Backport PR #2576: Specviz Parser handling HDULists

CHANGES.rst

@@ -21,6 +21,8 @@ Mosviz
 Specviz
 ^^^^^^^
 
+-  Fixed parser bug where an HDUList would load as SpectrumList, even though it was a Spectrum1D. [#2576]
+
 Specviz2d
 ^^^^^^^^^
 

jdaviz/configs/specviz/plugins/parsers.py

@@ -4,6 +4,7 @@
 import numpy as np
 from astropy.io.registry import IORegistryError
 from astropy.nddata import StdDevUncertainty
+from astropy.io import fits
 from specutils import Spectrum1D, SpectrumList, SpectrumCollection
 
 from jdaviz.core.events import SnackbarMessage
@@ -39,7 +40,6 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
     # If no data label is assigned, give it a unique name
     if not data_label:
         data_label = app.return_data_label(data, alt_name="specviz_data")
-
     if isinstance(data, SpectrumCollection):
         raise TypeError("SpectrumCollection detected."
                         " Please provide a Spectrum1D or SpectrumList")
@@ -50,7 +50,13 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
     elif isinstance(data, SpectrumList):
         pass
     elif isinstance(data, list):
-        data = SpectrumList.read(data, format=format)
+        # special processing for HDUList
+        if isinstance(data, fits.HDUList):
+            data = [Spectrum1D.read(data)]
+            data_label = [app.return_data_label(data_label, alt_name="specviz_data")]
+        else:
+            # list treated as SpectrumList if not an HDUList
+            data = SpectrumList.read(data, format=format)
     else:
         path = pathlib.Path(data)
 
@@ -127,7 +133,6 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
 
     with app.data_collection.delay_link_manager_update():
         for i, spec in enumerate(data):
-
             # note: if SpectrumList, this is just going to be the last unit when
             # combined in the next block. should put a check here to make sure
             # units are all the same or collect them in a list?

jdaviz/configs/specviz/tests/test_helper.py

@@ -3,6 +3,7 @@
 import numpy as np
 import pytest
 from astropy import units as u
+from astropy.io import fits
 from astropy.tests.helper import assert_quantity_allclose
 from glue.core.roi import XRangeROI
 from glue.core.edit_subset_mode import OrMode, AndMode, AndNotMode
@@ -36,6 +37,26 @@ def test_load_spectrum1d(self):
 
         assert isinstance(data, Spectrum1D)
 
+    def test_load_hdulist(self):
+        # Create a fake fits file with a 1D spectrum for testing.
+        primary_header = fits.Header({'TELESCOP': 'Fake Telescope'})
+        primary_hdu = fits.PrimaryHDU(header=primary_header)
+
+        # Image extension HDU with a 1D spectrum
+        wavelength = np.linspace(5000, 6000, 100)
+        flux = np.ones(100)
+        spectrum_table = fits.BinTableHDU.from_columns([
+            fits.Column(name='WAVELENGTH', array=wavelength, format='E', unit="Angstrom"),
+            fits.Column(name='FLUX', array=flux, format='E', unit="Jy")
+        ])
+        spectrum_table.header['INSTRUME'] = 'Fake Instrument'
+        fake_hdulist = fits.HDUList([primary_hdu, spectrum_table])
+        self.label = "Test 1D Spectrum"
+        self.spec_app.load_data(fake_hdulist)
+        data = self.spec_app.get_data(data_label=self.label)
+        # HDUList should load as Spectrum1D
+        assert isinstance(data, Spectrum1D)
+
     def test_load_spectrum_list_no_labels(self):
         # now load three more spectra from a SpectrumList, without labels
         self.spec_app.load_data(self.spec_list)