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Fix unit handling in continuum and moment calculations #3216

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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
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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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