Merge branch 'develop' into gs-inject-source

.github/workflows/autolabel.yml

@@ -10,5 +10,5 @@ jobs:
       - uses: Naturalclar/[email protected]
         with:
           title-or-body: "both"
-          parameters: '[ {"keywords": ["NIRCam Stage 1/2 Pipeline"], "labels": ["NIRCam"], "assignees": ["AarynnCarter","mperrin","JarronL"]}, {"keywords": ["MIRI Stage 1/2 Pipeline"], "labels": ["MIRI"], "assignees": ["AarynnCarter","mperrin","JarronL"]}, {"keywords": ["Image Tools"], "labels": ["image tools"], "assignees": ["kglidic","kammerje","AarynnCarter","wbalmer","kdlawson","JarronL"]}, {"keywords": ["PSF Subtraction"], "labels": ["PSF subtraction"], "assignees": ["kdlawson","wbalmer","AarynnCarter"]}, {"keywords": ["Analysis Tools"], "labels": ["analysis tools"], "assignees": ["kdlawson","wbalmer","AarynnCarter","juliengirard","kammerje","kglidic"]}, {"keywords": ["Other"], "labels": [], "assignees": ["kdlawson","AarynnCarter","juliengirard","JarronL","kglidic"]}, {"keywords": ["Documentation"], "labels": ["documentation"], "assignees": ["AarynnCarter","mperrin","kglidic"]}]'
+          parameters: '[ {"keywords": ["NIRCam Stage 1/2 Pipeline"], "labels": ["NIRCam"], "assignees": ["AarynnCarter","mperrin","JarronL"]}, {"keywords": ["MIRI Stage 1/2 Pipeline"], "labels": ["MIRI"], "assignees": ["AarynnCarter","mperrin","JarronL"]}, {"keywords": ["Image Tools"], "labels": ["image tools"], "assignees": ["kglidic","kammerje","AarynnCarter","wbalmer","kdlawson","JarronL"]}, {"keywords": ["PSF Subtraction"], "labels": ["PSF subtraction"], "assignees": ["kdlawson","wbalmer","AarynnCarter"]}, {"keywords": ["Analysis Tools"], "labels": ["analysis tools"], "assignees": ["kdlawson","wbalmer","AarynnCarter","juliengirard","kammerje","kglidic"]}, {"keywords": ["Other"], "labels": ["other"], "assignees": ["kdlawson","AarynnCarter","juliengirard","JarronL","kglidic"]}, {"keywords": ["Documentation"], "labels": ["documentation"], "assignees": ["AarynnCarter","mperrin","kglidic"]}]'
           github-token: "${{ secrets.GITHUB_TOKEN }}"

.gitignore

@@ -213,4 +213,9 @@ tests/ultranest
 tests/species_*
 
 # setuptools-scm
+
+# PyCharm files
+.idea/
+
+
 spaceKLIP/_version.py

README.rst

@@ -37,15 +37,11 @@ With the Anaconda environment created, move to the cloned directory and install
 ::
 
 	cd where/you/saved/the/git/repo
+	conda install conda-forge::git-lfs	
 	pip install -r requirements.txt
 	pip install -e .
 
-NEW AS OF 1 JUNE 2023: you also need to make the custom PSF mask files before running spaceKLIP for the first time:
-
-::
-
-	cd spaceKLIP/
-        python make_psfmasks.py
+Note that installing git-lfs from pip does not work as of 25 June 2024.
 
 Finally, and very importantly, you will need to download the reference files and set the environment variables supporting the functioning of :code:`webbpsf` and :code:`webbpsf_ext`. Instructions to do this can be found at the respective package websites (`WebbPSF <https://webbpsf.readthedocs.io/en/latest/installation.html#installing-the-required-data-files>`_, `WebbPSF_ext <https://github.com/JarronL/webbpsf_ext>`_). Ensure that if you edit your .bashrc file, close and reopen your terminal to fully apply the changes (:code:`source ~/.bashrc` or :code:`source ~/.zshrc` may also work).
 

requirements-dev.txt

@@ -1,6 +1,6 @@
 -r requirements.txt
-sphinx
-pandoc
-nbsphinx
-sphinx-rtd-theme
-sphinx_automodapi
+sphinx>=7.2.6
+pandoc>=2.3
+nbsphinx>=0.9.3
+sphinx-rtd-theme>=2.0.0
+sphinx_automodapi>=0.17.0

requirements.txt

@@ -1,12 +1,12 @@
-astropy
-astroquery
-jwst
+astropy>=6.0.1
+astroquery>=0.4.7
+jwst>=1.14.0
 matplotlib>=3.7.1
 numpy<2
-synphot
-stsynphot
-scipy
-stsci.stimage==0.2.6
-webbpsf
+synphot>=1.4.0
+stsynphot>=1.3.0
+scipy>=1.13.0
+stsci.stimage>=0.2.9
+webbpsf>=1.2.1
 webbpsf_ext>=1.2.0
-pyklip @ git+https://bitbucket.org/pyKLIP/pyklip.git@jwst
+pyklip>=2.7.1

spaceKLIP/coron2pipeline.py

@@ -344,7 +344,7 @@ def run_obs(database,
                                           verbose=verbose, **kwargs)
 
                 # Update spaceKLIP database.
-                database.update_obs(key, j, fitsout_path)
+                database.update_obs(key, j, fitsout_path, update_pxar=True)
 
             # Also process rate files?
             if do_rates:

spaceKLIP/database.py

@@ -20,8 +20,8 @@
 import webbpsf, webbpsf_ext
 
 from astropy.table import Table
-from astroquery.svo_fps import SvoFps
 from jwst.pipeline import Detector1Pipeline, Image2Pipeline, Coron3Pipeline
+from stdatamodels.jwst import datamodels
 
 from .utils import nircam_apname, get_nrcmask_from_apname, get_filter_info
 
@@ -191,6 +191,7 @@ def read_jwst_s012_data(self,
         APERNAME = []
         PPS_APER = []
         PIXSCALE = []  # arcsec
+        PIXAR_SR = []  # sr
         BUNIT = []
         CRPIX1 = []  # pix
         CRPIX2 = []  # pix
@@ -274,6 +275,7 @@ def read_jwst_s012_data(self,
                 raise UserWarning('Data originates from unknown telescope')
             BLURFWHM += [head.get('BLURFWHM', np.nan)]
             head = hdul['SCI'].header
+            PIXAR_SR += [head.get('PIXAR_SR', np.nan)]
             BUNIT += [head.get('BUNIT', 'NONE')]
             if cr_from_siaf:
                 CRPIX1 += [ap.XSciRef]
@@ -313,6 +315,7 @@ def read_jwst_s012_data(self,
         APERNAME = np.array(APERNAME)
         PPS_APER = np.array(PPS_APER)
         PIXSCALE = np.array(PIXSCALE)
+        PIXAR_SR = np.array(PIXAR_SR)
         BUNIT = np.array(BUNIT)
         CRPIX1 = np.array(CRPIX1)
         CRPIX2 = np.array(CRPIX2)
@@ -410,6 +413,7 @@ def read_jwst_s012_data(self,
                                'APERNAME',
                                'PPS_APER',
                                'PIXSCALE',
+                               'PIXAR_SR',
                                'BUNIT',
                                'CRPIX1',
                                'CRPIX2',
@@ -443,6 +447,7 @@ def read_jwst_s012_data(self,
                                'object',
                                'object', 
                                'float',
+                               'float',
                                'object',
                                'float',
                                'float',
@@ -481,10 +486,9 @@ def read_jwst_s012_data(self,
                 maskfile = allpaths[ww][j].replace('.fits', '_psfmask.fits')
                 if not os.path.exists(maskfile):    
                     if EXP_TYPE[ww][j] == 'NRC_CORON':
-                        maskpath = APERNAME[ww][j] + '_' + FILTER[ww][j] + '.fits'
-                        maskfile = os.path.join(maskbase, maskpath)
-                        if not os.path.exists(maskfile):
-                            maskfile = 'NONE'
+                        pipeline = Detector1Pipeline()
+                        input = datamodels.open(allpaths[ww][j])
+                        maskfile = pipeline.get_reference_file(input, 'psfmask')
                     elif EXP_TYPE[ww][j] == 'MIR_4QPM' or EXP_TYPE[ww][j] == 'MIR_LYOT':
                         if APERNAME[ww][j] == 'MIRIM_MASK1065':
                             maskpath = 'JWST_MIRI_F1065C_transmission_webbpsf-ext_v2.fits'
@@ -521,6 +525,7 @@ def read_jwst_s012_data(self,
                              APERNAME[ww][j],
                              PPS_APER[ww][j],
                              PIXSCALE[ww][j],
+                             PIXAR_SR[ww][j],
                              BUNIT[ww][j],
                              CRPIX1[ww][j],
                              CRPIX2[ww][j],
@@ -627,6 +632,7 @@ def read_jwst_s3_data(self,
         APERNAME = []
         PPS_APER = []
         PIXSCALE = []  # arcsec
+        PIXAR_SR = []  # sr
         MODE = []
         ANNULI = []
         SUBSECTS = []
@@ -723,6 +729,7 @@ def read_jwst_s3_data(self,
             BLURFWHM += [head.get('BLURFWHM', np.nan)]
             if TYPE[-1] == 'CORON3':
                 head = hdul['SCI'].header
+            PIXAR_SR += [head.get('PIXAR_SR', np.nan)]
             BUNIT += [head.get('BUNIT', 'NONE')]
             if cr_from_siaf:
                 CRPIX1 += [ap.XSciRef]
@@ -753,6 +760,7 @@ def read_jwst_s3_data(self,
         APERNAME = np.array(APERNAME)
         PPS_APER = np.array(PPS_APER)
         PIXSCALE = np.array(PIXSCALE)
+        PIXAR_SR = np.array(PIXAR_SR)
         MODE = np.array(MODE)
         ANNULI = np.array(ANNULI)
         SUBSECTS = np.array(SUBSECTS)
@@ -794,6 +802,7 @@ def read_jwst_s3_data(self,
                                    'APERNAME',
                                    'PPS_APER',
                                    'PIXSCALE',
+                                   'PIXAR_SR',
                                    'MODE',
                                    'ANNULI',
                                    'SUBSECTS',
@@ -823,6 +832,7 @@ def read_jwst_s3_data(self,
                                    'object',
                                    'object',
                                    'float',
+                                   'float',
                                    'object',
                                    'int',
                                    'int',
@@ -858,6 +868,7 @@ def read_jwst_s3_data(self,
                              APERNAME[ww[j]],
                              PPS_APER[ww[j]],
                              PIXSCALE[ww[j]],
+                             PIXAR_SR[ww[j]],
                              MODE[ww[j]],
                              ANNULI[ww[j]],
                              SUBSECTS[ww[j]],
@@ -1021,8 +1032,10 @@ def print_obs(self,
             else:
                 print_tab.remove_columns(['TARG_RA', 'TARG_DEC', 'EXPSTART', 'APERNAME', 'PPS_APER', 
                                           'CRPIX1', 'CRPIX2', 'RA_REF', 'DEC_REF', 'FITSFILE', 'MASKFILE'])
+            print_tab['XOFFSET'] *= 1e3
             print_tab['XOFFSET'] = np.round(print_tab['XOFFSET'])
             print_tab['XOFFSET'][print_tab['XOFFSET'] == 0.] = 0.
+            print_tab['YOFFSET'] *= 1e3
             print_tab['YOFFSET'] = np.round(print_tab['YOFFSET'])
             print_tab['YOFFSET'][print_tab['YOFFSET'] == 0.] = 0.
             print_tab.pprint()
@@ -1102,7 +1115,8 @@ def update_obs(self,
                    yoffset=None,
                    crpix1=None,
                    crpix2=None,
-                   blurfwhm=None):
+                   blurfwhm=None,
+                   update_pxar=False):
         """
         Update the content of the observations database.
         
@@ -1138,6 +1152,9 @@ def update_obs(self,
         blurfwhm : float, optional
             New FWHM for the Gaussian filter blurring (pix) for the observation
             to be updated. The default is None.
+        update_pxar : bool, optional
+            Update the pixel area column of the database based on the FITS file
+            header information? The default is False.
         
         Returns
         -------
@@ -1174,6 +1191,12 @@ def update_obs(self,
         self.obs[key]['FITSFILE'][index] = fitsfile
         if maskfile is not None:
             self.obs[key]['MASKFILE'][index] = maskfile
+        if update_pxar:
+            try:
+                pxar = pyfits.getheader(self.obs[key]['FITSFILE'][index], 'SCI')['PIXAR_SR']
+                self.obs[key]['PIXAR_SR'][index] = pxar
+            except:
+                pass
         hdul.close()
 
         pass