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Debug Cubeviz batch photometry (spacetelescope#3163)
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* Debugging Cubeviz batch photometry

* Fix changing units when in batch mode

* Working on adding cubeviz batch photometry test

* Add simple test

* Codestyle

* Add comment about future changes

* Move changelog to 3.10.4

* Don't convert if display unit hasn't been initialized

* Update test

* Codestyle

* Update jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>

---------

Co-authored-by: P. L. Lim <2090236+pllim@users.noreply.github.com>
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@rosteen @pllim @cshanahan1
2 people authored and cshanahan1 committed Sep 6, 2024
1 parent ae33f67 commit 6567880
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2 changes: 2 additions & 0 deletions CHANGES.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -233,6 +233,8 @@ Bug Fixes
Cubeviz
^^^^^^^

- Fixed multiple select handling for batch mode aperture photometry in Cubeviz. [#3163]

Imviz
^^^^^

Expand Down
64 changes: 39 additions & 25 deletions jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,8 @@ def valid_cubeviz_datasets(data):
acceptable_types = ['spectral flux density wav',
'photon flux density wav',
'spectral flux density',
'photon flux density']
'photon flux density',
'surface brightness']
return ((data.ndim in (2, 3)) and
((img_unit == (u.MJy / u.sr)) or
(img_unit.physical_type in acceptable_types)))
Expand Down Expand Up @@ -145,10 +146,19 @@ def _on_dataset_selected_changed(self, event={}):
if self.config != "cubeviz":
return
# self.dataset might not exist when app is setting itself up.
if hasattr(self, "dataset") and self.dataset.selected_dc_item.ndim > 2:
self.is_cube = True
else:
if hasattr(self, "dataset"):
if isinstance(self.dataset.selected_dc_item, list):
datasets = self.dataset.selected_dc_item
else:
datasets = [self.dataset.selected_dc_item]

self.is_cube = False
for dataset in datasets:
# This assumes all cubes, or no cubes. If we allow photometry on collapsed cubes
# or images this will need to change.
if dataset.ndim > 2:
self.is_cube = True
break

def _on_display_units_changed(self, event={}):

Expand Down Expand Up @@ -208,6 +218,8 @@ def _set_display_unit_of_selected_dataset(self):
return

data = self.dataset.selected_dc_item
if isinstance(data, list):
data = data[0]
comp = data.get_component(data.main_components[0])
if comp.units:
# if data is something-per-solid-angle, its a SB unit and we should
Expand Down Expand Up @@ -557,7 +569,7 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None,

# cubeviz: background_value set in plugin is in display units
# convert temporarily to image units for calculations
if (self.config == 'cubeviz') and (img_unit is not None):
if (self.config == 'cubeviz') and (img_unit is not None) and display_unit != '':
background_value = (background_value * display_unit).to_value(
img_unit, u.spectral_density(self._cube_wave))

Expand All @@ -568,7 +580,7 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None,

# cubeviz: background_value set in plugin is in display units
# convert temporarily to image units for calculations
if (self.config == 'cubeviz') and (img_unit is not None):
if (self.config == 'cubeviz') and (img_unit is not None) and display_unit != '':
background_value = (background_value * display_unit).to_value(
img_unit, u.spectral_density(self._cube_wave))
else:
Expand All @@ -578,7 +590,7 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None,

# cubeviz: computed background median will be in display units,
# convert temporarily back to image units for calculations
if (self.config == 'cubeviz') and (img_unit is not None):
if (self.config == 'cubeviz') and (img_unit is not None) and display_unit != '':
background_value = (background_value * display_unit).to_value(
img_unit, u.spectral_density(self._cube_wave))
try:
Expand Down Expand Up @@ -726,25 +738,26 @@ def calculate_photometry(self, dataset=None, aperture=None, background=None,
# convert units of certain columns in aperture phot. output table
# to reflect display units (i.e if data units are MJy / sr, but
# Jy / sr is selected in Unit Conversion plugin)
phot_table['background'] = phot_table['background'].to(
display_unit, u.spectral_density(self._cube_wave))

if include_pixarea_fac:
phot_table['sum'] = phot_table['sum'].to(
(display_unit * pixarea_fac).unit, u.spectral_density(self._cube_wave))
else:
phot_table['sum'] = phot_table['sum'].to(
if display_unit != '':
phot_table['background'] = phot_table['background'].to(
display_unit, u.spectral_density(self._cube_wave))
for key in ['min', 'max', 'mean', 'median', 'mode', 'std',
'mad_std', 'biweight_location']:
phot_table[key] = phot_table[key].to(
display_unit, u.spectral_density(self._cube_wave))
for key in ['var', 'biweight_midvariance']:
try:
phot_table[key] = phot_table[key].to(display_unit**2)
# FIXME: Can fail going between per-wave and per-freq
except u.UnitConversionError:
pass

if include_pixarea_fac:
phot_table['sum'] = phot_table['sum'].to(
(display_unit * pixarea_fac).unit, u.spectral_density(self._cube_wave))
else:
phot_table['sum'] = phot_table['sum'].to(
display_unit, u.spectral_density(self._cube_wave))
for key in ['min', 'max', 'mean', 'median', 'mode', 'std',
'mad_std', 'biweight_location']:
phot_table[key] = phot_table[key].to(
display_unit, u.spectral_density(self._cube_wave))
for key in ['var', 'biweight_midvariance']:
try:
phot_table[key] = phot_table[key].to(display_unit**2)
# FIXME: Can fail going between per-wave and per-freq
except u.UnitConversionError:
pass

if add_to_table:
try:
Expand Down Expand Up @@ -1060,6 +1073,7 @@ def calculate_batch_photometry(self, options=[], add_to_table=True, update_plots
option.setdefault('pixel_area', defaults.get('pixel_area', 0))
if self.flux_scaling_multi_auto:
option.setdefault('flux_scaling', defaults.get('flux_scaling', 0))

try:
self.calculate_photometry(add_to_table=add_to_table,
update_plots=this_update_plots,
Expand Down
30 changes: 30 additions & 0 deletions jdaviz/configs/imviz/tests/test_simple_aper_phot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -489,3 +489,33 @@ def test_curve_of_growth(with_unit):
with pytest.raises(TypeError, match='Unsupported aperture'):
_curve_of_growth(data, cen, EllipticalAnnulus(cen, 3, 8, 5), 100,
pixarea_fac=pixarea_fac)


def test_cubeviz_batch(cubeviz_helper, spectrum1d_cube_fluxunit_jy_per_steradian):
cubeviz_helper.load_data(spectrum1d_cube_fluxunit_jy_per_steradian, data_label='test')
phot_plugin = cubeviz_helper.plugins['Aperture Photometry']._obj
uc_plugin = cubeviz_helper.plugins['Unit Conversion']

cubeviz_helper.load_regions(CirclePixelRegion(center=PixCoord(x=5, y=5), radius=2))
cubeviz_helper.load_regions(CirclePixelRegion(center=PixCoord(x=3, y=3), radius=2))

phot_plugin.dataset_selected = 'test[FLUX]'
phot_plugin.multiselect = True
phot_plugin.aperture.selected = ['Subset 1', 'Subset 2']

phot_plugin.calculate_batch_photometry(full_exceptions=True)
assert len(phot_plugin.table) == 2
tbl = cubeviz_helper.get_aperture_photometry_results()
assert_quantity_allclose(tbl['sum'], [5.980836e-12, 2.037396e-10] * u.Jy, rtol=1e-4)

# Test that it still works after unit conversion
uc_plugin.flux_unit = 'MJy'

phot_plugin.calculate_batch_photometry(full_exceptions=True)

assert len(phot_plugin.table) == 4
tbl = cubeviz_helper.get_aperture_photometry_results()
# get_aperture_photometry_results converts all to the same units
assert_quantity_allclose(tbl['sum'],
[5.980836e-12, 2.037396e-10, 5.980836e-12, 2.037396e-10] * u.Jy,
rtol=1e-4)

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