TST: Fix failing tests in devdeps job

[pllim]

As seen in #1873. Need to investigate failures of Specviz2d tests that use https://stsci.box.com/shared/static/exnkul627fcuhy5akf2gswytud5tazmw.fits . Maybe the file is too old and we need to use a real JWST 2D spectrum from MAST.

[pllim]

I can reproduce the error when I install specreduce 1.2.1.dev36+g05a174d (as opposed to released version). There is no error from specreduce but it also does not show the collapsed spectrum.

[pllim]

Actually there is an extraction error but it was sent to snackbar, so automated test suite didn't catch it.

File .../jdaviz/configs/specviz2d/helper.py:195, in Specviz2d.load_data(self, spectrum_2d, spectrum_1d, spectrum_1d_label, spectrum_2d_label, show_in_viewer, ext, transpose)
    193 spext._trace_dataset_selected()
    194 try:
--> 195     spext.export_extract_spectrum(add_data=True)
    196 except Exception:
    197     raise

File .../jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py:892, in SpectralExtraction.export_extract_spectrum(self, add_data, **kwargs)
    882 def export_extract_spectrum(self, add_data=False, **kwargs):
    883     """
    884     Create an extracted 1D spectrum from the input parameters defined in the plugin.
    885 
   (...)
    890         defined in the plugin.
    891     """
--> 892     extract = self.export_extract(**kwargs)
    893     spectrum = extract.spectrum
    895     # Specreduce returns a spectral axis in pixels, so we'll replace with input spectral_axis
    896     # NOTE: this is currently disabled until proper handling of axes-limit linking between
    897     # the 2D spectrum image (plotted in pixels) and a 1D spectrum (plotted in freq or
    898     # wavelength) is implemented.
    899 
    900     # spectrum = Spectrum1D(spectral_axis=inp_sp2d.spectral_axis, flux=spectrum.flux)

File .../jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py:866, in SpectralExtraction.export_extract(self, **kwargs)
    863 if len(kwargs) and self.active_step != 'ext':
    864     self.update_marks(step='ext')
--> 866 trace = self._get_ext_trace()
    867 inp_sp2d = self._get_ext_input_spectrum()
    869 if self.ext_type_selected == 'Boxcar':

File .../jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py:831, in SpectralExtraction._get_ext_trace(self)
    829 def _get_ext_trace(self):
    830     if self.ext_trace_selected == 'From Plugin':
--> 831         return self.export_trace(add_data=False)
    832     else:
    833         return self.ext_trace.selected_obj

File .../jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py:654, in SpectralExtraction.export_trace(self, add_data, **kwargs)
    650         trace = tracing.ArrayTrace(self.trace_dataset.selected_obj.data,
    651                                    self.trace_trace.selected_obj.trace+self.trace_offset)
    653 elif self.trace_type_selected == 'Flat':
--> 654     trace = tracing.FlatTrace(self.trace_dataset.selected_obj.data,
    655                               self.trace_pixel)
    657 elif self.trace_type_selected == 'Auto':
    658     trace = tracing.KosmosTrace(self.trace_dataset.selected_obj.data,
    659                                 guess=self.trace_pixel,
    660                                 bins=int(self.trace_bins),
    661                                 window=self.trace_window,
    662                                 peak_method=self.trace_peak_method_selected.lower())

File <string>:5, in __init__(self, image, trace_pos)

File .../specreduce/tracing.py:100, in FlatTrace.__post_init__(self)
     99 def __post_init__(self):
--> 100     self.image = self._parse_image(self.image)
    102     self.set_position(self.trace_pos)

File .../specreduce/core.py:78, in _ImageParser._parse_image(self, image, disp_axis)
     73 unit = getattr(image, 'unit', u.Unit('DN'))
     75 spectral_axis = getattr(image, 'spectral_axis',
     76                         np.arange(img.shape[disp_axis]) * u.pix)
---> 78 return Spectrum1D(img * unit, spectral_axis=spectral_axis,
     79                   uncertainty=uncertainty, mask=mask)

File .../specutils/spectra/spectrum1d.py:268, in Spectrum1D.__init__(self, flux, spectral_axis, wcs, velocity_convention, rest_value, redshift, radial_velocity, bin_specification, **kwargs)
    265     size = flux.shape[-1] if not flux.isscalar else 1
    266     wcs = gwcs_from_array(np.arange(size) * u.Unit(""))
--> 268 super().__init__(
    269     data=flux.value if isinstance(flux, u.Quantity) else flux,
    270     wcs=wcs, **kwargs)
    272 # If no spectral_axis was provided, create a SpectralCoord based on
    273 # the WCS
    274 if spectral_axis is None:
    275     # If the WCS doesn't have a spectral attribute, we assume it's the
    276     # dummy GWCS we created or a solely spectral WCS

File .../ndcube/ndcube.py:208, in NDCubeBase.__init__(self, data, wcs, uncertainty, mask, meta, unit, copy, **kwargs)
    205 def __init__(self, data, wcs=None, uncertainty=None, mask=None, meta=None,
    206              unit=None, copy=False, **kwargs):
--> 208     super().__init__(data, uncertainty=uncertainty, mask=mask,
    209                      meta=meta, unit=unit, copy=copy, **kwargs)
    210     if not self.wcs:
    211         self.wcs = wcs  # This line is required as a patch for an astropy bug.

File .../astropy/nddata/nddata.py:251, in NDData.__init__(self, data, uncertainty, mask, wcs, meta, unit, copy, psf)
    249 # Store the attributes
    250 self._data = data
--> 251 self.mask = mask
    252 self._wcs = None
    253 if wcs is not None:
    254     # Validate the wcs

File .../specutils/spectra/spectrum1d.py:538, in Spectrum1D.mask(self, value)
    536     value = np.array(value)
    537     if not self.data.shape == value.shape:
--> 538         raise ValueError(
    539             "Flux axis ({}) and mask ({}) shapes must be the "
    540             "same.".format(self.data.shape, value.shape))
    541 self._mask = value

ValueError: Flux axis ((44, 387)) and mask (()) shapes must be the same.

[pllim]

I submitted astropy/specreduce#151 for the upstream portion.

After speaking with @kecnry , the rest of the errors in jdaviz is not worth fixing right now and should wait for these:

• spectral extraction: updates for Spectrum1D support in specreduce #1847
• spectral extraction: update with new model types #1695

Since specreduce dev is going through a lot of API changes right now, we should not test against it. Instead, I have advised specreduce dev to test locally against jdaviz (with --remote-data) during development and definitely before release.

FWIW, this will let you see the error:

--- a/jdaviz/configs/specviz2d/helper.py
+++ b/jdaviz/configs/specviz2d/helper.py
@@ -194,6 +194,7 @@ class Specviz2d(ConfigHelper, LineListMixin):
                 try:
                     spext.export_extract_spectrum(add_data=True)
                 except Exception:
+                    raise

And this fixed 3 of the 4 errors (together with the upstream patch mentioned above):

--- a/jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py
+++ b/jdaviz/configs/specviz2d/plugins/spectral_extraction/spectral_extraction.py
@@ -814,9 +814,12 @@ class SpectralExtraction(PluginTemplateMixin):
             defined in the plugin.
         """
         bg = self.export_bg(**kwargs)
-
-        bg_sub_spec = Spectrum1D(spectral_axis=self.bg_dataset.selected_obj.spectral_axis,
-                                 flux=bg.sub_image()*self.bg_dataset.selected_obj.flux.unit)
+        bg_sub_img = bg.sub_image()
+        if isinstance(bg_sub_img, Spectrum1D):
+            bg_sub_spec = bg_sub_img
+        else:
+            bg_sub_spec = Spectrum1D(spectral_axis=self.bg_dataset.selected_obj.spectral_axis,
+                                     flux=bg_sub_img*self.bg_dataset.selected_obj.flux.unit)