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get_data(use_display_units=True) to respect flux or sb selection #3129

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Aug 5, 2024
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get_data(use_display_units=True) to respect flux or sb selection #3129

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3b77edb
get_data(use_display_units) to respect flux or sb selection
kecnry Aug 2, 2024
cd60491
add to existing changelog entry
kecnry Aug 2, 2024
8a129d0
test coverage
kecnry Aug 2, 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 @@ -5,7 +5,7 @@ New Features
------------

- Added flux/surface brightness translation and surface brightness
unit conversion in Cubeviz and Specviz. [#2781, #2940, #3088, #3111, #3113]
unit conversion in Cubeviz and Specviz. [#2781, #2940, #3088, #3111, #3113, #3129]

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

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10 changes: 9 additions & 1 deletion jdaviz/configs/specviz/plugins/unit_conversion/tests/test_unit_conversion.py
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Expand Up @@ -137,7 +137,7 @@ def test_unit_translation(cubeviz_helper):
w = WCS(wcs_dict)
flux = np.zeros((30, 20, 3001), dtype=np.float32)
flux[5:15, 1:11, :] = 1
cube = Spectrum1D(flux=flux * u.MJy, wcs=w, meta=wcs_dict)
cube = Spectrum1D(flux=flux * u.MJy / u.sr, wcs=w, meta=wcs_dict)
cubeviz_helper.load_data(cube, data_label="test")

center = PixCoord(5, 10)
Expand All @@ -152,6 +152,10 @@ def test_unit_translation(cubeviz_helper):
# data collection item units will be used for translations.
assert uc_plg._obj.flux_or_sb_selected == 'Flux'

# accessing from get_data(use_display_units=True) should return flux-like units
assert cubeviz_helper.app._get_display_unit('spectral_y') == u.MJy
assert cubeviz_helper.get_data('Spectrum (sum)', use_display_units=True).unit == u.MJy

# to have access to display units
viewer_1d = cubeviz_helper.app.get_viewer(
cubeviz_helper._default_spectrum_viewer_reference_name)
Expand All @@ -165,6 +169,10 @@ def test_unit_translation(cubeviz_helper):
# check if units translated
assert y_display_unit == u.MJy / u.sr

# get_data(use_display_units=True) should return surface brightness-like units
assert cubeviz_helper.app._get_display_unit('spectral_y') == u.MJy / u.sr
assert cubeviz_helper.get_data('Spectrum (sum)', use_display_units=True).unit == u.MJy / u.sr


def test_sb_unit_conversion(cubeviz_helper):
# custom cube to have Surface Brightness units
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16 changes: 8 additions & 8 deletions jdaviz/core/helpers.py
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Expand Up @@ -470,7 +470,7 @@ def _handle_display_units(self, data, use_display_units=True):
spectral_unit = self.app._get_display_unit('spectral')
if not spectral_unit:
return data
flux_unit = self.app._get_display_unit('flux')
y_unit = self.app._get_display_unit('spectral_y')
# TODO: any other attributes (meta, wcs, etc)?
# TODO: implement uncertainty.to upstream
uncertainty = data.uncertainty
Expand All @@ -488,26 +488,26 @@ def _handle_display_units(self, data, use_display_units=True):
new_uncert = uncertainty
if ('_pixel_scale_factor' in data.meta):
new_uncert_converted = flux_conversion(data, new_uncert.quantity.value,
new_uncert.unit, flux_unit)
new_uncert = StdDevUncertainty(new_uncert_converted, unit=flux_unit)
new_uncert.unit, y_unit)
new_uncert = StdDevUncertainty(new_uncert_converted, unit=y_unit)
else:
new_uncert = StdDevUncertainty(new_uncert, unit=data.flux.unit)

else:
new_uncert = None
if ('_pixel_scale_factor' in data.meta):
new_flux = flux_conversion(data, data.flux.value, data.flux.unit,
flux_unit) * u.Unit(flux_unit)
new_y = flux_conversion(data, data.flux.value, data.flux.unit,
y_unit) * u.Unit(y_unit)
else:
new_flux = flux_conversion(data, data.flux.value, data.flux.unit,
data.flux.unit) * u.Unit(data.flux.unit)
new_y = flux_conversion(data, data.flux.value, data.flux.unit,
data.flux.unit) * u.Unit(data.flux.unit)
new_spec = (spectral_axis_conversion(data.spectral_axis.value,
data.spectral_axis.unit,
spectral_unit)
* u.Unit(spectral_unit))

data = Spectrum1D(spectral_axis=new_spec,
flux=new_flux,
flux=new_y,
uncertainty=new_uncert,
mask=data.mask)
else: # pragma: nocover
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11 changes: 0 additions & 11 deletions jdaviz/core/template_mixin.py
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Expand Up @@ -2955,17 +2955,6 @@ def _get_continuum(self, dataset, spectral_subset, update_marks=False, per_pixel
raise ValueError("per-pixel only supported for cubeviz")
full_spectrum = self.app._jdaviz_helper.get_data(self.dataset.selected,
use_display_units=True)
# TODO: Something like the following code may be needed to get continuum
# with display units working
# temp_spec = self.app._jdaviz_helper.get_data(self.dataset.selected,
# use_display_units=True)
# flux_values = np.sum(np.ones_like(temp_spec.flux.value), axis=(0, 1))
# pix_scale = self.dataset.selected_dc_item.meta.get('PIXAR_SR', 1.0)
# pix_scale_factor = (flux_values * pix_scale)
# temp_spec.meta['_pixel_scale_factor'] = pix_scale_factor
# full_spectrum = self._specviz_helper._handle_display_units(temp_spec,
# use_display_units=True)

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

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