expanded support of SB/Flux translations (#2940)

* UI functioning unit conversion, need to reconcile tests

* update syntax, remove unnecessary logic

* tests now pass, API functionality improved

* add additional equivalencies for coords info

* first pass at disabling specviz translations

* Remove dev flag, consolidate untranslatable units, multi-config support, styling changes

* Refactor moment map unit conversion
to not require spectrum, so nothing to centralize now.

Fix devdeps

Simplify flux_conversion logic
and other minor fixes. Add flux conversion tests.

Clarify which one should be reverted
in the future

* Remove SB/flux conversion for moment map
because moment map always in SB

* add os import

* remove duplicate import from rebase

* reconcile tests, change hints/docs, handle dimensionless case

* emit GlobalDisplayUnitChanged msg when toggling SB<>flux

* resolve most tests

* temporarily remove translation message

* add comments, reenable global display message, resolve tests

* force sb unit for line flux test

* add comments, clarify naming, add case handling for args

* remove args and loop, replaced with msg

* consolidate 2 translator functions into 1, consolidate _translate and _on_flux_unit_changed

* address test failures

* update marks.py equivalencies, resolving UnitConversion errors

* make sure not only translation equivalencies are in marks.py but also conversions

* add test coverage

* use astropy units, small logic tweaks, cache untranslatable units

* technical review changes

* add warning message in tray if PIXAR_SR not present in FITS header

* second pass at technical changes

* move flux_unit checks to beginning of _on_flux_unit_changed

* change _unit to flux.unit

---------

Co-authored-by: P. L. Lim <[email protected]>
Co-authored-by: Kyle Conroy <[email protected]>

CHANGES.rst

@@ -5,7 +5,7 @@ New Features
 ------------
 
 - Added flux/surface brightness translation and surface brightness
-  unit conversion in Cubeviz and Specviz. [#2781, #3088]
+  unit conversion in Cubeviz and Specviz. [#2781, #2940, #3088]
 
 - Plugin tray is now open by default. [#2892]
 

jdaviz/app.py

@@ -76,20 +76,17 @@ def equivalent_units(self, data, cid, units):
                     'Jy', 'mJy', 'uJy', 'MJy',
                     'W / (m2 Hz)', 'W / (Hz m2)',  # Order is different in astropy v5.3
                     'eV / (s m2 Hz)', 'eV / (Hz s m2)',
-                    'erg / (s cm2)',
                     'erg / (s cm2 Angstrom)', 'erg / (s cm2 Angstrom)',
                     'erg / (s cm2 Hz)', 'erg / (Hz s cm2)',
-                    'ph / (s cm2 Angstrom)', 'ph / (s cm2 Angstrom)',
+                    'ph / (Angstrom s cm2)',
                     'ph / (Hz s cm2)', 'ph / (Hz s cm2)', 'bol', 'AB', 'ST'
                 ]
                 + [
                     'Jy / sr', 'mJy / sr', 'uJy / sr', 'MJy / sr',
                     'W / (Hz sr m2)',
-                    'eV / (s m2 Hz sr)',
-                    'erg / (s cm2 sr)',
-                    'erg / (s cm2 Angstrom sr)', 'erg / (s cm2 Hz sr)',
-                    'ph / (s cm2 Angstrom sr)', 'ph / (s cm2 Hz sr)',
-                    'bol / sr', 'AB / sr', 'ST / sr'
+                    'eV / (Hz s sr m2)',
+                    'erg / (s sr cm2)',
+                    'AB / sr'
                 ])
         else:  # spectral axis
             # prefer Hz over Bq and um over micron

jdaviz/configs/cubeviz/plugins/moment_maps/moment_maps.py

@@ -22,8 +22,6 @@
                                         with_spinner)
 from jdaviz.core.validunits import check_if_unit_is_per_solid_angle
 from jdaviz.core.user_api import PluginUserApi
-from jdaviz.utils import flux_conversion
-
 
 __all__ = ['MomentMap']
 
@@ -358,18 +356,7 @@ def calculate_moment(self, add_data=True):
                 moment_new_unit = flux_or_sb_display_unit
             else:
                 moment_new_unit = flux_or_sb_display_unit * self.spectrum_viewer.state.x_display_unit  # noqa: E501
-
-            # Create a temporary Spectrum1D object with ability to convert from surface brightness
-            # to flux
-            temp_spec = Spectrum1D(flux=self.moment)
-            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
-            converted_spec = flux_conversion(temp_spec, self.moment.value,
-                                             self.moment.unit,
-                                             moment_new_unit) * moment_new_unit
-            self.moment = converted_spec
+            self.moment = self.moment.to(moment_new_unit)
 
         # Reattach the WCS so we can load the result
         self.moment = CCDData(self.moment, wcs=data_wcs)

jdaviz/configs/cubeviz/plugins/moment_maps/tests/test_moment_maps.py

@@ -334,7 +334,7 @@ def test_correct_output_flux_or_sb_units(cubeviz_helper, spectrum1d_cube_custom_
 
     # now change surface brightness units in the unit conversion plugin
 
-    uc.flux_or_sb_unit = 'Jy / sr'
+    uc.sb_unit = 'Jy / sr'
 
     # and make sure this change is propogated
     output_unit_moment_0 = mm.output_unit_items[0]
@@ -344,21 +344,3 @@ def test_correct_output_flux_or_sb_units(cubeviz_helper, spectrum1d_cube_custom_
     # and that calculated moment has the correct units
     mm.calculate_moment()
     assert mm.moment.unit == moment_unit
-
-    uc.flux_or_sb.selected = 'Flux'
-    mm._set_data_units()
-
-    # and make sure this change is propogated
-    output_unit_moment_0 = mm.output_unit_items[0]
-    assert output_unit_moment_0['label'] == 'Flux'
-    assert output_unit_moment_0['unit_str'] == 'Jy'
-
-    # TODO: Failing because of dev version of upstream dependency, figure
-    #  out which one
-    # assert mm.calculate_moment()
-
-    # TODO: This test should pass once continuum subtraction works with
-    #  flux to surface brightness conversion
-    # mm.continuum.selected = 'Surrounding'
-    #
-    # assert mm.calculate_moment()

jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py

@@ -516,6 +516,15 @@ def extract(self, return_bg=False, add_data=True, **kwargs):
         pix_scale_factor = self.aperture_area_along_spectral * self.spectral_cube.meta.get('PIXAR_SR', 1.0)  # noqa
         spec.meta['_pixel_scale_factor'] = pix_scale_factor
 
+        # inform the user if scale factor keyword not in metadata
+        if 'PIXAR_SR' not in self.spectral_cube.meta:
+            snackbar_message = SnackbarMessage(
+                ("PIXAR_SR FITS header keyword not found when parsing spectral cube. "
+                 "Flux/Surface Brightness will use default PIXAR_SR value of 1 sr/pix^2."),
+                color="warning",
+                sender=self)
+            self.hub.broadcast(snackbar_message)
+
         # stuff for exporting to file
         self.extracted_spec = spec
         self.extracted_spec_available = True

jdaviz/configs/imviz/plugins/coords_info/coords_info.py

@@ -17,6 +17,7 @@
 from jdaviz.core.marks import PluginScatter, PluginLine
 from jdaviz.core.registries import tool_registry
 from jdaviz.core.template_mixin import TemplateMixin, DatasetSelectMixin
+from jdaviz.utils import _eqv_pixar_sr
 
 __all__ = ['CoordsInfo']
 
@@ -561,10 +562,7 @@ def _copy_axes_to_spectral():
                 # temporarily here, may be removed after upstream units handling
                 # or will be generalized for any sb <-> flux
                 if '_pixel_scale_factor' in sp.meta:
-                    eqv = [(u.MJy / u.sr,
-                            u.MJy,
-                            lambda x: (x * sp.meta['_pixel_scale_factor']),
-                            lambda x: x)]
+                    eqv = u.spectral_density(sp.spectral_axis) + _eqv_pixar_sr(sp.meta['_pixel_scale_factor'])  # noqa
                     disp_flux = sp.flux.to_value(viewer.state.y_display_unit, eqv)
                 else:
                     disp_flux = sp.flux.to_value(viewer.state.y_display_unit,

jdaviz/configs/specviz/plugins/line_analysis/line_analysis.py

@@ -288,6 +288,11 @@ def _uncertainty(result):
             # don't need these if statements
             if function == "Line Flux":
                 flux_unit = spec_subtracted.flux.unit
+                if flux_unit == u.dimensionless_unscaled:
+                    add_flux = True
+                    flux_unit = u.Unit(self.spectrum_viewer.state.y_display_unit)
+                else:
+                    add_flux = False
                 # If the flux unit is equivalent to Jy, or Jy per spaxel for Cubeviz,
                 # enforce integration in frequency space
                 if (flux_unit.is_equivalent(u.Jy) or
@@ -300,7 +305,10 @@ def _uncertainty(result):
                         uncertainty=spec_subtracted.uncertainty)
 
                     try:
-                        raw_result = analysis.line_flux(freq_spec)
+                        if add_flux:
+                            raw_result = analysis.line_flux(freq_spec) * flux_unit
+                        else:
+                            raw_result = analysis.line_flux(freq_spec)
                     except ValueError as e:
                         # can happen if interpolation out-of-bounds or any error from specutils
                         # let's avoid the whole app crashing and instead expose the error to the
@@ -332,7 +340,10 @@ def _uncertainty(result):
                         flux=spec_subtracted.flux,
                         uncertainty=spec_subtracted.uncertainty)
                     try:
-                        raw_result = analysis.line_flux(wave_spec)
+                        if add_flux:
+                            raw_result = analysis.line_flux(wave_spec) * flux_unit
+                        else:
+                            raw_result = raw_result = analysis.line_flux(wave_spec)
                     except ValueError as e:
                         # can happen if interpolation out-of-bounds or any error from specutils
                         # let's avoid the whole app crashing and instead expose the error to the

jdaviz/configs/specviz/plugins/unit_conversion/tests/test_unit_conversion.py

@@ -89,14 +89,28 @@ def test_conv_wave_flux(specviz_helper, spectrum1d, uncert):
     assert u.Unit(viewer.state.y_display_unit) == u.Unit(new_flux)
 
 
-def test_conv_no_data(specviz_helper):
+def test_conv_no_data(specviz_helper, spectrum1d):
     """plugin unit selections won't have valid choices yet, preventing
     attempting to set display units."""
     plg = specviz_helper.plugins["Unit Conversion"]
+    # spectrum not load is in Flux units, sb_unit and flux_unit
+    # should be enabled, flux_or_sb should not be
+    assert hasattr(plg, 'sb_unit')
+    assert hasattr(plg, 'flux_unit')
+    assert not hasattr(plg, 'flux_or_sb')
     with pytest.raises(ValueError, match="no valid unit choices"):
         plg.spectral_unit = "micron"
     assert len(specviz_helper.app.data_collection) == 0
 
+    specviz_helper.load_data(spectrum1d, data_label="Test 1D Spectrum")
+    plg = specviz_helper.plugins["Unit Conversion"]
+
+    # spectrum loaded in Flux units, make sure sb_units don't
+    # display in the API and exposed translation isn't possible
+    assert hasattr(plg, 'flux_unit')
+    assert not hasattr(plg, 'sb_unit')
+    assert not hasattr(plg, 'flux_or_sb')
+
 
 @pytest.mark.skipif(ASTROPY_LT_5_3, reason='this feature relies on astropy v5.3+')
 def test_non_stddev_uncertainty(specviz_helper):
@@ -140,40 +154,21 @@ def test_unit_translation(cubeviz_helper):
     cubeviz_helper.load_regions(CirclePixelRegion(center, radius=2.5))
 
     uc_plg = cubeviz_helper.plugins['Unit Conversion']
-    # we can get rid of this after all spectra pass through
-    # spectral extraction plugin
-    extract_plg = cubeviz_helper.plugins['Spectral Extraction']
-
-    extract_plg.aperture = extract_plg.aperture.choices[-1]
-    extract_plg.aperture_method.selected = 'Exact'
-    extract_plg.wavelength_dependent = True
-    extract_plg.function = 'Sum'
-    # set so pixel scale factor != 1
-    extract_plg.reference_spectral_value = 0.000001
-
-    # all spectra will pass through spectral extraction,
-    # this will store a scale factor for use in translations.
-    collapsed_spec = extract_plg.extract()
 
     # test that the scale factor was set
-    assert np.all(collapsed_spec.meta['_pixel_scale_factor'] != 1)
+    assert np.all(cubeviz_helper.app.data_collection['Spectrum (sum)'].meta['_pixel_scale_factor'] != 1)  # noqa
 
     # When the dropdown is displayed, this ensures the loaded
     # data collection item units will be used for translations.
-    uc_plg._obj.show_translator = True
     assert uc_plg._obj.flux_or_sb_selected == 'Flux'
 
     # to have access to display units
     viewer_1d = cubeviz_helper.app.get_viewer(
         cubeviz_helper._default_spectrum_viewer_reference_name)
 
-    #  for testing _set_flux_or_sb()
-    uc_plg._obj.show_translator = False
-
     # change global y-units from Flux -> Surface Brightness
     uc_plg._obj.flux_or_sb_selected = 'Surface Brightness'
 
-    uc_plg._obj.show_translator = True
     assert uc_plg._obj.flux_or_sb_selected == 'Surface Brightness'
     y_display_unit = u.Unit(viewer_1d.state.y_display_unit)
 
@@ -196,42 +191,35 @@ def test_sb_unit_conversion(cubeviz_helper):
     uc_plg = cubeviz_helper.plugins['Unit Conversion']
     uc_plg.open_in_tray()
 
+    # ensure that per solid angle cube defaults to Flux spectrum
+    assert uc_plg.flux_or_sb == 'Flux'
+    # flux choices is populated with flux units
+    assert uc_plg.flux_unit.choices
+
     # to have access to display units
     viewer_1d = cubeviz_helper.app.get_viewer(
         cubeviz_helper._default_spectrum_viewer_reference_name)
 
-    uc_plg._obj.show_translator = True
     uc_plg.flux_or_sb.selected = 'Surface Brightness'
 
     # Surface Brightness conversion
-    uc_plg.flux_or_sb_unit = 'Jy / sr'
+    uc_plg.sb_unit = 'Jy / sr'
     y_display_unit = u.Unit(viewer_1d.state.y_display_unit)
     assert y_display_unit == u.Jy / u.sr
 
     # Try a second conversion
-    uc_plg.flux_or_sb_unit = 'W / Hz sr m2'
+    uc_plg.sb_unit = 'W / Hz sr m2'
     y_display_unit = u.Unit(viewer_1d.state.y_display_unit)
     assert y_display_unit == u.Unit("W / (Hz sr m2)")
 
     # really a translation test, test_unit_translation loads a Flux
     # cube, this test load a Surface Brightness Cube, this ensures
     # two-way translation
-    uc_plg.flux_or_sb_unit = 'MJy / sr'
+    uc_plg.sb_unit = 'MJy / sr'
     y_display_unit = u.Unit(viewer_1d.state.y_display_unit)
 
-    # we can get rid of this after all spectra pass through
-    # spectral extraction plugin
-    extract_plg = cubeviz_helper.plugins['Spectral Extraction']
-    extract_plg.aperture = extract_plg.aperture.choices[-1]
-    extract_plg.aperture_method.selected = 'Exact'
-    extract_plg.wavelength_dependent = True
-    extract_plg.function = 'Sum'
-    extract_plg.reference_spectral_value = 0.000001
-    extract_plg.extract()
-
-    uc_plg._obj.show_translator = True
     uc_plg._obj.flux_or_sb_selected = 'Flux'
-    uc_plg.flux_or_sb_unit = 'MJy'
+    uc_plg.flux_unit = 'MJy'
     y_display_unit = u.Unit(viewer_1d.state.y_display_unit)
 
     assert y_display_unit == u.MJy