Volume manager: add annotate functionality

Add front-end and back-end functionality to add annotations to a set of
volumes. A new checkbox column has been added to the volume table and an
"Annotate" button, that allows to annotate all selected volumes.

Worked on together with @aschampion, @clbarnes and @willp24.

See #1765

django/applications/catmaid/control/volume.py

@@ -8,6 +8,7 @@
 from django.conf import settings
 
 from catmaid.control.authentication import requires_user_role, user_can_edit
+from catmaid.control.common import get_request_list
 from catmaid.models import UserRole, Project, Volume
 from catmaid.serializers import VolumeSerializer
 
@@ -728,3 +729,34 @@ def intersects(request, project_id, volume_id):
     return JsonResponse({
         'intersects': result[0]
     })
+
+@api_view(['POST'])
+@requires_user_role([UserRole.Browse])
+def get_volume_entities(request, project_id):
+    """Retrieve a mapping of volume IDs to entity (class instance) IDs.
+    ---
+    parameters:
+      - name: volume_ids
+        description: A list of volume IDs to map
+        paramType: query
+    """
+    volume_ids = get_request_list(request.POST, 'volume_ids', map_fn=int)
+
+    cursor = connection.cursor()
+    cursor.execute("""
+        SELECT vci.volume_id, vci.class_instance_id
+        FROM volume_class_instance vci
+        JOIN UNNEST(%(volume_ids)s::int[]) volume(id)
+        ON volume.id = vci.volume_id
+        WHERE project_id = %(project_id)s
+        AND relation_id = (
+            SELECT id FROM relation
+            WHERE relation_name = 'model_of'
+            AND project_id = %(project_id)s
+        )
+    """, {
+        'volume_ids': volume_ids,
+        'project_id': project_id
+    })
+
+    return JsonResponse(dict(cursor.fetchall()))

django/applications/catmaid/static/js/widgets/volumewidget.js

@@ -85,6 +85,12 @@
         openFile.onclick = hiddenFileButton.click.bind(hiddenFileButton);
         controls.appendChild(openFile);
 
+        var annotate = document.createElement('button');
+        annotate.appendChild(document.createTextNode('Annotate'));
+        annotate.setAttribute('title', 'Annotate all selected volumes');
+        annotate.onclick = this.annotateSelectedVolumes.bind(this);
+        controls.appendChild(annotate);
+
         let self = this;
         CATMAID.DOM.appendNumericField(
             controls,
@@ -144,7 +150,7 @@
         table.style.width = "100%";
         var header = table.createTHead();
         var hrow = header.insertRow(0);
-        var columns = ['Name', 'Id', 'Comment', 'User', 'Creation time',
+        var columns = ['', 'Name', 'Id', 'Comment', 'User', 'Creation time',
             'Editor', 'Edition time', 'Action'];
         columns.forEach(function(c) {
           hrow.insertCell().appendChild(document.createTextNode(c));
@@ -171,6 +177,12 @@
               .catch(CATMAID.handleError);
           },
           columns: [
+            {
+              render: function(data, type, row, meta) {
+                return '<input type="checkbox" data-role="select" ' +
+                    (row.selected ? 'checked' : '') + ' />';
+              }
+            },
             {data: "title"},
             {data: "id"},
             {data: "comment"},
@@ -197,6 +209,12 @@
                   '<a href="#" data-action="export-STL">Export STL</a>'
             }
           ],
+        })
+        .on('change', 'input[data-role=select]', function() {
+          var table = $(this).closest('table');
+          var tr = $(this).closest('tr');
+          var data =  $(table).DataTable().row(tr).data();
+          data.selected = this.checked;
         });
 
         // Remove volume if 'remove' was clicked
@@ -331,7 +349,7 @@
 
         // Display a volume if clicked
         var self = this;
-        $(table).on('click', 'tbody td', function() {
+        $(table).on('dblclick', 'tbody td', function() {
           var tr = $(this).closest("tr");
           var volume = self.datatable.row(tr).data();
           self.loadVolume(volume.id)
@@ -623,6 +641,39 @@
   };
 
 
+  /**
+   * Annotate all currently selected volumes.
+   */
+  VolumeManagerWidget.prototype.annotateSelectedVolumes = function() {
+    if (!this.datatable) {
+      return;
+    }
+
+    let allVolumes = this.datatable.rows({'search': 'applied' }).data().toArray();
+    let selectedVolumeIds = allVolumes.filter(function(v) {
+      return v.selected;
+    }).map(function(v) {
+      return v.id;
+    });
+
+    if (selectedVolumeIds.length === 0) {
+      CATMAID.warn("No volumes selected");
+      return;
+    }
+
+    // Retrieve class instance IDs for volumes
+    CATMAID.fetch(project.id + '/volumes/entities/', 'POST', {
+        volume_ids: selectedVolumeIds
+      })
+      .then(function(ciMapping) {
+        return CATMAID.annotate(Object.values(ciMapping));
+      })
+      .then(function() {
+        CATMAID.msg("Success", "Annotations added");
+      })
+      .catch(CATMAID.handleError);
+  };
+
   var getVolumeType = function(volume) {
     if (volume instanceof CATMAID.AlphaShapeVolume) {
       return "alphashape";

django/applications/catmaid/urls.py

@@ -495,6 +495,7 @@
    url(r'^(?P<project_id>\d+)/volumes/$', volume.volume_collection),
    url(r'^(?P<project_id>\d+)/volumes/add$', record_view("volumes.create")(volume.add_volume)),
    url(r'^(?P<project_id>\d+)/volumes/import$', volume.import_volumes),
+   url(r'^(?P<project_id>\d+)/volumes/entities/$', volume.get_volume_entities),
    url(r'^(?P<project_id>\d+)/volumes/(?P<volume_id>\d+)/$', volume.volume_detail),
    url(r'^(?P<project_id>\d+)/volumes/(?P<volume_id>\d+)/intersect$', volume.intersects),
    url(r'^(?P<project_id>\d+)/volumes/(?P<volume_id>\d+)/export\.(?P<extension>\w+)', volume.export_volume),