Cubeviz spectral extraction through plugin

docs/cubeviz/plugins.rst

@@ -279,9 +279,6 @@ Spectral Extraction
 
 .. image:: ../img/cubeviz_spectral_extraction.png
 
-.. note::
-
-    Spectral Extraction requires at least version 5.3.2 of astropy.
 
 The Spectral Extraction plugin produces a 1D spectrum from a spectral
 cube. The 1D spectrum can be computed via the sum, mean, minimum, or

jdaviz/app.py

@@ -367,6 +367,8 @@ def __init__(self, configuration=None, *args, **kwargs):
         self._get_object_cache = {}
         self.hub.subscribe(self, SubsetUpdateMessage,
                            handler=self._on_subset_update_message)
+        self.hub.subscribe(self, SubsetDeleteMessage,
+                           handler=self._on_subset_delete_message)
 
         # Store for associations between Data entries:
         self._data_associations = self._init_data_associations()
@@ -378,8 +380,7 @@ def __init__(self, configuration=None, *args, **kwargs):
                            handler=self._on_layers_changed)
         self.hub.subscribe(self, SubsetCreateMessage,
                            handler=self._on_layers_changed)
-        self.hub.subscribe(self, SubsetDeleteMessage,
-                           handler=self._on_layers_changed)
+        # SubsetDeleteMessage will also call _on_layers_changed via _on_subset_delete_message
 
     def _on_plugin_table_added(self, msg):
         if msg.plugin._plugin_name is None:
@@ -388,7 +389,7 @@ def _on_plugin_table_added(self, msg):
         key = f"{msg.plugin._plugin_name}: {msg.table._table_name}"
         self._plugin_tables.setdefault(key, msg.table.user_api)
 
-    def _update_live_plugin_results(self, trigger_data_lbl=None, trigger_subset=None):
+    def _iter_live_plugin_results(self, trigger_data_lbl=None, trigger_subset=None):
         trigger_subset_lbl = trigger_subset.label if trigger_subset is not None else None
         for data in self.data_collection:
             plugin_inputs = data.meta.get('_update_live_plugin_results', None)
@@ -410,6 +411,10 @@ def _update_live_plugin_results(self, trigger_data_lbl=None, trigger_subset=None
                                for attr in data_subs]):
                     # trigger parent data of subset does not match subscribed data entries
                     continue
+            yield (data, plugin_inputs)
+
+    def _update_live_plugin_results(self, trigger_data_lbl=None, trigger_subset=None):
+        for data, plugin_inputs in self._iter_live_plugin_results(trigger_data_lbl, trigger_subset):
             # update and overwrite data
             # make a new instance of the plugin to avoid changing any UI settings
             plg = self._jdaviz_helper.plugins.get(data.meta.get('Plugin'))._obj.new()
@@ -422,6 +427,15 @@ def _update_live_plugin_results(self, trigger_data_lbl=None, trigger_subset=None
                 self.hub.broadcast(SnackbarMessage(
                     f"Auto-update for {plugin_inputs['add_results']['label']} failed: {e}",
                     sender=self, color="error"))
+                # TODO: should we delete the entry (but then any plot options, etc, are lost)
+                # self.vue_data_item_remove({'item_name': data.label})
+
+    def _remove_live_plugin_results(self, trigger_data_lbl=None, trigger_subset=None):
+        for data, plugin_inputs in self._iter_live_plugin_results(trigger_data_lbl, trigger_subset):
+            self.hub.broadcast(SnackbarMessage(
+                f"Removing {data.label} due to deletion of {trigger_subset.label if trigger_subset is not None else trigger_data_lbl}",  # noqa
+                sender=self, color="warning"))
+            self.vue_data_item_remove({'item_name': data.label})
 
     def _on_add_data_message(self, msg):
         self._on_layers_changed(msg)
@@ -433,6 +447,10 @@ def _on_subset_update_message(self, msg):
         if msg.attribute == 'subset_state':
             self._update_live_plugin_results(trigger_subset=msg.subset)
 
+    def _on_subset_delete_message(self, msg):
+        self._remove_live_plugin_results(trigger_subset=msg.subset)
+        self._on_layers_changed(msg)
+
     def _on_plugin_plot_added(self, msg):
         if msg.plugin._plugin_name is None:
             # plugin was instantiated after the app was created, ignore
@@ -2078,7 +2096,14 @@ def set_data_visibility(self, viewer_reference, data_label, visible=True, replac
 
             data = self.data_collection[data_label]
 
-            viewer.add_data(data, percentile=95, color=viewer.color_cycler())
+            # set the original color based on metadata preferences, if provided, and otherwise
+            # based on the colorcycler
+            # NOTE: this is intentionally not a single line to avoid incrementing the color-cycler
+            # unless it is used
+            color = data.meta.get('_default_color')
+            if color is None:
+                color = viewer.color_cycler()
+            viewer.add_data(data, percentile=95, color=color)
 
             # Specviz removes the data from collection in viewer.py if flux unit incompatible.
             if data_label not in self.data_collection:
@@ -2248,13 +2273,6 @@ def _on_data_deleted(self, msg):
             if data_item['name'] == msg.data.label:
                 self.state.data_items.remove(data_item)
 
-        # TODO: Fix bug with DataCollectionDeleteMessage not working with
-        #  a handler in cubeviz/plugins/viewers.py. This code is a temporary
-        #  workaround for that.
-        if self.config == 'cubeviz':
-            viewer = self.get_viewer(self._jdaviz_helper._default_spectrum_viewer_reference_name)
-            viewer._check_if_data_removed(msg=msg)
-
         self._clear_object_cache(msg.data.label)
 
     def _create_data_item(self, data):
@@ -2410,7 +2428,7 @@ def _create_viewer_item(self, viewer, vid=None, name=None, reference=None,
             'layer_options': "IPY_MODEL_" + viewer.layer_options.model_id,
             'viewer_options': "IPY_MODEL_" + viewer.viewer_options.model_id,
             'selected_data_items': {},  # noqa data_id: visibility state (visible, hidden, mixed), READ-ONLY
-            'visible_layers': {},  # label: {color, label_suffix}, READ-ONLY
+            'visible_layers': {},  # label: {color}, READ-ONLY
             'wcs_only_layers': wcs_only_layers,
             'reference_data_label': reference_data_label,
             'canvas_angle': 0,  # canvas rotation clockwise rotation angle in deg
@@ -2617,7 +2635,7 @@ def compose_viewer_area(viewer_area_items):
         for name in config.get('tray', []):
             tray = tray_registry.members.get(name)
 
-            tray_item_instance = tray.get('cls')(app=self)
+            tray_item_instance = tray.get('cls')(app=self, tray_instance=True)
 
             # store a copy of the tray name in the instance so it can be accessed by the
             # plugin itself

jdaviz/components/viewer_data_select.vue

@@ -208,12 +208,8 @@ module.exports = {
       } else if (this.$props.viewer.config === 'cubeviz') {
         if (this.$props.viewer.reference === 'spectrum-viewer') {
           if (item.meta.Plugin === undefined) {
-            // then the data can be a cube (auto-collapsed) as long as its the flux data
-            // if this logic moves to python, we could check directly against reference data instead
-            return (item.name.indexOf('[FLUX]') !== -1 || item.name.indexOf('[SCI]') !== -1) && this.dataItemInViewer(item, returnExtraItems)
-          } else if (item.meta.Plugin === 'GaussianSmooth') {
-            // spectrally smoothed would still be a collapsible cube
-            return item.ndims === 3 && this.dataItemInViewer(item, returnExtraItems)
+            // then only allow 1d spectra (not cubes or images)
+            return item.ndims === 1
           } else {
             // filter plugin results to only those that are spectra
             return item.ndims === 1 && this.dataItemInViewer(item, returnExtraItems)

jdaviz/components/viewer_data_select_item.vue

@@ -158,8 +158,6 @@ module.exports = {
           return ['IVAR', 'ERR'].indexOf(extension) !== -1
         } else if (this.$props.viewer.reference === 'mask-viewer') {
           return ['MASK', 'DQ'].indexOf(extension) !== -1
-        } else if (this.$props.viewer.reference === 'spectrum-viewer') {
-          return ['SCI', 'FLUX'].indexOf(extension) !== -1
         }
       } else if (this.$props.viewer.config === 'specviz2d') {
         if (this.$props.viewer.reference === 'spectrum-2d-viewer') {

jdaviz/configs/cubeviz/cubeviz.yaml

@@ -24,13 +24,13 @@ tray:
   - g-markers
   - cubeviz-slice
   - g-unit-conversion
+  - cubeviz-spectral-extraction
   - g-gaussian-smooth
   - g-collapse
   - g-model-fitting
   - g-line-list
   - specviz-line-analysis
   - cubeviz-moment-maps
-  - cubeviz-spectral-extraction
   - imviz-aper-phot-simple
   - export
 viewer_area:

jdaviz/configs/cubeviz/helper.py

@@ -1,10 +1,12 @@
+import logging
 import numpy as np
 from astropy.io import fits
 from astropy.io import registry as io_registry
 from astropy.utils.decorators import deprecated
 from specutils import Spectrum1D
 from specutils.io.registers import _astropy_has_priorities
 
+from jdaviz.core.events import SnackbarMessage
 from jdaviz.core.helpers import ImageConfigHelper
 from jdaviz.configs.default.plugins.line_lists.line_list_mixin import LineListMixin
 from jdaviz.configs.specviz import Specviz
@@ -79,6 +81,28 @@ def load_data(self, data, data_label=None, override_cube_limit=False, **kwargs):
 
         super().load_data(data, parser_reference="cubeviz-data-parser", **kwargs)
 
+        if 'Spectral Extraction' not in self.plugins.keys():  # pragma: nocov
+            msg = SnackbarMessage(
+                "Automatic spectral extraction requires the Spectral Extraction plugin to be enabled",  # noqa
+                color='error', sender=self, timeout=10000)
+            self.app.hub.broadcast(msg)
+        else:
+            try:
+                self.plugins['Spectral Extraction']._obj._create_auto_extract()
+            except Exception:
+                msg = SnackbarMessage(
+                    "Automatic spectrum extraction for the entire cube failed."
+                    " See the spectral extraction plugin to perform a custom extraction",
+                    color='error', sender=self, timeout=10000)
+                raise  # TODO: remove before merge
+            else:
+                msg = SnackbarMessage(
+                    "The extracted 1D spectrum was generated automatically for the entire cube."
+                    " See the spectral extraction plugin for details or to"
+                    " perform a custom extraction.",
+                    color='warning', sender=self, timeout=10000)
+            self.app.hub.broadcast(msg)
+
     @deprecated(since="3.9", alternative="select_wavelength")
     def select_slice(self, slice):
         """
@@ -124,20 +148,24 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, f
                  cls=None, use_display_units=False):
         """
         Returns data with name equal to ``data_label`` of type ``cls`` with subsets applied from
-        ``spatial_subset`` and/or ``spectral_subset`` using ``function`` if applicable.
+        ``spectral_subset``, if applicable.
 
         Parameters
         ----------
         data_label : str, optional
             Provide a label to retrieve a specific data set from data_collection.
         spatial_subset : str, optional
+            Deprecated as of 3.11.  Use the spectral extraction plugin and extract the extracted
+            spectrum instead.
             Spatial subset applied to data.
         spectral_subset : str, optional
             Spectral subset applied to data.
         function : {True, False, 'minimum', 'maximum', 'mean', 'median', 'sum'}, optional
+            Deprecated as of 3.11.  Use the spectral extraction plugin and extract the extracted
+            spectrum instead.
             Ignored if ``data_label`` does not point to cube-like data.
-            If True, will collapse according to the current collapse function defined in the
-            spectrum viewer.  If provided as a string, the cube will be collapsed with the provided
+            If True, will collapse using 'sum'.
+            If provided as a string, the cube will be collapsed with the provided
             function.  If False, None, or not passed, the entire cube will be returned (unless there
             are values for ``spatial_subset`` and ``spectral_subset``).
         cls : `~specutils.Spectrum1D`, `~astropy.nddata.CCDData`, optional
@@ -149,6 +177,11 @@ def get_data(self, data_label=None, spatial_subset=None, spectral_subset=None, f
             Data is returned as type cls with subsets applied.
 
         """
+        if function is not None or spatial_subset is not None:
+            logging.warning("DeprecationWarning: function and spatial_subset are deprecated and"
+                            " will be removed in a future release.  Use the spectral extraction"
+                            " plugin and access the extracted spectrum directly.")
+
         # If function is a value ('sum' or 'minimum') or True and spatial and spectral
         # are set, then we collapse the cube along the spatial subset using the function, then
         # we apply the mask from the spectral subset.

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

@@ -200,7 +200,6 @@ def _calculate_continuum(self, msg=None):
         # NOTE: there is no use in caching this, as the continuum will need to be re-computed
         # per-spaxel to use within calculating the moment map
         _ = self._get_continuum(self.dataset,
-                                None,
                                 self.spectral_subset,
                                 update_marks=True)
 
@@ -236,9 +235,9 @@ def calculate_moment(self, add_data=True):
                 cube = self.dataset.selected_obj
         else:
             _, _, cube = self._get_continuum(self.dataset,
-                                             'per-pixel',
                                              self.spectral_subset,
-                                             update_marks=False)
+                                             update_marks=False,
+                                             per_pixel=True)
 
         # slice out desired region
         # TODO: should we add a warning for a composite spectral subset?

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

@@ -70,15 +70,15 @@ def test_moment_calculation(cubeviz_helper, spectrum1d_cube, tmp_path):
     mm._obj.vue_calculate_moment()
 
     assert mm._obj.moment_available
-    assert dc[1].label == 'moment 0'
+    assert dc[-1].label == 'moment 0'
     mv_data = cubeviz_helper.app.get_viewer(
         cubeviz_helper._default_uncert_viewer_reference_name
     ).data()
     # by default, will overwrite the previous entry (so only one data entry)
     assert len(mv_data) == 1
     assert mv_data[0].label == 'moment 0'
 
-    assert len(dc.links) == 14
+    assert len(dc.links) == 19
 
     # label should remain unchanged but raise overwrite warnings
     assert mm._obj.results_label == 'moment 0'
@@ -99,9 +99,9 @@ def test_moment_calculation(cubeviz_helper, spectrum1d_cube, tmp_path):
         cubeviz_helper._default_flux_viewer_reference_name, 'moment 0'
     )
 
-    result = dc[1].get_object(cls=CCDData)
+    result = dc[-1].get_object(cls=CCDData)
     assert result.shape == (4, 2)  # Cube shape is (2, 2, 4)
-    assert isinstance(dc[1].coords, WCS)
+    assert isinstance(dc[-1].coords, WCS)
 
     # Make sure coordinate display now show moment map info (no WCS)
     label_mouseover._viewer_mouse_event(flux_viewer, {'event': 'mousemove',