Add unit conversion plugin with flux conversion disabled

Add message to flux conversion dropdown in cubeviz

Have moment map units update after conversion

Update continuum, moment maps, and spectral extraction

Fix model fitting and aperture plugins and add tests

jdaviz/configs/cubeviz/cubeviz.yaml

@@ -23,6 +23,7 @@ tray:
   - g-subset-plugin
   - g-markers
   - cubeviz-slice
+  - g-unit-conversion
   - g-gaussian-smooth
   - g-collapse
   - g-model-fitting

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

@@ -9,7 +9,7 @@
 from specutils import manipulation, analysis, Spectrum1D
 
 from jdaviz.core.custom_traitlets import IntHandleEmpty, FloatHandleEmpty
-from jdaviz.core.events import SnackbarMessage
+from jdaviz.core.events import SnackbarMessage, GlobalDisplayUnitChanged
 from jdaviz.core.registries import tray_registry
 from jdaviz.core.template_mixin import (PluginTemplateMixin,
                                         DatasetSelectMixin,
@@ -96,6 +96,8 @@ def __init__(self, *args, **kwargs):
 
         self.dataset.add_filter('is_cube')
         self.add_results.viewer.filters = ['is_image_viewer']
+        self.session.hub.subscribe(self, GlobalDisplayUnitChanged,
+                                   handler=self._set_data_units)
 
         if self.app.state.settings.get('server_is_remote', False):
             # when the server is remote, saving the file in python would save on the server, not
@@ -155,12 +157,16 @@ def _set_data_units(self, event={}):
         if self.dataset_selected != "":
             # Spectral axis is first in this list
             data = self.app.data_collection[self.dataset_selected]
-            if self.app.data_collection[self.dataset_selected].coords is not None:
+            if (self.spectrum_viewer and hasattr(self.spectrum_viewer.state, 'x_display_unit')
+                    and self.spectrum_viewer.state.x_display_unit is not None):
+                sunit = self.spectrum_viewer.state.x_display_unit
+            elif self.app.data_collection[self.dataset_selected].coords is not None:
                 sunit = data.coords.world_axis_units[0]
-                self.dataset_spectral_unit = sunit
-                unit_dict["Spectral Unit"] = sunit
             else:
-                self.dataset_spectral_unit = ""
+                sunit = ""
+            self.dataset_spectral_unit = sunit
+            unit_dict["Spectral Unit"] = sunit
+
             unit_dict["Flux"] = data.get_component('flux').units
 
         # Update units in selection item dictionary

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

@@ -147,7 +147,6 @@ def test_moment_velocity_calculation(cubeviz_helper, spectrum1d_cube):
     uncert_viewer.state._set_axes_aspect_ratio(1)
 
     mm = cubeviz_helper.plugins["Moment Maps"]
-    print(mm._obj.dataset_selected)
     mm._obj.dataset_selected = 'test[FLUX]'
 
     # Test moment 1 in velocity
@@ -170,6 +169,13 @@ def test_moment_velocity_calculation(cubeviz_helper, spectrum1d_cube):
                                          "World 13h39m59.9731s +27d00m00.3600s (ICRS)",
                                          "204.9998877673 27.0001000000 (deg)")
 
+    # Add test for unit conversion
+    assert mm._obj.output_radio_items[0]['unit_str'] == 'm'
+    uc_plugin = cubeviz_helper.plugins['Unit Conversion']._obj
+    uc_plugin.spectral_unit.selected = 'Angstrom'
+    assert mm._obj.output_radio_items[0]['unit_str'] == 'Angstrom'
+    uc_plugin.spectral_unit.selected = 'm'
+
     # Test moment 2 in velocity
     mm.n_moment = 2
     mm.calculate_moment()

jdaviz/configs/cubeviz/plugins/slice/slice.py

@@ -223,6 +223,24 @@ def _on_add_data(self, msg):
             # is updated (if enabled)
             self._on_value_updated({'new': self.value})
 
+    def _update_slice(self, x_all):
+        # Also update unit when data is updated
+        self.value_unit = x_all.unit.to_string()
+
+        # force value (wavelength/frequency) to update from the current slider slice
+        self._on_slider_updated({'new': self.slice})
+
+        # update data held inside slice indicator and force reverting to original active status
+        self.slice_indicator._update_data(x_all)
+
+    def _viewer_slices_changed(self, value):
+        # the slices attribute on the viewer state was changed,
+        # so we'll update the slider to match which will trigger
+        # the slider observer (_on_slider_updated) and sync across
+        # any other applicable viewers
+        if len(value) == 3:
+            self.slice = float(value[-1])
+
     def _on_select_slice_message(self, msg):
         with warnings.catch_warnings():
             warnings.simplefilter('ignore', category=UnitsWarning)

jdaviz/configs/cubeviz/plugins/slice/tests/test_slice.py

@@ -58,6 +58,13 @@ def test_slice(cubeviz_helper, spectrum1d_cube):
     cubeviz_helper.select_wavelength(4.62360028e-07)
     assert sl.value == slice_values[1]
 
+    # Add test for unit conversion
+    uc_plugin = cubeviz_helper.plugins['Unit Conversion']._obj
+    uc_plugin.spectral_unit.selected = 'Angstrom'
+    assert sl.value_unit == 'Angstrom'
+    cubeviz_helper.select_wavelength(4623.60028)
+    assert sl.slice == 1
+
     # Test player buttons API
 
     sl.vue_goto_first()

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

@@ -354,8 +354,7 @@ 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,
@@ -372,7 +371,7 @@ 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):

jdaviz/configs/default/plugins/model_fitting/model_fitting.py

@@ -315,7 +315,8 @@ def _warn_if_no_equation(self):
 
     def _get_1d_spectrum(self):
         # retrieves the 1d spectrum (accounting for spatial subset for cubeviz, if necessary)
-        return self.dataset.selected_spectrum_for_spatial_subset(self.spatial_subset_selected)  # noqa
+        return self.dataset.selected_spectrum_for_spatial_subset(self.spatial_subset_selected,
+                                                                 use_display_units=True)  # noqa
 
     @observe("dataset_selected", "spatial_subset_selected")
     def _dataset_selected_changed(self, event=None):
@@ -343,7 +344,6 @@ def _dataset_selected_changed(self, event=None):
         # Replace NaNs from collapsed Spectrum1D in Cubeviz
         # (won't affect calculations because these locations are masked)
         selected_spec.flux[np.isnan(selected_spec.flux)] = 0.0
-
         # TODO: can we simplify this logic?
         self._units["x"] = str(
             selected_spec.spectral_axis.unit)
@@ -518,6 +518,7 @@ def _initialize_model_component(self, model_comp, comp_label, poly_order=None):
         return new_model
 
     def _check_model_component_compat(self, axes=['x', 'y'], display_units=None):
+        print(display_units, self._units)
         if display_units is None:
             display_units = [u.Unit(self._units[ax]) for ax in axes]
 

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

@@ -127,18 +127,18 @@ def _on_glue_y_display_unit_changed(self, y_unit):
 
     @observe('spectral_unit_selected')
     def _on_spectral_unit_changed(self, *args):
-        self.hub.broadcast(GlobalDisplayUnitChanged('spectral',
-                                                    self.spectral_unit.selected,
-                                                    sender=self))
         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))
 
     @observe('flux_unit_selected')
     def _on_flux_unit_changed(self, *args):
-        self.hub.broadcast(GlobalDisplayUnitChanged('flux',
-                                                    self.flux_unit.selected,
-                                                    sender=self))
         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))

jdaviz/configs/specviz/plugins/unit_conversion/unit_conversion.vue

@@ -27,7 +27,13 @@
         label="Flux Unit"
         hint="Global display unit for flux."
         persistent-hint
+        :disabled="config === 'cubeviz'"
       ></v-select>
     </v-row>
+    <v-row v-if="config === 'cubeviz'">
+        <span class="v-messages v-messages__message text--secondary" style="color: red !important">
+          Flux conversion is not yet implemented in cubeviz
+        </span>
+    </v-row>
   </j-tray-plugin>
 </template>

jdaviz/core/helpers.py

@@ -490,7 +490,8 @@ 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

jdaviz/core/template_mixin.py

@@ -2632,7 +2632,8 @@ 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)
@@ -2719,7 +2720,7 @@ 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: