DQ support for Cubeviz

CHANGES.rst

@@ -8,6 +8,8 @@ New Features
 
 - The filename entry in the export plugin is now automatically populated based on the selection. [#2824]
 
+- Adding Data Quality plugin for Imviz and Cubeviz. [#2767, #2817]
+
 Cubeviz
 ^^^^^^^
 

docs/cubeviz/plugins.rst

@@ -46,6 +46,19 @@ To show axes on image viewers, toggle on the "Show axes" option at the bottom of
     :ref:`Spectral Plot Options <specviz-plot-settings>`
         Documentation on Specviz display settings in the Jdaviz viewers.
 
+.. _cubeviz-data-quality:
+
+Data Quality
+============
+
+Visualize data quality arrays for spectral cubes from JWST.
+
+.. seealso::
+
+    :ref:`Data Quality Plugin <imviz-data-quality>`
+        Follow the link to the rest of the Data Quality plugin documentation.
+
+
 .. _cubeviz-subset-plugin:
 
 Subset Tools

docs/imviz/plugins.rst

@@ -35,6 +35,32 @@ This plugin gives access to per-viewer and per-layer plotting options.
     :ref:`Display Settings <imviz-display-settings>`
         Documentation on various display settings in the Jdaviz viewers.
 
+.. _imviz-data-quality:
+
+Data Quality
+============
+
+Visualize data quality arrays for science data. The currently supported
+data quality flag mappings include JWST (all instruments) and Roman/WFI.
+
+Each science data layer can have one associated data quality layer.
+The visibility of the data quality layer can be toggled from the data
+dropdown menu, and toggling the science data visibility will do the
+same for the data quality layer. The mapping between bits and data quality
+flags is defined differently for each mission or instrument, and the
+plugin will infer the correct flag mapping from the file metadata.
+The opacity of the data quality layer can be changed relative to the
+opacity of the science data layer using the slider.
+
+The Quality Flag section contains a dropdown for applying a filter to the
+visualized bits. Select bits from the dropdown to visualize only flags
+containing those bits. The list of data quality flags beneath shows
+every flag in the data quality layer in bold, followed by the
+decomposed bits in that flag in parentheses. Clicking on a row
+will expand to flag to reveal the flag's short name and description,
+as well as a visibility toggle for that flag. Click on the color swatch
+to select a color for any flag.
+
 .. _imviz-subset-plugin:
 
 Subset Tools

jdaviz/app.py

@@ -2091,10 +2091,12 @@ def set_data_visibility(self, viewer_reference, data_label, visible=True, replac
                                               sender=self)
             self.hub.broadcast(add_data_message)
 
+        assoc_children = self._get_assoc_data_children(data_label)
+
         # set visibility state of all applicable layers
         for layer in viewer.layers:
             layer_is_wcs_only = getattr(layer.layer, 'meta', {}).get(_wcs_only_label, False)
-            if layer.layer.data.label == data_label:
+            if layer.layer.data.label in [data_label] + assoc_children:
                 if layer_is_wcs_only:
                     layer.visible = False
                     layer.update()
@@ -2112,7 +2114,22 @@ def set_data_visibility(self, viewer_reference, data_label, visible=True, replac
                     layer.visible = False
 
         # if Data has children, update their visibilities to match Data:
-        assoc_children = self._get_assoc_data_children(data_label)
+        available_plugins = [tray_item['name'] for tray_item in self.state.tray_items]
+        for child in assoc_children:
+            if child not in viewer.data_labels_loaded:
+                self.add_data_to_viewer(viewer.reference, child, visible=visible)
+
+            if 'g-data-quality' in available_plugins and visible:
+                # if we're adding a DQ layer to a viewer, make sure that
+                # the layer is appropriately colormapped as DQ:
+                data_quality_plugin = self.get_tray_item_from_name('g-data-quality')
+                old_viewer = data_quality_plugin.viewer_selected
+                data_quality_plugin.viewer_selected = viewer.reference
+                data_quality_plugin.science_layer_selected = data_label
+                data_quality_plugin.dq_layer_selected = child
+                data_quality_plugin.init_decoding(viewers=[viewer])
+                data_quality_plugin.viewer_selected = old_viewer
+
         for layer in viewer.layers:
             if layer.layer.data.label in assoc_children:
                 if visible and not layer.visible:
@@ -2121,14 +2138,19 @@ def set_data_visibility(self, viewer_reference, data_label, visible=True, replac
                 else:
                     layer.visible = visible
 
-        # update data menu - selected_data_items should be READ ONLY, not modified by the user/UI
+        # update data menu - selected_data_items should be READ ONLY, not modified by the user/UI.
+        # must update the visibility of `data_label` and its children:
         selected_items = viewer_item['selected_data_items']
-        data_id = self._data_id_from_label(data_label)
-        selected_items[data_id] = 'visible' if visible else 'hidden'
-        if replace:
-            for id in selected_items:
-                if id != data_id:
-                    selected_items[id] = 'hidden'
+        update_data_labels = [data_label] + assoc_children
+        for update_data_label in update_data_labels:
+            data_id = self._data_id_from_label(update_data_label)
+
+            if replace and update_data_label == data_label:
+                for id in selected_items:
+                    if id != data_id:
+                        selected_items[id] = 'hidden'
+
+            selected_items[data_id] = 'visible' if visible else 'hidden'
 
         # remove WCS-only data from selected items, add to wcs_only_layers:
         for layer in viewer.layers:
@@ -2316,7 +2338,9 @@ def _expose_meta(key):
             'has_wcs': data_has_valid_wcs(data),
             'is_astrowidgets_markers_table': (self.config == "imviz") and layer_is_table_data(data),
             'meta': {k: v for k, v in data.meta.items() if _expose_meta(k)},
-            'children': []}
+            'children': [],
+            'parent': None,
+        }
 
     @staticmethod
     def _create_stack_item(container='gl-stack', children=None, viewers=None):
@@ -2712,6 +2736,13 @@ def _add_assoc_data_as_parent(self, data_label):
     def _set_assoc_data_as_child(self, data_label, new_parent_label):
         # Data has a new parent:
         self._data_associations[data_label]['parent'] = new_parent_label
+
+        # update the data item so vue can see the change:
+        for data_item in self.state.data_items:
+            if data_item['name'] == data_label:
+                data_item['parent'] = new_parent_label
+                break
+
         # parent has a new child:
         self._data_associations[new_parent_label]['children'].append(data_label)
 

jdaviz/components/viewer_data_select.vue

@@ -50,7 +50,7 @@
             :icon="layer_icons[item.name]"
             :icons="icons"
             :viewer="viewer"
-            :multi_select="multi_select"
+            :multi_select="multi_select || isChild(item)"
             :is_wcs_only="false"
             :n_data_entries="nDataEntries"
             @data-item-visibility="$emit('data-item-visibility', $event)"
@@ -273,6 +273,10 @@ module.exports = {
     isRefData() {
       return this.$props.item.viewer.reference_data_label === this.$props.item.name
     },
+    isChild(item) {
+      // only override multi_select choice when data entry is a child:
+      return item.parent !== null
+    },
     selectRefData() {
       this.$emit('change-reference-data', {
         id: this.$props.viewer.id,
@@ -302,7 +306,7 @@ module.exports = {
       return this.$props.data_items.filter((item) => this.itemIsVisible(item, false))
     },
     extraDataItems() {
-      return this.$props.data_items.filter((item) => this.itemIsVisible(item, true))
+      return this.$props.data_items.filter((item) => this.itemIsVisible(item, true) && !this.isChild(item))
     },
     nDataEntries() {
       // return number of data entries in the entire plugin that were NOT created by a plugin

jdaviz/components/viewer_data_select_item.vue

@@ -191,7 +191,11 @@ module.exports = {
       } else {
         return 'gray'
       }
-    }
+    },
+    isChild(item) {
+      // only override multi_select choice when data entry is a child:
+      return item.parent !== null
+    },
   }
 };
 </script>

jdaviz/configs/cubeviz/cubeviz.yaml

@@ -20,6 +20,7 @@ toolbar:
 tray:
   - g-metadata-viewer
   - g-plot-options
+  - g-data-quality
   - g-subset-plugin
   - g-markers
   - cubeviz-slice

jdaviz/configs/cubeviz/plugins/parsers.py

@@ -10,6 +10,7 @@
 from astropy.wcs import WCS
 from specutils import Spectrum1D
 
+from jdaviz.configs.imviz.plugins.parsers import prep_data_layer_as_dq
 from jdaviz.core.registries import data_parser_registry
 from jdaviz.utils import standardize_metadata, PRIHDR_KEY
 
@@ -22,7 +23,7 @@
 
 
 @data_parser_registry("cubeviz-data-parser")
-def parse_data(app, file_obj, data_type=None, data_label=None):
+def parse_data(app, file_obj, data_type=None, data_label=None, parent=None):
     """
     Attempts to parse a data file and auto-populate available viewers in
     cubeviz.
@@ -84,10 +85,24 @@
                                          ('ERR', uncert_viewer_reference_name),
                                          ('DQ', None)):
                     data_label = app.return_data_label(file_name, ext)
+
+                    if ext == 'SCI':
+                        sci_ext = data_label
+
+                    # TODO: generalize/centralize this for use in other configs too
+
+                    if parent is not None:
+                        parent_data_label = parent
+                    elif ext == 'DQ':
+                        parent_data_label = sci_ext
+                    else:
+                        parent_data_label = None
+
                     _parse_jwst_s3d(
                         app, hdulist, data_label, ext=ext, viewer_name=viewer_name,
                         flux_viewer_reference_name=flux_viewer_reference_name,
-                        spectrum_viewer_reference_name=spectrum_viewer_reference_name
+                        spectrum_viewer_reference_name=spectrum_viewer_reference_name,
+                        parent=parent_data_label
                     )
             elif telescop == 'jwst' and filetype == 'r3d' and system == 'esa-pipeline':
                 for ext, viewer_name in (('DATA', flux_viewer_reference_name),
@@ -270,7 +285,7 @@
 
 def _parse_jwst_s3d(app, hdulist, data_label, ext='SCI',
                     viewer_name=None, flux_viewer_reference_name=None,
-                    spectrum_viewer_reference_name=None):
+                    spectrum_viewer_reference_name=None, parent=None):
     hdu = hdulist[ext]
     data_type = _get_data_type_by_hdu(hdu)
 
@@ -305,7 +320,13 @@
         metadata[PRIHDR_KEY] = standardize_metadata(hdulist['PRIMARY'].header)
 
     data = _return_spectrum_with_correct_units(flux, wcs, metadata, data_type, hdulist=hdulist)
-    app.add_data(data, data_label)
+    app.add_data(data, data_label, parent=parent)
+
+    # get glue data and update if DQ:
+    if ext == 'DQ':
+        data = app.data_collection[-1]
+        prep_data_layer_as_dq(data, component_id='flux')
+
     if data_type == 'flux':  # Forced wave unit conversion made it lose stuff, so re-add
         app.data_collection[-1].get_component("flux").units = flux.unit
 
@@ -315,6 +336,9 @@
     if viewer_name == flux_viewer_reference_name:
         app.add_data_to_viewer(spectrum_viewer_reference_name, data_label)
 
+    if ext == 'DQ':
+        app.add_data_to_viewer(flux_viewer_reference_name, data_label, visible=False)
+
     if data_type == 'flux':
         app._jdaviz_helper._loaded_flux_cube = app.data_collection[data_label]
     elif data_type == 'uncert':