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Fix unit handling in continuum and moment calculations #3216

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Oct 16, 2024
Merged

Fix unit handling in continuum and moment calculations #3216

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ff6c58f
Fix unit handling in continuum and moment calculations
rosteen Oct 8, 2024
5270ce4
Add test that fails on main
rosteen Oct 8, 2024
7911b26
Bump specutils pin
rosteen Oct 16, 2024
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2 changes: 1 addition & 1 deletion CHANGES.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ New Features

- Added flux/surface brightness translation and surface brightness
unit conversion in Cubeviz and Specviz. [#2781, #2940, #3088, #3111, #3113, #3129,
#3139, #3149, #3155, #3178, #3185, #3187, #3190, #3156, #3200, #3192, #3206, #3211]
#3139, #3149, #3155, #3178, #3185, #3187, #3190, #3156, #3200, #3192, #3206, #3211, #3216]

- Plugin tray is now open by default. [#2892]

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15 changes: 13 additions & 2 deletions jdaviz/configs/cubeviz/plugins/moment_maps/moment_maps.py
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Expand Up @@ -271,7 +271,13 @@ def calculate_moment(self, add_data=True):

# slice out desired region
# TODO: should we add a warning for a composite spectral subset?
spec_reg = self.spectral_subset.selected_obj
if self.spectral_subset.selected == "Entire Spectrum":
spec_reg = None
else:
spec_reg = self.app.get_subsets(self.spectral_subset.selected,
simplify_spectral=True,
use_display_units=True)
# We need to convert the spectral region to the display units

if spec_reg is None:
slab = cube
Expand Down Expand Up @@ -303,7 +309,12 @@ def calculate_moment(self, add_data=True):
ref_wavelength = self.reference_wavelength * u.Unit(self.dataset_spectral_unit)
slab_sa = slab.spectral_axis.to("km/s", doppler_convention="relativistic",
doppler_rest=ref_wavelength)
slab = Spectrum1D(slab.flux, slab_sa)
slab = Spectrum1D(slab.flux, slab_sa, uncertainty=slab.uncertainty)
# Otherwise convert spectral axis to display units, have to do frequency <-> wavelength
# before calculating
else:
slab_sa = slab.spectral_axis.to(self.app._get_display_unit('spectral'))
slab = Spectrum1D(slab.flux, slab_sa, uncertainty=slab.uncertainty)

# Finally actually calculate the moment
self.moment = analysis.moment(slab, order=n_moment).T
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4 changes: 4 additions & 0 deletions jdaviz/configs/cubeviz/plugins/moment_maps/tests/test_moment_maps.py
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Expand Up @@ -7,6 +7,7 @@
from astropy import units as u
from astropy.io import fits
from astropy.nddata import CCDData
from astropy.tests.helper import assert_quantity_allclose
from astropy.wcs import WCS
from numpy.testing import assert_allclose
from specutils import SpectralRegion
Expand Down Expand Up @@ -244,9 +245,12 @@ def test_moment_frequency_unit_conversion(cubeviz_helper, spectrum1d_cube_larger
mm.n_moment = 1
mm.output_unit = 'Spectral Unit'
moment_1_data = mm.calculate_moment()
mm.n_moment = 0
moment_0_data = mm.calculate_moment()

# Check to make sure there are no nans
assert len(np.where(moment_1_data.data > 0)[0]) == 8
assert_quantity_allclose(moment_0_data, -2.9607526e+09*u.Unit("Hz Jy / pix2"))


def test_write_momentmap(cubeviz_helper, spectrum1d_cube, tmp_path):
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6 changes: 4 additions & 2 deletions jdaviz/core/template_mixin.py
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Expand Up @@ -2970,7 +2970,8 @@ def _get_continuum(self, dataset, spectral_subset, update_marks=False, per_pixel
if per_pixel:
if self.app.config != 'cubeviz':
raise ValueError("per-pixel only supported for cubeviz")
full_spectrum = self.app._jdaviz_helper.get_data(self.dataset.selected)
full_spectrum = self.app._jdaviz_helper.get_data(self.dataset.selected,
use_display_units=True)
Comment on lines -2973 to +2974
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I feel like @cshanahan1 had just removed this. Was there a reason for that or did it just not seem to affect that use-case (see https://github.com/spacetelescope/jdaviz/pull/3211/files#r1787615549)

else:
full_spectrum = dataset.get_selected_spectrum(use_display_units=True)

Expand All @@ -2994,7 +2995,8 @@ def _get_continuum(self, dataset, spectral_subset, update_marks=False, per_pixel
spectrum = full_spectrum
else:
sr = self.app.get_subsets(spectral_subset.selected,
simplify_spectral=True)
simplify_spectral=True,
use_display_units=True)
spectrum = extract_region(full_spectrum, sr, return_single_spectrum=True)
sr_lower = np.nanmin(spectrum.spectral_axis[spectrum.spectral_axis >= sr.lower]) # noqa
sr_upper = np.nanmax(spectrum.spectral_axis[spectrum.spectral_axis <= sr.upper]) # noqa
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