diff --git a/.gitignore b/.gitignore index 0de9cb9..65a86c9 100644 --- a/.gitignore +++ b/.gitignore @@ -49,7 +49,11 @@ htmlcov/ .cache nosetests.xml coverage.xml +<<<<<<< HEAD +.pytest_cache/ +======= .pytest_cache/* +>>>>>>> master # Translations *.mo @@ -59,8 +63,7 @@ coverage.xml *.log # Sphinx documentation -# */_sources/* -# *.rst.txt +docs/build/ # PyBuilder target/ diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..3279f80 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,20 @@ +This software was developed by employees of the National Institute of Standards +and Technology (NIST), an agency of the Federal Government. Pursuant to +[title 17 United States Code Section 105](http://www.copyright.gov/title17/92chap1.html#105), +works of NIST employees are not subject to copyright protection in the United States and are +considered to be in the public domain. Permission to freely use, copy, modify, +and distribute this software and its documentation without fee is hereby granted, +provided that this notice and disclaimer of warranty appears in all copies. + +THE SOFTWARE IS PROVIDED 'AS IS' WITHOUT ANY WARRANTY OF ANY KIND, EITHER +EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY +THAT THE SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND FREEDOM FROM INFRINGEMENT, +AND ANY WARRANTY THAT THE DOCUMENTATION WILL CONFORM TO THE SOFTWARE, OR ANY +WARRANTY THAT THE SOFTWARE WILL BE ERROR FREE. IN NO EVENT SHALL NIST BE LIABLE +FOR ANY DAMAGES, INCLUDING, BUT NOT LIMITED TO, DIRECT, INDIRECT, SPECIAL OR +CONSEQUENTIAL DAMAGES, ARISING OUT OF, RESULTING FROM, OR IN ANY WAY CONNECTED +WITH THIS SOFTWARE, WHETHER OR NOT BASED UPON WARRANTY, CONTRACT, TORT, OR +OTHERWISE, WHETHER OR NOT INJURY WAS SUSTAINED BY PERSONS OR PROPERTY OR +OTHERWISE, AND WHETHER OR NOT LOSS WAS SUSTAINED FROM, OR AROSE OUT OF THE +RESULTS OF, OR USE OF, THE SOFTWARE OR SERVICES PROVIDED HEREUNDER. \ No newline at end of file diff --git a/NONLICENSE.md b/NONLICENSE.md deleted file mode 100644 index 1d4b574..0000000 --- a/NONLICENSE.md +++ /dev/null @@ -1,12 +0,0 @@ -This software was developed at the National Institute of Standards and Technology (NIST) by -employees of the Federal Government in the course of their official duties. Pursuant to -[Title 17 Section 105 of the United States Code](http://www.copyright.gov/title17/92chap1.html#105), -this software is not subject to copyright protection and is in the public domain. -NIST assumes no responsibility whatsoever for use by other parties of its source code, -and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. - -Specific software products identified in this open source project were used in order -to perform technology transfer and collaboration. In no case does such identification imply -recommendation or endorsement by the National Institute of Standards and Technology, nor -does it imply that the products identified are necessarily the best available for the -purpose. \ No newline at end of file diff --git a/README.md b/README.md index 7c91728..9cf429b 100644 --- a/README.md +++ b/README.md @@ -27,26 +27,17 @@ Note: These are the developmental system specs. Older versions of certain packages may work. * python >= 3.4 - * Tested with 3.4.4, 3.5.2, 3.6.1 -* SciPlot-PyQt >= 0.1.3 (>=0.1.4 for MPL2) + * Tested with 3.4.4, 3.5.2, 3.6.1, 3.7.2 +* NumPy +* PyQT5 + +* CVXOPT +* LazyHDF5 >= 0.2.1 + * Requires H5Py (>= 2.6) +* SciPlot-PyQt >= 0.2.2 * https://github.com/CCampJr/SciPlot-PyQt/releases -* numpy (1.9.3) - * Tested with 1.11.3+mkl -* PyQT5 (5.5.* or 5.6.*) - * Tested with 5.6, 5.8.1 -* matplotlib (1.5.0rc3, 2.0.0) (see below for MPL2) - * Tested with 1.5.2, 2.0.0 -* cvxopt (1.1.7) - * Tested with 1.1.7, 1.1.9 -* h5py (2.5) - * Tested with 2.6, 2.7 -* Sphinx (1.5.2) (Only for building documentation) - * Tested with 1.4.5, 1.6.4 - -### IMPORTANT: For Matplotlib 2 ### -You will need to use SciPlot-PyQT v0.1.4 -* Matplotlib 2 made numerous changes and deprecations that are being resolved -* See the installation instruction in the README.md file at https://github.com/CCampJr/SciPlot-PyQt + * Requires Matplotlib (v1.*, 2.*, or 3.*) +* Sphinx (only to build docs locally) ### IMPORTANT: For Python 3.4 ### You will need to manually install PyQt5 and Qt5 or get it through a distribution @@ -63,9 +54,6 @@ There is a bug in PyQt 5.7.* that will prevent SciPlot's tables from showing the * As WinPython 3.5.2.3Qt5 and 3.5.2.2Qt5 use PyQt 5.7.*, it is advised to use WinPython 3.5.2.1Qt5 or 3.4.4.5Qt5 until the matter is sorted out. * Alternatively, one can uninstall pyqt5.7.* and force an install of <= 5.6.*. -## SciPlot-PyQt ## -Currently, SciPlot >= 0.1.3 is not available through pip. You can however clone the repository from github. -(see https://github.com/CCampJr/SciPlot-PyQt) ## Installation ## ### Option 1: Easily updatable through git (dynamic copy)### diff --git a/TODO.md b/TODO.md index e52ce56..a2e246a 100644 --- a/TODO.md +++ b/TODO.md @@ -3,14 +3,16 @@ * Implement logging * Continue development of out-of-core analysis package * Carryover database package from SW into standalone and integrate +* GUI adjusts to screen resolution appropriately # Adjustment for External Package Updates -* Enhance ~~Implement~~ MPL2 testing and API (such as ax.hold deprecation) +* ~~Enhance ~~Implement~~ MPL2 testing and API (such as ax.hold deprecation)~~ # Enhancements * Carryover SVD auto-selection tools from SW package * Add rng functionality to all fcns * Move from ALS-only to ALS/ArPLS detrending +* Select sub-set of dark and NRB spectra # Minor updates * Fix model to use way less memory (and test 64 vs 128-bit complex) @@ -22,4 +24,29 @@ for now * ~~Minimum in qt_GrayScaleImgInfoBar is set to 0 -- needs to allow negative~~ * Undo also resets freq window (ie track frequency window settings) -* Re-evaluate how poisson noise is added to model inline. Very math-operation-order dependent. \ No newline at end of file +* Re-evaluate how poisson noise is added to model inline. Very math-operation-order dependent. + +# TODO +* ~~Tab describing history of processing steps~~ +* Create a set of feature-finding/selecting classes to take a lot of the computation out of the dialogSVD UI +* ~~Dark mean and fill-between~~ +* ~~NRB, L/R-NRB mean and fill-between~~ +* Delete linked plots (Delete all in-family) +* ~~Loading spectra/hsi into a spectrum averages~~ + * ~~Move from io.hdf5 to data.spectrum~~ +* Testing of spectrum, spectra, hsi when op_range defined +* Calculate Anscombe parameters +* Check bugs in SVD script text +* ~~When loading Dark or NRB, auto-open same HDF file as HSI. Cancel reverts to fileview~~ +* ~~Rename load file GUI title to whatever is being loaded (NRB, Dark, etc)~~ +* ~~Tab to view already performed tasks~~ + + +# REFACTORS +* ~~io.hdf5~~ + +# Known bugs +* spectrum, spectra, and hsi may only work properly when the spectral axis is -1 + * Test files only check axis = -1 case +* ~~subtract dark doesn't work when dark is multiple spectra~~ +* Calibration not correctly loaded from files that were later calibrated \ No newline at end of file diff --git a/crikit/CRIkitUI.py b/crikit/CRIkitUI.py index d095c40..83e098a 100644 --- a/crikit/CRIkitUI.py +++ b/crikit/CRIkitUI.py @@ -1,6 +1,6 @@ """ CRIKit2: Hyperspectral imaging toolkit -============================================================== +====================================== CRIKit2, formerly the Coherent Raman Imaging toolKit, is a hyperspectral imaging (HSI) platform (user interface, UI). @@ -32,9 +32,9 @@ import sys as _sys import webbrowser as _webbrowser -import h5py as _h5py import matplotlib as _mpl import numpy as _np +import h5py as _h5py import PyQt5.QtCore as _QtCore @@ -45,25 +45,30 @@ from PyQt5.QtWidgets import QMainWindow as _QMainWindow from PyQt5.QtWidgets import QMessageBox as _QMessageBox from PyQt5.QtWidgets import QWidget as _QWidget +from PyQt5.QtWidgets import QTableWidgetItem as _QTableWidgetItem + from scipy.signal import savgol_filter as _sg -from crikit.cri.error_correction import \ - PhaseErrCorrectALS as _PhaseErrCorrectALS +from crikit.cri.error_correction import (PhaseErrCorrectALS as _PhaseErrCorrectALS) from crikit.cri.error_correction import ScaleErrCorrectSG as _ScaleErrCorrectSG from crikit.cri.kk import KramersKronig from crikit.cri.merge_nrbs import MergeNRBs as _MergeNRBs -from crikit.data.frequency import calib_pix_wn as _calib_pix_wn +from crikit.data.frequency import (calib_pix_wn as _calib_pix_wn, + calib_pix_wl as _calib_pix_wl) from crikit.data.hsi import Hsi from crikit.data.spectra import Spectra from crikit.data.spectrum import Spectrum from crikit.datasets.model import Model as _Model -from crikit.io.hdf5 import hdf_is_valid_dsets from crikit.io.macros import import_csv_nist_special1 as io_nist_dlm from crikit.io.macros import import_hdf_nist_special as io_nist +from crikit.io.macros import import_hdf_nist_special_ooc as io_nist_ooc + +# from crikit.io.meta_configs import special_nist_bcars2 as _snb2 +# from crikit.io.meta_process import meta_process as _meta_process import crikit.measurement.peakamps as _peakamps @@ -80,11 +85,12 @@ from crikit.ui.dialog_kkOptions import DialogKKOptions from crikit.ui.dialog_model import DialogModel from crikit.ui.dialog_ploteffect import \ - DialogPlotEffectFuture as _DialogPlotEffect + DialogPlotEffect as _DialogPlotEffect from crikit.ui.dialog_save import DialogSave from crikit.ui.dialog_varstabAnscombeOptions import DialogAnscombeOptions from crikit.ui.qt_CRIkit import Ui_MainWindow -from crikit.ui.subui_hdf_load import SubUiHDFLoad +from crikit.ui.main_Mosaic import MainWindowMosaic + from crikit.ui.utils.roi import roimask as _roimask from crikit.ui.widget_Calibrate import widgetCalibrate as _widgetCalibrate from crikit.ui.widget_DeTrending import widgetALS as _widgetALS @@ -96,11 +102,12 @@ from crikit.ui.widget_SG import widgetSG as _widgetSG from crikit.utils.breadcrumb import BCPre as _BCPre -from crikit.utils.general import find_nearest, mean_nd_to_1d +from crikit.utils.general import find_nearest, mean_nd_to_1d, std_nd_to_1d from sciplot.sciplotUI import SciPlotUI as _SciPlotUI -_h5py.get_config().complex_names = ('Re', 'Im') +import lazy5 +from lazy5.ui.QtHdfLoad import HdfLoad force_not_sw = False @@ -133,8 +140,8 @@ print('No appropriate Jupyter/IPython installation found. Console will not be available') jupyter_flag = -1 -help_index = _os.path.abspath(_os.path.join(_os.path.dirname(__file__), - '../docs/build/html/index.html')) +str_doc = '../docs/build/html/index.html' +help_index = _os.path.abspath(_os.path.join(_os.path.dirname(__file__), str_doc)) if _os.path.exists(help_index): pass @@ -160,18 +167,19 @@ def __init__(self, **kwargs): parent = kwargs.get('parent') super(CRIkitUI_process, self).__init__(parent) ### EDIT ### - + self.parent = parent self.filename = kwargs.get('filename') self.path = kwargs.get('path') self.dataset_name = kwargs.get('dataset_name') + self.fid = None self.hsi = kwargs.get('hsi') if not isinstance(self.hsi, Hsi): self.hsi = Hsi() - + self.bcpre = _BCPre() self.dark = Spectra() @@ -181,6 +189,11 @@ def __init__(self, **kwargs): self.overlays = [] self.show_overlays = True + # ROI's to plot instead of random spectra + # Primarily affects dialogPlotEffect activities + # Also affected by setting actionUseSet + self.preview_rois = None + # Piecewise NRB's (not always used) self.nrb_left = Spectra() self.nrb_right = Spectra() @@ -190,7 +203,7 @@ def __init__(self, **kwargs): self.plotter = _SciPlotUI(show=False, parent=self.parent) - self._mpl_v2 = self.plotter._mpl_v2 + self._mpl_v1 = self.plotter._mpl_v1 self.ui = Ui_MainWindow() ### EDIT ### @@ -207,8 +220,12 @@ def __init__(self, **kwargs): self.img_BW.ui.spinBoxMax.setValue(self.img_BW.data.maxer) self.img_BW.ui.spinBoxMin.setValue(self.img_BW.data.minner) - self.ui.sweeperVL.insertWidget(0, self.img_BW) - self.img_BW.mpl.fig.tight_layout(pad=2) + self.ui.sweeperVL.insertWidget(0, self.img_BW, stretch=1, alignment=_QtCore.Qt.AlignHCenter) + try: + self.img_BW.mpl.fig.tight_layout(pad=2) + except: + print('tight_layout failed (CrikitUI: 1') + # ID used for matplotlib to connect to a figure self.cid = None @@ -231,7 +248,7 @@ def __init__(self, **kwargs): rgb_img.popimage.ui.pushButtonSpectrum.setEnabled(False) self.ui.tabColors.addTab(rgb_img, 'Color ' + str(count)) - + rgb_img.math.ui.pushButtonBasicMath.setEnabled(False) rgb_img.math.ui.pushButtonScripting.setEnabled(False) @@ -248,7 +265,7 @@ def __init__(self, **kwargs): rgb_img.math.ui.pushButtonBasicMath.pressed.connect(self.doMath) rgb_img.ui.spinBoxMax.editingFinished.connect(self.doComposite) rgb_img.ui.spinBoxMin.editingFinished.connect(self.doComposite) - rgb_img.math.ui.spinBoxGain.valueChanged.connect(self.doComposite) + rgb_img.math.ui.spinBoxGain.editingFinished.connect(self.doComposite) self.img_Composite = widgetCompositeColor(self.img_RGB_list, @@ -258,7 +275,7 @@ def __init__(self, **kwargs): self.ui.tabColors.addTab(self.img_Composite, 'Composite Image') - self.ui.sweeperVL_2.insertWidget(0, self.img_Composite2) + self.ui.sweeperVL_2.insertWidget(0, self.img_Composite2, stretch=1, alignment=_QtCore.Qt.AlignHCenter) self.ui.tabColors.currentChanged.connect(self.checkCompositeUpdate) @@ -267,6 +284,8 @@ def __init__(self, **kwargs): # Load Data self.ui.actionOpenHDFNIST.triggered.connect(self.fileOpenHDFNIST) + self.ui.actionOpenHDFNISTOOC.triggered.connect(self.fileOpenHDFNISTOOC) + self.ui.actionLoadNRB.triggered.connect(self.loadNRB) self.ui.actionLoadDark.triggered.connect(self.loadDark) @@ -285,6 +304,8 @@ def __init__(self, **kwargs): self.ui.actionMergeNRBs.triggered.connect(self.mergeNRBs) + self.ui.actionCreateMosaic.triggered.connect(self.mosaicTool) + # Settings self.ui.actionSettings.triggered.connect(self.settings) @@ -311,6 +332,7 @@ def __init__(self, **kwargs): # Calibrate Wavenumber self.ui.actionCalibrate.triggered.connect(self.calibrate) self.ui.actionResetCalibration.triggered.connect(self.calibrationReset) + self.ui.actionEstCalibration.triggered.connect(self.specialEstCalibration1) # Perform KK self.ui.actionKramersKronig.triggered.connect(self.doKK) @@ -332,6 +354,12 @@ def __init__(self, **kwargs): self.ui.actionAmpErrorCorrection.triggered.connect(self.errorCorrectAmp) self.ui.actionSubtractROI.triggered.connect(self.subtractROIStart) + # Preview ROIs + self.ui.actionSetPreviewROI.triggered.connect(self.set_preview_rois) + self.ui.actionDeletePreviewROI.triggered.connect(self.delete_preview_rois) + self.ui.actionShowPreviewROI.triggered.connect(self.changeSlider) + self.ui.actionShowPreviewROILegend.triggered.connect(self.changeSlider) + # SAVE self.ui.actionSave.triggered.connect(self.save) @@ -365,6 +393,9 @@ def __init__(self, **kwargs): self.ui.lineEditPix.setVisible(False) self.ui.labelFreqPixel.setVisible(False) + # Settings + self.ui.actionUseImagData.triggered.connect(self.changeSlider) + # Help if help_index is not None: self.ui.actionHelpManual.triggered.connect(lambda: _webbrowser.open('file:///' + help_index, new=1)) @@ -378,8 +409,8 @@ def __init__(self, **kwargs): if jupyter_flag == 1: try: - self.jupyterConsole = QJupyterWidget(customBanner='Welcome to the ' - 'embedded ipython console\n\n') + str_banner = 'Welcome to the embedded ipython console\n\n' + self.jupyterConsole = QJupyterWidget(customBanner=str_banner) except: print('Error loading embedded IPython Notebook') else: @@ -406,8 +437,10 @@ def __init__(self, **kwargs): # COMMAND LINE INTERPRETATION # file and dset info provided - if hdf_is_valid_dsets(self.path, self.filename, self.dataset_name): - self.fileOpenHDFNIST(dialog=False) + if (self.filename is not None) & (self.dataset_name is not None): + if lazy5.inspect.valid_dsets(filename=self.filename, + dset_list=self.dataset_name, pth=self.path): + self.fileOpenHDFNIST(dialog=False) # Hsi provided temp = kwargs.get('hsi') @@ -428,7 +461,7 @@ def __init__(self, **kwargs): except: print('Error in input x-array') self.hsi.x = None - + # y-array provided temp = kwargs.get('y') if temp is not None: @@ -461,6 +494,18 @@ def __init__(self, **kwargs): print('Error in input data') self.hsi = Hsi() + def mosaicTool(self): + win = MainWindowMosaic(parent=self) + win.show() + + def updateHistory(self): + self.ui.tableWidgetHistory.clearContents() + self.ui.tableWidgetHistory.setRowCount(len(self.bcpre.attr_dict)) + for num, q in enumerate(self.bcpre.attr_dict): + self.ui.tableWidgetHistory.setItem(num, 0, _QTableWidgetItem(q)) + self.ui.tableWidgetHistory.setItem(num, 1, + _QTableWidgetItem(str(self.bcpre.attr_dict[q]))) + def plotter_show(self): self.plotter.show() self.plotter.raise_() @@ -500,22 +545,24 @@ def toolbarSetting(self): self.ui.toolBar.addAction(self.ui.actionUndo) self.ui.toolBar.addSeparator() + # self.ui.toolBar.addActions([self.ui.actionLoadDark, + # self.ui.actionLoadNRB]) self.ui.toolBar.addActions([self.ui.actionLoadDark, - self.ui.actionLoadNRB]) + self.ui.actionLoad_NRB_Right_Side]) self.ui.toolBar.addSeparator() self.ui.toolBar.addActions([self.ui.actionDarkSubtract, - self.ui.actionResidualSubtract, + self.ui.actionEstCalibration, self.ui.actionFreqWindow, self.ui.actionAnscombe, self.ui.actionDeNoise, self.ui.actionInverseAnscombe, + self.ui.actionNRB_from_ROI_Left_Side, + self.ui.actionMergeNRBs, self.ui.actionKramersKronig, self.ui.actionPhaseErrorCorrection, self.ui.actionScaleErrorCorrection, - self.ui.actionSubtractROI, - self.ui.actionCalibrate, - self.ui.actionAmpErrorCorrection]) + self.ui.actionCalibrate]) elif sndr == self.ui.actionToolBarNIST1: self.ui.actionToolBarNIST2.setChecked(True) @@ -549,62 +596,40 @@ def toolbarSetting(self): def save(self): suffix = self.bcpre.dset_name_suffix - try: - ret = DialogSave.dialogSave(parent=self, - current_filename=self.filename, - current_path=self.path, - current_dataset_name=self.dataset_name[0], - suffix=suffix) - if ret is None: - pass # Save canceled - else: - self.save_filename = ret[0] - self.save_path = ret[1] - self.save_dataset_name = ret[2] - - self.save_grp = self.save_dataset_name.rpartition('/')[0] - self.save_dataset_name_no_grp = self.save_dataset_name.rpartition('/')[-1] - - - - try: - f_out = _h5py.File(self.save_path + self.save_filename, 'a') - loc = f_out.require_group(self.save_grp) - dset = loc.create_dataset(self.save_dataset_name_no_grp, data=self.hsi.data) - - meta = self.hsi.meta - for attr_key in meta: - val = meta[attr_key] - if isinstance(val, str): - dset.attrs[attr_key] = val - else: - try: - dset.attrs.create(attr_key, self.hsi.meta[attr_key]) - except: - print('Error in HSI attributes: {}'.format(attr_key)) + ret = DialogSave.dialogSave(parent=self, + current_filename=self.filename, + current_path=self.path, + current_dataset_name=self.dataset_name[0], + suffix=suffix) + if ret is None: + pass # Save canceled + else: + self.save_filename = ret[0] + self.save_path = ret[1] + self.save_dataset_name = ret[2] - bc_attr_dict = self.bcpre.attr_dict + self.save_grp = self.save_dataset_name.rpartition('/')[0] + self.save_dataset_name_no_grp = self.save_dataset_name.rpartition('/')[-1] - for attr_key in bc_attr_dict: - val = bc_attr_dict[attr_key] - if isinstance(val, str): - dset.attrs[attr_key] = val - else: - try: - dset.attrs.create(attr_key, bc_attr_dict[attr_key]) - except: - print('Could not create attribute') + if isinstance(self.hsi.meta, dict): + attr_dict = _copy.deepcopy(self.hsi.meta) + else: + print('Meta data (hsi.meta) is not a dictionary') + attr_dict = {} - except: - print('Something went wrong while saving') - else: - print('Saved without issues') - finally: - f_out.close() - self.setWindowTitle('{} -> {}'.format(self.windowTitle(), self.save_filename)) + attr_dict.update(self.bcpre.attr_dict) - except: - print('Couldn\'t open save dialog') + try: + ret_save = lazy5.create.save(self.save_filename, self.save_dataset_name, + self.hsi._data, pth=self.save_path, + attr_dict= attr_dict, sort_attrs=True, + chunks=True, verbose=True) + except: + print('Something went wrong saving...') + else: + print('Save succeeded with no errors.') + if ret_save: + self.setWindowTitle('{} -> {}'.format(self.windowTitle(), self.save_filename)) def tabMainChange(self): if self.ui.tabMain.currentIndex() == 4: # Jupyter console @@ -631,6 +656,15 @@ def closeEvent(self, event): else: print('Did not delete pickle file cut list... Something went wrong') + if self.fid: + print('Closing HDF File') + try: + self.fid.close() + except: + print('Something failed in closing the file') + else: + print('Successfully closed HDF File') + def fileOpenHDFNIST(self, *args, dialog=True): """ Open and load HDF5 File @@ -641,10 +675,14 @@ def fileOpenHDFNIST(self, *args, dialog=True): # Get data and load into CRI_HSI class # This will need to change to accomodate multiple-file selection - + if dialog: try: - to_open = SubUiHDFLoad.getFileDataSets(self.path) + if (self.filename is not None) & (self.path is not None): + to_open = HdfLoad.getFileDataSets(_os.path.join(self.path, self.filename), parent=self) + else: + to_open = HdfLoad.getFileDataSets(self.path, parent=self) + print('to_open: {}'.format(to_open)) if to_open is not None: self.path, self.filename, self.dataset_name = to_open @@ -655,6 +693,8 @@ def fileOpenHDFNIST(self, *args, dialog=True): self.hsi = Hsi() success = io_nist(self.path, self.filename, self.dataset_name, self.hsi) + print('Was successful: {}'.format(success)) + print('HSI shape: {}'.format(self.hsi.shape)) self.fileOpenSuccess(success) else: self.hsi = Hsi() @@ -662,6 +702,42 @@ def fileOpenHDFNIST(self, *args, dialog=True): self.hsi) self.fileOpenSuccess(success) + def fileOpenHDFNISTOOC(self, *args): + """ + Open and load HDF5 File OUT-OF-CORE + + dialog : bool + Present a gui for file and dataset selection + """ + + # Get data and load into CRI_HSI class + # This will need to change to accomodate multiple-file selection + + try: + if (self.filename is not None) & (self.path is not None): + to_open = HdfLoad.getFileDataSets(_os.path.join(self.path, self.filename), parent=self) + else: + to_open = HdfLoad.getFileDataSets(self.path, parent=self) + + print('to_open: {}'.format(to_open)) + if to_open is not None: + self.path, self.filename, self.dataset_name = to_open + self.dataset_name = self.dataset_name[0] + except: + print('Could not open file. Corrupt or not appropriate file format.') + else: + if to_open is not None: + self.hsi = Hsi() + success_fid = io_nist_ooc(self.path, self.filename, self.dataset_name, + self.hsi) + if success_fid: + self.fid = success_fid + print('HSI shape: {}'.format(self.hsi.shape)) + self.ui.actionUndo_Backup_Enabled.setChecked(False) + self.ui.actionUndo_Backup_Enabled.setEnabled(False) + + self.fileOpenSuccess(True) + def fileOpenDLMNIST(self): """ Open and load DLM File @@ -695,6 +771,11 @@ def fileOpenSuccess(self, success): activates or deactivates action (buttons) """ if success: + # * If HSI is integer dtype, convert to float + if (self.hsi.data.dtype.kind == 'i') & isinstance(self.hsi.data, _np.ndarray): + print('Converting HSI from int to float') + self.hsi.data = 1.0*self.hsi.data + self.setWindowTitle('{}: {}'.format(self.windowTitle(), self.filename)) # FILE self.ui.actionSave.setEnabled(True) @@ -711,6 +792,8 @@ def fileOpenSuccess(self, success): # VIEW self.ui.actionPointSpectrum.setEnabled(True) self.ui.actionROISpectrum.setEnabled(True) + self.ui.actionSetPreviewROI.setEnabled(True) + self.ui.actionDeletePreviewROI.setEnabled(True) # IMPORT/LOAD self.ui.actionLoadDark.setEnabled(True) @@ -731,8 +814,8 @@ def fileOpenSuccess(self, success): self.ui.actionNRB_from_ROI.setEnabled(True) self.ui.menuVariance_Stabilize.setEnabled(True) - # ANALYSIS - + # NIST SPECIAL + self.ui.actionEstCalibration.setEnabled(True) is_complex = _np.iscomplexobj(self.hsi.data) if is_complex: @@ -748,12 +831,16 @@ def fileOpenSuccess(self, success): # Backup for Undo self.bcpre.add_step(['Raw']) - try: - _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) - except: - print('Error in pickle backup (Undo functionality)') - else: - self.bcpre.backed_up() + self.updateHistory() + + if self.ui.actionUndo_Backup_Enabled.isChecked(): + try: + _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) + except: + print('Error in pickle backup (Undo functionality)') + else: + self.bcpre.backed_up() + # Set frequency slider and associated displays self.ui.freqSlider.setMinimum(self.hsi.freq.op_range_pix[0]) @@ -764,10 +851,18 @@ def fileOpenSuccess(self, success): self.ui.lineEditFreq.setText(str(round(self.hsi.f[0], 2))) # Set BW Class Data self.img_BW.initData() - self.img_BW.data.grayscaleimage = self.hsi.data_imag_over_real[:, :, pos] + + if _np.iscomplexobj(self.hsi.data): + if self.ui.actionUseImagData.isChecked(): + self.img_BW.data.grayscaleimage = _np.imag(self.hsi.data[:, :, pos]) + val_extrema = _np.max(_np.abs(self.img_BW.data.grayscaleimage)) + else: + self.img_BW.data.grayscaleimage = _np.real(self.hsi.data[:, :, pos]) + val_extrema = _np.max(_np.abs(self.img_BW.data.grayscaleimage)) + else: + self.img_BW.data.grayscaleimage = self.hsi.data[:, :, pos] + val_extrema = _np.max(_np.abs(self.img_BW.data.grayscaleimage)) - val_extrema = _np.max([_np.abs(self.hsi.data_imag_over_real.max()), - _np.abs(self.hsi.data_imag_over_real.min())]) self.img_BW.ui.spinBoxMin.setMinimum(-1.1*val_extrema) self.img_BW.ui.spinBoxMin.setMaximum(1.1*val_extrema) self.img_BW.ui.spinBoxMax.setMinimum(-1.1*val_extrema) @@ -813,7 +908,7 @@ def fileOpenSuccess(self, success): rgb_img.data.grayscaleimage = temp rgb_img.data.set_x(self.hsi.x, xlabel) rgb_img.data.set_y(self.hsi.y, ylabel) - + color_str = rgb_img.colormode.ui.comboBoxFGColor.itemText(num) rgb_img.data.colormap = _mpl.colors.colorConverter.to_rgb(_mpl.colors.cnames[color_str]) rgb_img.colormode.ui.comboBoxFGColor.setCurrentIndex(num) @@ -841,7 +936,7 @@ def fileOpenSuccess(self, success): rgb_img.gsinfo.ui.spinBoxMin.setMaximum(1.1*val_extrema) rgb_img.gsinfo.ui.spinBoxMax.setMinimum(-1.1*val_extrema) rgb_img.gsinfo.ui.spinBoxMax.setMaximum(1.1*val_extrema) - + # Set X- and Y- scales, labels, etc for composite color images self.img_Composite.data.set_x(self.hsi.x, xlabel) self.img_Composite.data.set_y(self.hsi.y, ylabel) @@ -853,7 +948,10 @@ def loadDark(self): Open HDF file and load dark spectrum(a) """ - to_open = SubUiHDFLoad.getFileDataSets(self.path) + if (self.filename is not None) & (self.path is not None): + to_open = HdfLoad.getFileDataSets(_os.path.join(self.path, self.filename), parent=self) + else: + to_open = HdfLoad.getFileDataSets(self.path, parent=self) print('To_open: {}'.format(to_open)) if to_open is not None: @@ -861,6 +959,11 @@ def loadDark(self): success = io_nist(pth, filename, datasets, self.dark) if success: + # If Dark is integer dtype, convert to float + if self.dark.data.dtype.kind == 'i': + print('Converting Dark from int to float') + self.dark.data = 1.0*self.dark.data + if self.dark.shape[-1] == self.hsi.freq.size: self.ui.actionDarkSubtract.setEnabled(True) self.ui.actionDarkSpectrum.setEnabled(True) @@ -899,6 +1002,11 @@ def loadDarkDLM(self): if success: + # If Dark is integer dtype, convert to float + if self.dark.data.dtype.kind == 'i': + print('Converting Dark from int to float') + self.dark.data = 1.0*self.dark.data + if self.dark.shape[-1] == self.hsi.freq.size: self.ui.actionDarkSubtract.setEnabled(True) self.ui.actionDarkSpectrum.setEnabled(True) @@ -926,12 +1034,21 @@ def loadNRB(self): nrb = self.nrb_right - to_open = SubUiHDFLoad.getFileDataSets(self.path) + if (self.filename is not None) & (self.path is not None): + to_open = HdfLoad.getFileDataSets(_os.path.join(self.path, self.filename), parent=self) + else: + to_open = HdfLoad.getFileDataSets(self.path, parent=self) + if to_open is not None: pth, filename, datasets = to_open success = io_nist(pth, filename, datasets, nrb) if success: + # If NRB is integer dtype, convert to float + if nrb.data.dtype.kind == 'i': + print('Converting NRB from int to float') + nrb.data = 1.0*nrb.data + if nrb.shape[-1] == self.hsi.freq.size: if sender == self.ui.actionLoadNRB: self.ui.menuCoherent_Raman_Imaging.setEnabled(True) @@ -1000,6 +1117,142 @@ def loadNRBDLM(self): self.ui.actionNRBSpectrum.setEnabled(False) self.ui.actionDeNoiseNRB.setEnabled(False) + def get_preview_spectra(self, full=False): + """ If self.preview_rois is set, output the mean spectra from thos regions """ + if full: + rng = self.hsi.freq.pix_vec + else: + rng = self.hsi.freq.op_range_pix + + if self.preview_rois: + prev_spectra = [] + + for prx, pry in self.preview_rois: + + mask, path = _roimask(self.hsi.x, self.hsi.y, prx, pry) + + mask_hits = _np.sum(mask) + if mask_hits > 0: # Len(mask) > 0 + temp = self.hsi.data[..., rng][mask == 1] + + + if mask_hits > 1: + prev_spectra.append(_np.mean(temp, axis=0)) + else: + prev_spectra.append(temp[self.hsi.freq.op_range_pix]) + return _np.array(prev_spectra) + + else: + return self.hsi.get_rand_spectra(2, pt_sz=3, quads=True) + + def set_preview_rois(self): + """ Set the preview ROIs. NOTE: this function just sets the signal for the MPL window """ + if self.cid is None: + # Updated by _roiClick + self.preview_rois = [] + self.x_loc_list = [] + self.y_loc_list = [] + + self.cid = self.img_BW.mpl.mpl_connect('button_press_event', + lambda event: self._roiPreviewClick(event)) + + self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.CrossCursor)) + self.setCursor(_QCursor(_QtCore.Qt.CrossCursor)) + pass + + def showPreviewRois(self): + lines = [] + if self.preview_rois: + for num, (prx, pry) in enumerate(self.preview_rois): + temp, = self.img_BW.mpl.ax.plot(prx, pry, label='Preview ROI {}'.format(num), + linestyle=':', color='C{}'.format(num % 10)) + lines.append(temp) + + if self.ui.actionShowPreviewROILegend.isChecked(): + # lg = self.img_BW.mpl.ax.legend(handles=lines, loc='lower left', mode='expand', + # bbox_to_anchor=(0.01, 1.02, 1., 0.2), + # ncol=2, fontsize=9) + lg = self.img_BW.mpl.ax.legend(handles=lines, loc='best', + ncol=2, fontsize=9) + self.img_BW.mpl.ax.add_artist(lg) + try: + self.img_BW.mpl.fig.tight_layout(pad=1) + except: + print('tight_layout failed (CrikitUI: 2') + self.img_BW.mpl.draw() + + def _roiPreviewClick(self, event, *args): + """ + Capture region-of-interest mouse click locations in MPL window. + """ + + getx = self.img_BW.mpl.ax.get_xlim() + gety = self.img_BW.mpl.ax.get_ylim() + + if event.button == 1: + if event.inaxes == self.img_BW.mpl.ax: + + self.x_loc_list.append(event.xdata) + self.y_loc_list.append(event.ydata) + + if len(self.x_loc_list) == 1: + self.img_BW.mpl.ax.plot(self.x_loc_list, self.y_loc_list, + markerfacecolor=[.9, .9, 0], + markeredgecolor=[.9, .9, 0], + marker='+', + markersize=10, + linestyle='None') + self.img_BW.mpl.ax.set_xlim(getx) + self.img_BW.mpl.ax.set_ylim(gety) + self.img_BW.mpl.draw() + else: + self.img_BW.mpl.ax.plot(self.x_loc_list[-2:], + self.y_loc_list[-2:], + linewidth=2, + marker='+', + markersize=10, + color=[.9, .9, 0], + markerfacecolor=[.9, .9, 0], + markeredgecolor=[.9, .9, 0]) + self.img_BW.mpl.ax.set_xlim(getx) + self.img_BW.mpl.ax.set_ylim(gety) + + self.img_BW.mpl.draw() + else: + if len(self.x_loc_list) > 0: # Insure at least 1 vertex + self.x_loc_list.append(self.x_loc_list[0]) + self.y_loc_list.append(self.y_loc_list[0]) + + self.img_BW.mpl.ax.plot(self.x_loc_list[-2:], + self.y_loc_list[-2:], + linewidth=2, + marker='+', + markersize=10, + color=[.9, .9, 0], + markerfacecolor=[.9, .9, 0], + markeredgecolor=[.9, .9, 0]) + self.img_BW.mpl.ax.set_xlim(getx) + self.img_BW.mpl.ax.set_ylim(gety) + self.img_BW.mpl.draw() + + self.preview_rois.append([self.x_loc_list, self.y_loc_list]) + + self.x_loc_list = [] + self.y_loc_list = [] + else: + del self.x_loc_list + del self.y_loc_list + + self.setCursor(_QCursor(_QtCore.Qt.ArrowCursor)) + self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.ArrowCursor)) + self.img_BW.mpl.mpl_disconnect(self.cid) + self.cid = None + self.changeSlider() + + def delete_preview_rois(self): + self.preview_rois = None + self.changeSlider() + def mergeNRBs(self): """ Interactive merge of the left- and right-side NRB @@ -1007,13 +1260,18 @@ def mergeNRBs(self): if self.nrb_left is not None and self.nrb_right is not None: rng = self.hsi.freq.op_range_pix + if (self.preview_rois is None) | (not self.ui.actionUsePreviewROI.isChecked()): + preview_spectra = self.hsi.get_rand_spectra(2, pt_sz=3, quads=True) + else: + preview_spectra = self.get_preview_spectra(full=False) - rand_spectra = self.hsi.get_rand_spectra(2, pt_sz=3, quads=True) + if _np.iscomplexobj(preview_spectra): + preview_spectra = preview_spectra.imag plugin = _widgetMergeNRBs(wn_vec=self.hsi.f, nrb_left=self.nrb_left.mean()[rng], nrb_right=self.nrb_right.mean()[rng]) - winPlotEffect = _DialogPlotEffect.dialogPlotEffect(data=rand_spectra, + winPlotEffect = _DialogPlotEffect.dialogPlotEffect(data=preview_spectra, x=self.hsi.f, plugin=plugin) @@ -1050,6 +1308,7 @@ def mergeNRBs(self): winPlotEffect.parameters['wn_switchpt'], 'scale_left', winPlotEffect.parameters['scale_left']]) + self.updateHistory() else: pass @@ -1066,12 +1325,16 @@ def calibrate(self): Calibrate spectra """ - rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, full=True) - if _np.iscomplexobj(rand_spectra): - rand_spectra = rand_spectra.imag + if (self.preview_rois is None) | (not self.ui.actionUsePreviewROI.isChecked()): + preview_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, full=True) + else: + preview_spectra = self.get_preview_spectra(full=True) + + if _np.iscomplexobj(preview_spectra): + preview_spectra = preview_spectra.imag plugin = _widgetCalibrate(calib_dict=self.hsi.freq.calib) - winPlotEffect = _DialogPlotEffect.dialogPlotEffect(rand_spectra, + winPlotEffect = _DialogPlotEffect.dialogPlotEffect(preview_spectra, x=self.hsi.f_full, plugin=plugin, parent=self) @@ -1091,6 +1354,26 @@ def calibrationReset(self): self.hsi.freq.update() self.changeSlider() + def specialEstCalibration1(self): + """ + For NIST BCARS 2, maximum raw spectrum occurs at approximately + 745.8 nm (18/07/11) + """ + msg = _QMessageBox(self) + msg.setIcon(_QMessageBox.Warning) + msg.setText('Estimate calibration for NIST BCARS2?') + msg.setWindowTitle('Confirm estimation of calibration') + msg.setInformativeText('This should only be applied to RAW BCARS2 data from NIST.') + msg.setStandardButtons(_QMessageBox.Ok | _QMessageBox.Cancel) + msg.setDefaultButton(_QMessageBox.Ok) + out = msg.exec() + + if out == _QMessageBox.Ok: + nm_diff = 745.8 - _calib_pix_wl(self.hsi.freq.calib)[0][self.hsi.mean().argmax()] + self.hsi.freq.calib['a_vec'][-1] = self.hsi.freq.calib['a_vec'][-1] + nm_diff + self.hsi.freq.update() + self.changeSlider() + def plotDarkSpectrum(self): """ Plot dark spectrum @@ -1098,8 +1381,18 @@ def plotDarkSpectrum(self): if self.dark.data is None: pass else: - self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.dark.data), - label='Mean Dark Spectrum') + meaner = mean_nd_to_1d(self.dark.data) + self.plotter.plot(self.hsi.f_full, meaner, + label='Mean Dark Spectrum ({})'.format(self.dark.n_pix)) + + if self.dark.n_pix > 1: + stder = std_nd_to_1d(self.dark.data) + color = self.plotter.list_all[-1].style_dict['color'] + std_label = r'Dark Spectrum $\pm$1 Std. Dev. ({})'.format(self.dark.n_pix) + self.plotter.fill_between(self.hsi.f_full, meaner - stder, + meaner + stder, color=color, + alpha=0.25, + label=std_label) self.plotter.show() self.plotter.raise_() @@ -1111,8 +1404,21 @@ def plotNRBSpectrum(self): if self.nrb.data is None: pass else: - self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.nrb.data), - label='Mean NRB Spectrum') + meaner = mean_nd_to_1d(self.nrb.data) + self.plotter.plot(self.hsi.f_full, meaner, + label='Mean NRB Spectrum ({})'.format(self.nrb.n_pix)) + + if self.nrb.n_pix > 1: + stder = std_nd_to_1d(self.nrb.data) + color = self.plotter.list_all[-1].style_dict['color'] + std_label = r'NRB Spectrum $\pm$1 Std. Dev. ({})'.format(self.nrb.n_pix) + self.plotter.fill_between(self.hsi.f_full, meaner - stder, + meaner + stder, color=color, + alpha=0.25, + label=std_label) + + # self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.nrb.data), + # label='Mean NRB Spectrum') self.plotter.show() self.plotter.raise_() @@ -1124,8 +1430,21 @@ def plotLeftNRBSpectrum(self): if self.nrb_left.data is None: pass else: - self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.nrb_left.data), - label='Mean Left-Side NRB Spectrum') + meaner = mean_nd_to_1d(self.nrb_left.data) + self.plotter.plot(self.hsi.f_full, meaner, + label='Mean Left-Side NRB Spectrum ({})'.format(self.nrb_left.n_pix)) + + if self.nrb_left.n_pix > 1: + stder = std_nd_to_1d(self.nrb_left.data) + color = self.plotter.list_all[-1].style_dict['color'] + std_label = r'Left-Side NRB Spectrum $\pm$1 Std. Dev. ({})'.format(self.nrb_left.n_pix) + self.plotter.fill_between(self.hsi.f_full, meaner - stder, + meaner + stder, color=color, + alpha=0.25, + label=std_label) + + # self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.nrb_left.data), + # label='Mean Left-Side NRB Spectrum') self.plotter.show() self.plotter.raise_() @@ -1137,8 +1456,18 @@ def plotRightNRBSpectrum(self): if self.nrb_right.data is None: pass else: - self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.nrb_right.data), - label='Mean Right-Side NRB Spectrum') + meaner = mean_nd_to_1d(self.nrb_right.data) + self.plotter.plot(self.hsi.f_full, meaner, + label='Mean Right-Side NRB Spectrum ({})'.format(self.nrb_right.n_pix)) + + if self.nrb_right.n_pix > 1: + stder = std_nd_to_1d(self.nrb_right.data) + color = self.plotter.list_all[-1].style_dict['color'] + std_label = r'Right-Side NRB Spectrum $\pm$1 Std. Dev. ({})'.format(self.nrb_right.n_pix) + self.plotter.fill_between(self.hsi.f_full, meaner - stder, + meaner + stder, color=color, + alpha=0.25, + label=std_label) self.plotter.show() self.plotter.raise_() @@ -1175,7 +1504,7 @@ def subtractROIStart(self): self.y_loc_list = [] - self.cid = self.img_BW.mpl.mpl_connect('button_press_event', + self.cid = self.img_BW.mpl.mpl_connect('button_press_event', lambda event: self._roiClick(event, self._roiSubtract)) self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.CrossCursor)) @@ -1205,7 +1534,7 @@ def _roiSubtract(self, locs): if mask_hits > 1: spectrum = _np.mean(spectra, axis=0) else: - spectrum = spectra + spectrum = _np.squeeze(spectra) spectrum = spectrum.astype(self.hsi.data.dtype) self.hsi.data -= spectrum[..., :] self.changeSlider() @@ -1213,6 +1542,7 @@ def _roiSubtract(self, locs): # Backup for Undo self.bcpre.add_step(['SubtractROI', 'Spectrum', spectrum]) + self.updateHistory() if self.ui.actionUndo_Backup_Enabled.isChecked(): try: _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) @@ -1254,7 +1584,7 @@ def nrbFromROI(self): # Need to send sender as the text name as the actual object # will change if self.cid is None: - self.cid = self.img_BW.mpl.mpl_connect('button_press_event', + self.cid = self.img_BW.mpl.mpl_connect('button_press_event', lambda event: self._roiClick(event, self._roiNRB, sender)) self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.CrossCursor)) @@ -1283,16 +1613,25 @@ def _roiNRB(self, locs, sender): mask_hits = _np.sum(mask) if mask_hits > 0: # Len(mask) > 0 - spectra = self.hsi.data_imag_over_real[mask == 1] + if isinstance(self.hsi.data, _h5py.Dataset): + spectra = self.hsi.data[_np.repeat(mask[...,None], + self.hsi.data.shape[-1], axis=-1) == 1] + else: + spectra = self.hsi.data[mask == 1] + + if _np.iscomplexobj(spectra) & self.ui.actionUseImagData.isChecked(): + spectra = spectra.imag + else: + spectra = spectra.real if mask_hits > 1: spectrum = _np.mean(spectra, axis=0) else: - spectrum = spectra + spectrum = _np.squeeze(spectra) spectrum = spectrum.astype(self.hsi.data.dtype) if sender == 'actionNRB_from_ROI': - self.nrb.data = spectrum + self.nrb.data = spectra self.ui.actionKramersKronig.setEnabled(True) self.ui.actionKKSpeedTest.setEnabled(True) self.ui.actionNRBSpectrum.setEnabled(True) @@ -1300,13 +1639,13 @@ def _roiNRB(self, locs, sender): elif sender == 'actionAppend_NRB_from_ROI': if self.nrb.size == 0: - self.nrb.data = spectrum + self.nrb.data = spectra else: self.nrb.data = (self.nrb.data + spectrum)/2 self.ui.actionKramersKronig.setEnabled(True) self.ui.actionNRBSpectrum.setEnabled(True) elif sender == 'actionNRB_from_ROI_Left_Side': - self.nrb_left.data = spectrum + self.nrb_left.data = spectra self.ui.actionLeftSideNRBSpect.setEnabled(True) if ((self.nrb_left.data is not None) and (self.nrb_right.data is not None)): @@ -1314,7 +1653,7 @@ def _roiNRB(self, locs, sender): self.ui.actionMergeNRBs.setEnabled(True) elif sender == 'actionNRB_from_ROI_Right_Side': - self.nrb_right.data = spectrum + self.nrb_right.data = spectra self.ui.actionRightSideNRBSpect.setEnabled(True) if ((self.nrb_left.data is not None) and (self.nrb_right.data is not None)): @@ -1399,9 +1738,14 @@ def _pointSpectrumPlot(self, locs): meta = {'x': x_loc, 'y': y_loc, 'x_pix': x_pix, 'y_pix': y_pix, 'overlay': True} - self.plotter.plot(self.hsi.f, - self.hsi.data_imag_over_real[y_pix, x_pix, rng], - label=label, meta=meta) + if _np.iscomplexobj(self.hsi.data) & self.ui.actionUseImagData.isChecked(): + self.plotter.plot(self.hsi.f, + self.hsi.data[y_pix, x_pix, rng].imag, + label=label, meta=meta) + else: + self.plotter.plot(self.hsi.f, + self.hsi.data[y_pix, x_pix, rng].real, + label=label, meta=meta) self.plotter.show() @@ -1426,13 +1770,31 @@ def _roiSpectrumPlot(self, locs): if mask_hits > 0: # Len(mask) > 0 rng = self.hsi.freq.op_range_pix - spectra = self.hsi.data_imag_over_real[mask == 1] + if isinstance(self.hsi.data, _h5py.Dataset): + + # * Can't do fancy boolean indexing with HDF + # * Make a square bounding box + m,n = _np.where(mask == 1) + rmin = m.min() + rmax = m.max()+1 + cmin = n.min() + cmax = n.max()+1 + + spectra = self.hsi.data[rmin:rmax, cmin:cmax,:][mask[rmin:rmax, cmin:cmax]==1] + + else: + spectra = self.hsi.data[mask == 1] + + if _np.iscomplexobj(spectra) & self.ui.actionUseImagData.isChecked(): + spectra = spectra.imag + else: + spectra = spectra.real if mask_hits > 1: spectrum = _np.mean(spectra[..., rng], axis=0) stddev = _np.std(spectra[..., rng], axis=0) else: - spectrum = spectra[..., rng] + spectrum = _np.squeeze(spectra[..., rng]) plot_num = self.plotter.n_lines @@ -1533,7 +1895,7 @@ def freqWindow(self): """ text, ok = _QInputDialog.getText(None, 'Frequency Window', 'Range Tuple (cm-1): ', - text='(500, 3400)') + text='(500, 3800)') if ok: text_str_list = text.strip('(').strip(')').strip().split(',') freqwin = [float(q) for q in text_str_list] @@ -1578,7 +1940,7 @@ def zeroFirstColumn(self): self.zc.transform(self.hsi.data) # Adjust mask - self.hsi._mask[:, self.zc.zero_col] *= 0 + # self.hsi._mask[:, self.zc.zero_col] *= 0 self.changeSlider() @@ -1591,7 +1953,7 @@ def zeroFirstRow(self): self.zr.transform(self.hsi.data) # Adjust mask - self.hsi._mask[self.zr.zero_row, :] *= 0 + # self.hsi._mask[self.zr.zero_row, :] *= 0 self.changeSlider() @@ -1604,7 +1966,7 @@ def zeroLastColumn(self): self.zc.transform(self.hsi.data) # Adjust mask - self.hsi._mask[:, self.zc.zero_col] *= 0 + # self.hsi._mask[:, self.zc.zero_col] *= 0 self.changeSlider() @@ -1617,7 +1979,7 @@ def zeroLastRow(self): self.zr.transform(self.hsi.data) # Adjust mask - self.hsi._mask[self.zr.zero_row, :] *= 0 + # self.hsi._mask[self.zr.zero_row, :] *= 0 self.changeSlider() @@ -1675,8 +2037,13 @@ def doKK(self): the Kramers-Kronig phase retrieval algorithm. """ - rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, - full=False) + if (self.preview_rois is None) | (not self.ui.actionUsePreviewROI.isChecked()): + preview_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, + full=False) + + else: + preview_spectra = self.get_preview_spectra(full=False) + nrb = self.nrb.mean() # Range of pixels to perform-over @@ -1684,7 +2051,7 @@ def doKK(self): out = DialogKKOptions.dialogKKOptions(data=[self.hsi.f, nrb[..., rng], - rand_spectra], parent=self) + preview_spectra], parent=self) if out is not None: cars_amp_offset = out['cars_amp'] @@ -1709,6 +2076,7 @@ def doKK(self): self.bcpre.add_step(['KK', 'CARSAmp', cars_amp_offset, 'NRBAmp', nrb_amp_offset, 'Phase', phase_offset, 'Norm', norm_to_nrb]) + self.updateHistory() if self.ui.actionUndo_Backup_Enabled.isChecked(): try: _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) @@ -1742,6 +2110,7 @@ def deNoiseNRB(self): self.bcpre.add_step(['DenoiseNrbSG', 'Win_size', win_size, 'Order', order]) + self.updateHistory() self.changeSlider() @@ -1770,7 +2139,7 @@ def deNoiseDark(self): self.bcpre.add_step(['DenoiseDarkSG', 'Win_size', win_size, 'Order', order]) - + self.updateHistory() self.changeSlider() @@ -1807,6 +2176,7 @@ def deNoise(self): # Backup for Undo self.bcpre.add_step(['SVD', 'SVs', svs]) + self.updateHistory() if self.ui.actionUndo_Backup_Enabled.isChecked(): try: @@ -1821,62 +2191,62 @@ def errorCorrectPhase(self): """ Error Correction: Phase """ - rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, - full=False) - if _np.iscomplexobj(rand_spectra): - rand_spectra = _np.angle(rand_spectra) + + if (self.preview_rois is None) | (not self.ui.actionUsePreviewROI.isChecked()): + preview_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, + full=True) + else: + preview_spectra = self.get_preview_spectra(full=True) + + if _np.iscomplexobj(preview_spectra): + preview_spectra = _np.angle(preview_spectra) rng = self.hsi.freq.op_range_pix - plugin = _widgetALS() - winPlotEffect = _DialogPlotEffect.dialogPlotEffect(rand_spectra, - x=self.hsi.f, + plugin = _widgetALS(x=self.hsi.f_full, rng=rng) + winPlotEffect = _DialogPlotEffect.dialogPlotEffect(preview_spectra, + x=self.hsi.f_full, plugin=plugin, parent=self) if winPlotEffect is not None: - asym_param = winPlotEffect.parameters['asym_param'] - smoothness_param = winPlotEffect.parameters['smoothness_param'] - redux_factor = winPlotEffect.parameters['redux'] - fix_end_points = winPlotEffect.parameters['fix_end_points'] - max_iter = winPlotEffect.parameters['max_iter'] - min_diff = winPlotEffect.parameters['min_diff'] - - phase_err_correct_als = _PhaseErrCorrectALS(smoothness_param=smoothness_param, - asym_param=asym_param, - redux=redux_factor, - order=2, - rng=rng, - fix_end_points=fix_end_points, - max_iter=max_iter, - min_diff=min_diff, - verbose=False) + # asym_param = winPlotEffect.parameters['asym_param'] + # smoothness_param = winPlotEffect.parameters['smoothness_param'] + # redux_factor = winPlotEffect.parameters['redux'] + # fix_end_points = winPlotEffect.parameters['fix_end_points'] + # max_iter = winPlotEffect.parameters['max_iter'] + # min_diff = winPlotEffect.parameters['min_diff'] + + phase_err_correct_als = _PhaseErrCorrectALS(**winPlotEffect.parameters) phase_err_correct_als.transform(self.hsi.data) + temp = ['PhaseErrorCorrectALS'] + [temp.extend(q) for q in winPlotEffect.parameters.items()] + self.bcpre.add_step(temp) # Backup for Undo - - if _np.size(asym_param) == 1: - self.bcpre.add_step(['PhaseErrorCorrectALS', - 'smoothness_param', smoothness_param, - 'asym_param', asym_param, - 'redux', redux_factor, - 'order', 2, - 'fix_end_points', fix_end_points, - 'max_iter', max_iter, - 'min_diff', min_diff]) - else: - self.bcpre.add_step(['PhaseErrorCorrectALS', - 'smoothness_param', smoothness_param, - 'asym_param_start', - winPlotEffect.parameters['asym_param_start'], - 'asym_param_end', - winPlotEffect.parameters['asym_param_end'], - 'redux', redux_factor, - 'order', 2, - 'fix_end_points', fix_end_points, - 'max_iter', max_iter, - 'min_diff', min_diff]) - + # if _np.size(asym_param) == 1: + # self.bcpre.add_step(['PhaseErrorCorrectALS', + # 'smoothness_param', smoothness_param, + # 'asym_param', asym_param, + # 'redux', redux_factor, + # 'order', 2, + # 'fix_end_points', fix_end_points, + # 'max_iter', max_iter, + # 'min_diff', min_diff]) + + # else: + # self.bcpre.add_step(['PhaseErrorCorrectALS', + # 'smoothness_param', smoothness_param, + # 'asym_param_start', + # winPlotEffect.parameters['asym_param_start'], + # 'asym_param_end', + # winPlotEffect.parameters['asym_param_end'], + # 'redux', redux_factor, + # 'order', 2, + # 'fix_end_points', fix_end_points, + # 'max_iter', max_iter, + # 'min_diff', min_diff]) + self.updateHistory() if self.ui.actionUndo_Backup_Enabled.isChecked(): try: _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) @@ -1891,15 +2261,20 @@ def errorCorrectScale(self): """ Error Correction: Scale """ - rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, - full=False) - if _np.iscomplexobj(rand_spectra): - rand_spectra = rand_spectra.real + + if (self.preview_rois is None) | (not self.ui.actionUsePreviewROI.isChecked()): + preview_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, + full=False) + else: + preview_spectra = self.get_preview_spectra(full=False) + + if _np.iscomplexobj(preview_spectra): + preview_spectra = preview_spectra.real rng = self.hsi.freq.op_range_pix plugin = _widgetSG(window_length=601, polyorder=2) - winPlotEffect = _DialogPlotEffect.dialogPlotEffect(rand_spectra, + winPlotEffect = _DialogPlotEffect.dialogPlotEffect(preview_spectra, x=self.hsi.f, plugin=plugin, parent=self) @@ -1916,6 +2291,7 @@ def errorCorrectScale(self): self.bcpre.add_step(['ScaleErrorCorrectSG', 'win_size', win_size, 'order', order]) + self.updateHistory() if self.ui.actionUndo_Backup_Enabled.isChecked(): try: @@ -1935,61 +2311,62 @@ def errorCorrectAmp(self): If data is complex, amplitude detrending occurs on and only on the \ imaginary portion """ - rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, - full=False) - if _np.iscomplexobj(rand_spectra): - rand_spectra = rand_spectra.imag + + if (self.preview_rois is None) | (not self.ui.actionUsePreviewROI.isChecked()): + preview_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, + full=True) + else: + preview_spectra = self.get_preview_spectra(full=True) + + if _np.iscomplexobj(preview_spectra): + preview_spectra = preview_spectra.imag rng = self.hsi.freq.op_range_pix - plugin = _widgetALS() - winPlotEffect = _DialogPlotEffect.dialogPlotEffect(rand_spectra, - x=self.hsi.f, + plugin = _widgetALS(x=self.hsi.f_full, rng=rng) + winPlotEffect = _DialogPlotEffect.dialogPlotEffect(preview_spectra, + x=self.hsi.f_full, plugin=plugin, parent=self) if winPlotEffect is not None: - asym_param = winPlotEffect.parameters['asym_param'] - smoothness_param = winPlotEffect.parameters['smoothness_param'] - redux_factor = winPlotEffect.parameters['redux'] - fix_end_points = winPlotEffect.parameters['fix_end_points'] - max_iter = winPlotEffect.parameters['max_iter'] - min_diff = winPlotEffect.parameters['min_diff'] - - - baseline_detrend = _SubtractBaselineALS(smoothness_param=smoothness_param, - asym_param=asym_param, - redux=redux_factor, - order=2, - rng=rng, - fix_end_points=fix_end_points, - max_iter=max_iter, - min_diff=min_diff, - verbose=False) + # asym_param = winPlotEffect.parameters['asym_param'] + # smoothness_param = winPlotEffect.parameters['smoothness_param'] + # redux_factor = winPlotEffect.parameters['redux'] + # fix_end_points = winPlotEffect.parameters['fix_end_points'] + # max_iter = winPlotEffect.parameters['max_iter'] + # min_diff = winPlotEffect.parameters['min_diff'] + + temp = ['AmpErrorCorrectALS'] + [temp.extend(q) for q in winPlotEffect.parameters.items()] + self.bcpre.add_step(temp) + + baseline_detrend = _SubtractBaselineALS(**winPlotEffect.parameters) + baseline_detrend.transform(self.hsi.data) # Backup for Undo - if _np.size(asym_param) == 1: - self.bcpre.add_step(['AmpErrorCorrectALS', - 'smoothness_param', smoothness_param, - 'asym_param', asym_param, - 'redux', redux_factor, - 'order', 2, - 'fix_end_points', fix_end_points, - 'max_iter', max_iter, - 'min_diff', min_diff]) - else: - self.bcpre.add_step(['AmpErrorCorrectALS', - 'smoothness_param', smoothness_param, - 'asym_param_start', - winPlotEffect.parameters['asym_param_start'], - 'asym_param_end', - winPlotEffect.parameters['asym_param_end'], - 'redux', redux_factor, - 'order', 2, - 'fix_end_points', fix_end_points, - 'max_iter', max_iter, - 'min_diff', min_diff]) - + # if _np.size(asym_param) == 1: + # self.bcpre.add_step(['AmpErrorCorrectALS', + # 'smoothness_param', smoothness_param, + # 'asym_param', asym_param, + # 'redux', redux_factor, + # 'order', 2, + # 'fix_end_points', fix_end_points, + # 'max_iter', max_iter, + # 'min_diff', min_diff]) + # else: + # self.bcpre.add_step(['AmpErrorCorrectALS', + # 'smoothness_param', smoothness_param, + # 'asym_param_start', + # winPlotEffect.parameters['asym_param_start'], + # 'asym_param_end', + # winPlotEffect.parameters['asym_param_end'], + # 'redux', redux_factor, + # 'order', 2, + # 'fix_end_points', fix_end_points, + # 'max_iter', max_iter, + # 'min_diff', min_diff]) + self.updateHistory() if self.ui.actionUndo_Backup_Enabled.isChecked(): try: @@ -2007,6 +2384,8 @@ def doUndo(self): """ self.bcpre.pop_to_last() self.hsi = _BCPre.load_pickle(self.bcpre.id_list[-1]) + self.updateHistory() + del_flag = 0 for count in self.bcpre.cut_list: @@ -2053,6 +2432,17 @@ def subDark(self): if out == _QMessageBox.Ok: sub_dark.transform(self.hsi.data) + # Backup for Undo + self.bcpre.add_step(['SubDark']) + self.updateHistory() + if self.ui.actionUndo_Backup_Enabled.isChecked(): + try: + _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) + except: + print('Error in pickle backup (Undo functionality)') + else: + self.bcpre.backed_up() + if nrbloaded: msg = _QMessageBox(self) msg.setIcon(_QMessageBox.Question) @@ -2089,18 +2479,6 @@ def subDark(self): if out == _QMessageBox.Ok: sub_dark.transform(self.nrb_right.data) - - # Backup for Undo - if darkloaded or nrbloaded: - self.bcpre.add_step(['SubDark']) - if self.ui.actionUndo_Backup_Enabled.isChecked(): - try: - _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) - except: - print('Error in pickle backup (Undo functionality)') - else: - self.bcpre.backed_up() - self.changeSlider() else: msg = _QMessageBox(self) @@ -2191,6 +2569,7 @@ def subResidual(self): self.bcpre.add_step(['SubResidual','RangeStart', freqwin[0], 'RangeEnd', freqwin[1]]) + self.updateHistory() if self.ui.actionUndo_Backup_Enabled.isChecked(): try: _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) @@ -2226,6 +2605,7 @@ def anscombe(self): self.bcpre.add_step(['Anscombe','Gauss_mean', 0.0, 'Gauss_std', out['stddev'], 'Poisson_multi', out['gain']]) + self.updateHistory() if self.ui.actionUndo_Backup_Enabled.isChecked(): try: _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) @@ -2257,6 +2637,7 @@ def inverseAnscombe(self): self.bcpre.add_step(['InvAnscombe','Gauss_mean', 0.0, 'Gauss_std', out['stddev'], 'Poisson_multi', out['gain']]) + self.updateHistory() if self.ui.actionUndo_Backup_Enabled.isChecked(): try: _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) @@ -2325,36 +2706,43 @@ def doMath(self): Mask = 1 else: if (operation_text == '') or (operation_text == ' '): # Return just a plane - Mask = _peakamps.MeasurePeak.measure(self.hsi.data_imag_over_real, + Mask = _peakamps.MeasurePeak.measure(self.hsi.data, condloc1) elif operation_text == '+': # Addition - Mask = _peakamps.MeasurePeakAdd.measure(self.hsi.data_imag_over_real, + Mask = _peakamps.MeasurePeakAdd.measure(self.hsi.data, condloc1, condloc2) elif operation_text == '-': # Subtraction - Mask = _peakamps.MeasurePeakMinus.measure(self.hsi.data_imag_over_real, + Mask = _peakamps.MeasurePeakMinus.measure(self.hsi.data, condloc1, condloc2) elif operation_text == '*': # Multiplication - Mask = _peakamps.MeasurePeakMultiply.measure(self.hsi.data_imag_over_real, + Mask = _peakamps.MeasurePeakMultiply.measure(self.hsi.data, condloc1, condloc2) elif operation_text == '/': # Division - Mask = _peakamps.MeasurePeakDivide.measure(self.hsi.data_imag_over_real, + Mask = _peakamps.MeasurePeakDivide.measure(self.hsi.data, condloc1, condloc2) elif operation_text == 'SUM': # Summation over range - Mask = _peakamps.MeasurePeakSummation.measure(self.hsi.data_imag_over_real, + Mask = _peakamps.MeasurePeakSummation.measure(self.hsi.data, condloc1, condloc2) elif operation_text == 'Peak b/w troughs': # Peak between troughs - Mask = _peakamps.MeasurePeakBWTroughs.measure(self.hsi.data_imag_over_real, + Mask = _peakamps.MeasurePeakBWTroughs.measure(self.hsi.data, condloc1, condloc2, condloc3) else: pass + if Mask is not None: + if _np.iscomplexobj(self.hsi.data) & self.ui.actionUseImagData.isChecked(): + Mask = Mask.imag + else: + Mask = Mask.real + + if cond_set is True: inequality_text = self.img_RGB_list[rgbnum].math.ui.comboBoxCondInEquality.currentText() inequality_val = self.img_RGB_list[rgbnum].math.ui.spinBoxInEquality.value() @@ -2418,50 +2806,58 @@ def doMath(self): if freq_set == True: if (operation_text == '') or (operation_text == ' '): # Return just a plane self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \ - _peakamps.MeasurePeak.measure(self.hsi.data_imag_over_real, + _peakamps.MeasurePeak.measure(self.hsi.data, oploc1) - self.img_RGB_list[rgbnum].changeColor() - #self.updateImgColorMinMax() elif operation_text == '+': # Addition self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \ - _peakamps.MeasurePeakAdd.measure(self.hsi.data_imag_over_real, + _peakamps.MeasurePeakAdd.measure(self.hsi.data, oploc1, oploc2) - self.img_RGB_list[rgbnum].changeColor() - #self.updateImgColorMinMax() elif operation_text == '-': # Subtraction self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \ - _peakamps.MeasurePeakMinus.measure(self.hsi.data_imag_over_real, + _peakamps.MeasurePeakMinus.measure(self.hsi.data, oploc1, oploc2) - self.img_RGB_list[rgbnum].changeColor() - #self.updateImgColorMinMax() elif operation_text == '*': # Multiplication self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \ - _peakamps.MeasurePeakMultiply.measure(self.hsi.data_imag_over_real, + _peakamps.MeasurePeakMultiply.measure(self.hsi.data, oploc1, oploc2) - self.img_RGB_list[rgbnum].changeColor() - #self.updateImgColorMinMax() elif operation_text == '/': # Division self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \ - _peakamps.MeasurePeakDivide.measure(self.hsi.data_imag_over_real, + _peakamps.MeasurePeakDivide.measure(self.hsi.data, oploc1, oploc2) - self.img_RGB_list[rgbnum].changeColor() - #self.updateImgColorMinMax() elif operation_text == 'SUM': # Division self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \ - _peakamps.MeasurePeakSummation.measure(self.hsi.data_imag_over_real, + _peakamps.MeasurePeakSummation.measure(self.hsi.data, oploc1, oploc2) - self.img_RGB_list[rgbnum].changeColor() - #self.updateImgColorMinMax() elif operation_text == 'Peak b/w troughs': # Division self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \ - _peakamps.MeasurePeakBWTroughs.measure(self.hsi.data_imag_over_real, + _peakamps.MeasurePeakBWTroughs.measure(self.hsi.data, oploc1, oploc2, - oploc3) - self.img_RGB_list[rgbnum].changeColor() - #self.updateImgColorMinMax() + oploc3) else: pass + + if (_np.iscomplexobj(self.img_RGB_list[rgbnum].data.grayscaleimage) & + self.ui.actionUseImagData.isChecked()): + + self.img_RGB_list[rgbnum].data.grayscaleimage = self.img_RGB_list[rgbnum].data.grayscaleimage.imag + else: + self.img_RGB_list[rgbnum].data.grayscaleimage = self.img_RGB_list[rgbnum].data.grayscaleimage.real + + + minner = self.img_RGB_list[rgbnum].data.grayscaleimage.min() + minner = _np.sign(minner)*(1.1*_np.abs(minner)) + + maxer = self.img_RGB_list[rgbnum].data.grayscaleimage.max() + maxer = _np.sign(maxer)*(1.1*_np.abs(maxer)) + + self.img_RGB_list[rgbnum].gsinfo.ui.spinBoxMin.setMinimum(minner) + self.img_RGB_list[rgbnum].gsinfo.ui.spinBoxMin.setMaximum(maxer) + self.img_RGB_list[rgbnum].gsinfo.ui.spinBoxMax.setMinimum(minner) + self.img_RGB_list[rgbnum].gsinfo.ui.spinBoxMax.setMaximum(maxer) + + self.img_RGB_list[rgbnum].changeColor() + else: pass self.doComposite() @@ -2478,6 +2874,18 @@ def setOpFreq1(self): self.img_RGB_list[rgbnum].data.opfreq1 = currentfreq self.img_RGB_list[rgbnum].math.ui.pushButtonOpFreq1.setText(str(round(currentfreq, 1))) self.img_RGB_list[rgbnum].data.grayscaleimage = self.img_BW.data.grayscaleimage + + minner = self.img_RGB_list[rgbnum].data.grayscaleimage.min() + minner = _np.sign(minner)*(1.1*_np.abs(minner)) + + maxer = self.img_RGB_list[rgbnum].data.grayscaleimage.max() + maxer = _np.sign(maxer)*(1.1*_np.abs(maxer)) + + self.img_RGB_list[rgbnum].gsinfo.ui.spinBoxMin.setMinimum(minner) + self.img_RGB_list[rgbnum].gsinfo.ui.spinBoxMin.setMaximum(maxer) + self.img_RGB_list[rgbnum].gsinfo.ui.spinBoxMax.setMinimum(minner) + self.img_RGB_list[rgbnum].gsinfo.ui.spinBoxMax.setMaximum(maxer) + self.img_RGB_list[rgbnum].changeColor() self.img_RGB_list[rgbnum].mpl.draw() @@ -2588,32 +2996,51 @@ def spectrumColorImg(self): mloc, nloc = _np.where(Mask) - if mask_hits > 1: - mean_spect = self.hsi.data_imag_over_real[mloc, nloc, :][:, self.hsi.freq.op_range_pix].mean(axis=0) - std_spect = self.hsi.data_imag_over_real[mloc, nloc, :][:, self.hsi.freq.op_range_pix].std(axis=0) - self.plotter.plot(self.hsi.f, mean_spect, label='Mean spectrum ({})'.format(mask_hits)) - elif mask_hits == 1: - mean_spect = _np.squeeze(self.hsi.data_imag_over_real[mloc,nloc,:])[self.hsi.freq.op_range_pix] + if mask_hits > 0: + rng = self.hsi.freq.op_range_pix - std_spect = 0 - # Plot spectrum + if isinstance(self.hsi.data, _h5py.Dataset): - self.plotter.plot(self.hsi.f, mean_spect, label='Spectrum ({})'.format(mask_hits)) + # * Can't do fancy boolean indexing with HDF + # * Make a square bounding box + rmin = mloc.min() + rmax = mloc.max()+1 + cmin = nloc.min() + cmax = nloc.max()+1 - # Check color of line b/c uses color cycler-- for fill_b/w - color = self.plotter.list_all[-1].style_dict['color'] + spectra = self.hsi.data[rmin:rmax, cmin:cmax,:][Mask[rmin:rmax, cmin:cmax]==1] + + else: + spectra = self.hsi.data[Mask == 1] + + if _np.iscomplexobj(spectra) & self.ui.actionUseImagData.isChecked(): + spectra = spectra.imag + else: + spectra = spectra.real - # Alternative - #color = self.plotter.modelLine._model_data[-1]['color'] + if mask_hits > 1: + spectrum = _np.mean(spectra[..., rng], axis=0) + stddev = _np.std(spectra[..., rng], axis=0) + else: + spectrum = _np.squeeze(spectra[..., rng]) + stddev = 0 + + self.plotter.plot(self.hsi.f, spectrum, label='Mean spectrum ({})'.format(mask_hits)) + + # Check color of line b/c uses color cycler-- for fill_b/w + color = self.plotter.list_all[-1].style_dict['color'] - # Plot +-1 std. dev. - if mask_hits > 1: - self.plotter.fill_between(self.hsi.f, mean_spect - std_spect, - mean_spect + std_spect, - color=color, - alpha=0.25, - label=r'$\pm$1 Std. Dev. ({})'.format(mask_hits)) + # Alternative + #color = self.plotter.modelLine._model_data[-1]['color'] + + # Plot +-1 std. dev. + if mask_hits > 1: + self.plotter.fill_between(self.hsi.f, spectrum - stddev, + spectrum + stddev, + color=color, + alpha=0.25, + label=r'$\pm$1 Std. Dev. ({})'.format(mask_hits)) self.plotter.show() @@ -2629,7 +3056,7 @@ def createImgBW(self, img): self.img_BW.createImg(img=img, xunits=xunits, yunits=yunits, - extent=extent, + extent=extent, cmap=self.img_BW.colormode.ui.comboBoxColormap.currentText()) if self.img_BW.ui.checkBoxFixed.checkState()==0: @@ -2659,7 +3086,18 @@ def changeSlider(self): self.ui.lineEditFreq.setText(str(round(self.hsi.f[pos],2))) # Set BW Class Data - self.img_BW.data.grayscaleimage = self.hsi.data_imag_over_real[:, :, pos+offset] + self.img_BW.data.grayscaleimage = self.hsi.data[:, :, pos+offset] + if _np.iscomplexobj(self.img_BW.data.grayscaleimage) & self.ui.actionUseImagData.isChecked(): + self.img_BW.data.grayscaleimage = self.img_BW.data.grayscaleimage.imag + else: + self.img_BW.data.grayscaleimage = self.img_BW.data.grayscaleimage.real + + val_extrema = _np.max(_np.abs(self.img_BW.data.grayscaleimage)) + + self.img_BW.ui.spinBoxMin.setMinimum(-1.1*val_extrema) + self.img_BW.ui.spinBoxMin.setMaximum(1.1*val_extrema) + self.img_BW.ui.spinBoxMax.setMinimum(-1.1*val_extrema) + self.img_BW.ui.spinBoxMax.setMaximum(1.1*val_extrema) xlabel = '' if isinstance(self.hsi.x_rep.label, str): @@ -2685,11 +3123,11 @@ def changeSlider(self): # if self.img_BW.ui.checkBoxFixed.checkState() == 0: # self.img_BW.data.setmax = None # self.img_BW.data.setmin = None - + # Set axis to original limits self.img_BW.mpl.ax.axis(orig_axis_lims) - if not self._mpl_v2: + if self._mpl_v1: self.img_BW.mpl.ax.hold(True) except: @@ -2723,16 +3161,29 @@ def changeSlider(self): ls=ls, ms=ms, alpha=a, label=label) - if self.ui.actionShowOverlayLegend.isChecked(): + if self.ui.actionShowOverlayLegend.isChecked(): + if self.overlays: try: - self.img_BW.mpl.ax.legend(loc='best') + # self.img_BW.mpl.ax.legend(loc='best') + lg = self.img_BW.mpl.ax.legend(loc='lower left', + mode='expand', + bbox_to_anchor=(0.01, 1.02, 1., 0.2), + ncol=2, fontsize=9) + self.img_BW.mpl.ax.add_artist(lg) + try: + self.img_BW.mpl.fig.tight_layout(pad=1) + except: + print('tight_layout failed (CrikitUI: 3') except: - pass + print('Error in showing overlay legend') except: print('Error in changeSlider: display overlays') self.img_BW.mpl.draw() + if self.ui.actionShowPreviewROI.isChecked(): + self.showPreviewRois() + if self.bcpre.backed_flag.count(True) > 1: self.ui.actionUndo.setEnabled(True) else: @@ -2793,7 +3244,7 @@ def doComposite(self): self.img_Composite2.initData(self.img_RGB_list) self.img_Composite2.changeMode() - + self.img_Composite2.data.set_x(self.hsi.x, xlabel) self.img_Composite2.data.set_y(self.hsi.y, ylabel) self.img_Composite2.createImg(img=self.img_Composite2.data.image, @@ -2831,7 +3282,7 @@ def makeRamanPhantom(self): dialog = DialogModel.dialogModel(cplx=cplx, parent=self) if dialog is not None: model = _Model(subsample=dialog['subsample']) - + wn_start = dialog['wn_start'] wn_end = dialog['wn_end'] @@ -2842,23 +3293,23 @@ def makeRamanPhantom(self): lam_end *= 1e9 # nm lam_ctr = (lam_start + lam_end) / 2 # nm - + n_pix = _np.ceil((lam_end-lam_start) / dialog['wl_slope']) # Make a properly linear frequency-vector and polyfit f = dialog['wl_slope'] * _np.arange(n_pix) # Temporary frequency vec f -= f.mean() f += lam_ctr - + a_vec = _np.polyfit(_np.arange(n_pix), f, 1) - + calib = {'a_vec': a_vec, 'ctr_wl': lam_ctr, 'ctr_wl0': lam_ctr, 'n_pix': n_pix, 'probe': dialog['probe'], 'units': 'nm'} - + f = _calib_pix_wn(calib)[0] model.make_hsi(f=f) @@ -2929,8 +3380,8 @@ def makeRamanPhantom(self): self.changeSlider() else: pass - - + + def makeBCARSPhantom(self): """ Generate a numerical phantom for BCARS @@ -2940,7 +3391,7 @@ def makeBCARSPhantom(self): dialog = DialogModel.dialogModel(cplx=cplx, parent=self) if dialog is not None: model = _Model(subsample=dialog['subsample']) - + wn_start = dialog['wn_start'] wn_end = dialog['wn_end'] @@ -2951,23 +3402,23 @@ def makeBCARSPhantom(self): lam_end *= 1e9 # nm lam_ctr = (lam_start + lam_end) / 2 # nm - + n_pix = _np.ceil((lam_end-lam_start) / dialog['wl_slope']) # Make a properly linear frequency-vector and polyfit f = dialog['wl_slope'] * _np.arange(n_pix) # Temporary frequency vec f -= f.mean() f += lam_ctr - + a_vec = _np.polyfit(_np.arange(n_pix), f, 1) - + calib = {'a_vec': a_vec, 'ctr_wl': lam_ctr, 'ctr_wl0': lam_ctr, 'n_pix': n_pix, 'probe': dialog['probe'], 'units': 'nm'} - + f = _calib_pix_wn(calib)[0] model.make_hsi(f=f) @@ -2990,7 +3441,7 @@ def makeBCARSPhantom(self): self.nrb.data = _np.abs(source*nrb)**2 self.nrb.freq = self.hsi.freq - + add_gnoise = dialog['gnoise_bool'] # AWGN (Gaussian) add_pnoise = dialog['pnoise_bool'] # Poisson noise add_dark = dialog['dark_bool'] # Dark background -- just a constant @@ -3054,13 +3505,13 @@ def makeBCARSPhantom(self): self.changeSlider() else: pass - + def crikit_launch(**kwargs): """ Command line launching of CRIkitUI. Input kwargs (Optional) - ------------ + ------------------------ hsi : crikit.data.Hsi Hsi instance @@ -3115,7 +3566,7 @@ def crikit_launch(**kwargs): obj = _QWidget() else: obj = parent - + kwargs['parent'] = obj # print('Kwargs: {}'.format(kwargs)) win = CRIkitUI_process(**kwargs) ### EDIT ### diff --git a/crikit/cri/algorithms/kk.py b/crikit/cri/algorithms/kk.py index b7a294b..2f79c1b 100644 --- a/crikit/cri/algorithms/kk.py +++ b/crikit/cri/algorithms/kk.py @@ -18,6 +18,8 @@ import numpy as _np from scipy import fftpack as _fftpack +from crikit.utils.general import pad as _pad + __all__ = ['kkrelation', 'hilbertfft'] _DEFAULT_THREADS = 1 @@ -119,7 +121,6 @@ def kkrelation(bg, cri, phase_offset=0.0, norm_by_bg=True, pad_factor=1): return out # return _ne.evaluate('sqrt(cri)*exp(1j*phase_offset + 1j*h)') - def hilbertfft(spectra, pad_factor=1, use_pyfftw=True): """ Compute the one-dimensional Hilbert Transform. @@ -158,18 +159,16 @@ def hilbertfft(spectra, pad_factor=1, use_pyfftw=True): freq_len = spectra.shape[-1] freq_pad_len = freq_len*(2*pad_factor+1) - pad_len = freq_len*(pad_factor) time_vec = _np.fft.fftfreq(freq_pad_len) if pad_factor > 0: - pad_left = _np.dot(spectra[..., 0][..., None], _np.ones((1, pad_len))) - pad_right = _np.dot(spectra[..., -1][..., None], _np.ones((1, pad_len))) - padded = _np.concatenate((pad_left, spectra, pad_right), axis=-1) + padded, window = _pad(spectra, pad_factor*spectra.shape[-1], 'edge') else: padded = spectra + window = None padded = padded.astype(_np.complex) - + # Use pyFFTW (supposed optimal) library or Scipy # Note (although not obvious with pyFFTW) these functions overwrite # the input variable-- saves memory and increases speed @@ -197,7 +196,10 @@ def hilbertfft(spectra, pad_factor=1, use_pyfftw=True): padded[_np.isnan(padded)] = 1e-8 padded[_np.isinf(padded)] = 1e-8 - return _np.real(padded[..., pad_len:pad_len + freq_len]) + if window is not None: + return padded[..., window == 1].real + else: + return padded.real if __name__ == '__main__': # pragma: no cover import timeit as _timeit diff --git a/crikit/cri/error_correction.py b/crikit/cri/error_correction.py index 5170c4b..a4a523d 100644 --- a/crikit/cri/error_correction.py +++ b/crikit/cri/error_correction.py @@ -27,7 +27,7 @@ class PhaseErrCorrectALS: def __init__(self, smoothness_param=1, asym_param=1e-2, redux=10, order=2, rng=None, fix_end_points=False, fix_rng=None, fix_const=1, max_iter=100, min_diff=1e-5, - **kwargs): + verbose=True, **kwargs): self.rng = _rng_is_pix_vec(rng) @@ -42,7 +42,8 @@ def __init__(self, smoothness_param=1, asym_param=1e-2, 'fix_rng' : fix_rng, 'fix_const' : fix_const, 'max_iter' : max_iter, - 'min_diff' : min_diff}) + 'min_diff' : min_diff, + 'verbose' : verbose}) def _calc(self, data, ret_obj, **kwargs): @@ -59,7 +60,8 @@ def _calc(self, data, ret_obj, **kwargs): counter = 1 for idx in _np.ndindex(shp): - print('Detrended iteration {} / {}'.format(counter, total_num)) + if self._k['verbose']: + print('Detrended iteration {} / {}'.format(counter, total_num)) ph = _np.unwrap(_np.angle(data[idx])) # if self.rng is None: err_phase = self._inst_als.calculate(ph) diff --git a/crikit/cri/tests/__init__.py b/crikit/cri/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/crikit/cri/tests/test_hilbert.py b/crikit/cri/tests/test_hilbert.py index 367a17e..659d0b2 100644 --- a/crikit/cri/tests/test_hilbert.py +++ b/crikit/cri/tests/test_hilbert.py @@ -16,6 +16,7 @@ def test_pyfftw_hilbert_no_pad(): y = 2/(2**2 + x**2) hilb_y = hilbertfft(y, pad_factor=0, use_pyfftw=True) hilb_y_analytical = x/(2**2 + x**2) + print(hilb_y.shape) assert_array_almost_equal(hilb_y_analytical, hilb_y, decimal=2) def test_pyfftw_hilbert_pad(): diff --git a/crikit/data/frequency.py b/crikit/data/frequency.py index 1132707..426e3d7 100644 --- a/crikit/data/frequency.py +++ b/crikit/data/frequency.py @@ -87,7 +87,7 @@ class Frequency: are items of interest or a large dynamic range across a spectrum. - For functions, methods, etc. that take into account _list_ \ - parameters, they should default to op_list_ if plot_list_ are set to \ + parameters, they should default to op_list_* if plot_list_* are set to \ None. """ @@ -214,7 +214,7 @@ def update(self): else: self.calib = self._calib_orig - self.data, self.units = self.calib_fcn(self.calib) + self.data, self.units = self.calib_fcn(self.calib) # pylint: disable=not-callable @property def op_list_pix(self): @@ -227,6 +227,7 @@ def op_list_pix(self,value): value = list(value) value.sort() self._op_list_pix = value + # if self.data is not None: # ! Allow setting without freq or not? self._op_list_freq = self.get_closest_freq(value) self._op_list_freq.sort() elif len(value) != 2 and _np.mod(len(value),2) == 0 and len(value) != 0: @@ -427,13 +428,17 @@ def calib_pix_wn(calib_obj): if 'units' not in calib: calib['units'] = 'nm' - factor = 1e7 - elif calib['units'] == 'nm': + elif isinstance(calib['units'], bytes): + calib['units'] = calib['units'].decode() + + if calib['units'] == 'nm': factor = 1e7 elif calib['units'] == 'um': factor = 1e4 else: - raise ValueError('Only nanometer (\'nm\') and micrometer (\'um\') units accepted') + errstr1 = 'Only nanometer (\'nm\') and micrometer (\'um\') units accepted. ' + errstr2 = '{} provided of type {}.'.format(calib['units'], type(calib['units'])) + raise ValueError(errstr1 + errstr2) wl_vec, _ = calib_pix_wl(calib_obj) wn_vec = factor/wl_vec - factor/calib['probe'] return (wn_vec, 'cm$^{-1}$') diff --git a/crikit/data/hsi.py b/crikit/data/hsi.py index 1716a68..16c190b 100644 --- a/crikit/data/hsi.py +++ b/crikit/data/hsi.py @@ -54,12 +54,6 @@ class Hsi(_Spectrum): Attributes ---------- - data_imag_over_real : ndarray (3D) - If data is complex, return the imaginary portion - - data_real_over_imag : ndarray (3D) - If data is complex, return the real portion - shape : tuple, read-only Shape of data @@ -81,12 +75,16 @@ class Hsi(_Spectrum): Notes ----- - * freq object contains some useful parameters such as op_range_\* and \ - plot_range_\*, which define spectral regions-of-interest. (It's debatable \ + * freq object contains some useful parameters such as op_range_* and \ + plot_range_*, which define spectral regions-of-interest. (It's debatable \ as to whether those parameters should be in Frequency or Spectrum classes) """ + # Configurations + config = {} + config['nd_axis'] = -1 + def __init__(self, data=None, freq=None, x=None, y=None, x_rep=None, y_rep=None, label=None, units=None, meta=None): @@ -103,6 +101,42 @@ def __init__(self, data=None, freq=None, x=None, y=None, x_rep=None, if y is None and y_rep is not None: self.y_rep = _copy.deepcopy(y_rep) + @staticmethod + def _mean_axes(*args, **kwargs): + """ Inhereted from Spectrum """ + raise NotImplementedError('Only applicable to Spectrum class.') + + @staticmethod + def _reshape_axes(shape, spectral_axis): + """ + Parameters + ---------- + shape : tuple + Input data shape + + spectral_axis : int + Spectral axis + + Returns + ------- + Reshape vector + """ + ndim = len(shape) + + if ndim == 1: + out = [1, 1, 1] + out[spectral_axis] = shape[0] + elif ndim == 2: # ! Super-wonky + out = [1, shape[0], shape[1]] + elif ndim == 3: + out = shape + elif ndim > 3: + out = [-1, shape[-2], shape[-1]] + else: + raise ValueError('Shape error') + + return tuple(out) + @property def mask(self): return self._mask @@ -152,35 +186,28 @@ def data(self): @data.setter def data(self, value): - if isinstance(value, _np.ndarray): - if value.ndim == 3: - if self.freq is None or self.freq.op_list_pix is None: - self._data = value - self._mask = _np.ones((self._data.shape[0], - self._data.shape[1]), - dtype=_np.int) - else: - if value.shape[-1] == self.freq.op_range_pix.size: - temp = _np.zeros((self._data.shape),dtype=value.dtype) - temp[:,:,self.freq.op_range_pix] = value - self._data = temp - self._mask = _np.ones((self._data.shape[0], - self._data.shape[1]), - dtype=_np.int) - elif value.shape[-1] == self._data.shape[-1]: - self._data = value - self._mask = _np.ones((self._data.shape[0], - self._data.shape[1]), - dtype=_np.int) - else: - #raise TypeError('data is of an unrecognized shape: {}'.format(value.shape)) - raise TypeError('pre-data: {}, value: {}'.format(self._data.shape,value.shape)) - else: - raise TypeError('data must be 3D') - else: - print('Assigning non-ndarray to data. Not shape checking') - self._data = value + if not isinstance(value, _np.ndarray): + raise TypeError('data must be of type ndarray') + + ax_rs = self._reshape_axes(value.shape, self.config['nd_axis']) + # self._mask = _np.ones(tuple([n for n in range(3) if n != self.config['nd_axis']]), + # dtype=_np.int) + + if self.freq is None or self.freq.op_list_pix is None: + self._data = value.reshape(ax_rs) + else: + if value.shape[self.config['nd_axis']] == self.freq.op_range_pix.size: + temp = _np.zeros((self._data.shape),dtype=value.dtype) + temp[:,:,self.freq.op_range_pix] = value.reshape(ax_rs) + self._data = 1*temp + del temp + elif value.shape[self.config['nd_axis']] == self._data.shape[self.config['nd_axis']]: + temp = _np.zeros((self._data.shape),dtype=value.dtype) + temp[..., self.freq.op_range_pix] = value.reshape(ax_rs)[..., self.freq.op_range_pix] + self._data = 1*temp + del temp + def check(self): """ Check x, y, and freq to make sure the dimensions agree with data diff --git a/crikit/data/mosaic.py b/crikit/data/mosaic.py new file mode 100644 index 0000000..747b8da --- /dev/null +++ b/crikit/data/mosaic.py @@ -0,0 +1,376 @@ +import numpy as _np +import h5py as _h5py + +class Mosaic: + """ + Mosaic Class + + Notes + ----- + + - input objects mts be ndarray + - input objects must be 2D/3D # ! Higher-D? + - For 3D objects, assumed to be Y, X, Color + + """ + def __init__(self): + self._data = None + + self.parameters = {} + self.parameters['StartC'] = 0 + self.parameters['StartR'] = 0 + self.parameters['EndC'] = -0 + self.parameters['EndR'] = -0 + self.parameters['Transpose'] = False + self.parameters['FlipVertical'] = False + self.parameters['FlipHorizontally'] = False + self.parameters['Order'] = 'R' + self.parameters['Compress'] = False + self.parameters['Shape'] = [1, 1] + + def __repr__(self): # pragma: no cover + if self._data: + return 'Mosaic contains {} component(s)'.format(self.size) + else: + return 'Empty Collection' + + def attr_dict(self, prefix='Mosaic.'): + temp = {} + for k in self.parameters: + temp.update({prefix+k:self.parameters[k]}) + return temp + + @property + def shape(self): + if self._data: + return tuple([q.shape for q in self._data]) + + @property + def size(self): + if isinstance(self._data, list): + return len(self._data) + + def append(self, obj): + """ Append new object to data. Check dimensions """ + if not (isinstance(obj, _np.ndarray) | isinstance(obj, _h5py.Dataset)): + raise TypeError('Appended object must be a numpy array') + if not ((obj.ndim > 1) & (obj.ndim <= 3)): + raise TypeError('Appended object must be a numpy array with ndim 2 or 3') + + if not self._data: + self._data = [] + + if self._data: + if not _np.unique([q.ndim for q in self._data])[0] == obj.ndim: + err_str1 = 'New component ndim must match existing ndim' + err_str2 = ' ({})'.format(self._data[0].ndim) + raise TypeError(err_str1 + err_str2) + + self._data.append(obj) + + @property + def issamedim(self): + if self._data: + return _np.unique([q.ndim for q in self._data]).size == 1 + + @property + def is2d(self): + if self._data: + if not self.issamedim: + raise TypeError('Not every component is of the same dimension') + return len(self.unitshape) == 2 + + @property + def is3d(self): + if self._data: + if not self.issamedim: + raise TypeError('Not every component is of the same dimension') + return len(self.unitshape) == 3 + + + @property + def unitshape(self): + if self.parameters['EndR'] > 0: + raise ValueError('parameter EndR must be <= 0') + if self.parameters['EndC'] > 0: + raise ValueError('parameter EndC must be <= 0') + + if self._data: + temp = list(self.unitshape_orig) + + sr = self.parameters['StartR'] + er = self.parameters['EndR'] + sc = self.parameters['StartC'] + ec = self.parameters['EndC'] + + temp[0] -= (sr - er) + temp[1] -= (sc - ec) + + return tuple(temp) + + @property + def unitshape_orig(self): + if self._data: + return tuple(_np.array(self.shape).max(axis=0).tolist()) + + + @property + def dtype(self): + """ Return the highest dtype """ + if self._data: + dt = [q.dtype.kind for q in self._data] + + if dt.count('c') > 0: + return _np.complex + elif dt.count('f') > 0: + return _np.float + elif dt.count('i') > 0: + return _np.int + + + def mosaic_shape(self, shape=None, idx=None): + """ Return the shape of a would-be mosaic """ + if shape is None: + shape = self.parameters['Shape'] + else: + self.parameters['Shape'] = shape + + if self._data: + if not len(shape) == 2: + raise ValueError('Shape must be a tuple/list with 2 entries (Y, X)') + + if _np.prod(shape) < self.size: + raise ValueError('The total number of subimages (shape) need be >= number of components ({})'.format(self.size)) + + us = list(self.unitshape) + + if self.parameters['Transpose']: + temp = 1*us[0] + us[0] = us[1] + us[1] = temp + + if (len(us) == 3): + if idx is None: + out_is2d = False + else: + out_is2d = True + else: + out_is2d = True + + if out_is2d: + return (shape[0]*us[0], shape[1]*us[1]) + else: + return (shape[0]*us[0], shape[1]*us[1], us[2]) + + def _mosaic(self, shape=None, idx=None, out=None, mask=False): + """ Mosaic super method """ + if shape is None: + shape = self.parameters['Shape'] + else: + self.parameters['Shape'] = shape + + compress = self.parameters['Compress'] + + if self._data: + if mask: + idx = 0 + + if not len(shape) == 2: + raise ValueError('Shape must be a tuple/list with 2 entries (Y, X)') + + if _np.prod(shape) < self.size: + raise ValueError('The total number of subimages (shape) need be >= number of components ({})'.format(self.size)) + + if out is None: + if not mask: + out = _np.zeros(self.mosaic_shape(shape=shape, idx=idx), + dtype=self.dtype) + else: + # For mask, start at -1 + out = -1 + _np.zeros(self.mosaic_shape(shape=shape, idx=idx), + dtype=self.dtype) + out_provided = False + else: + out_provided = True + + sr = 1*self.parameters['StartR'] + sc = 1*self.parameters['StartC'] + er = 1*self.parameters['EndR'] + ec = 1*self.parameters['EndC'] + if sr == 0: + sr = None + if sc == 0: + sc = None + if er == 0: + er = None + if ec == 0: + ec = None + + # Slice to take on each sub-image + slice_sub_r = slice(sr, er, 1) + slice_sub_c = slice(sc, ec, 1) + + sub_img_counter = 0 + num_components = self.size + + order = self.parameters['Order'] + + if order == 'C': + sh_outter = shape[0] + sh_inner = shape[1] + else: # Order == 'R' + sh_outter = shape[1] + sh_inner = shape[0] + + # * h5 write_direct has strict limitations + cannot_write_direct = (self.parameters['Transpose'] | + self.parameters['FlipVertical'] | + self.parameters['FlipHorizontally']) + + # * Only used by out matrix + us = list(self.unitshape) + if self.parameters['Transpose']: + temp = 1*us[0] + us[0] = us[1] + us[1] = temp + + for num_outter in range(sh_outter): + for num_inner in range(sh_inner): + if order == 'C': + numR = num_outter + numC = num_inner + else: # Order == 'R' + numC = num_outter + numR = num_inner + + if sub_img_counter < num_components: + if mask: + data = sub_img_counter * \ + _np.ones(self._data[sub_img_counter][slice_sub_r, + slice_sub_c].shape[0:2], + dtype=_np.int) + elif idx is None: + data = self._data[sub_img_counter][slice_sub_r, slice_sub_c] + else: + data = self._data[sub_img_counter][slice_sub_r, slice_sub_c, idx] + + data_is2d = (data.ndim == 2) + + if self.parameters['FlipHorizontally']: + data = _np.flip(data, axis=1) + if self.parameters['FlipVertical']: + data = _np.flip(data, axis=0) + if self.parameters['Transpose']: + if data_is2d: + data = data.T + else: + data = _np.transpose(data, axes=(1,0,2)) + + # * Using this in case m/ndata is smaller than u[0/1] + mdata, ndata = data.shape[0], data.shape[1] + + if isinstance(out, _h5py.Dataset) & (not cannot_write_direct): + out.write_direct(source=data, + dest_sel=_np.s_[(numR*us[0]):(numR*us[0] + mdata), + (numC*us[1]):(numC*us[1] + ndata)]) + else: + out[(numR*us[0]):(numR*us[0] + mdata), + (numC*us[1]):(numC*us[1] + ndata)] = 1*data + sub_img_counter += 1 + + if not out_provided: + if not compress: + return out + else: + if mask: # Cute trick since first ROI is +0 and blank is -1 + out += 1 + + if out.ndim == 3: + out = out[:, (out.sum(axis=0)[:, 0] != 0), :] + out = out[(out.sum(axis=1)[:, 0] != 0), :, :] + + else: # 2D + out = out[:, (out.sum(axis=0) != 0)] + out = out[(out.sum(axis=1) != 0), :] + if mask: # Cute trick since first ROI is +0 and blank is -1 + out -= 1 + return out + + def mosaic2d(self, shape=None, idx=None, out=None): + """ Return 2D mosaic image""" + + if self._data: + if (self.is3d & (idx is None)): + raise ValueError('With 3D components, idx must be provided') + + return self._mosaic(shape=shape, idx=idx, out=out) + + def mosaic_mask(self, shape=None, out=None): + """ Returns a 2D mosaic image with integer values for which img is where """ + + return self._mosaic(shape=shape, out=out, mask=True) + + def mosaicfull(self, shape=None, out=None): + """ Return full mosaic """ + + if self._data: + return self._mosaic(shape=shape, idx=None, out=out) + +if __name__ == '__main__': + mos = Mosaic() + mos.parameters['StartR'] = 1 + mos.parameters['EndR'] = -1 + mos.parameters['StartC'] = 1 + mos.parameters['EndC'] = -1 + mos.parameters['Transpose'] = True + mos.parameters['FlipVertical'] = True + mos.parameters['FlipHorizontally'] = True + + m_obj = 3 + n_obj = 4 + p_obj = 5 + + # MANUALLY SET BASED ON PARAMS ABOVE + m_obj_crop = m_obj - 2 + n_obj_crop = n_obj - 2 + p_obj_crop = p_obj + + new_obj = _np.ones((m_obj, n_obj, p_obj)) + m_side = 2 + n_side = 2 + + n = m_side * n_side + + for ct in range(n): + mos.append(new_obj) + + # NOT AFFECTED BY START* END* + assert mos.shape == tuple(n*[new_obj.shape]) + assert mos.size == n + assert mos.issamedim + assert mos.dtype == _np.float + + # AFFECTED BY START* END* + assert mos.unitshape == (m_obj_crop, n_obj_crop, p_obj_crop) + assert mos.unitshape_orig == (m_obj, n_obj, p_obj) + + mos.parameters['Order'] = 'R' + assert mos.mosaic2d((m_side, n_side), idx=0).T.shape == (m_side * m_obj_crop, + n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, + n_side))[:-1] + mos.parameters['Order'] = 'C' + assert mos.mosaic2d((m_side, n_side), idx=0).T.shape == (m_side * m_obj_crop, + n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, n_side))[:-1] + + mos.parameters['Order'] = 'R' + assert mos.mosaicfull((m_side, n_side)).transpose(1,0,2).shape == (m_side * m_obj_crop, + n_side * n_obj_crop, p_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + + mos.parameters['Order'] = 'C' + assert mos.mosaicfull((m_side, n_side)).transpose(1,0,2).shape == (m_side * m_obj_crop, + n_side * n_obj_crop, + p_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) \ No newline at end of file diff --git a/crikit/data/spectra.py b/crikit/data/spectra.py index 0f7dc4b..3d15340 100644 --- a/crikit/data/spectra.py +++ b/crikit/data/spectra.py @@ -62,43 +62,77 @@ class Spectra(_Spectrum): Notes ----- - * freq object contains some useful parameters such as op_range_\* and \ - plot_range_\*, which define spectral regions-of-interest. (It's debatable \ + * freq object contains some useful parameters such as op_range* and \ + plot_range*, which define spectral regions-of-interest. (It's debatable \ as to whether those parameters should be in Frequency or Spectrum classes) """ + # Configurations + config = {} + config['nd_axis'] = -1 + def __init__(self, data=None, freq=None, label=None, units=None, meta=None): super().__init__(data, freq, label, units, meta) self._reps = _Replicate() + @staticmethod + def _mean_axes(*args, **kwargs): + """ Inhereted from Spectrum """ + raise NotImplementedError('Only applicable to Spectrum class.') + + @staticmethod + def _reshape_axes(shape, spectral_axis): + """ + Parameters + ---------- + shape : tuple + Input data shape + + spectral_axis : int + Spectral axis + + Returns + ------- + Reshape vector + """ + ndim = len(shape) + + if ndim >= 2: + out = [-1, -1] + else: + out = [1, 1] + + out[spectral_axis] = shape[spectral_axis] + return tuple(out) + @property def data(self): return self._data @data.setter def data(self, value): - if isinstance(value, _np.ndarray): - if self.freq.data is None or self.freq.op_list_pix is None: - if value.ndim == 1: - print('Spectra: converting data input from 1D to 2D ndarray') - self._data = value[None,:] - elif value.ndim == 2: - self._data = value - else: - print('Spectra: converting data input from {}D to 2D ndarray'.format(value.ndim)) - f_sh = value.shape[-1] - self._data = value.reshape((-1, f_sh)) - else: - if value.shape[-1] == self.freq.op_range_pix.size: - temp = _np.zeros((self._data.shape),dtype=value.dtype) - temp[:,self.freq.op_range_pix] = value - self._data = temp - else: - raise TypeError('data is of an unrecognized shape: {}'.format(value.shape)) + if not isinstance(value, _np.ndarray): + raise TypeError('data must be of type ndarray') + + if self.freq.data is None or self.freq.op_list_pix is None: + if value.ndim != 2: + print('Spectra: converting data input from {}D to 2D ndarray'.format(value.ndim)) + ax_rs = self._reshape_axes(value.shape, spectral_axis=self.config['nd_axis']) + self._data = value.reshape(ax_rs) else: - print('Assigning non-ndarray to data. Not shape checking') - self._data = value + if value.ndim != 2: + print('Spectra: converting data input from {}D to 2D ndarray'.format(value.ndim)) + if value.shape[-1] == self.freq.op_range_pix.size: + temp = _np.zeros((self._data.shape), dtype=value.dtype) + temp[:,self.freq.op_range_pix] = value + self._data = temp + elif value.shape[-1] == self.freq.size: + temp = _np.zeros((self._data.shape), dtype=value.dtype) + temp[..., self.freq.op_range_pix] = value[..., self.freq.op_range_pix].reshape((-1, len(self.freq.op_range_pix))) + self._data = temp + else: + raise TypeError('data is of an unrecognized shape: {}'.format(value.shape)) @property def n_pix(self): diff --git a/crikit/data/spectrum.py b/crikit/data/spectrum.py index e46d070..4abc8d1 100644 --- a/crikit/data/spectrum.py +++ b/crikit/data/spectrum.py @@ -60,12 +60,17 @@ class Spectrum: Notes ----- - * freq object contains some useful parameters such as op_range_\* and \ - plot_range_\*, which define spectral regions-of-interest. (It's debatable \ + * freq object contains some useful parameters such as op_range* and \ + plot_range*, which define spectral regions-of-interest. (It's debatable \ as to whether those parameters should be in Frequency or Spectrum classes) """ + # Configurations + config = {} + config['nd_axis'] = -1 + config['nd_fcn'] = _np.mean + def __init__(self, data=None, freq=None, label=None, units=None, meta=None): self._data = None @@ -87,47 +92,68 @@ def __init__(self, data=None, freq=None, label=None, units=None, meta=None): if meta is not None: self._meta = _copy.deepcopy(meta) + @staticmethod + def _mean_axes(ndim, axis): + """ + Parameters + ---------- + ndim : int + Number of dimensions of input data (target is 1D spectrum) + + axis : int + For ND data, axis is remaining axis + + Returns + ------- + Vector that describes what axes to operate (using a mean or similar method) with + axis parameter + """ + if axis < 0: + axis2 = ndim + axis + else: + axis2 = axis + return tuple([n for n in range(ndim) if n != axis2]) + @property def data(self): return self._data @data.setter def data(self, value): - if isinstance(value, _np.ndarray): - if value.ndim == 1: - if self.freq is not None and self.freq.op_list_pix is not None: - if value.shape[-1] == self.freq.op_range_pix.size: - temp = _np.zeros((self.freq.size),dtype=value.dtype) - temp[self.freq.op_range_pix] = value - self._data = temp - else: - raise TypeError('data is of an unrecognized shape: {}'.format(value.shape)) + if not isinstance(value, _np.ndarray): + raise TypeError('data must be of type ndarray') + + # If sub-range of operation is defined. Only perform action over op_range_pix + if self.freq is not None and self.freq.op_list_pix is not None: + if value.shape[self.config['nd_axis']] == self.freq.op_range_pix.size: + temp = _np.zeros((self.freq.size), dtype=value.dtype) + if value.ndim == 1: + temp[self.freq.op_range_pix] = value else: - self._data = value - else: - raise TypeError('data must be a 1D ndarray') - else: - raise TypeError('data must be a 1D ndarray') + print('Input data is {}-dim. Performing {}'.format(value.ndim, self.config['nd_fcn'].__name__)) + nd_ax = self._mean_axes(value.ndim, axis=self.config['nd_axis']) + temp[self.freq.op_range_pix] = self.config['nd_fcn'](value, axis=nd_ax) + elif value.shape[self.config['nd_axis']] == self.freq.size: + temp = _np.zeros((self.freq.size), dtype=value.dtype) + if value.ndim == 1: + temp[self.freq.op_range_pix] = value[self.freq.op_range_pix] + else: + print('Input data is {}-dim. Performing {}'.format(value.ndim, self.config['nd_fcn'].__name__)) + nd_ax = self._mean_axes(value.ndim, axis=self.config['nd_axis']) + temp[self.freq.op_range_pix] = self.config['nd_fcn'](value, axis=nd_ax)[self.freq.op_range_pix] - @property - def data_imag_over_real(self): - if _np.iscomplexobj(self._data): - if isinstance(self._data, _np.ndarray): - return self._data.imag else: - return _np.imag(self._data) + raise TypeError('data is of an unrecognized shape: {}'.format(value.shape)) + self._data = 1*temp + del temp else: - return self._data - - @property - def data_real_over_imag(self): - if _np.iscomplexobj(self._data): - if isinstance(self._data, _np.ndarray): - return self._data.real + if value.ndim == 1: + self._data = value else: - return _np.real(self._data) - else: - return self._data + print('Input data is {}-dim. Performing {}'.format(value.ndim, self.config['nd_fcn'].__name__)) + nd_ax = self._mean_axes(value.ndim, axis=self.config['nd_axis']) + self._data = self.config['nd_fcn'](value, axis=nd_ax) + @property def freq(self): @@ -364,10 +390,3 @@ def __sub__(self, spectrum): sp.data[200:500] tmr -= _timeit.default_timer() print(-tmr) - - tmr = _timeit.default_timer() - locs = _np.arange(sp.freq.get_index_of_closest_freq(500), - sp.freq.get_index_of_closest_freq(600)) - sp.data_imag_over_real[locs] - tmr -= _timeit.default_timer() - print(-tmr) diff --git a/crikit/data/tests/test_hsi.py b/crikit/data/tests/test_hsi.py new file mode 100644 index 0000000..13e9437 --- /dev/null +++ b/crikit/data/tests/test_hsi.py @@ -0,0 +1,121 @@ +import os +import numpy as np +import numpy.testing + +import pytest +import lazy5 + +from crikit.io.hdf5 import hdf_import_data +from crikit.data.spectrum import Spectrum +from crikit.data.spectra import Spectra +from crikit.data.hsi import Hsi + +@pytest.fixture(scope="function") +def make_datasets(): + """ Setups and tears down a series of datasets """ + + data_m, data_n, data_p = [20, 22, 24] + spectrum = np.random.randn(data_p)**2 + 1 + spectra = np.random.randn(data_n, data_p)**2 + 1 + hsi = np.random.randn(data_m, data_n, data_p)**2 + 1 + + return spectrum, spectra, hsi, np.array([data_m, data_n, data_p]) + +def test_mean_axes_static(): + """ Ensure mean_axes_static raises an error""" + + with pytest.raises(NotImplementedError): + Hsi._mean_axes() + +def test_reshape_axes_static(make_datasets): + """ Test reshape axes static method """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + Hsi._reshape_axes(shape=hsi.shape, spectral_axis=-1) == (-1, hsi.shape[-1]) + Hsi._reshape_axes(shape=spectra.shape, spectral_axis=-1) == (-1, spectra.shape[-1]) + Hsi._reshape_axes(shape=spectrum.shape, spectral_axis=-1) == (-1, spectrum.shape[-1]) + +def test_hsi_to_hsi(make_datasets): + """ Import an hsi into an hsi """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + new_dataset = Hsi() + new_dataset.data = hsi + + assert new_dataset.size == hsi.size + np.testing.assert_array_equal(new_dataset.data, hsi) + +def test_hsi_to_hsi_rng(make_datasets): + """ Import an hsi into an hsi -- defined range""" + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + rng = [10,11] + + new_dataset = Hsi() + new_dataset.freq.data = np.arange(hsi.shape[-1]) + new_dataset.data = hsi + new_dataset.freq.op_list_pix = rng + new_dataset.data = hsi + + assert new_dataset.size == hsi.size + assert (new_dataset.data != 0).sum() == len(rng)*np.prod(hsi.shape[:-1]) + np.testing.assert_almost_equal(new_dataset.data[..., rng], hsi[..., rng]) + +def test_spectrum_to_hsi(make_datasets): + """ Import a spectrum into an hsi """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + new_dataset = Hsi() + new_dataset.data = spectrum + + assert new_dataset.size == spectrum.size + np.testing.assert_array_equal(np.squeeze(new_dataset.data), spectrum) + +def test_spectrum_to_hsi_rng(make_datasets): + """ Import a spectrum into an hsi -- defined range""" + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + rng = [10,11] + + new_dataset = Hsi() + new_dataset.freq.data = np.arange(hsi.shape[-1]) + new_dataset.data = spectrum + new_dataset.freq.op_list_pix = rng + new_dataset.data = spectrum + + assert new_dataset.size == spectrum.size + assert (new_dataset.data != 0).sum() == len(rng) + np.testing.assert_almost_equal(np.squeeze(new_dataset.data[..., rng]), spectrum[rng]) + +def test_spectra_to_hsi(make_datasets): + """ Import spectra into an hsi """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + new_dataset = Hsi() + new_dataset.data = spectra + + assert new_dataset.size == spectra.size + np.testing.assert_array_equal(np.squeeze(new_dataset.data), spectra) + +def test_spectra_to_hsi_rng(make_datasets): + """ Import spectra into an hsi -- defined range""" + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + rng = [10,11] + + new_dataset = Hsi() + new_dataset.freq.data = np.arange(hsi.shape[-1]) + new_dataset.data = spectra + new_dataset.freq.op_list_pix = rng + new_dataset.data = spectra + + assert new_dataset.size == spectra.size + assert (new_dataset.data != 0).sum() == len(rng)*spectra.shape[0] + np.testing.assert_almost_equal(np.squeeze(new_dataset.data[..., rng]), spectra[..., rng]) diff --git a/crikit/data/tests/test_mosaic.py b/crikit/data/tests/test_mosaic.py new file mode 100644 index 0000000..639aa44 --- /dev/null +++ b/crikit/data/tests/test_mosaic.py @@ -0,0 +1,469 @@ +import numpy as np +import pytest + +from crikit.data.mosaic import Mosaic + +def test_blank(): + mos = Mosaic() + assert mos.shape is None + assert mos.size is None + assert mos.issamedim is None + assert mos.issamedim is None + assert mos.dtype is None + assert mos.mosaic_shape((2,2)) is None + assert mos.mosaic2d((2,2)) is None + assert mos.mosaicfull((2,2)) is None + +def test_crop_2D(): + """ Test a 2D dataset with cropped rows and columns """ + mos = Mosaic() + mos.parameters['StartR'] = 1 + mos.parameters['EndR'] = -1 + mos.parameters['StartC'] = 1 + mos.parameters['EndC'] = -1 + + m_obj = 3 + n_obj = 4 + + # MANUALLY SET BASED ON PARAMS ABOVE + m_obj_crop = m_obj - 2 + n_obj_crop = n_obj - 2 + + new_obj = np.ones((m_obj, n_obj)) + m_side = 2 + n_side = 2 + + n = m_side * n_side + + for ct in range(n): + mos.append(new_obj) + + # NOT AFFECTED BY START* END* + assert mos.shape == tuple(n*[new_obj.shape]) + assert mos.size == n + assert mos.issamedim + assert mos.dtype == np.float + + # AFFECTED BY START* END* + assert mos.unitshape == (m_obj_crop, n_obj_crop) + assert mos.unitshape_orig == (m_obj, n_obj) + + mos.parameters['Order'] = 'R' + assert mos.mosaic2d((m_side, n_side)).shape == (m_side * m_obj_crop, n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + assert mos.mosaicfull((m_side, n_side)).shape == (m_side * m_obj_crop, n_side * n_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + + mos.parameters['Order'] = 'C' + assert mos.mosaic2d((m_side, n_side)).shape == (m_side * m_obj_crop, n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + assert mos.mosaicfull((m_side, n_side)).shape == (m_side * m_obj_crop, n_side * n_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + +def test_crop_3D(): + """ Test a 2D dataset with cropped rows and columns """ + mos = Mosaic() + mos.parameters['StartR'] = 1 + mos.parameters['EndR'] = -1 + mos.parameters['StartC'] = 1 + mos.parameters['EndC'] = -1 + + m_obj = 3 + n_obj = 4 + p_obj = 5 + + # MANUALLY SET BASED ON PARAMS ABOVE + m_obj_crop = m_obj - 2 + n_obj_crop = n_obj - 2 + p_obj_crop = p_obj + + new_obj = np.ones((m_obj, n_obj, p_obj)) + m_side = 2 + n_side = 2 + + n = m_side * n_side + + for ct in range(n): + mos.append(new_obj) + + # NOT AFFECTED BY START* END* + assert mos.shape == tuple(n*[new_obj.shape]) + assert mos.size == n + assert mos.issamedim + assert mos.dtype == np.float + + # AFFECTED BY START* END* + assert mos.unitshape == (m_obj_crop, n_obj_crop, p_obj_crop) + assert mos.unitshape_orig == (m_obj, n_obj, p_obj) + + mos.parameters['Order'] = 'R' + assert mos.mosaic2d((m_side, n_side), idx=0).shape == (m_side * m_obj_crop, n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, n_side))[:-1] + assert mos.mosaicfull((m_side, n_side)).shape == (m_side * m_obj_crop, n_side * n_obj_crop, + p_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + + mos.parameters['Order'] = 'C' + assert mos.mosaic2d((m_side, n_side), idx=0).shape == (m_side * m_obj_crop, n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, n_side))[:-1] + assert mos.mosaicfull((m_side, n_side)).shape == (m_side * m_obj_crop, n_side * n_obj_crop, + p_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + +def test_3D_crop_transpose_flips(): + """ Test a 2D dataset with cropped rows and columns """ + mos = Mosaic() + mos.parameters['StartR'] = 1 + mos.parameters['EndR'] = -1 + mos.parameters['StartC'] = 1 + mos.parameters['EndC'] = -1 + mos.parameters['Transpose'] = True + mos.parameters['FlipVertical'] = True + mos.parameters['FlipHorizontally'] = True + + m_obj = 3 + n_obj = 4 + p_obj = 5 + + # MANUALLY SET BASED ON PARAMS ABOVE + m_obj_crop = m_obj - 2 + n_obj_crop = n_obj - 2 + p_obj_crop = p_obj + + new_obj = np.ones((m_obj, n_obj, p_obj)) + m_side = 2 + n_side = 2 + + n = m_side * n_side + + for ct in range(n): + mos.append(new_obj) + + # NOT AFFECTED BY START* END* + assert mos.shape == tuple(n*[new_obj.shape]) + assert mos.size == n + assert mos.issamedim + assert mos.dtype == np.float + + # AFFECTED BY START* END* + assert mos.unitshape == (m_obj_crop, n_obj_crop, p_obj_crop) + assert mos.unitshape_orig == (m_obj, n_obj, p_obj) + + mos.parameters['Order'] = 'R' + assert mos.mosaic2d((m_side, n_side), idx=0).T.shape == (m_side * m_obj_crop, + n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, n_side))[:-1] + assert mos.mosaicfull((m_side, n_side)).transpose(1,0,2).shape == (m_side * m_obj_crop, + n_side * n_obj_crop, + p_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + + mos.parameters['Order'] = 'C' + assert mos.mosaic2d((m_side, n_side), idx=0).T.shape == (m_side * m_obj_crop, + n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, n_side))[:-1] + assert mos.mosaicfull((m_side, n_side)).transpose(1,0,2).shape == (m_side * m_obj_crop, + n_side * n_obj_crop, + p_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + +def test_3D_crop_transpose_flips_2(): + """ Test a 2D dataset with cropped rows and columns (asymmetrically) """ + mos = Mosaic() + mos.parameters['StartR'] = 2 + mos.parameters['EndR'] = -1 + mos.parameters['StartC'] = 1 + mos.parameters['EndC'] = -1 + mos.parameters['Transpose'] = True + mos.parameters['FlipVertical'] = True + mos.parameters['FlipHorizontally'] = True + + m_obj = 5 + n_obj = 6 + p_obj = 7 + + # MANUALLY SET BASED ON PARAMS ABOVE + m_obj_crop = m_obj - 3 + n_obj_crop = n_obj - 2 + p_obj_crop = p_obj + + new_obj = np.ones((m_obj, n_obj, p_obj)) + m_side = 2 + n_side = 2 + + n = m_side * n_side + + for ct in range(n): + mos.append(new_obj) + + # NOT AFFECTED BY START* END* + assert mos.shape == tuple(n*[new_obj.shape]) + assert mos.size == n + assert mos.issamedim + assert mos.dtype == np.float + + # AFFECTED BY START* END* + assert mos.unitshape == (m_obj_crop, n_obj_crop, p_obj_crop) + assert mos.unitshape_orig == (m_obj, n_obj, p_obj) + + mos.parameters['Order'] = 'R' + assert mos.mosaic2d((m_side, n_side), idx=0).T.shape == (m_side * m_obj_crop, + n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, n_side))[:-1] + assert mos.mosaicfull((m_side, n_side)).transpose(1,0,2).shape == (m_side * m_obj_crop, + n_side * n_obj_crop, + p_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + + mos.parameters['Order'] = 'C' + assert mos.mosaic2d((m_side, n_side), idx=0).T.shape == (m_side * m_obj_crop, + n_side * n_obj_crop) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, n_side))[:-1] + assert mos.mosaicfull((m_side, n_side)).transpose(1,0,2).shape == (m_side * m_obj_crop, + n_side * n_obj_crop, + p_obj_crop) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + +def test_2D_uniform_obj(): + mos = Mosaic() + + m_obj = 3 + n_obj = 4 + + new_obj = np.ones((m_obj, n_obj)) + m_side = 2 + n_side = 2 + + n = m_side * n_side + + for ct in range(n): + mos.append(new_obj) + + assert mos.shape == tuple(n*[new_obj.shape]) + assert mos.size == n + assert mos.issamedim + assert mos.dtype == np.float + assert mos.unitshape == (m_obj, n_obj) + assert mos.unitshape_orig == (m_obj, n_obj) + + mos.parameters['Order'] = 'R' + assert mos.mosaic2d((m_side, n_side)).shape == (m_side * m_obj, n_side * n_obj) + assert mos.mosaic2d((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + assert mos.mosaicfull((m_side, n_side)).shape == (m_side * m_obj, n_side * n_obj) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + + mos.parameters['Order'] = 'C' + assert mos.mosaic2d((m_side, n_side)).shape == (m_side * m_obj, n_side * n_obj) + assert mos.mosaic2d((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + assert mos.mosaicfull((m_side, n_side)).shape == (m_side * m_obj, n_side * n_obj) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + +def test_3D_uniform_obj(): + mos = Mosaic() + + m_obj = 3 + n_obj = 4 + p_obj = 2 + + new_obj = np.ones((m_obj, n_obj, p_obj)) + + m_side = 2 + n_side = 2 + + n = m_side * n_side + + for ct in range(n): + mos.append(new_obj) + + assert mos.shape == tuple(n*[new_obj.shape]) + assert mos.size == n + assert mos.issamedim + assert mos.dtype == np.float + with pytest.raises(ValueError): + mos.mosaic2d((m_side, n_side)).shape + + mos.parameters['Order'] = 'R' + assert mos.mosaic2d((m_side, n_side), idx=0).shape == (m_side * m_obj, n_side * n_obj) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, n_side), idx=0) + assert mos.mosaicfull((m_side, n_side)).shape == (m_side * m_obj, n_side * n_obj, p_obj) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + + mos.parameters['Order'] = 'C' + assert mos.mosaic2d((m_side, n_side), idx=0).shape == (m_side * m_obj, n_side * n_obj) + assert mos.mosaic2d((m_side, n_side), idx=0).shape == mos.mosaic_shape((m_side, n_side), idx=0) + assert mos.mosaicfull((m_side, n_side)).shape == (m_side * m_obj, n_side * n_obj, p_obj) + assert mos.mosaicfull((m_side, n_side)).shape == mos.mosaic_shape((m_side, n_side)) + +def test_err_wrong_dim(): + mos = Mosaic() + + with pytest.raises(TypeError): + mos.append(np.random.randn(5)) + + with pytest.raises(TypeError): + mos.append(np.random.randn(2,2,2,2)) + +def test_err_wrong_dim_append(): + + # Start with 2D + mos = Mosaic() + mos.append(np.random.randn(3,4)) + + with pytest.raises(TypeError): + mos.append(np.random.randn(5)) + + with pytest.raises(TypeError): + mos.append(np.random.randn(3,4,5)) + + # Start with 3D + mos = Mosaic() + mos.append(np.random.randn(3,4,2)) + + with pytest.raises(TypeError): + mos.append(np.random.randn(5)) + + with pytest.raises(TypeError): + mos.append(np.random.randn(3,5)) + +def test_big_to_small_2d(): + orig_data = np.random.randn(40,5) + + mos = Mosaic() + + m_unit_size = 10 + n_unit_size = 5 + + m_ct = orig_data.shape[0]//m_unit_size + n_ct = orig_data.shape[1]//n_unit_size + + for ct in range(m_ct): + mos.append(orig_data[ct*m_unit_size:(ct+1)*m_unit_size,:]) + + mos.parameters['Order'] = 'R' + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct)), orig_data) + assert np.allclose(mos.mosaicfull(shape=(m_ct, n_ct)), orig_data) + + mos.parameters['Order'] = 'C' + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct)), orig_data) + assert np.allclose(mos.mosaicfull(shape=(m_ct, n_ct)), orig_data) + +def test_big_to_small_2d_2(): + orig_data = np.random.randn(40,10) + + mos = Mosaic() + + m_unit_size = 10 + n_unit_size = 5 + + m_ct = orig_data.shape[0]//m_unit_size + n_ct = orig_data.shape[1]//n_unit_size + + for ni in range(n_ct): + for mi in range(m_ct): + mos.append(orig_data[mi*m_unit_size:(mi+1)*m_unit_size, + ni*n_unit_size:(ni+1)*n_unit_size]) + + mos.parameters['Order'] = 'R' + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct)), orig_data) + assert np.allclose(mos.mosaicfull(shape=(m_ct, n_ct)), orig_data) + + mos.parameters['Order'] = 'C' + assert not np.allclose(mos.mosaic2d(shape=(m_ct, n_ct)), orig_data) + assert not np.allclose(mos.mosaicfull(shape=(m_ct, n_ct)), orig_data) + +def test_big_to_small_3d(): + orig_data = np.random.randn(40,5,3) + + mos = Mosaic() + + m_unit_size = 10 + n_unit_size = 5 + + m_ct = orig_data.shape[0]//m_unit_size + n_ct = orig_data.shape[1]//n_unit_size + + for ct in range(m_ct): + mos.append(orig_data[ct*m_unit_size:(ct+1)*m_unit_size, ...]) + + mos.parameters['Order'] = 'R' + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=0), orig_data[...,0]) + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=1), orig_data[...,1]) + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=2), orig_data[...,2]) + assert np.allclose(mos.mosaicfull(shape=(m_ct, n_ct)), orig_data) + + mos.parameters['Order'] = 'C' + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=0), orig_data[...,0]) + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=1), orig_data[...,1]) + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=2), orig_data[...,2]) + assert np.allclose(mos.mosaicfull(shape=(m_ct, n_ct)), orig_data) + +def test_big_to_small_3d_2(): + orig_data = np.random.randn(40,10, 3) + + mos = Mosaic() + + m_unit_size = 10 + n_unit_size = 5 + + m_ct = orig_data.shape[0]//m_unit_size + n_ct = orig_data.shape[1]//n_unit_size + + for ni in range(n_ct): + for mi in range(m_ct): + mos.append(orig_data[mi*m_unit_size:(mi+1)*m_unit_size, + ni*n_unit_size:(ni+1)*n_unit_size, :]) + + mos.parameters['Order'] = 'R' + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=0), orig_data[..., 0]) + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=1), orig_data[..., 1]) + assert np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=2), orig_data[..., 2]) + assert np.allclose(mos.mosaicfull(shape=(m_ct, n_ct)), orig_data) + + mos.parameters['Order'] = 'C' + assert not np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=0), orig_data[..., 0]) + assert not np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=1), orig_data[..., 1]) + assert not np.allclose(mos.mosaic2d(shape=(m_ct, n_ct), idx=2), orig_data[..., 2]) + assert not np.allclose(mos.mosaicfull(shape=(m_ct, n_ct)), orig_data) + + +def test_big_to_small_3d_output_given(): + orig_data = np.random.randn(40,10, 3) + + mos = Mosaic() + + m_unit_size = 10 + n_unit_size = 5 + + m_ct = orig_data.shape[0]//m_unit_size + n_ct = orig_data.shape[1]//n_unit_size + + for ni in range(n_ct): + for mi in range(m_ct): + mos.append(orig_data[mi*m_unit_size:(mi+1)*m_unit_size, + ni*n_unit_size:(ni+1)*n_unit_size, :]) + + output_data = np.zeros(orig_data.shape[:-1], dtype=orig_data.dtype) + id_in = id(output_data) + + mos.parameters['Order'] = 'R' + mos.mosaic2d(shape=(m_ct, n_ct), idx=0, out=output_data) + id_out = id(output_data) + assert np.allclose(output_data, orig_data[..., 0]) + assert id_in == id_out + + output_data = np.zeros(orig_data.shape[:-1], dtype=orig_data.dtype) + mos.mosaic2d(shape=(m_ct, n_ct), idx=1, out=output_data) + assert np.allclose(output_data, orig_data[..., 1]) + + output_data = np.zeros(orig_data.shape[:-1], dtype=orig_data.dtype) + mos.mosaic2d(shape=(m_ct, n_ct), idx=2, out=output_data) + assert np.allclose(output_data, orig_data[..., 2]) + + output_data = np.zeros(orig_data.shape, dtype=orig_data.dtype) + mos.mosaicfull(shape=(m_ct, n_ct), out=output_data) + assert np.allclose(output_data, orig_data) + + mos.parameters['Order'] = 'C' + output_data = np.zeros(orig_data.shape, dtype=orig_data.dtype) + mos.mosaicfull(shape=(m_ct, n_ct), out=output_data) + assert not np.allclose(output_data, orig_data) diff --git a/crikit/data/tests/test_mosaic_hdf.py b/crikit/data/tests/test_mosaic_hdf.py new file mode 100644 index 0000000..3f685f8 --- /dev/null +++ b/crikit/data/tests/test_mosaic_hdf.py @@ -0,0 +1,254 @@ +import os +import time + +import numpy as np +import pytest +import h5py + +import lazy5 + +from crikit.data.mosaic import Mosaic + +@pytest.fixture(scope="module") +def hdf_dataset2(): + """ Setups and tears down a sample HDF5 file """ + filename = 'temp_test.h5' + fid = h5py.File(filename, 'w') + # data_m, data_n, data_p = [3, 4, 24] + data_m, data_n = [3, 4] + data = np.random.randn(data_m, data_n) + + N = 10 + for n in range(N): + fid.create_dataset('img_z{}'.format(n), data=data) + + yield filename, fid + + # Tear-down + if lazy5.utils.hdf_is_open(fid): + fid.close() + + time.sleep(1) + try: + os.remove(filename) + except: + print('Could not delete {}'.format(filename)) + +def test_hdf2(hdf_dataset2): + filename, fid = hdf_dataset2 + + dset_list = lazy5.inspect.get_datasets(fid) + mos = Mosaic() + for n in range(10): + mos.append(fid[dset_list[n]]) + + # assert mos.shape is None + assert mos.size == 10 + assert mos.issamedim + + mos.parameters['Order'] = 'R' + assert mos.mosaic2d((5, 2)).shape == (5*3, 2*4) + + mos.parameters['Order'] = 'C' + assert mos.mosaic2d((5, 2)).shape == (5*3, 2*4) + +def test_big_to_small_3d_output_given(): + orig_data_np = np.random.randn(40, 10, 3) + + filename_in = 'test_h5mosaic_in.h5' + dset_in_prefix = 'dset_' + fid_in = h5py.File(filename_in, 'w') + + m_unit_size = 10 + n_unit_size = 5 + + m_ct = orig_data_np.shape[0]//m_unit_size + n_ct = orig_data_np.shape[1]//n_unit_size + + ct = 0 + for ni in range(n_ct): + for mi in range(m_ct): + temp = orig_data_np[mi*m_unit_size:(mi+1)*m_unit_size, + ni*n_unit_size:(ni+1)*n_unit_size, :] + fid_in.create_dataset(dset_in_prefix+'{}'.format(ct), shape=temp.shape, data=temp) + ct += 1 + + fid_in.close() + + fid_in = h5py.File(filename_in, 'r') + mos = Mosaic() + + ct = 0 + for ni in range(n_ct): + for mi in range(m_ct): + mos.append(fid_in[dset_in_prefix+'{}'.format(ct)]) + ct += 1 + + filename_out = 'test_h5mosaic_out.h5' + dset_out_name = 'dset' + + fid_out = h5py.File(filename_out, 'w') + fid_out.create_dataset(dset_out_name, shape=orig_data_np.shape, data=np.zeros(orig_data_np.shape)) + + mos.parameters['Order'] = 'R' + mos.mosaicfull((m_ct, n_ct), out=fid_out[dset_out_name]) + + assert np.allclose(fid_out[dset_out_name], orig_data_np) + + fid_in.close() + fid_out.close() + + time.sleep(1) + try: + os.remove(filename_in) + except: + print('Could not delete {}'.format(filename_in)) + + time.sleep(1) + try: + os.remove(filename_out) + except: + print('Could not delete {}'.format(filename_out)) + +def test_big_to_small_3d_output_given_crop(): + """ 3D big dataset, divied up into small chunks -- WITH CROPPING """ + orig_data_np = np.random.randn(40, 10, 3) + + filename_in = 'test_h5mosaic_in.h5' + dset_in_prefix = 'dset_' + fid_in = h5py.File(filename_in, 'w') + + m_unit_size = 10 + n_unit_size = 5 + + m_ct = orig_data_np.shape[0]//m_unit_size + n_ct = orig_data_np.shape[1]//n_unit_size + + ct = 0 + for ni in range(n_ct): + for mi in range(m_ct): + temp = orig_data_np[mi*m_unit_size:(mi+1)*m_unit_size, + ni*n_unit_size:(ni+1)*n_unit_size, :] + fid_in.create_dataset(dset_in_prefix+'{}'.format(ct), shape=temp.shape, data=temp) + ct += 1 + + fid_in.close() + + fid_in = h5py.File(filename_in, 'r') + + mos = Mosaic() + mos.parameters['StartR'] = 1 + mos.parameters['EndR'] = -1 + mos.parameters['StartC'] = 1 + mos.parameters['EndC'] = -1 + + ct = 0 + for ni in range(n_ct): + for mi in range(m_ct): + mos.append(fid_in[dset_in_prefix+'{}'.format(ct)]) + ct += 1 + + filename_out = 'test_h5mosaic_out.h5' + dset_out_name = 'dset' + + fid_out = h5py.File(filename_out, 'w') + fid_out.create_dataset(dset_out_name, shape=mos.mosaic_shape((m_ct, n_ct)), + dtype=orig_data_np.dtype) + + mos.parameters['Order'] = 'R' + mos.mosaicfull((m_ct, n_ct), out=fid_out[dset_out_name]) + + assert np.allclose(fid_out[dset_out_name][0:3,0:3,:], + orig_data_np[1:4, 1:4, :]) + assert np.allclose(fid_out[dset_out_name][8:11, 0:3, :], + orig_data_np[11:14, 1:4, :]) + + assert np.allclose(fid_out[dset_out_name][0:3, 8:11, :], + orig_data_np[1:4, 11:14, :]) + + fid_in.close() + fid_out.close() + + time.sleep(1) + try: + os.remove(filename_in) + except: + print('Could not delete {}'.format(filename_in)) + + time.sleep(1) + try: + os.remove(filename_out) + except: + print('Could not delete {}'.format(filename_out)) + +def test_big_to_small_3d_output_given_crop_transpose_flips(): + """ + 3D big dataset, divied up into small chunks -- WITH CROPPING, TRANSPOSING + AND FLIPPING H & V + + Note: This test does not assert anything, but rather just ensures the methods + can run without raising errors + """ + orig_data_np = np.random.randn(40, 10, 3) + + filename_in = 'test_h5mosaic_in.h5' + dset_in_prefix = 'dset_' + fid_in = h5py.File(filename_in, 'w') + + m_unit_size = 10 + n_unit_size = 5 + + m_ct = orig_data_np.shape[0]//m_unit_size + n_ct = orig_data_np.shape[1]//n_unit_size + + ct = 0 + for ni in range(n_ct): + for mi in range(m_ct): + temp = orig_data_np[mi*m_unit_size:(mi+1)*m_unit_size, + ni*n_unit_size:(ni+1)*n_unit_size, :] + fid_in.create_dataset(dset_in_prefix+'{}'.format(ct), shape=temp.shape, data=temp) + ct += 1 + + fid_in.close() + + fid_in = h5py.File(filename_in, 'r') + + mos = Mosaic() + mos.parameters['StartR'] = 1 + mos.parameters['EndR'] = -1 + mos.parameters['StartC'] = 1 + mos.parameters['EndC'] = -1 + mos.parameters['Transpose'] = True + mos.parameters['FlipVertical'] = True + mos.parameters['FlipHorizontally'] = True + + ct = 0 + for ni in range(n_ct): + for mi in range(m_ct): + mos.append(fid_in[dset_in_prefix+'{}'.format(ct)]) + ct += 1 + + filename_out = 'test_h5mosaic_out.h5' + dset_out_name = 'dset' + + fid_out = h5py.File(filename_out, 'w') + fid_out.create_dataset(dset_out_name, shape=mos.mosaic_shape((m_ct, n_ct)), + dtype=orig_data_np.dtype) + + mos.parameters['Order'] = 'R' + mos.mosaicfull((m_ct, n_ct), out=fid_out[dset_out_name]) + + fid_in.close() + fid_out.close() + + time.sleep(1) + try: + os.remove(filename_in) + except: + print('Could not delete {}'.format(filename_in)) + + time.sleep(1) + try: + os.remove(filename_out) + except: + print('Could not delete {}'.format(filename_out)) diff --git a/crikit/data/tests/test_spectra.py b/crikit/data/tests/test_spectra.py new file mode 100644 index 0000000..61555d8 --- /dev/null +++ b/crikit/data/tests/test_spectra.py @@ -0,0 +1,121 @@ +import os +import numpy as np +import numpy.testing + +import pytest +import lazy5 + +from crikit.io.hdf5 import hdf_import_data +from crikit.data.spectrum import Spectrum +from crikit.data.spectra import Spectra +from crikit.data.hsi import Hsi + +@pytest.fixture(scope="function") +def make_datasets(): + """ Setups and tears down a series of datasets """ + + data_m, data_n, data_p = [20, 22, 24] + spectrum = np.random.randn(data_p)**2 + 1 + spectra = np.random.randn(data_n, data_p)**2 + 1 + hsi = np.random.randn(data_m, data_n, data_p)**2 + 1 + + return spectrum, spectra, hsi, np.array([data_m, data_n, data_p]) + +def test_mean_axes_static(): + """ Ensure mean_axes_static raises an error""" + + with pytest.raises(NotImplementedError): + Spectra._mean_axes() + +def test_reshape_axes_static(make_datasets): + """ Test reshape axes static method """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + Spectra._reshape_axes(shape=hsi.shape, spectral_axis=-1) == (-1, hsi.shape[-1]) + Spectra._reshape_axes(shape=spectra.shape, spectral_axis=-1) == (-1, spectra.shape[-1]) + Spectra._reshape_axes(shape=spectrum.shape, spectral_axis=-1) == (-1, spectrum.shape[-1]) + +def test_spectra_to_spectra(make_datasets): + """ Import a spectrum into a spectrum """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + new_dataset = Spectra() + new_dataset.data = spectra + + assert new_dataset.size == spectra.size + np.testing.assert_array_equal(new_dataset.data, spectra) + +def test_spectra_to_spectra_rng(make_datasets): + """ Import spectra into spectra -- defined range""" + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + rng = [10,11] + + new_dataset = Spectra() + new_dataset.freq.data = np.arange(spectra.shape[-1]) + new_dataset.data = spectra + new_dataset.freq.op_list_pix = rng + new_dataset.data = spectra + + assert new_dataset.size == spectra.size + assert (new_dataset.data != 0).sum() == len(rng)*spectra.shape[0] + np.testing.assert_almost_equal(new_dataset.data[..., rng], spectra[..., rng]) + +def test_spectrum_to_spectra(make_datasets): + """ Import a spectrum into a spectrum """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + new_dataset = Spectra() + new_dataset.data = spectrum + + assert new_dataset.size == spectrum.size + np.testing.assert_array_equal(np.squeeze(new_dataset.data), spectrum) + +def test_spectrum_to_spectra_rng(make_datasets): + """ Import spectrum into spectra -- defined range""" + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + rng = [10,11] + + new_dataset = Spectra() + new_dataset.freq.data = np.arange(spectra.shape[-1]) + new_dataset.data = spectrum + new_dataset.freq.op_list_pix = rng + new_dataset.data = spectrum + + assert new_dataset.size == spectrum.size + assert (new_dataset.data != 0).sum() == len(rng) + np.testing.assert_almost_equal(np.squeeze(new_dataset.data[..., rng]), spectrum[rng]) + +def test_hsi_to_spectra(make_datasets): + """ Import an hsi into spectra """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + new_dataset = Spectra() + new_dataset.data = hsi + + assert new_dataset.size == hsi.size + np.testing.assert_array_equal(hsi.reshape((-1, hsi.shape[-1])), new_dataset.data) + +def test_hsi_to_spectra_rng(make_datasets): + """ Import an hsi into spectra -- defined range""" + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + rng = [10,11] + + new_dataset = Spectra() + new_dataset.freq.data = np.arange(spectra.shape[-1]) + new_dataset.data = hsi + new_dataset.freq.op_list_pix = rng + new_dataset.data = hsi + + assert new_dataset.size == hsi.size + assert (new_dataset.data != 0).sum() == len(rng)*np.prod(hsi.shape[:-1]) + np.testing.assert_almost_equal(new_dataset.data[..., rng], hsi[..., rng].reshape((-1, len(rng)))) diff --git a/crikit/data/tests/test_spectrum.py b/crikit/data/tests/test_spectrum.py new file mode 100644 index 0000000..7c0a68d --- /dev/null +++ b/crikit/data/tests/test_spectrum.py @@ -0,0 +1,115 @@ +import os +import numpy as np +import numpy.testing + +import pytest +import lazy5 + +from crikit.io.hdf5 import hdf_import_data +from crikit.data.spectrum import Spectrum +from crikit.data.spectra import Spectra +from crikit.data.hsi import Hsi + +@pytest.fixture(scope="function") +def make_datasets(): + """ Setups and tears down a series of datasets """ + + data_m, data_n, data_p = [20, 22, 24] + spectrum = np.random.randn(data_p)**2 + 1 + spectra = np.random.randn(data_n, data_p)**2 + 1 + hsi = np.random.randn(data_m, data_n, data_p)**2 + 1 + + return spectrum, spectra, hsi, np.array([data_m, data_n, data_p]) + +def test_mean_axes_static(make_datasets): + """ Import a spectrum into a spectrum """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + Spectrum._mean_axes(3, 2) == [0,1] + Spectrum._mean_axes(3, -1) == [0,1] + Spectrum._mean_axes(3, 0) == [1,2] + Spectrum._mean_axes(3, 1) == [0,2] + +def test_spectrum_to_spectrum(make_datasets): + """ Import a spectrum into a spectrum """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + new_dataset = Spectrum() + new_dataset.data = spectrum + + assert new_dataset.size == spectrum.size + np.testing.assert_almost_equal(new_dataset.data, spectrum) + +def test_spectrum_to_spectrum_rng(make_datasets): + """ Import a spectrum into a spectrum -- defined range""" + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + rng = [10,11] + + new_dataset = Spectrum() + new_dataset.freq.data = np.arange(spectrum.size) + new_dataset.freq.op_list_pix = rng + new_dataset.data = spectrum + + assert new_dataset.size == spectrum.size + assert (new_dataset.data != 0).sum() == len(rng) + np.testing.assert_almost_equal(new_dataset.data[rng], spectrum[rng]) + +def test_spectra_to_spectrum(make_datasets): + """ Import spectra into a spectrum """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + new_dataset = Spectrum() + new_dataset.data = spectra + + assert new_dataset.size == spectrum.size + np.testing.assert_almost_equal(new_dataset.data, spectra.mean(axis=0)) + +def test_spectra_to_spectrum_rng(make_datasets): + """ Import spectra into a spectrum -- defined range""" + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + rng = [10,11] + + new_dataset = Spectrum() + new_dataset.freq.data = np.arange(spectrum.size) + new_dataset.freq.op_list_pix = rng + new_dataset.data = spectra + + assert new_dataset.size == spectrum.size + assert (new_dataset.data != 0).sum() == len(rng) + np.testing.assert_almost_equal(new_dataset.data[rng], spectra[:,rng].mean(axis=0)) + +def test_hsi_to_spectrum(make_datasets): + """ Import hsi into a spectrum """ + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + new_dataset = Spectrum() + new_dataset.data = hsi + + assert new_dataset.size == spectrum.size + np.testing.assert_almost_equal(new_dataset.data, hsi.mean(axis=(0,1))) + +def test_hsi_to_spectrum_rng(make_datasets): + """ Import an hsi into a spectrum -- defined range""" + + spectrum, spectra, hsi, make_dataset_shape = make_datasets + + rng = [10,11] + + new_dataset = Spectrum() + new_dataset.freq.data = np.arange(spectrum.size) + new_dataset.freq.op_list_pix = rng + new_dataset.data = hsi + + assert new_dataset.size == spectrum.size + assert (new_dataset.data != 0).sum() == len(rng) + + print('A - B: {}'.format(new_dataset.data[rng] - hsi[..., rng].mean(axis=(0,1)))) + np.testing.assert_almost_equal(new_dataset.data[rng], hsi[..., rng].mean(axis=(0,1))) \ No newline at end of file diff --git a/crikit/io/hdf5.py b/crikit/io/hdf5.py index 0827193..9dd4235 100644 --- a/crikit/io/hdf5.py +++ b/crikit/io/hdf5.py @@ -9,146 +9,15 @@ import os as _os +import numpy as _np + from crikit.data.spectrum import Spectrum as _Spectrum from crikit.data.spectra import Spectra as _Spectra from crikit.data.hsi import Hsi as _Hsi +import lazy5 as _lazy5 -import h5py as _h5py -_h5py.get_config().complex_names = ('Re','Im') - -import numpy as _np - -__all__ = ['hdf_dset_list_rep','hdf_is_valid_dsets', - 'hdf_attr_to_dict','hdf_import_data'] - -def hdf_dset_list_rep(prefix,suffixes): - """ - Create a list of dataset names - """ - dset_list = [] - - assert isinstance(prefix,str) - - for sfx in suffixes: - dset_list.append(prefix + str(sfx)) - - return dset_list - -def hdf_is_valid_dsets(pth, filename, dset_list): - """ - Validate file and datasets exist. Return boolean as to whether valid - - """ - - isvalid = False - fileexists = False - - try: - # Join path and filename in an os-independant way - pfname = _os.path.normpath(_os.path.join(pth, filename)) - f = _h5py.File(pfname, 'r') - print('File exists: \'{}\''.format(pfname)) - fileexists = True - except OSError: - print('File does not exist: \'{}\''.format(pfname)) - fileexists = False - else: - if isinstance(dset_list, list): # List of dataset(s) - try: - for count in dset_list: - f[count] - except: - print('dataset: {} is invalid'.format(count)) - else: - print('All datasets are valid') - isvalid = True - elif isinstance(dset_list, str): # Single dataset string name - try: - f[dset_list] - except: - print('dataset {} is invalid'.format(count)) - else: - print('Dataset is valid') - isvalid = True - else: - print('dset_list is unrecognized type') - finally: - if fileexists: - f.close() - - return isvalid - -def _convert_to_np_dtype(dset): - """ - Given an HDF5 dataset, return the values in a numpy-builtin datatype - - Parameters - ---------- - dset : h5py.Dataset - HDF5 (h5py) dataset - - Returns - ------- - out : numpy.ndarray (dtype = numpy built-in) - - Notes - ----- - The software accounts for big-/little-endianness, and the inability of \ - hdf5 to natively store complex numbers. - - """ - assert isinstance(dset, _h5py.Dataset), 'Input is not of type h5py.Dataset' - # Single datatype - if len(dset.dtype) == 0: - converted = _np.ndarray(dset.shape, dtype = dset.dtype.newbyteorder('=')) - dset.read_direct(converted) - if issubclass(converted.dtype.type, _np.integer): # Integer to float - converted = converted.astype(_np.float) - return converted - #Compound datatype of length 2-- assumed ('Re','Im') - elif len(dset.dtype) == 2: - print('Warning: h5py.complex_names set incorrectly using \'{}\' and \'{}\' \ -for Re and Im, respectively'.format(dset.dtype.names[0], dset.dtype.names[1])) - _h5py.get_config().complex_names = (dset.dtype.names[0],dset.dtype.names[1]) - dset = dset.file[dset.name] - converted = _np.ndarray(dset.shape, dtype = dset.dtype.newbyteorder('=')) - dset.read_direct(converted) - # Unknown datatype - else: - print('Warning: Unknown datatype. Returning dataset values as is.') - return dset.value - return converted - -def hdf_attr_to_dict(attr): - """ - Convert from HDF attributes to valid dict - """ - - try: - output_dict = dict(attr) - except: - output_dict = {} - for count in attr: - try: - output_dict[count] = attr[count] - except: - print('Fail: {}'.format(count)) - - # String in HDF are treated as numpy bytes_ literals - # We want out instance in memeory to have Python Strings - # This does a simple conversion - # Also will check to see if a string is burried in an array - for k in output_dict: - if isinstance(output_dict[k], _np.bytes_): - output_dict[k] = output_dict[k].decode('UTF-8') - elif isinstance(output_dict[k], _np.ndarray): - if output_dict[k].dtype.kind == 'S': # String array - # This is a cute way of taking an array of charcters and merging - # them into a string. If just a single-element array, - # will also return a string - output_dict[k] = ''.join(output_dict[k].astype(_np.str)) - return output_dict +__all__ = ['hdf_import_data'] def hdf_import_data(pth, filename, dset_list, output_cls_instance=None): """ @@ -178,176 +47,194 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None): """ # Join path and filename in an os-independant way - pfname = _os.path.normpath(_os.path.join(pth, filename)) + pfname = _lazy5.utils.fullpath(filename, pth=pth) - if hdf_is_valid_dsets(pth, filename,dset_list) == False: - print('Invalid filename or dataset list') + if not _lazy5.inspect.valid_file(filename, pth=pth, verbose=True): + return False + elif not _lazy5.inspect.valid_dsets(filename, dset_list, pth=pth, verbose=True): return False else: - try: - f = _h5py.File(pfname,'r') - - if type(output_cls_instance) == _Hsi: - print('Type Hsi') - if isinstance(dset_list, str): - output_cls_instance.data = _convert_to_np_dtype(f[dset_list]) - output_cls_instance.meta = hdf_attr_to_dict(f[dset_list].attrs) - elif isinstance(dset_list, list): - if len(dset_list) > 1: - print('Cannot accept more than 1 HSI image at this time') - else: - for num, dname in enumerate(dset_list): - if num == 0: - output_cls_instance.data = _convert_to_np_dtype(f[dname]) - output_cls_instance.meta = hdf_attr_to_dict(f[dname].attrs) - else: - output_cls_instance.data = _np.vstack((output_cls_instance.data, _convert_to_np_dtype(f[dname]))) - ret = True - elif type(output_cls_instance) == _Spectra: - print('Type Spectra') - if isinstance(dset_list,str): - output_cls_instance.data = _convert_to_np_dtype(f[dset_list]) - output_cls_instance.meta = hdf_attr_to_dict(f[dset_list].attrs) - - elif isinstance(dset_list, list): + fof = _lazy5.utils.FidOrFile(pfname, mode='r') + fid = fof.fid + + if type(output_cls_instance) == _Hsi: + print('Type Hsi') + if isinstance(dset_list, str): + # Convert to hardware-oriented dtype (endianess) + dset_dtype_import = fid[dset_list].dtype.newbyteorder('=') + dset_shp = fid[dset_list].shape + output_cls_instance.data = _np.zeros(dset_shp, dtype=dset_dtype_import) + fid[dset_list].read_direct(output_cls_instance.data) + + # output_cls_instance.data = fid[dset_list].value + output_cls_instance.meta = _lazy5.inspect.get_attrs_dset(fid, dset_list) + elif isinstance(dset_list, list): + if len(dset_list) > 1: + print('Cannot accept more than 1 HSI image at this time') + else: for num, dname in enumerate(dset_list): + # Convert to hardware-oriented dtype (endianess) + dset_dtype_import = fid[dname].dtype.newbyteorder('=') + dset_shp = fid[dname].shape if num == 0: - output_cls_instance.data = _convert_to_np_dtype(f[dname]) - output_cls_instance.meta = hdf_attr_to_dict(f[dname].attrs) + output_cls_instance.data = _np.zeros(dset_shp, + dtype=dset_dtype_import) + fid[dname].read_direct(output_cls_instance.data) + + # output_cls_instance.data = fid[dname].value + output_cls_instance.meta = _lazy5.inspect.get_attrs_dset(fid, dname) else: - output_cls_instance.data = _np.vstack((output_cls_instance.data, _convert_to_np_dtype(f[dname]))) - ret = True - elif type(output_cls_instance) == _Spectrum: - print('Type Spectrum') - if isinstance(dset_list, str): - output_cls_instance.data = _convert_to_np_dtype(f[dset_list]) - output_cls_instance.meta = hdf_attr_to_dict(f[dset_list].attrs) - elif isinstance(dset_list, list): - if len > 1: - print('Will average spectra into a single spectrum') + output_cls_instance.data = _np.vstack((output_cls_instance.data, + fid[dname].value.astype(dset_dtype_import))) + ret = True + elif type(output_cls_instance) == _Spectra: + print('Type Spectra') + if isinstance(dset_list, str): + # Convert to hardware-oriented dtype (endianess) + dset_dtype_import = fid[dset_list].dtype.newbyteorder('=') + if fid[dset_list].ndim == 2: # Compatible dimensions-- use read-direct + dset_shp = fid[dset_list].shape + output_cls_instance.data = _np.zeros(dset_shp, dtype=dset_dtype_import) + fid[dset_list].read_direct(output_cls_instance.data) + else: + output_cls_instance.data = fid[dset_list].value.astype(dset_dtype_import) + + # output_cls_instance.data = fid[dset_list].value + output_cls_instance.meta = _lazy5.inspect.get_attrs_dset(fid, dset_list) + + elif isinstance(dset_list, list): + for num, dname in enumerate(dset_list): + # Convert to hardware-oriented dtype (endianess) + dset_dtype_import = fid[dname].dtype.newbyteorder('=') + if num == 0: + output_cls_instance.data = fid[dname].value.astype(dset_dtype_import) + output_cls_instance.meta = _lazy5.inspect.get_attrs_dset(fid, dname) else: - for num, dname in enumerate(dset_list): - if num == 0: - output_cls_instance.data = _convert_to_np_dtype(f[dname]) - output_cls_instance.meta = hdf_attr_to_dict(f[dname].attrs) - else: - output_cls_instance.data += _convert_to_np_dtype(f[dname]) - output_cls_instance.data /= num+1 - ret = True - elif output_cls_instance is None: - if isinstance(dset_list, str): - data = _convert_to_np_dtype(f[dset_list]) - meta = hdf_attr_to_dict(f[dset_list].attrs) - elif isinstance(dset_list, list): + output_cls_instance.data = _np.vstack((output_cls_instance.data, + fid[dname].value.astype(dset_dtype_import))) + ret = True + elif type(output_cls_instance) == _Spectrum: + print('Type Spectrum') + if isinstance(dset_list, str): + # Convert to hardware-oriented dtype (endianess) + dset_dtype_import = fid[dset_list].dtype.newbyteorder('=') + dset_shp = fid[dset_list].shape + output_cls_instance.data = _np.zeros(dset_shp, dtype=dset_dtype_import) + fid[dset_list].read_direct(output_cls_instance.data) + + # output_cls_instance.data = fid[dset_list].value + output_cls_instance.meta = _lazy5.inspect.get_attrs_dset(fid, dset_list) + elif isinstance(dset_list, list): + if len > 1: + print('Will average spectra into a single spectrum') + else: for num, dname in enumerate(dset_list): + # Convert to hardware-oriented dtype (endianess) + dset_dtype_import = fid[dname].dtype.newbyteorder('=') + dset_shp = fid[dname].shape if num == 0: - data = _convert_to_np_dtype(f[dname]) - meta = hdf_attr_to_dict(f[dname].attrs) + output_cls_instance.data = _np.zeros(dset_shp, + dtype=dset_dtype_import) + fid[dname].read_direct(output_cls_instance.data) + # output_cls_instance.data = fid[dname].value + output_cls_instance.meta = _lazy5.inspect.get_attrs_dset(fid, dname) else: - data = _np.vstack((data, _convert_to_np_dtype(f[dname]))) - ret = [data, meta] - else: - raise TypeError('output_cls must be Spectrum, Spectra, or Hsi') - except: - raise TypeError('Something failed in import_hdf_nist_special') - ret = False - - finally: - f.close() - return ret - -def hdf_export_data(self, output_cls_instance, pth, filename, dsetname): - """ + output_cls_instance.data += fid[dname].value.astype(dset_dtype_import) + output_cls_instance.data /= num+1 + ret = True + elif output_cls_instance is None: + if isinstance(dset_list, str): + # Convert to hardware-oriented dtype (endianess) + dset_dtype_import = fid[dset_list].dtype.newbyteorder('=') + dset_shp = fid[dset_list].shape + data = _np.zeros(dset_shp, dtype=dset_dtype_import) + fid[dset_list].read_direct(data) + + # data = fid[dset_list].value + meta = _lazy5.inspect.get_attrs_dset(fid, dset_list) + elif isinstance(dset_list, list): + for num, dname in enumerate(dset_list): + # Convert to hardware-oriented dtype (endianess) + dset_dtype_import = fid[dname].dtype.newbyteorder('=') + dset_shp = fid[dname].shape + if num == 0: + data = _np.zeros(dset_shp, + dtype=dset_dtype_import) + fid[dname].read_direct(data) + # data = fid[dname].value + meta = _lazy5.inspect.get_attrs_dset(fid, dname) + else: + data = _np.vstack((data, fid[dname].value.astype(dset_dtype_import))) + ret = [data, meta] + else: + raise TypeError('output_cls must be Spectrum, Spectra, or Hsi') - """ - save_grp = dsetname.rpartition('/')[0] - save_dataset_name_no_grp = dsetname.rpartition('/')[-1] - - try: - # Join path and filename in an os-independant way - pfname_out = _os.path.normpath(_os.path.join(pth, filename)) - - f_out = _h5py.File(pfname_out, 'a') - loc = f_out.require_group(save_grp) - dset = loc.create_dataset(save_dataset_name_no_grp, data=output_cls_instance.data) - - for attr_key in output_cls_instance.meta: - try: - attribute = output_cls_instance.meta[attr_key] - if isinstance(attribute, str): - attribute = _np.array(attribute, dtype='S') - dset.attrs.create(attr_key,attribute) - except: - print('Error in attributes') - - # Breadcrumb attributes - bc_attr_dict = self.bcpre.attr_dict - for attr_key in bc_attr_dict: - try: - attribute = bc_attr_dict[attr_key] - if isinstance(attribute, str): - attribute = _np.array(attribute, dtype='S') - dset.attrs.create(attr_key,attribute) - except: - print('Error in attributes') - -# #print('Key: {}, Val: {}'.format(attr_key, bc_attr_dict[attr_key])) -# val = bc_attr_dict[attr_key] -# if isinstance(val, str): -# dset.attrs[attr_key] = val -# else: -# try: -# dset.attrs.create(attr_key,bc_attr_dict[attr_key]) -# except: -# print('Could not create attribute') - - except: - print('Something went wrong while saving') - else: - print('Saved without issues') - finally: - f_out.close() + fid.close() + return ret if __name__ == '__main__': # pragma: no cover - from crikit.io.meta_configs import (special_nist_bcars2 - as _snb) + from crikit.io.meta_configs import (special_nist_bcars2 as _snb) rosetta = _snb() - pth = '../../../' + pth = '../' filename = 'mP2_w_small.h5' - dset = '/Spectra/Dark_3_5ms_2' - tester = hdf_is_valid_dsets(pth, 'fake.h5','fake') - assert tester == False - tester = hdf_is_valid_dsets(pth, filename,'fake_dset') - assert tester == False + dset = '/Spectra/Dark_3_5ms_2' + tester = _lazy5.inspect.valid_dsets(pth=pth, file='fake.h5', dset_list='fake') + assert not tester - tester = hdf_is_valid_dsets(pth, filename,['fake_dset1','fake_dset2']) - assert tester == False + tester = _lazy5.inspect.valid_dsets(pth=pth, file='fake.h5', dset_list='fake_dset') + assert not tester - tester = hdf_is_valid_dsets(pth, filename,dset) - assert tester == True + tester = _lazy5.inspect.valid_dsets(pth=pth, file='fake.h5', + dset_list=['fake_dset1', 'fake_dset2']) + assert not tester - dset_list = hdf_dset_list_rep('/Spectra/Dark_3_5ms_',_np.arange(2)) - tester = hdf_is_valid_dsets(pth, filename,dset_list) - assert tester == True + print('Path: {}'.format(pth)) + tester = _lazy5.inspect.valid_dsets(pth=pth, file=filename, dset_list=dset, verbose=True) + assert tester print('--------------\n\n') spect_dark = _Spectra() - tester = hdf_is_valid_dsets(pth, filename,['/Spectra/Dark_3_5ms_2']) - hdf_import_data(pth, filename,'/Spectra/Dark_3_5ms_2',spect_dark) + tester = _lazy5.inspect.valid_dsets(pth=pth, file=filename, + dset_list=['/Spectra/Dark_3_5ms_2']) + hdf_import_data(pth, filename, '/Spectra/Dark_3_5ms_2', spect_dark) #hdf_process_attr(rosetta, spect_dark) print('Shape of dark spectra: {}'.format(spect_dark.shape)) print('Shape of dark spectra.mean(): {}'.format(spect_dark.mean().shape)) - + print('Dtype of dark spectra: {}'.format(spect_dark._data.dtype)) print('') img = _Hsi() - hdf_import_data(pth, filename,'/BCARSImage/mP2_3_5ms_Pos_2_0/mP2_3_5ms_Pos_2_0_small',img) + hdf_import_data(pth, filename, '/BCARSImage/mP2_3_5ms_Pos_2_0/mP2_3_5ms_Pos_2_0_small', img) print('Shape of img: {}'.format(img.shape)) print('Shape of img.mean(): {}'.format(img.mean().shape)) + print('Dtype of img: {}'.format(img._data.dtype)) + print('Dtype of img.mean(): {}'.format(img.mean().dtype)) + + print('--------------\n\n') + pth = 'C:/Users/chc/Documents/Data/2018/OliverJonas/180629/' + filename = 'L1d1_pos0.h5' + dsetname = '/BCARSImage/L1d1_pos0_0/NRB_Post_0' + spect_nrb = _Spectra() + tester = _lazy5.inspect.valid_dsets(pth=pth, file=filename, + dset_list=[dsetname]) + out = hdf_import_data(pth, filename, dsetname, spect_nrb) + print('HDF_import_data returned: {}'.format(out)) + # hdf_process_attr(rosetta, spect_nrb) + + # print('Shape of dark spectra: {}'.format(spect_dark.shape)) + # print('Shape of dark spectra.mean(): {}'.format(spect_dark.mean().shape)) + # print('Dtype of dark spectra: {}'.format(spect_dark._data.dtype)) + # print('') + # img = _Hsi() + # hdf_import_data(pth, filename, '/BCARSImage/mP2_3_5ms_Pos_2_0/mP2_3_5ms_Pos_2_0_small', img) + # print('Shape of img: {}'.format(img.shape)) + # print('Shape of img.mean(): {}'.format(img.mean().shape)) + # print('Dtype of img: {}'.format(img._data.dtype)) + # print('Dtype of img.mean(): {}'.format(img.mean().dtype)) \ No newline at end of file diff --git a/crikit/io/macros.py b/crikit/io/macros.py index dcab6e9..8c5eb0b 100644 --- a/crikit/io/macros.py +++ b/crikit/io/macros.py @@ -3,9 +3,9 @@ @author: chc """ +import os as _os -import h5py as _h5py -_h5py.get_config().complex_names = ('Re','Im') +import lazy5 from crikit.io.meta_configs import (special_nist_bcars2 as _snb, special_nist_bcars1_sample_scan as _snb1ss) @@ -13,7 +13,7 @@ from crikit.io.hdf5 import hdf_import_data as _hdf_import_data from crikit.io.csv_nist import csv_nist_import_data as _csv_nist_import_data -__all__ = [] +__all__ = ['import_hdf_nist_special', 'import_csv_nist_special1'] def import_hdf_nist_special(pth, filename, dset, output_cls_instance): @@ -27,17 +27,35 @@ def import_hdf_nist_special(pth, filename, dset, output_cls_instance): """ print('\n') + import_success = _hdf_import_data(pth, filename, dset, output_cls_instance) + if import_success is False: + raise ValueError('hdf_import_data failed') + return False + _meta_process(_snb(), output_cls_instance) + return True + +def import_hdf_nist_special_ooc(pth, filename, dset, output_cls_instance): + """ + Import data from HDF File (OUT-OF-CORE) as specified by NIST-specific settings + + Returns + ------- + Success : bool + Whether import was successful + """ + + print('\n') + try: - import_success = _hdf_import_data(pth, filename, dset, output_cls_instance) - if import_success is None or import_success is False: - raise ValueError('hdf_import_data returned None') + fid = lazy5.utils.FidOrFile(lazy5.utils.fullpath(filename, pth=pth)).fid + output_cls_instance._data = fid[dset] + output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset) _meta_process(_snb(), output_cls_instance) except: - print('Something failed in import_hdf_nist_special') + raise ValueError('hdf_import_data failed') return False else: - print('\n') - return True + return fid def import_csv_nist_special1(pth, filename_header, filename_data, output_cls_instance): @@ -66,7 +84,7 @@ def import_csv_nist_special1(pth, filename_header, filename_data, from crikit.data.hsi import Hsi as _Hsi - pth = _os.path.abspath('../../../') + '/' + pth = '../' filename = 'mP2_w_small.h5' img = _Hsi() import_hdf_nist_special(pth, filename,'/BCARSImage/mP2_3_5ms_Pos_2_0/mP2_3_5ms_Pos_2_0_small',img) @@ -74,13 +92,13 @@ def import_csv_nist_special1(pth, filename_header, filename_data, print('Shape of img.mean(): {}'.format(img.mean().shape)) print(img.y_rep.data) - from crikit.data.spectrum import Spectrum as _Spectrum + # from crikit.data.spectrum import Spectrum as _Spectrum - sp = _Spectrum() - pth = '../../../Young_150617/' - filename_header = 'SH-03.h' - filename_data = 'base061715_152213_60ms.txt' + # sp = _Spectrum() + # pth = '../../../Young_150617/' + # filename_header = 'SH-03.h' + # filename_data = 'base061715_152213_60ms.txt' - import_csv_nist_special1(pth, filename_header, filename_data, - output_cls_instance=sp) + # import_csv_nist_special1(pth, filename_header, filename_data, + # output_cls_instance=sp) \ No newline at end of file diff --git a/crikit/io/meta_configs.py b/crikit/io/meta_configs.py index ea45397..bcb9e85 100644 --- a/crikit/io/meta_configs.py +++ b/crikit/io/meta_configs.py @@ -16,7 +16,7 @@ def special_nist_bcars2(): rosetta = {} rosetta['XPixelSize'] = ['RasterScanParams.FastAxisStepSize', - 'Raster.Fast.StepSize'] + 'Raster.Fast.StepSize','!',1] rosetta['XStart'] = ['RasterScanParams.FastAxisStart', 'Raster.Fast.Start'] rosetta['XStop'] = ['RasterScanParams.FastAxisStop', 'Raster.Fast.Stop'] rosetta['XLength'] = ['RasterScanParams.FastAxisSteps', 'Raster.Fast.Steps'] @@ -24,7 +24,7 @@ def special_nist_bcars2(): rosetta['XUnits'] = ['RasterScanParams.FastAxisUnits','!','$\\mu$m'] rosetta['YPixelSize'] = ['RasterScanParams.SlowAxisStepSize', - 'Raster.Slow.StepSize'] + 'Raster.Slow.StepSize','!',1] rosetta['YStart'] = ['RasterScanParams.SlowAxisStart', 'Raster.Slow.Start'] rosetta['YStop'] = ['RasterScanParams.SlowAxisStop', 'Raster.Slow.Stop'] rosetta['YLength'] = ['RasterScanParams.SlowAxisSteps', 'Raster.Slow.Steps'] diff --git a/crikit/io/meta_process.py b/crikit/io/meta_process.py index abff806..f6b8d2f 100644 --- a/crikit/io/meta_process.py +++ b/crikit/io/meta_process.py @@ -34,7 +34,6 @@ def rosetta_query(key, rosetta, output_cls_instance): temp_key = count temp_val = output_cls_instance._meta[temp_key] break -# print('{}:{}'.format(count, temp_val)) else: pass except: @@ -63,29 +62,26 @@ def meta_process(rosetta, output_cls_instance): """ # Frequency-calibration - try: - calib_dict = {} - - calib_dict['a_vec'] = rosetta_query('ColorPolyVals',rosetta, output_cls_instance)[0] - calib_dict['n_pix'] = rosetta_query('ColorChannels',rosetta, output_cls_instance)[0] - calib_dict['ctr_wl'] = rosetta_query('ColorCenterWL',rosetta, output_cls_instance)[0] - calib_dict['ctr_wl0'] = rosetta_query('ColorCalibWL',rosetta, output_cls_instance)[0] - calib_dict['probe'] = rosetta_query('ColorProbe',rosetta, output_cls_instance)[0] - calib_dict['units'] = rosetta_query('ColorUnits',rosetta, output_cls_instance)[0] + calib_dict = {} - output_cls_instance.freq.calib = calib_dict + calib_dict['a_vec'] = rosetta_query('ColorPolyVals',rosetta, output_cls_instance)[0] + calib_dict['n_pix'] = rosetta_query('ColorChannels',rosetta, output_cls_instance)[0] + calib_dict['ctr_wl'] = rosetta_query('ColorCenterWL',rosetta, output_cls_instance)[0] + calib_dict['ctr_wl0'] = rosetta_query('ColorCalibWL',rosetta, output_cls_instance)[0] + calib_dict['probe'] = rosetta_query('ColorProbe',rosetta, output_cls_instance)[0] + calib_dict['units'] = rosetta_query('ColorUnits',rosetta, output_cls_instance)[0] - use_wn = rosetta_query('ColorWnMode',rosetta, output_cls_instance)[0] - print('Use wavenumber: {}'.format(use_wn)) - if use_wn: # Use wavenumber? - output_cls_instance.freq.calib_fcn = _calib_pix_wn - else: # Use wavelength - output_cls_instance.freq.calib_fcn = _calib_pix_wl + output_cls_instance.freq.calib = calib_dict - output_cls_instance.freq.update() - except: - print('Something failed in meta_process: freq-calib') + use_wn = rosetta_query('ColorWnMode',rosetta, output_cls_instance)[0] + print('Use wavenumber: {}'.format(use_wn)) + if use_wn: # Use wavenumber? + output_cls_instance.freq.calib_fcn = _calib_pix_wn + else: # Use wavelength + output_cls_instance.freq.calib_fcn = _calib_pix_wl + output_cls_instance.freq.update() + # See if an original calibration is found try: calib_orig_dict = {} @@ -118,11 +114,29 @@ def meta_process(rosetta, output_cls_instance): if type(output_cls_instance) == _Hsi: print('Type Hsi') try: - start = rosetta_query('XStart',rosetta, output_cls_instance)[0] - stop = rosetta_query('XStop',rosetta, output_cls_instance)[0] - steps = rosetta_query('XLength',rosetta, output_cls_instance)[0] - units = rosetta_query('XUnits',rosetta, output_cls_instance)[0] - label = rosetta_query('XLabel',rosetta, output_cls_instance)[0] + units = rosetta_query('XUnits',rosetta, output_cls_instance) + label = rosetta_query('XLabel',rosetta, output_cls_instance) + if units is not None: + units = units[0] + if label is not None: + label = label[0] + + start = rosetta_query('XStart',rosetta, output_cls_instance) + stop = rosetta_query('XStop',rosetta, output_cls_instance) + steps = rosetta_query('XLength',rosetta, output_cls_instance) + if (start is not None) & (stop is not None) & (steps is not None): + start = start[0] + stop = stop[0] + steps = steps[0] + else: + temp = output_cls_instance.shape + start = 0 + stop = temp[1] - 1 + steps = temp[1] + units = 'pix' + label = 'X' + + # HDF files store strings in np.bytes format if isinstance(units, bytes): @@ -137,11 +151,27 @@ def meta_process(rosetta, output_cls_instance): del start, stop, steps, units, label - start = rosetta_query('YStart',rosetta, output_cls_instance)[0] - stop = rosetta_query('YStop',rosetta, output_cls_instance)[0] - steps = rosetta_query('YLength',rosetta, output_cls_instance)[0] - units = rosetta_query('YUnits',rosetta, output_cls_instance)[0] - label = rosetta_query('YLabel',rosetta, output_cls_instance)[0] + units = rosetta_query('YUnits',rosetta, output_cls_instance) + label = rosetta_query('YLabel',rosetta, output_cls_instance) + if units is not None: + units = units[0] + if label is not None: + label = label[0] + + start = rosetta_query('YStart',rosetta, output_cls_instance) + stop = rosetta_query('YStop',rosetta, output_cls_instance) + steps = rosetta_query('YLength',rosetta, output_cls_instance) + if (start is not None) & (stop is not None) & (steps is not None): + start = start[0] + stop = stop[0] + steps = steps[0] + else: + temp = output_cls_instance.shape + start = 0 + stop = temp[0] - 1 + steps = temp[0] + units = 'pix' + label = 'Y' # HDF files store strings in np.bytes format if isinstance(units, bytes): diff --git a/crikit/io/tests/test_hdf5.py b/crikit/io/tests/test_hdf5.py new file mode 100644 index 0000000..7e2747e --- /dev/null +++ b/crikit/io/tests/test_hdf5.py @@ -0,0 +1,188 @@ +import os +import numpy as np +import numpy.testing + +import pytest +import h5py +import lazy5 + +from crikit.io.hdf5 import hdf_import_data +from crikit.data.spectrum import Spectrum +from crikit.data.spectra import Spectra +from crikit.data.hsi import Hsi + +@pytest.fixture(scope="module") +def hdf_dataset(): + """ Setups and tears down a sample HDF5 file """ + filename = 'temp_test.h5' + fid = h5py.File(filename, 'w') + + data_m, data_n, data_p = [20, 22, 24] + spectrum = np.random.randn(data_p) + spectra = np.random.randn(data_n, data_p) + hsi = np.random.randn(data_m, data_n, data_p) + + fid.create_dataset('hsi', data=hsi) + fid.create_dataset('spectra', data=spectra) + fid.create_dataset('spectrum', data=spectrum) + + yield filename, fid, (data_m, data_n, data_p) + + # Tear-down + if lazy5.utils.hdf_is_open(fid): + fid.close() + os.remove(filename) + +def test_hdf_import_spectrum_to_spectrum(hdf_dataset): + """ Import a spectrum into a spectrum """ + + filename, fid, hdf_data_shape = hdf_dataset + hdf_data_shape = np.array(hdf_data_shape) + + dname = 'spectrum' + dataset = Spectrum() + + out = hdf_import_data('.', filename, dname, output_cls_instance=dataset) + assert out is True + assert dataset.size == hdf_data_shape[-1] + np.testing.assert_array_equal(dataset.data, fid[dname].value) + +def test_hdf_import_spectra_to_spectra(hdf_dataset): + """ Import a spectra into a spectra """ + + filename, fid, hdf_data_shape = hdf_dataset + hdf_data_shape = np.array(hdf_data_shape) + + dname = 'spectra' + dataset = Spectra() + + out = hdf_import_data('.', filename, dname, output_cls_instance=dataset) + assert out is True + assert dataset.size == hdf_data_shape[1:].prod() + np.testing.assert_array_equal(dataset.data, fid[dname].value) + +def test_hdf_import_hsi_to_hsi(hdf_dataset): + """ Import an hsi into an hsi """ + + filename, fid, hdf_data_shape = hdf_dataset + hdf_data_shape = np.array(hdf_data_shape) + + dname = 'hsi' + dataset = Hsi() + + out = hdf_import_data('.', filename, dname, output_cls_instance=dataset) + assert out is True + assert dataset.size == hdf_data_shape.prod() + np.testing.assert_array_equal(dataset.data, fid[dname].value) +def test_hdf_import_no_output_cls_given(hdf_dataset): + """ Import a spectrum, spectra, and hsi when no instantiated class is provided """ + + filename, fid, hdf_data_shape = hdf_dataset + hdf_data_shape = np.array(hdf_data_shape) + + # Spectrum + dname = 'spectrum' + dataset, dset_meta = hdf_import_data('.', filename, dname, output_cls_instance=None) + assert dataset.size == hdf_data_shape[-1] + np.testing.assert_array_equal(dataset, fid[dname].value) + + # Spectra + dname = 'spectra' + dataset, dset_meta = hdf_import_data('.', filename, dname, output_cls_instance=None) + assert dataset.size == hdf_data_shape[1:].prod() + np.testing.assert_array_equal(dataset, fid[dname].value) + + # HSI + dname = 'hsi' + dataset, dset_meta = hdf_import_data('.', filename, dname, output_cls_instance=None) + assert dataset.size == hdf_data_shape.prod() + np.testing.assert_array_equal(dataset, fid[dname].value) + +# def test_hdf_import_spectra_to_spectrum(hdf_dataset): +# """ Import spectra into a spectrum """ + +# filename, fid, hdf_data_shape = hdf_dataset +# hdf_data_shape = np.array(hdf_data_shape) + +# dname = 'spectra' +# dataset = Spectrum() + +# out = hdf_import_data('.', filename, dname, output_cls_instance=dataset) +# assert out is True +# assert dataset.size == hdf_data_shape[-1] +# np.testing.assert_equal(dataset.data, fid[dname].value.mean(axis=0)) + +# def test_hdf_import_hsi_to_spectrum(hdf_dataset): +# """ Import hsi into a spectrum """ + +# filename, fid, hdf_data_shape = hdf_dataset +# hdf_data_shape = np.array(hdf_data_shape) + +# dname = 'hsi' +# dataset = Spectrum() + +# out = hdf_import_data('.', filename, dname, output_cls_instance=dataset) +# assert out is True +# assert dataset.size == hdf_data_shape[-1] +# np.testing.assert_equal(dataset.data, fid[dname].value.mean(axis=(0,1))) + + +# def test_hdf_import_spectrum_to_spectra(hdf_dataset): +# """ Import a spectrum into a spectra """ + +# filename, fid, hdf_data_shape = hdf_dataset +# hdf_data_shape = np.array(hdf_data_shape) + +# dname = 'spectrum' +# dataset = Spectra() + +# out = hdf_import_data('.', filename, dname, output_cls_instance=dataset) +# assert out is True +# assert dataset.size == hdf_data_shape[-1] +# assert dataset.ndim == 2 +# np.testing.assert_equal(dataset.data, fid[dname].value) + +# def test_hdf_import_hsi_to_spectra(hdf_dataset): +# """ Import hsi into spectra """ + +# filename, fid, hdf_data_shape = hdf_dataset +# hdf_data_shape = np.array(hdf_data_shape) + +# dname = 'hsi' +# dataset = Spectra() + +# out = hdf_import_data('.', filename, dname, output_cls_instance=dataset) +# assert out is True +# assert dataset.size == hdf_data_shape.prod() +# assert dataset.ndim == 2 +# np.testing.assert_equal(dataset.data, fid[dname].value.reshape((-1, hdf_data_shape[-1]))) + +# def test_hdf_import_spectrum_to_hsi(hdf_dataset): +# """ Import a spectrum into an hsi """ + +# filename, fid, hdf_data_shape = hdf_dataset +# hdf_data_shape = np.array(hdf_data_shape) + +# dname = 'spectrum' +# dataset = Hsi() + +# out = hdf_import_data('.', filename, dname, output_cls_instance=dataset) +# assert out is True +# assert dataset.size == hdf_data_shape[-1] +# assert dataset.ndim == 3 +# np.testing.assert_equal(dataset.data, fid[dname].value) + +# def test_hdf_import_spectra_to_hsi(hdf_dataset): +# """ Import spectra into an hsi """ + +# filename, fid, hdf_data_shape = hdf_dataset +# hdf_data_shape = np.array(hdf_data_shape) + +# dname = 'spectra' +# dataset = Hsi() + +# out = hdf_import_data('.', filename, dname, output_cls_instance=dataset) +# assert out is True +# assert dataset.size == hdf_data_shape[1:].prod() +# assert dataset.ndim == 3 +# np.testing.assert_equal(dataset.data, fid[dname].value.reshape((0, -1, hdf_data_shape[-1]))) \ No newline at end of file diff --git a/crikit/preprocess/algorithms/als.py b/crikit/preprocess/algorithms/als.py index 7036c3b..e9ba112 100644 --- a/crikit/preprocess/algorithms/als.py +++ b/crikit/preprocess/algorithms/als.py @@ -17,15 +17,17 @@ class AlsCvxopt(AbstractBaseline): def __init__(self, smoothness_param=1e3, asym_param=1e-4, redux=1, order=2, rng=None, fix_end_points=False, fix_rng=None, - fix_const=1, max_iter=100, min_diff=1e-5, verbose=False): + fix_const=1, max_iter=100, min_diff=1e-5, verbose=False, + **kwargs): """ Parameters ---------- smoothness_param : float, optional (default, 1e3) Smoothness parameter - asym_param : float, optional (default, 1e-4) - Assymetry parameter + asym_param : float, ndarray, optional (default, 1e-4) + Assymetry parameter. Note: if vector, length of signal/frequency + vector (i.e., not relative to rng) redux : int, optional (default, 1) Reduction parameter to sub-sample input signal @@ -43,7 +45,7 @@ def __init__(self, smoothness_param=1e3, asym_param=1e-4, redux=1, fix_rng : ndarray (1D), optional (default, None) Pixels to weight so that the baseline strongly approaches the data - at these pixels. + at these pixels. Note: pixel number relative to rng max_iter : int, optional (default, 100) Maximum number of least-squares iterations to perform @@ -54,6 +56,13 @@ def __init__(self, smoothness_param=1e3, asym_param=1e-4, redux=1, verbose : bool, optional (default, False) Display progress of detrending + Notes + ----- + Vector spaces: + + - asym_param, x + - fix_rng, x[rng] + """ self.smoothness_param=smoothness_param @@ -168,7 +177,11 @@ def _calc(self, signal): penalty_vector[-1] = 1 if self.fix_rng is not None: - penalty_vector[self.fix_rng] = self.fix_const + # ! Dirty fix to the problem of @property fix_rng being + # ! equal to the size of penalty_vector + fix_rng = 1*self.fix_rng + fix_rng = fix_rng[fix_rng < penalty_vector.size] + penalty_vector[fix_rng] = self.fix_const baseline_output[coords] = baseline_current @@ -180,53 +193,14 @@ def _calc(self, signal): return baseline_output if __name__ == '__main__': # pragma: no cover - import matplotlib.pyplot as _plt - - x = _np.linspace(0,1000,800) - data = _np.exp(-(x-500)**2/300**2) + _np.abs(5/(300 - x -1j*10) + .005) - - N = 1 - D = 2 - - if D == 3: - data = _np.dot((_np.random.rand(N,N)*_np.ones((N,N)))[...,None], data[None,:]) - else: - data = _np.dot((_np.random.rand(N)*_np.ones((N)))[...,None], data[None,:]) - -# print('Data.shape: {}\n'.format(data.shape)) - -# asym_param = _np.logspace(-4, -7, x.size) - - _plt.plot(x,data.T) - - sp_vec = _np.logspace(0,6,7) - for num, sp in enumerate(sp_vec): -# for ap in _np.logspace(-6,0,10): - ap = sp/1e6 - als = AlsCvxopt(smoothness_param=sp, asym_param=ap, redux=1, - max_iter=1000, - verbose=False) + x = _np.linspace(-100, 100, 1000) + y = 10*_np.exp(-(x**2/(2*20**2))) - baseline = als.calculate(data) - - scaled_num = (num)/(sp_vec.size) - color = _plt.cm.jet(scaled_num) - - _plt.plot(x, baseline.T, c=color, label='{:.1e}'.format(sp)) - _plt.legend() - _plt.show() -# print('Internal Timer: {:.4f} sec ({:.4f} per)'.format(als.t, -# als.t_per_iter)) - -# als = AlsCvxopt(smoothness_param=1, asym_param=1e-3, redux=10, -# max_iter=1000, -# verbose=False) -# -# baseline = als.calculate(data) -# print('Internal Timer: {:.4f} sec ({:.4f} per)'.format(als.t, -# als.t_per_iter)) -# -# if (D <= 2) & (N<21): -# _plt.plot(data.T,'k') -# _plt.plot(baseline.T,'r') -# _plt.show() + rng = _np.arange(200,800) + asym_vec = 0*x + 1e-7 + fix_rng = _np.arange(600) + + als = AlsCvxopt(smoothness_param=1, asym_param=asym_vec, rng=rng, + redux=10, fix_end_points=False, fix_rng=fix_rng, + verbose=True) + y_als = als.calculate(y) diff --git a/crikit/preprocess/subtract_dark.py b/crikit/preprocess/subtract_dark.py index 0324f0a..6db990c 100644 --- a/crikit/preprocess/subtract_dark.py +++ b/crikit/preprocess/subtract_dark.py @@ -1,9 +1,7 @@ """ Subtract mean value (optionally, over a range from all spectrum/spectra/hsi) -Created on Thu May 26 14:31:39 2016 - -@author: chc +Note: If dark > 1D, averaged -- even if data has same shape. """ import numpy as _np @@ -36,6 +34,12 @@ def transform(self, data): Returns the success state (True=success) """ + + if not _np.can_cast(self.dark.dtype, data.dtype): + err_str1 = 'Cannot transform input data type {}'.format(data.dtype) + err_str2 = ' with dark type {}'.format(self.dark.dtype) + raise TypeError(err_str1 + err_str2) + success = self._calc(data, ret_obj=data) return success @@ -69,12 +73,9 @@ def _calc(self, data, ret_obj): # Expand dark dimensionality to match data.ndim self.dark = _expand_1d_to_ndim(self.dark, data.ndim) - try: - ret_obj -= self.dark - except: - return False - else: - return True + ret_obj -= self.dark + return True + if __name__ == '__main__': # pragma: no cover diff --git a/crikit/preprocess/tests/test_als.py b/crikit/preprocess/tests/test_als.py index 6e27f05..5dfbfe9 100644 --- a/crikit/preprocess/tests/test_als.py +++ b/crikit/preprocess/tests/test_als.py @@ -165,18 +165,43 @@ def test_rng_redux_fix_rng(): x = np.linspace(-100, 100, 1000) y = 10*np.exp(-(x**2/(2*20**2))) - als = AlsCvxopt(smoothness_param=1, asym_param=1e-7, + rng = np.arange(200,800) + + als = AlsCvxopt(smoothness_param=1, asym_param=1e-7, rng=rng, redux=10, fix_end_points=False, fix_rng=None, verbose=True) y_als = als.calculate(y) assert np.max(y[250:750] - y_als[250:750]) > 9 - fix_rng = np.arange(200,800) - - als = AlsCvxopt(smoothness_param=1, asym_param=1e-7, + fix_rng = np.arange(600) + # fix_rng = np.hstack((np.arange(100), np.arange(500,600))) + + als = AlsCvxopt(smoothness_param=1, asym_param=1e-7, rng=rng, redux=10, fix_end_points=False, fix_rng=fix_rng, verbose=True) y_als = als.calculate(y) assert np.max(y[250:750] - y_als[250:750]) < 0.004 - + +def test_rng_redux_fix_rng_vecasym(): + x = np.linspace(-100, 100, 1000) + y = 10*np.exp(-(x**2/(2*20**2))) + + rng = np.arange(200,800) + + asym_vec = 0*x + 1e-7 + als = AlsCvxopt(smoothness_param=1, asym_param=asym_vec, rng=rng, + redux=10, fix_end_points=False, fix_rng=None, + verbose=True) + y_als = als.calculate(y) + + assert np.max(y[250:750] - y_als[250:750]) > 9 + + fix_rng = np.arange(600) + # fix_rng = np.hstack((np.arange(100), np.arange(500,600))) + + als = AlsCvxopt(smoothness_param=1, asym_param=1e-7, rng=rng, + redux=10, fix_end_points=False, fix_rng=fix_rng, + verbose=True) + y_als = als.calculate(y) + assert np.max(y[250:750] - y_als[250:750]) < 0.004 \ No newline at end of file diff --git a/crikit/preprocess/tests/test_subtract_dark.py b/crikit/preprocess/tests/test_subtract_dark.py new file mode 100644 index 0000000..a560d74 --- /dev/null +++ b/crikit/preprocess/tests/test_subtract_dark.py @@ -0,0 +1,327 @@ +import os +import numpy as np +import numpy.testing + +import pytest + +from crikit.preprocess.subtract_dark import SubtractDark + +@pytest.fixture(scope="function") +def make_datasets(): + """ Setups and tears down a series of datasets """ + + data_m, data_n, data_p = [20, 22, 24] + spectrum = np.random.randn(data_p)**2 + 1 + spectra = np.random.randn(data_n, data_p)**2 + 1 + hsi = np.random.randn(data_m, data_n, data_p)**2 + 1 + + return spectrum, spectra, hsi, np.array([data_m, data_n, data_p]) + +def test_sub_spectrum_from_spectrum(make_datasets): + """ Dark is spectrum. Data is spectrum. """ + + spectrum, spectra, hsi, shape = make_datasets + data = 1*spectrum + dark = 1*spectrum + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + np.testing.assert_array_almost_equal(out, 0.0) + np.testing.assert_array_almost_equal(out, data - dark) + + # Transform + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_sub_spectra_from_spectrum(make_datasets): + """ Dark is spectra. Data is spectrum. """ + + spectrum, spectra, hsi, shape = make_datasets + data = 1*spectrum + dark = 1*spectra + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + np.testing.assert_array_almost_equal(out, data - dark.mean(axis=0)) + + # Transform + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_sub_hsi_from_spectrum(make_datasets): + """ Dark is HSI. Data is spectrum. """ + + spectrum, spectra, hsi, shape = make_datasets + data = 1*spectrum + dark = 1*hsi + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + np.testing.assert_array_almost_equal(out, data - dark.mean(axis=(0,1))) + + # Transform + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_sub_spectrum_from_spectra(make_datasets): + """ Dark is spectrum. Data is spectra. """ + + spectrum, spectra, hsi, shape = make_datasets + data = 1*spectra + dark = 1*spectrum + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + np.testing.assert_array_almost_equal(out, data - dark[None,:]) + + # Transform + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_sub_spectra_from_spectra(make_datasets): + """ Dark is spectra. Data is spectra. """ + + spectrum, spectra, hsi, shape = make_datasets + data = 1*spectra + dark = 1*spectra + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + + # * Even though the data and dark have same dimensions, the dark is averaged + np.testing.assert_array_almost_equal(out, data - dark.mean(axis=0)[None,:]) + + # Transform + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_sub_hsi_from_spectra(make_datasets): + """ Dark is HSI. Data is spectrum. """ + + spectrum, spectra, hsi, shape = make_datasets + data = 1*spectra + dark = 1*hsi + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + np.testing.assert_array_almost_equal(out, data - dark.mean(axis=(0,1))[None,:]) + + # Transform + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_sub_spectrum_from_hsi(make_datasets): + """ Dark is spectrum. Data is HSI. """ + + spectrum, spectra, hsi, shape = make_datasets + data = 1*hsi + dark = 1*spectrum + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + np.testing.assert_array_almost_equal(out, data - dark[None,None,:]) + + # Transform + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_sub_spectra_from_hsi(make_datasets): + """ Dark is spectra. Data is HSI. """ + + spectrum, spectra, hsi, shape = make_datasets + data = 1*hsi + dark = 1*spectra + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + + np.testing.assert_array_almost_equal(out, data - dark.mean(axis=0)[None,None,:]) + + # Transform + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_sub_hsi_from_hsi(make_datasets): + """ Dark is HSI. Data is HSI. """ + + spectrum, spectra, hsi, shape = make_datasets + data = 1*hsi + dark = 1*hsi + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + + # * Even though the data and dark have same dimensions, the dark is averaged + np.testing.assert_array_almost_equal(out, data - dark.mean(axis=(0,1))[None,None,:]) + + # Transform + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_sub_hsi_int_from_hsi_float(make_datasets): + """ Dark is HSI. Data is HSI. """ + + spectrum, spectra, hsi, shape = make_datasets + data = (1*hsi).astype(np.float) + dark = (1*hsi).astype(np.int) + + subdark = SubtractDark(dark) + + # Calculate + meaner = data.mean() + out = subdark.calculate(data) + assert meaner == data.mean() + assert out.mean() != data.mean() + assert out.size == data.size + + # * Even though the data and dark have same dimensions, the dark is averaged + np.testing.assert_array_almost_equal(out, data - dark.mean(axis=(0,1))[None,None,:]) + + # Transform + dark = (1*hsi).astype(np.int) + subdark = SubtractDark(dark) + success = subdark.transform(data) + np.testing.assert_array_almost_equal(data, out) + assert meaner != data.mean() + assert success is True + +def test_transform_incompatible_dtypes(make_datasets): + """ + Test that TypeError is raised when Dark and Data have incompatible + dtypes for in-place transformation + + Note: if spectra or hsi is used for dark, will convert to float due to mean + """ + + spectrum, spectra, hsi, shape = make_datasets + + # DOES NOT RAISE ERROR + data = (1*hsi).astype(np.int) + dark = (1*spectrum).astype(np.int) + subdark = SubtractDark(dark) + subdark.transform(data) + + # DOES NOT RAISE ERROR + data = (1*hsi).astype(np.float) + dark = (1*spectrum).astype(np.int) + subdark = SubtractDark(dark) + subdark.transform(data) + + # DOES NOT RAISE ERROR + data = (1*hsi).astype(np.complex) + dark = (1*spectrum).astype(np.int) + subdark = SubtractDark(dark) + subdark.transform(data) + + # DOES RAISE ERROR + data = (1*hsi).astype(np.int) + dark = (1*spectrum).astype(np.float) + subdark = SubtractDark(dark) + with pytest.raises(TypeError): + subdark.transform(data) + + # DOES NOT RAISE ERROR + data = (1*hsi).astype(np.float) + dark = (1*spectrum).astype(np.float) + subdark = SubtractDark(dark) + subdark.transform(data) + + # DOES NOT RAISE ERROR + data = (1*hsi).astype(np.complex) + dark = (1*spectrum).astype(np.float) + subdark = SubtractDark(dark) + subdark.transform(data) + + # DOES RAISE ERROR + data = (1*hsi).astype(np.int) + dark = (1*spectrum).astype(np.complex) + subdark = SubtractDark(dark) + with pytest.raises(TypeError): + subdark.transform(data) + + # DOES RAISE ERROR + data = (1*hsi).astype(np.float) + dark = (1*spectrum).astype(np.complex) + subdark = SubtractDark(dark) + with pytest.raises(TypeError): + subdark.transform(data) + + # DOES NOT RAISE ERROR + data = (1*hsi).astype(np.complex) + dark = (1*spectrum).astype(np.complex) + subdark = SubtractDark(dark) + subdark.transform(data) + + \ No newline at end of file diff --git a/crikit/ui/deprecated/dialog_SVD.py b/crikit/ui/deprecated/dialog_SVD.py deleted file mode 100644 index 29abec6..0000000 --- a/crikit/ui/deprecated/dialog_SVD.py +++ /dev/null @@ -1,363 +0,0 @@ -""" -SVD Dialog - -References ------------ -[1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \ - Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \ - Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543. - -""" - -import sys as _sys -import numpy as _np - -from PyQt5 import QtWidgets as _QtWidgets -from PyQt5.QtWidgets import (QApplication as _QApplication, - QDialog as _QDialog) -import PyQt5.QtCore as _QtCore - -from scipy.linalg import (svd as _svd, diagsvd as _diagsvd) - -# Import from Designer-based GUI -from crikit.ui.qt_Factorization import Ui_Dialog ### EDIT ### - -# Generic imports for MPL-incorporation -import matplotlib as _mpl - -from sciplot.ui.widget_mpl import MplCanvas as _MplCanvas - -_mpl.use('Qt5Agg') -_mpl.rcParams['font.family'] = 'sans-serif' -_mpl.rcParams['font.size'] = 12 - -class DialogSVD(_QDialog): - """ - SubUiSVD : SVD SubUI - """ - - def __init__(self, data=None, parent = None): - - # Generic load/init designer-based GUI - super(DialogSVD, self).__init__(parent) ### EDIT ### - - self.ui = Ui_Dialog() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - self.ui.pushButtonNext.clicked.connect(self.advance) - self.ui.pushButtonPrev.clicked.connect(self.advance) - self.ui.pushButtonGoTo.clicked.connect(self.advance) - self.ui.pushButtonCancel.clicked.connect(self.reject) - self.ui.pushButtonOk.clicked.connect(self.accept) - self.ui.pushButtonClear.clicked.connect(self.clear) - self.ui.pushButtonApply.clicked.connect(self.applyCheckBoxes) - self.ui.pushButtonScript.clicked.connect(self.runScript) - - self.firstSV = 0 - self.spanSV = 6 - - self.Mlen = 0 - self.Nlen = 0 - self.Olen = 0 - - self.data = _np.zeros([self.Mlen, self.Nlen, self.Olen]) - - self.selected_svs = set() - self.ui.lcdSelectedFactors.display(len(self.selected_svs)) - - self.svWins = [] - self.svLabelCheckBoxes = [self.ui.checkBox, - self.ui.checkBox_2, - self.ui.checkBox_3, - self.ui.checkBox_4, - self.ui.checkBox_5, - self.ui.checkBox_6] - - for count in range(self.spanSV): - self.svWins.append(_MplCanvas(subplot=211)) - self.svWins[count].ax[0].axis('Off') - self.svWins[count].ax[1].hold('Off') - - self.ui.gridLayout.addWidget(self.svWins[0],1,0) - self.ui.gridLayout.addWidget(self.svWins[1],1,1) - self.ui.gridLayout.addWidget(self.svWins[2],1,2) - - self.ui.gridLayout.addWidget(self.svWins[3],3,0) - self.ui.gridLayout.addWidget(self.svWins[4],3,1) - self.ui.gridLayout.addWidget(self.svWins[5],3,2) - - self.reconCurrent = _MplCanvas(subplot=211) - self.reconCurrent.ax[0].axis('Off') - self.reconCurrent.ax[1].hold('Off') - - self.reconRemainder = _MplCanvas(subplot=211) - self.reconRemainder.ax[0].axis('Off') - self.reconRemainder.ax[1].hold('Off') - - - self.ui.verticalLayout_3.insertWidget(1,self.reconCurrent) - self.ui.verticalLayout_3.insertWidget(4,self.reconRemainder) - - for count in range(self.spanSV): - self.svLabelCheckBoxes[count].setText('Keep: ' + str(count)) - - if data is not None: - self.data = data - if data.ndim == 3: - self.Mlen, self.Nlen, self.Olen = data.shape - self.reconCurrent.ax[0].imshow(_np.mean(data, axis=-1),interpolation='none', origin='lower') - self.reconCurrent.draw() - - data = data.reshape([-1, self.Olen]) - - self.svddata = self.SvdData() - self.svddata.orig_shape = [self.Mlen, self.Nlen, self.Olen] - self.svddata.U, self.svddata.S, self.svddata.Vh = _svd(data, full_matrices=False) - - self.maxsvs = self.svddata.S.size - - self.ui.lcdMaxFactors.display(self.maxsvs) - self.ui.spinBoxGoTo.setMaximum(self.maxsvs) - - self.updateCurrentRemainder() - - #print('U: {}, S: {}, Vh: {}'.format(self.svddata.U.shape, self.svddata.S.shape, self.svddata.Vh.shape)) - - self.updateSVPlots() - - @staticmethod - def dialogSVD(data, parent = None): - """ - Executes DialogSVD dialog and returns values - """ - dialog = DialogSVD(data, parent) - dialog.showMaximized() - result = dialog.exec_() # 1 = Aceepted, 0 = Rejected/Canceled - - if result == 1: - svs = list(dialog.selected_svs) - svs.sort() - svs = _np.array(svs) - - if svs.size == 0: - return None - else: - return svs - else: - return None - - class SvdData: - """ - Hold SVD factorized components of input data - """ - def __init__(self): - self.U = _np.zeros((0,0)) - self.S = _np.zeros((0)) - self.Vh = _np.zeros((0,0)) - self.orig_shape = [0,0,0] - - def return_svd(self, Select_list=None): - #print('Select_list:{}'.format(Select_list)) - temp = self.s_from_selected(self.S, self.U.shape[-1], self.Vh.shape[0], Select_list) - #print(temp[0:10,0]) - - return _np.dot(self.U, _np.dot(temp, self.Vh)) - - def return_remainder(self, Select_list=None): - return _np.dot(self.U, _np.dot(self.s_from_unselected(self.S, - self.U.shape[-1], - self.Vh.shape[0], - Select_list), - self.Vh)) - - @staticmethod - def s_from_selected(S, M, N, Select_list=None): - """ - Return SVD S-matrix of SELECTED singular values - """ - if Select_list is None: - return _diagsvd(S, M, N) - else: - if type(Select_list) is set: - Select_list = list(Select_list) - - #print(Select_list) - P = _np.zeros(S.size) - #print('P-shape:{}'.format(P.shape)) - #print('Select List:{}'.format(Select_list)) - #print('S-of-select:{}'.format(S[Select_list])) - P[Select_list] = S[Select_list] - #print('P:{}'.format(P[0:10])) - temp = _diagsvd(P, M, N) - return temp - - @staticmethod - def s_from_unselected(S, M, N, Select_list=None): - """ - Return SVD S-matrix of UNselected singular values - """ - if Select_list is None: - return _diagsvd(0*S, M, N) - else: - if type(Select_list) is set: - Select_list = list(Select_list) - P = S.copy() - P[Select_list] = 0 - return _diagsvd(P, M, N) - - def applyCheckBoxes(self): - """ - Add checked singular values (and remove un-checked SVs) - """ - for count, checkBox in enumerate(self.svLabelCheckBoxes): - if checkBox.isChecked() == True: - self.selected_svs.add(self.firstSV+count) - else: - try: - self.selected_svs.remove(self.firstSV+count) - except: - pass - - #print('Self.S: {}'.format(self.svddata.S[0:3])) - self.ui.lcdSelectedFactors.display(len(self.selected_svs)) - self.updateCurrentRemainder() - - def advance(self): - """ - View next set of SVs - """ - sender = self.sender().objectName() - if sender == 'pushButtonPrev': - self.updateSVPlots(startnum=self.firstSV-self.spanSV) - elif sender == 'pushButtonNext': - self.updateSVPlots(startnum=self.firstSV+self.spanSV) - elif sender == 'pushButtonGoTo': - self.updateSVPlots(startnum=self.ui.spinBoxGoTo.value()) - else: - pass - def runScript(self): - """ - Run "script" of singular value selection - - Example: - [1,2,3,5:7] = 1,2,3,5,6,7 - """ - script = self.ui.lineEditSelections.text() - script = script.strip('[').strip(']') - script = script.split(',') - for count in script: - if ':' in count: - temp = count.split(':') - self.selected_svs.update(set(_np.arange(int(temp[0]),int(temp[1])+1))) - elif count.strip() == '': - pass - else: - self.selected_svs.add(int(count)) - self.updateSVPlots(startnum=self.firstSV) - self.ui.lcdSelectedFactors.display(len(self.selected_svs)) - self.updateCurrentRemainder() - - def updateCurrentRemainder(self): - """ - Update image reconstructed (mean over spectral vector) using remaining \ - (unselected) singular values - """ - #print(self.selected_svs) - temp = self.svddata.return_svd(self.selected_svs) - #print(temp[0:10]) - self.showMeanImg(temp, - self.reconCurrent.ax[0], - self.reconCurrent.ax[1], - self.reconCurrent) - - self.showMeanImg(self.svddata.return_remainder(self.selected_svs), - self.reconRemainder.ax[0], - self.reconRemainder.ax[1], - self.reconRemainder) - - def updateSVPlots(self, startnum=0): - """ - Update images and spectra of set of singular values starting at SV \ - number startnum - """ - if startnum <= 0: - startnum = 0 - self.ui.pushButtonPrev.setEnabled(False) - self.ui.pushButtonNext.setEnabled(True) - elif startnum > self.Olen - self.spanSV: - startnum = self.Olen - self.spanSV - self.ui.pushButtonPrev.setEnabled(True) - self.ui.pushButtonNext.setEnabled(False) - else: - self.ui.pushButtonPrev.setEnabled(True) - self.ui.pushButtonNext.setEnabled(True) - - self.firstSV = startnum - - for count in range(self.spanSV): - self.svWins[count].ax[0].clear() - temp = self.svddata.U[:,count + self.firstSV].copy() - temp = _np.reshape(temp,[self.Mlen, self.Nlen]) - - self.svWins[count].ax[0].imshow(-temp*self.svddata.S[count + self.firstSV], interpolation='none', cmap = _mpl.cm.gray , origin='lower') - - self.svWins[count].ax[0].axis('Off') - - self.svWins[count].ax[1].clear() - self.svWins[count].ax[1].plot(-self.svddata.Vh[count + self.firstSV,:]*self.svddata.S[count + self.firstSV]) - #if count == 0: - # print(_np.min(self.svddata.Vh[count + self.firstSV,:])) - self.svLabelCheckBoxes[count].setText('Keep: ' + str(startnum + count)) - self.svWins[count].draw() - if self.firstSV + count in self.selected_svs: - self.svLabelCheckBoxes[count].setChecked(True) - else: - self.svLabelCheckBoxes[count].setChecked(False) - - - def showMeanImg(self, data, ax_img, ax_spectrum, canvas): - """ - Update image reconstructed (mean over spectral vector) using selected \ - singular values - """ - temp = _np.reshape(_np.sum(data,axis=-1),[self.Mlen, self.Nlen]) - #print(temp[0:10,0]) - ax_img.clear() - ax_img.imshow(temp, interpolation='none', cmap = _mpl.cm.gray , origin='lower') - #ax_img.figure.colorbar(img) - #ax_img.imshow(_np.random.rand(100,100), interpolation='none', cmap = _mpl.cm.gray , origin='lower') - ax_spectrum.clear() - ax_spectrum.plot(_np.mean(data,axis=0)) - canvas.draw() - - def clear(self): - """ - Clear selected singular values (i.e., none will be selected) - """ - self.selected_svs = set() - self.ui.lcdSelectedFactors.display(len(self.selected_svs)) - self.updateCurrentRemainder() - self.updateSVPlots(startnum=self.firstSV) - - -if __name__ == '__main__': - app = _QApplication(_sys.argv) - app.setStyle('Cleanlooks') - x = _np.linspace(100,200,50) - y = _np.linspace(200,300,50) - f = _np.linspace(500,3000,800) - Ex = 30*_np.exp((-(f-1750)**2/(200**2))) - Spectrum = _np.convolve(_np.flipud(Ex),Ex,mode='same') - - data = _np.zeros((y.size,x.size,f.size)) - - for count in range(y.size): - data[count,:,:] = y[count]*_np.random.poisson(_np.dot(x[:,None],Spectrum[None,:])) - - win = DialogSVD.dialogSVD(data) ### EDIT ### - - print(win) - - - _sys.exit(app.exec_()) -# _sys.exit() \ No newline at end of file diff --git a/crikit/ui/deprecated/dialog_options.py b/crikit/ui/deprecated/dialog_options.py deleted file mode 100644 index 3d4d962..0000000 --- a/crikit/ui/deprecated/dialog_options.py +++ /dev/null @@ -1,322 +0,0 @@ -""" -CRIkit Options Dialogs (crikit.ui.dialog_options) -======================================================= - -Classes that present dialog boxes that retrieve options - -DialogDarkOptions : Dark subtraction options dialog - -DialogKKOptions : Phase retrieval options dialog. Note: this class only\ - considers the Kramers-Kronig currently - -References ----------- -[1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \ - Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \ - Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543. - -""" - -# Append sys path -import sys as _sys -import os as _os - -# Generic imports for QT-based programs -from PyQt5.QtWidgets import (QApplication as _QApplication, - QWidget as _QWidget, QDialog as _QDialog, - QMainWindow as _QMainWindow, - QSizePolicy as _QSizePolicy) -import PyQt5.QtCore as _QtCore - -# Other imports -import numpy as _np - -# Import from Designer-based GUI -from crikit.ui.qt_DarkOptions import Ui_Dialog as Ui_DarkOptions ### EDIT ### -from crikit.ui.qt_KKOptions import Ui_Dialog as Ui_KKOptions -from crikit.ui.qt_AnscombeOptions import Ui_Dialog as Ui_AnscombeOptions - -from crikit.ui.subui_ploteffect import DialogPlotEffect as _DialogPlotEffect -from crikit.ui.widget_ploteffect import widgetKK as _widgetKK - -# Generic imports for MPL-incorporation -import matplotlib as _mpl -_mpl.use('Qt5Agg') -_mpl.rcParams['font.family'] = 'sans-serif' -_mpl.rcParams['font.size'] = 10 -#import matplotlib.pyplot as plt - -from matplotlib.backends.backend_qt5agg import (FigureCanvasQTAgg as _FigureCanvas, \ - NavigationToolbar2QT as _NavigationToolbar) - -from matplotlib.figure import Figure as _Figure - -class DialogDarkOptions(_QDialog): - """ - DialogDarkOptions : Dark subtraction options dialog - - Methods - -------- - dialogDarkOptions : Used to call UI and retrieve results of dialog - - References - ---------- - [1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \ - Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \ - Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543. - - """ - SUB_DARK = True - SUB_DARK_IMG = True - SUB_DARK_NRB = True - - RESIDUAL_FREQ = [-1500, -400] - SUB_RESIDUAL = True - - def __init__(self, parent = None): - super(DialogDarkOptions, self).__init__(parent) ### EDIT ### - self.ui = Ui_DarkOptions() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - self.ui.frameResidual.setEnabled(self.SUB_RESIDUAL) - self.ui.spinBoxMax.setValue(self.RESIDUAL_FREQ[0]) - self.ui.spinBoxMax.setValue(self.RESIDUAL_FREQ[1]) - - self.subdark = self.SUB_DARK - self.subdarkimg = self.SUB_DARK_IMG - self.subdarknrb = self.SUB_DARK_NRB - - self.subresidual = self.SUB_RESIDUAL - self.freq0 = self.RESIDUAL_FREQ[0] - self.freq1 = self.RESIDUAL_FREQ[1] - - self.ui.checkBoxResidualDarkSub.stateChanged.connect(self.checkBoxResidualSub) - self.ui.checkBoxDarkSub.stateChanged.connect(self.checkBoxDarkSub) - self.ui.checkBoxDarkSubImg.stateChanged.connect(self.checkBoxDarkSubImg) - self.ui.checkBoxDarkSubNRB.stateChanged.connect(self.checkBoxDarkSubNRB) - - self.ui.spinBoxMin.editingFinished.connect(self.checkMinMax) - self.ui.spinBoxMax.editingFinished.connect(self.checkMinMax) - - @staticmethod - def dialogDarkOptions(parent = None, darkloaded = False, nrbloaded = False): - """ - Retrieve dark subtraction dialog results - - Parameters - ---------- - nrbloaded : (bool) - Is there an NRB loaded? - - darkloaded : (bool) - Is there a Dark spectrum(a) loaded? - - Returns - ---------- - out : (tuple) - Subtract Dark : (bool) - Subtract Dark from HSData: (bool) - Subtract Dark from NRB: (bool) - Subtract Residual over Frequency Range: (bool) - Frequency Range : (list[str]) - """ - dialog = DialogDarkOptions(parent) - dialog.ui.checkBoxDarkSubNRB.setChecked(nrbloaded) - dialog.ui.checkBoxDarkSubNRB.setEnabled(nrbloaded) - dialog.ui.checkBoxDarkSub.setChecked(darkloaded) - dialog.ui.checkBoxDarkSubImg.setChecked(darkloaded) - dialog.ui.checkBoxDarkSub.setEnabled(darkloaded) - #dialog.ui.checkBoxDarkSubNRB.setEnabled(nrbloaded) - - result = dialog.exec_() - - subdark = dialog.subdark - subresidual = dialog.subresidual - - if result == 1: - if subdark == True: - subdarkimg = dialog.subdarkimg - subdarknrb = dialog.subdarknrb - else: - subdarkimg = None - subdarknrb = None - - if subresidual == True: - freq = [dialog.freq0, dialog.freq1] - freq.sort() - else: - subresidual = False - freq = None - return (subdark, subdarkimg, subdarknrb, subresidual, freq) - else: - return (None, None, None, None, None) - - def checkBoxDarkSubImg(self): - if self.ui.checkBoxDarkSubImg.isChecked() == True: - self.subdarkimg = True - else: - self.subdarkimg = False - - - def checkBoxDarkSubNRB(self): - - if self.ui.checkBoxDarkSubNRB.isChecked() == True: - self.subdarknrb = True - else: - self.subdarknrb = False - - def checkBoxDarkSub(self): - if self.ui.checkBoxDarkSub.isChecked() == True: - self.ui.frameDark.setEnabled(True) - self.subdark = True - else: - self.ui.frameDark.setEnabled(False) - self.subdark = False - self.ui.checkBoxDarkSubImg.setChecked(False) - self.ui.checkBoxDarkSubNRB.setChecked(False) - - def checkBoxResidualSub(self): - if self.ui.checkBoxResidualDarkSub.isChecked() == True: - self.ui.frameResidual.setEnabled(True) - self.subresidual = True - else: - self.ui.frameResidual.setEnabled(False) - self.subresidual = False - - def checkMinMax(self): - self.freq0 = self.ui.spinBoxMin.value() - self.freq1 = self.ui.spinBoxMax.value() - -class DialogKKOptions(_QDialog): - """ - DialogKKOptions : Phase-Retrieval (only Kramers-Kronig currently \ - supported) options dialog - - Methods - -------- - dialogKKOptions : Used to call UI and retrieve results of dialog - - References - ---------- - [1] Y. Liu, Y. J. Lee, and M. T. Cicerone, "Broadband CARS spectral \ - phase retrieval using a time-domain Kramers-Kronig transform," \ - Opt. Lett. 34, 1363-1365 (2009). - - [2] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \ - Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \ - Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543. - - """ - NORM_TO_NRB = True - NRB_AMP = 0.0 - CARS_AMP = 0.0 - PHASE_OFFSET = 0.0 - PAD_FACTOR = 1 - - def __init__(self, parent=None, data=None): - super(DialogKKOptions, self).__init__(parent) ### EDIT ### - self.ui = Ui_KKOptions() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - self.ui.doubleSpinBoxCARSAmp.setValue(self.CARS_AMP) - self.ui.doubleSpinBoxNRBAmp.setValue(self.NRB_AMP) - self.ui.doubleSpinBoxPhase.setValue(self.PHASE_OFFSET) - self.ui.checkBoxNormToNRB.setChecked(self.NORM_TO_NRB) - self.ui.spinBoxPadFactor.setValue(self.PAD_FACTOR) - - self.ui.checkBoxNormToNRB.stateChanged.connect(self.checkBoxNormToNRB) - - self.norm_to_nrb = self.NORM_TO_NRB - - self.data = data - - if data is None: - self.ui.pushButtonInteractive.setEnabled(False) - else: - self.ui.pushButtonInteractive.pressed.connect(self.goInteractive) - - def checkBoxNormToNRB(self): - if self.ui.checkBoxNormToNRB.isChecked() == True: - self.norm_to_nrb = True - else: - self.norm_to_nrb = False - - def goInteractive(self): - - plugin = _widgetKK() - - winPlotEffect = _DialogPlotEffect.dialogPlotEffect(self.data, x=self.data[0], plugin=plugin, xlabel='Wavenumber (cm$^{-1}$)', ylabel='Imag. {$\chi_R$} (au)') - - if winPlotEffect is not None: - self.ui.doubleSpinBoxCARSAmp.setValue(winPlotEffect.cars_bias) - self.ui.doubleSpinBoxNRBAmp.setValue(winPlotEffect.nrb_bias) - self.ui.checkBoxNormToNRB.setChecked(winPlotEffect.nrb_norm) - self.ui.doubleSpinBoxPhase.setValue(winPlotEffect.phaselin) - self.ui.spinBoxPadFactor.setValue(winPlotEffect.pad_factor) - - @staticmethod - def dialogKKOptions(parent=None, data=None): - """ - Retrieve dark subtraction dialog results - - Parameters - ---------- - None : None - - Returns - ---------- - out : (tuple) - HSData amp offset : (float) - NRB amp offset : (float) - Phase offset : (float) - Normalize by NRB : (bool) - Pad factor : (int) - """ - dialog = DialogKKOptions(parent=parent,data=data) - - result = dialog.exec_() - - if result == 1: - - return (dialog.ui.doubleSpinBoxCARSAmp.value(), - dialog.ui.doubleSpinBoxNRBAmp.value(), - dialog.ui.doubleSpinBoxPhase.value(), - dialog.norm_to_nrb, - dialog.ui.spinBoxPadFactor.value()) - else: - return (None, None, None, None, None) - -if __name__ == '__main__': - - - app = _QApplication(_sys.argv) - app.setStyle('Cleanlooks') - - - winDark = DialogDarkOptions.dialogDarkOptions(darkloaded=True) - - from crikit.data.hsi import Hsi as _Hsi - - temp = _Hsi() - - WN = _np.linspace(500,4000,1000) - - CARS = _np.zeros((20,20,WN.size)) - CARS[:,:,:] = _np.abs(1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055) - temp.data = CARS - temp.freq.data = WN - - - NRB = 0*WN + .055 - - - winKK = DialogKKOptions.dialogKKOptions(data=[WN, NRB, - temp.get_rand_spectra(10, pt_sz=3, quads=False)]) -# -# winAnscombe = DialogAnscombeOptions.dialogAnscombeOptions() - - print('Dark return: {}'.format(winDark)) -# print('KK return:{}'.format(winKK)) -# print('Anscombe return:{}'.format(winAnscombe)) - - _sys.exit() \ No newline at end of file diff --git a/crikit/ui/deprecated/dialog_ploteffect.py b/crikit/ui/deprecated/dialog_ploteffect.py deleted file mode 100644 index cd30a82..0000000 --- a/crikit/ui/deprecated/dialog_ploteffect.py +++ /dev/null @@ -1,371 +0,0 @@ -""" -Plot-Effect Interface (crikit.ui.subui_ploteffect) -======================================================= - - -TODO: Do some manual tight layout assessment to make sure labels and titles \ -are fully visible - -""" - -# Append sys path -import sys as _sys -import os as _os - -# Generic imports for QT-based programs -from PyQt5.QtWidgets import (QApplication as _QApplication, - QDialog as _QDialog, - QColorDialog as _QColorDialog, - QDoubleSpinBox as _QDoubleSpinBox, - QComboBox as _QComboBox, - QLineEdit as _QLineEdit, - QStyledItemDelegate as _QStyledItemDelegate, - QWidget as _QWidget) - -from PyQt5.QtCore import (QAbstractTableModel as _QAbstractTableModel, - QModelIndex as _QModelIndex, - QVariant as _QVariant, - Qt as _Qt, - pyqtSignal as _pyqtSignal, - QObject as _QObject) - -from PyQt5.QtGui import (QPixmap as _QPixmap, - QIcon as _QIcon, - QColor as _QColor) - -# Other imports -import numpy as _np - -# Import from Designer-based GUI -from crikit.ui.qt_PlotEffect import Ui_Dialog as Ui_DialogPlotEffect -from crikit.ui.helper_plotOptions import plotStyle - -# Generic imports for MPL-incorporation -import matplotlib as _mpl -_mpl.use('Qt5Agg') -_mpl.rcParams['font.family'] = 'sans-serif' -_mpl.rcParams['font.size'] = 10 -_mpl.rcParams['savefig.dpi'] = 300 -_mpl.rcParams['figure.figsize'] = (4, 4) -#_mpl.rcParams['figure.autolayout'] = True -_mpl.rcParams['legend.fontsize'] = 10 - -from matplotlib.backends.backend_qt5agg import \ - (FigureCanvasQTAgg as _FigureCanvas, - NavigationToolbar2QT as _NavigationToolbar) - -from matplotlib.figure import Figure as _Figure - - -class _winMpl: - def __init__(self): - self.fig = None - self.ax = None - self.img = None - self.canvas = None - self.toolbar = None - -class DialogPlotEffect(_QDialog): - """ - Plotter subUI class - """ - XLABEL = 'X (au)' - YLABEL = 'Y (au)' - - def __init__(self, data, x=None, plugin=None, xlabel=None, ylabel=None, show_difference=False, parent=None): - super(DialogPlotEffect, self).__init__(parent) - self.ui = Ui_DialogPlotEffect() - self.ui.setupUi(self) - - self.data = data - - self.mpl_orig = _winMpl() - self.mpl_orig.fig = _Figure(facecolor=[1, 1, 1]) - self.mpl_orig.ax = self.mpl_orig.fig.add_subplot(111) - self.mpl_orig.canvas = _FigureCanvas(self.mpl_orig.fig) - self.mpl_orig.toolbar = _NavigationToolbar(self.mpl_orig.canvas, None) - - self.mpl_affected = _winMpl() - self.mpl_affected.fig = _Figure(facecolor=[1, 1, 1]) - self.mpl_affected.ax = self.mpl_affected.fig.add_subplot(111) - self.mpl_affected.canvas = _FigureCanvas(self.mpl_affected.fig) - self.mpl_affected.toolbar = _NavigationToolbar(self.mpl_affected.canvas, None) - - self.ui.verticalLayout.insertWidget(1, self.mpl_orig.canvas) - self.ui.verticalLayout.insertWidget(1, self.mpl_orig.toolbar) - - self.ui.verticalLayout.insertWidget(3, self.mpl_affected.canvas) - self.ui.verticalLayout.insertWidget(3, self.mpl_affected.toolbar) - - # Plugin that brings functionality to PlotEffect - self.plugin = plugin - - # Signal emited when something changes in the plugin widget - self.plugin.changed.connect(self.widget_changed) - - if xlabel is None: - self.ui.xlabel = self.XLABEL - else: - self.ui.xlabel = xlabel - - if ylabel is None: - self.ui.ylabel = self.YLABEL - else: - self.ui.ylabel = ylabel - - if x is None: - self.x = _np.linspace(0,data.shape[0],self.data.shape[0]) - else: - self.x = x - - self.show_diff = show_difference - - - if not isinstance(data, list): - try: - self.mpl_orig.ax.plot(self.x,data) - except: - self.mpl_orig.ax.plot(self.x,data.T) - - self.mpl_orig.ax.xaxis.set_label_text(self.ui.xlabel) - self.mpl_orig.ax.yaxis.set_label_text(self.ui.ylabel) -# self.mpl_orig.fig.tight_layout(rect=[-.05,0.05,1,.95]) - self.mpl_orig.ax.set_title('Original') - else: - if self.plugin is not None: - - try: - self.mpl_orig.ax.plot(self.x,self.plugin.fcn(self.data)) - except: - self.mpl_orig.ax.plot(self.x,self.plugin.fcn(self.data).T) - - self.mpl_orig.ax.xaxis.set_label_text(self.ui.xlabel) - self.mpl_orig.ax.yaxis.set_label_text(self.ui.ylabel) -# self.mpl_orig.fig.tight_layout(rect=[0,0.05,1,.9]) - self.mpl_orig.ax.set_title('Original') - - if self.plugin is not None: - self.ui.verticalLayout.insertWidget(8, plugin) - - self.widget_changed() - self.mpl_orig.canvas.draw() - self.mpl_affected.canvas.draw() - - self.ui.pushButtonOk.clicked.connect(self.accept) - self.ui.pushButtonCancel.clicked.connect(self.reject) - - def widget_changed(self): - """ - Plugin widget has changed. Re-submit data to plugin function. - """ -# try: -# print(self.data.shape) -# except: -# pass - if self.plugin is not None: - self.mpl_affected.ax.clear() - try: -# print('Here 1') - affected_data = self.plugin.fcn(self.data).T - self.mpl_affected.ax.plot(self.x,affected_data) - except: - try: -# print('Here 2') - affected_data = self.plugin.fcn(self.data) - self.mpl_affected.ax.plot(self.x,affected_data) - except: - pass - self.mpl_affected.ax.xaxis.set_label_text(self.ui.xlabel) - self.mpl_affected.ax.yaxis.set_label_text(self.ui.ylabel) - self.mpl_affected.ax.set_title('Processed') -# self.mpl_affected.fig.tight_layout(rect=[0,0.05,1,.95]) - - self.mpl_affected.canvas.draw() - - if self.show_diff: - self.mpl_orig.ax.clear() - if not isinstance(self.data, list): - try: - self.mpl_orig.ax.plot(self.x,self.data.T) - except: - try: - self.mpl_orig.ax.plot(self.x,self.data) - except: - pass - - try: - self.mpl_orig.ax.plot(self.x,self.data.T-affected_data, linestyle='dashed') - except: - try: - self.mpl_orig.ax.plot(self.x,self.data-affected_data, linestyle='dashed') - except: - pass - - - self.mpl_orig.ax.xaxis.set_label_text(self.ui.xlabel) - self.mpl_orig.ax.yaxis.set_label_text(self.ui.ylabel) - # self.mpl_orig.fig.tight_layout(rect=[-.05,0.05,1,.95]) - self.mpl_orig.ax.set_title('Original') - self.mpl_orig.canvas.draw() - - @staticmethod - def dialogPlotEffect(data, x = None, plugin=None, xlabel=None, ylabel=None, - show_difference=False, parent = None): - """ - Executes DialogPlotEffect - - Parameters - ---------- - data : (np.ndarray, list) - Array for straightforward plotting, list if plugin.fcn requires \ - multiple inputs - plugin : object - Plugin container class - xlabel : str - String describing independent variable - ylabel : str - String describing dependent variable - show_difference : bool - Plot the difference between the original data and the affected \ - (perfomed-on) data overlaid with the original data. Note: \ - difference shown with dashed line - parent : object - Parent object - - Returns - ------- - out : object - Returns access to the plugin variables - - """ - dialog = DialogPlotEffect(data, x=x, plugin=plugin, xlabel=xlabel, - ylabel=ylabel, show_difference=show_difference, - parent=parent) - - result = dialog.exec_() # 1 = Aceepted, 0 = Rejected/Canceled - - if result == 1: - #print('----------------\nReturned: Ok!\n') - #print(dialog.plugin.__dict__) - - return dialog.plugin - - else: - #print('----------------\nReturned: Cancel!\n') - return None - - -if __name__ == '__main__': - - from crikit.ui.widget_ploteffect import (widgetNothing, widgetKK, - widgetALS, widgetSG, - widgetCalibrate) - - app = _QApplication(_sys.argv) - - - ################# - # KK Demo - plugin = widgetKK() - - WN = _np.linspace(500,4000,800) - CARS = _np.abs(1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055) - NRB = 0*WN + .055 - - winPlotEffect = DialogPlotEffect.dialogPlotEffect([WN, NRB, CARS], x=WN, - plugin=plugin, - xlabel='Wavenumber (cm$^{-1}$)', - ylabel='Imag. {$\chi_R$} (au)') - - if winPlotEffect is not None: - print('CARS Bias: {}'.format(winPlotEffect.cars_bias)) - print('NRB Bias: {}'.format(winPlotEffect.nrb_bias)) - print('Norm by NRB: {}'.format(winPlotEffect.nrb_norm)) - print('Phase correction constant: {}'.format(winPlotEffect.phaselin)) - print('KK algorithm pad factor: {}'.format(winPlotEffect.pad_factor)) - print('Phase correction constant type: {}'.format(winPlotEffect.phase_type)) - ################## - - ################ - # ALS Demo - plugin = widgetALS() - - WN = _np.linspace(500,4000,800) - CARS = _np.abs(1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055) - NRB = 0*WN + .055 - CARS = _np.dot(_np.ones((5,1)),CARS[None,:]) - winPlotEffect = DialogPlotEffect.dialogPlotEffect(CARS, x=WN, plugin=plugin, - xlabel='Wavenumber (cm$^{-1}$)', - ylabel='Imag. {$\chi_R$} (au)', - show_difference=True) - - if winPlotEffect is not None: - print('P-Value: {}'.format(winPlotEffect.p)) - print('Lambda-Value: {}'.format(winPlotEffect.lam)) - print('Redux: {}'.format(winPlotEffect.redux)) - - ################ - # SG Demo - plugin = widgetSG(win_size=501, order=5) - - WN = _np.linspace(500,4000,800) - CARS = _np.abs(1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055) - NRB = 0*WN + .055 - CARS = _np.dot(_np.ones((5,1)),CARS[None,:]) - winPlotEffect = DialogPlotEffect.dialogPlotEffect(CARS, x=WN, plugin=plugin, - xlabel='Wavenumber (cm$^{-1}$)', - ylabel='Imag. {$\chi_R$} (au)', - show_difference=True) - - if winPlotEffect is not None: - print('Window Size: {}'.format(winPlotEffect.win_size)) - print('Order: {}'.format(winPlotEffect.order)) - - - ################ - # Calibrate Demo - plugin = widgetCalibrate() - - - calib_dict = {} - calib_dict['n_pix'] = 1600 - calib_dict['ctr_wl'] = 730.0 - calib_dict['ctr_wl0'] = 730.0 - calib_dict['probe'] = 771.461 - calib_dict['units'] = 'nm' - calib_dict['a_vec'] = (-0.167740721307557, 863.8736708961577) # slope, intercept - - from crikit.data.frequency import calib_pix_wl, calib_pix_wn - wl_vec, units_wl = calib_pix_wl(calib_dict) - WN, units_wn = calib_pix_wn(calib_dict) - - #WN = _np.linspace(500,4000,800) - CARS = _np.abs(1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055) - NRB = 0*WN + .055 -# CARS = _np.dot(_np.ones((5,1)),CARS[None,:]) - winPlotEffect = DialogPlotEffect.dialogPlotEffect(CARS, x=WN, plugin=plugin, - xlabel='Wavenumber (cm$^{-1}$)', - ylabel='Imag. {$\chi_R$} (au)', - show_difference=False) - - if winPlotEffect is not None: - print('New Calibration Dictionary: {}'.format(winPlotEffect.new_calib_dict)) -# print('Order: {}'.format(winPlotEffect.order)) - - - ################# - # Nothing Demo - plugin = widgetNothing() - - x = _np.linspace(1,100,100) - data = _np.random.randn(100) - - winPlotEffect = DialogPlotEffect.dialogPlotEffect(data, x=x, plugin=plugin, xlabel='Wavenumber (cm$^{-1}$)', ylabel='Imag. {$\chi_R$} (au)') - - if winPlotEffect is not None: - print('This plugin did nothing, as expected.') - ################## - -# print(winPlotEffect.__dict__) - - _sys.exit() \ No newline at end of file diff --git a/crikit/ui/deprecated/dialog_plugin.py b/crikit/ui/deprecated/dialog_plugin.py deleted file mode 100644 index a2961ea..0000000 --- a/crikit/ui/deprecated/dialog_plugin.py +++ /dev/null @@ -1,254 +0,0 @@ -""" -Created on Tue Feb 16 15:51:32 2016 - -@author: camp -""" - -import sys as _sys -import os as _os - -# Generic imports for QT-based programs -from PyQt5.QtWidgets import (QApplication as _QApplication, - QWidget as _QWidget, QDialog as _QDialog, - QMainWindow as _QMainWindow, - QSizePolicy as _QSizePolicy) -import PyQt5.QtCore as _QtCore - -# Other imports -import numpy as _np - -from yapsy.PluginManager import (PluginManager as _PluginManager, - PluginInfo as _PluginInfo) - -from crikit.ui.helper_plugin_categories import DeNoiser, ErrorCorrect -#import logging -#logging.basicConfig(level=logging.DEBUG) - -# Import from Designer-based GUI -from crikit.ui.qt_PluginSelector import Ui_Dialog - - -# Generic imports for MPL-incorporation -import matplotlib as _mpl -_mpl.use('Qt5Agg') -_mpl.rcParams['font.family'] = 'sans-serif' -_mpl.rcParams['font.size'] = 10 -#import matplotlib.pyplot as plt - -#from matplotlib.backends.backend_qt5agg import (FigureCanvasQTAgg as _FigureCanvas, \ -# NavigationToolbar2QT as _NavigationToolbar) - -#from matplotlib.figure import Figure as _Figure - -class DialogDenoisePlugins(_QDialog): - """ - DialogDenoisePlugins : Denoise plugin selector - - Methods - ------------- - dialogDenoisePlugins : Used to call UI and retrieve results of dialog - - References - ---------- - [1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \ - Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \ - Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543. - - """ - - def __init__(self, parent = None): - super(DialogDenoisePlugins, self).__init__(parent) ### EDIT ### - self.ui = Ui_Dialog() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - self.temp = 0 - - # Create plugin manager - self.manager = _PluginManager() - - - if _os.path.isdir(_os.path.abspath('./plugins')): - plugins_loc = 'plugins' - elif _os.path.isdir(_os.path.abspath('./crikit/ui/plugins')): - plugins_loc = './crikit/ui/plugins' - elif _os.path.isdir(_os.path.abspath('./ui/plugins')): - plugins_loc = './ui/plugins' - else: - plugins_loc = None - - self.manager.setPluginPlaces([plugins_loc]) - self.manager.setCategoriesFilter({'DeNoiser' : DeNoiser}) - - self.manager.collectPlugins() - - # Load plugins - self.manager.locatePlugins() - - self.manager.loadPlugins() - self.denoisers = {} - self.denoiser_desc = {} - - for plugin in self.manager.getPluginsOfCategory('DeNoiser'): - self.ui.comboBox.addItem(plugin.plugin_object.name) - self.denoisers[plugin.plugin_object.name] = plugin.plugin_object - self.denoiser_desc[plugin.plugin_object.name] = plugin._PluginInfo__details['Documentation']['description'] - - #print(self.denoiser_desc[self.ui.comboBox.currentText]) - self.ui.plainTextEditDescription.setPlainText(self.denoiser_desc[self.ui.comboBox.currentText()]) - self.ui.comboBox.currentIndexChanged.connect(self.changeDesc) - - def changeDesc(self): - self.ui.plainTextEditDescription.setPlainText(self.denoiser_desc[self.ui.comboBox.currentText()]) - - @staticmethod - def dialogDenoisePlugins(parent = None): - """ - - """ - - dialog = DialogDenoisePlugins(parent) - - result = dialog.exec_() - - - if result == 1: # Accepted - return (dialog.denoisers[dialog.ui.comboBox.currentText()]) - else: # Rejected/Cancel - return None - -class DialogErrCorrPlugins(_QDialog): - """ - DialogErrCorrPlugins : Error correction plugin selector - - Methods - ------------- - dialogErrCorrPlugins : Used to call UI and retrieve results of dialog - - References - ---------- - [1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \ - Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \ - Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543. - - """ - - def __init__(self, parent = None): - super(DialogErrCorrPlugins, self).__init__(parent) ### EDIT ### - self.ui = Ui_Dialog() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - self.temp = 0 - - # Create plugin manager - self.manager = _PluginManager() - - - if _os.path.isdir(_os.path.abspath('./plugins')): - plugins_loc = 'plugins' - elif _os.path.isdir(_os.path.abspath('./crikit/ui/plugins')): - plugins_loc = './crikit/ui/plugins' - elif _os.path.isdir(_os.path.abspath('./ui/plugins')): - plugins_loc = './ui/plugins' - else: - plugins_loc = None - - self.manager.setPluginPlaces([plugins_loc]) - self.manager.setCategoriesFilter({'ErrorCorrect' : ErrorCorrect}) - - self.manager.collectPlugins() - - # Load plugins - self.manager.locatePlugins() - - self.manager.loadPlugins() - self.errcorrectors = {} - self.errcorrectors_desc = {} - - for plugin in self.manager.getPluginsOfCategory('ErrorCorrect'): - self.ui.comboBox.addItem(plugin.plugin_object.name) - self.errcorrectors[plugin.plugin_object.name] = plugin.plugin_object - self.errcorrectors_desc[plugin.plugin_object.name] = plugin._PluginInfo__details['Documentation']['description'] - - self.ui.comboBox.currentIndexChanged.connect(self.changeDesc) - - try: - self.ui.plainTextEditDescription.setPlainText(self.errcorrectors_desc[self.ui.comboBox.currentText()]) - - except: # Fails if no plugins found - pass - - def changeDesc(self): - - try: - self.ui.plainTextEditDescription.setPlainText(self.errcorrectors_desc[self.ui.comboBox.currentText()]) - except: # Fails if no plugins found - pass - - @staticmethod - def dialogErrCorrPlugins(parent = None): - """ - - """ - - dialog = DialogErrCorrPlugins(parent) - - result = dialog.exec_() - - - if result == 1: # Accepted - return (dialog.errcorrectors[dialog.ui.comboBox.currentText()]) - else: # Rejected/Cancel - return None - - -if __name__ == '__main__': - - -# from crikit.data.classes import HSData -# - x = _np.linspace(100,200,50) - y = _np.linspace(200,300,50) - f = _np.linspace(500,3000,800) - Ex = 30*_np.exp((-(f-1750)**2/(200**2))) - Spectrum = _np.convolve(_np.flipud(Ex),Ex,mode='same') - - data = _np.zeros((y.size,x.size,f.size)) - for count in range(y.size): - data[count,:,:] = y[count]*_np.random.poisson(_np.dot(x[:,None],Spectrum[None,:])) - - #temp = HSData() - #temp.spectrafull = data - - app = _QApplication(_sys.argv) - app.setStyle('Cleanlooks') - - ### DeNoise Demo - win = DialogDenoisePlugins.dialogDenoisePlugins() - - if win is not None: - retwin = win.denoiseHSData(data) - print('RetWin:{}'.format(retwin)) - -# ### Error Correction Demo -# win = DialogErrCorrPlugins.dialogErrCorrPlugins() -# -## temp = HSData() -# -# WN = _np.linspace(500,4000,1000) -# -# CARS = _np.zeros((20,20,WN.size), dtype=complex) -# CARS[:,:,:] = (1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055) -# temp.spectrafull = CARS -# temp.freqvecfull = WN -# -# -# NRB = 0*WN + .055 -# -# if win is not None: -# retwin = win.errorCorrectHSData(data) -# #if win is not None: -# #retwin = win.denoiseHSData(temp) -# #print('RetWin:{}'.format(retwin)) -# -# _sys.exit() - app.exec_() \ No newline at end of file diff --git a/crikit/ui/deprecated/qt_BWImage.py b/crikit/ui/deprecated/qt_BWImage.py deleted file mode 100644 index 48667fa..0000000 --- a/crikit/ui/deprecated/qt_BWImage.py +++ /dev/null @@ -1,108 +0,0 @@ -# -*- coding: utf-8 -*- - -# Form implementation generated from reading ui file 'ui_BWImage.ui' -# -# Created by: PyQt5 UI code generator 5.5 -# -# WARNING! All changes made in this file will be lost! - -from PyQt5 import QtCore, QtGui, QtWidgets - -class Ui_Form(object): - def setupUi(self, Form): - Form.setObjectName("Form") - Form.resize(635, 480) - Form.setStyleSheet("font: 10pt \"Arial\";") - self.gridLayout = QtWidgets.QGridLayout(Form) - self.gridLayout.setObjectName("gridLayout") - self.verticalLayout = QtWidgets.QVBoxLayout() - self.verticalLayout.setObjectName("verticalLayout") - self.frame_2 = QtWidgets.QFrame(Form) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.frame_2.sizePolicy().hasHeightForWidth()) - self.frame_2.setSizePolicy(sizePolicy) - self.frame_2.setFrameShape(QtWidgets.QFrame.StyledPanel) - self.frame_2.setFrameShadow(QtWidgets.QFrame.Plain) - self.frame_2.setObjectName("frame_2") - self.horizontalLayout = QtWidgets.QHBoxLayout(self.frame_2) - self.horizontalLayout.setObjectName("horizontalLayout") - self.verticalLayout_5 = QtWidgets.QVBoxLayout() - self.verticalLayout_5.setObjectName("verticalLayout_5") - self.checkBoxFixed = QtWidgets.QCheckBox(self.frame_2) - self.checkBoxFixed.setChecked(False) - self.checkBoxFixed.setObjectName("checkBoxFixed") - self.verticalLayout_5.addWidget(self.checkBoxFixed) - self.checkBoxCompress = QtWidgets.QCheckBox(self.frame_2) - self.checkBoxCompress.setChecked(False) - self.checkBoxCompress.setObjectName("checkBoxCompress") - self.verticalLayout_5.addWidget(self.checkBoxCompress) - self.horizontalLayout.addLayout(self.verticalLayout_5) - self.verticalLayout_2 = QtWidgets.QVBoxLayout() - self.verticalLayout_2.setObjectName("verticalLayout_2") - self.label_2 = QtWidgets.QLabel(self.frame_2) - self.label_2.setObjectName("label_2") - self.verticalLayout_2.addWidget(self.label_2) - self.lineEditMin = QtWidgets.QLineEdit(self.frame_2) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.lineEditMin.sizePolicy().hasHeightForWidth()) - self.lineEditMin.setSizePolicy(sizePolicy) - self.lineEditMin.setMinimumSize(QtCore.QSize(0, 25)) - self.lineEditMin.setMaximumSize(QtCore.QSize(16777215, 25)) - self.lineEditMin.setObjectName("lineEditMin") - self.verticalLayout_2.addWidget(self.lineEditMin) - self.horizontalLayout.addLayout(self.verticalLayout_2) - self.verticalLayout_3 = QtWidgets.QVBoxLayout() - self.verticalLayout_3.setSpacing(6) - self.verticalLayout_3.setObjectName("verticalLayout_3") - self.label = QtWidgets.QLabel(self.frame_2) - self.label.setObjectName("label") - self.verticalLayout_3.addWidget(self.label) - self.lineEditMax = QtWidgets.QLineEdit(self.frame_2) - self.lineEditMax.setMinimumSize(QtCore.QSize(0, 25)) - self.lineEditMax.setMaximumSize(QtCore.QSize(16777215, 25)) - self.lineEditMax.setObjectName("lineEditMax") - self.verticalLayout_3.addWidget(self.lineEditMax) - self.horizontalLayout.addLayout(self.verticalLayout_3) - self.frame = QtWidgets.QFrame(self.frame_2) - self.frame.setFrameShape(QtWidgets.QFrame.VLine) - self.frame.setFrameShadow(QtWidgets.QFrame.Raised) - self.frame.setObjectName("frame") - self.horizontalLayout.addWidget(self.frame) - self.checkBoxRemOutliers = QtWidgets.QCheckBox(self.frame_2) - self.checkBoxRemOutliers.setObjectName("checkBoxRemOutliers") - self.horizontalLayout.addWidget(self.checkBoxRemOutliers) - self.verticalLayout_4 = QtWidgets.QVBoxLayout() - self.verticalLayout_4.setObjectName("verticalLayout_4") - self.label_3 = QtWidgets.QLabel(self.frame_2) - self.label_3.setObjectName("label_3") - self.verticalLayout_4.addWidget(self.label_3) - self.spinBoxStdDevs = QtWidgets.QDoubleSpinBox(self.frame_2) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.spinBoxStdDevs.sizePolicy().hasHeightForWidth()) - self.spinBoxStdDevs.setSizePolicy(sizePolicy) - self.spinBoxStdDevs.setProperty("value", 3.0) - self.spinBoxStdDevs.setObjectName("spinBoxStdDevs") - self.verticalLayout_4.addWidget(self.spinBoxStdDevs) - self.horizontalLayout.addLayout(self.verticalLayout_4) - self.verticalLayout.addWidget(self.frame_2, 0, QtCore.Qt.AlignHCenter) - self.gridLayout.addLayout(self.verticalLayout, 0, 0, 1, 1) - - self.retranslateUi(Form) - QtCore.QMetaObject.connectSlotsByName(Form) - - def retranslateUi(self, Form): - _translate = QtCore.QCoreApplication.translate - Form.setWindowTitle(_translate("Form", "Form")) - self.checkBoxFixed.setText(_translate("Form", "Fixed")) - self.checkBoxCompress.setText(_translate("Form", "Compress")) - self.label_2.setText(_translate("Form", "Minimum")) - self.label.setText(_translate("Form", "Maximum")) - self.checkBoxRemOutliers.setText(_translate("Form", "Outlier Removal")) - self.label_3.setText(_translate("Form", "Std. Dev\'s")) - diff --git a/crikit/ui/deprecated/qt_ColorMath.py b/crikit/ui/deprecated/qt_ColorMath.py deleted file mode 100644 index f3608dd..0000000 --- a/crikit/ui/deprecated/qt_ColorMath.py +++ /dev/null @@ -1,209 +0,0 @@ -# -*- coding: utf-8 -*- - -# Form implementation generated from reading ui file '.\ui_ColorMath.ui' -# -# Created by: PyQt5 UI code generator 5.5.1 -# -# WARNING! All changes made in this file will be lost! - -from PyQt5 import QtCore, QtGui, QtWidgets - -class Ui_Form(object): - def setupUi(self, Form): - Form.setObjectName("Form") - Form.resize(785, 202) - Form.setStyleSheet("font: 10pt \"Arial\";") - self.gridLayout_5 = QtWidgets.QGridLayout(Form) - self.gridLayout_5.setObjectName("gridLayout_5") - self.frame_3 = QtWidgets.QFrame(Form) - self.frame_3.setFrameShape(QtWidgets.QFrame.StyledPanel) - self.frame_3.setFrameShadow(QtWidgets.QFrame.Plain) - self.frame_3.setObjectName("frame_3") - self.gridLayout_3 = QtWidgets.QGridLayout(self.frame_3) - self.gridLayout_3.setObjectName("gridLayout_3") - self.verticalLayout_3 = QtWidgets.QVBoxLayout() - self.verticalLayout_3.setObjectName("verticalLayout_3") - self.label_3 = QtWidgets.QLabel(self.frame_3) - self.label_3.setObjectName("label_3") - self.verticalLayout_3.addWidget(self.label_3) - self.horizontalLayout = QtWidgets.QHBoxLayout() - self.horizontalLayout.setObjectName("horizontalLayout") - self.pushButtonOpFreq1 = QtWidgets.QPushButton(self.frame_3) - self.pushButtonOpFreq1.setMaximumSize(QtCore.QSize(100, 16777215)) - self.pushButtonOpFreq1.setObjectName("pushButtonOpFreq1") - self.horizontalLayout.addWidget(self.pushButtonOpFreq1) - self.comboBoxOperations = QtWidgets.QComboBox(self.frame_3) - self.comboBoxOperations.setEnabled(True) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.comboBoxOperations.sizePolicy().hasHeightForWidth()) - self.comboBoxOperations.setSizePolicy(sizePolicy) - self.comboBoxOperations.setObjectName("comboBoxOperations") - self.horizontalLayout.addWidget(self.comboBoxOperations) - self.pushButtonOpFreq2 = QtWidgets.QPushButton(self.frame_3) - self.pushButtonOpFreq2.setEnabled(False) - self.pushButtonOpFreq2.setMaximumSize(QtCore.QSize(100, 16777215)) - self.pushButtonOpFreq2.setObjectName("pushButtonOpFreq2") - self.horizontalLayout.addWidget(self.pushButtonOpFreq2) - self.pushButtonOpFreq3 = QtWidgets.QPushButton(self.frame_3) - self.pushButtonOpFreq3.setEnabled(False) - self.pushButtonOpFreq3.setMaximumSize(QtCore.QSize(100, 16777215)) - self.pushButtonOpFreq3.setObjectName("pushButtonOpFreq3") - self.horizontalLayout.addWidget(self.pushButtonOpFreq3) - self.verticalLayout_3.addLayout(self.horizontalLayout) - self.gridLayout_3.addLayout(self.verticalLayout_3, 0, 0, 1, 1) - self.gridLayout_5.addWidget(self.frame_3, 0, 0, 1, 1) - self.frame = QtWidgets.QFrame(Form) - self.frame.setFrameShape(QtWidgets.QFrame.StyledPanel) - self.frame.setFrameShadow(QtWidgets.QFrame.Plain) - self.frame.setLineWidth(1) - self.frame.setMidLineWidth(0) - self.frame.setObjectName("frame") - self.gridLayout = QtWidgets.QGridLayout(self.frame) - self.gridLayout.setObjectName("gridLayout") - self.verticalLayout_5 = QtWidgets.QVBoxLayout() - self.verticalLayout_5.setObjectName("verticalLayout_5") - self.checkBox = QtWidgets.QCheckBox(self.frame) - self.checkBox.setEnabled(False) - self.checkBox.setObjectName("checkBox") - self.verticalLayout_5.addWidget(self.checkBox) - self.pushButtonDoMath = QtWidgets.QPushButton(self.frame) - self.pushButtonDoMath.setEnabled(True) - self.pushButtonDoMath.setMaximumSize(QtCore.QSize(100, 16777215)) - self.pushButtonDoMath.setObjectName("pushButtonDoMath") - self.verticalLayout_5.addWidget(self.pushButtonDoMath) - self.gridLayout.addLayout(self.verticalLayout_5, 0, 0, 1, 1) - self.gridLayout_5.addWidget(self.frame, 0, 1, 1, 1) - self.frame_2 = QtWidgets.QFrame(Form) - self.frame_2.setFrameShape(QtWidgets.QFrame.StyledPanel) - self.frame_2.setFrameShadow(QtWidgets.QFrame.Plain) - self.frame_2.setObjectName("frame_2") - self.gridLayout_2 = QtWidgets.QGridLayout(self.frame_2) - self.gridLayout_2.setObjectName("gridLayout_2") - self.verticalLayout_6 = QtWidgets.QVBoxLayout() - self.verticalLayout_6.setObjectName("verticalLayout_6") - self.verticalLayout = QtWidgets.QVBoxLayout() - self.verticalLayout.setSpacing(0) - self.verticalLayout.setObjectName("verticalLayout") - self.verticalLayout_2 = QtWidgets.QVBoxLayout() - self.verticalLayout_2.setSpacing(0) - self.verticalLayout_2.setObjectName("verticalLayout_2") - self.label = QtWidgets.QLabel(self.frame_2) - self.label.setObjectName("label") - self.verticalLayout_2.addWidget(self.label) - self.lineEditMax = QtWidgets.QLineEdit(self.frame_2) - self.lineEditMax.setMinimumSize(QtCore.QSize(0, 25)) - self.lineEditMax.setMaximumSize(QtCore.QSize(16777215, 25)) - self.lineEditMax.setReadOnly(False) - self.lineEditMax.setObjectName("lineEditMax") - self.verticalLayout_2.addWidget(self.lineEditMax) - self.verticalLayout.addLayout(self.verticalLayout_2) - self.label_2 = QtWidgets.QLabel(self.frame_2) - self.label_2.setObjectName("label_2") - self.verticalLayout.addWidget(self.label_2) - self.lineEditMin = QtWidgets.QLineEdit(self.frame_2) - self.lineEditMin.setMinimumSize(QtCore.QSize(0, 25)) - self.lineEditMin.setMaximumSize(QtCore.QSize(16777215, 25)) - self.lineEditMin.setReadOnly(False) - self.lineEditMin.setObjectName("lineEditMin") - self.verticalLayout.addWidget(self.lineEditMin) - self.verticalLayout_6.addLayout(self.verticalLayout) - self.gridLayout_2.addLayout(self.verticalLayout_6, 1, 0, 1, 1) - self.verticalLayout_8 = QtWidgets.QVBoxLayout() - self.verticalLayout_8.setObjectName("verticalLayout_8") - self.checkBoxFixed = QtWidgets.QCheckBox(self.frame_2) - self.checkBoxFixed.setEnabled(True) - self.checkBoxFixed.setChecked(False) - self.checkBoxFixed.setObjectName("checkBoxFixed") - self.verticalLayout_8.addWidget(self.checkBoxFixed) - self.checkBoxCompress = QtWidgets.QCheckBox(self.frame_2) - self.checkBoxCompress.setEnabled(True) - self.checkBoxCompress.setChecked(False) - self.checkBoxCompress.setObjectName("checkBoxCompress") - self.verticalLayout_8.addWidget(self.checkBoxCompress) - self.gridLayout_2.addLayout(self.verticalLayout_8, 0, 0, 1, 1) - self.gridLayout_5.addWidget(self.frame_2, 0, 2, 3, 1) - self.frame_4 = QtWidgets.QFrame(Form) - self.frame_4.setFrameShape(QtWidgets.QFrame.StyledPanel) - self.frame_4.setFrameShadow(QtWidgets.QFrame.Plain) - self.frame_4.setObjectName("frame_4") - self.gridLayout_4 = QtWidgets.QGridLayout(self.frame_4) - self.gridLayout_4.setObjectName("gridLayout_4") - self.verticalLayout_4 = QtWidgets.QVBoxLayout() - self.verticalLayout_4.setSpacing(0) - self.verticalLayout_4.setObjectName("verticalLayout_4") - self.label_4 = QtWidgets.QLabel(self.frame_4) - self.label_4.setObjectName("label_4") - self.verticalLayout_4.addWidget(self.label_4) - self.horizontalLayout_2 = QtWidgets.QHBoxLayout() - self.horizontalLayout_2.setObjectName("horizontalLayout_2") - self.pushButtonCondFreq1 = QtWidgets.QPushButton(self.frame_4) - self.pushButtonCondFreq1.setEnabled(False) - self.pushButtonCondFreq1.setMaximumSize(QtCore.QSize(100, 16777215)) - self.pushButtonCondFreq1.setObjectName("pushButtonCondFreq1") - self.horizontalLayout_2.addWidget(self.pushButtonCondFreq1) - self.comboBoxCondOps = QtWidgets.QComboBox(self.frame_4) - self.comboBoxCondOps.setEnabled(True) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.comboBoxCondOps.sizePolicy().hasHeightForWidth()) - self.comboBoxCondOps.setSizePolicy(sizePolicy) - self.comboBoxCondOps.setObjectName("comboBoxCondOps") - self.horizontalLayout_2.addWidget(self.comboBoxCondOps) - self.pushButtonCondFreq2 = QtWidgets.QPushButton(self.frame_4) - self.pushButtonCondFreq2.setEnabled(False) - self.pushButtonCondFreq2.setMaximumSize(QtCore.QSize(100, 16777215)) - self.pushButtonCondFreq2.setObjectName("pushButtonCondFreq2") - self.horizontalLayout_2.addWidget(self.pushButtonCondFreq2) - self.pushButtonCondFreq3 = QtWidgets.QPushButton(self.frame_4) - self.pushButtonCondFreq3.setEnabled(False) - self.pushButtonCondFreq3.setMaximumSize(QtCore.QSize(100, 16777215)) - self.pushButtonCondFreq3.setObjectName("pushButtonCondFreq3") - self.horizontalLayout_2.addWidget(self.pushButtonCondFreq3) - self.comboBoxCondInEquality = QtWidgets.QComboBox(self.frame_4) - self.comboBoxCondInEquality.setEnabled(False) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Fixed) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.comboBoxCondInEquality.sizePolicy().hasHeightForWidth()) - self.comboBoxCondInEquality.setSizePolicy(sizePolicy) - self.comboBoxCondInEquality.setObjectName("comboBoxCondInEquality") - self.horizontalLayout_2.addWidget(self.comboBoxCondInEquality) - self.spinBoxInEquality = QtWidgets.QDoubleSpinBox(self.frame_4) - self.spinBoxInEquality.setEnabled(False) - self.spinBoxInEquality.setMinimumSize(QtCore.QSize(100, 0)) - self.spinBoxInEquality.setButtonSymbols(QtWidgets.QAbstractSpinBox.NoButtons) - self.spinBoxInEquality.setDecimals(5) - self.spinBoxInEquality.setMinimum(-1000000000000.0) - self.spinBoxInEquality.setMaximum(1000000000000.0) - self.spinBoxInEquality.setObjectName("spinBoxInEquality") - self.horizontalLayout_2.addWidget(self.spinBoxInEquality) - self.verticalLayout_4.addLayout(self.horizontalLayout_2) - self.gridLayout_4.addLayout(self.verticalLayout_4, 1, 0, 1, 1) - self.gridLayout_5.addWidget(self.frame_4, 2, 0, 1, 2) - spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) - self.gridLayout_5.addItem(spacerItem, 1, 0, 1, 1) - - self.retranslateUi(Form) - QtCore.QMetaObject.connectSlotsByName(Form) - - def retranslateUi(self, Form): - _translate = QtCore.QCoreApplication.translate - Form.setWindowTitle(_translate("Form", "Form")) - self.label_3.setText(_translate("Form", "Basic Math")) - self.pushButtonOpFreq1.setText(_translate("Form", "Freq 1")) - self.pushButtonOpFreq2.setText(_translate("Form", "Freq 2")) - self.pushButtonOpFreq3.setText(_translate("Form", "Freq 3")) - self.checkBox.setText(_translate("Form", "Norm. Intensity")) - self.pushButtonDoMath.setText(_translate("Form", "Perform Math")) - self.label.setText(_translate("Form", "Maximum")) - self.label_2.setText(_translate("Form", "Minimum")) - self.checkBoxFixed.setText(_translate("Form", "Fixed")) - self.checkBoxCompress.setText(_translate("Form", "Compress")) - self.label_4.setText(_translate("Form", "Conditional")) - self.pushButtonCondFreq1.setText(_translate("Form", "Freq 1")) - self.pushButtonCondFreq2.setText(_translate("Form", "Freq 2")) - self.pushButtonCondFreq3.setText(_translate("Form", "Freq 3")) - diff --git a/crikit/ui/deprecated/qt_SglColorImage.py b/crikit/ui/deprecated/qt_SglColorImage.py deleted file mode 100644 index 9771aba..0000000 --- a/crikit/ui/deprecated/qt_SglColorImage.py +++ /dev/null @@ -1,113 +0,0 @@ -# -*- coding: utf-8 -*- - -# Form implementation generated from reading ui file '.\ui_SglColorImage.ui' -# -# Created by: PyQt5 UI code generator 5.5.1 -# -# WARNING! All changes made in this file will be lost! - -from PyQt5 import QtCore, QtGui, QtWidgets - -class Ui_Form(object): - def setupUi(self, Form): - Form.setObjectName("Form") - Form.resize(642, 579) - Form.setMouseTracking(False) - Form.setStyleSheet("font: 10pt \"Arial\";") - self.gridLayout = QtWidgets.QGridLayout(Form) - self.gridLayout.setContentsMargins(-1, 0, -1, 0) - self.gridLayout.setObjectName("gridLayout") - self.verticalLayoutMain = QtWidgets.QVBoxLayout() - self.verticalLayoutMain.setObjectName("verticalLayoutMain") - self.widgetImgOpt = QtWidgets.QWidget(Form) - self.widgetImgOpt.setEnabled(True) - self.widgetImgOpt.setObjectName("widgetImgOpt") - self.horizontalLayout_3 = QtWidgets.QHBoxLayout(self.widgetImgOpt) - self.horizontalLayout_3.setContentsMargins(-1, 0, -1, 0) - self.horizontalLayout_3.setObjectName("horizontalLayout_3") - self.pushButtonPop = QtWidgets.QPushButton(self.widgetImgOpt) - self.pushButtonPop.setEnabled(True) - self.pushButtonPop.setObjectName("pushButtonPop") - self.horizontalLayout_3.addWidget(self.pushButtonPop) - self.pushButtonSpectrum = QtWidgets.QPushButton(self.widgetImgOpt) - self.pushButtonSpectrum.setEnabled(True) - self.pushButtonSpectrum.setObjectName("pushButtonSpectrum") - self.horizontalLayout_3.addWidget(self.pushButtonSpectrum) - self.pushButtonGSPop = QtWidgets.QPushButton(self.widgetImgOpt) - self.pushButtonGSPop.setEnabled(True) - self.pushButtonGSPop.setObjectName("pushButtonGSPop") - self.horizontalLayout_3.addWidget(self.pushButtonGSPop) - self.comboBox = QtWidgets.QComboBox(self.widgetImgOpt) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.comboBox.sizePolicy().hasHeightForWidth()) - self.comboBox.setSizePolicy(sizePolicy) - self.comboBox.setMinimumSize(QtCore.QSize(140, 0)) - self.comboBox.setLayoutDirection(QtCore.Qt.LeftToRight) - self.comboBox.setEditable(False) - self.comboBox.setObjectName("comboBox") - self.horizontalLayout_3.addWidget(self.comboBox, 0, QtCore.Qt.AlignHCenter) - self.pushButtonSpectrum.raise_() - self.pushButtonGSPop.raise_() - self.comboBox.raise_() - self.pushButtonPop.raise_() - self.verticalLayoutMain.addWidget(self.widgetImgOpt) - self.horizontalLayoutGainImg = QtWidgets.QHBoxLayout() - self.horizontalLayoutGainImg.setContentsMargins(10, -1, -1, -1) - self.horizontalLayoutGainImg.setObjectName("horizontalLayoutGainImg") - self.groupBox = QtWidgets.QGroupBox(Form) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Preferred) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.groupBox.sizePolicy().hasHeightForWidth()) - self.groupBox.setSizePolicy(sizePolicy) - self.groupBox.setMinimumSize(QtCore.QSize(120, 0)) - self.groupBox.setMaximumSize(QtCore.QSize(120, 16777215)) - self.groupBox.setObjectName("groupBox") - self.gridLayout_2 = QtWidgets.QGridLayout(self.groupBox) - self.gridLayout_2.setObjectName("gridLayout_2") - self.verticalLayoutGain = QtWidgets.QVBoxLayout() - self.verticalLayoutGain.setContentsMargins(-1, 6, -1, -1) - self.verticalLayoutGain.setSpacing(6) - self.verticalLayoutGain.setObjectName("verticalLayoutGain") - self.gainSlider = QtWidgets.QSlider(self.groupBox) - self.gainSlider.setMaximum(100) - self.gainSlider.setProperty("value", 10) - self.gainSlider.setSliderPosition(10) - self.gainSlider.setOrientation(QtCore.Qt.Vertical) - self.gainSlider.setInvertedAppearance(False) - self.gainSlider.setTickPosition(QtWidgets.QSlider.TicksAbove) - self.gainSlider.setTickInterval(10) - self.gainSlider.setObjectName("gainSlider") - self.verticalLayoutGain.addWidget(self.gainSlider, 0, QtCore.Qt.AlignHCenter) - self.lineEditGainSlider = QtWidgets.QLineEdit(self.groupBox) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.lineEditGainSlider.sizePolicy().hasHeightForWidth()) - self.lineEditGainSlider.setSizePolicy(sizePolicy) - self.lineEditGainSlider.setMaximumSize(QtCore.QSize(30, 16777215)) - self.lineEditGainSlider.setObjectName("lineEditGainSlider") - self.verticalLayoutGain.addWidget(self.lineEditGainSlider, 0, QtCore.Qt.AlignHCenter) - self.pushButtonGain1 = QtWidgets.QPushButton(self.groupBox) - self.pushButtonGain1.setObjectName("pushButtonGain1") - self.verticalLayoutGain.addWidget(self.pushButtonGain1, 0, QtCore.Qt.AlignHCenter) - self.gridLayout_2.addLayout(self.verticalLayoutGain, 0, 0, 1, 1) - self.horizontalLayoutGainImg.addWidget(self.groupBox) - self.verticalLayoutMain.addLayout(self.horizontalLayoutGainImg) - self.gridLayout.addLayout(self.verticalLayoutMain, 0, 0, 1, 1) - - self.retranslateUi(Form) - QtCore.QMetaObject.connectSlotsByName(Form) - - def retranslateUi(self, Form): - _translate = QtCore.QCoreApplication.translate - Form.setWindowTitle(_translate("Form", "Form")) - self.pushButtonPop.setText(_translate("Form", "Pop")) - self.pushButtonSpectrum.setText(_translate("Form", "Mean Spectrum")) - self.pushButtonGSPop.setText(_translate("Form", "Grayscale")) - self.groupBox.setTitle(_translate("Form", "Gain")) - self.lineEditGainSlider.setText(_translate("Form", "1.0")) - self.pushButtonGain1.setText(_translate("Form", "1.0")) - diff --git a/crikit/ui/deprecated/widget_ploteffect.py b/crikit/ui/deprecated/widget_ploteffect.py deleted file mode 100644 index 805ba8c..0000000 --- a/crikit/ui/deprecated/widget_ploteffect.py +++ /dev/null @@ -1,722 +0,0 @@ -""" -Widgets for Plot-Effect Interface (crikit.ui.widget_ploteffect) -=============================================================== - -widgetNothing : This demo widget does nothing - -widgetKK : This applies the Kramers-Kronig relation phase retrieval operation - -widgetALS : Controls alternating least square parameters - -widgetCalibrate : Controls calibration parameters - - -Operation ---------- -PlotEffect subUI widgets are essentially 3 parts: a visual component that \ -controls any necessary variables, a function (fcn) that performs the \ -mathemtical operation on the input data, and a signal (changed) that conveys \ -that some change has occurred to the variables within the widget UI. - -data_in : (np.array, list) - For function (fcn) with single-input, data_in should be a numpy array. For \ - fcn with multiple input variables, data_in of type list - -changed : QtCore.pyqtSignal - -""" - -# Append sys path -import sys as _sys -import os as _os - -# Generic imports for QT-based programs -from PyQt5.QtWidgets import (QApplication as _QApplication, - QWidget as _QWidget) - -from PyQt5.QtCore import pyqtSignal as _pyqtSignal - -# Other imports -import numpy as _np -from scipy.signal import savgol_filter as _sg -from scipy.interpolate import UnivariateSpline as _UnivariateSpline -import copy as _copy - -# Import from Designer-based GUI - -from crikit.ui.qt_PlotEffect_Nothing import Ui_Form as Ui_Nothing_Form -from crikit.ui.qt_PlotEffect_KK import Ui_Form as Ui_KK_Form -from crikit.ui.qt_PlotEffect_ALS import Ui_Form as Ui_ALS_Form -from crikit.ui.qt_PlotEffect_SG import Ui_Form as Ui_SG_Form -from crikit.ui.qt_PlotEffect_Calibrate import Ui_Form as Ui_Calibrate_Form - - -from crikit.cri.algorithms.kk import kkrelation as _kk -from crikit.preprocess.algorithms.als import als_baseline_redux as _als - -from crikit.data.frequency import (calib_pix_wn as _calib_pix_wn) - -from crikit.utils.general import find_nearest as _find_nearest - -class widgetNothing(_QWidget): - """ - Plugin widget for PlotEffect subUI. - - This plugin does nothing (i.e., it is a template and for demonstration \ - purposes). - - """ - - changed = _pyqtSignal() - - def __init__(self, parent = None): - super(widgetNothing, self).__init__(parent) ### EDIT ### - self.ui = Ui_Nothing_Form() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - def fcn(self, data_in): - return data_in - -class widgetCalibrate(_QWidget): - """ - This plugin widget provides calibration functionality. - - """ - DEFAULT_N_PIX = 1600 - DEFAULT_CTR_WL = 730.0 - DEFAULT_CTR_WL0 = 730.0 - DEFAULT_A_VEC = (-0.167740721307557, 863.8736708961577) - DEFAULT_PROBE = 771.461 - - DEFAULT_MEAS = 1004.0 - - CALIB_DICT = {'n_pix' : DEFAULT_N_PIX, 'ctr_wl' : DEFAULT_CTR_WL, - 'ctr_wl0' : DEFAULT_CTR_WL0, 'a_vec' : DEFAULT_A_VEC, - 'probe' : DEFAULT_PROBE} - - changed = _pyqtSignal() - - def __init__(self, calib_dict=None, parent = None): - super(widgetCalibrate, self).__init__(parent) ### EDIT ### - self.ui = Ui_Calibrate_Form() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - if calib_dict is None: - self.calib_dict = self.CALIB_DICT - else: - self.calib_dict = calib_dict - if isinstance(self.calib_dict['a_vec'], tuple): - self.calib_dict['a_vec'] = list(self.calib_dict['a_vec']) - - self.new_calib_dict = _copy.deepcopy(self.calib_dict) - - self.updateUI() - self.WN, _ = _calib_pix_wn(self.calib_dict) - self.WN_2, _ = _calib_pix_wn(self.new_calib_dict) - -# self.WN, self.WL, _ = _make_freq_vector(self.calib_dict) -# self.WN_2, self.WL_2, _ = _make_freq_vector(self.new_calib_dict) - - self.ui.spinBoxMeas.setValue(self.DEFAULT_MEAS) - self.ui.spinBoxCorrect.setValue(self.DEFAULT_MEAS) - - self.meas = self.DEFAULT_MEAS - self.correct = self.DEFAULT_MEAS - - self.ui.spinBoxCorrect.editingFinished.connect(self.calcCalibDict) - self.ui.spinBoxMeas.editingFinished.connect(self.calcCalibDict) - - def fcn(self, data_in): - """ - Performs the KK. - - Parameters - ---------- - data : list - data[0] : Wavenumber vector - data[1] : NRB spectrum(a) - data[2] : CARS spectrum(a) - - Returns - ------- - out : np.array - Imaginary component the of KK-retrieved spectrum(a) - - See also - -------- - crikit.process.phase_retr, crikit.process.maths.kk - - """ - if data_in.ndim == 1: - spl = _UnivariateSpline(self.WN_2, data_in, s=0, ext=0) - output = spl(self.WN) - elif data_in.ndim == 2: - output = _np.zeros(data_in.shape) - for num, spect in enumerate(data_in): - spl = _UnivariateSpline(self.WN_2, spect, s=0, ext=0) - output[num,:] = spl(self.WN) - return output - #return data_in - - def calcCalibDict(self): - """ - (Re)-Calculate calibration dictionary components and recalculate \ - wavenumber/wavelength vector - """ - self.meas = self.ui.spinBoxMeas.value() - self.correct = self.ui.spinBoxCorrect.value() - - delta_lambda = 1/(((self.correct)/1e7) + 1/self.calib_dict['probe']) - \ - 1/(((self.meas)/1e7) + 1/self.calib_dict['probe']) - - self.new_calib_dict['a_vec'][1] = self.calib_dict['a_vec'][1] + delta_lambda - - self.WN_2, _ = _calib_pix_wn(self.new_calib_dict) - - self.updateUI() - self.changed.emit() - - def updateUI(self): - # Set calibration values - - self.ui.spinBoxNPix.setValue(self.calib_dict['n_pix']) - self.ui.spinBoxNPix_2.setValue(self.new_calib_dict['n_pix']) - - self.ui.spinBoxCenterWL.setValue(self.calib_dict['ctr_wl']) - self.ui.spinBoxCenterWL_2.setValue(self.new_calib_dict['ctr_wl']) - - self.ui.spinBoxCalibWL.setValue(self.calib_dict['ctr_wl0']) - self.ui.spinBoxCalibWL_2.setValue(self.new_calib_dict['ctr_wl0']) - - self.ui.spinBoxSlope.setValue(self.calib_dict['a_vec'][0]) - self.ui.spinBoxSlope_2.setValue(self.new_calib_dict['a_vec'][0]) - - self.ui.spinBoxIntercept.setValue(self.calib_dict['a_vec'][1]) - self.ui.spinBoxIntercept_2.setValue(self.new_calib_dict['a_vec'][1]) - - self.ui.spinBoxProbeWL.setValue(self.calib_dict['probe']) - self.ui.spinBoxProbeWL_2.setValue(self.new_calib_dict['probe']) - - - -class widgetKK(_QWidget): - """ - Plugin widget for PlotEffect subUI. - - This plugin performs the Kramers-Kronig (KK) relation phase retrieval. - - Attributes - ---------- - nrb_norm : bool - Normalize by the NRB flag - - cars_bias : (int, float) - Constant added to the input CARS spectrum(a) - - nrb_bias : (int, float) - Constant added to the input NRB spectrum(a) - - phaselin : (int, float) - Constant phase correction to the retrieved phase - - phasesig1 : (int, float) - For sigmoidal phase correction, the is the starting phase - - phasesig2 : (int, float) - For sigmoidal phase correction, the is the ending phase - - sigrate : (int, float) - For sigmoidal phase correction, this is the rate of change from \ - phasesig1 to phasesig2 - - pad_factor : int - Padding factor to use with the KK algorithm - - phase_type : str - Global phase addition type: 'linear' or 'sigmoidal' - - - Methods - --------- - fcn : Performs the KK - - Signals : - changed : a value in the UI has changed - - """ - - changed = _pyqtSignal() - - NRB_NORM = True - PHASE_TYPE = 'Linear' - - CARS_BIAS = 0 - NRB_BIAS = 0 - PHASELIN = 0 - - PHASESIG1 = 0 - PHASESIG2 = 0 - SIGRATE = 1 - - PADFACTOR = 1 - - def __init__(self, parent = None): - super(widgetKK, self).__init__(parent) ### EDIT ### - self.ui = Ui_KK_Form() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - self.setupKK() - - def setupKK(self): - - self.ui.checkBoxNRBNorm.setChecked(self.NRB_NORM) - self.nrb_norm = self.NRB_NORM - - self.ui.spinBoxCARSBias.setValue(self.CARS_BIAS) - self.ui.sliderCARSBias.setValue(self.CARS_BIAS) - self.cars_bias = self.CARS_BIAS - - self.ui.spinBoxNRBBias.setValue(self.NRB_BIAS) - self.ui.sliderNRBBias.setValue(self.NRB_BIAS) - self.nrb_bias = self.NRB_BIAS - - self.ui.spinBoxPhaseLin.setValue(self.PHASELIN) - self.ui.sliderPhaseLin.setValue(self.PHASELIN) - self.phaselin = self.PHASELIN - - self.ui.spinBoxSigPhase1.setValue(self.PHASESIG1) - self.ui.sliderSigPhase1.setValue(self.PHASESIG1) - self.phasesig1 = self.PHASESIG1 - - self.ui.spinBoxSigPhase2.setValue(self.PHASESIG2) - self.ui.sliderSigPhase2.setValue(self.PHASESIG2) - self.phasesig2 = self.PHASESIG2 - - self.ui.spinBoxSigRate.setValue(self.SIGRATE) - self.ui.sliderSigRate.setValue(self.SIGRATE) - self.sigrate = self.SIGRATE - - self.ui.spinBoxPadFactor.setValue(self.PADFACTOR) - self.pad_factor = self.PADFACTOR - - if self.PHASE_TYPE.lower() == 'linear': - self.ui.tabWidget.setCurrentIndex(0) - self.phase_type = 'linear' - elif self.PHASE_TYPE.lower() == 'sigmoidal': - self.ui.tabWidget.setCurrentIndex(1) - self.phase_type = 'sigmoidal' - else: - self.ui.tabWidget.setCurrentIndex(0) - self.phase_type = 'linear' - - # Signals-Slots - self.ui.sliderCARSBias.valueChanged.connect(self.changeSliderCARSBiasPre) - self.ui.sliderCARSBias.sliderReleased.connect(self.changeSliderCARSBiasFinal) - self.ui.spinBoxCARSBias.valueChanged.connect(self.changeSpinBoxCARSBias) - - self.ui.sliderNRBBias.valueChanged.connect(self.changeSliderNRBBiasPre) - self.ui.sliderNRBBias.sliderReleased.connect(self.changeSliderNRBBiasFinal) - self.ui.spinBoxNRBBias.valueChanged.connect(self.changeSpinBoxNRBBias) - - self.ui.sliderPhaseLin.valueChanged.connect(self.changeSliderPhaseLinPre) - self.ui.sliderPhaseLin.sliderReleased.connect(self.changeSliderPhaseLinFinal) - self.ui.spinBoxPhaseLin.valueChanged.connect(self.changeSpinBoxPhaseLin) - - self.ui.sliderSigPhase1.valueChanged.connect(self.changeSliderSigPhase1Pre) - self.ui.sliderSigPhase1.sliderReleased.connect(self.changeSliderSigPhase1Final) - self.ui.spinBoxSigPhase1.valueChanged.connect(self.changeSpinBoxSigPhase1) - - self.ui.sliderSigPhase2.valueChanged.connect(self.changeSliderSigPhase2Pre) - self.ui.sliderSigPhase2.sliderReleased.connect(self.changeSliderSigPhase2Final) - self.ui.spinBoxSigPhase2.valueChanged.connect(self.changeSpinBoxSigPhase2) - - self.ui.sliderSigRate.valueChanged.connect(self.changeSliderSigRatePre) - self.ui.sliderSigRate.sliderReleased.connect(self.changeSliderSigRateFinal) - self.ui.spinBoxSigRate.valueChanged.connect(self.changeSpinBoxSigRate) - - self.ui.spinBoxPadFactor.valueChanged.connect(self.changeSpinBoxPadFactor) - - self.ui.checkBoxNRBNorm.clicked.connect(self.changeCheckBoxNRBNorm) - self.ui.checkBoxLockBias.clicked.connect(self.changeCheckBoxLockBias) - - self.ui.radioButtonPhaseLin.clicked.connect(self.changeRadioPhaseLin) - self.ui.radioButtonPhaseSig.clicked.connect(self.changeRadioPhaseSig) - - # Disabled sigmoidal phase correction for now - self.ui.radioButtonPhaseSig.setEnabled(False) - - self.ui.sliderNRBBias.setEnabled(False) - self.ui.spinBoxNRBBias.setEnabled(False) - self.ui.sliderCARSBias.sliderReleased.connect(self.sliderBiasLock) - self.ui.spinBoxCARSBias.valueChanged.connect(self.spinBoxBiasLock) - - - - def fcn(self, data_in): - """ - Performs the KK. - - Parameters - ---------- - data : list - data[0] : Wavenumber vector - data[1] : NRB spectrum(a) - data[2] : CARS spectrum(a) - - Returns - ------- - out : np.array - Imaginary component the of KK-retrieved spectrum(a) - - See also - -------- - crikit.process.phase_retr, crikit.process.maths.kk - - """ - assert isinstance(data_in, list), 'KK plot effect fcn requires the data input be a list with length 3: WN, NRB, CARS' - - out = _kk(data_in[1] + self.nrb_bias, data_in[2] + - self.cars_bias, phase_offset=self.phaselin*_np.pi/360, - norm_by_bg=self.nrb_norm, pad_factor=self.pad_factor) - return out.imag - - - - def changeSliderCARSBiasPre(self): - self.ui.spinBoxCARSBias.setValue(self.ui.sliderCARSBias.value()) - self.cars_bias = self.ui.sliderCARSBias.value() - self.changed.emit() - - def changeSliderCARSBiasFinal(self): - self.ui.spinBoxCARSBias.setValue(self.ui.sliderCARSBias.value()) - self.cars_bias = self.ui.sliderCARSBias.value() - self.changed.emit() - - def changeSpinBoxCARSBias(self): - self.ui.sliderCARSBias.setValue(self.ui.spinBoxCARSBias.value()) - self.cars_bias = self.ui.spinBoxCARSBias.value() - self.changed.emit() - - def changeSliderNRBBiasPre(self): - self.ui.spinBoxNRBBias.setValue(self.ui.sliderNRBBias.value()) - self.nrb_bias = self.ui.sliderNRBBias.value() - self.changed.emit() - - def changeSliderNRBBiasFinal(self): - self.ui.spinBoxNRBBias.setValue(self.ui.sliderNRBBias.value()) - self.nrb_bias = self.ui.sliderNRBBias.value() - self.changed.emit() - - def changeSpinBoxNRBBias(self): - self.ui.sliderNRBBias.setValue(self.ui.spinBoxNRBBias.value()) - self.nrb_bias = self.ui.spinBoxNRBBias.value() - self.changed.emit() - - def changeSliderPhaseLinPre(self): - self.ui.spinBoxPhaseLin.setValue(self.ui.sliderPhaseLin.value()) - self.phaselin = self.ui.sliderPhaseLin.value() - self.changed.emit() - - def changeSliderPhaseLinFinal(self): - self.ui.spinBoxPhaseLin.setValue(self.ui.sliderPhaseLin.value()) - self.phaselin = self.ui.sliderPhaseLin.value() - self.changed.emit() - - def changeSpinBoxPhaseLin(self): - self.ui.sliderPhaseLin.setValue(self.ui.spinBoxPhaseLin.value()) - self.phaselin = self.ui.spinBoxPhaseLin.value() - self.changed.emit() - - def changeSliderSigPhase1Pre(self): - self.ui.spinBoxSigPhase1.setValue(self.ui.sliderSigPhase1.value()) - self.phasesig1 = self.ui.sliderSigPhase1.value() - self.changed.emit() - - def changeSliderSigPhase1Final(self): - self.ui.spinBoxSigPhase1.setValue(self.ui.sliderSigPhase1.value()) - self.phasesig1 = self.ui.sliderSigPhase1.value() - self.changed.emit() - - def changeSpinBoxSigPhase1(self): - self.ui.sliderSigPhase1.setValue(self.ui.spinBoxSigPhase1.value()) - self.phasesig1 = self.ui.spinBoxSigPhase1.value() - self.changed.emit() - - def changeSliderSigPhase2Pre(self): - self.ui.spinBoxSigPhase2.setValue(self.ui.sliderSigPhase2.value()) - self.phasesig2 = self.ui.sliderSigPhase2.value() - self.changed.emit() - - def changeSliderSigPhase2Final(self): - self.ui.spinBoxSigPhase2.setValue(self.ui.sliderSigPhase2.value()) - self.phasesig2 = self.ui.sliderSigPhase2.value() - self.changed.emit() - - def changeSpinBoxSigPhase2(self): - self.ui.sliderSigPhase2.setValue(self.ui.spinBoxSigPhase2.value()) - self.phasesig2 = self.ui.spinBoxSigPhase2.value() - self.changed.emit() - - def changeSliderSigRatePre(self): - self.ui.spinBoxSigRate.setValue(self.ui.sliderSigRate.value()) - self.sigrate = self.ui.sliderSigRate.value() - self.changed.emit() - - def changeSliderSigRateFinal(self): - self.ui.spinBoxSigRate.setValue(self.ui.sliderSigRate.value()) - self.sigrate = self.ui.sliderSigRate.value() - self.changed.emit() - - def changeSpinBoxSigRate(self): - self.ui.sliderSigRate.setValue(self.ui.spinBoxSigRate.value()) - self.sigrate = self.ui.spinBoxSigRate.value() - self.changed.emit() - - def changeCheckBoxLockBias(self): - if self.ui.checkBoxLockBias.isChecked(): - self.ui.sliderNRBBias.setEnabled(False) - self.ui.spinBoxNRBBias.setEnabled(False) - self.ui.sliderCARSBias.sliderReleased.connect(self.sliderBiasLock) - self.ui.spinBoxCARSBias.valueChanged.connect(self.spinBoxBiasLock) - self.sliderBiasLock() - self.spinBoxBiasLock() - - else: - self.ui.sliderNRBBias.setEnabled(True) - self.ui.spinBoxNRBBias.setEnabled(True) - self.ui.sliderCARSBias.sliderReleased.disconnect(self.sliderBiasLock) - self.ui.spinBoxCARSBias.valueChanged.disconnect(self.spinBoxBiasLock) - self.changed.emit() - - def sliderBiasLock(self): - self.ui.sliderNRBBias.setValue(self.ui.sliderCARSBias.value()) - self.nrb_bias = self.ui.sliderCARSBias.value() - self.changed.emit() - - def spinBoxBiasLock(self): - self.ui.spinBoxNRBBias.setValue(self.ui.spinBoxCARSBias.value()) - self.nrb_bias = self.ui.sliderCARSBias.value() - self.changed.emit() - - def changeCheckBoxNRBNorm(self): - if self.ui.checkBoxNRBNorm.isChecked(): - self.nrb_norm = True - else: - self.nrb_norm = False - self.changed.emit() - - def changeRadioPhaseLin(self): - self.phase_type = 'linear' - self.ui.tabWidget.setCurrentIndex(0) - - def changeRadioPhaseSig(self): - self.phase_type = 'sigmoidal' - self.ui.tabWidget.setCurrentIndex(1) - - def changeSpinBoxPadFactor(self): - self.pad_factor = self.ui.spinBoxPadFactor.value() - self.changed.emit() - - - - - - - -class widgetALS(_QWidget): - """ - Plugin widget for PlotEffect subUI. - - This performs detrending with the asymmetric least squares algorithms - - Attributes - ---------- - p : float - ALS asymmetry parameter - - lam : float - ALS smoothness parameter - - redux : int - - - - Methods - --------- - fcn : Performs the Asymmetric Least Squares - - Signals: - changed : a value in the UI has changed - - Notes - ----- - Please cite the C. H. Camp Jr., et al. reference (below) if you - use this software. - - References - ---------- - [1] C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative, - Comparable Coherent Anti-Stokes Raman Scattering (CARS) - Spectroscopy: Correcting Errors in Phase Retrieval" - - [2] P. H. C. Eilers, "A perfect smoother," Anal. Chem. 75, - 3631-3636 (2003). - - [3] P. H. C. Eilers and H. F. M. Boelens, "Baseline correction with - asymmetric least squares smoothing," Report. October 21, 2005. - - """ - - changed = _pyqtSignal() - - P_VAL = 1e-3 # Asymmetry - LAMBDA_VAL = 1 # Smothness - REDUX = 10 # Interpolation step size (pixels) - - def __init__(self, parent = None): - super(widgetALS, self).__init__(parent) ### EDIT ### - self.ui = Ui_ALS_Form() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - self.ui.spinBoxP.setValue(self.P_VAL) - self.ui.spinBoxLambda.setValue(self.LAMBDA_VAL) - self.ui.spinBoxRedux.setValue(self.REDUX) - - self.p = self.P_VAL - self.lam = self.LAMBDA_VAL - self.redux = self.REDUX - - self.ui.spinBoxP.valueChanged.connect(self.changeP) - self.ui.spinBoxLambda.valueChanged.connect(self.changeLambda) - self.ui.spinBoxRedux.valueChanged.connect(self.changeRedux) - - - def fcn(self, data_in): - data_out = _np.zeros(data_in.shape) - - if data_in.ndim == 1: - baseline = _als(data_in, redux_factor=self.redux, - redux_full=False, - smoothness_param=self.lam, - asym_param=self.p)[0] - data_out = data_in - baseline - else: - for num, spectrum in enumerate(data_in): - baseline = _als(spectrum, redux_factor=self.redux, - redux_full=False, smoothness_param=self.lam, - asym_param=self.p, print_iteration=False)[0] - data_out[num,:] = spectrum - baseline - return data_out - - def changeP(self): - self.p = self.ui.spinBoxP.value() - self.changed.emit() - - def changeLambda(self): - self.lam = self.ui.spinBoxLambda.value() - self.changed.emit() - - def changeRedux(self): - self.redux = self.ui.spinBoxRedux.value() - self.changed.emit() - -class widgetSG(_QWidget): - """ - Plugin widget for PlotEffect subUI. - - This performs the Savitky-Golay filtering - - Attributes - ---------- - win_size : int - Window size - - order : int - Order (polynomial) - - Methods - --------- - fcn : Performs the Savitky-Golay - - Signals: - changed : a value in the UI has changed - - References - ---------- - [1] C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative, - Comparable Coherent Anti-Stokes Raman Scattering (CARS) - Spectroscopy: Correcting Errors in Phase Retrieval" - - """ - - changed = _pyqtSignal() - -# WIN_SIZE = 601 # Window size -# ORDER = 2 # Order - - def __init__(self, win_size=601, order=2, parent = None): - super(widgetSG, self).__init__(parent) ### EDIT ### - self.ui = Ui_SG_Form() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - self.win_size = win_size - self.order = order - - # Window size must be > order - if self.win_size <= self.order: - self.win_size = self.order + 1 - - # Window size must be odd - if self.win_size%2 == 1: - pass - else: - self.win_size += 1 - - self.ui.spinBoxWinSize.setValue(self.win_size) - self.ui.spinBoxOrder.setValue(self.order) - - self.ui.spinBoxWinSize.valueChanged.connect(self.changeWinSize) - self.ui.spinBoxOrder.valueChanged.connect(self.changeOrder) - - def fcn(self, data_in): - - baseline = _sg(data_in, window_length=self.win_size, polyorder=self.order, axis=-1) - data_out = data_in - baseline - - return data_out - - def changeWinSize(self): - temp_win_size = self.ui.spinBoxWinSize.value() - if temp_win_size%2 == 1: - self.win_size = temp_win_size - else: - self.ui.spinBoxWinSize.setValue(temp_win_size+1) - self.win_size = temp_win_size+1 - self.changed.emit() - - def changeOrder(self): - self.order = self.ui.spinBoxOrder.value() - self.changed.emit() - - -if __name__ == '__main__': - app = _QApplication(_sys.argv) - app.setStyle('Cleanlooks') - - winNothing = widgetNothing() - winNothing.show() - - winKK = widgetKK() - winKK.show() - - winALS = widgetALS() - winALS.show() - - winSG = widgetSG(win_size=3, order=3) - winSG.show() - - winCalib = widgetCalibrate() - winCalib.show() - - - app.exec_() - _sys.exit() \ No newline at end of file diff --git a/crikit/ui/dialog_AbstractFactorization.py b/crikit/ui/dialog_AbstractFactorization.py index 2765833..04cb7f8 100644 --- a/crikit/ui/dialog_AbstractFactorization.py +++ b/crikit/ui/dialog_AbstractFactorization.py @@ -33,7 +33,7 @@ class DialogAbstractFactorization(_QDialog): """ def __init__(self, parent=None): super(DialogAbstractFactorization, self).__init__(parent=parent) - + self._mpl_v1 = _mpl.__version__.split('.')[0] == 1 ## def __init__(self, parent=None): # raise NotImplementedError('This is an abstract class.') ## super(DialogAbstractFactorization, self).__init__(parent=parent) ### EDIT ### @@ -99,7 +99,8 @@ def setup(self, parent = None): for count in range(self._num_factor_visible): self.factorWins.append(_MplCanvas(subplot=211)) self.factorWins[count].ax[0].axis('Off') - self.factorWins[count].ax[1].hold('Off') + if self._mpl_v1: + self.factorWins[count].ax[1].hold('Off') self.ui.gridLayout.addWidget(self.factorWins[0],1,0) self.ui.gridLayout.addWidget(self.factorWins[1],1,1) @@ -111,11 +112,13 @@ def setup(self, parent = None): self.reconCurrent = _MplCanvas(subplot=211) self.reconCurrent.ax[0].axis('Off') - self.reconCurrent.ax[1].hold('Off') + if self._mpl_v1: + self.reconCurrent.ax[1].hold('Off') self.reconRemainder = _MplCanvas(subplot=211) self.reconRemainder.ax[0].axis('Off') - self.reconRemainder.ax[1].hold('Off') + if self._mpl_v1: + self.reconRemainder.ax[1].hold('Off') self.ui.verticalLayout_3.insertWidget(1,self.reconCurrent) diff --git a/crikit/ui/dialog_kkOptions.py b/crikit/ui/dialog_kkOptions.py index eaa3d78..51576c6 100644 --- a/crikit/ui/dialog_kkOptions.py +++ b/crikit/ui/dialog_kkOptions.py @@ -21,7 +21,7 @@ # Import from Designer-based GUI from crikit.ui.qt_KKOptions import Ui_Dialog as Ui_KKOptions -from crikit.ui.dialog_ploteffect import (DialogPlotEffectFuture as +from crikit.ui.dialog_ploteffect import (DialogPlotEffect as _DialogPlotEffect) from crikit.ui.widget_KK import (widgetKK as _widgetKK) diff --git a/crikit/ui/dialog_ploteffect.py b/crikit/ui/dialog_ploteffect.py index 050e495..34bbac2 100644 --- a/crikit/ui/dialog_ploteffect.py +++ b/crikit/ui/dialog_ploteffect.py @@ -9,6 +9,7 @@ from PyQt5.QtWidgets import (QApplication as _QApplication, QDialog as _QDialog) +from PyQt5 import QtWidgets as _QtWidgets from crikit.ui.qt_PlotEffect import Ui_Dialog as Ui_DialogPlotEffect @@ -18,7 +19,7 @@ from sciplot.ui.widget_mpl import MplCanvas as _MplCanvas -class DialogPlotEffectFuture(_QDialog): +class DialogPlotEffect(_QDialog): """ Extensible Dialog that shows the effect of a plugin on input data. @@ -37,23 +38,30 @@ class DialogPlotEffectFuture(_QDialog): parent : QObject Parent """ + + TRANSPOSE_ARR = True - def __init__(self, data, x=None, plugin=None, parent=None): - super(DialogPlotEffectFuture, self).__init__(parent) + def __init__(self, data, x=None, plugin=None, mpl_kwargs={'width':8, 'height':2}, parent=None): + super(DialogPlotEffect, self).__init__(parent) self.ui = Ui_DialogPlotEffect() self.ui.setupUi(self) self.data = data # Setup MPL containers - self.mpl_orig = _MplCanvas(subplot=111) - self.mpl_affected = _MplCanvas(subplot=111) - + self.mpl_orig = _MplCanvas(subplot=111, **mpl_kwargs) + self.mpl_orig.fig.canvas.setMinimumSize(100,200) + self.mpl_orig.fig.canvas.setSizePolicy(_QtWidgets.QSizePolicy.Expanding, _QtWidgets.QSizePolicy.Minimum) + + self.mpl_affected = _MplCanvas(subplot=111, **mpl_kwargs) + self.mpl_affected.fig.canvas.setMinimumSize(100,200) + self.mpl_affected.fig.canvas.setSizePolicy(_QtWidgets.QSizePolicy.Expanding, _QtWidgets.QSizePolicy.Minimum) + # Show(), although not needed, enables mpl-tight_layout # to work later on self.show() - self.ui.verticalLayout.insertWidget(1, self.mpl_orig) + self.ui.verticalLayout.insertWidget(1, self.mpl_orig, stretch=1) self.ui.verticalLayout.insertWidget(1, self.mpl_orig.toolbar) self.ui.verticalLayout.insertWidget(3, self.mpl_affected) @@ -71,23 +79,8 @@ def __init__(self, data, x=None, plugin=None, parent=None): self.x = _np.linspace(0,data.shape[0],self.data.shape[0]) else: self.x = x - - # If data is a list (assumed to be a list of ndarrays), - # plot each item in list - if isinstance(data, _np.ndarray): - try: - self.mpl_orig.ax.plot(self.x,data) - except: - self.mpl_orig.ax.plot(self.x,data.T) - elif isinstance(data, list): - for d in data: - try: - self.mpl_orig.ax.plot(self.x,d) - except: - self.mpl_orig.ax.plot(self.x,d.T) - - - self.plot_labels() + + self.make_orig_plots(self.data) if self.plugin is not None: self.ui.verticalLayout.insertWidget(8, plugin) @@ -100,14 +93,69 @@ def __init__(self, data, x=None, plugin=None, parent=None): self.ui.pushButtonOk.clicked.connect(self.accept) self.ui.pushButtonCancel.clicked.connect(self.reject) + def make_orig_plots(self, data, lw=1, ls='-'): + """ + + """ + self.make_plots(self.mpl_orig, data, lw=lw, ls=ls) + + def make_affected_plots(self, data, lw=1, ls='-'): + """ + + """ + self.make_plots(self.mpl_affected, data, lw=lw, ls=ls) + + def make_plots(self, canvas, data, lw=1, ls='-'): + """ + + """ + # If data is a list (assumed to be a list of ndarrays), + # plot each item in list + if isinstance(data, _np.ndarray): + # TRANSPOSE ARRAY in case of plt.plot(data) -- in a for-loop, this is opposite + if self.TRANSPOSE_ARR: + if data.ndim > 1: + for num, d in enumerate(data): + canvas.ax.plot(self.x,d, lw=lw, ls=ls, color='C{}'.format(num % 10)) + else: + canvas.ax.plot(self.x,data, lw=lw, ls=ls, color='C0') + else: + if data.ndim > 1: + for num, d in enumerate(data.T): + canvas.ax.plot(self.x,d, lw=lw, color='C{}'.format(num % 10)) + else: + canvas.ax.plot(self.x,data, lw=lw, color='C0') + + elif isinstance(data, list): + for d in data: + if d.ndim > 1: + if self.TRANSPOSE_ARR: + for num, d2 in enumerate(d): + canvas.ax.plot(self.x, d2, lw=lw, ls=ls, color='C{}'.format(num % 10)) + else: + for num, d2 in enumerate(d.T): + canvas.ax.plot(self.x, d2, lw=lw, ls=ls, color='C{}'.format(num % 10)) + else: + canvas.ax.plot(self.x, d, lw=lw, ls=ls, color='C0') + + self.plot_labels() + try: + canvas.fig.tight_layout() + except: + print('Tight layout failed (dialog_ploteffect') + + @staticmethod - def dialogPlotEffect(data, x = None, plugin=None, parent = None): + def dialogPlotEffect(data, x=None, plugin=None, parent=None): """ Static method that is actually called """ - dialog = DialogPlotEffectFuture(data, x=x, plugin=plugin, + dialog = DialogPlotEffect(data, x=x, plugin=plugin, parent=parent) - + # Resize to fit plugin + if dialog.width() < dialog.plugin.width(): + dialog.resize(int(dialog.plugin.width()*1.1), dialog.height()) + result = dialog.exec_() # 1 = Accepted, 0 = Rejected/Canceled if result == 1: @@ -144,28 +192,11 @@ def widget_changed(self): self.mpl_orig.ax.clear() + self.make_orig_plots(self.data) - if isinstance(self.data, _np.ndarray): - try: - self.mpl_orig.ax.plot(self.x,self.data) - except: - self.mpl_orig.ax.plot(self.x,self.data.T) - - # If data is a list (assumed to be a list of ndarrays), - # plot each item in list - elif isinstance(self.data, list): - for d in self.data: - try: - self.mpl_orig.ax.plot(self.x,d) - except: - self.mpl_orig.ax.plot(self.x,d.T) - if orig_data_addon is not None: - try: - self.mpl_orig.ax.plot(self.x,orig_data_addon, lw=2) - except: - self.mpl_orig.ax.plot(self.x,orig_data_addon.T, lw=2) - + self.make_orig_plots(orig_data_addon, lw=0.75, ls=':') + # If there already exists an affected plot, keep those # axis limits upon re-plotting if len(self.mpl_affected.ax.lines) > 0: @@ -182,15 +213,7 @@ def widget_changed(self): self.mpl_affected.toolbar.setVisible(True) self.mpl_affected.ax.clear() - try: - self.mpl_affected.ax.plot(self.x,affected_data) - except: - self.mpl_affected.ax.plot(self.x,affected_data.T) - - self.plot_labels() # Update x-,y-, and title-labels on plots - - self.mpl_orig.fig.tight_layout() - self.mpl_affected.fig.tight_layout() + self.make_affected_plots(affected_data) # Reset axis limits to previous setting before re-plotting if lim_orig is not None: @@ -274,47 +297,48 @@ def fcn(self, data_in): CARS = _np.abs(1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055) NRB = 0*WN + .055 - CARS = _np.dot(_np.ones((5,1)),CARS[None,:]) + CARS = _np.dot(_np.arange(1,4)[:,None],CARS[None,:]) - NRB_LEFT = 20e3*_np.exp(-(WN)**2/(1000**2)) + 500 - NRB_RIGHT = 6e3*_np.exp(-(WN-2500)**2/(400**2)) + 500 + # NRB_LEFT = 20e3*_np.exp(-(WN)**2/(1000**2)) + 500 + # NRB_RIGHT = 6e3*_np.exp(-(WN-2500)**2/(400**2)) + 500 - NRB_LEFT[WN<500] *= 0 - NRB_LEFT[WN<500] += 1e-6 - NRB_RIGHT[WN<500] *= 0 - NRB_RIGHT[WN<500] += 1e-6 + # NRB_LEFT[WN<500] *= 0 + # NRB_LEFT[WN<500] += 1e-6 + # NRB_RIGHT[WN<500] *= 0 + # NRB_RIGHT[WN<500] += 1e-6 - from crikit.cri.merge_nrbs import MergeNRBs as _MergeNRBs + # from crikit.cri.merge_nrbs import MergeNRBs as _MergeNRBs from crikit.utils.general import find_nearest as _find_nearest - NRB2 = _MergeNRBs(nrb_left=NRB_LEFT, nrb_right=NRB_RIGHT, - pix=_find_nearest(WN, 1885.0)[1], - left_side_scale=False).calculate() + # NRB2 = _MergeNRBs(nrb_left=NRB_LEFT, nrb_right=NRB_RIGHT, + # pix=_find_nearest(WN, 1885.0)[1], + # left_side_scale=False).calculate() - CARS2 = _np.abs(500*(1/(1000-WN-1j*20) + 1/(2700-WN-1j*20)) + NRB2**0.5)**2 - CARS2 = _np.dot(_np.ones((10,1), dtype=_np.double),CARS2[None,:]) + # CARS2 = _np.abs(500*(1/(1000-WN-1j*20) + 1/(2700-WN-1j*20)) + NRB2**0.5)**2 + # CARS2 = _np.dot(_np.ones((3,1), dtype=_np.double),CARS2[None,:]) # # Demo # plugin = widgetDemoPlotEffectPlugin() -# winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN, +# winPlotEffect = DialogPlotEffect.dialogPlotEffect(CARS, x=WN, # plugin=plugin) # if winPlotEffect is not None: # print(winPlotEffect.parameters) # ## # ALS -## from crikit.ui.widget_ALS import widgetALS as _widgetALS -## -## plugin = _widgetALS() -## winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN, -## plugin=plugin) -## if winPlotEffect is not None: -## print(winPlotEffect.parameters) + from crikit.ui.widget_ALS import widgetALS as _widgetALS + + rng = _np.arange(*_find_nearest(WN, [500, 3800])[1]) + plugin = _widgetALS(x=WN, rng=rng) + winPlotEffect = DialogPlotEffect.dialogPlotEffect(CARS, x=WN, + plugin=plugin) + if winPlotEffect is not None: + print(winPlotEffect.parameters) # # # ArPLS # from crikit.ui.widget_ArPLS import widgetArPLS as _widgetArPLS # plugin = _widgetArPLS() -# winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN, +# winPlotEffect = DialogPlotEffect.dialogPlotEffect(CARS, x=WN, # plugin=plugin) # if winPlotEffect is not None: # print(winPlotEffect.parameters) @@ -323,7 +347,7 @@ def fcn(self, data_in): # from crikit.ui.widget_DeTrending import (widgetDeTrending as # _widgetDeTrending) # plugin = _widgetDeTrending() -# winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN, +# winPlotEffect = DialogPlotEffect.dialogPlotEffect(CARS, x=WN, # plugin=plugin) # if winPlotEffect is not None: # print(winPlotEffect.parameters) @@ -331,7 +355,7 @@ def fcn(self, data_in): # # SG # from crikit.ui.widget_SG import (widgetSG as _widgetSG) # plugin = _widgetSG() -# winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN, +# winPlotEffect = DialogPlotEffect.dialogPlotEffect(CARS, x=WN, # plugin=plugin) # if winPlotEffect is not None: # print(winPlotEffect.parameters) @@ -339,7 +363,7 @@ def fcn(self, data_in): # # KK # from crikit.ui.widget_KK import (widgetKK as _widgetKK) # plugin = _widgetKK() -# winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect([NRB,CARS], x=WN, +# winPlotEffect = DialogPlotEffect.dialogPlotEffect([NRB,CARS], x=WN, # plugin=plugin) # if winPlotEffect is not None: # print(winPlotEffect.parameters) @@ -348,19 +372,19 @@ def fcn(self, data_in): # from crikit.ui.widget_Calibrate import (widgetCalibrate as # _widgetCalibrate) # plugin = _widgetCalibrate(calib_dict) -# winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN, +# winPlotEffect = DialogPlotEffect.dialogPlotEffect(CARS, x=WN, # plugin=plugin) # if winPlotEffect is not None: # print(winPlotEffect.parameters) # Merge NRBs - from crikit.ui.widget_mergeNRBs import (widgetMergeNRBs as - _widgetMergeNRBs) - plugin = _widgetMergeNRBs(WN, NRB_LEFT, NRB_RIGHT) - winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS2, x=WN, - plugin=plugin) - if winPlotEffect is not None: - print(winPlotEffect.parameters) + # from crikit.ui.widget_mergeNRBs import (widgetMergeNRBs as + # _widgetMergeNRBs) + # plugin = _widgetMergeNRBs(WN, NRB_LEFT, NRB_RIGHT) + # winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS2, x=WN, + # plugin=plugin) + # if winPlotEffect is not None: + # print(winPlotEffect.parameters) diff --git a/crikit/ui/dialog_save.py b/crikit/ui/dialog_save.py index d83a8ac..7db3790 100644 --- a/crikit/ui/dialog_save.py +++ b/crikit/ui/dialog_save.py @@ -217,7 +217,7 @@ def dialogSave(current_filename=None, current_path=None, suffix : str Suffix to append to _dataset_name based on processing steps - NOTE : save_ parameters supercede current_ parameters + NOTE : save* parameters supercede current* parameters Returns ---------- diff --git a/crikit/ui/main_Mosaic.py b/crikit/ui/main_Mosaic.py new file mode 100644 index 0000000..8d4c9dc --- /dev/null +++ b/crikit/ui/main_Mosaic.py @@ -0,0 +1,695 @@ +""" +MainWindow program that allows construction of stitched images from +multiple dataset +""" + +import sys as _sys +import os as _os +import copy as _copy + +from collections import OrderedDict + +import h5py +import numpy as _np + +from PyQt5 import QtWidgets as _QtWidgets +from PyQt5.QtWidgets import (QApplication as _QApplication, + QMainWindow as _QMainWindow, + QWidget as _QWidget, + QListWidget as _QListWidget, + QMessageBox as _QMessageBox) + +import PyQt5.QtCore as _QtCore +from PyQt5.QtCore import (pyqtSignal as _pyqtSignal) + +from crikit.ui.qt_Mosaic import Ui_MainWindow + +from crikit.data.frequency import calib_pix_wl, calib_pix_wn +from crikit.data.mosaic import Mosaic +from crikit.ui.dialog_save import DialogSave + +from sciplot.ui.widget_mpl import MplCanvas as _MplCanvas + +import lazy5 +from lazy5.utils import FidOrFile, fullpath +from lazy5.ui.QtHdfLoad import HdfLoad + + +class DnDReorderListWidget(_QListWidget): + """ List widget with drag-n-drop reordering """ + + reordered = _pyqtSignal() + + def __init__(self, parent): + super(DnDReorderListWidget, self).__init__(parent) + + self.setAcceptDrops(True) + self.setEditTriggers(_QtWidgets.QAbstractItemView.NoEditTriggers) + self.setDragEnabled(True) + self.setDragDropMode(_QtWidgets.QAbstractItemView.InternalMove) + self.setDefaultDropAction(_QtCore.Qt.MoveAction) + self.setAlternatingRowColors(False) + self.setSelectionMode(_QtWidgets.QAbstractItemView.SingleSelection) + self.setObjectName("listWidgetDatasets") + + item = _QtWidgets.QListWidgetItem() + self.addItem(item) + item = _QtWidgets.QListWidgetItem() + self.addItem(item) + + self.setSortingEnabled(False) + item = self.item(0) + item.setText('A') + item = self.item(1) + item.setText('B') + + def dropEvent(self, e): + super().dropEvent(e) + self.reordered.emit() + +class MainWindowMosaic(_QMainWindow): + """ + + """ + + frequency_calib = {'Slope':-0.165955456, 'Intercept':832.5510120093941, + 'Probe': 771.461, 'Calib_WL': 700.0, 'Center_WL': 700.0} + + config = {'allow_duplicates':False} + + def __init__(self, parent=None): + super(MainWindowMosaic, self).__init__(parent) + self.ui = Ui_MainWindow() + self.ui.setupUi(self) + self.setupListWidget() + + self.ui.spinBoxIntercept.setValue(self.frequency_calib['Intercept']) + self.ui.spinBoxSlope.setValue(self.frequency_calib['Slope']) + self.ui.spinBoxProbe.setValue(self.frequency_calib['Probe']) + self.ui.spinBoxCalibWL.setValue(self.frequency_calib['Calib_WL']) + self.ui.spinBoxCenterWL.setValue(self.frequency_calib['Center_WL']) + + # Internal data + self.init_internals() + + self.mpl = _MplCanvas(parent=self) + self.ui.verticalLayoutMPL.insertWidget(0, self.mpl, _QtCore.Qt.AlignCenter) + self.ui.verticalLayoutMPL.insertWidget(0,self.mpl.toolbar, _QtCore.Qt.AlignHCenter) + + # SIGNALS AND SLOTS + self.ui.actionAddFromHDF.triggered.connect(self.addDataset) + self.ui.pushButtonAddDataset.pressed.connect(self.addDataset) + + self.ui.actionSaveToHDF5.triggered.connect(self.save) + + self.ui.sliderFreq.valueChanged.connect(self.updateSlider) + self.ui.sliderFreq.sliderReleased.connect(self.updateMosaicImage) + + self.ui.lineEditPix.editingFinished.connect(self.lineEditPixChange) + + self.ui.spinBoxMRows.editingFinished.connect(self.updateParams) + self.ui.spinBoxNCols.editingFinished.connect(self.updateParams) + self.ui.comboBoxRowCol.currentIndexChanged.connect(self.updateParams) + self.ui.checkBoxFlipH.stateChanged.connect(self.updateParams) + self.ui.checkBoxFlipV.stateChanged.connect(self.updateParams) + self.ui.checkBoxTranspose.stateChanged.connect(self.updateParams) + self.ui.spinBoxStartRow.editingFinished.connect(self.updateParams) + self.ui.spinBoxStartCol.editingFinished.connect(self.updateParams) + self.ui.spinBoxEndRow.editingFinished.connect(self.updateParams) + self.ui.spinBoxEndCol.editingFinished.connect(self.updateParams) + + # ! Currently, cannot save compress in HDF5 + self.ui.checkBoxCompress.setEnabled(False) + # self.ui.checkBoxCompress.stateChanged.connect(self.updateParams) + + self.ui.spinBoxSlope.editingFinished.connect(self.updateFrequency) + self.ui.spinBoxIntercept.editingFinished.connect(self.updateFrequency) + self.ui.spinBoxProbe.editingFinished.connect(self.updateFrequency) + self.ui.spinBoxCalibWL.editingFinished.connect(self.updateFrequency) + self.ui.spinBoxCenterWL.editingFinished.connect(self.updateFrequency) + + # self.ui.spinBoxXStepSize.editingFinished.connect(self.updateSpace) + # self.ui.spinBoxYStepSize.editingFinished.connect(self.updateSpace) + + self.ui.pushButtonMoveUp.pressed.connect(self.promote_demote_list_item) + self.ui.pushButtonMoveDown.pressed.connect(self.promote_demote_list_item) + self.ui.pushButtonDeleteDataset.pressed.connect(self.deleteDataset) + + self.ui.listWidgetDatasets.reordered.connect(self.list_reordered) + + # Close event + self.ui.closeEvent = self.closeEvent + self.ui.actionExit.triggered.connect(self.closeEvent) + + def setupListWidget(self): + + self.ui.listWidgetDatasets = DnDReorderListWidget(parent=self.ui.frame) + self.ui.verticalLayout_4.insertWidget(2, self.ui.listWidgetDatasets) + + def deleteDataset(self): + if self.data._data: + row = self.ui.listWidgetDatasets.currentRow() + + if row < 0: + # print('No selection') + pass + else: + # print('Current row: {}'.format(row)) + + it = self.ui.listWidgetDatasets.takeItem(row) + out = self.data_list.pop(row) + out = self.data._data.pop(row) + out = self.h5dlist.pop(row) + out.file.close() + + if self.data.size > 0: + self.list_reordered() + else: + self.init_internals() + self.mpl.ax.clear() + self.mpl.draw() + + def promote_demote_list_item(self): + if self.data._data: + sndr = self.sender() + row = self.ui.listWidgetDatasets.currentRow() + isup = None + + if sndr == self.ui.pushButtonMoveUp: + isup = True + elif sndr == self.ui.pushButtonMoveDown: + isup = False + + if row < 0: + # print('No selection') + pass + else: + # print('Current row: {}'.format(row)) + pass + if isup & (row == 0): + # print('Can\'t promote first') + pass + elif (isup == False) & (row + 1 == self.ui.listWidgetDatasets.count()): + # print('Can\'t demote last') + pass + elif row < 0: + # print('Can\'t promote/demote no selection') + pass + elif isup: + # print('Promoting') + it = self.ui.listWidgetDatasets.takeItem(row) + self.ui.listWidgetDatasets.insertItem(row - 1, it) + self.list_reordered() + elif not isup: + # print('Demoting') + it = self.ui.listWidgetDatasets.takeItem(row) + self.ui.listWidgetDatasets.insertItem(row + 1, it) + self.list_reordered() + + def list_reordered(self): + if self.data._data: + if self.data.size >= 1: + dset_list = [] + for num in range(self.ui.listWidgetDatasets.count()): + dset_list.append(self.ui.listWidgetDatasets.item(num).text().split(' : ')) + + new_order = [] + for q in self.data_list: + new_order.append(dset_list.index(q)) + + assert len(new_order) == self.data.size + assert len(new_order) == _np.unique(new_order).size + + self.data_list = [self.data_list[idx] for idx in new_order] + self.data._data = [self.data._data[idx] for idx in new_order] + self.h5dlist = [self.h5dlist[idx] for idx in new_order] + self.updateMosaicImage() + + else: + pass + + def init_internals(self): + """ Initialize internal variables """ + self.data = Mosaic() + self.data_list = [] # List of list [pth, fname, dsetname] + self.h5dlist = [] # List of dataset pointers + + self.pix = None + self.wl = None + self.freq = None + + self.last_path = None + self.last_fname = None + self.last_dsetname = None + + self.imported_calib_vec = None + self.imported_spatial_vec = None + + def lineEditPixChange(self): + """ + Frequency manually entered in frequency-slider-display + """ + + freq_in = int(float(self.ui.lineEditPix.text())) + + max_freq = self.ui.sliderFreq.maximum() + min_freq = self.ui.sliderFreq.minimum() + + if freq_in > max_freq: + freq_in = max_freq + elif freq_in < min_freq: + freq_in = min_freq + else: + pass + + self.ui.sliderFreq.setValue(freq_in) + + def updateSlider(self): + idx = self.ui.sliderFreq.value() + self.ui.lineEditPix.setText(str(idx)) + + if self.freq is not None: + self.ui.lineEditFreq.setText(str(self.freq[idx])) + + # In case incremented by the arrow buttons + if not self.ui.sliderFreq.isSliderDown(): + self.updateMosaicImage() + + def addDataset(self): + if (self.last_path is None) | (self.last_fname is None) | (self.last_dsetname is None): + first_dset = True + to_open = HdfLoad.getFileDataSets(parent=self) + else: + first_dset = False + to_open = HdfLoad.getFileDataSets(pth=_os.path.join(self.last_path, self.last_fname), + parent=self) + + if to_open is not None: + temp_last_path, temp_last_fname, _ = to_open + + # Since to_open's dsets will be lists, this is an unraveled version + to_import = [[temp_last_path, temp_last_fname, q] for q in to_open[-1]] + to_import2 = [] # Duplicates removed if NOT allowing duplicates + + for q in to_import: + if not self.config['allow_duplicates']: + if self.is_duplicate_import([q[0], q[1], q[2]]): + msg = _QMessageBox(self) + msg.setIcon(_QMessageBox.Critical) + str1 = 'Cannot import duplicate image:\n\n' + str2 = '{} : {} : {}\n\n'.format(*q) + str3 = '\n\nNot importing this dataset' + msg.setText(str1 + str2 + str3) + msg.setWindowTitle('Duplicate Image Found.') + msg.setStandardButtons(_QMessageBox.Ok) + msg.setDefaultButton(_QMessageBox.Ok) + out = msg.exec() + else: + to_import2.append(q) + + else: + to_import2.append(q) + + for q in to_import2: + fof = FidOrFile(fullpath(pth=q[0], filename=q[1])) + if fof.fid[q[-1]].ndim != 3: + msg = _QMessageBox(self) + msg.setIcon(_QMessageBox.Critical) + str1 = 'Dataset is not 3D:\n\n' + str2 = '{} : {} : {}'.format(*q) + str3 = '\n\nNot importing this dataset' + msg.setText(str1 + str2 + str3) + msg.setWindowTitle('Cannot Load Non-3D Datasets.') + msg.setStandardButtons(_QMessageBox.Ok) + msg.setDefaultButton(_QMessageBox.Ok) + out = msg.exec() + fof.fid.close() + else: + self.h5dlist.append(fof.fid[q[-1]]) + self.data.append(fof.fid[q[-1]]) + self.last_path = q[0] + self.last_fname = q[1] + self.last_dsetname = q[2] + self.data_list.append(q) + + if first_dset: + flen = self.data.unitshape_orig[-1] + self.ui.sliderFreq.setMinimum(0) + self.ui.sliderFreq.setMaximum(flen-1) + self.ui.sliderFreq.setValue(0) + + self.pix = _np.arange(flen) + calib_vec = self.check_for_spectral_calib(fof.fid[q[-1]]) + self.check_for_spatial_calib(fof.fid[q[-1]]) + + self.updateFrequency(calib_vec) + first_dset = False + + self.updateDatasets() + + def check_for_spatial_calib(self, dset): + """ See if dataset has spatial calibration meta data """ + if not isinstance(dset, h5py.Dataset): + return None + if not hasattr(dset, 'attrs'): + return None + + spatial_vec = [] # X, Y + + attrs_dict = lazy5.inspect.get_attrs_dset(dset.file, dset.name) + list_of_keys = list(attrs_dict) + + ct = 0 + temp = [] + to_check = ['Raster.Fast.StepSize', 'Raster.Slow.StepSize'] # X, Y + for num, tc in enumerate(to_check): + if list_of_keys.count(tc) > 0: + ct += 1 + temp.append(attrs_dict[tc]) + if ct == len(to_check): + print('Has StepSize info (New)') + spatial_vec = temp + else: + ct = 0 + temp = [] + to_check = ['RasterScanParams.FastAxisStepSize', 'RasterScanParams.SlowAxisStepSize'] # X, Y + for num, tc in enumerate(to_check): + if list_of_keys.count(tc) > 0: + ct += 1 + temp.append(attrs_dict[tc]) + if ct == len(to_check): + print('Has StepSize info (Old)') + spatial_vec = temp + else: + ct = 0 + temp = [] + to_check = ['Raster.Fast.Start', 'Raster.Fast.Stop', 'Raster.Fast.Steps', + 'Raster.Slow.Start', 'Raster.Slow.Stop', 'Raster.Slow.Steps'] + for num, tc in enumerate(to_check): + if list_of_keys.count(tc) > 0: + ct += 1 + temp.append(attrs_dict[tc]) + if ct == len(to_check): + print('Has Start-Stop-Steps info (New)') + x_stepsize = (temp[1] - temp[0])/(temp[2]-1) + y_stepsize = (temp[4] - temp[3])/(temp[5]-1) + spatial_vec = [x_stepsize, y_stepsize] + else: + ct = 0 + temp = [] + to_check = ['RasterScanParams.FastAxisStart', 'RasterScanParams.FastAxisStop', + 'RasterScanParams.FastAxisSteps', + 'RasterScanParams.SlowAxisStart', 'RasterScanParams.SlowAxisStop', + 'RasterScanParams.SlowAxisSteps'] + for num, tc in enumerate(to_check): + if list_of_keys.count(tc) > 0: + ct += 1 + temp.append(attrs_dict[tc]) + if ct == len(to_check): + print('Has Start-Stop-Steps info (Old)') + x_stepsize = (temp[1] - temp[0])/(temp[2]-1) + y_stepsize = (temp[4] - temp[3])/(temp[5]-1) + spatial_vec = [x_stepsize, y_stepsize] + + if spatial_vec: + self.imported_spatial_vec = spatial_vec + self.ui.checkBoxSpaceFromData.setChecked(True) + self.ui.spinBoxXStepSize.setValue(spatial_vec[0]) + self.ui.spinBoxYStepSize.setValue(spatial_vec[1]) + + def check_for_spectral_calib(self, dset): + """ See if dataset has spectral calibration meta data """ + if not isinstance(dset, h5py.Dataset): + return None + if not hasattr(dset, 'attrs'): + return None + + calib_vec = [] + + attrs_dict = lazy5.inspect.get_attrs_dset(dset.file, dset.name) + list_of_keys = list(attrs_dict) + + ct = 0 + temp = [] + to_check = ['Calib.a_vec', 'Calib.ctr_wl', 'Calib.ctr_wl0', 'Calib.n_pix', + 'Calib.probe'] + for num, tc in enumerate(to_check): + if list_of_keys.count(tc) > 0: + ct += 1 + temp.append(attrs_dict[tc]) + if ct == len(to_check): + print('Has Calib series') + calib_vec = temp + else: + ct = 0 + temp = [] + to_check = ['Spectro.Avec', 'Spectro.CurrentWavelength', 'Spectro.CalibWavelength', + 'Spectro.SpectralPixels', 'Spectro.ProbeWavelength'] + for num, tc in enumerate(to_check): + if list_of_keys.count(tc) > 0: + ct += 1 + temp.append(attrs_dict[tc]) + if ct == len(to_check): + print('Has Spectro series') + calib_vec = temp + if calib_vec: + self.ui.checkBoxSpectFromData.setChecked(True) + return calib_vec + + def is_duplicate_import(self, to_open): + if self.data._data: + return self.data_list.count(to_open) > 0 + else: + return False + + def updateFrequency(self, calib_vec=None): + if self.pix is not None: + if calib_vec is None: + probe = self.ui.spinBoxProbe.value() * 1e-9 + intercept = self.ui.spinBoxIntercept.value() * 1e-9 + slope = self.ui.spinBoxSlope.value() * 1e-9 + ctr_wl = self.ui.spinBoxCenterWL.value() * 1e-9 + calib_wl = self.ui.spinBoxCalibWL.value() * 1e-9 + + self.frequency_calib['Probe'] = probe + self.frequency_calib['Intercept'] = intercept + self.frequency_calib['Slope'] = slope + self.frequency_calib['Center_WL'] = ctr_wl + self.frequency_calib['Calib_WL'] = calib_wl + + self.wl = slope*self.pix + intercept + (ctr_wl - calib_wl) + + if probe != 0.0: + self.freq = 0.01 / self.wl - 0.01 / probe + else: + self.freq = 0.01 / self.wl + else: + a_vec = calib_vec[0] + if len(a_vec) == 2: + slope = a_vec[0] * 1e-9 + intercept = a_vec[1] * 1e-9 + else: # Linearizes higher order polynomial + a_vec = _np.polyfit(self.pix, _np.polyval(a_vec, self.pix), 1) + slope = a_vec[0] * 1e-9 + intercept = a_vec[1] * 1e-9 + + ctr_wl = calib_vec[1] * 1e-9 + calib_wl = calib_vec[2] * 1e-9 + local_pix = calib_vec[3] + probe = calib_vec[4] * 1e-9 + + self.ui.spinBoxProbe.setValue(probe * 1e9) + self.ui.spinBoxIntercept.setValue(intercept * 1e9) + self.ui.spinBoxSlope.setValue(slope * 1e9) + self.ui.spinBoxCenterWL.setValue(ctr_wl * 1e9) + self.ui.spinBoxCalibWL.setValue(calib_wl * 1e9) + + self.wl = slope*self.pix + intercept + (ctr_wl - calib_wl) + if probe != 0.0: + self.freq = 0.01 / self.wl - 0.01 / probe + else: + self.freq = 0.01 / self.wl + + self.imported_calib_vec = _copy.deepcopy(calib_vec) + + self.updateSlider() + + @staticmethod + def _create_list_names(item_list): + temp = [] + for q in item_list: + temp.append(q[0] + ' : ' + q[1] + ' : ' + q[-1]) + return temp + + def updateDatasets(self): + """ Update the listWidget of datasets """ + self.ui.listWidgetDatasets.clear() + + temp = self._create_list_names(self.data_list) + + for q in temp: + self.ui.listWidgetDatasets.addItem(q) + + self.updateParams() + # self.updateMosaicImage() + + def updateMosaicImage(self): + if self.data._data: + + idx = self.ui.sliderFreq.value() + self.ui.lineEditPix.setText(str(idx)) + if self.freq is not None: + self.ui.lineEditFreq.setText(str(self.freq[idx])) + + self.mpl.ax.clear() + temp = self.data.mosaic2d(idx=idx) + if _np.iscomplexobj(temp): + self.mpl.ax.imshow(temp.imag) + else: + self.mpl.ax.imshow(temp) + + self.mpl.draw() + + def closeEvent(self, event): + print('Closing') + + if self.h5dlist: + for q in self.h5dlist: + print('Closing: {}'.format(q)) + q.file.close() + self.init_internals() + + app = _QApplication.instance() + app.closeAllWindows() + app.quit() + + + + def updateParams(self): + """ Update Mosaic object parameters """ + self.data.parameters['StartC'] = self.ui.spinBoxStartCol.value() + self.data.parameters['StartR'] = self.ui.spinBoxStartRow.value() + self.data.parameters['EndC'] = -1*self.ui.spinBoxEndCol.value() + self.data.parameters['EndR'] = -1*self.ui.spinBoxEndRow.value() + self.data.parameters['Transpose'] = self.ui.checkBoxTranspose.isChecked() + self.data.parameters['FlipVertical'] = self.ui.checkBoxFlipV.isChecked() + self.data.parameters['FlipHorizontally'] = self.ui.checkBoxFlipH.isChecked() + self.data.parameters['Compress'] = self.ui.checkBoxCompress.isChecked() + self.data.parameters['Shape'] = [self.ui.spinBoxMRows.value(), self.ui.spinBoxNCols.value()] + + idx = self.ui.comboBoxRowCol.currentIndex() + if idx == 0: + self.data.parameters['Order'] = 'R' + else: + self.data.parameters['Order'] = 'C' + + mrows = self.ui.spinBoxMRows.value() + ncols = self.ui.spinBoxNCols.value() + n_dsets = len(self.data_list) + + if (mrows * ncols) < n_dsets: + mrows = int(_np.ceil(n_dsets / ncols)) + + self.ui.spinBoxMRows.setValue(mrows) + self.ui.spinBoxNCols.setValue(ncols) + + self.data.parameters['Shape'] = [mrows, ncols] + + if self.data._data: + self.updateMosaicImage() + + def save(self): + + if self.data.parameters['Compress']: + msg = _QMessageBox(self) + msg.setIcon(_QMessageBox.Information) + str1 = 'Currently, HDF5-saving with compression is not supported. Saving full data.' + msg.setText(str1) + msg.setWindowTitle('Compression not supported.') + msg.setStandardButtons(_QMessageBox.Ok) + msg.setDefaultButton(_QMessageBox.Ok) + msg.exec() + + ret = DialogSave.dialogSave(parent=self, + current_filename='MOSAIC_' + self.last_fname, + current_path=self.last_path, + current_dataset_name=self.last_dsetname, + suffix='') + if ret is None: + pass # Save canceled + else: + save_filename = ret[0] + save_path = ret[1] + save_dataset_name = ret[2] + + save_grp = save_dataset_name.rpartition('/')[0] + save_dataset_name_no_grp = save_dataset_name.rpartition('/')[-1] + save_dataset_mask = save_grp + '/' + 'MASK_' + save_dataset_name_no_grp + mask = self.data.mosaic_mask() + + new_attrs = OrderedDict() + new_attrs.update(self.data.attr_dict()) + + if self.imported_calib_vec: + new_attrs.update({'Calib.a_vec':self.imported_calib_vec[0], + 'Calib.ctr_wl':self.imported_calib_vec[1], + 'Calib.ctr_wl0':self.imported_calib_vec[2], + 'Calib.n_pix':self.imported_calib_vec[3], + 'Calib.probe':self.imported_calib_vec[4], + 'Calib.units':'nm'}) + + if self.imported_spatial_vec: + temp = self.data.mosaic_shape() + x_stepsize = self.imported_spatial_vec[0] + y_stepsize = self.imported_spatial_vec[0] + x_start = 0 + y_start = 0 + x_stop = (temp[1]-1)*x_stepsize + y_stop = (temp[0]-1)*y_stepsize + x_steps = temp[1] + y_steps = temp[0] + + # ['Raster.Fast.Start', 'Raster.Fast.Stop', 'Raster.Fast.Steps', + # 'Raster.Slow.Start', 'Raster.Slow.Stop', 'Raster.Slow.Steps'] + new_attrs.update({'Raster.Fast.StepSize':x_stepsize, 'Raster.Fast.Steps':x_steps, + 'Raster.Fast.Start':x_start, 'Raster.Fast.Stop':x_stop, + 'Raster.Slow.StepSize':y_stepsize, 'Raster.Slow.Steps':y_steps, + 'Raster.Slow.Start':y_start, 'Raster.Slow.Stop':y_stop}) + + for num, q in enumerate(self.data._data): + curr_shape = [(mask == num).sum(axis=0).max(), (mask == num).sum(axis=1).max()] + new_attrs.update({'Mosaic.shape.{}'.format(num):curr_shape}) + new_attrs.update({'Mosaic.path.{}'.format(num):self.data_list[num][0]}) + new_attrs.update({'Mosaic.filename.{}'.format(num):self.data_list[num][1]}) + new_attrs.update({'Mosaic.datasetname.{}'.format(num):self.data_list[num][2]}) + if hasattr(q, 'attrs'): + orig_attrs = lazy5.inspect.get_attrs_dset(q.file, q.name) + for k in orig_attrs: + new_attrs.update({'Mosaic.{}.{}'.format(num, k):orig_attrs[k]}) + + # try: + fid = h5py.File(_os.path.join(save_path, save_filename), 'a') + fid.require_group(save_grp) + fid.create_dataset(save_dataset_name, shape=self.data.mosaic_shape(), + dtype=self.data.dtype, chunks=True) + self.data.mosaicfull(out=fid[save_dataset_name]) + lazy5.alter.write_attr_dict(fid[save_dataset_name], new_attrs) + fid.close() + + lazy5.create.save(save_filename, save_dataset_mask, self.data.mosaic_mask(), + pth=save_path, attr_dict=new_attrs) + +if __name__ == '__main__': + app = _QApplication(_sys.argv) + app.setStyle('Cleanlooks') + app.setQuitOnLastWindowClosed(True) + + win = MainWindowMosaic(parent=None) + win.show() + app.exec_() + + + + print(win) + + _sys.exit() \ No newline at end of file diff --git a/crikit/ui/old/dialog_plugin (2).py b/crikit/ui/old/dialog_plugin (2).py deleted file mode 100644 index 6349333..0000000 --- a/crikit/ui/old/dialog_plugin (2).py +++ /dev/null @@ -1,254 +0,0 @@ -""" -Created on Tue Feb 16 15:51:32 2016 - -@author: camp -""" - -import sys as _sys -import os as _os - -# Generic imports for QT-based programs -from PyQt5.QtWidgets import (QApplication as _QApplication, - QWidget as _QWidget, QDialog as _QDialog, - QMainWindow as _QMainWindow, - QSizePolicy as _QSizePolicy) -import PyQt5.QtCore as _QtCore - -# Other imports -import numpy as _np - -from yapsy.PluginManager import (PluginManager as _PluginManager, - PluginInfo as _PluginInfo) - -from crikit.ui.helper_plugin_categories import DeNoiser, ErrorCorrect -#import logging -#logging.basicConfig(level=logging.DEBUG) - -# Import from Designer-based GUI -from crikit.ui.qt_PluginSelector import Ui_Dialog - - -# Generic imports for MPL-incorporation -import matplotlib as _mpl -_mpl.use('Qt5Agg') -_mpl.rcParams['font.family'] = 'sans-serif' -_mpl.rcParams['font.size'] = 10 -#import matplotlib.pyplot as plt - -#from matplotlib.backends.backend_qt5agg import (FigureCanvasQTAgg as _FigureCanvas, \ -# NavigationToolbar2QT as _NavigationToolbar) - -#from matplotlib.figure import Figure as _Figure - -class DialogDenoisePlugins(_QDialog): - """ - DialogDenoisePlugins : Denoise plugin selector - - Methods - -------- - dialogDenoisePlugins : Used to call UI and retrieve results of dialog - - References - ---------- - [1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \ - Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \ - Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543. - - """ - - def __init__(self, parent = None): - super(DialogDenoisePlugins, self).__init__(parent) ### EDIT ### - self.ui = Ui_Dialog() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - self.temp = 0 - - # Create plugin manager - self.manager = _PluginManager() - - - if _os.path.isdir(_os.path.abspath('./plugins')): - plugins_loc = 'plugins' - elif _os.path.isdir(_os.path.abspath('./crikit/ui/plugins')): - plugins_loc = './crikit/ui/plugins' - elif _os.path.isdir(_os.path.abspath('./ui/plugins')): - plugins_loc = './ui/plugins' - else: - plugins_loc = None - - self.manager.setPluginPlaces([plugins_loc]) - self.manager.setCategoriesFilter({'DeNoiser' : DeNoiser}) - - self.manager.collectPlugins() - - # Load plugins - self.manager.locatePlugins() - - self.manager.loadPlugins() - self.denoisers = {} - self.denoiser_desc = {} - - for plugin in self.manager.getPluginsOfCategory('DeNoiser'): - self.ui.comboBox.addItem(plugin.plugin_object.name) - self.denoisers[plugin.plugin_object.name] = plugin.plugin_object - self.denoiser_desc[plugin.plugin_object.name] = plugin._PluginInfo__details['Documentation']['description'] - - #print(self.denoiser_desc[self.ui.comboBox.currentText]) - self.ui.plainTextEditDescription.setPlainText(self.denoiser_desc[self.ui.comboBox.currentText()]) - self.ui.comboBox.currentIndexChanged.connect(self.changeDesc) - - def changeDesc(self): - self.ui.plainTextEditDescription.setPlainText(self.denoiser_desc[self.ui.comboBox.currentText()]) - - @staticmethod - def dialogDenoisePlugins(parent = None): - """ - - """ - - dialog = DialogDenoisePlugins(parent) - - result = dialog.exec_() - - - if result == 1: # Accepted - return (dialog.denoisers[dialog.ui.comboBox.currentText()]) - else: # Rejected/Cancel - return None - -class DialogErrCorrPlugins(_QDialog): - """ - DialogErrCorrPlugins : Error correction plugin selector - - Methods - ------- - dialogErrCorrPlugins : Used to call UI and retrieve results of dialog - - References - ---------- - [1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \ - Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \ - Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543. - - """ - - def __init__(self, parent = None): - super(DialogErrCorrPlugins, self).__init__(parent) ### EDIT ### - self.ui = Ui_Dialog() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - self.temp = 0 - - # Create plugin manager - self.manager = _PluginManager() - - - if _os.path.isdir(_os.path.abspath('./plugins')): - plugins_loc = 'plugins' - elif _os.path.isdir(_os.path.abspath('./crikit/ui/plugins')): - plugins_loc = './crikit/ui/plugins' - elif _os.path.isdir(_os.path.abspath('./ui/plugins')): - plugins_loc = './ui/plugins' - else: - plugins_loc = None - - self.manager.setPluginPlaces([plugins_loc]) - self.manager.setCategoriesFilter({'ErrorCorrect' : ErrorCorrect}) - - self.manager.collectPlugins() - - # Load plugins - self.manager.locatePlugins() - - self.manager.loadPlugins() - self.errcorrectors = {} - self.errcorrectors_desc = {} - - for plugin in self.manager.getPluginsOfCategory('ErrorCorrect'): - self.ui.comboBox.addItem(plugin.plugin_object.name) - self.errcorrectors[plugin.plugin_object.name] = plugin.plugin_object - self.errcorrectors_desc[plugin.plugin_object.name] = plugin._PluginInfo__details['Documentation']['description'] - - self.ui.comboBox.currentIndexChanged.connect(self.changeDesc) - - try: - self.ui.plainTextEditDescription.setPlainText(self.errcorrectors_desc[self.ui.comboBox.currentText()]) - - except: # Fails if no plugins found - pass - - def changeDesc(self): - - try: - self.ui.plainTextEditDescription.setPlainText(self.errcorrectors_desc[self.ui.comboBox.currentText()]) - except: # Fails if no plugins found - pass - - @staticmethod - def dialogErrCorrPlugins(parent = None): - """ - - """ - - dialog = DialogErrCorrPlugins(parent) - - result = dialog.exec_() - - - if result == 1: # Accepted - return (dialog.errcorrectors[dialog.ui.comboBox.currentText()]) - else: # Rejected/Cancel - return None - - -if __name__ == '__main__': - - -# from crikit.data.classes import HSData -# - x = _np.linspace(100,200,50) - y = _np.linspace(200,300,50) - f = _np.linspace(500,3000,800) - Ex = 30*_np.exp((-(f-1750)**2/(200**2))) - Spectrum = _np.convolve(_np.flipud(Ex),Ex,mode='same') - - data = _np.zeros((y.size,x.size,f.size)) - for count in range(y.size): - data[count,:,:] = y[count]*_np.random.poisson(_np.dot(x[:,None],Spectrum[None,:])) - - #temp = HSData() - #temp.spectrafull = data - - app = _QApplication(_sys.argv) - app.setStyle('Cleanlooks') - - ### DeNoise Demo - win = DialogDenoisePlugins.dialogDenoisePlugins() - - if win is not None: - retwin = win.denoiseHSData(data) - print('RetWin:{}'.format(retwin)) - -# ### Error Correction Demo -# win = DialogErrCorrPlugins.dialogErrCorrPlugins() -# -## temp = HSData() -# -# WN = _np.linspace(500,4000,1000) -# -# CARS = _np.zeros((20,20,WN.size), dtype=complex) -# CARS[:,:,:] = (1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055) -# temp.spectrafull = CARS -# temp.freqvecfull = WN -# -# -# NRB = 0*WN + .055 -# -# if win is not None: -# retwin = win.errorCorrectHSData(data) -# #if win is not None: -# #retwin = win.denoiseHSData(temp) -# #print('RetWin:{}'.format(retwin)) -# -# _sys.exit() - app.exec_() \ No newline at end of file diff --git a/crikit/ui/old/helper_plugin_categories.py b/crikit/ui/old/helper_plugin_categories.py deleted file mode 100644 index 47f15ad..0000000 --- a/crikit/ui/old/helper_plugin_categories.py +++ /dev/null @@ -1,26 +0,0 @@ -""" -Created on Tue Feb 16 16:07:39 2016 - -@author: camp -""" - -class DeNoiser(object): - """ - Plugins of this class denoise hyperspectral data (crikit.data.HSData) - """ - - name = 'Do Nothing' - - def denoiseHSData(self, hsdatacls): - return 1 - -class ErrorCorrect(object): - """ - Plugins of this class perform error correction (phase, baseline, etc) on - hyperspectral data - """ - - name = 'Do Nothing' - - def errorCorrectHSData(self, hsdatacls): - return 1 \ No newline at end of file diff --git a/crikit/ui/old/plugins/__init__.py b/crikit/ui/old/plugins/__init__.py deleted file mode 100644 index c745558..0000000 --- a/crikit/ui/old/plugins/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -""" -CRIkit User Interfaces (crikit.ui) -======================================================= - -""" diff --git a/crikit/ui/old/plugins/denoise_Anscombe_SVD.py b/crikit/ui/old/plugins/denoise_Anscombe_SVD.py deleted file mode 100644 index aaddf0f..0000000 --- a/crikit/ui/old/plugins/denoise_Anscombe_SVD.py +++ /dev/null @@ -1,37 +0,0 @@ -""" -Created on Mon Feb 22 15:27:50 2016 - -@author: chc -""" - -from crikit.ui.helper_plugin_categories import DeNoiser -import crikit.ui.subui_SVD -from crikit.process.varstabilize import gen_anscombe_forward -from crikit.process.varstabilize import gen_anscombe_inverse_exact_unbiased - -from crikit.ui.dialog_options import DialogAnscombeOptions - -import copy as _copy - -class DeNoiseSVD(DeNoiser): - name = 'Anscombe SVD' - - def denoiseHSData(self, hsdatacls): - data = _copy.deepcopy(hsdatacls.spectra) - result = DialogAnscombeOptions.dialogAnscombeOptions() - if result[0] is not None: - stddev = result[0] - gain = result[1] - data = gen_anscombe_forward(data, gauss_std=stddev, poisson_multi=gain) - ret = crikit.ui.subui_SVD.DialogSVD.dialogSVD(data=data) - if ret is None: - return None - else: - data = gen_anscombe_inverse_exact_unbiased(ret[0], gauss_std=stddev, poisson_multi=gain) - hsdatacls.spectra = data - ret[1][0] = 'AnscSVD' - return ret[1] - else: - return None - - diff --git a/crikit/ui/old/plugins/denoise_Anscombe_SVD.yapsy-plugin b/crikit/ui/old/plugins/denoise_Anscombe_SVD.yapsy-plugin deleted file mode 100644 index 726b2b5..0000000 --- a/crikit/ui/old/plugins/denoise_Anscombe_SVD.yapsy-plugin +++ /dev/null @@ -1,8 +0,0 @@ -[Core] -Name = Anscombe SVD -Module = denoise_Anscombe_SVD - -[Documentation] -Author = Charles H. Camp Jr. -Version = 16.02.22 -Description = Anscombe-Transformed Singular Value Decomposition diff --git a/crikit/ui/old/plugins/denoise_SVD.py b/crikit/ui/old/plugins/denoise_SVD.py deleted file mode 100644 index 6845945..0000000 --- a/crikit/ui/old/plugins/denoise_SVD.py +++ /dev/null @@ -1,19 +0,0 @@ -""" -Created on Tue Feb 16 17:23:25 2016 - -@author: camp -""" -from crikit.ui.helper_plugin_categories import DeNoiser -import crikit.ui.subui_SVD - -class DeNoiseSVD(DeNoiser): - name = 'SVD' - - def denoiseHSData(self, hsdatacls): - ret = crikit.ui.subui_SVD.DialogSVD.dialogSVD(data=hsdatacls.spectra) - if ret is None: - return None - else: - hsdatacls.spectra = ret[0] - return ret[1] - diff --git a/crikit/ui/old/plugins/denoise_SVD.yapsy-plugin b/crikit/ui/old/plugins/denoise_SVD.yapsy-plugin deleted file mode 100644 index dee4653..0000000 --- a/crikit/ui/old/plugins/denoise_SVD.yapsy-plugin +++ /dev/null @@ -1,8 +0,0 @@ -[Core] -Name = SVD -Module = denoise_SVD - -[Documentation] -Author = Charles H. Camp Jr. -Version = 16.02.16 -Description = Singular Value Decomposition diff --git a/crikit/ui/old/plugins/errcorrect_amp_ALS.py b/crikit/ui/old/plugins/errcorrect_amp_ALS.py deleted file mode 100644 index 31cd847..0000000 --- a/crikit/ui/old/plugins/errcorrect_amp_ALS.py +++ /dev/null @@ -1,78 +0,0 @@ -""" -Created on Tue Mar 2 2016 - -@author: chc -""" - -from crikit.ui.helper_plugin_categories import ErrorCorrect -from crikit.ui.subui_ploteffect import DialogPlotEffect -from crikit.ui.widget_ploteffect import widgetALS - -from crikit.process.maths.als_methods import als_baseline_redux as _als -from crikit.process.maths.kk import hilbertfft as _hilbert - -import numpy as _np -import numexpr as _ne -import timeit as _ti -#import copy as _copy - -class ErrCorrectAmpALS(ErrorCorrect): - name = 'Amp Error: ALS' - - def errorCorrectHSData(self, hsdatacls): - temp_spectra = hsdatacls._get_rand_spectra(10, pt_sz=3, quads=True) - - plugin = widgetALS() - - result = DialogPlotEffect.dialogPlotEffect(temp_spectra, x=hsdatacls.freqvec, - plugin=plugin, xlabel='Wavenumber (cm$^{-1}$)', - ylabel='Imag. {$\chi_R$} (au)', show_difference=True) - if result is not None: - p = result.p - lam = result.lam - redux = result.redux - - data_out = _np.zeros(hsdatacls.spectra.shape, dtype=hsdatacls.spectrafull.dtype) - - detrend_ct = 0 - detrend_tot = hsdatacls.mlen * hsdatacls.nlen - - for count_col in _np.arange(0, hsdatacls.nlen): - start = _ti.default_timer() - for count_row in _np.arange(0, hsdatacls.mlen): -# start2 = _ti.default_timer() - - # Most efficient system - if len(hsdatacls.pixrange) != 0: - sig = hsdatacls.spectrafull[count_row, count_col, hsdatacls.pixrange[0]:hsdatacls.pixrange[1]+1] - else: - sig = hsdatacls.spectrafull[count_row, count_col,:] - - # MUCH LESS EFFICIENT - #ph = hsdatacls.spectraphase[count_row, count_col,:] - -# stop2 = _ti.default_timer() - -# start3 = _ti.default_timer() - if isinstance(sig, complex): - err_amp, als_type = _als(sig.imag, redux_factor=redux, redux_full=False, - smoothness_param=lam, asym_param=p, print_iteration=False) - data_out[count_row, count_col, :] = hsdatacls.spectracomplex[count_row, count_col, :] - 1j*err_amp - else: - err_amp, als_type = _als(sig, redux_factor=redux, redux_full=False, - smoothness_param=lam, asym_param=p, print_iteration=False) - data_out[count_row, count_col, :] = hsdatacls.spectracomplex[count_row, count_col, :] - err_amp - - detrend_ct += 1 - stop = _ti.default_timer() -# print('2: {}'.format(stop2-start2)) -# print('3: {}'.format(stop3-start3)) -# print('4: {}'.format(stop4-start4)) -# print('5: {}'.format(stop5-start5)) -# - print('Detrended {} / {} ({:.5f} sec/spect)'.format(detrend_ct, detrend_tot, (stop-start)/hsdatacls.mlen )) - - hsdatacls.spectra = data_out - return ['AmpErrorCorect','Type', 'ALS', 'p', p, 'lambda', lam, 'redux', redux, 'alg', als_type] - else: - return None \ No newline at end of file diff --git a/crikit/ui/old/plugins/errcorrect_amp_ALS.yapsy-plugin b/crikit/ui/old/plugins/errcorrect_amp_ALS.yapsy-plugin deleted file mode 100644 index 68a24e9..0000000 --- a/crikit/ui/old/plugins/errcorrect_amp_ALS.yapsy-plugin +++ /dev/null @@ -1,9 +0,0 @@ -[Core] -Name = Amp Error: ALS -Module = errcorrect_amp_ALS - -[Documentation] -Author = Charles H. Camp Jr. -Version = 16.03.02 -Description = Amplitude error correction with alternating least squares. If complex, performed on imag component. - diff --git a/crikit/ui/old/plugins/errcorrect_phase_ALS.py b/crikit/ui/old/plugins/errcorrect_phase_ALS.py deleted file mode 100644 index 680fbf0..0000000 --- a/crikit/ui/old/plugins/errcorrect_phase_ALS.py +++ /dev/null @@ -1,87 +0,0 @@ -""" -Created on Tue Mar 1 11:12:12 2016 - -@author: chc -""" - -from crikit.ui.helper_plugin_categories import ErrorCorrect -from crikit.ui.subui_ploteffect import DialogPlotEffect -from crikit.ui.widget_ploteffect import widgetALS - -from crikit.process.maths.als_methods import als_baseline_redux as _als -from crikit.process.maths.kk import hilbertfft as _hilbert - -import numpy as _np -import numexpr as _ne -import timeit as _ti -#import copy as _copy - -class ErrCorrectPhaseALS(ErrorCorrect): - name = 'Phase Error: ALS' - - def errorCorrectHSData(self, hsdatacls): - temp_spectra = hsdatacls._get_rand_spectra_phase(10, pt_sz=3, quads=True) - - plugin = widgetALS() - - result = DialogPlotEffect.dialogPlotEffect(temp_spectra, x=hsdatacls.freqvec, - plugin=plugin, xlabel='Wavenumber (cm$^{-1}$)', - ylabel='Imag. {$\chi_R$} (au)', show_difference=True) - if result is not None: - p = result.p - lam = result.lam - redux = result.redux - - data_out = _np.zeros(hsdatacls.spectra.shape, dtype=complex) - - detrend_ct = 0 - detrend_tot = hsdatacls.mlen * hsdatacls.nlen - - for count_col in _np.arange(0, hsdatacls.nlen): - start = _ti.default_timer() - for count_row in _np.arange(0, hsdatacls.mlen): -# start2 = _ti.default_timer() - - # Most efficient system - if len(hsdatacls.pixrange) != 0: - ph = _np.angle(hsdatacls.spectrafull[count_row, count_col, hsdatacls.pixrange[0]:hsdatacls.pixrange[1]+1]) - else: - ph = _np.angle(hsdatacls.spectrafull[count_row, count_col,:]) - - # MUCH LESS EFFICIENT - #ph = hsdatacls.spectraphase[count_row, count_col,:] - -# stop2 = _ti.default_timer() - -# start3 = _ti.default_timer() - err_phase, als_type = _als(ph, redux_factor=redux, redux_full=False, - smoothness_param=lam, asym_param=p, print_iteration=False) -# stop3 = _ti.default_timer() - -# start4 = _ti.default_timer() - h = _hilbert(err_phase) -# stop4 = _ti.default_timer() - #err_amp = _np.exp(_hilbert(err_phase).imag) - #err_amp = _ne.evaluate('exp(imag(h))') - #correction_factor = 1/err_amp * _np.exp(-1j*err_phase) - -# start5 = _ti.default_timer() - correction_factor = _ne.evaluate('1/exp(imag(h)) * exp(-1j*err_phase)') -# stop5 = _ti.default_timer() - - - data_out[count_row, count_col, :] = hsdatacls.spectracomplex[count_row, count_col, :]*correction_factor - - detrend_ct += 1 - stop = _ti.default_timer() -# print('2: {}'.format(stop2-start2)) -# print('3: {}'.format(stop3-start3)) -# print('4: {}'.format(stop4-start4)) -# print('5: {}'.format(stop5-start5)) -# - print('Detrended {} / {} ({:.5f} sec/spect)'.format(detrend_ct, detrend_tot, (stop-start)/hsdatacls.mlen )) - - hsdatacls.spectra = data_out - return ['PhaseErrorCorect','Type', 'ALS', 'p', p, 'lambda', lam, 'redux', redux, 'alg', als_type] - else: - return None \ No newline at end of file diff --git a/crikit/ui/old/plugins/errcorrect_phase_ALS.yapsy-plugin b/crikit/ui/old/plugins/errcorrect_phase_ALS.yapsy-plugin deleted file mode 100644 index 22b918e..0000000 --- a/crikit/ui/old/plugins/errcorrect_phase_ALS.yapsy-plugin +++ /dev/null @@ -1,8 +0,0 @@ -[Core] -Name = Phase Error: ALS -Module = errcorrect_phase_ALS - -[Documentation] -Author = Charles H. Camp Jr. -Version = 16.03.01 -Description = Phase error correction with alternating least squares diff --git a/crikit/ui/old/plugins/errcorrect_scale_SG.py b/crikit/ui/old/plugins/errcorrect_scale_SG.py deleted file mode 100644 index 436eae3..0000000 --- a/crikit/ui/old/plugins/errcorrect_scale_SG.py +++ /dev/null @@ -1,63 +0,0 @@ -""" -Created on Wed Mar 2 12:39:53 2016 - -@author: chc -""" - -from crikit.ui.helper_plugin_categories import ErrorCorrect -from crikit.ui.subui_ploteffect import DialogPlotEffect -from crikit.ui.widget_ploteffect import widgetSG - -from crikit.process.maths.als_methods import als_baseline_redux as _als -from crikit.process.maths.kk import hilbertfft as _hilbert - -import numpy as _np -import numexpr as _ne -import timeit as _ti -#import scipy as _scipy -from scipy.signal import savgol_filter as _sg -#import copy as _copy - -class ErrCorrectScaleSG(ErrorCorrect): - name = 'Scaling: Savitky-Golay' - - def errorCorrectHSData(self, hsdatacls): - temp_spectra = hsdatacls._get_rand_spectra_real(10, pt_sz=3, quads=True) - - plugin = widgetSG() - - result = DialogPlotEffect.dialogPlotEffect(temp_spectra, x=hsdatacls.freqvec, - plugin=plugin, xlabel='Wavenumber (cm$^{-1}$)', - ylabel='Real {$\chi_R$} (au)', show_difference=True) - if result is not None: - win_size = result.win_size - order = result.order - - - detrend_ct = 0 - detrend_tot = hsdatacls.mlen * hsdatacls.nlen - - # Most efficient system - if len(hsdatacls.pixrange) != 0: - data_out = hsdatacls.spectrafull[:,:, hsdatacls.pixrange[0]:hsdatacls.pixrange[1]+1] - else: - data_out = hsdatacls.spectrafull - - start = _ti.default_timer() - - correction = (1/_sg(data_out.real, window_length=win_size, polyorder=order, axis=-1)) - - data_out = data_out*correction - - stop = _ti.default_timer() -# print('2: {}'.format(stop2-start2)) -# print('3: {}'.format(stop3-start3)) -# print('4: {}'.format(stop4-start4)) -# print('5: {}'.format(stop5-start5)) -# - print('Scaled {} spectra ({:.5f} sec/spect)'.format(detrend_tot, (stop-start)/(hsdatacls.mlen*hsdatacls.nlen))) - - hsdatacls.spectra = data_out - return ['Scaling','Type', 'SG', 'win_size', win_size, 'order', order] - else: - return None \ No newline at end of file diff --git a/crikit/ui/old/plugins/errcorrect_scale_SG.yapsy-plugin b/crikit/ui/old/plugins/errcorrect_scale_SG.yapsy-plugin deleted file mode 100644 index 8989d4e..0000000 --- a/crikit/ui/old/plugins/errcorrect_scale_SG.yapsy-plugin +++ /dev/null @@ -1,9 +0,0 @@ -[Core] -Name = Scaling: SG -Module = errcorrect_scale_SG - -[Documentation] -Author = Charles H. Camp Jr. -Version = 16.03.02 -Description = Scaling determined and applied by a Savitky-Golay filter. - diff --git a/crikit/ui/old/qt_PluginSelector.py b/crikit/ui/old/qt_PluginSelector.py deleted file mode 100644 index cc32f3f..0000000 --- a/crikit/ui/old/qt_PluginSelector.py +++ /dev/null @@ -1,59 +0,0 @@ -# -*- coding: utf-8 -*- - -# Form implementation generated from reading ui file 'ui_PluginSelector.ui' -# -# Created by: PyQt5 UI code generator 5.5.1 -# -# WARNING! All changes made in this file will be lost! - -from PyQt5 import QtCore, QtGui, QtWidgets - -class Ui_Dialog(object): - def setupUi(self, Dialog): - Dialog.setObjectName("Dialog") - Dialog.resize(389, 239) - Dialog.setStyleSheet("font: 10pt \"Arial\";") - self.gridLayout = QtWidgets.QGridLayout(Dialog) - self.gridLayout.setObjectName("gridLayout") - self.buttonBox = QtWidgets.QDialogButtonBox(Dialog) - self.buttonBox.setOrientation(QtCore.Qt.Horizontal) - self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok) - self.buttonBox.setObjectName("buttonBox") - self.gridLayout.addWidget(self.buttonBox, 1, 0, 1, 1) - self.verticalLayout = QtWidgets.QVBoxLayout() - self.verticalLayout.setObjectName("verticalLayout") - self.label = QtWidgets.QLabel(Dialog) - font = QtGui.QFont() - font.setFamily("Arial") - font.setPointSize(10) - font.setItalic(False) - self.label.setFont(font) - self.label.setObjectName("label") - self.verticalLayout.addWidget(self.label, 0, QtCore.Qt.AlignTop) - self.comboBox = QtWidgets.QComboBox(Dialog) - self.comboBox.setObjectName("comboBox") - self.verticalLayout.addWidget(self.comboBox) - spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) - self.verticalLayout.addItem(spacerItem) - spacerItem1 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) - self.verticalLayout.addItem(spacerItem1) - self.label_2 = QtWidgets.QLabel(Dialog) - self.label_2.setObjectName("label_2") - self.verticalLayout.addWidget(self.label_2) - self.plainTextEditDescription = QtWidgets.QPlainTextEdit(Dialog) - self.plainTextEditDescription.setReadOnly(True) - self.plainTextEditDescription.setObjectName("plainTextEditDescription") - self.verticalLayout.addWidget(self.plainTextEditDescription) - self.gridLayout.addLayout(self.verticalLayout, 0, 0, 1, 1) - - self.retranslateUi(Dialog) - self.buttonBox.accepted.connect(Dialog.accept) - self.buttonBox.rejected.connect(Dialog.reject) - QtCore.QMetaObject.connectSlotsByName(Dialog) - - def retranslateUi(self, Dialog): - _translate = QtCore.QCoreApplication.translate - Dialog.setWindowTitle(_translate("Dialog", "Plugin Selector")) - self.label.setText(_translate("Dialog", "Plugin")) - self.label_2.setText(_translate("Dialog", "Description")) - diff --git a/crikit/ui/qt5/ui_BlankLayout.ui b/crikit/ui/qt5/ui_BlankLayout.ui index 8936f23..2c45408 100644 --- a/crikit/ui/qt5/ui_BlankLayout.ui +++ b/crikit/ui/qt5/ui_BlankLayout.ui @@ -6,8 +6,8 @@ 0 0 - 802 - 1128 + 600 + 54 @@ -17,8 +17,24 @@ - 2 + 10 + + + 10 + + + 10 + + + 10 + + 10 + + + + + 2 @@ -34,7 +50,17 @@ - + + + Qt::Vertical + + + + 20 + 40 + + + diff --git a/crikit/ui/qt5/ui_CRIkit.ui b/crikit/ui/qt5/ui_CRIkit.ui index 7dcbc4d..aa509d6 100644 --- a/crikit/ui/qt5/ui_CRIkit.ui +++ b/crikit/ui/qt5/ui_CRIkit.ui @@ -6,8 +6,8 @@ 0 0 - 1691 - 905 + 1200 + 800 @@ -152,7 +152,55 @@ - + + + History + + + + + + QAbstractItemView::NoEditTriggers + + + 0 + + + 2 + + + false + + + 200 + + + true + + + false + + + false + + + 37 + + + + Process Attributes + + + + + Value + + + + + + + Notes @@ -347,8 +395,8 @@ This will be saved to the processed file. 0 0 - 1691 - 22 + 1200 + 19 @@ -359,6 +407,10 @@ This will be saved to the processed file. + + + + @@ -473,6 +525,11 @@ This will be saved to the processed file. + + + + + @@ -483,6 +540,8 @@ This will be saved to the processed file. Settings + + @@ -493,6 +552,12 @@ This will be saved to the processed file. + + + NIST Special + + + @@ -500,6 +565,7 @@ This will be saved to the processed file. + @@ -1044,29 +1110,61 @@ This will be saved to the processed file. + + + :/icons/open-iconic-master/png/account-login-4x.png:/icons/open-iconic-master/png/account-login-4x.png + - Load NRB (HDF; Left-Side) + Load NRB (HDF; Left) + + + Load NRB (HDF; Left) + + + :/icons/open-iconic-master/png/account-login-4x.png:/icons/open-iconic-master/png/account-login-4x.png + - Load NRB (HDF; Right-Side) + Load NRB (HDF; Right) + + + Load NRB (HDF; Right) + + + :/icons/open-iconic-master/png/globe-4x.png:/icons/open-iconic-master/png/globe-4x.png + - NRB from ROI (Left-Side) + NRB from ROI (Left) + + + NRB from ROI (Left) + + + :/icons/open-iconic-master/png/globe-4x.png:/icons/open-iconic-master/png/globe-4x.png + - NRB from ROI (Right-Side) + NRB from ROI (Right) + + + NRB from ROI (Right) false + + + :/icons/open-iconic-master/png/wrench-4x.png:/icons/open-iconic-master/png/wrench-4x.png + Merge NRBs @@ -1157,6 +1255,90 @@ This will be saved to the processed file. BCARS Numerical Phantom + + + true + + + true + + + Use Preview ROI(s) + + + + + false + + + Set Preview ROI(s) + + + + + false + + + false + + + Delete Preview ROI(s) + + + + + true + + + Show Preview ROI(s) + + + + + true + + + Show Preview ROI Legend + + + + + false + + + + :/icons/open-iconic-master/png/compass-4x.png:/icons/open-iconic-master/png/compass-4x.png + + + Est. Calibration + + + + + + :/icons/open-iconic-master/png/grid-three-up-4x.png + + + + Create Mosaic + + + + + true + + + true + + + Use Imaginary if Exists + + + + + Open HDF OOC (NIST) + + diff --git a/crikit/ui/qt5/ui_CompositeColor.ui b/crikit/ui/qt5/ui_CompositeColor.ui index 9c0df3c..1a033c7 100644 --- a/crikit/ui/qt5/ui_CompositeColor.ui +++ b/crikit/ui/qt5/ui_CompositeColor.ui @@ -6,8 +6,8 @@ 0 0 - 767 - 594 + 600 + 100 @@ -128,6 +128,19 @@ + + + + Qt::Vertical + + + + 20 + 40 + + + + diff --git a/crikit/ui/qt5/ui_HDFLoad.ui b/crikit/ui/qt5/ui_HDFLoad.ui deleted file mode 100644 index f5abf36..0000000 --- a/crikit/ui/qt5/ui_HDFLoad.ui +++ /dev/null @@ -1,279 +0,0 @@ - - - Dialog - - - - 0 - 0 - 845 - 588 - - - - HDF File Inspector - - - font: 10pt "Arial"; - - - - - - QLayout::SetNoConstraint - - - - - QLayout::SetNoConstraint - - - - - - - Groups Containing Datasets - - - - - - - - - - Datasets - - - - - - - QAbstractItemView::DoubleClicked|QAbstractItemView::EditKeyPressed|QAbstractItemView::SelectedClicked - - - QAbstractItemView::ExtendedSelection - - - - - - - <html><head/><body><p><span style=" font-weight:600;">Include</span> Entires with Substring (separate by ',' [comma])</p></body></html> - - - - - - - - - - <html><head/><body><p><span style=" font-weight:600;">Exclude</span> Entires with Substring (separate by ',' [comma])</p></body></html> - - - - - - - - - - - - Filter List - - - - - - - Reset List - - - - - - - - - - - - - Current Selection - - - - - - - - 0 - 0 - - - - - 16777215 - 100 - - - - - - - - Atrribute Table - - - - - - - - - - true - - - 2 - - - true - - - 200 - - - false - - - true - - - true - - - false - - - false - - - - Attribute - - - - 10 - - - - - 121 - 121 - 121 - - - - - - 91 - 91 - 91 - - - - - - - Value - - - - 123 - 123 - 123 - - - - - - 91 - 91 - 91 - - - - - - - - - - Dataset Information (Memo) - - - - - - - - 0 - 0 - - - - - 16777215 - 100 - - - - - - - - - - - - 10 - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - OK - - - - - - - Cancel - - - - - - - - - - - - diff --git a/crikit/ui/qt5/ui_Mosaic.ui b/crikit/ui/qt5/ui_Mosaic.ui new file mode 100644 index 0000000..595c0fe --- /dev/null +++ b/crikit/ui/qt5/ui_Mosaic.ui @@ -0,0 +1,1185 @@ + + + MainWindow + + + + 0 + 0 + 1200 + 915 + + + + + 2000 + 16777215 + + + + Make Mosaic Dataset + + + Qt::ToolButtonTextUnderIcon + + + + + + + 0 + + + + + + 0 + 0 + + + + + 500 + 0 + + + + + 500 + 16777215 + + + + QFrame::StyledPanel + + + QFrame::Plain + + + + 3 + + + 3 + + + 3 + + + 3 + + + + + 1 + + + + + 0 + + + 0 + + + + + 0 + + + + + M Rows + + + + + + + + 50 + 0 + + + + + 50 + 16777215 + + + + 1 + + + + + + + + + + + N Cols + + + + + + + + 50 + 0 + + + + + 50 + 16777215 + + + + 1 + + + 300 + + + 1 + + + + + + + + + + + Qt::Vertical + + + + 20 + 15 + + + + + + + + Trim Row Start + + + + + + + + 50 + 0 + + + + + 50 + 16777215 + + + + 500 + + + + + + + Qt::Vertical + + + + 20 + 15 + + + + + + + + Trim Row End + + + + + + + + 50 + 0 + + + + + 50 + 16777215 + + + + 500 + + + + + + + Qt::Vertical + + + + 20 + 15 + + + + + + + + Trim Col Start + + + + + + + + 50 + 0 + + + + + 50 + 16777215 + + + + 500 + + + + + + + Qt::Vertical + + + + 20 + 15 + + + + + + + + Trim Col End + + + + + + + + 50 + 0 + + + + + 50 + 16777215 + + + + 500 + + + + + + + Compress + + + + + + + Qt::Vertical + + + + 20 + 5 + + + + + + + + Row / Column First + + + + + + + + 100 + 16777215 + + + + + Row + + + + + Column + + + + + + + + + 120 + 16777215 + + + + Flip Horizontally + + + + + + + + 110 + 16777215 + + + + Flip Vertically + + + + + + + + 110 + 16777215 + + + + Transpose + + + + + + + + + Order of Inputs (Drag to Move) + + + + + + + 2 + + + 0 + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + 50 + 16777215 + + + + + + + + :/icons/open-iconic-master/png/arrow-circle-top-4x.png:/icons/open-iconic-master/png/arrow-circle-top-4x.png + + + + + + + + 50 + 16777215 + + + + + + + + :/icons/open-iconic-master/png/arrow-circle-bottom-4x.png:/icons/open-iconic-master/png/arrow-circle-bottom-4x.png + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + 50 + 16777215 + + + + + + + + :/icons/open-iconic-master/png/minus-4x.png:/icons/open-iconic-master/png/minus-4x.png + + + + + + + + 50 + 16777215 + + + + + + + + :/icons/open-iconic-master/png/plus-4x.png:/icons/open-iconic-master/png/plus-4x.png + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + + 0 + 0 + + + + + 120 + 20 + + + + + 1000 + 20 + + + + Frequency Pixel + + + Qt::AutoText + + + Qt::AlignCenter + + + 0 + + + + + + + + 0 + 0 + + + + + 100 + 30 + + + + + 100 + 30 + + + + + Arial + 14 + 50 + false + false + + + + font: 14pt "Arial"; + + + + + + + true + + + + 100 + 30 + + + + + 100 + 30 + + + + + + + + + 198 + 198 + 198 + + + + + + + + + 198 + 198 + 198 + + + + + + + + + 240 + 240 + 240 + + + + + + + + + + + true + + + + + + + Estimated Frequency (cm-1) + + + + + + + + 200 + 30 + + + + 10 + + + Qt::Horizontal + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + QFrame::StyledPanel + + + QFrame::Plain + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + 500 + 0 + + + + + 500 + 16777215 + + + + 0 + + + + Spectral Calibration + + + + + + + 400 + 16777215 + + + + QFrame::StyledPanel + + + QFrame::Plain + + + + + + Wavelength Intercept (nm) + + + + + + + 10 + + + -100000000.000000000000000 + + + 100000000.000000000000000 + + + 832.551012000000014 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + Wavelength Slope (nm/pix) + + + + + + + 10 + + + -100000000.000000000000000 + + + 100000000.000000000000000 + + + -0.165956000000000 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + Probe Wavelength (nm) + + + + + + + 5 + + + -1000000000.000000000000000 + + + 1000000000.000000000000000 + + + 771.461000000000013 + + + + + + + Calibration Wavelength (nm) + + + + + + + 10 + + + -100000000.000000000000000 + + + 10000000.000000000000000 + + + 700.000000000000000 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + Current Center Wavelength (nm) + + + + + + + 10 + + + -100000000.000000000000000 + + + 10000000.000000000000000 + + + 700.000000000000000 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + false + + + + 10 + + + + Loaded from Data + + + + 20 + 20 + + + + true + + + + + + + + Spatial Calibration + + + + + + QFrame::StyledPanel + + + QFrame::Plain + + + + + + X Step Size (um) + + + + + + + false + + + false + + + QAbstractSpinBox::NoButtons + + + 10 + + + -1.000000000000000 + + + 1000000.000000000000000 + + + 0.100000000000000 + + + -1.000000000000000 + + + + + + + Y Step Size (um) + + + + + + + false + + + false + + + QAbstractSpinBox::NoButtons + + + 10 + + + -1.000000000000000 + + + 1000000.000000000000000 + + + 0.100000000000000 + + + -1.000000000000000 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + false + + + + 10 + + + + Loaded from Data + + + true + + + + + + + + + + + + + 0 + 0 + 1200 + 26 + + + + + File + + + + + + + + + + + + toolBar + + + TopToolBarArea + + + false + + + + + + + + + + :/icons/open-iconic-master/png/envelope-open-4x.png:/icons/open-iconic-master/png/envelope-open-4x.png + + + Add from HDF5 + + + Ctrl+O + + + + + + :/icons/open-iconic-master/png/envelope-closed-4x.png:/icons/open-iconic-master/png/envelope-closed-4x.png + + + Save to HDF5 + + + Ctrl+S + + + + + + :/icons/open-iconic-master/png/account-logout-4x.png + + + + Exit + + + + + + + + diff --git a/crikit/ui/qt5/ui_PlotEffect.ui b/crikit/ui/qt5/ui_PlotEffect.ui index 51c2c0f..6f97f1a 100644 --- a/crikit/ui/qt5/ui_PlotEffect.ui +++ b/crikit/ui/qt5/ui_PlotEffect.ui @@ -6,8 +6,8 @@ 0 0 - 640 - 977 + 650 + 200 diff --git a/crikit/ui/qt5/ui_PlotEffect_ALS.ui b/crikit/ui/qt5/ui_PlotEffect_ALS.ui index 9521f6a..cf1f947 100644 --- a/crikit/ui/qt5/ui_PlotEffect_ALS.ui +++ b/crikit/ui/qt5/ui_PlotEffect_ALS.ui @@ -6,7 +6,7 @@ 0 0 - 738 + 800 180 diff --git a/crikit/ui/qt5/ui_PlotEffect_ALS2.ui b/crikit/ui/qt5/ui_PlotEffect_ALS2.ui new file mode 100644 index 0000000..ec244ca --- /dev/null +++ b/crikit/ui/qt5/ui_PlotEffect_ALS2.ui @@ -0,0 +1,487 @@ + + + Form + + + + 0 + 0 + 800 + 282 + + + + Form + + + font: 10pt "Arial"; + + + + + + + 0 + 0 + + + + + 0 + 10 + + + + + 0 + 140 + + + + QFrame::Plain + + + Qt::ScrollBarAsNeeded + + + 0 + + + true + + + 80 + + + false + + + 20 + + + true + + + + Start X + + + + + End X + + + + + P (Asymmetry) Value + + + + + + + + QFrame::StyledPanel + + + QFrame::Plain + + + + 5 + + + 5 + + + 5 + + + 5 + + + + + + + Sub-Sampling Factor + + + + + + + 1 + + + 10000 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + + Arial + 10 + 50 + false + false + + + + Lambda (smoothness) + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + Fix End-Points + + + + + + + + 20 + 20 + + + + + + + true + + + + + + + + + + + + + 0 + 0 + + + + QFrame::StyledPanel + + + QFrame::Plain + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + + Define P (Asymmetry) + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + P Subsections + + + + + + + 5 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + + Fixed=P + + + + + + + QFrame::StyledPanel + + + QFrame::Plain + + + + 5 + + + 5 + + + 5 + + + 5 + + + + + 0 + + + 0 + + + + + Max Iterations + + + + + + + 1 + + + 1000000 + + + 100 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + Min Difference + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + QLayout::SetNoConstraint + + + + + 0 + + + 0 + + + + + 0 + + + + + Weighted (Subsections) + + + + + + + 5 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + Weight Value + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + + 0 + 0 + + + + + 0 + 70 + + + + + 0 + 65 + + + + 80 + + + true + + + + Start X + + + + + + + + + + + + diff --git a/crikit/ui/qt5/ui_PlotEffect_Calibrate.ui b/crikit/ui/qt5/ui_PlotEffect_Calibrate.ui index b61e8ac..50eed61 100644 --- a/crikit/ui/qt5/ui_PlotEffect_Calibrate.ui +++ b/crikit/ui/qt5/ui_PlotEffect_Calibrate.ui @@ -6,8 +6,8 @@ 0 0 - 643 - 415 + 800 + 300 diff --git a/crikit/ui/qt_BlankLayout.py b/crikit/ui/qt_BlankLayout.py index 449d4a2..df9c9cc 100644 --- a/crikit/ui/qt_BlankLayout.py +++ b/crikit/ui/qt_BlankLayout.py @@ -2,26 +2,30 @@ # Form implementation generated from reading ui file '.\ui_BlankLayout.ui' # -# Created by: PyQt5 UI code generator 5.8.1 +# Created by: PyQt5 UI code generator 5.12 # # WARNING! All changes made in this file will be lost! from PyQt5 import QtCore, QtGui, QtWidgets + class Ui_Form(object): def setupUi(self, Form): Form.setObjectName("Form") - Form.resize(802, 1128) + Form.resize(600, 54) self.verticalLayout_2 = QtWidgets.QVBoxLayout(Form) self.verticalLayout_2.setObjectName("verticalLayout_2") self.verticalLayout = QtWidgets.QVBoxLayout() - self.verticalLayout.setContentsMargins(2, 2, 2, 2) - self.verticalLayout.setSpacing(2) + self.verticalLayout.setContentsMargins(10, 10, 10, 10) + self.verticalLayout.setSpacing(10) self.verticalLayout.setObjectName("verticalLayout") self.verticalLayout_2.addLayout(self.verticalLayout) self.gridLayout = QtWidgets.QGridLayout() + self.gridLayout.setContentsMargins(2, 2, 2, 2) self.gridLayout.setObjectName("gridLayout") self.verticalLayout_2.addLayout(self.gridLayout) + spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_2.addItem(spacerItem) self.retranslateUi(Form) QtCore.QMetaObject.connectSlotsByName(Form) @@ -30,3 +34,4 @@ def retranslateUi(self, Form): _translate = QtCore.QCoreApplication.translate Form.setWindowTitle(_translate("Form", "Form")) + diff --git a/crikit/ui/qt_CRIkit.py b/crikit/ui/qt_CRIkit.py index fb4000f..b04ef61 100644 --- a/crikit/ui/qt_CRIkit.py +++ b/crikit/ui/qt_CRIkit.py @@ -2,16 +2,17 @@ # Form implementation generated from reading ui file '.\ui_CRIkit.ui' # -# Created by: PyQt5 UI code generator 5.8.1 +# Created by: PyQt5 UI code generator 5.12 # # WARNING! All changes made in this file will be lost! from PyQt5 import QtCore, QtGui, QtWidgets + class Ui_MainWindow(object): def setupUi(self, MainWindow): MainWindow.setObjectName("MainWindow") - MainWindow.resize(1691, 905) + MainWindow.resize(1200, 800) palette = QtGui.QPalette() brush = QtGui.QBrush(QtGui.QColor(240, 240, 240)) brush.setStyle(QtCore.Qt.SolidPattern) @@ -51,7 +52,6 @@ def setupUi(self, MainWindow): self.tab = QtWidgets.QWidget() self.tab.setObjectName("tab") self.gridLayout_3 = QtWidgets.QGridLayout(self.tab) - self.gridLayout_3.setContentsMargins(0, 0, 0, 0) self.gridLayout_3.setObjectName("gridLayout_3") self.sweeperVL = QtWidgets.QVBoxLayout() self.sweeperVL.setSizeConstraint(QtWidgets.QLayout.SetDefaultConstraint) @@ -63,7 +63,6 @@ def setupUi(self, MainWindow): self.tabCompositeLarge = QtWidgets.QWidget() self.tabCompositeLarge.setObjectName("tabCompositeLarge") self.gridLayout_4 = QtWidgets.QGridLayout(self.tabCompositeLarge) - self.gridLayout_4.setContentsMargins(0, 0, 0, 0) self.gridLayout_4.setObjectName("gridLayout_4") self.sweeperVL_2 = QtWidgets.QVBoxLayout() self.sweeperVL_2.setSizeConstraint(QtWidgets.QLayout.SetDefaultConstraint) @@ -75,24 +74,43 @@ def setupUi(self, MainWindow): self.tabSettings = QtWidgets.QWidget() self.tabSettings.setObjectName("tabSettings") self.gridLayout_6 = QtWidgets.QGridLayout(self.tabSettings) - self.gridLayout_6.setContentsMargins(0, 0, 0, 0) self.gridLayout_6.setObjectName("gridLayout_6") self.gridLayout_5 = QtWidgets.QGridLayout() self.gridLayout_5.setObjectName("gridLayout_5") self.gridLayout_6.addLayout(self.gridLayout_5, 0, 0, 1, 1) self.tabMain.addTab(self.tabSettings, "") - self.tab_3 = QtWidgets.QWidget() - self.tab_3.setObjectName("tab_3") - self.gridLayout_2 = QtWidgets.QGridLayout(self.tab_3) - self.gridLayout_2.setContentsMargins(0, 0, 0, 0) + self.tabHistory = QtWidgets.QWidget() + self.tabHistory.setObjectName("tabHistory") + self.verticalLayout_4 = QtWidgets.QVBoxLayout(self.tabHistory) + self.verticalLayout_4.setObjectName("verticalLayout_4") + self.tableWidgetHistory = QtWidgets.QTableWidget(self.tabHistory) + self.tableWidgetHistory.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) + self.tableWidgetHistory.setRowCount(0) + self.tableWidgetHistory.setColumnCount(2) + self.tableWidgetHistory.setObjectName("tableWidgetHistory") + item = QtWidgets.QTableWidgetItem() + self.tableWidgetHistory.setHorizontalHeaderItem(0, item) + item = QtWidgets.QTableWidgetItem() + self.tableWidgetHistory.setHorizontalHeaderItem(1, item) + self.tableWidgetHistory.horizontalHeader().setCascadingSectionResizes(False) + self.tableWidgetHistory.horizontalHeader().setDefaultSectionSize(200) + self.tableWidgetHistory.horizontalHeader().setStretchLastSection(True) + self.tableWidgetHistory.verticalHeader().setVisible(False) + self.tableWidgetHistory.verticalHeader().setCascadingSectionResizes(False) + self.tableWidgetHistory.verticalHeader().setDefaultSectionSize(37) + self.verticalLayout_4.addWidget(self.tableWidgetHistory) + self.tabMain.addTab(self.tabHistory, "") + self.tabNotes = QtWidgets.QWidget() + self.tabNotes.setObjectName("tabNotes") + self.gridLayout_2 = QtWidgets.QGridLayout(self.tabNotes) self.gridLayout_2.setObjectName("gridLayout_2") self.gridLayout = QtWidgets.QGridLayout() self.gridLayout.setObjectName("gridLayout") - self.plainTextEdit = QtWidgets.QPlainTextEdit(self.tab_3) + self.plainTextEdit = QtWidgets.QPlainTextEdit(self.tabNotes) self.plainTextEdit.setObjectName("plainTextEdit") self.gridLayout.addWidget(self.plainTextEdit, 0, 0, 1, 1) self.gridLayout_2.addLayout(self.gridLayout, 0, 0, 1, 1) - self.tabMain.addTab(self.tab_3, "") + self.tabMain.addTab(self.tabNotes, "") self.verticalLayout_3.addWidget(self.tabMain) self.freqSlider = QtWidgets.QScrollBar(self.centralwidget) self.freqSlider.setMinimumSize(QtCore.QSize(400, 30)) @@ -168,7 +186,7 @@ def setupUi(self, MainWindow): self.gridLayout_7.addLayout(self.verticalLayout_3, 0, 0, 1, 1) MainWindow.setCentralWidget(self.centralwidget) self.menubar = QtWidgets.QMenuBar(MainWindow) - self.menubar.setGeometry(QtCore.QRect(0, 0, 1691, 22)) + self.menubar.setGeometry(QtCore.QRect(0, 0, 1200, 19)) self.menubar.setObjectName("menubar") self.menuFile = QtWidgets.QMenu(self.menubar) self.menuFile.setObjectName("menuFile") @@ -197,6 +215,8 @@ def setupUi(self, MainWindow): self.menuSettings.setObjectName("menuSettings") self.menuHelp = QtWidgets.QMenu(self.menubar) self.menuHelp.setObjectName("menuHelp") + self.menuNIST_Special = QtWidgets.QMenu(self.menubar) + self.menuNIST_Special.setObjectName("menuNIST_Special") MainWindow.setMenuBar(self.menubar) self.statusbar = QtWidgets.QStatusBar(MainWindow) self.statusbar.setObjectName("statusbar") @@ -416,15 +436,22 @@ def setupUi(self, MainWindow): self.actionUndo_Backup_Enabled.setChecked(True) self.actionUndo_Backup_Enabled.setObjectName("actionUndo_Backup_Enabled") self.actionLoad_NRB_Left_Side = QtWidgets.QAction(MainWindow) + self.actionLoad_NRB_Left_Side.setIcon(icon1) self.actionLoad_NRB_Left_Side.setObjectName("actionLoad_NRB_Left_Side") self.actionLoad_NRB_Right_Side = QtWidgets.QAction(MainWindow) + self.actionLoad_NRB_Right_Side.setIcon(icon1) self.actionLoad_NRB_Right_Side.setObjectName("actionLoad_NRB_Right_Side") self.actionNRB_from_ROI_Left_Side = QtWidgets.QAction(MainWindow) + self.actionNRB_from_ROI_Left_Side.setIcon(icon15) self.actionNRB_from_ROI_Left_Side.setObjectName("actionNRB_from_ROI_Left_Side") self.actionNRB_from_ROI_Right_Side = QtWidgets.QAction(MainWindow) + self.actionNRB_from_ROI_Right_Side.setIcon(icon15) self.actionNRB_from_ROI_Right_Side.setObjectName("actionNRB_from_ROI_Right_Side") self.actionMergeNRBs = QtWidgets.QAction(MainWindow) self.actionMergeNRBs.setEnabled(False) + icon24 = QtGui.QIcon() + icon24.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/wrench-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.actionMergeNRBs.setIcon(icon24) self.actionMergeNRBs.setObjectName("actionMergeNRBs") self.actionMerge_NRBs_KK_Preview = QtWidgets.QAction(MainWindow) self.actionMerge_NRBs_KK_Preview.setObjectName("actionMerge_NRBs_KK_Preview") @@ -448,24 +475,62 @@ def setupUi(self, MainWindow): self.actionShowOverlayLegend.setCheckable(True) self.actionShowOverlayLegend.setObjectName("actionShowOverlayLegend") self.actionHelpManual = QtWidgets.QAction(MainWindow) - icon24 = QtGui.QIcon() - icon24.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/question-mark-2x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) - self.actionHelpManual.setIcon(icon24) + icon25 = QtGui.QIcon() + icon25.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/question-mark-2x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.actionHelpManual.setIcon(icon25) self.actionHelpManual.setObjectName("actionHelpManual") self.actionRamanPhantom = QtWidgets.QAction(MainWindow) - icon25 = QtGui.QIcon() - icon25.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/person-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) - self.actionRamanPhantom.setIcon(icon25) + icon26 = QtGui.QIcon() + icon26.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/person-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.actionRamanPhantom.setIcon(icon26) self.actionRamanPhantom.setObjectName("actionRamanPhantom") self.actionBCARSPhantom = QtWidgets.QAction(MainWindow) - icon26 = QtGui.QIcon() - icon26.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/people-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) - self.actionBCARSPhantom.setIcon(icon26) + icon27 = QtGui.QIcon() + icon27.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/people-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.actionBCARSPhantom.setIcon(icon27) self.actionBCARSPhantom.setObjectName("actionBCARSPhantom") + self.actionUsePreviewROI = QtWidgets.QAction(MainWindow) + self.actionUsePreviewROI.setCheckable(True) + self.actionUsePreviewROI.setChecked(True) + self.actionUsePreviewROI.setObjectName("actionUsePreviewROI") + self.actionSetPreviewROI = QtWidgets.QAction(MainWindow) + self.actionSetPreviewROI.setEnabled(False) + self.actionSetPreviewROI.setObjectName("actionSetPreviewROI") + self.actionDeletePreviewROI = QtWidgets.QAction(MainWindow) + self.actionDeletePreviewROI.setCheckable(False) + self.actionDeletePreviewROI.setEnabled(False) + self.actionDeletePreviewROI.setObjectName("actionDeletePreviewROI") + self.actionShowPreviewROI = QtWidgets.QAction(MainWindow) + self.actionShowPreviewROI.setCheckable(True) + self.actionShowPreviewROI.setObjectName("actionShowPreviewROI") + self.actionShowPreviewROILegend = QtWidgets.QAction(MainWindow) + self.actionShowPreviewROILegend.setCheckable(True) + self.actionShowPreviewROILegend.setObjectName("actionShowPreviewROILegend") + self.actionEstCalibration = QtWidgets.QAction(MainWindow) + self.actionEstCalibration.setEnabled(False) + icon28 = QtGui.QIcon() + icon28.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/compass-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.actionEstCalibration.setIcon(icon28) + self.actionEstCalibration.setObjectName("actionEstCalibration") + self.actionCreateMosaic = QtWidgets.QAction(MainWindow) + icon29 = QtGui.QIcon() + icon29.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/grid-three-up-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.On) + self.actionCreateMosaic.setIcon(icon29) + self.actionCreateMosaic.setObjectName("actionCreateMosaic") + self.actionUseImagData = QtWidgets.QAction(MainWindow) + self.actionUseImagData.setCheckable(True) + self.actionUseImagData.setChecked(True) + self.actionUseImagData.setObjectName("actionUseImagData") + self.actionOpenHDFNISTOOC = QtWidgets.QAction(MainWindow) + self.actionOpenHDFNISTOOC.setObjectName("actionOpenHDFNISTOOC") self.menuFile.addAction(self.actionOpenHDFNIST) self.menuFile.addAction(self.actionOpenDLMNIST) self.menuFile.addAction(self.actionSave) self.menuFile.addSeparator() + self.menuFile.addAction(self.actionOpenHDFNISTOOC) + self.menuFile.addSeparator() + self.menuFile.addAction(self.actionCreateMosaic) + self.menuFile.addSeparator() self.menuFile.addAction(self.actionSettings) self.menuPiece_wise_NRB.addAction(self.actionMergeNRBs) self.menuPiece_wise_NRB.addSeparator() @@ -526,15 +591,23 @@ def setupUi(self, MainWindow): self.menuView.addAction(self.actionPointSpectrum) self.menuView.addAction(self.actionROISpectrum) self.menuView.addSeparator() + self.menuView.addAction(self.actionSetPreviewROI) + self.menuView.addAction(self.actionDeletePreviewROI) + self.menuView.addAction(self.actionShowPreviewROI) + self.menuView.addAction(self.actionShowPreviewROILegend) + self.menuView.addSeparator() self.menuView.addAction(self.actionDarkSpectrum) self.menuView.addAction(self.actionNRBSpectrum) self.menuView.addAction(self.actionLeftSideNRBSpect) self.menuView.addAction(self.actionRightSideNRBSpect) self.menuSettings.addAction(self.actionUndo_Backup_Enabled) + self.menuSettings.addAction(self.actionUsePreviewROI) + self.menuSettings.addAction(self.actionUseImagData) self.menuHelp.addAction(self.actionHelpManual) self.menuHelp.addSeparator() self.menuHelp.addAction(self.actionRamanPhantom) self.menuHelp.addAction(self.actionBCARSPhantom) + self.menuNIST_Special.addAction(self.actionEstCalibration) self.menubar.addAction(self.menuFile.menuAction()) self.menubar.addAction(self.menuEdit.menuAction()) self.menubar.addAction(self.menuView.menuAction()) @@ -542,6 +615,7 @@ def setupUi(self, MainWindow): self.menubar.addAction(self.menuPre_Process.menuAction()) self.menubar.addAction(self.menuAnalysis.menuAction()) self.menubar.addAction(self.menuSettings.menuAction()) + self.menubar.addAction(self.menuNIST_Special.menuAction()) self.menubar.addAction(self.menuHelp.menuAction()) self.retranslateUi(MainWindow) @@ -555,10 +629,15 @@ def retranslateUi(self, MainWindow): self.tabMain.setTabText(self.tabMain.indexOf(self.tab), _translate("MainWindow", "Single Frequency")) self.tabMain.setTabText(self.tabMain.indexOf(self.tabCompositeLarge), _translate("MainWindow", "Composite")) self.tabMain.setTabText(self.tabMain.indexOf(self.tabSettings), _translate("MainWindow", "Settings")) + item = self.tableWidgetHistory.horizontalHeaderItem(0) + item.setText(_translate("MainWindow", "Process Attributes")) + item = self.tableWidgetHistory.horizontalHeaderItem(1) + item.setText(_translate("MainWindow", "Value")) + self.tabMain.setTabText(self.tabMain.indexOf(self.tabHistory), _translate("MainWindow", "History")) self.plainTextEdit.setPlainText(_translate("MainWindow", "This is where you enter notes....\n" "\n" "This will be saved to the processed file.")) - self.tabMain.setTabText(self.tabMain.indexOf(self.tab_3), _translate("MainWindow", "Notes")) + self.tabMain.setTabText(self.tabMain.indexOf(self.tabNotes), _translate("MainWindow", "Notes")) self.labelFreqPixel.setText(_translate("MainWindow", "Freq Pixel")) self.labelWavenumber.setText(_translate("MainWindow", "Wavenumber (cm-1)")) self.menuFile.setTitle(_translate("MainWindow", "File")) @@ -573,6 +652,7 @@ def retranslateUi(self, MainWindow): self.menuToolbar.setTitle(_translate("MainWindow", "Toolbar")) self.menuSettings.setTitle(_translate("MainWindow", "Settings")) self.menuHelp.setTitle(_translate("MainWindow", "Help")) + self.menuNIST_Special.setTitle(_translate("MainWindow", "NIST Special")) self.toolBar.setWindowTitle(_translate("MainWindow", "toolBar")) self.actionOpenHDFNIST.setText(_translate("MainWindow", "Open HDF (NIST)...")) self.actionOpenHDFNIST.setShortcut(_translate("MainWindow", "Ctrl+O")) @@ -632,10 +712,14 @@ def retranslateUi(self, MainWindow): self.actionLoadNRBDLM.setToolTip(_translate("MainWindow", "Load NRB (DLM)")) self.actionToolBarNIST1.setText(_translate("MainWindow", "NIST CRI Workflow (BCARS1)")) self.actionUndo_Backup_Enabled.setText(_translate("MainWindow", "Undo/Backup Enabled")) - self.actionLoad_NRB_Left_Side.setText(_translate("MainWindow", "Load NRB (HDF; Left-Side)")) - self.actionLoad_NRB_Right_Side.setText(_translate("MainWindow", "Load NRB (HDF; Right-Side)")) - self.actionNRB_from_ROI_Left_Side.setText(_translate("MainWindow", "NRB from ROI (Left-Side)")) - self.actionNRB_from_ROI_Right_Side.setText(_translate("MainWindow", "NRB from ROI (Right-Side)")) + self.actionLoad_NRB_Left_Side.setText(_translate("MainWindow", "Load NRB (HDF; Left)")) + self.actionLoad_NRB_Left_Side.setToolTip(_translate("MainWindow", "Load NRB (HDF; Left)")) + self.actionLoad_NRB_Right_Side.setText(_translate("MainWindow", "Load NRB (HDF; Right)")) + self.actionLoad_NRB_Right_Side.setToolTip(_translate("MainWindow", "Load NRB (HDF; Right)")) + self.actionNRB_from_ROI_Left_Side.setText(_translate("MainWindow", "NRB from ROI (Left)")) + self.actionNRB_from_ROI_Left_Side.setToolTip(_translate("MainWindow", "NRB from ROI (Left)")) + self.actionNRB_from_ROI_Right_Side.setText(_translate("MainWindow", "NRB from ROI (Right)")) + self.actionNRB_from_ROI_Right_Side.setToolTip(_translate("MainWindow", "NRB from ROI (Right)")) self.actionMergeNRBs.setText(_translate("MainWindow", "Merge NRBs")) self.actionMerge_NRBs_KK_Preview.setText(_translate("MainWindow", "Merge NRBs (KK Preview)")) self.actionLeftSideNRBSpect.setText(_translate("MainWindow", "Left-Side NRB Spect")) @@ -648,5 +732,15 @@ def retranslateUi(self, MainWindow): self.actionHelpManual.setShortcut(_translate("MainWindow", "F1")) self.actionRamanPhantom.setText(_translate("MainWindow", "Raman Numerical Phantom")) self.actionBCARSPhantom.setText(_translate("MainWindow", "BCARS Numerical Phantom")) + self.actionUsePreviewROI.setText(_translate("MainWindow", "Use Preview ROI(s)")) + self.actionSetPreviewROI.setText(_translate("MainWindow", "Set Preview ROI(s)")) + self.actionDeletePreviewROI.setText(_translate("MainWindow", "Delete Preview ROI(s)")) + self.actionShowPreviewROI.setText(_translate("MainWindow", "Show Preview ROI(s)")) + self.actionShowPreviewROILegend.setText(_translate("MainWindow", "Show Preview ROI Legend")) + self.actionEstCalibration.setText(_translate("MainWindow", "Est. Calibration")) + self.actionCreateMosaic.setText(_translate("MainWindow", "Create Mosaic")) + self.actionUseImagData.setText(_translate("MainWindow", "Use Imaginary if Exists")) + self.actionOpenHDFNISTOOC.setText(_translate("MainWindow", "Open HDF OOC (NIST)")) + from . import icons_all_rc diff --git a/crikit/ui/qt_CompositeColor.py b/crikit/ui/qt_CompositeColor.py index 6232e18..7cf1b7b 100644 --- a/crikit/ui/qt_CompositeColor.py +++ b/crikit/ui/qt_CompositeColor.py @@ -2,16 +2,17 @@ # Form implementation generated from reading ui file '.\ui_CompositeColor.ui' # -# Created by: PyQt5 UI code generator 5.8.1 +# Created by: PyQt5 UI code generator 5.12 # # WARNING! All changes made in this file will be lost! from PyQt5 import QtCore, QtGui, QtWidgets + class Ui_Form(object): def setupUi(self, Form): Form.setObjectName("Form") - Form.resize(767, 594) + Form.resize(600, 100) Form.setStyleSheet("font: 10pt \"Arial\";") self.verticalLayout = QtWidgets.QVBoxLayout(Form) self.verticalLayout.setObjectName("verticalLayout") @@ -56,6 +57,8 @@ def setupUi(self, Form): self.verticalLayoutBGColor.addWidget(self.comboBoxBGColor) self.horizontalLayout.addLayout(self.verticalLayoutBGColor) self.verticalLayout.addWidget(self.frame) + spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout.addItem(spacerItem) self.retranslateUi(Form) QtCore.QMetaObject.connectSlotsByName(Form) @@ -69,3 +72,4 @@ def retranslateUi(self, Form): self.comboBoxColorMode.setItemText(2, _translate("Form", "Absorption v2")) self.labelBGColor.setText(_translate("Form", "Background Color")) + diff --git a/crikit/ui/qt_HDFLoad.py b/crikit/ui/qt_HDFLoad.py deleted file mode 100644 index 7d3e15d..0000000 --- a/crikit/ui/qt_HDFLoad.py +++ /dev/null @@ -1,157 +0,0 @@ -# -*- coding: utf-8 -*- - -# Form implementation generated from reading ui file '.\ui_HDFLoad.ui' -# -# Created by: PyQt5 UI code generator 5.5.1 -# -# WARNING! All changes made in this file will be lost! - -from PyQt5 import QtCore, QtGui, QtWidgets - -class Ui_Dialog(object): - def setupUi(self, Dialog): - Dialog.setObjectName("Dialog") - Dialog.resize(845, 588) - Dialog.setStyleSheet("font: 10pt \"Arial\";") - self.verticalLayout_2 = QtWidgets.QVBoxLayout(Dialog) - self.verticalLayout_2.setObjectName("verticalLayout_2") - self.verticalLayout = QtWidgets.QVBoxLayout() - self.verticalLayout.setSizeConstraint(QtWidgets.QLayout.SetNoConstraint) - self.verticalLayout.setObjectName("verticalLayout") - self.topHL = QtWidgets.QHBoxLayout() - self.topHL.setSizeConstraint(QtWidgets.QLayout.SetNoConstraint) - self.topHL.setObjectName("topHL") - self.dataSetVL = QtWidgets.QVBoxLayout() - self.dataSetVL.setObjectName("dataSetVL") - self.label_1 = QtWidgets.QLabel(Dialog) - self.label_1.setObjectName("label_1") - self.dataSetVL.addWidget(self.label_1) - self.dataGroupSelect = QtWidgets.QComboBox(Dialog) - self.dataGroupSelect.setObjectName("dataGroupSelect") - self.dataSetVL.addWidget(self.dataGroupSelect) - self.label_2 = QtWidgets.QLabel(Dialog) - self.label_2.setObjectName("label_2") - self.dataSetVL.addWidget(self.label_2) - self.dataSetList = QtWidgets.QListWidget(Dialog) - self.dataSetList.setEditTriggers(QtWidgets.QAbstractItemView.DoubleClicked|QtWidgets.QAbstractItemView.EditKeyPressed|QtWidgets.QAbstractItemView.SelectedClicked) - self.dataSetList.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection) - self.dataSetList.setObjectName("dataSetList") - self.dataSetVL.addWidget(self.dataSetList) - self.label_3 = QtWidgets.QLabel(Dialog) - self.label_3.setObjectName("label_3") - self.dataSetVL.addWidget(self.label_3) - self.filterIncludeString = QtWidgets.QLineEdit(Dialog) - self.filterIncludeString.setObjectName("filterIncludeString") - self.dataSetVL.addWidget(self.filterIncludeString) - self.label_4 = QtWidgets.QLabel(Dialog) - self.label_4.setObjectName("label_4") - self.dataSetVL.addWidget(self.label_4) - self.filterExcludeString = QtWidgets.QLineEdit(Dialog) - self.filterExcludeString.setObjectName("filterExcludeString") - self.dataSetVL.addWidget(self.filterExcludeString) - self.horizontalLayout = QtWidgets.QHBoxLayout() - self.horizontalLayout.setObjectName("horizontalLayout") - self.filterButton = QtWidgets.QPushButton(Dialog) - self.filterButton.setObjectName("filterButton") - self.horizontalLayout.addWidget(self.filterButton) - self.resetFilter = QtWidgets.QPushButton(Dialog) - self.resetFilter.setObjectName("resetFilter") - self.horizontalLayout.addWidget(self.resetFilter) - self.dataSetVL.addLayout(self.horizontalLayout) - self.topHL.addLayout(self.dataSetVL) - self.attribVL = QtWidgets.QVBoxLayout() - self.attribVL.setObjectName("attribVL") - self.label_5 = QtWidgets.QLabel(Dialog) - self.label_5.setObjectName("label_5") - self.attribVL.addWidget(self.label_5) - self.currentDatasetText = QtWidgets.QTextBrowser(Dialog) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Maximum) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.currentDatasetText.sizePolicy().hasHeightForWidth()) - self.currentDatasetText.setSizePolicy(sizePolicy) - self.currentDatasetText.setMaximumSize(QtCore.QSize(16777215, 100)) - self.currentDatasetText.setObjectName("currentDatasetText") - self.attribVL.addWidget(self.currentDatasetText) - self.label_6 = QtWidgets.QLabel(Dialog) - self.label_6.setObjectName("label_6") - self.attribVL.addWidget(self.label_6) - self.dataSetAttribs = QtWidgets.QTableWidget(Dialog) - self.dataSetAttribs.setStyleSheet("") - self.dataSetAttribs.setColumnCount(2) - self.dataSetAttribs.setObjectName("dataSetAttribs") - self.dataSetAttribs.setRowCount(0) - item = QtWidgets.QTableWidgetItem() - font = QtGui.QFont() - font.setPointSize(10) - item.setFont(font) - item.setBackground(QtGui.QColor(121, 121, 121)) - brush = QtGui.QBrush(QtGui.QColor(91, 91, 91)) - brush.setStyle(QtCore.Qt.SolidPattern) - item.setForeground(brush) - self.dataSetAttribs.setHorizontalHeaderItem(0, item) - item = QtWidgets.QTableWidgetItem() - item.setBackground(QtGui.QColor(123, 123, 123)) - brush = QtGui.QBrush(QtGui.QColor(91, 91, 91)) - brush.setStyle(QtCore.Qt.SolidPattern) - item.setForeground(brush) - self.dataSetAttribs.setHorizontalHeaderItem(1, item) - self.dataSetAttribs.horizontalHeader().setCascadingSectionResizes(True) - self.dataSetAttribs.horizontalHeader().setDefaultSectionSize(200) - self.dataSetAttribs.horizontalHeader().setHighlightSections(False) - self.dataSetAttribs.horizontalHeader().setSortIndicatorShown(True) - self.dataSetAttribs.horizontalHeader().setStretchLastSection(True) - self.dataSetAttribs.verticalHeader().setVisible(False) - self.dataSetAttribs.verticalHeader().setHighlightSections(False) - self.attribVL.addWidget(self.dataSetAttribs) - self.label_7 = QtWidgets.QLabel(Dialog) - self.label_7.setObjectName("label_7") - self.attribVL.addWidget(self.label_7) - self.dataSetMemo = QtWidgets.QTextBrowser(Dialog) - sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Maximum) - sizePolicy.setHorizontalStretch(0) - sizePolicy.setVerticalStretch(0) - sizePolicy.setHeightForWidth(self.dataSetMemo.sizePolicy().hasHeightForWidth()) - self.dataSetMemo.setSizePolicy(sizePolicy) - self.dataSetMemo.setMaximumSize(QtCore.QSize(16777215, 100)) - self.dataSetMemo.setObjectName("dataSetMemo") - self.attribVL.addWidget(self.dataSetMemo) - self.topHL.addLayout(self.attribVL) - self.verticalLayout.addLayout(self.topHL) - self.horizontalLayout_2 = QtWidgets.QHBoxLayout() - self.horizontalLayout_2.setContentsMargins(-1, 10, -1, -1) - self.horizontalLayout_2.setObjectName("horizontalLayout_2") - spacerItem = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum) - self.horizontalLayout_2.addItem(spacerItem) - self.pushButtonOk = QtWidgets.QPushButton(Dialog) - self.pushButtonOk.setObjectName("pushButtonOk") - self.horizontalLayout_2.addWidget(self.pushButtonOk) - self.pushButtonCancel = QtWidgets.QPushButton(Dialog) - self.pushButtonCancel.setObjectName("pushButtonCancel") - self.horizontalLayout_2.addWidget(self.pushButtonCancel) - self.verticalLayout.addLayout(self.horizontalLayout_2) - self.verticalLayout_2.addLayout(self.verticalLayout) - - self.retranslateUi(Dialog) - QtCore.QMetaObject.connectSlotsByName(Dialog) - - def retranslateUi(self, Dialog): - _translate = QtCore.QCoreApplication.translate - Dialog.setWindowTitle(_translate("Dialog", "HDF File Inspector")) - self.label_1.setText(_translate("Dialog", "Groups Containing Datasets")) - self.label_2.setText(_translate("Dialog", "Datasets")) - self.label_3.setText(_translate("Dialog", "

Include Entires with Substring (separate by \',\' [comma])

")) - self.label_4.setText(_translate("Dialog", "

Exclude Entires with Substring (separate by \',\' [comma])

")) - self.filterButton.setText(_translate("Dialog", "Filter List")) - self.resetFilter.setText(_translate("Dialog", "Reset List")) - self.label_5.setText(_translate("Dialog", "Current Selection")) - self.label_6.setText(_translate("Dialog", "Atrribute Table")) - self.dataSetAttribs.setSortingEnabled(True) - item = self.dataSetAttribs.horizontalHeaderItem(0) - item.setText(_translate("Dialog", "Attribute")) - item = self.dataSetAttribs.horizontalHeaderItem(1) - item.setText(_translate("Dialog", "Value")) - self.label_7.setText(_translate("Dialog", "Dataset Information (Memo)")) - self.pushButtonOk.setText(_translate("Dialog", "OK")) - self.pushButtonCancel.setText(_translate("Dialog", "Cancel")) - diff --git a/crikit/ui/qt_Mosaic.py b/crikit/ui/qt_Mosaic.py new file mode 100644 index 0000000..284bdd4 --- /dev/null +++ b/crikit/ui/qt_Mosaic.py @@ -0,0 +1,485 @@ +# -*- coding: utf-8 -*- + +# Form implementation generated from reading ui file '.\ui_Mosaic.ui' +# +# Created by: PyQt5 UI code generator 5.9.2 +# +# WARNING! All changes made in this file will be lost! + +from PyQt5 import QtCore, QtGui, QtWidgets + +class Ui_MainWindow(object): + def setupUi(self, MainWindow): + MainWindow.setObjectName("MainWindow") + MainWindow.resize(1200, 915) + MainWindow.setMaximumSize(QtCore.QSize(2000, 16777215)) + MainWindow.setToolButtonStyle(QtCore.Qt.ToolButtonTextUnderIcon) + self.centralwidget = QtWidgets.QWidget(MainWindow) + self.centralwidget.setObjectName("centralwidget") + self.gridLayout_2 = QtWidgets.QGridLayout(self.centralwidget) + self.gridLayout_2.setObjectName("gridLayout_2") + self.verticalLayout_5 = QtWidgets.QVBoxLayout() + self.verticalLayout_5.setContentsMargins(0, -1, -1, -1) + self.verticalLayout_5.setObjectName("verticalLayout_5") + self.frame = QtWidgets.QFrame(self.centralwidget) + sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred) + sizePolicy.setHorizontalStretch(0) + sizePolicy.setVerticalStretch(0) + sizePolicy.setHeightForWidth(self.frame.sizePolicy().hasHeightForWidth()) + self.frame.setSizePolicy(sizePolicy) + self.frame.setMinimumSize(QtCore.QSize(500, 0)) + self.frame.setMaximumSize(QtCore.QSize(500, 16777215)) + self.frame.setFrameShape(QtWidgets.QFrame.StyledPanel) + self.frame.setFrameShadow(QtWidgets.QFrame.Plain) + self.frame.setObjectName("frame") + self.verticalLayout_4 = QtWidgets.QVBoxLayout(self.frame) + self.verticalLayout_4.setContentsMargins(3, 3, 3, 3) + self.verticalLayout_4.setObjectName("verticalLayout_4") + self.verticalLayoutOptions = QtWidgets.QVBoxLayout() + self.verticalLayoutOptions.setSpacing(1) + self.verticalLayoutOptions.setObjectName("verticalLayoutOptions") + self.horizontalLayout_2 = QtWidgets.QHBoxLayout() + self.horizontalLayout_2.setContentsMargins(0, 0, -1, -1) + self.horizontalLayout_2.setObjectName("horizontalLayout_2") + self.verticalLayout = QtWidgets.QVBoxLayout() + self.verticalLayout.setContentsMargins(-1, 0, -1, -1) + self.verticalLayout.setObjectName("verticalLayout") + self.label_5 = QtWidgets.QLabel(self.frame) + self.label_5.setObjectName("label_5") + self.verticalLayout.addWidget(self.label_5, 0, QtCore.Qt.AlignRight) + self.spinBoxMRows = QtWidgets.QSpinBox(self.frame) + self.spinBoxMRows.setMinimumSize(QtCore.QSize(50, 0)) + self.spinBoxMRows.setMaximumSize(QtCore.QSize(50, 16777215)) + self.spinBoxMRows.setMinimum(1) + self.spinBoxMRows.setObjectName("spinBoxMRows") + self.verticalLayout.addWidget(self.spinBoxMRows, 0, QtCore.Qt.AlignRight) + self.horizontalLayout_2.addLayout(self.verticalLayout) + self.verticalLayout_3 = QtWidgets.QVBoxLayout() + self.verticalLayout_3.setObjectName("verticalLayout_3") + self.label_6 = QtWidgets.QLabel(self.frame) + self.label_6.setObjectName("label_6") + self.verticalLayout_3.addWidget(self.label_6, 0, QtCore.Qt.AlignRight) + self.spinBoxNCols = QtWidgets.QSpinBox(self.frame) + self.spinBoxNCols.setMinimumSize(QtCore.QSize(50, 0)) + self.spinBoxNCols.setMaximumSize(QtCore.QSize(50, 16777215)) + self.spinBoxNCols.setMinimum(1) + self.spinBoxNCols.setMaximum(300) + self.spinBoxNCols.setProperty("value", 1) + self.spinBoxNCols.setObjectName("spinBoxNCols") + self.verticalLayout_3.addWidget(self.spinBoxNCols, 0, QtCore.Qt.AlignRight) + self.horizontalLayout_2.addLayout(self.verticalLayout_3) + self.verticalLayoutOptions.addLayout(self.horizontalLayout_2) + spacerItem = QtWidgets.QSpacerItem(20, 15, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayoutOptions.addItem(spacerItem) + self.label = QtWidgets.QLabel(self.frame) + self.label.setObjectName("label") + self.verticalLayoutOptions.addWidget(self.label, 0, QtCore.Qt.AlignRight) + self.spinBoxStartRow = QtWidgets.QSpinBox(self.frame) + self.spinBoxStartRow.setMinimumSize(QtCore.QSize(50, 0)) + self.spinBoxStartRow.setMaximumSize(QtCore.QSize(50, 16777215)) + self.spinBoxStartRow.setMaximum(500) + self.spinBoxStartRow.setObjectName("spinBoxStartRow") + self.verticalLayoutOptions.addWidget(self.spinBoxStartRow, 0, QtCore.Qt.AlignRight) + spacerItem1 = QtWidgets.QSpacerItem(20, 15, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayoutOptions.addItem(spacerItem1) + self.label_2 = QtWidgets.QLabel(self.frame) + self.label_2.setObjectName("label_2") + self.verticalLayoutOptions.addWidget(self.label_2, 0, QtCore.Qt.AlignRight) + self.spinBoxEndRow = QtWidgets.QSpinBox(self.frame) + self.spinBoxEndRow.setMinimumSize(QtCore.QSize(50, 0)) + self.spinBoxEndRow.setMaximumSize(QtCore.QSize(50, 16777215)) + self.spinBoxEndRow.setMaximum(500) + self.spinBoxEndRow.setObjectName("spinBoxEndRow") + self.verticalLayoutOptions.addWidget(self.spinBoxEndRow, 0, QtCore.Qt.AlignRight) + spacerItem2 = QtWidgets.QSpacerItem(20, 15, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayoutOptions.addItem(spacerItem2) + self.label_3 = QtWidgets.QLabel(self.frame) + self.label_3.setObjectName("label_3") + self.verticalLayoutOptions.addWidget(self.label_3, 0, QtCore.Qt.AlignRight) + self.spinBoxStartCol = QtWidgets.QSpinBox(self.frame) + self.spinBoxStartCol.setMinimumSize(QtCore.QSize(50, 0)) + self.spinBoxStartCol.setMaximumSize(QtCore.QSize(50, 16777215)) + self.spinBoxStartCol.setMaximum(500) + self.spinBoxStartCol.setObjectName("spinBoxStartCol") + self.verticalLayoutOptions.addWidget(self.spinBoxStartCol, 0, QtCore.Qt.AlignRight) + spacerItem3 = QtWidgets.QSpacerItem(20, 15, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayoutOptions.addItem(spacerItem3) + self.label_4 = QtWidgets.QLabel(self.frame) + self.label_4.setObjectName("label_4") + self.verticalLayoutOptions.addWidget(self.label_4, 0, QtCore.Qt.AlignRight) + self.spinBoxEndCol = QtWidgets.QSpinBox(self.frame) + self.spinBoxEndCol.setMinimumSize(QtCore.QSize(50, 0)) + self.spinBoxEndCol.setMaximumSize(QtCore.QSize(50, 16777215)) + self.spinBoxEndCol.setMaximum(500) + self.spinBoxEndCol.setObjectName("spinBoxEndCol") + self.verticalLayoutOptions.addWidget(self.spinBoxEndCol, 0, QtCore.Qt.AlignRight) + self.checkBoxCompress = QtWidgets.QCheckBox(self.frame) + self.checkBoxCompress.setObjectName("checkBoxCompress") + self.verticalLayoutOptions.addWidget(self.checkBoxCompress, 0, QtCore.Qt.AlignRight) + spacerItem4 = QtWidgets.QSpacerItem(20, 5, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayoutOptions.addItem(spacerItem4) + self.label_8 = QtWidgets.QLabel(self.frame) + self.label_8.setObjectName("label_8") + self.verticalLayoutOptions.addWidget(self.label_8, 0, QtCore.Qt.AlignLeft) + self.comboBoxRowCol = QtWidgets.QComboBox(self.frame) + self.comboBoxRowCol.setMaximumSize(QtCore.QSize(100, 16777215)) + self.comboBoxRowCol.setObjectName("comboBoxRowCol") + self.comboBoxRowCol.addItem("") + self.comboBoxRowCol.addItem("") + self.verticalLayoutOptions.addWidget(self.comboBoxRowCol, 0, QtCore.Qt.AlignLeft) + self.checkBoxFlipH = QtWidgets.QCheckBox(self.frame) + self.checkBoxFlipH.setMaximumSize(QtCore.QSize(120, 16777215)) + self.checkBoxFlipH.setObjectName("checkBoxFlipH") + self.verticalLayoutOptions.addWidget(self.checkBoxFlipH, 0, QtCore.Qt.AlignLeft) + self.checkBoxFlipV = QtWidgets.QCheckBox(self.frame) + self.checkBoxFlipV.setMaximumSize(QtCore.QSize(110, 16777215)) + self.checkBoxFlipV.setObjectName("checkBoxFlipV") + self.verticalLayoutOptions.addWidget(self.checkBoxFlipV, 0, QtCore.Qt.AlignLeft) + self.checkBoxTranspose = QtWidgets.QCheckBox(self.frame) + self.checkBoxTranspose.setMaximumSize(QtCore.QSize(110, 16777215)) + self.checkBoxTranspose.setObjectName("checkBoxTranspose") + self.verticalLayoutOptions.addWidget(self.checkBoxTranspose, 0, QtCore.Qt.AlignLeft) + self.verticalLayout_4.addLayout(self.verticalLayoutOptions) + self.label_7 = QtWidgets.QLabel(self.frame) + self.label_7.setObjectName("label_7") + self.verticalLayout_4.addWidget(self.label_7, 0, QtCore.Qt.AlignLeft) + self.horizontalLayout_3 = QtWidgets.QHBoxLayout() + self.horizontalLayout_3.setContentsMargins(-1, 0, -1, -1) + self.horizontalLayout_3.setSpacing(2) + self.horizontalLayout_3.setObjectName("horizontalLayout_3") + spacerItem5 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum) + self.horizontalLayout_3.addItem(spacerItem5) + self.pushButtonMoveUp = QtWidgets.QPushButton(self.frame) + self.pushButtonMoveUp.setMaximumSize(QtCore.QSize(50, 16777215)) + self.pushButtonMoveUp.setText("") + icon = QtGui.QIcon() + icon.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/arrow-circle-top-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.pushButtonMoveUp.setIcon(icon) + self.pushButtonMoveUp.setObjectName("pushButtonMoveUp") + self.horizontalLayout_3.addWidget(self.pushButtonMoveUp) + self.pushButtonMoveDown = QtWidgets.QPushButton(self.frame) + self.pushButtonMoveDown.setMaximumSize(QtCore.QSize(50, 16777215)) + self.pushButtonMoveDown.setText("") + icon1 = QtGui.QIcon() + icon1.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/arrow-circle-bottom-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.pushButtonMoveDown.setIcon(icon1) + self.pushButtonMoveDown.setObjectName("pushButtonMoveDown") + self.horizontalLayout_3.addWidget(self.pushButtonMoveDown) + spacerItem6 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum) + self.horizontalLayout_3.addItem(spacerItem6) + self.pushButtonDeleteDataset = QtWidgets.QPushButton(self.frame) + self.pushButtonDeleteDataset.setMaximumSize(QtCore.QSize(50, 16777215)) + self.pushButtonDeleteDataset.setText("") + icon2 = QtGui.QIcon() + icon2.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/minus-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.pushButtonDeleteDataset.setIcon(icon2) + self.pushButtonDeleteDataset.setObjectName("pushButtonDeleteDataset") + self.horizontalLayout_3.addWidget(self.pushButtonDeleteDataset) + self.pushButtonAddDataset = QtWidgets.QPushButton(self.frame) + self.pushButtonAddDataset.setMaximumSize(QtCore.QSize(50, 16777215)) + self.pushButtonAddDataset.setText("") + icon3 = QtGui.QIcon() + icon3.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/plus-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.pushButtonAddDataset.setIcon(icon3) + self.pushButtonAddDataset.setObjectName("pushButtonAddDataset") + self.horizontalLayout_3.addWidget(self.pushButtonAddDataset) + spacerItem7 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum) + self.horizontalLayout_3.addItem(spacerItem7) + self.verticalLayout_4.addLayout(self.horizontalLayout_3) + self.verticalLayout_5.addWidget(self.frame, 0, QtCore.Qt.AlignRight) + spacerItem8 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_5.addItem(spacerItem8) + self.gridLayout_2.addLayout(self.verticalLayout_5, 0, 2, 1, 1) + self.gridLayout_3 = QtWidgets.QGridLayout() + self.gridLayout_3.setObjectName("gridLayout_3") + self.labelWavenumber_2 = QtWidgets.QLabel(self.centralwidget) + sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Maximum) + sizePolicy.setHorizontalStretch(0) + sizePolicy.setVerticalStretch(0) + sizePolicy.setHeightForWidth(self.labelWavenumber_2.sizePolicy().hasHeightForWidth()) + self.labelWavenumber_2.setSizePolicy(sizePolicy) + self.labelWavenumber_2.setMinimumSize(QtCore.QSize(120, 20)) + self.labelWavenumber_2.setMaximumSize(QtCore.QSize(1000, 20)) + self.labelWavenumber_2.setTextFormat(QtCore.Qt.AutoText) + self.labelWavenumber_2.setAlignment(QtCore.Qt.AlignCenter) + self.labelWavenumber_2.setObjectName("labelWavenumber_2") + self.gridLayout_3.addWidget(self.labelWavenumber_2, 1, 0, 1, 1, QtCore.Qt.AlignHCenter|QtCore.Qt.AlignBottom) + self.lineEditPix = QtWidgets.QLineEdit(self.centralwidget) + sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) + sizePolicy.setHorizontalStretch(0) + sizePolicy.setVerticalStretch(0) + sizePolicy.setHeightForWidth(self.lineEditPix.sizePolicy().hasHeightForWidth()) + self.lineEditPix.setSizePolicy(sizePolicy) + self.lineEditPix.setMinimumSize(QtCore.QSize(100, 30)) + self.lineEditPix.setMaximumSize(QtCore.QSize(100, 30)) + font = QtGui.QFont() + font.setFamily("Arial") + font.setPointSize(14) + font.setBold(False) + font.setItalic(False) + font.setWeight(50) + self.lineEditPix.setFont(font) + self.lineEditPix.setStyleSheet("font: 14pt \"Arial\";") + self.lineEditPix.setObjectName("lineEditPix") + self.gridLayout_3.addWidget(self.lineEditPix, 0, 0, 1, 1, QtCore.Qt.AlignHCenter|QtCore.Qt.AlignBottom) + self.lineEditFreq = QtWidgets.QLineEdit(self.centralwidget) + self.lineEditFreq.setEnabled(True) + self.lineEditFreq.setMinimumSize(QtCore.QSize(100, 30)) + self.lineEditFreq.setMaximumSize(QtCore.QSize(100, 30)) + palette = QtGui.QPalette() + brush = QtGui.QBrush(QtGui.QColor(198, 198, 198)) + brush.setStyle(QtCore.Qt.SolidPattern) + palette.setBrush(QtGui.QPalette.Active, QtGui.QPalette.Base, brush) + brush = QtGui.QBrush(QtGui.QColor(198, 198, 198)) + brush.setStyle(QtCore.Qt.SolidPattern) + palette.setBrush(QtGui.QPalette.Inactive, QtGui.QPalette.Base, brush) + brush = QtGui.QBrush(QtGui.QColor(240, 240, 240)) + brush.setStyle(QtCore.Qt.SolidPattern) + palette.setBrush(QtGui.QPalette.Disabled, QtGui.QPalette.Base, brush) + self.lineEditFreq.setPalette(palette) + self.lineEditFreq.setText("") + self.lineEditFreq.setReadOnly(True) + self.lineEditFreq.setObjectName("lineEditFreq") + self.gridLayout_3.addWidget(self.lineEditFreq, 0, 1, 1, 1, QtCore.Qt.AlignHCenter|QtCore.Qt.AlignBottom) + self.label_9 = QtWidgets.QLabel(self.centralwidget) + self.label_9.setObjectName("label_9") + self.gridLayout_3.addWidget(self.label_9, 1, 1, 1, 1, QtCore.Qt.AlignHCenter|QtCore.Qt.AlignBottom) + self.sliderFreq = QtWidgets.QScrollBar(self.centralwidget) + self.sliderFreq.setMinimumSize(QtCore.QSize(200, 30)) + self.sliderFreq.setProperty("value", 10) + self.sliderFreq.setOrientation(QtCore.Qt.Horizontal) + self.sliderFreq.setObjectName("sliderFreq") + self.gridLayout_3.addWidget(self.sliderFreq, 2, 0, 1, 2, QtCore.Qt.AlignBottom) + spacerItem9 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.gridLayout_3.addItem(spacerItem9, 3, 0, 1, 1) + self.gridLayout_2.addLayout(self.gridLayout_3, 2, 0, 1, 1) + self.frameMosaicImg = QtWidgets.QFrame(self.centralwidget) + self.frameMosaicImg.setFrameShape(QtWidgets.QFrame.StyledPanel) + self.frameMosaicImg.setFrameShadow(QtWidgets.QFrame.Plain) + self.frameMosaicImg.setObjectName("frameMosaicImg") + self.gridLayout = QtWidgets.QGridLayout(self.frameMosaicImg) + self.gridLayout.setObjectName("gridLayout") + self.verticalLayoutMPL = QtWidgets.QVBoxLayout() + self.verticalLayoutMPL.setObjectName("verticalLayoutMPL") + spacerItem10 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum) + self.verticalLayoutMPL.addItem(spacerItem10) + self.gridLayout.addLayout(self.verticalLayoutMPL, 0, 0, 1, 1) + spacerItem11 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.gridLayout.addItem(spacerItem11, 1, 0, 1, 1) + self.gridLayout_2.addWidget(self.frameMosaicImg, 0, 0, 1, 1) + self.tabWidget = QtWidgets.QTabWidget(self.centralwidget) + self.tabWidget.setMinimumSize(QtCore.QSize(500, 0)) + self.tabWidget.setMaximumSize(QtCore.QSize(500, 16777215)) + self.tabWidget.setObjectName("tabWidget") + self.tab_3 = QtWidgets.QWidget() + self.tab_3.setObjectName("tab_3") + self.horizontalLayout = QtWidgets.QHBoxLayout(self.tab_3) + self.horizontalLayout.setObjectName("horizontalLayout") + self.frame_2 = QtWidgets.QFrame(self.tab_3) + self.frame_2.setMaximumSize(QtCore.QSize(400, 16777215)) + self.frame_2.setFrameShape(QtWidgets.QFrame.StyledPanel) + self.frame_2.setFrameShadow(QtWidgets.QFrame.Plain) + self.frame_2.setObjectName("frame_2") + self.verticalLayout_2 = QtWidgets.QVBoxLayout(self.frame_2) + self.verticalLayout_2.setObjectName("verticalLayout_2") + self.label_10 = QtWidgets.QLabel(self.frame_2) + self.label_10.setObjectName("label_10") + self.verticalLayout_2.addWidget(self.label_10) + self.spinBoxIntercept = QtWidgets.QDoubleSpinBox(self.frame_2) + self.spinBoxIntercept.setDecimals(10) + self.spinBoxIntercept.setMinimum(-100000000.0) + self.spinBoxIntercept.setMaximum(100000000.0) + self.spinBoxIntercept.setProperty("value", 832.551012) + self.spinBoxIntercept.setObjectName("spinBoxIntercept") + self.verticalLayout_2.addWidget(self.spinBoxIntercept) + spacerItem12 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_2.addItem(spacerItem12) + self.label_11 = QtWidgets.QLabel(self.frame_2) + self.label_11.setObjectName("label_11") + self.verticalLayout_2.addWidget(self.label_11) + self.spinBoxSlope = QtWidgets.QDoubleSpinBox(self.frame_2) + self.spinBoxSlope.setDecimals(10) + self.spinBoxSlope.setMinimum(-100000000.0) + self.spinBoxSlope.setMaximum(100000000.0) + self.spinBoxSlope.setProperty("value", -0.165956) + self.spinBoxSlope.setObjectName("spinBoxSlope") + self.verticalLayout_2.addWidget(self.spinBoxSlope) + spacerItem13 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_2.addItem(spacerItem13) + self.label_12 = QtWidgets.QLabel(self.frame_2) + self.label_12.setObjectName("label_12") + self.verticalLayout_2.addWidget(self.label_12) + self.spinBoxProbe = QtWidgets.QDoubleSpinBox(self.frame_2) + self.spinBoxProbe.setDecimals(5) + self.spinBoxProbe.setMinimum(-1000000000.0) + self.spinBoxProbe.setMaximum(1000000000.0) + self.spinBoxProbe.setProperty("value", 771.461) + self.spinBoxProbe.setObjectName("spinBoxProbe") + self.verticalLayout_2.addWidget(self.spinBoxProbe) + self.label_13 = QtWidgets.QLabel(self.frame_2) + self.label_13.setObjectName("label_13") + self.verticalLayout_2.addWidget(self.label_13) + self.spinBoxCalibWL = QtWidgets.QDoubleSpinBox(self.frame_2) + self.spinBoxCalibWL.setDecimals(10) + self.spinBoxCalibWL.setMinimum(-100000000.0) + self.spinBoxCalibWL.setMaximum(10000000.0) + self.spinBoxCalibWL.setProperty("value", 700.0) + self.spinBoxCalibWL.setObjectName("spinBoxCalibWL") + self.verticalLayout_2.addWidget(self.spinBoxCalibWL) + spacerItem14 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_2.addItem(spacerItem14) + self.label_14 = QtWidgets.QLabel(self.frame_2) + self.label_14.setObjectName("label_14") + self.verticalLayout_2.addWidget(self.label_14) + self.spinBoxCenterWL = QtWidgets.QDoubleSpinBox(self.frame_2) + self.spinBoxCenterWL.setDecimals(10) + self.spinBoxCenterWL.setMinimum(-100000000.0) + self.spinBoxCenterWL.setMaximum(10000000.0) + self.spinBoxCenterWL.setProperty("value", 700.0) + self.spinBoxCenterWL.setObjectName("spinBoxCenterWL") + self.verticalLayout_2.addWidget(self.spinBoxCenterWL) + spacerItem15 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_2.addItem(spacerItem15) + self.horizontalLayout.addWidget(self.frame_2) + self.checkBoxSpectFromData = QtWidgets.QCheckBox(self.tab_3) + self.checkBoxSpectFromData.setEnabled(False) + font = QtGui.QFont() + font.setPointSize(10) + self.checkBoxSpectFromData.setFont(font) + self.checkBoxSpectFromData.setIconSize(QtCore.QSize(20, 20)) + self.checkBoxSpectFromData.setCheckable(True) + self.checkBoxSpectFromData.setObjectName("checkBoxSpectFromData") + self.horizontalLayout.addWidget(self.checkBoxSpectFromData) + self.tabWidget.addTab(self.tab_3, "") + self.tab_4 = QtWidgets.QWidget() + self.tab_4.setObjectName("tab_4") + self.horizontalLayout_4 = QtWidgets.QHBoxLayout(self.tab_4) + self.horizontalLayout_4.setObjectName("horizontalLayout_4") + self.frame_3 = QtWidgets.QFrame(self.tab_4) + self.frame_3.setFrameShape(QtWidgets.QFrame.StyledPanel) + self.frame_3.setFrameShadow(QtWidgets.QFrame.Plain) + self.frame_3.setObjectName("frame_3") + self.verticalLayout_6 = QtWidgets.QVBoxLayout(self.frame_3) + self.verticalLayout_6.setObjectName("verticalLayout_6") + self.label_15 = QtWidgets.QLabel(self.frame_3) + self.label_15.setObjectName("label_15") + self.verticalLayout_6.addWidget(self.label_15) + self.spinBoxXStepSize = QtWidgets.QDoubleSpinBox(self.frame_3) + self.spinBoxXStepSize.setEnabled(False) + self.spinBoxXStepSize.setReadOnly(False) + self.spinBoxXStepSize.setButtonSymbols(QtWidgets.QAbstractSpinBox.NoButtons) + self.spinBoxXStepSize.setDecimals(10) + self.spinBoxXStepSize.setMinimum(-1.0) + self.spinBoxXStepSize.setMaximum(1000000.0) + self.spinBoxXStepSize.setSingleStep(0.1) + self.spinBoxXStepSize.setProperty("value", -1.0) + self.spinBoxXStepSize.setObjectName("spinBoxXStepSize") + self.verticalLayout_6.addWidget(self.spinBoxXStepSize) + self.label_16 = QtWidgets.QLabel(self.frame_3) + self.label_16.setObjectName("label_16") + self.verticalLayout_6.addWidget(self.label_16) + self.spinBoxYStepSize = QtWidgets.QDoubleSpinBox(self.frame_3) + self.spinBoxYStepSize.setEnabled(False) + self.spinBoxYStepSize.setReadOnly(False) + self.spinBoxYStepSize.setButtonSymbols(QtWidgets.QAbstractSpinBox.NoButtons) + self.spinBoxYStepSize.setDecimals(10) + self.spinBoxYStepSize.setMinimum(-1.0) + self.spinBoxYStepSize.setMaximum(1000000.0) + self.spinBoxYStepSize.setSingleStep(0.1) + self.spinBoxYStepSize.setProperty("value", -1.0) + self.spinBoxYStepSize.setObjectName("spinBoxYStepSize") + self.verticalLayout_6.addWidget(self.spinBoxYStepSize) + spacerItem16 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_6.addItem(spacerItem16) + self.horizontalLayout_4.addWidget(self.frame_3) + self.checkBoxSpaceFromData = QtWidgets.QCheckBox(self.tab_4) + self.checkBoxSpaceFromData.setEnabled(False) + font = QtGui.QFont() + font.setPointSize(10) + self.checkBoxSpaceFromData.setFont(font) + self.checkBoxSpaceFromData.setCheckable(True) + self.checkBoxSpaceFromData.setObjectName("checkBoxSpaceFromData") + self.horizontalLayout_4.addWidget(self.checkBoxSpaceFromData) + self.tabWidget.addTab(self.tab_4, "") + self.gridLayout_2.addWidget(self.tabWidget, 2, 2, 1, 1, QtCore.Qt.AlignRight) + MainWindow.setCentralWidget(self.centralwidget) + self.menubar = QtWidgets.QMenuBar(MainWindow) + self.menubar.setGeometry(QtCore.QRect(0, 0, 1200, 26)) + self.menubar.setObjectName("menubar") + self.menuFile = QtWidgets.QMenu(self.menubar) + self.menuFile.setObjectName("menuFile") + MainWindow.setMenuBar(self.menubar) + self.statusbar = QtWidgets.QStatusBar(MainWindow) + self.statusbar.setObjectName("statusbar") + MainWindow.setStatusBar(self.statusbar) + self.toolBar = QtWidgets.QToolBar(MainWindow) + self.toolBar.setObjectName("toolBar") + MainWindow.addToolBar(QtCore.Qt.TopToolBarArea, self.toolBar) + self.actionAddFromHDF = QtWidgets.QAction(MainWindow) + icon4 = QtGui.QIcon() + icon4.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/envelope-open-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.actionAddFromHDF.setIcon(icon4) + self.actionAddFromHDF.setObjectName("actionAddFromHDF") + self.actionSaveToHDF5 = QtWidgets.QAction(MainWindow) + icon5 = QtGui.QIcon() + icon5.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/envelope-closed-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off) + self.actionSaveToHDF5.setIcon(icon5) + self.actionSaveToHDF5.setObjectName("actionSaveToHDF5") + self.actionExit = QtWidgets.QAction(MainWindow) + icon6 = QtGui.QIcon() + icon6.addPixmap(QtGui.QPixmap(":/icons/open-iconic-master/png/account-logout-4x.png"), QtGui.QIcon.Normal, QtGui.QIcon.On) + self.actionExit.setIcon(icon6) + self.actionExit.setObjectName("actionExit") + self.menuFile.addAction(self.actionAddFromHDF) + self.menuFile.addAction(self.actionSaveToHDF5) + self.menuFile.addSeparator() + self.menuFile.addAction(self.actionExit) + self.menubar.addAction(self.menuFile.menuAction()) + self.toolBar.addAction(self.actionAddFromHDF) + self.toolBar.addAction(self.actionSaveToHDF5) + self.toolBar.addSeparator() + self.toolBar.addAction(self.actionExit) + + self.retranslateUi(MainWindow) + self.tabWidget.setCurrentIndex(0) + QtCore.QMetaObject.connectSlotsByName(MainWindow) + + def retranslateUi(self, MainWindow): + _translate = QtCore.QCoreApplication.translate + MainWindow.setWindowTitle(_translate("MainWindow", "Make Mosaic Dataset")) + self.label_5.setText(_translate("MainWindow", "M Rows")) + self.label_6.setText(_translate("MainWindow", "N Cols")) + self.label.setText(_translate("MainWindow", "Trim Row Start")) + self.label_2.setText(_translate("MainWindow", "Trim Row End")) + self.label_3.setText(_translate("MainWindow", "Trim Col Start")) + self.label_4.setText(_translate("MainWindow", "Trim Col End")) + self.checkBoxCompress.setText(_translate("MainWindow", "Compress")) + self.label_8.setText(_translate("MainWindow", "Row / Column First")) + self.comboBoxRowCol.setItemText(0, _translate("MainWindow", "Row")) + self.comboBoxRowCol.setItemText(1, _translate("MainWindow", "Column")) + self.checkBoxFlipH.setText(_translate("MainWindow", "Flip Horizontally")) + self.checkBoxFlipV.setText(_translate("MainWindow", "Flip Vertically")) + self.checkBoxTranspose.setText(_translate("MainWindow", "Transpose")) + self.label_7.setText(_translate("MainWindow", "Order of Inputs (Drag to Move)")) + self.labelWavenumber_2.setText(_translate("MainWindow", "Frequency Pixel")) + self.label_9.setText(_translate("MainWindow", "Estimated Frequency (cm-1)")) + self.label_10.setText(_translate("MainWindow", "Wavelength Intercept (nm)")) + self.label_11.setText(_translate("MainWindow", "Wavelength Slope (nm/pix)")) + self.label_12.setText(_translate("MainWindow", "Probe Wavelength (nm)")) + self.label_13.setText(_translate("MainWindow", "Calibration Wavelength (nm)")) + self.label_14.setText(_translate("MainWindow", "Current Center Wavelength (nm)")) + self.checkBoxSpectFromData.setText(_translate("MainWindow", "Loaded from Data")) + self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_3), _translate("MainWindow", "Spectral Calibration")) + self.label_15.setText(_translate("MainWindow", "X Step Size (um)")) + self.label_16.setText(_translate("MainWindow", "Y Step Size (um)")) + self.checkBoxSpaceFromData.setText(_translate("MainWindow", "Loaded from Data")) + self.tabWidget.setTabText(self.tabWidget.indexOf(self.tab_4), _translate("MainWindow", "Spatial Calibration")) + self.menuFile.setTitle(_translate("MainWindow", "File")) + self.toolBar.setWindowTitle(_translate("MainWindow", "toolBar")) + self.actionAddFromHDF.setText(_translate("MainWindow", "Add from HDF5")) + self.actionAddFromHDF.setShortcut(_translate("MainWindow", "Ctrl+O")) + self.actionSaveToHDF5.setText(_translate("MainWindow", "Save to HDF5")) + self.actionSaveToHDF5.setShortcut(_translate("MainWindow", "Ctrl+S")) + self.actionExit.setText(_translate("MainWindow", "Exit")) + +from . import icons_all_rc diff --git a/crikit/ui/qt_PlotEffect.py b/crikit/ui/qt_PlotEffect.py index f331c95..d59376d 100644 --- a/crikit/ui/qt_PlotEffect.py +++ b/crikit/ui/qt_PlotEffect.py @@ -1,17 +1,18 @@ # -*- coding: utf-8 -*- -# Form implementation generated from reading ui file '.\qt5-creator\ui_PlotEffect.ui' +# Form implementation generated from reading ui file '.\ui_PlotEffect.ui' # -# Created by: PyQt5 UI code generator 5.5.1 +# Created by: PyQt5 UI code generator 5.12 # # WARNING! All changes made in this file will be lost! from PyQt5 import QtCore, QtGui, QtWidgets + class Ui_Dialog(object): def setupUi(self, Dialog): Dialog.setObjectName("Dialog") - Dialog.resize(640, 977) + Dialog.resize(650, 200) self.verticalLayout = QtWidgets.QVBoxLayout(Dialog) self.verticalLayout.setObjectName("verticalLayout") self.horizontalLayout = QtWidgets.QHBoxLayout() @@ -57,4 +58,5 @@ def retranslateUi(self, Dialog): self.pushButtonOk.setText(_translate("Dialog", "Ok")) self.pushButtonCancel.setText(_translate("Dialog", "Cancel")) + from . import icons_all_rc diff --git a/crikit/ui/qt_PlotEffect_ALS.py b/crikit/ui/qt_PlotEffect_ALS.py index 3cbc607..98c3c7c 100644 --- a/crikit/ui/qt_PlotEffect_ALS.py +++ b/crikit/ui/qt_PlotEffect_ALS.py @@ -2,16 +2,17 @@ # Form implementation generated from reading ui file '.\ui_PlotEffect_ALS.ui' # -# Created by: PyQt5 UI code generator 5.5.1 +# Created by: PyQt5 UI code generator 5.12 # # WARNING! All changes made in this file will be lost! from PyQt5 import QtCore, QtGui, QtWidgets + class Ui_Form(object): def setupUi(self, Form): Form.setObjectName("Form") - Form.resize(738, 180) + Form.resize(800, 180) Form.setStyleSheet("font: 10pt \"Arial\";") self.gridLayout = QtWidgets.QGridLayout(Form) self.gridLayout.setObjectName("gridLayout") @@ -178,3 +179,4 @@ def retranslateUi(self, Form): self.label_2.setText(_translate("Form", "Lambda (smoothness)")) self.label_4.setText(_translate("Form", "Fix End-Points")) + diff --git a/crikit/ui/qt_PlotEffect_ALS2.py b/crikit/ui/qt_PlotEffect_ALS2.py new file mode 100644 index 0000000..a1baf3e --- /dev/null +++ b/crikit/ui/qt_PlotEffect_ALS2.py @@ -0,0 +1,225 @@ +# -*- coding: utf-8 -*- + +# Form implementation generated from reading ui file '.\ui_PlotEffect_ALS2.ui' +# +# Created by: PyQt5 UI code generator 5.12 +# +# WARNING! All changes made in this file will be lost! + +from PyQt5 import QtCore, QtGui, QtWidgets + + +class Ui_Form(object): + def setupUi(self, Form): + Form.setObjectName("Form") + Form.resize(800, 282) + Form.setStyleSheet("font: 10pt \"Arial\";") + self.gridLayout = QtWidgets.QGridLayout(Form) + self.gridLayout.setObjectName("gridLayout") + self.tableWidgetAsym = QtWidgets.QTableWidget(Form) + sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Maximum) + sizePolicy.setHorizontalStretch(0) + sizePolicy.setVerticalStretch(0) + sizePolicy.setHeightForWidth(self.tableWidgetAsym.sizePolicy().hasHeightForWidth()) + self.tableWidgetAsym.setSizePolicy(sizePolicy) + self.tableWidgetAsym.setMinimumSize(QtCore.QSize(0, 10)) + self.tableWidgetAsym.setBaseSize(QtCore.QSize(0, 140)) + self.tableWidgetAsym.setFrameShadow(QtWidgets.QFrame.Plain) + self.tableWidgetAsym.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAsNeeded) + self.tableWidgetAsym.setRowCount(0) + self.tableWidgetAsym.setObjectName("tableWidgetAsym") + self.tableWidgetAsym.setColumnCount(3) + item = QtWidgets.QTableWidgetItem() + self.tableWidgetAsym.setHorizontalHeaderItem(0, item) + item = QtWidgets.QTableWidgetItem() + self.tableWidgetAsym.setHorizontalHeaderItem(1, item) + item = QtWidgets.QTableWidgetItem() + self.tableWidgetAsym.setHorizontalHeaderItem(2, item) + self.tableWidgetAsym.horizontalHeader().setCascadingSectionResizes(True) + self.tableWidgetAsym.horizontalHeader().setDefaultSectionSize(80) + self.tableWidgetAsym.horizontalHeader().setHighlightSections(False) + self.tableWidgetAsym.horizontalHeader().setMinimumSectionSize(20) + self.tableWidgetAsym.horizontalHeader().setStretchLastSection(True) + self.gridLayout.addWidget(self.tableWidgetAsym, 3, 0, 1, 1) + self.frame_3 = QtWidgets.QFrame(Form) + self.frame_3.setFrameShape(QtWidgets.QFrame.StyledPanel) + self.frame_3.setFrameShadow(QtWidgets.QFrame.Plain) + self.frame_3.setObjectName("frame_3") + self.gridLayout_2 = QtWidgets.QGridLayout(self.frame_3) + self.gridLayout_2.setContentsMargins(5, 5, 5, 5) + self.gridLayout_2.setObjectName("gridLayout_2") + self.verticalLayout_3 = QtWidgets.QVBoxLayout() + self.verticalLayout_3.setObjectName("verticalLayout_3") + self.label_3 = QtWidgets.QLabel(self.frame_3) + self.label_3.setObjectName("label_3") + self.verticalLayout_3.addWidget(self.label_3, 0, QtCore.Qt.AlignLeft|QtCore.Qt.AlignTop) + self.spinBoxRedux = QtWidgets.QSpinBox(self.frame_3) + self.spinBoxRedux.setMinimum(1) + self.spinBoxRedux.setMaximum(10000) + self.spinBoxRedux.setObjectName("spinBoxRedux") + self.verticalLayout_3.addWidget(self.spinBoxRedux, 0, QtCore.Qt.AlignTop) + spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_3.addItem(spacerItem) + self.gridLayout_2.addLayout(self.verticalLayout_3, 0, 1, 1, 1) + self.verticalLayout_2 = QtWidgets.QVBoxLayout() + self.verticalLayout_2.setObjectName("verticalLayout_2") + self.label_2 = QtWidgets.QLabel(self.frame_3) + font = QtGui.QFont() + font.setFamily("Arial") + font.setPointSize(10) + font.setBold(False) + font.setItalic(False) + font.setWeight(50) + self.label_2.setFont(font) + self.label_2.setObjectName("label_2") + self.verticalLayout_2.addWidget(self.label_2, 0, QtCore.Qt.AlignLeft) + spacerItem1 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_2.addItem(spacerItem1) + self.gridLayout_2.addLayout(self.verticalLayout_2, 0, 0, 1, 1) + self.verticalLayout_4 = QtWidgets.QVBoxLayout() + self.verticalLayout_4.setObjectName("verticalLayout_4") + self.label_4 = QtWidgets.QLabel(self.frame_3) + self.label_4.setObjectName("label_4") + self.verticalLayout_4.addWidget(self.label_4, 0, QtCore.Qt.AlignHCenter|QtCore.Qt.AlignVCenter) + self.checkBox = QtWidgets.QCheckBox(self.frame_3) + self.checkBox.setMinimumSize(QtCore.QSize(20, 20)) + self.checkBox.setText("") + self.checkBox.setChecked(True) + self.checkBox.setObjectName("checkBox") + self.verticalLayout_4.addWidget(self.checkBox, 0, QtCore.Qt.AlignHCenter|QtCore.Qt.AlignTop) + self.gridLayout_2.addLayout(self.verticalLayout_4, 1, 1, 1, 1) + self.gridLayout.addWidget(self.frame_3, 1, 1, 2, 1) + self.frame = QtWidgets.QFrame(Form) + sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Preferred) + sizePolicy.setHorizontalStretch(0) + sizePolicy.setVerticalStretch(0) + sizePolicy.setHeightForWidth(self.frame.sizePolicy().hasHeightForWidth()) + self.frame.setSizePolicy(sizePolicy) + self.frame.setFrameShape(QtWidgets.QFrame.StyledPanel) + self.frame.setFrameShadow(QtWidgets.QFrame.Plain) + self.frame.setObjectName("frame") + self.horizontalLayout_2 = QtWidgets.QHBoxLayout(self.frame) + self.horizontalLayout_2.setContentsMargins(0, 0, 0, 0) + self.horizontalLayout_2.setObjectName("horizontalLayout_2") + self.verticalLayout = QtWidgets.QVBoxLayout() + self.verticalLayout.setObjectName("verticalLayout") + self.label = QtWidgets.QLabel(self.frame) + self.label.setObjectName("label") + self.verticalLayout.addWidget(self.label, 0, QtCore.Qt.AlignLeft) + spacerItem2 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout.addItem(spacerItem2) + self.label_6 = QtWidgets.QLabel(self.frame) + self.label_6.setObjectName("label_6") + self.verticalLayout.addWidget(self.label_6) + self.spinBoxAsymSubSections = QtWidgets.QSpinBox(self.frame) + self.spinBoxAsymSubSections.setMaximum(5) + self.spinBoxAsymSubSections.setObjectName("spinBoxAsymSubSections") + self.verticalLayout.addWidget(self.spinBoxAsymSubSections) + spacerItem3 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout.addItem(spacerItem3) + self.horizontalLayout_2.addLayout(self.verticalLayout) + self.gridLayout.addWidget(self.frame, 1, 0, 1, 1) + self.label_5 = QtWidgets.QLabel(Form) + self.label_5.setObjectName("label_5") + self.gridLayout.addWidget(self.label_5, 0, 0, 1, 1) + self.frame_4 = QtWidgets.QFrame(Form) + self.frame_4.setFrameShape(QtWidgets.QFrame.StyledPanel) + self.frame_4.setFrameShadow(QtWidgets.QFrame.Plain) + self.frame_4.setObjectName("frame_4") + self.verticalLayout_8 = QtWidgets.QVBoxLayout(self.frame_4) + self.verticalLayout_8.setContentsMargins(5, 5, 5, 5) + self.verticalLayout_8.setObjectName("verticalLayout_8") + self.verticalLayout_9 = QtWidgets.QVBoxLayout() + self.verticalLayout_9.setContentsMargins(-1, 0, -1, -1) + self.verticalLayout_9.setSpacing(0) + self.verticalLayout_9.setObjectName("verticalLayout_9") + self.label_9 = QtWidgets.QLabel(self.frame_4) + self.label_9.setObjectName("label_9") + self.verticalLayout_9.addWidget(self.label_9) + self.spinBoxMaxIter = QtWidgets.QSpinBox(self.frame_4) + self.spinBoxMaxIter.setMinimum(1) + self.spinBoxMaxIter.setMaximum(1000000) + self.spinBoxMaxIter.setProperty("value", 100) + self.spinBoxMaxIter.setObjectName("spinBoxMaxIter") + self.verticalLayout_9.addWidget(self.spinBoxMaxIter) + spacerItem4 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_9.addItem(spacerItem4) + self.label_10 = QtWidgets.QLabel(self.frame_4) + self.label_10.setObjectName("label_10") + self.verticalLayout_9.addWidget(self.label_10) + self.verticalLayout_8.addLayout(self.verticalLayout_9) + spacerItem5 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_8.addItem(spacerItem5) + self.gridLayout.addWidget(self.frame_4, 1, 3, 1, 1) + self.verticalLayout_5 = QtWidgets.QVBoxLayout() + self.verticalLayout_5.setSizeConstraint(QtWidgets.QLayout.SetNoConstraint) + self.verticalLayout_5.setObjectName("verticalLayout_5") + self.horizontalLayout = QtWidgets.QHBoxLayout() + self.horizontalLayout.setContentsMargins(-1, 0, 0, -1) + self.horizontalLayout.setObjectName("horizontalLayout") + self.verticalLayout_6 = QtWidgets.QVBoxLayout() + self.verticalLayout_6.setContentsMargins(-1, 0, -1, -1) + self.verticalLayout_6.setObjectName("verticalLayout_6") + self.label_7 = QtWidgets.QLabel(Form) + self.label_7.setObjectName("label_7") + self.verticalLayout_6.addWidget(self.label_7) + self.spinBoxWSubSections = QtWidgets.QSpinBox(Form) + self.spinBoxWSubSections.setMaximum(5) + self.spinBoxWSubSections.setObjectName("spinBoxWSubSections") + self.verticalLayout_6.addWidget(self.spinBoxWSubSections) + spacerItem6 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_6.addItem(spacerItem6) + self.horizontalLayout.addLayout(self.verticalLayout_6) + self.verticalLayout_7 = QtWidgets.QVBoxLayout() + self.verticalLayout_7.setObjectName("verticalLayout_7") + self.label_8 = QtWidgets.QLabel(Form) + self.label_8.setObjectName("label_8") + self.verticalLayout_7.addWidget(self.label_8) + spacerItem7 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding) + self.verticalLayout_7.addItem(spacerItem7) + self.horizontalLayout.addLayout(self.verticalLayout_7) + self.verticalLayout_5.addLayout(self.horizontalLayout) + self.tableWidgetWeights = QtWidgets.QTableWidget(Form) + sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Maximum) + sizePolicy.setHorizontalStretch(0) + sizePolicy.setVerticalStretch(0) + sizePolicy.setHeightForWidth(self.tableWidgetWeights.sizePolicy().hasHeightForWidth()) + self.tableWidgetWeights.setSizePolicy(sizePolicy) + self.tableWidgetWeights.setMinimumSize(QtCore.QSize(0, 70)) + self.tableWidgetWeights.setBaseSize(QtCore.QSize(0, 65)) + self.tableWidgetWeights.setObjectName("tableWidgetWeights") + self.tableWidgetWeights.setColumnCount(2) + self.tableWidgetWeights.setRowCount(0) + item = QtWidgets.QTableWidgetItem() + self.tableWidgetWeights.setHorizontalHeaderItem(0, item) + self.tableWidgetWeights.horizontalHeader().setDefaultSectionSize(80) + self.tableWidgetWeights.horizontalHeader().setStretchLastSection(True) + self.verticalLayout_5.addWidget(self.tableWidgetWeights) + self.gridLayout.addLayout(self.verticalLayout_5, 3, 1, 1, 2) + + self.retranslateUi(Form) + QtCore.QMetaObject.connectSlotsByName(Form) + + def retranslateUi(self, Form): + _translate = QtCore.QCoreApplication.translate + Form.setWindowTitle(_translate("Form", "Form")) + item = self.tableWidgetAsym.horizontalHeaderItem(0) + item.setText(_translate("Form", "Start X")) + item = self.tableWidgetAsym.horizontalHeaderItem(1) + item.setText(_translate("Form", "End X")) + item = self.tableWidgetAsym.horizontalHeaderItem(2) + item.setText(_translate("Form", "P (Asymmetry) Value")) + self.label_3.setText(_translate("Form", "Sub-Sampling Factor")) + self.label_2.setText(_translate("Form", "Lambda (smoothness)")) + self.label_4.setText(_translate("Form", "Fix End-Points")) + self.label.setText(_translate("Form", "Define P (Asymmetry)")) + self.label_6.setText(_translate("Form", "P Subsections")) + self.label_5.setText(_translate("Form", "Fixed=P")) + self.label_9.setText(_translate("Form", "Max Iterations")) + self.label_10.setText(_translate("Form", "Min Difference")) + self.label_7.setText(_translate("Form", "Weighted (Subsections)")) + self.label_8.setText(_translate("Form", "Weight Value")) + item = self.tableWidgetWeights.horizontalHeaderItem(0) + item.setText(_translate("Form", "Start X")) + + diff --git a/crikit/ui/qt_PlotEffect_Calibrate.py b/crikit/ui/qt_PlotEffect_Calibrate.py index 8b4d7a7..a95f182 100644 --- a/crikit/ui/qt_PlotEffect_Calibrate.py +++ b/crikit/ui/qt_PlotEffect_Calibrate.py @@ -2,16 +2,17 @@ # Form implementation generated from reading ui file '.\ui_PlotEffect_Calibrate.ui' # -# Created by: PyQt5 UI code generator 5.5.1 +# Created by: PyQt5 UI code generator 5.12 # # WARNING! All changes made in this file will be lost! from PyQt5 import QtCore, QtGui, QtWidgets + class Ui_Form(object): def setupUi(self, Form): Form.setObjectName("Form") - Form.resize(643, 415) + Form.resize(800, 300) Form.setStyleSheet("font: 10pt \"Arial\";") self.horizontalLayout = QtWidgets.QHBoxLayout(Form) self.horizontalLayout.setObjectName("horizontalLayout") @@ -263,3 +264,4 @@ def retranslateUi(self, Form): self.label_15.setText(_translate("Form", "Measured WN")) self.label_16.setText(_translate("Form", "Correct WN")) + diff --git a/crikit/ui/subui_hdf_load.py b/crikit/ui/subui_hdf_load.py deleted file mode 100644 index 69458a2..0000000 --- a/crikit/ui/subui_hdf_load.py +++ /dev/null @@ -1,223 +0,0 @@ -""" -HDF5 LOAD DATA QDialog (crikit.vis.subguis.h5loadgui) -======================================================= - - H5LoadGUI : A graphical user interface (GUI) to select HDF5 dataset(s) - - Method : H5LoadGUI.getFileDataSets() - - Return (tuple) : (path [str], filename [str], dataset(s) [list], selection_made [bool]) - -""" - - -# Append sys path -import sys as _sys -import os as _os - -# Generic imports for QT-based programs -from PyQt5.QtWidgets import (QApplication as _QApplication, \ -QDialog as _QDialog, QFileDialog as _QFileDialog, \ -QTableWidgetItem as _QTableWidgetItem) - -# Other imports -import numpy as _np -import crikit.utils.h5 as _h5utils - -# Import from Designer-based GUI -from crikit.ui.qt_HDFLoad import Ui_Dialog ### EDIT ### - -class SubUiHDFLoad(_QDialog): ### EDIT ### - """ GUI Loader Class for H5 Files """ - - def __init__(self, parent = None): - - # Generic load/init designer-based GUI - super(SubUiHDFLoad, self).__init__(parent) ### EDIT ### - self.ui = Ui_Dialog() ### EDIT ### - self.ui.setupUi(self) ### EDIT ### - - # Set static GUI parameters - - # Set signal(s)-slot(s) connection/actions - - self.ui.pushButtonOk.clicked.connect(self.accept) - self.ui.pushButtonCancel.clicked.connect(self.reject) - self.ui.dataGroupSelect.currentTextChanged.connect(self.datagroupchange) - self.ui.dataSetList.itemClicked.connect(self.datasetselected) - self.ui.filterButton.clicked.connect(self.filterlist) - self.ui.resetFilter.clicked.connect(self.datagroupchange) - # Setup GUI variables - self.path = None - self.filename = None - self.allselect=None - # Initial Actions - - @staticmethod - def getFileDataSets(start_path='./', parent = None): - """ - Retrieve the filename and datasets selected by the user (via GUI) - - Parameters - ---------- - start_path : str - Home directory to start in - - Returns - ---------- - out : (tuple) - path : str - filename : (str) - dataset(s) : (list[str]) - """ - if start_path is None: - start_path = './' - - dialog = SubUiHDFLoad(parent) - - ret_fileopen = dialog.fileopen(start_path) - - if ret_fileopen is None: - return None - - # Execute dialog, which defined by QDialog class returns - # QDialog.Accepted or QDialog.Rejected - ret_dset_select = dialog.exec_() - if ret_dset_select == _QDialog.Rejected: - return None - elif dialog.allselect is None: - return None - else: - return (dialog.path, dialog.filename, dialog.allselect) - - def fileopen(self, start_path='./'): - """ Select HDF5 File """ - - if start_path is None: - start_path = './' - - filename = _QFileDialog.getOpenFileName(self, "Open H5 File", - start_path,\ - "HDF5 Files (*.h5 *.hdf);;All Files (*.*)") - - if filename[0]: - self.filename = filename[0] - self.path = _os.path.dirname(self.filename) + '/' - self.filename = self.filename.split(_os.path.dirname(self.filename))[1][1::] - - self.group_dset_dict = _h5utils.retrieve_group_dataset_dict(self.path + self.filename) - self.ui.dataGroupSelect.clear() - for count in self.group_dset_dict: - self.ui.dataGroupSelect.addItem(count) - return [self.path, self.filename] - else: - return None - def datagroupchange(self): - """ Action : ComboBox containing Groups with DataSets has changed""" - - #self.dsetlist = QListWidget(self.verticalLayoutWidget) - self.ui.dataSetList.clear() - self.ui.dataSetList.addItems(self.group_dset_dict[self.ui.dataGroupSelect.currentText()]) - #print('Changed') - - def datasetselected(self): - """ Action : One or more DataSets were selected from the list """ - - #print('Selection changed') - self.currentdset = self.ui.dataGroupSelect.currentText() + '/' + \ - self.ui.dataSetList.currentItem().text() - -# print('Current Selection : {}'.format(self.currentdset)) - self.allselect = ['/' + str(self.ui.dataGroupSelect.currentText() +\ - '/' + i.text()) for i in self.ui.dataSetList.selectedItems()] - - - if len(self.allselect) == 0: - self.allselect = None - self.ui.currentDatasetText.setText('') - attrs = {} - self.ui.dataSetAttribs.setRowCount(0) - self.ui.dataSetMemo.setText('') - else: - if len(self.allselect) == 1: - self.ui.currentDatasetText.setText(self.currentdset) - else: - self.ui.currentDatasetText.setText(self.currentdset + ' ( + ' +\ - str(len(self.allselect)-1) + ' others)' ) - - self.ui.dataSetAttribs.setSortingEnabled(False) - self.ui.dataSetAttribs.setRowCount(0) - self.ui.dataSetAttribs.setColumnCount(2) - - attrs = _h5utils.retrieve_dataset_attribute_dict(self.path + self.filename,self.currentdset) - - for count, key in enumerate(attrs.keys()): - self.ui.dataSetAttribs.insertRow(self.ui.dataSetAttribs.rowCount()) - self.ui.dataSetAttribs.setItem(count,0,_QTableWidgetItem(str(key))) - temp = attrs[key] - if isinstance(temp,_np.bytes_): - self.ui.dataSetAttribs.setItem(count,1,_QTableWidgetItem(temp.decode())) - else: - self.ui.dataSetAttribs.setItem(count,1,_QTableWidgetItem(str(temp))) - - self.ui.dataSetAttribs.setSortingEnabled(True) - self.ui.dataSetAttribs.sortItems(0) - - try: - self.ui.dataSetMemo.setText(attrs['Memo'].decode()) - except: - pass - - def filterlist(self): - """ Action : Filter available dataset list (.ui.dataSetList) based on - include or exclude strings (or comma-separated strings) - """ - - temp_list = [] - - for count in range(self.ui.dataSetList.count()): - temp_list.append(self.ui.dataSetList.item(count).text()) - - temp_list_filt = temp_list - - # Has strings to Exclude - if self.ui.filterExcludeString.text() != '': - # Convert comma-separated string to list-of-strings - strexclude = str.split(self.ui.filterExcludeString.text(),',') - - # Strip white-space - strexclude = [str.strip(strexclude) for strexclude in strexclude] - - # Exclude Filter - for count in strexclude[0::]: - temp_list_filt = ([i for i in temp_list_filt if str.find(i,count) == -1]) - #print(count) - else: - pass - - # Has strings to Include - if self.ui.filterIncludeString.text() != '': - # Convert comma-separated string to list-of-strings - strinclude = str.split(self.ui.filterIncludeString.text(),',') - - # Strip white-space - strinclude = [str.strip(strinclude) for strinclude in strinclude] - - # Include Filter - for count in strinclude: - temp_list_filt = ([i for i in temp_list_filt if str.find(i,count) != -1]) - else: - pass - - # Update GUI - self.ui.dataSetList.clear() - self.ui.dataSetList.addItems(temp_list_filt) - -if __name__ == '__main__': - - app = _QApplication(_sys.argv) - #win = H5LoadGUI() ### EDIT ### - result = SubUiHDFLoad.getFileDataSets() - print('Result: {}'.format(result)) - - _sys.exit() diff --git a/crikit/ui/widget_ALS.py b/crikit/ui/widget_ALS.py index 2cee0b6..4696973 100644 --- a/crikit/ui/widget_ALS.py +++ b/crikit/ui/widget_ALS.py @@ -8,21 +8,24 @@ """ import numpy as _np +from PyQt5.QtWidgets import QTableWidgetItem as _QTableWidgetItem + from crikit.ui.dialog_AbstractPlotEffect import (AbstractPlotEffectPlugin as _AbstractPlotEffectPlugin) -from crikit.ui.qt_PlotEffect_ALS import Ui_Form as _Ui_Form +from crikit.ui.qt_PlotEffect_ALS2 import Ui_Form as _Ui_Form from crikit.ui.widget_scientificspin import (ScientificDoubleSpinBox as _SciSpin) from crikit.preprocess.algorithms.als import AlsCvxopt as _Als +from crikit.utils.general import find_nearest as _find_nearest class widgetALS(_AbstractPlotEffectPlugin): """ Widget for PlotEffect that adjusts the parameters appropriate for asymmetric least squares (ALS) - + Parameters ---------- smoothness_param : float, optional (default, 1e3) @@ -30,131 +33,258 @@ class widgetALS(_AbstractPlotEffectPlugin): asym_param : float, optional (default, 1e-4) Assymetry parameter - + redux : int, optional (default, 1) Reduction parameter to sub-sample input signal - + order : int, optional (default, 2) Derivative regularization term. Order=2 for Whittaker-smoother - + fix_end_points : bool, optional (default, False) Weight the baseline endpoints to approach equally the end-points of the data. - + max_iter : int, optional (default, 100) Maximum number of least-squares iterations to perform - + min_diff : float, optional (default, 1e-5) Break iterative calculations if difference is less than min_diff - + parent: QObject Parent - + Methods ------- fcn : Perform ALS detrending - + Signals: changed : a value in the UI has changed """ - + # Parameter dict that will be returned from PlotEffect # Will be updated later in program to contain all parameters # to pass to underlying algorithm - parameters = {'name' : 'ALS', + parameters = {'name' : 'ALS', 'long_name' : 'Asymmetric least squares'} - + # Labeling options for original data plot labels_orig = { 'x_label' : 'Wavenumber (cm$^{-1}$)', 'y_label' : 'Input Int (au)', 'title' : 'Original' } - - # Labeling options for affected data plot + + # Labeling options for affected data plot labels_affected = { 'x_label' : labels_orig['x_label'], 'y_label' : 'Output Int (au)', 'title' : 'Detrended' } - - def __init__(self, asym_param=1e-3, smoothness_param=1, redux=10, - pstart=1e-2, pend=1e-3, fixed_p=True, fix_end_points=True, - max_iter=100, min_diff=1e-6, parent = None): - + + def __init__(self, x=None, rng=None, smoothness_param=1, asym_param=1e-3, redux=10, + order=2, fix_end_points=True, fix_const=1, fix_rng=None, + max_iter=100, min_diff=1e-6, verbose=False, sub_asym_list=None, + sub_w_list=None, parent = None): + super(widgetALS, self).__init__(parent) ### EDIT ### + + self._x = x + self.rng = rng + self.ui = _Ui_Form() self.ui.setupUi(self) - + + + self.sub_asym_list = sub_asym_list + self.sub_w_list = sub_w_list + + # ! Change this into its own function after + # ! the asym table widget is all setup + if not self.sub_asym_list: + self.parameters['asym_param'] = asym_param + else: + self.parameters['asym_param'] = 0*self.x + asym_param + # Update parameter dict self.parameters['smoothness_param'] = smoothness_param - self.parameters['asym_param'] = asym_param - self.parameters['fixed_p'] = fixed_p - self.parameters['asym_param_start'] = pstart - self.parameters['asym_param_end'] = pend + self.parameters['rng'] = rng self.parameters['redux'] = redux + self.parameters['order'] = order self.parameters['fix_end_points'] = fix_end_points + self.parameters['fix_rng'] = fix_rng + self.parameters['fix_const'] = fix_const self.parameters['max_iter'] = max_iter self.parameters['min_diff'] = min_diff - + self.parameters['verbose'] = verbose + self.setup_asym() # Setup controls for asymmetry parameter self.setup_smoothness() # Setup controls for smoothness parameter - + # Redux factor self.ui.spinBoxRedux.setValue(self.parameters['redux']) # Fixed ends self.ui.checkBox.setChecked(self.parameters['fix_end_points']) - + # Max iterations self.ui.spinBoxMaxIter.setValue(self.parameters['max_iter']) - + # Min Difference self.ui.spinBoxMinDiff = _SciSpin() self.ui.verticalLayout_9.insertWidget(4, self.ui.spinBoxMinDiff) self.ui.spinBoxMinDiff.setValue(self.parameters['min_diff']) - + # SIGNALS & SLOTS self.ui.spinBoxP.editingFinished.connect(self.spinBoxChanged) self.ui.spinBoxLambda.editingFinished.connect(self.spinBoxChanged) self.ui.spinBoxRedux.editingFinished.connect(self.spinBoxChanged) - - self.ui.spinBoxPStart.editingFinished.connect(self.spinBoxChanged) - self.ui.spinBoxPEnd.editingFinished.connect(self.spinBoxChanged) + self.ui.spinBoxMaxIter.editingFinished.connect(self.spinBoxChanged) self.ui.spinBoxMinDiff.editingFinished.connect(self.spinBoxChanged) - - self.ui.radioButtonFixedP.clicked.connect(self.selectFixedOrLog) - self.ui.radioButtonLogLinearP.clicked.connect(self.selectFixedOrLog) + self.ui.checkBox.clicked.connect(self.selectFixedEnds) - - + + self.ui.spinBoxAsymSubSections.valueChanged.connect(self.asym_sub_val_change) + self.ui.spinBoxWSubSections.valueChanged.connect(self.weight_sub_val_change) + + self.ui.spinBoxWeight = _SciSpin() + self.ui.spinBoxWeight.setMinimum(0) + self.ui.spinBoxWeight.setMaximum(1e10) + self.ui.spinBoxWeight.setValue(1) + self.ui.spinBoxWeight.editingFinished.connect(self.weightspinboxchanged) + self.ui.verticalLayout_7.insertWidget(1, self.ui.spinBoxWeight) + + @property + def x(self): + if self.rng is None: + return self._x + else: + return self._x[self.rng] + + def weight_sub_val_change(self): + """ Weights Subsections spinbox has changed value """ + sbval = self.ui.spinBoxWSubSections.value() + n_rows = self.ui.tableWidgetWeights.rowCount() + n_cols = self.ui.tableWidgetWeights.columnCount() + + max_x = _np.max(self.x) + min_x = _np.min(self.x) + + if sbval > n_rows: + for nr in _np.arange(n_rows, sbval): + self.ui.tableWidgetWeights.setRowCount(sbval) + n_rows = self.ui.tableWidgetWeights.rowCount() + + # Start X + scispin = _SciSpin() + scispin.setMinimum(self._x.min()) + scispin.setMaximum(self._x.max()) + scispin.setValue(min_x) + scispin.editingFinished.connect(self.weightspinboxchanged) + self.ui.tableWidgetWeights.setCellWidget(nr, 0, scispin) + + # Stop X + scispin = _SciSpin() + scispin.setMinimum(self._x.min()) + scispin.setMaximum(self._x.max()) + scispin.setValue(max_x) + scispin.editingFinished.connect(self.weightspinboxchanged) + self.ui.tableWidgetWeights.setCellWidget(nr, 1, scispin) + + # Weight Parameter + # scispin = _SciSpin() + # scispin.setMinimum(0) + # scispin.setMaximum(1e4) + # scispin.setValue(1) + # scispin.editingFinished.connect(self.weightspinboxchanged) + # self.ui.tableWidgetWeights.setCellWidget(nr, 2, scispin) + elif sbval < n_rows: + for nr in _np.arange(sbval, n_rows): + for nc in range(n_cols): + sw = self.ui.tableWidgetWeights.cellWidget(nr, nc) + sw.editingFinished.disconnect() + + self.ui.tableWidgetWeights.setRowCount(sbval) + n_rows = self.ui.tableWidgetWeights.rowCount() + + self.weightspinboxchanged() + + def asym_sub_val_change(self): + """ P Subsections spinbox has changed value """ + sbval = self.ui.spinBoxAsymSubSections.value() + n_rows = self.ui.tableWidgetAsym.rowCount() + n_cols = self.ui.tableWidgetAsym.columnCount() + + max_x = _np.max(self.x) + min_x = _np.min(self.x) + + if sbval > n_rows: + for nr in _np.arange(n_rows, sbval): + self.ui.tableWidgetAsym.setRowCount(sbval) + n_rows = self.ui.tableWidgetAsym.rowCount() + + # Start X + scispin = _SciSpin() + scispin.setMinimum(self._x.min()) + scispin.setMaximum(self._x.max()) + scispin.setValue(min_x) + scispin.editingFinished.connect(self.asymspinboxchanged) + self.ui.tableWidgetAsym.setCellWidget(nr, 0, scispin) + + # Stop X + scispin = _SciSpin() + scispin.setMinimum(self._x.min()) + scispin.setMaximum(self._x.max()) + scispin.setValue(max_x) + scispin.editingFinished.connect(self.asymspinboxchanged) + self.ui.tableWidgetAsym.setCellWidget(nr, 1, scispin) + + # Asym Parameter + scispin = _SciSpin() + scispin.setMinimum(0) + scispin.setMaximum(1e20) + scispin.setValue(self.ui.spinBoxP.value()) + scispin.editingFinished.connect(self.asymspinboxchanged) + self.ui.tableWidgetAsym.setCellWidget(nr, 2, scispin) + elif sbval < n_rows: + for nr in _np.arange(sbval, n_rows): + for nc in range(n_cols): + sw = self.ui.tableWidgetAsym.cellWidget(nr, nc) + sw.editingFinished.disconnect() + + self.ui.tableWidgetAsym.setRowCount(sbval) + n_rows = self.ui.tableWidgetAsym.rowCount() + + self.asymspinboxchanged() + def fcn(self, data_in): """ If return list, [0] goes to original, [1] goes to affected """ - + data_out = _np.zeros(data_in.shape) baseline = _np.zeros(data_in.shape) - - if callable(self.parameters['asym_param']): - self.parameters['asym_param'] = \ - self.parameters['asym_param'](data_in.shape[-1]) - - smoothness_param = self.parameters['smoothness_param'] - asym_param = self.parameters['asym_param'] - redux = self.parameters['redux'] - fep = self.parameters['fix_end_points'] - max_iter = self.parameters['max_iter'] - min_diff = self.parameters['min_diff'] - - _als = _Als(smoothness_param=smoothness_param, - asym_param=asym_param, - redux=redux, fix_end_points=fep, - max_iter=max_iter, - min_diff=min_diff) - + + # if callable(self.parameters['asym_param']): + # self.parameters['asym_param'] = \ + # self.parameters['asym_param'](data_in.shape[-1]) + + # smoothness_param = self.parameters['smoothness_param'] + # asym_param = self.parameters['asym_param'] + # redux = self.parameters['redux'] + # fep = self.parameters['fix_end_points'] + # max_iter = self.parameters['max_iter'] + # min_diff = self.parameters['min_diff'] + # order = self.parameters['order'] + # rng = self.parameters['rng'] + # fix_rng = self.parameters['fix_rng'] + # smoothness_param=1e3, asym_param=1e-4, redux=1, + # order=2, rng=None, fix_end_points=False, fix_rng=None, + # fix_const=1, max_iter=100, min_diff=1e-5, verbose=False + + _als = _Als(**self.parameters) + if data_in.ndim == 1: baseline = _als.calculate(data_in) data_out = data_in - baseline @@ -163,121 +293,134 @@ def fcn(self, data_in): baseline[num,:] = _als.calculate(spectrum) data_out[num,:] = spectrum - baseline[num,:] return [baseline, data_out] - - + + def setup_smoothness(self): - """ + """ Lambda/smoothness parameter rlated """ - + self.ui.label_2.setText('{} (Smoothness)'.format(u'\u03BB')) self.ui.spinBoxLambda = _SciSpin() self.ui.verticalLayout_2.insertWidget(1, self.ui.spinBoxLambda) self.ui.spinBoxLambda.setValue(self.parameters['smoothness_param']) - + def setup_asym(self): """ P/asymmetry parameter related """ - - + self.ui.spinBoxP = _SciSpin() self.ui.verticalLayout.insertWidget(1, self.ui.spinBoxP) self.ui.spinBoxP.setValue(self.parameters['asym_param']) - if self.parameters['fixed_p']: - self.ui.radioButtonFixedP.setChecked(True) - self.ui.radioButtonLogLinearP.setChecked(False) - else: - self.ui.radioButtonFixedP.setChecked(False) - self.ui.radioButtonLogLinearP.setChecked(True) - self.selectFixedOrLog() - - self.ui.spinBoxPStart = _SciSpin() - self.ui.verticalLayout_5.insertWidget(1, self.ui.spinBoxPStart) - self.ui.spinBoxPStart.setValue(self.parameters['asym_param_start']) + + def asymspinboxchanged(self): + """ + Asymetry parameter-related values have changed + """ + n_rows = self.ui.tableWidgetAsym.rowCount() - self.ui.spinBoxPEnd = _SciSpin() - self.ui.verticalLayout_6.insertWidget(1, self.ui.spinBoxPEnd) - self.ui.spinBoxPEnd.setValue(self.parameters['asym_param_end']) + # * Currently, asym_param in ALS is in the full vector space + x = self._x + + self.sub_asym_list = [] + + if n_rows == 0: + self.parameters['asym_param'] = self.ui.spinBoxP.value() + else: + self.parameters['asym_param'] = self.ui.spinBoxP.value() + 0*x + for rc in range(n_rows): + xstart_pix = _find_nearest(x, + self.ui.tableWidgetAsym.cellWidget(rc, 0).value())[1] + xstop_pix = _find_nearest(x, + self.ui.tableWidgetAsym.cellWidget(rc, 1).value())[1] + asym = self.ui.tableWidgetAsym.cellWidget(rc, 2).value() + + self.parameters['asym_param'][xstart_pix:xstop_pix+1] = 1*asym + print('XStart: {}, XStop: {}, ASym: {}'.format(xstart_pix, xstop_pix, asym)) + self.sub_asym_list.append([xstart_pix, xstop_pix, asym]) + + print('---------') + self.changed.emit() + + def weightspinboxchanged(self): + """ + Weight parameter-related values have changed + """ + n_rows = self.ui.tableWidgetWeights.rowCount() + # * Currently, fix_rng (weight parameters) in ALS is in the rng vector space + x = self.x + + self.sub_w_list = [] + + if n_rows == 0: + self.parameters['fix_rng'] = None + else: + self.parameters['fix_rng'] = [] + for rc in range(n_rows): + xstart_pix = _find_nearest(x, + self.ui.tableWidgetWeights.cellWidget(rc, 0).value())[1] + xstop_pix = _find_nearest(x, + self.ui.tableWidgetWeights.cellWidget(rc, 1).value())[1] + weight = self.ui.spinBoxWeight.value() + + # self.parameters['fix_rng'].extend(_np.arange(xstart_pix, xstop_pix+1).tolist()) + self.parameters['fix_rng'].extend(_np.arange(xstart_pix, xstop_pix).tolist()) # No +1 + + # self.parameters['asym_param'][xstart_pix:xstop_pix+1] = 1*asym + # print('XStart: {}, XStop: {}, ASym: {}'.format(xstart_pix, xstop_pix, asym)) + self.sub_w_list.append([xstart_pix, xstop_pix, weight]) + self.parameters['fix_rng'] = _np.array(self.parameters['fix_rng']) + self.parameters['fix_const'] = self.ui.spinBoxWeight.value() + print('---------') + self.changed.emit() + def spinBoxChanged(self): """ Controller for all spinBoxes """ - sdr = self.sender() - - if sdr == self.ui.spinBoxPStart: - self.parameters['asym_param_start'] = self.ui.spinBoxPStart.value() - self.selectFixedOrLog() - - elif sdr == self.ui.spinBoxPEnd: - self.parameters['asym_param_end'] = self.ui.spinBoxPEnd.value() - self.selectFixedOrLog() - - elif sdr == self.ui.spinBoxLambda: + + if sdr == self.ui.spinBoxLambda: self.parameters['smoothness_param'] = self.ui.spinBoxLambda.value() - + elif sdr == self.ui.spinBoxP: - self.parameters['asym_param'] = self.ui.spinBoxP.value() - + self.asymspinboxchanged() + elif sdr == self.ui.spinBoxRedux: self.parameters['redux'] = self.ui.spinBoxRedux.value() - + elif sdr == self.ui.spinBoxMaxIter: self.parameters['max_iter'] = self.ui.spinBoxMaxIter.value() - + elif sdr == self.ui.spinBoxMinDiff: self.parameters['min_diff'] = self.ui.spinBoxMinDiff.value() - + self.changed.emit() - + def selectFixedEnds(self): """ Check selection of fixed end-points """ - + self.parameters['fix_end_points'] =self.ui.checkBox.isChecked() self.changed.emit() - - def selectFixedOrLog(self): - """ - Check fixed or log-linear asymmetry parameter - """ - - self.parameters['fixed_p'] = self.ui.radioButtonFixedP.isChecked() - if self.parameters['fixed_p']: - self.ui.radioButtonFixedP.setChecked(True) - self.ui.radioButtonLogLinearP.setChecked(False) - self.ui.frame_2.setEnabled(False) - self.ui.frame.setEnabled(True) -# self.p = lambda x: self.ui.spinBoxP.value() - self.parameters['asym_param'] = self.ui.spinBoxP.value() - - else: - self.ui.radioButtonFixedP.setChecked(False) - self.ui.radioButtonLogLinearP.setChecked(True) - self.ui.frame_2.setEnabled(True) - self.ui.frame.setEnabled(False) - self.parameters['asym_param'] = \ - lambda x: _np.logspace(_np.log10(self.parameters['asym_param_start']), - _np.log10(self.parameters['asym_param_end']),x) - self.changed.emit() - - + if __name__ == '__main__': import sys as _sys from PyQt5.QtWidgets import (QApplication as _QApplication) - - + + app = _QApplication(_sys.argv) app.setStyle('Cleanlooks') - winALS = widgetALS() - + x = _np.linspace(500, 4000, 1001) + winALS = widgetALS(x=x) + winALS.show() - + app.exec_() print(winALS.parameters) _sys.exit() \ No newline at end of file diff --git a/crikit/ui/widget_Jupyter.py b/crikit/ui/widget_Jupyter.py index 91eca55..cbdc455 100644 --- a/crikit/ui/widget_Jupyter.py +++ b/crikit/ui/widget_Jupyter.py @@ -23,9 +23,14 @@ class QJupyterWidget(RichJupyterWidget): """ Convenience class for a live IPython console widget. We can replace the standard banner using the customBanner argument""" def __init__(self,customBanner=None,*args,**kwargs): super(QJupyterWidget, self).__init__(*args,**kwargs) - if customBanner!=None: self.banner=customBanner + if customBanner!=None: + self.banner=customBanner self.kernel_manager = kernel_manager = QtInProcessKernelManager() kernel_manager.start_kernel() + def _abort_queues(kernel): + # ! See IPython Issue: https://github.com/ipython/ipykernel/issues/370 + pass + kernel_manager.kernel._abort_queues = _abort_queues kernel_manager.kernel.gui = 'qt' self.kernel_client = kernel_client = self._kernel_manager.client() diff --git a/crikit/ui/widget_images.py b/crikit/ui/widget_images.py index b70cd1d..f4a3a41 100644 --- a/crikit/ui/widget_images.py +++ b/crikit/ui/widget_images.py @@ -39,7 +39,9 @@ # Generic imports for MPL-incorporation import matplotlib as _mpl from matplotlib.pyplot import colormaps as _plt_colormaps -import sciplot as _sciplot + +from sciplot.sciplotUI import SciPlotUI as _SciPlotUI + #import matplotlib.pyplot as _plt _mpl.use('Qt5Agg') @@ -81,7 +83,7 @@ def clear(self): Resets the ui to it's initial state """ self.ui.checkBoxDisable.setChecked(False) - + self.ui.spinBoxGain.setValue(1.0) self.ui.tabWidgetMath.setCurrentIndex(0) @@ -96,7 +98,7 @@ def clear(self): self.ui.comboBoxCondOps.setCurrentIndex(0) self.ui.comboBoxCondInEquality.setCurrentIndex(0) self.ui.spinBoxInEquality.setValue(0.0) - + def condOpsChange(self): index = self.ui.comboBoxCondOps.currentIndex() @@ -137,7 +139,7 @@ def operationchange(self): self.ui.pushButtonOpFreq3.setEnabled(True) class widgetPopSpectrumGS(_QWidget): - """ + """ Panel that let's user pop the current image, an average spectrum, or a grayscale image to SciPlot """ @@ -165,7 +167,7 @@ def __init__(self, parent=None, **kwargs): self.ui.setupUi(self) # Get all MPL named colors - color_list = ['red', 'green', 'blue', 'magenta', 'cyan', 'yellow', + color_list = ['red', 'green', 'blue', 'magenta', 'cyan', 'yellow', 'black', 'white', 'CUSTOM'] color_list.extend(sorted(set(_mpl.colors.cnames.keys()) - set(color_list))) self.ui.comboBoxBGColor.addItems(color_list) @@ -188,11 +190,11 @@ def __init__(self, parent = None, **kwargs): self.win = Ui_Blank() self.win.setupUi(self) self.win.gridLayout.setEnabled(False) - + self._img_defaults = {'showcbar': True, 'axison': True} self.gsinfo = widgetGrayScaleInfoBar(parent=self) - + self.colormode = widgetColorMode(parent=self) self.colormode.ui.comboBoxColorMode.setCurrentIndex(1) self.colormode.ui.comboBoxColormap.setVisible(True) @@ -213,9 +215,9 @@ def __init__(self, parent = None, **kwargs): self.win.horizLayout.setContentsMargins(2,2,2,2) self.win.verticalLayout.insertLayout(0, self.win.horizLayout) - - self.win.horizLayout.insertWidget(0, self.gsinfo, _QtCore.Qt.AlignHCenter) - self.win.horizLayout.insertWidget(0, self.colormode, _QtCore.Qt.AlignBottom) + + self.win.horizLayout.insertWidget(0, self.gsinfo, alignment=_QtCore.Qt.AlignHCenter) + self.win.horizLayout.insertWidget(0, self.colormode, alignment=_QtCore.Qt.AlignBottom) # Initialize underlying data self.initData() @@ -225,31 +227,34 @@ def __init__(self, parent = None, **kwargs): self.data.grayscaleimage = _np.dot(_np.ones([100,1]),_np.linspace(1,100,100)[None,:]) self.data.set_x(_np.linspace(1,400,self.data.xlen)) self.data.set_y(_np.linspace(1,400,self.data.ylen)) - + # Calculate extent of image winextent = (self.data.x.min(), self.data.x.max(), self.data.y.min(), self.data.y.max()) # MPL canvas self.mpl = _MplCanvas(**kwargs) self.mpl.cbar = None # Monkey patch on a cbar object - + # Create stand-image plot self.createImg(img=self.data.image, xunits=self.data.xunits, yunits=self.data.yunits, extent=winextent, cmap=self.colormode.ui.comboBoxColormap.currentText()) - self.mpl.fig.tight_layout() - + try: + self.mpl.fig.tight_layout() + except: + print('tight_layout failed (widget_images 1') + # Insert canvas widget into this widget - self.win.verticalLayout.insertWidget(0,self.mpl,_QtCore.Qt.AlignCenter) - self.win.verticalLayout.insertWidget(0,self.popimage,_QtCore.Qt.AlignCenter) - self.win.verticalLayout.insertWidget(0,self.mpl.toolbar, _QtCore.Qt.AlignHCenter) + self.win.verticalLayout.insertWidget(0,self.mpl, alignment=_QtCore.Qt.AlignCenter) + self.win.verticalLayout.insertWidget(0,self.popimage, alignment=_QtCore.Qt.AlignCenter) + self.win.verticalLayout.insertWidget(0,self.mpl.toolbar, alignment=_QtCore.Qt.AlignHCenter) # # SIGNAL & SLOTS self.ui.checkBoxFixed.stateChanged.connect(self.checkBoxFixed) self.ui.checkBoxRemOutliers.stateChanged.connect(self.checkBoxRemOutliers) self.ui.spinBoxStdDevs.editingFinished.connect(self.checkBoxRemOutliers) - + # New self.ui.comboBoxAboveMax.currentIndexChanged.connect(self.comboBoxCompress) self.ui.comboBoxBelowMin.currentIndexChanged.connect(self.comboBoxCompress) @@ -276,15 +281,15 @@ def createImg_Ext(self, img, xunits = None, yunits = None, Create new figure window and show image of img """ - self.external_plots.append(_sciplot.main(parent=parent)) - self.external_plots[-1].imshow(img, x_label=xunits, y_label=yunits, + self.external_plots.append(_SciPlotUI(parent=parent)) + self.external_plots[-1].imshow(img, x_label=xunits, y_label=yunits, cmap=cmap, cbar=showcbar, extent=extent) def createImg(self, img, xunits = None, yunits = None, extent = None, cmap = _mpl.cm.gray): self.mpl.ax.clear() self.mpl.img = self.mpl.ax.imshow(img, interpolation = 'none', - extent = extent, cmap = cmap, + extent = extent, cmap = cmap, origin='lower') if xunits is not None: self.mpl.ax.xaxis.set_label_text(xunits) @@ -304,13 +309,13 @@ def createImg(self, img, xunits = None, yunits = None, if self.ui.checkBoxFixed.isChecked() == False: self.ui.spinBoxMax.setValue(self.data.maxer) self.ui.spinBoxMin.setValue(self.data.minner) - + def spinBoxMinMaxSet(self): try: self.data.setmin = self.ui.spinBoxMin.value() self.data.setmax = self.ui.spinBoxMax.value() self.ui.checkBoxFixed.setChecked(True) - + # Spin-Box call from Outlier-related widgets? sent_by = self.sender() if ((sent_by == self.ui.checkBoxRemOutliers) | @@ -344,10 +349,10 @@ def checkBoxRemOutliers(self): self.ui.spinBoxMax.setValue(new_max) self.ui.spinBoxMin.setValue(new_min) self.spinBoxMinMaxSet() - + self.createImg(img=self.data.image, xunits=self.data.xunits, yunits=self.data.yunits, - extent=self.data.winextent, + extent=self.data.winextent, cmap=self.colormode.ui.comboBoxColormap.currentText()) self.mpl.draw() @@ -382,7 +387,7 @@ def checkBoxFixed(self): self.createImg(img=self.data.image, xunits=self.data.xunits, yunits=self.data.yunits, - extent=self.data.winextent, + extent=self.data.winextent, cmap=self.colormode.ui.comboBoxColormap.currentText()) self.mpl.draw() @@ -412,6 +417,8 @@ class widgetSglColor(widgetBWImg): """ def __init__(self, parent=None, **kwargs): super().__init__(parent) + self.win.gridLayout.setEnabled(False) + self._img_defaults = {'showcbar': False, 'axison': True} self.initData() self.data.grayscaleimage = _np.dot(_np.ones([100,1]),_np.linspace(1,100,100)[None,:]) @@ -419,13 +426,13 @@ def __init__(self, parent=None, **kwargs): self.data.set_y(_np.linspace(1,400,self.data.ylen)) self.changeColor() self.colormode.setMaximumHeight(130) - + self.math = widgetImageGainMath(parent=self) self.win.verticalLayout.insertWidget(3, self.math) # Disconnect colormap-related (from BW parent) self.colormode.ui.comboBoxColormap.currentIndexChanged.disconnect() - + self.colormode.ui.comboBoxColorMode.setCurrentIndex(0) self.colormode.ui.comboBoxColormap.setVisible(False) self.colormode.ui.labelColormap.setVisible(False) @@ -438,7 +445,7 @@ def __init__(self, parent=None, **kwargs): self.colormode.ui.comboBoxFGColor.currentIndexChanged.connect(self.changeColor) self.colormode.ui.comboBoxBGColor.currentIndexChanged.connect(self.changeColor) - self.math.ui.spinBoxGain.valueChanged.connect(self.applyGain) + self.math.ui.spinBoxGain.editingFinished.connect(self.applyGain) self.math.ui.pushButtonGain1.pressed.connect(self.gain1) self.math.ui.checkBoxDisable.stateChanged.connect(self.disabled) @@ -449,11 +456,11 @@ def __init__(self, parent=None, **kwargs): pass self.popimage.ui.pushButtonPop.pressed.connect(lambda: self.createImg_Ext(img = self.data.image, showcbar=False, - extent=self.data.winextent, + extent=self.data.winextent, xunits=self.data.xunits, yunits=self.data.yunits, parent=parent)) - + try: self.popimage.ui.pushButtonGSPop.pressed.disconnect() except TypeError: @@ -470,11 +477,11 @@ def initData(self): (Re)-initialize self.data """ self.data = SingleColor() - - + + def changeColor(self): # try: - + if self.sender() == self.colormode.ui.comboBoxFGColor: color_str = self.colormode.ui.comboBoxFGColor.currentText() if color_str == 'CUSTOM': @@ -496,12 +503,12 @@ def changeColor(self): else: self.data.bgcolor = _mpl.colors.colorConverter.to_rgb(_mpl.colors.cnames[bgcolor_str]) - + self.createImg(img = self.data.image, xunits = self.data.xunits, yunits = self.data.yunits, extent = self.data.winextent) self.mpl.draw() - + def applyGain(self): self.data.setgain = self.math.ui.spinBoxGain.value() self.changeColor() @@ -535,7 +542,7 @@ def __init__(self, sgl_color_widget_list = None, parent = None, **kwargs): self.data.grayscaleimage = _np.dot(_np.ones([100,1]),_np.linspace(1,100,100)[None,:]) self.data.set_x(_np.linspace(1,400,self.data.xlen)) self.data.set_y(_np.linspace(1,400,self.data.ylen)) - + winextent = (self.data.x.min(), self.data.x.max(), self.data.y.min(), self.data.y.max()) # Instantiate mpl widget @@ -549,7 +556,7 @@ def __init__(self, sgl_color_widget_list = None, parent = None, **kwargs): color_list.extend(sorted(set(_mpl.colors.cnames.keys()) - set(color_list))) self.ui.comboBoxBGColor.addItems(color_list) self.ui.comboBoxBGColor.setCurrentIndex(color_list.index('black')) - + # Emission/Absorption mode settings self.ui.comboBoxColorMode.setCurrentIndex(0) # Emission mode is default @@ -557,17 +564,20 @@ def __init__(self, sgl_color_widget_list = None, parent = None, **kwargs): self.createImg(img = self.data.image, xunits = self.data.xunits, yunits = self.data.yunits, extent = winextent) - self.mpl.fig.tight_layout() + try: + self.mpl.fig.tight_layout() + except: + print('tight_layout failed (widget_image: 3') # Insert mpl widget into this widget - self.ui.verticalLayout.insertWidget(0,self.mpl,_QtCore.Qt.AlignHCenter) - self.ui.verticalLayout.insertWidget(0,self.mpl.toolbar, _QtCore.Qt.AlignHCenter) + self.ui.verticalLayout.insertWidget(0,self.mpl, alignment=_QtCore.Qt.AlignHCenter) + self.ui.verticalLayout.insertWidget(0,self.mpl.toolbar, alignment=_QtCore.Qt.AlignHCenter) self.popimage = widgetPopSpectrumGS(self) - self.ui.verticalLayout.insertWidget(1, self.popimage, _QtCore.Qt.AlignLeft) + self.ui.verticalLayout.insertWidget(1, self.popimage, alignment=_QtCore.Qt.AlignHCenter) self.popimage.ui.pushButtonPop.pressed.connect(lambda: self.createImg_Ext(img = self.data.image, showcbar=False, - extent=self.data.winextent, + extent=self.data.winextent, xunits=self.data.xunits, yunits=self.data.yunits, parent=parent)) @@ -582,7 +592,7 @@ def initData(self, sgl_color_widget_list): """ (Re)-initialize self.data """ - + if sgl_color_widget_list is None: self.data = CompositeColor() else: @@ -618,8 +628,8 @@ def createImg_Ext(self, img, xunits = None, yunits = None, Create new figure window and show image of img """ - self.external_plots.append(_sciplot.main(parent=parent)) - self.external_plots[-1].imshow(img, x_label=xunits, y_label=yunits, + self.external_plots.append(_SciPlotUI(parent=parent)) + self.external_plots[-1].imshow(img, x_label=xunits, y_label=yunits, cmap=cmap, cbar=showcbar, extent=extent) # BROKEN -- May never work @@ -635,7 +645,7 @@ def createImg_Ext(self, img, xunits = None, yunits = None, # extent = self.data.winextent) # self.mpl.fig.tight_layout() # self.mpl.draw() - + def changeMode(self): self.data.mode = self.ui.comboBoxColorMode.currentIndex() # self.data.mode = _np.abs(self.data.mode - 1).astype(int) @@ -643,7 +653,10 @@ def changeMode(self): self.createImg(img = self.data.image, xunits = self.data.xunits, yunits = self.data.yunits, extent = self.data.winextent) - self.mpl.fig.tight_layout() + try: + self.mpl.fig.tight_layout() + except: + print('tight_layout failed (widget_image: 3') self.mpl.draw() @@ -655,7 +668,7 @@ def changeMode(self): winBWImg = widgetBWImg() winBWImg.setWindowTitle('BW Image') winBWImg.show() - + winSglColor = widgetSglColor() winSglColor.setWindowTitle('Single Color') winSglColor.colormode.ui.comboBoxBGColor.setCurrentIndex(7) @@ -666,8 +679,8 @@ def changeMode(self): winSglColor2.colormode.ui.comboBoxBGColor.setCurrentIndex(7) winSglColor2.setWindowTitle('Single Color') winSglColor2.show() - - + + winColorMath = widgetImageGainMath() winColorMath.setWindowTitle('Color Math') winColorMath.show() diff --git a/crikit/utils/breadcrumb.py b/crikit/utils/breadcrumb.py index 331b012..d88af19 100644 --- a/crikit/utils/breadcrumb.py +++ b/crikit/utils/breadcrumb.py @@ -14,11 +14,12 @@ import time as _time import copy as _copy import pickle as _pickle +from collections import OrderedDict as _OrderedDict class BCPre: """ Container that describes processing steps (ie it contains "breadcrumbs") - + Attributes ---------- process_list : list @@ -26,68 +27,70 @@ class BCPre: ['Process Name', 'Var1 Name', Val1, 'Var2 Name', Val2, ...]. The \ variable names and values may be input values to the pre-processing \ step. Only the Process Name is mnadatory: the rest are optional. - + backed_flag : list Flag identifying which steps were backed-up to disk (e.g., for undo) - + id_list : list (read-only) Unique identifier for each step. Can be used to name back-up/undo files cut_list : list (read-only) Identifier of id's cut with pop_to_last method - + num_steps : int Number of processing steps - + attr_dict : dict Dictionary-version of process_list that can be written to HDF5 dataset metadata (properties) - + Methods ------- add_step : Add a new processing step - + backed_up : Mark most recent process step as backed up in backed_flag list - + pop_to_last : Remove entries until nearest backup point (excluding current \ step). - + """ - - HDF_PREFIX = 'Processing.Steps' - + + PREFIX = 'Processing.Steps' + def __init__(self): self.process_list = [] self._id_list = [] self.backed_flag = [] self._cut_list = [] - + # PROPERTIES @property def id_list(self): - # Use shallow-copy to prevent ability to append + # Use shallow-copy to prevent ability to append # to _id_list via id_list return self._id_list.copy() - + @property def cut_list(self): - # Use shallow-copy to prevent ability to append + # Use shallow-copy to prevent ability to append # to _cut_list via cut_list return self._cut_list.copy() - + @cut_list.deleter def cut_list(self): self._cut_list = [] - + @property def num_steps(self): return len(self.process_list) - + @property def attr_dict(self): - temp = {} + temp = _OrderedDict() + temp[self.PREFIX] = self.num_steps + for num, item in enumerate(self.process_list): - temp_key_process_prefix = self.HDF_PREFIX + '.' + str(num+1) + '.' + str(item[0]) + temp_key_process_prefix = self.PREFIX + '.' + str(num+1) + '.' + str(item[0]) temp_val = 'NA' temp[temp_key_process_prefix] = temp_val if len(item) > 1: @@ -97,9 +100,9 @@ def attr_dict(self): temp_key = temp_key_process_prefix + '.' + str(var) temp_val = item[2*num_var+2] temp[temp_key] = temp_val - temp[self.HDF_PREFIX] = self.num_steps + return temp - + @property def dset_name_suffix(self): temp = '' @@ -116,14 +119,14 @@ def dset_name_suffix(self): return temp except: return None - + # METHODS @staticmethod def backup_pickle(data, fname, addl_attr = None): """ - Dump current state of data (class of type crikit.data.spectrum or - subclass)to pickle file (filename= fname). - + Dump current state of data (class of type crikit.data.spectrum or + subclass)to pickle file (filename= fname). + Can append additional attributes (addl_attr) to \ attribute dictionary (self.attr) """ @@ -137,7 +140,7 @@ def backup_pickle(data, fname, addl_attr = None): # Pickle with highest protocol # Surpasses the default protocol 3 4Gb limit _pickle.dump(data, f, protocol=-1) - + @staticmethod def load_pickle(fname): """ @@ -151,11 +154,11 @@ def load_pickle(fname): with open(fname, 'rb') as f: return _pickle.load(f) - + def add_step(self, process_desc): """ Adds a steps to the list - + Parameters ------ process_desc : list @@ -164,54 +167,59 @@ def add_step(self, process_desc): variable names and values may be input values to the \ pre-processing step. Only the Process Name is mnadatory: the rest \ are optional. - + Returns ------- None : None - + """ - assert isinstance(process_desc,list), 'The input need be a list' - assert len(process_desc)%2 != 0, 'The input needs to be an odd length (title, var name 1, var value 1, etc)' - - # Ensures unique IDs based on time. Note some systems only report in - # seconds, not sub-seconds + + if not isinstance(process_desc,list): + raise TypeError('Added step need be of type list') + + if len(process_desc)%2 == 0: + err_str = 'The input needs to be an odd length (title, var name 1, var value 1, etc)' + raise ValueError(err_str) + + # Ensures unique IDs based on time. Note some systems only report in + # seconds, not sub-seconds _time.sleep(1) self.process_list.append(process_desc) self._id_list.append(str(_time.time())) self.backed_flag.append(False) - + def backed_up(self): """ Marks most recent process step as backed up in backed_flag list - + Parameters ------ None : None - + Returns ------- None : None - + """ self.backed_flag[-1] = True - + def pop_to_last(self, all=False): """ - Remove entries until nearest backup point (excluding current step). + Remove entries until nearest backup point (excluding current step). That is, if current step IS a backup point, moves to previous one. If \ current step is NOT a backup point, moves to nearest point. - + If all = True, will cut everything """ temp = _copy.deepcopy(self.backed_flag) - backup_locs = [] + backup_locs = [] for num, val in enumerate(temp): if val is True: backup_locs.append(num) - + current_loc = len(temp) - 1 - + if all is False: if temp[-1] == True: # Current is backed-up, go to previous num_to_pop = backup_locs[-1] - backup_locs[-2] @@ -219,7 +227,7 @@ def pop_to_last(self, all=False): num_to_pop = current_loc - backup_locs[-1] else: num_to_pop = len(temp) - + for count in range(num_to_pop): self.process_list.pop() is_backed_up = self.backed_flag.pop() @@ -227,8 +235,8 @@ def pop_to_last(self, all=False): self._cut_list.append(self._id_list.pop()) else: self._id_list.pop() - - + + if __name__ == '__main__': import sys as _sys test = BCPre() @@ -240,41 +248,41 @@ def pop_to_last(self, all=False): test.add_step(['Test',1]) except: print('Expected Error\n') - + test.add_step(['Raw']) test.add_step(['SubDark','RangeStart',-1500,'RangeEnd',-400]) test.add_step(['NormKK','Amp',100.0,'Phase',10.0]) #test.add_step(['DeTrend','Lambda',1000.0,'p',0.001,'Method','ALS','Type','Phase']) #test.add_step(['DeTrend','Order',2,'win',601,'Method','sg','Type','Scale']) - + #print('Attempting to append \'1\' to the end of id_list (it should not work)') #test.id_list.append(1) #print(test.id_list) - + print('\nProcess list: {}'.format(test.process_list)) print('\nID list: {}'.format(test.id_list)) print('\nNumber of process steps: {}'.format(test.num_steps)) print('\n\nReturned attribute dict: {}'.format(test.attr_dict)) print('\n\nGenerated dataset name: {}'.format(test.dset_name_suffix)) _sys.exit() - + #[['Raw'], ['SubDark'], ['SubResidual', 'RangeStart', -1500, 'RangeEnd', -400]] - - + + # print('\n\n\nWritten to backup file: {}'.format(test.backed_flag)) # print('\n...Apply backed_up...') # test.backed_up() # print('\nWritten to backup file: {}'.format(test.backed_flag)) -# +# # print('\nAdjust backup') # test.backed_flag[0] = True # print('Written to backup file: {}'.format(test.backed_flag)) -# +# # print('\n Test Pop-to-last') # print('Process List: {}'.format(test.process_list)) # print('ID List: {}'.format(test.id_list)) # print('Written to backup file: {}\n'.format(test.backed_flag)) -# +# # test.pop_to_last() # print('Process List: {}'.format(test.process_list)) # print('ID List: {}'.format(test.id_list)) @@ -282,7 +290,7 @@ def pop_to_last(self, all=False): # print('Cut List:{}'.format(test.cut_list)) # del test.cut_list # print('Cut List:{}'.format(test.cut_list)) -# +# # print('\nCut all') # test.pop_to_last(all=True) # print('Process List: {}'.format(test.process_list)) @@ -291,4 +299,4 @@ def pop_to_last(self, all=False): # print('Cut List:{}'.format(test.cut_list)) # del test.cut_list # print('Cut List:{}'.format(test.cut_list)) -# \ No newline at end of file +# \ No newline at end of file diff --git a/crikit/utils/general.py b/crikit/utils/general.py index 0670914..6016323 100644 --- a/crikit/utils/general.py +++ b/crikit/utils/general.py @@ -9,11 +9,86 @@ find_nearest : Given a vector and a value, find the index and value of the closest match + pad : Wrapper around numpy.pad that also returns a window defining the + original signal + Notes ----- """ import numpy as _np +def pad(y, pad_width, mode): + """ + Pad array with either constants or edge values. + + Note: For N-D arrays, pads the -1 axis + + Parameters + ---------- + y : ndarray + Input array + + pad_width : int + Size of padding on each side of y + + mode : str + 'constant' (0), 'edge' currently accepted + + Returns + ------- + y_pad, window + Padded array and window. Window defines the region of the original signal + """ + if pad_width <= 0: + return y, _np.ones(y.shape[-1]) + else: + shaper = list(y.shape) + shaper_out = list(y.shape) + shaper_out[-1] += 2*pad_width + y_pad = _np.zeros(shaper_out, dtype=y.dtype) + window = _np.zeros(shaper_out[-1], dtype=_np.integer) + + y_pad[...,pad_width:shaper[-1]+pad_width] = 1*y + window[pad_width:shaper[-1]+pad_width] = 1 + + if (mode == 'zeros') | (mode == 'constant') | (mode == 'zero'): + pass + elif mode == 'edge': + y_pad[...,:pad_width] = _np.dot(y[...,0:1], _np.ones((1, pad_width))) + y_pad[..., -pad_width:] = _np.dot(y[...,-1:-2:-1], _np.ones((1, pad_width))) + + return y_pad, window + +def pad_dual(y, edge_pad_width, constant_pad_width): + """ + Pad array with edge values followed by constant 0's. + + Note: For N-D arrays, pads the -1 axis + + Parameters + ---------- + y : ndarray + Input array + + edge_pad_width : int + Size of edge-value padding on each side of y + + constant_pad_width : int + Size of 0-padding on each side of y after edge-value padding + + Returns + ------- + y_pad, window + Padded array and window. Window defines the region of the original signal + """ + y_pad_edge, win_edge = pad(y, edge_pad_width, 'edge') + y_pad, win_constant = pad(y_pad_edge, constant_pad_width, 'constant') + + window = 0*win_constant + window[_np.where(win_constant == 1)[0][win_edge == 1]] = 1 + + return y_pad, window + def np_fcn_nd_to_1d(fcn, data, axis=-1): """ Take in an n-dimensional array and return a 1D version operated on by fcn.\ @@ -172,7 +247,7 @@ def lin_from_row_col(row, col, sh): x = _np.random.rand(10,11) for ct in range(x.size): - row, col = lin_count_row_col(ct, x.shape) + row, col = row_col_from_lin(ct, x.shape) print('R: {} C: {}'.format(row,col)) print('Total number iterated through: {}'.format(ct+1)) @@ -202,7 +277,7 @@ def lin_from_row_col(row, col, sh): space_shp = _np.array(x.shape)[0:-1] num_sp = space_shp.prod() for num in range(num_sp): - rc, cc = lin_count_row_col(num, space_shp) + rc, cc = row_col_from_lin(num, space_shp) y[rc, cc, :] = _np.fft.fft(x[rc, cc, :]) tmr -= _timeit.default_timer() print('Time with 1 for-loops: {:.3g} sec'.format(-tmr)) diff --git a/crikit/utils/h5.py b/crikit/utils/h5.py deleted file mode 100644 index 3ba637a..0000000 --- a/crikit/utils/h5.py +++ /dev/null @@ -1,436 +0,0 @@ -""" -hdf5 utilities (crikit.utils.h5) -======================================================= - - Utilities for for reading and writing data to HDF5 files - -Methods --------- - convert_to_np_dtype : convert from HDF5 dataset to numpy ndarray with \ - numpy-builtin and native datatype - - retrieve_group_dataset_dict : Retrieve dictionary describing groups that \ - contain data [key] and the datasets [value]. {group : [dataset(s)]} - - retrieve_dataset_attribute_dict : Retrieve dictionary describing \ - attributes that contain data [key] and the datasets [value]. \ - {group : [dataset(s)]} - -""" - -import h5py as _h5py -_h5py.get_config().complex_names = ('Re','Im') - -import numpy as _np - -def convert_to_np_dtype(dset): - """ - Given an HDF5 dataset, return the values in a numpy-builtin datatype - - Parameters - ---------- - dset : h5py.Dataset - HDF5 (h5py) dataset - - Returns - ------- - out : numpy.ndarray (dtype = numpy built-in) - - Notes - ----- - The software accounts for big-/little-endianness, and the inability of \ - hdf5 to natively store complex numbers. - - """ - assert isinstance(dset, _h5py.Dataset), 'Input is not of type h5py.Dataset' - # Single datatype - if len(dset.dtype) == 0: - converted = _np.ndarray(dset.shape, dtype = dset.dtype.newbyteorder('=')) - dset.read_direct(converted) - if issubclass(converted.dtype.type, _np.integer): # Integer to float - converted = converted.astype(_np.float) - return converted - #Compound datatype of length 2-- assumed ('Re','Im') - elif len(dset.dtype) == 2: - print('Warning: h5py.complex_names set incorrectly using \'{}\' and \'{}\' \ -for Re and Im, respectively'.format(dset.dtype.names[0], dset.dtype.names[1])) - _h5py.get_config().complex_names = (dset.dtype.names[0],dset.dtype.names[1]) - dset = dset.file[dset.name] - converted = _np.ndarray(dset.shape, dtype = dset.dtype.newbyteorder('=')) - dset.read_direct(converted) - # Unknown datatype - else: - print('Warning: Unknown datatype. Returning dataset values as is.') - return dset.value - return converted - - -def retrieve_group_dataset_dict(filename): - """ - Given an HDF5 filename, return a dictionary with keys named with full \ - paths to datasets (values) - - Parameters - ---------- - filename : str - filename of HDF5 file - - Returns - ------- - out : dict - {group path : [dataset list]} - - Notes - ----- - - """ - try: - f = _h5py.File(filename,'r') - except OSError as err: - print(err) - else: - list_of_items = ['/'] - f.visit(list_of_items.append) - - groups_all = [] - datasets_all = [] - - for count in list_of_items: - if isinstance(f[count],_h5py.Group) == True: - groups_all.append(count) - if isinstance(f[count],_h5py.Dataset) == True: - datasets_all.append(count) - - groups_with_datasets = [] - - for group_count in groups_all: - for item_count in f[group_count]: - if isinstance(f[group_count][item_count],_h5py.Dataset): - groups_with_datasets.append(group_count) - break - - # Setup dictionary group_with_dataset : datasetnames - group_dataset_dict = [] - for group_count in groups_with_datasets: - dataset_list = [] - for item_count in f[group_count]: - if isinstance(f[group_count][item_count],_h5py.Dataset): - dataset_list.append(item_count) - group_dataset_dict.append([group_count,dataset_list]) - - group_dataset_dict = dict(group_dataset_dict) - - #print('Returning {0} groups covering {1} datasets'.format\ - # (len(groups_with_datasets), len(datasets_all))) - - - - f.close() - return group_dataset_dict - -def retrieve_dataset_attribute_dict(filename,datasetfullname): - """ - Given an HDF5 filename and dataset, return a dictionary with keys named \ - with parameters and values - - Parameters - ---------- - filename : str - filename of HDF5 file - - datasetfullname : str - full pathname to dataset (e.g., /group/subgroup/dataset) - - Returns - ------- - out : dict - {parameter : value} - - Notes - ----- - - """ - try: - f = _h5py.File(filename,'r') - except OSError as err: - print(err) - else: - try: - attrs = f[datasetfullname].attrs - temp = dict(attrs) - except: - print('Error in attributes... Usually an empty one') - temp = {} - for count in attrs: - try: - temp[count] = attrs[count] - except: - pass - return temp - f.close() - return None - -def special_exclude_datasets(filename, str_excl = '_background', new_filename = None): - """ - Removes any datasets with '_background' in the name. Creates a new - h5 file with '_excl*_.h5' appended (unless specified) - - Parameters - ---------- - filename (str) : name of file to analyze/repack/copy - - str_excl (str) : (default: '_background') exclude datasets with this string in the name - - new_filename (str) : (Optional) Output filename - - Returns - ------- - str : filename of new HDF5 file - - Writes a new file filename(-.h5) + '_excl_' + str_exclude + '.h5' - - Notes - ----- - SPECIAL : Only likely useful for the NIST developers - - """ - - if new_filename == None: - new_filename = str.strip(filename,'.h5') + '_excl_' + str_excl.strip('_') + '.h5' - else: - pass - - dataset_dict = retrieve_group_dataset_dict(filename) - - f_input = _h5py.File(filename, 'r') - f_output = _h5py.File(new_filename, 'w-') - - try: - # Interate trhough groups/subgroups - for groups in dataset_dict: - dsets_in_group = dataset_dict[groups] - - # Iterate through each filename in this group - for dset_name in dsets_in_group: - if str.find(dset_name,str_excl) == -1: - temp_name = groups + '/' + dset_name - loc = f_output.require_group(f_input[temp_name].parent.name) - print('Copying: {}'.format(temp_name)) - f_input.copy(temp_name,loc) - del temp_name - except: - print('There was an error') - return None - f_input.close() - f_output.close() - return new_filename - -def special_repack(filename, repack_str = '_Movie_', new_filename = None): - """ - Find datasets (1D) with a given repack_str and concatenates them into - a larger array. Other datasets are copied as is. - - Creates a new h5 file with '_repack_' + repack_str(-'_') + .h5' appended - - Parameters - ---------- - filename (str) : name of file to analyze/repack/copy - - repack_str (str) : string to find in datasets to concatenate - - new_filename (str) : (Optional) Output filename - - Returns - ------- - str : filename of new HDF5 file - - Writes a new file filename + '_repack_' + repack_str(-'_') + .h5' - - Notes - ----- - The output file cannot already exist - - SPECIAL : Only likely useful for the NIST developers - - """ - - if new_filename == None: - new_filename = str.strip(filename,'.h5') + '_repack_' + \ - repack_str.strip('_') + '.h5' - else: - pass - - dataset_dict = retrieve_group_dataset_dict(filename) - - f_input = _h5py.File(filename, 'r') - f_output = _h5py.File(new_filename, 'w-') - - try: - # Iterate through each data-containing group - for groups in dataset_dict: - dsets_in_group = dataset_dict[groups] - # Turn dataset list into one long string and look for - # repack_str if there are none, copy the whole group - if str(dsets_in_group).find(repack_str) == -1: - loc = f_output.require_group(groups) - for dset in dsets_in_group: - name = groups + '/' + dset - f_input.copy(name,loc) - else: - # Create a set from the list to remove identical entries - unique_dset_prefix_list = \ - list(set([str.split(dset_names,repack_str)[0] \ - for dset_names in dsets_in_group])) - - for unique_dset_prefix in unique_dset_prefix_list: - dset_w_prefix = [dset_names for dset_names in \ - dsets_in_group \ - if dset_names.find(unique_dset_prefix) != -1] - - name = groups + '/' + dset_w_prefix[0] - - # Init larger array with expanded size, same dtype - repack_array = _np.ndarray([len(dset_w_prefix), \ - f_input[name].value.shape[0]], dtype = \ - f_input[name].dtype) - - # Fill in columns - for count in enumerate(dset_w_prefix): - name = groups + '/' + count[1] - repack_array[count[0],:] = f_input[name].value - - loc = f_output.require_group(groups) - f_output[str(groups + '/' + unique_dset_prefix)] = repack_array - name = groups + '/' + dset_w_prefix[0] - input_attrs = f_input[str(groups + '/' + \ - dset_w_prefix[0])].attrs - - # Copy attribute from first dataset to the repack_array - for attr in input_attrs: - try: - f_output[str(groups + '/' + \ - unique_dset_prefix)].attrs.create(attr, \ - input_attrs[attr]) - except: - pass - except: - print('There was an error') - - f_input.close() - f_output.close() - - return new_filename - -def special_shrink_datasets(filename, dset_path, dset_name, stepsize, - xstep_attr='RasterScanParams.FastAxisSteps', - xstep_size_attr='RasterScanParams.FastAxisStepSize', - ystep_attr='RasterScanParams.SlowAxisSteps', - ystep_size_attr='RasterScanParams.SlowAxisStepSize'): - """ - Find a particular dataset and shrink it by stepping over pixels - - Parameters - ---------- - filename : str - Name of file to analyze/repack/copy - - dset_path : str - Path to dataset - - dset_attr : str - Dataset name - - stepsize : int - Step size to take (1::stepsize) - - xstep_attr : str - Name of HDF attribute that describes number of steps in the \ - X-direction - - xstep_size_attr : str - Name of HDF attribute that describes step size in the \ - X-direction - - ystep_attr : str - Name of HDF attribute that describes number of steps in the \ - Y-direction - - ystep_size_attr : str - Name of HDF attribute that describes step size in the \ - Y-direction - - Returns - ------- - str : filename of new HDF5 file - - Writes a new file filename + '_repack_' + repack_str(-'_') + .h5' - - Notes - ----- - The output file cannot already exist - - SPECIAL : Only likely useful for the NIST developers - - Example - ------- - _shrink('../mP2_w_small.h5','/BCARSImage/mP2_3_5ms_Pos_2_0/','mP2_3_5ms_Pos_2_0',10) - - """ - - f = _h5py.File(filename,'r') - - try: - dset_fullname = dset_path + dset_name - - dset_name_small = dset_name + '_small' - dset_fullname_small = dset_path + dset_name_small - - temp = _np.zeros(f[dset_fullname].shape, dtype=f[dset_fullname].dtype) - - - f[dset_fullname].read_direct(temp) - f.close() - - f = _h5py.File(filename,'r+') - temp2 = temp[0::stepsize,0::stepsize,:] - - lg_xsteps = temp.shape[1] - lg_ysteps = temp.shape[0] - sm_xsteps = temp2.shape[1] - sm_ysteps = temp2.shape[0] - - - ds = f[dset_path] - ds.create_dataset(dset_name_small, data = temp2) - except: - print('Failed') - else: - input_attrs = f[dset_fullname].attrs - - # Copy attribute from first dataset to the repack_array - for attr in input_attrs: - try: - if attr == xstep_attr: - f[dset_fullname_small].attrs.create(attr, \ - sm_xsteps) - elif attr == xstep_size_attr: - temp = input_attrs[attr] - - f[dset_fullname_small].attrs.create(attr, \ - temp*(lg_xsteps/sm_xsteps)) - - elif attr == ystep_attr: - f[dset_fullname_small].attrs.create(attr, \ - sm_ysteps) - elif attr == ystep_size_attr: - temp = input_attrs[attr] - - f[dset_fullname_small].attrs.create(attr, \ - temp*(lg_ysteps/sm_ysteps)) - else: - f[dset_fullname_small].attrs.create(attr, \ - input_attrs[attr]) - except: - pass - finally: - f.close() \ No newline at end of file diff --git a/crikit/utils/tests/test_breadcrumb.py b/crikit/utils/tests/test_breadcrumb.py new file mode 100644 index 0000000..2a64db2 --- /dev/null +++ b/crikit/utils/tests/test_breadcrumb.py @@ -0,0 +1,23 @@ +import numpy as np + +import pytest + +from crikit.utils.breadcrumb import BCPre + +def test_breadcrumb(): + + atrdict = BCPre() + prefix = BCPre.PREFIX + + with pytest.raises(TypeError): + atrdict.add_step('Test1') + with pytest.raises(ValueError): + atrdict.add_step(['Test',1]) + + atrdict.add_step(['Raw']) + atrdict.add_step(['SubDark','RangeStart',-1500,'RangeEnd',-400]) + atrdict.add_step(['NormKK','Amp',100.0,'Phase',10.0]) + + assert atrdict.attr_dict[prefix] == 3 + + \ No newline at end of file diff --git a/crikit/utils/tests/test_general.py b/crikit/utils/tests/test_general.py new file mode 100644 index 0000000..a05dccc --- /dev/null +++ b/crikit/utils/tests/test_general.py @@ -0,0 +1,130 @@ +import numpy as np + +import pytest + +from crikit.utils.general import pad, pad_dual + +def test_pad_1d(): + x = np.arange(-1000,1001) + y = np.real(1/(-500 - x - 1j*100)) + + y_pad_edge, window_edge = pad(y, 10, 'edge') + assert np.allclose(y_pad_edge[10:-10], y) + assert np.allclose(y_pad_edge[:10], y[0]) + assert np.allclose(y_pad_edge[-10:], y[-1]) + + assert np.allclose(window_edge[10:-10], 1) + assert np.allclose(window_edge[:10], 0) + assert np.allclose(window_edge[-10:], 0) + + assert np.allclose(y_pad_edge[..., window_edge==1], y) + + y_pad_constant, window_constant = pad(y, 10, 'constant') + assert np.allclose(y_pad_constant[10:-10], y) + assert np.allclose(y_pad_constant[:10], 0) + assert np.allclose(y_pad_constant[-10:], 0) + + assert np.allclose(window_constant[10:-10], 1) + assert np.allclose(window_constant[:10], 0) + assert np.allclose(window_constant[-10:], 0) + + assert np.allclose(y_pad_constant[..., window_constant==1], y) + +def test_pad_1d_0_width(): + x = np.arange(-1000,1001) + y = np.real(1/(-500 - x - 1j*100)) + + y_pad_edge, window_edge = pad(y, 0, 'edge') + assert np.allclose(y_pad_edge, y) + assert np.allclose(y_pad_edge[..., window_edge==1], y) + assert np.allclose(window_edge, 1) + + y_pad_constant, window_constant = pad(y, 0, 'constant') + assert np.allclose(y_pad_constant, y) + assert np.allclose(y_pad_constant[..., window_constant==1], y) + assert np.allclose(window_constant, 1) + +def test_pad_2d(): + x = np.arange(-1000,1001) + y = np.real(1/(-500 - x - 1j*100)) + y = np.vstack((y, y)) + + assert y.shape[0] == 2 + assert y.shape[-1] == x.size + + y_pad_edge, window_edge = pad(y, 10, 'edge') + assert np.allclose(y_pad_edge[..., 10:-10], y) + + assert np.allclose(y_pad_edge[..., :10], np.dot(y[..., 0:1], np.ones((1, 10)))) + assert np.allclose(y_pad_edge[..., -10:], np.dot(y[..., -1:-2:-1], np.ones((1, 10)))) + + assert np.allclose(window_edge[10:-10], 1) + assert np.allclose(window_edge[:10], 0) + assert np.allclose(window_edge[-10:], 0) + + assert np.allclose(y_pad_edge[..., window_edge==1], y) + + y_pad_constant, window_constant = pad(y, 10, 'constant') + assert np.allclose(y_pad_constant[..., 10:-10], y) + assert np.allclose(y_pad_constant[..., :10], 0) + assert np.allclose(y_pad_constant[..., -10:], 0) + + assert np.allclose(window_constant[10:-10], 1) + assert np.allclose(window_constant[:10], 0) + assert np.allclose(window_constant[-10:], 0) + + assert np.allclose(y_pad_constant[..., window_constant==1], y) + +def test_pad_2d_0_width(): + x = np.arange(-1000,1001) + y = np.real(1/(-500 - x - 1j*100)) + y = np.vstack((y, y)) + + assert y.shape[0] == 2 + assert y.shape[-1] == x.size + + y_pad_edge, window_edge = pad(y, 0, 'edge') + assert np.allclose(y_pad_edge, y) + assert np.allclose(window_edge, 1) + assert np.allclose(y_pad_edge[..., window_edge==1], y) + + y_pad_constant, window_constant = pad(y, 0, 'constant') + assert np.allclose(y_pad_constant, y) + assert np.allclose(window_constant, 1) + assert np.allclose(y_pad_constant[..., window_constant==1], y) + + +def test_pad_dual_1d(): + x = np.arange(-1000,1001) + y = np.real(1/(-500 - x - 1j*100)) + + y_pad, window = pad_dual(y, 10, 20) + + assert np.allclose(y_pad[..., window==1], y) + assert np.allclose(y_pad[..., :20], 0) + assert np.allclose(y_pad[..., -20:], 0) + assert np.allclose(y_pad[..., 20:30], y[0]) + assert np.allclose(y_pad[..., -30:-20], y[-1]) + +def test_pad_dual_1d_all_0s(): + x = np.arange(-1000,1001) + y = np.real(1/(-500 - x - 1j*100)) + + y_pad, window = pad_dual(y, 0, 0) + + assert np.allclose(y_pad[..., window==1], y) + assert np.allclose(window, 1) + +def test_pad_dual_2d(): + x = np.arange(-1000,1001) + y = np.real(1/(-500 - x - 1j*100)) + y = np.vstack((y,y)) + + y_pad, window = pad_dual(y, 10, 20) + + assert np.allclose(y_pad[..., window==1], y) + assert np.allclose(y_pad[..., :20], 0) + assert np.allclose(y_pad[..., -20:], 0) + assert np.allclose(y_pad[..., 20:30], np.dot(y[..., 0:1], np.ones((1, 10)))) + assert np.allclose(y_pad[..., -30:-20], np.dot(y[..., -1:-2:-1], np.ones((1, 10)))) + diff --git a/docs/build/doctrees/algorithms.doctree b/docs/build/doctrees/algorithms.doctree deleted file mode 100644 index 7b82936..0000000 Binary files a/docs/build/doctrees/algorithms.doctree and /dev/null differ diff --git a/docs/build/doctrees/api.doctree b/docs/build/doctrees/api.doctree deleted file mode 100644 index f35477b..0000000 Binary files a/docs/build/doctrees/api.doctree and /dev/null differ diff --git a/docs/build/doctrees/cri_walkthru.doctree b/docs/build/doctrees/cri_walkthru.doctree deleted file mode 100644 index 48fb53f..0000000 Binary files a/docs/build/doctrees/cri_walkthru.doctree and /dev/null differ diff --git a/docs/build/doctrees/crikit.cri.algorithms.doctree b/docs/build/doctrees/crikit.cri.algorithms.doctree deleted file mode 100644 index f085f03..0000000 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- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- - - - -
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-
-
- -

Source code for crikit.CRIkitUI

-"""
-CRIKit2: Hyperspectral imaging toolkit
-==============================================================
-
-CRIKit2, formerly the Coherent Raman Imaging toolKit, is a hyperspectral
-imaging (HSI) platform (user interface, UI).
-
-HSI Processing:
-    * Dark subtraction
-    * Detrending
-    * Denoising
-
-Coherent Raman-Specific Processing:
-    * Kramers-Kronig phase retrieval
-    * Phase- and scale-error correction
-
-Analysis:
-    * Coming soon
-
-Usage
------
-From ./crikit2 directory
-python3 main.py
-
-Authors
--------
-* Charles H. Camp Jr. <charles.camp@nist.gov>
-"""
-
-import copy as _copy
-import os as _os
-import sys as _sys
-import webbrowser as _webbrowser
-
-import h5py as _h5py
-import matplotlib as _mpl
-import numpy as _np
-
-import PyQt5.QtCore as _QtCore
-
-from PyQt5.QtGui import QCursor as _QCursor
-from PyQt5.QtWidgets import QApplication as _QApplication
-from PyQt5.QtWidgets import QFileDialog as _QFileDialog
-from PyQt5.QtWidgets import QInputDialog as _QInputDialog
-from PyQt5.QtWidgets import QMainWindow as _QMainWindow
-from PyQt5.QtWidgets import QMessageBox as _QMessageBox
-from PyQt5.QtWidgets import QWidget as _QWidget
-from scipy.signal import savgol_filter as _sg
-
-
-from crikit.cri.error_correction import \
-    PhaseErrCorrectALS as _PhaseErrCorrectALS
-from crikit.cri.error_correction import ScaleErrCorrectSG as _ScaleErrCorrectSG
-from crikit.cri.kk import KramersKronig
-from crikit.cri.merge_nrbs import MergeNRBs as _MergeNRBs
-
-from crikit.data.frequency import calib_pix_wn as _calib_pix_wn
-from crikit.data.hsi import Hsi
-from crikit.data.spectra import Spectra
-from crikit.data.spectrum import Spectrum
-
-from crikit.datasets.model import Model as _Model
-
-from crikit.io.hdf5 import hdf_is_valid_dsets
-from crikit.io.macros import import_csv_nist_special1 as io_nist_dlm
-from crikit.io.macros import import_hdf_nist_special as io_nist
-
-import crikit.measurement.peakamps as _peakamps
-
-from crikit.preprocess.crop import ZeroColumn as _ZeroColumn
-from crikit.preprocess.crop import ZeroRow as _ZeroRow
-from crikit.preprocess.denoise import SVDDecompose, SVDRecompose
-from crikit.preprocess.standardize import Anscombe as _Anscombe
-from crikit.preprocess.standardize import AnscombeInverse as _AnscombeInverse
-from crikit.preprocess.subtract_baseline import \
-    SubtractBaselineALS as _SubtractBaselineALS
-from crikit.preprocess.subtract_dark import SubtractDark
-from crikit.preprocess.subtract_mean import SubtractMeanOverRange
-
-from crikit.ui.dialog_kkOptions import DialogKKOptions
-from crikit.ui.dialog_model import DialogModel
-from crikit.ui.dialog_ploteffect import \
-    DialogPlotEffectFuture as _DialogPlotEffect
-from crikit.ui.dialog_save import DialogSave
-from crikit.ui.dialog_varstabAnscombeOptions import DialogAnscombeOptions
-from crikit.ui.qt_CRIkit import Ui_MainWindow
-from crikit.ui.subui_hdf_load import SubUiHDFLoad
-from crikit.ui.utils.roi import roimask as _roimask
-from crikit.ui.widget_Calibrate import widgetCalibrate as _widgetCalibrate
-from crikit.ui.widget_DeTrending import widgetALS as _widgetALS
-from crikit.ui.widget_DeTrending import widgetArPLS as _widgetArPLS
-from crikit.ui.widget_DeTrending import widgetDeTrending as _widgetDeTrending
-from crikit.ui.widget_images import (widgetBWImg, widgetCompositeColor, widgetSglColor)
-
-from crikit.ui.widget_mergeNRBs import widgetMergeNRBs as _widgetMergeNRBs
-from crikit.ui.widget_SG import widgetSG as _widgetSG
-
-from crikit.utils.breadcrumb import BCPre as _BCPre
-from crikit.utils.general import find_nearest, mean_nd_to_1d
-
-from sciplot.sciplotUI import SciPlotUI as _SciPlotUI
-
-_h5py.get_config().complex_names = ('Re', 'Im')
-
-force_not_sw = False
-
-try:
-    import crikit2_sw
-except:
-    __sw_installed = False
-    print('SW package not installed, using standard')
-    from crikit.ui.dialog_SVD import DialogSVD
-else:
-    __sw_installed = True
-
-    if force_not_sw:
-        print('SW package installed, but forced off -- using standard')
-        from crikit.ui.dialog_SVD import DialogSVD
-    else:
-        print('SW package installed, let\'s rock!')
-        from crikit2_sw.ui.dialog_SVD import DialogSVD
-
-
-_mpl.use('Qt5Agg')
-_mpl.rcParams['font.family'] = 'sans-serif'
-_mpl.rcParams['font.size'] = 12
-
-jupyter_flag = 0
-try:
-    from crikit.ui.widget_Jupyter import QJupyterWidget
-    jupyter_flag = 1
-except:
-    print('No appropriate Jupyter/IPython installation found. Console will not be available')
-    jupyter_flag = -1
-
-help_index = _os.path.abspath(_os.path.join(_os.path.dirname(__file__), 
-                              '../docs/build/html/index.html'))
-
-if _os.path.exists(help_index):
-    pass
-else:
-    help_index = None
-
-
[docs]class CRIkitUI_process(_QMainWindow):
-    """
-    CRIkitUI_process : CRIkitUI for image (pre-)processing
-
-    References
-    ----------
-    [1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \
-    Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \
-    Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543.
-    """
-
-    NUMCOLORS = 4  # Number of single-color windows to auto-generate
-
-    def __init__(self, **kwargs):
-
-        # Generic load/init designer-based GUI
-        parent = kwargs.get('parent')
-
-        super(CRIkitUI_process, self).__init__(parent) ### EDIT ###
-               
-
-        self.parent = parent
-
-        self.filename = kwargs.get('filename')
-        self.path = kwargs.get('path')
-        self.dataset_name = kwargs.get('dataset_name')
-
-        self.hsi = kwargs.get('hsi')
-        if not isinstance(self.hsi, Hsi):
-            self.hsi = Hsi()
-        
-        self.bcpre = _BCPre()
-
-        self.dark = Spectra()
-        self.nrb = Spectra()
-
-        # Overlays
-        self.overlays = []
-        self.show_overlays = True
-
-        # Piecewise NRB's (not always used)
-        self.nrb_left = Spectra()
-        self.nrb_right = Spectra()
-
-        # Internal Parameters
-        self._anscombe_params = None
-
-
-        self.plotter = _SciPlotUI(show=False, parent=self.parent)
-        self._mpl_v2 = self.plotter._mpl_v2
-
-        self.ui = Ui_MainWindow() ### EDIT ###
-
-
-        self.ui.setupUi(self)     ### EDIT ###
-
-        # Match UI Show overlays to attribute of this class
-        self.ui.actionShowOverlays.setChecked(self.show_overlays)
-
-
-        # Initialize Intensity image (single frequency B&W)
-        self.img_BW = widgetBWImg(parent=self, figfacecolor=[1, 1, 1])
-        if self.img_BW.ui.checkBoxFixed.checkState() == 0:
-            self.img_BW.ui.spinBoxMax.setValue(self.img_BW.data.maxer)
-            self.img_BW.ui.spinBoxMin.setValue(self.img_BW.data.minner)
-
-        self.ui.sweeperVL.insertWidget(0, self.img_BW)
-        self.img_BW.mpl.fig.tight_layout(pad=2)
-        # ID used for matplotlib to connect to a figure
-        self.cid = None
-
-        # Initialize Single-Color RGB widgets
-        self.img_RGB_list = []
-
-        for count in range(self.NUMCOLORS):
-            self.img_RGB_list.append(widgetSglColor(figfacecolor=[1, 1, 1],
-                                                    parent=self))
-
-        # Split from previous for-loop for compactness of code
-        for count, rgb_img in enumerate(self.img_RGB_list):
-            color_str = rgb_img.colormode.ui.comboBoxFGColor.itemText(count)
-
-            # Note: colors.to_rgb exists in MPL 2*, but is under colorConverter
-            # in MPL < 2.
-            rgb_img.data.colormap = _mpl.colors.colorConverter.to_rgb(_mpl.colors.cnames[color_str])
-            rgb_img.colormode.ui.comboBoxFGColor.setCurrentIndex(count)
-
-            rgb_img.popimage.ui.pushButtonSpectrum.setEnabled(False)
-            self.ui.tabColors.addTab(rgb_img, 'Color ' + str(count))
-
-            
-            rgb_img.math.ui.pushButtonBasicMath.setEnabled(False)
-            rgb_img.math.ui.pushButtonScripting.setEnabled(False)
-
-            rgb_img.math.ui.pushButtonOpFreq1.pressed.connect(self.setOpFreq1)
-            rgb_img.math.ui.pushButtonOpFreq2.pressed.connect(self.setOpFreq2)
-            rgb_img.math.ui.pushButtonOpFreq3.pressed.connect(self.setOpFreq3)
-            rgb_img.math.ui.comboBoxOperations.currentIndexChanged.connect(self.opChange)
-            rgb_img.math.ui.pushButtonCondFreq1.pressed.connect(self.setCondFreq1)
-            rgb_img.math.ui.pushButtonCondFreq2.pressed.connect(self.setCondFreq2)
-            rgb_img.math.ui.pushButtonCondFreq3.pressed.connect(self.setCondFreq3)
-            rgb_img.math.ui.comboBoxCondOps.currentIndexChanged.connect(self.condOpChange)
-            rgb_img.math.ui.comboBoxCondInEquality.currentIndexChanged.connect(self.condInEqualityChange)
-            rgb_img.math.ui.spinBoxInEquality.editingFinished.connect(self.spinBoxInEqualityChange)
-            rgb_img.math.ui.pushButtonBasicMath.pressed.connect(self.doMath)
-            rgb_img.ui.spinBoxMax.editingFinished.connect(self.doComposite)
-            rgb_img.ui.spinBoxMin.editingFinished.connect(self.doComposite)
-            rgb_img.math.ui.spinBoxGain.valueChanged.connect(self.doComposite)
-
-
-        self.img_Composite = widgetCompositeColor(self.img_RGB_list,
-                                                  figfacecolor=[1, 1, 1])
-        self.img_Composite2 = widgetCompositeColor(self.img_RGB_list,
-                                                   figfacecolor=[1, 1, 1])
-
-        self.ui.tabColors.addTab(self.img_Composite, 'Composite Image')
-
-        self.ui.sweeperVL_2.insertWidget(0, self.img_Composite2)
-
-        self.ui.tabColors.currentChanged.connect(self.checkCompositeUpdate)
-
-
-        # SIGNALS & SLOTS
-
-        # Load Data
-        self.ui.actionOpenHDFNIST.triggered.connect(self.fileOpenHDFNIST)
-        self.ui.actionLoadNRB.triggered.connect(self.loadNRB)
-        self.ui.actionLoadDark.triggered.connect(self.loadDark)
-
-        self.ui.actionOpenDLMNIST.triggered.connect(self.fileOpenDLMNIST)
-        self.ui.actionLoadNRBDLM.triggered.connect(self.loadNRBDLM)
-        self.ui.actionLoadDarkDLM.triggered.connect(self.loadDarkDLM)
-
-        self.ui.actionNRB_from_ROI.triggered.connect(self.nrbFromROI)
-        self.ui.actionAppend_NRB_from_ROI.triggered.connect(self.nrbFromROI)
-
-        self.ui.actionLoad_NRB_Left_Side.triggered.connect(self.loadNRB)
-        self.ui.actionNRB_from_ROI_Left_Side.triggered.connect(self.nrbFromROI)
-
-        self.ui.actionLoad_NRB_Right_Side.triggered.connect(self.loadNRB)
-        self.ui.actionNRB_from_ROI_Right_Side.triggered.connect(self.nrbFromROI)
-
-        self.ui.actionMergeNRBs.triggered.connect(self.mergeNRBs)
-
-        # Settings
-        self.ui.actionSettings.triggered.connect(self.settings)
-
-        # Undo
-        self.ui.actionUndo.triggered.connect(self.doUndo)
-
-        # Close event
-        self.ui.closeEvent = self.closeEvent
-
-        # Subtract DARK-Related
-        self.ui.actionDarkSubtract.triggered.connect(self.subDark)
-        self.ui.actionResidualSubtract.triggered.connect(self.subResidual)
-
-
-        # ZERO first column or row
-        self.ui.actionZeroFirstColumn.triggered.connect(self.zeroFirstColumn)
-        self.ui.actionZeroFirstRow.triggered.connect(self.zeroFirstRow)
-        self.ui.actionZeroLastColumn.triggered.connect(self.zeroLastColumn)
-        self.ui.actionZeroLastRow.triggered.connect(self.zeroLastRow)
-
-        # Set frequency WINDOW
-        self.ui.actionFreqWindow.triggered.connect(self.freqWindow)
-
-        # Calibrate Wavenumber
-        self.ui.actionCalibrate.triggered.connect(self.calibrate)
-        self.ui.actionResetCalibration.triggered.connect(self.calibrationReset)
-
-        # Perform KK
-        self.ui.actionKramersKronig.triggered.connect(self.doKK)
-
-        self.ui.actionKKSpeedTest.setEnabled(False)
-
-        # Variance Stabilize
-        self.ui.actionAnscombe.triggered.connect(self.anscombe)
-        self.ui.actionInverseAnscombe.triggered.connect(self.inverseAnscombe)
-
-        # DeNoise
-        self.ui.actionDeNoise.triggered.connect(self.deNoise)
-        self.ui.actionDeNoiseNRB.triggered.connect(self.deNoiseNRB)
-        self.ui.actionDeNoiseDark.triggered.connect(self.deNoiseDark)
-
-        # Error Correction
-        self.ui.actionPhaseErrorCorrection.triggered.connect(self.errorCorrectPhase)
-        self.ui.actionScaleErrorCorrection.triggered.connect(self.errorCorrectScale)
-        self.ui.actionAmpErrorCorrection.triggered.connect(self.errorCorrectAmp)
-        self.ui.actionSubtractROI.triggered.connect(self.subtractROIStart)
-
-        # SAVE
-
-        self.ui.actionSave.triggered.connect(self.save)
-
-        # Plotting spectra-related
-        self.ui.actionPointSpectrum.triggered.connect(self.pointSpectrum)
-        self.ui.actionROISpectrum.triggered.connect(self.roiSpectrum)
-
-        self.ui.actionDarkSpectrum.triggered.connect(self.plotDarkSpectrum)
-        self.ui.actionNRBSpectrum.triggered.connect(self.plotNRBSpectrum)
-        self.ui.actionLeftSideNRBSpect.triggered.connect(self.plotLeftNRBSpectrum)
-        self.ui.actionRightSideNRBSpect.triggered.connect(self.plotRightNRBSpectrum)
-        self.ui.actionShowPlotter.triggered.connect(self.plotter_show)
-
-        # Overlays
-        self.plotter.modelLine.dataDeleted.connect(self.updateOverlays)
-        self.plotter.modelLine.dataChanged.connect(self.updateOverlays)
-        self.plotter.all_cleared.connect(self.deleteOverlays)
-        self.ui.actionShowOverlays.triggered.connect(self.checkShowOverlays)
-        self.ui.actionShowOverlayLegend.triggered.connect(self.changeSlider)
-
-       # Frequency-slider related
-        self.ui.freqSlider.valueChanged.connect(self.changeSlider)
-        self.ui.freqSlider.sliderPressed.connect(self.sliderPressed)
-        self.ui.freqSlider.sliderReleased.connect(self.sliderReleased)
-        self.ui.freqSlider.setTracking(True)
-
-       # Frequency-slider display boxes
-        self.ui.lineEditFreq.editingFinished.connect(self.lineEditFreqChanged)
-        self.ui.lineEditPix.editingFinished.connect(self.lineEditPixChanged)
-        self.ui.lineEditPix.setVisible(False)
-        self.ui.labelFreqPixel.setVisible(False)
-
-        # Help
-        if help_index is not None:
-            self.ui.actionHelpManual.triggered.connect(lambda: _webbrowser.open('file:///' + help_index, new=1))
-        else:
-            self.ui.actionHelpManual.setEnabled(False)
-
-        self.ui.actionRamanPhantom.triggered.connect(self.makeRamanPhantom)
-        self.ui.actionBCARSPhantom.triggered.connect(self.makeBCARSPhantom)
-
-        # Jupyter console
-
-        if jupyter_flag == 1:
-            try:
-                self.jupyterConsole = QJupyterWidget(customBanner='Welcome to the '
-                                                    'embedded ipython console\n\n')
-            except:
-                print('Error loading embedded IPython Notebook')
-            else:
-                self.ui.tabMain.addTab(self.jupyterConsole, 'Jupyter/IPython Console')
-
-                self.jupyterConsole.pushVariables({'ui':self.ui,
-                                                'bcpre':self.bcpre,
-                                                'dark':self.dark,
-                                                'nrb':self.nrb,
-                                                'crikit_data':self})
-                self.ui.tabMain.currentChanged.connect(self.tabMainChange)
-
-
-        # Temporary toolbar setup
-        self.ui.toolBar.setVisible(True)
-        self.ui.toolBar.setToolButtonStyle(_QtCore.Qt.ToolButtonTextUnderIcon)
-        self.ui.actionToolBarNIST1.triggered.connect(self.toolbarSetting)
-        self.ui.actionToolBarNIST2.triggered.connect(self.toolbarSetting)
-        self.ui.actionToolBarNone.triggered.connect(self.toolbarSetting)
-
-        # Default toolbar is NIST Workflow
-        self.ui.actionToolBarNIST2.trigger()
-
-        # COMMAND LINE INTERPRETATION
-
-        # file and dset info provided
-        if hdf_is_valid_dsets(self.path, self.filename, self.dataset_name):
-            self.fileOpenHDFNIST(dialog=False)
-
-        # Hsi provided
-        temp = kwargs.get('hsi')
-        if temp is not None:
-            try:
-                self.fileOpenSuccess(True)
-            except:
-                print('Error in input hsi')
-                self.hsi = Hsi()
-
-        # x-array provided
-        temp = kwargs.get('x')
-        if temp is not None:
-            try:
-                self.hsi.x = temp
-                self.hsi._x_rep.units = kwargs.get('x_units')
-                self.hsi._x_rep.label = kwargs.get('x_label')
-            except:
-                print('Error in input x-array')
-                self.hsi.x = None
-            
-        # y-array provided
-        temp = kwargs.get('y')
-        if temp is not None:
-            try:
-                self.hsi.y = temp
-                self.hsi._y_rep.units = kwargs.get('y_units')
-                self.hsi._y_rep.label = kwargs.get('y_label')
-            except:
-                print('Error in input y-array')
-                self.hsi.y = None
-
-        # freq-array provided
-        temp = kwargs.get('f')
-        if temp is not None:
-            try:
-                self.hsi.freq._data = temp
-                self.hsi.freq._units = kwargs.get('f_units')
-                self.hsi.freq._label = kwargs.get('f_label')
-            except:
-                print('Error in input freq-array (f)')
-                self.hsi.freq._data = None
-
-        # data provided
-        if isinstance(kwargs.get('data'), _np.ndarray):
-            try:
-                self.hsi.data = kwargs.get('data')
-                self.hsi.check()
-                self.fileOpenSuccess(True)
-            except:
-                print('Error in input data')
-                self.hsi = Hsi()
-
-
[docs]    def plotter_show(self):
-        self.plotter.show()
-        self.plotter.raise_()

-
-
[docs]    def toolbarSetting(self):
-        """
-        Toolbar settings through View menu.
-        """
-        toolbar_actions = [self.ui.actionToolBarNone,
-                           self.ui.actionToolBarNIST2,
-                           self.ui.actionToolBarNIST1]
-
-        sndr = self.sender()
-        for tb in toolbar_actions:
-            if sndr == tb:
-                tb.setChecked(True)
-            else:
-                tb.setChecked(False)
-
-        # Hide toolbar if None
-        if sndr == self.ui.actionToolBarNone:
-            self.ui.toolBar.setVisible(False)
-        else:
-            self.ui.toolBar.clear()
-            self.ui.toolBar.setVisible(True)
-
-        # So far only NIST toolbar setup
-        if sndr == self.ui.actionToolBarNIST2:
-            self.ui.actionToolBarNIST2.setChecked(True)
-            self.ui.toolBar.addActions([self.ui.actionOpenHDFNIST,
-                                        self.ui.actionSave])
-
-            self.ui.toolBar.addSeparator()
-            self.ui.toolBar.addActions([self.ui.actionPointSpectrum,
-                                        self.ui.actionROISpectrum])
-            self.ui.toolBar.addSeparator()
-            self.ui.toolBar.addAction(self.ui.actionUndo)
-
-            self.ui.toolBar.addSeparator()
-            self.ui.toolBar.addActions([self.ui.actionLoadDark,
-                                        self.ui.actionLoadNRB])
-
-            self.ui.toolBar.addSeparator()
-            self.ui.toolBar.addActions([self.ui.actionDarkSubtract,
-                                        self.ui.actionResidualSubtract,
-                                        self.ui.actionFreqWindow,
-                                        self.ui.actionAnscombe,
-                                        self.ui.actionDeNoise,
-                                        self.ui.actionInverseAnscombe,
-                                        self.ui.actionKramersKronig,
-                                        self.ui.actionPhaseErrorCorrection,
-                                        self.ui.actionScaleErrorCorrection,
-                                        self.ui.actionSubtractROI,
-                                        self.ui.actionCalibrate,
-                                        self.ui.actionAmpErrorCorrection])
-
-        elif sndr == self.ui.actionToolBarNIST1:
-            self.ui.actionToolBarNIST2.setChecked(True)
-            self.ui.toolBar.addActions([self.ui.actionOpenDLMNIST,
-                                        self.ui.actionSave])
-
-            self.ui.toolBar.addSeparator()
-            self.ui.toolBar.addActions([self.ui.actionPointSpectrum,
-                                        self.ui.actionROISpectrum])
-            self.ui.toolBar.addSeparator()
-            self.ui.toolBar.addAction(self.ui.actionUndo)
-
-            self.ui.toolBar.addSeparator()
-            self.ui.toolBar.addActions([self.ui.actionLoadDarkDLM,
-                                        self.ui.actionLoadNRBDLM])
-
-            self.ui.toolBar.addSeparator()
-            self.ui.toolBar.addActions([self.ui.actionDarkSubtract,
-                                        self.ui.actionResidualSubtract,
-                                        self.ui.actionFreqWindow,
-                                        self.ui.actionAnscombe,
-                                        self.ui.actionDeNoise,
-                                        self.ui.actionInverseAnscombe,
-                                        self.ui.actionKramersKronig,
-                                        self.ui.actionPhaseErrorCorrection,
-                                        self.ui.actionScaleErrorCorrection,
-                                        self.ui.actionSubtractROI,
-                                        self.ui.actionCalibrate,
-                                        self.ui.actionAmpErrorCorrection])

-
-
[docs]    def save(self):
-        suffix = self.bcpre.dset_name_suffix
-
-        try:
-            ret = DialogSave.dialogSave(parent=self,
-                                        current_filename=self.filename,
-                                        current_path=self.path,
-                                        current_dataset_name=self.dataset_name[0],
-                                        suffix=suffix)
-            if ret is None:
-                pass # Save canceled
-            else:
-                self.save_filename = ret[0]
-                self.save_path = ret[1]
-                self.save_dataset_name = ret[2]
-
-                self.save_grp = self.save_dataset_name.rpartition('/')[0]
-                self.save_dataset_name_no_grp = self.save_dataset_name.rpartition('/')[-1]
-
-
-
-                try:
-                    f_out = _h5py.File(self.save_path + self.save_filename, 'a')
-                    loc = f_out.require_group(self.save_grp)
-                    dset = loc.create_dataset(self.save_dataset_name_no_grp, data=self.hsi.data)
-
-                    meta = self.hsi.meta
-                    for attr_key in meta:
-                        val = meta[attr_key]
-                        if isinstance(val, str):
-                            dset.attrs[attr_key] = val
-                        else:
-                            try:
-                                dset.attrs.create(attr_key, self.hsi.meta[attr_key])
-                            except:
-                                print('Error in HSI attributes: {}'.format(attr_key))
-
-                    bc_attr_dict = self.bcpre.attr_dict
-
-                    for attr_key in bc_attr_dict:
-                        val = bc_attr_dict[attr_key]
-                        if isinstance(val, str):
-                            dset.attrs[attr_key] = val
-                        else:
-                            try:
-                                dset.attrs.create(attr_key, bc_attr_dict[attr_key])
-                            except:
-                                print('Could not create attribute')
-
-                except:
-                    print('Something went wrong while saving')
-                else:
-                    print('Saved without issues')
-                finally:
-                    f_out.close()
-                    self.setWindowTitle('{} -> {}'.format(self.windowTitle(), self.save_filename))
-
-        except:
-            print('Couldn\'t open save dialog')

-
-
[docs]    def tabMainChange(self):
-        if self.ui.tabMain.currentIndex() == 4:  # Jupyter console
-            self.jupyterConsole._control.setFocus()

-
-
[docs]    def closeEvent(self, event):
-        print('Closing')
-        app = _QApplication.instance()
-        app.closeAllWindows()
-        app.quit()
-        self.bcpre.pop_to_last(all=True)
-
-        del_flag = 0
-
-        for count in self.bcpre.cut_list:
-            try:
-                _os.remove(count + '.pickle')
-            except:
-                print('Error in deleting old pickle files')
-            else:
-                del_flag += 1
-        if del_flag == len(self.bcpre.cut_list):
-            del self.bcpre.cut_list
-        else:
-            print('Did not delete pickle file cut list... Something went wrong')

-
-
[docs]    def fileOpenHDFNIST(self, *args, dialog=True):
-        """
-        Open and load HDF5 File
-
-        dialog : bool
-            Present a gui for file and dataset selection
-        """
-
-        # Get data and load into CRI_HSI class
-        # This will need to change to accomodate multiple-file selection
-        
-        if dialog:
-            try:
-                to_open = SubUiHDFLoad.getFileDataSets(self.path)
-                print('to_open: {}'.format(to_open))
-                if to_open is not None:
-                    self.path, self.filename, self.dataset_name = to_open
-            except:
-                print('Could not open file. Corrupt or not appropriate file format.')
-            else:
-                if to_open is not None:
-                    self.hsi = Hsi()
-                    success = io_nist(self.path, self.filename, self.dataset_name,
-                                    self.hsi)
-                    self.fileOpenSuccess(success)
-        else:
-            self.hsi = Hsi()
-            success = io_nist(self.path, self.filename, self.dataset_name,
-                              self.hsi)
-            self.fileOpenSuccess(success)

-
-
[docs]    def fileOpenDLMNIST(self):
-        """
-        Open and load DLM File
-        """
-
-        # Get data and load into CRI_HSI class
-        # This will need to change to accomodate multiple-file selection
-        filename_header,_ = _QFileDialog.getOpenFileName(self, 'Open Header File',
-                                                         './', 'All Files (*.*)')
-
-
-        if filename_header != '':
-            self.path = _os.path.dirname(filename_header) + '/'
-            filename_data,_ = _QFileDialog.getOpenFileName(self, 'Open Data File',
-                                                           self.path,
-                                                           'All Files (*.*)')
-
-            if filename_data != '':
-                self.path = _os.path.dirname(filename_data) + '/'
-                self.filename = filename_data.split(_os.path.dirname(filename_data))[1][1::]
-                self.filename_header = filename_header
-
-                success = io_nist_dlm(self.path, self.filename_header,
-                                      self.filename,
-                                      self.hsi)
-                self.fileOpenSuccess(success)

-
-
[docs]    def fileOpenSuccess(self, success):
-        """
-        Executed after a file is loaded. Checks success and appropriately
-        activates or deactivates action (buttons)
-        """
-        if success:
-            self.setWindowTitle('{}: {}'.format(self.windowTitle(), self.filename))
-            # FILE
-            self.ui.actionSave.setEnabled(True)
-
-            # EDIT
-            self.ui.actionZeroFirstColumn.setEnabled(True)
-            self.ui.actionZeroFirstRow.setEnabled(True)
-            self.ui.actionZeroLastColumn.setEnabled(True)
-            self.ui.actionZeroLastRow.setEnabled(True)
-            self.ui.actionFreqWindow.setEnabled(True)
-            self.ui.actionCalibrate.setEnabled(True)
-            self.ui.actionResetCalibration.setEnabled(True)
-
-            # VIEW
-            self.ui.actionPointSpectrum.setEnabled(True)
-            self.ui.actionROISpectrum.setEnabled(True)
-
-            # IMPORT/LOAD
-            self.ui.actionLoadDark.setEnabled(True)
-            self.ui.actionLoadNRB.setEnabled(True)
-            self.ui.actionLoadDarkDLM.setEnabled(True)
-            self.ui.actionLoadNRBDLM.setEnabled(True)
-            self.ui.actionNRB_from_ROI.setEnabled(True)
-            # self.ui.actionAppend_NRB_from_ROI.setEnabled(True)
-            self.ui.menuPiece_wise_NRB.setEnabled(True)
-
-            # PREPROCESS
-            self.ui.actionResidualSubtract.setEnabled(True)
-            self.ui.actionAnscombe.setEnabled(True)
-            self.ui.actionInverseAnscombe.setEnabled(True)
-            self.ui.actionDeNoise.setEnabled(True)
-            self.ui.actionAmpErrorCorrection.setEnabled(True)
-            self.ui.actionSubtractROI.setEnabled(True)
-            self.ui.actionNRB_from_ROI.setEnabled(True)
-            self.ui.menuVariance_Stabilize.setEnabled(True)
-
-            # ANALYSIS
-
-
-            is_complex = _np.iscomplexobj(self.hsi.data)
-            if is_complex:
-                self.ui.actionPhaseErrorCorrection.setEnabled(True)
-                self.ui.actionScaleErrorCorrection.setEnabled(True)
-        else:
-            self.ui.actionLoadDark.setEnabled(False)
-            self.ui.actionLoadNRB.setEnabled(False)
-            self.ui.actionZeroFirstColumn.setEnabled(False)
-            self.ui.actionZeroFirstRow.setEnabled(False)
-            self.ui.actionZeroLastColumn.setEnabled(False)
-            self.ui.actionZeroLastRow.setEnabled(False)
-
-        # Backup for Undo
-        self.bcpre.add_step(['Raw'])
-        try:
-            _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-        except:
-            print('Error in pickle backup (Undo functionality)')
-        else:
-            self.bcpre.backed_up()
-
-        # Set frequency slider and associated displays
-        self.ui.freqSlider.setMinimum(self.hsi.freq.op_range_pix[0])
-        self.ui.freqSlider.setMaximum(self.hsi.freq.op_range_pix[-1])
-        self.ui.freqSlider.setSliderPosition(self.hsi.freq.op_range_pix[0])
-        pos = self.ui.freqSlider.sliderPosition()
-        self.ui.lineEditPix.setText(str(self.ui.freqSlider.sliderPosition()))
-        self.ui.lineEditFreq.setText(str(round(self.hsi.f[0], 2)))
-        # Set BW Class Data
-        self.img_BW.initData()
-        self.img_BW.data.grayscaleimage = self.hsi.data_imag_over_real[:, :, pos]
-        
-        val_extrema = _np.max([_np.abs(self.hsi.data_imag_over_real.max()),
-                                _np.abs(self.hsi.data_imag_over_real.min())])
-        self.img_BW.ui.spinBoxMin.setMinimum(-1.1*val_extrema)
-        self.img_BW.ui.spinBoxMin.setMaximum(1.1*val_extrema)
-        self.img_BW.ui.spinBoxMax.setMinimum(-1.1*val_extrema)
-        self.img_BW.ui.spinBoxMax.setMaximum(1.1*val_extrema)
-
-        xlabel = ''
-        if isinstance(self.hsi.x_rep.label, str):
-            xlabel += self.hsi.x_rep.label.strip()
-        if isinstance(self.hsi.x_rep.units, str):
-            xlabel += ' ('
-            xlabel += self.hsi.x_rep.units.strip()
-            xlabel += ')'
-
-        # print('Xlabel: {}'.format(xlabel))
-        ylabel = ''
-        if isinstance(self.hsi.y_rep.label, str):
-            ylabel += self.hsi.y_rep.label.strip()
-        if isinstance(self.hsi.y_rep.units, str):
-            ylabel += ' ('
-            ylabel += self.hsi.y_rep.units.strip()
-            ylabel += ')'
-        # xlabel = r'{} ({})'.format(self.hsi.x_rep.label.strip(), self.hsi.x_rep.units.strip())
-        # ylabel = r'{} ({})'.format(self.hsi.y_rep.label.strip(), self.hsi.y_rep.units.strip())
-
-        # print('Ylabel: {}'.format(ylabel))
-        self.img_BW.data.set_x(self.hsi.x, xlabel)
-        self.img_BW.data.set_y(self.hsi.y, ylabel)
-        # Set min/max, fixed, compress, etc buttons to defaults
-        self.img_BW.ui.checkBoxFixed.setChecked(False)
-        # self.img_BW.ui.checkBoxCompress.setChecked(False)
-        self.img_BW.ui.comboBoxAboveMax.setCurrentIndex(0)
-        self.img_BW.ui.checkBoxRemOutliers.setChecked(False)
-        self.createImgBW(self.img_BW.data.image)
-        self.img_BW.mpl.draw()
-        # RGB images
-        temp = 0*self.img_BW.data.grayscaleimage
-
-        # Re-initialize RGB images
-
-        for num, rgb_img in enumerate(self.img_RGB_list):
-            rgb_img.initData()
-            rgb_img.math.clear()
-            rgb_img.data.grayscaleimage = temp
-            rgb_img.data.set_x(self.hsi.x, xlabel)
-            rgb_img.data.set_y(self.hsi.y, ylabel)
-            
-            color_str = rgb_img.colormode.ui.comboBoxFGColor.itemText(num)
-            rgb_img.data.colormap = _mpl.colors.colorConverter.to_rgb(_mpl.colors.cnames[color_str])
-            rgb_img.colormode.ui.comboBoxFGColor.setCurrentIndex(num)
-
-            # Cute way of setting the colormap to last setting and replotting
-            rgb_img.changeColor()
-
-            # Enable Math
-            # rgb_img.math.ui.pushButtonDoMath.setEnabled(True)
-            rgb_img.math.ui.pushButtonBasicMath.setEnabled(True)
-
-            # Enable mean spectrum from RGB images
-            # Note: if load new file after one has already loaded, need to disconnect
-            # signal then reconnect (or could have ignored, but this is easier)
-            try:
-                rgb_img.popimage.ui.pushButtonSpectrum.pressed.disconnect()
-            except:
-                pass
-
-            rgb_img.popimage.ui.pushButtonSpectrum.pressed.connect(self.spectrumColorImg)
-
-            rgb_img.popimage.ui.pushButtonSpectrum.setEnabled(True)
-
-            rgb_img.gsinfo.ui.spinBoxMin.setMinimum(-1.1*val_extrema)
-            rgb_img.gsinfo.ui.spinBoxMin.setMaximum(1.1*val_extrema)
-            rgb_img.gsinfo.ui.spinBoxMax.setMinimum(-1.1*val_extrema)
-            rgb_img.gsinfo.ui.spinBoxMax.setMaximum(1.1*val_extrema)
-            
-        # Set X- and Y- scales, labels, etc for composite color images
-        self.img_Composite.data.set_x(self.hsi.x, xlabel)
-        self.img_Composite.data.set_y(self.hsi.y, ylabel)
-        self.img_Composite2.data.set_x(self.hsi.x, xlabel)
-        self.img_Composite2.data.set_y(self.hsi.y, ylabel)

-
-
[docs]    def loadDark(self):
-        """
-        Open HDF file and load dark spectrum(a)
-        """
-
-        to_open = SubUiHDFLoad.getFileDataSets(self.path)
-        print('To_open: {}'.format(to_open))
-
-        if to_open is not None:
-            pth, filename, datasets = to_open
-            success = io_nist(pth, filename, datasets, self.dark)
-
-            if success:
-                if self.dark.shape[-1] == self.hsi.freq.size:
-                    self.ui.actionDarkSubtract.setEnabled(True)
-                    self.ui.actionDarkSpectrum.setEnabled(True)
-                    self.ui.actionDeNoiseDark.setEnabled(True)
-                else:
-                    self.dark = Spectra()
-                    print('Dark was the wrong shape')
-            else:
-                self.dark = Spectra()
-                self.ui.actionDarkSubtract.setEnabled(False)
-                self.ui.actionDarkSpectrum.setEnabled(False)
-                self.ui.actionDeNoiseDark.setEnabled(False)

-
-
-
[docs]    def loadDarkDLM(self):
-        """
-        Open DLM file and load dark spectrum(a)
-        """
-
-
-        filename,_ = _QFileDialog.getOpenFileName(self, 'Open Dark File',
-                                                  self.path,
-                                                  'All Files (*.*)')
-        if filename != '':
-            filename = filename.split(_os.path.dirname(filename))[1][1::]
-
-
-            # Spectra first
-            self.dark = Spectra()
-            success = io_nist_dlm(self.path, self.filename_header, filename,
-                                  self.dark)
-            if not success: # Maybe Spectrum
-                self.dark = Spectrum()
-                success = io_nist_dlm(self.path, self.filename_header, filename,
-                                      self.dark)
-
-
-            if success:
-                if self.dark.shape[-1] == self.hsi.freq.size:
-                    self.ui.actionDarkSubtract.setEnabled(True)
-                    self.ui.actionDarkSpectrum.setEnabled(True)
-                else:
-                    self.dark = Spectra()
-                    print('Dark was the wrong shape')
-            else:
-                self.dark = Spectra()
-                self.ui.actionDarkSubtract.setEnabled(False)
-                self.ui.actionDarkSpectrum.setEnabled(False)

-
-
-
[docs]    def loadNRB(self):
-        """
-        Open HDF file and load NRB spectrum(a)
-        """
-
-        sender = self.sender()
-
-        if sender == self.ui.actionLoadNRB:
-            nrb = self.nrb
-        elif sender == self.ui.actionLoad_NRB_Left_Side:
-            nrb = self.nrb_left
-        elif sender == self.ui.actionLoad_NRB_Right_Side:
-            nrb = self.nrb_right
-
-
-        to_open = SubUiHDFLoad.getFileDataSets(self.path)
-        if to_open is not None:
-            pth, filename, datasets = to_open
-
-            success = io_nist(pth, filename, datasets, nrb)
-            if success:
-                if nrb.shape[-1] == self.hsi.freq.size:
-                    if sender == self.ui.actionLoadNRB:
-                        self.ui.menuCoherent_Raman_Imaging.setEnabled(True)
-                        self.ui.actionKramersKronig.setEnabled(True)
-                        self.ui.actionKKSpeedTest.setEnabled(True)
-                        self.ui.actionNRBSpectrum.setEnabled(True)
-                        self.ui.actionDeNoiseNRB.setEnabled(True)
-                    elif sender == self.ui.actionLoad_NRB_Left_Side:
-                        self.ui.actionLeftSideNRBSpect.setEnabled(True)
-                        if ((self.nrb_left.data is not None) and
-                                (self.nrb_right.data is not None)):
-                            if self.nrb_right.mean().size == self.nrb_left.mean().size:
-                                self.ui.actionMergeNRBs.setEnabled(True)
-                    elif sender == self.ui.actionLoad_NRB_Right_Side:
-                        self.ui.actionRightSideNRBSpect.setEnabled(True)
-                        if ((self.nrb_left.data is not None) and
-                                (self.nrb_right.data is not None)):
-                            if self.nrb_right.mean().size == self.nrb_left.mean().size:
-                                self.ui.actionMergeNRBs.setEnabled(True)
-                else:
-                    nrb = Spectra()
-                    print('NRB was the wrong shape')
-            else:
-                nrb = Spectra()
-                if sender == self.ui.actionLoadNRB:
-                    self.ui.actionKramersKronig.setEnabled(False)
-                    self.ui.actionKKSpeedTest.setEnabled(False)
-                    self.ui.actionNRBSpectrum.setEnabled(False)

-
-
[docs]    def loadNRBDLM(self):
-        """
-        Open DLM file and load NRB spectrum(a)
-        """
-
-
-        filename, _ = _QFileDialog.getOpenFileName(self, 'Open NRB File',
-                                                   self.path,
-                                                   'All Files (*.*)')
-        if filename != '':
-            filename = filename.split(_os.path.dirname(filename))[1][1::]
-
-
-            # Spectra first
-            self.nrb = Spectra()
-            success = io_nist_dlm(self.path, self.filename_header, filename,
-                                  self.nrb)
-            if not success: # Maybe Spectrum
-                self.nrb = Spectrum()
-                success = io_nist_dlm(self.path, self.filename_header, filename,
-                                      self.nrb)
-            print('Success: {}'.format(success))
-
-            if success:
-                if self.dark.shape[-1] == self.hsi.freq.size:
-                    self.ui.actionKramersKronig.setEnabled(True)
-                    self.ui.actionKKSpeedTest.setEnabled(True)
-                    self.ui.actionNRBSpectrum.setEnabled(True)
-                    self.ui.actionDeNoiseNRB.setEnabled(True)
-                else:
-                    self.nrb = Spectra()
-                    print('NRB was the wrong shape')
-            else:
-                self.nrb = Spectra()
-                self.ui.actionKramersKronig.setEnabled(False)
-                self.ui.actionKKSpeedTest.setEnabled(False)
-                self.ui.actionNRBSpectrum.setEnabled(False)
-                self.ui.actionDeNoiseNRB.setEnabled(False)

-
-
[docs]    def mergeNRBs(self):
-        """
-        Interactive merge of the left- and right-side NRB
-        """
-        if self.nrb_left is not None and self.nrb_right is not None:
-            rng = self.hsi.freq.op_range_pix
-
-
-            rand_spectra = self.hsi.get_rand_spectra(2, pt_sz=3, quads=True)
-
-            plugin = _widgetMergeNRBs(wn_vec=self.hsi.f,
-                                      nrb_left=self.nrb_left.mean()[rng],
-                                      nrb_right=self.nrb_right.mean()[rng])
-            winPlotEffect = _DialogPlotEffect.dialogPlotEffect(data=rand_spectra,
-                                                               x=self.hsi.f,
-                                                               plugin=plugin)
-
-            if winPlotEffect is not None:
-                print('NRB merge pixel: {}'.format(winPlotEffect.parameters['pix_switchpt']))
-                print('NRB merge WN: {}'.format(winPlotEffect.parameters['wn_switchpt']))
-                print('NRB merge scale left side: {}'.format(winPlotEffect.parameters['scale_left']))
-
-                self.nrb.data = _np.squeeze(0*self.nrb_left.mean())
-                print('nrb shape: {}'.format(self.nrb.shape))
-
-                inst_nrb_merge = _MergeNRBs(nrb_left=self.nrb_left.mean()[rng],
-                                            nrb_right=self.nrb_right.mean()[rng],
-                                            pix=winPlotEffect.parameters['pix_switchpt'],
-                                            left_side_scale=winPlotEffect.parameters['scale_left'])
-                nrb_merge = inst_nrb_merge.calculate()
-
-                # Need 2D because of class Spectra NOT Spectrum
-                self.nrb.data[:, self.hsi.freq.op_range_pix] = nrb_merge
-
-                self.ui.actionNRBSpectrum.setEnabled(True)
-                self.ui.actionKramersKronig.setEnabled(True)
-                self.ui.actionKKSpeedTest.setEnabled(True)
-                self.ui.menuCoherent_Raman_Imaging.setEnabled(True)
-                self.ui.actionDeNoiseNRB.setEnabled(True)
-
-                wn, pix = find_nearest(self.hsi.f_full, \
-                   self.hsi.f[winPlotEffect.parameters['pix_switchpt']])
-
-                # Backup for Undo
-                self.bcpre.add_step(['MergeNRBs',
-                                     'pix_switchpt', pix,
-                                     'wn_switchpt',
-                                     winPlotEffect.parameters['wn_switchpt'],
-                                     'scale_left',
-                                     winPlotEffect.parameters['scale_left']])
-
-        else:
-            pass

-
-
[docs]    def settings(self):
-        """
-        Go to settings tab
-        """
-        index = self.ui.tabMain.indexOf(self.ui.tabSettings)
-        self.ui.tabMain.setCurrentIndex(index)

-
-
[docs]    def calibrate(self):
-        """
-        Calibrate spectra
-        """
-
-        rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True, full=True)
-        if _np.iscomplexobj(rand_spectra):
-            rand_spectra = rand_spectra.imag
-
-        plugin = _widgetCalibrate(calib_dict=self.hsi.freq.calib)
-        winPlotEffect = _DialogPlotEffect.dialogPlotEffect(rand_spectra,
-                                                           x=self.hsi.f_full,
-                                                           plugin=plugin,
-                                                           parent=self)
-
-        if winPlotEffect is not None:
-            #print('New Calibration Dictionary: {}'.format(winPlotEffect.new_calib_dict))
-            self.hsi.freq.calib = winPlotEffect.parameters['new_calib_dict']
-            self.hsi.freq.update()
-        self.changeSlider()

-
-
-
[docs]    def calibrationReset(self):
-        """
-        Set self.hsi.freqcalib back to self.hsi.freqcaliborig
-        """
-        self.hsi.freq.calib = None
-        self.hsi.freq.update()
-        self.changeSlider()

-
-
[docs]    def plotDarkSpectrum(self):
-        """
-        Plot dark spectrum
-        """
-        if self.dark.data is None:
-            pass
-        else:
-            self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.dark.data),
-                              label='Mean Dark Spectrum')
-
-            self.plotter.show()
-            self.plotter.raise_()

-
-
[docs]    def plotNRBSpectrum(self):
-        """
-        Plot NRB spectrum
-        """
-        if self.nrb.data is None:
-            pass
-        else:
-            self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.nrb.data),
-                              label='Mean NRB Spectrum')
-
-            self.plotter.show()
-            self.plotter.raise_()

-
-
[docs]    def plotLeftNRBSpectrum(self):
-        """
-        Plot Left-Side NRB spectrum
-        """
-        if self.nrb_left.data is None:
-            pass
-        else:
-            self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.nrb_left.data),
-                              label='Mean Left-Side NRB Spectrum')
-
-            self.plotter.show()
-            self.plotter.raise_()

-
-
[docs]    def plotRightNRBSpectrum(self):
-        """
-        Plot NRB spectrum
-        """
-        if self.nrb_right.data is None:
-            pass
-        else:
-            self.plotter.plot(self.hsi.f_full, mean_nd_to_1d(self.nrb_right.data),
-                              label='Mean Right-Side NRB Spectrum')
-
-            self.plotter.show()
-            self.plotter.raise_()

-
-
[docs]    def pointSpectrum(self):
-        """
-        Get spectrum of selected point.
-
-        Note: This function just sets up the signal-slot connection for the \
-        MPL window. It executes all the way through
-
-        Action:
-            Left mouse-click : Select vertex point
-        """
-        if self.cid is None:
-            self.cid = self.img_BW.mpl.mpl_connect('button_press_event',
-                                                   lambda event: self._pointClick(event, self._pointSpectrumPlot))
-
-            self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.CrossCursor))
-            self.setCursor(_QCursor(_QtCore.Qt.CrossCursor))

-
-
[docs]    def subtractROIStart(self):
-        """
-        Acquire an average spectrum from a user-selected ROI and subtract.
-
-        Note: This function just sets up the signal-slot connection for the \
-        MPL window. It executes all the way through
-
-        """
-
-        if self.cid is None:
-            # Updated by _roiClick
-            self.x_loc_list = []
-            self.y_loc_list = []
-
-
-            self.cid = self.img_BW.mpl.mpl_connect('button_press_event', 
-                                                   lambda event: self._roiClick(event, self._roiSubtract))
-
-            self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.CrossCursor))
-            self.setCursor(_QCursor(_QtCore.Qt.CrossCursor))

-
-
[docs]    def _roiSubtract(self, locs):
-        """
-        Acquire an average spectrum from a user-selected ROI and subtract.
-
-        """
-        x_loc_list, y_loc_list = locs
-
-        x_pix = find_nearest(self.hsi.x, x_loc_list)[1]
-        y_pix = find_nearest(self.hsi.y, y_loc_list)[1]
-
-        mask, path = _roimask(self.hsi.x, self.hsi.y,
-                              x_loc_list, y_loc_list)
-
-
-        mask_hits = _np.sum(mask)
-
-
-        if mask_hits > 0:  # Len(mask) > 0
-
-            spectra = self.hsi.data[mask == 1]
-
-            if mask_hits > 1:
-                spectrum = _np.mean(spectra, axis=0)
-            else:
-                spectrum = spectra
-            spectrum = spectrum.astype(self.hsi.data.dtype)
-            self.hsi.data -= spectrum[..., :]
-            self.changeSlider()
-
-
-            # Backup for Undo
-            self.bcpre.add_step(['SubtractROI', 'Spectrum', spectrum])
-            if self.ui.actionUndo_Backup_Enabled.isChecked():
-                try:
-                    _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                except:
-                    print('Error in pickle backup (Undo functionality)')
-                else:
-                    self.bcpre.backed_up()
-
-
-            del spectrum
-
-        del x_pix
-        del y_pix

-
-
[docs]    def nrbFromROI(self):
-        """
-        Acquire an average spectrum from a user-selected ROI and apply to the \
-        NRB-- either as the new NRB or averaged with the existing (sender- \
-        dependent)
-
-        Note: This function just sets up the signal-slot connection for the \
-        MPL window. It executes all the way through
-
-        """
-
-        # I found that the objectName is a better way than a reference to the
-        # actual action (e.g., self.ui.action_*) as the reference may change
-        # depending on the call location or how this method is called
-        sender = self.sender().objectName()
-
-        if ((sender == 'actionNRB_from_ROI') or
-                (sender == 'actionAppend_NRB_from_ROI') or
-                (sender == 'actionNRB_from_ROI_Left_Side') or
-                (sender == 'actionNRB_from_ROI_Right_Side')):
-            # Updated by _roiClick
-            self.x_loc_list = []
-            self.y_loc_list = []
-
-            # Need to send sender as the text name as the actual object
-            # will change
-            if self.cid is None:
-                self.cid = self.img_BW.mpl.mpl_connect('button_press_event', 
-                                                       lambda event: self._roiClick(event, self._roiNRB, sender))
-
-                self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.CrossCursor))
-                self.setCursor(_QCursor(_QtCore.Qt.CrossCursor))
-
-        else:
-            print('Unknown action send to nrbFromROI')

-
-
[docs]    def _roiNRB(self, locs, sender):
-        """
-        Acquire an average spectrum from a user-selected ROI and subtract.
-
-        """
-        # Sender was sent as a text reference to the actual sender
-        # the pass of sender put it in a tuple; thus the [0]
-        sender = sender[0]
-
-        x_loc_list, y_loc_list = locs
-
-        x_pix = find_nearest(self.hsi.x, x_loc_list)[1]
-        y_pix = find_nearest(self.hsi.y, y_loc_list)[1]
-
-        mask, path = _roimask(self.hsi.x, self.hsi.y,
-                              x_loc_list, y_loc_list)
-
-
-        mask_hits = _np.sum(mask)
-        if mask_hits > 0:  # Len(mask) > 0
-            spectra = self.hsi.data_imag_over_real[mask == 1]
-
-            if mask_hits > 1:
-                spectrum = _np.mean(spectra, axis=0)
-            else:
-                spectrum = spectra
-
-            spectrum = spectrum.astype(self.hsi.data.dtype)
-            if sender == 'actionNRB_from_ROI':
-                self.nrb.data = spectrum
-                self.ui.actionKramersKronig.setEnabled(True)
-                self.ui.actionKKSpeedTest.setEnabled(True)
-                self.ui.actionNRBSpectrum.setEnabled(True)
-                self.ui.menuCoherent_Raman_Imaging.setEnabled(True)
-
-            elif sender == 'actionAppend_NRB_from_ROI':
-                if self.nrb.size == 0:
-                    self.nrb.data = spectrum
-                else:
-                    self.nrb.data = (self.nrb.data + spectrum)/2
-                self.ui.actionKramersKronig.setEnabled(True)
-                self.ui.actionNRBSpectrum.setEnabled(True)
-            elif sender == 'actionNRB_from_ROI_Left_Side':
-                self.nrb_left.data = spectrum
-                self.ui.actionLeftSideNRBSpect.setEnabled(True)
-                if ((self.nrb_left.data is not None) and
-                        (self.nrb_right.data is not None)):
-                    if self.nrb_right.mean().size == self.nrb_left.mean().size:
-                        self.ui.actionMergeNRBs.setEnabled(True)
-
-            elif sender == 'actionNRB_from_ROI_Right_Side':
-                self.nrb_right.data = spectrum
-                self.ui.actionRightSideNRBSpect.setEnabled(True)
-                if ((self.nrb_left.data is not None) and
-                        (self.nrb_right.data is not None)):
-                    if self.nrb_right.mean().size == self.nrb_left.mean().size:
-                        self.ui.actionMergeNRBs.setEnabled(True)
-            else:
-                print('Unknown action sent to _roiNRB')
-
-            del spectrum
-
-        del x_pix
-        del y_pix

-
-
[docs]    def roiSpectrum(self):
-        """
-        Plot spectrum over selected region-of-interest (ROI).
-
-        Note: This function just sets up the signal-slot connection for the \
-        MPL window. It executes all the way through
-
-        Action:
-            Left mouse-click : Select vertex point
-            Right mouse-click : Close polygon
-        """
-        if self.cid is None:
-            # Updated by _roiClick
-            self.x_loc_list = []
-            self.y_loc_list = []
-
-
-            self.cid = self.img_BW.mpl.mpl_connect('button_press_event',
-                                                   lambda event: self._roiClick(event, self._roiSpectrumPlot))
-
-            self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.CrossCursor))
-            self.setCursor(_QCursor(_QtCore.Qt.CrossCursor))

-
-
[docs]    def _pointClick(self, event, pass_fcn):
-        """
-        Capture single mouse click location in MPL window.
-
-        After this function completes, it sends the data (x_pt, y_pt) on to \
-        the pass_fcn function.
-        """
-        if event.button == 1:
-            if event.inaxes == self.img_BW.mpl.ax:
-                    #self.tempverts += [[event.xdata, event.ydata]]
-                x_loc = event.xdata
-                y_loc = event.ydata
-
-                # Send on to a function that will use the collected data
-                pass_fcn((x_loc, y_loc))
-
-                self.setCursor(_QCursor(_QtCore.Qt.ArrowCursor))
-                self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.ArrowCursor))
-                self.img_BW.mpl.mpl_disconnect(self.cid)
-                self.cid = None
-            else:  # Clicked out-of-bounds
-                pass
-
-        else: # Right-or-middle clicked; thus, cancel
-            self.setCursor(_QCursor(_QtCore.Qt.ArrowCursor))
-            self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.ArrowCursor))
-            self.img_BW.mpl.mpl_disconnect(self.cid)
-            self.cid = None

-
-
[docs]    def _pointSpectrumPlot(self, locs):
-        """
-        Add a plot (in plotter) of a point spectrum
-        """
-
-        x_loc, y_loc = locs
-        x_pix = find_nearest(self.hsi.x, x_loc)[1]
-        y_pix = find_nearest(self.hsi.y, y_loc)[1]
-
-        self.changeSlider()
-
-        plot_num = self.plotter.n_lines
-        label = 'Point ' + str(plot_num)
-
-        rng = self.hsi.freq.op_range_pix
-
-        meta = {'x': x_loc, 'y': y_loc, 'x_pix': x_pix, 'y_pix': y_pix,
-                'overlay': True}
-
-        self.plotter.plot(self.hsi.f,
-                          self.hsi.data_imag_over_real[y_pix, x_pix, rng],
-                          label=label, meta=meta)
-
-
-        self.plotter.show()
-        self.plotter.raise_()
-        self.updateOverlays()

-
-
[docs]    def _roiSpectrumPlot(self, locs):
-        """
-        Add a plot (in plotter) of the mean spectrum over a region
-        """
-        x_loc_list, y_loc_list = locs
-
-        x_pix = find_nearest(self.hsi.x, x_loc_list)[1]
-        y_pix = find_nearest(self.hsi.y, y_loc_list)[1]
-
-
-        mask, path = _roimask(self.hsi.x, self.hsi.y,
-                              x_loc_list, y_loc_list)
-
-
-        mask_hits = _np.sum(mask)
-        if mask_hits > 0:  # Len(mask) > 0
-            rng = self.hsi.freq.op_range_pix
-
-            spectra = self.hsi.data_imag_over_real[mask == 1]
-
-            if mask_hits > 1:
-                spectrum = _np.mean(spectra[..., rng], axis=0)
-                stddev = _np.std(spectra[..., rng], axis=0)
-            else:
-                spectrum = spectra[..., rng]
-
-            plot_num = self.plotter.n_lines
-
-            label_plot = 'ROI {} ({})'.format(plot_num, mask_hits)
-            label_std = r'$\pm$1 Std. Dev. ROI {} ({})'.format(plot_num, mask_hits)
-
-            # Plot line
-            meta = {'x': x_loc_list, 'y': y_loc_list, 'x_pix': x_pix,
-                    'y_pix': y_pix, 'overlay': True}
-            self.plotter.plot(self.hsi.f, spectrum, label=label_plot, meta=meta)
-
-            # Check color of line b/c uses color cycler-- for fill_b/w
-            color = self.plotter.list_all[-1].style_dict['color']
-
-
-            # Alternative
-            #color = self.plotter.modelLine._model_data[-1]['color']
-
-            # Plot +-1 std. dev.
-            if mask_hits > 1:
-                self.plotter.fill_between(self.hsi.f, spectrum-stddev,
-                                          spectrum+stddev, color=color,
-                                          alpha=0.25,
-                                          label=label_std,
-                                          meta=meta)
-
-            del spectrum
-            self.plotter.show()
-            self.plotter.raise_()
-            self.updateOverlays()
-
-
-        del x_pix
-        del y_pix

-
-
[docs]    def _roiClick(self, event, pass_fcn, *args):
-        """
-        Capture region-of-interest mouse click locations in MPL window.
-        """
-
-
-        if event.button == 1:
-            if event.inaxes == self.img_BW.mpl.ax:
-
-                self.x_loc_list.append(event.xdata)
-                self.y_loc_list.append(event.ydata)
-
-                getx = self.img_BW.mpl.ax.get_xlim()
-                gety = self.img_BW.mpl.ax.get_ylim()
-
-                if len(self.x_loc_list) == 1:
-                    self.img_BW.mpl.ax.plot(self.x_loc_list, self.y_loc_list,
-                                            markerfacecolor=[.9, .9, 0],
-                                            markeredgecolor=[.9, .9, 0],
-                                            marker='+',
-                                            markersize=10,
-                                            linestyle='None')
-                    self.img_BW.mpl.ax.set_xlim(getx)
-                    self.img_BW.mpl.ax.set_ylim(gety)
-                    self.img_BW.mpl.draw()
-                else:
-                    self.img_BW.mpl.ax.plot(self.x_loc_list[-2:],
-                                            self.y_loc_list[-2:],
-                                            linewidth=2,
-                                            marker='+',
-                                            markersize=10,
-                                            color=[.9, .9, 0],
-                                            markerfacecolor=[.9, .9, 0],
-                                            markeredgecolor=[.9, .9, 0])
-                    self.img_BW.mpl.ax.set_xlim(getx)
-                    self.img_BW.mpl.ax.set_ylim(gety)
-
-                    self.img_BW.mpl.draw()
-        else:
-            if len(self.x_loc_list) > 0: # Insure at least 1 vertex
-                self.x_loc_list.append(self.x_loc_list[0])
-                self.y_loc_list.append(self.y_loc_list[0])
-
-                # Pass on roi data
-                if not args:
-                    pass_fcn((self.x_loc_list, self.y_loc_list))
-                else:
-                    pass_fcn((self.x_loc_list, self.y_loc_list), args)
-
-            del self.x_loc_list
-            del self.y_loc_list
-
-            self.setCursor(_QCursor(_QtCore.Qt.ArrowCursor))
-            self.img_BW.mpl.setCursor(_QCursor(_QtCore.Qt.ArrowCursor))
-            self.img_BW.mpl.mpl_disconnect(self.cid)
-            self.cid = None
-            self.changeSlider()

-
-
-
[docs]    def freqWindow(self):
-        """
-        Limit the frequency window displayed and analyzed
-        """
-        text, ok = _QInputDialog.getText(None, 'Frequency Window',
-                                         'Range Tuple (cm-1): ',
-                                         text='(500, 3400)')
-        if ok:
-            text_str_list = text.strip('(').strip(')').strip().split(',')
-            freqwin = [float(q) for q in text_str_list]
-            freqwin.sort()
-            self.hsi.freq.op_list_freq = freqwin
-            self.ui.freqSlider.setMinimum(0)
-            self.ui.freqSlider.setMaximum(self.hsi.freq.op_size-1)
-            self.changeSlider()

-
-
-
[docs]    def lineEditFreqChanged(self):
-        """
-        Frequency manually entered in frequency-slider-display
-        """
-
-        try:
-            freq_in = float(self.ui.lineEditFreq.text())
-            pos = self.hsi.freq.get_index_of_closest_freq(freq_in)
-            if self.hsi.freq.op_list_pix is not None:
-                pos -= self.hsi.freq.op_list_pix[0]
-
-            self.ui.freqSlider.setSliderPosition(pos)
-            self.changeSlider()
-        except:
-            pass

-
-
[docs]    def lineEditPixChanged(self):
-        """
-        Frequency in pixel units manually entered in frequency-slider-display
-        """
-        pos = int(self.ui.lineEditPix.text())
-
-        self.ui.freqSlider.setSliderPosition(pos)
-        self.changeSlider()

-
-
[docs]    def zeroFirstColumn(self):
-        """
-        Zero first non-all-zero column. (Rather than crop)
-
-        """
-        self.zc = _ZeroColumn(first_or_last=0)
-        self.zc.transform(self.hsi.data)
-
-        # Adjust mask
-        self.hsi._mask[:, self.zc.zero_col] *= 0
-
-        self.changeSlider()

-
-
[docs]    def zeroFirstRow(self):
-        """
-        Zero first non-all-zero row. (Rather than crop)
-
-        """
-        self.zr = _ZeroRow(first_or_last=0)
-        self.zr.transform(self.hsi.data)
-
-        # Adjust mask
-        self.hsi._mask[self.zr.zero_row, :] *= 0
-
-        self.changeSlider()

-
-
[docs]    def zeroLastColumn(self):
-        """
-        Zero first non-all-zero column. (Rather than crop)
-
-        """
-        self.zc = _ZeroColumn(first_or_last=-1)
-        self.zc.transform(self.hsi.data)
-
-        # Adjust mask
-        self.hsi._mask[:, self.zc.zero_col] *= 0
-
-        self.changeSlider()

-
-
[docs]    def zeroLastRow(self):
-        """
-        Zero first non-all-zero row. (Rather than crop)
-
-        """
-        self.zr = _ZeroRow(first_or_last=-1)
-        self.zr.transform(self.hsi.data)
-
-        # Adjust mask
-        self.hsi._mask[self.zr.zero_row, :] *= 0
-
-        self.changeSlider()

-
-
[docs]    def opChange(self):
-        """
-        Math operation performed on single-color images changed.
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            currentop = self.img_RGB_list[rgbnum].math.ui.comboBoxOperations.currentText()
-            self.img_RGB_list[rgbnum].data.operation = currentop
-        except:
-            pass

-
-
[docs]    def condOpChange(self):
-        """
-        Conditional math operation performed on single-color images changed.
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            currentop = self.img_RGB_list[rgbnum].math.ui.comboBoxCondOps.currentText()
-            self.img_RGB_list[rgbnum].data.condoperation = currentop
-        except:
-            pass

-
-
[docs]    def condInEqualityChange(self):
-        """
-        Conditional inequality changed.
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            currentop = self.img_RGB_list[rgbnum].math.ui.comboBoxCondInEquality.currentText()
-            self.img_RGB_list[rgbnum].data.inequality = currentop
-        except:
-            pass

-
-
[docs]    def spinBoxInEqualityChange(self):
-        """
-        Conditional inequality value changed.
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            self.img_RGB_list[rgbnum].data.inequalityval = \
-                self.img_RGB_list[rgbnum].math.ui.spinBoxInEquality.value()
-        except:
-            pass

-
-
[docs]    def doKK(self):
-        """
-        Pop-up Kramers-Kronig parameter entry dialog and perform
-        the Kramers-Kronig phase retrieval algorithm.
-        """
-
-        rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True,
-                                                 full=False)
-        nrb = self.nrb.mean()
-
-        # Range of pixels to perform-over
-        rng = self.hsi.freq.op_range_pix
-
-        out = DialogKKOptions.dialogKKOptions(data=[self.hsi.f,
-                                                    nrb[..., rng],
-                                                    rand_spectra], parent=self)
-
-        if out is not None:
-            cars_amp_offset = out['cars_amp']
-            nrb_amp_offset = out['nrb_amp']
-            phase_offset = out['phase_offset']
-            norm_to_nrb = out['norm_to_nrb']
-            pad_factor = out['pad_factor']
-
-            kk = KramersKronig(cars_amp_offset=cars_amp_offset,
-                               nrb_amp_offset=nrb_amp_offset,
-                               phase_offset=phase_offset, norm_to_nrb=norm_to_nrb,
-                               pad_factor=pad_factor,
-                               rng=rng)
-
-            self.hsi.data = kk.calculate(self.hsi.data, self.nrb.data)
-            self.changeSlider()
-
-            self.ui.actionPhaseErrorCorrection.setEnabled(True)
-            self.ui.actionScaleErrorCorrection.setEnabled(True)
-
-            # Backup for Undo
-            self.bcpre.add_step(['KK', 'CARSAmp', cars_amp_offset, 'NRBAmp',
-                                 nrb_amp_offset, 'Phase', phase_offset,
-                                 'Norm', norm_to_nrb])
-            if self.ui.actionUndo_Backup_Enabled.isChecked():
-                try:
-                    _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                except:
-                    print('Error in pickle backup (Undo functionality)')
-                else:
-                    self.bcpre.backed_up()

-
-
[docs]    def deNoiseNRB(self):
-        """
-        Denoise NRB with Savitky-Golay
-        """
-        # Range of pixels to perform-over
-        rng = self.hsi.freq.op_range_pix
-
-        plugin = _widgetSG(window_length=11, polyorder=3)
-        winPlotEffect = _DialogPlotEffect.dialogPlotEffect(self.nrb.mean()[rng],
-                                                           x=self.hsi.f,
-                                                           plugin=plugin,
-                                                           parent=self)
-        if winPlotEffect is not None:
-            win_size = winPlotEffect.parameters['window_length']
-            order = winPlotEffect.parameters['polyorder']
-
-            nrb_denoise = _copy.deepcopy(_np.squeeze(self.nrb.data))
-            nrb_denoise[..., rng] = _sg(nrb_denoise[..., rng], win_size, order)
-
-            self.nrb.data = nrb_denoise
-
-            # Backup for Undo
-            self.bcpre.add_step(['DenoiseNrbSG',
-                                 'Win_size', win_size,
-                                 'Order', order])
-
-        self.changeSlider()

-
-
[docs]    def deNoiseDark(self):
-        """
-        Denoise Dark with Savitky-Golay
-        """
-        # Range of pixels to perform-over
-        rng = self.hsi.freq.op_range_pix
-
-        plugin = _widgetSG(window_length=201, polyorder=3)
-        winPlotEffect = _DialogPlotEffect.dialogPlotEffect(self.dark.mean()[rng],
-                                                           x=self.hsi.f,
-                                                           plugin=plugin,
-                                                           parent=self)
-        if winPlotEffect is not None:
-            win_size = winPlotEffect.parameters['window_length']
-            order = winPlotEffect.parameters['polyorder']
-
-            dark_denoise = _copy.deepcopy(_np.squeeze(self.dark.data))
-            dark_denoise[..., rng] = _sg(dark_denoise[..., rng], win_size, order)
-
-            self.dark.data = dark_denoise
-
-            # Backup for Undo
-            self.bcpre.add_step(['DenoiseDarkSG',
-                                 'Win_size', win_size,
-                                 'Order', order])
-
-
-        self.changeSlider()

-
-
[docs]    def deNoise(self):
-        """
-        SVD
-        """
-        # Range of pixels to perform-over
-        rng = self.hsi.freq.op_range_pix
-        # SVD Decompose
-        svd_decompose = SVDDecompose(rng=rng)
-        UsVh = svd_decompose.calculate(self.hsi.data)
-
-        # Class method route
-        if rng is None:
-            # Note: .main in dialog_AbstractFactorization
-            svs = DialogSVD.dialogSVD(UsVh, self.hsi.data.shape, mask=self.hsi.mask,
-                                      img_all=self.hsi.data.mean(axis=-1),
-                                      spect_all=self.hsi.data.mean(axis=(0,1)),
-                                      parent=self)
-        else:
-            svs = DialogSVD.dialogSVD(UsVh, self.hsi.data[..., rng].shape,
-                                      mask=self.hsi.mask,
-                                      img_all=self.hsi.data[..., rng].mean(axis=-1),
-                                      spect_all=self.hsi.data[..., rng].mean(axis=(0,1)),
-                                      parent=self)
-
-        print('SV\'s:{}'.format(svs))
-
-        if svs is not None:
-            svd_recompose = SVDRecompose(rng=rng)
-            svd_recompose.transform(self.hsi.data, UsVh[0], UsVh[1], UsVh[2],
-                                    svs=svs)
-
-            # Backup for Undo
-            self.bcpre.add_step(['SVD', 'SVs', svs])
-
-            if self.ui.actionUndo_Backup_Enabled.isChecked():
-                try:
-                    _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                except:
-                    print('Error in pickle backup (Undo functionality)')
-                else:
-                    self.bcpre.backed_up()
-            self.changeSlider()

-
-
[docs]    def errorCorrectPhase(self):
-        """
-        Error Correction: Phase
-        """
-        rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True,
-                                                 full=False)
-        if _np.iscomplexobj(rand_spectra):
-            rand_spectra = _np.angle(rand_spectra)
-
-        rng = self.hsi.freq.op_range_pix
-
-        plugin = _widgetALS()
-        winPlotEffect = _DialogPlotEffect.dialogPlotEffect(rand_spectra,
-                                                           x=self.hsi.f,
-                                                           plugin=plugin,
-                                                           parent=self)
-        if winPlotEffect is not None:
-            asym_param = winPlotEffect.parameters['asym_param']
-            smoothness_param = winPlotEffect.parameters['smoothness_param']
-            redux_factor = winPlotEffect.parameters['redux']
-            fix_end_points = winPlotEffect.parameters['fix_end_points']
-            max_iter = winPlotEffect.parameters['max_iter']
-            min_diff = winPlotEffect.parameters['min_diff']
-
-            phase_err_correct_als = _PhaseErrCorrectALS(smoothness_param=smoothness_param,
-                                                        asym_param=asym_param,
-                                                        redux=redux_factor,
-                                                        order=2,
-                                                        rng=rng,
-                                                        fix_end_points=fix_end_points,
-                                                        max_iter=max_iter,
-                                                        min_diff=min_diff,
-                                                        verbose=False)
-
-            phase_err_correct_als.transform(self.hsi.data)
-
-            # Backup for Undo
-
-            if _np.size(asym_param) == 1:
-                self.bcpre.add_step(['PhaseErrorCorrectALS',
-                                     'smoothness_param', smoothness_param,
-                                     'asym_param', asym_param,
-                                     'redux', redux_factor,
-                                     'order', 2,
-                                     'fix_end_points', fix_end_points,
-                                     'max_iter', max_iter,
-                                     'min_diff', min_diff])
-            else:
-                self.bcpre.add_step(['PhaseErrorCorrectALS',
-                                     'smoothness_param', smoothness_param,
-                                     'asym_param_start',
-                                     winPlotEffect.parameters['asym_param_start'],
-                                     'asym_param_end',
-                                     winPlotEffect.parameters['asym_param_end'],
-                                     'redux', redux_factor,
-                                     'order', 2,
-                                     'fix_end_points', fix_end_points,
-                                     'max_iter', max_iter,
-                                     'min_diff', min_diff])
-
-            if self.ui.actionUndo_Backup_Enabled.isChecked():
-                try:
-                    _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                except:
-                    print('Error in pickle backup (Undo functionality)')
-                else:
-                    self.bcpre.backed_up()
-
-        self.changeSlider()

-
-
[docs]    def errorCorrectScale(self):
-        """
-        Error Correction: Scale
-        """
-        rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True,
-                                                 full=False)
-        if _np.iscomplexobj(rand_spectra):
-            rand_spectra = rand_spectra.real
-
-        rng = self.hsi.freq.op_range_pix
-
-        plugin = _widgetSG(window_length=601, polyorder=2)
-        winPlotEffect = _DialogPlotEffect.dialogPlotEffect(rand_spectra,
-                                                           x=self.hsi.f,
-                                                           plugin=plugin,
-                                                           parent=self)
-        if winPlotEffect is not None:
-            win_size = winPlotEffect.parameters['window_length']
-            order = winPlotEffect.parameters['polyorder']
-
-            scale_err_correct_sg = _ScaleErrCorrectSG(win_size=win_size,
-                                                      order=order,
-                                                      rng=rng)
-            scale_err_correct_sg.transform(self.hsi.data)
-
-            # Backup for Undo
-            self.bcpre.add_step(['ScaleErrorCorrectSG',
-                                 'win_size', win_size,
-                                 'order', order])
-
-            if self.ui.actionUndo_Backup_Enabled.isChecked():
-                try:
-                    _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                except:
-                    print('Error in pickle backup (Undo functionality)')
-                else:
-                    self.bcpre.backed_up()
-        self.changeSlider()

-
-
[docs]    def errorCorrectAmp(self):
-        """
-        Error Correction: Amp aka Baseline Detrending
-
-        Notes
-        -----
-        If data is complex, amplitude detrending occurs on and only on the \
-        imaginary portion
-        """
-        rand_spectra = self.hsi.get_rand_spectra(5, pt_sz=3, quads=True,
-                                                 full=False)
-        if _np.iscomplexobj(rand_spectra):
-            rand_spectra = rand_spectra.imag
-
-        rng = self.hsi.freq.op_range_pix
-
-        plugin = _widgetALS()
-        winPlotEffect = _DialogPlotEffect.dialogPlotEffect(rand_spectra,
-                                                           x=self.hsi.f,
-                                                           plugin=plugin,
-                                                           parent=self)
-        if winPlotEffect is not None:
-            asym_param = winPlotEffect.parameters['asym_param']
-            smoothness_param = winPlotEffect.parameters['smoothness_param']
-            redux_factor = winPlotEffect.parameters['redux']
-            fix_end_points = winPlotEffect.parameters['fix_end_points']
-            max_iter = winPlotEffect.parameters['max_iter']
-            min_diff = winPlotEffect.parameters['min_diff']
-
-
-            baseline_detrend = _SubtractBaselineALS(smoothness_param=smoothness_param,
-                                                    asym_param=asym_param,
-                                                    redux=redux_factor,
-                                                    order=2,
-                                                    rng=rng,
-                                                    fix_end_points=fix_end_points,
-                                                    max_iter=max_iter,
-                                                    min_diff=min_diff,
-                                                    verbose=False)
-            baseline_detrend.transform(self.hsi.data)
-
-            # Backup for Undo
-            if _np.size(asym_param) == 1:
-                self.bcpre.add_step(['AmpErrorCorrectALS',
-                                     'smoothness_param', smoothness_param,
-                                     'asym_param', asym_param,
-                                     'redux', redux_factor,
-                                     'order', 2,
-                                     'fix_end_points', fix_end_points,
-                                     'max_iter', max_iter,
-                                     'min_diff', min_diff])
-            else:
-                self.bcpre.add_step(['AmpErrorCorrectALS',
-                                     'smoothness_param', smoothness_param,
-                                     'asym_param_start',
-                                     winPlotEffect.parameters['asym_param_start'],
-                                     'asym_param_end',
-                                     winPlotEffect.parameters['asym_param_end'],
-                                     'redux', redux_factor,
-                                     'order', 2,
-                                     'fix_end_points', fix_end_points,
-                                     'max_iter', max_iter,
-                                     'min_diff', min_diff])
-
-
-            if self.ui.actionUndo_Backup_Enabled.isChecked():
-                try:
-                    _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                except:
-                    print('Error in pickle backup (Undo functionality)')
-                else:
-                    self.bcpre.backed_up()
-
-        self.changeSlider()

-
-
[docs]    def doUndo(self):
-        """
-        Undo last operation back to last backup point
-        """
-        self.bcpre.pop_to_last()
-        self.hsi = _BCPre.load_pickle(self.bcpre.id_list[-1])
-        del_flag = 0
-
-        for count in self.bcpre.cut_list:
-            try:
-                _os.remove(count + '.pickle')
-            except:
-                print('Error in deleting old pickle files')
-            else:
-                del_flag += 1
-        if del_flag == len(self.bcpre.cut_list):
-            del self.bcpre.cut_list
-        else:
-            print('Did not delete pickle file cut list... Something went wrong')
-
-        self.ui.freqSlider.setMinimum(0)
-
-        self.ui.freqSlider.setMaximum(self.hsi.freq.size-1)
-
-        self.changeSlider()

-
-
[docs]    def subDark(self):
-        """
-        Subtract loaded dark spectrum from HSI data.
-        """
-
-        nrbloaded = self.nrb.data is not None
-        nrbloaded_left = self.nrb_left.data is not None
-        nrbloaded_right = self.nrb_right.data is not None
-        darkloaded = self.dark.data is not None
-
-        if self.hsi.data is not None:
-            if darkloaded:
-                # Instantiate SubtractDark
-                sub_dark = SubtractDark(self.dark.data)
-
-                msg = _QMessageBox(self)
-                msg.setIcon(_QMessageBox.Question)
-                msg.setText('Subtract Dark Spectrum from Image?')
-                msg.setWindowTitle('Confirm dark subtract from image')
-                msg.setStandardButtons(_QMessageBox.Ok | _QMessageBox.Cancel)
-                msg.setDefaultButton(_QMessageBox.Ok)
-                out = msg.exec()
-
-                if out == _QMessageBox.Ok:
-                    sub_dark.transform(self.hsi.data)
-
-                if nrbloaded:
-                    msg = _QMessageBox(self)
-                    msg.setIcon(_QMessageBox.Question)
-                    msg.setText('Subtract Dark Spectrum from NRB Spectrum(a)?')
-                    msg.setWindowTitle('Confirm dark subtract from NRB spectrum(a)')
-                    msg.setStandardButtons(_QMessageBox.Ok | _QMessageBox.Cancel)
-                    msg.setDefaultButton(_QMessageBox.Ok)
-                    out = msg.exec()
-
-                    if out == _QMessageBox.Ok:
-                        sub_dark.transform(self.nrb.data)
-
-                if nrbloaded_left:
-                    msg = _QMessageBox(self)
-                    msg.setIcon(_QMessageBox.Question)
-                    msg.setText('Subtract Dark Spectrum from Left-Side NRB Spectrum(a)?')
-                    msg.setWindowTitle('Confirm dark subtract from Left-Side NRB spectrum(a)')
-                    msg.setStandardButtons(_QMessageBox.Ok | _QMessageBox.Cancel)
-                    msg.setDefaultButton(_QMessageBox.Ok)
-                    out = msg.exec()
-
-                    if out == _QMessageBox.Ok:
-                        sub_dark.transform(self.nrb_left.data)
-
-                if nrbloaded_right:
-                    msg = _QMessageBox(self)
-                    msg.setIcon(_QMessageBox.Question)
-                    msg.setText('Subtract Dark Spectrum from Right-Side NRB Spectrum(a)?')
-                    msg.setWindowTitle('Confirm dark subtract from Right-Side NRB spectrum(a)')
-                    msg.setStandardButtons(_QMessageBox.Ok | _QMessageBox.Cancel)
-                    msg.setDefaultButton(_QMessageBox.Ok)
-                    out = msg.exec()
-
-                    if out == _QMessageBox.Ok:
-                        sub_dark.transform(self.nrb_right.data)
-
-
-                # Backup for Undo
-                if darkloaded or nrbloaded:
-                    self.bcpre.add_step(['SubDark'])
-                    if self.ui.actionUndo_Backup_Enabled.isChecked():
-                        try:
-                            _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                        except:
-                            print('Error in pickle backup (Undo functionality)')
-                        else:
-                            self.bcpre.backed_up()
-
-                self.changeSlider()
-            else:
-                msg = _QMessageBox(self)
-                msg.setIcon(_QMessageBox.Information)
-                msg.setText('Dark spectrum not loaded.')
-                msg.setStandardButtons(_QMessageBox.Ok)
-                msg.setDefaultButton(_QMessageBox.Ok)
-                msg.exec()
-        else:
-            msg = _QMessageBox(self)
-            msg.setIcon(_QMessageBox.Information)
-            msg.setText('Image data not loaded. Cannot subtract dark spectrum.')
-            msg.setStandardButtons(_QMessageBox.Ok)
-            msg.setDefaultButton(_QMessageBox.Ok)
-            msg.exec()

-
-
[docs]    def subResidual(self):
-        """
-        Subtract a linear residual over range
-        """
-        nrbloaded = self.nrb.data is not None
-        nrbloaded_left = self.nrb_left.data is not None
-        nrbloaded_right = self.nrb_right.data is not None
-        imgloaded = self.hsi.data is not None
-
-        if nrbloaded or imgloaded:
-            text, ok = _QInputDialog.getText(None, 'Frequency Window',
-                                             'Range Tuple (cm-1): ',
-                                             text='(-1500, -500)')
-            if ok:
-                text_str_list = text.strip('(').strip(')').strip().split(',')
-                freqwin = [float(q) for q in text_str_list]
-                freqwin.sort()
-
-                rng = self.hsi.freq.get_index_of_closest_freq(freqwin)
-                sub_residual = SubtractMeanOverRange(rng)
-
-                if imgloaded:
-                    msg = _QMessageBox(self)
-                    msg.setIcon(_QMessageBox.Question)
-                    msg.setText('Subtract Residual Dark Spectrum from Image?')
-                    msg.setWindowTitle('Confirm residual subtraction from Image')
-                    msg.setStandardButtons(_QMessageBox.Ok | _QMessageBox.Cancel)
-                    msg.setDefaultButton(_QMessageBox.Ok)
-                    out_img = msg.exec()
-
-                    if out_img == _QMessageBox.Ok:
-                        sub_residual.transform(self.hsi.data)
-
-                if nrbloaded:
-                    msg = _QMessageBox(self)
-                    msg.setIcon(_QMessageBox.Question)
-                    msg.setText('Subtract Residual Dark Spectrum from NRB?')
-                    msg.setWindowTitle('Confirm residual subtraction from NRB')
-                    msg.setStandardButtons(_QMessageBox.Ok | _QMessageBox.Cancel)
-                    msg.setDefaultButton(_QMessageBox.Ok)
-                    out = msg.exec()
-
-                    if out == _QMessageBox.Ok:
-                        sub_residual.transform(self.nrb.data)
-
-                if nrbloaded_left:
-                    msg = _QMessageBox(self)
-                    msg.setIcon(_QMessageBox.Question)
-                    msg.setText('Subtract Residual Dark Spectrum from Left-Side NRB?')
-                    msg.setWindowTitle('Confirm residual subtraction from Left-Side NRB')
-                    msg.setStandardButtons(_QMessageBox.Ok | _QMessageBox.Cancel)
-                    msg.setDefaultButton(_QMessageBox.Ok)
-                    out = msg.exec()
-
-                    if out == _QMessageBox.Ok:
-                        sub_residual.transform(self.nrb_left.data)
-
-                if nrbloaded_right:
-                    msg = _QMessageBox(self)
-                    msg.setIcon(_QMessageBox.Question)
-                    msg.setText('Subtract Residual Dark Spectrum from Right-Side NRB?')
-                    msg.setWindowTitle('Confirm residual subtraction from Right-Side NRB')
-                    msg.setStandardButtons(_QMessageBox.Ok | _QMessageBox.Cancel)
-                    msg.setDefaultButton(_QMessageBox.Ok)
-                    out = msg.exec()
-
-                    if out == _QMessageBox.Ok:
-                        sub_residual.transform(self.nrb_right.data)
-
-                # Backup for Undo
-                if out_img == _QMessageBox.Ok:
-                    self.bcpre.add_step(['SubResidual','RangeStart',
-                                         freqwin[0], 'RangeEnd',
-                                         freqwin[1]])
-                    if self.ui.actionUndo_Backup_Enabled.isChecked():
-                        try:
-                            _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                        except:
-                            print('Error in pickle backup (Undo functionality)')
-                        else:
-                            self.bcpre.backed_up()
-                self.changeSlider()
-        else:
-            msg = _QMessageBox(self)
-            msg.setIcon(_QMessageBox.Information)
-            msg.setText('Image or NRB data need be loaded.')
-            msg.setStandardButtons(_QMessageBox.Ok)
-            msg.setDefaultButton(_QMessageBox.Ok)
-            msg.exec()

-
-
[docs]    def anscombe(self):
-        """
-        Performance Anscombe transformation
-        """
-        out = DialogAnscombeOptions.dialogAnscombeOptions(parent=self)
-
-        if out is not None:
-            self._anscombe_params = _copy.deepcopy(out)
-
-            rng = self.hsi.freq.op_range_pix
-
-            ansc = _Anscombe(gauss_std=out['stddev'], gauss_mean=0.0,
-                             poisson_multi=out['gain'], rng=rng)
-            ansc.transform(self.hsi.data)
-
-            # Backup for Undo
-            self.bcpre.add_step(['Anscombe','Gauss_mean', 0.0,
-                                 'Gauss_std', out['stddev'],
-                                 'Poisson_multi', out['gain']])
-            if self.ui.actionUndo_Backup_Enabled.isChecked():
-                try:
-                    _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                except:
-                    print('Error in pickle backup (Undo functionality)')
-                else:
-                    self.bcpre.backed_up()
-            self.changeSlider()

-
-
[docs]    def inverseAnscombe(self):
-        """
-        Performance an Inverse Anscombe transformation
-        """
-        if self._anscombe_params is None:
-            out = DialogAnscombeOptions.dialogAnscombeOptions(parent=self)
-        else:
-            out = DialogAnscombeOptions.dialogAnscombeOptions(stddev=self._anscombe_params['stddev'],
-                                                              gain=self._anscombe_params['gain'],
-                                                              parent=self)
-
-        if out is not None:
-            rng = self.hsi.freq.op_range_pix
-
-            iansc = _AnscombeInverse(gauss_std=out['stddev'], gauss_mean=0.0,
-                                     poisson_multi=out['gain'], rng=rng)
-            iansc.transform(self.hsi.data)
-
-            # Backup for Undo
-            self.bcpre.add_step(['InvAnscombe','Gauss_mean', 0.0,
-                                 'Gauss_std', out['stddev'],
-                                 'Poisson_multi', out['gain']])
-            if self.ui.actionUndo_Backup_Enabled.isChecked():
-                try:
-                    _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-                except:
-                    print('Error in pickle backup (Undo functionality)')
-                else:
-                    self.bcpre.backed_up()
-            self.changeSlider()

-
-
[docs]    def doMath(self):
-        """
-        Perform selected math operation on single-color imagery.
-        """
-
-        # Which RGB image is it
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        # Which operation is selected
-        operation_index = self.img_RGB_list[rgbnum].math.ui.comboBoxCondOps.currentIndex()
-        operation_text = self.img_RGB_list[rgbnum].math.ui.comboBoxCondOps.currentText()
-
-
-        if operation_index == 0:
-            num_freq_needed = 0
-        else:
-            # num_freq_needed = widgetColorMath.OPERATION_FREQ_COUNT[operation_index-1]
-            num_freq_needed = self.img_RGB_list[rgbnum].math.OPERATION_FREQ_COUNT[operation_index-1]
-        # Check conditional frequencies are set
-        cond_set = False
-
-        if (num_freq_needed == 1 and
-                self.img_RGB_list[rgbnum].data.condfreq1 is not None):
-
-            # Conditional frequency LOCATION 1
-            condloc1 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.condfreq1)
-
-            # All frequencies set
-            cond_set = True
-        elif (num_freq_needed == 2 and
-              self.img_RGB_list[rgbnum].data.condfreq1 is not None and
-              self.img_RGB_list[rgbnum].data.condfreq2 is not None):
-
-            # Conditional frequency LOCATIONS
-            condloc1 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.condfreq1)
-            condloc2 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.condfreq2)
-
-            # All frequencies set
-            cond_set = True
-        elif (num_freq_needed == 3 and
-              self.img_RGB_list[rgbnum].data.condfreq1 is not None and
-              self.img_RGB_list[rgbnum].data.condfreq2 is not None and
-              self.img_RGB_list[rgbnum].data.condfreq3 is not None):
-
-            # Conditional frequency LOCATIONS
-            condloc1 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.condfreq1)
-            condloc2 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.condfreq2)
-            condloc3 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.condfreq3)
-
-            # All frequencies set
-            cond_set = True
-        else:
-            cond_set = False
-
-        if cond_set is False:
-            self.img_RGB_list[rgbnum].math.ui.comboBoxCondOps.setCurrentIndex(0)
-            Mask = 1
-        else:
-            if (operation_text == '') or (operation_text == ' '):  # Return just a plane
-                Mask = _peakamps.MeasurePeak.measure(self.hsi.data_imag_over_real,
-                                                     condloc1)
-
-
-            elif operation_text == '+':  # Addition
-                Mask = _peakamps.MeasurePeakAdd.measure(self.hsi.data_imag_over_real,
-                                                        condloc1, condloc2)
-
-            elif operation_text == '-':  # Subtraction
-                Mask = _peakamps.MeasurePeakMinus.measure(self.hsi.data_imag_over_real,
-                                                          condloc1, condloc2)
-
-            elif operation_text == '*':  # Multiplication
-                Mask = _peakamps.MeasurePeakMultiply.measure(self.hsi.data_imag_over_real,
-                                                             condloc1, condloc2)
-
-            elif operation_text == '/':  # Division
-                Mask = _peakamps.MeasurePeakDivide.measure(self.hsi.data_imag_over_real,
-                                                           condloc1, condloc2)
-
-            elif operation_text == 'SUM':  # Summation over range
-                Mask = _peakamps.MeasurePeakSummation.measure(self.hsi.data_imag_over_real,
-                                                              condloc1, condloc2)
-
-            elif operation_text == 'Peak b/w troughs':  # Peak between troughs
-                Mask = _peakamps.MeasurePeakBWTroughs.measure(self.hsi.data_imag_over_real,
-                                                              condloc1, condloc2, condloc3)
-            else:
-                pass
-
-        if cond_set is True:
-            inequality_text = self.img_RGB_list[rgbnum].math.ui.comboBoxCondInEquality.currentText()
-            inequality_val = self.img_RGB_list[rgbnum].math.ui.spinBoxInEquality.value()
-            if inequality_text == '<':
-                Mask = Mask < inequality_val
-            elif inequality_text == '>':
-                Mask = Mask > inequality_val
-            elif inequality_text == '=':
-                Mask = Mask == inequality_val
-            elif inequality_text == '>=':
-                Mask = Mask >= inequality_val
-            elif inequality_text == '<=':
-                Mask = Mask <= inequality_val
-            else:
-                print('Inequality type error... setting to 1')
-                Mask = 1
-        # Check frequencies are set
-        operation_index = self.img_RGB_list[rgbnum].math.ui.comboBoxOperations.currentIndex()
-        operation_text = self.img_RGB_list[rgbnum].math.ui.comboBoxOperations.currentText()
-
-        # num_freq_needed = widgetColorMath.OPERATION_FREQ_COUNT[operation_index]
-        num_freq_needed = self.img_RGB_list[rgbnum].math.OPERATION_FREQ_COUNT[operation_index]
-
-        freq_set = False
-
-        if (num_freq_needed == 1 and
-                self.img_RGB_list[rgbnum].data.opfreq1 is not None):
-
-            # Operating frequency LOCATION 1
-            oploc1 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.opfreq1)
-
-            # All frequencies set
-            freq_set = True
-        elif (num_freq_needed == 2 and
-              self.img_RGB_list[rgbnum].data.opfreq1 is not None and
-              self.img_RGB_list[rgbnum].data.opfreq2 is not None):
-
-            # Operating frequency LOCATIONS
-            oploc1 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.opfreq1)
-            oploc2 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.opfreq2)
-
-            # All frequencies set
-            freq_set = True
-
-        elif (num_freq_needed == 3 and
-              self.img_RGB_list[rgbnum].data.opfreq1 is not None and
-              self.img_RGB_list[rgbnum].data.opfreq2 is not None and
-              self.img_RGB_list[rgbnum].data.opfreq3 is not None):
-
-            # Operating frequency LOCATIONS
-            oploc1 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.opfreq1)
-            oploc2 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.opfreq2)
-            oploc3 = self.hsi.freq.get_index_of_closest_freq(self.img_RGB_list[rgbnum].data.opfreq3)
-
-            # All frequencies set
-            freq_set = True
-
-        else:
-            freq_set = False
-
-        if freq_set == True:
-            if (operation_text == '') or (operation_text == ' '):  # Return just a plane
-                self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \
-                    _peakamps.MeasurePeak.measure(self.hsi.data_imag_over_real,
-                                                  oploc1)
-                self.img_RGB_list[rgbnum].changeColor()
-                #self.updateImgColorMinMax()
-            elif operation_text == '+':  # Addition
-                self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \
-                    _peakamps.MeasurePeakAdd.measure(self.hsi.data_imag_over_real,
-                                                     oploc1, oploc2)
-
-                self.img_RGB_list[rgbnum].changeColor()
-                #self.updateImgColorMinMax()
-            elif operation_text == '-':  # Subtraction
-                self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \
-                    _peakamps.MeasurePeakMinus.measure(self.hsi.data_imag_over_real,
-                                                       oploc1, oploc2)
-                self.img_RGB_list[rgbnum].changeColor()
-                #self.updateImgColorMinMax()
-            elif operation_text == '*':  # Multiplication
-                self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \
-                    _peakamps.MeasurePeakMultiply.measure(self.hsi.data_imag_over_real,
-                                                          oploc1, oploc2)
-                self.img_RGB_list[rgbnum].changeColor()
-                #self.updateImgColorMinMax()
-            elif operation_text == '/':  # Division
-                self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \
-                    _peakamps.MeasurePeakDivide.measure(self.hsi.data_imag_over_real,
-                                                        oploc1, oploc2)
-                self.img_RGB_list[rgbnum].changeColor()
-                #self.updateImgColorMinMax()
-            elif operation_text == 'SUM':  # Division
-                self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \
-                    _peakamps.MeasurePeakSummation.measure(self.hsi.data_imag_over_real,
-                                                           oploc1, oploc2)
-                self.img_RGB_list[rgbnum].changeColor()
-                #self.updateImgColorMinMax()
-            elif operation_text == 'Peak b/w troughs':  # Division
-                self.img_RGB_list[rgbnum].data.grayscaleimage = Mask * \
-                    _peakamps.MeasurePeakBWTroughs.measure(self.hsi.data_imag_over_real,
-                                                           oploc1, oploc2,
-                                                           oploc3)
-                self.img_RGB_list[rgbnum].changeColor()
-                #self.updateImgColorMinMax()
-            else:
-                pass
-        else:
-            pass
-        self.doComposite()

-
-
[docs]    def setOpFreq1(self):
-        """
-        Set color math frequency #1 (the primary frequency)
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            currentfreq = float(self.ui.lineEditFreq.text())
-
-            self.img_RGB_list[rgbnum].data.opfreq1 = currentfreq
-            self.img_RGB_list[rgbnum].math.ui.pushButtonOpFreq1.setText(str(round(currentfreq, 1)))
-            self.img_RGB_list[rgbnum].data.grayscaleimage = self.img_BW.data.grayscaleimage
-            self.img_RGB_list[rgbnum].changeColor()
-
-            self.img_RGB_list[rgbnum].mpl.draw()
-
-        except:
-            print('Error')
-        self.doComposite()

-
-
[docs]    def setOpFreq2(self):
-        """
-        Set color math frequency #2 (e.g., freq #1 + freq #2)
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            currentfreq = float(self.ui.lineEditFreq.text())
-
-            self.img_RGB_list[rgbnum].data.opfreq2 = currentfreq
-            self.img_RGB_list[rgbnum].math.ui.pushButtonOpFreq2.setText(str(round(currentfreq, 1)))
-        except:
-            pass

-
-
[docs]    def setOpFreq3(self):
-        """
-        Set color math frequency #3 (e.g., Amplitude at freq #1 - interpolation [freq #2, freq #3])
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            currentfreq = float(self.ui.lineEditFreq.text())
-
-            self.img_RGB_list[rgbnum].data.opfreq3 = currentfreq
-            self.img_RGB_list[rgbnum].math.ui.pushButtonOpFreq3.setText(str(round(currentfreq, 1)))
-
-        except:
-            pass

-
-
[docs]    def setCondFreq1(self):
-        """
-        Set color math conditional frequency #1
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            currentfreq = float(self.ui.lineEditFreq.text())
-
-            self.img_RGB_list[rgbnum].data.condfreq1 = currentfreq
-            self.img_RGB_list[rgbnum].math.ui.pushButtonCondFreq1.setText(str(round(currentfreq, 1)))
-
-        except:
-            print('Error')

-
-
[docs]    def setCondFreq2(self):
-        """
-        Set color math conditional frequency #2
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            currentfreq = float(self.ui.lineEditFreq.text())
-
-            self.img_RGB_list[rgbnum].data.condfreq2 = currentfreq
-            self.img_RGB_list[rgbnum].math.ui.pushButtonCondFreq2.setText(str(round(currentfreq, 1)))
-
-        except:
-            print('Error')

-
-
[docs]    def setCondFreq3(self):
-        """
-        Set color math conditional frequency #1
-        """
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        try:
-            currentfreq = float(self.ui.lineEditFreq.text())
-
-            self.img_RGB_list[rgbnum].data.condfreq3 = currentfreq
-            self.img_RGB_list[rgbnum].math.ui.pushButtonCondFreq3.setText(str(round(currentfreq, 1)))
-
-        except:
-            print('Error')

-
-
[docs]    def spectrumColorImg(self):
-        """
-        Generate plot of mean
-        """
-        # Which RGB image is it
-        rgbnum = self.ui.tabColors.currentIndex()
-
-        Mask = _copy.deepcopy(self.img_RGB_list[rgbnum].data.grayscaleimage)
-
-        if self.img_RGB_list[rgbnum].data.setmin is not None:
-            Mask *= Mask >= self.img_RGB_list[rgbnum].data.setmin
-
-        if self.img_RGB_list[rgbnum].data.setmax is not None:
-            Mask *= Mask <= self.img_RGB_list[rgbnum].data.setmax
-
-        if Mask.max() <= 0:
-            pass
-        else:
-
-            Mask = Mask > 0
-            Mask = Mask.astype(_np.integer)
-
-            mask_hits = Mask.sum()
-
-
-            mloc, nloc = _np.where(Mask)
-
-
-            if mask_hits > 1:
-                mean_spect = self.hsi.data_imag_over_real[mloc, nloc, :][:, self.hsi.freq.op_range_pix].mean(axis=0)
-                std_spect = self.hsi.data_imag_over_real[mloc, nloc, :][:, self.hsi.freq.op_range_pix].std(axis=0)
-                self.plotter.plot(self.hsi.f, mean_spect, label='Mean spectrum ({})'.format(mask_hits))
-            elif mask_hits == 1:
-                mean_spect = _np.squeeze(self.hsi.data_imag_over_real[mloc,nloc,:])[self.hsi.freq.op_range_pix]
-
-                std_spect = 0
-                # Plot spectrum
-
-                self.plotter.plot(self.hsi.f, mean_spect, label='Spectrum ({})'.format(mask_hits))
-
-
-            # Check color of line b/c uses color cycler-- for fill_b/w
-            color = self.plotter.list_all[-1].style_dict['color']
-
-            # Alternative
-            #color = self.plotter.modelLine._model_data[-1]['color']
-
-            # Plot +-1 std. dev.
-            if mask_hits > 1:
-                self.plotter.fill_between(self.hsi.f, mean_spect - std_spect,
-                                          mean_spect + std_spect,
-                                          color=color,
-                                          alpha=0.25,
-                                          label=r'$\pm$1 Std. Dev. ({})'.format(mask_hits))
-
-
-            self.plotter.show()
-            self.plotter.raise_()

-
-
[docs]    def createImgBW(self, img):
-        """
-        Generate the single-frequency grayscale image
-        """
-        xunits = self.img_BW.data.xunits
-        yunits = self.img_BW.data.yunits
-        extent = self.img_BW.data.winextent
-
-        self.img_BW.createImg(img=img, xunits=xunits,
-                              yunits=yunits,
-                              extent=extent, 
-                              cmap=self.img_BW.colormode.ui.comboBoxColormap.currentText())
-
-        if self.img_BW.ui.checkBoxFixed.checkState()==0:
-            self.img_BW.ui.spinBoxMax.setValue(self.img_BW.data.maxer)
-            self.img_BW.ui.spinBoxMin.setValue(self.img_BW.data.minner)

-
-
[docs]    def changeSlider(self):
-        """
-        Respond to change in frequency slider
-        """
-
-        # Get current axis limits to reset to these
-        # after refresh is performed
-        orig_axis_lims = self.img_BW.mpl.ax.axis()
-
-        pos = self.ui.freqSlider.sliderPosition()
-        assert isinstance(pos, int), 'Slider position need be an integer'
-
-        if self.hsi.freq.op_list_pix is not None:
-            offset = self.hsi.freq.op_list_pix[0]
-        else:
-            offset = 0
-
-        self.ui.lineEditPix.setText(str(pos))
-
-        try:
-            self.ui.lineEditFreq.setText(str(round(self.hsi.f[pos],2)))
-            # Set BW Class Data
-
-            self.img_BW.data.grayscaleimage = self.hsi.data_imag_over_real[:, :, pos+offset]
-
-            xlabel = ''
-            if isinstance(self.hsi.x_rep.label, str):
-                xlabel += self.hsi.x_rep.label.strip()
-            if isinstance(self.hsi.x_rep.units, str):
-                xlabel += ' ('
-                xlabel += self.hsi.x_rep.units.strip()
-                xlabel += ')'
-
-            # print('Xlabel: {}'.format(xlabel))
-            ylabel = ''
-            if isinstance(self.hsi.y_rep.label, str):
-                ylabel += self.hsi.y_rep.label.strip()
-            if isinstance(self.hsi.y_rep.units, str):
-                ylabel += ' ('
-                ylabel += self.hsi.y_rep.units.strip()
-                ylabel += ')'
-
-            self.img_BW.data.set_x(self.hsi.x, xlabel)
-            self.img_BW.data.set_y(self.hsi.y, ylabel)
-
-            self.img_BW.checkBoxRemOutliers()
-            # if self.img_BW.ui.checkBoxFixed.checkState() == 0:
-            #     self.img_BW.data.setmax = None
-            #     self.img_BW.data.setmin = None
-            
-            # Set axis to original limits
-            self.img_BW.mpl.ax.axis(orig_axis_lims)
-
-            if not self._mpl_v2:
-                self.img_BW.mpl.ax.hold(True)
-
-        except:
-            print('Error in changeSlider: display img_BW')
-
-        try:
-            if self.show_overlays:
-                for ol in self.overlays:
-                    x = ol['meta']['x']
-                    y = ol['meta']['y']
-
-                    color = ol['color']
-                    mfc = color  # Marker face color
-                    mec = color  # Marker edge color
-                    lw = ol['linewidth']  # Linewidth
-                    label = ol['label']
-                    ls = ol['linestyle']  # Linestyle
-                    ms = ol['markersize']  # Markersize
-                    a = ol['alpha']
-                    marker = ol['marker']
-
-                    # Need some sort of marker if just a point
-                    if _np.size(x) == 1:
-                        if isinstance(marker, str):
-                            if marker.lower() == 'none':
-                                marker = 'x'
-
-                    self.img_BW.mpl.ax.plot(x, y, marker=marker,
-                                            mfc=mfc, mec=mec,
-                                            color=color, lw=lw,
-                                            ls=ls, ms=ms, alpha=a,
-                                            label=label)
-
-                    if self.ui.actionShowOverlayLegend.isChecked():
-                        try:
-                            self.img_BW.mpl.ax.legend(loc='best')
-                        except:
-                            pass
-        except:
-            print('Error in changeSlider: display overlays')
-
-        self.img_BW.mpl.draw()
-
-        if self.bcpre.backed_flag.count(True) > 1:
-            self.ui.actionUndo.setEnabled(True)
-        else:
-            self.ui.actionUndo.setEnabled(False)

-
-
[docs]    def sliderPressed(self):
-        """
-        Respond to press of frequency slider (set tracking of location)
-        """
-        self.ui.freqSlider.setTracking(False)

-
-
[docs]    def sliderReleased(self):
-        """
-        Respond to release of frequency slider (end tracking of location)
-        """
-        self.ui.freqSlider.setTracking(True)

-
-
[docs]    def checkCompositeUpdate(self,num):
-        """
-        Update color composite only if appropriate tab is selected.
-        """
-        if num == self.ui.tabColors.count()-1:
-            self.doComposite()

-
-
[docs]    def doComposite(self):
-        """
-        Update color composite image.
-        """
-        try:
-            self.img_Composite.initData(self.img_RGB_list)
-            self.img_Composite.changeMode()  # This checks what mode is set
-
-            xlabel = ''
-            if isinstance(self.hsi.x_rep.label, str):
-                xlabel += self.hsi.x_rep.label.strip()
-            if isinstance(self.hsi.x_rep.units, str):
-                xlabel += ' ('
-                xlabel += self.hsi.x_rep.units.strip()
-                xlabel += ')'
-
-            # print('Xlabel: {}'.format(xlabel))
-            ylabel = ''
-            if isinstance(self.hsi.y_rep.label, str):
-                ylabel += self.hsi.y_rep.label.strip()
-            if isinstance(self.hsi.y_rep.units, str):
-                ylabel += ' ('
-                ylabel += self.hsi.y_rep.units.strip()
-                ylabel += ')'
-
-            self.img_Composite.data.set_x(self.hsi.x, xlabel)
-            self.img_Composite.data.set_y(self.hsi.y, ylabel)
-
-            self.img_Composite.createImg(img=self.img_Composite.data.image,
-                                         xunits=self.img_Composite.data.xunits,
-                                         yunits=self.img_Composite.data.yunits,
-                                         extent=self.img_BW.data.winextent)
-            self.img_Composite.mpl.draw()
-
-            self.img_Composite2.initData(self.img_RGB_list)
-            self.img_Composite2.changeMode()
-            
-            self.img_Composite2.data.set_x(self.hsi.x, xlabel)
-            self.img_Composite2.data.set_y(self.hsi.y, ylabel)
-            self.img_Composite2.createImg(img=self.img_Composite2.data.image,
-                                          xunits=self.img_Composite2.data.xunits,
-                                          yunits=self.img_Composite2.data.yunits,
-                                          extent=self.img_BW.data.winextent)
-            self.img_Composite2.mpl.draw()
-        except:
-            print('Error in doComposite')

-
-
[docs]    def updateOverlays(self):
-        self.overlays=[]
-        for ln in self.plotter.list_line_objs:
-            ms = ln.model_style
-
-            # Make sure there is the appropriate meta data
-            if ms.get('meta').get('overlay') is not None:
-                if ms['meta']['overlay'] == True:
-                    self.overlays.append(ms)
-        self.changeSlider()

-
-
[docs]    def deleteOverlays(self):
-        self.updateOverlays()

-
-
[docs]    def checkShowOverlays(self):
-        self.show_overlays = self.ui.actionShowOverlays.isChecked()
-        self.changeSlider()

-
-
[docs]    def makeRamanPhantom(self):
-        """
-        Generate a numerical phantom for Raman
-        """
-        cplx = False  # Is model complex-valued -- False for Raman
-
-        dialog = DialogModel.dialogModel(cplx=cplx, parent=self)
-        if dialog is not None:
-            model = _Model(subsample=dialog['subsample'])
-        
-            wn_start = dialog['wn_start']
-            wn_end = dialog['wn_end']
-
-            lam_start = 0.01 / (wn_start + 0.01/(dialog['probe']*1e-9))  # meters
-            lam_start *= 1e9  # nm
-
-            lam_end = 0.01 / (wn_end + 0.01/(dialog['probe']*1e-9))  # meters
-            lam_end *= 1e9  # nm
-
-            lam_ctr = (lam_start + lam_end) / 2  # nm
-            
-            n_pix = _np.ceil((lam_end-lam_start) / dialog['wl_slope'])
-
-            # Make a properly linear frequency-vector and polyfit
-            f = dialog['wl_slope'] * _np.arange(n_pix)  # Temporary frequency vec
-            f -= f.mean()
-            f += lam_ctr
-        
-            a_vec = _np.polyfit(_np.arange(n_pix), f, 1)
-        
-            calib = {'a_vec': a_vec,
-                     'ctr_wl': lam_ctr,
-                     'ctr_wl0': lam_ctr,
-                     'n_pix': n_pix,
-                     'probe': dialog['probe'],
-                     'units': 'nm'}
-        
-            f = _calib_pix_wn(calib)[0]
-            model.make_hsi(f=f)
-
-            if cplx:
-                model.hsi = model.hsi.astype(_np.complex64)
-                self.hsi = Hsi(data=model.hsi, x=model.x, y=model.y)
-            else:
-                model.hsi = 1*model.hsi.imag
-                model.hsi = model.hsi.astype(_np.float32)
-                self.hsi = Hsi(data=model.hsi, x=model.x, y=model.y)
-
-            # For Raman -- make the Hsi more intense
-            # This is ARBITRARY
-            self.hsi._data *= 50e3
-
-            self.hsi.freq.calib_fcn = _calib_pix_wn
-            self.hsi.freq.calib = calib
-            self.hsi.freq.update()
-
-            add_gnoise = dialog['gnoise_bool']  # AWGN (Gaussian)
-            add_pnoise = dialog['pnoise_bool']  # Poisson noise
-            add_dark = dialog['dark_bool']  # Dark background -- just a constant
-
-            # These values correspond to the defaults of the
-            # Anscombe UI
-            g_noise = dialog['gnoise_stddev']  # Std Dev of Gaussian noise
-            p_amp = dialog['pnoise_gain']  # Multiplier of Poisson noise
-            dark_amp = dialog['dark_level']
-
-            if add_pnoise:  # Add Poisson noise
-                # NOTE: CORRECT is p_amp*poisson(signal)
-                # DEFINITELY NOT p_amp*(poisson(signal)-signal) + signal
-                self.hsi._data += p_amp*(_np.random.poisson(self.hsi._data)) - self.hsi._data
-            if add_gnoise:  # Add AGWN
-                self.hsi._data += _np.random.randn(*self.hsi._data.shape)
-            if add_dark:  # Add a constant dark background
-                self.hsi._data += dark_amp
-                self.dark._data = dark_amp + 0*f
-                self.dark.freq = self.hsi.freq
-
-            self.filename = 'Phantom.h5'
-            self.path = _os.path.abspath('./')
-            self.dataset_name = '/BCARSImage/Phantom_v0/Phantom_v0'
-
-            meta = {'Calib.a_vec': a_vec,
-                    'Calib.ctr_wl': lam_ctr,
-                    'Calib.ctr_wl0': lam_ctr,
-                    'Calib.n_pix': n_pix,
-                    'Calib.probe': calib['probe'],
-                    'Calib.units': 'nm',
-                    'Memo': 'Numerical phantom from murine pancreas artery. See Camp et al, JRS (2016).',
-                    'RasterScanParams.FastAxis': 'X',
-                    'RasterScanParams.FastAxisStart': model.x[0],
-                    'RasterScanParams.FastAxisStepSize': _np.diff(model.x).mean(),
-                    'RasterScanParams.FastAxisSteps': model.x.size,
-                    'RasterScanParams.FastAxisStop': model.x[-1],
-                    'RasterScanParams.FixedAxis': 'Z',
-                    'RasterScanParams.FixedAxisPosition': 0,
-                    'RasterScanParams.SlowAxis': 'Y',
-                    'RasterScanParams.SlowAxisStart': model.y[0],
-                    'RasterScanParams.SlowAxisStepSize': _np.diff(model.y).mean(),
-                    'RasterScanParams.SlowAxisSteps': model.y.size,
-                    'RasterScanParams.SlowAxisStop': model.y[-1],
-                    'Spectro.CenterWavelength': lam_ctr,
-                    }
-            self.hsi._meta = meta
-            self.fileOpenSuccess(True)
-            self.changeSlider()
-        else:
-            pass

-        
-    
-
[docs]    def makeBCARSPhantom(self):
-        """
-        Generate a numerical phantom for BCARS
-        """
-        cplx = True  # Is model complex-valued -- True for BCARS
-
-        dialog = DialogModel.dialogModel(cplx=cplx, parent=self)
-        if dialog is not None:
-            model = _Model(subsample=dialog['subsample'])
-        
-            wn_start = dialog['wn_start']
-            wn_end = dialog['wn_end']
-
-            lam_start = 0.01 / (wn_start + 0.01/(dialog['probe']*1e-9))  # meters
-            lam_start *= 1e9  # nm
-
-            lam_end = 0.01 / (wn_end + 0.01/(dialog['probe']*1e-9))  # meters
-            lam_end *= 1e9  # nm
-
-            lam_ctr = (lam_start + lam_end) / 2  # nm
-            
-            n_pix = _np.ceil((lam_end-lam_start) / dialog['wl_slope'])
-
-            # Make a properly linear frequency-vector and polyfit
-            f = dialog['wl_slope'] * _np.arange(n_pix)  # Temporary frequency vec
-            f -= f.mean()
-            f += lam_ctr
-        
-            a_vec = _np.polyfit(_np.arange(n_pix), f, 1)
-        
-            calib = {'a_vec': a_vec,
-                     'ctr_wl': lam_ctr,
-                     'ctr_wl0': lam_ctr,
-                     'n_pix': n_pix,
-                     'probe': dialog['probe'],
-                     'units': 'nm'}
-        
-            f = _calib_pix_wn(calib)[0]
-            model.make_hsi(f=f)
-
-            if cplx:
-                model.hsi = model.hsi.astype(_np.complex64)
-                self.hsi = Hsi(data=model.hsi, x=model.x, y=model.y)
-            else:
-                model.hsi = 1*model.hsi.imag
-                model.hsi = model.hsi.astype(_np.float32)
-                self.hsi = Hsi(data=model.hsi, x=model.x, y=model.y)
-
-            # Simple Gaussian 0-centered source profile
-            source = 1e2*_np.exp(-f**2/(2*1500**2))
-            nrb = 10*_np.exp(-(f-20e3)**2/(2*10e3**2))
-
-            self.hsi.data = _np.abs((self.hsi.data+nrb)*source)**2
-            self.hsi.freq.calib_fcn = _calib_pix_wn
-            self.hsi.freq.calib = calib
-            self.hsi.freq.update()
-
-            self.nrb.data = _np.abs(source*nrb)**2
-            self.nrb.freq = self.hsi.freq
-            
-            add_gnoise = dialog['gnoise_bool']  # AWGN (Gaussian)
-            add_pnoise = dialog['pnoise_bool']  # Poisson noise
-            add_dark = dialog['dark_bool']  # Dark background -- just a constant
-
-            # These values correspond to the defaults of the
-            # Anscombe UI
-            g_noise = dialog['gnoise_stddev']  # Std Dev of Gaussian noise
-            p_amp = dialog['pnoise_gain']  # Multiplier of Poisson noise
-            dark_amp = dialog['dark_level']
-
-            # Only dark added to NRB
-            # Others only to Hsi data
-            if add_pnoise:  # Add Poisson noise
-                # NOTE: CORRECT is p_amp*poisson(signal)
-                # DEFINITELY NOT p_amp*(poisson(signal)-signal) + signal
-                self.hsi._data += p_amp*(_np.random.poisson(self.hsi._data)) - self.hsi._data
-            if add_gnoise:  # Add AGWN
-                self.hsi._data += _np.random.randn(*self.hsi._data.shape)
-            if add_dark:  # Add a constant dark background
-                self.hsi._data += dark_amp
-                self.nrb._data += dark_amp
-                self.dark._data = dark_amp + 0*f
-                self.dark.freq = self.hsi.freq
-
-            self.filename = 'Phantom.h5'
-            self.path = _os.path.abspath('./')
-            self.dataset_name = '/BCARSImage/Phantom_v0/Phantom_v0'
-
-            meta = {'Calib.a_vec': a_vec,
-                    'Calib.ctr_wl': lam_ctr,
-                    'Calib.ctr_wl0': lam_ctr,
-                    'Calib.n_pix': n_pix,
-                    'Calib.probe': calib['probe'],
-                    'Calib.units': 'nm',
-                    'Memo': 'Numerical phantom from murine pancreas artery. See Camp et al, JRS (2016).',
-                    'RasterScanParams.FastAxis': 'X',
-                    'RasterScanParams.FastAxisStart': model.x[0],
-                    'RasterScanParams.FastAxisStepSize': _np.diff(model.x).mean(),
-                    'RasterScanParams.FastAxisSteps': model.x.size,
-                    'RasterScanParams.FastAxisStop': model.x[-1],
-                    'RasterScanParams.FixedAxis': 'Z',
-                    'RasterScanParams.FixedAxisPosition': 0,
-                    'RasterScanParams.SlowAxis': 'Y',
-                    'RasterScanParams.SlowAxisStart': model.y[0],
-                    'RasterScanParams.SlowAxisStepSize': _np.diff(model.y).mean(),
-                    'RasterScanParams.SlowAxisSteps': model.y.size,
-                    'RasterScanParams.SlowAxisStop': model.y[-1],
-                    'Spectro.CenterWavelength': lam_ctr,
-                    }
-            self.hsi._meta = meta
-
-            self.ui.actionDarkSpectrum.setEnabled(True)
-            self.ui.actionNRBSpectrum.setEnabled(True)
-            self.ui.actionDarkSubtract.setEnabled(True)
-            self.ui.actionKramersKronig.setEnabled(True)
-            self.ui.actionPhaseErrorCorrection.setEnabled(True)
-            self.ui.actionScaleErrorCorrection.setEnabled(True)
-            self.ui.menuCoherent_Raman_Imaging.setEnabled(True)
-
-            self.fileOpenSuccess(True)
-            self.changeSlider()
-        else:
-            pass

-                
-
[docs]def crikit_launch(**kwargs):
-    """
-    Command line launching of CRIkitUI.
-
-    Input kwargs (Optional)
-    ------------
-    hsi : crikit.data.Hsi
-        Hsi instance
-
-    data : ndarray (3D)
-        Numpy array (Y,X,Freq) hsi
-
-    x : ndarray (1D)
-        x-array
-
-    x_units : str
-        Units of x (e.g. r'$\mu$m')
-
-    x_label : str
-        Label of x (e.g. 'X')
-
-    y : ndarray (1D)
-        y-array
-
-    y_units : str
-        Units of y (e.g. r'$\mu$m')
-
-    y_label : str
-        Label of y (e.g. 'Y')
-
-    f : ndarray (1D)
-        frequency-array
-
-    f_units : str
-        Units of frequency (e.g. r'cm$^{-1}$')
-
-    f_label : str
-        Label of frequency (e.g. 'Wavenumber')
-
-    filename : str
-        Filename of HDF data to auto-load (requires path and dataset_name as well)
-
-    path : str
-        Path of HDF data to auto-load (requires filename and dataset_name as well)
-
-    dataset_name : str
-        Dataset name(s) of HDF data to auto-load (requires path and filename as well)
-
-    """
-
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-    app.setQuitOnLastWindowClosed(False)
-
-    parent = kwargs.get('parent')
-
-    if parent is None:
-        obj = _QWidget()
-    else:
-        obj = parent
-        
-    kwargs['parent'] = obj
-    # print('Kwargs: {}'.format(kwargs))
-    win = CRIkitUI_process(**kwargs) ### EDIT ###
-
-    # Insert other stuff to do
-
-    # Final stuff
-    win.showMaximized()
-    #win.plotter.lower()
-    #win.raise_()
-    app.exec_()
-    return None

-
-if __name__ == '__main__':
-
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-    app.setQuitOnLastWindowClosed(False)
-
-    obj = _QWidget()
-    win = CRIkitUI_process(parent=obj) ### EDIT ###
-
-    # Insert other stuff to do
-
-
-    # Final stuff
-    win.showMaximized()
-    #win.plotter.lower()
-    #win.raise_()
-    app.exec_()
-#    _sys.exit(app.exec_())
-    #app.closeAllWindows()
-
- -
-
- -
-
- - -
-
- -
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Source code for crikit.cri.algorithms.kk

-"""
-Kramers-Kronig Relation Phase Retrieval (crikit.process.maths.kk)
-=================================================================
-
-    kkrelation : Retrieve real and imaginary components from a
-    spectrum that is the modulus of a function
-
-    hilbertfft : Fourier-domain Hilbert transform
-
-References
-----------
-[1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent 
-    Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase 
-    Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543.
-
-"""
-
-import numpy as _np
-from scipy import fftpack as _fftpack
-
-__all__ = ['kkrelation', 'hilbertfft']
-
-_DEFAULT_THREADS = 1
-
-# Conditional modules
-# Check for and load pyFFTW if available (kkrelation, hilbertfft)
-try:  # pragma: no cover
-    import pyfftw as _pyfftw
-    _pyfftw_available = True
-except ImportError:  # pragma: no cover
-    print("No pyFFTW found. Using Scipy instead. \n\
-    You may want to install pyFFTW and FFTW for [potentially]\n\
-    significant performance enhancement")
-    _pyfftw_available = False
-
-
-
-# Check for and load multiprocessing to determine number of CPUs
-try:
-    import multiprocessing as _multiprocessing
-    _thread_num = _multiprocessing.cpu_count()
-except ImportError:  # pragma: no cover
-    print("No multiprocessing module found. \n\
-    Default thread number set to 1. This can be\n\
-    changed within the .py file")
-    _thread_num = _DEFAULT_THREADS
-
-
-
[docs]def kkrelation(bg, cri, phase_offset=0.0, norm_by_bg=True, pad_factor=1):
-    """
-    Retrieve the real and imaginary components of a CRI spectra(um) via
-    the Kramers-Kronig (KK) relation.
-
-    Parameters
-    ----------
-    bg : ndarray
-        Coherent background (bg) spectra(um) array that can be one-, two-, \
-        or three-dimensional
-    cri : ndarray
-        CRI spectra(um) array that can be one-,two-,or three-dimensional \
-    (phase_offset) : int, float, or ndarray, optional
-        Global phase offset applied to the KK, which effecively controls \
-        the real-to-imaginary components relationship
-    (norm_by_bg) : bool
-        Should the output be normalized by the square-root of the \
-        background (bg) spectrum(a)
-    (pad_factor) : int
-        The multiple number of spectra-length pads that will be
-        applied before and after the original spectra
-
-
-    Returns
-    -------
-    out : complex ndarray
-        The real and imaginary components of KK.
-
-    Notes
-    -----
-    (1) The imaginary components provides the sponatenous Raman-like \
-    spectra(um).
-
-    (2) This module assumes the spectra are oriented as such that the \
-    frequency (wavenumber) increases with increasing index.  If this is \
-    not the case for your spectra(um), apply a phase_offset of _np.pi
-
-    References
-    ----------
-    Y Liu, Y J Lee, and M T Cicerone, "Broadband CARS spectral phase \
-    retrieval using a time-domain Kramers-Kronig transform," Opt. Lett. 34, \
-    1363-1365 (2009).
-
-    C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable \
-    Coherent Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting \
-    Errors in Phase Retrieval," Journal of Raman Spectroscopy (2016). \
-    arXiv:1507.06543.
-    """
-
-    ratio = cri / bg
-    ratio[_np.isnan(ratio)] = 1e-8
-    ratio[_np.isinf(ratio)] = 1e-8
-
-    ratio[ratio <= 0] = 1e-8
-
-    if ratio.ndim == 3:
-        h = _np.zeros(ratio.shape, dtype=float)
-        for row_num, blk in enumerate(ratio):
-            h[row_num, :, :] = hilbertfft(0.5 * _np.log(blk),
-                                          pad_factor=pad_factor)
-    else:
-        h = hilbertfft(0.5 * _np.log(ratio), pad_factor=pad_factor)
-
-    # Note: disabled numexpr eval due to stability issues
-    if norm_by_bg is True:
-        out = _np.sqrt(ratio) * _np.exp(1j * phase_offset + 1j * h)
-        # out = _ne.evaluate('sqrt(ratio)*exp(1j*phase_offset + 1j*h)')
-        return out
-    else:
-        out = _np.sqrt(cri) * _np.exp(1j * phase_offset + 1j * h)
-        return out

-        # return _ne.evaluate('sqrt(cri)*exp(1j*phase_offset + 1j*h)')
-
-
-
[docs]def hilbertfft(spectra, pad_factor=1, use_pyfftw=True):
-    """
-    Compute the one-dimensional Hilbert Transform.
-
-    This function computes the one-dimentional Hilbert transform
-    using the Fourier-domain implementation.
-
-    Parameters
-    ----------
-    spectra : ndarray
-        Input array that can be one-,two-,or three-dimensional
-    pad_factor : int, optional
-        The multiple number of spectra-length pads that will be
-        applied before and after the original spectra
-    use_pyfftw : bool, optional
-        If available, use pyfftw. Else use scipy scipack implementation
-
-    Returns
-    -------
-    ndarray
-        Hilbert transformed data
-
-    References
-    ----------
-    C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable \
-    Coherent Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting \
-    Errors in Phase Retrieval," Journal of Raman Spectroscopy (2016). \
-    arXiv:1507.06543.
-
-    A D Poularikas, "The Hilbert Transform," in The Handbook of \
-    Formulas and Tables for Signal Processing (ed., A. D. Poularikas), \
-    Boca Raton, CRC Press LLC (1999).
-    """
-
-    assert spectra.ndim <= 2, 'Input data need be 1D or 2D for memory'
-
-    freq_len = spectra.shape[-1]
-    freq_pad_len = freq_len*(2*pad_factor+1)
-    pad_len = freq_len*(pad_factor)
-    time_vec = _np.fft.fftfreq(freq_pad_len)
-
-    if pad_factor > 0:
-        pad_left = _np.dot(spectra[..., 0][..., None], _np.ones((1, pad_len)))
-        pad_right = _np.dot(spectra[..., -1][..., None], _np.ones((1, pad_len)))
-        padded = _np.concatenate((pad_left, spectra, pad_right), axis=-1)
-    else:
-        padded = spectra
-
-    padded = padded.astype(_np.complex)
-
-    # Use pyFFTW (supposed optimal) library or Scipy
-    # Note (although not obvious with pyFFTW) these functions overwrite
-    # the input variable-- saves memory and increases speed
-    if _pyfftw_available and use_pyfftw:
-        _pyfftw.interfaces.cache.enable()
-        padded = _pyfftw.interfaces.scipy_fftpack.ifft(padded, axis=-1,
-                                                       overwrite_x=True,
-                                                       threads=_thread_num,
-                                                       auto_align_input=True,
-                                                       planner_effort='FFTW_MEASURE')
-
-        padded *= 1j*_np.sign(time_vec)
-
-        padded = _pyfftw.interfaces.scipy_fftpack.fft(padded, axis=-1,
-                                                      overwrite_x=True,
-                                                      threads=_thread_num,
-                                                      auto_align_input=True,
-                                                      planner_effort='FFTW_MEASURE')
-    else: # Perform Hilbert Transform with Scipy FFTPACK
-        _fftpack.ifft(padded, axis=-1, overwrite_x=True)
-        padded *= 1j*_np.sign(time_vec)
-        _fftpack.fft(padded, axis=-1, overwrite_x=True)
-
-    # Set inf's and NaN's to arbitrarily small value
-    padded[_np.isnan(padded)] = 1e-8
-    padded[_np.isinf(padded)] = 1e-8
-
-    return _np.real(padded[..., pad_len:pad_len + freq_len])

-
-if __name__ == '__main__':  # pragma: no cover
-    import timeit as _timeit
-
-    x = _np.random.rand(300,900)
-    print(x.dtype)
-    y = _np.random.rand(300,900)
-    
-    
-    if _pyfftw_available:
-        start = _timeit.default_timer()
-        #out = kkrelation(x,y)
-        out = hilbertfft(x)
-        start -= _timeit.default_timer()
-        print('PyFFTW Time (Trial 1): {:.3g} sec'.format(-start))
-
-        start = _timeit.default_timer()
-        #out = kkrelation(x,y)
-        out = hilbertfft(x)
-        start -= _timeit.default_timer()
-        print('PyFFTW Time (Trial 2): {:.3g} sec'.format(-start))
-
-    start = _timeit.default_timer()
-    #out = kkrelation(x,y)
-    out = hilbertfft(x, use_pyfftw=False)
-    start -= _timeit.default_timer()
-    print('Scipy Time (Trial 1): {:.3g} sec'.format(-start))
-
-    start = _timeit.default_timer()
-    #out = kkrelation(x,y)
-    out = hilbertfft(x, use_pyfftw=False)
-    start -= _timeit.default_timer()
-    print('Scipy Time (Trial 2): {:.3g} sec'.format(-start))
-
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/cri/error_correction.html b/docs/build/html/_modules/crikit/cri/error_correction.html deleted file mode 100644 index bacb94c..0000000 --- a/docs/build/html/_modules/crikit/cri/error_correction.html +++ /dev/null @@ -1,446 +0,0 @@ - - - - - - - - - - - crikit.cri.error_correction — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.cri.error_correction

-"""
-Created on Mon Jun  6 11:20:35 2016
-
-@author: chc
-"""
-
-import numpy as _np
-import copy as _copy
-
-from scipy.signal import savgol_filter as _sg
-
-from crikit.cri.algorithms.kk import hilbertfft as _hilbert
-
-from crikit.preprocess.algorithms.als import AlsCvxopt as _AlsCvxopt
-
-from crikit.utils.datacheck import _rng_is_pix_vec
-
-
-
[docs]class PhaseErrCorrectALS:
-    """
-    Phase error correction using alternating least squares (ALS)
-
-    References
-    -----------
-    * C H Camp Jr, Y J Lee, and M T Cicerone, JRS (2016).
-    """
-    def __init__(self, smoothness_param=1, asym_param=1e-2,
-                 redux=10, order=2, rng=None, fix_end_points=False,
-                 fix_rng=None, max_iter=100, min_diff=1e-5, **kwargs):
-
-
-        self.rng = _rng_is_pix_vec(rng)
-        self._k = kwargs
-
-        self._k.update({'smoothness_param' : smoothness_param,
-                        'asym_param' : asym_param,
-                        'redux' : redux,
-                        'order' : order,
-                        'fix_end_points' : fix_end_points,
-                        'fix_rng' : fix_rng,
-                        'max_iter' : max_iter,
-                        'min_diff' : min_diff})
-
-
-
[docs]    def _calc(self, data, ret_obj, **kwargs):
-
-        self._inst_als = _AlsCvxopt(**kwargs)
-
-        try:
-            shp = data.shape[0:-2]
-            total_num = _np.array(shp).prod()
-
-            counter = 1
-            for idx in _np.ndindex(shp):
-                print('Detrended iteration {} / {}'.format(counter, total_num))
-                ph = _np.unwrap(_np.angle(data[idx]))
-                if self.rng is None:
-                    err_phase = self._inst_als.calculate(ph)
-                else:
-                    err_phase = self._inst_als.calculate(ph[..., self.rng])
-
-                h = _np.zeros(err_phase.shape)
-                h += _hilbert(err_phase)
-
-                correction_factor = 1/_np.exp(h) * _np.exp(-1j*err_phase)
-
-                if self.rng is None:
-                    ret_obj[idx] *= correction_factor
-                else:
-                    ret_obj[idx][..., self.rng] *= correction_factor
-                counter += 1
-        except:
-            return False
-        else:
-#            print(self._inst_als.__dict__)
-            return True

-
-
[docs]    def calculate(self, data, **kwargs):
-
-        data_copy = _copy.deepcopy(data)
-        self._k.update(kwargs)
-
-        success = self._calc(data, ret_obj=data_copy, **self._k)
-        if success:
-            return data_copy
-        else:
-            return None

-
-
[docs]    def transform(self, data, **kwargs):
-        self._k.update(kwargs)
-
-        success = self._calc(data, ret_obj=data, **self._k)
-        return success

-
-
[docs]class ScaleErrCorrectSG:
-    """
-    Scale error correction using Savitky-Golay
-
-    References
-    -----------
-    * C H Camp Jr, Y J Lee, and M T Cicerone, JRS (2016).
-    """
-    def __init__(self, win_size=601, order=2, rng=None):
-        self.win_size = win_size
-        self.order = order
-        self.rng = _rng_is_pix_vec(rng)
-
-
[docs]    def _calc(self, data, ret_obj):
-        try:
-            if self.rng is None:
-                correction_factor = _sg(data.real, window_length=self.win_size,
-                                        polyorder=self.order, axis=-1)
-            else:
-                correction_factor = _sg(data[..., self.rng].real,
-                                        window_length=self.win_size,
-                                        polyorder=self.order, axis=-1)
-
-            correction_factor[correction_factor == 0] = 1
-            correction_factor **= -1
-
-            if self.rng is None:
-                ret_obj *= correction_factor
-            else:
-                ret_obj[..., self.rng] *= correction_factor
-        except:
-            return False
-        else:
-            return True

-
-
[docs]    def calculate(self, data):
-
-        data_copy = _copy.deepcopy(data)
-        success = self._calc(data, ret_obj=data_copy)
-        if success:
-            return data_copy
-        else:
-            return None

-
-
[docs]    def transform(self, data):
-        success = self._calc(data, ret_obj=data)
-        return success

-
-
-if __name__ == '__main__':  # pragma: no cover
-    import matplotlib.pyplot as plt
-    from crikit.cri.kk import KramersKronig
-    import timeit
-
-    SPECT_LEN = 878
-    WN = _np.linspace(4000, 500, SPECT_LEN)
-    chi = (1 / ((WN - 1000 - 1j * 10)) +
-           1 / ((WN - 1020 - 1j * 10)) +
-           1 / ((WN - 2800 - 1j * 10)))
-    chiNR = 0*chi + 0.055
-    exc = WN
-    sig = _np.abs(chi + chiNR)**2
-
-    sigNR = _np.abs(chiNR)**2
-    sigRef = chiNR*(WN/1e3)**.5
-
-    NUM_REPS = 10
-
-    kk = KramersKronig()
-    kkd = kk.calculate(sig, sigRef)
-    kkd = _np.dot(_np.random.rand(NUM_REPS,NUM_REPS,1)*_np.ones((NUM_REPS, NUM_REPS, 1)), kkd[None, :])
-
-#    plt.plot(chi.imag/chiNR.real, label='Ideal')
-    plt.plot(kkd[5, 5, :].imag, label='Before Correction')
-
-    start = timeit.default_timer()
-    phase_err_correct_als = PhaseErrCorrectALS(fix_end_points=True,
-                                               smoothness_param=1e8,
-                                               asym_param=1e-3,
-                                               redux=1)
-    success = phase_err_correct_als.transform(kkd, verbose=False)
-    print('Success? : {}'.format(success))
-    stop = timeit.default_timer()
-    print('Sec/spectrum: {:.3g}'.format((stop-start)/NUM_REPS**2))
-
-
-#
-    plt.plot(kkd[5,5,:].imag, label='After PhErr Corr.')
-    plt.legend()
-    plt.show()
-#    scale_err_correct_sg = ScaleErrCorrectSG()
-#    success = scale_err_correct_sg.transform(kkd)
-#    print('Success? : {}'.format(success))
-#    plt.plot(kkd[5, 5, :].imag, label='After Correction')
-#    plt.legend(loc='best')
-#    plt.show()
-
-#    scale_err_correct_sg = ScaleErrCorrectSG()
-#    out = scale_err_correct_sg.calculate(kkd[0,0,:])
-#    plt.plot(out.imag)
-#
-#    scale_err_correct_sg = ScaleErrCorrectSG(win_size=11, order=2)
-#    out = scale_err_correct_sg.calculate(kkd[0,0,:])
-#    plt.plot(out.imag)
-#
-#    plt.show()
-
-#
-#    phase_err_correct_als = PhaseErrCorrectALS(print_iteration=False)
-#    out = phase_err_correct_als.calculate(kkd)
-#
-#    plt.plot(out[0,0,:].imag)
-#
-#    phase_err_correct_als = PhaseErrCorrectALS(smoothness_param=1e1,
-#                                                asym_param=1e-2,
-#                                                redux_factor=1)
-
-
-#    print(phase_err_correct_als._k)
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/cri/kk.html b/docs/build/html/_modules/crikit/cri/kk.html deleted file mode 100644 index a6c2991..0000000 --- a/docs/build/html/_modules/crikit/cri/kk.html +++ /dev/null @@ -1,481 +0,0 @@ - - - - - - - - - - - crikit.cri.kk — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
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-
- - - - - - - - - - - - - - - - -
- - - - -
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-
-
- -

Source code for crikit.cri.kk

-"""
-Kramers-Kronig relation phase retrieval.
-
-References
-----------
-[1] Y. Liu, Y. J. Lee, and M. T. Cicerone, "Broadband CARS spectral
-phase retrieval using a time-domain Kramers-Kronig transform,"
-Opt. Lett. 34, 1363-1365 (2009).
-
-[2] C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative, \
-Comparable Coherent Anti-Stokes Raman Scattering (CARS) \
-Spectroscopy: Correcting Errors in Phase Retrieval," Journal of Raman \
-Spectroscopy 47, 408-415 (2016). arXiv:1507.06543.
-
-
-"""
-
-import timeit as _timeit
-
-import numpy as _np
-
-from crikit.cri.algorithms.kk import kkrelation as _kkrelation
-from crikit.utils.datacheck import _rng_is_pix_vec
-from crikit.utils.general import find_nearest as _find_nearest
-from crikit.utils.general import mean_nd_to_1d as _mean_nd_to_1d
-
-
[docs]class KramersKronig:
-    """
-    Retrieve the real and imaginary components of coherent Raman data via the \
-    Kramers-Kronig (KK) relation. See References.
-
-    Parameters
-    ----------
-    cars_amp_offset : float, optional (default=0.0)
-        DC offset applied to CARS spectrum(a) prior to KK relation. See Notes \
-        and Ref. [2].
-
-    nrb_amp_offset : float, optional (default=0.0)
-        DC offset applied to NRB spectrum(a) prior to KK relation. See Notes \
-        and Ref. [2].
-
-    phase_offset : float or ndarray, optional (default=0.0)
-        Phase constant or ndarray applied to retrieved phase prior to \
-        separating the real and imaginary components. See Notes \
-        and Ref. [2].
-
-    norm_to_nrb : bool, optional (default=True)
-        Normalize the amplitude by sqrt(NRB). This effectively removes several \
-        system reponse functions. Highly recommended. See Ref. [2]
-
-    pad_factor : int, optional (default=1)
-        Multiple size of spectral-length to pad the ends of each spectra with. \
-        Padded with a constant value corresponding to the value at that end of \
-        the spectrum. See Ref. [1].
-
-    rng : ndarray (1D), optional (default=None)
-        Range of pixels/frequencies (if freq provided) to perform over
-
-    rng_list : list/tuple, optional (default=None)
-        First and Last pixels/frequencies (if freq provided) to perform over
-
-    freq : ndarray (1D), optional (default=None)
-        Frequency vector
-
-    Returns
-    -------
-    ndarray
-        KK of cars
-
-    Notes
-    -----
-    * This function does NOT overwrite input data
-    * The imaginary components provides the sponatenous Raman-like spectra(um).
-    * This module assumes the spectra are oriented as such that the frequency \
-    (wavenumber) increases with increasing index.  If this is not the case for \
-    your spectra(um), apply a phase_offset of pi.
-
-    References
-    ----------
-    [1] Y. Liu, Y. J. Lee, and M. T. Cicerone, "Broadband CARS spectral
-    phase retrieval using a time-domain Kramers-Kronig transform,"
-    Opt. Lett. 34, 1363-1365 (2009).
-
-    [2] C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative, \
-    Comparable Coherent Anti-Stokes Raman Scattering (CARS) \
-    Spectroscopy: Correcting Errors in Phase Retrieval," Journal of Raman \
-    Spectroscopy 47, 408-415 (2016). arXiv:1507.06543.
-
-    """
-    def __init__(self, cars_amp_offset=0.0, nrb_amp_offset=0.0,
-                 phase_offset=0.0, norm_to_nrb=True, pad_factor=1, rng=None):
-
-        self.cars_amp_offset = cars_amp_offset
-        self.nrb_amp_offset = nrb_amp_offset
-        self.phase_offset = phase_offset
-        self.norm_to_nrb = norm_to_nrb
-        self.pad_factor = pad_factor
-
-        # Check range of operation
-        self.rng = _rng_is_pix_vec(rng)
-
-
-
[docs]    def _calc(self, cars, nrb, ret_obj):
-
-        # Assume that an nD nrb should be averaged to be 1D
-        nrb = _mean_nd_to_1d(nrb)
-
-        shp = cars.shape[0:-2]
-
-        #  Step row-by-row through image
-        for idx in _np.ndindex(shp):
-            if self.rng is None:
-                kkd = _kkrelation(bg=nrb + self.nrb_amp_offset,
-                                  cri=cars[idx] + self.cars_amp_offset,
-                                  phase_offset=self.phase_offset,
-                                  norm_by_bg=self.norm_to_nrb,
-                                  pad_factor=self.pad_factor)
-            else:
-                kkd = _kkrelation(bg=nrb[self.rng] + self.nrb_amp_offset,
-                                      cri=cars[idx][..., self.rng] + self.cars_amp_offset,
-                                      phase_offset=self.phase_offset,
-                                      norm_by_bg=self.norm_to_nrb,
-                                      pad_factor=self.pad_factor)
-
-            try:
-                ret_obj[idx] *= 0
-                if self.rng is None:
-                    ret_obj[idx] += kkd
-                elif ret_obj[idx].size == kkd.size:
-                    ret_obj[idx] += kkd
-                else:
-                    ret_obj[idx][..., self.rng] += kkd
-            except:
-                return False
-            else:
-                pass
-        return True

-
-
[docs]    def calculate(self, cars, nrb):
-        """
-        cars : ndarray
-        Coherent Raman signal.
-
-        nrb : ndarray
-            Nonresonant background (NRB)
-        """
-
-        kkd = _np.zeros(cars.shape, dtype=_np.complex)
-        success = self._calc(cars, nrb, ret_obj=kkd)
-        if success:
-            return kkd
-        else:
-            return None

-
-
[docs]    def _transform(self, cars, nrb):
-        if issubclass(cars.dtype.type, _np.complex):
-            success = self._calc(cars, nrb, ret_obj=cars)
-            return success
-        else:
-            return False

-
-
-if __name__ == '__main__': # pragma: no cover
-
-    from crikit.data.spectrum import Spectrum as _Spectrum
-    from crikit.data.spectra import Spectra as _Spectra
-    from crikit.data.hsi import Hsi as _Hsi
-
-    hsi = _Hsi()
-    nrb = _Spectra()
-
-    WN = _np.linspace(-1386,3826,400)
-    X = .055 + 1/(1000-WN-1j*20) + 1/(3000-WN-1j*20)
-    XNR = 0*X + 0.055
-    E = 1*_np.exp(-(WN-2000)**2/(2*3000**2))
-
-    # Simulated spectrum
-    CARS = _np.abs(E+X)**2
-    NRB = _np.abs(E+XNR)**2
-    nrb.data = NRB
-
-    # Copies of spectrum
-    temp = _np.dot(_np.ones((30,30,1)),CARS[None,:])
-
-    # Create an HSData class instance
-    hsi.data = temp
-    num_spectra = int(hsi.size/WN.size)
-
-    hsi.freq.data = WN
-
-    start = _timeit.default_timer()
-    kkd = _kkrelation(NRB,CARS)
-    stop = _timeit.default_timer()
-    print('Single spectrum -- Total time: {:.6f} sec'.format(stop-start))
-    _timeit.time.sleep(2)
-
-    start = _timeit.default_timer()
-    kkd = _kkrelation(NRB,temp)
-    stop = _timeit.default_timer()
-    print('Data-based -- Total time: {:.6f} sec ({:.6f} sec/spectrum)'.format(stop-start,
-          (stop-start)/num_spectra))
-    _timeit.time.sleep(2)
-
-
-    kk = KramersKronig(cars_amp_offset=0, nrb_amp_offset=0, norm_to_nrb=False, pad_factor=1)
-    start = _timeit.default_timer()
-    kk.calculate(hsi.data, nrb.data)
-    stop = _timeit.default_timer()
-    print('Class-based -- Total time: {:.6f} sec ({:.6f} sec/spectrum)'.format(stop-start,
-          (stop-start)/num_spectra))
-
-    hsi.data = temp
-    _timeit.time.sleep(2)
-
-
-    import matplotlib as mpl
-    mpl.rcParams['font.size'] = 14
-    import matplotlib.pyplot as plt
-
-    hsi.freq.op_list_freq = [500, 4000]
-
-    #plt.plot(hsi.freq.freq_vec[hsi.freq.op_range_pix], hsi.data[0,0,hsi.freq.op_range_pix])
-
-    kk = KramersKronig(cars_amp_offset=0, nrb_amp_offset=0,
-                       norm_to_nrb=False, rng=hsi.freq.op_range_pix,
-                       pad_factor=1)
-    start = _timeit.default_timer()
-    del kkd
-    kkd = kk.calculate(hsi.data, nrb.data)
-    stop = _timeit.default_timer()
-    print('Pixrange Class-based -- Total time: {:.6f} sec ({:.6f} sec/spectrum)'.format(stop-start,
-          (stop-start)/num_spectra))
-
-    hsi.data = kkd
-    del kkd
-    _timeit.time.sleep(2)
-
-    plt.plot(WN, X.imag, label='Imag.{$\chi_{R}$}')
-    plt.plot(hsi.freq.data[hsi.freq.op_range_pix],
-             hsi.data[10,10,hsi.freq.op_range_pix].imag, 'r*',
-             label='KK-Retrieved')
-    plt.legend(loc='best')
-    plt.xlabel('Wavenumber (cm$^{-1}$)')
-    plt.ylabel('Raman Int. (au)')
-    plt.title('Raman vs KK-Retrieved CARS')
-    plt.show()
-
-    print(_np.allclose(X.imag[hsi.freq.op_range_pix], hsi.data[10,10,hsi.freq.op_range_pix].imag,rtol=1))
-
- -
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- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/cri/merge_nrbs.html b/docs/build/html/_modules/crikit/cri/merge_nrbs.html deleted file mode 100644 index 969345f..0000000 --- a/docs/build/html/_modules/crikit/cri/merge_nrbs.html +++ /dev/null @@ -1,336 +0,0 @@ - - - - - - - - - - - crikit.cri.merge_nrbs — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.cri.merge_nrbs

-"""
-Created on Wed Nov  2 11:04:43 2016
-
-@author: chc
-"""
-
-import copy as _copy
-
-if __name__ == '__main__':
-    import matplotlib.pyplot as _plt
-    import numpy as _np
-
-    
-
[docs]class MergeNRBs:
-    """
-    Merge two NRBs: a left-side and a right-side
-    
-    """
-    def __init__(self, nrb_left, nrb_right, pix, left_side_scale=True):
-        """
-        Attributes
-        ----------
-        pix : int
-            Pixel number to make the merge
-            
-        left_side_scale : bool
-            Scale the left-side to match the right-side. If FALSE, scales the
-            right-side. If None, scales neither.
-            
-        """
-        self.nrb_left = nrb_left
-        self.nrb_right = nrb_right
-        self.nrb_merge = None
-        
-        self.pix = pix
-        self.scale_left = left_side_scale
-
-
[docs]    def calculate(self):
-        """
-        
-        """
-        if self.nrb_left.size != self.nrb_right.size:
-            print('NRB size mismatch')
-            return None
-        else:
-            pass
-        
-        self.nrb_merge = _copy.deepcopy(0*self.nrb_left)
-        
-        success = self._calc(self.nrb_merge, ret_obj=self.nrb_merge)
-        if success:
-            return self.nrb_merge
-        else:
-            return None

-        
-
[docs]    def _calc(self, data, ret_obj):
-        try:
-            ret_obj *= 0
-            scaler = self.nrb_left[self.pix]/self.nrb_right[self.pix]
-            if self.scale_left == True:
-                ret_obj += self.nrb_left/scaler
-                ret_obj[self.pix::] = self.nrb_right[self.pix::]
-            elif self.scale_left == False:
-                ret_obj += self.nrb_left
-                ret_obj[self.pix::] = self.nrb_right[self.pix::]*scaler
-            elif self.scale_left is None:
-                ret_obj[0:self.pix+1] = self.nrb_left[0:self.pix+1]
-                ret_obj[self.pix+1::] = self.nrb_right[self.pix+1::]
-                
-            else:
-                raise ValueError('self.scale_left must be 0 or 1')
-        except:
-            return False
-        else:
-            return True

-           
-if __name__ == '__main__':
-    x = _np.arange(0,1000)
-    
-    nrb_left = _np.exp(-(x-500)**2/(100**2))
-    nrb_right = _np.exp(-(x-700)**2/(120**2))
-    
-    pix = 625
-    
-    _plt.plot(x, nrb_left, label='left')
-    _plt.plot(x, nrb_right, label='right')
-    _plt.title('Raw NRBs')
-    
-    
-    merge = MergeNRBs(nrb_left, nrb_right, pix, left_side_scale=True)
-    out_scaled_left = merge.calculate()
-    _plt.plot(x, out_scaled_left, ls='--', label='Left Scaled')
-    
-    merge = MergeNRBs(nrb_left, nrb_right, pix, left_side_scale=False)
-    out_scaled_right = merge.calculate()
-    _plt.plot(x, out_scaled_right, ls='--', label='Right Scaled')
-    
-    merge = MergeNRBs(nrb_left, nrb_right, pix, left_side_scale=None)
-    out_scaled_none = merge.calculate()
-    _plt.plot(x, out_scaled_none, ls='--', lw=3, label='NOT Scaled')
-    
-    _plt.legend(loc='best')
-    _plt.show()
-
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- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/cri/tests/test_hilbert.html b/docs/build/html/_modules/crikit/cri/tests/test_hilbert.html deleted file mode 100644 index 731bbb0..0000000 --- a/docs/build/html/_modules/crikit/cri/tests/test_hilbert.html +++ /dev/null @@ -1,273 +0,0 @@ - - - - - - - - - - - crikit.cri.tests.test_hilbert — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    • - - -
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Source code for crikit.cri.tests.test_hilbert

-"""
-Testing for Hilbert transform method
-
-Using the math relation a^2 / (a^2 + x^2) (Lorentz/Cauchy) has an 
-analytical Hilbert transform: x^2 / (a^2 + x^2)
-"""
-
-import numpy as np
-from numpy.testing import assert_array_almost_equal
-
-from crikit.cri.algorithms.kk import hilbertfft
-
-
-
[docs]def test_pyfftw_hilbert_no_pad():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-    hilb_y = hilbertfft(y, pad_factor=0, use_pyfftw=True)
-    hilb_y_analytical = x/(2**2 + x**2)
-    assert_array_almost_equal(hilb_y_analytical, hilb_y, decimal=2)

-
-
[docs]def test_pyfftw_hilbert_pad():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-    hilb_y = hilbertfft(y, pad_factor=10, use_pyfftw=True)
-    hilb_y_analytical = x/(2**2 + x**2)
-    assert_array_almost_equal(hilb_y_analytical, hilb_y, decimal=4)

-
-
[docs]def test_hilbert_no_pad():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-    hilb_y = hilbertfft(y, pad_factor=0, use_pyfftw=False)
-    hilb_y_analytical = x/(2**2 + x**2)
-    assert_array_almost_equal(hilb_y_analytical, hilb_y, decimal=2)

-
-
[docs]def test_hilbert_pad():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-    hilb_y = hilbertfft(y, pad_factor=10, use_pyfftw=False)
-    hilb_y_analytical = x/(2**2 + x**2)
-    assert_array_almost_equal(hilb_y_analytical, hilb_y, decimal=4)

-
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- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/cri/tests/test_kk.html b/docs/build/html/_modules/crikit/cri/tests/test_kk.html deleted file mode 100644 index 2e2556e..0000000 --- a/docs/build/html/_modules/crikit/cri/tests/test_kk.html +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - - - - - - crikit.cri.tests.test_kk — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.cri.tests.test_kk

-"""
-Testing for Kramers-Kronig Phase Retrieval Method
-
-Using the math relation a^2 / (a^2 + x^2) (Lorentz/Cauchy) has an 
-analytical Hilbert transform: x^2 / (a^2 + x^2)-- and how that plays into
-the KK
-
-"""
-
-import numpy as np
-from numpy.testing import assert_array_almost_equal
-
-from crikit.cri.kk import KramersKronig
-
-
-
[docs]def test_kk():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-    hilb_y_analytical = x/(2**2 + x**2)
-    
-    kk = KramersKronig(pad_factor=10)
-    kkd = kk.calculate(np.exp(2*y), 0*y + 1)
-    
-    kkd_angle = np.angle(kkd)
-    assert_array_almost_equal(hilb_y_analytical, kkd_angle, decimal=4)

-
-
[docs]def test_kk_no_bg_norm():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-
-    kk = KramersKronig(norm_to_nrb=False)
-    kkd = kk.calculate(y, 0*y + 1)
-
-    assert_array_almost_equal(np.abs(kkd), np.sqrt(y))

-
-
[docs]def test_kk_rng():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-
-    rng = np.arange(5, x.size)
-
-    kk = KramersKronig(norm_to_nrb=False, rng=rng)
-    kkd = kk.calculate(y, 0*y + 1)
-
-    assert_array_almost_equal(np.abs(kkd[rng]), np.sqrt(y[rng]))

-
-
[docs]def test_kk_transform():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-    y_complex = y.astype(np.complex)
-
-    kk = KramersKronig(norm_to_nrb=False)
-    success = kk._transform(y_complex, 0*y_complex + 1)
-
-    assert success
-    assert_array_almost_equal(np.abs(y_complex), np.sqrt(y))

-
-
[docs]def test_kk_transform_fail():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-    y_complex = y.astype(np.complex)
-
-    kk = KramersKronig(norm_to_nrb=False)
-    
-    success = kk._transform(y, 0*y + 1)
-    assert not success

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- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/cri/tests/test_kk_alg.html b/docs/build/html/_modules/crikit/cri/tests/test_kk_alg.html deleted file mode 100644 index b23ee2c..0000000 --- a/docs/build/html/_modules/crikit/cri/tests/test_kk_alg.html +++ /dev/null @@ -1,270 +0,0 @@ - - - - - - - - - - - crikit.cri.tests.test_kk_alg — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.cri.tests.test_kk_alg

-"""
-Testing for Kramers-Kronig Phase Retrieval Method
-
-Using the math relation a^2 / (a^2 + x^2) (Lorentz/Cauchy) has an 
-analytical Hilbert transform: x^2 / (a^2 + x^2)-- and how that plays into
-the KK
-
-"""
-
-import numpy as np
-from numpy.testing import assert_array_almost_equal
-
-from crikit.cri.algorithms.kk import kkrelation
-
-
-
[docs]def test_kk():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-    hilb_y_analytical = x/(2**2 + x**2)
-    kkd = kkrelation(0*y + 1, np.exp(2*y), pad_factor=10)
-    kkd_angle = np.angle(kkd)
-    assert_array_almost_equal(hilb_y_analytical, kkd_angle, decimal=4)

-
-
[docs]def test_kk_no_bg_norm():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-
-    kkd = kkrelation(0*y + 1, y, norm_by_bg=False)
-    assert_array_almost_equal(np.abs(kkd), np.sqrt(y))

-
-
[docs]def test_kk_3d():
-    x = np.linspace(-100, 100, 1000)
-    y = 2/(2**2 + x**2)
-    y = y[:, None, None]
-
-    kkd = kkrelation(0*y + 1, y, norm_by_bg=False)
-    assert_array_almost_equal(np.abs(kkd), np.sqrt(y))

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- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/data/factorized.html b/docs/build/html/_modules/crikit/data/factorized.html deleted file mode 100644 index 2104dfc..0000000 --- a/docs/build/html/_modules/crikit/data/factorized.html +++ /dev/null @@ -1,293 +0,0 @@ - - - - - - - - - - - crikit.data.factorized — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.data.factorized

-"""
-Factored data class
-
-Created on Fri Apr 22 23:42:40 2016
-
-@author: chc
-"""
-
-import numpy as _np
-
-from crikit.data.frequency import Frequency as _Frequency
-from crikit.data.spectrum import Spectrum as _Spectrum
-from crikit.data.spectra import Spectra as _Spectra
-from crikit.data.replicate import Replicate as _Replicate
-from crikit.data.hsi import Hsi as _Hsi
-
-
[docs]class _Factorized:
-    """
-    Factorized class. Contains items unique to factorized spectral data.
-    """
-
-    def __init__(self):
-        raise NotImplementedError

-
-
[docs]class FactorizedHsi(_Hsi, _Factorized):
-    """
-    Factorized Hsi Class
-
-    Attributes
-    ----------
-
-    Methods
-    -------
-
-    Notes
-    -----
-    * TODO: deside on
-
-    """
-    def __init__(self):
-        raise NotImplementedError

-
-
[docs]class FactorizedSpectra(_Spectra, _Factorized):
-    """
-    Factorized Spectra Class
-
-    Attributes
-    ----------
-
-    Methods
-    -------
-
-    Notes
-    -----
-    * TODO: deside on
-
-    """
-    def __init__(self):
-        raise NotImplementedError

-
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Source code for crikit.data.frequency

-"""
-"Frequency" [,wavelength, and wavenumber] class and function.
-
-"""
-
-import numpy as _np
-import copy as _copy
-from crikit.utils.general import find_nearest as _find_nearest
-
-__all__ = ['Frequency', 'calib_pix_wn', 'calib_pix_wl']
-
-
[docs]class Frequency:
-    """
-    Frequency [,wavelength, and waevnumber] class
-
-    Attributes
-    ----------
-    data : 1D ndarray, optional (see note)
-        Frequency vector
-
-    calib : object, optional (see note)
-        Calibration object that is passed to calib_fcn
-
-    calib_orig : object, optional (see note)
-        Calibration object ('original'). Set during initial setting of calib. \
-        Useful for backing-up calibration)
-
-    calib_fcn : fcn, optional (see note)
-        Function that accepts a calibration object and returns data and \
-        units
-
-    units : str, optional
-        Units of data (the default is 'Frequency'). Over-written by return \
-        from calib_fcn
-
-    op_list_pix : list or tuple or 1D ndarray
-        Range of pixels to perform operations over. Must be even lengthed.
-
-    op_list_freq : list or tuple or 1D ndarray
-        Range of frequencies (or wavelength, or wavenumber) to perform \
-        operations over. Must be even lengthed.
-
-    plot_list_pix : list or tuple or 1D ndarray
-        Range of pixels to plot. Must be even lengthed.
-
-    plot_list_freq : list or tuple or 1D ndarray
-        Range of frequencies (or wavelength, or wavenumber) to plot. \
-        Must be even lengthed.
-
-    size : int, read-only
-        Length of data
-
-    pix_vec : 1D ndarray, read-only
-        Pixel vector (0-indexed)
-
-    op_range_freq : 1D ndarray, read-only
-        Range of operarational frequencies
-
-    plot_range_freq : 1D ndarray, read-only
-        Range of printing frequencies (not implemented)
-
-    Methods
-    -------
-    update
-        Updates data based on contents of calib (or calib_orig) and calib_fcn
-
-    get_index_of_closest_freq
-        Find the closest frequency in freq to a given freq value and RETURN
-        the pixel value.
-
-    get_closest_freq
-        Find the closest frequency in freq to a given freq value.
-
-    Notes
-    -----
-    Currently, this implementation does not check whether the 
-    attributes/parameters are contradictory:
-    - calib
-    - calib_orig
-    - data
-
-    - The purpose of _list_ is to limit the range over which operation \
-    or plotting is performed. In some instances, for example, one may collect \
-    a larger set of frequencies that of interest or there may be blank (i.e., \
-    no signal) regions. Limiting these regions enables faster computation, may \
-    minimize "edge effects", and may allow for zoomed-in plotting when there \
-    are items of interest or a large dynamic range across a spectrum.
-
-    - For functions, methods, etc. that take into account _list_ \
-    parameters, they should default to op_list_ if plot_list_ are set to \
-    None.
-
-    """
-
-    def __init__(self, data=None, calib=None, calib_orig=None,
-                 calib_fcn=None, units=None):
-
-
-        self._data = None
-        self._calib = None
-        self._calib_orig = None
-        self._calib_fcn = None
-        self._label = None
-        self._units = None
-        self._op_list_pix = None
-        self._op_list_freq = None
-        self._plot_list_pix = None
-        self._plot_list_freq = None
-
-        if data is not None:
-            self.data = data
-        if calib is not None:
-            self.calib = calib
-        if calib_orig is not None:
-            self.calib_orig = calib_orig
-        if calib_fcn is not None:
-            self.calib_fcn = calib_fcn
-        if units is not None:
-            self.units = units
-
-        if (self._data is None) and (self._calib is not None) and \
-            (self._calib_fcn is not None):
-            self.update()
-
-    @property
-    def data(self):
-        return self._data
-
-    @data.setter
-    def data(self, value):
-        if isinstance(value, _np.ndarray):
-            if value.ndim == 1:
-                self._data = value
-            else:
-                raise TypeError('data must be a 1D ndarray')
-        elif value is None:
-            self._data = None
-        else:
-            raise TypeError('data must be a 1D ndarray')
-
-    @property
-    def calib(self):
-        return self._calib
-
-    @calib.setter
-    def calib(self, value):
-        if isinstance(value, dict):
-            self._calib = value
-            if self._calib_orig is None:
-                self._calib_orig = value
-        elif value is None:
-            self._calib = None
-            self.update()
-        else:
-            raise TypeError('calib must be of type dict')
-            
-    @calib.deleter
-    def calib(self):
-        self._calib = None
-        self.update()
-
-
-    @property
-    def calib_orig(self):
-        return self._calib_orig
-
-    @calib_orig.setter
-    def calib_orig(self, value):
-        if isinstance(value, dict):
-            self._calib_orig = value
-        else:
-            raise TypeError('calib_orig must be of type dict')
-
-
-    @property
-    def calib_fcn(self):
-        return self._calib_fcn
-
-    @calib_fcn.setter
-    def calib_fcn(self, value):
-        if callable(value):
-            self._calib_fcn = value
-        else:
-            raise TypeError('calib_fcn must be a callable function')
-
-    @property
-    def units(self):
-        return self._units
-
-    @units.setter
-    def units(self, value):
-        if isinstance(value, str):
-            self._units = value
-        else:
-            raise TypeError('units must be of type str')
-
-    @property
-    def size(self):
-        return self.data.size
-
-    @property
-    def pix_vec(self):
-        return _np.arange(self.data.size)
-
-
[docs]    def update(self):
-        """
-        Update data with calib and calib_fcn.
-        """
-        if self._calib_fcn is None:
-            raise TypeError('Calibration function not set')
-        if self._calib is None:
-            if self._calib_orig is None:
-                raise TypeError('Calibration object not set')
-            else:
-                self.calib = self._calib_orig
-
-        self.data, self.units = self.calib_fcn(self.calib)

-
-    @property
-    def op_list_pix(self):
-        return self._op_list_pix
-
-    @op_list_pix.setter
-    def op_list_pix(self,value):
-        if isinstance(value, list) or isinstance(value, tuple) or isinstance(value, _np.ndarray):
-            if len(value) == 2:
-                value = list(value)
-                value.sort()
-                self._op_list_pix = value
-                self._op_list_freq = self.get_closest_freq(value)
-                self._op_list_freq.sort()
-            elif len(value) != 2 and _np.mod(len(value),2) == 0 and len(value) != 0:
-                raise NotImplementedError('op_list_pix can only currently handle 2 entries')
-            else:
-                raise TypeError('op_list_pix should be a list, tuple, or ndarray with an even number of entries')
-        else:
-            raise TypeError('op_list_pix should be a list, tuple, or ndarray')
-
-    @op_list_pix.deleter
-    def op_list_pix(self):
-        self._op_list_pix = None
-        self._op_list_freq = None
-
-    @property
-    def op_list_freq(self):
-        return self._op_list_freq
-
-    @op_list_freq.setter
-    def op_list_freq(self,value):
-        if isinstance(value, list) or isinstance(value, tuple) or isinstance(value, _np.ndarray):
-            if len(value) == 2:
-                value = list(value)
-                value.sort()
-                self._op_list_pix = self.get_index_of_closest_freq(value)
-                self._op_list_pix.sort()
-                self._op_list_freq = self.get_closest_freq(value)
-                self._op_list_freq.sort()
-            elif len(value) != 2 and _np.mod(len(value),2) == 0 and len(value) != 0:
-                raise NotImplementedError('op_list_freq can only currently handle 2 entries')
-            elif len(value) == 0:
-                self._op_list_freq = None
-                self._op_list_pix = None
-            else:
-                raise TypeError('op_list_freq should be a list, tuple, or ndarray with an even number of entries')
-        else:
-            raise TypeError('op_list_freq should be a list, tuple, or ndarray')
-
-    @op_list_freq.deleter
-    def op_list_freq(self):
-        self._op_list_pix = None
-        self._op_list_freq = None
-
-    @property
-    def op_range_pix(self):
-        if self._op_list_pix is not None:
-            return _np.arange(self._op_list_pix[0],self._op_list_pix[1]+1)
-        else:
-            return self.pix_vec
-
-    @property
-    def op_range_freq(self):
-        if self._op_list_pix is not None:
-            return self.data[self.op_range_pix]
-        else:
-            return self.data
-
-    @property
-    def op_size(self):
-        if self._op_list_pix is None:
-            return self.data.size
-        else:
-            return self._op_list_pix[-1] - self._op_list_pix[0] + 1
-
-    @property
-    def plot_list_pix(self):
-        raise NotImplementedError('plot_list_pix is not yet implemented')
-
-    @property
-    def plot_list_freq(self):
-        raise NotImplementedError('plot_list_freq is not yet implemented')
-
-
-
[docs]    def get_index_of_closest_freq(self, in_freqs):
-        """
-        Return index(-es) of frequency(-ies) in freq closest to in_freqs
-        """
-        return _find_nearest(self.data, in_freqs)[1]

-
-
[docs]    def get_closest_freq(self, in_freqs):
-        """
-        Return frequency(-ies) in freq closest to in_freqs
-        """
-        return _find_nearest(self.data, in_freqs)[0]

-
-
[docs]def calib_pix_wl(calib_obj):
-    """
-    Return a wavelength (wl) vector based on calibration (calib) object
-
-    Parameters
-    ----------
-    calib_obj : dict or list or 1D ndarray
-        Calibration object (see below).
-
-    calib_obj : dict {'n_pix', 'ctr_wl', 'ctr_wl0', 'units', 'a_vec'}
-        Calibration dict with 5 key-value pairs (see Notes)
-
-    calib_obj : list or 1D ndarray
-        Calibration array ['n_pix', 'ctr_wl', 'ctr_wl0', 'units',
-        'a_0', 'a_1', ..., 'a_n']
-    Returns
-    -------
-    wl_vec : 1D ndarray
-        Wavelength vector
-    units : str
-        Units string 'Wavelength (' + calib_obj['units'] + ')'
-
-    Notes
-    -----
-    calib_obj dict key-value pairs:
-        * n_pix : int, number of pixels (0-index)
-        * ctr_wl : float, center wavelength
-        * ctr_wl0 : float, center calibration wavelength
-        * units : str, wavelength units, optional (default is 'nm')
-        * a_vec : list or 1D ndarray, polynomial coefficients, [a_n, a_n-1,..., \
-        a_1, a_0]. a_2...a_n, optional.
-
-    calibration model:
-        .. math::
-            wl\_{vec} = a_n*(n\_{pix})^n + a_{n-1}*(n\_{pix})^{n-1} + ~...~ +  \
-            n\_{pix}*a_1 + a_0 + ctr\_{wl} - ctr\_{wl0}
-
-    """
-
-
-    calib = {}
-
-    if len(calib_obj) < 4:
-        raise TypeError('Calibration object does not contain enough entries')
-
-    if isinstance(calib_obj, dict):
-        key_list = ['n_pix','ctr_wl', 'ctr_wl0', 'a_vec']
-        for k in key_list:
-            if k not in calib_obj:
-                raise KeyError('Calibration dict missing: {}'.format(k))
-            else:
-                calib[k] = calib_obj[k]
-        if 'units' in calib_obj:
-            calib['units'] = calib_obj['units']
-        else:
-            calib['units'] = 'nm'
-
-    pix = _np.arange(calib['n_pix'])
-    wl_vec = _np.polyval(calib['a_vec'], pix)
-    wl_vec += calib['ctr_wl'] - calib['ctr_wl0']
-
-    return (wl_vec, calib['units'])

-
-
[docs]def calib_pix_wn(calib_obj):
-    """
-    Return a wavenumber (wn) vector based on calibration (calib) object
-
-    Parameters
-    ----------
-    calib_obj : dict or list or 1D ndarray
-        Calibration object (see below).
-
-    calib_obj : dict {'n_pix', 'ctr_wl', 'ctr_wl0', 'probe', 'units', 'a_vec'}
-        Calibration dict with 6 key-value pairs (see Notes)
-
-    calib_obj : list or 1D ndarray
-        Calibration array ['n_pix', 'ctr_wl', 'ctr_wl0', 'probe', 'units',
-        'a_0', 'a_1', ..., 'a_n']
-
-    Returns
-    -------
-    wn_vec : 1D ndarray
-        Wavenumber vector
-    units : str
-        Wavenumber units. Always 'cm$^-1$'
-
-    Notes
-    -----
-    calib_obj dict key-value pairs:
-        * n_pix : int, number of pixels (0-index)
-        * ctr_wl : float, center wavelength
-        * ctr_wl0 : float, center calibration wavelength
-        * probe : float, center wavelength of probe source (in units)
-        * units : {'nm', 'um'}, wavelength units, optional (default is 'nm')
-        * a_vec : list or 1D ndarray, polynomial coefficients, [a_n, a_n-1,..., \
-        a_1, a_0]. a_2...a_n, optional.
-
-    calibration model :
-        Wavelength vector:
-            .. math::
-                wl\_{vec} = a_n*(n\_{pix})^n + a_{n-1}*(n\_{pix})^{n-1} + ~...~ +  \
-                n\_{pix}*a_1 + a_0 + ctr\_{wl} - ctr\_{wl0}
-        Wavenumber vector:
-            .. math::
-                wl\_{vec} = a_n*(n\_{pix})^n + a_{n-1}*(n\_{pix})^{n-1} + ~...~ +  \
-                n\_{pix}*a_1 + a_0 + ctr\_{wl} - ctr\_{wl0}
-
-    """
-    calib = _copy.deepcopy(calib_obj)
-
-    if 'probe' not in calib:
-        raise KeyError('\'probe\' key not in calib_obj')
-
-    if 'units' not in calib:
-        calib['units'] = 'nm'
-        factor = 1e7
-    elif calib['units'] == 'nm':
-        factor = 1e7
-    elif calib['units'] == 'um':
-        factor = 1e4
-    else:
-        raise ValueError('Only nanometer (\'nm\') and micrometer (\'um\') units accepted')
-    wl_vec, _ = calib_pix_wl(calib_obj)
-    wn_vec = factor/wl_vec - factor/calib['probe']
-    return (wn_vec, 'cm$^{-1}$')

-
-if __name__ == '__main__':  # pragma: no cover
-    import matplotlib as _mpl
-    _mpl.use('Qt5Agg')
-    _mpl.rcParams['font.family'] = 'sans-serif'
-    _mpl.rcParams['font.size'] = 12
-    import matplotlib.pyplot as _plt
-
-    _calib_dict = {}
-    _calib_dict['n_pix'] = 1600
-    _calib_dict['ctr_wl'] = 730.0
-    _calib_dict['ctr_wl0'] = 730.0
-    _calib_dict['probe'] = 771.461
-    _calib_dict['units'] = 'nm'
-    _calib_dict['a_vec'] = (-0.167740721307557, 863.8736708961577)  # slope, intercept
-
-    _wl_vec, _units_wl = calib_pix_wl(_calib_dict)
-    _wn_vec, _units_wn = calib_pix_wn(_calib_dict)
-    _plt.plot(_wl_vec, _wn_vec)
-    _plt.xlabel('Wavelength ({})'.format(_units_wl))
-    _plt.ylabel('Wavenumber ({})'.format(_units_wn))
-    _plt.title('Wavenumber vs Wavelength')
-    _plt.show()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/data/hsi.html b/docs/build/html/_modules/crikit/data/hsi.html deleted file mode 100644 index 29f9291..0000000 --- a/docs/build/html/_modules/crikit/data/hsi.html +++ /dev/null @@ -1,579 +0,0 @@ - - - - - - - - - - - crikit.data.hsi — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- - - - -
-
-
-
- -

Source code for crikit.data.hsi

-"""
-Hyperspectral imagery (hsi) class
-
-Created on Tue Apr 12 13:06:30 2016
-
-@author: chc
-"""
-
-import numpy as _np
-import copy as _copy
-
-from crikit.data.frequency import Frequency as _Frequency
-from crikit.data.spectrum import Spectrum as _Spectrum
-from crikit.data.replicate import Replicate as _Replicate
-
-__all__ = ['Hsi']
-
-
[docs]class Hsi(_Spectrum):
-    """
-    Hyperspectral imagery class
-
-    Parameters
-    ----------
-    data : 3D ndarray [y_pix, x_pix, f_pix]
-        HSI image
-
-    mask : 3D ndarray (int) [y_pix, x_pix, f_pix]
-        0,1 mask with 1 is a usable pixel and 0 is not
-
-    freq : crikit.data.frequency.Frequency instance
-        Frequency [wavelength, wavenumber] object (i.e., the independent \
-        variable)
-
-    label : str
-        Image label (i.e., a string describing what the image is)
-
-    units : str
-        Units of image (e.g., intensity)
-
-    x_rep : crikit.data.replicate.Replicate instance, Not implemented yet
-        x-axis spatial object
-
-    y_rep : crikit.data.replicate.Replicate instance, Not implemented yet
-        x-axis spatial object
-
-    x : 1D ndarray
-        x-axis spatial vector
-
-    y : 1D ndarray
-        y-axis spatial vector
-
-    meta : dict
-        Meta-data dictionary
-
-    Attributes
-    ----------
-    data_imag_over_real : ndarray (3D)
-        If data is complex, return the imaginary portion
-
-    data_real_over_imag : ndarray (3D)
-        If data is complex, return the real portion
-
-    shape : tuple, read-only
-        Shape of data
-
-    size : int, read-only
-        Size of data (i.e., total number of entries)
-
-    Methods
-    -------
-    mean : 1D ndarray
-        Mean spectrum. If extent [a,b] is provided, calculate mean over that\
-        inclusive region.
-
-    std : 1D ndarray
-        Standard deviation of spectrum. If extent [a,b] is provided, calculate standard\
-        deviation over that inclusive region.
-
-    subtract : 3D ndarray or None
-        Subtract spectrum or object
-
-    Notes
-    -----
-    * freq object contains some useful parameters such as op_range_\* and \
-    plot_range_\*, which define spectral regions-of-interest. (It's debatable \
-    as to whether those parameters should be in Frequency or Spectrum classes)
-
-    """
-
-    def __init__(self, data=None, freq=None, x=None, y=None, x_rep=None,
-                 y_rep=None, label=None, units=None, meta=None):
-
-        super().__init__(data, freq, label, units, meta)
-        self._x_rep = _Replicate()
-        self._y_rep = _Replicate()
-        self._mask = None
-
-        self._x_rep = _Replicate(data=x)
-        self._y_rep = _Replicate(data=y)
-
-        if x is None and x_rep is not None:
-            self.x_rep = _copy.deepcopy(x_rep)
-        if y is None and y_rep is not None:
-            self.y_rep = _copy.deepcopy(y_rep)
-
-    @property
-    def mask(self):
-        return self._mask
-
-    @property
-    def x_rep(self):
-        return self._x_rep
-
-    @x_rep.setter
-    def x_rep(self, value):
-        if isinstance(value, _Replicate):
-            self._x_rep = value
-        elif isinstance(value, _np.ndarray):
-            self._x_rep.data = value
-
-    @property
-    def y_rep(self):
-        return self._y_rep
-
-    @property
-    def x(self):
-        return self._x_rep.data
-
-    @x.setter
-    def x(self, value):
-        self._x_rep.data = value
-
-    @property
-    def y(self):
-        return self._y_rep.data
-
-    @y.setter
-    def y(self, value):
-        self._y_rep.data = value
-
-
-    @y_rep.setter
-    def y_rep(self, value):
-        if isinstance(value, _Replicate):
-            self._y_rep = value
-        elif isinstance(value, _np.ndarray):
-            self._y_rep.data = value
-
-    @property
-    def data(self):
-        return self._data
-
-    @data.setter
-    def data(self, value):
-        if isinstance(value, _np.ndarray):
-            if value.ndim == 3:
-                if self.freq is None or self.freq.op_list_pix is None:
-                    self._data = value
-                    self._mask = _np.ones((self._data.shape[0],
-                                           self._data.shape[1]),
-                                          dtype=_np.int)
-                else:
-                    if value.shape[-1] == self.freq.op_range_pix.size:
-                        temp = _np.zeros((self._data.shape),dtype=value.dtype)
-                        temp[:,:,self.freq.op_range_pix] = value
-                        self._data = temp
-                        self._mask = _np.ones((self._data.shape[0],
-                                               self._data.shape[1]),
-                                              dtype=_np.int)
-                    elif value.shape[-1] == self._data.shape[-1]:
-                        self._data = value
-                        self._mask = _np.ones((self._data.shape[0],
-                                               self._data.shape[1]),
-                                              dtype=_np.int)
-                    else:
-                        #raise TypeError('data is of an unrecognized shape: {}'.format(value.shape))
-                        raise TypeError('pre-data: {}, value: {}'.format(self._data.shape,value.shape))
-            else:
-                raise TypeError('data must be 3D')
-        else:
-            print('Assigning non-ndarray to data. Not shape checking')
-            self._data = value
-
-
[docs]    def check(self):
-        """
-        Check x, y, and freq to make sure the dimensions agree with data
-        """
-        if self._data is None:
-            print('Hsi check: data is None, not checking')
-        else:
-            if self._x_rep._data is None:
-                self._x_rep._data = _np.arange(self.shape[1])
-                self._x_rep._label = 'X'
-                self._x_rep._units = 'pix'
-                print('Hsi check: setting x to pixels')
-            elif self._x_rep._data.size != self._data.shape[1]:
-                self._x_rep = _Replicate()
-                self._x_rep._data = _np.arange(self.shape[1])
-                self._x_rep._label = 'X'
-                self._x_rep._units = 'pix'
-                print('Hsi check: setting x to pixels')
-
-            if self._y_rep._data is None:
-                self._y_rep._data = _np.arange(self.shape[0])
-                self._y_rep._label = 'Y'
-                self._y_rep._units = 'pix'
-                print('Hsi check: setting y to pixels')
-            elif self._y_rep._data.size != self._data.shape[0]:
-                self._y_rep = _Replicate()
-                self._y_rep._data = _np.arange(self.shape[0])
-                self._y_rep._label = 'Y'
-                self._y_rep._units = 'pix'
-                print('Hsi check: setting y to pixels')
-
-            if self.freq._data is None:
-                self.freq._data = _np.arange(self.shape[-1])
-                self.freq._label = 'Frequency'
-                self.freq._units = 'pix'
-                print('Hsi check: setting freq to pixels')
-            elif self.freq._data.size != self._data.shape[-1]:
-                self.freq = _Frequency()
-                self.freq._data = _np.arange(self.shape[-1])
-                print('Hsi check: setting freq to pixels')
-        return None

-
-
[docs]    def subtract(self, spectra, overwrite=True):
-        """
-        Subtract spectrum from data
-        """
-        # Order IS important
-        if isinstance(spectra, Hsi):
-            if overwrite:
-                self.data -= spectra.data
-                return None
-            else:
-                return self.data - spectra.data
-        elif isinstance(spectra, _Spectrum):
-            if overwrite:
-                self.data -= spectra.data[None,None,:]
-                return None
-            else:
-                return self.data - spectra.data
-        elif isinstance(spectra, _np.ndarray):
-            if spectra.shape == self.data.shape:
-                if overwrite:
-                    self.data -= spectra
-                    return None
-                else:
-                    return self.data - spectra
-            else:
-                if overwrite:
-                    self.data -= spectra[None,None,:]
-                    return None
-                else:
-                    return self.data - spectra[None,None,:]

-
-
[docs]    def get_rand_spectra(self, num, pt_sz=1, quads=False, full=False):
-
-        mlen, nlen, freqlen = self.data.shape
-
-        if quads:
-            num_spectra = num + 5
-        else:
-            num_spectra = num
-
-        if _np.iscomplexobj(self.data):
-            dtype = _np.complex
-        else:
-            dtype = _np.float
-
-        temp = _np.zeros((num_spectra, self.data.shape[-1]), dtype=dtype)
-
-        quad_mid_row = int(_np.round(mlen/2))
-        quad_mid_col = int(_np.round(nlen/2))
-        center_row = (int(_np.round(mlen/3)), int(_np.round(2*mlen/3)))
-        center_col = (int(_np.round(nlen/3)), int(_np.round(2*nlen/3)))
-
-        start_count = 0
-        if quads:
-            # QUADS
-            # Bottom-left
-            temp[0, :] = _np.mean(self.data[0:quad_mid_row, 0:quad_mid_col, :], axis=(0, 1))
-
-            # Upper-left
-            temp[1, :] = _np.mean(self.data[0:quad_mid_row, quad_mid_col+1::, :], axis=(0, 1))
-
-            # Upper-right
-            temp[2, :] = _np.mean(self.data[quad_mid_row+1::, quad_mid_col+1::, :], axis=(0, 1))
-
-            # Bottom-right
-            temp[3, :] = _np.mean(self.data[quad_mid_row+1::, 0:quad_mid_col, :], axis=(0, 1))
-
-            # Center
-            temp[4, :] = _np.mean(self.data[center_row[0]:center_row[1], center_col[0]:center_col[1], :], axis=(0, 1))
-
-            start_count += 5
-        else:
-            pass
-
-        rand_rows = ((mlen-pt_sz-1)*_np.random.rand(num_spectra)).astype(int)
-        rand_cols = ((nlen-pt_sz-1)*_np.random.rand(num_spectra)).astype(int)
-
-        for count in _np.arange(start_count,num_spectra):
-            if pt_sz == 1:
-                temp[count, :] = _np.squeeze(self.data[rand_rows[count-start_count],
-                                            rand_cols[count-start_count]])
-            else:
-
-                rows = [rand_rows[count-start_count]-(pt_sz-1),
-                        rand_rows[count-start_count]+pt_sz]
-                cols = [rand_cols[count-start_count]-(pt_sz-1),
-                                 rand_cols[count-start_count]+pt_sz]
-
-                if rows[0] < 0:
-                    rows[0] = 0
-                if rows[1] >= mlen:
-                    rows[1] = mlen-1
-                if cols[0] < 0:
-                    cols[0] = 0
-                if cols[1] >= nlen:
-                    cols[1] = nlen-1
-
-                if cols[0] == cols[1] or rows[0] == rows[1]:
-                    pass
-                else:
-                    temp[count,:] = _np.squeeze(_np.mean(self.data[rows[0]:rows[1], cols[0]:cols[1], :], axis=(0, 1)))
-
-        if (not full) and (self.freq.data is not None):
-            temp = temp[..., self.freq.op_range_pix]
-
-        return temp

-
-    def __sub__(self, spectrum):
-        return self.subtract(spectrum, overwrite=False)

-
-if __name__ == '__main__': # pragma: no cover
-
-    x = _np.linspace(0,100,10)
-    y = _np.linspace(0,100,10)
-    freq = _np.arange(20)
-    data = _np.random.rand(10,10,20)
-
-
-    hs = Hsi(data=data, freq=freq, x=x, y=y)
-    print(hs.shape)
-    print(isinstance(hs, _Spectrum))
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/data/replicate.html b/docs/build/html/_modules/crikit/data/replicate.html deleted file mode 100644 index 32f60d4..0000000 --- a/docs/build/html/_modules/crikit/data/replicate.html +++ /dev/null @@ -1,416 +0,0 @@ - - - - - - - - - - - crikit.data.replicate — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    • - -
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    • - - -
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- -

Source code for crikit.data.replicate

-"""
-Replicate class used for things such as repetitive measurements or even spatial \
-vectors (e.g., x and y)
-
-Created on Tue Apr 12 11:42:56 2016
-
-@author: chc
-"""
-
-import numpy as _np
-
-__all__ = ['Replicate']
-
-
[docs]class Replicate:
-    """
-    Replicate class
-
-    Attributes
-    ----------
-    data : 1D ndarray [size]
-        Replicate data
-
-    calib : list [(start), stop, (step size)]
-        Calibration descriptor. See Note.
-
-    units : str
-        Units of replicate data
-
-    size : int, read-only
-
-    Methods
-    -------
-    update_calib_from_data
-        Calculate and set calib parameter from data
-
-    update_data_from_calib
-        Calculate and set data from calib parameter
-
-    calib_data_agree
-        Return bool as to whether data and that derived from calib agree
-
-    Notes
-    -----
-    * input to calib can be a list or tuple or 1D ndarray or int or float
-
-    Setting calib can take up to 3 entries :
-        * 1 entry: stop = entry; start = 0, step size = 1
-        * 2 entries: start = entry[0], stop = entry[1], step size = 1
-        * 3 entries: [start, stop, step size]
-
-    """
-
-
-    def __init__(self, data=None, calib=None, units=None, label=None):
-        self._data = None
-        self._calib = None
-        self._units = None
-        self._label = None
-
-        if data is not None:
-            self.data = data
-        if calib is not None:
-            self.calib = calib
-        if units is not None:
-            self.units = units
-        if label is not None:
-            self.label = label
-
-    @property
-    def data(self):
-        return self._data
-
-    @data.setter
-    def data(self, value):
-        if isinstance(value, _np.ndarray):
-            if value.ndim == 1:
-                self._data = value
-            else:
-                raise TypeError('data must be 1D ndarray')
-        elif value is None:
-            self._data = None
-        else:
-            raise TypeError('data must be 1D ndarray')
-
-    @property
-    def size(self):
-        return self._data.size
-
-    @property
-    def calib(self):
-        return self._calib
-
-    @calib.setter
-    def calib(self, value):
-        if isinstance(value, _np.ndarray) or isinstance(value, list) or isinstance(value, tuple):
-            if len(value) == 3:
-                self._calib = list(value)
-            elif len(value) == 2:
-                temp = list(value)
-                temp.append(1)
-                self._calib = temp
-            elif len(value) == 1:
-                temp = [0]
-                temp.append(value[0])
-                temp.append(1)
-                self._calib = temp
-            else:
-                raise TypeError('calib should have 1-3 components: [(start), stop, (step size)]')
-        elif isinstance(value, int) or isinstance(value, float):
-            temp = [0]
-            temp.append(value)
-            temp.append(1)
-            self._calib = temp
-        else:
-            raise TypeError('calib should be an int or float [stop]; or a \
-            1D ndarray, tuple, or list with 1-3 entires: [start, stop, step size]')
-
-    @property
-    def units(self):
-        return self._units
-
-    @units.setter
-    def units(self, value):
-        if isinstance(value, str) | (value is None):
-            self._units = value
-        else:
-            raise TypeError('units should be of type str')
-
-    @property
-    def label(self):
-        return self._label
-
-    @label.setter
-    def label(self, value):
-        if isinstance(value, str) | (value is None):
-            self._label = value
-        else:
-            raise TypeError('label should be of type str')
-
-
[docs]    def update_data_from_calib(self):
-        """
-        Calculate and set data from calib parameter
-        """
-        if self._calib is not None:
-            self.data = _np.arange(self._calib[0],self._calib[1], self._calib[2])
-        else:
-            raise TypeError('calib is not set')

-
-
[docs]    def update_calib_from_data(self):
-        """
-        Calculate and set calib parameter from data. Note: assumes uniform \
-        spacing of data.
-        """
-        if self._data is not None:
-            delta = self._data[1] - self._data[0]
-            self.calib = [self._data[0], self._data[-1]+delta, delta]
-        else:
-            raise TypeError('data is not set')

-
-
[docs]    def calib_data_agree(self):
-        if self._data is None:
-            raise TypeError('data not set')
-        if self._calib is None:
-            raise TypeError('calib not set')
-
-        temp = _np.arange(self._calib[0],self._calib[1],self._calib[2])
-
-        if temp.size != self._data.size:
-            return False
-        else:
-            return _np.allclose(temp, self._data)

-
-if __name__ == '__main__':  # pragma: no cover
-
-    start = 0
-    stop = 10
-    step_size = .1
-
-    x = _np.arange(start, stop, step_size)
-
-    rep = Replicate(data=x,calib=[start, stop, step_size])
-
-    print('Calib and data agree: {}'.format(rep.calib_data_agree()))
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/data/spectra.html b/docs/build/html/_modules/crikit/data/spectra.html deleted file mode 100644 index 70899a6..0000000 --- a/docs/build/html/_modules/crikit/data/spectra.html +++ /dev/null @@ -1,392 +0,0 @@ - - - - - - - - - - - crikit.data.spectra — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- - - - -
-
-
-
- -

Source code for crikit.data.spectra

-"""
-Spectra class and function (very similar to Spetcrum except this deals with
-multiple entries)
-
-"""
-
-import numpy as _np
-import copy as _copy
-
-from crikit.data.frequency import Frequency as _Frequency
-from crikit.data.spectrum import Spectrum as _Spectrum
-from crikit.data.replicate import Replicate as _Replicate
-
-__all__ = ['Spectra']
-
-
[docs]class Spectra(_Spectrum):
-    """
-    Spectra class
-
-    Attributes
-    ----------
-    data : 2D ndarray [n_pix, f_pix]
-        Spectra. Note: input can be a ndarray of any dimension: it will be \
-        CONVERTED to [n_pix, f_pix] shape, assuming that shape[-1] is the f_pix \
-        long.
-
-    freq : crikit.data.frequency.Frequency instance
-        Frequency [wavelength, wavenumber] object (i.e., the independent \
-        variable)
-
-    label : str
-        Spectrum label (i.e., a string describing what the spectrum is)
-
-    units : str
-        Units of spectrum
-
-    reps : crikit.data.replicate.Replicate instance, Not implemented yet
-        Object describing the meaning of multiple spectra (i.e., the physical \
-        meaning of n_pix).
-
-    meta : dict
-        Meta-data dictionary
-
-    shape : tuple, read-only
-        Shape of data
-
-    n_pix : int, read-only
-        Size of data's replicate/spectral number axis.
-
-    Methods
-    -------
-    mean : 1D ndarray
-        Mean spectrum. If extent [a,b] is provided, calculate mean over that\
-        inclusive region.
-
-    std : 1D ndarray
-        Standard deviation of spectrum. If extent [a,b] is provided, calculate standard\
-        deviation over that inclusive region.
-
-    subtract : 2D ndarray or None
-        Subtract spectrum or object
-
-    Notes
-    -----
-    * freq object contains some useful parameters such as op_range_\* and \
-    plot_range_\*, which define spectral regions-of-interest. (It's debatable \
-    as to whether those parameters should be in Frequency or Spectrum classes)
-
-    """
-
-    def __init__(self, data=None, freq=None, label=None, units=None, meta=None):
-        super().__init__(data, freq, label, units, meta)
-        self._reps = _Replicate()
-
-    @property
-    def data(self):
-        return self._data
-
-    @data.setter
-    def data(self, value):
-        if isinstance(value, _np.ndarray):
-            if self.freq.data is None or self.freq.op_list_pix is None:
-                if value.ndim == 1:
-                    print('Spectra: converting data input from 1D to 2D ndarray')
-                    self._data = value[None,:]
-                elif value.ndim == 2:
-                    self._data = value
-                else:
-                    print('Spectra: converting data input from {}D to 2D ndarray'.format(value.ndim))
-                    f_sh = value.shape[-1]
-                    self._data = value.reshape((-1, f_sh))
-            else:
-                if value.shape[-1] == self.freq.op_range_pix.size:
-                    temp = _np.zeros((self._data.shape),dtype=value.dtype)
-                    temp[:,self.freq.op_range_pix] = value
-                    self._data = temp
-                else:
-                    raise TypeError('data is of an unrecognized shape: {}'.format(value.shape))
-        else:
-            print('Assigning non-ndarray to data. Not shape checking')
-            self._data = value
-
-    @property
-    def n_pix(self):
-        return self._data.shape[0]
-
-    @property
-    def reps(self):
-        return self._reps
-
-    @reps.setter
-    def reps(self, value):
-        if isinstance(value, _Replicate):
-            self._reps = value
-        elif isinstance(value, _np.ndarray):
-            self._reps.data = value
-
-
[docs]    def subtract(self, spectra, overwrite=True):
-        """
-        Subtract spectrum from data
-        """
-        # Order IS important
-        if isinstance(spectra, Spectra):
-            if overwrite:
-                self.data -= spectra.data
-                return None
-            else:
-                return self.data - spectra.data
-        elif isinstance(spectra, _Spectrum):
-            if overwrite:
-                self.data -= spectra.data[None,:]
-                return None
-            else:
-                return self.data - spectra.data[None,:]
-        elif isinstance(spectra, _np.ndarray):
-            if spectra.shape == self.data.shape:
-                if overwrite:
-                    self.data -= spectra
-                    return None
-                else:
-                    return self.data - spectra
-            else:
-                if overwrite:
-                    self.data -= spectra[None,:]
-                    return None
-                else:
-                    return self.data - spectra[None,:]

-
-    def __sub__(self, spectrum):
-        return self.subtract(spectrum, overwrite=False)

-
-if __name__ == '__main__': # pragma: no cover
-    sp = Spectra()
-    print(sp.__dict__)
-    print('Subclass? : {}'.format(issubclass(Spectra,_Spectrum)))
-    print('Instance of Spectra? : {}'.format(isinstance(sp,Spectra)))
-    print('Instance of Spectrum? : {}'.format(isinstance(sp,_Spectrum)))
-    print('Type(sp) == Spectrum? : {}'.format(type(sp)==_Spectrum))
-    print('Type(sp) == Spectra? : {}'.format(type(sp)==Spectra))
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/data/spectrum.html b/docs/build/html/_modules/crikit/data/spectrum.html deleted file mode 100644 index 3508f17..0000000 --- a/docs/build/html/_modules/crikit/data/spectrum.html +++ /dev/null @@ -1,606 +0,0 @@ - - - - - - - - - - - crikit.data.spectrum — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
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- -
    - -
  • Docs »
    • - -
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    • - -
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-
-
- -

Source code for crikit.data.spectrum

-"""
-Spectrum class and function
-
-"""
-
-import numpy as _np
-import copy as _copy
-
-from crikit.data.frequency import Frequency as _Frequency
-
-__all__ = ['Spectrum']
-
-
[docs]class Spectrum:
-    """
-    Spectrum class
-
-    Attributes
-    ----------
-    data : 1D ndarray [f_pix]
-        Spectrum
-
-    freq : crikit.data.Frequency instance
-        Frequency [wavelength, wavenumber] object (i.e., the independent \
-        variable)
-
-    label : str
-        Spectrum label (i.e., a string describing what the spectrum is)
-
-    units : str
-        Units of spectrum
-
-    meta : dict
-        Meta-data dictionary
-
-    f_pix : int, read-only
-        Size of data. Note: this matches the size of data and does NOT check \
-        the size of freq.freq_vec.
-
-    ndim : int, read-only
-        Number of data dimensions
-
-    shape : tuple, read-only
-        Shape of data
-
-    size : int, read-only
-        Size of data (i.e., total number of entries)
-
-    Methods
-    -------
-    mean : int
-        Mean value. If extent [a,b] is provided, calculate mean over that\
-        inclusive region.
-
-    std : int
-        Standard deviation. If extent [a,b] is provided, calculate standard\
-        deviation over that inclusive region.
-
-    subtract : 1D ndarray or None
-        Subtract spectrum or object
-
-    Notes
-    -----
-    * freq object contains some useful parameters such as op_range_\* and \
-    plot_range_\*, which define spectral regions-of-interest. (It's debatable \
-    as to whether those parameters should be in Frequency or Spectrum classes)
-
-    """
-
-    def __init__(self, data=None, freq=None, label=None, units=None, meta=None):
-
-        self._data = None
-        self._freq = _Frequency()
-        self._label = None
-        self._units = None
-        self._meta = {}
-
-        if data is not None:
-            self.data = _copy.deepcopy(data)
-        if freq is not None:
-            self.freq = _copy.deepcopy(freq)
-        else:
-            self.freq = _Frequency()
-        if label is not None:
-            self.label = _copy.deepcopy(label)
-        if units is not None:
-            self.units = _copy.deepcopy(units)
-        if meta is not None:
-            self._meta = _copy.deepcopy(meta)
-
-    @property
-    def data(self):
-        return self._data
-
-    @data.setter
-    def data(self, value):
-        if isinstance(value, _np.ndarray):
-            if value.ndim == 1:
-                if self.freq is not None and self.freq.op_list_pix is not None:
-                    if value.shape[-1] == self.freq.op_range_pix.size:
-                        temp = _np.zeros((self.freq.size),dtype=value.dtype)
-                        temp[self.freq.op_range_pix] = value
-                        self._data = temp
-                    else:
-                        raise TypeError('data is of an unrecognized shape: {}'.format(value.shape))
-                else:
-                    self._data = value
-            else:
-                raise TypeError('data must be a 1D ndarray')
-        else:
-               raise TypeError('data must be a 1D ndarray')
-
-    @property
-    def data_imag_over_real(self):
-        if _np.iscomplexobj(self._data):
-            if isinstance(self._data, _np.ndarray):
-                return self._data.imag
-            else:
-                return _np.imag(self._data)
-        else:
-            return self._data
-
-    @property
-    def data_real_over_imag(self):
-        if _np.iscomplexobj(self._data):
-            if isinstance(self._data, _np.ndarray):
-                return self._data.real
-            else:
-                return _np.real(self._data)
-        else:
-            return self._data
-
-    @property
-    def freq(self):
-        return self._freq
-
-    @freq.setter
-    def freq(self, value):
-        if isinstance(value, _Frequency):
-            self._freq = value
-        elif isinstance(value, _np.ndarray):
-            self.freq = _Frequency(data=value)
-        else:
-            raise TypeError('freq must be of type crikit.data.Frequency')
-
-    @property
-    def f(self):
-        """
-        Convenience attribute: return frequency vector within operating (op) \
-        range
-        """
-        return self.freq.op_range_freq
-
-    @property
-    def f_full(self):
-        """
-        Convenience attribute: return full frequency vector
-        """
-        return self.freq.data
-
-    @property
-    def units(self):
-        return self._units
-
-    @units.setter
-    def units(self, value):
-        if isinstance(value, str):
-            self._units = value
-        else:
-            raise TypeError('units must be of type str')
-
-    @property
-    def label(self):
-        return self._label
-
-    @label.setter
-    def label(self, value):
-        if isinstance(value, str):
-            self._label = value
-        else:
-            raise TypeError('label must be of type str')
-
-    @property
-    def meta(self):
-        temp_dict = self._meta.copy()
-
-        if self.freq.calib is not None:
-            try:
-                calib_dict = {}
-                calib_prefix = 'Calib.'
-
-                calib_dict[calib_prefix + 'a_vec'] = self.freq.calib['a_vec']
-                calib_dict[calib_prefix + 'ctr_wl'] = self.freq.calib['ctr_wl']
-                calib_dict[calib_prefix + 'ctr_wl0'] = self.freq.calib['ctr_wl0']
-                calib_dict[calib_prefix + 'n_pix'] = self.freq.calib['n_pix']
-                calib_dict[calib_prefix + 'probe'] = self.freq.calib['probe']
-
-                try:  # Doesn't really matter if we have the units
-                    calib_dict[calib_prefix + 'units'] = self.freq.calib['units']
-                except:
-                    pass
-
-            except:
-                print('Could not get calibration information')
-            else:
-                temp_dict.update(calib_dict)
-
-        if self.freq.calib_orig is not None:
-            try:
-                calib_dict = {}
-                calib_prefix = 'CalibOrig.'
-
-                calib_dict[calib_prefix + 'a_vec'] = self.freq.calib_orig['a_vec']
-                calib_dict[calib_prefix + 'ctr_wl'] = self.freq.calib_orig['ctr_wl']
-                calib_dict[calib_prefix + 'ctr_wl0'] = self.freq.calib_orig['ctr_wl0']
-                calib_dict[calib_prefix + 'n_pix'] = self.freq.calib_orig['n_pix']
-                calib_dict[calib_prefix + 'probe'] = self.freq.calib_orig['probe']
-
-                try:  # Doesn't really matter if we have the units
-                    calib_dict[calib_prefix + 'units'] = self.freq.calib_orig['units']
-                except:
-                    pass
-
-            except:
-                print('Could not get calibration information')
-            else:
-                temp_dict.update(calib_dict)
-
-        # return self._meta
-        return temp_dict
-
-    @meta.setter
-    def meta(self, value):
-        if isinstance(value, dict):
-            self._meta = value
-        else:
-            raise TypeError('meta must be of type dict')
-
-    @property
-    def f_pix(self):
-        if self._data is not None:
-            return self._data.shape[-1]
-
-    @property
-    def ndim(self):
-        if self._data is None:
-            return None
-        elif isinstance(self._data, _np.ndarray):
-            return self._data.ndim
-        else:
-            return len(self._data.shape)
-
-    @property
-    def shape(self):
-        if self._data is None:
-            return None
-        else:
-            return self._data.shape
-
-    @property
-    def size(self):
-        if self._data is None:
-            return None
-        else:
-            return self._data.size
-
-
[docs]    def mean(self, extent=None, over_space=True):
-        """
-        Return mean spectrum (or mean over extent [list with 2 elements]). If\
-        over_space is False, returns reps-number of mean spectra
-        """
-        if self._data is None:
-            return None
-
-        ndim = len(self._data.shape)
-
-        if ndim == 1:
-            if isinstance(self._data, _np.ndarray):
-                return self._data.mean()
-            else:
-                return _np.mean(self._data)
-
-        if ndim > 1:
-            if over_space == True:
-                axes = tuple(_np.arange(ndim-1))
-            else:
-                axes = -1
-
-        if isinstance(self._data, _np.ndarray):
-            if extent is None:
-                return self._data.mean(axis=axes)
-            else:
-                return self._data[:,extent[0]:extent[1]+1].mean(axis=axes)
-        else:
-            if extent is None:
-                return _np.mean(self._data, axis=axes)
-            else:
-                return _np.mean(self._data[:,extent[0]:extent[1]+1],
-                                axis=axes)

-
-
[docs]    def std(self, extent=None, over_space=True):
-        """
-        Return standard deviation (std) spectrum (or std over extent
-        [list with 2 elements]). If over_space is False, reps (or reps x reps)
-        number of std's.
-        """
-        if self._data is None:
-            return None
-
-        ndim = len(self._data.shape)
-
-        if ndim == 1:
-            if isinstance(self._data, _np.ndarray):
-                return self._data.std()
-            else:
-                return _np.std(self._data)
-
-        if ndim > 1:
-            if over_space == True:
-                axes = tuple(_np.arange(ndim-1))
-            else:
-                axes = -1
-
-        if isinstance(self._data, _np.ndarray):
-            if extent is None:
-                return self._data.std(axis=axes)
-            else:
-                return self._data[:,extent[0]:extent[1]+1].std(axis=axes)
-        else:
-            if extent is None:
-                return _np.std(self._data, axis=axes)
-            else:
-                return _np.std(self._data[:,extent[0]:extent[1]+1],
-                                axis=axes)

-
-
[docs]    def subtract(self, spectrum, overwrite=True):
-        """
-        Subtract spectrum from data
-        """
-        if isinstance(spectrum, Spectrum):
-            if overwrite:
-                self.data -= spectrum.data
-                return None
-            else:
-                return self.data - spectrum.data
-        elif isinstance(spectrum, _np.ndarray):
-            if overwrite:
-                self.data -= spectrum
-                return None
-            else:
-                return self.data - spectrum

-
-    def __sub__(self, spectrum):
-        return self.subtract(spectrum, overwrite=False)

-
-
-if __name__ == '__main__':  # pragma: no cover
-    import timeit as _timeit
-
-    N = 10001
-    wn = _np.linspace(500,3000,N)
-    sp = Spectrum(data=_np.random.rand(N) + 1j*_np.random.rand(N), freq=wn)
-
-    tmr = _timeit.default_timer()
-    sp.data[200:500]
-    tmr -= _timeit.default_timer()
-    print(-tmr)
-
-    tmr = _timeit.default_timer()
-    locs = _np.arange(sp.freq.get_index_of_closest_freq(500),
-                     sp.freq.get_index_of_closest_freq(600))
-    sp.data_imag_over_real[locs]
-    tmr -= _timeit.default_timer()
-    print(-tmr)
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/datasets/model.html b/docs/build/html/_modules/crikit/datasets/model.html deleted file mode 100644 index 0393de4..0000000 --- a/docs/build/html/_modules/crikit/datasets/model.html +++ /dev/null @@ -1,385 +0,0 @@ - - - - - - - - - - - crikit.datasets.model — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.datasets.model
    • - - -
  • - - - -
    • - -
- - -
-
-
-
- -

Source code for crikit.datasets.model

-import numpy as _np
-from pkgutil import get_data as _get_data
-from io import BytesIO as _BytesIO
-import copy as _copy
-
-
[docs]class Model:
-    """
-    Model class
-
-    Parameters
-    ----------
-    subsample : int
-        Subsample the spatial dimenension (ie x[::subsample], y[::subsample])
-
-    dtype : numpy dtype
-        Dtype to set final image
-
-    """
-    _M = 300
-    _N = 300
-
-    def __init__(self, subsample=1, dtype=_np.complex):
-        self.n_layers = 7  # Number of components
-        self.img_shape = [300, 300]  # Spaital imaging shape
-
-        self.x = _np.linspace(1,199,self._N)
-        self.y = _np.linspace(1,199,self._M)
-
-        if subsample > 1:
-            self.x = self.x[::subsample]
-            self.y = self.y[::subsample]
-            self.img_shape = [self.y.size, self.x.size]
-
-        self.dtype = dtype
-
-        # Order of spectral array
-        # A: amplitude
-        # Omega: center frequency
-        # Gamma: peak frequency width
-        self.spec_order = ['Omega','A','Gamma']
-
-        # Filename prefix for concentration images
-        self.__conc_img_prefix = 'Chem_Conc_'
-
-        # Filename prefix for spectral array
-        self.__spec_prefix = 'Chem_Spec_'
-
-        self.layers = _np.zeros(self.img_shape + [self.n_layers])
-        self.spec_list = []
-        self.n_peak_list = []
-
-        # Final hyperspectral image
-        self.hsi = None
-
-        # Spectra array
-        self.spectra = None
-
-        # Frequency vector
-        # For convenicence self.f or self.wn will work
-        self._f = None
-
-        try:
-            for num in range(self.n_layers):
-                gd_layer = _get_data('crikit.datasets', '{}{}{}'.format(self.__conc_img_prefix,
-                                                                    num, '.csv'))
-                self.layers[:,:,num] = _np.genfromtxt(_BytesIO(gd_layer), delimiter=',')[::subsample,::subsample]
-
-                gd_spec = _get_data('crikit.datasets', '{}{}{}'.format(self.__spec_prefix,
-                                                                    num, '.csv'))
-                self.spec_list.append(_np.genfromtxt(_BytesIO(gd_spec), delimiter=','))
-        except:
-            print('Failed to import model layer and/or spectral information')
-        else:
-            print('Model spatial size: {}'.format(self.img_shape))
-            print('Model components/layers: {}'.format(self.n_layers))
-
-    @property
-    def f(self):
-        return self._f
-
-    @property
-    def wn(self):
-        return self._f
-
-    @property
-    def hsi_i(self):
-        """Return imag{hsi}"""
-        return self.hsi.imag
-
-    @property
-    def hsi_r(self):
-        """Return real{hsi}"""
-        return self.hsi.real
-
-
[docs]    def make_spectra(self, f):
-        """
-        Parameters
-        ----------
-        f : ndarray (1D)
-            Frequency vector
-        """
-        self._f = f
-
-        a_loc = self.spec_order.index('A')
-        o_loc = self.spec_order.index('Omega')
-        g_loc = self.spec_order.index('Gamma')
-
-        self.spectra = _np.zeros((self.n_layers, f.size), dtype=self.dtype)
-
-        try:
-            for num, arr in enumerate(self.spec_list):
-                omega_vec = arr[:,o_loc]
-                a_vec = arr[:,a_loc]
-                gamma_vec = arr[:,g_loc]
-                self.n_peak_list.append(a_vec.size)
-
-                self.spectra[num, :] = _np.sum(a_vec[:,None] / (omega_vec [:,None] - f[None,:] - 1j*gamma_vec[:,None]), axis=0)
-        except:
-            print('Failed to make model spectra')
-        else:
-            print('Model spectral size: {}'.format(self.f.size))

-
-
[docs]    def make_hsi(self, f=None):
-        """
-        Make the HSI image
-
-        Parameters
-        ----------
-        f : ndarray (1D)
-            Frequency vector
-        """
-        try:
-            if f is not None:
-                self.make_spectra(f=f)
-
-            # self.hsi = _np.zeros(self.img_shape + [self._f.size], dtype=self.dtype)
-            self.hsi = _np.dot(self.layers, self.spectra)
-            print('Model HSI shape: {}'.format(self.hsi.shape))
-        except:
-            print('Faled to make model HSI')

-
-#%%
-if __name__ == '__main__':
-    model = Model(subsample=4)
-    print('Layer shape: {}'.format(model.layers.shape))
-
-    wn = _np.linspace(500, 3400, 100)
-    model.make_hsi(f=wn)
-
-    print('Model shape: {}'.format(model.hsi.shape))
-    print('Model is complex: {}'.format(_np.iscomplexobj(model.hsi)))
-
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/io/csv_nist.html b/docs/build/html/_modules/crikit/io/csv_nist.html deleted file mode 100644 index 476ff2c..0000000 --- a/docs/build/html/_modules/crikit/io/csv_nist.html +++ /dev/null @@ -1,488 +0,0 @@ - - - - - - - - - - - crikit.io.csv_nist — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- - - - -
-
-
-
- -

Source code for crikit.io.csv_nist

-"""
-Created on Wed Sep  7 12:36:36 2016
-
-@author: chc
-"""
-
-import os as _os
-import csv as _csv
-import numpy as _np
-import copy as _copy
-
-from crikit.data.spectrum import Spectrum as _Spectrum
-from crikit.data.spectra import Spectra as _Spectra
-from crikit.data.hsi import Hsi as _Hsi
-
-from configparser import ConfigParser as _ConfigParser
-#
-#__all__ = ['hdf_dset_list_rep','hdf_is_valid_dsets',
-#           'hdf_attr_to_dict','hdf_import_data']
-#
-
-
[docs]def csv_nist_import_data(pth, filename_header, filename_data,
-                    output_cls_instance=None):
-    """
-    Import dataset(s) from HDF file
-
-    Parameters
-    ----------
-    pth : str
-        Path
-
-    filename_header : str
-        File name of header
-        
-    filename_data : str
-        File name of data
-
-    output_cls_instance : crikit.data.spectrum.Spectrum (or subclass)
-        Spectrum class (or sub) object
-
-    Returns
-    -------
-        Success : bool
-            Success of import
-        Data, Meta : list (ndarray, dict)
-            If output_cls_instance is None and import is successful, will \
-            return the data from dset_list and associated meta data.
-
-    """
-    # Join path and filename in an os-independant way
-    pfname_header = _os.path.normpath(_os.path.join(pth, filename_header))
-    pfname_data = _os.path.normpath(_os.path.join(pth, filename_data))
-
-    valid_import_locs = 0
-    
-    try:
-        with open(pfname_header,'r') as _:
-            pass
-    except:
-        print('Invalid header filename')
-    else:
-        valid_import_locs += 1
-        
-    try:
-        with open(pfname_data,'r') as _:
-            pass
-    except:
-        print('Invalid data filename')
-    else:
-        valid_import_locs += 1
-        
-    if valid_import_locs != 2:
-        return False
-    else:
-        try:
-            config = _ConfigParser()
-            config.read(pfname_header)
-            
-            # Frequency calibration
-            probe = config.getfloat('Frequency Calibration','probe(nm)')
-            wl1 = config.getfloat('Frequency Calibration','wavelength1(nm)')
-            wl2 = config.getfloat('Frequency Calibration','wavelength2(nm)')
-            pixel1 = config.getint('Frequency Calibration','pixel1')
-            pixel2 = config.getint('Frequency Calibration','pixel2')
-            f_begin = config.getfloat('Frequency Calibration','freq index begin')
-            f_size = config.getint('Frequency Calibration','freq index length')
-            f_min = config.getfloat('Frequency Calibration','freq Min')
-            f_max = config.getfloat('Frequency Calibration','freq Max')
-            
-            pix = _np.linspace(pixel1,pixel2,f_size)
-            wl = _np.linspace(wl1,wl2,f_size)
-            wn = 1e7*(1/wl - 1/probe)
-            
-            # Config is apparently backwards so flip order
-            pix = _np.flipud(pix)
-            wl = _np.flipud(wl)
-            wn = _np.flipud(wn)
-            
-            # Frequency calibration stuff
-            wl_center = wl.mean()
-            wl_slope, wl_intercept = _np.polyfit(pix, wl,1)
-            
-                
-            # Get data
-            with open(pfname_data,'r') as csvfile:
-                reader = _csv.reader(csvfile, delimiter='\t')
-                data = []
-                for count in reader:
-                    data.append(count)
-            data = _np.array(data).astype(float)
-            
-            if (data.shape[-1] == 3) | (data.shape[-1] == 2):  # Spectra
-                print('Spectra')
-                wn = data[:,0]
-                temp = data[:,-1]
-                if data.shape[-1] == 3:
-                    wl = data[:,1]
-                data = temp
-                
-                # Meta data
-                attr = {}
-                for each_section in config.sections():
-                    #print('Section: {}'.format(each_section))
-                    for (each_key, each_val) in config.items(each_section):
-                        k = each_section + '.' + each_key
-                        try:  # int
-                            v = int(each_val)
-                            #print('Integer')
-                        except:
-                            try:  # float
-                                v = float(each_val)
-                            except:  # string
-                                v = str.strip(each_val,'"')
-                        #print('{}.{}: {}'.format(each_section,each_key, v))
-                        attr.update({k:v})
-                    
-                # Add in frequency calibration info
-                attr['Frequency Calibration.Slope'] = wl_slope
-                attr['Frequency Calibration.Intercept'] = wl_intercept
-                attr['Frequency Calibration.CenterWavelength'] = wl_center
-    
-                # Convert meta keys to match those of HDF5 version
-                # Note: will not overwrite, just add-to
-                # Note: Subject to change
-                
-                output_cls_instance.data = data
-                output_cls_instance.meta = attr
-                return True
-                
-            else:
-                data = data.reshape((data.shape[0],-1,f_size))
-                # Spatial Info
-                x_start = config.getfloat('X scan Parameters','X start (um)')
-                x_steps = config.getint('X scan Parameters','X steps')
-                x_step_size = config.getfloat('X scan Parameters','X step size (um)')
-                x = _np.linspace(x_start, x_start + x_step_size * (x_steps-1), x_steps)
-    
-                try:  # Exists a typo in header info in LabView program
-                    y_start = config.getfloat('Y scan Paramters','Y start (um)')
-                    y_steps = config.getint('Y scan Paramters','Y steps')
-                    y_step_size = config.getfloat('Y scan Paramters','Y step size (um)')
-                    y = _np.linspace(y_start, y_start + y_step_size * (y_steps-1), y_steps)
-                except:  # In case typo is corrected in the future
-                    y_start = config.getfloat('Y scan Parameters','Y start (um)')
-                    y_steps = config.getint('Y scan Parameters','Y steps')
-                    y_step_size = config.getfloat('Y scan Parameters','Y step size (um)')
-                    y = _np.linspace(y_start, y_start + y_step_size * (y_steps-1), y_steps)
-                
-                # Meta data
-                attr = {}
-                for each_section in config.sections():
-                    #print('Section: {}'.format(each_section))
-                    for (each_key, each_val) in config.items(each_section):
-                        k = each_section + '.' + each_key
-                        try:  # int
-                            v = int(each_val)
-                            #print('Integer')
-                        except:
-                            try:  # float
-                                v = float(each_val)
-                            except:  # string
-                                v = str.strip(each_val,'"')
-                        #print('{}.{}: {}'.format(each_section,each_key, v))
-                        attr.update({k:v})
-                    
-                # Add in frequency calibration info
-                attr['Frequency Calibration.Slope'] = wl_slope
-                attr['Frequency Calibration.Intercept'] = wl_intercept
-                attr['Frequency Calibration.CenterWavelength'] = wl_center
-    
-                # Convert meta keys to match those of HDF5 version
-                # Note: will not overwrite, just add-to
-                # Note: Subject to change
-                try:
-                    ax1 = attr['Image data.1st axis']
-    
-                    if ax1 == 0:
-                        attr['RasterScanParams.FastAxis'] = 'X'
-                    elif ax1 == 1:
-                        attr['RasterScanParams.FastAxis'] = 'Y'
-                    elif ax1 == 2:
-                        attr['RasterScanParams.FastAxis'] = 'Z'
-                        
-                    attr['RasterScanParams.FastAxisStart'] = x_start
-                    attr['RasterScanParams.FastAxisStepSize'] = x_step_size
-                    attr['RasterScanParams.FastAxisSteps'] = x_steps
-                    attr['RasterScanParams.FastAxisStop'] = x[-1]
-    
-                    ax2 = attr['Image data.2nd axis']
-                    
-                    if ax2 == 0:
-                        attr['RasterScanParams.SlowAxis'] = 'X'
-                    elif ax2 == 1:
-                        attr['RasterScanParams.SlowAxis'] = 'Y'
-                    elif ax2 == 2:
-                        attr['RasterScanParams.SlowAxis'] = 'Z'
-                        
-                    attr['RasterScanParams.SlowAxisStart'] = y_start
-                    attr['RasterScanParams.SlowAxisStepSize'] = y_step_size
-                    attr['RasterScanParams.SlowAxisSteps'] = y_steps
-                    attr['RasterScanParams.SlowAxisStop'] = y[-1]
-    
-                    ax3 = attr['Image data.3rd axis']
-    
-                    if ax3 == 0:
-                        attr['RasterScanParams.FixedAxis'] = 'X'
-                    elif ax3 == 1:
-                        attr['RasterScanParams.FixedAxis'] = 'Y'
-                    elif ax3 == 2:
-                        attr['RasterScanParams.FixedAxis'] = 'Z'
-                        
-                    # Figure out fixed positions later
-                    
-                except:
-                    pass
-                else:
-                    output_cls_instance.data = data
-                    output_cls_instance.meta = attr
-                    return True
-
-        except:
-            print('Something failed in import')

-
-if __name__ == '__main__':
-    #from crikit.data.spectra import Spectra as _Spectra
-    
-    sp = _Spectra()
-    pth = '../../../Young_150617/'
-    filename_header = 'SH-03.h'
-    filename_data = 'base061715_152213_60ms.txt'
-    
-    csv_nist_import_data(pth, filename_header, filename_data,
-                    output_cls_instance=sp)
-    
-    print(sp.__dict__)
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/io/hdf5.html b/docs/build/html/_modules/crikit/io/hdf5.html deleted file mode 100644 index a238c08..0000000 --- a/docs/build/html/_modules/crikit/io/hdf5.html +++ /dev/null @@ -1,586 +0,0 @@ - - - - - - - - - - - crikit.io.hdf5 — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- - - - -
-
-
-
- -

Source code for crikit.io.hdf5

-"""
-
-
-
-Created on Mon May 23 10:17:16 2016
-
-@author: chc
-"""
-
-import os as _os
-
-from crikit.data.spectrum import Spectrum as _Spectrum
-from crikit.data.spectra import Spectra as _Spectra
-from crikit.data.hsi import Hsi as _Hsi
-
-
-import h5py as _h5py
-_h5py.get_config().complex_names = ('Re','Im')
-
-import numpy as _np
-
-__all__ = ['hdf_dset_list_rep','hdf_is_valid_dsets',
-           'hdf_attr_to_dict','hdf_import_data']
-
-
[docs]def hdf_dset_list_rep(prefix,suffixes):
-    """
-    Create a list of dataset names
-    """
-    dset_list = []
-
-    assert isinstance(prefix,str)
-
-    for sfx in suffixes:
-        dset_list.append(prefix + str(sfx))
-
-    return dset_list

-
-
[docs]def hdf_is_valid_dsets(pth, filename, dset_list):
-    """
-    Validate file and datasets exist. Return boolean as to whether valid
-
-    """
-    
-    isvalid = False
-    fileexists = False
-
-    try:
-        # Join path and filename in an os-independant way
-        pfname = _os.path.normpath(_os.path.join(pth, filename))
-        f = _h5py.File(pfname, 'r')
-        print('File exists: \'{}\''.format(pfname))
-        fileexists = True
-    except OSError:
-        print('File does not exist: \'{}\''.format(pfname))
-        fileexists = False
-    else:
-        if isinstance(dset_list, list):  # List of dataset(s)
-            try:
-                for count in dset_list:
-                    f[count]
-            except:
-                print('dataset: {} is invalid'.format(count))
-            else:
-                print('All datasets are valid')
-                isvalid = True
-        elif isinstance(dset_list, str):  # Single dataset string name
-            try:
-                f[dset_list]
-            except:
-                print('dataset {} is invalid'.format(count))
-            else:
-                print('Dataset is valid')
-                isvalid = True
-        else:
-            print('dset_list is unrecognized type')
-    finally:
-        if fileexists:
-            f.close()
-
-        return isvalid

-
-def _convert_to_np_dtype(dset):
-    """
-    Given an HDF5 dataset, return the values in a numpy-builtin datatype
-
-    Parameters
-    ----------
-    dset : h5py.Dataset
-        HDF5 (h5py) dataset
-
-    Returns
-    -------
-    out : numpy.ndarray (dtype = numpy built-in)
-
-    Notes
-    -----
-    The software accounts for big-/little-endianness, and the inability of \
-    hdf5 to natively store complex numbers.
-
-    """
-    assert isinstance(dset, _h5py.Dataset), 'Input is not of type h5py.Dataset'
-    # Single datatype
-    if len(dset.dtype) == 0:
-        converted = _np.ndarray(dset.shape, dtype = dset.dtype.newbyteorder('='))
-        dset.read_direct(converted)
-        if issubclass(converted.dtype.type, _np.integer):  # Integer to float
-            converted = converted.astype(_np.float)
-        return converted
-    #Compound datatype of length 2-- assumed ('Re','Im')
-    elif len(dset.dtype) == 2:
-        print('Warning: h5py.complex_names set incorrectly using \'{}\' and \'{}\' \
-for Re and Im, respectively'.format(dset.dtype.names[0], dset.dtype.names[1]))
-        _h5py.get_config().complex_names = (dset.dtype.names[0],dset.dtype.names[1])
-        dset = dset.file[dset.name]
-        converted = _np.ndarray(dset.shape, dtype = dset.dtype.newbyteorder('='))
-        dset.read_direct(converted)
-    # Unknown datatype
-    else:
-        print('Warning: Unknown datatype. Returning dataset values as is.')
-        return dset.value
-    return converted
-
-
[docs]def hdf_attr_to_dict(attr):
-    """
-    Convert from HDF attributes to valid dict
-    """
-
-    try:
-        output_dict = dict(attr)
-    except:
-        output_dict = {}
-        for count in attr:
-            try:
-                output_dict[count] = attr[count]
-            except:
-                print('Fail: {}'.format(count))
-    
-    # String in HDF are treated as numpy bytes_ literals
-    # We want out instance in memeory to have Python Strings
-    # This does a simple conversion
-    # Also will check to see if a string is burried in an array
-    for k in output_dict:
-        if isinstance(output_dict[k], _np.bytes_):
-            output_dict[k] = output_dict[k].decode('UTF-8')
-        elif isinstance(output_dict[k], _np.ndarray):
-            if output_dict[k].dtype.kind == 'S':  # String array
-                # This is a cute way of taking an array of charcters and merging
-                # them into a string. If just a single-element array,
-                # will also return a string
-                output_dict[k] = ''.join(output_dict[k].astype(_np.str))
-    return output_dict

-
-
[docs]def hdf_import_data(pth, filename, dset_list, output_cls_instance=None):
-    """
-    Import dataset(s) from HDF file
-
-    Parameters
-    ----------
-    pth : str
-        Path
-
-    filename : str
-        File name
-
-    dset_list : list
-        List of 1 or more datasets
-
-    output_cls_instance : crikit.data.spectrum.Spectrum (or subclass)
-        Spectrum class (or sub) object
-
-    Returns
-    -------
-        Success : bool
-            Success of import
-        Data, Meta : list (ndarray, dict)
-            If output_cls_instance is None and import is successful, will \
-            return the data from dset_list and associated meta data.
-
-    """
-    # Join path and filename in an os-independant way
-    pfname = _os.path.normpath(_os.path.join(pth, filename))
-
-    if hdf_is_valid_dsets(pth, filename,dset_list) == False:
-        print('Invalid filename or dataset list')
-        return False
-    else:
-        try:
-            f = _h5py.File(pfname,'r')
-
-            if type(output_cls_instance) == _Hsi:
-                print('Type Hsi')
-                if isinstance(dset_list, str):
-                    output_cls_instance.data = _convert_to_np_dtype(f[dset_list])
-                    output_cls_instance.meta = hdf_attr_to_dict(f[dset_list].attrs)
-                elif isinstance(dset_list, list):
-                    if len(dset_list) > 1:
-                        print('Cannot accept more than 1 HSI image at this time')
-                    else:
-                        for num, dname in enumerate(dset_list):
-                            if num == 0:
-                                output_cls_instance.data = _convert_to_np_dtype(f[dname])
-                                output_cls_instance.meta = hdf_attr_to_dict(f[dname].attrs)
-                            else:
-                                output_cls_instance.data = _np.vstack((output_cls_instance.data, _convert_to_np_dtype(f[dname])))
-                ret = True
-            elif type(output_cls_instance) == _Spectra:
-                print('Type Spectra')
-                if isinstance(dset_list,str):
-                    output_cls_instance.data = _convert_to_np_dtype(f[dset_list])
-                    output_cls_instance.meta = hdf_attr_to_dict(f[dset_list].attrs)
-
-                elif isinstance(dset_list, list):
-                    for num, dname in enumerate(dset_list):
-                        if num == 0:
-                            output_cls_instance.data = _convert_to_np_dtype(f[dname])
-                            output_cls_instance.meta = hdf_attr_to_dict(f[dname].attrs)
-                        else:
-                            output_cls_instance.data = _np.vstack((output_cls_instance.data, _convert_to_np_dtype(f[dname])))
-                ret = True
-            elif type(output_cls_instance) == _Spectrum:
-                print('Type Spectrum')
-                if isinstance(dset_list, str):
-                    output_cls_instance.data = _convert_to_np_dtype(f[dset_list])
-                    output_cls_instance.meta = hdf_attr_to_dict(f[dset_list].attrs)
-                elif isinstance(dset_list, list):
-                    if len > 1:
-                        print('Will average spectra into a single spectrum')
-                    else:
-                        for num, dname in enumerate(dset_list):
-                            if num == 0:
-                                output_cls_instance.data = _convert_to_np_dtype(f[dname])
-                                output_cls_instance.meta = hdf_attr_to_dict(f[dname].attrs)
-                            else:
-                                output_cls_instance.data += _convert_to_np_dtype(f[dname])
-                        output_cls_instance.data /= num+1
-                ret = True
-            elif output_cls_instance is None:
-                if isinstance(dset_list, str):
-                    data = _convert_to_np_dtype(f[dset_list])
-                    meta = hdf_attr_to_dict(f[dset_list].attrs)
-                elif isinstance(dset_list, list):
-                    for num, dname in enumerate(dset_list):
-                        if num == 0:
-                            data = _convert_to_np_dtype(f[dname])
-                            meta = hdf_attr_to_dict(f[dname].attrs)
-                        else:
-                            data = _np.vstack((data, _convert_to_np_dtype(f[dname])))
-                ret = [data, meta]
-            else:
-                raise TypeError('output_cls must be Spectrum, Spectra, or Hsi')
-        except:
-            raise TypeError('Something failed in import_hdf_nist_special')
-            ret = False
-
-        finally:
-            f.close()
-            return ret

-
-def hdf_export_data(self, output_cls_instance, pth, filename, dsetname):
-    """
-
-    """
-
-    save_grp = dsetname.rpartition('/')[0]
-    save_dataset_name_no_grp = dsetname.rpartition('/')[-1]
-
-    try:
-        # Join path and filename in an os-independant way
-        pfname_out = _os.path.normpath(_os.path.join(pth, filename))
-        
-        f_out = _h5py.File(pfname_out, 'a')
-        loc = f_out.require_group(save_grp)
-        dset = loc.create_dataset(save_dataset_name_no_grp, data=output_cls_instance.data)
-
-        for attr_key in output_cls_instance.meta:
-            try:
-                attribute = output_cls_instance.meta[attr_key]
-                if isinstance(attribute, str):
-                    attribute = _np.array(attribute, dtype='S')
-                dset.attrs.create(attr_key,attribute)
-            except:
-                print('Error in attributes')
-
-        #  Breadcrumb attributes
-        bc_attr_dict = self.bcpre.attr_dict
-        for attr_key in bc_attr_dict:
-            try:
-                attribute = bc_attr_dict[attr_key]
-                if isinstance(attribute, str):
-                    attribute = _np.array(attribute, dtype='S')
-                dset.attrs.create(attr_key,attribute)
-            except:
-                print('Error in attributes')
-                
-#            #print('Key: {}, Val: {}'.format(attr_key, bc_attr_dict[attr_key]))
-#            val = bc_attr_dict[attr_key]
-#            if isinstance(val, str):
-#                dset.attrs[attr_key] = val
-#            else:
-#                try:
-#                    dset.attrs.create(attr_key,bc_attr_dict[attr_key])
-#                except:
-#                    print('Could not create attribute')
-
-    except:
-        print('Something went wrong while saving')
-    else:
-        print('Saved without issues')
-    finally:
-        f_out.close()
-
-if __name__ == '__main__':  # pragma: no cover
-
-    from crikit.io.meta_configs import (special_nist_bcars2
-                                            as _snb)
-    rosetta = _snb()
-
-    pth = '../../../'
-    filename = 'mP2_w_small.h5'
-
-    dset = '/Spectra/Dark_3_5ms_2'
-    tester = hdf_is_valid_dsets(pth, 'fake.h5','fake')
-    assert tester == False
-
-    tester = hdf_is_valid_dsets(pth, filename,'fake_dset')
-    assert tester == False
-
-    tester = hdf_is_valid_dsets(pth, filename,['fake_dset1','fake_dset2'])
-    assert tester == False
-
-    tester = hdf_is_valid_dsets(pth, filename,dset)
-    assert tester == True
-
-    dset_list = hdf_dset_list_rep('/Spectra/Dark_3_5ms_',_np.arange(2))
-    tester = hdf_is_valid_dsets(pth, filename,dset_list)
-    assert tester == True
-
-    print('--------------\n\n')
-
-    spect_dark = _Spectra()
-    tester = hdf_is_valid_dsets(pth, filename,['/Spectra/Dark_3_5ms_2'])
-    hdf_import_data(pth, filename,'/Spectra/Dark_3_5ms_2',spect_dark)
-    #hdf_process_attr(rosetta, spect_dark)
-
-    print('Shape of dark spectra: {}'.format(spect_dark.shape))
-    print('Shape of dark spectra.mean(): {}'.format(spect_dark.mean().shape))
-
-    print('')
-    img = _Hsi()
-    hdf_import_data(pth, filename,'/BCARSImage/mP2_3_5ms_Pos_2_0/mP2_3_5ms_Pos_2_0_small',img)
-    print('Shape of img: {}'.format(img.shape))
-    print('Shape of img.mean(): {}'.format(img.mean().shape))
-
-
- -
-
- -
-
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-
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- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/io/meta_configs.html b/docs/build/html/_modules/crikit/io/meta_configs.html deleted file mode 100644 index cc90dc5..0000000 --- a/docs/build/html/_modules/crikit/io/meta_configs.html +++ /dev/null @@ -1,338 +0,0 @@ - - - - - - - - - - - crikit.io.meta_configs — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.io.meta_configs

-"""
-Configuration settings for HDF imports
-
-Use '!' as the first entry in a list to denote to use the value rather \
-than querying for it
-
-Created on Mon May 23 10:35:19 2016
-
-@author: chc
-"""
-
-
[docs]def special_nist_bcars2():
-    """
-    Return import attributes particular to the "BCARS 2" system at NIST
-    """
-    rosetta = {}
-
-    rosetta['XPixelSize'] = ['RasterScanParams.FastAxisStepSize', 
-                             'Raster.Fast.StepSize']
-    rosetta['XStart'] = ['RasterScanParams.FastAxisStart', 'Raster.Fast.Start']
-    rosetta['XStop'] = ['RasterScanParams.FastAxisStop', 'Raster.Fast.Stop']
-    rosetta['XLength'] = ['RasterScanParams.FastAxisSteps', 'Raster.Fast.Steps']
-    rosetta['XLabel'] = ['RasterScanParams.FastAxis','Raster.Fast.Axis','!','X']
-    rosetta['XUnits'] = ['RasterScanParams.FastAxisUnits','!','$\\mu$m']
-
-    rosetta['YPixelSize'] = ['RasterScanParams.SlowAxisStepSize', 
-                            'Raster.Slow.StepSize']
-    rosetta['YStart'] = ['RasterScanParams.SlowAxisStart', 'Raster.Slow.Start']
-    rosetta['YStop'] = ['RasterScanParams.SlowAxisStop', 'Raster.Slow.Stop']
-    rosetta['YLength'] = ['RasterScanParams.SlowAxisSteps', 'Raster.Slow.Steps']
-    rosetta['YLabel'] = ['RasterScanParams.SlowAxis','Raster.Slow.Axis','!','Y']
-    rosetta['YUnits'] = ['RasterScanParams.SlowAxisUnits','!','$\\mu$m']
-
-    rosetta['ZPosition'] = ['RasterScanParams.FixedAxisPosition', 
-                            'Raster.Stack.Position','!',0]
-    rosetta['ZLabel'] = ['RasterScanParams.FixedAxis', 'Raster.Stack.Axis','!','Z']
-
-    # Color Calibration
-    rosetta['ColorCenterWL'] = ['Spectro.CenterWavelength', 
-                                'Spectro.CurrentWavelength', 'Calib.ctr_wl',
-                                '!', 729.994]
-    rosetta['ColorUnits'] = ['Calib.units', '!', 'nm']
-    rosetta['ColorChannels'] = ['Calib.n_pix', '!', 1600]
-    rosetta['ColorCalibWL'] = ['Calib.ctr_wl', 'Spectro.CalibWavelength', '!', 729.994]
-    rosetta['ColorPolyVals'] = ['Spectro.Avec', 'Calib.a_vec', '!', [-0.167740721307557,
-                                                     863.8736708961577]]
-
-    rosetta['ColorProbe'] = ['Spectro.ProbeWavelength', 'Calib.probe', '!', 771.461]
-    rosetta['ColorWnMode'] = ['!', True]
-
-    # Color Calibration Original
-    rosetta['OrigColorCenterWL'] = ['Spectro.CenterWavelength',
-                                    'Spectro.CurrentWavelength',
-                                    'CalibOrig.ctr_wl']
-    rosetta['OrigColorUnits'] = ['CalibOrig.units']
-    rosetta['OrigColorChannels'] = ['CalibOrig.n_pix']
-    rosetta['OrigColorCalibWL'] = ['CalibOrig.ctr_wl']
-
-    rosetta['OrigColorPolyVals'] = ['CalibOrig.a_vec']
-
-    rosetta['OrigColorProbe'] = ['CalibOrig.probe']
-    rosetta['OrigColorWnMode'] = ['!', True]
-
-    return rosetta

-
-
[docs]def special_nist_bcars1_sample_scan():
-    """
-    Return import attributes particular to the "BCARS 1" system at NIST
-    """
-    rosetta = {}
-
-    rosetta['XPixelSize'] = 'X scan Parameters.x step size (um)'
-    rosetta['XStart'] = 'X scan Parameters.x start (um)'
-    rosetta['XStop'] = 'RasterScanParams.FastAxisStop'
-    rosetta['XLength'] = 'X scan Parameters.x steps'
-    rosetta['XLabel'] = 'RasterScanParams.FastAxis'
-    rosetta['XUnits'] = ['RasterScanParams.FastAxisUnits', '!', '$\mu m$']
-
-    rosetta['YPixelSize'] = 'Y scan Paramters.y step size (um)'
-    rosetta['YStart'] = 'Y scan Paramters.y start (um)'
-    rosetta['YStop'] = 'RasterScanParams.SlowAxisStop'
-    rosetta['YLength'] = 'Y scan Paramters.y steps'
-    rosetta['YLabel'] = 'RasterScanParams.SlowAxis'
-    rosetta['YUnits'] = ['RasterScanParams.SlowAxisUnits', '!', '$\mu m$']
-
-    rosetta['ZPosition'] = 'Z scan parameters.z start (um)'
-    rosetta['ZLabel'] = 'RasterScanParams.FixedAxis'
-
-    rosetta['ColorCenterWL'] = ['Frequency Calibration.CenterWavelength', '!', 696.831]
-    rosetta['ColorUnits'] = ['!','nm']
-    rosetta['ColorChannels'] = ['Frequency Calibration.freq index length', '!', 512]
-    rosetta['ColorCalibWL'] = ['Frequency Calibration.CenterWavelength', '!', 696.831]
-
-    # Will become deprecated in favor of ColorPolyVals
-    rosetta['ColorSlope'] = ['Frequency Calibration.Slope', '!', -0.50418919]
-    rosetta['ColorIntercept'] = ['Frequency Calibration.Intercept', '!', 825.651318]
-
-    rosetta['ColorPolyVals'] = ['Frequency Calibration.Polyvals', '!',
-                                [-0.50418919, 825.651318]]
-
-    rosetta['ColorProbe'] = ['Frequency Calibration.probe(nm)','!', 830.0]
-    rosetta['ColorWnMode'] = ['!', True]
-    # rosetta['ColorCalibWN'] = ['Processing.WNCalib','Processing.WNCalibOrig']
-
-    return rosetta

-
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- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/io/meta_process.html b/docs/build/html/_modules/crikit/io/meta_process.html deleted file mode 100644 index 69f214d..0000000 --- a/docs/build/html/_modules/crikit/io/meta_process.html +++ /dev/null @@ -1,429 +0,0 @@ - - - - - - - - - - - crikit.io.meta_process — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.io.meta_process

-"""
-Created on Mon May 23 16:55:09 2016
-
-@author: chc
-"""
-
-from crikit.data.frequency import (calib_pix_wn as _calib_pix_wn,
-                                   calib_pix_wl as _calib_pix_wl)
-
-from crikit.data.spectrum import Spectrum as _Spectrum
-from crikit.data.spectra import Spectra as _Spectra
-from crikit.data.hsi import Hsi as _Hsi
-
-import numpy as _np
-
-
[docs]def rosetta_query(key, rosetta, output_cls_instance):
-    """
-    Return the highest-priority value
-    """
-
-    if isinstance(rosetta[key],list):  # There is a priority list
-        for num, count in enumerate(rosetta[key]):
-            temp_val = None
-            temp_key = None
-
-            try:
-                if isinstance(count,str):
-                    if count == '!':
-                        temp_key = key
-                        temp_val = rosetta[key][num+1]
-                        print('Using default meta_configs value for: {}'.format(key))
-                        break
-                    else:
-                        temp_key = count
-                        temp_val = output_cls_instance._meta[temp_key]
-                        break
-#                        print('{}:{}'.format(count, temp_val))
-                else:
-                    pass
-            except:
-                temp_val = None
-                temp_key = None
-
-        if temp_val is not None:
-            return(temp_val, temp_key)
-        else:
-            return None
-
-    elif isinstance(rosetta[key],str):
-        try:
-            temp = output_cls_instance._meta[rosetta[key]]
-        except:
-            return None
-        else:
-            return (temp, rosetta[key])
-    else:  # the value is likely a predefined answer-- no need to query meta
-        return None

-
-
[docs]def meta_process(rosetta, output_cls_instance):
-    """
-    Uses a conversion dict (rosetta) to process the meta data in \
-    output_cls_instance
-    """
-
-    # Frequency-calibration
-    try:
-        calib_dict = {}
-
-        calib_dict['a_vec'] = rosetta_query('ColorPolyVals',rosetta, output_cls_instance)[0]
-        calib_dict['n_pix'] = rosetta_query('ColorChannels',rosetta, output_cls_instance)[0]
-        calib_dict['ctr_wl'] = rosetta_query('ColorCenterWL',rosetta, output_cls_instance)[0]
-        calib_dict['ctr_wl0'] = rosetta_query('ColorCalibWL',rosetta, output_cls_instance)[0]
-        calib_dict['probe'] = rosetta_query('ColorProbe',rosetta, output_cls_instance)[0]
-        calib_dict['units'] = rosetta_query('ColorUnits',rosetta, output_cls_instance)[0]
-
-        output_cls_instance.freq.calib = calib_dict
-
-        use_wn = rosetta_query('ColorWnMode',rosetta, output_cls_instance)[0]
-        print('Use wavenumber: {}'.format(use_wn))
-        if use_wn:  # Use wavenumber?
-            output_cls_instance.freq.calib_fcn = _calib_pix_wn
-        else:  # Use wavelength
-            output_cls_instance.freq.calib_fcn = _calib_pix_wl
-
-        output_cls_instance.freq.update()
-    except:
-        print('Something failed in meta_process: freq-calib')
-
-    # See if an original calibration is found
-    try:
-        calib_orig_dict = {}
-
-        calib_orig_dict['a_vec'] = rosetta_query('OrigColorPolyVals',rosetta, output_cls_instance)[0]
-        if calib_orig_dict['a_vec'] is None:
-            raise ValueError
-        calib_orig_dict['n_pix'] = rosetta_query('OrigColorChannels',rosetta, output_cls_instance)[0]
-        if calib_orig_dict['n_pix'] is None:
-            raise ValueError
-        calib_orig_dict['ctr_wl'] = rosetta_query('OrigColorCenterWL',rosetta, output_cls_instance)[0]
-        if calib_orig_dict['ctr_wl'] is None:
-            raise ValueError
-        calib_orig_dict['ctr_wl0'] = rosetta_query('OrigColorCalibWL',rosetta, output_cls_instance)[0]
-        if calib_orig_dict['ctr_wl0'] is None:
-            raise ValueError
-        
-        # Probe and Units are not necessary for calibration
-        # Probe is only needed for wavelength-to-wavenumber conversion
-        calib_orig_dict['probe'] = rosetta_query('OrigColorProbe',rosetta, output_cls_instance)[0]
-        calib_orig_dict['units'] = rosetta_query('OrigColorUnits',rosetta, output_cls_instance)[0]
-
-    except:
-        print('Original calibration not found.')
-    else:
-        print('Original calibration found.')
-        output_cls_instance.freq.calib_orig = calib_orig_dict
-    
-    # Spatial for HSI
-    if type(output_cls_instance) == _Hsi:
-        print('Type Hsi')
-        try:
-            start = rosetta_query('XStart',rosetta, output_cls_instance)[0]
-            stop = rosetta_query('XStop',rosetta, output_cls_instance)[0]
-            steps = rosetta_query('XLength',rosetta, output_cls_instance)[0]
-            units = rosetta_query('XUnits',rosetta, output_cls_instance)[0]
-            label = rosetta_query('XLabel',rosetta, output_cls_instance)[0]
-
-            # HDF files store strings in np.bytes format
-            if isinstance(units, bytes):
-                units = units.decode()
-            if isinstance(label, bytes):
-                label = label.decode()
-
-            output_cls_instance.x_rep.data = _np.linspace(start, stop, steps)
-            output_cls_instance.x_rep.units = units
-            output_cls_instance.x_rep.label = label
-            output_cls_instance.x_rep.update_calib_from_data()
-
-            del start, stop, steps, units, label
-
-            start = rosetta_query('YStart',rosetta, output_cls_instance)[0]
-            stop = rosetta_query('YStop',rosetta, output_cls_instance)[0]
-            steps = rosetta_query('YLength',rosetta, output_cls_instance)[0]
-            units = rosetta_query('YUnits',rosetta, output_cls_instance)[0]
-            label = rosetta_query('YLabel',rosetta, output_cls_instance)[0]
-
-            # HDF files store strings in np.bytes format
-            if isinstance(units, bytes):
-                units = units.decode()
-            if isinstance(label, bytes):
-                label = label.decode()
-
-            output_cls_instance.y_rep.data = _np.linspace(start, stop, steps)
-            output_cls_instance.y_rep.units = units
-            output_cls_instance.y_rep.label = label
-            output_cls_instance.y_rep.update_calib_from_data()
-
-            del start, stop, steps, units
-        except:
-            print('Something failed in meta_process: HSI-spatial calib')
-
-    elif type(output_cls_instance) == _Spectra:
-        try:
-            print('Type Spectra')
-            output_cls_instance.reps.units = None
-            output_cls_instance.reps.label = 'Acq Number'
-            output_cls_instance.reps.data = _np.arange(output_cls_instance.data.shape[0])
-    #        print(output_cls_instance.reps.data.shape)
-            output_cls_instance.reps.update_calib_from_data()
-        except:
-            print('Something failed in meta_process: Spectra rep-calib')
-
-    elif type(output_cls_instance) == _Spectrum:
-        print('Type Spectrum')

-
-if __name__ == '__main__':
-
-    from crikit.io.meta_configs import (special_nist_bcars2
-                                            as _snb)
-
-    from crikit.io.hdf5 import hdf_import_data as _hdf_import_data
-    rosetta = _snb()
-
-    filename = _os.path.abspath('../../../mP2_w_small.h5')
-
-    spect_dark = _Spectra()
-    _hdf_import_data(filename,'/Spectra/Dark_3_5ms_2',spect_dark)
-    meta_process(rosetta, spect_dark)
-    print(spect_dark.reps)
-
-    print('')
-    img = _Hsi()
-    _hdf_import_data(filename,'/BCARSImage/mP2_3_5ms_Pos_2_0/mP2_3_5ms_Pos_2_0_small',img)
-    meta_process(rosetta, img)
-    print(img.freq.__dict__)
-
-
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/measurement/fftspatialnoise.html b/docs/build/html/_modules/crikit/measurement/fftspatialnoise.html deleted file mode 100644 index 188f20b..0000000 --- a/docs/build/html/_modules/crikit/measurement/fftspatialnoise.html +++ /dev/null @@ -1,340 +0,0 @@ - - - - - - - - - - - crikit.measurement.fftspatialnoise — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.measurement.fftspatialnoise
    • - - -
  • - - - -
    • - -
- - -
-
-
-
- -

Source code for crikit.measurement.fftspatialnoise

-"""
-Created on Fri Jun 10 16:16:17 2016
-
-@author: chc
-"""
-
-import numpy as _np
-
-
[docs]class FFTSignalMetric:
-    """
-    FFT Spatial Noise Metric (Ratio - 1)
-    """
-    def __init__(self, img_shp, cutoff=0.5, img=None):
-
-        self.value = None
-        self.cutoff = cutoff
-        self.img_shape = img_shp
-        self.img_size = self.img_shape[0]*self.img_shape[1]
-
-        self._calc_mtxs()
-
-        if img is None:
-            pass
-        else:
-            self.calc(img)
-
-
[docs]    def _calc_mtxs(self):
-        """
-        Calculate binary spatial weight maxtrix, wij.
-
-        Note: Currently only supports 1st-order "rook's" case continuity
-        """
-
-        self.cutoff_row = [int(self.img_shape[0]/2*self.cutoff),
-                           int(self.img_shape[0]/2*(1+self.cutoff))]
-        self.cutoff_col = [int(self.img_shape[1]/2*self.cutoff),
-                           int(self.img_shape[1]/2*(1+self.cutoff))]
-
-        self.n_inner_pix = (self.cutoff_row[1]-self.cutoff_row[0]+1) * \
-                           (self.cutoff_col[1]-self.cutoff_col[0]+1)
-
-        self.n_outter_pix = self.img_size - self.n_inner_pix
-
-        self.scaler = self.n_outter_pix/self.n_inner_pix

-
-
[docs]    def calc(self, img):
-        """
-
-        """
-        self.value = None
-
-        f_img = _np.abs(_np.fft.fftshift(_np.fft.fft2(img-img.mean())))
-        sum_inner = f_img[self.cutoff_row[0]:self.cutoff_row[1]+1,
-                          self.cutoff_col[0]:self.cutoff_col[1]+1].sum()
-        sum_outter = f_img.sum() - sum_inner
-        
-        if sum_outter == 0:
-            self.value = 1e6
-        else:
-            self.value = self.scaler*sum_inner/sum_outter
-
-        self.value -= 1

-
-if __name__ == '__main__':
-
-    import timeit as _timeit
-
-    side_len = 301
-    img = _np.zeros(side_len**2)
-    img[::1] = 1.0
-    img = img.reshape((side_len, side_len))
-
-    tmr = _timeit.default_timer()
-    fmet = FFTSignalMetric(img_shp=(side_len, side_len))
-    fmet.calc(img)
-    tmr -= _timeit.default_timer()
-
-    print('---------')
-    print('Calculated in {:.3g} sec'.format(-tmr))
-    print('FFT Signal Metric of checkerboard: {:.3g}'.format(fmet.value))
-    print('Is close to ideal -1 value (?) (+/- .1): {}'.format(_np.isclose(fmet.value, -1, atol=1e-1)))
-
-    img = _np.random.rand(side_len, side_len)
-
-    tmr = _timeit.default_timer()
-    fmet = FFTSignalMetric(img_shp=(side_len, side_len))
-    fmet.calc(img)
-    tmr -= _timeit.default_timer()
-
-    print('\n---------')
-    print('Calculated in {:.3g} sec'.format(-tmr))
-    print('FFT Signal Metric of random: {:.3g}'.format(fmet.value))
-    print('Is close to ideal 0 value (+/- .1): {}'.format(_np.isclose(fmet.value, 0,
-          atol=1e-1)))
-    
-    img = _np.random.rand(1, side_len)
-
-    tmr = _timeit.default_timer()
-    fmet = FFTSignalMetric(img_shp=(1, side_len))
-    fmet.calc(img)
-    tmr -= _timeit.default_timer()
-
-    print('\n---------')
-    print('Calculated in {:.3g} sec'.format(-tmr))
-    print('FFT Signal Metric of random: {:.3g}'.format(fmet.value))
-    print('Is close to ideal 0 value (+/- .1): {}'.format(_np.isclose(fmet.value, 0,
-          atol=1e-1)))
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/measurement/peakamps.html b/docs/build/html/_modules/crikit/measurement/peakamps.html deleted file mode 100644 index f7a034f..0000000 --- a/docs/build/html/_modules/crikit/measurement/peakamps.html +++ /dev/null @@ -1,683 +0,0 @@ - - - - - - - - - - - crikit.measurement.peakamps — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.measurement.peakamps
    • - - -
  • - - - -
    • - -
- - -
-
-
-
- -

Source code for crikit.measurement.peakamps

-"""
-Created on Wed Jun 29 01:28:44 2016
-
-@author: chc
-"""
-
-import numpy as _np
-
-
[docs]class MeasurePeak:
-    """
-    Meausure peak amplitude.
-    
-    Parameters
-    ----------
-    pk : int
-        Peak location in pixel coordinates
-    
-    Attributes
-    ----------
-    amp : float or ndarray
-        Amplitude of peak
-    
-    Methods
-    -------
-    calculate : Calculate the amplitude
-    
-    Static Methods
-    --------------
-    measure : Same as calculate but static (returns the amplitude directly)
-    
-    """
-    def __init__(self, pk):
-        self.amp = None
-
-        self.pk = pk
-        
-
[docs]    def calculate(self, signal):
-        self.amp = self._calc(signal)
-
-        return self.amp

-        
-
[docs]    @staticmethod
-    def measure(signal, pk):
-        inst = MeasurePeak(pk)
-        return inst.calculate(signal)

-
-
[docs]    def _calc(self, signal):
-        amp = signal[..., self.pk]
-
-        return amp

-
-
[docs]class MeasurePeakBWTroughs:
-    """
-    Meausure the amplitude of a peak between troughs.
-    
-    Parameters
-    ----------
-    pk : int
-        Peak location in pixel coordinates
-    tr1 : int
-        Trough 1 location in pixel coordinates
-    tr2 : int
-        Trough 2 location in pixel coordinates
-    
-    Attributes
-    ----------
-    amp : float or ndarray
-        Amplitude of peak
-    
-    Methods
-    -------
-    calculate : Calculate the amplitude
-    
-    Static Methods
-    --------------
-    measure : Same as calculate but static (returns the amplitude directly)
-    
-    """
-    def __init__(self, pk, tr1, tr2):
-        self.amp = None
-
-        self.pk = pk
-
-        if tr1 < tr2:
-            self.tr_left = tr1
-            self.tr_right = tr2
-        else:
-            self.tr_left = tr2
-            self.tr_right = tr1
-
-
[docs]    def calculate(self, signal):
-#        try:
-        self.amp = self._calc(signal)
-#        except:
-#            return None
-#        else:
-        return self.amp

-        
-
[docs]    @staticmethod
-    def measure(signal, pk, tr1, tr2):
-        inst = MeasurePeakBWTroughs(pk, tr1, tr2)
-        return inst.calculate(signal)

-
-
[docs]    def _calc(self, signal):
-        slope = (signal[..., self.tr_right]-signal[..., self.tr_left])/ \
-                 (self.tr_right - self.tr_left)
-        amp = signal[..., self.pk] - (slope*(self.pk - self.tr_left) + \
-                signal[..., self.tr_left])
-
-        return amp

-        
-
[docs]class MeasurePeakMinus:
-    """
-    Meausure the difference (subtraction) of two peaks (pk1 - pk2).
-    
-    Parameters
-    ----------
-    pk1 : int
-        Peak location in pixel coordinates
-    pk2 : int
-        Peak location in pixel coordinates
-    
-    Attributes
-    ----------
-    amp : float or ndarray
-        Amplitude of peak
-    
-    Methods
-    -------
-    calculate : Calculate the amplitude
-    
-    Static Methods
-    --------------
-    measure : Same as calculate but static (returns the amplitude directly)
-    
-    """
-    def __init__(self, pk1, pk2):
-        self.amp = None
-
-        self.pk1 = pk1
-        self.pk2 = pk2
-        
-
[docs]    def calculate(self, signal):
-        self.amp = self._calc(signal)
-
-        return self.amp

-        
-
[docs]    @staticmethod
-    def measure(signal, pk1, pk2):
-        inst = MeasurePeakMinus(pk1, pk2)
-        return inst.calculate(signal)

-
-
[docs]    def _calc(self, signal):
-        amp = signal[..., self.pk1] - signal[..., self.pk2]
-
-        return amp

-        
-
[docs]class MeasurePeakAdd:
-    """
-    Meausure the addition of two peaks (pk1 + pk2).
-    
-    Parameters
-    ----------
-    pk1 : int
-        Peak location in pixel coordinates
-    pk2 : int
-        Peak location in pixel coordinates
-    
-    Attributes
-    ----------
-    amp : float or ndarray
-        Amplitude of peak
-    
-    Methods
-    -------
-    calculate : Calculate the amplitude
-    
-    Static Methods
-    --------------
-    measure : Same as calculate but static (returns the amplitude directly)
-    
-    """
-    def __init__(self, pk1, pk2):
-        self.amp = None
-
-        self.pk1 = pk1
-        self.pk2 = pk2
-        
-
[docs]    def calculate(self, signal):
-        self.amp = self._calc(signal)
-
-        return self.amp

-        
-
[docs]    @staticmethod
-    def measure(signal, pk1, pk2):
-        inst = MeasurePeakAdd(pk1, pk2)
-        return inst.calculate(signal)

-
-
[docs]    def _calc(self, signal):
-        amp = signal[..., self.pk1] + signal[..., self.pk2]
-
-        return amp

-        
-
[docs]class MeasurePeakMultiply:
-    """
-    Meausure the multiplication of two peak.
-    
-    Parameters
-    ----------
-    pk1 : int
-        Peak location in pixel coordinates
-    pk2 : int
-        Peak location in pixel coordinates
-    
-    Attributes
-    ----------
-    amp : float or ndarray
-        Amplitude of peak
-    
-    Methods
-    -------
-    calculate : Calculate the amplitude
-    
-    Static Methods
-    --------------
-    measure : Same as calculate but static (returns the amplitude directly)
-    
-    """
-    def __init__(self, pk1, pk2):
-        self.amp = None
-
-        self.pk1 = pk1
-        self.pk2 = pk2
-        
-
[docs]    def calculate(self, signal):
-        self.amp = self._calc(signal)
-
-        return self.amp

-        
-
[docs]    @staticmethod
-    def measure(signal, pk1, pk2):
-        inst = MeasurePeakMultiply(pk1, pk2)
-        return inst.calculate(signal)

-
-
[docs]    def _calc(self, signal):
-        amp = signal[..., self.pk1] * signal[..., self.pk2]
-
-        return amp

-        
-
[docs]class MeasurePeakDivide:
-    """
-    Meausure the ratio (division) of two peaks. pk1/pk2
-    
-    Parameters
-    ----------
-    pk1 : int
-        Peak location in pixel coordinates
-    pk2 : int
-        Peak location in pixel coordinates
-    
-    Attributes
-    ----------
-    amp : float or ndarray
-        Amplitude of peak
-    
-    Methods
-    -------
-    calculate : Calculate the amplitude
-    
-    Static Methods
-    --------------
-    measure : Same as calculate but static (returns the amplitude directly)
-    
-    """
-    def __init__(self, pk1, pk2):
-        self.amp = None
-
-        self.pk1 = pk1
-        self.pk2 = pk2
-        
-
[docs]    def calculate(self, signal):
-        self.amp = self._calc(signal)
-
-        return self.amp

-        
-
[docs]    @staticmethod
-    def measure(signal, pk1, pk2):
-        inst = MeasurePeakDivide(pk1, pk2)
-        return inst.calculate(signal)

-
-
[docs]    def _calc(self, signal):
-        amp = signal[..., self.pk1] / signal[..., self.pk2]
-
-        return amp

-        
-
[docs]class MeasurePeakSummation:
-    """
-    Meausure the summation of all amplitudes between (inclusive) two peak
-    locations.
-    
-    Parameters
-    ----------
-    pk1 : int
-        Peak location in pixel coordinates
-    pk2 : int
-        Peak location in pixel coordinates
-    
-    Attributes
-    ----------
-    amp : float or ndarray
-        Amplitude of peak
-    
-    Methods
-    -------
-    calculate : Calculate the amplitude
-    
-    Static Methods
-    --------------
-    measure : Same as calculate but static (returns the amplitude directly)
-    
-    """
-    def __init__(self, pk1, pk2):
-        self.amp = None
-
-        self.pk1 = pk1
-        self.pk2 = pk2
-        
-
[docs]    def calculate(self, signal):
-        self.amp = self._calc(signal)
-
-        return self.amp

-        
-
[docs]    @staticmethod
-    def measure(signal, pk1, pk2):
-        inst = MeasurePeakSummation(pk1, pk2)
-        return inst.calculate(signal)

-
-
[docs]    def _calc(self, signal):
-        amp = _np.sum(signal[..., self.pk1:self.pk2+1], axis=-1)
-
-        return amp

-        
-if __name__ == '__main__':
-    import matplotlib.pyplot as _plt
-
-    print('\n\n--------- 1-Signal Test--------')
-    amp = 100
-    pk = 50
-    tr1 = 20
-    tr2 = 80
-    
-    x = _np.arange(100)
-    signal = amp*_np.exp(-(x-pk)**2/(10**2))
-    baseline = x
-    y = signal + baseline
-
-    _plt.plot(x, y.T, label='Signal')
-    _plt.plot(x,baseline, label='baseline')
-    _plt.plot(x, signal.T,label='Signal - Baseline')
-
-    # non-static method
-    #pbwt = MeasurePeakBWTroughs(pk=pk, tr1=tr1, tr2=tr2)
-    #out = pbwt.calculate(y)
-
-    # static method
-    out = MeasurePeakBWTroughs.measure(signal, pk, tr1, tr2)
-    
-    _plt.plot((pk, pk), (0, out), 'k', lw=3, label='Calculated Amp')
-    _plt.xlabel('X')
-    _plt.ylabel('Amplitude (au)')
-    _plt.legend(loc='best')
-    _plt.show()
-    
-    print('Actual peak amp: {:.2f}. Retrieved peak amp: {:.2f}.'.format(amp, out))
-    print('Within 1% agreement: {}'.format(_np.isclose(amp, out, rtol=.01)))
-   
-    print('\n\n--------- 2D Simple Test--------')
-    _plt.figure()
-    
-    amp = 100
-    pk = 50
-    tr1 = 20
-    tr2 = 80
-    
-    N=2
-    
-    x = _np.arange(100)
-    signal = amp*_np.exp(-(x-pk)**2/(10**2))
-    baseline = x
-    y = signal + baseline
-    mask = _np.ones((N,N))
-    y = _np.dot(mask[...,None], y[None,:])
-
-    _plt.plot(y.reshape((-1,x.size)).T, label='Signal')
-    _plt.plot(x,baseline, label='baseline')
-    _plt.plot(x, signal.T,label='Signal - Baseline')
-
-    out = MeasurePeakBWTroughs.measure(signal, pk, tr1, tr2)
-    
-    for out_pk in out.ravel():
-        _plt.plot((pk, pk), (0, out_pk), 'k', lw=3, label='Calculated Amp')
-    _plt.xlabel('X')
-    _plt.ylabel('Amplitude (au)')
-    _plt.legend(loc='best')
-    
-    print('Actual peak(s) amp: {:.2f}. Retrieved peak amps: {}.'.format(amp, out.ravel()))
-    print('Within 1% agreement: {}'.format(_np.isclose(amp, out.ravel(), rtol=.01)))
-    print('All agree within 1%: {}'.format(_np.allclose(amp, out.ravel(), rtol=.01)))
-
-    _plt.show()
-    
-    print('\n\n--------- 2D More Complicated Test--------')
-    _plt.figure()
-    
-    amp = 100
-    pk = 50
-    tr1 = 20
-    tr2 = 80
-    
-    N=2
-    
-    x = _np.arange(100)
-    signal = amp*_np.exp(-(x-pk)**2/(10**2))
-    mask = _np.ones((N,N))
-    rndm = _np.random.randint(0,10,size=(N,N))
-    baseline = _np.dot((rndm*mask)[...,None],x[None,:])
-    
-    y = signal[None,None,:] + baseline
-    
-    #y = _np.dot(mask[...,None], y[None,:])
-
-    _plt.plot(y.reshape((-1,x.size)).T, label='Signal')
-    _plt.plot(x,baseline.reshape((-1,x.size)).T, label='baseline')
-    _plt.plot(x, signal.T,label='Signal - Baseline')
-
-    #pbwt = MeasurePeakBWTroughs(pk=pk, tr1=tr1, tr2=tr2)
-    #out = pbwt.calculate(y)
-    out = MeasurePeakBWTroughs.measure(signal, pk, tr1, tr2)
-    
-    for out_pk in out.ravel():
-        _plt.plot((pk, pk), (0, out_pk), 'k', lw=3, label='Calculated Amp')
-    _plt.xlabel('X')
-    _plt.ylabel('Amplitude (au)')
-    _plt.legend(loc='best')
-    
-    print('Actual peak(s) amp: {:.2f}. Retrieved peak amps: {}.'.format(amp, out.ravel()))
-    print('Within 1% agreement: {}'.format(_np.isclose(amp, out.ravel(), rtol=.01)))
-    print('All agree within 1%: {}'.format(_np.allclose(amp, out.ravel(), rtol=.01)))
-
-    _plt.show()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/measurement/peakfind.html b/docs/build/html/_modules/crikit/measurement/peakfind.html deleted file mode 100644 index 961d294..0000000 --- a/docs/build/html/_modules/crikit/measurement/peakfind.html +++ /dev/null @@ -1,501 +0,0 @@ - - - - - - - - - - - crikit.measurement.peakfind — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.measurement.peakfind

-"""
-Peak-finding utilities
-
-
-Notes
------
-"""
-import copy as _copy
-import numpy as _np
-import timeit as _timeit
-
-from scipy.signal import (convolve as _convolve,
-                          argrelmin as _argrelmin)
-
-
[docs]class PeakFinder:
-    """
-    Find peaks and shoulders of a signal.
-    
-    Parameters
-    ----------
-    QQ : int
-        Peak location in pixel coordinates
-    
-    Attributes
-    ----------
-    amp : float or ndarray
-        Amplitude of peak
-    
-    Methods
-    -------
-    calculate : Calculate the amplitude
-    
-    Static Methods
-    --------------
-    measure : Same as calculate but static (returns the amplitude directly)
-    
-    """
-    def __init__(self, noise_sigma, cwt_width=10, n_noise_tests=1000,
-                 cutoff_d1=None, cutoff_d2=None, verbose=True):
-        self.cwt_width = cwt_width  # Width, in pixels, of wavelet
-        self.noise_sigma = noise_sigma  # Standard deviation of signal noise
-        
-        # If cutoffs not specified, # of Monte Carlo tests to estimate cutoff values
-        self.n_noise_tests = n_noise_tests
-        self.cutoff_d1 = cutoff_d1  # Amplitude cutoff for 1st derivative
-        self.cutoff_d2 = cutoff_d2  # Amplitude cutoff for 2nd derivative
-
-        self.verbose = verbose
-
-        # Array elements
-        self.x = None  # Independent variable
-        self.y = None  # Dependent variable
-        self.x_pix = None # Independent variable (pixel-units)
-
-        self.amps = None  # Retrieved amplitudes
-        self.centers = None  # Retrieved peak centers (x-units)
-        self.sigmas = None  # Retrieved Gaussian widths (x-units)
-        self.shoulder = None  # Is a peak a shoulder
-
-        self.centers_pix = None  # Retrieved peak centers (pixel-units)
-        self.sigmas_pix = None  # Retrieved peak widths (standard deviation) (pixel-units)
-
-        self.y_retrieved = None  # Estimated coarse peak fitting
-
-    @property
-    def cwt_width(self):
-        return self._cwt_width
-
-    @cwt_width.setter
-    def cwt_width(self, value):
-        if value <= 0:
-            raise ValueError('cwt_width must be positive')
-        else:
-            self._cwt_width = value
-
-    @property
-    def noise_sigma(self):
-        return self._noise_sigma
-
-    @noise_sigma.setter
-    def noise_sigma(self, value):
-        if value < 0:
-            raise ValueError('noise_sigma must be non-negtaive')
-        else:
-            self._noise_sigma = value
-
-
[docs]    @staticmethod
-    def haar(width):
-        """
-        Create Haar wavelet (wv) with specified width (width)
-        """
-        wv = _np.zeros((width))
-        midpoint = int(_np.floor(width/2))
-        wv[0:midpoint] = 1
-        wv[midpoint::] = -1
-
-        # Set midpoint == 0 for odd-length. Not technically correct, but needed
-        # for computations
-        if width % 2 == 1:
-            wv[midpoint] = 0
-    
-        return wv

-
-
[docs]    @staticmethod
-    def cwt_diff(signal, wv_width, order=1, method='auto'):
-        """
-        Take a numerical derivative using a Haar wavelet (noise-supression)
-        
-        Parameters
-        ----------
-        signal : ndarray (1D)
-            Signal data
-        
-        wv_width : int
-            Width of wavelet to use (balance noise suppression and distortion)
-            
-        order : int, optional (default=1)
-            Order of derivative (e.g., 1st-order derivative)
-
-        method : str {'auto' (default), 'fft', 'direct'}
-            
-        Returns
-        -------
-        deriv : ndarray (1D)
-            Derivative of input signal
-        """
-        deriv = _copy.deepcopy(signal)
-        for count in range(order):
-            try:
-                deriv = _convolve(deriv, PeakFinder.haar(wv_width), mode='same', 
-                                  method=method)
-            except:
-                print('peakfind.py | cwt_diff: Likely using an old version of SciPy (no convolve method parameter)')
-                deriv = _convolve(deriv, PeakFinder.haar(wv_width), mode='same')
-        return deriv

-
-    # @staticmethod
-    # def measure(signal, noise_sigma, x=None, cwt_width=10, n_noise_tests=1000,
-    #             cutoff_d1=None, cutoff_d2=None, verbose=True):
-    #     pass
-
-
[docs]    def calculate(self, y, x=None, recalc_cutoff=True, method='auto'):
-        """ Find peaks """
-        self.y = y
-        self.x_pix = _np.arange(self.y.size)
-
-        # Will update in the future for 1D x and ND y
-        if x is not None:
-            if x.size == y.size:
-                self.x = x
-            else:
-                self.x = None
-            
-        self._calc_cutoff(recalc_cutoff=recalc_cutoff, method=method)
-        
-        tmr = _timeit.default_timer()
-        d1 = PeakFinder.cwt_diff(self.y, wv_width=self._cwt_width, order=1, method=method)
-        d2 = PeakFinder.cwt_diff(self.y, wv_width=self._cwt_width, order=2, method=method)
-
-        loc_mins_d2 = _argrelmin(d2, order=10)[0]
-        loc_mins_d2 = loc_mins_d2[d2[loc_mins_d2] < 0]
-        loc_mins_d2 = loc_mins_d2[_np.abs(d2[loc_mins_d2]) > self.cutoff_d2]
-        loc_mins_d2 = loc_mins_d2[loc_mins_d2 > 10]
-        loc_mins_d2 = loc_mins_d2[loc_mins_d2 < (d2.size - 10)]
-        peak = _np.sign(d1[loc_mins_d2-10])+_np.sign(d1[loc_mins_d2+10])==0
-        shoulder = ~peak
-        
-        
-        loc_mins_d1 = _argrelmin(d1, order=10)[0]
-        loc_mins_d1 = loc_mins_d1[d1[loc_mins_d1] < 0]
-        loc_mins_d1 = loc_mins_d1[_np.abs(d1[loc_mins_d1]) > self.cutoff_d1]
-
-        sigma_retr = []
-        sigma_retr_locs = []
-        for l in loc_mins_d2:
-            if self.x is not None:
-                sigma_retr.append(x[l] - x[loc_mins_d1[_np.argmin(_np.abs(l - loc_mins_d1))]])
-            sigma_retr_locs.append(loc_mins_d1[_np.argmin(_np.abs(l - loc_mins_d1))])
-        
-        if self.x is not None:
-            sigma_retr = _np.abs(_np.array(sigma_retr))
-            omegas_retr = x[loc_mins_d2]
-        sigma_retr_locs = _np.array(sigma_retr_locs)       
-        omegas_retr_locs = loc_mins_d2
-        
-        amps_retr = []
-        for l, s in zip(omegas_retr_locs, sigma_retr_locs):
-            dl = _np.abs(_np.ceil((l - s)/10)).astype(_np.integer)
-            amps_retr.append(_np.median(y[l-dl:l+dl+1]))
-        amps_retr = _np.array(amps_retr)
-
-        tmr -= _timeit.default_timer()
-        self._timer = 1*tmr
-
-        if self.verbose:
-            print('Time for peak finding: {:.2e} sec'.format(-tmr))
-        
-        y_retrieved = _np.zeros(*self.x_pix.shape)
-
-        for num, (a, o, s) in enumerate(zip(amps_retr, omegas_retr_locs, sigma_retr_locs)):
-            y_retrieved += a*_np.exp(-(self.x_pix-o)**2/(2*(s)**2))
-        
-        self.amps = 1*amps_retr  # Retrieved amplitudes
-
-        if self.x is not None:
-            self.centers = 1*omegas_retr  # Retrieved peak centers (x-units)
-            self.sigmas = 1*sigma_retr  # Retrieved Gaussian widths (x-units)
-        self.shoulder = shoulder  # Is a peak a shoulder
-
-        self.centers_pix = 0+omegas_retr_locs  # Retrieved peak centers (pixel-units)
-        self.sigmas_pix = 1*sigma_retr_locs  # Retrieved peak widths (standard deviation) (pixel-units)
-
-        self.y_retrieved = 1*y_retrieved  # Estimated coarse peak fitting

-
-
[docs]    def _calc_cutoff(self, recalc_cutoff=True, method='auto'):
-        if (self.cutoff_d1 is None) or (self.cutoff_d2 is None) or (recalc_cutoff == True):
-            y_blank = self._noise_sigma*_np.random.randn(self.n_noise_tests,self.x_pix.size)
-            y_blank_d2 = _np.zeros(y_blank.shape)
-            y_blank_d1 = _np.zeros(y_blank.shape)
-            for num, temp in enumerate(y_blank):
-                y_blank_d1[num, :] = PeakFinder.cwt_diff(temp, wv_width=self._cwt_width, order=1, method=method)
-                y_blank_d2[num, :] = PeakFinder.cwt_diff(temp, wv_width=self._cwt_width, order=2, method=method)
-
-            if (self.cutoff_d2 is None) or (recalc_cutoff == True):
-                self.cutoff_d2 = _np.max(_np.abs(y_blank_d2))
-            if (self.cutoff_d1 is None) or (recalc_cutoff == True):
-                self.cutoff_d1 = _np.max(_np.abs(y_blank_d1))
-            
-        if self.verbose:
-            print('1st-Deriv cutoff: {:.2f}'.format(self.cutoff_d1))
-            print('2nd-Deriv cutoff: {:.2f}'.format(self.cutoff_d2))

-        
-if __name__ == '__main__':
-
-    x = _np.linspace(0,100,1000)
-
-    A = _np.array([80, 100, 40])
-    Omega = _np.array([30, 50, 60])
-    Sigma = _np.array([3, 4, 4])
-
-    y = _np.zeros(x.shape)
-
-    for a, o, s in zip(A, Omega, Sigma):
-        y += a*_np.exp(-(x-o)**2/(2*s**2))
-    
-    noise_sigma = 3
-    noise = noise_sigma*_np.random.randn(*x.shape)
-    y_noisy = y + noise
-    
-    pkfind = PeakFinder(noise_sigma=noise_sigma, cwt_width=50, n_noise_tests=1000,
-                        cutoff_d1=None, cutoff_d2=None, verbose=True)
-
-    print('\n====================================\n')
-    pkfind.calculate(y, x=x, recalc_cutoff=True, method='fft')
-
-    
-    print('\nActual Center: {}'.format(Omega))
-    print('Calculated Centers: {}\n'.format(['{:.2f}'.format(x) for x in pkfind.centers]))
-
-    print('\nActual Amplitudes: {}'.format(A))
-    print('Calculated Amplitudes: {}\n'.format(['{:.2f}'.format(x) for x in pkfind.amps]))
-
-    print('\nActual Widths: {}'.format(Sigma))
-    print('Calculated Widths: {}\n'.format(['{:.2f}'.format(x) for x in pkfind.sigmas]))
-
-    print('Is Shoulder: {}\n'.format(pkfind.shoulder))
-    # print(pkfind.sigmas)
-    # print(pkfind.__dict__)
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/measurement/tests/test_peakfind.html b/docs/build/html/_modules/crikit/measurement/tests/test_peakfind.html deleted file mode 100644 index cfebe31..0000000 --- a/docs/build/html/_modules/crikit/measurement/tests/test_peakfind.html +++ /dev/null @@ -1,284 +0,0 @@ - - - - - - - - - - - crikit.measurement.tests.test_peakfind — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.measurement.tests.test_peakfind

-"""
-Testing for Hilbert transform method
-
-Using the math relation a^2 / (a^2 + x^2) (Lorentz/Cauchy) has an 
-analytical Hilbert transform: x^2 / (a^2 + x^2)
-"""
-
-import numpy as np
-from numpy.testing import assert_allclose
-
-from crikit.measurement.peakfind import PeakFinder
-
-
[docs]def test_peakfind():
-    x = np.linspace(0,100,1000)
-
-    A = np.array([80, 100])
-    Omega = np.array([30, 50])
-    Sigma = np.array([3, 4])
-
-    y = np.zeros(x.shape)
-
-    for a, o, s in zip(A, Omega, Sigma):
-        y += a*np.exp(-(x-o)**2/(2*s**2))
-    
-    noise_sigma = 0.001
-    noise = noise_sigma*np.random.randn(*x.shape)
-    y_noisy = y + noise
-    
-    pkfind = PeakFinder(noise_sigma=noise_sigma, cwt_width=50, n_noise_tests=1000,
-                        cutoff_d1=None, cutoff_d2=None, verbose=False)
-
-    print('\n====================================\n')
-    pkfind.calculate(y, x=x, recalc_cutoff=True, method='fft')
-
-    assert_allclose(np.array(Omega), pkfind.centers, rtol=0.01)
-    assert_allclose(np.array(A), pkfind.amps, rtol=0.01)
-    assert_allclose(np.array(Sigma), pkfind.sigmas, rtol=0.1)
-    assert_allclose(np.array([False, False]), pkfind.shoulder)
-       
-    print('\nActual Center: {}'.format(Omega))
-    print('Calculated Centers: {}\n'.format(['{:.2f}'.format(x) for x in pkfind.centers]))
-
-    print('\nActual Amplitudes: {}'.format(A))
-    print('Calculated Amplitudes: {}\n'.format(['{:.2f}'.format(x) for x in pkfind.amps]))
-
-    print('\nActual Widths: {}'.format(Sigma))
-    print('Calculated Widths: {}\n'.format(['{:.2f}'.format(x) for x in pkfind.sigmas]))
-
-    print('Is Shoulder: {}\n'.format(pkfind.shoulder))

-if __name__ == '__main__':
-    test_peakfind()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/preprocess/algorithms/abstract_als.html b/docs/build/html/_modules/crikit/preprocess/algorithms/abstract_als.html deleted file mode 100644 index 6a947d8..0000000 --- a/docs/build/html/_modules/crikit/preprocess/algorithms/abstract_als.html +++ /dev/null @@ -1,301 +0,0 @@ - - - - - - - - - - - crikit.preprocess.algorithms.abstract_als — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.preprocess.algorithms.abstract_als

-"""
-Created on Mon Dec  5 13:44:58 2016
-
-@author: chc
-"""
-import numpy as _np
-import timeit as _timeit
-
-from scipy.interpolate import UnivariateSpline as _USpline
-
-
[docs]class AbstractBaseline:
-    
-
[docs]    def setup(self, redux=1, verbose=False, order=2, fix_end_points=False, 
-              fix_rng=None, max_iter=100, min_diff=1e-5):
-        self.redux = redux
-        self.order = order
-        self.fix_end_points = fix_end_points
-        self.fix_rng = fix_rng
-        self.max_iter = max_iter
-        self.min_diff = min_diff
-        
-        self.verbose = verbose
-        self.t = None
-        self.t_per_iter = None

-        
-
[docs]    def calculate(self, signal):
-        sig_shape = signal.shape  # Shape of input signal
-        sig_size = signal.shape[-1]  # Length of spectral axis
-        
-        # N signals to detrend
-        sig_n_to_detrend = int(signal.size/signal.shape[-1])
-        
-        tmr = _timeit.default_timer()
-        if self.redux == 1:
-            output = self._calc(signal)
-        else:  # Sub-sample
-            # Dummy indep variable
-            x = _np.arange(sig_size)
-            x_sub = _np.linspace(x[0], x[-1], _np.round(x.size / 
-                                 self.redux).astype(_np.integer))
-
-            sub_shape = list(sig_shape)
-            sub_shape[-1] = x_sub.size
-            
-            signal_sampled = _np.zeros(sub_shape)
-            
-            # Spline interpolation/sub-sampling
-            for coords in _np.ndindex(signal.shape[0:-1]):
-                spl = _USpline(x,signal[coords],s=0)
-                signal_sampled[coords] = spl(x_sub)
-            
-            # Baseline from sub-sampled signal
-            output_sampled = self._calc(signal_sampled)
-            
-            output = _np.zeros(signal.shape)
-            # Spline interpolation/super-sampling
-            for coords in _np.ndindex(output_sampled.shape[0:-1]):
-                spl2 = _USpline(x_sub,output_sampled[coords],s=0)
-                output[coords] = spl2(x)
-            
-        tmr -= _timeit.default_timer()
-        self.t = -tmr
-        self.t_per_iter = self.t/sig_n_to_detrend
-        
-        return output

-
-
[docs]    def _calc(self, signal):
-        raise NotImplementedError

-
- -
-
- -
-
- - -
-
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- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/preprocess/algorithms/als.html b/docs/build/html/_modules/crikit/preprocess/algorithms/als.html deleted file mode 100644 index e80dd8c..0000000 --- a/docs/build/html/_modules/crikit/preprocess/algorithms/als.html +++ /dev/null @@ -1,453 +0,0 @@ - - - - - - - - - - - crikit.preprocess.algorithms.als — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.preprocess.algorithms.als

-"""
-Created on Mon Dec  5 12:12:51 2016
-
-@author: chc
-"""
-import numpy as _np
-
-import cvxopt as _cvxopt
-import cvxopt.cholmod as _cholmod
-_cvxopt.cholmod.options['supernodal'] = 1
-_cvxopt.cholmod.options['postorder'] = False
-
-from crikit.preprocess.algorithms.abstract_als import AbstractBaseline
-    
-
[docs]class AlsCvxopt(AbstractBaseline):   
-    def __init__(self, smoothness_param=1e3, asym_param=1e-4, redux=1,
-                 order=2, fix_end_points=False, fix_rng=None, max_iter=100, min_diff=1e-5, 
-                 verbose=False):
-        """
-        Parameters
-        ----------
-        smoothness_param : float, optional (default, 1e3)
-            Smoothness parameter
-    
-        asym_param : float, optional (default, 1e-4)
-            Assymetry parameter
-            
-        redux : int, optional (default, 1)
-            Reduction parameter to sub-sample input signal
-            
-        order : int, optional (default, 2)
-            Derivative regularization term. Order=2 for Whittaker-smoother
-        
-        fix_end_points : bool, optional (default, False)
-            Weight the baseline endpoints to approach equally the end-points
-            of the data.
-
-        fix_rng : ndarray (1D), optional (default, None)
-            Pixels to weight so that the baseline strongly approaches the data
-            at these pixels.
-        
-        max_iter : int, optional (default, 100)
-            Maximum number of least-squares iterations to perform
-            
-        min_diff : float, optional (default, 1e-5)
-            Break iterative calculations if difference is less than min_diff
-            
-        verbose : bool, optional (default, False)
-            Display progress of detrending
-    
-        """
-        
-        self.smoothness_param=smoothness_param
-        self._asym_param=asym_param
-        
-        self.setup(redux=redux, verbose=verbose, order=order, 
-                   fix_end_points=fix_end_points, fix_rng=fix_rng, 
-                   max_iter=max_iter, min_diff=min_diff)
-
-    @property
-    def asym_param(self):
-        if _np.size(self._asym_param) == 1:
-            return self._asym_param
-        elif self.redux == 1:
-            return self._asym_param
-        elif self.redux > 1:
-            x = _np.arange(0, self._asym_param.size, self.redux, 
-                           dtype=_np.integer)
-            
-            
-            return self._asym_param[x]
-            
-    @asym_param.setter
-    def asym_param(self, value):
-        self._asym_param = value
-        
-
[docs]    def _calc(self, signal):
-        """
-        Perform the ALS. Called from self.calculate (defined in 
-        AbstractBaseline parent class)
-        
-        Parameters
-        ----------
-        signal : ndarray (>= 1D)
-            Input signal
-            
-        Returns
-        -------
-        baseline : ndarray
-            Baseline of input signal
-        """
-        sig_shape = signal.shape  # Shape of input signal
-#        sig_ndim = signal.ndim  # N Signal dimensions
-        sig_size = signal.shape[-1]  # Length of spectral axis
-        
-        # N signals to detrend
-        sig_n_to_detrend = int(signal.size/signal.shape[-1])
-        
-        baseline_output = _np.zeros(sig_shape) 
-        
-        # Cute linalg trick to create 2nd-order derivative transform matrix
-        difference_matrix = _np.diff(_np.eye(sig_size), 
-                                     n=self.order, axis=0)
-        
-        # Convert into sparse matrix
-        difference_matrix = _cvxopt.sparse(_cvxopt.matrix(difference_matrix))
-    
-        for ct, coords in enumerate(_np.ndindex(signal.shape[0:-1])):
-            signal_current = signal[coords]
-    
-            penalty_vector = _np.ones([sig_size])
-            baseline_current = _np.zeros([sig_size])
-            baseline_last = _np.zeros([sig_size])
-    
-            # Iterative asymmetric least squares smoothing
-            for ct_iter in range(self.max_iter):
-                penalty_matrix = _cvxopt.spdiag(list(penalty_vector))
-                
-                minimazation_matrix = (penalty_matrix + 
-                                       _cvxopt.mul(self.smoothness_param, 
-                                                   difference_matrix.T) *
-                                       difference_matrix)
-                                       
-                x = _cvxopt.matrix(penalty_vector[:]*signal_current)
-    
-                try:
-                    # Cholesky factorization A = LL'
-                    # Solve A * baseline_current = w_sp * Signal
-                    _cholmod.linsolve(minimazation_matrix,x,uplo='U')
-                    
-                except:
-                    print('Failure in Cholesky factorization')
-                    break
-                else:
-                    if ct_iter > 0:
-                        baseline_last = baseline_current
-        
-                    baseline_current = _np.array(x).squeeze()
-        
-                    if ct_iter > 0: # Difference check b/w iterations
-                        differ = _np.abs(_np.sum(baseline_current - 
-                                                 baseline_last, axis=0))
-                        
-                        if differ < self.min_diff:
-                            break
-                    
-                    # Apply asymmetric penalization
-                    penalty_vector = _np.squeeze(self.asym_param * 
-                                                 (signal_current >= 
-                                                  baseline_current) + 
-                                                 (1-self.asym_param) * 
-                                                 (signal_current < 
-                                                  baseline_current))
-                    if self.fix_end_points:
-                        penalty_vector[0] = 1
-                        penalty_vector[-1] = 1
-
-                    if self.fix_rng is not None:
-                        penalty_vector[self.fix_rng] = 1
-            
-            baseline_output[coords] = baseline_current
-            
-            if self.verbose:
-                print('Number of iterations to converge: {}'.format(ct_iter))
-                print('Finished detrending spectra {}/{}'.format(ct + 1,
-                      sig_n_to_detrend))
-    
-        return baseline_output

-    
-if __name__ == '__main__':
-    import matplotlib.pyplot as _plt
-
-    x = _np.linspace(0,1000,800)
-    data = _np.exp(-(x-500)**2/300**2) + _np.abs(5/(300 - x -1j*10) + .005)
-    
-    N = 1
-    D = 2
-    
-    if D == 3:
-        data = _np.dot((_np.random.rand(N,N)*_np.ones((N,N)))[...,None], data[None,:])
-    else:
-        data = _np.dot((_np.random.rand(N)*_np.ones((N)))[...,None], data[None,:])
-    
-#    print('Data.shape: {}\n'.format(data.shape))
-    
-#    asym_param = _np.logspace(-4, -7, x.size)
-    
-    _plt.plot(x,data.T)
-    
-    sp_vec = _np.logspace(0,6,7)
-    for num, sp in enumerate(sp_vec):
-#        for ap in _np.logspace(-6,0,10):
-        ap = sp/1e6
-        als = AlsCvxopt(smoothness_param=sp, asym_param=ap, redux=1,
-                        max_iter=1000,
-                        verbose=False)
-
-        baseline = als.calculate(data)
-        
-        scaled_num = (num)/(sp_vec.size)
-        color = _plt.cm.jet(scaled_num)
-        
-        _plt.plot(x, baseline.T, c=color, label='{:.1e}'.format(sp))
-    _plt.legend()
-    _plt.show()
-#    print('Internal Timer: {:.4f} sec ({:.4f} per)'.format(als.t, 
-#                                                           als.t_per_iter))
-    
-#    als = AlsCvxopt(smoothness_param=1, asym_param=1e-3, redux=10, 
-#                    max_iter=1000,
-#                    verbose=False)
-#    
-#    baseline = als.calculate(data)
-#    print('Internal Timer: {:.4f} sec ({:.4f} per)'.format(als.t, 
-#                                                           als.t_per_iter))
-#    
-#    if (D <= 2) & (N<21):
-#        _plt.plot(data.T,'k')
-#        _plt.plot(baseline.T,'r')
-#        _plt.show()
-
- -
-
- -
-
- - -
-
- -
- -
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Source code for crikit.preprocess.algorithms.anscombe

-"""Variance Stabilization
-
-Routines:
-    gen_anscombe_forward
-        Generalized forward Anscombe transformation
-
-    gen_anscombe_inverse_closed_form
-        Closed-form approximation of the exact unbiased inverse of Generalized \
-        Anscombe variance-stabilizing transformation
-
-    gen_anscombe_exact_unbiased
-        Exact unbiased inverse of Generalized Anscombe variance-stabilizing
-
-Notes
------
-This software is a direct translation (with minor alterations) of the \
-original MATLAB software created by Alessandro Foi and Markku Mäkitalo \
-(Tampere University of Technology - 2011-2012). Please cite the references \
-below if using this software. http://www.cs.tut.fi/~foi/
-
-References
-----------
-[1] M. Mäkitalo and A. Foi, "Optimal inversion of the generalized Anscombe
-    transformation for Poisson-Gaussian noise", IEEE Trans. Image Process.,
-    doi:10.1109/TIP.2012.2202675
-
-[2] J.L. Starck, F. Murtagh, and A. Bijaoui, Image  Processing  and  Data
-    Analysis, Cambridge University Press, Cambridge, 1998)
-
-"""
-
-import numpy as _np
-#import numexpr as _ne
-import os as _os
-
-resource_dir = None
-resource_dir = _os.path.join(_os.path.abspath(_os.path.dirname(__file__)),
-                             'resources')
-
-if _os.path.exists(resource_dir):
-    #print('Resource directory: {}'.format(_os.path.abspath(resource_dir)))
-    pass
-else:  # pragma: no cover
-    raise IOError('Cannot find resource directory for Anscombe')
-
-
[docs]def gen_anscombe_forward(signal, gauss_std, gauss_mean = 0, poisson_multi = 1):
-    """
-    Applies the generalized Anscombe variance-stabilization transform
-    assuming a mixed Poisson-Gaussian noise model as:
-
-    signal = poisson_multi*Poisson{signal0} + Gauss{gauss_mean, gauss_std},
-
-    where Poisson{} and Gauss{} are generalized descriptions of Poisson and
-    Gaussian noise.
-
-    Parameters
-    ----------
-    signal : ndarray
-        Noisy signal (1-,2-,3D)
-
-    gauss_std : float, int
-        Standard deviation of Gaussian noise
-
-    poisson_multi : float or int, optional (default = 1)
-        Effectively a multiplier that scales the effect of the Poisson
-        noise
-
-    gauss_mean : float or int, optional (default = 0)
-        Mean Gaussian noise level
-
-    Returns
-    -------
-    fsignal : ndarray (matched to signal shape)
-        "Anscombe-transformed" signal with an approximate unity standard \
-        deviation/variance (~ 1)
-
-    Notes
-    -----
-    This software is a direct translation (with minor alterations) of the
-    original MATLAB software created by Alessandro Foi and Markku Mäkitalo
-    (Tampere University of Technology - 2011-2012). Please cite the references
-    below if using this software. http://www.cs.tut.fi/~foi/
-
-    References
-    ----------
-    [1] J.L. Starck, F. Murtagh, and A. Bijaoui, Image  Processing  and
-    Data Analysis, Cambridge University Press, Cambridge, 1998)
-
-    """
-
-    SMALL_VAL = 1
-
-    fsignal = 2/poisson_multi * _np.sqrt(_np.fmax(SMALL_VAL,poisson_multi*signal +
-                                    (3/8)*poisson_multi**2 +
-                                    gauss_std**2 -
-                                    poisson_multi*gauss_mean))
-#    fsignal = _ne.evaluate('2/poisson_multi * sqrt(where(poisson_multi*signal + (3/8)*poisson_multi**2 +\
-#                            gauss_std**2 - poisson_multi*gauss_mean > SMALL_VAL,\
-#                            poisson_multi*signal + (3/8)*poisson_multi**2 +\
-#                            gauss_std**2 - poisson_multi*gauss_mean, SMALL_VAL))')
-    #fsignal = 2/poisson_multi * _np.sqrt(_np.fmax(SMALL_VAL,fsignal))
-    return fsignal

-
-
[docs]def gen_anscombe_inverse_closed_form(fsignal, gauss_std, gauss_mean = 0,
-                                     poisson_multi = 1):
-    """
-    Applies a closed-form approximation of the exact unbiased inverse of the
-    generalized Anscombe variance-stabilizing transformation assuming a
-    mixed Poisson-Gaussian noise model as:
-
-    signal = poisson_multi*Poisson{signal0} + Gauss{gauss_mean, gauss_std},
-
-    where Poisson{} and Gauss{} are generalized descriptions of Poisson and
-    Gaussian noise.
-
-    Parameters
-    ----------
-    fsignal : ndarray
-        Forward Anscombe-transformed noisy signal (1-,2-,3D)
-
-    gauss_std : float, int
-        Standard deviation of Gaussian noise
-
-    (poisson_multi) : float, int (default = 1)
-        Effectively a multiplier that scales the effect of the Poisson
-        noise
-
-    (gauss_mean) : float, int (default = 0)
-        Mean Gaussian noise level
-
-    Returns
-    -------
-    signal : ndarray (matched to signal shape)
-        Inverse Anscombe-transformed signal with mixed Gaussian-Poisson
-        noise
-
-    Notes
-    -----
-    This software is a direct translation (with minor alterations) of the
-    original MATLAB software created by Alessandro Foi and Markku Mäkitalo
-    (Tampere University of Technology - 2011-2012). Please cite the references
-    below if using this software. http://www.cs.tut.fi/~foi/
-
-    References
-    ----------
-    [1] M. Mäkitalo and A. Foi, "Optimal inversion of the generalized Anscombe
-        transformation for Poisson-Gaussian noise", IEEE Trans. Image Process.,
-        doi:10.1109/TIP.2012.2202675
-
-    [2] J.L. Starck, F. Murtagh, and A. Bijaoui, Image  Processing  and  Data
-        Analysis, Cambridge University Press, Cambridge, 1998)
-
-    """
-
-    SMALL_VAL = 0
-
-    gauss_std = gauss_std/poisson_multi
-
-#    signal = _ne.evaluate('poisson_multi*where((fsignal/2)**2 + \
-#                    1/4*sqrt(3/2)*fsignal**-1 -\
-#                    (11/8)*fsignal**-2 + 5/8*sqrt(3/2)*fsignal**-3 -\
-#                    (1/8) - gauss_std**2 > SMALL_VAL, (fsignal/2)**2 + \
-#                    1/4*sqrt(3/2)*fsignal**-1 -\
-#                    (11/8)*fsignal**-2 + 5/8*sqrt(3/2)*fsignal**-3 -\
-#                    (1/8) - gauss_std**2, SMALL_VAL) + gauss_mean')
-    
-    signal = _np.fmax(SMALL_VAL, (fsignal/2)**2 + 1/4*_np.sqrt(3/2)*fsignal**-1 - 
-              (11/8)*fsignal**-2 + 5/8*_np.sqrt(3/2)*fsignal**-3 - 
-              (1/8) - gauss_std**2)
-    #signal[signal < SMALL_VAL] = SMALL_VAL
-    signal *= poisson_multi
-    
-#    signal = poisson_multi*where((fsignal/2)**2 + \
-#                                1/4*sqrt(3/2)*fsignal**-1 -\
-#                                (11/8)*fsignal**-2 + 5/8*sqrt(3/2)*fsignal**-3 -\
-#                                (1/8) - gauss_std**2 > SMALL_VAL, (fsignal/2)**2 + \
-#                                1/4*sqrt(3/2)*fsignal**-1 -\
-#                                (11/8)*fsignal**-2 + 5/8*sqrt(3/2)*fsignal**-3 -\
-#                                (1/8) - gauss_std**2, SMALL_VAL) \
-#                     + gauss_mean')
-
-    return signal

-
-
[docs]def gen_anscombe_inverse_exact_unbiased(fsignal, gauss_std, gauss_mean = 0,
-                                        poisson_multi = 1):
-    """
-    Applies an exact, unbiased inverse of the generalized Anscombe
-    variance-stabilizing transformation assuming a mixed Poisson-Gaussian
-    noise model as:
-
-    signal = poisson_multi*Poisson{signal0} + Gauss{gauss_mean, gauss_std},
-
-    where Poisson{} and Gauss{} are generalized descriptions of Poisson and
-    Gaussian noise.
-
-    Parameters
-    ----------
-    fsignal : ndarray
-        Forward Anscombe-transformed noisy signal (1-,2-,3D)
-
-    gauss_std : float, int
-        Standard deviation of Gaussian noise
-
-    (poisson_multi) : float, int (default = 1)
-        Effectively a multiplier that scales the effect of the Poisson
-        noise
-
-    (gauss_mean) : float, int (default = 0)
-        Mean Gaussian noise level
-
-    Returns
-    -------
-    signal : ndarray (matched to signal shape)
-        Inverse Anscombe-transformed signal with mixed Gaussian-Poisson
-        noise
-
-    Notes
-    -----
-    This software is a direct translation (with minor alterations) of the
-    original MATLAB software created by Alessandro Foi and Markku Mäkitalo
-    (Tampere University of Technology - 2011-2012). Please cite the references
-    below if using this software. http://www.cs.tut.fi/~foi/
-
-    References
-    ----------
-    [1] M. Mäkitalo and A. Foi, "Optimal inversion of the generalized Anscombe
-        transformation for Poisson-Gaussian noise", IEEE Trans. Image Process.,
-        doi:10.1109/TIP.2012.2202675
-
-    [2] J.L. Starck, F. Murtagh, and A. Bijaoui, Image  Processing  and  Data
-        Analysis, Cambridge University Press, Cambridge, 1998)
-
-    """
-    from scipy.io import loadmat
-    from scipy.interpolate import InterpolatedUnivariateSpline, interp2d
-
-    SMALL_VAL = 0
-
-    mat_dict = loadmat(_os.path.join(resource_dir,'GenAnscombe_vectors.mat'))
-
-    Efzmatrix = _np.squeeze(mat_dict['Efzmatrix'])
-    Ez = _np.squeeze(mat_dict['Ez'])
-    sigmas = _np.squeeze(mat_dict['sigmas'])
-
-    gauss_std = gauss_std/poisson_multi;
-
-
-    # interpolate the exact unbiased inverse for the desired gauss_std
-    # gauss_std is given as input parameter
-    if (gauss_std > _np.max(sigmas)):
-        # for very large sigmas, use the exact unbiased inverse of
-        # Anscombe modified by a -gauss_std^2 addend
-        exact_inverse = anscombe_inverse_exact_unbiased(fsignal) - gauss_std**2
-
-        # this should be necessary, since anscombe_inverse_exact_unbiased(fsignal) is >=0 and gauss_std>=0.
-
-        exact_inverse = _np.fmax(_np.zeros(exact_inverse.shape),exact_inverse)
-
-    elif gauss_std > 0:
-        # interpolate Efz
-
-        Efz = interp2d(sigmas,Ez,Efzmatrix,kind='linear')(gauss_std,Ez)
-
-        # apply the exact unbiased inverse
-        exact_inverse = InterpolatedUnivariateSpline(Efz,Ez,k=1)(fsignal)
-
-        # outside the pre-computed domain, use the exact unbiased inverse
-        # of Anscombe modified by a -gauss_std^2 addend
-        # (the exact unbiased inverse of Anscombe takes care of asymptotics)
-        outside_exact_inverse_domain = fsignal > _np.max(Efz.flatten())
-        asymptotic = anscombe_inverse_exact_unbiased(fsignal) - gauss_std**2
-        exact_inverse[outside_exact_inverse_domain] = asymptotic[outside_exact_inverse_domain]
-        outside_exact_inverse_domain = fsignal < _np.min(Efz);
-        exact_inverse[outside_exact_inverse_domain] = 0;
-    elif gauss_std == 0:
-        # if gauss_std is zero, then use exact unbiased inverse of Anscombe
-        # transformation (higher numerical precision)
-        exact_inverse = anscombe_inverse_exact_unbiased(fsignal);
-    else:  # gauss_std < 0
-        raise ValueError('Error: gauss_std must be non-negative!')
-
-    # reverse the initial variable change
-
-    exact_inverse *= poisson_multi;
-    exact_inverse += gauss_mean;
-
-    return exact_inverse

-
-
[docs]def anscombe_inverse_exact_unbiased(fsignal):
-    """
-    Applies an exact, unbiased inverse of the Anscombe
-    variance-stabilizing transformation assuming a mixed Poisson-Gaussian
-    noise model as:
-
-    signal = poisson_multi*Poisson{signal0} + Gauss{gauss_mean, gauss_std},
-
-    where Poisson{} and Gauss{} are generalized descriptions of Poisson and
-    Gaussian noise.
-
-    Parameters
-    ----------
-    fsignal : ndarray
-        Forward Anscombe-transformed noisy signal (1-,2-,3D)
-
-    Returns
-    -------
-    signal : ndarray (matched to signal shape)
-        Inverse Anscombe-transformed signal
-
-    Notes
-    -----
-    This software is a direct translation (with minor alterations) of the
-    original MATLAB software created by Alessandro Foi and Markku Mäkitalo
-    (Tampere University of Technology - 2011-2012). Please cite the references
-    below if using this software. http://www.cs.tut.fi/~foi/
-
-    References
-    ----------
-    [1] M. Mäkitalo and A. Foi, "On the inversion of the Anscombe
-        transformation in low-count Poisson image denoising", Proc. Int.
-        Workshop on Local and Non-Local Approx. in Image Process., LNLA 2009,
-        Tuusula, Finland, pp. 26-32, August 2009. doi:10.1109/LNLA.2009.5278406
-
-    [2] M. Mäkitalo and A. Foi, "Optimal inversion of the Anscombe
-        transformation in low-count Poisson image denoising", IEEE Trans.
-        Image Process., vol. 20, no. 1, pp. 99-109, January 2011.
-        doi:10.1109/TIP.2010.2056693
-
-    [3] Anscombe, F.J., "The transformation of Poisson, binomial and
-        negative-binomial data", Biometrika, vol. 35, no. 3/4, pp. 246-254,
-        Dec. 1948.
-
-    """
-    import time
-
-    from scipy.io import loadmat
-    from scipy.interpolate import InterpolatedUnivariateSpline
-
-    mat_dict = loadmat(_os.path.join(resource_dir,'Anscombe_vectors.mat'))
-
-    Efz = mat_dict['Efz']
-    Ez = mat_dict['Ez']
-
-    asymptotic = (fsignal/2)**2 - 1/8;  # asymptotically unbiased inverse [3]
-#    asymptotic = _ne.evaluate('(fsignal/2)**2 - 1/8')  # asymptotically unbiased inverse [3]
-
-    #start = time.process_time()
-    signal = InterpolatedUnivariateSpline(Efz,Ez,k=1)(fsignal)   # exact unbiased inverse [1,2]
-    #stop = time.process_time()
-    #print(stop-start)
-
-    outside_exact_inverse_domain = fsignal > _np.max(Efz)    # for large values use asymptotically unbiased inverse instead of linear extrapolation of exact unbiased inverse outside of pre-computed domain
-
-    signal[outside_exact_inverse_domain] = asymptotic[outside_exact_inverse_domain];
-
-    outside_exact_inverse_domain = fsignal < 2*_np.sqrt(3/8) # min(Efz(:));
-
-    signal[outside_exact_inverse_domain] = 0;
-    return signal

-
-if __name__ == '__main__':  # pragma: no cover
-    import numpy as np
-    import matplotlib as mpl
-    import matplotlib.pyplot as plt
-
-    stddev = 20
-    gain = 1
-
-    x = np.linspace(500,4000,10000)
-    y = 10e4*np.exp(-(x-2000)**2/(500**2))
-    gnoise = stddev*np.random.randn(x.size)
-    ygn = y + gnoise
-    ymix = np.random.poisson(y) + gnoise
-#    ymix = _np.dot(_np.ones((1000,1)), ymix[None,:])
-    ymix_ansc = gen_anscombe_forward(ymix, gauss_std=stddev, poisson_multi=gain)
-    y_ansc = gen_anscombe_forward(y, gauss_std=stddev, poisson_multi=gain)
-
-    y_inv_ansc = gen_anscombe_inverse_exact_unbiased(y_ansc, gauss_std=stddev,
-                                                     poisson_multi=gain)
-
-    if ymix.ndim == 1:
-        plt.subplot(211)
-        plt.plot(x,y, label='Signal')
-        plt.hold(True)
-        plt.plot(x,ymix, label='Mixed Noise Signal')
-        plt.title('Signal')
-        plt.legend(loc='best')
-    
-        plt.subplot(212)
-        plt.plot(x,ymix-y, label='Mixed - Signal')
-        plt.title('Difference ($\sigma =$ {:.3f})'.format((ymix - y).std()))
-        plt.legend(loc='best')
-    
-        plt.figure()
-        plt.subplot(211)
-        plt.plot(x,ymix_ansc, label='Anscombe Mixed Signal')
-        plt.plot(x,y_ansc, label='Anscombe Signal')
-        plt.title('Anscombe Transformed')
-        plt.legend(loc='best')
-    
-        plt.subplot(212)
-        plt.plot(x,ymix_ansc - y_ansc, label='Ansc. Mixed - Ansc. Signal')
-        plt.title('Difference ($\sigma =$ {:.3f})'.format((ymix_ansc - y_ansc).std()))
-        plt.legend(loc='best')
-    
-        plt.figure()
-        plt.subplot(211)
-        plt.plot(x,y_inv_ansc, label='Inv. Anscombe Signal')
-        plt.plot(x,y, label='Signal')
-        plt.title('Inverse Anscombe Transformed')
-        plt.legend(loc='best')
-    
-        plt.subplot(212)
-        plt.plot(x,y_inv_ansc - ymix, label='Inv. Ansc. Signal - Mixed')
-        plt.title('Difference ($\sigma =$ {:.3f})'.format((y_inv_ansc - ymix).std()))
-        plt.legend(loc='best')
-        plt.show()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/preprocess/algorithms/arpls.html b/docs/build/html/_modules/crikit/preprocess/algorithms/arpls.html deleted file mode 100644 index ca663ea..0000000 --- a/docs/build/html/_modules/crikit/preprocess/algorithms/arpls.html +++ /dev/null @@ -1,410 +0,0 @@ - - - - - - - - - - - crikit.preprocess.algorithms.arpls — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.preprocess.algorithms.arpls

-"""
-Created on Mon Dec  5 13:53:49 2016
-
-@author: chc
-"""
-
-import numpy as _np
-
-import cvxopt as _cvxopt
-import cvxopt.cholmod as _cholmod
-_cvxopt.cholmod.options['supernodal'] = 1
-_cvxopt.cholmod.options['postorder'] = False
-
-from crikit.preprocess.algorithms.abstract_als import AbstractBaseline
-    
-
[docs]class ArPlsCvxopt(AbstractBaseline):
-    def __init__(self, smoothness_param=1e-8, redux=1, order=2, 
-                 fix_end_points=False, max_iter=100, min_diff=1e-5, 
-                 verbose=False):
-        """
-        Parameters
-        ----------
-        smoothness_param : float, optional (default, 1e3)
-            Smoothness parameter
-    
-        redux : int, optional (default, 1)
-            Reduction parameter to sub-sample input signal
-            
-        order : int, optional (default, 2)
-            Derivative regularization term. Order=2 for Whittaker-smoother
-            
-        max_iter : int, optional (default, 100)
-            Maximum number of least-squares iterations to perform
-            
-        min_diff : float, optional (default, 1e-5)
-            Break iterative calculations if difference is less than min_diff
-            
-        verbose : bool, optional (default, False)
-            Display progress of detrending
-    
-        """
-        
-        self.smoothness_param=smoothness_param
-        
-        self.setup(redux=redux, verbose=verbose, order=order,
-                   fix_end_points=fix_end_points, max_iter=max_iter, 
-                   min_diff=min_diff)
-
-
[docs]    def _calc(self, signal):
-        # Shut-off over-flow warning temporarily
-        _np.seterr(over = 'ignore')
-        
-        sig_shape = signal.shape  # Shape of input signal
-#        sig_ndim = signal.ndim  # N Signal dimensions
-        sig_size = signal.shape[-1]  # Length of spectral axis
-        
-        # N signals to detrend
-        sig_n_to_detrend = int(signal.size/signal.shape[-1])
-        
-        baseline_output = _np.zeros(sig_shape) 
-        
-        # Cute linalg trick to create 2nd-order derivative transform matrix
-        difference_matrix = _np.diff(_np.eye(sig_size), 
-                                     n=self.order, axis=0)
-        
-        # Convert into sparse matrix
-        difference_matrix = _cvxopt.sparse(_cvxopt.matrix(difference_matrix))
-    
-        for ct, coords in enumerate(_np.ndindex(signal.shape[0:-1])):
-            signal_current = signal[coords]
-    
-            penalty_vector = _np.ones([sig_size])
-            baseline_current = _np.zeros([sig_size])
-#            baseline_last = _np.zeros([sig_size])
-    
-            # Iterative asymmetric least squares smoothing
-            for ct_iter in range(self.max_iter):
-                penalty_matrix = _cvxopt.spdiag(list(penalty_vector))
-                
-                minimazation_matrix = (penalty_matrix + 
-                                       _cvxopt.mul(self.smoothness_param, 
-                                                   difference_matrix.T) *
-                                       difference_matrix)
-                                       
-                x = _cvxopt.matrix(penalty_vector[:]*signal_current)
-    
-                # Cholesky factorization A = LL'
-                # Solve A * baseline_current = w_sp * Signal
-                _cholmod.linsolve(minimazation_matrix,x,uplo='U')
-    
-#                if ct_iter > 0:
-#                    baseline_last = baseline_current
-    
-                baseline_current = _np.array(x).squeeze()
-    
-                signal_baseline_differ = signal_current - baseline_current
-                neg_signal_baseline_differ = signal_baseline_differ[signal_baseline_differ < 0]
-                mean_neg_signal_baseline_differ = _np.mean(neg_signal_baseline_differ)
-                std_neg_signal_baseline_differ = _np.std(neg_signal_baseline_differ)
-                
-                penalty_vector_temp = 1 / (1 + 
-                                           _np.exp(2*(signal_baseline_differ -
-                                                      (2*std_neg_signal_baseline_differ -
-                                                       mean_neg_signal_baseline_differ)) / 
-                                           std_neg_signal_baseline_differ))
-                
-                if ct_iter > 0:
-                    norm_differ = (_np.linalg.norm(penalty_vector - 
-                                                  penalty_vector_temp) / 
-                                   _np.linalg.norm(penalty_vector))
-#                    print('Norm differ: {:.2f}'.format(norm_differ))
-#                    print(norm_differ)
-#                    print('norm: {:.6e}'.format(_np.linalg.norm(penalty_vector)))
-                    if (norm_differ < self.min_diff) | (_np.isnan(norm_differ)):
-                        break
-                    
-                penalty_vector = penalty_vector_temp
-
-                if self.fix_end_points:
-                    penalty_vector[0] = 1
-                    penalty_vector[-1] = 1
-
-            if self.verbose:
-                print('Number of iterations to converge: {}'.format(ct_iter))
-                        
-            baseline_output[coords] = baseline_current
-            
-            if self.verbose:
-                print('Finished detrending spectra {}/{}'.format(ct + 1,
-                      sig_n_to_detrend))
-    
-        return baseline_output

-    
-if __name__ == '__main__':
-    import matplotlib.pyplot as _plt
-
-    x = _np.linspace(0,1000,800)
-    data_orig = _np.abs(5/(300 - x -1j*10) + .005)
-    bg = _np.exp(-(x-500)**2/700**2)
-    data = bg + data_orig
-    
-    N = 1
-    D = 2
-    
-    if N > 1:
-        if D == 3:
-            data = _np.dot((_np.random.rand(N,N)*_np.ones((N,N)))[...,None], data[None,:])
-        else:
-            data = _np.dot((_np.random.rand(N)*_np.ones((N)))[...,None], data[None,:])
-    
-    print('Data.shape: {}\n'.format(data.shape))
-    
-    arpls = ArPlsCvxopt(smoothness_param=1e-11, redux=1, max_iter=1000, 
-                        min_diff=1e-6,
-                        verbose=False)
-    
-    baseline = arpls.calculate(data)
-    print('Internal Timer: {:.4f} sec ({:.4f} per)'.format(arpls.t, 
-                                                           arpls.t_per_iter))
-    
-#    arpls = ArPlsCvxopt(smoothness_param=1e-15, redux=10, max_iter=50,
-#                        verbose=False)
-#    
-#    baseline = arpls.calculate(data)
-#    print('Internal Timer: {:.4f} sec ({:.4f} per)'.format(arpls.t, 
-#                                                           arpls.t_per_iter))
-#    
-
-    if (D <= 2) & (N<21):
-        _plt.figure()
-        _plt.plot(data.T,'k')
-        _plt.plot(baseline.T,'r')
-        
-        _plt.figure()
-        _plt.plot(data_orig.T, 'k')
-        _plt.plot((data-baseline).T, 'r')
-        _plt.show()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/preprocess/crop.html b/docs/build/html/_modules/crikit/preprocess/crop.html deleted file mode 100644 index 759a60d..0000000 --- a/docs/build/html/_modules/crikit/preprocess/crop.html +++ /dev/null @@ -1,356 +0,0 @@ - - - - - - - - - - - crikit.preprocess.crop — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    • - -
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    • - -
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    • - - -
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-
- -

Source code for crikit.preprocess.crop

-"""
-Created on Tue Jun 21 14:28:49 2016
-
-@author: chc
-"""
-
-import numpy as _np
-import copy as _copy
-
-
-
[docs]class ZeroColumn:
-    """
-    Set first or last column that is not all 0's to 0.
-
-    Parameters
-    ----------
-    first_or_last : int, optional (default = 0 [first])
-        Find first (= 0) or last (= -1)
-
-    zero_col : int, optional (default = None)
-        Zero a specified column
-    """
-    def __init__(self, first_or_last=0, zero_col=None):
-        self.zero_col = zero_col
-        self.fol = first_or_last
-
-
[docs]    def _calc(self, data, ret_obj):
-        assert data.ndim == 3
-        try:
-            if self.zero_col is None:
-                row_sums = data.sum(axis=(0, -1))
-                self.zero_col = _np.nonzero(row_sums)[0][self.fol]
-
-            ret_obj[:, self.zero_col, :] *= 0
-        except:
-            return False
-        else:
-            return True

-
-
[docs]    def transform(self, data):
-        success = self._calc(data, ret_obj=data)
-        return success

-
-
[docs]    def calculate(self, data):
-        data_copy = _copy.deepcopy(data)
-        success = self._calc(data, ret_obj=data_copy)
-        if success:
-            return data_copy
-        else:
-            return None

-
-
-
[docs]class ZeroRow:
-    """
-    Set first or last row that is not all 0's to 0.
-
-    Parameters
-    ----------
-    first_or_last : int, optional (default = 0 [first])
-        Find first (= 0) or last (= -1)
-
-    zero_row : int, optional (default = None)
-        Zero a specified row
-    """
-    def __init__(self, first_or_last=0, zero_row=None):
-        self.zero_row = zero_row
-        self.fol = first_or_last
-
-
[docs]    def _calc(self, data, ret_obj):
-        assert data.ndim == 3
-        try:
-            if self.zero_row is None:
-                col_sums = data.sum(axis=(1, -1))
-                self.zero_row = _np.nonzero(col_sums)[0][self.fol]
-
-            ret_obj[self.zero_row, :, :] *= 0
-        except:
-            return False
-        else:
-            return True

-
-
[docs]    def transform(self, data):
-        success = self._calc(data, ret_obj=data)
-        return success

-
-
[docs]    def calculate(self, data):
-        data_copy = _copy.deepcopy(data)
-        success = self._calc(data, ret_obj=data_copy)
-        if success:
-            return data_copy
-        else:
-            return None

-
-if __name__ == '__main__':
-
-
-    temp = _np.random.rand(3,4,5)
-    z = ZeroColumn(first_or_last=0)
-    z.transform(temp)
-    print('Zero First Column')
-    print('Is first column sum-0?: {}'.format(temp.sum(axis=(0,-1))[0] == 0))
-    print('Is first row sum-0?: {}'.format(temp.sum(axis=(1,-1))[0] == 0))
-
-    temp = _np.random.rand(3,4,5)
-    z = ZeroRow(first_or_last=0)
-    z.transform(temp)
-    print('\n\nZero First Row')
-    print('Is first column sum-0?: {}'.format(temp.sum(axis=(0,-1))[0] == 0))
-    print('Is first row sum-0?: {}'.format(temp.sum(axis=(1,-1))[0] == 0))
-
-    temp = _np.random.rand(3,4,5)
-    z = ZeroColumn(first_or_last=-1)
-    z.transform(temp)
-    print('\n\nZero Last Column')
-    print('Is last column sum-0?: {}'.format(temp.sum(axis=(0,-1))[-1] == 0))
-    print('Is last row sum-0?: {}'.format(temp.sum(axis=(1,-1))[-1] == 0))
-
-    temp = _np.random.rand(3,4,5)
-    z = ZeroRow(first_or_last=-1)
-    z.transform(temp)
-    print('\n\nZero First Row')
-    print('Is last column sum-0?: {}'.format(temp.sum(axis=(0,-1))[-1] == 0))
-    print('Is last row sum-0?: {}'.format(temp.sum(axis=(1,-1))[-1] == 0))
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/preprocess/denoise.html b/docs/build/html/_modules/crikit/preprocess/denoise.html deleted file mode 100644 index 1670a3d..0000000 --- a/docs/build/html/_modules/crikit/preprocess/denoise.html +++ /dev/null @@ -1,495 +0,0 @@ - - - - - - - - - - - crikit.preprocess.denoise — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
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-
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    • - -
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    • - - -
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- -

Source code for crikit.preprocess.denoise

-"""
-Denoising
-
-Created on Fri Apr 22 23:55:22 2016
-
-@author: chc
-"""
-
-import copy as _copy
-
-import numpy as _np
-
-from numpy.linalg import svd as _svd
-
-from crikit.utils.datacheck import _rng_is_pix_vec
-
-__all__ = ['SVDDecompose', 'SVDRecompose']
-
-
-
[docs]class SVDDecompose:
-    """
-    Compute the SVD of a signal (just wraps numpy.linalg.svd) i.e., decompose \
-    the input into components.
-
-    Parameters
-    ----------
-    data : ndarray (2D or 3D).
-        Input array.
-
-    rng : ndarray (1D), optional
-        Range of pixels to perform operation over.
-
-    Returns
-    -------
-    ndarray, ndarray, ndarray
-        U, s, Vh
-
-    Notes
-    -----
-
-    U : ndarray (2D)
-        U-component from SVD decomposition (spatial componenet with crikit)
-
-    Vh : ndarray (2D)
-        Vh-component from SVD decomposition (spectral componenet with crikit).
-        NOTE: this is the Hermitial/conjugate transpose of the normal
-        V-component in SVD
-
-    s : ndarray (1D)
-        Diagonal elements of S-matrix describing the relative contributions
-        of each singular value
-
-    S : ndarray (2D)
-        S-matrix derived from s
-
-    References
-    ----------
-
-    """
-    def __init__(self, rng=None):
-        self._U = None
-        self._s = None
-        self._Vh = None
-
-        self.rng = _rng_is_pix_vec(rng)
-
-
-
[docs]    def _calc(self, data, ret_obj):
-        """
-        Calculate SVD (wrap numpy SVD).
-        """
-        try:
-            if self.rng is None:
-                self._U, self._s, self._Vh = _svd(data, full_matrices=False)
-            else:
-                self._U, self._s, self._Vh = _svd(data[..., self.rng],
-                                               full_matrices=False)
-        except:
-            return False
-        else:
-            return True

-
-
[docs]    def calculate(self, data):
-        """
-        Calculate SVD and return U, s, and Vh.
-        """
-
-        # If 3D -> 2D
-        if data.ndim == 3:
-            success = self._calc(data.reshape((-1,data.shape[-1])), ret_obj=None)
-        else:
-            success = self._calc(data, ret_obj=None)
-        if success:
-            return self._U, self._s, self._Vh
-        else:
-            return None

-
-
-
[docs]class SVDRecompose:
-    """
-    Reconstruct the original data using the SVD components. The reconstructed \
-    signal shape is 2D (or if provided) or matches data_obj.
-
-    Parameters
-    ----------
-    U : ndarray (2D)
-        U-component from SVD decomposition (spatial componenet with crikit)
-
-    s : ndarray (1D)
-        Diagonal elements of S-matrix describing the relative contributions
-        of each singular value
-
-    Vh : ndarray (2D)
-        Vh-component from SVD decomposition (spectral componenet with crikit).
-        NOTE: this is the Hermitial/conjugate transpose of the normal
-        V-component in SVD
-
-    data : ndarray (2D or 3D)
-        Original data (for overwrite if selected).
-
-    rng : ndarray (1D), optional
-        Range of pixels to perform operation over.
-
-    overwrite : bool, optional (default=True)
-        Overwrite the original data in data_obj
-
-    Returns
-    -------
-    ndarray (2D or 3D)
-        Recomposed data (U*S*Vh). If data_obj is not None, returned object \
-        shape matches data_obj. Else 2D.
-
-    None
-        Returns None if overwrite is True and overwrites input data_obj.
-
-    Notes
-    -----
-
-    S : ndarray (2D)
-        S-matrix derived from s
-
-    References
-    ----------
-
-    """
-    def __init__(self, rng=None):
-        self.rng = _rng_is_pix_vec(rng)
-        self.svs = None
-        self.s_keep = None
-
-
-
[docs]    def _calc(self, U, s, Vh, ret_obj):
-        """
-        Perform data reconstruction from U*S*Vh with selected s-values.
-        """
-
-        try:
-            ret_obj *= 0
-            if ret_obj.ndim == 2:
-                if self.rng is None:
-                # out = U*S*Vh
-                    # ret_obj += _np.dot(U, _np.dot(_np.diag(s), Vh))
-                    ret_obj += _np.dot(U[:, self.svs], _np.dot(_np.diag(s[self.svs]), Vh[self.svs, :]))
-                else:
-                    # ret_obj[..., self.rng] += _np.dot(U, _np.dot(_np.diag(s), Vh))
-                    ret_obj[..., self.rng] += _np.dot(U[:, self.svs], _np.dot(_np.diag(s[self.svs]), Vh[self.svs, :]))
-            elif ret_obj.ndim == 3:
-                # If 3D (calculate is performed in 2D), reshape.
-                if self.rng is None:
-                    # out = U*S*Vh
-                    # ret_obj += _np.reshape(_np.dot(U, _np.dot(_np.diag(s), Vh)),
-                    #                        ret_obj.shape)
-                    ret_obj += _np.reshape(_np.dot(U[:, self.svs], 
-                                                   _np.dot(_np.diag(s[self.svs]),
-                                                           Vh[self.svs, :])), ret_obj.shape)               
-                else:
-                    shp = list(ret_obj.shape)
-                    shp[-1] = self.rng.size
-                    # ret_obj[..., self.rng] += _np.reshape(_np.dot(U, _np.dot(_np.diag(s), Vh)),
-                    #                        shp)
-                    ret_obj[..., self.rng] += _np.reshape(_np.dot(U[:, self.svs], _np.dot(_np.diag(s[self.svs]),Vh[self.svs, :])), shp)
-
-        except:
-            return False
-        else:
-            return True

-
-
[docs]    def _set_s_keep(self, s, svs):
-        """
-        Set the singular value vector (s_keep) based on svs list/ndarray
-        """
-        if svs is not None:
-            self.svs = svs
-        if self.svs is None:
-            self.svs = _np.arange(s.size)
-        
-        self.s_keep = 0*s
-        self.s_keep[self.svs] = s[self.svs]

-        # print(self.s_keep)
-        # self.s_keep = s[svs]
-
-
[docs]    def transform(self, data, U, s, Vh, svs=None):
-        # Set what singular values to keep
-        self._set_s_keep(s, svs)
-
-
-        success = self._calc(U, self.s_keep, Vh, ret_obj=data)
-        return success

-
-
[docs]    def calculate(self, data, U, s, Vh, svs=None):
-        # Set what singular values to keep
-        self._set_s_keep(s, svs)
-
-        data_copy = _copy.deepcopy(data)
-        success = self._calc(U, self.s_keep, Vh, ret_obj=data_copy)
-        if success:
-            return data_copy
-        else:
-            return None

-
-
-if __name__ == '__main__':  # pragma: no cover
-
-    y = _np.random.randn(100,1000)
-
-    svd_decompose = SVDDecompose()
-    svd_recompose = SVDRecompose()
-
-    U, s, Vh = svd_decompose.calculate(y)
-
-    y2 = svd_recompose.calculate(y,U,s,Vh,svs=[])
-    print('0 singular values selected...')
-    print('Returns matrix is all 0\'s: {}'.format(_np.allclose(y2,0) == True))
-    
-    [U,s,Vh] = svd_decompose.calculate(y)
-    y2 = svd_recompose.calculate(y, U, s, Vh, svs=[1])
-    print('\n1 singular value selected...')
-    print('Returns matrix is NOT all 0\'s: {}'.format(_np.allclose(y2,0) == False))
-    print('Return matrix is all based on 1 component: {}'.format(_np.isclose(\
-        _np.median(y2[0,:]/y2[50,:]),y2[0,0]/y2[50,0])))
-
-    print('\nReturned matrix is same shape {} as that entered: {}'.format(y.shape, y.shape == y2.shape))
-
-    y = _np.random.randn(10,10,1600)
-    rng = _np.arange(300,600)
-    svd_decompose = SVDDecompose(rng=rng)
-    svd_recompose = SVDRecompose(rng=rng)
-    U, s, Vh = svd_decompose.calculate(y)
-
-    y2 = svd_recompose.calculate(y, U, s, Vh, svs=[])
-    print('\nReturned matrix is same shape {} as that entered: {}'.format(y.shape, y.shape == y2.shape))
-
-    y = _np.random.randn(10,1000)
-    y_copy = _copy.deepcopy(y)
-
-    [U,s,Vh] = svd_decompose.calculate(y)
-    y2 = svd_recompose.transform(y, U, s, Vh, svs=[])
-    print('\nOverwrite input data...')
-    print('0 singular values selected...')
-    print('Input is NOT same as output: {}'.format(not _np.allclose(y,y_copy)))
-    print('Returns matrix is all 0\'s: {}'.format(_np.allclose(y,0) == True))
-
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/preprocess/standardize.html b/docs/build/html/_modules/crikit/preprocess/standardize.html deleted file mode 100644 index 6dab92e..0000000 --- a/docs/build/html/_modules/crikit/preprocess/standardize.html +++ /dev/null @@ -1,589 +0,0 @@ - - - - - - - - - - - crikit.preprocess.standardize — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
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    • - -
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- -

Source code for crikit.preprocess.standardize

-"""
-Standardization
-
-Created on Thu Apr 14 08:53:08 2016
-
-@author: chc
-"""
-
-__all__ = ['Anscombe', 'AnscombeInverse']
-
-import copy as _copy
-import numpy as _np
-
-from crikit.preprocess.algorithms.anscombe import (gen_anscombe_forward as ansc,
-                                                   gen_anscombe_inverse_exact_unbiased as inv_ansc)
-
-from crikit.utils.datacheck import _rng_is_pix_vec
-
-
[docs]class Anscombe:
-    """
-    Implement the generalized forward Anscombe transformation.
-
-    Signal : :math:`X`
-
-    Mean of Gaussian noise :  :math:`<g>`
-
-    Standard deviation of Gaussian noise :  :math:`\sigma_g`
-
-    Noise of type 'type' : :math:`N_{type}`
-
-    Poisson noise multiplier : :math:`\\alpha`
-
-    Model : :math:`X = \\alpha*N_{Poisson}\{X\} + N_{Gauss}\{<g>, \sigma_g\},`
-
-    Parameters
-    ----------
-    data : ndarray.
-        Signal with mixed Gaussian and Poisson noise to transform.
-
-    gauss_std : float
-        Standard deviation of Gaussian noise. :math:`\sigma_g` in model.
-
-    poisson_multi : float, optional (default=1.0)
-        A multiplier that scales the effect of the Poisson noise. \
-        :math:`\\alpha` in model.
-
-    gauss_mean : float, optional (default=0.0)
-        Mean Gaussian noise level. :math:`<g>` in model.
-
-    rng : ndarray (1D), optional
-        Range of pixels to perform operation over.
-
-    overwrite : bool, optional (default=True)
-
-    Returns
-    -------
-    ndarray
-        Altered data if overwrite is False
-
-    None
-        Return None if overwrite is True
-
-    See Also
-    -----
-    * See the docstring of ./algorithms/anscombe for more information.
-
-    References
-    -----------
-    [1] M. Mäkitalo and A. Foi, "Optimal inversion of the generalized Anscombe \
-        transformation for Poisson-Gaussian noise", IEEE Trans. Image Process., \
-        doi:10.1109/TIP.2012.2202675
-
-    [2] J.L. Starck, F. Murtagh, and A. Bijaoui, Image  Processing  and  Data \
-        Analysis, Cambridge University Press, Cambridge, 1998)
-
-    [3] C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative, \
-        comparable coherent anti-Stokes Raman scattering (CARS) \
-        spectroscopy: Correcting errors in phase retrieval," Journal of Raman \
-        Spectroscopy 47, 408-415 (2016). arXiv:1507.06543.
-    """
-    def __init__(self, gauss_std, gauss_mean=0.0, poisson_multi=1.0, rng=None):
-
-        self.gauss_std = gauss_std
-        self.gauss_mean = gauss_mean
-        self.poisson_multi = poisson_multi
-
-        self.rng = _rng_is_pix_vec(rng)
-
-
[docs]    def _calc(self, data, ret_obj):
-        # Anscombe transform
-        if self.rng is None:
-            self.rng = _np.arange(data.shape[-1])
-            out = ansc(data, gauss_std=self.gauss_std,
-                       gauss_mean=self.gauss_mean,
-                       poisson_multi=self.poisson_multi)
-        else:
-            out = ansc(data[..., self.rng], gauss_std=self.gauss_std,
-                       gauss_mean=self.gauss_mean,
-                       poisson_multi=self.poisson_multi)
-
-        try:
-            ret_obj *= 0
-            ret_obj[..., self.rng] = out
-        except:
-            return False
-        else:
-            return True

-
-
[docs]    def transform(self, data):
-        """
-        Generalized Anscombe transform (Overwrite data).
-
-        Parameters
-        ----------
-        data : ndarray
-            Input data.
-
-        Returns
-        -------
-        bool
-            Returns the success state (True=success)
-
-        """
-        success = self._calc(data, ret_obj=data)
-        return success

-
-
[docs]    def calculate(self, data):
-        """
-        Generalized Anscombe transform (Return copy).
-
-        Parameters
-        ----------
-        data : ndarray
-            Input data.
-
-        Returns
-        -------
-        ndarray
-            Returns Anscombe-transformed data (or None if fails)
-
-        """
-        data_copy = _copy.deepcopy(data)
-        success = self._calc(data, ret_obj=data_copy)
-        if success:
-            return data_copy
-        else:
-            return None

-
-
-
[docs]class AnscombeInverse:
-    """
-    Applies an exact, unbiased inverse of the generalized Anscombe \
-    variance-stabilizing transformation assuming a mixed Poisson-Gaussian \
-    noise model as:
-
-
-    Signal : :math:`X`
-
-    Mean of Gaussian noise :  :math:`<g>`
-
-    Standard deviation of Gaussian noise :  :math:`\sigma_g`
-
-    Noise of type 'type' : :math:`N_{type}`
-
-    Poisson noise multiplier : :math:`\\alpha`
-
-    Model : :math:`X = \\alpha*N_{Poisson}\{X\} + N_{Gauss}\{<g>, \sigma_g\},`
-
-    Parameters
-    ----------
-    data : Spectrum (or subclass) object or ndarray.
-        Signal with mixed Gaussian and Poisson noise to transform.
-
-    gauss_std : float
-        Standard deviation of Gaussian noise. :math:`\sigma_g` in model.
-
-    poisson_multi : float, optional (default=1.0)
-        A multiplier that scales the effect of the Poisson noise. \
-        :math:`\\alpha` in model.
-
-    gauss_mean : float, optional (default=0.0)
-        Mean Gaussian noise level. :math:`<g>` in model.
-
-    rng : ndarray (1D), optional
-        Range of pixels to perform operation over.
-
-    overwrite : bool, optional (default=True)
-
-    See Also
-    -----
-    * See the docstring of ./algorithms/anscombe for more information.
-
-    References
-    ----------
-    [1] M. Mäkitalo and A. Foi, "Optimal inversion of the generalized Anscombe \
-        transformation for Poisson-Gaussian noise", IEEE Trans. Image Process., \
-        doi:10.1109/TIP.2012.2202675
-
-    [2] J.L. Starck, F. Murtagh, and A. Bijaoui, Image  Processing  and  Data \
-        Analysis, Cambridge University Press, Cambridge, 1998)
-
-    [3] C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative, \
-        comparable coherent anti-Stokes Raman scattering (CARS) \
-        spectroscopy: Correcting errors in phase retrieval," Journal of Raman \
-        Spectroscopy 47, 408-415 (2016). arXiv:1507.06543.
-    """
-
-    def __init__(self, gauss_std, gauss_mean=0.0, poisson_multi=1.0, rng=None):
-        self.gauss_std = gauss_std
-        self.gauss_mean = gauss_mean
-        self.poisson_multi = poisson_multi
-
-        self.rng = _rng_is_pix_vec(rng)
-
-
[docs]    def _calc(self, data, ret_obj):
-
-        # Inverse Anscombe transform
-        if self.rng is None:
-            self.rng = _np.arange(data.shape[-1])
-            out = inv_ansc(data, gauss_std=self.gauss_std,
-                       gauss_mean=self.gauss_mean,
-                       poisson_multi=self.poisson_multi)
-        else:
-            out = inv_ansc(data[..., self.rng], gauss_std=self.gauss_std,
-                       gauss_mean=self.gauss_mean,
-                       poisson_multi=self.poisson_multi)
-
-        try:
-            ret_obj *= 0
-            ret_obj[..., self.rng] = out
-        except:
-            return False
-        else:
-            return True

-
-
[docs]    def transform(self, data):
-        """
-        Generalized Inverse Anscombe transform (Overwrite data).
-
-        Parameters
-        ----------
-        data : ndarray
-            Input data.
-
-        Returns
-        -------
-        bool
-            Returns the success state (True=success)
-
-        """
-        success = self._calc(data, ret_obj=data)
-        return success

-
-
[docs]    def calculate(self, data):
-        """
-        Generalized Inverse Anscombe transform (Return copy).
-
-        Parameters
-        ----------
-        data : ndarray
-            Input data.
-
-        Returns
-        -------
-        ndarray
-            Returns Anscombe-transformed data (or None if fails)
-
-        """
-        data_copy = _copy.deepcopy(data)
-        success = self._calc(data, ret_obj=data_copy)
-        if success:
-            return data_copy
-        else:
-            return None

-
-if __name__ == '__main__': # pragma: no cover
-
-    from crikit.data.spectrum import Spectrum as _Spectrum
-
-    stddev = 20
-    gain = 1
-
-    f = _np.linspace(500,4000,1000)
-    sig = 10e4*_np.exp(-(f-2000)**2/(500**2))
-
-    gnoise = stddev*_np.random.randn(f.size)
-
-    sig_mix = _np.random.poisson(sig) + gnoise
-
-    import matplotlib.pyplot as _plt
-
-    anscombe = Anscombe(gauss_std=stddev, gauss_mean=0, poisson_multi=gain)
-
-    sig2 = _Spectrum(sig)
-
-    out = anscombe.calculate(sig2.data)
-    _plt.subplot(211)
-    _plt.plot(sig2.data, label='Data')
-    _plt.title('Untransformed Space')
-    _plt.legend(loc='best')
-
-    _plt.subplot(212)
-    _plt.plot(out, label='Calculate')
-
-    out2 = anscombe.transform(sig2.data)
-    _plt.plot(sig2.data, label='Transform')
-    _plt.legend(loc='best')
-    _plt.title('Anscombe Transform')
-    _plt.show()
-
-    print('Transform and Calculate Equivalent: {}'.format(_np.allclose(out,
-          sig2.data)))
-
-    inverse_anscombe = AnscombeInverse(gauss_std=stddev, gauss_mean=0,
-                                       poisson_multi=gain)
-
-    sig2 = _Spectrum(sig)
-    sig2_ansc = anscombe.calculate(sig2.data)
-
-    out = inverse_anscombe.calculate(sig2_ansc)
-    _plt.subplot(211)
-    _plt.plot(sig2.data, label='Data')
-    _plt.plot(out, label='Calculate')
-    _plt.title('Untransformed Space/Inverse Anscombe')
-
-    _plt.legend(loc='best')
-
-    _plt.subplot(212)
-    _plt.plot(sig2_ansc, label='Anscombe')
-
-
-    _plt.legend(loc='best')
-    _plt.title('Anscombe Transform')
-    _plt.show()
-
-#    print('Data and Inverse of Anscombe Close: {}'.format(_np.allclose(out,
-#          sig2.data)))
-
-    _plt.figure()
-    _plt.plot(out-sig2.data)
-    _plt.title('Inverse Anscombe - Original Data')
-    _plt.show()
-#
-#    print((out-sig2.data)[0])
-
-#    # Recalc sig
-#    sig = 10e4*_np.exp(-(f-2000)**2/(500**2))
-#
-#    _plt.figure()
-#    sig_ansc = anscombe(sig.data, gauss_std=stddev, poisson_multi=gain, overwrite=False)
-#    out = anscombe_inverse(sig_ansc, gauss_std=stddev, poisson_multi=gain, overwrite=False)
-#    _plt.plot(sig)
-#    _plt.plot(out)
-#    anscombe_inverse(sig_ansc, gauss_std=stddev, poisson_multi=gain, overwrite=True)
-#    _plt.plot(sig_ansc)
-#    _plt.show()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/preprocess/subtract_baseline.html b/docs/build/html/_modules/crikit/preprocess/subtract_baseline.html deleted file mode 100644 index 3256118..0000000 --- a/docs/build/html/_modules/crikit/preprocess/subtract_baseline.html +++ /dev/null @@ -1,387 +0,0 @@ - - - - - - - - - - - crikit.preprocess.subtract_baseline — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.preprocess.subtract_baseline
    • - - -
  • - - - -
    • - -
- - -
-
-
-
- -

Source code for crikit.preprocess.subtract_baseline

-"""
-
-Subtract baseline
-
-Created on Sat May 28 00:41:41 2016
-
-@author: chc
-"""
-
-import copy as _copy
-
-import numpy as _np
-
-from crikit.preprocess.algorithms.als import (AlsCvxopt as _AlsCvxopt)
-
-from crikit.utils.datacheck import _rng_is_pix_vec
-
-
-
[docs]class SubtractBaselineALS:
-    """
-    Subtract baseline using asymmetric least squares algorithm
-    
-    Parameters
-    ----------
-    smoothness_param : float, optional (default=1.0)
-        Smoothness parameter aka 'lambda'
-        
-    asym_param : float, optional (default=1e-2)
-        Asymmetry parameter aka 'p'
-        
-    redux_factor : int, optional (default=10)
-        Down-sampling factor (more down-sampling leads to faster detrending,
-        but with more chance of non-optimal detrending)
-        
-    rng : ndarray (1D), optional (default=None)
-        Range in pixels to perform action over
-    
-    use_imag : bool, optional (default=True)
-        If spectrum(a) are complex-values, use the imaginary portion?
-    """
-    def __init__(self, smoothness_param=1, asym_param=1e-2,
-                 redux=10, order=2, rng=None, fix_end_points=False, 
-                 max_iter=100, min_diff=1e-5, use_imag=True, 
-                 **kwargs):
-
-        self.rng = _rng_is_pix_vec(rng)
-        self._k = kwargs
-        
-        self._k.update({'smoothness_param' : smoothness_param, 
-                        'asym_param' : asym_param,
-                        'redux' : redux,
-                        'order' : order,
-                        'fix_end_points' : fix_end_points,
-                        'max_iter' : max_iter,
-                        'min_diff' : min_diff})
-        
-        self.use_imag = use_imag
-        
-
[docs]    def _calc(self, data, ret_obj, **kwargs):
-        
-        self._inst_als = _AlsCvxopt(**kwargs)
-        
-        try:
-            # Get the subarray shape
-            shp = data.shape[0:-2]
-            total_num = _np.array(shp).prod()
-   
-            # Iterate over the sub-array -- super slick way of doing it
-            for num, idx in enumerate(_np.ndindex(shp)):
-                print('Detrended iteration {} / {}'.format(num+1, total_num))
-                # Imaginary portion set
-                if self.use_imag and _np.iscomplexobj(data):
-                    if self.rng is None:
-                        ret_obj[idx] -= 1j*self._inst_als.calculate(data[idx].imag)
-                    else:
-                        ret_obj[idx][..., self.rng] -= 1j*self._inst_als.calculate(data[idx][..., self.rng].imag)
-                else:  # Real portion set or real object
-                    if self.rng is None:
-                        ret_obj[idx] -= self._inst_als.calculate(data[idx].real)
-                    else:
-                        ret_obj[idx][..., self.rng] -= self._inst_als.calculate(data[idx][..., self.rng].real)
-        except:
-            return False
-        else:
-#            print(self._inst_als.__dict__)
-            return True

-
-
[docs]    def transform(self, data, **kwargs):
-        self._k.update(kwargs)
-        
-        success = self._calc(data, ret_obj=data, **self._k)
-        return success

-
-
[docs]    def calculate(self, data, **kwargs):
-
-        data_copy = _copy.deepcopy(data)
-        self._k.update(kwargs)
-        
-        success = self._calc(data, ret_obj=data_copy, **self._k)
-        if success:
-            return data_copy
-        else:
-            return None

-
-
-if __name__ == '__main__':
-
-    from crikit.data.spectrum import Spectrum as _Spectrum
-    from crikit.data.spectra import Spectra as _Spectra
-    from crikit.data.hsi import Hsi as _Hsi
-
-    import matplotlib.pyplot as _plt
-    sp = _Spectrum()
-    sp.data = _np.exp(-(_np.arange(1000)-500)**2/100**2)
-
-    sub_baseline_als = SubtractBaselineALS(smoothness_param=1, asym_param=1e-1)
-
-    _plt.plot(sp.data, label='Original')
-    out = sub_baseline_als.transform(sp.data)
-    _plt.plot(sp.data, label='Detrended')
-    _plt.title('Spectrum')
-    _plt.legend(loc='best')
-    _plt.show()
-
-    sp.data = _np.exp(-(_np.arange(1000)-500)**2/100**2)
-    _plt.plot(sp.data, label='Original')
-    sub_baseline_als.redux_factor = 10
-    out = sub_baseline_als.transform(sp.data)
-    _plt.plot(sp.data, label='Detrended (Redux)')
-    _plt.title('Spectrum')
-    _plt.legend(loc='best')
-    _plt.show()
-#
-    spa = _Spectra()
-    sub_baseline_als = SubtractBaselineALS(smoothness_param=1e2, asym_param=1e-4)
-    spa.data = _np.dot(_np.ones((2,1)),_np.exp(-(_np.arange(1000)-500)**2/100**2)[None,:])
-    _plt.plot(spa.data.T, label='Original')
-    out = sub_baseline_als.transform(spa.data)
-    _plt.plot(spa.data.T, label='Detrended')
-    _plt.title('Spectra')
-    _plt.legend(loc='upper right')
-    _plt.show()
-
-    hsi = _Hsi()
-    sub_baseline_als.redux_factor = 10
-    hsi.data = _np.dot(_np.ones((1,1,1)),_np.exp(-(_np.arange(1000)-500)**2/100**2)[None,:])
-
-    _plt.plot(hsi.data.reshape((-1,1000)).T, label='Original')
-    out = sub_baseline_als.calculate(hsi.data)
-    _plt.plot(out.reshape((-1,1000)).T, label='Detrended (Redux)')
-    _plt.plot(hsi.data.reshape((-1,1000)).T, label='Original (No Overwrite)')
-    _plt.title('HSI')
-    _plt.legend(loc='upper right')
-    _plt.show()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/preprocess/subtract_dark.html b/docs/build/html/_modules/crikit/preprocess/subtract_dark.html deleted file mode 100644 index 7aef6fb..0000000 --- a/docs/build/html/_modules/crikit/preprocess/subtract_dark.html +++ /dev/null @@ -1,372 +0,0 @@ - - - - - - - - - - - crikit.preprocess.subtract_dark — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.preprocess.subtract_dark
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Source code for crikit.preprocess.subtract_dark

-"""
-Subtract mean value (optionally, over a range from all spectrum/spectra/hsi)
-
-Created on Thu May 26 14:31:39 2016
-
-@author: chc
-"""
-
-import numpy as _np
-import copy as _copy
-
-from crikit.data.spectrum import Spectrum as _Spectrum
-from crikit.data.spectra import Spectra as _Spectra
-from crikit.data.hsi import Hsi as _Hsi
-
-from crikit.utils.general import (expand_1d_to_ndim as _expand_1d_to_ndim,
-                                  mean_nd_to_1d as _mean_nd_to_1d)
-
-
[docs]class SubtractDark:
-    def __init__(self, dark):
-        self.dark = dark
-
-
[docs]    def transform(self, data):
-        """
-        Subtract dark spectrum (overwrite original data).
-
-
-        Parameters
-        ----------
-        data : ndarray
-            Data from which dark is subtracted.
-
-        Returns
-        -------
-        bool
-            Returns the success state (True=success)
-
-        """
-        success = self._calc(data, ret_obj=data)
-        return success

-
-
-
[docs]    def calculate(self, data):
-        """
-        Subtract dark spectrum (return copy).
-
-        Parameters
-        ----------
-        data : ndarray
-            Data from which dark is subtracted.
-
-        Returns
-        -------
-        ndarray
-            Returns data with dark subtracted (or None if fails)
-
-        """
-        data_copy = _copy.deepcopy(data)
-        success = self._calc(data, ret_obj=data_copy)
-        if success:
-            return data_copy
-        else:
-            return None

-
-
[docs]    def _calc(self, data, ret_obj):
-        # Assume that an nD dark should be averaged to be 1D
-        self.dark = _mean_nd_to_1d(self.dark, axis=-1)
-
-        # Expand dark dimensionality to match data.ndim
-        self.dark = _expand_1d_to_ndim(self.dark, data.ndim)
-
-        try:
-            ret_obj -= self.dark
-        except:
-            return False
-        else:
-            return True

-
-if __name__ == '__main__': # pragma: no cover
-
-    x = _np.linspace(0,100,10)
-    y = _np.linspace(0,100,10)
-    freq = _np.arange(20)
-    data = _np.ones((10,10,20))
-
-    # OVERWRITE TEST
-    hs = _Hsi(data=_copy.deepcopy(data), freq=freq, x=x, y=y)
-    spa = _Spectra(data=_copy.deepcopy(data)[0,:,:], freq=freq)
-    sp = _Spectrum(data=_copy.deepcopy(data)[0,0,:], freq=freq)
-
-    dark=0.5 * _copy.deepcopy(data)
-    dark_sub = SubtractDark(dark)
-
-    print('\n---------TRANSFORM TEST----------\n')
-    print('\n3D----------')
-    print('Initial mean: {}'.format(hs.data.mean()))
-    out = dark_sub.transform(hs.data)
-    print('Success?: {}'.format(out))
-    print('Final mean: {}\n'.format(hs.data.mean()))
-
-    print('2D----------')
-    print('Initial mean: {}'.format(spa.data.mean()))
-    out = dark_sub.transform(spa.data)
-    print('Success?: {}'.format(out))
-    print('Final mean: {}\n'.format(spa.data.mean()))
-
-    print('1D----------')
-    print('Initial mean: {}'.format(sp.data.mean()))
-    out = dark_sub.transform(sp.data)
-    print('Success?: {}'.format(out))
-    print('Final mean: {}'.format(sp.data.mean()))
-
-    # NOT-OVERWRITE TEST
-    print('\n---------CALCULATE TEST----------\n')
-
-    hs = _Hsi(data=_copy.deepcopy(data), freq=freq, x=x, y=y)
-    spa = _Spectra(data=_copy.deepcopy(data)[0,:,:], freq=freq)
-    sp = _Spectrum(data=_copy.deepcopy(data)[0,0,:], freq=freq)
-
-    dark=0.5 * _copy.deepcopy(data)
-    dark_sub = SubtractDark(dark)
-
-    print('\n3D----------')
-    print('Initial Data Mean: {}'.format(hs.data.mean()))
-    out = dark_sub.calculate(hs.data)
-    print('Returned Mean: {}'.format(out.mean()))
-    print('Final Data Mean: {}'.format(hs.data.mean()))
-
-    print('2D----------')
-    print('Initial Data Mean: {}'.format(spa.data.mean()))
-    out = dark_sub.calculate(spa.data)
-    print('Returned Mean: {}'.format(out.mean()))
-    print('Final Data Mean: {}'.format(spa.data.mean()))
-
-    print('1D----------')
-    print('Initial Data Mean: {}'.format(sp.data.mean()))
-    out = dark_sub.calculate(sp.data)
-    print('Returned Mean: {}'.format(out.mean()))
-    print('Final Data Mean: {}'.format(sp.data.mean()))
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/preprocess/subtract_mean.html b/docs/build/html/_modules/crikit/preprocess/subtract_mean.html deleted file mode 100644 index f11d665..0000000 --- a/docs/build/html/_modules/crikit/preprocess/subtract_mean.html +++ /dev/null @@ -1,372 +0,0 @@ - - - - - - - - - - - crikit.preprocess.subtract_mean — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.preprocess.subtract_mean

-"""
-Subtract mean value (optionally, over a range from all spectrum/spectra/hsi)
-
-Created on Thu May 26 14:31:39 2016
-
-@author: chc
-"""
-import copy as _copy
-import numpy as _np
-
-from crikit.utils.general import find_nearest as _find_nearest
-from crikit.utils.datacheck import _rng_is_pix_vec
-
-
-
[docs]class SubtractMeanOverRange:
-    def __init__(self, rng=None):
-        self.rng = _rng_is_pix_vec(rng)
-
-
-
[docs]    def _calc(self, data, ret_obj):
-        if self.rng is None:
-            meaner = data.mean(axis=-1)
-        else:
-            meaner = data[..., self.rng].mean(axis=-1)
-
-        try:
-            ret_obj -= meaner[..., None]
-        except:
-            return False
-        else:
-            return True

-
-
-
[docs]    def transform(self, data):
-        """
-        Subtract the mean intensity over a pixel range (rng). \
-        (Overwrite data).
-
-        Parameters
-        ----------
-        data : ndarray
-            Input data.
-
-        Returns
-        -------
-        bool
-            Returns the success state (True=success)
-
-        """
-        success = self._calc(data, ret_obj=data)
-        return success

-
-
[docs]    def calculate(self, data):
-        """
-        Subtract the mean intensity over a pixel range (rng). \
-        (Return copy).
-
-        Parameters
-        ----------
-        data : ndarray
-            Input data.
-
-        Returns
-        -------
-        ndarray
-            Returns data with mean subtracted (or None if fails)
-
-        """
-        data_copy = _copy.deepcopy(data)
-        success = self._calc(data, ret_obj=data_copy)
-        if success:
-            return data_copy
-        else:
-            return None

-
-if __name__ == '__main__':  # pragma: no cover
-
-    from crikit.data.spectrum import Spectrum as _Spectrum
-    from crikit.data.spectra import Spectra as _Spectra
-    from crikit.data.hsi import Hsi as _Hsi
-
-    
-
-    x = _np.linspace(0, 100, 10)
-    y = _np.linspace(0, 100, 10)
-    freq = _np.arange(20)
-    data = _np.ones((10, 10, 20))
-
-    hs = _Hsi(data=_copy.deepcopy(data), freq=freq, x=x, y=y)
-    spa = _Spectra(data=_copy.deepcopy(data), freq=freq)
-    sp = _Spectrum(data=_copy.deepcopy(data)[0, 0, :], freq=freq)
-
-    mean_sub = SubtractMeanOverRange([5, 8])
-
-    print('\n---------TRANSFORM TEST----------\n')
-    print('\n3D----------')
-    print('Initial mean: {}'.format(hs.data.mean()))
-    out = mean_sub.transform(hs.data)
-    print('Success?: {}'.format(out))
-    print('Final mean: {}\n'.format(hs.data.mean()))
-
-    print('2D----------')
-    print('Initial mean: {}'.format(spa.data.mean()))
-    out = mean_sub.transform(spa.data)
-    print('Success?: {}'.format(out))
-    print('Final mean: {}\n'.format(spa.data.mean()))
-
-    print('1D----------')
-    print('Initial mean: {}'.format(sp.data.mean()))
-    out = mean_sub.transform(sp.data)
-    print('Success?: {}'.format(out))
-    print('Final mean: {}'.format(sp.data.mean()))
-
-    # NOT-OVERWRITE TEST
-    print('\n---------CALCULATE TEST----------\n')
-
-    hs = _Hsi(data=_copy.deepcopy(data), freq=freq, x=x, y=y)
-    spa = _Spectra(data=_copy.deepcopy(data)[0, :, :], freq=freq)
-    sp = _Spectrum(data=_copy.deepcopy(data)[0, 0, :], freq=freq)
-
-    mean_sub = SubtractMeanOverRange([5, 8])
-
-    print('\n3D----------')
-    print('Initial Data Mean: {}'.format(hs.data.mean()))
-    out = mean_sub.calculate(hs.data)
-    print('Returned Mean: {}'.format(out.mean()))
-    print('Final Data Mean: {}'.format(hs.data.mean()))
-
-    print('2D----------')
-    print('Initial Data Mean: {}'.format(spa.data.mean()))
-    out = mean_sub.calculate(spa.data)
-    print('Returned Mean: {}'.format(out.mean()))
-    print('Final Data Mean: {}'.format(spa.data.mean()))
-
-    print('1D----------')
-    print('Initial Data Mean: {}'.format(sp.data.mean()))
-    out = mean_sub.calculate(sp.data)
-    print('Returned Mean: {}'.format(out.mean()))
-    print('Final Data Mean: {}'.format(sp.data.mean()))
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/classes_ui.html b/docs/build/html/_modules/crikit/ui/classes_ui.html deleted file mode 100644 index 5f7126c..0000000 --- a/docs/build/html/_modules/crikit/ui/classes_ui.html +++ /dev/null @@ -1,655 +0,0 @@ - - - - - - - - - - - crikit.ui.classes_ui — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.ui.classes_ui

-"""
-User Interface and Visualization Classes (crikit.ui.classes_ui)
-===============================================================
-
-BW : Grayscale images
-
-SingleColor : Single-color images
-
-_ColorMath : Container of math operations
-
-"""
-
-import numpy as _np
-import copy as _copy
-import matplotlib as _mpl
-
-
[docs]class BW:
-    """
-
-    """
-    
-    def __init__(self, **kwargs):
-        self._default_attributes = {
-            'title':None,
-            'setflag':0,
-            'setmax':None,
-            'setmin':None,
-            'compress_low':None,
-            'compress_high':None,
-            'setgain':1,
-            'xunits':'Pixels',
-            'yunits':'Pixels'
-        }
-        self._default_attributes.update(kwargs)
-
-        self._grayscaleimage = None
-        self.title = self._default_attributes['title']
-        self.setflag = self._default_attributes['setflag']
-        self.setmax = self._default_attributes['setmax']
-        self.setmin = self._default_attributes['setmin']
-        self.compress_high = self._default_attributes['compress_high']
-        self.compress_low = self._default_attributes['compress_low']
-        self.setgain = self._default_attributes['setgain']
-        self.xunits = self._default_attributes['xunits']
-        self.yunits = self._default_attributes['yunits']
-        self._x = None
-        self._y = None
-
-    @property
-    def image(self):
-        """
-        For image from property settings (limits, compression, etc)
-        """    
-        img = self.grayscaleimage
-
-        if (self.setmax is None or self.setmin is None):
-            return img*self.setgain
-        else:
-            mask_pass = (img >= self.setmin)*(img <= self.setmax)
-            mask_low = (img < self.setmin)
-            mask_high = (img > self.setmax)
-            img = (mask_pass*img + self.compress_low*mask_low*self.setmin + 
-                    self.compress_high*mask_high*self.setmax)
-            return img*self.setgain
-
-    @property
-    def winextent(self):
-        return (self.x.min(), self.x.max(), self.y.min(), self.y.max())
-
-    @property
-    def maxer(self):
-        return self.grayscaleimage.max()
-
-    @property
-    def minner(self):
-        return self.grayscaleimage.min()
-
-    @property
-    def std(self):
-        try:
-            temp = self.grayscaleimage.std()
-            return temp
-        except:
-            return None
-
-    @property
-    def mean(self):
-        try:
-            temp = self.grayscaleimage.mean()
-            return temp
-        except:
-            return None
-
-    @property
-    def ylen(self):
-        return self._grayscaleimage.shape[0]
-
-    @property
-    def xlen(self):
-        return self._grayscaleimage.shape[1]
-
-    @property
-    def grayscaleimage(self):
-        return self._grayscaleimage
-
-    @grayscaleimage.setter
-    def grayscaleimage(self, value):
-        try:
-            if value.ndim == 2:
-                self._grayscaleimage = value
-                if (_np.equal(self._x,None).any() or
-                    _np.equal(self._y,None).any() or
-                    self._x.size != value.shape[1] or
-                    self._y.size != value.shape[0]):
-
-                    self._x = _np.linspace(1, value.shape[1], value.shape[1])
-                    self._y = _np.linspace(1, value.shape[0], value.shape[0])
-                    
-
-                else:
-                    pass
-        except:
-            print('Set grayscaleimage error')
-
-    @grayscaleimage.deleter
-    def grayscaleimage(self):
-        self.__init__()
-
-    @property
-    def x(self):
-        if self._x is not None:
-            return self._x
-        else:
-            self._x = _np.arange(self.xlen)
-            self.xunits = self._default_attributes['xunits']
-            return self._x
-
-    @x.deleter
-    def x(self):
-        self._x = _np.linspace(1, self.xlen, self.xlen)
-        self.xunits = self.XUNITS
-
-    @property
-    def y(self):
-        if self._y is not None:
-            return self._y
-        else:
-            self._y = _np.arange(self.ylen)
-            self.yunits = self._default_attributes['yunits']
-            return self._y
-
-    @y.deleter
-    def y(self):
-        self._y = _np.linspace(1, self.ylen, self.ylen)
-        self.yunits = self.YUNITS
-
-
[docs]    def set_x(self, value, units = None):
-        if value is None:
-            pass
-        else:
-            if self.xlen == value.size:
-                self._x = value
-                if units is not None:
-                    self.xunits = units
-            else:
-                pass

-
-
[docs]    def set_y(self, value, units = None):
-        if value is None:
-            pass
-        else:
-            if self.ylen == value.size:
-                self._y = value
-                if units is not None:
-                    self.yunits = units
-            else:
-                pass

-
-
-
[docs]class _ColorMath:
-
-    opfreq1 = None
-    opfreq2 = None
-    opfreq3 = None
-
-    operation = None
-
-    condfreq1 = None
-    condfreq2 = None
-    condfreq3 = None
-
-    condoperation = None
-    inequality = None
-    inequalityval = None
-
-    def __init__(self):
-        pass

-
-
[docs]class CompositeColor(BW):
-    """
-
-    """
-    def __init__(self, sgl_color_list = None):
-        BW.__init__(self)
-        self.bgcolor = [0,0,0]
-        self.mode = 0  # 0: emission; 1: absorption
-
-        if sgl_color_list is None:
-            self.sgl_color_list = []
-        else:
-            self.sgl_color_list = sgl_color_list
-
-    @property
-    def mode_txt(self):
-        if self.mode == 0:
-            return 'Emission'
-        else:
-            return 'Absorption'
-        
-    @property
-    def image(self):
-        #print(self.sgl_color_list)
-        if len(self.sgl_color_list) == 0:
-            return _np.zeros(self.grayscaleimage.shape)
-        else:
-            if self.mode == 0:  # Emission
-                img_emission = _np.zeros(self.sgl_color_list[0].image.shape)
-            
-                list_imgs = _copy.deepcopy(self.sgl_color_list)
-            
-                for img in list_imgs:
-                    img.bgcolor = [0,0,0]
-                    img_emission += img.image
-                img_emission[img_emission>1] = 1
-                return img_emission
-            elif self.mode == 1:  # Absorption
-                img_absorption = _np.zeros(self.sgl_color_list[0].image.shape)
-                img_frac_coverage = _np.zeros(self.sgl_color_list[0].grayscaleimage.shape)
-                img_num_covered = _np.zeros(self.sgl_color_list[0].grayscaleimage.shape)
-
-                list_imgs = _copy.deepcopy(self.sgl_color_list)
-                
-                for img in list_imgs:
-                    if (img.grayscaleimage.nonzero()[0].size == 0) | (img.setgain == 0.0):
-                        pass
-                    else:
-                        img.bgcolor = [0,0,0]
-
-                        temp = 1*img.imageGS
-                        temp -= temp.min()
-                        if temp.max() != 0:
-                            temp /= temp.max()
-
-                        img_absorption += temp[:,:,None]*img.colormap
-                        img_frac_coverage += temp
-                        img_num_covered += (temp > 0)
-                img_frac_coverage[img_frac_coverage>1] = 1
-                img_absorb_bg = (1-img_frac_coverage)[:,:,None]*[1,1,1]
-                img_absorb_bg[img_absorb_bg<0] = 0
-                img_absorption /= (img_num_covered+1e-10)[:,:,None]
-                img_absorption += img_absorb_bg
-                return img_absorption
-            elif self.mode == 2: # Absorption version 2
-                
-                img_emission = _np.zeros(self.sgl_color_list[0].image.shape)
-                list_imgs = _copy.deepcopy(self.sgl_color_list)
-            
-                # Start with emission image BUT white background
-                # This addition will BRIGHTEN as well
-                # thus needs contrast enhancement later
-                num = 0
-                for img in list_imgs:
-                    img.bgcolor = [1,1,1]
-                    temp = img.image
-                    if (temp.max() != temp.min()) & (img.setgain != 0.0):
-                        img_emission += temp
-                        num += 1
-
-                # Average
-                if num != 0:
-                    img_emission /= num
-                    
-                    # This enhances contrast
-                    # Yes, the first step cancels out the step above
-                    # but this keep the norm. and contrast steps separate
-                    img_emission *= num
-                    img_emission -= (num-1)
-
-                img_emission[img_emission<0] = 0
-                img_emission[img_emission>1] = 1
-                
-                return img_emission
-
-    @property
-    def ylen(self):
-        return self.sgl_color_list[0].image.shape[0]
-#        return self.grayscaleimage.shape[0]
-
-    @property
-    def xlen(self):
-        return self.sgl_color_list[0].image.shape[1]

-#        return self.grayscaleimage.shape[1]
-
-
[docs]class SingleColor(BW, _ColorMath):
-    """
-
-    """
-    
-    def __init__(self):
-        BW.__init__(self)
-        self.bgcolor = [0,0,0]
-        self.colormap = [1,0,0]
-
-    def __add__(self, other):
-        return self.image + other.image
-
-    @property
-    def image(self):
-        
-        if (self.setmax is None or self.setmin is None):
-            scaled_gs = SingleColor._imgnorm(self.grayscaleimage)
-            scaled_gain_gs = scaled_gs*self.setgain
-            final_scaled_gs = SingleColor._imgnormcompress(scaled_gain_gs)
-            return SingleColor._bwtocolor(final_scaled_gs, self.colormap, self.bgcolor)
-
-        else:
-            fudge_factor = .001
-            fudge_amt = _np.abs((self.setmax - self.setmin)*fudge_factor)
-            fudged_min = self.setmin - fudge_amt
-            fudged_max = self.setmax + fudge_amt
-            
-            # if self.compress == True:
-            mask_pass = (self.grayscaleimage >= fudged_min) * \
-                        (self.grayscaleimage <= fudged_max)
-            mask_low = (self.grayscaleimage < fudged_min)
-            mask_high = (self.grayscaleimage > fudged_max)
-            masked_img = mask_pass*self.grayscaleimage + \
-                            self.compress_low*mask_low*fudged_min + \
-                            self.compress_high*mask_high*fudged_max
-
-            scaled_gs = SingleColor._imgnorm(masked_img)
-            scaled_gain_gs = scaled_gs*self.setgain
-            final_scaled_gs = SingleColor._imgnormcompress(scaled_gain_gs)
-            return SingleColor._bwtocolor(final_scaled_gs, self.colormap, self.bgcolor)
-
-            # else:
-            #     mask = (self.grayscaleimage >= fudged_min) * \
-            #            (self.grayscaleimage <= fudged_max)
-            #     masked_img = self.grayscaleimage*mask
-
-            #     scaled_gs = SingleColor._imgnorm(masked_img)
-            #     scaled_gain_gs = scaled_gs*self.setgain
-            #     final_scaled_gs = SingleColor._imgnormcompress(scaled_gain_gs)
-            #     return SingleColor._bwtocolor(final_scaled_gs, self.colormap)
-
-    @property
-    def imageGS(self):
-        """
-        Returns self.grayscaleimage with limits applied
-        """
-        if (self.setmax is None or self.setmin is None):
-            return self.grayscaleimage
-
-        else:
-            # if self.compress == True:
-            mask_pass = (self.grayscaleimage >= self.setmin)*(self.grayscaleimage <= self.setmax)
-            mask_low = (self.grayscaleimage < self.setmin)
-            mask_high = (self.grayscaleimage > self.setmax)
-            masked_img = (mask_pass*self.grayscaleimage + self.compress_low*mask_low*self.setmin +
-                          self.compress_high*mask_high*self.setmax)
-
-            return masked_img
-
-            # else:
-            #     mask = (self.grayscaleimage >= self.setmin)*(self.grayscaleimage <= self.setmax)
-            #     masked_img = self.grayscaleimage*mask
-
-            #     return masked_img
-
-
[docs]    @staticmethod
-    def _imgnorm(img, low = None, high = None):
-        """
-        Normalize intensity (B&W) image. Values at
-        low -> 0
-        high -> 1
-
-        """
-
-        # If now provided low or high values, set to min() and max()
-        if low is None:
-            low = img.min()
-        if high is None:
-            high = img.max()
-
-        # Ensure high and low values are different
-        if high == low:
-            return 0*img  # Return 0's, if same
-        else:
-            return (img - low)/(high - low)

-
-
[docs]    @staticmethod
-    def _imgnormcompress(img):
-        """
-        Compress normalized image. Values:
-        > 1 -> 1
-        < 0 -> 0
-        """
-        mask_pass = (img <= 1)*(img >= 0)
-        mask_high = (img > 1)
-
-        return mask_pass*img + mask_high

-
-
[docs]    @staticmethod
-    def _bwtocolor(gs, colormap, bgcolor=[0,0,0]):
-        """
-        Convert normalized [0,1] B&W image (gs) to color, applying a
-        3-value list colormap (colormap)
-        """
-        # img = _np.ones((gs.shape[0], gs.shape[1], 3))
-        # gs_3d = _np.dot(gs[:,:,None],_np.ones((1,3)))
-        # return (img*colormap)*gs_3d
-        return (1-gs[:,:,None])*bgcolor + gs[:,:,None]*colormap

-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/dialog_AbstractFactorization.html b/docs/build/html/_modules/crikit/ui/dialog_AbstractFactorization.html deleted file mode 100644 index aedad7e..0000000 --- a/docs/build/html/_modules/crikit/ui/dialog_AbstractFactorization.html +++ /dev/null @@ -1,548 +0,0 @@ - - - - - - - - - - - crikit.ui.dialog_AbstractFactorization — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
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Source code for crikit.ui.dialog_AbstractFactorization

-"""
-Abstract Factorization Class
-
-Created on Mon Jul 25 10:44:03 2016
-
-@author: chc
-"""
-
-import sys as _sys
-import numpy as _np
-
-from PyQt5 import QtWidgets as _QtWidgets
-from PyQt5.QtWidgets import (QApplication as _QApplication,
-                             QDialog as _QDialog)
-import PyQt5.QtCore as _QtCore
-
-# Import from Designer-based GUI
-from crikit.ui.qt_Factorization import Ui_Dialog ### EDIT ###
-
-# Generic imports for MPL-incorporation
-import matplotlib as _mpl
-
-
-from sciplot.ui.widget_mpl import MplCanvas as _MplCanvas
-
-_mpl.use('Qt5Agg')
-_mpl.rcParams['font.family'] = 'sans-serif'
-_mpl.rcParams['font.size'] = 12
-
-
[docs]class DialogAbstractFactorization(_QDialog):
-    """
-    SubUiSVD : SVD SubUI
-    """
-    def __init__(self, parent=None):
-        super(DialogAbstractFactorization, self).__init__(parent=parent)
-
-##    def __init__(self, parent=None):
-#        raise NotImplementedError('This is an abstract class.')
-##        super(DialogAbstractFactorization, self).__init__(parent=parent) ### EDIT ###
-##        self.setup()
-##        self.setupData(img_shape=img_shape)
-##        self.ui_changes()
-#        pass
-
-        
-
[docs]    def ui_changes(self):
-        """
-        Any changes to ui labels or otherwise for particular implementation
-        """
-        pass

-    
-
[docs]    def setupData(self, img_shape):
-        self._img_shape = img_shape
-        self._img_size = int(_np.array(img_shape).prod())
-        self._img_shape2D = tuple(_np.array(img_shape)[0:2])
-        self._img_size2D = int(_np.array(img_shape)[0:2].prod())
-        self._n_y = img_shape[0]
-        self._n_x = img_shape[1]
-        self._n_spectra = img_shape[2]
-        self._n_factors = self.max_factors()
-
-        self.selected_factors = set()
-        self.cube_all = None
-        self.img_all = None
-        self.spect_all = None

-
-        
-
[docs]    def setup(self, parent = None):
-
-        # Generic load/init designer-based GUI
-        # super(DialogAbstractFactorization, self).__init__(parent) ### EDIT ###
-
-        self.ui = Ui_Dialog() ### EDIT ###
-        self.ui.setupUi(self)     ### EDIT ###
-
-        self.ui.pushButtonNext.clicked.connect(self.advance)
-        self.ui.pushButtonPrev.clicked.connect(self.advance)
-        self.ui.pushButtonGoTo.clicked.connect(self.advance)
-        self.ui.pushButtonCancel.clicked.connect(self.reject)
-        self.ui.pushButtonOk.clicked.connect(self.accept)
-        self.ui.pushButtonClear.clicked.connect(self.clear)
-        self.ui.pushButtonApply.clicked.connect(self.applyCheckBoxes)
-        self.ui.pushButtonScript.clicked.connect(self.runScript)
-
-        self._first_factor_visible = 0
-        self._num_factor_visible = 6
-
-        self.ui.lcdSelectedFactors.display(0)
-        self.ui.lcdMaxFactors.display(self.max_factors())
-
-        self.factorWins = []
-        self.factorLabelCheckBoxes = [self.ui.checkBox,
-                                  self.ui.checkBox_2,
-                                  self.ui.checkBox_3,
-                                  self.ui.checkBox_4,
-                                  self.ui.checkBox_5,
-                                  self.ui.checkBox_6]
-
-        for count in range(self._num_factor_visible):
-            self.factorWins.append(_MplCanvas(subplot=211))
-            self.factorWins[count].ax[0].axis('Off')
-            self.factorWins[count].ax[1].hold('Off')
-
-        self.ui.gridLayout.addWidget(self.factorWins[0],1,0)
-        self.ui.gridLayout.addWidget(self.factorWins[1],1,1)
-        self.ui.gridLayout.addWidget(self.factorWins[2],1,2)
-
-        self.ui.gridLayout.addWidget(self.factorWins[3],3,0)
-        self.ui.gridLayout.addWidget(self.factorWins[4],3,1)
-        self.ui.gridLayout.addWidget(self.factorWins[5],3,2)
-
-        self.reconCurrent = _MplCanvas(subplot=211)
-        self.reconCurrent.ax[0].axis('Off')
-        self.reconCurrent.ax[1].hold('Off')
-
-        self.reconRemainder = _MplCanvas(subplot=211)
-        self.reconRemainder.ax[0].axis('Off')
-        self.reconRemainder.ax[1].hold('Off')
-
-
-        self.ui.verticalLayout_3.insertWidget(1,self.reconCurrent)
-        self.ui.verticalLayout_3.insertWidget(-1,self.reconRemainder)
-
-        for count in range(self._num_factor_visible):
-            self.factorLabelCheckBoxes[count].setText('Keep: ' + str(count))

-
-    @property
-    def unselected_factors(self):
-        all_factors = set(_np.arange(self._n_factors))
-        return all_factors - self.selected_factors
-
-
[docs]    def applyCheckBoxes(self):
-        """
-        Add checked singular values (and remove un-checked SVs)
-        """
-        for count, checkBox in enumerate(self.factorLabelCheckBoxes):
-            if checkBox.isChecked() == True:
-                self.selected_factors.add(self._first_factor_visible+count)
-            else:
-                try:
-                    self.selected_factors.remove(self._first_factor_visible+count)
-                except:
-                    pass
-
-        #print('Self.S: {}'.format(self.svddata.S[0:3]))
-        self.ui.lcdSelectedFactors.display(len(self.selected_factors))
-        self.updateCurrentRemainder()

-
-
[docs]    def advance(self):
-        """
-        View next set of SVs
-        """
-        sender = self.sender().objectName()
-        if sender == 'pushButtonPrev':
-            self.updatePlots(startnum=self._first_factor_visible-self._num_factor_visible)
-        elif sender == 'pushButtonNext':
-            self.updatePlots(startnum=self._first_factor_visible+self._num_factor_visible)
-        elif sender == 'pushButtonGoTo':
-            self.updatePlots(startnum=self.ui.spinBoxGoTo.value())
-        else:
-            pass

-
[docs]    def runScript(self):
-        """
-        Run "script" of singular value selection
-
-        Example:
-            [1,2,3,5:7] = 1,2,3,5,6,7
-        """
-        script = self.ui.lineEditSelections.text()
-        script = script.strip('[').strip(']')
-        script = script.split(',')
-        for count in script:
-            if ':' in count:
-                temp = count.split(':')
-                self.selected_factors.update(set(_np.arange(int(temp[0]),int(temp[1])+1)))
-            elif count.strip() == '':
-                pass
-            else:
-                self.selected_factors.add(int(count))
-        self.updatePlots(startnum=self._first_factor_visible)
-        self.ui.lcdSelectedFactors.display(len(self.selected_factors))
-        self.updateCurrentRemainder()

-
-
[docs]    def max_factors(self):
-        raise NotImplementedError('max_factors method not implemented')

-        
-
[docs]    def combiner(self, factors=None):
-        raise NotImplementedError('combiner method not implemented')

-
-
[docs]    def mean_spatial(self, cube):
-        raise NotImplementedError('mean_spatial method not implemented')

-        
-
[docs]    def mean_spectral(self, cube):
-        raise NotImplementedError('mean_spectral method not implemented')

-               
-
[docs]    def get_spatial_slice(self, num):
-        raise NotImplementedError('get_spatial_slice method not implemented.')

-        
-
[docs]    def get_spectral_slice(self, num):
-        raise NotImplementedError('get_spectral_slice method not implemented.')

-        
-
[docs]    def updateCurrentRemainder(self):
-        """
-        Update image reconstructed (mean over spectral vector) using remaining \
-        (unselected) singular values
-        """
-        cube_select = self.combiner(self.selected_factors)
-        img_select = self.mean_spatial(cube_select)
-        spect_select = self.mean_spectral(cube_select)
-        
-        # cube_nonselect = self.combiner(self.unselected_factors)
-        
-        # cube_nonselect = self.cube_all - cube_select
-        # img_nonselect = self.mean_spatial(cube_nonselect)
-        # spect_nonselect = self.mean_spectral(cube_nonselect)
-        img_nonselect = self.img_all - img_select
-        print('Spect_select: {}'.format(spect_select))
-        print('Spect_select is None: {}'.format(spect_select is None))
-        spect_nonselect = self.spect_all - spect_select
-        
-        self.reconCurrent.ax[0].cla()
-        self.reconCurrent.ax[1].cla()
-        
-        # s_lim = _np.abs(img_select).max()
-        s_lim = _np.abs(img_select.mean() + 3*img_select.std())
-
-        self.reconCurrent.ax[0].imshow(img_select, interpolation='None', 
-                                       cmap = 'bwr', origin='lower', vmin=0, vmax=s_lim)
-        self.reconCurrent.ax[1].plot(spect_select)
-        self.reconCurrent.draw()
-        
-        self.reconRemainder.ax[0].cla()
-        self.reconRemainder.ax[1].cla()
-
-        # s_lim = _np.abs(img_nonselect).max()
-        s_lim = _np.abs(img_nonselect.mean() + 3*img_nonselect.std())
-        self.reconRemainder.ax[0].imshow(img_nonselect, interpolation='None', 
-                                         cmap = 'bwr', origin='lower', vmin=-s_lim, vmax=s_lim)
-        self.reconRemainder.ax[1].plot(spect_nonselect)
-        self.reconRemainder.draw()

-        
-
-
[docs]    def updatePlots(self, startnum=0):
-        """
-        Update images and spectra of set of singular values starting at SV \
-        number startnum
-        """
-        if startnum <= 0:
-            startnum = 0
-            self.ui.pushButtonPrev.setEnabled(False)
-            self.ui.pushButtonNext.setEnabled(True)
-        elif startnum > self._n_factors - self._num_factor_visible:
-            startnum = self._n_factors - self._num_factor_visible
-            self.ui.pushButtonPrev.setEnabled(True)
-            self.ui.pushButtonNext.setEnabled(False)
-        else:
-            self.ui.pushButtonPrev.setEnabled(True)
-            self.ui.pushButtonNext.setEnabled(True)
-
-        self._first_factor_visible = startnum
-
-        for count in range(self._num_factor_visible):
-            self.factorWins[count].ax[0].clear()
-
-            sl = self.get_spatial_slice(count + self._first_factor_visible)
-            # sl_lim = _np.abs(sl).max()
-            sl_lim = _np.abs(sl.mean() + 3*sl.std())
-            self.factorWins[count].ax[0].imshow(sl, vmin=-sl_lim, vmax=sl_lim, 
-                                                interpolation='none',
-                                                cmap = 'bwr' , origin='lower')
-
-            self.factorWins[count].ax[0].axis('Off')
-
-            self.factorWins[count].ax[1].clear()
-            self.factorWins[count].ax[1].plot(self.get_spectral_slice(count + self._first_factor_visible))
-
-            self.factorLabelCheckBoxes[count].setText('Keep: ' + str(startnum + count))
-            self.factorWins[count].draw()
-            if self._first_factor_visible + count in self.selected_factors:
-                self.factorLabelCheckBoxes[count].setChecked(True)
-            else:
-                self.factorLabelCheckBoxes[count].setChecked(False)

-
-
[docs]    def clear(self):
-        """
-        Clear selected singular values (i.e., none will be selected)
-        """
-        self.selected_factors = set()
-        self.ui.lcdSelectedFactors.display(len(self.selected_factors))
-        self.updateCurrentRemainder()
-        self.updatePlots(startnum=self._first_factor_visible)

-
-
-if __name__ == '__main__':
-    pass
-#     app = _QApplication(_sys.argv)
-#     app.setStyle('Cleanlooks')
-#     x = _np.linspace(100,200,50)
-#     y = _np.linspace(200,300,50)
-#     f = _np.linspace(500,3000,800)
-#     Ex = 30*_np.exp((-(f-1750)**2/(200**2)))
-#     Spectrum = _np.convolve(_np.flipud(Ex),Ex,mode='same')
-
-#     data = _np.zeros((y.size,x.size,f.size))
-
-#     for count in range(y.size):
-#         data[count,:,:] = y[count]*_np.random.poisson(_np.dot(x[:,None],Spectrum[None,:]))
-
-#     win = DialogAbstractFactorization.dialogAbstractFactorization(data, data.shape) ### EDIT ###
-
-#     print(win)
-
-
-#     _sys.exit(app.exec_())
-# #    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/dialog_AbstractPlotEffect.html b/docs/build/html/_modules/crikit/ui/dialog_AbstractPlotEffect.html deleted file mode 100644 index 148eab9..0000000 --- a/docs/build/html/_modules/crikit/ui/dialog_AbstractPlotEffect.html +++ /dev/null @@ -1,268 +0,0 @@ - - - - - - - - - - - crikit.ui.dialog_AbstractPlotEffect — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
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    • - -
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    • - -
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    • - - -
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Source code for crikit.ui.dialog_AbstractPlotEffect

-"""
-Created on Thu Dec 22 10:04:39 2016
-
-@author: chc
-"""
-
-from PyQt5.QtWidgets import (QWidget as _QWidget)
-from PyQt5.QtCore import (pyqtSignal as _pyqtSignal)
-
-
[docs]class AbstractPlotEffectPlugin(_QWidget):
-    
-    parameters = {
-                  'name' : 'Name',
-                  'long_name' : 'Longer Name'
-                  }
-    
-    labels_orig = {
-                   'x_label' : 'x',
-                   'y_label' : 'y',
-                   'title' : 'Original'
-                   }
-                   
-    labels_affected = {
-                       'x_label' : 'x',
-                       'y_label' : 'y',
-                       'title' : 'Affected'
-                      }
-                   
-    changed = _pyqtSignal()
-    
-#    def __init__(self):
-#        raise NotImplementedError
-        
-
[docs]    def fcn(self, data_in):
-        raise NotImplementedError

-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/dialog_SVD.html b/docs/build/html/_modules/crikit/ui/dialog_SVD.html deleted file mode 100644 index f543a3a..0000000 --- a/docs/build/html/_modules/crikit/ui/dialog_SVD.html +++ /dev/null @@ -1,438 +0,0 @@ - - - - - - - - - - - crikit.ui.dialog_SVD — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
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    • - - -
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Source code for crikit.ui.dialog_SVD

-"""
-Created on Mon Jul 25 13:57:24 2016
-
-@author: chc
-"""
-import sys as _sys
-# import timeit
-import numpy as _np
-
-from PyQt5.QtWidgets import (QApplication as _QApplication, QWidget as _QWidget)
-
-from crikit.ui.dialog_AbstractFactorization import DialogAbstractFactorization
-
-from scipy.linalg import diagsvd as _diagsvd
-
-
[docs]class DialogSVD(DialogAbstractFactorization):
-    """
-    SVD Class
-    """
-    def __init__(self, data, img_shape, mask=None, use_imag=True, img_all=None, spect_all=None,
-                 parent=None):
-        super(DialogSVD, self).__init__(parent=parent) ### EDIT ###
-        self.setup(parent=parent)
-        self.setupData(img_shape=img_shape)
-        self.ui_changes()
-
-        self.U = data[0]
-        self.s = data[1]
-        self.Vh = data[2]
-        self._n_factors = self.s.size
-
-        self.mask = mask
-
-        self._use_imag = use_imag # By default, use imag portion of complex data
-
-        if (img_all is None) and (spect_all is None):
-            cube_all = self.combiner(selections=_np.arange(self._n_factors))
-            self.img_all = self.mean_spatial(cube_all)
-            self.spect_all = self.mean_spectral(cube_all)
-        else:
-            self.img_all = img_all.real
-            if _np.iscomplexobj(spect_all):
-                if self._use_imag:    
-                    self.spect_all = spect_all.imag
-                else:
-                    self.spect_all = spect_all.real
-            else: 
-                self.spect_all = spect_all
-
-        self.updatePlots(0)
-        self.updateCurrentRemainder()
-
-
[docs]    @staticmethod
-    def dialogSVD(data, img_shape, mask=None, use_imag=True, img_all=None, spect_all=None, parent=None):
-        dialog = DialogSVD(data=data, img_shape=img_shape, mask=mask,
-                           use_imag=use_imag, img_all=img_all, spect_all=spect_all, parent=parent)
-        result = dialog.exec_()
-
-        if result == 1:
-            svs = list(dialog.selected_factors)
-            if len(svs) == 0:
-                svs = None
-            else:
-                svs.sort()
-                svs = _np.array(svs)
-        else:
-            svs = None
-        return svs

-
-
[docs]    def max_factors(self):
-        """
-        Return maximum number of factors. Since DialogAbstractFactorization
-        (parent) is initialized first (before self.s), need to return None
-        at first.
-        """
-        try:
-            return self.s.size
-        except:
-            return None

-
-
[docs]    def combiner(self, selections=None):
-        """Performs U*S*Vh"""
-
-        # Straight-forward way, but slow
-        # tmr = timeit.default_timer()
-        # S = self.s_from_selected(selections=selections)
-        # ret = _np.dot(self.U, _np.dot(S, self.Vh))
-        # tmr -= timeit.default_timer()
-        # # print('Selections: {}'.format(selections))
-        # print('S (head): {}'.format(_np.diag(S)[0:10]))
-        # print('Old way: {}'.format(-tmr))
-
-        # New faster method
-        # tmr = timeit.default_timer()
-        ret = _np.dot(self.U[:, list(selections)], _np.dot(_np.diag(self.s[list(selections)]), self.Vh[list(selections), :]))
-        # tmr -= timeit.default_timer()
-        # print('S (head): {}'.format(self.s[list(selections)]))
-        # print('New way: {}'.format(-tmr))
-        # print('Old == New: {}\n'.format(_np.allclose(ret,ret2)))
-        
-        return ret

-
-
[docs]    def mean_spatial(self, cube):
-        ret = cube.mean(axis=-1)
-        ret = ret.reshape((self._n_y, self._n_x))
-        if _np.iscomplexobj(ret):
-            if self._use_imag:
-                return _np.imag(ret)
-            else:
-                return _np.real(ret)
-        else:
-            return ret

-
-
[docs]    def mean_spectral(self, cube):
-        ret = cube.mean(axis=0)
-
-        if _np.iscomplexobj(ret):
-            if self._use_imag:
-                return _np.imag(ret)
-            else:
-                return _np.real(ret)
-        else:
-            return ret

-
-
[docs]    def s_from_selected(self, selections=None):
-        """
-        Return SVD S-matrix of SELECTED singular values
-        """
-        M = self.U.shape[-1]
-        N = self.Vh.shape[0]
-
-        if selections is None:
-            S = _diagsvd(self.s, M, N)
-            return S
-        else:
-            if isinstance(selections, set):
-                selections = list(selections)
-            s_select = _np.zeros(self.s.size)
-            s_select[selections] = self.s[selections]
-
-            S = _diagsvd(s_select, M, N)
-            return S

-
-
[docs]    def get_spatial_slice(self, num):
-        img = self.U[...,num].reshape((self._n_y, self._n_x))
-        return _np.real(img)

-
-        # Used to return complex, but the SVD of complex numbers tends to
-        # shove everything in U into the real component
-
-        # if _np.iscomplexobj(img):
-        #     if self._use_imag:
-        #         return _np.imag(img)
-        #     else:
-        #         return _np.real(img)
-        # else:
-        #     return img
-
-
-
-
[docs]    def get_spectral_slice(self, num):
-        spect = self.Vh[num,:]
-
-        if _np.iscomplexobj(spect):
-            if self._use_imag:
-                return _np.imag(spect)
-            else:
-                return _np.real(spect)
-        else:
-            return spect

-
-if __name__ == '__main__':
-    from scipy.linalg import svd as _svd
-
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-    x = _np.linspace(100, 200, 100)
-    y = _np.linspace(200, 300, 100)
-
-
-    f = _np.linspace(500,3000,900)
-    Ex = 30*_np.exp((-(f-1750)**2/(200**2)))
-    Spectrum = _np.convolve(_np.flipud(Ex),Ex,mode='same')
-#
-    hsi = _np.zeros((y.size,x.size,f.size))
-#
-    for count in range(y.size):
-        # hsi[count,:,:] = y[count]*_np.random.poisson(_np.dot(x[:,None],Spectrum[None,:]))
-        hsi[count,:,:] = y[count]*_np.dot(x[:,None],Spectrum[None,:])
-    hsi = 0*hsi + 1j*hsi
-
-    data = _svd(hsi.reshape((-1,f.size)), full_matrices=False)
-
-    # Class method route
-    #ret = DialogSVD.main(data, hsi.shape)
-    #print(ret)
-
-    # Full route
-    obj = _QWidget()
-    svs = DialogSVD.dialogSVD(data, hsi.shape, img_all=hsi.mean(axis=-1), spect_all=hsi.mean(axis=(0,1)) ,parent=obj)
-
-    print('Factors selected: {}'.format(svs))
-
-##    app.exec_()
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/dialog_kkOptions.html b/docs/build/html/_modules/crikit/ui/dialog_kkOptions.html deleted file mode 100644 index 854e56e..0000000 --- a/docs/build/html/_modules/crikit/ui/dialog_kkOptions.html +++ /dev/null @@ -1,391 +0,0 @@ - - - - - - - - - - - crikit.ui.dialog_kkOptions — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.ui.dialog_kkOptions

-"""
-Kramers-Kronig phase retrieval
-
-References
-----------
-[1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \
-Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \
-Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543.
-
-"""
-
-import sys as _sys
-import os as _os
-import numpy as _np
-
-# Generic imports for QT-based programs
-from PyQt5.QtWidgets import (QApplication as _QApplication,
-                             QDialog as _QDialog)
-
-
-# Import from Designer-based GUI
-from crikit.ui.qt_KKOptions import Ui_Dialog as Ui_KKOptions
-
-from crikit.ui.dialog_ploteffect import (DialogPlotEffectFuture as 
-                                                _DialogPlotEffect)
-from crikit.ui.widget_KK import (widgetKK as _widgetKK)
-
-# Generic imports for MPL-incorporation
-import matplotlib as _mpl
-_mpl.use('Qt5Agg')
-_mpl.rcParams['font.family'] = 'sans-serif'
-_mpl.rcParams['font.size'] = 10
-
-
-
[docs]class DialogKKOptions(_QDialog):
-    """
-    DialogKKOptions : Phase-Retrieval (only Kramers-Kronig currently \
-        supported) options dialog
-
-    Methods
-    --------
-    dialogKKOptions : Used to call UI and retrieve results of dialog
-
-    References
-    ----------
-    [1] Y. Liu, Y. J. Lee, and M. T. Cicerone, "Broadband CARS spectral \
-        phase retrieval using a time-domain Kramers-Kronig transform," \
-        Opt. Lett. 34, 1363-1365 (2009).
-
-    [2] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \
-        Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \
-        Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543.
-
-    """
-    NORM_TO_NRB = True
-    NRB_AMP = 0.0
-    CARS_AMP = 0.0
-    PHASE_OFFSET = 0.0
-    PAD_FACTOR = 1
-
-    def __init__(self, parent=None, data=None):
-        super(DialogKKOptions, self).__init__(parent) ### EDIT ###
-        self.ui = Ui_KKOptions() ### EDIT ###
-        self.ui.setupUi(self)     ### EDIT ###
-
-        self.ui.doubleSpinBoxCARSAmp.setValue(self.CARS_AMP)
-        self.ui.doubleSpinBoxNRBAmp.setValue(self.NRB_AMP)
-        self.ui.doubleSpinBoxPhase.setValue(self.PHASE_OFFSET)
-        self.ui.checkBoxNormToNRB.setChecked(self.NORM_TO_NRB)
-        self.ui.spinBoxPadFactor.setValue(self.PAD_FACTOR)
-
-        self.norm_to_nrb = self.NORM_TO_NRB
-
-        self.data = data
-
-        if data is None:
-            self.ui.pushButtonInteractive.setEnabled(False)
-        else:
-            self.ui.pushButtonInteractive.pressed.connect(self.goInteractive)
-
-
[docs]    def goInteractive(self):
-
-        plugin = _widgetKK()
-
-        winPlotEffect = _DialogPlotEffect.dialogPlotEffect(self.data[1:], 
-                                                           x=self.data[0], 
-                                                           plugin=plugin,
-                                                           parent=self)
-
-        if winPlotEffect is not None:
-            self.ui.doubleSpinBoxCARSAmp.setValue(winPlotEffect.parameters['cars_amp_offset'])
-            self.ui.doubleSpinBoxNRBAmp.setValue(winPlotEffect.parameters['nrb_amp_offset'])
-            self.ui.checkBoxNormToNRB.setChecked(winPlotEffect.parameters['norm_to_nrb'])
-            self.ui.doubleSpinBoxPhase.setValue(winPlotEffect.parameters['phase_offset'])
-            self.ui.spinBoxPadFactor.setValue(winPlotEffect.parameters['pad_factor'])

-
-
[docs]    @staticmethod
-    def dialogKKOptions(parent=None, data=None):
-        """
-        Retrieve dark subtraction dialog results
-
-        Parameters
-        ----------
-        None : None
-
-        Returns
-        ----------
-        out : dict{'cars_amp' : float, 'nrb_amp' : float,
-                   'phase_offset' : float, 'norm_to_nrb' : bool,
-                   'pad_factor' : int}
-            In order: CARS amp offset, NRB amp offset, phase offset, normalize
-                by NRB, pad factor
-        """
-        dialog = DialogKKOptions(parent=parent,data=data)
-
-        result = dialog.exec_()
-
-        if result == 1:
-            ret = {}
-            ret['cars_amp'] = dialog.ui.doubleSpinBoxCARSAmp.value()
-            ret['nrb_amp'] = dialog.ui.doubleSpinBoxNRBAmp.value()
-            ret['phase_offset'] = dialog.ui.doubleSpinBoxPhase.value()
-            ret['norm_to_nrb'] = dialog.ui.checkBoxNormToNRB.isChecked()
-            ret['pad_factor'] = dialog.ui.spinBoxPadFactor.value()
-            return ret
-        else:
-            return None

-
-if __name__ == '__main__':
-
-
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-
-#    winDark = DialogDarkOptions.dialogDarkOptions(darkloaded=True)
-
-    from crikit.data.hsi import Hsi as _Hsi
-
-    temp = _Hsi()
-
-    WN = _np.linspace(500,4000,1000)
-
-    CARS = _np.zeros((20,20,WN.size))
-    CARS[:,:,:] = _np.abs(1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055)
-    temp.data = CARS
-    temp.freq.data = WN
-
-
-    NRB = 0*WN + .055
-
-
-    winKK = DialogKKOptions.dialogKKOptions(data=[WN, NRB,
-        temp.get_rand_spectra(10, pt_sz=3, quads=False)])
-
-    print('KK return: {}'.format(winKK))
-
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/dialog_model.html b/docs/build/html/_modules/crikit/ui/dialog_model.html deleted file mode 100644 index f049dd5..0000000 --- a/docs/build/html/_modules/crikit/ui/dialog_model.html +++ /dev/null @@ -1,349 +0,0 @@ - - - - - - - - - - - crikit.ui.dialog_model — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.ui.dialog_model

-"""
-Dialog for creating BCARS or Raman numerical phantom
-"""
-import sys as _sys
-
-import numpy as _np
-
-# Generic imports for QT-based programs
-from PyQt5.QtWidgets import (QApplication as _QApplication,
-                             QWidget as _QWidget, QDialog as _QDialog,
-                             QMainWindow as _QMainWindow,
-                             QSizePolicy as _QSizePolicy,
-                             QFileDialog as _QFileDialog)
-import PyQt5.QtCore as _QtCore
-
-from crikit.ui.qt_Model import Ui_Dialog
-from crikit.datasets.model import Model
-
-
[docs]class DialogModel(_QDialog):
-    """
-    Dialog for creating BCARS or Raman numerical phantom
-    """
-    def __init__(self, cplx=True, parent=None):
-        super().__init__(parent)
-        self.cplx = cplx  # Is dataset complex-valued
-
-        self.ui = Ui_Dialog()
-        self.ui.setupUi(self)
-        self.ui.pushButtonCancel.setDefault(False)
-        self.ui.pushButtonCancel.setAutoDefault(False)
-        self.ui.pushButtonOk.setDefault(False)
-        self.ui.pushButtonOk.setAutoDefault(False)
-        self.ui.spinBoxSubsample.setFocus()
-
-        self.ui.pushButtonOk.pressed.connect(self.accept)
-        self.ui.pushButtonCancel.pressed.connect(self.reject)
-
-        self.ui.spinBoxSubsample.valueChanged.connect(self.changeSize)
-        self.ui.spinBoxStart.valueChanged.connect(self.changeSize)
-        self.ui.spinBoxEnd.valueChanged.connect(self.changeSize)
-        self.ui.spinBoxSpectrographStep.valueChanged.connect(self.changeSize)
-        self.ui.spinBoxProbe.valueChanged.connect(self.changeSize)
-
-        self.changeSize()
-
-
[docs]    def changeSize(self):
-        subsample = self.ui.spinBoxSubsample.value()
-        start = self.ui.spinBoxStart.value()
-        stop = self.ui.spinBoxEnd.value()
-        slope = self.ui.spinBoxSpectrographStep.value()
-        probe = self.ui.spinBoxProbe.value()
-
-        m = Model._M
-        n = Model._N
-
-        x = _np.arange(n)
-        y = _np.arange(m)
-
-        rows = y[::subsample].size
-        cols = x[::subsample].size
-        
-        lam_start = 0.01 / (start + 0.01/(probe*1e-9))  # meters
-        lam_start *= 1e9  # nm
-
-        lam_end = 0.01 / (stop + 0.01/(probe*1e-9))  # meters
-        lam_end *= 1e9  # nm
-
-        lam_ctr = (lam_start + lam_end) / 2  # nm
-        
-        n_pix = _np.abs(_np.ceil((lam_end-lam_start) / slope)).astype(int)
-
-        datasize = rows * cols * n_pix
-        if self.cplx:
-            datasize *= (128/8)  # Assume complex128, for now
-        else:
-            datasize *= (64/8)  # Assume float64, for now
-        datasize *= 1e-9  # Gigbytes (Gb)
-
-        self.ui.spinBoxOutputColors.setValue(n_pix)
-        self.ui.spinBoxOutputRows.setValue(rows)
-        self.ui.spinBoxOutputCols.setValue(cols)
-        self.ui.spinBoxMemory.setValue(datasize)

-
[docs]    @staticmethod
-    def dialogModel(cplx=True, parent=None):
-        """
-
-        """
-        dialog = DialogModel(cplx=cplx, parent=parent)
-        result = dialog.exec_()
-        if result == 1:
-            settings = {}
-            settings['subsample'] = dialog.ui.spinBoxSubsample.value()
-            settings['wn_start'] = dialog.ui.spinBoxStart.value()
-            settings['wn_end'] = dialog.ui.spinBoxEnd.value()
-            settings['wl_slope'] = dialog.ui.spinBoxSpectrographStep.value()
-            settings['probe'] = dialog.ui.spinBoxProbe.value()
-
-            settings['gnoise_bool'] = dialog.ui.checkBoxGNoise.isChecked()
-            settings['pnoise_bool'] = dialog.ui.checkBoxPNoise.isChecked()
-            settings['dark_bool'] = dialog.ui.checkBoxDark.isChecked()
-
-            settings['gnoise_stddev'] = dialog.ui.spinBoxGStdDev.value()
-            settings['pnoise_gain'] = dialog.ui.spinBoxPMulti.value()
-            settings['dark_level'] = dialog.ui.spinBoxDark.value()
-            return settings
-        else:
-            return None

-
-if __name__ == '__main__':
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    win = DialogModel.dialogModel(cplx=False, parent=None)
-    print(win)
-    
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/dialog_ploteffect.html b/docs/build/html/_modules/crikit/ui/dialog_ploteffect.html deleted file mode 100644 index 23aada2..0000000 --- a/docs/build/html/_modules/crikit/ui/dialog_ploteffect.html +++ /dev/null @@ -1,608 +0,0 @@ - - - - - - - - - - - crikit.ui.dialog_ploteffect — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.ui.dialog_ploteffect

-"""
-Extensible Dialog that shows the effect of a plugin on input data.
-
-Created on Wed Dec 21 21:36:00 2016
-
-@author: chc
-"""
-import numpy as _np
-
-from PyQt5.QtWidgets import (QApplication as _QApplication,
-                             QDialog as _QDialog)
-
-from crikit.ui.qt_PlotEffect import Ui_Dialog as Ui_DialogPlotEffect
-
-from crikit.ui.dialog_AbstractPlotEffect import (AbstractPlotEffectPlugin 
-                                                     as
-                                                     _AbstractPlotEffectPlugin)
-
-from sciplot.ui.widget_mpl import MplCanvas as _MplCanvas
-
-
[docs]class DialogPlotEffectFuture(_QDialog):
-    """
-    Extensible Dialog that shows the effect of a plugin on input data.
-    
-    Parameters
-    ----------
-    
-    data : ndarray (ND)
-        Input data
-    
-    x : ndarray (1D)
-        Independent variable
-        
-    plugin : sub-class of AbstractPlotEffectPlugin
-        Plugin class instance
-        
-    parent : QObject
-        Parent
-    """
-    
-    def __init__(self, data, x=None, plugin=None, parent=None):
-        super(DialogPlotEffectFuture, self).__init__(parent)
-        self.ui = Ui_DialogPlotEffect()
-        self.ui.setupUi(self)
-
-        self.data = data
-        
-        # Setup MPL containers
-        self.mpl_orig = _MplCanvas(subplot=111)        
-        self.mpl_affected = _MplCanvas(subplot=111)
-        
-        # Show(), although not needed, enables mpl-tight_layout 
-        # to work later on
-        self.show()
-        
-        self.ui.verticalLayout.insertWidget(1, self.mpl_orig)
-        self.ui.verticalLayout.insertWidget(1, self.mpl_orig.toolbar)
-        
-        self.ui.verticalLayout.insertWidget(3, self.mpl_affected)
-        self.ui.verticalLayout.insertWidget(3, self.mpl_affected.toolbar)
-
-        # Plugin that brings functionality to PlotEffect
-        self.plugin = plugin
-        
-        
-        # Signal emited when something changes in the plugin widget
-        self.plugin.changed.connect(self.widget_changed)
-            
-        # Setup indep. variable
-        if x is None:
-            self.x = _np.linspace(0,data.shape[0],self.data.shape[0])
-        else:
-            self.x = x
-        
-        # If data is a list (assumed to be a list of ndarrays),
-        # plot each item in list
-        if isinstance(data, _np.ndarray):
-            try:
-                self.mpl_orig.ax.plot(self.x,data)
-            except:
-                self.mpl_orig.ax.plot(self.x,data.T)
-        elif isinstance(data, list):
-            for d in data:
-                try:
-                    self.mpl_orig.ax.plot(self.x,d)
-                except:
-                    self.mpl_orig.ax.plot(self.x,d.T)
-                
-            
-        self.plot_labels()
-                
-        if self.plugin is not None:
-            self.ui.verticalLayout.insertWidget(8, plugin)
-        
-        self.show()
-        self.widget_changed()
-        self.mpl_orig.draw()
-        self.mpl_affected.draw()
-
-        self.ui.pushButtonOk.clicked.connect(self.accept)
-        self.ui.pushButtonCancel.clicked.connect(self.reject)
-        
-
[docs]    @staticmethod
-    def dialogPlotEffect(data, x = None, plugin=None, parent = None):
-        """
-        Static method that is actually called
-        """        
-        dialog = DialogPlotEffectFuture(data, x=x, plugin=plugin, 
-                                  parent=parent)
-        
-        result = dialog.exec_()  # 1 = Accepted, 0 = Rejected/Canceled
-        
-        if result == 1:
-            return dialog.plugin
-        else:
-            return None

-            
-
[docs]    def widget_changed(self):
-        """
-        Plugin widget has changed. Re-submit data to plugin function.
-        """
-        try:
-            affected_data = self.plugin.fcn(self.data)
-        except:
-            print('Error in plugin.fcn')
-        else:
-            # If affected_data is a list, [0] is added to the original data
-            # plots and is bolded
-            if isinstance(affected_data, list):
-                # Split affected data into the addon and te affected axis
-                # data
-                orig_data_addon = affected_data[0]
-                affected_data = affected_data[1]
-                
-            else:
-                orig_data_addon = None
-            
-            # If there already exists an original plot, keep those
-            # axis limits upon re-plotting
-            if len(self.mpl_orig.ax.lines) > 0:
-                lim_orig = self.mpl_orig.ax.axis()
-            else:
-                lim_orig = None
-                
-            self.mpl_orig.ax.clear()
-            
-            
-            if isinstance(self.data, _np.ndarray):
-                try:
-                    self.mpl_orig.ax.plot(self.x,self.data)
-                except:
-                    self.mpl_orig.ax.plot(self.x,self.data.T)
-                    
-            # If data is a list (assumed to be a list of ndarrays),
-            # plot each item in list
-            elif isinstance(self.data, list):
-                for d in self.data:
-                    try:
-                        self.mpl_orig.ax.plot(self.x,d)
-                    except:
-                        self.mpl_orig.ax.plot(self.x,d.T)
-                
-            if orig_data_addon is not None:
-                try:
-                    self.mpl_orig.ax.plot(self.x,orig_data_addon, lw=2)
-                except:
-                    self.mpl_orig.ax.plot(self.x,orig_data_addon.T, lw=2)
-                    
-            # If there already exists an affected plot, keep those
-            # axis limits upon re-plotting
-            if len(self.mpl_affected.ax.lines) > 0:
-                lim_affected = self.mpl_affected.ax.axis()
-            else:
-                lim_affected = None
-                
-            # If affected data return is None, hide the affected axis
-            if affected_data is None:
-                self.mpl_affected.setVisible(False)
-                self.mpl_affected.toolbar.setVisible(False)
-            else:
-                self.mpl_affected.setVisible(True)
-                self.mpl_affected.toolbar.setVisible(True)
-                
-                self.mpl_affected.ax.clear()
-                try:
-                    self.mpl_affected.ax.plot(self.x,affected_data)
-                except:
-                    self.mpl_affected.ax.plot(self.x,affected_data.T)
-            
-            self.plot_labels()  # Update x-,y-, and title-labels on plots
-            
-            self.mpl_orig.fig.tight_layout()
-            self.mpl_affected.fig.tight_layout()
-            
-            # Reset axis limits to previous setting before re-plotting
-            if lim_orig is not None:
-                self.mpl_orig.ax.axis(lim_orig)
-                
-            # Reset axis limits to previous setting before re-plotting
-            if lim_affected is not None:
-                self.mpl_affected.ax.axis(lim_affected)
-                
-            self.mpl_orig.draw()
-            self.mpl_affected.draw()

-            
-
[docs]    def plot_labels(self):
-        """
-        Add axis labels and titles
-        """
-        self._plot_labels_ax(self.mpl_orig.ax, self.plugin.labels_orig)
-        self._plot_labels_ax(self.mpl_affected.ax, self.plugin.labels_affected)

-    
-
[docs]    def _plot_labels_ax(self, ax, labels):
-        for k in labels:
-            val = labels[k]
-            k_lower = k.lower()
-            if k_lower == 'x_label':
-                ax.set_xlabel(val)
-            elif k_lower == 'y_label':
-                ax.set_ylabel(val)
-            elif k_lower == 'title':
-                ax.set_title(val)

-                
-        
-
[docs]class widgetDemoPlotEffectPlugin(_AbstractPlotEffectPlugin):
-    """
-    Very simple demo of a plugin
-    """
-    
-    parameters = {'name' : 'DEMO', 
-                  'long_name' : 'Demo of PlotEffectPlugins'}
-    
-    labels_orig = {
-                   'x_label' : 'Wavenumber (cm$^{-1}$)',
-                   'y_label' : 'Input Int (au)',
-                   'title' : 'Original'
-                   }
-                   
-    labels_affected = {
-                       'x_label' : labels_orig['x_label'],
-                       'y_label' : 'Output Int (au)',
-                       'title' : 'Affected'
-                      }
-                    
-    def __init__(self, offset=0.1, parent=None):
-        super(widgetDemoPlotEffectPlugin, self).__init__(parent) ### EDIT ###
-        
-        self.parameters['offset'] = offset 
-    
-
[docs]    def fcn(self, data_in):
-        """
-        If return list, [0] goes to original, [1] goes to affected
-        """
-        return [0*data_in + .1, data_in + .1]

-        
-    
-if __name__ == '__main__':
-    
-    import sys as _sys
-
-    app = _QApplication(_sys.argv)
-    
-#    WN = _np.linspace(500,4000,800)
-
-    calib_dict = {'n_pix' : 1600,
-                  'ctr_wl' : 730,
-                  'ctr_wl0' : 730,
-                  'a_vec' : [-0.167740721307557, 863.8736708961577],
-                  'probe': 771.461}
-                  
-    pix = _np.arange(calib_dict['n_pix'])
-    wl = calib_dict['a_vec'][0]*pix + calib_dict['a_vec'][1]
-    WN = .01/(wl*1e-9) - .01/(calib_dict['probe']*1e-9)
-    
-    CARS = _np.abs(1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055)
-    NRB = 0*WN + .055
-    CARS = _np.dot(_np.ones((5,1)),CARS[None,:])
-    
-    
-    
-    NRB_LEFT = 20e3*_np.exp(-(WN)**2/(1000**2)) + 500
-    NRB_RIGHT = 6e3*_np.exp(-(WN-2500)**2/(400**2)) + 500
-    
-    NRB_LEFT[WN<500] *= 0
-    NRB_LEFT[WN<500] += 1e-6
-    NRB_RIGHT[WN<500] *= 0
-    NRB_RIGHT[WN<500] += 1e-6
-    
-    from crikit.cri.merge_nrbs import MergeNRBs as _MergeNRBs
-    from crikit.utils.general import find_nearest as _find_nearest
-    NRB2 = _MergeNRBs(nrb_left=NRB_LEFT, nrb_right=NRB_RIGHT, 
-                     pix=_find_nearest(WN, 1885.0)[1],
-                     left_side_scale=False).calculate()
-    
-    CARS2 = _np.abs(500*(1/(1000-WN-1j*20) + 1/(2700-WN-1j*20)) + NRB2**0.5)**2
-    CARS2 = _np.dot(_np.ones((10,1), dtype=_np.double),CARS2[None,:])
-    
-#    # Demo
-#    plugin = widgetDemoPlotEffectPlugin()
-#    winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN,
-#                                                            plugin=plugin)
-#    if winPlotEffect is not None:
-#        print(winPlotEffect.parameters)
-#
-##    # ALS
-##    from crikit.ui.widget_ALS import widgetALS as _widgetALS
-##    
-##    plugin = _widgetALS()
-##    winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN,
-##                                                            plugin=plugin)
-##    if winPlotEffect is not None:
-##        print(winPlotEffect.parameters)
-#
-#    # ArPLS
-#    from crikit.ui.widget_ArPLS import widgetArPLS as _widgetArPLS
-#    plugin = _widgetArPLS()
-#    winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN,
-#                                                            plugin=plugin)
-#    if winPlotEffect is not None:
-#        print(winPlotEffect.parameters)
-#    
-#    # Detrending
-#    from crikit.ui.widget_DeTrending import (widgetDeTrending as 
-#                                                  _widgetDeTrending)
-#    plugin = _widgetDeTrending()
-#    winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN,
-#                                                            plugin=plugin)
-#    if winPlotEffect is not None:
-#        print(winPlotEffect.parameters)
-#    
-#    # SG
-#    from crikit.ui.widget_SG import (widgetSG as _widgetSG)
-#    plugin = _widgetSG()
-#    winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN,
-#                                                            plugin=plugin)
-#    if winPlotEffect is not None:
-#        print(winPlotEffect.parameters)
-#    
-#    # KK
-#    from crikit.ui.widget_KK import (widgetKK as _widgetKK)
-#    plugin = _widgetKK()
-#    winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect([NRB,CARS], x=WN,
-#                                                            plugin=plugin)
-#    if winPlotEffect is not None:
-#        print(winPlotEffect.parameters)
-#        
-#    # Calibrate
-#    from crikit.ui.widget_Calibrate import (widgetCalibrate as 
-#                                                _widgetCalibrate)
-#    plugin = _widgetCalibrate(calib_dict)
-#    winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS, x=WN,
-#                                                            plugin=plugin)
-#    if winPlotEffect is not None:
-#        print(winPlotEffect.parameters)
-    
-    # Merge NRBs
-    from crikit.ui.widget_mergeNRBs import (widgetMergeNRBs as 
-                                            _widgetMergeNRBs)
-    plugin = _widgetMergeNRBs(WN, NRB_LEFT, NRB_RIGHT)
-    winPlotEffect = DialogPlotEffectFuture.dialogPlotEffect(CARS2, x=WN,
-                                                            plugin=plugin)
-    if winPlotEffect is not None:
-        print(winPlotEffect.parameters)
-        
-    
-    
-    
-    
-    
-    
-#        print('P-Value: {}'.format(winPlotEffect.p))
-#        print('Lambda-Value: {}'.format(winPlotEffect.lam))
-#        print('Redux: {}'.format(winPlotEffect.redux))
-#        
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/dialog_save.html b/docs/build/html/_modules/crikit/ui/dialog_save.html deleted file mode 100644 index 4de2d8f..0000000 --- a/docs/build/html/_modules/crikit/ui/dialog_save.html +++ /dev/null @@ -1,488 +0,0 @@ - - - - - - - - - - - crikit.ui.dialog_save — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
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    • - -
  • Module code »
    • - -
  • crikit.ui.dialog_save
    • - - -
  • - - - -
    • - -
- - -
-
-
-
- -

Source code for crikit.ui.dialog_save

-"""
-CRIkit Save Dialog (crikit.ui.dialog_save)
-=======================================================
-
-Classes that present dialog boxes that retrieve options
-
-DialogSave : Save Dialog
-
-"""
-
-# Append sys path
-import sys as _sys
-import os as _os
-import datetime as _datetime
-
-# Generic imports for QT-based programs
-from PyQt5.QtWidgets import (QApplication as _QApplication,
-                             QWidget as _QWidget, QDialog as _QDialog,
-                             QMainWindow as _QMainWindow,
-                             QSizePolicy as _QSizePolicy,
-                             QFileDialog as _QFileDialog)
-import PyQt5.QtCore as _QtCore
-
-# Other imports
-import numpy as _np
-
-# Import from Designer-based GUI
-from crikit.ui.qt_Save import Ui_Dialog
-
-
[docs]class DialogSave(_QDialog):
-    """
-    DialogDarkOptions : Dark subtraction options dialog
-    
-    Methods
-    --------
-    dialogSave : Used to call UI and retrieve results of dialog
-    
-    """
-
-    def __init__(self, current_filename=None, current_path=None,
-                 current_dataset_name=None, save_filename=None,
-                 save_path=None, save_dataset_name=None, suffix=None,
-                 parent=None):
-        super(DialogSave, self).__init__(parent) ### EDIT ###
-        self.ui = Ui_Dialog() ### EDIT ###
-        self.ui.setupUi(self)     ### EDIT ###
-        self.ui.lineEditFilename.setFocus()
-        
-#        print('Current filename: {}'.format(current_filename))
-        if save_filename is not None and save_filename != '':
-            self.filename = save_filename
-        elif current_filename is not None and current_filename != '':
-            self.filename = current_filename
-        else:
-            self.filename = None
-            
-        if save_path is not None and save_path != '':
-            self.path = save_path
-        elif current_path is not None and current_path != '':
-            self.path = current_path
-        else:
-            self.path = None
-            
-        if save_dataset_name is not None and save_dataset_name != '':
-            self.dataset_name = save_dataset_name
-        elif current_dataset_name is not None and current_dataset_name != '':
-            self.dataset_name = current_dataset_name
-        else:
-            self.dataset_name = None
-        
-        
-        self.current_filename=current_filename
-        self.current_path=current_path
-        self.current_dataset_name=current_dataset_name
-        self.save_filename=save_filename
-        self.save_path=save_path
-        self.save_dataset_name=save_dataset_name
-        
-        self.suffix = suffix
-        
-        self.ui.lineEditFilename.setText(self.filename)
-        self.generateFilename()
-        self.ui.lineEditPath.setText(self.path)
-        self.ui.lineEditDataset.setText(self.dataset_name)
-        self.ui.lineReadDataset.setText(self.dataset_name)
-        self.generateDatasetName()
-            
-        self.ui.buttonCancel.pressed.connect(self.reject)
-        self.ui.buttonOK.pressed.connect(self.accept)
-        
-        self.ui.lineEditFilename.editingFinished.connect(self.changeFilename)
-        self.ui.lineEditPath.editingFinished.connect(self.changePath)
-        self.ui.lineEditDataset.editingFinished.connect(self.changeDataset)
-        self.ui.buttonGetFilename.pressed.connect(self.getFilename)
-        self.ui.buttonGetPath.pressed.connect(self.getPath)
-        self.ui.buttonGenerateFilename.pressed.connect(self.generateFilename)
-        self.ui.buttonGenerateDatasetname.pressed.connect(self.generateDatasetName)
-        
-
[docs]    def changeFilename(self):
-        self.filename = self.ui.lineEditFilename.text()
-        self.filename = self.filename.split('.h5')[0]
-        self.filename = self.filename + '.h5'
-        
-        self.ui.lineEditFilename.setText(self.filename)
-        
-        if self.path is None or self.path == '':        
-            self.ui.lineReadFileNamePath.setText('./' + self.filename)
-        else:
-            self.ui.lineReadFileNamePath.setText(self.path + self.filename)

-                
-
[docs]    def changePath(self):
-        self.path = self.ui.lineEditPath.text()
-        self.changeFilename()

-        
-
[docs]    def changeDataset(self):
-        self.dataset_name = self.ui.lineEditDataset.text()
-        self.ui.lineReadDataset.setText(self.dataset_name)

-        
-
[docs]    def getFilename(self):
-        filename,_ = _QFileDialog.getSaveFileName(self, "Open H5 File", "./",\
-            "HDF5 Files (*.h5 *.hdf);;All Files (*.*)",options=_QFileDialog.Options(4))
-        
-        if filename != '':
-            self.path = _os.path.dirname(filename) + '/'
-            self.filename = filename.split(_os.path.dirname(filename))[1][1::]
-            self.ui.lineEditFilename.setText(self.filename)
-            self.ui.lineReadFileNamePath.setText(self.path + self.filename)
-            self.ui.lineEditPath.setText(self.path)

-        
-
[docs]    def getPath(self):
-        path = _QFileDialog.getExistingDirectory(self)
-        
-        if path != '':
-            self.path = path + '/'
-            self.ui.lineEditPath.setText(self.path)
-            self.changeFilename()

-    
-
[docs]    def generateFilename(self):
-        curr_time = _datetime.datetime.now()
-        rnd_fname = 'PROCESS_' + str(curr_time.year) + str(curr_time.month) + \
-        str(curr_time.day) + '_' + str(curr_time.hour) + '_' + \
-        str(curr_time.minute) + '_' + str(curr_time.second) + '_' + \
-        str(curr_time.microsecond) + '.h5'
-        if self.filename is None or self.filename == '':
-            self.filename = rnd_fname
-            self.ui.lineEditFilename.setText(self.filename)
-        else:
-            self.filename = self.filename.split('.h5')[0] + '_' + rnd_fname
-            self.ui.lineEditFilename.setText(self.filename)
-                        
-        if self.path is None or self.path == '':
-            self.ui.lineReadFileNamePath.setText('./' + self.filename)
-        else:
-            self.ui.lineReadFileNamePath.setText(self.path + self.filename)

-
[docs]    def generateDatasetName(self):
-        if self.save_dataset_name is not None:
-            if self.suffix is not None:
-                self.dataset_name = self.save_dataset_name + self.suffix
-            else:
-                curr_time = _datetime.datetime.now()
-                self.dataset_name = self.save_dataset_name + '_' + str(curr_time.year) + str(curr_time.month) + \
-                str(curr_time.day) + '_' + str(curr_time.hour) + '_' + \
-                str(curr_time.minute) + '_' + str(curr_time.second) + '_' + \
-                str(curr_time.microsecond)
-        elif self.current_dataset_name is not None:
-            if self.suffix is not None:
-                self.dataset_name = self.current_dataset_name + self.suffix
-            else:
-                curr_time = _datetime.datetime.now()
-                self.dataset_name = self.current_dataset_name + '_PROCESS_' + str(curr_time.year) + str(curr_time.month) + \
-                str(curr_time.day) + '_' + str(curr_time.hour) + '_' + \
-                str(curr_time.minute) + '_' + str(curr_time.second) + '_' + \
-                str(curr_time.microsecond)
-        else:
-            if self.suffix is not None:
-                self.dataset_name = 'PROCESS_' + self.suffix
-            else:
-                curr_time = _datetime.datetime.now()
-                self.dataset_name = 'PROCESS_' + str(curr_time.year) + str(curr_time.month) + \
-                str(curr_time.day) + '_' + str(curr_time.hour) + '_' + \
-                str(curr_time.minute) + '_' + str(curr_time.second) + '_' + \
-                str(curr_time.microsecond)
-        
-        self.ui.lineEditDataset.setText(self.dataset_name)
-        self.ui.lineReadDataset.setText(self.dataset_name)

-            
-        
-        
-
[docs]    @staticmethod
-    def dialogSave(current_filename=None, current_path=None,
-                 current_dataset_name=None, save_filename=None,
-                 save_path=None, save_dataset_name=None, suffix=None,
-                 parent=None):
-        """
-        Retrieve save dialog results
-
-        Parameters
-        ----------
-        current_filename : str
-            Filename of HDF5 file from where current data resided
-        
-        current_path : str
-            Path to HDF5 file from where current data resided
-            
-        current_dataset_name : str
-            Dataset path and name where current data resided
-            
-        save_filename : str
-            Filename of HDF5 file where previously saved (if so)
-            
-        save_path : str
-            Path of HDF5 file where previously saved (if so)
-        
-        save_dataset_name : str
-            Dataset path and name where previously saved (if so)
-        
-        suffix : str
-            Suffix to append to _dataset_name based on processing steps
-            
-        NOTE : save_ parameters supercede current_ parameters
-
-        Returns
-        ----------
-        out : (tuple)
-            Filename : str
-            Path : str
-            Dataset_name_path : str
-        """
-        dialog = DialogSave(current_filename=current_filename,
-                            current_path=current_path,
-                            current_dataset_name=current_dataset_name,
-                            save_filename=save_filename,
-                            save_path=save_path,
-                            save_dataset_name=save_dataset_name,
-                            suffix=suffix, parent=parent)
-        
-        result = dialog.exec_()
-        if result == 1:
-            if dialog.filename is not None and dialog.path is not None and dialog.dataset_name is not None:
-                return (dialog.filename, dialog.path, dialog.dataset_name)
-            else:
-                return None
-        else:
-            return None

-
-if __name__ == '__main__':
-
-        
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    win = DialogSave.dialogSave()
-    print(win)
-
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/dialog_subResidualOptions.html b/docs/build/html/_modules/crikit/ui/dialog_subResidualOptions.html deleted file mode 100644 index eeb2177..0000000 --- a/docs/build/html/_modules/crikit/ui/dialog_subResidualOptions.html +++ /dev/null @@ -1,330 +0,0 @@ - - - - - - - - - - - crikit.ui.dialog_subResidualOptions — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
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    • - -
  • Module code »
    • - -
  • crikit.ui.dialog_subResidualOptions
    • - - -
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-
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Source code for crikit.ui.dialog_subResidualOptions

-"""
-
-
-References
-----------
-[1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \
-Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \
-Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543.
-"""
-
-import sys as _sys
-
-# Generic imports for QT-based programs
-from PyQt5.QtWidgets import (QApplication as _QApplication,
-                             QDialog as _QDialog)
-
-# Import from Designer-based GUI
-from crikit.ui.qt_SubResidualOptions import Ui_Dialog as Ui_ResidualOptions ### EDIT ###
-
-# Generic imports for MPL-incorporation
-import matplotlib as _mpl
-_mpl.use('Qt5Agg')
-_mpl.rcParams['font.family'] = 'sans-serif'
-_mpl.rcParams['font.size'] = 10
-
-
[docs]class DialogSubResidualOptions(_QDialog):
-    """
-    
-    """
-    RESIDUAL_FREQ = [-1500, -400]
-
-    def __init__(self, parent = None):
-        super(DialogSubResidualOptions, self).__init__(parent) ### EDIT ###
-        self.ui = Ui_ResidualOptions() ### EDIT ###
-        self.ui.setupUi(self)     ### EDIT ###
-
-        self.ui.spinBoxMax.setValue(self.RESIDUAL_FREQ[0])
-        self.ui.spinBoxMax.setValue(self.RESIDUAL_FREQ[1])
-        
-        
-
[docs]    @staticmethod
-    def dialogSubResidualOptions(parent = None,
-                                 imgloaded = False,
-                                 nrbloaded = False):
-        """
-        Retrieve dark subtraction dialog results
-
-        Parameters
-        ----------
-        imgloaded : (bool)
-            Is there an HSI image loaded?
-            
-        nrbloaded : (bool)
-            Is there an NRB loaded?
-
-        Returns
-        ----------
-        out : dict{'submain' : bool, 'subnrb' : bool, 'subrange' : list}
-            In order: subtract residual from image, subtract residual from NRB,
-            range to subtract from.
-        """
-        dialog = DialogSubResidualOptions(parent)
-        
-        # If nrb loaded, check and enable checkbox
-        dialog.ui.checkBoxBG.setChecked(nrbloaded)
-        dialog.ui.checkBoxBG.setEnabled(nrbloaded)
-        dialog.subnrb = nrbloaded
-        
-        # If img is loaded, check and enable checkbox
-        dialog.ui.checkBoxMain.setChecked(imgloaded)
-        dialog.ui.checkBoxMain.setEnabled(imgloaded)
-        dialog.submain = imgloaded
-        
-        result = dialog.exec_()
-
-        if result == 1:
-            ret = {}
-            freq = [dialog.ui.spinBoxMin.value(),
-                    dialog.ui.spinBoxMax.value()]
-            ret['subrange'] = freq
-            ret['submain'] = dialog.ui.checkBoxMain.isChecked()
-            ret['subnrb'] = dialog.ui.checkBoxBG.isChecked()
-            
-            return ret
-        else:
-            return None

-
-if __name__ == '__main__':
-
-
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    out = DialogSubResidualOptions.dialogSubResidualOptions(imgloaded=True, nrbloaded=True)
-    print(out)
-    app.exec_()
-    
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/dialog_varstabAnscombeOptions.html b/docs/build/html/_modules/crikit/ui/dialog_varstabAnscombeOptions.html deleted file mode 100644 index 1a9113b..0000000 --- a/docs/build/html/_modules/crikit/ui/dialog_varstabAnscombeOptions.html +++ /dev/null @@ -1,308 +0,0 @@ - - - - - - - - - - - crikit.ui.dialog_varstabAnscombeOptions — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.ui.dialog_varstabAnscombeOptions
    • - - -
  • - - - -
    • - -
- - -
-
-
-
- -

Source code for crikit.ui.dialog_varstabAnscombeOptions

-"""
-Created on Sat Jul 23 21:38:08 2016
-
-@author: chc
-"""
-import sys as _sys
-from PyQt5.QtWidgets import QApplication as _QApplication
-from PyQt5.QtWidgets import QDialog as _QDialog
-from crikit.ui.qt_AnscombeOptions import Ui_Dialog as Ui_AnscombeOptions
-
-
[docs]class DialogAnscombeOptions(_QDialog):
-    """
-    DialogAnscombeOptions : Anscombe Transformation options dialog
-
-    Methods
-    -------
-    dialogAnscombeOptions : Used to call UI and retrieve results of dialog
-
-    References
-    ----------
-    [1] C H Camp Jr, Y J Lee, and M T Cicerone, "Quantitative, Comparable Coherent \
-    Anti-Stokes Raman Scattering (CARS) Spectroscopy: Correcting Errors in Phase \
-    Retrieval," Journal of Raman Spectroscopy (2016). arXiv:1507.06543.
-
-    """
-    
-    def __init__(self, stddev=12.44, gain=1.4, parent = None):
-        super(DialogAnscombeOptions, self).__init__(parent) ### EDIT ###
-        self.ui = Ui_AnscombeOptions() ### EDIT ###
-        self.ui.setupUi(self)     ### EDIT ###
-
-        self.ui.spinBoxGain.setValue(gain)
-        self.ui.spinBoxStdDev.setValue(stddev)
-
-
-
[docs]    @staticmethod
-    def dialogAnscombeOptions(stddev=12.44, gain=1.4, parent=None):
-        """
-        Retrieve Anscombe Transform dialog results
-
-        Parameters
-        ----------
-        None : None
-
-        Returns
-        ----------
-        out : dict{'gain' : float, 'stddev' : float}
-            Standard deviation of Gaussian noise : (float)
-            Detector gain of Poisson noise : (float)
-        """
-        dialog = DialogAnscombeOptions(stddev=stddev, gain=gain, 
-                                       parent=parent)
-
-        result = dialog.exec_()
-
-        ret = {}
-
-        ret['stddev'] = dialog.ui.spinBoxStdDev.value()
-        ret['gain'] = dialog.ui.spinBoxGain.value()
-
-        if result == 1:
-            return ret
-        else:
-            return None

-            
-            
-if __name__ == '__main__':
-
-
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    out = DialogAnscombeOptions.dialogAnscombeOptions()
-    print(out)
-    app.exec_()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/helper_plotOptions.html b/docs/build/html/_modules/crikit/ui/helper_plotOptions.html deleted file mode 100644 index 96c6400..0000000 --- a/docs/build/html/_modules/crikit/ui/helper_plotOptions.html +++ /dev/null @@ -1,348 +0,0 @@ - - - - - - - - - - - crikit.ui.helper_plotOptions — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
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    • - -
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    • - -
  • crikit.ui.helper_plotOptions
    • - - -
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- - -
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-
-
- -

Source code for crikit.ui.helper_plotOptions

-"""
-Created on Sun Oct  4 00:28:16 2015
-
-@author: camp
-"""
-
-import numpy as _np
-from PyQt5.QtGui import (QColor as _QColor)
-
-
[docs]class plotStyle:
-
-    COLOR_DICT = {'Blue':[0, 0, 1],
-                  'Red':[1, 0, 0],
-                  'Green':[0, .5, 0],
-                  'Cyan':[0, .8, .8],
-                  'Magenta':[1, 0, 1],
-                  'Yellow':[.8, .8, 0]
-                  }
-
-    COLOR_VEC = ['Blue', 'Green', 'Red', 'Magenta', 'Yellow', 'Cyan']
-
-    LINEWIDTH = 1.0
-
-    MARKER_VEC = ['None',  #none
-                  '.',  #point
-                  ',',  #pixel
-                  'o',  #circle
-                  'v',  #triangle_down
-                  '^',  #triangle_up
-                  '<',  #triangle_left
-                  '>',  #triangle_right
-                  '8',  #octagon
-                  's',  #square
-                  'p',  #pentagon
-                  '*',  #star
-                  'h',  #hexagon1
-                  'H',  #hexagon2
-                  '+',  #plus
-                  'x',  #x
-                  'D',  #diamond
-                  'd',  #thin_diamond
-                  '|',  #vline
-                  '_']  #hline
-
-    MARKER_VEC_STR = ['None',
-                  'Point',
-                  'Pixel',
-                  'Circle',
-                  'Triangle Down',
-                  'Triangle Up',
-                  'Triangle Left',
-                  'Triangle Right',
-                  'Octagon',
-                  'Square',
-                  'Pentagon',
-                  'Star',
-                  'Hexagon 1',
-                  'Hexagon 2',
-                  'Plus',
-                  'X',
-                  'Diamond',
-                  'Thin Diamondd',
-                  'Vert Line',
-                  'Horiz Line']
-
-    MARKERSIZE=5.0
-    LINESTYLE_VEC = ['-', '--', '-.', ':', 'None']
-    LINESTYLE_VEC_STR = ['Solid','Dashed','Dash-Dot','Dotted','None']
-
-    def __init__(self, num_current_plots=0):
-
-        color, linestyle, marker = self.getLineStyle(num_current_plots=num_current_plots)
-
-        self.color = color
-        self.linewidth = self.LINEWIDTH
-        self.linestyle = linestyle
-        self.marker = marker
-        self.markersize = self.MARKERSIZE
-
-    @property
-    def linestyle_str(self):
-        index = self.LINESTYLE_VEC.index(self.linestyle)
-        return self.LINESTYLE_VEC_STR[index]
-
-    @property
-    def qcolor(self):
-        color = self.color
-        color_256 = [color[0]*255, color[1]*255, color[2]*255]
-        return _QColor(color_256[0], color_256[1], color_256[2])
-
-    @property
-    def marker_str(self):
-        index = self.MARKER_VEC.index(self.marker)
-        return self.MARKER_VEC_STR[index]
-
-
[docs]    def getLineStyle(self, num_current_plots = 0):
-        num_colors = len(self.COLOR_VEC)
-        num_linestyles = len(self.LINESTYLE_VEC)
-        num_markers = len(self.MARKER_VEC)
-
-        max_styles = num_colors*num_linestyles*num_markers
-
-        if num_current_plots > max_styles:
-            num_current_plots = num_current_plots - max_styles
-
-        color_iter = num_current_plots%num_colors
-        style_iter = int(_np.floor(num_current_plots/num_colors))%num_linestyles
-        marker_iter = int(_np.floor(num_current_plots/(num_colors*num_linestyles)))%num_markers
-
-        color = self.COLOR_DICT[self.COLOR_VEC[color_iter]]
-        #print(style_iter)
-        linestyle = self.LINESTYLE_VEC[style_iter]
-        marker = self.MARKER_VEC[marker_iter]
-
-        return (color, linestyle, marker)

-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/helper_roiselect.html b/docs/build/html/_modules/crikit/ui/helper_roiselect.html deleted file mode 100644 index fe40ba1..0000000 --- a/docs/build/html/_modules/crikit/ui/helper_roiselect.html +++ /dev/null @@ -1,428 +0,0 @@ - - - - - - - - - - - crikit.ui.helper_roiselect — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.ui.helper_roiselect

-"""
-"""
-
-# Append sys path
-import sys as _sys
-import os as _os
-
-
-# Generic imports for QT-based programs
-from PyQt5.QtWidgets import (QApplication as _QApplication,
-                             QWidget as _QWidget,
-                             QDialog as _QDialog,
-                             QMainWindow as _QMainWindow,
-                             QSizePolicy as _QSizePolicy,
-                             QTableWidgetItem as _QTableWidgetItem,
-                             QTableView as _QTableView,
-                             QColorDialog as _QColorDialog,
-                             QDoubleSpinBox as _QDoubleSpinBox,
-                             QComboBox as _QComboBox,
-                             QPushButton as _QPushButton,
-                             QLineEdit as _QLineEdit,
-                             QStyle as _QStyle,
-                             QStyledItemDelegate as _QStyledItemDelegate)
-
-from PyQt5.QtCore import (QAbstractItemModel as _QAbstractItemModel,
-                          QAbstractTableModel as _QAbstractTableModel,
-                          QModelIndex as _QModelIndex,
-                          QVariant as _QVariant,
-                          Qt as _Qt)
-
-from PyQt5.QtGui import (QPixmap as _QPixmap,
-                         QIcon as _QIcon,
-                         QColor as _QColor)
-
-# Other imports
-import numpy as _np
-
-# Import from Designer-based GUI
-from crikit.ui.helper_plotOptions import plotStyle
-
-# Generic imports for MPL-incorporation
-import matplotlib as _mpl
-_mpl.use('Qt5Agg')
-_mpl.rcParams['font.family'] = 'sans-serif'
-_mpl.rcParams['font.size'] = 10
-_mpl.rcParams['savefig.dpi'] = 300
-_mpl.rcParams['figure.figsize'] = (4, 4)
-#_mpl.rcParams['figure.autolayout'] = True
-_mpl.rcParams['legend.fontsize'] = 10
-
-from matplotlib.backends.backend_qt5agg import (FigureCanvasQTAgg as _FigureCanvas, \
-    NavigationToolbar2QT as _NavigationToolbar)
-
-from matplotlib.figure import Figure as _Figure
-
-
[docs]class _PointsData:
-    def __init__(self, num_current_plots=0):
-        self.x = None
-        self.y = None
-        self.xpix = None
-        self.ypix = None
-
-        self.style = plotStyle(num_current_plots)

-
-
-
[docs]class ImageSelection:
-    def __init__(self, parent=None):
-        self.pointdata_list = []
-
-    @property
-    def num_selections(self):
-        return len(self.pointdata_list)
-
-
[docs]    def clear_all(self):
-        self.__init__()

-
-
[docs]    def append_selection(self, xpix, ypix, x=None, y=None):
-        pt = _PointsData(self.num_selections)
-        if xpix is not None:
-            pt.xpix = xpix
-            pt.ypix = ypix
-
-            if (x is not None and y is not None):
-                pt.x = x
-                pt.y = y
-            else:
-                pt.x = xpix
-                pt.y = ypix
-        else:
-            pass
-        self.pointdata_list.append(pt)

-
-if __name__ == '__main__':
-
-    from PyQt5 import QtCore, QtGui, QtWidgets
-
-    class Ui_MainWindow(object):
-
-        def setupUi(self, MainWindow):
-            MainWindow.setObjectName("MainWindow")
-            MainWindow.resize(984, 658)
-            self.centralwidget = QtWidgets.QWidget(MainWindow)
-            self.centralwidget.setObjectName("centralwidget")
-            self.gridLayout = QtWidgets.QGridLayout(self.centralwidget)
-            self.gridLayout.setObjectName("gridLayout")
-            self.verticalLayout = QtWidgets.QVBoxLayout()
-            self.verticalLayout.setObjectName("verticalLayout")
-            self.pushbutton = QtWidgets.QPushButton('Test')
-            self.verticalLayout.addWidget(self.pushbutton)
-            self.gridLayout.addLayout(self.verticalLayout, 0, 0, 1, 1)
-            MainWindow.setCentralWidget(self.centralwidget)
-            self.menubar = QtWidgets.QMenuBar(MainWindow)
-            self.menubar.setGeometry(QtCore.QRect(0, 0, 984, 21))
-            self.menubar.setObjectName("menubar")
-            MainWindow.setMenuBar(self.menubar)
-            self.statusbar = QtWidgets.QStatusBar(MainWindow)
-            self.statusbar.setObjectName("statusbar")
-            MainWindow.setStatusBar(self.statusbar)
-
-            self.retranslateUi(MainWindow)
-            QtCore.QMetaObject.connectSlotsByName(MainWindow)
-
-        def retranslateUi(self, MainWindow):
-            _translate = QtCore.QCoreApplication.translate
-            MainWindow.setWindowTitle(_translate("MainWindow", "MainWindow"))
-
-    class testWindow(_QMainWindow):
-        def __init__(self, parent=None):
-            super(testWindow, self).__init__(parent) ### EDIT ###
-            self.ui = Ui_MainWindow() ### EDIT ###
-            self.ui.setupUi(self)     ### EDIT ###
-
-    def buttonPress():
-        winTest.cid = winTest.ui.mpl.canvas.mpl_connect('button_press_event', pointClick)
-
-    def pointClick(event):
-        if event.inaxes == winTest.ui.mpl.ax:
-            x = int(_np.round(event.xdata))
-            y = int(_np.round(event.ydata))
-
-
-            selectiondata.append_selection(x,y)
-            updatePlot()
-            winTest.ui.mpl.canvas.mpl_disconnect(winTest.cid)
-
-    def updatePlot():
-        winTest.ui.mpl.ax.clear()
-        winTest.ui.mpl.img = winTest.ui.mpl.ax.imshow(data_slice, interpolation='none', cmap = _mpl.cm.gray , origin='lower')
-        getx = winTest.ui.mpl.ax.get_xlim()
-        gety = winTest.ui.mpl.ax.get_ylim()
-
-        winTest.ui.mpl.ax.hold(True)
-        for pts in selectiondata.pointdata_list:
-            winTest.ui.mpl.ax.plot(pts.x, pts.y,
-                                   marker='+',
-                                   markersize=pts.style.markersize,
-                                   markerfacecolor=pts.style.color,
-                                   markeredgecolor=pts.style.color,
-                                   linestyle='None')
-
-        winTest.ui.mpl.ax.set_xlim(getx)
-        winTest.ui.mpl.ax.set_ylim(gety)
-
-        winTest.ui.mpl.canvas.draw()
-
-    class _winMpl:
-        def __init__(self):
-            self.fig = None
-            self.ax = None
-            self.img = None
-            self.canvas = None
-            self.toolbar = None
-
-    app = _QApplication(_sys.argv)
-
-    winTest = testWindow()
-    winTest.ui.mpl = _winMpl()
-    winTest.ui.mpl.fig = _Figure()
-    winTest.ui.mpl.ax = winTest.ui.mpl.fig.add_subplot(111)
-
-    data = _np.random.rand(20,20,50)
-    data_slice = data[:,:,25]
-
-    winTest.ui.mpl.img = winTest.ui.mpl.ax.imshow(data_slice, interpolation='none', cmap = _mpl.cm.gray , origin='lower')
-    winTest.ui.mpl.canvas = _FigureCanvas(winTest.ui.mpl.fig)
-
-    winTest.ui.verticalLayout.insertWidget(0,winTest.ui.mpl.canvas)
-
-    winTest.ui.pushbutton.pressed.connect(buttonPress)
-
-    winTest.show()
-
-    selectiondata = ImageSelection()
-
-    _sys.exit(app.exec_())
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/subui_hdf_load.html b/docs/build/html/_modules/crikit/ui/subui_hdf_load.html deleted file mode 100644 index 3dded26..0000000 --- a/docs/build/html/_modules/crikit/ui/subui_hdf_load.html +++ /dev/null @@ -1,456 +0,0 @@ - - - - - - - - - - - crikit.ui.subui_hdf_load — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
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Source code for crikit.ui.subui_hdf_load

-"""
-HDF5 LOAD DATA QDialog (crikit.vis.subguis.h5loadgui)
-=======================================================
-
-    H5LoadGUI : A graphical user interface (GUI) to select HDF5 dataset(s)
-
-    Method : H5LoadGUI.getFileDataSets()
-
-    Return (tuple) : (path [str], filename [str], dataset(s) [list], selection_made [bool])
-
-"""
-
-
-# Append sys path
-import sys as _sys
-import os as _os
-
-# Generic imports for QT-based programs
-from PyQt5.QtWidgets import (QApplication as _QApplication, \
-QDialog as _QDialog, QFileDialog as _QFileDialog, \
-QTableWidgetItem as _QTableWidgetItem)
-
-# Other imports
-import numpy as _np
-import crikit.utils.h5 as _h5utils
-
-# Import from Designer-based GUI
-from crikit.ui.qt_HDFLoad import Ui_Dialog ### EDIT ###
-
-
[docs]class SubUiHDFLoad(_QDialog): ### EDIT ###
-    """ GUI Loader Class for H5 Files """
-
-    def __init__(self, parent = None):
-
-        # Generic load/init designer-based GUI
-        super(SubUiHDFLoad, self).__init__(parent) ### EDIT ###
-        self.ui = Ui_Dialog() ### EDIT ###
-        self.ui.setupUi(self)     ### EDIT ###
-
-        # Set static GUI  parameters
-
-        # Set signal(s)-slot(s) connection/actions
-
-        self.ui.pushButtonOk.clicked.connect(self.accept)
-        self.ui.pushButtonCancel.clicked.connect(self.reject)
-        self.ui.dataGroupSelect.currentTextChanged.connect(self.datagroupchange)
-        self.ui.dataSetList.itemClicked.connect(self.datasetselected)
-        self.ui.filterButton.clicked.connect(self.filterlist)
-        self.ui.resetFilter.clicked.connect(self.datagroupchange)
-        # Setup GUI variables
-        self.path = None
-        self.filename = None
-        self.allselect=None
-        # Initial Actions
-
-
[docs]    @staticmethod
-    def getFileDataSets(start_path='./', parent = None):
-        """
-        Retrieve the filename and datasets selected by the user (via GUI)
-
-        Parameters
-        ----------
-        start_path : str
-            Home directory to start in
-
-        Returns
-        ----------
-        out : (tuple)
-            path : str
-            filename : (str)
-            dataset(s) : (list[str])
-        """
-        if start_path is None:
-            start_path = './'
-            
-        dialog = SubUiHDFLoad(parent)
-
-        ret_fileopen = dialog.fileopen(start_path)
-
-        if ret_fileopen is None:
-            return None
-
-        # Execute dialog, which defined by QDialog class returns
-        # QDialog.Accepted or QDialog.Rejected
-        ret_dset_select = dialog.exec_()
-        if ret_dset_select == _QDialog.Rejected:
-            return None
-        elif dialog.allselect is None:
-            return None
-        else:
-            return (dialog.path, dialog.filename, dialog.allselect)

-
-
[docs]    def fileopen(self, start_path='./'):
-        """ Select HDF5 File """
-
-        if start_path is None:
-            start_path = './'
-            
-        filename = _QFileDialog.getOpenFileName(self, "Open H5 File", 
-                                                start_path,\
-            "HDF5 Files (*.h5 *.hdf);;All Files (*.*)")
-
-        if filename[0]:
-            self.filename = filename[0]
-            self.path = _os.path.dirname(self.filename) + '/'
-            self.filename = self.filename.split(_os.path.dirname(self.filename))[1][1::]
-
-            self.group_dset_dict = _h5utils.retrieve_group_dataset_dict(self.path + self.filename)
-            self.ui.dataGroupSelect.clear()
-            for count in self.group_dset_dict:
-                self.ui.dataGroupSelect.addItem(count)
-            return [self.path, self.filename]
-        else:
-            return None

-
[docs]    def datagroupchange(self):
-        """ Action : ComboBox containing Groups with DataSets has changed"""
-
-        #self.dsetlist = QListWidget(self.verticalLayoutWidget)
-        self.ui.dataSetList.clear()
-        self.ui.dataSetList.addItems(self.group_dset_dict[self.ui.dataGroupSelect.currentText()])

-        #print('Changed')
-
-
[docs]    def datasetselected(self):
-        """ Action : One or more DataSets were selected from the list """
-
-        #print('Selection changed')
-        self.currentdset = self.ui.dataGroupSelect.currentText() + '/' + \
-            self.ui.dataSetList.currentItem().text()
-
-#        print('Current Selection : {}'.format(self.currentdset))
-        self.allselect = ['/' + str(self.ui.dataGroupSelect.currentText() +\
-            '/' + i.text()) for i in self.ui.dataSetList.selectedItems()]
-
-
-        if len(self.allselect) == 0:
-            self.allselect = None
-            self.ui.currentDatasetText.setText('')
-            attrs = {}
-            self.ui.dataSetAttribs.setRowCount(0)
-            self.ui.dataSetMemo.setText('')
-        else:
-            if len(self.allselect) == 1:
-                self.ui.currentDatasetText.setText(self.currentdset)
-            else:
-                self.ui.currentDatasetText.setText(self.currentdset + ' ( + ' +\
-                    str(len(self.allselect)-1) + ' others)' )
-
-            self.ui.dataSetAttribs.setSortingEnabled(False)
-            self.ui.dataSetAttribs.setRowCount(0)
-            self.ui.dataSetAttribs.setColumnCount(2)
-
-            attrs = _h5utils.retrieve_dataset_attribute_dict(self.path + self.filename,self.currentdset)
-
-            for count, key in enumerate(attrs.keys()):
-                self.ui.dataSetAttribs.insertRow(self.ui.dataSetAttribs.rowCount())
-                self.ui.dataSetAttribs.setItem(count,0,_QTableWidgetItem(str(key)))
-                temp = attrs[key]
-                if isinstance(temp,_np.bytes_):
-                    self.ui.dataSetAttribs.setItem(count,1,_QTableWidgetItem(temp.decode()))
-                else:
-                    self.ui.dataSetAttribs.setItem(count,1,_QTableWidgetItem(str(temp)))
-
-            self.ui.dataSetAttribs.setSortingEnabled(True)
-            self.ui.dataSetAttribs.sortItems(0)
-
-            try:
-                self.ui.dataSetMemo.setText(attrs['Memo'].decode())
-            except:
-                pass

-
-
[docs]    def filterlist(self):
-        """ Action : Filter available dataset list (.ui.dataSetList) based on
-        include or exclude strings (or comma-separated strings)
-        """
-
-        temp_list = []
-
-        for count in range(self.ui.dataSetList.count()):
-            temp_list.append(self.ui.dataSetList.item(count).text())
-
-        temp_list_filt = temp_list
-
-        # Has strings to Exclude
-        if self.ui.filterExcludeString.text() != '':
-            # Convert comma-separated string to list-of-strings
-            strexclude = str.split(self.ui.filterExcludeString.text(),',')
-
-            # Strip white-space
-            strexclude = [str.strip(strexclude) for strexclude in strexclude]
-
-            # Exclude Filter
-            for count in strexclude[0::]:
-                temp_list_filt = ([i for i in temp_list_filt if str.find(i,count) == -1])
-                #print(count)
-        else:
-            pass
-
-        # Has strings to Include
-        if self.ui.filterIncludeString.text() != '':
-            # Convert comma-separated string to list-of-strings
-            strinclude = str.split(self.ui.filterIncludeString.text(),',')
-
-            # Strip white-space
-            strinclude = [str.strip(strinclude) for strinclude in strinclude]
-
-            # Include Filter
-            for count in strinclude:
-                temp_list_filt = ([i for i in temp_list_filt if str.find(i,count) != -1])
-        else:
-            pass
-
-        # Update GUI
-        self.ui.dataSetList.clear()
-        self.ui.dataSetList.addItems(temp_list_filt)

-
-if __name__ == '__main__':
-
-    app = _QApplication(_sys.argv)
-    #win = H5LoadGUI() ### EDIT ###
-    result = SubUiHDFLoad.getFileDataSets()
-    print('Result: {}'.format(result))
-
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/utils/roi.html b/docs/build/html/_modules/crikit/ui/utils/roi.html deleted file mode 100644 index 25e3ede..0000000 --- a/docs/build/html/_modules/crikit/ui/utils/roi.html +++ /dev/null @@ -1,307 +0,0 @@ - - - - - - - - - - - crikit.ui.utils.roi — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
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- - - - - - - - - - - - - - - - -
- - - - -
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- -

Source code for crikit.ui.utils.roi

-"""
-Visualization General Utilities (crikit.ui.visgentuils)
-=======================================================
-
-    roimask : Create a region-of-interest binary mask
-
-"""
-
-from matplotlib.path import Path as _Path
-import numpy as _np
-
-
-
[docs]def roimask(imgx, imgy, xvec, yvec):
-    """
-    Create a region-of-interest binary mask from vertices.
-
-    Parameters
-    ----------
-    imgx : ndarray
-        X-axis vector in physical units
-
-    imgy : ndarray
-        Y-axis vector in physical units
-
-    xvec : ndarray
-        Vector of x-locations of selected points
-
-    yvec : ndarray
-        Vector of y-locations of selected points
-
-    Returns
-    -------
-    mask : ndarray
-        Binary mask
-
-    path : MPL path object
-        Matplotlib path object describing ROI
-    """
-    verts = _pts_to_verts(xvec, yvec)
-    path = _verts_to_path(verts)
-    mask = _mask_from_path(imgx, imgy, path)
-    return (mask, path)

-
-
-
[docs]def _pts_to_verts(xvec, yvec):
-    """
-    Convert points to vertices, i.e., convert from 2 1D arrays (or list) of \
-    x- and y-coordinates to a list-of-lists of [x,y] pairs
-    """
-    verts = []
-    for count in range(len(xvec)):
-        verts.append([xvec[count],yvec[count]])
-    return verts

-
-
-
[docs]def _verts_to_path(verts, isclose = True):
-    """
-    Convert vertices to paths
-    """
-    if not isclose:
-        verts += verts[0]
-    else:
-        pass
-    codes = [_Path.MOVETO] + [_Path.LINETO]*(len(verts)-2) + [_Path.CLOSEPOLY]
-    return _Path(verts, codes)

-
-
-
[docs]def _mask_from_path(x, y, path):
-    """
-    Create mask from path
-    """
-    X, Y = _np.meshgrid(x, y)
-    allpts = _np.hstack((X.flatten()[:, None], Y.flatten()[:, None]))
-    return _np.reshape(path.contains_points(allpts, radius=1e-12),[y.size, x.size])

-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_ALS.html b/docs/build/html/_modules/crikit/ui/widget_ALS.html deleted file mode 100644 index 844d2e2..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_ALS.html +++ /dev/null @@ -1,516 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_ALS — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
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- - - - - - - - - - - - - - - - -
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    - -
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    • - -
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    • - -
  • crikit.ui.widget_ALS
    • - - -
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    • - -
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- -

Source code for crikit.ui.widget_ALS

-"""
-Widget for PlotEffect that adjusts the parameters appropriate for
-asymmetric least squares (ALS)
-
-Created on Thu Dec 22 01:16:01 2016
-
-@author: chc
-"""
-import numpy as _np
-
-from crikit.ui.dialog_AbstractPlotEffect import (AbstractPlotEffectPlugin
-                                                 as _AbstractPlotEffectPlugin)
-
-from crikit.ui.qt_PlotEffect_ALS import Ui_Form as _Ui_Form
-
-from crikit.ui.widget_scientificspin import (ScientificDoubleSpinBox as
-                                             _SciSpin)
-
-from crikit.preprocess.algorithms.als import AlsCvxopt as _Als
-
-
[docs]class widgetALS(_AbstractPlotEffectPlugin):
-    """
-    Widget for PlotEffect that adjusts the parameters appropriate for
-    asymmetric least squares (ALS)
-    
-    Parameters
-    ----------
-    smoothness_param : float, optional (default, 1e3)
-        Smoothness parameter
-
-    asym_param : float, optional (default, 1e-4)
-        Assymetry parameter
-        
-    redux : int, optional (default, 1)
-        Reduction parameter to sub-sample input signal
-        
-    order : int, optional (default, 2)
-        Derivative regularization term. Order=2 for Whittaker-smoother
-    
-    fix_end_points : bool, optional (default, False)
-        Weight the baseline endpoints to approach equally the end-points
-        of the data.
-    
-    max_iter : int, optional (default, 100)
-        Maximum number of least-squares iterations to perform
-        
-    min_diff : float, optional (default, 1e-5)
-        Break iterative calculations if difference is less than min_diff
-        
-    parent: QObject
-        Parent
-        
-    Methods
-    -------
-    fcn : Perform ALS detrending
-    
-    Signals:
-        changed : a value in the UI has changed
-    """
-    
-    # Parameter dict that will be returned from PlotEffect
-    # Will be updated later in program to contain all parameters
-    # to pass to underlying algorithm
-    parameters = {'name' : 'ALS', 
-                  'long_name' : 'Asymmetric least squares'}
-    
-    # Labeling options for original data plot
-    labels_orig = {
-                   'x_label' : 'Wavenumber (cm$^{-1}$)',
-                   'y_label' : 'Input Int (au)',
-                   'title' : 'Original'
-                   }
-    
-    # Labeling options for affected data plot              
-    labels_affected = {
-                       'x_label' : labels_orig['x_label'],
-                       'y_label' : 'Output Int (au)',
-                       'title' : 'Detrended'
-                      }
-                      
-    def __init__(self, asym_param=1e-2, smoothness_param=1, redux=10,
-                 pstart=1e-2, pend=1e-3, fixed_p=False, fix_end_points=True, 
-                 max_iter=100, min_diff=1e-6, parent = None):
-                      
-        super(widgetALS, self).__init__(parent) ### EDIT ###
-        
-        self.ui = _Ui_Form()
-        self.ui.setupUi(self)
-        
-        # Update parameter dict
-        self.parameters['smoothness_param'] = smoothness_param
-        self.parameters['asym_param'] = asym_param
-        self.parameters['fixed_p'] = fixed_p
-        self.parameters['asym_param_start'] = pstart
-        self.parameters['asym_param_end'] = pend
-        self.parameters['redux'] = redux
-        self.parameters['fix_end_points'] = fix_end_points
-        self.parameters['max_iter'] = max_iter
-        self.parameters['min_diff'] = min_diff
-        
-        self.setup_asym()  # Setup controls for asymmetry parameter
-        self.setup_smoothness()  # Setup controls for smoothness parameter
-        
-        # Redux factor
-        self.ui.spinBoxRedux.setValue(self.parameters['redux'])
-
-        # Fixed ends
-        self.ui.checkBox.setChecked(self.parameters['fix_end_points'])
-        
-        # Max iterations
-        self.ui.spinBoxMaxIter.setValue(self.parameters['max_iter'])
-        
-        # Min Difference
-        self.ui.spinBoxMinDiff = _SciSpin()
-        self.ui.verticalLayout_9.insertWidget(4, self.ui.spinBoxMinDiff)
-        self.ui.spinBoxMinDiff.setValue(self.parameters['min_diff'])
-        
-        # SIGNALS & SLOTS
-        self.ui.spinBoxP.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxLambda.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxRedux.editingFinished.connect(self.spinBoxChanged)
-        
-        self.ui.spinBoxPStart.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxPEnd.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxMaxIter.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxMinDiff.editingFinished.connect(self.spinBoxChanged)
-        
-        self.ui.radioButtonFixedP.clicked.connect(self.selectFixedOrLog)
-        self.ui.radioButtonLogLinearP.clicked.connect(self.selectFixedOrLog)
-        self.ui.checkBox.clicked.connect(self.selectFixedEnds)
-        
-    
-
[docs]    def fcn(self, data_in):
-        """
-        If return list, [0] goes to original, [1] goes to affected
-        """
-        
-        data_out = _np.zeros(data_in.shape)
-        baseline = _np.zeros(data_in.shape)
-        
-        if callable(self.parameters['asym_param']):
-            self.parameters['asym_param'] = \
-                self.parameters['asym_param'](data_in.shape[-1])
-        
-        smoothness_param = self.parameters['smoothness_param']
-        asym_param = self.parameters['asym_param']
-        redux = self.parameters['redux']
-        fep = self.parameters['fix_end_points']
-        max_iter = self.parameters['max_iter']
-        min_diff = self.parameters['min_diff']
-        
-        _als = _Als(smoothness_param=smoothness_param, 
-                    asym_param=asym_param, 
-                    redux=redux, fix_end_points=fep, 
-                    max_iter=max_iter, 
-                    min_diff=min_diff)
-        
-        if data_in.ndim == 1:
-            baseline = _als.calculate(data_in)
-            data_out = data_in - baseline
-        else:
-            for num, spectrum in enumerate(data_in):
-                baseline[num,:] = _als.calculate(spectrum)
-                data_out[num,:] = spectrum - baseline[num,:]
-        return [baseline, data_out]

-        
-    
-
[docs]    def setup_smoothness(self):
-        """ 
-        Lambda/smoothness parameter rlated
-        """
-        
-        self.ui.label_2.setText('{} (Smoothness)'.format(u'\u03BB'))
-        self.ui.spinBoxLambda = _SciSpin()
-        self.ui.verticalLayout_2.insertWidget(1, self.ui.spinBoxLambda)
-        self.ui.spinBoxLambda.setValue(self.parameters['smoothness_param'])

-        
-
[docs]    def setup_asym(self):
-        """
-        P/asymmetry parameter related
-        """
-        
-        
-        self.ui.spinBoxP = _SciSpin()
-        self.ui.verticalLayout.insertWidget(1, self.ui.spinBoxP)
-        self.ui.spinBoxP.setValue(self.parameters['asym_param'])
-        if self.parameters['fixed_p']:
-            self.ui.radioButtonFixedP.setChecked(True)
-            self.ui.radioButtonLogLinearP.setChecked(False)
-        else:
-            self.ui.radioButtonFixedP.setChecked(False)
-            self.ui.radioButtonLogLinearP.setChecked(True)
-        self.selectFixedOrLog()
-            
-        self.ui.spinBoxPStart = _SciSpin()
-        self.ui.verticalLayout_5.insertWidget(1, self.ui.spinBoxPStart)
-        self.ui.spinBoxPStart.setValue(self.parameters['asym_param_start'])
-        
-        self.ui.spinBoxPEnd = _SciSpin()
-        self.ui.verticalLayout_6.insertWidget(1, self.ui.spinBoxPEnd)
-        self.ui.spinBoxPEnd.setValue(self.parameters['asym_param_end'])

-        
-
[docs]    def spinBoxChanged(self):
-        """
-        Controller for all spinBoxes
-        """
-
-        sdr = self.sender()
-        
-        if sdr == self.ui.spinBoxPStart:
-            self.parameters['asym_param_start'] = self.ui.spinBoxPStart.value()
-            self.selectFixedOrLog()
-            
-        elif sdr == self.ui.spinBoxPEnd:
-            self.parameters['asym_param_end'] = self.ui.spinBoxPEnd.value()
-            self.selectFixedOrLog()
-            
-        elif sdr == self.ui.spinBoxLambda:
-            self.parameters['smoothness_param'] = self.ui.spinBoxLambda.value()
-        
-        elif sdr == self.ui.spinBoxP:
-            self.parameters['asym_param'] = self.ui.spinBoxP.value()
-    
-        elif sdr == self.ui.spinBoxRedux:
-            self.parameters['redux'] = self.ui.spinBoxRedux.value()
-            
-        elif sdr == self.ui.spinBoxMaxIter:
-            self.parameters['max_iter'] = self.ui.spinBoxMaxIter.value()
-            
-        elif sdr == self.ui.spinBoxMinDiff:
-            self.parameters['min_diff'] = self.ui.spinBoxMinDiff.value()
-            
-        self.changed.emit()

-        
-
[docs]    def selectFixedEnds(self):
-        """
-        Check selection of fixed end-points
-        """
-        
-        self.parameters['fix_end_points'] =self.ui.checkBox.isChecked()
-        self.changed.emit()

-        
-
[docs]    def selectFixedOrLog(self):
-        """
-        Check fixed or log-linear asymmetry parameter
-        """
-        
-        self.parameters['fixed_p'] = self.ui.radioButtonFixedP.isChecked()
-        if self.parameters['fixed_p']:
-            self.ui.radioButtonFixedP.setChecked(True)
-            self.ui.radioButtonLogLinearP.setChecked(False)
-            self.ui.frame_2.setEnabled(False)
-            self.ui.frame.setEnabled(True)
-#            self.p = lambda x: self.ui.spinBoxP.value()
-            self.parameters['asym_param'] = self.ui.spinBoxP.value()
-            
-        else:
-            self.ui.radioButtonFixedP.setChecked(False)
-            self.ui.radioButtonLogLinearP.setChecked(True)
-            self.ui.frame_2.setEnabled(True)
-            self.ui.frame.setEnabled(False)
-            self.parameters['asym_param'] = \
-                lambda x: _np.logspace(_np.log10(self.parameters['asym_param_start']),
-                                       _np.log10(self.parameters['asym_param_end']),x) 
-
-        self.changed.emit()

-        
-        
-if __name__ == '__main__':
-    import sys as _sys
-    from PyQt5.QtWidgets import (QApplication as _QApplication)
-    
-    
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    winALS = widgetALS()
-    
-    winALS.show()
-    
-    app.exec_()
-    print(winALS.parameters)
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_ArPLS.html b/docs/build/html/_modules/crikit/ui/widget_ArPLS.html deleted file mode 100644 index ad780ca..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_ArPLS.html +++ /dev/null @@ -1,432 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_ArPLS — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    • - -
  • crikit.ui.widget_ArPLS
    • - - -
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Source code for crikit.ui.widget_ArPLS

-"""
-Widget for PlotEffect that adjusts the parameters appropriate for
-asymmetrically reweights penalized least squares (arPLS)
-
-Created on Thu Dec 22 01:16:01 2016
-
-@author: chc
-"""
-import numpy as _np
-
-from crikit.ui.dialog_AbstractPlotEffect import (AbstractPlotEffectPlugin
-                                                     as
-                                                     _AbstractPlotEffectPlugin)
-
-from crikit.ui.qt_PlotEffect_ArPLS import Ui_Form as _Ui_Form
-
-from crikit.ui.widget_scientificspin import (ScientificDoubleSpinBox as
-                                             _SciSpin)
-
-from crikit.preprocess.algorithms.arpls import ArPlsCvxopt as _Arpls
-
-
[docs]class widgetArPLS(_AbstractPlotEffectPlugin):
-    """
-    Widget for PlotEffect that adjusts the parameters appropriate for
-    asymmetrically reweights penalized least squares (arPLS)
-    
-    Parameters
-    ----------
-    smoothness_param : float, optional (default, 1e3)
-        Smoothness parameter
-
-    redux : int, optional (default, 1)
-        Reduction parameter to sub-sample input signal
-        
-    order : int, optional (default, 2)
-        Derivative regularization term. Order=2 for Whittaker-smoother
-    
-    fix_end_points : bool, optional (default, False)
-        Weight the baseline endpoints to approach equally the end-points
-        of the data.
-    
-    max_iter : int, optional (default, 100)
-        Maximum number of least-squares iterations to perform
-        
-    min_diff : float, optional (default, 1e-5)
-        Break iterative calculations if difference is less than min_diff
-        
-    parent: QObject
-        Parent
-        
-    Methods
-    -------
-    fcn : Perform arPLS detrending
-    
-    Signals:
-        changed : a value in the UI has changed
-    """
-    
-    # Parameter dict that will be returned from PlotEffect
-    # Will be updated later in program to contain all parameters
-    # to pass to underlying algorithm
-    parameters = {'name' : 'arPLS', 
-                  'long_name' : 'Asymmetrically reweighted penalized least \
-                  squares'}
-    
-    # Labeling options for original data plot
-    labels_orig = {
-                   'x_label' : 'Wavenumber (cm$^{-1}$)',
-                   'y_label' : 'Input Int (au)',
-                   'title' : 'Original'
-                   }
-    
-    # Labeling options for affected data plot                             
-    labels_affected = {
-                       'x_label' : labels_orig['x_label'],
-                       'y_label' : 'Output Int (au)',
-                       'title' : 'Detrended'
-                      }
-                      
-    def __init__(self, smoothness_param=1, redux=1, fix_end_points=True, 
-                 max_iter=100, min_diff=1e-6, parent = None):
-                      
-        super(widgetArPLS, self).__init__(parent) ### EDIT ###
-        
-        self.ui = _Ui_Form()
-        self.ui.setupUi(self)##
-        
-        # Update parameter dict
-        self.parameters['smoothness_param'] = smoothness_param
-        self.parameters['redux'] = redux
-        self.parameters['fix_end_points'] = fix_end_points
-        self.parameters['max_iter'] = max_iter
-        self.parameters['min_diff'] = min_diff
-        
-        
-        # Lambda/smoothness parameter rlated
-        self.ui.label_2.setText('{} (Smoothness)'.format(u'\u03BB'))
-        self.ui.spinBoxLambda = _SciSpin()
-        self.ui.verticalLayout_2.insertWidget(1, self.ui.spinBoxLambda)
-        self.ui.spinBoxLambda.setValue(self.parameters['smoothness_param'])
-                
-        # Redux factor
-        self.ui.spinBoxRedux.setValue(self.parameters['redux'])
-
-        # Fixed ends
-        self.ui.checkBox.setChecked(self.parameters['fix_end_points'])
-        
-        # Max iterations
-        self.ui.spinBoxMaxIter.setValue(self.parameters['max_iter'])
-        
-        # Min Difference
-        self.ui.spinBoxMinDiff = _SciSpin()
-        self.ui.verticalLayout_9.insertWidget(4, self.ui.spinBoxMinDiff)
-        self.ui.spinBoxMinDiff.setValue(self.parameters['min_diff'])
-        
-        # SIGNALS & SLOTS
-        self.ui.spinBoxLambda.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxRedux.editingFinished.connect(self.spinBoxChanged)
-        
-        self.ui.spinBoxMaxIter.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxMinDiff.editingFinished.connect(self.spinBoxChanged)
-        
-        self.ui.checkBox.clicked.connect(self.selectFixedEnds)
-        
-    
-
[docs]    def fcn(self, data_in):
-        """
-        If return list, [0] goes to original, [1] goes to affected
-        """
-        
-        data_out = _np.zeros(data_in.shape)
-        baseline = _np.zeros(data_in.shape)
-               
-        smoothness_param = self.parameters['smoothness_param']
-        redux = self.parameters['redux']
-        fep = self.parameters['fix_end_points']
-        max_iter = self.parameters['max_iter']
-        min_diff = self.parameters['min_diff']
-        
-        _arpls = _Arpls(smoothness_param=smoothness_param, 
-                        redux=redux, fix_end_points=fep, 
-                        max_iter=max_iter, 
-                        min_diff=min_diff, verbose=False)
-        
-        if data_in.ndim == 1:
-            baseline = _arpls.calculate(data_in)
-            data_out = data_in - baseline
-        else:
-            for num, spectrum in enumerate(data_in):
-                baseline[num,:] = _arpls.calculate(spectrum)
-                data_out[num,:] = spectrum - baseline[num,:]
-        return [baseline, data_out]

-        
-    
-
[docs]    def spinBoxChanged(self):
-        """
-        Controller for all spinBoxes
-        """
-        
-        sdr = self.sender()
-        
-        if sdr == self.ui.spinBoxLambda:
-            self.parameters['smoothness_param'] = self.ui.spinBoxLambda.value()
-        
-        elif sdr == self.ui.spinBoxRedux:
-            self.parameters['redux'] = self.ui.spinBoxRedux.value()
-            
-        elif sdr == self.ui.spinBoxMaxIter:
-            self.parameters['max_iter'] = self.ui.spinBoxMaxIter.value()
-            
-        elif sdr == self.ui.spinBoxMinDiff:
-            self.parameters['min_diff'] = self.ui.spinBoxMinDiff.value()
-            
-        self.changed.emit()

-        
-
[docs]    def selectFixedEnds(self):
-        """
-        Check selection of fixed end-points
-        """
-        
-        self.parameters['fix_end_points'] =self.ui.checkBox.isChecked()
-        self.changed.emit()

-        
-        
-if __name__ == '__main__':
-    import sys as _sys
-    from PyQt5.QtWidgets import (QApplication as _QApplication)
-    
-    
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    winArPLS = widgetArPLS()
-    
-    winArPLS.show()
-    
-    app.exec_()
-    print(winArPLS.parameters)
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_Calibrate.html b/docs/build/html/_modules/crikit/ui/widget_Calibrate.html deleted file mode 100644 index f8b657a..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_Calibrate.html +++ /dev/null @@ -1,446 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_Calibrate — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.ui.widget_Calibrate

-"""
-Widget for PlotEffect that adjusts the parameters appropriate for
-calibration
-
-Created on Thu Dec 22 14:27:46 2016
-
-@author: chc
-"""
-import copy as _copy
-
-import numpy as _np
-
-from crikit.ui.dialog_AbstractPlotEffect import (AbstractPlotEffectPlugin
-                                                 as _AbstractPlotEffectPlugin)
-
-from scipy.interpolate import UnivariateSpline as _UnivariateSpline
-
-from crikit.data.frequency import (calib_pix_wn as _calib_pix_wn)
-
-#from crikit.utils.general import find_nearest as _find_nearest
-
-from crikit.ui.qt_PlotEffect_Calibrate import Ui_Form as _Ui_Form
-
-
-
[docs]class widgetCalibrate(_AbstractPlotEffectPlugin):
-    """
-    Widget for PlotEffect that adjusts the parameters appropriate for
-    calibration
-    
-    Parameters
-    ----------
-    calib_dict : dict
-        Calibration dictionary
-        
-    Methods
-    -------
-    fcn : Perform arPLS detrending
-    
-    Signals:
-        changed : a value in the UI has changed
-        
-    """
-    # Parameter dict that will be returned from PlotEffect
-    # Will be updated later in program to contain all parameters
-    # to pass to underlying algorithm
-    parameters = {'name' : 'Calibrate', 
-                  'long_name' : 'Spectral Calibration'}
-    
-    # Labeling options for original data plot
-    labels_orig = {
-                   'x_label' : 'Wavenumber (cm$^{-1}$)',
-                   'y_label' : 'Input Int (au)',
-                   'title' : 'Uncalibrated'
-                   }
-    
-    # Labeling options for affected data plot                             
-    labels_affected = {
-                       'x_label' : labels_orig['x_label'],
-                       'y_label' : 'Output Int (au)',
-                       'title' : 'Calibrated'
-                      }
-
-    def __init__(self, calib_dict, parent=None):
-        super(widgetCalibrate, self).__init__(parent) ### EDIT ###
-        
-        self.ui = _Ui_Form() 
-        self.ui.setupUi(self)    
-
-        self.parameters['orig_calib_dict'] = calib_dict
-        
-        if isinstance(self.parameters['orig_calib_dict']['a_vec'], tuple):
-            self.parameters['orig_calib_dict']['a_vec'] = \
-                list(self.parameters['orig_calib_dict']['a_vec'])
-
-        self.parameters['new_calib_dict'] = \
-            _copy.deepcopy(self.parameters['orig_calib_dict'])
-
-        self.setup_calib()
-#        self.orig_wn = _calib_pix_wn(self.parameters['orig_calib_dict'])
-#        self.new_wn = _calib_pix_wn(self.parameters['new_calib_dict'])
-
-        self.ui.spinBoxMeas.setValue(1004.0)
-        self.ui.spinBoxCorrect.setValue(1004.0)
-
-        # SIGNALS & SLOTS    
-        # New
-        self.ui.spinBoxNPix_2.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxCenterWL_2.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxProbeWL_2.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxIntercept_2.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxSlope_2.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxCalibWL_2.editingFinished.connect(self.spinBoxChanged)
-        
-        self.ui.spinBoxCorrect.editingFinished.connect(self.meas_vs_ideal)
-        self.ui.spinBoxMeas.editingFinished.connect(self.meas_vs_ideal)
-
-
[docs]    def spinBoxChanged(self):
-        """
-        Controller for all spinBoxes
-        """
-        
-        sdr = self.sender()
-        
-        # Original
-        if sdr == self.ui.spinBoxNPix_2:
-            self.parameters['new_calib_dict']['n_pix'] = \
-                self.ui.spinBoxNPix_2.value()
-        
-        elif sdr == self.ui.spinBoxCenterWL_2:
-            self.parameters['new_calib_dict']['ctr_wl'] = \
-                self.ui.spinBoxCenterWL_2.value()
-            
-        elif sdr == self.ui.spinBoxCalibWL_2:
-            self.parameters['new_calib_dict']['ctr_wl0'] = \
-                self.ui.spinBoxCalibWL_2.value()
-                
-        elif sdr == self.ui.spinBoxSlope_2:
-            self.parameters['new_calib_dict']['a_vec'][0] = \
-                self.ui.spinBoxSlope_2.value()
-                
-        elif sdr == self.ui.spinBoxIntercept_2:
-            self.parameters['new_calib_dict']['a_vec'][1] = \
-                self.ui.spinBoxIntercept_2.value()
-                
-        elif sdr == self.ui.spinBoxProbeWL_2:
-            self.parameters['new_calib_dict']['probe'] = \
-                self.ui.spinBoxProbeWL_2.value()
-        
-        self.changed.emit()

-        
-
[docs]    def meas_vs_ideal(self):
-        meas = self.ui.spinBoxMeas.value()
-        ideal = self.ui.spinBoxCorrect.value()
-
-        delta_lambda = (1 / ((ideal / 1e7) + 
-                            (1 / self.parameters['orig_calib_dict']['probe']))
-                        - 1 / ((meas/1e7) + 
-                               (1 / self.parameters['orig_calib_dict']['probe'])))
-    
-        self.parameters['new_calib_dict']['a_vec'][1] = \
-            self.parameters['orig_calib_dict']['a_vec'][1] + delta_lambda
-
-        self.setup_calib()
-        self.changed.emit()

-        
-
[docs]    def fcn(self, data_in):
-        """
-        Returns a shifted version of the input spectrum to mimic the effect
-        of calibration. (Real calibration doesn't shift the spectrum, but 
-        rather the independent variable)
-
-        """
-        orig_wn = _calib_pix_wn(self.parameters['orig_calib_dict'])[0]
-        new_wn = _calib_pix_wn(self.parameters['new_calib_dict'])[0]
-        
-        if data_in.ndim == 1:
-            spl = _UnivariateSpline(new_wn, data_in, s=0, ext=0)
-            output = spl(orig_wn)
-        elif data_in.ndim == 2:
-            output = _np.zeros(data_in.shape)
-            for num, spect in enumerate(data_in):
-                spl = _UnivariateSpline(new_wn, spect, s=0, ext=0)
-                output[num,:] = spl(orig_wn)
-        return output

-
-
[docs]    def setup_calib(self):
-        
-        # Original
-        self.ui.spinBoxNPix.setValue(self.parameters['orig_calib_dict']['n_pix'])
-        self.ui.spinBoxCenterWL.setValue(self.parameters['orig_calib_dict']['ctr_wl'])
-        self.ui.spinBoxCalibWL.setValue(self.parameters['orig_calib_dict']['ctr_wl0'])
-        self.ui.spinBoxSlope.setValue(self.parameters['orig_calib_dict']['a_vec'][0])
-        self.ui.spinBoxIntercept.setValue(self.parameters['orig_calib_dict']['a_vec'][1])
-        self.ui.spinBoxProbeWL.setValue(self.parameters['orig_calib_dict']['probe'])
-        
-        # New
-        self.ui.spinBoxNPix_2.setValue(self.parameters['new_calib_dict']['n_pix'])
-        self.ui.spinBoxCenterWL_2.setValue(self.parameters['new_calib_dict']['ctr_wl'])
-        self.ui.spinBoxProbeWL_2.setValue(self.parameters['new_calib_dict']['probe'])
-        self.ui.spinBoxIntercept_2.setValue(self.parameters['new_calib_dict']['a_vec'][1])
-        self.ui.spinBoxSlope_2.setValue(self.parameters['new_calib_dict']['a_vec'][0])
-        self.ui.spinBoxCalibWL_2.setValue(self.parameters['new_calib_dict']['ctr_wl0'])

-
-    
-if __name__ == '__main__':
-    import sys as _sys
-    from PyQt5.QtWidgets import (QApplication as _QApplication)
-    
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-    
-    
-    calib_dict = {'n_pix' : 1600,
-                  'ctr_wl' : 730,
-                  'ctr_wl0' : 730,
-                  'a_vec' : [-0.167740721307557, 863.8736708961577],
-                  'probe': 771.461}
-                  
-    pix = _np.arange(calib_dict['n_pix'])
-    wl = calib_dict['a_vec'][0]*pix + calib_dict['a_vec'][1]
-    WN = .01/(wl*1e-9) - .01/(calib_dict['probe']*1e-9)
-    
-    CARS = _np.abs(1/(1000-WN-1j*20) + 1/(3000-WN-1j*20) + .055)
-    NRB = 0*WN + .055
-    CARS = _np.dot(_np.ones((5,1)),CARS[None,:])
-
-        
-    winCalib = widgetCalibrate(calib_dict)
-    winCalib.show()
-
-    
-    app.exec_()
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_DeTrending.html b/docs/build/html/_modules/crikit/ui/widget_DeTrending.html deleted file mode 100644 index 89bf74e..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_DeTrending.html +++ /dev/null @@ -1,378 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_DeTrending — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
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    • - -
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    • - -
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    • - - -
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-
-
-
- -

Source code for crikit.ui.widget_DeTrending

-"""
-Widget for PlotEffect that contains and presents different detrending
-algorithms. Whichever algorithm is plugged in effectively acts as the
-widget as far as PlotEffect is concerned.
-
-Created on Wed Dec  7 13:36:48 2016
-
-@author: chc
-"""
-
-# Generic imports for QT-based programs
-from PyQt5.QtWidgets import (QApplication as _QApplication,
-                             QRadioButton as _QRadioButton,
-                             QButtonGroup as _QButtonGroup)
-
-from crikit.ui.qt_PlotEffect_DeTrending import Ui_Form as _Ui_Form
-
-# At Minimum import ALS
-from crikit.ui.widget_ALS import widgetALS
-_widget_list_names = ['ALS']
-_widget_list_classes = [widgetALS]
-
-# Try to add arPLS to detrend options
-try:
-    from crikit.ui.widget_ArPLS import widgetArPLS
-except:
-    pass
-else:
-    _widget_list_names.append('ArPLS')
-    _widget_list_classes.append(widgetArPLS)
-    
-from crikit.ui.dialog_AbstractPlotEffect import (AbstractPlotEffectPlugin
-                                                 as _AbstractPlotEffectPlugin)
-
-
[docs]class widgetDeTrending(_AbstractPlotEffectPlugin):
-    """
-    Widget for PlotEffect that contains and presents different detrending
-    algorithms. Whichever algorithm is plugged in effectively acts as the
-    widget as far as PlotEffect is concerned.
-    
-    """
-        
-    def __init__(self, parent = None):
-        super(widgetDeTrending, self).__init__(parent) ### EDIT ###
-        self.ui = _Ui_Form() ### EDIT ###
-        self.ui.setupUi(self)     ### EDIT ###
-
-        self.ui.widget_list_names = _widget_list_names
-        self.ui.widget_list = []
-        for cl in _widget_list_classes:
-            self.ui.widget_list.append(cl())
-        
-        self.ui.buttonGroup = _QButtonGroup()
-        self.ui.radio_button_list = []
-        
-        for num, (wdgt, name) in enumerate(zip(self.ui.widget_list, 
-                                               self.ui.widget_list_names)):
-
-            self.ui.verticalLayoutWidgets.insertWidget(num, wdgt)
-            self.ui.radio_button_list.append(_QRadioButton(name))
-            self.ui.verticalLayoutButtons.insertWidget(num, self.ui.radio_button_list[num])
-            self.ui.buttonGroup.addButton(self.ui.radio_button_list[num],0)
-            if num == 0:
-                wdgt.setVisible(True)
-                self.ui.radio_button_list[0].setChecked(True)
-                self.fcn = wdgt.fcn
-                self.parameters = wdgt.parameters
-                self.labels_orig = wdgt.labels_orig
-                self.labels_affected = wdgt.labels_affected
-                
-                # Connect the changed-signal from the active widget
-                # to this container's version of the change-signal
-                try:
-                    wdgt.changed.connect(self.widgetOptionsChanged)
-                except:
-                    pass
-            else:
-                wdgt.setVisible(False)
-                try:
-                    wdgt.changed.disconnect(self.widgetOptionsChanged)
-                except:
-                    pass
-                
-        # SIGNALS & SLOTS
-        
-        # Active widget changed
-        self.ui.buttonGroup.buttonClicked.connect(self.changeWidget)
-        
-
[docs]    def widgetOptionsChanged(self):
-        """
-        Options within the active widget were changed
-        """
-        self.changed.emit()

-        
-
[docs]    def changeWidget(self, buttonId):
-        """
-        Change active widget
-        """
-        
-        selection = self.ui.radio_button_list.index(buttonId)
-        
-        for num, (wdgt, name) in enumerate(zip(self.ui.widget_list, 
-                                             self.ui.widget_list_names)):
-            if num == selection:
-                wdgt.setVisible(True)
-                self.ui.radio_button_list[num].setChecked(True)
-                self.fcn = wdgt.fcn
-                self.parameters = wdgt.parameters
-                self.labels_orig = wdgt.labels_orig
-                self.labels_affected = wdgt.labels_affected
-                
-                # Connect the changed-signal from the active widget
-                # to this container's version of the change-signal
-                try:
-                    wdgt.changed.connect(self.widgetOptionsChanged)
-                except:
-                    pass
-            else:
-                wdgt.setVisible(False)
-                
-                # Disconnect non-active widget's changed-signal
-                try:
-                    wdgt.changed.disconnect(self.widgetOptionsChanged)
-                except:
-                    pass
-                
-        self.changed.emit()

-        
-
-if __name__ == '__main__':
-    
-    import sys as _sys
-    
-    
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    win = widgetDeTrending()
-    
-    win.show()
-    
-    app.exec_()
-    print(win.parameters)
-    _sys.exit()
-    
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_Jupyter.html b/docs/build/html/_modules/crikit/ui/widget_Jupyter.html deleted file mode 100644 index e6ad1b7..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_Jupyter.html +++ /dev/null @@ -1,328 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_Jupyter — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
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    • - -
  • Module code »
    • - -
  • crikit.ui.widget_Jupyter
    • - - -
  • - - - -
    • - -
- - -
-
-
-
- -

Source code for crikit.ui.widget_Jupyter

-"""
-Created on Wed Mar  2 17:12:54 2016
-
-@author: chc
-"""
-
-import os
-os.environ['QT_API'] = 'pyqt5'
-
-from PyQt5 import QtWidgets
-from PyQt5 import QtGui
-# ipython won't work if this is not correctly installed. And the error message will be misleading
-from PyQt5 import QtSvg 
-
-# Import the console machinery from ipython
-from qtconsole.rich_jupyter_widget import RichJupyterWidget
-from qtconsole.inprocess import QtInProcessKernelManager
-#from IPython.qt.console.rich_ipython_widget import RichIPythonWidget
-#from IPython.qt.inprocess import QtInProcessKernelManager
-
-
-
[docs]class QJupyterWidget(RichJupyterWidget):
-    """ Convenience class for a live IPython console widget. We can replace the standard banner using the customBanner argument"""
-    def __init__(self,customBanner=None,*args,**kwargs):
-        super(QJupyterWidget, self).__init__(*args,**kwargs)
-        if customBanner!=None: self.banner=customBanner
-        self.kernel_manager = kernel_manager = QtInProcessKernelManager()
-        kernel_manager.start_kernel()
-        kernel_manager.kernel.gui = 'qt'
-        
-        self.kernel_client = kernel_client = self._kernel_manager.client()
-        kernel_client.start_channels()
-
-        def stop():
-            kernel_client.stop_channels()
-            kernel_manager.shutdown_kernel()
-            #get_app_qt5().exit()            
-        self.exit_requested.connect(stop)
-
-
[docs]    def pushVariables(self,variableDict):
-        """ Given a dictionary containing name / value pairs, push those variables to the IPython console widget """
-        self.kernel_manager.kernel.shell.push(variableDict)

-
[docs]    def clearTerminal(self):
-        """ Clears the terminal """
-        self._control.clear()    

-
[docs]    def printText(self,text):
-        """ Prints some plain text to the console """
-        self._append_plain_text(text, False)

-        
-        
-        
-
[docs]    def executeCommand(self,command):
-        """ Execute a command in the frame of the console widget """
-        self._execute(command,False)

-        
-if __name__ == '__main__':
-    class ExampleWidget(QtWidgets.QMainWindow):
-        """ Main GUI Window including a button and IPython Console widget inside vertical layout """
-        def __init__(self, parent=None):
-            super(ExampleWidget, self).__init__(parent)
-            self.setWindowTitle('iPython in PyQt5 app example')
-            self.mainWidget = QtWidgets.QWidget(self)
-            self.setCentralWidget(self.mainWidget)
-            layout = QtWidgets.QVBoxLayout(self.mainWidget)
-            self.button = QtWidgets.QPushButton('Another widget')
-            self.ipyConsole = QJupyterWidget(customBanner="Welcome to the embedded ipython console\n")
-            layout.addWidget(self.button)
-            layout.addWidget(self.ipyConsole)        
-            # This allows the variable foo and method print_process_id to be accessed from the ipython console
-            self.ipyConsole.pushVariables({"foo":43,"print_process_id":print_process_id})
-            self.ipyConsole.printText("The variable 'foo' and the method 'print_process_id()' are available. Use the 'whos' command for information.\n\nTo push variables run this before starting the UI:\n ipyConsole.pushVariables({\"foo\":43,\"print_process_id\":print_process_id})")
-            self.setGeometry(300, 300, 800, 600)
-
-    def print_process_id():
-        print('Process ID is:', os.getpid())
-    
-    def get_app_qt5(*args, **kwargs):
-        """Create a new qt5 app or return an existing one."""
-        app = QtWidgets.QApplication.instance()
-        if app is None:
-            if not args:
-                args = ([''],)
-            app = QtWidgets.QApplication(*args, **kwargs)
-        return app
-        
-
-    app  = get_app_qt5()
-    widget = ExampleWidget()
-      
-    widget.show()
-    
-   
-    app.exec_()
-    
-    
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_KK.html b/docs/build/html/_modules/crikit/ui/widget_KK.html deleted file mode 100644 index 4d2f50c..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_KK.html +++ /dev/null @@ -1,437 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_KK — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- - - - -
-
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-
- -

Source code for crikit.ui.widget_KK

-"""
-Widget for PlotEffect that adjusts the parameters appropriate for
-the Kramers-Kronig relation
-
-Created on Thu Dec 22 11:43:42 2016
-
-@author: chc
-"""
-import numpy as _np
-
-from crikit.ui.dialog_AbstractPlotEffect import (AbstractPlotEffectPlugin
-                                                 as _AbstractPlotEffectPlugin)
-
-from crikit.ui.qt_PlotEffect_KK import Ui_Form as _Ui_Form
-
-from crikit.cri.kk import KramersKronig as _KramersKronig
-
-
[docs]class widgetKK(_AbstractPlotEffectPlugin):
-    """
-    Widget for PlotEffect that adjusts the parameters appropriate for
-    the Kramers-Kronig (KK) relation phase retrieval.
-
-    Attributes
-    ----------
-    cars_amp_offset : float, optional (default=0.0)
-        DC offset applied to CARS spectrum(a) prior to KK relation.
-
-    nrb_amp_offset : float, optional (default=0.0)
-        DC offset applied to NRB spectrum(a) prior to KK relation. 
-
-    phase_offset : float or ndarray, optional (default=0.0)
-        Phase constant or ndarray applied to retrieved phase prior to 
-        separating the real and imaginary components.
-
-    norm_to_nrb : bool, optional (default=True)
-        Normalize the amplitude by sqrt(NRB). This effectively removes several \
-        system reponse functions.
-        
-    pad_factor : int, optional (default=1)
-        Multiple size of spectral-length to pad the ends of each spectra with. \
-        Padded with a constant value corresponding to the value at that end of \
-        the spectrum.
-
-    Methods
-    ---------
-        fcn : Performs the KK
-
-    Signals:
-        changed : a value in the UI has changed
-
-    """
-    
-    # Parameter dict that will be returned from PlotEffect
-    # Will be updated later in program to contain all parameters
-    # to pass to underlying algorithm
-    parameters = {'name' : 'KK', 
-                  'long_name' : 'Kramers-Kronig Relation'}
-    
-    # Labeling options for original data plot
-    labels_orig = {
-                   'x_label' : 'Wavenumber (cm$^{-1}$)',
-                   'y_label' : 'Input Int (au)',
-                   'title' : 'Original'
-                   }
-    
-    # Labeling options for affected data plot              
-    labels_affected = {
-                       'x_label' : labels_orig['x_label'],
-                       'y_label' : 'Raman-Like Int (au)',
-                       'title' : 'KK-Raman'
-                      }
-                      
-    def __init__(self, cars_amp_offset=0.0, nrb_amp_offset=0.0,
-                 phase_offset=0.0, norm_to_nrb=True, pad_factor=1, 
-                 parent = None):
-        
-        super(widgetKK, self).__init__(parent)
-        
-        self.ui = _Ui_Form()
-        self.ui.setupUi(self)
-        
-        self.lock_cars_nrb_bias = True
-        
-        # Update parameter dict
-        self.parameters['cars_amp_offset'] = cars_amp_offset
-        self.parameters['nrb_amp_offset'] = nrb_amp_offset
-        self.parameters['phase_offset'] = phase_offset
-        self.parameters['norm_to_nrb'] = norm_to_nrb
-        self.parameters['pad_factor'] = pad_factor
-                
-        self.setupKK()
-        
-
[docs]    def setupKK(self):
-
-        self.ui.checkBoxNRBNorm.setChecked(self.parameters['norm_to_nrb'])
-        self.ui.checkBoxLockBias.setChecked(self.lock_cars_nrb_bias)
-        
-        self.ui.spinBoxCARSBias.setValue(self.parameters['cars_amp_offset'])
-        self.ui.spinBoxNRBBias.setValue(self.parameters['nrb_amp_offset'])
-        self.ui.spinBoxPhaseLin.setValue(self.parameters['phase_offset'])
-        self.ui.spinBoxPadFactor.setValue(self.parameters['pad_factor'])
-
-        # SIGNALS & SLOTS
-        self.ui.spinBoxCARSBias.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxNRBBias.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxPhaseLin.editingFinished.connect(self.spinBoxChanged)
-        self.ui.spinBoxPadFactor.editingFinished.connect(self.spinBoxChanged)
-        
-        self.ui.checkBoxNRBNorm.clicked.connect(self.changeCheckBoxNRBNorm)
-        self.ui.checkBoxLockBias.clicked.connect(self.changeCheckBoxLockBias)
-
-        self.ui.spinBoxNRBBias.setEnabled(not self.lock_cars_nrb_bias)

-        
-
-
[docs]    def fcn(self, data_in):
-        """
-        If return list, [0] goes to original, [1] goes to affected
-        """
-        
-        assert isinstance(data_in, list), 'KK plot effect fcn requires the \
-            data input be a list with length 2: NRB, CARS'
-
-        assert len(data_in), 'KK plot effect fcn requires the \
-            data input be a list with length 2: NRB, CARS'
-            
-        nrb = data_in[0]
-        cars = data_in[1]
-        
-        data_out = _np.zeros(cars.shape, dtype=_np.complex)
-               
-        cars_amp_offset = self.parameters['cars_amp_offset']
-        nrb_amp_offset = self.parameters['nrb_amp_offset'] 
-        phase_offset = self.parameters['phase_offset'] 
-        norm_to_nrb = self.parameters['norm_to_nrb']
-        pad_factor = self.parameters['pad_factor']
-        
-        _kk = _KramersKronig(cars_amp_offset=cars_amp_offset,
-                             nrb_amp_offset=nrb_amp_offset,
-                             phase_offset=phase_offset,
-                             norm_to_nrb=norm_to_nrb,
-                             pad_factor=pad_factor)
-
-        data_out = _kk.calculate(cars, nrb)
-        
-        return data_out.imag

-
-
[docs]    def spinBoxChanged(self):
-        """
-        Controller for all spinBoxes
-        """
-        
-        sdr = self.sender()
-        
-        if sdr == self.ui.spinBoxCARSBias:
-            self.parameters['cars_amp_offset'] = self.ui.spinBoxCARSBias.value()
-            if self.lock_cars_nrb_bias:
-                self.parameters['nrb_amp_offset'] = \
-                    self.ui.spinBoxCARSBias.value()
-                self.ui.spinBoxNRBBias.setValue(self.parameters['nrb_amp_offset'])
-                
-        elif sdr == self.ui.spinBoxNRBBias:
-            self.parameters['nrb_amp_offset'] = self.ui.spinBoxNRBBias.value()
-            
-        elif sdr == self.ui.spinBoxPhaseLin:
-            self.parameters['phase_offset'] = self.ui.spinBoxPhaseLin.value()
-            
-        elif sdr == self.ui.spinBoxPadFactor:
-            self.parameters['pad_factor'] = self.ui.spinBoxPadFactor.value()
-            
-        self.changed.emit()

-
-
[docs]    def changeCheckBoxLockBias(self):
-        if self.ui.checkBoxLockBias.isChecked():
-            self.ui.spinBoxNRBBias.setEnabled(False)
-            self.lock_cars_nrb_bias = True
-        else:
-            self.ui.spinBoxNRBBias.setEnabled(True)
-            self.lock_cars_nrb_bias = False
-        self.changed.emit()

-
-
[docs]    def changeCheckBoxNRBNorm(self):
-        if self.ui.checkBoxNRBNorm.isChecked():
-            self.parameters['norm_to_nrb'] = True
-        else:
-            self.parameters['norm_to_nrb'] = False
-        self.changed.emit()

-
-
[docs]    def changeSpinBoxPadFactor(self):
-        self.parameters['pad_factor'] = self.ui.spinBoxPadFactor.value()
-        self.changed.emit()

-        
-        
-if __name__ == '__main__':
-    import sys as _sys
-    from PyQt5.QtWidgets import (QApplication as _QApplication)
-    
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    win = widgetKK()
-    win.show()
-
-    app.exec_()
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_SG.html b/docs/build/html/_modules/crikit/ui/widget_SG.html deleted file mode 100644 index be31d86..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_SG.html +++ /dev/null @@ -1,361 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_SG — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- - - - -
-
-
-
- -

Source code for crikit.ui.widget_SG

-"""
-Widget for PlotEffect that adjusts the parameters appropriate for
-Savitky-Golay filtering
-
-Created on Thu Dec 22 11:18:36 2016
-
-@author: chc
-"""
-
-from scipy.signal import savgol_filter as _sg
-
-from crikit.ui.dialog_AbstractPlotEffect import (AbstractPlotEffectPlugin
-                                                 as _AbstractPlotEffectPlugin)
-
-from crikit.ui.qt_PlotEffect_SG import Ui_Form as _Ui_Form
-
-
[docs]class widgetSG(_AbstractPlotEffectPlugin):
-    """
-    Widget for PlotEffect that adjusts the parameters appropriate for
-    Savitky-Golay filtering
-
-
-    Parameters
-    ----------
-    window_length : int
-        Window length
-
-    polyorder : int
-        Polynomial order
-        
-    parent : QObject
-        Parent
-        
-    Methods
-    ---------
-    fcn : Performs the Savitky-Golay
-
-    Signals:
-        changed : a value in the UI has changed
-
-    """
-
-    # Parameter dict that will be returned from PlotEffect
-    # Will be updated later in program to contain all parameters
-    # to pass to underlying algorithm
-    parameters = {'name' : 'SG', 
-                  'long_name' : 'Savitky-Golay filtering'}
-    
-    # Labeling options for original data plot
-    labels_orig = {
-                   'x_label' : 'Wavenumber (cm$^{-1}$)',
-                   'y_label' : 'Input Int (au)',
-                   'title' : 'Original'
-                   }
-    
-    # Labeling options for affected data plot              
-    labels_affected = {
-                       'x_label' : labels_orig['x_label'],
-                       'y_label' : 'Difference (au)',
-                       'title' : 'Difference'
-                      }
-                      
-
-    def __init__(self, window_length=601, polyorder=2, parent = None):
-        super(widgetSG, self).__init__(parent)
-        self.ui = _Ui_Form() ### EDIT ###
-        self.ui.setupUi(self)     ### EDIT ###
-
-        # Update parameter dict
-        self.parameters['window_length'] = window_length
-        self.parameters['polyorder'] = polyorder
-                
-        # Window size must be > polyorder
-        if self.parameters['window_length'] <= self.parameters['polyorder']:
-            self.parameters['window_length'] = self.parameters['polyorder'] + 1
-            
-        # Window size must be odd
-        if self.parameters['window_length'] % 2 == 1:
-            pass
-        else:
-            self.parameters['window_length'] += 1
-
-        self.ui.spinBoxWinSize.setValue(self.parameters['window_length'])
-        self.ui.spinBoxOrder.setValue(self.parameters['polyorder'])
-
-        # SIGNALS & SLOTS
-        self.ui.spinBoxWinSize.editingFinished.connect(self.changeWinSize)
-        self.ui.spinBoxOrder.editingFinished.connect(self.changeOrder)
-
-
[docs]    def fcn(self, data_in):
-        """
-        If return list, [0] goes to original, [1] goes to affected
-        """
-
-        baseline = _sg(data_in, window_length=self.parameters['window_length'],
-                       polyorder=self.parameters['polyorder'], axis=-1)
-        data_out = data_in - baseline
-
-        return [baseline, data_out]

-
-
[docs]    def changeWinSize(self):
-        temp_win_size = self.ui.spinBoxWinSize.value()
-        if temp_win_size % 2 == 1:
-            self.parameters['window_length'] = temp_win_size
-        else:
-            self.ui.spinBoxWinSize.setValue(temp_win_size + 1)
-            self.parameters['window_length'] = temp_win_size + 1
-        self.changed.emit()

-
-
[docs]    def changeOrder(self):
-        self.parameters['polyorder'] = self.ui.spinBoxOrder.value()
-        self.changed.emit()

-        
-if __name__ == '__main__':
-    import sys as _sys
-    from PyQt5.QtWidgets import (QApplication as _QApplication)
-    
-    
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    win = widgetSG()
-    
-    win.show()
-    
-    app.exec_()
-    print(win.parameters)
-    _sys.exit()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_images.html b/docs/build/html/_modules/crikit/ui/widget_images.html deleted file mode 100644 index 3dc5304..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_images.html +++ /dev/null @@ -1,912 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_images — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.ui.widget_images
    • - - -
  • - - - -
    • - -
- - -
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- -

Source code for crikit.ui.widget_images

-"""
-Visualization Widgets (crikit.ui.widget_images)
-=======================================================
-
-widgetColorMath : Mathematical operations on raw data leading to color \
-    images
-
-widgetBWImg : Grayscale imagery
-
-widgetSglColor : Single-color imagery
-
-widgetCompositeColor : Composite-color imagery
-
-_mplWin : Matplotlib window container
-
-"""
-
-import sys as _sys
-import numpy as _np
-
-# Generic imports for QT-based programs
-from PyQt5.QtWidgets import (QApplication as _QApplication,
-                             QWidget as _QWidget,
-                             QSizePolicy as _QSizePolicy,
-                             QColorDialog as _QColorDialog,
-                             QHBoxLayout as _QHBoxLayout)
-
-import PyQt5.QtCore as _QtCore
-
-# Import from Designer-based GUI
-from crikit.ui.qt_CompositeColor import Ui_Form as Ui_CompositeColor_Form
-from sciplot.ui.widget_mpl import MplCanvas as _MplCanvas
-from crikit.ui.qt_GrayScaleImgInfoBar import Ui_formWidgetGrayScaleImgInfoBar as Ui_GrayImgInfoBar
-from crikit.ui.qt_ColorModeSetting import Ui_Form as Ui_ColorModeSetting
-from crikit.ui.qt_BlankLayout import Ui_Form as Ui_Blank
-from crikit.ui.qt_PopSpectrumGS import Ui_Form as Ui_PopSpectrumGS
-from crikit.ui.qt_ImageGainMath import Ui_Form as Ui_ImageGainMath
-
-# Generic imports for MPL-incorporation
-import matplotlib as _mpl
-from matplotlib.pyplot import colormaps as _plt_colormaps
-import sciplot as _sciplot
-#import matplotlib.pyplot as _plt
-
-_mpl.use('Qt5Agg')
-_mpl.rcParams['font.family'] = 'sans-serif'
-_mpl.rcParams['font.size'] = 10
-
-from matplotlib.backends.backend_qt5agg import (NavigationToolbar2QT as _NavigationToolbar)
-
-from crikit.ui.classes_ui import BW, SingleColor, CompositeColor
-
-
-
[docs]class widgetImageGainMath(_QWidget):
-    """
-    Panel that controle image gain and applies math
-    """
-    OPERATION_STRINGS = ['','+','-','*','/','Peak b/w troughs','SUM']
-    OPERATION_FREQ_COUNT = [1, 2, 2, 2,2, 3, 2]
-    COND_TYPE_STRINGS = ['>','<','=','<=','>=']
-
-    def __init__(self, parent=None, **kwargs):
-        super().__init__(parent)
-        self.ui = Ui_ImageGainMath()
-        self.ui.setupUi(self)
-
-        self.ui.comboBoxCondOps.addItem('OFF')
-
-        for item in widgetImageGainMath.OPERATION_STRINGS:
-            self.ui.comboBoxOperations.addItem(item)
-            self.ui.comboBoxCondOps.addItem(item)
-
-        for item in widgetImageGainMath.COND_TYPE_STRINGS:
-            self.ui.comboBoxCondInEquality.addItem(item)
-
-        self.ui.comboBoxOperations.currentIndexChanged.connect(self.operationchange)
-        self.ui.comboBoxCondOps.currentIndexChanged.connect(self.condOpsChange)
-
-
[docs]    def clear(self):
-        """
-        Resets the ui to it's initial state
-        """
-        self.ui.checkBoxDisable.setChecked(False)
-        
-        self.ui.spinBoxGain.setValue(1.0)
-        self.ui.tabWidgetMath.setCurrentIndex(0)
-
-        self.ui.pushButtonOpFreq1.setText('Freq 1')
-        self.ui.pushButtonOpFreq2.setText('Freq 2')
-        self.ui.pushButtonOpFreq3.setText('Freq 3')
-        self.ui.comboBoxOperations.setCurrentIndex(0)
-
-        self.ui.pushButtonCondFreq1.setText('Freq 1')
-        self.ui.pushButtonCondFreq2.setText('Freq 2')
-        self.ui.pushButtonCondFreq3.setText('Freq 3')
-        self.ui.comboBoxCondOps.setCurrentIndex(0)
-        self.ui.comboBoxCondInEquality.setCurrentIndex(0)
-        self.ui.spinBoxInEquality.setValue(0.0)

-        
-
[docs]    def condOpsChange(self):
-        index = self.ui.comboBoxCondOps.currentIndex()
-
-        if index == 0:
-            num_freq = 0
-        else:
-            num_freq = widgetImageGainMath.OPERATION_FREQ_COUNT[index-1]
-
-        self.ui.pushButtonCondFreq1.setEnabled(False)
-        self.ui.pushButtonCondFreq2.setEnabled(False)
-        self.ui.pushButtonCondFreq3.setEnabled(False)
-        self.ui.comboBoxCondInEquality.setEnabled(False)
-        self.ui.spinBoxInEquality.setEnabled(False)
-
-        if num_freq >= 1:
-            self.ui.pushButtonCondFreq1.setEnabled(True)
-            self.ui.comboBoxCondInEquality.setEnabled(True)
-            self.ui.spinBoxInEquality.setEnabled(True)
-        if num_freq >= 2:
-            self.ui.pushButtonCondFreq2.setEnabled(True)
-        if num_freq >= 3:
-            self.ui.pushButtonCondFreq3.setEnabled(True)

-
-
[docs]    def operationchange(self):
-        index = self.ui.comboBoxOperations.currentIndex()
-
-        num_freq = widgetImageGainMath.OPERATION_FREQ_COUNT[index]
-
-        self.ui.pushButtonOpFreq1.setEnabled(False)
-        self.ui.pushButtonOpFreq2.setEnabled(False)
-        self.ui.pushButtonOpFreq3.setEnabled(False)
-
-        if num_freq >= 1:
-            self.ui.pushButtonOpFreq1.setEnabled(True)
-        if num_freq >= 2:
-            self.ui.pushButtonOpFreq2.setEnabled(True)
-        if num_freq >= 3:
-            self.ui.pushButtonOpFreq3.setEnabled(True)

-
-
[docs]class widgetPopSpectrumGS(_QWidget):
-    """ 
-    Panel that let's user pop the current image, an average spectrum,
-    or a grayscale image to SciPlot
-    """
-    def __init__(self, parent=None, **kwargs):
-        super().__init__(parent)
-        self.ui = Ui_PopSpectrumGS()
-        self.ui.setupUi(self)

-
-
[docs]class widgetGrayScaleInfoBar(_QWidget):
-    """
-    Grayscale image info bar
-    """
-    def __init__(self, parent = None, **kwargs):
-        super().__init__(parent)
-        self.ui = Ui_GrayImgInfoBar()
-        self.ui.setupUi(self)

-
-
[docs]class widgetColorMode(_QWidget):
-    """
-    Color mode selector
-    """
-    def __init__(self, parent=None, **kwargs):
-        super().__init__(parent)
-        self.ui = Ui_ColorModeSetting()
-        self.ui.setupUi(self)
-
-        # Get all MPL named colors
-        color_list = ['red', 'green', 'blue', 'magenta', 'cyan', 'yellow', 
-                      'black', 'white', 'CUSTOM']
-        color_list.extend(sorted(set(_mpl.colors.cnames.keys()) - set(color_list)))
-        self.ui.comboBoxBGColor.addItems(color_list)
-        self.ui.comboBoxFGColor.addItems(color_list)
-        self.ui.comboBoxBGColor.setCurrentIndex(color_list.index('black'))
-        # Get all mpl colormaps and set combo box
-        list_of_colormaps = sorted(_plt_colormaps())
-        self.ui.comboBoxColormap.addItems(list_of_colormaps)
-
-        # Set default colormap to 'gray'
-        idx = self.ui.comboBoxColormap.findText('gray')
-        self.ui.comboBoxColormap.setCurrentIndex(idx)

-
-
[docs]class widgetBWImg(_QWidget):
-    """
-    Grayscale image widget
-    """
-    def __init__(self, parent = None, **kwargs):
-        super().__init__(parent)
-        self.win = Ui_Blank()
-        self.win.setupUi(self)
-        self.win.gridLayout.setEnabled(False)
-        
-        self._img_defaults = {'showcbar': True, 'axison': True}
-
-        self.gsinfo = widgetGrayScaleInfoBar(parent=self)
-        
-        self.colormode = widgetColorMode(parent=self)
-        self.colormode.ui.comboBoxColorMode.setCurrentIndex(1)
-        self.colormode.ui.comboBoxColormap.setVisible(True)
-        self.colormode.ui.labelColormap.setVisible(True)
-        self.colormode.ui.comboBoxFGColor.setVisible(False)
-        self.colormode.ui.comboBoxBGColor.setVisible(False)
-        self.colormode.ui.comboBoxColorMode.setVisible(False)
-        self.colormode.ui.labelBGColor.setVisible(False)
-        self.colormode.ui.labelFGColor.setVisible(False)
-        self.colormode.ui.labelColorMode.setVisible(False)
-
-        self.popimage = widgetPopSpectrumGS(parent=self)
-        self.popimage.ui.pushButtonGSPop.setVisible(False)
-
-        self.ui = self.gsinfo.ui  # Alias
-
-        self.win.horizLayout = _QHBoxLayout()
-        self.win.horizLayout.setContentsMargins(2,2,2,2)
-
-        self.win.verticalLayout.insertLayout(0, self.win.horizLayout)
-        
-        self.win.horizLayout.insertWidget(0, self.gsinfo, _QtCore.Qt.AlignHCenter)
-        self.win.horizLayout.insertWidget(0, self.colormode, _QtCore.Qt.AlignBottom)
-
-        # Initialize underlying data
-        self.initData()
-        self.external_plots = []
-
-        # Stand-in image data
-        self.data.grayscaleimage = _np.dot(_np.ones([100,1]),_np.linspace(1,100,100)[None,:])
-        self.data.set_x(_np.linspace(1,400,self.data.xlen))
-        self.data.set_y(_np.linspace(1,400,self.data.ylen))
-        
-        # Calculate extent of image
-        winextent = (self.data.x.min(), self.data.x.max(), self.data.y.min(), self.data.y.max())
-
-        # MPL canvas
-        self.mpl = _MplCanvas(**kwargs)
-        self.mpl.cbar = None  # Monkey patch on a cbar object
-        
-        # Create stand-image plot
-        self.createImg(img=self.data.image, xunits=self.data.xunits,
-                       yunits=self.data.yunits,
-                       extent=winextent,
-                       cmap=self.colormode.ui.comboBoxColormap.currentText())
-        self.mpl.fig.tight_layout()
-        
-        # Insert canvas widget into this widget
-        self.win.verticalLayout.insertWidget(0,self.mpl,_QtCore.Qt.AlignCenter)
-        self.win.verticalLayout.insertWidget(0,self.popimage,_QtCore.Qt.AlignCenter)
-        self.win.verticalLayout.insertWidget(0,self.mpl.toolbar, _QtCore.Qt.AlignHCenter)
-
-        # # SIGNAL & SLOTS
-        self.ui.checkBoxFixed.stateChanged.connect(self.checkBoxFixed)
-        self.ui.checkBoxRemOutliers.stateChanged.connect(self.checkBoxRemOutliers)
-        self.ui.spinBoxStdDevs.editingFinished.connect(self.checkBoxRemOutliers)
-        
-        # New
-        self.ui.comboBoxAboveMax.currentIndexChanged.connect(self.comboBoxCompress)
-        self.ui.comboBoxBelowMin.currentIndexChanged.connect(self.comboBoxCompress)
-        self.ui.spinBoxMax.editingFinished.connect(self.spinBoxMinMaxSet)
-        self.ui.spinBoxMin.editingFinished.connect(self.spinBoxMinMaxSet)
-        self.colormode.ui.comboBoxColormap.currentIndexChanged.connect(self.checkBoxFixed)
-        self.popimage.ui.pushButtonPop.pressed.connect(lambda: self.createImg_Ext(img=self.data.image,
-                                                      cmap=self.colormode.ui.comboBoxColormap.currentText(),
-                                                      showcbar=True,
-                                                      extent=self.data.winextent,
-                                                      xunits=self.data.xunits,
-                                                      yunits=self.data.yunits,
-                                                      parent=parent))
-
[docs]    def initData(self):
-        """
-        (Re)-initialize self.data
-        """
-        self.data = BW()

-
-
[docs]    def createImg_Ext(self, img, xunits = None, yunits = None,
-                  extent = None, showcbar = True, axison = True,
-                  cmap = _mpl.cm.gray, parent=None):
-        """
-        Create new figure window and show image of img
-        """
-
-        self.external_plots.append(_sciplot.main(parent=parent))
-        self.external_plots[-1].imshow(img, x_label=xunits, y_label=yunits, 
-                      cmap=cmap, cbar=showcbar, extent=extent)

-
-
[docs]    def createImg(self, img, xunits = None, yunits = None,
-                  extent = None, cmap = _mpl.cm.gray):
-        self.mpl.ax.clear()
-        self.mpl.img = self.mpl.ax.imshow(img, interpolation = 'none',
-                                          extent = extent, cmap = cmap, 
-                                          origin='lower')
-        if xunits is not None:
-            self.mpl.ax.xaxis.set_label_text(xunits)
-        if yunits is not None:
-            self.mpl.ax.yaxis.set_label_text(yunits)
-
-        if self._img_defaults['axison'] == False:
-            self.mpl.ax.set_axis_off()
-
-        # print(self.mpl.cbar)
-        if self.mpl.cbar is not None:
-            self.mpl.cbar.remove()
-            self.mpl.cbar = None
-        if self._img_defaults['showcbar'] == True:
-            self.mpl.cbar = self.mpl.fig.colorbar(self.mpl.img)
-
-        if self.ui.checkBoxFixed.isChecked() == False:
-            self.ui.spinBoxMax.setValue(self.data.maxer)
-            self.ui.spinBoxMin.setValue(self.data.minner)

-           
-
[docs]    def spinBoxMinMaxSet(self):
-        try:
-            self.data.setmin = self.ui.spinBoxMin.value()
-            self.data.setmax = self.ui.spinBoxMax.value()
-            self.ui.checkBoxFixed.setChecked(True)
-            
-            # Spin-Box call from Outlier-related widgets?
-            sent_by = self.sender()
-            if ((sent_by == self.ui.checkBoxRemOutliers) |
-                (sent_by == self.ui.spinBoxStdDevs)):
-                pass
-            elif ((sent_by == self.ui.spinBoxMax) |
-                  (sent_by == self.ui.spinBoxMin)):
-                  self.ui.checkBoxRemOutliers.setChecked(False)
-            else:
-                pass
-
-            self.createImg(img=self.data.image, xunits=self.data.xunits,
-                           yunits=self.data.yunits,
-                           extent=self.data.winextent,
-                           cmap=self.colormode.ui.comboBoxColormap.currentText())
-            self.mpl.draw()
-
-        except:
-            print('Error in spinBoxMinMaxSet')

-
-
[docs]    def checkBoxRemOutliers(self):
-        """
-        """
-        if self.ui.checkBoxRemOutliers.isChecked() == False:
-            pass
-        else:
-            new_max = self.data.mean + self.ui.spinBoxStdDevs.value()* \
-                      self.data.std
-            new_min = self.data.mean - self.ui.spinBoxStdDevs.value()* \
-                      self.data.std
-            self.ui.spinBoxMax.setValue(new_max)
-            self.ui.spinBoxMin.setValue(new_min)
-            self.spinBoxMinMaxSet()
-           
-        self.createImg(img=self.data.image, xunits=self.data.xunits,
-                       yunits=self.data.yunits,
-                       extent=self.data.winextent, 
-                       cmap=self.colormode.ui.comboBoxColormap.currentText())
-        self.mpl.draw()

-
-
[docs]    def checkBoxFixed(self):
-        """
-        See if the min and max are identified as being fixed by
-        checkbox
-        """
-
-        # See if there is a min and max in the textBrowsers
-
-        if self.ui.checkBoxFixed.isChecked() == True:  # Checked
-            try:
-                self.data.setmin = self.ui.spinBoxMin.value()
-                self.data.setmax = self.ui.spinBoxMax.value()
-                if self.ui.comboBoxAboveMax.currentIndex() == 0:
-                    self.data.compress_high = False
-                else:
-                    self.data.compress_high = True
-                if self.ui.comboBoxBelowMin.currentIndex() == 0:
-                    self.data.compress_low = False
-                else:
-                    self.data.compress_low = True
-            except:
-                pass
-        else:
-            self.data.setmin = None
-            self.data.setmax = None
-            self.data.compress_low = None
-            self.data.compress_high = None
-            self.ui.checkBoxRemOutliers.setChecked(False)
-
-        self.createImg(img=self.data.image, xunits=self.data.xunits,
-                       yunits=self.data.yunits,
-                       extent=self.data.winextent, 
-                       cmap=self.colormode.ui.comboBoxColormap.currentText())
-        self.mpl.draw()

-
-
[docs]    def comboBoxCompress(self):
-        """
-        See if compression is activated via the comboBoxAboveMax
-        """
-        if self.ui.comboBoxAboveMax.currentIndex() == 0:
-            self.data.compress_high = False
-        else:
-            self.data.compress_high = True
-
-        if self.ui.comboBoxBelowMin.currentIndex() == 0:
-            self.data.compress_low = False
-        else:
-            self.data.compress_low = True
-
-        self.createImg(img=self.data.image, xunits=self.data.xunits,
-                       yunits=self.data.yunits,
-                       extent=self.data.winextent,
-                       cmap=self.colormode.ui.comboBoxColormap.currentText())
-        self.mpl.draw()

-
-
[docs]class widgetSglColor(widgetBWImg):
-    """
-    Single-color widget
-    """
-    def __init__(self, parent=None, **kwargs):
-        super().__init__(parent)
-        self._img_defaults = {'showcbar': False, 'axison': True}
-        self.initData()
-        self.data.grayscaleimage = _np.dot(_np.ones([100,1]),_np.linspace(1,100,100)[None,:])
-        self.data.set_x(_np.linspace(1,400,self.data.xlen))
-        self.data.set_y(_np.linspace(1,400,self.data.ylen))
-        self.changeColor()
-        self.colormode.setMaximumHeight(130)
-        
-        self.math = widgetImageGainMath(parent=self)
-        self.win.verticalLayout.insertWidget(3, self.math)
-
-        # Disconnect colormap-related (from BW parent)
-        self.colormode.ui.comboBoxColormap.currentIndexChanged.disconnect()
-        
-        self.colormode.ui.comboBoxColorMode.setCurrentIndex(0)
-        self.colormode.ui.comboBoxColormap.setVisible(False)
-        self.colormode.ui.labelColormap.setVisible(False)
-        self.colormode.ui.comboBoxFGColor.setVisible(True)
-        self.colormode.ui.comboBoxBGColor.setVisible(True)
-        self.colormode.ui.comboBoxColorMode.setVisible(False)
-        self.colormode.ui.labelBGColor.setVisible(True)
-        self.colormode.ui.labelFGColor.setVisible(True)
-        self.colormode.ui.labelColorMode.setVisible(True)
-
-        self.colormode.ui.comboBoxFGColor.currentIndexChanged.connect(self.changeColor)
-        self.colormode.ui.comboBoxBGColor.currentIndexChanged.connect(self.changeColor)
-        self.math.ui.spinBoxGain.valueChanged.connect(self.applyGain)
-        self.math.ui.pushButtonGain1.pressed.connect(self.gain1)
-        self.math.ui.checkBoxDisable.stateChanged.connect(self.disabled)
-
-        self.popimage.ui.pushButtonGSPop.setVisible(True)
-        try:
-            self.popimage.ui.pushButtonPop.pressed.disconnect()
-        except:
-            pass
-        self.popimage.ui.pushButtonPop.pressed.connect(lambda: self.createImg_Ext(img = self.data.image,
-                                                                                  showcbar=False,
-                                                                                  extent=self.data.winextent, 
-                                                                                  xunits=self.data.xunits,
-                                                                                  yunits=self.data.yunits,
-                                                                                  parent=parent))
-        
-        try:
-            self.popimage.ui.pushButtonGSPop.pressed.disconnect()
-        except TypeError:
-            pass  # Just means pushButtonGSPop wasn't connected to anything
-        self.popimage.ui.pushButtonGSPop.pressed.connect(lambda: self.createImg_Ext(img = self.data.imageGS,
-                                                                                    showcbar=True,
-                                                                                    extent=self.data.winextent,
-                                                                                    xunits=self.data.xunits,
-                                                                                    yunits=self.data.yunits,
-                                                                                    parent=parent))
-
-
[docs]    def initData(self):
-        """
-        (Re)-initialize self.data
-        """
-        self.data = SingleColor()

-        
-        
-
[docs]    def changeColor(self):
-        # try:
-        
-        if self.sender() == self.colormode.ui.comboBoxFGColor:
-            color_str = self.colormode.ui.comboBoxFGColor.currentText()
-            if color_str == 'CUSTOM':
-                color = _QColorDialog.getColor().getRgb()
-                color = [round(color[0]/255,2), round(color[1]/255,2), round(color[2]/255,2)]
-
-                self.data.colormap = color
-
-            else:
-                self.data.colormap = _mpl.colors.colorConverter.to_rgb(_mpl.colors.cnames[color_str])
-
-        elif self.sender() == self.colormode.ui.comboBoxBGColor:
-            bgcolor_str = self.colormode.ui.comboBoxBGColor.currentText()
-            if bgcolor_str == 'CUSTOM':
-                bgcolor = _QColorDialog.getColor().getRgb()
-                bgcolor = [round(bgcolor[0]/255,2), round(bgcolor[1]/255,2), round(bgcolor[2]/255,2)]
-
-                self.data.bgcolor = bgcolor
-
-            else:
-                self.data.bgcolor = _mpl.colors.colorConverter.to_rgb(_mpl.colors.cnames[bgcolor_str])
-        
-        self.createImg(img = self.data.image, xunits = self.data.xunits,
-                                yunits = self.data.yunits,
-                                extent = self.data.winextent)
-        self.mpl.draw()

-        
-
[docs]    def applyGain(self):
-        self.data.setgain = self.math.ui.spinBoxGain.value()
-        self.changeColor()
-        if self.data.setgain == 0.0:
-            self.math.ui.checkBoxDisable.setChecked(True)
-        else:
-            self.math.ui.checkBoxDisable.setChecked(False)

-
-
[docs]    def gain1(self):
-        self.math.ui.spinBoxGain.setValue(1.0)

-
-
[docs]    def disabled(self):
-        if self.math.ui.checkBoxDisable.isChecked():
-            self.math.ui.spinBoxGain.setValue(0.0)
-        else:
-            self.math.ui.spinBoxGain.setValue(1.0)

-
-
[docs]class widgetCompositeColor(_QWidget):
-    def __init__(self, sgl_color_widget_list = None, parent = None, **kwargs):
-        super(widgetCompositeColor, self).__init__(parent)
-        ## Double check the spellings
-        self._img_defaults = {'showcbar':False, 'axison':True}
-        self.ui = Ui_CompositeColor_Form()
-        self.ui.setupUi(self)
-
-        # Initialize underlying data
-        self.initData(sgl_color_widget_list)
-        self.external_plots = []
-
-        # Create stand-in image data
-        self.data.grayscaleimage = _np.dot(_np.ones([100,1]),_np.linspace(1,100,100)[None,:])
-        self.data.set_x(_np.linspace(1,400,self.data.xlen))
-        self.data.set_y(_np.linspace(1,400,self.data.ylen))
-        
-        winextent = (self.data.x.min(), self.data.x.max(), self.data.y.min(), self.data.y.max())
-
-        # Instantiate mpl widget
-        self.mpl = _MplCanvas(**kwargs)
-        self.mpl.cbar = None  # Monkey patch on a cbar object
-
-        # Background color-related
-        # Get all MPL named colors
-        color_list = ['black', 'white', 'CUSTOM', 'red', 'green', 'blue',
-                      'magenta', 'cyan', 'yellow']
-        color_list.extend(sorted(set(_mpl.colors.cnames.keys()) - set(color_list)))
-        self.ui.comboBoxBGColor.addItems(color_list)
-        self.ui.comboBoxBGColor.setCurrentIndex(color_list.index('black'))
-        
-        # Emission/Absorption mode settings
-        self.ui.comboBoxColorMode.setCurrentIndex(0)  # Emission mode is default
-
-        # Create stand-in image data
-        self.createImg(img = self.data.image, xunits = self.data.xunits,
-                              yunits = self.data.yunits,
-                              extent = winextent)
-        self.mpl.fig.tight_layout()
-
-        # Insert mpl widget into this widget
-        self.ui.verticalLayout.insertWidget(0,self.mpl,_QtCore.Qt.AlignHCenter)
-        self.ui.verticalLayout.insertWidget(0,self.mpl.toolbar, _QtCore.Qt.AlignHCenter)
-
-        self.popimage = widgetPopSpectrumGS(self)
-        self.ui.verticalLayout.insertWidget(1, self.popimage, _QtCore.Qt.AlignLeft)
-        self.popimage.ui.pushButtonPop.pressed.connect(lambda: self.createImg_Ext(img = self.data.image,
-                                                                                  showcbar=False,
-                                                                                  extent=self.data.winextent, 
-                                                                                  xunits=self.data.xunits,
-                                                                                  yunits=self.data.yunits,
-                                                                                  parent=parent))
-        self.popimage.ui.pushButtonGSPop.setEnabled(False)
-        self.popimage.ui.pushButtonSpectrum.setEnabled(False)
-        self.ui.comboBoxBGColor.setEnabled(False)
-        self.ui.comboBoxBGColor.setVisible(False)  # Broken -- don't know if it will ever work
-        self.ui.labelBGColor.setVisible(False)  # Broken
-        self.ui.comboBoxColorMode.currentIndexChanged.connect(self.changeMode)
-
-
[docs]    def initData(self, sgl_color_widget_list):
-        """
-        (Re)-initialize self.data
-        """
-        
-        if sgl_color_widget_list is None:
-            self.data = CompositeColor()
-        else:
-            temp = []
-            for count in sgl_color_widget_list:
-                temp.append(count.data)
-
-            self.data = CompositeColor(temp)

-
-
[docs]    def createImg(self, img, xunits = None, yunits = None,
-                  extent = None,
-                  cmap = _mpl.cm.gray):
-        self.mpl.ax.clear()
-        self.mpl.img = self.mpl.ax.imshow(img, interpolation = 'none',
-                                      extent = extent, cmap = cmap, origin='lower')
-        if xunits is not None:
-            self.mpl.ax.xaxis.set_label_text(xunits)
-        if yunits is not None:
-            self.mpl.ax.yaxis.set_label_text(yunits)
-
-        if self._img_defaults['axison'] == False:
-            self.mpl.ax.set_axis_off()
-
-        if self.mpl.cbar is not None:
-                self.mpl.cbar.remove()
-        if self._img_defaults['showcbar'] == True:
-            self.mpl.cbar = self.mpl.fig.colorbar(self.mpl.img)

-
-
[docs]    def createImg_Ext(self, img, xunits = None, yunits = None,
-                  extent = None, showcbar = True, axison = True,
-                  cmap = _mpl.cm.gray, parent=None):
-        """
-        Create new figure window and show image of img
-        """
-
-        self.external_plots.append(_sciplot.main(parent=parent))
-        self.external_plots[-1].imshow(img, x_label=xunits, y_label=yunits, 
-                      cmap=cmap, cbar=showcbar, extent=extent)

-
-    # BROKEN -- May never work
-    # def changeBGColor(self):
-    #     """
-    #     Does not work as expected
-    #     """
-    #     color_str = self.ui.comboBoxBGColor.currentText()
-    #     self.data.bgcolor = _mpl.colors.to_rgb(_mpl.colors.cnames[color_str])
-
-    #     self.createImg(img = self.data.image, xunits = self.data.xunits,
-    #                           yunits = self.data.yunits,
-    #                           extent = self.data.winextent)
-    #     self.mpl.fig.tight_layout()
-    #     self.mpl.draw()
-    
-
[docs]    def changeMode(self):
-        self.data.mode = self.ui.comboBoxColorMode.currentIndex()
-        # self.data.mode = _np.abs(self.data.mode - 1).astype(int)
-        self.mpl.ax.clear()
-        self.createImg(img = self.data.image, xunits = self.data.xunits,
-                              yunits = self.data.yunits,
-                              extent = self.data.winextent)
-        self.mpl.fig.tight_layout()
-        self.mpl.draw()

-
-
-if __name__ == '__main__':
-
-    app = _QApplication(_sys.argv)
-    app.setStyle('Cleanlooks')
-
-    winBWImg = widgetBWImg()
-    winBWImg.setWindowTitle('BW Image')
-    winBWImg.show()
-    
-    winSglColor = widgetSglColor()
-    winSglColor.setWindowTitle('Single Color')
-    winSglColor.colormode.ui.comboBoxBGColor.setCurrentIndex(7)
-    winSglColor.show()
-
-    winSglColor2 = widgetSglColor()
-    winSglColor2.colormode.ui.comboBoxFGColor.setCurrentIndex(1)
-    winSglColor2.colormode.ui.comboBoxBGColor.setCurrentIndex(7)
-    winSglColor2.setWindowTitle('Single Color')
-    winSglColor2.show()
-    
-    
-    winColorMath = widgetImageGainMath()
-    winColorMath.setWindowTitle('Color Math')
-    winColorMath.show()
-
-    winCompositeColor = widgetCompositeColor(sgl_color_widget_list=[winSglColor, winSglColor2])
-    winCompositeColor.setWindowTitle('Composite Color')
-    winCompositeColor.show()
-
-    _sys.exit(app.exec_())
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_mergeNRBs.html b/docs/build/html/_modules/crikit/ui/widget_mergeNRBs.html deleted file mode 100644 index cdbde3f..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_mergeNRBs.html +++ /dev/null @@ -1,428 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_mergeNRBs — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
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Source code for crikit.ui.widget_mergeNRBs

-"""
-Widget for PlotEffect that adjusts the parameters appropriate for
-merging 2 NRBs
-
-Created on Thu Dec 22 22:20:06 2016
-
-@author: chc
-"""
-
-import numpy as _np
-
-from crikit.ui.dialog_AbstractPlotEffect import (AbstractPlotEffectPlugin
-                                                     as
-                                                     _AbstractPlotEffectPlugin)
-
-
-from crikit.ui.widget_KK import (widgetKK as _widgetKK)
-from crikit.ui.qt_PlotEffect_MergeNRBs import Ui_Form as _Ui_Form
-from crikit.utils.general import find_nearest as _find_nearest
-from crikit.cri.merge_nrbs import MergeNRBs as _MergeNRBs
-
-
[docs]class widgetMergeNRBs(_AbstractPlotEffectPlugin):
-    """
-    Widget for PlotEffect that adjusts the parameters appropriate for
-    merging 2 NRBs
-    """
-    # Parameter dict that will be returned from PlotEffect
-    # Will be updated later in program to contain all parameters
-    # to pass to underlying algorithm
-    parameters = {'name' : 'mergeNRBs', 
-                  'long_name' : 'Merge 2 NRBs'}
-    
-    # Labeling options for original data plot
-    labels_orig = {
-                   'x_label' : 'Wavenumber (cm$^{-1}$)',
-                   'y_label' : 'Input Int (au)',
-                   'title' : 'Original'
-                   }
-    
-    # Labeling options for affected data plot              
-    labels_affected = {
-                       'x_label' : labels_orig['x_label'],
-                       'y_label' : 'Raman-Like Int (au)',
-                       'title' : 'KK-Raman'
-                      }
-  
-    def __init__(self, wn_vec, nrb_left, nrb_right, scale_left=False, 
-                 wn_switchpt=2800.0, parent = None):
-                      
-        super(widgetMergeNRBs, self).__init__(parent)
-        
-        self.ui = _Ui_Form()
-        self.ui.setupUi(self)
-        
-        self.wn = wn_vec
-        self.nrb_left = nrb_left
-        self.nrb_right = nrb_right
-        
-        # Update parameter dict
-        self.parameters['scale_left'] = scale_left
-        self.parameters['wn_switchpt'] = wn_switchpt
-        self.parameters['pix_switchpt'] = \
-            _find_nearest(self.wn, self.parameters['wn_switchpt'])[1]
-        
-        self.kk_widget = _widgetKK()
-        
-        self.ui.horizontalLayoutKK.insertWidget(0, self.kk_widget)
-        
-        self.ui.spinBoxWN.setMinimum(self.wn.min())
-        self.ui.spinBoxWN.setMaximum(self.wn.max())
-        self.ui.spinBoxPix.setMinimum(0)
-        self.ui.spinBoxPix.setMaximum(self.wn.size-1)
-        
-        # Set range
-        self.ui.spinBoxLowRange.setValue(self.wn.min())
-        self.ui.spinBoxHighRange.setValue(self.wn.max())
-        self.rng = None
-        self.rangeChanged()
-        
-        if self.parameters['scale_left']:
-            self.ui.comboBoxScaleLeftRight.setCurrentIndex(0)
-        elif self.parameters['scale_left'] == False:
-            self.ui.comboBoxScaleLeftRight.setCurrentIndex(1)
-        elif self.parameters['scale_left'] is None:
-            self.ui.comboBoxScaleLeftRight.setCurrentIndex(2)
-            
-        self.ui.spinBoxWN.setValue(self.parameters['wn_switchpt'])
-        self.ui.spinBoxPix.setValue(self.parameters['pix_switchpt'])
-        
-        # SIGNALS & SLOTS
-        self.kk_widget.changed.connect(self.kkChanged)
-        
-        self.ui.comboBoxScaleLeftRight.currentIndexChanged.connect(self.scaleChanged)
-        self.ui.spinBoxWN.editingFinished.connect(self.wnChanged)
-        self.ui.spinBoxPix.editingFinished.connect(self.pixChanged)
-        
-        self.ui.spinBoxLowRange.editingFinished.connect(self.rangeChanged)
-        self.ui.spinBoxHighRange.editingFinished.connect(self.rangeChanged)
-        
-
[docs]    def rangeChanged(self):
-        low = self.ui.spinBoxLowRange.value()
-        high = self.ui.spinBoxHighRange.value()
-        self.rng = [low, high]
-        self.rng.sort()
-        self.changed.emit()

-        
-    @property
-    def fullRange(self):
-        low = self.rng[0]
-        high = self.rng[1]
-        
-        if (_np.isclose(self.wn.min(), low, atol=.1) & 
-            _np.isclose(self.wn.max(), high, atol=.1)):
-            return True
-        else:
-            return False
-        
-
[docs]    def kkChanged(self):
-        self.changed.emit()

-    
-
[docs]    def scaleChanged(self):
-        idx = self.ui.comboBoxScaleLeftRight.currentIndex()
-        
-        if idx == 0:
-            self.parameters['scale_left'] = True
-        elif idx == 1:
-            self.parameters['scale_left'] = False
-        else:
-            self.parameters['scale_left'] = None
-        self.changed.emit()

-
-
[docs]    def wnChanged(self):
-#        print('WN Changed')
-        self.parameters['wn_switchpt'], self.parameters['pix_switchpt'] = \
-            _find_nearest(self.wn, self.ui.spinBoxWN.value())
-            
-        self.ui.spinBoxWN.setValue(self.parameters['wn_switchpt'])
-        self.ui.spinBoxPix.setValue(self.parameters['pix_switchpt'])
-        self.changed.emit()

-    
-
[docs]    def pixChanged(self):
-        self.parameters['pix_switchpt'] = self.ui.spinBoxPix.value()
-        self.parameters['wn_switchpt'] = self.wn[self.parameters['pix_switchpt']]
-
-        self.ui.spinBoxWN.setValue(self.parameters['wn_switchpt'])
-        
-        self.changed.emit()

-
-
[docs]    def fcn(self, data_in):
-        """
-        If return list, [0] goes to original, [1] goes to affected
-        """
-        inst_nrb_merge = _MergeNRBs(nrb_left=self.nrb_left, 
-                                        nrb_right=self.nrb_right,
-                                        pix=self.parameters['pix_switchpt'],
-                                        left_side_scale=self.parameters['scale_left'])
-        
-        if self.fullRange:
-            pix = _np.arange(self.wn.size, dtype=_np.integer)
-            
-        else:
-            list_rng_pix = _find_nearest(self.wn, self.rng)[1]
-            pix = _np.arange(list_rng_pix[0],list_rng_pix[1]+1,
-                             dtype=_np.integer)
-            
-        nrb_merged = inst_nrb_merge.calculate()
-        kkd = _np.zeros(data_in.shape)
-
-        # Note: kk_widget.fcn return imag part
-        kkd[..., pix] = self.kk_widget.fcn([nrb_merged[pix], data_in[..., pix]])
-        
-        return [_np.vstack((self.nrb_left, self.nrb_right, nrb_merged)),
-                kkd]

-        
-if __name__ == '__main__':
-    import sys as _sys
-    from PyQt5.QtWidgets import QApplication as _QApplication
-    app = _QApplication(_sys.argv)
-    
-    WN = _np.linspace(-1500,3600,1600)
-    
-    NRB_LEFT = 20e3*_np.exp(-(WN)**2/(1000**2)) + 500
-    NRB_RIGHT = 6e3*_np.exp(-(WN-2500)**2/(400**2)) + 500
-    
-    NRB_LEFT[WN<500] *= 0
-    NRB_LEFT[WN<500] += 1e-6
-    NRB_RIGHT[WN<500] *= 0
-    NRB_RIGHT[WN<500] += 1e-6
-    
-    win = widgetMergeNRBs(WN, NRB_LEFT, NRB_RIGHT)
-    win.show()
-    
-    app.exec_()
-    _sys.exit()
-    
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/ui/widget_scientificspin.html b/docs/build/html/_modules/crikit/ui/widget_scientificspin.html deleted file mode 100644 index 1f67518..0000000 --- a/docs/build/html/_modules/crikit/ui/widget_scientificspin.html +++ /dev/null @@ -1,303 +0,0 @@ - - - - - - - - - - - crikit.ui.widget_scientificspin — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.ui.widget_scientificspin

-"""
-From https://gist.github.com/jdreaver -- scientificspin.py
-
-Created on Wed Dec  7 10:39:26 2016
-
-@author: chc
-"""
-
-import re
-
-from PyQt5 import QtWidgets, QtGui
-
-# Regular expression to find floats. Match groups are the whole string, the
-# whole coefficient, the decimal part of the coefficient, and the exponent
-# part.
-_float_re = re.compile(r'(([+-]?\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)')
-
-
[docs]def valid_float_string(string):
-    match = _float_re.search(string)
-    return match.groups()[0] == string if match else False

-
-
[docs]class FloatValidator(QtGui.QValidator):
-
-
[docs]    def validate(self, string, position):
-        if valid_float_string(string):
-            state = QtGui.QValidator.Acceptable
-        elif string == "" or string[position-1] in 'e.-+':
-            state = QtGui.QValidator.Intermediate
-        else:
-            state = QtGui.QValidator.Invalid
-        return (state, string, position)

-    
-
[docs]    def fixup(self, text):
-        match = _float_re.search(text)
-        return match.groups()[0] if match else ""

-
-
[docs]class ScientificDoubleSpinBox(QtWidgets.QDoubleSpinBox):
-
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.setMinimum(-1e20)
-        self.setMaximum(1e20)
-        self.validator = FloatValidator()
-        self.setDecimals(100)
-        
-
[docs]    def validate(self, text, position):
-        return self.validator.validate(text, position)

-    
-
[docs]    def fixup(self, text):
-        return self.validator.fixup(text)

-    
-
[docs]    def valueFromText(self, text):
-        return float(text)

-    
-
[docs]    def textFromValue(self, value):
-        return format_float(value)

-    
-
[docs]    def stepBy(self, steps):
-        text = self.cleanText()
-        groups = _float_re.search(text).groups()
-        decimal = float(groups[1])
-        decimal += steps
-        new_string = "{:g}".format(decimal) + (groups[3] if groups[3] else "")
-        self.lineEdit().setText(new_string)

-        
-
[docs]def format_float(value):
-    """Modified form of the 'g' format specifier."""
-    string = "{:g}".format(value).replace("e+", "e")
-    string = re.sub("e(-?)0*(\d+)", r"e\1\2", string)
-    return string

-
- -
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- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/utils/breadcrumb.html b/docs/build/html/_modules/crikit/utils/breadcrumb.html deleted file mode 100644 index 237ed9b..0000000 --- a/docs/build/html/_modules/crikit/utils/breadcrumb.html +++ /dev/null @@ -1,527 +0,0 @@ - - - - - - - - - - - crikit.utils.breadcrumb — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Source code for crikit.utils.breadcrumb

-"""
-Breadcrumb Module
-=================
-
-    BCPre : Container describing pre-processing steps
-
-Class Methods
---------------
-    HDFtoClass(filename [str], datasetname [str]) : Load dataset in HDF
-        file into the HSI Class
-
-"""
-
-import time as _time
-import copy as _copy
-import pickle as _pickle
-
-
[docs]class BCPre:
-    """
-    Container that describes processing steps (ie it contains "breadcrumbs")
-    
-    Attributes
-    ----------
-    process_list : list
-        A list-of-lists. Each contained list follows the format \
-        ['Process Name', 'Var1 Name', Val1, 'Var2 Name', Val2, ...]. The \
-        variable names and values may be input values to the pre-processing \
-        step. Only the Process Name is mnadatory: the rest are optional.
-    
-    backed_flag : list
-        Flag identifying which steps were backed-up to disk (e.g., for undo)
-        
-    id_list : list (read-only)
-        Unique identifier for each step. Can be used to name back-up/undo files
-
-    cut_list : list (read-only)
-        Identifier of id's cut with pop_to_last method
-        
-    num_steps : int
-        Number of processing steps
-        
-    attr_dict : dict
-        Dictionary-version of process_list that can be written to HDF5 dataset
-        metadata (properties)
-    
-    Methods
-    -------
-    add_step : Add a new processing step
-    
-    backed_up : Mark most recent process step as backed up in backed_flag list
-    
-    pop_to_last : Remove entries until nearest backup point (excluding current \
-        step).
-    
-    """
-    
-    HDF_PREFIX = 'Processing.Steps'
-    
-    def __init__(self):
-        self.process_list = []
-        self._id_list = []
-        self.backed_flag = []
-        self._cut_list = []
-    
-    # PROPERTIES
-    @property
-    def id_list(self):
-        # Use shallow-copy to prevent ability to append 
-        # to _id_list via id_list
-        return self._id_list.copy()
-        
-    @property
-    def cut_list(self):
-        # Use shallow-copy to prevent ability to append 
-        # to _cut_list via cut_list
-        return self._cut_list.copy()
-    
-    @cut_list.deleter
-    def cut_list(self):
-        self._cut_list = []
-            
-    @property
-    def num_steps(self):
-        return len(self.process_list)
-    
-    @property
-    def attr_dict(self):
-        temp = {}
-        for num, item in enumerate(self.process_list):
-            temp_key_process_prefix = self.HDF_PREFIX + '.' + str(num+1) + '.' + str(item[0])
-            temp_val = 'NA'
-            temp[temp_key_process_prefix] = temp_val
-            if len(item) > 1:
-                #print('ITEM: {}'.format(item))
-                for num_var, var in enumerate(item[1::2]):
-                    #print('KEY: {}, VAL: {}'.format(var, item[2*num_var+2]))
-                    temp_key = temp_key_process_prefix + '.' + str(var)
-                    temp_val = item[2*num_var+2]
-                    temp[temp_key] = temp_val
-        temp[self.HDF_PREFIX] = self.num_steps
-        return temp
-        
-    @property
-    def dset_name_suffix(self):
-        temp = ''
-        #print('QQQ: {}'.format(self.process_list))
-        try:
-            for num, step in enumerate(self.process_list):
-                #print('Step: {}'.format(step[0]))
-                #print(num)
-                if num == 0:
-                    pass
-                else:
-                    #print(step[0])
-                    temp = temp + '_' + step[0]
-            return temp
-        except:
-            return None
-    
-    # METHODS
-
[docs]    @staticmethod
-    def backup_pickle(data, fname, addl_attr = None):
-        """
-        Dump current state of data (class of type crikit.data.spectrum or 
-        subclass)to pickle file (filename= fname). 
-        
-        Can append additional attributes (addl_attr) to \
-        attribute dictionary (self.attr)
-        """
-        if fname.find('.pickle') == -1:
-            fname += '.pickle'
-
-        if addl_attr is not None:
-            data.attr.update(addl_attr)
-
-        with open(fname, 'xb') as f:
-            # Pickle with highest protocol
-            # Surpasses the default protocol 3 4Gb limit
-            _pickle.dump(data, f, protocol=-1)

-            
-
[docs]    @staticmethod
-    def load_pickle(fname):
-        """
-        Static method.
-
-        Return a loaded pickled version of this class (filename= fname).
-
-        """
-        if fname.find('.pickle') == -1:
-            fname += '.pickle'
-
-        with open(fname, 'rb') as f:
-            return _pickle.load(f)

-            
-
[docs]    def add_step(self, process_desc):
-        """
-        Adds a steps to the list
-        
-        Parameters
-        ------
-        process_desc : list
-            List containing elements of new process with format: \
-            ['Process Name', 'Var1 Name', Val1, 'Var2 Name', Val2, ...]. The \
-            variable names and values may be input values to the \
-            pre-processing step. Only the Process Name is mnadatory: the rest \
-            are optional.
-            
-        Returns
-        -------
-        None : None
-            
-        """
-        assert isinstance(process_desc,list), 'The input need be a list'
-        assert len(process_desc)%2 != 0, 'The input needs to be an odd length (title, var name 1, var value 1, etc)'
-        
-        # Ensures unique IDs based on time. Note some systems only report in 
-        # seconds, not sub-seconds        
-        _time.sleep(1)
-
-        self.process_list.append(process_desc)
-        self._id_list.append(str(_time.time()))
-        self.backed_flag.append(False)

-        
-
[docs]    def backed_up(self):
-        """
-        Marks most recent process step as backed up in backed_flag list
-        
-        Parameters
-        ------
-        None : None
-            
-        Returns
-        -------
-        None : None
-            
-        """
-        self.backed_flag[-1] = True

-        
-
[docs]    def pop_to_last(self, all=False):
-        """
-        Remove entries until nearest backup point (excluding current step). 
-        That is, if current step IS a backup point, moves to previous one. If \
-        current step is NOT a backup point, moves to nearest point.
-        
-        If all = True, will cut everything
-        """
-        temp = _copy.deepcopy(self.backed_flag)
-        backup_locs = []        
-        for num, val in enumerate(temp):
-            if val is True:
-                backup_locs.append(num)
-        
-        current_loc = len(temp) - 1
-        
-        if all is False:
-            if temp[-1] == True:  # Current is backed-up, go to previous
-                num_to_pop = backup_locs[-1] - backup_locs[-2]
-            else: # Current is not backed-up, return to nearest
-                num_to_pop = current_loc - backup_locs[-1]
-        else:
-            num_to_pop = len(temp)
-        
-        for count in range(num_to_pop):
-            self.process_list.pop()
-            is_backed_up = self.backed_flag.pop()
-            if is_backed_up:
-                self._cut_list.append(self._id_list.pop())
-            else:
-                self._id_list.pop()

-              
-        
-if __name__ == '__main__':
-    import sys as _sys
-    test = BCPre()
-    try:
-        test.add_step('Test1')
-    except:
-        print('Expected Error\n')
-    try:
-        test.add_step(['Test',1])
-    except:
-        print('Expected Error\n')
-    
-    test.add_step(['Raw'])
-    test.add_step(['SubDark','RangeStart',-1500,'RangeEnd',-400])
-    test.add_step(['NormKK','Amp',100.0,'Phase',10.0])
-    #test.add_step(['DeTrend','Lambda',1000.0,'p',0.001,'Method','ALS','Type','Phase'])
-    #test.add_step(['DeTrend','Order',2,'win',601,'Method','sg','Type','Scale'])
-    
-    #print('Attempting to append \'1\' to the end of id_list (it should not work)')
-    #test.id_list.append(1)
-    #print(test.id_list)
-    
-    print('\nProcess list: {}'.format(test.process_list))
-    print('\nID list: {}'.format(test.id_list))
-    print('\nNumber of process steps: {}'.format(test.num_steps))
-    print('\n\nReturned attribute dict: {}'.format(test.attr_dict))
-    print('\n\nGenerated dataset name: {}'.format(test.dset_name_suffix))
-    _sys.exit()
-    
-    #[['Raw'], ['SubDark'], ['SubResidual', 'RangeStart', -1500, 'RangeEnd', -400]]
-    
-    
-#    print('\n\n\nWritten to backup file: {}'.format(test.backed_flag))
-#    print('\n...Apply backed_up...')
-#    test.backed_up()
-#    print('\nWritten to backup file: {}'.format(test.backed_flag))
-#    
-#    print('\nAdjust backup')
-#    test.backed_flag[0] = True
-#    print('Written to backup file: {}'.format(test.backed_flag))
-#    
-#    print('\n Test Pop-to-last')
-#    print('Process List: {}'.format(test.process_list))
-#    print('ID List: {}'.format(test.id_list))
-#    print('Written to backup file: {}\n'.format(test.backed_flag))
-#            
-#    test.pop_to_last()
-#    print('Process List: {}'.format(test.process_list))
-#    print('ID List: {}'.format(test.id_list))
-#    print('Written to backup file: {}'.format(test.backed_flag))
-#    print('Cut List:{}'.format(test.cut_list))
-#    del test.cut_list
-#    print('Cut List:{}'.format(test.cut_list))
-#    
-#    print('\nCut all')
-#    test.pop_to_last(all=True)
-#    print('Process List: {}'.format(test.process_list))
-#    print('ID List: {}'.format(test.id_list))
-#    print('Written to backup file: {}'.format(test.backed_flag))
-#    print('Cut List:{}'.format(test.cut_list))
-#    del test.cut_list
-#    print('Cut List:{}'.format(test.cut_list))
-#    
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/utils/datacheck.html b/docs/build/html/_modules/crikit/utils/datacheck.html deleted file mode 100644 index a0632c1..0000000 --- a/docs/build/html/_modules/crikit/utils/datacheck.html +++ /dev/null @@ -1,271 +0,0 @@ - - - - - - - - - - - crikit.utils.datacheck — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.utils.datacheck
    • - - -
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- -

Source code for crikit.utils.datacheck

-"""
-Functions to check and (if needed) convert input variables
-
-Created on Sat Jun 18 00:16:27 2016
-
-@author: chc
-"""
-
-import numpy as _np
-
-
-
[docs]def _rng_is_pix_vec(rng, vec_size=None):
-    """
-    Make sure rng is a vector, unless None (then returns None).
-
-    Parameters
-    ----------
-
-    rng : int, list, tuple, or ndarray(1D)
-        * int: number of pixels in rng
-        * list, tuple, ndarray with length 2: Start and end of rng
-        * ndarray (length > 2): actual rng vector
-
-    Returns
-    -------
-
-    rng : ndarray (1D)
-        Array of pixel range
-    """
-    if rng is None:
-        return None
-    elif isinstance(rng, (int, float)):
-        return _np.arange(rng)
-    elif len(rng) == 2:
-        rng.sort()
-        return _np.arange(rng[0], rng[1])
-    else:
-        return rng

-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/utils/general.html b/docs/build/html/_modules/crikit/utils/general.html deleted file mode 100644 index e5681c8..0000000 --- a/docs/build/html/_modules/crikit/utils/general.html +++ /dev/null @@ -1,442 +0,0 @@ - - - - - - - - - - - crikit.utils.general — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.utils.general
    • - - -
  • - - - -
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-
- -

Source code for crikit.utils.general

-"""
-General utilities
-
-    expand_1d_to_ndim_data : Match 1D data array dimensionality to that of \
-        another array
-
-    expand_1d_to_ndim : Expand 1D data array dimensionality to ndim
-
-    find_nearest : Given a vector and a value, find the index and value
-        of the closest match
-
-Notes
------
-"""
-import numpy as _np
-
-
[docs]def np_fcn_nd_to_1d(fcn, data, axis=-1):
-    """
-    Take in an n-dimensional array and return a 1D version operated on by fcn.\
-    Works with many numpy functions that can take an "axis" parameter
-    """
-    if data.ndim > 1:
-        dims = list(range(data.ndim))
-        dims.pop(axis)
-        vec = fcn(data, axis=tuple(dims))
-    else:
-        vec = data
-
-    return vec

-
-
[docs]def mean_nd_to_1d(data, axis=-1):
-    """
-    Take the mean of an nd array, except axis, returning a 1D array
-    """
-    vec = np_fcn_nd_to_1d(_np.mean, data, axis=axis)
-
-    return vec

-
-
[docs]def std_nd_to_1d(data, axis=-1):
-    """
-    Take the mean of an nd array, except axis, returning a 1D array
-    """
-    vec = np_fcn_nd_to_1d(_np.std, data, axis=axis)
-
-    return vec

-
-
-
[docs]def arange_nonzero(start, stop, dtype=_np.float):
-    """
-    Similar to numpy arange but only returns non-zero elements
-    """
-    vec = _np.arange(start, stop+1)
-    vec = vec[vec != 0]
-    return vec

-
-
-
[docs]def expand_1d_to_ndim_data(data, data_to_match):
-    """
-    Make 1D data array equal in dimensions to data_to_match
-    """
-    if data.ndim > 1:
-        print('data must be 1D')
-    else:
-        nd = data_to_match.ndim
-        return expand_1d_to_ndim(data, nd)

-
-
-
[docs]def expand_1d_to_ndim(data, ndim):
-    """
-    Make 1D array into ndim dimensions
-    """
-    if data.ndim > 1:
-        print('data must be 1D')
-    else:
-        sh = _np.ones((ndim-1),dtype=int)
-        sh = _np.append(sh,-1)
-        return data.reshape(sh)

-
-
[docs]def find_nearest(np_vec,to_find = 0):
-    """
-    Given a vector and a value (or list/vector of values), find the index and
-    value of the closest match
-
-
-    Parameters
-    ----------
-    np_vec : numpy.ndarray
-        Numpy array (list) of values
-
-    to_find : int, float, numpy.ndarray, or list
-
-    Returns
-    -------
-    out : tuple (nearest_value(s), index(es))
-        Closest value (nearest_value) and index (index)
-
-    """
-
-    # Number of values (to_find) to find
-    len_to_find = 0
-
-    if isinstance(to_find, int) or isinstance(to_find, float):
-        len_to_find = 1
-    elif isinstance(to_find, list) or isinstance(to_find, tuple):
-        len_to_find = len(to_find)
-    elif isinstance(to_find, _np.ndarray):
-        len_to_find = to_find.size
-    else:
-        pass
-
-    if len_to_find == 0:
-        return (None, None)
-    elif len_to_find == 1:  # Single value
-        test = _np.abs(_np.array(np_vec)-to_find)
-        nearest_loc = test.argmin()
-        nearest_val = np_vec[nearest_loc]
-    else:  # Series of values
-        nearest_val = []
-        nearest_loc = []
-
-        for val in to_find:
-            loc = _np.argmin(_np.abs(_np.array(np_vec)-val))
-            nearest_loc.append(loc)
-            nearest_val.append(np_vec[loc])
-
-    return (nearest_val, nearest_loc)

-
-
-
[docs]def row_col_from_lin(ct, sh):
-    """
-    Convert a 1D counter into a col and row counter
-    """
-
-    assert len(sh) == 2, 'Shape must be 2D'
-
-    tot_rows = sh[0]
-    tot_cols = sh[1]
-
-    if isinstance(ct, _np.ndarray):
-        if (ct > tot_rows*tot_cols).any():
-            print('Count is out-of-range. Returning None.')
-            return None
-    else:
-        if ct > tot_rows*tot_cols:
-            print('Count is out-of-range. Returning None.')
-            return None
-
-    row = _np.mod(ct, tot_rows)
-    col = ct//tot_rows
-
-    return [row, col]

-
-
-
[docs]def lin_from_row_col(row, col, sh):
-    """
-    Convert a col and row counter to 1D linear count
-    """
-
-    assert len(sh) == 2, 'Shape must be 2D'
-
-    tot_rows = sh[0]
-    # tot_cols = sh[1]
-
-    ct = col*tot_rows + row
-
-    return ct

-
-if __name__ == '__main__':
-    import timeit as _timeit
-
-    print('Test 1.....')
-    x = _np.random.rand(10,11)
-
-    for ct in range(x.size):
-        row, col = lin_count_row_col(ct, x.shape)
-        print('R: {} C: {}'.format(row,col))
-    print('Total number iterated through: {}'.format(ct+1))
-
-    print('Test 2...')
-    x = _np.random.rand(100,100,878)
-    y = _np.zeros(x.shape, dtype=complex)
-
-    tmr = _timeit.default_timer()
-    for rc, blk in enumerate(x):
-        for cc, sp in enumerate(blk):
-            y[rc,cc,:] = _np.fft.fft(sp)
-    tmr -= _timeit.default_timer()
-    print('Time with 2 for-loops: {:.3g} sec'.format(-tmr))
-
-    tmr = _timeit.default_timer()
-    shp = x.shape
-    x = x.reshape((-1, shp[-1]))
-    y = _np.zeros(x.shape, dtype=complex)
-    for num, sp in enumerate(x):
-        y[num,:] = _np.fft.fft(sp)
-    y = y.reshape(shp)
-    tmr -= _timeit.default_timer()
-    print('Time with reshaping and 1 for-loops: {:.3g} sec'.format(-tmr))
-    x = x.reshape(shp)
-
-    tmr = _timeit.default_timer()
-    space_shp = _np.array(x.shape)[0:-1]
-    num_sp = space_shp.prod()
-    for num in range(num_sp):
-        rc, cc = lin_count_row_col(num, space_shp)
-        y[rc, cc, :] = _np.fft.fft(x[rc, cc, :])
-    tmr -= _timeit.default_timer()
-    print('Time with 1 for-loops: {:.3g} sec'.format(-tmr))
-
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/utils/h5.html b/docs/build/html/_modules/crikit/utils/h5.html deleted file mode 100644 index 727c0b9..0000000 --- a/docs/build/html/_modules/crikit/utils/h5.html +++ /dev/null @@ -1,669 +0,0 @@ - - - - - - - - - - - crikit.utils.h5 — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- - - - -
-
-
-
- -

Source code for crikit.utils.h5

-"""
-hdf5 utilities (crikit.utils.h5)
-=======================================================
-
-    Utilities for for reading and writing data to HDF5 files
-
-Methods
---------
-    convert_to_np_dtype : convert from HDF5 dataset to numpy ndarray with \
-    numpy-builtin and native datatype
-
-    retrieve_group_dataset_dict : Retrieve dictionary describing groups that \
-    contain data [key] and the datasets [value]. {group : [dataset(s)]}
-
-    retrieve_dataset_attribute_dict : Retrieve dictionary describing \
-    attributes that contain data [key] and the datasets [value]. \
-    {group : [dataset(s)]}
-
-"""
-
-import h5py as _h5py
-_h5py.get_config().complex_names = ('Re','Im')
-
-import numpy as _np
-
-
[docs]def convert_to_np_dtype(dset):
-    """
-    Given an HDF5 dataset, return the values in a numpy-builtin datatype
-
-    Parameters
-    ----------
-    dset : h5py.Dataset
-        HDF5 (h5py) dataset
-
-    Returns
-    -------
-    out : numpy.ndarray (dtype = numpy built-in)
-
-    Notes
-    -----
-    The software accounts for big-/little-endianness, and the inability of \
-    hdf5 to natively store complex numbers.
-
-    """
-    assert isinstance(dset, _h5py.Dataset), 'Input is not of type h5py.Dataset'
-    # Single datatype
-    if len(dset.dtype) == 0:
-        converted = _np.ndarray(dset.shape, dtype = dset.dtype.newbyteorder('='))
-        dset.read_direct(converted)
-        if issubclass(converted.dtype.type, _np.integer):  # Integer to float
-            converted = converted.astype(_np.float)
-        return converted
-    #Compound datatype of length 2-- assumed ('Re','Im')
-    elif len(dset.dtype) == 2:
-        print('Warning: h5py.complex_names set incorrectly using \'{}\' and \'{}\' \
-for Re and Im, respectively'.format(dset.dtype.names[0], dset.dtype.names[1]))
-        _h5py.get_config().complex_names = (dset.dtype.names[0],dset.dtype.names[1])
-        dset = dset.file[dset.name]
-        converted = _np.ndarray(dset.shape, dtype = dset.dtype.newbyteorder('='))
-        dset.read_direct(converted)
-    # Unknown datatype
-    else:
-        print('Warning: Unknown datatype. Returning dataset values as is.')
-        return dset.value
-    return converted

-
-
-
[docs]def retrieve_group_dataset_dict(filename):
-    """
-    Given an HDF5 filename, return a dictionary with keys named with full \
-    paths to datasets (values)
-
-    Parameters
-    ----------
-    filename : str
-        filename of HDF5 file
-
-    Returns
-    -------
-    out : dict
-        {group path : [dataset list]}
-
-    Notes
-    -----
-
-    """
-    try:
-        f = _h5py.File(filename,'r')
-    except OSError as err:
-        print(err)
-    else:
-        list_of_items = ['/']
-        f.visit(list_of_items.append)
-
-        groups_all = []
-        datasets_all = []
-
-        for count in list_of_items:
-            if isinstance(f[count],_h5py.Group) == True:
-                groups_all.append(count)
-            if isinstance(f[count],_h5py.Dataset) == True:
-                datasets_all.append(count)
-
-        groups_with_datasets = []
-
-        for group_count in groups_all:
-            for item_count in f[group_count]:
-                if isinstance(f[group_count][item_count],_h5py.Dataset):
-                    groups_with_datasets.append(group_count)
-                    break
-
-        # Setup dictionary group_with_dataset : datasetnames
-        group_dataset_dict = []
-        for group_count in groups_with_datasets:
-            dataset_list = []
-            for item_count in f[group_count]:
-                if isinstance(f[group_count][item_count],_h5py.Dataset):
-                    dataset_list.append(item_count)
-            group_dataset_dict.append([group_count,dataset_list])
-
-        group_dataset_dict = dict(group_dataset_dict)
-
-        #print('Returning {0} groups covering {1} datasets'.format\
-        #        (len(groups_with_datasets), len(datasets_all)))
-
-
-
-        f.close()
-        return group_dataset_dict

-
-
[docs]def retrieve_dataset_attribute_dict(filename,datasetfullname):
-    """
-    Given an HDF5 filename and dataset, return a dictionary with keys named \
-    with parameters and values
-
-    Parameters
-    ----------
-    filename : str
-        filename of HDF5 file
-
-    datasetfullname : str
-        full pathname to dataset (e.g., /group/subgroup/dataset)
-
-    Returns
-    -------
-    out : dict
-        {parameter : value}
-
-    Notes
-    -----
-
-    """
-    try:
-        f = _h5py.File(filename,'r')
-    except OSError as err:
-        print(err)
-    else:
-        try:
-            attrs = f[datasetfullname].attrs
-            temp =  dict(attrs)
-        except:
-            print('Error in attributes... Usually an empty one')
-            temp = {}
-            for count in attrs:
-                try:
-                    temp[count] = attrs[count]
-                except:
-                    pass
-        return temp
-    f.close()
-    return None

-
-
[docs]def special_exclude_datasets(filename, str_excl = '_background', new_filename = None):
-    """
-    Removes any datasets with '_background' in the name. Creates a new
-    h5 file with '_excl*_.h5' appended (unless specified)
-
-    Parameters
-    ----------
-        filename (str) : name of file to analyze/repack/copy
-
-        str_excl (str) : (default: '_background') exclude datasets with this string in the name
-
-        new_filename (str) : (Optional) Output filename
-
-    Returns
-    -------
-        str : filename of new HDF5 file
-
-        Writes a new file filename(-.h5) + '_excl_' + str_exclude + '.h5'
-
-    Notes
-    -----
-    SPECIAL : Only likely useful for the NIST developers
-
-    """
-
-    if new_filename == None:
-        new_filename = str.strip(filename,'.h5') + '_excl_' + str_excl.strip('_') + '.h5'
-    else:
-        pass
-
-    dataset_dict = retrieve_group_dataset_dict(filename)
-
-    f_input = _h5py.File(filename, 'r')
-    f_output = _h5py.File(new_filename, 'w-')
-
-    try:
-        # Interate trhough groups/subgroups
-        for groups in dataset_dict:
-            dsets_in_group = dataset_dict[groups]
-
-            # Iterate through each filename in this group
-            for dset_name in dsets_in_group:
-                if str.find(dset_name,str_excl) == -1:
-                    temp_name = groups + '/' + dset_name
-                    loc = f_output.require_group(f_input[temp_name].parent.name)
-                    print('Copying: {}'.format(temp_name))
-                    f_input.copy(temp_name,loc)
-                    del temp_name
-    except:
-        print('There was an error')
-        return None
-    f_input.close()
-    f_output.close()
-    return new_filename

-
-
[docs]def special_repack(filename, repack_str = '_Movie_', new_filename = None):
-    """
-    Find datasets (1D) with a given repack_str and concatenates them into
-    a larger array. Other datasets are copied as is.
-
-    Creates a new h5 file with '_repack_' + repack_str(-'_') + .h5' appended
-
-    Parameters
-    ----------
-        filename (str) : name of file to analyze/repack/copy
-
-        repack_str (str) : string to find in datasets to concatenate
-
-        new_filename (str) : (Optional) Output filename
-
-    Returns
-    -------
-        str : filename of new HDF5 file
-
-        Writes a new file filename + '_repack_' + repack_str(-'_') + .h5'
-
-    Notes
-    -----
-    The output file cannot already exist
-
-    SPECIAL : Only likely useful for the NIST developers
-
-    """
-
-    if new_filename == None:
-        new_filename = str.strip(filename,'.h5') + '_repack_' + \
-            repack_str.strip('_') + '.h5'
-    else:
-        pass
-
-    dataset_dict = retrieve_group_dataset_dict(filename)
-
-    f_input = _h5py.File(filename, 'r')
-    f_output = _h5py.File(new_filename, 'w-')
-
-    try:
-        # Iterate through each data-containing group
-        for groups in dataset_dict:
-            dsets_in_group = dataset_dict[groups]
-            # Turn dataset list into one long string and look for
-            # repack_str if there are none, copy the whole group
-            if str(dsets_in_group).find(repack_str) == -1:
-                loc = f_output.require_group(groups)
-                for dset in dsets_in_group:
-                    name = groups + '/' + dset
-                    f_input.copy(name,loc)
-            else:
-                # Create a set from the list to remove identical entries
-                unique_dset_prefix_list = \
-                    list(set([str.split(dset_names,repack_str)[0] \
-                    for dset_names in dsets_in_group]))
-
-                for unique_dset_prefix in unique_dset_prefix_list:
-                    dset_w_prefix = [dset_names for dset_names in \
-                        dsets_in_group \
-                        if dset_names.find(unique_dset_prefix) != -1]
-
-                    name = groups + '/' + dset_w_prefix[0]
-
-                    # Init larger array with expanded size, same dtype
-                    repack_array = _np.ndarray([len(dset_w_prefix), \
-                        f_input[name].value.shape[0]], dtype = \
-                        f_input[name].dtype)
-
-                    # Fill in columns
-                    for count in enumerate(dset_w_prefix):
-                        name = groups + '/' + count[1]
-                        repack_array[count[0],:] = f_input[name].value
-
-                    loc = f_output.require_group(groups)
-                    f_output[str(groups + '/' + unique_dset_prefix)] = repack_array
-                    name = groups + '/' + dset_w_prefix[0]
-                    input_attrs = f_input[str(groups + '/' + \
-                        dset_w_prefix[0])].attrs
-
-                    # Copy attribute from first dataset to the repack_array
-                    for attr in input_attrs:
-                        try:
-                            f_output[str(groups + '/' + \
-                                unique_dset_prefix)].attrs.create(attr, \
-                                input_attrs[attr])
-                        except:
-                            pass
-    except:
-        print('There was an error')
-
-    f_input.close()
-    f_output.close()
-
-    return new_filename

-
-
[docs]def special_shrink_datasets(filename, dset_path, dset_name, stepsize,
-                            xstep_attr='RasterScanParams.FastAxisSteps',
-                            xstep_size_attr='RasterScanParams.FastAxisStepSize',
-                            ystep_attr='RasterScanParams.SlowAxisSteps',
-                            ystep_size_attr='RasterScanParams.SlowAxisStepSize'):
-    """
-    Find a particular dataset and shrink it by stepping over pixels
-
-    Parameters
-    ----------
-        filename : str
-            Name of file to analyze/repack/copy
-
-        dset_path : str
-            Path to dataset
-            
-        dset_attr : str
-            Dataset name
-
-        stepsize : int
-            Step size to take (1::stepsize)
-        
-        xstep_attr : str
-            Name of HDF attribute that describes number of steps in the \
-            X-direction
-            
-        xstep_size_attr : str
-            Name of HDF attribute that describes step size in the \
-            X-direction
-            
-        ystep_attr : str
-            Name of HDF attribute that describes number of steps in the \
-            Y-direction
-        
-        ystep_size_attr : str
-            Name of HDF attribute that describes step size in the \
-            Y-direction
-
-    Returns
-    -------
-        str : filename of new HDF5 file
-
-        Writes a new file filename + '_repack_' + repack_str(-'_') + .h5'
-
-    Notes
-    -----
-    The output file cannot already exist
-
-    SPECIAL : Only likely useful for the NIST developers
-    
-    Example
-    -------
-    _shrink('../mP2_w_small.h5','/BCARSImage/mP2_3_5ms_Pos_2_0/','mP2_3_5ms_Pos_2_0',10)
-    
-    """
-    
-    f = _h5py.File(filename,'r')
-    
-    try:
-        dset_fullname = dset_path + dset_name
-        
-        dset_name_small = dset_name + '_small'
-        dset_fullname_small = dset_path + dset_name_small
-        
-        temp = _np.zeros(f[dset_fullname].shape, dtype=f[dset_fullname].dtype)
-        
-        
-        f[dset_fullname].read_direct(temp)
-        f.close()
-        
-        f = _h5py.File(filename,'r+')
-        temp2 = temp[0::stepsize,0::stepsize,:]
-
-        lg_xsteps = temp.shape[1]
-        lg_ysteps = temp.shape[0]        
-        sm_xsteps = temp2.shape[1]
-        sm_ysteps = temp2.shape[0]
-        
-        
-        ds = f[dset_path]
-        ds.create_dataset(dset_name_small, data = temp2)    
-    except:
-        print('Failed')
-    else:
-        input_attrs = f[dset_fullname].attrs
-
-        # Copy attribute from first dataset to the repack_array
-        for attr in input_attrs:
-            try:
-                if attr == xstep_attr:
-                    f[dset_fullname_small].attrs.create(attr, \
-                        sm_xsteps)
-                elif attr == xstep_size_attr:
-                    temp = input_attrs[attr]
-                    
-                    f[dset_fullname_small].attrs.create(attr, \
-                        temp*(lg_xsteps/sm_xsteps))
-                    
-                elif attr == ystep_attr:
-                    f[dset_fullname_small].attrs.create(attr, \
-                        sm_ysteps)
-                elif attr == ystep_size_attr:
-                    temp = input_attrs[attr]
-                    
-                    f[dset_fullname_small].attrs.create(attr, \
-                        temp*(lg_ysteps/sm_ysteps))
-                else:
-                    f[dset_fullname_small].attrs.create(attr, \
-                        input_attrs[attr])
-            except:
-                pass
-    finally:
-        f.close()    

-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/utils/mplstyle.html b/docs/build/html/_modules/crikit/utils/mplstyle.html deleted file mode 100644 index ffb1ffd..0000000 --- a/docs/build/html/_modules/crikit/utils/mplstyle.html +++ /dev/null @@ -1,381 +0,0 @@ - - - - - - - - - - - crikit.utils.mplstyle — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Module code »
    • - -
  • crikit.utils.mplstyle
    • - - -
  • - - - -
    • - -
- - -
-
-
-
- -

Source code for crikit.utils.mplstyle

-"""
-Created on Thu Jun 30 10:23:03 2016
-
-@author: chc
-"""
-
-from cycler import cycler
-import copy as _copy
-import numpy as _np
-
-
[docs]class CrikitMplStyle:
-    """
-
-    """
-
-    _tableau20 = _np.array([[31, 119, 180],
-                           [174, 199, 232],
-                           [255, 127, 14],
-                           [255, 187, 120],
-                           [44, 160, 44],
-                           [152, 223, 138],
-                           [214, 39, 40],
-                           [255, 152, 150],
-                           [148, 103, 189],
-                           [197, 176, 213],
-                           [140, 86, 75],
-                           [196, 156, 148],
-                           [227, 119, 194],
-                           [247, 182, 210],
-                           [127, 127, 127],
-                           [199, 199, 199],
-                           [188, 189, 34],
-                           [219, 219, 141],
-                           [23, 190, 207],
-                           [158, 218, 229]], dtype=_np.float)/255
-
-    _tableau10 = _tableau20[::2,:]
-
-    _tableau10_med = _np.array([[114, 158, 206],
-                                [255, 158, 74],
-                                [103, 191, 92],
-                                [237, 102, 93],
-                                [173, 139, 201],
-                                [168, 120, 110],
-                                [237, 151, 202],
-                                [162, 162, 162],
-                                [205, 204, 93],
-                                [109, 204, 218]], dtype = _np.float)/255
-
-
-    _base_crikit = {'font.family': ['sans-serif'],
-                    'font.sans-serif': ['Arial',
-                                        'Bitstream Vera Sans',
-                                        'DejaVu Sans',
-                                        'Lucida Grande',
-                                        'Verdana',
-                                        'Geneva',
-                                        'Lucid',
-                                        'Avant Garde',
-                                        'sans-serif'],
-                    'axes.prop_cycle': cycler('color', _tableau10),
-#                    'axes.prop_cycle': plt.style.library['ggplot']['axes.prop_cycle'],
-                    'image.cmap': 'viridis',
-                    'image.interpolation': 'none'}
-
-    _paper_halfwidth = {'axes.labelsize': 8.8,
-                 'axes.titlesize': 9.6,
-                 'figure.figsize': [3.3, 4.4],
-                 'grid.linewidth': 0.8,
-                 'legend.fontsize': 8.0,
-                 'lines.linewidth': 1.4,
-                 'lines.markeredgewidth': 0.0,
-                 'lines.markersize': 5.6,
-                 'patch.linewidth': 0.24,
-                 'xtick.labelsize': 8.0,
-                 'xtick.major.pad': 5.6,
-                 'xtick.major.width': 0.8,
-                 'xtick.minor.width': 0.4,
-                 'ytick.labelsize': 8.0,
-                 'ytick.major.pad': 5.6,
-                 'ytick.major.width': 0.8,
-                 'ytick.minor.width': 0.4}
-
-    _paper_fullwidth = {'axes.labelsize': 8.8,
-                 'axes.titlesize': 9.6,
-                 'figure.figsize': [6.4, 4.4],
-                 'grid.linewidth': 0.8,
-                 'legend.fontsize': 8.8,
-                 'lines.linewidth': 1.4,
-                 'lines.markeredgewidth': 0.0,
-                 'lines.markersize': 5.6,
-                 'patch.linewidth': 0.24,
-                 'xtick.labelsize': 8.0,
-                 'xtick.major.pad': 5.6,
-                 'xtick.major.width': 0.8,
-                 'xtick.minor.width': 0.4,
-                 'ytick.labelsize': 8.0,
-                 'ytick.major.pad': 5.6,
-                 'ytick.major.width': 0.8,
-                 'ytick.minor.width': 0.4}
-
-    _poster = {'axes.labelsize': 17.6,
-               'axes.titlesize': 19.2,
-               'figure.figsize': [12.8, 8.8],
-              'grid.linewidth': 1.6,
-              'legend.fontsize': 16.0,
-              'lines.linewidth': 2.8,
-              'lines.markeredgewidth': 0.0,
-              'lines.markersize': 11.2,
-              'patch.linewidth': 0.48,
-              'xtick.labelsize': 16.0,
-              'xtick.major.pad': 11.2,
-              'xtick.major.width': 1.6,
-              'xtick.minor.width': 0.8,
-              'ytick.labelsize': 16.0,
-              'ytick.major.pad': 11.2,
-              'ytick.major.width': 1.6,
-              'ytick.minor.width': 0.8}
-
-    basic_halfwidth = _copy.deepcopy(_base_crikit)
-    basic_halfwidth.update(_paper_halfwidth)
-
-    basic_fullwidth = _copy.deepcopy(_base_crikit)
-    basic_fullwidth.update(_paper_fullwidth)
-
-    basic_poster = _copy.deepcopy(_base_crikit)
-    basic_poster.update(_poster)

-
-
-if __name__ == '__main__':
-    import matplotlib.pyplot as _plt
-    import numpy as _np
-
-    x = _np.arange(100)
-    _plt.style.use('classic')
-    style = CrikitMplStyle.basic_fullwidth
-    _plt.style.use(style)
-
-    _plt.figure()
-
-    _plt.plot((_np.random.rand(10,1)*x).T, label='test')
-    _plt.legend()
-    _plt.show()
-
-    _plt.figure()
-    _plt.imshow(_np.random.rand(100,100))
-    _plt.colorbar()
-    _plt.show()
-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/crikit/utils/roi.html b/docs/build/html/_modules/crikit/utils/roi.html deleted file mode 100644 index 4da6510..0000000 --- a/docs/build/html/_modules/crikit/utils/roi.html +++ /dev/null @@ -1,302 +0,0 @@ - - - - - - - - - - - crikit.utils.roi — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- - - - -
-
-
-
- -

Source code for crikit.utils.roi

-"""
-Created on Wed Jun 15 23:33:41 2016
-
-@author: chc
-"""
-import numpy as _np
-from matplotlib.path import Path as _Path
-
-
-
[docs]def verts_to_path(verts, isclosed=True):
-    """
-    Convert vertices to paths
-    """
-    if not isclosed:
-        verts += [verts[0]]
-    else:
-        pass
-    codes = [_Path.MOVETO] + [_Path.LINETO] * (len(verts)-2) + \
-            [_Path.CLOSEPOLY]
-
-    return _Path(verts, codes)

-
-
-
[docs]def pts_in_path(path):
-    """
-    Return points (pixels) that fall within path (but not on boundary)
-    """
-
-    # Get bounding box of path (simplify geometry)
-    exts = path.get_extents()
-
-    # Bottom-left, top-right coordinates
-    bl, tr = exts.get_points()
-
-    # Temporary x- and y-vectors and meshgrids
-    x = _np.arange(bl[0], tr[0])
-    y = _np.arange(bl[1], tr[1])
-    X, Y = _np.meshgrid(x, y)
-
-    # Linearize meshgrid
-    allpts = _np.hstack((X.flatten()[:, None], Y.flatten()[:, None]))
-
-    # Mask of points within path (NOT including boundary)
-    mask_allpts = path.contains_points(allpts)
-
-    # Get and return x- and y-pixels
-    x_pts, y_pts = _np.array([X.flatten()[mask_allpts],
-                              Y.flatten()[mask_allpts]])
-    return x_pts, y_pts

-
-
-
[docs]def pts_to_verts(xvec, yvec):
-    """
-    Convert points to vertices, i.e., convert from 2 1D arrays (or list) of \
-    x- and y-coordinates to a list-of-lists of [x,y] pairs
-    """
-    verts = []
-    for count in range(len(xvec)):
-        verts.append([xvec[count], yvec[count]])
-    return verts

-
-
-
[docs]def verts_to_points_in_roi(verts):
-    """
-    Vertice list defining ROI in, points within returned.
-    """
-    path = verts_to_path(verts, isclosed=False)
-    x_pts, y_pts = pts_in_path(path)
-    return x_pts, y_pts

-
- -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html deleted file mode 100644 index 79d033e..0000000 --- a/docs/build/html/_modules/index.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - - - - - - Overview: module code — CRIKit2 17.10b1 documentation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - - - - -
-
- - - - - - - - - - - - - - - - -
- -
    - -
  • Docs »
    • - -
  • Overview: module code
    • - - -
  • - - - -
    • - -
- - -
-
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- -

All modules for which code is available

- - -
-
- -
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/build/html/_sources/algorithms.rst.txt b/docs/build/html/_sources/algorithms.rst.txt deleted file mode 100644 index 5d79315..0000000 --- a/docs/build/html/_sources/algorithms.rst.txt +++ /dev/null @@ -1,16 +0,0 @@ -.. _algorithms: - -.. image:: _static/CRIkit2_Logo.png - :align: left - -| -| -| -| -| -| -| - -Command Line Tools & Algorthms -=============================== - diff --git a/docs/build/html/_sources/api.rst.txt b/docs/build/html/_sources/api.rst.txt deleted file mode 100644 index d25df71..0000000 --- a/docs/build/html/_sources/api.rst.txt +++ /dev/null @@ -1,161 +0,0 @@ -.. _api: - -.. image:: _static/CRIkit2_Logo.png - :align: left - -| -| -| -| -| -| -| - -API Reference -============= - -This is not an exhaustive list of classes and functions, -but rather those most likely to be of interest to users and developer. -See :ref:`genindex` and :ref:`modindex` for a full list. - -:mod:`crikit.cri`: Coherent Raman Imagery (CRI) classes and functions ---------------------------------------------------------------------- - -.. automodule:: crikit.cri - -Classes -~~~~~~~ -.. currentmodule:: crikit - -.. autosummary:: - - - cri.kk.KramersKronig - cri.error_correction.PhaseErrCorrectALS - cri.error_correction.ScaleErrCorrectSG - -Functions -~~~~~~~~~ -.. currentmodule:: crikit - -.. autosummary:: - - - cri.algorithms.kk.kkrelation - cri.algorithms.kk.hilbertfft - -:mod:`crikit.data`: Data container classes ------------------------------------------- - -.. automodule:: crikit.data - -Classes -~~~~~~~ -.. currentmodule:: crikit - -.. autosummary:: - - data.frequency.Frequency - data.replicate.Replicate - - data.spectrum.Spectrum - data.spectra.Spectra - data.hsi.Hsi - -:mod:`crikit.io`: Input/Output (IO) functions ----------------------------------------------- - -.. automodule:: crikit.io - -Functions -~~~~~~~~~ -.. currentmodule:: crikit - -.. autosummary:: - - io.csv_nist.csv_nist_import_data - io.hdf5.hdf_is_valid_dsets - io.hdf5.hdf_attr_to_dict - io.hdf5.hdf_import_data - io.meta_configs.special_nist_bcars1_sample_scan - io.meta_configs.special_nist_bcars2 - io.meta_process.meta_process - io.meta_process.rosetta_query - -:mod:`crikit.measurement`: Measurement classes ----------------------------------------------- - -.. automodule:: crikit.measurement - -Classes -~~~~~~~ -.. currentmodule:: crikit - -.. autosummary:: - - measurement.fftspatialnoise.FFTSignalMetric - measurement.peakamps.MeasurePeak - measurement.peakamps.MeasurePeakAdd - measurement.peakamps.MeasurePeakBWTroughs - measurement.peakamps.MeasurePeakMinus - measurement.peakamps.MeasurePeakDivide - measurement.peakamps.MeasurePeakMultiply - measurement.peakamps.MeasurePeakSummation - measurement.peakfind.PeakFinder - -:mod:`crikit.preprocess`: Preprocessing classes and functions -------------------------------------------------------------- - -.. automodule:: crikit.preprocess - -Classes -~~~~~~~ -.. currentmodule:: crikit - -.. autosummary:: - - preprocess.algorithms.als.AlsCvxopt - preprocess.algorithms.anscombe.anscombe_inverse_exact_unbiased - preprocess.algorithms.anscombe.gen_anscombe_forward - preprocess.algorithms.anscombe.gen_anscombe_inverse_closed_form - preprocess.algorithms.anscombe.gen_anscombe_inverse_exact_unbiased - preprocess.algorithms.arpls.ArPlsCvxopt - preprocess.crop.ZeroColumn - preprocess.crop.ZeroRow - preprocess.denoise.SVDDecompose - preprocess.denoise.SVDRecompose - preprocess.standardize.Anscombe - preprocess.standardize.AnscombeInverse - preprocess.subtract_baseline.SubtractBaselineALS - preprocess.subtract_dark.SubtractDark - preprocess.subtract_mean.SubtractMeanOverRange - -:mod:`crikit.utils`: Utility functions ---------------------------------------- - -.. automodule:: crikit.utils - -Classes -~~~~~~~ -.. currentmodule:: crikit - -.. autosummary:: - - utils.breadcrumb.BCPre - -Functions -~~~~~~~~~ -.. currentmodule:: crikit - -.. autosummary:: - - utils.general.arange_nonzero - utils.general.expand_1d_to_ndim - utils.general.expand_1d_to_ndim_data - utils.general.find_nearest - utils.general.lin_from_row_col - utils.general.mean_nd_to_1d - utils.general.np_fcn_nd_to_1d - utils.general.row_col_from_lin - utils.general.std_nd_to_1d - diff --git a/docs/build/html/_sources/cri_walkthru.rst.txt b/docs/build/html/_sources/cri_walkthru.rst.txt deleted file mode 100644 index bbeb867..0000000 --- a/docs/build/html/_sources/cri_walkthru.rst.txt +++ /dev/null @@ -1,597 +0,0 @@ -.. _cri_walkthru: - -.. image:: _static/CRIkit2_Logo.png - :align: left - -| -| -| -| -| -| -| - -Walk-Thru: CRI Processing -========================= - -This walk-thru will take you through several steps: - -- `Overview`_ -- `Generating the built-in Raman/BCARS numerical phantom`_ -- `Viewing dark, NRB, and dataset spectra`_ -- `Dark subtraction`_ -- `Residual dark subtraction (Optional)`_ -- `Variance stabilization`_ -- `Denoising via singular value decomposition (SVD)`_ -- `The inverse Anscombe transformation`_ -- `Phase retrieval via Kramers-Kronig relation`_ -- `Phase error correction`_ -- `Scale error correction`_ -- `Calibration`_ -- `Saving`_ -- `Pseudo-color imagery`_ -- `Skipped actions in a normal CRI workflow`_ - - `Loading HDF file Hsi dataset`_ - - `Loading Dark dataset`_ - -`Denoise Dark (Optional)`_ - - `Loading an NRB dataset`_ - - From HDF - - From an ROI within the **Hsi** dataset - -The screenshots within this manual may or may not reflect the exact look of the -version of CRIkit2 UI that you are using. - -Overview --------- - -.. image:: _static/cri_wt/Overview.png - :align: center - -Generating the built-in Raman/BCARS numerical phantom ------------------------------------------------------ -CRIkit2 comes with a built-in numerical phantom, which is dervived from an -actual BCARS image collected from murine pancreas tissue [Camp16]_. This -numerical phantom may be used as a **Raman** or a **BCARS** model. The Raman -model produces an HSI wherein each pixel contains a Raman spectrum. The BCARS -model incorporates a nonresonant background (NRB) and excitation source profile; -thus, generating raw BCARS spectra, similar to those generated here at NIST [Camp14]_. - -1. **Help** >> **BCARS Numerical Phantom** -2. Check Noise and Dark check boxes. - - **Check** Gaussian (AWGN) - - **Std Dev**: 12.44 - - **Check** Poisson - - **Multiplier (alpha)**: 1.4 - - **Check** Dark Constant - - **Level**: 1600.0 -3. Select Subsampling - - Subsampling will reduce the memory and performance burden on your computer. - - This tutorial will demonstrate with 1x (no sub-sampling), but you can feel - free to use up to 4x to make things speedier. -4. Press **Ok** pushbutton. - -.. image:: _static/cri_wt/LoadModel.png - :align: center - -There now is a fully loaded BCARS phantom. Additionally, the **NRB** reference -is loaded (**View** >> **NRB Spect**) and the **Dark** spectrum is loaded -(**View** >> **Dark Spect**). - -.. image:: _static/cri_wt/Overview_post_gen_BCARS.png - :align: center - -Viewing dark, NRB, and dataset spectra --------------------------------------- -To view the loaded **Dark** spectrum(a): - -- **View** >> **Dark Spect** - -To view the loaded **NRB** spectrum(a): - -- **View** >> **NRB Spect** - -There are two primary methods to view spectra from within the dataset: point -spectra and ROI spectra. - -To view the spectrum from a single point within the dataset (2 methods): - -- **View** >> **Pt Spect** -- Click the **Pt Spect** button on the main ribbon - -Either method will change your cursor into a cross. Select a pixel within the -**single-frequency (SF) image** and **left-click**. This will pop-up the plotter window with the -spectrum. - -To view the mean spectrum from within an ROI (2 methods): - -- **View** >> **ROI Spect** -- Click the **ROI Spect** button on the main ribbon - -Again, either method will change your cursor into a cross. The ROI is defined by -a polyhedron within the **single-frequency (SF) image**. Select vertices with -a **left-click** with your mouse. Close the polyhedrom with a single -**right-click**. The location of the right-click does not matter as this only -indicates to connect the last selected vertex and the first. This will pop-up -the plotter window with 2 components: the mean spectrum (dark, solid line) and -a patch (lighter, solid shading) that indicates plus-minus 1 standard deviation. - -.. image:: _static/cri_wt/RoiRawSpectra.png - :align: center - -Dark subtraction ----------------- -The dark signal is the intrinsic signal level generated by the detector, even -when no photons are incident on the detector. Typically, a measurement is made -with the detector (or incident) sources blocked. - -Under normal operation, you would load a dark spectrum(a) from an external -file. During the generation of the BCARS numerical phantom, the dark signal -is co-generated. - -To subtract the dark spectrum(a) from the HSI (2 methods): - -- **Pre-Process** >> **Dark Sub...** -- Click the **Dark Sub** button on the main ribbon - -Two pop-up dialog boxes will appear: - -- Subtract Dark Spectrum from Image?: **Click**: OK -- Subtract Dark Spectrum from NRB Spectrum(a)?: **Click**: OK - -.. image:: _static/cri_wt/Sub_dark_dialogs.png - :align: center - -Variance stabilization ----------------------- -CRIkit2 provides variance stabilitization through the forward Anscombe -transformation that enables signals with mixed additive white Gaussian noise -(AWGN) and shot-noise (Poisson) to be transformed into a signal with -approximately uniform AWGN only [Foi13]_. Conversely, CRIkit2 provides an -exact, unbiased inverse of the generalized Anscombe variance-stabilizing -transform [Foi13]_. - -Many denoising and factorization methods, such as principle component analysis -(PCA), singular value decomposition (SVD), nonnegative matrix factorization -(NMF); explicitly or implicitly assume a normal (i.e., Gaussian) distribution -of noise (and signals). Thus, variance stabilization may aid actions involving -such tasks [Camp16]_. - -In this tutorial, we will use the Anscombe transformation prior to -**SVD denoising**. Additionally, we will apply the **inverse Anscombe** -transform **after** SVD denoising. - -To perform the forward Anscombe transformation (2 methods): - -- **Pre-Process** >> **Standardize** >> **Anscombe** -- Click the **Anscombe** button on the main ribbon - -A pop-up dialog will appear asking for two necessary pieces of information: - -- The standard deviation of the AWGN -- The shot-noise (Poisson) noise multiplier - -Normally, one would need to calculate/measure or estimate these parameters, but -the **numerical phantom, by default, applies**: - -- Gaussian noise standard deviation: 12.44 -- Poisson noise gain: 1.4 - -.. image:: _static/cri_wt/Anscombe.png - :align: center - - -Denoising via singular value decomposition (SVD) ------------------------------------------------- -SVD is a linear algebra method that transforms a matrix into the multiplication -of three matrices: the left-singular vectors matrix, the singular value matrix, -and the right-singular vector matrix. The use of SVD for denoising has been -extensively explored for both traditional computer imagery -[Narendra75]_ [Patterson75]_, and CRI [Camp16]_ [Lee11]_. - -In short, SVD will decompose the CRI image into a series of images and spectra. -Ideally, the spectra/images that contain real (ie non-noise) signal -contributions are totally separate from those containing noise. One can thus -reconstruct a noiseless image from the noise-free images/spectra decompositions. - -CRIkit2 performs the SVD decomposition and raises a new user interface (UI) -that displays the decomposed images and spectra, providing information to the -user to interactively select those with minimal noise. - -.. image:: _static/cri_wt/SVD_Ui.png - :align: center - -Recommendations: - -- Select all singular values with visible spatial **or** spectral components -- Remember to press **Apply** button after selections to-keep of current 6 - displayed. -- Press **Next** pushbutton to view next 6 components. -- Press **Ok** pushbutton to recompose the CRI image with only selected - components. - -In this tutorial, selections [0,1,2,3,4,5,6] are kept (7 total). - -.. image:: _static/cri_wt/Spectrum_Before_After_SVD.png - :align: center - -**Note**: The example spectra are before Anscombe-SVD; and after -Anscombe-SVD-inverse Anscombe. - -The inverse Anscombe transformation ------------------------------------ -CRIkit2 provides an exact, unbiased inverse of the generalized Anscombe -variance-stabilizing transform to convert the variance-stabilized image -back into a mixed-noise version [Foi13]_. - -To perform the inverse Anscombe transformation (2 methods): - -- **Pre-Process** >> **Standardize** >> **Inv Anscombe** -- Click the **Inv Anscombe** button on the main ribbon - -A pop-up dialog will appear asking for two necessary pieces of information: - -- The standard deviation of the AWGN -- The shot-noise (Poisson) noise multiplier - -**Note**: these values will be pre-filled with the values entered from the -forward Anscombe transformation. It would be unusual to not use these values. - -Phase retrieval via Kramers-Kronig relation -------------------------------------------- -In CRI imagery acquired through CARS methods, phase retrieval methods are -used to separate CARS and NRB signal contribution, i.e. to extract the Raman -spectral signatures [Liu09]_ [Camp16]_. - -CRIkit2 provides access to a Kramers-Kronig (KK) relation implemented using a -Fourier transform-based Hilbert transform [Camp16]_. - -This KK implementation requires an approximate NRB, which may be imported -through several means: - -- Selection of a ROI (e.g., selecting an ROI of water) -- Spectra imported from an external file -- Merging two NRB spectra from ROI's or external files. - -During the generation of the BCARS numerical phantom, the NRB signal -is co-generated and loaded. - -To perform the KK (2 methods): - -- **Pre-Process** >> **Coherent Raman Imaging** >> **KK** -- Click the **KK** button on the main ribbon - -.. image:: _static/cri_wt/KKOptions.png - :align: center - -This dialog enables fine-tuning of several parameters: - -- NRB bias (constant to add/subract from NRB spectrum) -- CARS bias (constant to add/subract from all HSI spectra) -- Phase offset (constant phase to add/subtract to all KK'd spectra) -- Pad factor (window-padding multiple of spectral length [Liu09]_) - -The **Interative Setting Selection** provides preview spectra of several spectra. -These spectra are the mean of the 4 quandrants (i.e. fourths) of the total image -and the center fourth. - -.. image:: _static/cri_wt/KKInteractive.png - :align: center - -For this tutorial: - -- CARS/NRB bias: 0 -- Phase Offset: 0 -- Pad Factor: 1 - -When **finished** press **Ok** pushbutton. - -Phase error correction ----------------------- -The KK relation will extract Raman signatures accurately under certain conditions, -one being that the NRB can be separately measured and provided -- **at every -pixel**. This condition, however, can not readily be met; thus, reference NRB -are typically utilized. An ideal reference NRB should not contain any Raman peaks -within the spectral region of interest. Typical examples are glasses, salts, and -water [Camp14]_ [Camp16]_ [Karuna16]_. - -Unfortunately, the use of a reference (i.e., non-exact) NRB results in amplitude -and phase error. Phase error correction **and** scale error correction correct -for these complex errors. Phase error correction is performed by finding the -slowly varying baseline of the spectral phase at each pixel. - -CRIkit2 uses an asymmetric least-squares (ALS) method [Eilers05]_. The -custom implementation 3 main parameters: - -- P (asymmetry parameter) -- Lambda (smoothness parameter) -- Sub-sampling factor (sub-sample the spectra to improve speed) - -**Note**: This is typically the **slowest processing step** in the workflow. A -300 x 300 x 900 pixel image with no sub-sampling of the ALS may require 45 -**minutes** or longer to complete. - -Additionally, this dialog allows for a **fixed P-value** across the spectrum -or a **log-linear P-value** that varies across the spectrum. For this tutorial -we will use the **Fixed-P**. - -To perform phase error correction (2 methods): - -- **Pre-Process** >> **Coherent Raman Imaging** >> **Phase Err...** -- Click the **Phase Err** button on the main ribbon - -Recommendations: - -- The sub-sampling parameter will increase the speed of the detrending - (potentially quadratically), but at the expense of accuracy. -- Though P- and Lambda-values are independent, the most important factor - is the ratio of the two. -- There may be window-edge errors at the extreme points of spectra. The - **Fix End-Points** option may correct these distortions; though, for extremely - minor baseline correction, this may cause more harm than help. -- The exact settings are a function of the particular optical system's - resolution, spectral sampling, and reference material used. - -This tutorial and the numerical phantom, **unlike real experiments**, provides -the exact NRB; thus, phase-error is extremely small (numerical error). - -For this tutorial: - -- **Fixed-P**: 1e-6 -- **Lambda*: 1 -- **Sub-Sampling Factor**: 10 -- **Max Iterations**: 100 -- **Min Difference**: 1e-6 -- **Fix End-Points**: False (Unchecked) - -For typical experiments: - -- **Fixed-P**: 1e-4 to 1e-2 (increment by half order-of-magnitude) -- **Lambda*: 1 -- **Sub-Sampling Factor**: 10 -- **Max Iterations**: 100 -- **Min Difference**: 1e-6 -- **Fix End-Points**: True (Checked) - -When **finished** press **Ok** pushbutton. - -.. image:: _static/cri_wt/ALS.png - :align: center - -Scale error correction ------------------------ -The use of a reference (i.e., non-exact) NRB results in amplitude -and phase error. Phase error correction **and** scale error correction correct -for these complex errors. Scale error correction is performed by finding the -median trend line that bisects the real portion of the complex spectra at each -pixel [Camp16]_. - -CRIkit2 uses a Savitky-Golay filter to find a smooth median line, which requires -2 parameters: - -- Window width (sliding-window width to polynomial fit). Must be odd-valued. -- Order (order of polynomial to fit) - -To perform phase error correction (2 methods): - -- **Pre-Process** >> **Coherent Raman Imaging** >> **Scale Err...** -- Click the **Scale Err** button on the main ribbon - -Recommendations: - -- Set the **order** to 1 or 2 -- Expand the **window width** to a large enough value that the median line - approximately bisects the shown spectra. -- The exact settings are a function of the particular optical system's - resolution, spectral sampling, and reference material used. - -Typical experimental values: - -- **Window width**: 601 -- **Order**: 2 - -When **finished** press **Ok** pushbutton. - -.. image:: _static/cri_wt/SG.png - :align: center - -Calibration ------------ -CRIkit2 provides a UI for single-peak calibration that properly accounts -for the nonlinear relationship between wavenumber and wavelength (i.e. what -spectrometers measure across) in BCARS. - -In typical bio-experiments, we utilize the 1,004 cm-1 peak (phenylalanine) [DeGelder07]_. - -To use a different peak, change the **Correct WN** value to the new peak wavenumber -and fill-in the **Measured WN** with what the average spectra show within the -upper plot. - -To perform calibration (2 methods): - -- **Edit** >> **Calibrate** -- Click the **Calibrate** button on the main ribbon - -Recommendations - -- Click the **Zoom** button on the upper plot and select around the 1,004 cm-1 - region. -- Enter the actual peak location in the **Measured WN** box. -- If the spectra do not reveal a feature of interest, return (click **Cancel**) - to the main UI and use the **ROI Spect** or **Pt Spect** to plot the spectrum - from a pixel(s) of interest. Identify the location of the particular - calibration peak. Re-open the **calibration** tool (ignore the plots) and enter - the **Correct WN** and **Measured WN** values. - -For this tutorial there is no calibration necessary. Click **Cancel** pushbutton. - -.. image:: _static/cri_wt/Calibration.png - :align: center - -Saving -------- - -.. image:: _static/cri_wt/Save.png - :align: center - -Pseudo-color imagery --------------------- -Nuclei: - -- **Color 0** tab -- **Color** drop-down box setting: Yellow -- Math function: "Peak b/w Troughs" -- Peak (Freq 1 button): 786 cm-1 -- Trough 1 (Freq 2 button): 767 cm-1 -- Trough 2 (Freq 3 button): 809 cm-1 -- **Conditional** math function: "SUM" -- Start freq (Freq 1 button): 2700 cm-1 -- Stop freq (Freq 1 button): 3000 cm-1 -- **Conditional** comparitor: ">" -- **Conditional** value: 1.0 -- **Minimum** value setting: 0.002 - -.. image:: _static/cri_wt/SingleColorExample.png - :align: center - -.. image:: _static/cri_wt/Nuclei.png - :align: center - -Phenylalanine: - -- **Color 1** tab -- **Color** drop-down box setting: Magenta -- Math function: "Peak b/w Troughs" -- Peak (Freq 1 button): 1002 cm-1 -- Trough 1 (Freq 2 button): 986 cm-1 -- Trough 2 (Freq 3 button): 1019 cm-1 -- **Conditional** math function: "SUM" -- Start freq (Freq 1 button): 2700 cm-1 -- Stop freq (Freq 1 button): 3000 cm-1 -- **Conditional** comparitor: ">" -- **Conditional** value: 1.0 -- **Minimum** value setting: 0.002 - -.. image:: _static/cri_wt/Phenylalanine.png - :align: center - -Structural Proteins: - -- **Color 2** tab -- **Color** drop-down box setting: Cyan -- Math function: "Peak b/w Troughs" -- Peak (Freq 1 button): 937 cm-1 -- Trough 1 (Freq 2 button): 902 cm-1 -- Trough 2 (Freq 3 button): 980 cm-1 -- **Conditional** math function: "SUM" -- Start freq (Freq 1 button): 2700 cm-1 -- Stop freq (Freq 1 button): 3000 cm-1 -- **Conditional** comparitor: ">" -- **Conditional** value: 1.0 -- **Minimum** value setting: 0.002 - -.. image:: _static/cri_wt/StructuralProtein.png - :align: center - -Elastin: - -- **Color 3** tab -- **Color** drop-down box setting: B&W (Black-and-white) -- Math function: "Peak b/w Troughs" -- Peak (Freq 1 button): 525 cm-1 -- Trough 1 (Freq 2 button): 513 cm-1 -- Trough 2 (Freq 3 button): 540 cm-1 -- **Conditional** math function: " / " -- Start freq (Freq 1 button): 1003 cm-1 -- Stop freq (Freq 1 button): 1029 cm-1 -- **Conditional** comparitor: ">" -- **Conditional** value: 1.4 -- **Minimum** value setting: 0.0006 - -.. image:: _static/cri_wt/Elastin.png - :align: center - -.. image:: _static/cri_wt/CompositeColorExample.png - :align: center - -Skipped actions in a normal CRI workflow ----------------------------------------- - -Loading HDF file Hsi dataset -~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -.. image:: _static/cri_wt/Open.png - :align: center - - - -Loading Dark dataset -~~~~~~~~~~~~~~~~~~~~ - -.. image:: _static/cri_wt/OpenDark.png - :align: center - -Denoise Dark (Optional) -~~~~~~~~~~~~~~~~~~~~~~~ - -.. image:: _static/cri_wt/denoise_dark.jpg - :align: center - -Loading an NRB from HDF file -~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -.. image:: _static/cri_wt/OpenNRB.png - :align: center - -Load an NRB from a region-of-interest (ROI) -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -.. image:: _static/cri_wt/load_nrb_roi.jpg - :align: center - -Merge two NRB datasets -~~~~~~~~~~~~~~~~~~~~~~ - -Residual dark subtraction (Optional) -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -References ----------- - -.. [Camp14] C. H. Camp Jr, Y. J. Lee, J. M. Heddleston, C. M. Hartshorn, A. R. - Hight Walker, J. N. Rich, J. D. Lathia, and M. T. Cicerone, "High-Speed - Coherent Raman Fingerprint Imaging of Biological Tissues," Nat. Photonics 8, - 627–634 (2014). - -.. [Camp16] C. H. Camp Jr, Y. J. Lee, and M. T. Cicerone, "Quantitative, - comparable coherent anti-Stokes Raman scattering (CARS) spectroscopy: - correcting errors in phase retrieval," J. Raman Spectrosc. 47, 408–415 (2016). - -.. [DeGelder07] J. De Gelder, K. De Gussem, P. Vandenabeele, and L. Moens, - "Reference database of Raman spectra of biological molecules," J. Raman - Spectrosc. 38, 1133–1147 (2007). - -.. [Eilers05] P. H. C. Eilers and H. F. M. Boelens, "Baseline Correction with - Asymmetric Least Squares Smoothing," (Unpublished, 2005). - https://zanran_storage.s3.amazonaws.com/www.science.uva.nl/ContentPages/443199618.pdf - -.. [Foi13] M. Mäkitalo and A. Foi, "Optimal inversion of the generalized - anscombe transformation for Poisson-Gaussian noise," IEEE Trans. Image - Process. 22, 91–103 (2013). - -.. [Karuna16] A. Karuna, F. Masia, P. Borri, and W. Langbein, "Hyperspectral - volumetric coherent anti-Stokes Raman scattering microscopy: quantitative - volume determination and NaCl as non-resonant standard," J. Raman Spectrosc. - 47, 1167–1173 (2016). - -.. [Lee11] Y. J. Lee, D. Moon, K. B. Migler, and M. T. Cicerone, "Quantitative - image analysis of broadband CARS hyperspectral images of polymer blends," - Anal. Chem. 83, 2733–2739 (2011). - -.. [Liu09] Y. X. Liu, Y. J. Lee, and M. T. Cicerone, "Broadband CARS spectral - phase retrieval using a time-domain Kramers-Kronig transform," Opt. Lett. 34, - 1363–1365 (2009). - -.. [Narendra75] T. S. Huang and P. M. Narendra, "Image restoration by singular - value decomposition.," Appl. Opt. 14, 2213–6 (1975). - -.. [Patterson75] H. C. Andrews and C. L. Patterson, "Outer Product Expansions - and Their Uses in Digital Image Processing," Am. Math. Mon. 82, 1–13 (1975). diff --git a/docs/build/html/_sources/crikit.cri.algorithms.rst.txt b/docs/build/html/_sources/crikit.cri.algorithms.rst.txt deleted file mode 100644 index a1cdb1f..0000000 --- a/docs/build/html/_sources/crikit.cri.algorithms.rst.txt +++ /dev/null @@ -1,22 +0,0 @@ -crikit\.cri\.algorithms package -=============================== - -Submodules ----------- - -crikit\.cri\.algorithms\.kk module ----------------------------------- - -.. automodule:: crikit.cri.algorithms.kk - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.cri.algorithms - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.cri.rst.txt b/docs/build/html/_sources/crikit.cri.rst.txt deleted file mode 100644 index a1cade9..0000000 --- a/docs/build/html/_sources/crikit.cri.rst.txt +++ /dev/null @@ -1,46 +0,0 @@ -crikit\.cri package -=================== - -Subpackages ------------ - -.. toctree:: - - crikit.cri.algorithms - crikit.cri.tests - -Submodules ----------- - -crikit\.cri\.error\_correction module -------------------------------------- - -.. automodule:: crikit.cri.error_correction - :members: - :undoc-members: - :show-inheritance: - -crikit\.cri\.kk module ----------------------- - -.. automodule:: crikit.cri.kk - :members: - :undoc-members: - :show-inheritance: - -crikit\.cri\.merge\_nrbs module -------------------------------- - -.. automodule:: crikit.cri.merge_nrbs - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.cri - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.cri.tests.rst.txt b/docs/build/html/_sources/crikit.cri.tests.rst.txt deleted file mode 100644 index 54b35ac..0000000 --- a/docs/build/html/_sources/crikit.cri.tests.rst.txt +++ /dev/null @@ -1,38 +0,0 @@ -crikit\.cri\.tests package -========================== - -Submodules ----------- - -crikit\.cri\.tests\.test\_hilbert module ----------------------------------------- - -.. automodule:: crikit.cri.tests.test_hilbert - :members: - :undoc-members: - :show-inheritance: - -crikit\.cri\.tests\.test\_kk module ------------------------------------ - -.. automodule:: crikit.cri.tests.test_kk - :members: - :undoc-members: - :show-inheritance: - -crikit\.cri\.tests\.test\_kk\_alg module ----------------------------------------- - -.. automodule:: crikit.cri.tests.test_kk_alg - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.cri.tests - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.data.rst.txt b/docs/build/html/_sources/crikit.data.rst.txt deleted file mode 100644 index 2163611..0000000 --- a/docs/build/html/_sources/crikit.data.rst.txt +++ /dev/null @@ -1,62 +0,0 @@ -crikit\.data package -==================== - -Submodules ----------- - -crikit\.data\.factorized module -------------------------------- - -.. automodule:: crikit.data.factorized - :members: - :undoc-members: - :show-inheritance: - -crikit\.data\.frequency module ------------------------------- - -.. automodule:: crikit.data.frequency - :members: - :undoc-members: - :show-inheritance: - -crikit\.data\.hsi module ------------------------- - -.. automodule:: crikit.data.hsi - :members: - :undoc-members: - :show-inheritance: - -crikit\.data\.replicate module ------------------------------- - -.. automodule:: crikit.data.replicate - :members: - :undoc-members: - :show-inheritance: - -crikit\.data\.spectra module ----------------------------- - -.. automodule:: crikit.data.spectra - :members: - :undoc-members: - :show-inheritance: - -crikit\.data\.spectrum module ------------------------------ - -.. automodule:: crikit.data.spectrum - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.data - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.datasets.rst.txt b/docs/build/html/_sources/crikit.datasets.rst.txt deleted file mode 100644 index ed42e31..0000000 --- a/docs/build/html/_sources/crikit.datasets.rst.txt +++ /dev/null @@ -1,22 +0,0 @@ -crikit\.datasets package -======================== - -Submodules ----------- - -crikit\.datasets\.model module ------------------------------- - -.. automodule:: crikit.datasets.model - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.datasets - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.io.rst.txt b/docs/build/html/_sources/crikit.io.rst.txt deleted file mode 100644 index d2ecf2c..0000000 --- a/docs/build/html/_sources/crikit.io.rst.txt +++ /dev/null @@ -1,54 +0,0 @@ -crikit\.io package -================== - -Submodules ----------- - -crikit\.io\.csv\_nist module ----------------------------- - -.. automodule:: crikit.io.csv_nist - :members: - :undoc-members: - :show-inheritance: - -crikit\.io\.hdf5 module ------------------------ - -.. automodule:: crikit.io.hdf5 - :members: - :undoc-members: - :show-inheritance: - -crikit\.io\.macros module -------------------------- - -.. automodule:: crikit.io.macros - :members: - :undoc-members: - :show-inheritance: - -crikit\.io\.meta\_configs module --------------------------------- - -.. automodule:: crikit.io.meta_configs - :members: - :undoc-members: - :show-inheritance: - -crikit\.io\.meta\_process module --------------------------------- - -.. automodule:: crikit.io.meta_process - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.io - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.measurement.rst.txt b/docs/build/html/_sources/crikit.measurement.rst.txt deleted file mode 100644 index 4fccd03..0000000 --- a/docs/build/html/_sources/crikit.measurement.rst.txt +++ /dev/null @@ -1,45 +0,0 @@ -crikit\.measurement package -=========================== - -Subpackages ------------ - -.. toctree:: - - crikit.measurement.tests - -Submodules ----------- - -crikit\.measurement\.fftspatialnoise module -------------------------------------------- - -.. automodule:: crikit.measurement.fftspatialnoise - :members: - :undoc-members: - :show-inheritance: - -crikit\.measurement\.peakamps module ------------------------------------- - -.. automodule:: crikit.measurement.peakamps - :members: - :undoc-members: - :show-inheritance: - -crikit\.measurement\.peakfind module ------------------------------------- - -.. automodule:: crikit.measurement.peakfind - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.measurement - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.measurement.tests.rst.txt b/docs/build/html/_sources/crikit.measurement.tests.rst.txt deleted file mode 100644 index 9815a7e..0000000 --- a/docs/build/html/_sources/crikit.measurement.tests.rst.txt +++ /dev/null @@ -1,22 +0,0 @@ -crikit\.measurement\.tests package -================================== - -Submodules ----------- - -crikit\.measurement\.tests\.test\_peakfind module -------------------------------------------------- - -.. automodule:: crikit.measurement.tests.test_peakfind - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.measurement.tests - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.preprocess.algorithms.rst.txt b/docs/build/html/_sources/crikit.preprocess.algorithms.rst.txt deleted file mode 100644 index 5521b2d..0000000 --- a/docs/build/html/_sources/crikit.preprocess.algorithms.rst.txt +++ /dev/null @@ -1,46 +0,0 @@ -crikit\.preprocess\.algorithms package -====================================== - -Submodules ----------- - -crikit\.preprocess\.algorithms\.abstract\_als module ----------------------------------------------------- - -.. automodule:: crikit.preprocess.algorithms.abstract_als - :members: - :undoc-members: - :show-inheritance: - -crikit\.preprocess\.algorithms\.als module ------------------------------------------- - -.. automodule:: crikit.preprocess.algorithms.als - :members: - :undoc-members: - :show-inheritance: - -crikit\.preprocess\.algorithms\.anscombe module ------------------------------------------------ - -.. automodule:: crikit.preprocess.algorithms.anscombe - :members: - :undoc-members: - :show-inheritance: - -crikit\.preprocess\.algorithms\.arpls module --------------------------------------------- - -.. automodule:: crikit.preprocess.algorithms.arpls - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.preprocess.algorithms - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.preprocess.rst.txt b/docs/build/html/_sources/crikit.preprocess.rst.txt deleted file mode 100644 index 805e9fe..0000000 --- a/docs/build/html/_sources/crikit.preprocess.rst.txt +++ /dev/null @@ -1,69 +0,0 @@ -crikit\.preprocess package -========================== - -Subpackages ------------ - -.. toctree:: - - crikit.preprocess.algorithms - -Submodules ----------- - -crikit\.preprocess\.crop module -------------------------------- - -.. automodule:: crikit.preprocess.crop - :members: - :undoc-members: - :show-inheritance: - -crikit\.preprocess\.denoise module ----------------------------------- - -.. automodule:: crikit.preprocess.denoise - :members: - :undoc-members: - :show-inheritance: - -crikit\.preprocess\.standardize module --------------------------------------- - -.. automodule:: crikit.preprocess.standardize - :members: - :undoc-members: - :show-inheritance: - -crikit\.preprocess\.subtract\_baseline module ---------------------------------------------- - -.. automodule:: crikit.preprocess.subtract_baseline - :members: - :undoc-members: - :show-inheritance: - -crikit\.preprocess\.subtract\_dark module ------------------------------------------ - -.. automodule:: crikit.preprocess.subtract_dark - :members: - :undoc-members: - :show-inheritance: - -crikit\.preprocess\.subtract\_mean module ------------------------------------------ - -.. automodule:: crikit.preprocess.subtract_mean - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.preprocess - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.rst.txt b/docs/build/html/_sources/crikit.rst.txt deleted file mode 100644 index d401f59..0000000 --- a/docs/build/html/_sources/crikit.rst.txt +++ /dev/null @@ -1,37 +0,0 @@ -crikit package -============== - -Subpackages ------------ - -.. toctree:: - - crikit.cri - crikit.data - crikit.datasets - crikit.io - crikit.measurement - crikit.preprocess - crikit.transform - crikit.ui - crikit.utils - -Submodules ----------- - -crikit\.CRIkitUI module ------------------------ - -.. automodule:: crikit.CRIkitUI - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.transform.rst.txt b/docs/build/html/_sources/crikit.transform.rst.txt deleted file mode 100644 index 0b8b464..0000000 --- a/docs/build/html/_sources/crikit.transform.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -crikit\.transform package -========================= - -Module contents ---------------- - -.. automodule:: crikit.transform - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.ui.rst.txt b/docs/build/html/_sources/crikit.ui.rst.txt deleted file mode 100644 index b06fcb9..0000000 --- a/docs/build/html/_sources/crikit.ui.rst.txt +++ /dev/null @@ -1,205 +0,0 @@ -crikit\.ui package -================== - -Subpackages ------------ - -.. toctree:: - - crikit.ui.utils - -Submodules ----------- - -crikit\.ui\.classes\_ui module ------------------------------- - -.. automodule:: crikit.ui.classes_ui - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.dialog\_AbstractFactorization module ------------------------------------------------- - -.. automodule:: crikit.ui.dialog_AbstractFactorization - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.dialog\_AbstractPlotEffect module ---------------------------------------------- - -.. automodule:: crikit.ui.dialog_AbstractPlotEffect - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.dialog\_SVD module ------------------------------- - -.. automodule:: crikit.ui.dialog_SVD - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.dialog\_kkOptions module ------------------------------------- - -.. automodule:: crikit.ui.dialog_kkOptions - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.dialog\_model module --------------------------------- - -.. automodule:: crikit.ui.dialog_model - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.dialog\_ploteffect module -------------------------------------- - -.. automodule:: crikit.ui.dialog_ploteffect - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.dialog\_save module -------------------------------- - -.. automodule:: crikit.ui.dialog_save - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.dialog\_subResidualOptions module ---------------------------------------------- - -.. automodule:: crikit.ui.dialog_subResidualOptions - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.dialog\_varstabAnscombeOptions module -------------------------------------------------- - -.. automodule:: crikit.ui.dialog_varstabAnscombeOptions - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.helper\_plotOptions module --------------------------------------- - -.. automodule:: crikit.ui.helper_plotOptions - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.helper\_roiselect module ------------------------------------- - -.. automodule:: crikit.ui.helper_roiselect - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.subui\_hdf\_load module ------------------------------------ - -.. automodule:: crikit.ui.subui_hdf_load - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_ALS module ------------------------------- - -.. automodule:: crikit.ui.widget_ALS - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_ArPLS module --------------------------------- - -.. automodule:: crikit.ui.widget_ArPLS - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_Calibrate module ------------------------------------- - -.. automodule:: crikit.ui.widget_Calibrate - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_DeTrending module -------------------------------------- - -.. automodule:: crikit.ui.widget_DeTrending - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_Jupyter module ----------------------------------- - -.. automodule:: crikit.ui.widget_Jupyter - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_KK module ------------------------------ - -.. automodule:: crikit.ui.widget_KK - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_SG module ------------------------------ - -.. automodule:: crikit.ui.widget_SG - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_images module ---------------------------------- - -.. automodule:: crikit.ui.widget_images - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_mergeNRBs module ------------------------------------- - -.. automodule:: crikit.ui.widget_mergeNRBs - :members: - :undoc-members: - :show-inheritance: - -crikit\.ui\.widget\_scientificspin module ------------------------------------------ - -.. automodule:: crikit.ui.widget_scientificspin - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.ui - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.ui.utils.rst.txt b/docs/build/html/_sources/crikit.ui.utils.rst.txt deleted file mode 100644 index 1ee92bf..0000000 --- a/docs/build/html/_sources/crikit.ui.utils.rst.txt +++ /dev/null @@ -1,22 +0,0 @@ -crikit\.ui\.utils package -========================= - -Submodules ----------- - -crikit\.ui\.utils\.roi module ------------------------------ - -.. automodule:: crikit.ui.utils.roi - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.ui.utils - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/crikit.utils.rst.txt b/docs/build/html/_sources/crikit.utils.rst.txt deleted file mode 100644 index a87fc54..0000000 --- a/docs/build/html/_sources/crikit.utils.rst.txt +++ /dev/null @@ -1,62 +0,0 @@ -crikit\.utils package -===================== - -Submodules ----------- - -crikit\.utils\.breadcrumb module --------------------------------- - -.. automodule:: crikit.utils.breadcrumb - :members: - :undoc-members: - :show-inheritance: - -crikit\.utils\.datacheck module -------------------------------- - -.. automodule:: crikit.utils.datacheck - :members: - :undoc-members: - :show-inheritance: - -crikit\.utils\.general module ------------------------------ - -.. automodule:: crikit.utils.general - :members: - :undoc-members: - :show-inheritance: - -crikit\.utils\.h5 module ------------------------- - -.. automodule:: crikit.utils.h5 - :members: - :undoc-members: - :show-inheritance: - -crikit\.utils\.mplstyle module ------------------------------- - -.. automodule:: crikit.utils.mplstyle - :members: - :undoc-members: - :show-inheritance: - -crikit\.utils\.roi module -------------------------- - -.. automodule:: crikit.utils.roi - :members: - :undoc-members: - :show-inheritance: - - -Module contents ---------------- - -.. automodule:: crikit.utils - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt deleted file mode 100644 index 5ebb9c2..0000000 --- a/docs/build/html/_sources/index.rst.txt +++ /dev/null @@ -1,56 +0,0 @@ -.. CRIKit2 documentation master file, created by - sphinx-quickstart on Wed Jul 20 22:31:57 2016. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -.. image:: _static/CRIkit2_Logo.png - :align: left - - -| -| -| -| -| -| -| - -Welcome to CRIKit2's documentation! -=================================== - -CRIkit2 is a numerical and graphical package for processing hyperspectral -imagery (HSI). Originally developed for coherent Raman imaginery (CRI), -CRIkit2 is appropriate for all HSI. - -The main components of CRIkit2: - -- **CRIkitUI_process** : the [graphical] user interface (UI) for (pre-)processing - HSI. -- **CRIkitUI_analyze** : *Coming soon*. A UI for analysis and visualization. Out-of-core - computation enabled. Does not alter the original data. -- Numerical packages that can be used from the command line. - -Contents: - -.. toctree:: - :maxdepth: 2 - :caption: User Documentation - - installing - running - cri_walkthru - algorithms - io - nonlicense - -.. toctree:: - :maxdepth: 2 - :caption: Developer Documentation - - api - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` diff --git a/docs/build/html/_sources/installing.rst.txt b/docs/build/html/_sources/installing.rst.txt deleted file mode 100644 index 24719e2..0000000 --- a/docs/build/html/_sources/installing.rst.txt +++ /dev/null @@ -1,104 +0,0 @@ -.. _installing: - -.. image:: _static/CRIkit2_Logo.png - :align: left - -| -| -| -| -| -| -| - -Installation -============ - -Dependencies ---------------------- -Note: the versions are those that have been tested, but older/newer -versions may also work. - -- Python 3.4, 3.5, 3.6 (3.4.4, 3.5.2, 3.6.1) -- `SciPlot-PyQt `__ >= 0.1.3 (>=0.1.4 for MPL2) -- numpy (1.9.3, 1.11.1, 1.11.3+mkl) -- PyQt5 (5.5, 5.6, 5.8.1) -- matplotlib (1.5, 2.0 -- see below for MPL2) -- cvxopt (1.1.7, 1.1.9) -- h5py (2.5, 2.6, 2.7) -- Sphinx (1.4.5, 1.5.2, 1.6.4) -- only for documentation building - -Notes and Known Issues ----------------------- - -Matplotlib 2 -~~~~~~~~~~~~ -You will need to use SciPlot-PyQT v0.1.4 (or higher) -- Matplotlib 2 made numerous changes and deprecations that are being resolved -- See the installation instruction in the `SciPlot-pyQt README.md `__ - -Python 3.4 -~~~~~~~~~~~ -You will need to manually install PyQt5 and Qt5 or get it through a distribution -* PyQt5: https://www.riverbankcomputing.com/software/pyqt/download5 -* Qt: https://www.qt.io/ - -PyQt 5.7 and WinPython 3.5 -~~~~~~~~~~~~~~~~~~~~~~~~~~ -There is a bug in PyQt 5.7.* that will prevent SciPlot's tables from showing the individual plot entries -(see https://www.riverbankcomputing.com/pipermail/pyqt/2017-January/038483.html). Apparently, this will be fixed in 5.7.2. - -- As WinPython 3.5.2.3Qt5 and 3.5.2.2Qt5 use PyQt 5.7.*, it is advised to use WinPython 3.5.2.1Qt5 or 3.4.4.5Qt5 until the matter is sorted out. -- Alternatively, one can uninstall pyqt5.7.* and force an install of <= 5.6.*. - -SciPlot-PyQt -~~~~~~~~~~~~ -Currently, SciPlot >= 0.1.3 is not available through pip. You can however clone the repository from github. -(see https://github.com/CCampJr/SciPlot-PyQt) - -Instructions ------------- - -Git Dynamic copy -~~~~~~~~~~~~~~~~~~~ -:: - - # Make new directory for crikit2 (DIR) - # Clone from github - git clone https://github.com/CoherentRamanNIST/crikit2.git ./DIR - - # Within install directory (DIR) - pip3 install -e . - - # To update installation, from within crikit2 directory - git pull - -Git Static copy -~~~~~~~~~~~~~~~~~~~ -:: - - # Make new directory for crikit2 (DIR) - # Clone from github - git clone https://github.com/CoherentRamanNIST/crikit2.git ./DIR - - # Within install directory (DIR) - pip3 install . - - # You can now delete the source files you downloaded - -(Re)-Building documentation -~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -The documentation was built using Sphinx. A pre-built version of the html -files is included with this module, but you may wish to rebuild on your own -system.:: - - # Build all APIs - # From within the docs/ directory - sphinx-apidoc -o ./source/ ../crikit/ - - # Build API w/o pyuic5-generated files - sphinx-apidoc -f -o .\source\ ..\crikit\ ..\crikit\ui\qt_* ..\crikit\ui\*_rc* ..\crikit\ui\old\** - - make html - # On Windows - make.bat html diff --git a/docs/build/html/_sources/io.rst.txt b/docs/build/html/_sources/io.rst.txt deleted file mode 100644 index f1d2a24..0000000 --- a/docs/build/html/_sources/io.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _io: - -.. image:: _static/CRIkit2_Logo.png - :align: left - -| -| -| -| -| -| -| - -Input/Output (IO) File Types and Specs -====================================== - -Coming Soon \ No newline at end of file diff --git a/docs/build/html/_sources/modules.rst.txt b/docs/build/html/_sources/modules.rst.txt deleted file mode 100644 index fcf390b..0000000 --- a/docs/build/html/_sources/modules.rst.txt +++ /dev/null @@ -1,7 +0,0 @@ -crikit -====== - -.. toctree:: - :maxdepth: 4 - - crikit diff --git a/docs/build/html/_sources/nonlicense.rst.txt b/docs/build/html/_sources/nonlicense.rst.txt deleted file mode 100644 index be3bde8..0000000 --- a/docs/build/html/_sources/nonlicense.rst.txt +++ /dev/null @@ -1,28 +0,0 @@ -.. _nonlicense: - -.. image:: _static/CRIkit2_Logo.png - :align: left - -| -| -| -| -| -| -| - -Nonlicense -=========== -This software was developed at the National Institute of Standards and Technology (NIST) by -employees of the Federal Government in the course of their official duties. Pursuant to -`Title 17 Section 105 of the United States Code `_, -this software is not subject to copyright protection and is in the public domain. -NIST assumes no responsibility whatsoever for use by other parties of its source code, -and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. - -Specific software products identified in this open source project were used in order -to perform technology transfer and collaboration. In no case does such identification imply -recommendation or endorsement by the National Institute of Standards and Technology, nor -does it imply that the products identified are necessarily the best available for the -purpose. - diff --git a/docs/build/html/_sources/running.rst.txt b/docs/build/html/_sources/running.rst.txt deleted file mode 100644 index 25d7d3a..0000000 --- a/docs/build/html/_sources/running.rst.txt +++ /dev/null @@ -1,52 +0,0 @@ -.. _running: - -.. image:: _static/CRIkit2_Logo.png - :align: left - -| -| -| -| -| -| -| - -Running the CRIkit2 Graphical User Interface -============================================ - -As a module ------------ -:: - - python3 -m crikit - - # OR - - python -m crikit - -From within a Python/IPython/Jupyter shell ------------------------------------------- - -.. code:: python - - from crikit.CRIkitUI import crikit_launch - crikit_launch() - - -A longer example: - -.. code:: python - - import numpy as np - - from crikit.CRIkitUI import crikit_launch - - # Random hsi image - data = np.random.randn(10,21,100) - f = np.linspace(500,1000,100) - x = 1e3*np.arange(21) - y = 1e3*np.arange(10) - - crikit_launch(data=data, x=x, y=y, x_units='Feet', y_units='M', - x_label='Test', y_label='Test2', f_units=r'$\mu$m', - f_label='Frequency') \ No newline at end of file diff --git a/docs/build/html/_static/CRIkit2_Logo.png b/docs/build/html/_static/CRIkit2_Logo.png deleted file mode 100644 index b3cde5e..0000000 Binary files a/docs/build/html/_static/CRIkit2_Logo.png and /dev/null differ diff --git a/docs/build/html/_static/ajax-loader.gif b/docs/build/html/_static/ajax-loader.gif deleted file mode 100644 index 61faf8c..0000000 Binary files a/docs/build/html/_static/ajax-loader.gif and /dev/null differ diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css deleted file mode 100644 index 6df76b0..0000000 --- a/docs/build/html/_static/basic.css +++ /dev/null @@ -1,639 +0,0 @@ -/* - * basic.css - * ~~~~~~~~~ - * - * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -/* -- main layout ----------------------------------------------------------- */ - -div.clearer { - clear: both; -} - -/* -- relbar ---------------------------------------------------------------- */ - -div.related { - width: 100%; - font-size: 90%; -} - -div.related h3 { - display: none; -} - -div.related ul { - margin: 0; - padding: 0 0 0 10px; - list-style: none; -} - -div.related li { - display: inline; -} - -div.related li.right { - float: right; - margin-right: 5px; -} - -/* -- sidebar --------------------------------------------------------------- */ - -div.sphinxsidebarwrapper { - padding: 10px 5px 0 10px; -} - -div.sphinxsidebar { - float: left; - width: 230px; - margin-left: -100%; - font-size: 90%; - word-wrap: break-word; - overflow-wrap : break-word; -} - -div.sphinxsidebar ul { - list-style: 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b/docs/build/html/_static/doctools.js deleted file mode 100644 index 5654977..0000000 --- a/docs/build/html/_static/doctools.js +++ /dev/null @@ -1,287 +0,0 @@ -/* - * doctools.js - * ~~~~~~~~~~~ - * - * Sphinx JavaScript utilities for all documentation. - * - * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -/** - * select a different prefix for underscore - */ -$u = _.noConflict(); - -/** - * make the code below compatible with browsers without - * an installed firebug like debugger -if (!window.console || !console.firebug) { - var names = ["log", "debug", "info", "warn", "error", "assert", "dir", - "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace", - "profile", "profileEnd"]; - window.console = {}; - for (var i = 0; i < names.length; ++i) - window.console[names[i]] = function() {}; -} - */ - -/** - * small helper function to urldecode strings - */ -jQuery.urldecode = function(x) { - return decodeURIComponent(x).replace(/\+/g, ' '); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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' + _('Hide Search Matches') + '

') - .appendTo($('#searchbox')); - } - }, - - /** - * init the domain index toggle buttons - */ - initIndexTable : function() { - var togglers = $('img.toggler').click(function() { - var src = $(this).attr('src'); - var idnum = $(this).attr('id').substr(7); - $('tr.cg-' + idnum).toggle(); - if (src.substr(-9) == 'minus.png') - $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); - else - $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); - }).css('display', ''); - if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { - togglers.click(); - } - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords : function() { - $('#searchbox .highlight-link').fadeOut(300); - $('span.highlighted').removeClass('highlighted'); - }, - - /** - * make the url absolute - */ - makeURL : function(relativeURL) { - return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; - }, - - /** - * get the current relative url - */ - getCurrentURL : function() { - var path = document.location.pathname; - var parts = path.split(/\//); - $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { - if (this == '..') - parts.pop(); - }); - var url = parts.join('/'); - return path.substring(url.lastIndexOf('/') + 1, path.length - 1); - }, - - initOnKeyListeners: function() { - $(document).keyup(function(event) { - var activeElementType = document.activeElement.tagName; - // don't navigate when in search box or textarea - if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') { - switch (event.keyCode) { - case 37: // left - var prevHref = $('link[rel="prev"]').prop('href'); - if (prevHref) { - window.location.href = prevHref; - return false; - } - case 39: // right - var nextHref = $('link[rel="next"]').prop('href'); - if (nextHref) { - window.location.href = nextHref; - return false; - } - } - } - }); - } -}; - -// quick alias for translations -_ = Documentation.gettext; - -$(document).ready(function() { - Documentation.init(); -}); 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- - if ( typeof module === "object" && typeof module.exports === "object" ) { - - // For CommonJS and CommonJS-like environments where a proper `window` - // is present, execute the factory and get jQuery. - // For environments that do not have a `window` with a `document` - // (such as Node.js), expose a factory as module.exports. - // This accentuates the need for the creation of a real `window`. - // e.g. var jQuery = require("jquery")(window); - // See ticket #14549 for more info. - module.exports = global.document ? - factory( global, true ) : - function( w ) { - if ( !w.document ) { - throw new Error( "jQuery requires a window with a document" ); - } - return factory( w ); - }; - } else { - factory( global ); - } - -// Pass this if window is not defined yet -} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) { - -// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1 -// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode -// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common -// enough that all such attempts are guarded in a try block. -"use strict"; - -var arr = []; - -var document = window.document; - -var getProto = Object.getPrototypeOf; - -var slice = arr.slice; - -var concat = arr.concat; - -var push = arr.push; - -var indexOf = arr.indexOf; - -var class2type = {}; - -var toString = class2type.toString; - -var hasOwn = class2type.hasOwnProperty; - -var fnToString = hasOwn.toString; - -var ObjectFunctionString = fnToString.call( Object ); - -var support = {}; - - - - function DOMEval( code, doc ) { - doc = doc || document; - - var script = doc.createElement( "script" ); - - script.text = code; - doc.head.appendChild( script ).parentNode.removeChild( script ); - } -/* global Symbol */ -// Defining this global in .eslintrc would create a danger of using the global -// unguarded in another place, it seems safer to define global only for this module - - - -var - version = "3.1.0", - - // Define a local copy of jQuery - jQuery = function( selector, context ) { - - // The jQuery object is actually just the init constructor 'enhanced' - // Need init if jQuery is called (just allow error to be thrown if not included) - return new jQuery.fn.init( selector, context ); - }, - - // Support: Android <=4.0 only - // Make sure we trim BOM and NBSP - rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g, - - // Matches dashed string for camelizing - rmsPrefix = /^-ms-/, - rdashAlpha = /-([a-z])/g, - - // Used by jQuery.camelCase as callback to replace() - fcamelCase = function( all, letter ) { - return letter.toUpperCase(); - }; - -jQuery.fn = jQuery.prototype = { - - // The current version of jQuery being used - jquery: version, - - constructor: jQuery, - - // The default length of a jQuery object is 0 - length: 0, - - toArray: function() { - return slice.call( this ); - }, - - // Get the Nth element in the matched element set OR - // Get the whole matched element set as a clean array - get: function( num ) { - return num != null ? - - // Return just the one element from the set - ( num < 0 ? this[ num + this.length ] : this[ num ] ) : - - // Return all the elements in a clean array - slice.call( this ); - }, - - // Take an array of elements and push it onto the stack - // (returning the new matched element set) - pushStack: function( elems ) { - - // Build a new jQuery matched element set - var ret = jQuery.merge( this.constructor(), elems ); - - // Add the old object onto the stack (as a reference) - ret.prevObject = this; - - // Return the newly-formed element set - return ret; - }, - - // Execute a callback for every element in the matched set. - each: function( callback ) { - return jQuery.each( this, callback ); - }, - - map: function( callback ) { - return this.pushStack( jQuery.map( this, function( elem, i ) { - return callback.call( elem, i, elem ); - } ) ); - }, - - slice: function() { - return this.pushStack( slice.apply( this, arguments ) ); - }, - - first: function() { - return this.eq( 0 ); - }, - - last: function() { - return this.eq( -1 ); - }, - - eq: function( i ) { - var len = this.length, - j = +i + ( i < 0 ? len : 0 ); - return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] ); - }, - - end: function() { - return this.prevObject || this.constructor(); - }, - - // For internal use only. - // Behaves like an Array's method, not like a jQuery method. - push: push, - sort: arr.sort, - splice: arr.splice -}; - -jQuery.extend = jQuery.fn.extend = function() { - var options, name, src, copy, copyIsArray, clone, - target = arguments[ 0 ] || {}, - i = 1, - length = arguments.length, - deep = false; - - // Handle a deep copy situation - if ( typeof target === "boolean" ) { - deep = target; - - // Skip the boolean and the target - target = arguments[ i ] || {}; - i++; - } - - // Handle case when target is a string or something (possible in deep copy) - if ( typeof target !== "object" && !jQuery.isFunction( target ) ) { - target = {}; - } - - // Extend jQuery itself if only one argument is passed - if ( i === length ) { - target = this; - i--; - } - - for ( ; i < length; i++ ) { - - // Only deal with non-null/undefined values - if ( ( options = arguments[ i ] ) != null ) { - - // Extend the base object - for ( name in options ) { - src = target[ name ]; - copy = options[ name ]; - - // Prevent never-ending loop - if ( target === copy ) { - continue; - } - - // Recurse if we're merging plain objects or arrays - if ( deep && copy && ( jQuery.isPlainObject( copy ) || - ( copyIsArray = jQuery.isArray( copy ) ) ) ) { - - if ( copyIsArray ) { - copyIsArray = false; - clone = src && jQuery.isArray( src ) ? src : []; - - } else { - clone = src && jQuery.isPlainObject( src ) ? src : {}; - } - - // Never move original objects, clone them - target[ name ] = jQuery.extend( deep, clone, copy ); - - // Don't bring in undefined values - } else if ( copy !== undefined ) { - target[ name ] = copy; - } - } - } - } - - // Return the modified object - return target; -}; - -jQuery.extend( { - - // Unique for each copy of jQuery on the page - expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), - - // Assume jQuery is ready without the ready module - isReady: true, - - error: function( msg ) { - throw new Error( msg ); - }, - - noop: function() {}, - - isFunction: function( obj ) { - return jQuery.type( obj ) === "function"; - }, - - isArray: Array.isArray, - - isWindow: function( obj ) { - return obj != null && obj === obj.window; - }, - - isNumeric: function( obj ) { - - // As of jQuery 3.0, isNumeric is limited to - // strings and numbers (primitives or objects) - // that can be coerced to finite numbers (gh-2662) - var type = jQuery.type( obj ); - return ( type === "number" || type === "string" ) && - - // parseFloat NaNs numeric-cast false positives ("") - // ...but misinterprets leading-number strings, particularly hex literals ("0x...") - // subtraction forces infinities to NaN - !isNaN( obj - parseFloat( obj ) ); - }, - - isPlainObject: function( obj ) { - var proto, Ctor; - - // Detect obvious negatives - // Use toString instead of jQuery.type to catch host objects - if ( !obj || toString.call( obj ) !== "[object Object]" ) { - return false; - } - - proto = getProto( obj ); - - // Objects with no prototype (e.g., `Object.create( null )`) are plain - if ( !proto ) { - return true; - } - - // Objects with prototype are plain iff they were constructed by a global Object function - Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; - return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; - }, - - isEmptyObject: function( obj ) { - - /* eslint-disable no-unused-vars */ - // See https://github.com/eslint/eslint/issues/6125 - var name; - - for ( name in obj ) { - return false; - } - return true; - }, - - type: function( obj ) { - if ( obj == null ) { - return obj + ""; - } - - // Support: Android <=2.3 only (functionish RegExp) - return typeof obj === "object" || typeof obj === "function" ? - class2type[ toString.call( obj ) ] || "object" : - typeof obj; - }, - - // Evaluates a script in a global context - globalEval: function( code ) { - DOMEval( code ); - }, - - // Convert dashed to camelCase; used by the css and data modules - // Support: IE <=9 - 11, Edge 12 - 13 - // Microsoft forgot to hump their vendor prefix (#9572) - camelCase: function( string ) { - return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); - }, - - nodeName: function( elem, name ) { - return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); - }, - - each: function( obj, callback ) { - var length, i = 0; - - if ( isArrayLike( obj ) ) { - length = obj.length; - for ( ; i < length; i++ ) { - if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { - break; - } - } - } else { - for ( i in obj ) { - if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { - break; - } - } - } - - return obj; - }, - - // Support: Android <=4.0 only - trim: function( text ) { - return text == null ? - "" : - ( text + "" ).replace( rtrim, "" ); - }, - - // results is for internal usage only - makeArray: function( arr, results ) { - var ret = results || []; - - if ( arr != null ) { - if ( isArrayLike( Object( arr ) ) ) { - jQuery.merge( ret, - typeof arr === "string" ? - [ arr ] : arr - ); - } else { - push.call( ret, arr ); - } - } - - return ret; - }, - - inArray: function( elem, arr, i ) { - return arr == null ? -1 : indexOf.call( arr, elem, i ); - }, - - // Support: Android <=4.0 only, PhantomJS 1 only - // push.apply(_, arraylike) throws on ancient WebKit - merge: function( first, second ) { - var len = +second.length, - j = 0, - i = first.length; - - for ( ; j < len; j++ ) { - first[ i++ ] = second[ j ]; - } - - first.length = i; - - return first; - }, - - grep: function( elems, callback, invert ) { - var callbackInverse, - matches = [], - i = 0, - length = elems.length, - callbackExpect = !invert; - - // Go through the array, only saving the items - // that pass the validator function - for ( ; i < length; i++ ) { - callbackInverse = !callback( elems[ i ], i ); - if ( callbackInverse !== callbackExpect ) { - matches.push( elems[ i ] ); - } - } - - return matches; - }, - - // arg is for internal usage only - map: function( elems, callback, arg ) { - var length, value, - i = 0, - ret = []; - - // Go through the array, translating each of the items to their new values - if ( isArrayLike( elems ) ) { - length = elems.length; - for ( ; i < length; i++ ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - - // Go through every key on the object, - } else { - for ( i in elems ) { - value = callback( elems[ i ], i, arg ); - - if ( value != null ) { - ret.push( value ); - } - } - } - - // Flatten any nested arrays - return concat.apply( [], ret ); - }, - - // A global GUID counter for objects - guid: 1, - - // Bind a function to a context, optionally partially applying any - // arguments. - proxy: function( fn, context ) { - var tmp, args, proxy; - - if ( typeof context === "string" ) { - tmp = fn[ context ]; - context = fn; - fn = tmp; - } - - // Quick check to determine if target is callable, in the spec - // this throws a TypeError, but we will just return undefined. - if ( !jQuery.isFunction( fn ) ) { - return undefined; - } - - // Simulated bind - args = slice.call( arguments, 2 ); - proxy = function() { - return fn.apply( context || this, args.concat( slice.call( arguments ) ) ); - }; - - // Set the guid of unique handler to the same of original handler, so it can be removed - proxy.guid = fn.guid = fn.guid || jQuery.guid++; - - return proxy; - }, - - now: Date.now, - - // jQuery.support is not used in Core but other projects attach their - // properties to it so it needs to exist. - support: support -} ); - -if ( typeof Symbol === "function" ) { - jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; -} - -// Populate the class2type map -jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), -function( i, name ) { - class2type[ "[object " + name + "]" ] = name.toLowerCase(); -} ); - -function isArrayLike( obj ) { - - // Support: real iOS 8.2 only (not reproducible in simulator) - // `in` check used to prevent JIT error (gh-2145) - // hasOwn isn't used here due to false negatives - // regarding Nodelist length in IE - var length = !!obj && "length" in obj && obj.length, - type = jQuery.type( obj ); - - if ( type === "function" || jQuery.isWindow( obj ) ) { - return false; - } - - return type === "array" || length === 0 || - typeof length === "number" && length > 0 && ( length - 1 ) in obj; -} -var Sizzle = -/*! - * Sizzle CSS Selector Engine v2.3.0 - * https://sizzlejs.com/ - * - * Copyright jQuery Foundation and other contributors - * Released under the MIT license - * http://jquery.org/license - * - * Date: 2016-01-04 - */ -(function( window ) { - -var i, - support, - Expr, - getText, - isXML, - tokenize, - compile, - select, - outermostContext, - sortInput, - hasDuplicate, - - // Local document vars - setDocument, - document, - docElem, - documentIsHTML, - rbuggyQSA, - rbuggyMatches, - matches, - contains, - - // Instance-specific data - expando = "sizzle" + 1 * new Date(), - preferredDoc = window.document, - dirruns = 0, - done = 0, - classCache = createCache(), - tokenCache = createCache(), - compilerCache = createCache(), - sortOrder = function( a, b ) { - if ( a === b ) { - hasDuplicate = true; - } - return 0; - }, - - // Instance methods - hasOwn = ({}).hasOwnProperty, - arr = [], - pop = arr.pop, - push_native = arr.push, - push = arr.push, - slice = arr.slice, - // Use a stripped-down indexOf as it's faster than native - // https://jsperf.com/thor-indexof-vs-for/5 - indexOf = function( list, elem ) { - var i = 0, - len = list.length; - for ( ; i < len; i++ ) { - if ( list[i] === elem ) { - return i; - } - } - return -1; - }, - - booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped", - - // Regular expressions - - // http://www.w3.org/TR/css3-selectors/#whitespace - whitespace = "[\\x20\\t\\r\\n\\f]", - - // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier - identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+", - - // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors - attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + - // Operator (capture 2) - "*([*^$|!~]?=)" + whitespace + - // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]" - "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace + - "*\\]", - - pseudos = ":(" + identifier + ")(?:\\((" + - // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: - // 1. quoted (capture 3; capture 4 or capture 5) - "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + - // 2. simple (capture 6) - "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + - // 3. anything else (capture 2) - ".*" + - ")\\)|)", - - // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter - rwhitespace = new RegExp( whitespace + "+", "g" ), - rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ), - - rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), - rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ), - - rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ), - - rpseudo = new RegExp( pseudos ), - ridentifier = new RegExp( "^" + identifier + "$" ), - - matchExpr = { - "ID": new RegExp( "^#(" + identifier + ")" ), - "CLASS": new RegExp( "^\\.(" + identifier + ")" ), - "TAG": new RegExp( "^(" + identifier + "|[*])" ), - "ATTR": new RegExp( "^" + attributes ), - "PSEUDO": new RegExp( "^" + pseudos ), - "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace + - "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace + - "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), - "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), - // For use in libraries implementing .is() - // We use this for POS matching in `select` - "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + - whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) - }, - - rinputs = /^(?:input|select|textarea|button)$/i, - rheader = /^h\d$/i, - - rnative = /^[^{]+\{\s*\[native \w/, - - // Easily-parseable/retrievable ID or TAG or CLASS selectors - rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, - - rsibling = /[+~]/, - - // CSS escapes - // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters - runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ), - funescape = function( _, escaped, escapedWhitespace ) { - var high = "0x" + escaped - 0x10000; - // NaN means non-codepoint - // Support: Firefox<24 - // Workaround erroneous numeric interpretation of +"0x" - return high !== high || escapedWhitespace ? - escaped : - high < 0 ? - // BMP codepoint - String.fromCharCode( high + 0x10000 ) : - // Supplemental Plane codepoint (surrogate pair) - String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); - }, - - // CSS string/identifier serialization - // https://drafts.csswg.org/cssom/#common-serializing-idioms - rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\x80-\uFFFF\w-]/g, - fcssescape = function( ch, asCodePoint ) { - if ( asCodePoint ) { - - // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER - if ( ch === "\0" ) { - return "\uFFFD"; - } - - // Control characters and (dependent upon position) numbers get escaped as code points - return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; - } - - // Other potentially-special ASCII characters get backslash-escaped - return "\\" + ch; - }, - - // Used for iframes - // See setDocument() - // Removing the function wrapper causes a "Permission Denied" - // error in IE - unloadHandler = function() { - setDocument(); - }, - - disabledAncestor = addCombinator( - function( elem ) { - return elem.disabled === true; - }, - { dir: "parentNode", next: "legend" } - ); - -// Optimize for push.apply( _, NodeList ) -try { - push.apply( - (arr = slice.call( preferredDoc.childNodes )), - preferredDoc.childNodes - ); - // Support: Android<4.0 - // Detect silently failing push.apply - arr[ preferredDoc.childNodes.length ].nodeType; -} catch ( e ) { - push = { apply: arr.length ? - - // Leverage slice if possible - function( target, els ) { - push_native.apply( target, slice.call(els) ); - } : - - // Support: IE<9 - // Otherwise append directly - function( target, els ) { - var j = target.length, - i = 0; - // Can't trust NodeList.length - while ( (target[j++] = els[i++]) ) {} - target.length = j - 1; - } - }; -} - -function Sizzle( selector, context, results, seed ) { - var m, i, elem, nid, match, groups, newSelector, - newContext = context && context.ownerDocument, - - // nodeType defaults to 9, since context defaults to document - nodeType = context ? context.nodeType : 9; - - results = results || []; - - // Return early from calls with invalid selector or context - if ( typeof selector !== "string" || !selector || - nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { - - return results; - } - - // Try to shortcut find operations (as opposed to filters) in HTML documents - if ( !seed ) { - - if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) { - setDocument( context ); - } - context = context || document; - - if ( documentIsHTML ) { - - // If the selector is sufficiently simple, try using a "get*By*" DOM method - // (excepting DocumentFragment context, where the methods don't exist) - if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) { - - // ID selector - if ( (m = match[1]) ) { - - // Document context - if ( nodeType === 9 ) { - if ( (elem = context.getElementById( m )) ) { - - // Support: IE, Opera, Webkit - // TODO: identify versions - // getElementById can match elements by name instead of ID - if ( elem.id === m ) { - results.push( elem ); - return results; - } - } else { - return results; - } - - // Element context - } else { - - // Support: IE, Opera, Webkit - // TODO: identify versions - // getElementById can match elements by name instead of ID - if ( newContext && (elem = newContext.getElementById( m )) && - contains( context, elem ) && - elem.id === m ) { - - results.push( elem ); - return results; - } - } - - // Type selector - } else if ( match[2] ) { - push.apply( results, context.getElementsByTagName( selector ) ); - return results; - - // Class selector - } else if ( (m = match[3]) && support.getElementsByClassName && - context.getElementsByClassName ) { - - push.apply( results, context.getElementsByClassName( m ) ); - return results; - } - } - - // Take advantage of querySelectorAll - if ( support.qsa && - !compilerCache[ selector + " " ] && - (!rbuggyQSA || !rbuggyQSA.test( selector )) ) { - - if ( nodeType !== 1 ) { - newContext = context; - newSelector = selector; - - // qSA looks outside Element context, which is not what we want - // Thanks to Andrew Dupont for this workaround technique - // Support: IE <=8 - // Exclude object elements - } else if ( context.nodeName.toLowerCase() !== "object" ) { - - // Capture the context ID, setting it first if necessary - if ( (nid = context.getAttribute( "id" )) ) { - nid = nid.replace( rcssescape, fcssescape ); - } else { - context.setAttribute( "id", (nid = expando) ); - } - - // Prefix every selector in the list - groups = tokenize( selector ); - i = groups.length; - while ( i-- ) { - groups[i] = "#" + nid + " " + toSelector( groups[i] ); - } - newSelector = groups.join( "," ); - - // Expand context for sibling selectors - newContext = rsibling.test( selector ) && testContext( context.parentNode ) || - context; - } - - if ( newSelector ) { - try { - push.apply( results, - newContext.querySelectorAll( newSelector ) - ); - return results; - } catch ( qsaError ) { - } finally { - if ( nid === expando ) { - context.removeAttribute( "id" ); - } - } - } - } - } - } - - // All others - return select( selector.replace( rtrim, "$1" ), context, results, seed ); -} - -/** - * Create key-value caches of limited size - * @returns {function(string, object)} Returns the Object data after storing it on itself with - * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) - * deleting the oldest entry - */ -function createCache() { - var keys = []; - - function cache( key, value ) { - // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) - if ( keys.push( key + " " ) > Expr.cacheLength ) { - // Only keep the most recent entries - delete cache[ keys.shift() ]; - } - return (cache[ key + " " ] = value); - } - return cache; -} - -/** - * Mark a function for special use by Sizzle - * @param {Function} fn The function to mark - */ -function markFunction( fn ) { - fn[ expando ] = true; - return fn; -} - -/** - * Support testing using an element - * @param {Function} fn Passed the created element and returns a boolean result - */ -function assert( fn ) { - var el = document.createElement("fieldset"); - - try { - return !!fn( el ); - } catch (e) { - return false; - } finally { - // Remove from its parent by default - if ( el.parentNode ) { - el.parentNode.removeChild( el ); - } - // release memory in IE - el = null; - } -} - -/** - * Adds the same handler for all of the specified attrs - * @param {String} attrs Pipe-separated list of attributes - * @param {Function} handler The method that will be applied - */ -function addHandle( attrs, handler ) { - var arr = attrs.split("|"), - i = arr.length; - - while ( i-- ) { - Expr.attrHandle[ arr[i] ] = handler; - } -} - -/** - * Checks document order of two siblings - * @param {Element} a - * @param {Element} b - * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b - */ -function siblingCheck( a, b ) { - var cur = b && a, - diff = cur && a.nodeType === 1 && b.nodeType === 1 && - a.sourceIndex - b.sourceIndex; - - // Use IE sourceIndex if available on both nodes - if ( diff ) { - return diff; - } - - // Check if b follows a - if ( cur ) { - while ( (cur = cur.nextSibling) ) { - if ( cur === b ) { - return -1; - } - } - } - - return a ? 1 : -1; -} - -/** - * Returns a function to use in pseudos for input types - * @param {String} type - */ -function createInputPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return name === "input" && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for buttons - * @param {String} type - */ -function createButtonPseudo( type ) { - return function( elem ) { - var name = elem.nodeName.toLowerCase(); - return (name === "input" || name === "button") && elem.type === type; - }; -} - -/** - * Returns a function to use in pseudos for :enabled/:disabled - * @param {Boolean} disabled true for :disabled; false for :enabled - */ -function createDisabledPseudo( disabled ) { - // Known :disabled false positives: - // IE: *[disabled]:not(button, input, select, textarea, optgroup, option, menuitem, fieldset) - // not IE: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable - return function( elem ) { - - // Check form elements and option elements for explicit disabling - return "label" in elem && elem.disabled === disabled || - "form" in elem && elem.disabled === disabled || - - // Check non-disabled form elements for fieldset[disabled] ancestors - "form" in elem && elem.disabled === false && ( - // Support: IE6-11+ - // Ancestry is covered for us - elem.isDisabled === disabled || - - // Otherwise, assume any non-