Use get_data internally instead of get_data_from_viewer

CHANGES.rst

@@ -32,6 +32,9 @@ API Changes
 
 - Export plot plugin now exposes the ``viewer`` dropdown in the user API. [#2037]
 
+- Replaced internal ``get_data_from_viewer()`` calls, ``specviz.get_spectra`` now returns
+  spectra for all data+subset combinations. [#2072]
+
 Cubeviz
 ^^^^^^^
 

jdaviz/configs/cubeviz/plugins/tests/test_regions.py

@@ -69,6 +69,8 @@ def test_spatial_spectral_mix(self):
         # https://github.com/spacetelescope/jdaviz/issues/1584
         with pytest.warns(UserWarning, match='Applying the value from the redshift slider'):
             spectral_subsets = self.cubeviz.specviz.get_spectra()
-        assert list(spectral_subsets.keys()) == ['has_microns[FLUX]', 'Subset 1', 'Subset 2'], spectral_subsets  # noqa
+        assert list(spectral_subsets.keys()) == ['has_microns[FLUX]',
+                                                 'has_microns[FLUX] (Subset 1)',
+                                                 'has_microns[FLUX] (Subset 2)'], spectral_subsets  # noqa
         for sp in spectral_subsets.values():
             assert isinstance(sp, Spectrum1D)

jdaviz/configs/default/plugins/line_lists/line_lists.py

@@ -166,9 +166,7 @@ def _on_viewer_data_changed(self, msg=None):
 
         label = msg.data.label
         try:
-            viewer_data = self.app.get_data_from_viewer(
-                self._default_spectrum_viewer_reference_name
-            ).get(label)
+            viewer_data = self.app._jdaviz_helper.get_data(data_label=label)
         except TypeError:
             warn_message = SnackbarMessage("Line list plugin could not retrieve data from viewer",
                                            sender=self, color="error")

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

@@ -294,15 +294,20 @@ def _warn_if_no_equation(self):
 
     def _get_1d_spectrum(self):
         # retrieves the 1d spectrum (accounting for spatial subset for cubeviz, if necessary)
-        if self.config == 'cubeviz' and self.spatial_subset_selected != 'Entire Cube':
-            # then we're acting on the auto-collapsed data in the spectrum-viewer
-            # of a spatial subset.  In the future, we may want to expose on-the-fly
-            # collapse options... but right now these will follow the settings of the
-            # spectrum-viewer itself
-            return self.app.get_data_from_viewer(
-                                                 self._default_spectrum_viewer_reference_name,
-                                                 self.spatial_subset_selected
-                                                 )
+        if self.config == 'cubeviz':
+            stat = self.app.get_viewer(self._default_spectrum_viewer_reference_name).state.function
+            if self.spatial_subset_selected == 'Entire Cube':
+                return self.app._jdaviz_helper.get_data(data_label=self.dataset_selected,
+                                                        statistic=stat)
+            else:
+                # then we're acting on the auto-collapsed data in the spectrum-viewer
+                # of a spatial subset.  In the future, we may want to expose on-the-fly
+                # collapse options... but right now these will follow the settings of the
+                # spectrum-viewer itself
+                kwargs = {"data_label": self.dataset_selected,
+                          "subset_to_apply": self.spatial_subset_selected,
+                          "statistic": stat}
+                return self.app._jdaviz_helper.get_data(**kwargs)
         else:
             return self.dataset.selected_obj
 
@@ -321,7 +326,7 @@ def _dataset_selected_changed(self, event=None):
             IPyWidget callback event object. In this case, represents the data
             label of the data collection object selected by the user.
         """
-        if not hasattr(self, 'dataset'):
+        if not hasattr(self, 'dataset') or self.app._jdaviz_helper is None:
             # during initial init, this can trigger before the component is initialized
             return
 

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

@@ -327,9 +327,14 @@ def _spectrum_viewer_update(self, viewer, x, y):
                 if not isinstance(lyr.layer.subset_state, RoiSubsetState):
                     # then this is a SPECTRAL subset
                     continue
-            elif ((not isinstance(lyr.layer, BaseData)) or (lyr.layer.ndim not in (1, 3))
-                    or (not lyr.visible)):
+                # For use later in data retrieval
+                subset_label = lyr.layer.label
+                data_label = lyr.layer.data.label
+            elif ((not isinstance(lyr.layer, BaseData)) or (lyr.layer.ndim not in (1, 3))):
                 continue
+            else:
+                subset_label = None
+                data_label = lyr.layer.label
 
             try:
                 # Cache should have been populated when spectrum was first plotted.
@@ -339,7 +344,9 @@ def _spectrum_viewer_update(self, viewer, x, y):
                 if cache_key in self.app._get_object_cache:
                     sp = self.app._get_object_cache[cache_key]
                 else:
-                    sp = self.app.get_data_from_viewer('spectrum-viewer', lyr.layer.label)
+                    sp = self.app._jdaviz_helper.get_data(data_label=data_label,
+                                                          statistic=statistic,
+                                                          subset_to_apply=subset_label)
                     self.app._get_object_cache[cache_key] = sp
 
                 # Out of range in spectral axis.

jdaviz/configs/specviz/helper.py

@@ -2,6 +2,7 @@
 
 from astropy import units as u
 from astropy.utils.decorators import deprecated
+from glue.core.subset_group import GroupedSubset
 from specutils import SpectralRegion, Spectrum1D
 
 from jdaviz.core.helpers import ConfigHelper
@@ -67,20 +68,50 @@ def load_spectrum(self, data, data_label=None, format=None, show_in_viewer=True,
                           show_in_viewer=show_in_viewer,
                           concat_by_file=concat_by_file)
 
-    def get_spectra(self, data_label=None, apply_slider_redshift="Warn"):
+    def get_spectra(self, data_label=None, subset_to_apply=None, apply_slider_redshift="Warn"):
         """Returns the current data loaded into the main viewer
 
         """
-        spectra = self.app.get_data_from_viewer(
-            self._default_spectrum_viewer_reference_name, data_label=data_label
-        )
+        spectra = {}
+        # Just to save line length
+        get_data_method = self.app._jdaviz_helper.get_data
+        viewer = self.app.get_viewer(self._default_spectrum_viewer_reference_name)
+        statistic = getattr(viewer, "function", None)
+
+        if data_label is not None:
+            spectrum = get_data_method(data_label=data_label,
+                                       subset_to_apply=subset_to_apply,
+                                       statistic=statistic)
+            spectra[data_label] = spectrum
+        else:
+            for layer_state in viewer.state.layers:
+                lyr = layer_state.layer
+                if subset_to_apply is not None:
+                    if lyr.label == subset_to_apply:
+                        spectrum = get_data_method(data_label=lyr.data.label,
+                                                   subset_to_apply=subset_to_apply,
+                                                   statistic=statistic)
+                        spectra[lyr.data.label] = spectrum
+                    else:
+                        continue
+                else:
+                    if isinstance(lyr, GroupedSubset):
+                        spectrum = get_data_method(data_label=lyr.data.label,
+                                                   subset_to_apply=lyr.label,
+                                                   statistic=statistic)
+                        spectra[f'{lyr.data.label} ({lyr.label})'] = spectrum
+                    else:
+                        spectrum = get_data_method(data_label=lyr.label,
+                                                   statistic=statistic)
+                        spectra[lyr.label] = spectrum
+
         if not apply_slider_redshift:
+            if data_label is not None:
+                return spectra[data_label]
             return spectra
         else:
             output_spectra = {}
             # We need to create new Spectrum1D outputs with the redshifts set
-            if data_label is not None:
-                spectra = {data_label: spectra}
             for key in spectra.keys():
                 output_spectra[key] = _apply_redshift_to_spectra(spectra[key], self._redshift)
 

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

@@ -173,9 +173,10 @@ def _on_viewer_data_changed(self, msg):
         if msg is None or msg.viewer_id != viewer_id or msg.data is None:
             return
 
-        viewer_data = self.app.get_data_from_viewer(
-            self._default_spectrum_viewer_reference_name
-        ).get(msg.data.label)
+        viewer = self.app.get_viewer(self._default_spectrum_viewer_reference_name)
+        statistic = getattr(viewer, 'function', None)
+        viewer_data = self.app._jdaviz_helper.get_data(data_label=msg.data.label,
+                                                       statistic=statistic)
 
         # If no data is currently plotted, don't attempt to update
         if viewer_data is None:
@@ -300,7 +301,7 @@ def _calculate_statistics(self, *args, **kwargs):
         Run the line analysis functions on the selected data/subset and
         display the results.
         """
-        if not hasattr(self, 'dataset'):
+        if not hasattr(self, 'dataset') or self.app._jdaviz_helper is None:
             # during initial init, this can trigger before the component is initialized
             return
 
@@ -314,16 +315,25 @@ def _calculate_statistics(self, *args, **kwargs):
         # show spinner with overlay
         self.results_computing = True
 
-        if (self.config == 'cubeviz' and self.spatial_subset_selected not in
-                (SPATIAL_DEFAULT_TEXT, "")):
-            # then we're acting on the auto-collapsed data in the spectrum-viewer
-            # of a spatial subset.  In the future, we may want to expose on-the-fly
-            # collapse options... but right now these will follow the settings of the
-            # spectrum-viewer itself
-            full_spectrum = self.app.get_data_from_viewer(
-                self._default_spectrum_viewer_reference_name,
-                self.spatial_subset_selected
-            )
+        if self.config == 'cubeviz':
+            statistic = None
+            for viewer in self.dataset.viewers:
+                if hasattr(viewer.state, "function"):
+                    statistic = viewer.state.function
+                    break
+            subset_to_apply = None
+            if self.spatial_subset_selected not in (SPATIAL_DEFAULT_TEXT, ""):
+                # then we're acting on the auto-collapsed data in the spectrum-viewer
+                # of a spatial subset.  In the future, we may want to expose on-the-fly
+                # collapse options... but right now these will follow the settings of the
+                # spectrum-viewer itself
+                subset_to_apply = self.spatial_subset_selected
+
+            full_spectrum = self.app._jdaviz_helper.get_data(
+                data_label=self.dataset.selected,
+                subset_to_apply=subset_to_apply,
+                statistic=statistic)
+
         else:
             full_spectrum = self.dataset.selected_obj
 
@@ -390,10 +400,8 @@ def _calculate_statistics(self, *args, **kwargs):
                       'right': np.array([sr.upper.value, max(spectral_axis.value[continuum_mask])])}
 
         else:
-            continuum_mask = ~self.app.get_data_from_viewer(
-                self._default_spectrum_viewer_reference_name,
-                data_label=self.continuum_subset_selected
-            ).mask
+            continuum_mask = ~self.app._jdaviz_helper.get_data(
+                subset_to_apply=self.continuum_subset_selected).mask
             spectral_axis_nanmasked = spectral_axis.value.copy()
             spectral_axis_nanmasked[~continuum_mask] = np.nan
             if self.spectral_subset_selected == "Entire Spectrum":

jdaviz/configs/specviz/plugins/parsers.py

@@ -76,13 +76,13 @@ def specviz_spectrum1d_parser(app, data, data_label=None, format=None, show_in_v
             raise ValueError(f"Length of data labels list ({len(data_label)}) is different"
                              f" than length of list of data ({len(data)})")
 
-    # If there's already data in the viewer, convert units if needed
+    # If there's already visible data in the viewer, convert units if needed
     current_unit = None
     if spectrum_viewer_reference_name in app.get_viewer_reference_names():
-        current_spec = app.get_data_from_viewer(spectrum_viewer_reference_name)
-        if current_spec != {} and current_spec is not None:
-            spec_key = list(current_spec.keys())[0]
-            current_unit = current_spec[spec_key].spectral_axis.unit
+        sv = app.get_viewer(spectrum_viewer_reference_name)
+        for layer_state in sv.state.layers:
+            if layer_state.visible:
+                current_unit = sv.state.x_display_unit
 
     with app.data_collection.delay_link_manager_update():
         # these are used to build a combined spectrum with all

jdaviz/configs/specviz/tests/test_helper.py

@@ -175,13 +175,13 @@ def test_get_spectra_no_spectra_redshift_error(specviz_helper, spectrum1d):
 
 def test_get_spectra_no_spectra_label(specviz_helper, spectrum1d):
     label = "label"
-    with pytest.raises(AttributeError):
+    with pytest.raises(ValueError):
         specviz_helper.get_spectra(data_label=label)
 
 
 def test_get_spectra_no_spectra_label_redshift_error(specviz_helper, spectrum1d):
     label = "label"
-    with pytest.raises(AttributeError):
+    with pytest.raises(ValueError):
         specviz_helper.get_spectra(data_label=label, apply_slider_redshift=True)
 
 

jdaviz/core/template_mixin.py

@@ -984,30 +984,21 @@ def selected_subset_state(self):
 
     @property
     def selected_subset_mask(self):
-        if self._allowed_type == 'spatial':
-            viewer_ref = getattr(self.plugin,
-                                 '_default_flux_viewer_reference_name',
-                                 self.viewers[0].reference_id)
+        if self._allowed_type == 'spatial' or self.app.config != 'cubeviz':
+            statistic = None
         elif self._allowed_type == 'spectral':
             viewer_ref = getattr(self.plugin,
                                  '_default_spectrum_viewer_reference_name',
                                  self.viewers[0].reference_id)
+            statistic = self.app.get_viewer(viewer_ref).state.function
 
-        subset = self.app.get_data_from_viewer(
-            viewer_ref, data_label=self.selected
-        )
+        data_label = self.plugin.dataset.selected
 
-        if hasattr(subset, 'mask'):
-            # the mask attr is available for spectral subsets:
-            subset_mask = subset.mask
-        else:
-            # `subset` is a GroupedSubset.
-            # We take the logical-not of the mask here, since the glue subset masks
-            # are True in selected regions and False outside. This is the opposite of
-            # the numpy/astropy/specutils convention where True is masked-out.
-            subset_mask = ~subset.to_mask()
+        subset = self.app._jdaviz_helper.get_data(data_label=data_label,
+                                                  subset_to_apply=self.selected,
+                                                  statistic=statistic)
 
-        return subset_mask
+        return subset.mask
 
     def selected_min_max(self, spectrum1d):
         if self.selected_obj is None:
@@ -1420,17 +1411,9 @@ def selected_obj(self):
         if self.selected not in self.labels:
             # _apply_default_selection will override shortly anyways
             return None
-        for viewer_ref in self.viewer_refs:
-            if viewer_ref is None:
-                # image viewers might not have a reference, but get_data_from_viewer
-                # does not take id
-                continue
-            match = self.app.get_data_from_viewer(viewer_ref, data_label=self.selected)
-            if match is not None:
-                if hasattr(match, 'get_object'):
-                    # cube viewers return the data collection instance from get_data_from_viewer
-                    return match.get_object(cls=self.default_data_cls)
-                return match
+        match = self.app._jdaviz_helper.get_data(data_label=self.selected)
+        if match is not None:
+            return match
         # handle the case of empty Application with no viewer, we'll just pull directly
         # from the data collection
         return self.get_object(cls=self.default_data_cls)