integrate into cubeviz spectral extraction for future cone support

CHANGES.rst

@@ -45,6 +45,9 @@ API Changes
 Cubeviz
 ^^^^^^^
 
+- ``spatial_subset`` in the spectral extraction plugin is now renamed to ``aperture`` and will
+  be removed in a future release. [#2664]
+
 Imviz
 ^^^^^
 

docs/dev/ui_style_guide.rst

@@ -22,7 +22,7 @@ try to adhere to the following principles:
   components are necessary in a single row.  Always emphasize readability at the default/minimum
   width of the plugin tray, rather than using columns that result in a ton of text overflow.
 * Use ``<v-row justify="end">`` to align content to the right (such as action buttons).
-* Action buttons should use ``<plugin-action-button :results_isolated_to_plugin="true/false">text</v-btn>``
+* Action buttons should use ``<plugin-action-button :results_isolated_to_plugin="true/false">text</plugin-action-button>``
   to control the color depending on whether the button affects things outside the plugin itself
   (adding/modifying data collection or subset entries, etc) or are isolated to within the plugin
   (adding model components in model fitting, etc).  These buttons can be wrapped in tooltip components

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

@@ -11,7 +11,8 @@
 from specutils.spectra.spectrum1d import Spectrum1D
 
 from jdaviz.core.events import (AddDataMessage, SliceToolStateMessage,
-                                SliceSelectSliceMessage, GlobalDisplayUnitChanged)
+                                SliceSelectSliceMessage, SliceWavelengthUpdatedMessage,
+                                GlobalDisplayUnitChanged)
 from jdaviz.core.registries import tray_registry
 from jdaviz.core.template_mixin import PluginTemplateMixin
 from jdaviz.core.user_api import PluginUserApi
@@ -217,6 +218,10 @@ def _on_slider_updated(self, event):
         for viewer in self._indicator_viewers:
             viewer._update_slice_indicator(value)
 
+        self.hub.broadcast(SliceWavelengthUpdatedMessage(slice=value,
+                                                         wavelength=self.wavelength,
+                                                         sender=self))
+
     def vue_goto_first(self, *args):
         if self.is_playing:
             return

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

@@ -5,17 +5,19 @@
 import numpy as np
 import astropy
 import astropy.units as u
+from astropy.utils.decorators import deprecated
 from astropy.nddata import (
     NDDataArray, StdDevUncertainty, NDUncertainty
 )
-from traitlets import Bool, List, Unicode, observe
+from traitlets import Bool, Float, List, Unicode, observe
 
-from jdaviz.core.events import SnackbarMessage
+from jdaviz.core.custom_traitlets import FloatHandleEmpty
+from jdaviz.core.events import SnackbarMessage, SliceWavelengthUpdatedMessage
 from jdaviz.core.registries import tray_registry
 from jdaviz.core.template_mixin import (PluginTemplateMixin,
                                         DatasetSelectMixin,
                                         SelectPluginComponent,
-                                        SpatialSubsetSelectMixin,
+                                        ApertureSubsetSelectMixin,
                                         AddResultsMixin,
                                         with_spinner)
 from jdaviz.core.user_api import PluginUserApi
@@ -31,7 +33,7 @@
     'cubeviz-spectral-extraction', label="Spectral Extraction", viewer_requirements='spectrum'
 )
 class SpectralExtraction(PluginTemplateMixin, DatasetSelectMixin,
-                         SpatialSubsetSelectMixin, AddResultsMixin):
+                         ApertureSubsetSelectMixin, AddResultsMixin):
     """
     See the :ref:`Spectral Extraction Plugin Documentation <spex>` for more details.
 
@@ -41,12 +43,20 @@ class SpectralExtraction(PluginTemplateMixin, DatasetSelectMixin,
     * :meth:`~jdaviz.core.template_mixin.PluginTemplateMixin.show`
     * :meth:`~jdaviz.core.template_mixin.PluginTemplateMixin.open_in_tray`
     * :meth:`~jdaviz.core.template_mixin.PluginTemplateMixin.close_in_tray`
-    * ``spatial_subset`` (:class:`~jdaviz.core.template_mixin.SubsetSelect`):
-      Subset to use for the spectral extraction, or ``No Subset``.
+    * ``aperture`` (:class:`~jdaviz.core.template_mixin.SubsetSelect`):
+      Subset to use for the spectral extraction, or ``Entire Cube``.
     * ``add_results`` (:class:`~jdaviz.core.template_mixin.AddResults`)
     * :meth:`collapse`
     """
     template_file = __file__, "spectral_extraction.vue"
+    uses_active_status = Bool(True).tag(sync=True)
+
+    # feature flag for cone support
+    dev_cone_support = Bool(False).tag(sync=True)
+    wavelength_dependent = Bool(False).tag(sync=True)
+    reference_wavelength = FloatHandleEmpty().tag(sync=True)
+    slice_wavelength = Float().tag(sync=True)
+
     function_items = List().tag(sync=True)
     function_selected = Unicode('Sum').tag(sync=True)
     filename = Unicode().tag(sync=True)
@@ -68,6 +78,12 @@ def __init__(self, *args, **kwargs):
 
         self.extracted_spec = None
 
+        # TODO: in the future this could be generalized with support in SelectPluginComponent
+        self.aperture._default_text = 'Entire Cube'
+        self.aperture._manual_options = ['Entire Cube']
+        self.aperture.items = [{"label": "Entire Cube"}]
+        self.aperture.select_default()
+
         self.function = SelectPluginComponent(
             self,
             items='function_items',
@@ -77,6 +93,9 @@ def __init__(self, *args, **kwargs):
         self._set_default_results_label()
         self.add_results.viewer.filters = ['is_spectrum_viewer']
 
+        self.session.hub.subscribe(self, SliceWavelengthUpdatedMessage,
+                                   handler=self._on_slice_changed)
+
         if ASTROPY_LT_5_3_2:
             self.disabled_msg = "Spectral Extraction in Cubeviz requires astropy>=5.3.2"
 
@@ -95,11 +114,46 @@ def user_api(self):
         return PluginUserApi(
             self,
             expose=(
-                'function', 'spatial_subset',
+                'function', 'spatial_subset', 'aperture',
                 'add_results', 'collapse_to_spectrum'
             )
         )
 
+    @property
+    @deprecated(since="3.9", alternative="aperture")
+    def spatial_subset(self):
+        return self.user_api.aperture
+
+    @property
+    def slice_plugin(self):
+        return self.app._jdaviz_helper.plugins['Slice']
+
+    @observe('wavelength_dependent')
+    def _wavelength_dependent_changed(self, *args):
+        if self.wavelength_dependent:
+            self.reference_wavelength = self.slice_plugin.wavelength
+        # NOTE: this can be redundant in the case where reference_wavelength changed and triggers
+        # the observe, but we need to ensure it is updated if reference_wavelength is unchanged
+        self._update_mark_scale()
+
+    def _on_slice_changed(self, msg):
+        self.slice_wavelength = msg.wavelength
+
+    def vue_goto_reference_wavelength(self, *args):
+        self.slice_plugin.wavelength = self.reference_wavelength
+        # TODO: can we get rid of this extra call after properly observing wavelength?
+#        self._update_mark_scale()
+
+    def vue_adopt_slice_as_reference(self, *args):
+        self.reference_wavelength = self.slice_plugin.wavelength
+
+    @observe('reference_wavelength', 'slice_wavelength')
+    def _update_mark_scale(self, *args):
+        if not self.wavelength_dependent:
+            self.aperture.scale_factor = 1.0
+            return
+        self.aperture.scale_factor = self.slice_wavelength/self.reference_wavelength
+
     @with_spinner()
     def collapse_to_spectrum(self, add_data=True, **kwargs):
         """
@@ -121,12 +175,12 @@ def collapse_to_spectrum(self, add_data=True, **kwargs):
         # defaults to ``No Subset``). Since the Cubeviz parser puts the fluxes
         # and uncertainties in different glue Data objects, we translate the spectral
         # cube and its uncertainties into separate NDDataArrays, then combine them:
-        if self.spatial_subset_selected != self.spatial_subset.default_text:
+        if self.aperture.selected != self.spatial_subset.default_text:
             nddata = spectral_cube.get_subset_object(
-                subset_id=self.spatial_subset_selected, cls=NDDataArray
+                subset_id=self.aperture.selected, cls=NDDataArray
             )
             uncertainties = uncert_cube.get_subset_object(
-                subset_id=self.spatial_subset_selected, cls=StdDevUncertainty
+                subset_id=self.aperture.selected, cls=StdDevUncertainty
             )
         else:
             nddata = spectral_cube.get_object(cls=NDDataArray)
@@ -242,15 +296,15 @@ def _save_extracted_spec_to_fits(self, overwrite=False, *args):
             f"Extracted spectrum saved to {os.path.abspath(filename)}",
                            sender=self, color="success"))
 
-    @observe('spatial_subset_selected')
+    @observe('aperture_selected')
     def _set_default_results_label(self, event={}):
         label = "Spectral extraction"
 
         if (
-            hasattr(self, 'spatial_subset') and
-            self.spatial_subset.selected != self.spatial_subset.default_text
+            hasattr(self, 'aperture') and
+            self.aperture.selected != self.aperture.default_text
         ):
-            label += f' ({self.spatial_subset_selected})'
+            label += f' ({self.aperture_selected})'
         self.results_label_default = label
 
 

jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.vue

@@ -2,6 +2,9 @@
   <j-tray-plugin
     description='Extract a spectrum from a spectral cube.'
     :link="docs_link || 'https://jdaviz.readthedocs.io/en/'+vdocs+'/'+config+'/plugins.html#spectral-extraction'"
+    :uses_active_status="uses_active_status"
+    @plugin-ping="plugin_ping($event)"
+    :keep_active.sync="keep_active"
     :popout_button="popout_button"
     :disabled_msg="disabled_msg">
 
@@ -18,13 +21,53 @@
     </v-row>
 
     <plugin-subset-select 
-      :items="spatial_subset_items"
-      :selected.sync="spatial_subset_selected"
+      :items="aperture_items"
+      :selected.sync="aperture_selected"
       :show_if_single_entry="true"
-      label="Spatial region"
+      label="Spatial aperture"
       hint="Select a spatial region to extract its spectrum."
     />
 
+    <div v-if="aperture_selected !== 'Entire Cube' && dev_cone_support">
+      <v-alert type='warning'>cone support is under active development and hidden from users</v-alert>
+      <v-row>
+        <v-switch
+          v-model="wavelength_dependent"
+          label="Wavelength dependent"
+          hint="Vary aperture linearly with wavelength"
+          persistent-hint>
+        </v-switch>
+      </v-row>
+      <div v-if="wavelength_dependent">
+        <v-row justify="end">
+          <j-tooltip tooltipcontent="Adopt the current slice as the reference wavelength">
+            <plugin-action-button :results_isolated_to_plugin="true" @click="adopt_slice_as_reference">
+              Adopt Current Slice
+            </plugin-action-button>
+          </j-tooltip>
+        </v-row>
+        <v-row>
+          <v-text-field
+            v-model.number="reference_wavelength"
+            type="number"
+            :step="0.1"
+            class="mt-0 pt-0"
+            label="Wavelength"
+            hint="Wavelength at which the aperture matches the selected subset."
+            persistent-hint
+          ></v-text-field>
+        </v-row>
+        <v-row justify="end">
+          <j-tooltip tooltipcontent="Select the slice nearest the reference wavelength">
+            <plugin-action-button :results_isolated_to_plugin="true" @click="goto_reference_wavelength">
+              Slice to Reference Wavelength
+            </plugin-action-button>
+          </j-tooltip>
+        </v-row>
+      </div>
+
+    </div>
+
     <plugin-add-results
       :label.sync="results_label"
       :label_default="results_label_default"

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

@@ -85,7 +85,7 @@ def test_gauss_smooth_before_spec_extract(cubeviz_helper, spectrum1d_cube_with_u
     extract_plugin.function = "Sum"
     expected_uncert = 2
 
-    extract_plugin.spatial_subset = 'Subset 1'
+    extract_plugin.aperture = 'Subset 1'
     collapsed_spec = extract_plugin.collapse_to_spectrum()
 
     # this single pixel has two wavelengths, and all uncertainties are unity
@@ -94,7 +94,7 @@ def test_gauss_smooth_before_spec_extract(cubeviz_helper, spectrum1d_cube_with_u
     assert np.all(np.equal(collapsed_spec.uncertainty.array, 1))
 
     # this two-pixel region has four unmasked data points per wavelength:
-    extract_plugin.spatial_subset = 'Subset 2'
+    extract_plugin.aperture = 'Subset 2'
     collapsed_spec_2 = extract_plugin.collapse_to_spectrum()
     assert np.all(np.equal(collapsed_spec_2.uncertainty.array, expected_uncert))
 
@@ -129,7 +129,7 @@ def test_subset(
     plg.function = function
 
     # single pixel region:
-    plg.spatial_subset = 'Subset 1'
+    plg.aperture = 'Subset 1'
     collapsed_spec_1 = plg.collapse_to_spectrum()
 
     # this single pixel has two wavelengths, and all uncertainties are unity
@@ -138,7 +138,7 @@ def test_subset(
     assert np.all(np.equal(collapsed_spec_1.uncertainty.array, 1))
 
     # this two-pixel region has four unmasked data points per wavelength:
-    plg.spatial_subset = 'Subset 2'
+    plg.aperture = 'Subset 2'
     collapsed_spec_2 = plg.collapse_to_spectrum()
 
     assert np.all(np.equal(collapsed_spec_2.uncertainty.array, expected_uncert))

jdaviz/core/events.py

@@ -4,7 +4,7 @@
 __all__ = ['NewViewerMessage', 'ViewerAddedMessage', 'ViewerRemovedMessage', 'LoadDataMessage',
            'AddDataMessage', 'SnackbarMessage', 'RemoveDataMessage',
            'AddLineListMessage', 'RowLockMessage',
-           'SliceSelectSliceMessage',
+           'SliceSelectSliceMessage', 'SliceWavelengthUpdatedMessage',
            'SliceToolStateMessage',
            'TableClickMessage', 'LinkUpdatedMessage', 'ExitBatchLoadMessage',
            'MarkersChangedMessage', 'CanvasRotationChangedMessage',
@@ -288,6 +288,14 @@ def slice(self):
         return self._slice
 
 
+class SliceWavelengthUpdatedMessage(Message):
+    '''Message generated by the slice plugin when the selected slice and wavelength are updated'''
+    def __init__(self, slice, wavelength, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.slice = slice
+        self.wavelength = wavelength
+
+
 class SliceToolStateMessage(Message):
     '''Message generated by the select slice plot plugin when activated/deactivated'''
     def __init__(self, change, *args, **kwargs):

jdaviz/core/template_mixin.py

@@ -1938,7 +1938,6 @@ def __init__(self, plugin, items, selected, scale_factor, multiselect=None,
                          selected=selected,
                          multiselect=multiselect,
                          filters=['is_spatial', 'is_not_composite', 'is_not_annulus'],
-                         dataset=dataset,
                          viewers=viewers,
                          default_text=None)
 
@@ -1988,10 +1987,12 @@ def marks(self):
         return all_aperture_marks
 
     def _get_mark_coords(self, viewer):
-        if not len(self.selected) or not len(self.dataset.selected):
+        if not len(self.selected):
+            return [], []
+        if self.selected in self.manual_options:
             return [], []
 
-        subset_dicts = self.selected_obj if self.multiselect else [self.selected_obj]
+        subset_dicts = self.selected_obj if getattr(self, 'multiselect', False) else [self.selected_obj]  # noqa
 
         x_coords, y_coords = np.array([]), np.array([])
         for subset_dict in subset_dicts:
@@ -2063,7 +2064,6 @@ def __init__(self, *args, **kwargs):
                                              'aperture_items',
                                              'aperture_selected',
                                              'aperture_scale_factor',
-                                             dataset='dataset' if hasattr(self, 'dataset') else None,  # noqa
                                              multiselect='multiselect' if hasattr(self, 'multiselect') else None)  # noqa