BUG: Fix specviz2d loader with ext keyword (#2830)

* BUG: Let Specviz2d choose ext

* TST: Add a regression test that fails on main
but should pass with this patch

* BUG: 2D spec might not have valid WCS
but that should not crash the mouseover display.

CHANGES.rst

@@ -61,6 +61,8 @@ Specviz
 Specviz2d
 ^^^^^^^^^
 
+- Loading a specific extension with ``ext`` keyword no longer crashes. [#2830]
+
 Other Changes and Additions
 ---------------------------
 

jdaviz/configs/imviz/plugins/coords_info/coords_info.py

@@ -397,16 +397,20 @@ def _image_viewer_update(self, viewer, x, y):
             self._dict['world'] = (sky.ra.value, sky.dec.value)
             self._dict['world:unreliable'] = unreliable_world
         elif isinstance(viewer, MosvizProfile2DView) and hasattr(getattr(image, 'coords', None),
-                                                                 'pixel_to_world_values'):
+                                                                 'pixel_to_world'):
             # use WCS to expose the wavelength for a 2d spectrum shown in pixel space
-            wave, pixel = image.coords.pixel_to_world(x, y)
-            self.row2_title = 'Wave'
-            self.row2_text = f'{wave.value:10.5e} {wave.unit.to_string()}'
-            self.row2_unreliable = False
+            try:
+                wave, pixel = image.coords.pixel_to_world(x, y)
+            except Exception:  # WCS might not be valid  # pragma: no cover
+                coords_status = False
+            else:
+                self.row2_title = 'Wave'
+                self.row2_text = f'{wave.value:10.5e} {wave.unit.to_string()}'
+                self.row2_unreliable = False
 
-            self.row3_title = '\u00A0'
-            self.row3_text = ""
-            self.row3_unreliable = False
+                self.row3_title = '\u00A0'
+                self.row3_text = ""
+                self.row3_unreliable = False
         else:
             self.row2_title = '\u00A0'
             self.row2_text = ""
@@ -484,7 +488,7 @@ def _image_viewer_update(self, viewer, x, y):
             self.marks[viewer._reference_id].visible = True
 
             for matched_marker_id in self._matched_markers.get(viewer._reference_id, []):
-                if hasattr(getattr(image, 'coords', None), 'pixel_to_world_values'):
+                if coords_status and hasattr(getattr(image, 'coords', None), 'pixel_to_world'):
                     # should already have wave computed from setting the coords-info
                     matched_viewer = self.app.get_viewer(matched_marker_id.split(':matched')[0])
                     wave = wave.to_value(matched_viewer.state.x_display_unit)

jdaviz/configs/mosviz/plugins/parsers.py

@@ -326,7 +326,7 @@ def _parse_as_spectrum1d(hdulist, ext, transpose):
         data_obj = [data_obj]
 
     # See if this is a multi s2d file
-    if len(data_obj) == 1 and _check_is_file(data_obj[0]):
+    if app.config == "mosviz" and len(data_obj) == 1 and _check_is_file(data_obj[0]):
         if identify_jwst_s2d_multi_fits("test", data_obj[0]):
             data_obj = SpectrumList.read(data_obj[0])
 

jdaviz/configs/specviz2d/tests/test_parsers.py

@@ -1,8 +1,10 @@
 import pytest
+import stdatamodels
 from astropy.io import fits
 from astropy.utils.data import download_file
 
 from jdaviz.utils import PRIHDR_KEY
+from jdaviz.configs.imviz.tests.utils import create_example_gwcs
 
 
 @pytest.mark.remote_data
@@ -89,6 +91,37 @@ def test_2d_parser_no_unit(specviz2d_helper, mos_spectrum2d):
     assert label_mouseover.icon == 'b'
 
 
+def test_2d_parser_hdulist_ext(tmp_path, specviz2d_helper, mos_spectrum2d_as_hdulist):
+    in_filename = tmp_path / "my_2d_spec.fits"
+
+    # Create a dummy ASDF extension to trick specutil to use JWST s2d parser.
+    # The actual values do not matter here; they are currently nonsense.
+    w = create_example_gwcs(mos_spectrum2d_as_hdulist['SCI'].data.shape)
+    w.bounding_box = ((-1, 2.9), (6, 7.5))
+    tree = {
+        'model': {
+            'sci': {
+                'data': mos_spectrum2d_as_hdulist['SCI'].data
+            }
+        },
+        'meta': {'wcs': w}
+    }
+    stdatamodels.asdf_in_fits.write(in_filename, tree, mos_spectrum2d_as_hdulist, overwrite=True)
+
+    specviz2d_helper.load_data(in_filename, ext=1)
+    assert len(specviz2d_helper.app.data_collection) == 2
+
+    dc_0 = specviz2d_helper.app.data_collection[0]
+    assert dc_0.label == 'Spectrum 2D'
+    assert dc_0.get_component('flux').units == 'ct'
+
+    dc_1 = specviz2d_helper.app.data_collection[1]
+    assert dc_1.label == 'Spectrum 1D'
+    assert dc_1.get_component('flux').units == dc_0.get_component('flux').units
+
+    # The rest already checked in test_2d_parser_no_unit above.
+
+
 def test_1d_parser(specviz2d_helper, spectrum1d):
     specviz2d_helper.load_data(spectrum_1d=spectrum1d)
     assert len(specviz2d_helper.app.data_collection) == 1

jdaviz/conftest.py

@@ -288,15 +288,7 @@ def spectrum2d():
     return Spectrum1D(flux=data*u.MJy, spectral_axis=data[3]*u.um)
 
 
-@pytest.fixture
-def mos_spectrum2d():
-    '''
-    A specially defined 2D (spatial) Spectrum1D whose wavelength range matches the
-    mos-specific 1D spectrum.
-
-    TODO: This should be reformed to match the global Spectrum1D defined above so that we may
-    deprecate the mos-specific spectrum1d.
-    '''
+def _generate_mos_spectrum2d():
     header = {
         'WCSAXES': 2,
         'CRPIX1': 0.0, 'CRPIX2': 1024.5,
@@ -305,12 +297,42 @@ def mos_spectrum2d():
         'CTYPE1': 'WAVE', 'CTYPE2': 'OFFSET',
         'CRVAL1': 0.0, 'CRVAL2': 5.0,
         'RADESYS': 'ICRS', 'SPECSYS': 'BARYCENT'}
-    wcs = WCS(header)
     np.random.seed(42)
     data = np.random.sample((1024, 15)) * u.one
+    return data, header
+
+
+@pytest.fixture
+def mos_spectrum2d():
+    '''
+    A specially defined 2D (spatial) Spectrum1D whose wavelength range matches the
+    mos-specific 1D spectrum.
+
+    TODO: This should be reformed to match the global Spectrum1D defined above so that we may
+    deprecate the mos-specific spectrum1d.
+    '''
+    data, header = _generate_mos_spectrum2d()
+    wcs = WCS(header)
     return Spectrum1D(data, wcs=wcs, meta=header)
 
 
+@pytest.fixture
+def mos_spectrum2d_as_hdulist():
+    data, header = _generate_mos_spectrum2d()
+    hdu = fits.ImageHDU(data.value)
+    hdu.header.update(header)
+
+    # This layout is to trick specutils to think it is JWST s2d
+    hdulist = fits.HDUList([fits.PrimaryHDU(), hdu, hdu])
+    hdulist[0].header["TELESCOP"] = "JWST"
+    hdulist[1].name = "SCI"
+    hdulist[1].ver = 1
+    hdulist[2].name = "SCI"
+    hdulist[2].ver = 2
+
+    return hdulist
+
+
 @pytest.fixture
 def mos_image():
     header = {