Use stdatamodels

TST: Update test_parse_jwst_niriss_grism
because asdf_in_fits do the invalid WCS handling natively now.

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -70,6 +70,7 @@ body:
         import scipy; print("scipy", scipy.__version__)
         import skimage; print("scikit-image", skimage.__version__)
         import asdf; print("asdf", asdf.__version__)
+        import stdatamodels; print("stdatamodels", stdatamodels.__version__)
         import gwcs; print("gwcs", gwcs.__version__)
         import regions; print("regions", regions.__version__)
         import specutils; print("specutils", specutils.__version__)

CHANGES.rst

@@ -38,6 +38,8 @@ Cubeviz
 Imviz
 ^^^^^
 
+- ASDF parser for JWST images now uses ``stdatamodels``. [#2052]
+
 Mosviz
 ^^^^^^
 

conftest.py

@@ -32,5 +32,6 @@ def pytest_configure(config):
     PYTEST_HEADER_MODULES['vispy'] = 'vispy'
     PYTEST_HEADER_MODULES['gwcs'] = 'gwcs'
     PYTEST_HEADER_MODULES['asdf'] = 'asdf'
+    PYTEST_HEADER_MODULES['stdatamodels'] = 'stdatamodels'
 
     TESTED_VERSIONS['jdaviz'] = __version__

jdaviz/configs/default/plugins/metadata_viewer/metadata_viewer.py

@@ -122,7 +122,8 @@ def get_comment(key):
             self.reset()
 
 
-# TODO: If this is natively supported by asdf in the future, replace with native function.
+# TODO: If this generalized in stdatamodels in the future, replace with native function.
+#       See https://github.com/spacetelescope/stdatamodels/issues/131
 # This code below is taken code from stdatamodels/model_base.py, and the method to_flat_dict()
 def flatten_nested_dict(asdfnode, include_arrays=True):
     """

jdaviz/configs/imviz/helper.py

@@ -87,7 +87,7 @@ def load_data(self, data, data_label=None, do_link=True, show_in_viewer=True, **
             * ``'filename.fits[SCI,2]'`` (loads the second SCI extension)
             * ``'filename.jpg'`` (requires ``scikit-image``; grayscale only)
             * ``'filename.png'`` (requires ``scikit-image``; grayscale only)
-            * JWST ASDF-in-FITS file (requires ``asdf`` and ``gwcs``; ``data`` or given
+            * JWST ASDF-in-FITS file (requires ``stdatamodels`` and ``gwcs``; ``data`` or given
               ``ext`` + GWCS)
             * `~astropy.io.fits.HDUList` object (first image extension found
               is loaded unless ``ext`` keyword is also given)

jdaviz/configs/imviz/plugins/parsers.py

@@ -1,13 +1,13 @@
 import os
 
 import numpy as np
-from asdf.fits_embed import AsdfInFits
 from astropy import units as u
 from astropy.io import fits
 from astropy.nddata import NDData
 from astropy.wcs import WCS
 from glue.core.data import Component, Data
 from gwcs.wcs import WCS as GWCS
+from stdatamodels import asdf_in_fits
 
 from jdaviz.core.registries import data_parser_registry
 from jdaviz.core.events import SnackbarMessage
@@ -229,7 +229,7 @@ def _jwst2data(file_obj, ext, data_label):
 
     try:
         # This is very specific to JWST pipeline image output.
-        with AsdfInFits.open(file_obj) as af:
+        with asdf_in_fits.open(file_obj) as af:
             dm = af.tree
             dm_meta = af.tree["meta"]
             data.meta.update(standardize_metadata(dm_meta))

jdaviz/configs/imviz/tests/test_parser.py

@@ -1,6 +1,5 @@
 import numpy as np
 import pytest
-from asdf.fits_embed import AsdfInFits
 from astropy import units as u
 from astropy.io import fits
 from astropy.nddata import NDData, StdDevUncertainty
@@ -11,6 +10,7 @@
 from numpy.testing import assert_allclose, assert_array_equal
 from regions import CirclePixelRegion, RectanglePixelRegion
 from skimage.io import imsave
+from stdatamodels import asdf_in_fits
 
 from jdaviz.configs.imviz.helper import split_filename_with_fits_ext
 from jdaviz.configs.imviz.plugins.parsers import (
@@ -221,14 +221,13 @@ def test_filelist(self, imviz_helper, tmp_path):
         with pytest.raises(ValueError, match='Do not manually overwrite data_label'):
             imviz_helper.load_data(flist, data_label='foo', show_in_viewer=False)
 
-    def test_parse_asdf_in_fits_4d(self, imviz_helper, tmpdir):
+    def test_parse_asdf_in_fits_4d(self, imviz_helper, tmp_path):
         hdulist = fits.HDUList([
             fits.PrimaryHDU(),
             fits.ImageHDU(np.zeros((1, 2, 5, 5)), name='SCI')])
         tree = {'data': {'data': hdulist['SCI'].data}}
-        filename = str(tmpdir.join('myasdf.fits'))
-        ff = AsdfInFits(hdulist, tree)
-        ff.write_to(filename, overwrite=True)
+        filename = str(tmp_path / 'myasdf.fits')
+        asdf_in_fits.write(filename, tree, hdulist=hdulist, overwrite=True)
 
         with pytest.raises(ValueError, match='Imviz cannot load this HDU'):
             parse_data(imviz_helper.app, filename)
@@ -360,16 +359,15 @@ def test_parse_jwst_nircam_level2(self, imviz_helper):
 
     @pytest.mark.remote_data
     def test_parse_jwst_niriss_grism(self, imviz_helper):
-        """No valid image GWCS for Imviz, will fall back to FITS loading without WCS."""
+        """No valid image GWCS for Imviz, will fall back to loading without WCS."""
         filename = download_file(self.jwst_asdf_url_2, cache=True)
 
         imviz_helper.load_data(filename, show_in_viewer=False)
         data = imviz_helper.app.data_collection[0]
-        comp = data.get_component('SCI,1')
-        assert data.label == 'contents[SCI,1]'  # download_file returns cache loc
+        comp = data.get_component('DATA')
+        assert data.label == 'contents[DATA]'  # download_file returns cache loc
         assert data.shape == (2048, 2048)
         assert data.coords is None
-        assert data.meta['RADESYS'] == 'ICRS'
         assert comp.units == 'DN/s'
         assert comp.data.shape == (2048, 2048)
 

jdaviz/conftest.py

@@ -309,5 +309,6 @@ def pytest_configure(config):
     PYTEST_HEADER_MODULES['vispy'] = 'vispy'
     PYTEST_HEADER_MODULES['gwcs'] = 'gwcs'
     PYTEST_HEADER_MODULES['asdf'] = 'asdf'
+    PYTEST_HEADER_MODULES['stdatamodels'] = 'stdatamodels'
 
     TESTED_VERSIONS['jdaviz'] = __version__

setup.cfg

@@ -44,6 +44,8 @@ install_requires =
     # vispy is an indirect dependency, but older vispy's don't play nice with jdaviz install
     vispy>=0.6.5
     asdf>=2.14.3
+    # TODO: update stdatamodels to version without stcal
+    stdatamodels>=1.1
     gwcs>=0.16.1
     regions>=0.6
     scikit-image
@@ -98,7 +100,6 @@ filterwarnings =
     ignore:.*With traitlets 4\.1, metadata should be set using the \.tag\(\) method:DeprecationWarning
     ignore:Widget.* is deprecated:DeprecationWarning
     ignore:zmq\.eventloop\.ioloop is deprecated in pyzmq:DeprecationWarning
-    ignore:AsdfInFits has been deprecated
     ignore:The unit 'Angstrom' has been deprecated in the VOUnit standard\. Suggested.* 0\.1nm\.
     ignore:specutils uses the deprecated entry point asdf_extensions
     ignore::DeprecationWarning:glue

tox.ini

@@ -48,6 +48,7 @@ deps =
     devdeps: git+https://github.com/astropy/photutils.git
     devdeps: git+https://github.com/spacetelescope/gwcs.git
     devdeps: git+https://github.com/asdf-format/asdf.git
+    devdeps: git+https://github.com/spacetelescope/stdatamodels.git
     devdeps: git+https://github.com/bqplot/[email protected]
     devdeps: git+https://github.com/glue-viz/glue.git
     devdeps: git+https://github.com/voila-dashboards/voila.git