Update continuum, moment maps, and spectral extraction

spacetelescope · Mar 19, 2024 · 9257b59 · 9257b59
1 parent 70a27fd
commit 9257b59
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Showing 4 changed files with 13 additions and 12 deletions.
diff --git a/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py b/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py
@@ -349,8 +349,7 @@ def get_aperture(self):
         # Retrieve flux cube and create an array to represent the cone mask
         flux_cube = self._app._jdaviz_helper._loaded_flux_cube.get_object(cls=Spectrum1D,
                                                                           statistic=None)
-        # TODO: Replace with code for retrieving display_unit in cubeviz when it is available
-        display_unit = flux_cube.spectral_axis.unit
+        display_unit = astropy.units.Unit(self.app._get_display_unit('spectral'))
 
         # Center is reverse coordinates
         center = (self.aperture.selected_spatial_region.center.y,
@@ -367,7 +366,7 @@ def get_aperture(self):
                     f'Spectral axis unit physical type is {display_unit.physical_type}, '
                     'must be length for cone aperture')
 
-            fac = flux_cube.spectral_axis.value / self.reference_wavelength
+            fac = flux_cube.spectral_axis.to(display_unit).value / self.reference_wavelength
 
             # TODO: Use flux_cube.spectral_axis.to_value(display_unit) when we have unit conversion.
             if isinstance(aperture, CircularAperture):

diff --git a/jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py b/jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.py
@@ -130,15 +130,15 @@ def _on_spectral_unit_changed(self, *args):
         xunit = _valid_glue_display_unit(self.spectral_unit.selected, self.spectrum_viewer, 'x')
         if self.spectrum_viewer.state.x_display_unit != xunit:
             self.spectrum_viewer.state.x_display_unit = xunit
-        self.hub.broadcast(GlobalDisplayUnitChanged('spectral',
-                                                    self.spectral_unit.selected,
-                                                    sender=self))
+            self.hub.broadcast(GlobalDisplayUnitChanged('spectral',
+                                                        self.spectral_unit.selected,
+                                                        sender=self))
 
     @observe('flux_unit_selected')
     def _on_flux_unit_changed(self, *args):
         yunit = _valid_glue_display_unit(self.flux_unit.selected, self.spectrum_viewer, 'y')
         if self.spectrum_viewer.state.y_display_unit != yunit:
             self.spectrum_viewer.state.y_display_unit = yunit
-        self.hub.broadcast(GlobalDisplayUnitChanged('flux',
-                                                    self.flux_unit.selected,
-                                                    sender=self))
+            self.hub.broadcast(GlobalDisplayUnitChanged('flux',
+                                                        self.flux_unit.selected,
+                                                        sender=self))
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
@@ -483,7 +483,8 @@ def _handle_display_units(data, use_display_units):
                                                                           u.spectral()),
                                       flux=data.flux.to(flux_unit,
                                                         u.spectral_density(data.spectral_axis)),
-                                      uncertainty=new_uncert)
+                                      uncertainty=new_uncert,
+                                      mask=data.mask)
                 else:  # pragma: nocover
                     raise NotImplementedError(f"converting {data.__class__.__name__} to display units is not supported")  # noqa
             return data

diff --git a/jdaviz/core/template_mixin.py b/jdaviz/core/template_mixin.py
@@ -2446,7 +2446,8 @@ def _get_continuum(self, dataset, spatial_subset, spectral_subset, update_marks=
         if spatial_subset == 'per-pixel':
             if self.app.config != 'cubeviz':
                 raise ValueError("per-pixel only supported for cubeviz")
-            full_spectrum = self.dataset.selected_obj
+            full_spectrum = self.app._jdaviz_helper.get_data(self.dataset.selected,
+                                                             use_display_units=True)
         else:
             full_spectrum = dataset.selected_spectrum_for_spatial_subset(spatial_subset.selected if spatial_subset is not None else None,  # noqa
                                                                          use_display_units=True)
@@ -2533,7 +2534,7 @@ def _get_continuum(self, dataset, spatial_subset, spectral_subset, update_marks=
             continuum_mask = ~self._specviz_helper.get_data(
                 dataset.selected,
                 spectral_subset=self.continuum_subset_selected,
-                use_display_units=False).mask
+                use_display_units=True).mask
             spectral_axis_nanmasked = spectral_axis.value.copy()
             spectral_axis_nanmasked[~continuum_mask] = np.nan
             if not update_marks: