Merge branch '0.2.X'

.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/

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.

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)###

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.
+* 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