working on initial DQ plugin UI

jdaviz/configs/default/default.yaml

@@ -15,4 +15,4 @@ toolbar:
 tray:
   - g-subset-plugin
   - g-gaussian-smooth
-  - export
+  - export

jdaviz/configs/default/plugins/__init__.py

@@ -11,3 +11,4 @@
 from .export.export import *  # noqa
 from .plot_options.plot_options import *  # noqa
 from .markers.markers import * # noqa
+from .data_quality.data_quality import *  # noqa

jdaviz/configs/default/plugins/data_quality/__init__.py

@@ -1 +1 @@
-from .dq_utils import *  # noqa
+from .data_quality import *  # noqa

jdaviz/configs/default/plugins/data_quality/data_quality.py

@@ -0,0 +1,197 @@
+import os
+from traitlets import Any, Dict, Bool, List, Unicode, observe
+
+import numpy as np
+from glue_jupyter.common.toolbar_vuetify import read_icon
+from echo import delay_callback
+from matplotlib.colors import hex2color
+
+from jdaviz.core.registries import tray_registry
+from jdaviz.core.template_mixin import (
+    PluginTemplateMixin, ViewerSelect, LayerSelect
+)
+from jdaviz.core.tools import ICON_DIR
+from jdaviz.configs.default.plugins.data_quality.dq_utils import (
+    decode_flags, generate_listed_colormap, dq_flag_map_paths, load_flag_map
+)
+
+__all__ = ['DataQuality']
+
+telescope_names = {
+    "jwst": "JWST",
+    "roman": "Roman"
+}
+
+
+@tray_registry('g-data-quality', label="Data Quality", viewer_requirements="image")
+class DataQuality(PluginTemplateMixin):
+    template_file = __file__, "data_quality.vue"
+
+    viewer_multiselect = Bool(False).tag(sync=True)
+    viewer_items = List().tag(sync=True)
+    viewer_selected = Any().tag(sync=True)  # Any needed for multiselect
+    viewer_limits = Dict().tag(sync=True)
+
+    # `layer` is the science data layer
+    science_layer_multiselect = Bool(False).tag(sync=True)
+    science_layer_items = List().tag(sync=True)
+    science_layer_selected = Any().tag(sync=True)  # Any needed for multiselect
+
+    # `dq_layer` is teh data quality layer corresponding to the
+    # science data in `layer`
+    dq_layer_multiselect = Bool(False).tag(sync=True)
+    dq_layer_items = List().tag(sync=True)
+    dq_layer_selected = Any().tag(sync=True)  # Any needed for multiselect
+
+    flag_map_definitions = Dict().tag(sync=True)
+    flag_map_selected = Any().tag(sync=True)
+    flag_map_items = List().tag(sync=True)
+    viewer_selected = Any().tag(sync=True)  # Any needed for multiselect
+    decoded_flags = List().tag(sync=True)
+
+    icons = Dict().tag(sync=True)
+    icon_radialtocheck = Unicode(read_icon(os.path.join(ICON_DIR, 'radialtocheck.svg'), 'svg+xml')).tag(sync=True)  # noqa
+    icon_checktoradial = Unicode(read_icon(os.path.join(ICON_DIR, 'checktoradial.svg'), 'svg+xml')).tag(sync=True)  # noqa
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        self.icons = {k: v for k, v in self.app.state.icons.items()}
+
+        self.viewer = ViewerSelect(
+            self, 'viewer_items', 'viewer_selected', 'viewer_multiselect'
+        )
+        self.science_layer = LayerSelect(
+            self, 'science_layer_items', 'science_layer_selected',
+            'viewer_selected', 'science_layer_multiselect', is_root=True
+        )
+
+        self.dq_layer = LayerSelect(
+            self, 'dq_layer_items', 'dq_layer_selected',
+            'viewer_selected', 'dq_layer_multiselect', is_root=False,
+            is_child_of=self.science_layer.selected
+        )
+
+        self.load_default_flag_maps()
+        self.init_decoding()
+
+    @observe('science_layer_selected')
+    def update_dq_layer(self, *args):
+        if not hasattr(self, 'dq_layer'):
+            return
+
+        self.dq_layer.filter_is_child_of = self.science_layer_selected
+        self.dq_layer._update_layer_items()
+
+    def load_default_flag_maps(self):
+        for name in dq_flag_map_paths:
+            self.flag_map_definitions[name] = load_flag_map(name)
+            self.flag_map_items = self.flag_map_items + [telescope_names[name]]
+
+    @property
+    def multiselect(self):
+        logging.warning(f"DeprecationWarning: multiselect has been replaced by separate viewer_multiselect and layer_multiselect and will be removed in the future.  This currently evaluates viewer_multiselect or layer_multiselect")  # noqa
+        return self.viewer_multiselect or self.layer_multiselect
+
+    @multiselect.setter
+    def multiselect(self, value):
+        logging.warning(f"DeprecationWarning: multiselect has been replaced by separate viewer_multiselect and layer_multiselect and will be removed in the future.  This currently sets viewer_multiselect and layer_multiselect")  # noqa
+        self.viewer_multiselect = value
+        self.layer_multiselect = value
+
+    def vue_set_value(self, data):
+        attr_name = data.get('name')
+        value = data.get('value')
+        setattr(self, attr_name, value)
+
+    @property
+    def unique_flags(self):
+        selected_dq = self.dq_layer.selected_obj
+        if not len(selected_dq):
+            return []
+
+        dq = selected_dq[0].get_image_data()
+        return np.unique(dq[~np.isnan(dq)])
+
+    @property
+    def flag_map_definitions_selected(self):
+        return self.flag_map_definitions[self.flag_map_selected.lower()]
+
+    @property
+    def validate_flag_decode_possible(self):
+        return (
+            self.flag_map_selected is not None and
+            len(self.dq_layer.selected_obj) > 0
+        )
+
+    @observe('dq_layer_selected')
+    def init_decoding(self, event={}):
+        if not self.validate_flag_decode_possible:
+            return
+
+        unique_flags = self.unique_flags
+        cmap, rgba_colors = generate_listed_colormap(n_flags=len(unique_flags))
+        self.decoded_flags = decode_flags(
+            flag_map=self.flag_map_definitions_selected,
+            unique_flags=unique_flags,
+            rgba_colors=rgba_colors
+        )
+
+        viewer = self.viewer.selected_obj
+        [dq_layer] = [
+            layer for layer in viewer.layers if
+            layer.layer.label == self.dq_layer_selected
+        ]
+        dq_layer.composite._allow_bad_alpha = True
+
+        flag_bits = np.float32([flag['flag'] for flag in self.decoded_flags])
+
+        with delay_callback(dq_layer.state, 'alpha', 'cmap', 'v_min', 'v_max', 'stretch'):
+            dq_layer.state.cmap = cmap
+
+            dq_layer.state.stretch = 'lookup'
+            stretch_object = dq_layer.state.stretch_object
+            stretch_object.flags = flag_bits
+
+            dq_layer.state.v_min = min(flag_bits)
+            dq_layer.state.v_max = max(flag_bits)
+            dq_layer.state.alpha = 0.9
+
+    @observe('decoded_flags')
+    def update_cmap(self, event={}):
+        viewer = self.viewer.selected_obj
+        [dq_layer] = [
+            layer for layer in viewer.layers if
+            layer.layer.label == self.dq_layer_selected
+        ]
+        flag_bits = np.float32([flag['flag'] for flag in self.decoded_flags])
+        rgb_colors = [hex2color(flag['color']) for flag in self.decoded_flags]
+
+        # update the colors of the listed colormap without
+        # reassigning the layer.state.cmap object
+        cmap = dq_layer.state.cmap
+        cmap.colors = rgb_colors
+        cmap._init()
+
+        with delay_callback(dq_layer.state, 'v_min', 'v_max', 'alpha'):
+            # trigger updates to cmap in viewer:
+            dq_layer.update()
+
+            # set correct stretch and limits:
+            dq_layer.state.stretch = 'lookup'
+            dq_layer.state.v_min = min(flag_bits)
+            dq_layer.state.v_max = max(flag_bits)
+            dq_layer.state.alpha = 0.9
+
+    @observe('science_layer_selected')
+    def mission_or_instrument_from_meta(self, event):
+        if not hasattr(self, 'science_layer'):
+            return
+
+        layer = self.science_layer.selected_obj
+        if len(layer):
+            # this is defined for JWST and ROMAN, should be upper case:
+            telescope = layer[0].layer.meta.get('telescope', None)
+
+            if telescope is not None:
+                self.flag_map_selected = telescope_names[telescope.lower()]

jdaviz/configs/default/plugins/data_quality/data_quality.vue

@@ -0,0 +1,124 @@
+<template>
+  <j-tray-plugin
+    :description="docs_description || 'Viewer and data/layer options.'"
+    :link="docs_link || 'https://jdaviz.readthedocs.io/en/'+vdocs+'/'+config+'/plugins.html#plot-options'"
+    @plugin-ping="plugin_ping($event)"
+    :popout_button="popout_button">
+
+    <!-- VIEWER OPTIONS -->
+    <plugin-viewer-select
+      :items="viewer_items"
+      :selected.sync="viewer_selected"
+      :multiselect.sync="viewer_multiselect"
+      :show_multiselect_toggle="viewer_multiselect || viewer_items.length > 1"
+      :icon_checktoradial="icon_checktoradial"
+      :icon_radialtocheck="icon_radialtocheck"
+      :label="viewer_multiselect ? 'Viewers' : 'Viewer'"
+      :show_if_single_entry="viewer_multiselect"
+      :hint="viewer_multiselect ? 'Select viewers to set options simultaneously' : 'Select the viewer to set options.'"
+    />
+
+    <plugin-layer-select
+      :items="science_layer_items"
+      :selected.sync="science_layer_selected"
+      :multiselect="science_layer_multiselect"
+      :icons="icons"
+      :show_if_single_entry="true"
+      :label="'Science data'"
+      :hint="'Select the science data'"
+    />
+
+    <plugin-layer-select
+      :items="dq_layer_items"
+      :selected.sync="dq_layer_selected"
+      :multiselect="dq_layer_multiselect"
+      :label="'Data quality'"
+      :show_if_single_entry="true"
+      :hint="'Select the data quality'"
+      :icons="icons"
+    />
+
+    <v-row>
+    <v-select
+      attach
+      :menu-props="{ left: true }"
+      :items="flag_map_items"
+      v-model="flag_map_selected"
+      label="Flag definitions"
+    ></v-select>
+    </v-row>
+
+    <j-plugin-section-header>Quality Flags</j-plugin-section-header>
+    <v-row style="max-width: calc(100% - 80px)">
+      <v-col>
+        Color
+      </v-col>
+      <v-col>
+        <strong>Flag</strong>
+      </v-col>
+      <v-col>
+        (Decomposed)
+      </v-col>
+    </v-row>
+    <v-row>
+      <v-expansion-panels accordion>
+        <v-expansion-panel v-for="(item, index) in decoded_flags" key=":item">
+          <v-expansion-panel-header v-slot="{ open }">
+            <v-row no-gutters align="center" style="...">
+              <v-col cols=1>
+              </v-col>
+                <v-col cols=2>
+                <j-tooltip tipid='plugin-line-lists-color-picker'>
+                  <v-menu>
+                    <template v-slot:activator="{ on }">
+                        <span class="color-menu"
+                              :style="`background:${item.color}; cursor: pointer`"
+                              @click.stop="on.click"
+                        > </span>
+                    </template>
+                    <div @click.stop="" style="text-align: end; background-color: white">
+                        <v-color-picker v-model="decoded_flags[index].color"
+                                        @update:color="throttledSetColor($event.hexa)">
+                        ></v-color-picker>
+                    </div>
+                  </v-menu>
+                </j-tooltip>
+              </v-col>
+              <v-col>
+                <div> <strong>{{item.flag}}</strong> ({{Object.keys(item.decomposed).join(', ')}})</div>
+              </v-col>
+          </v-row>
+          </v-expansion-panel-header>
+          <v-expansion-panel-content>
+              <v-col v-for="(item, key, index) in item.decomposed">
+                <span>{{item.name}} ({{key}}): {{item.description}}</span>
+              </v-col>
+          </v-expansion-panel-content>
+        <v-expansion-panel>
+      </v-expansion-panels>
+    </v-row>
+  </j-tray-plugin>
+</template>
+
+
+<script>
+  module.exports = {
+    created() {
+      this.throttledSetColor = _.throttle(
+        (v) => { this.color = v },
+        100);
+    }
+  }
+</script>
+
+<style>
+  .v-slider {
+    margin: 0px !important;
+  }
+
+  .color-menu {
+      font-size: 16px;
+      padding-left: 16px;
+      border: 2px solid rgba(0,0,0,0.54);
+  }
+</style>

jdaviz/configs/default/plugins/data_quality/dq_utils.py

@@ -45,7 +45,7 @@ def load_flag_map(mission_or_instrument=None, path=None):
 
     flag_mapping = {}
     for flag, name, desc in flag_table.iterrows():
-        flag_mapping[flag] = dict(name=name, description=desc)
+        flag_mapping[int(flag)] = dict(name=name, description=desc)
 
     return flag_mapping
 
@@ -77,7 +77,7 @@ def write_flag_map(flag_mapping, csv_path, **kwargs):
     table.write(csv_path, format='ascii.csv', **kwargs)
 
 
-def generate_listed_colormap(n_flags, seed=42):
+def generate_listed_colormap(n_flags=None, seed=3):
     """
     Generate a list of random "light" colors of length ``n_flags``.
 
@@ -103,14 +103,14 @@ def generate_listed_colormap(n_flags, seed=42):
     # Generate random colors that are generally "light", i.e. with
     # RGB values in the upper half of the interval (0, 1):
     rgba_colors = [
-        tuple(rng.uniform(low=0.5, high=1, size=3).tolist() + [default_alpha])
+        tuple(np.insert(rng.uniform(size=2), rng.integers(0, 3), 1).tolist() + [default_alpha])
         for _ in range(n_flags)
     ]
 
     cmap = ListedColormap(rgba_colors)
 
     # setting `bad` alpha=0 will make NaNs transparent:
-    cmap.set_bad(alpha=0)
+    cmap.set_bad(color='k', alpha=0)
     return cmap, rgba_colors