BUG: Gaussian smooth plugin incompatible with unreleased upstream package

[pllim]

This started happening over the weekend in dev job, so must have been some recent unreleased upstream changes (probably glue-viz/glue-astronomy#36). We need to fix this incompatibility before it is too late.

Example log: https://github.com/spacetelescope/jdaviz/runs/3460019342?check_suite_focus=true

Package versions: 
Numpy: 1.22.0.dev0+949.ga90677a0b
Scipy: 1.7.1
Matplotlib: 3.4.3
h5py: 3.4.0
Pandas: 1.3.2
astropy: 5.0.dev702+g5942ac3a2
pyyaml: 5.4.1
scikit-image: 0.18.3
specutils: 1.3.1
spectral-cube: 0.5.1.dev215+gc3a9ece
asteval: 0.9.25
click: 8.0.1
echo: 0.5
idna: 2.10
traitlets: 5.0.5
bqplot: 0.12.30
bqplot-image-gl: 1.4.4
glue-core: 1.2.1
glue-jupyter: 0.8
glue-astronomy: 0.3.dev6+g03e439a
ipyvue: 1.5.0
ipyvuetify: 1.8.1
ipysplitpanes: 0.2.0
ipygoldenlayout: 0.4.0
voila: 0.2.10
vispy: 0.8.1
gwcs: 0.16.2a1.dev31+g0f3d750
asdf: 2.9.0.dev11+g9e64fbe

______________________ test_linking_after_spectral_smooth ______________________

spectral_cube_wcs = WCS Keywords

Number of WCS axes: 3
CTYPE : 'RA---TAN'  'DEC--TAN'  'FREQ'  
CRVAL : 0.0  0.0  0.0  
CRPIX : 0.0  0.0 ...0  0.0  
PC2_1 PC2_2 PC2_3  : 0.0  1.0  0.0  
PC3_1 PC3_2 PC3_3  : 0.0  0.0  1.0  
CDELT : 1.0  1.0  1.0  
NAXIS : 0  0

    def test_linking_after_spectral_smooth(spectral_cube_wcs):
    
        app = Application(configuration="cubeviz")
        dc = app.data_collection
        dc.append(Data(x=np.ones((3, 4, 5)), label='test', coords=spectral_cube_wcs))
    
        gs = GaussianSmooth(app=app)
    
        gs._on_data_selected({'new': 'test'})
        gs.stddev = '3.2'
>       gs.vue_spectral_smooth()

../../.tox/py38-test-devdeps/lib/python3.8/site-packages/jdaviz/configs/default/plugins/gaussian_smooth/tests/test_gaussian_smooth.py:20: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../.tox/py38-test-devdeps/lib/python3.8/site-packages/jdaviz/configs/default/plugins/gaussian_smooth/gaussian_smooth.py:64: in vue_spectral_smooth
    spec = self._selected_data.get_object(cls=Spectrum1D)
../../.tox/py38-test-devdeps/lib/python3.8/site-packages/glue/core/data.py:289: in get_object
    return handler.to_object(self, **kwargs)
../../.tox/py38-test-devdeps/lib/python3.8/site-packages/glue_astronomy/translators/spectrum1d.py:168: in to_object
    return Spectrum1D(**data_kwargs, **kwargs)
../../.tox/py38-test-devdeps/lib/python3.8/site-packages/specutils/spectra/spectrum1d.py:252: in __init__
    spec_axis = self.wcs.pixel_to_world(np.arange(self.flux.shape[-1]))
../../.tox/py38-test-devdeps/lib/python3.8/site-packages/astropy/wcs/wcsapi/high_level_api.py:239: in pixel_to_world
    world = self.low_level_wcs.pixel_to_world_values(*pixel_arrays)
../../.tox/py38-test-devdeps/lib/python3.8/site-packages/astropy/wcs/wcsapi/fitswcs.py:322: in pixel_to_world_values
    world = self.all_pix2world(*pixel_arrays, 0)
../../.tox/py38-test-devdeps/lib/python3.8/site-packages/astropy/wcs/wcs.py:1347: in all_pix2world
    return self._array_converter(
../../.tox/py38-test-devdeps/lib/python3.8/site-packages/astropy/wcs/wcs.py:1323: in _array_converter
    return _return_list_of_arrays([xy], origin)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

axes = [array([0, 1, 2])], origin = 0

    def _return_list_of_arrays(axes, origin):
        if any([x.size == 0 for x in axes]):
            return axes
    
        try:
            axes = np.broadcast_arrays(*axes)
        except ValueError:
            raise ValueError(
                "Coordinate arrays are not broadcastable to each other")
    
        xy = np.hstack([x.reshape((x.size, 1)) for x in axes])
    
        if ra_dec_order and sky == 'input':
            xy = self._denormalize_sky(xy)
>       output = func(xy, origin)
E       ValueError: Wrong number of dimensions in input array.  Expected 2.

../../.tox/py38-test-devdeps/lib/python3.8/site-packages/astropy/wcs/wcs.py:1291: ValueError
----------------------------- Captured stderr call -----------------------------
WARNING:specutils.spectra.spectrum1d:Input WCS indicates that the spectral axis is not last. Reshaping arrays to put spectral axis last.
------------------------------ Captured log call -------------------------------
WARNING  specutils.spectra.spectrum1d:spectrum1d.py:188 Input WCS indicates that the spectral axis is not last. Reshaping arrays to put spectral axis last.

[pllim]

Minimally reproducible code snippet as follows. Must have dev version of glue-astronomy installed:

import numpy as np
from astropy.wcs import WCS
from glue.config import data_translator
from glue.core import Data
from specutils import Spectrum1D

# This indirectly enables the necessary data translator
from jdaviz.configs.default.plugins.gaussian_smooth.gaussian_smooth import GaussianSmooth

wcs = WCS(naxis=3)
wcs.wcs.ctype = 'RA---TAN', 'DEC--TAN', 'FREQ'
wcs.wcs.set()
data = Data(x=np.ones((3, 4, 5)), label='test', coords=wcs)
handler, _ = data_translator.get_handler_for(Spectrum1D)
spec = data.get_object(cls=Spectrum1D)  # See traceback

.../glue/core/data.py in get_object(self, cls, **kwargs)
    287         handler, _ = data_translator.get_handler_for(cls)
    288
--> 289         return handler.to_object(self, **kwargs)
    290
    291     @property

.../glue_astronomy/translators/spectrum1d.py in to_object(self, data_or_subset, attribute, statistic)
    168         return Spectrum1D(**data_kwargs, **kwargs)

.../specutils/spectra/spectrum1d.py in __init__(self, flux, spectral_axis, wcs, velocity_convention, rest_value, redshift, radial_velocity, bin_specification, **kwargs)
    250             # If spectral_axis wasn't provided, set _spectral_axis based on
    251             # the WCS
--> 252             spec_axis = self.wcs.pixel_to_world(np.arange(self.flux.shape[-1]))
    253
    254             if spec_axis.unit.is_equivalent(u.one):

.../astropy/wcs/wcsapi/high_level_api.py in pixel_to_world(self, *pixel_arrays)
    237
    238         # Compute the world coordinate values
--> 239         world = self.low_level_wcs.pixel_to_world_values(*pixel_arrays)
    240
    241         if self.world_n_dim == 1:

.../astropy/wcs/wcsapi/fitswcs.py in pixel_to_world_values(self, *pixel_arrays)
    320
    321     def pixel_to_world_values(self, *pixel_arrays):
--> 322         world = self.all_pix2world(*pixel_arrays, 0)
    323         return world[0] if self.world_n_dim == 1 else tuple(world)
    324

..../astropy/wcs/wcs.py in all_pix2world(self, *args, **kwargs)
   1345
   1346     def all_pix2world(self, *args, **kwargs):
-> 1347         return self._array_converter(
   1348             self._all_pix2world, 'output', *args, **kwargs)
   1349     all_pix2world.__doc__ = """

.../astropy/wcs/wcs.py in _array_converter(self, func, sky, ra_dec_order, *args)
   1321                     "(coords[N][{}], origin)".format(self.naxis))
   1322             if xy.shape == () or len(xy.shape) == 1:
-> 1323                 return _return_list_of_arrays([xy], origin)
   1324             return _return_single_array(xy, origin)
   1325

.../astropy/wcs/wcs.py in _return_list_of_arrays(axes, origin)
   1289             if ra_dec_order and sky == 'input':
   1290                 xy = self._denormalize_sky(xy)
-> 1291             output = func(xy, origin)
   1292             if ra_dec_order and sky == 'output':
   1293                 output = self._normalize_sky(output)

ValueError: Wrong number of dimensions in input array.  Expected 2.

which narrows down to:

from astropy import units as u

flux = np.ones((3, 4, 5)) * u.dimensionless_unscaled
spec = Spectrum1D(flux=flux, mask=None, wcs=wcs)  # traceback

which narrows down to:

wcs.pixel_to_world([0, 1, 2, 3, 4])  # traceback

[pllim]

I traced this error to statistic set to None instead of 'mean'. See glue-viz/glue-astronomy#40

[astrofrog]

I think the change of default of None in glue-astronomy actually makes sense, however the exception we are running into here is a bug in specutils: astropy/specutils#857 - so for now I think reverting the default in glue-astronomy makes sense.

[pllim]

Thanks! I opened glue-viz/glue-astronomy#43 upstream as a follow-up. I don't think there is anything Jdaviz can do in this matter.