Label stack support

django/applications/catmaid/control/stack.py

@@ -8,7 +8,7 @@
 from django.shortcuts import get_object_or_404
 
 from ..models import UserRole, Project, Stack, ProjectStack, \
-        BrokenSlice, StackMirror
+        BrokenSlice, StackMirror, StackStackGroup
 from .authentication import requires_user_role
 
 logger = logging.getLogger(__name__)
@@ -152,3 +152,15 @@ def stacks(request, project_id=None):
         'sort_keys': True,
         'indent': 4
     })
+
+@requires_user_role([UserRole.Annotate, UserRole.Browse])
+def stack_groups(request, project_id=None, stack_id=None):
+    stackgroup_links = StackStackGroup.objects \
+        .filter(stack=stack_id) \
+        .select_related('group_relation')
+
+    result = {
+        'stack_group_ids': [l.stack_group_id for l in stackgroup_links]
+    }
+
+    return JsonResponse(result)

django/applications/catmaid/control/stackgroup.py

@@ -17,7 +17,6 @@ def get_stackgroup_info(request, project_id, stackgroup_id):
         .filter(stack_group=stackgroup_id) \
         .order_by('position') \
         .select_related('group_relation')
-    stacks = [l.stack_id for l in stackgroup_links]
 
     result = {
         'id': stackgroup.id,

django/applications/catmaid/static/css/stack.css

@@ -118,16 +118,16 @@ div.smallMapView_hidden div.smallMapRect div {
 }
 
 div.LayerControl {
-  border: solid 1px #00F;
+  border-right: solid 1px #00F;
   margin: 0;
   padding: 8px;
   position: relative;
-  top: 10px;
-  left: 10px;
-  width: 40em;
+  top: 0;
+  left: 0;
+  width: 42em;
   min-width: 13em;
   max-width: 80%;
-  height: 65%;
+  height: 100%;
   overflow-x: hidden;
   overflow-y: auto;
   color: #FFFFFF;
@@ -207,7 +207,7 @@ div.LayerControl li.highlight {
 
 .layerControl .layerFilterControl input.remove {
   position: absolute;
-  left: 0.5em;
+  left: 2em;
 }
 
 .layerControl .layerFilterControl h5 {

django/applications/catmaid/static/js/init.js

@@ -1362,13 +1362,13 @@ var project;
                       stacks: stacks
                     };
                     CATMAID.layoutStackViewers();
-                    // Make all tile layers visible, they have been initialized
+                    // Make all stack layers visible, they have been initialized
                     // invisible.
                     for (var i=0; i<loadedStackViewers.length; ++i) {
                       var sv = loadedStackViewers[i];
-                      var tileLayers = sv.getLayersOfType(CATMAID.TileLayer);
-                      for (var j=0; j<tileLayers.length; ++j) {
-                        var tl = tileLayers[j];
+                      var stackLayers = sv.getLayersOfType(CATMAID.StackLayer);
+                      for (var j=0; j<stackLayers.length; ++j) {
+                        var tl = stackLayers[j];
                         tl.setOpacity(1.0);
                         tl.redraw();
                       }
@@ -1517,7 +1517,7 @@ var project;
    * @param  {StackViewer} stackViewer Viewer to which to add the stack.
    * @param  {number}      mirrorIndex Optional mirror index, defaults to
    *                                   the first available.
-   * @param  {Boolean} hide            The stack's tile layer will initially be
+   * @param  {Boolean} hide            The stack's layer will initially be
    *                                   hidden.
    * @return {Promise}                 A promise yielding the stack viewer
    *                                   containing the new stack.
@@ -1590,40 +1590,45 @@ var project;
       });
     }
 
-    function loadStack(e, stackViewer, hideTileLayer) {
+    function loadStack(e, stackViewer, hideStackLayer) {
       var useExistingViewer = typeof stackViewer !== 'undefined';
 
       var stack = new CATMAID.Stack.fromStackInfoJson(e);
 
+      // If this is a label stack, not a raw stack, create a label annotation
+      // manager.
+      // TODO: should eventually use a backend image label space instead.
+      if (!!stack.labelMetadata()) {
+        CATMAID.LabelAnnotations.get(stack);
+      }
+
       if (!useExistingViewer) {
         stackViewer = new CATMAID.StackViewer(project, stack);
       }
 
       document.getElementById( "toolbox_project" ).style.display = "block";
 
-      var tilelayerConstructor = CATMAID.TileLayer.Settings.session.prefer_webgl ?
-          CATMAID.PixiTileLayer :
-          CATMAID.TileLayer;
-      var tilelayer = new tilelayerConstructor(
+      var stackLayerConstructor = CATMAID.StackLayer.preferredConstructorForStack();
+      var stackLayer = new stackLayerConstructor(
           stackViewer,
           "Image data (" + stack.title + ")",
           stack,
           mirrorIndex,
-          !hideTileLayer,
-          hideTileLayer ? 0 : 1,
+          !hideStackLayer,
+          hideStackLayer ? 0 : 1,
           !useExistingViewer,
-          CATMAID.TileLayer.Settings.session.linear_interpolation,
+          CATMAID.StackLayer.INTERPOLATION_MODES.INHERIT,
           true);
 
       if (!useExistingViewer) {
-        stackViewer.addLayer( "TileLayer", tilelayer );
+        stackViewer.addLayer("StackLayer", stackLayer);
 
         project.addStackViewer( stackViewer );
 
         // refresh the overview handler to also register the mouse events on the buttons
         stackViewer.layercontrol.refresh();
       } else {
-        stackViewer.addStackLayer(stack, tilelayer);
+        stackViewer.addStackLayer(stack, stackLayer);
       }
 
       CATMAID.ui.releaseEvents();

django/applications/catmaid/static/js/label-annotations.js

@@ -0,0 +1,171 @@
+(function (CATMAID) {
+
+  "use strict";
+
+  class LabelAnnotations {
+    constructor() {
+      this.groupManagingStack = new Map();
+      this.managers = new Map();
+      this.active = undefined;
+    }
+
+    activate(stackID) {
+      this.active = stackID;
+    }
+
+    clear() {
+      for (const [_stack, manager] of this.managers.entries()) manager.unregister();
+      this.managers.clear();
+      this.groupManagingStack.clear();
+      this.active = undefined;
+    }
+
+    get(stack) {
+      let manager = this.managers.get(stack.id);
+
+      if (!manager) {
+        // Find all stack groups to which this stack belongs.
+        return CATMAID.fetch(project.id + '/stack/' + stack.id + '/groups')
+            .then(response =>
+              // Get the info of all of these groups.
+              Promise.all(response.stack_group_ids.map(
+                  sg_id => CATMAID.fetch(project.id + '/stackgroup/' + sg_id + '/info')))
+            )
+            .then(sg_infos => {
+              // Find stack groups where this stack is an (ortho)view.
+              let ortho_sgs = sg_infos
+                  .filter(sg_info => sg_info.stacks
+                      .find(s => s.id === stack.id)
+                      .relation === 'view');
+
+              // Find if an existing manager for any of these stack groups exists.
+              let managing_stack_id = ortho_sgs.find(sg => this.groupManagingStack.get(sg.id));
+
+              if (typeof managing_stack_id !== 'undefined') {
+                manager = this.managers.get(managing_stack_id);
+              } else {
+                // If no manager exists, create a new one.
+                managing_stack_id = stack.id;
+                manager = new LabelStackAnnotations(stack);
+                ortho_sgs.forEach(sg => this.groupManagingStack.set(sg.id, managing_stack_id));
+                // Add all other stack (ortho)views in all (ortho)view groups
+                // to this manager.
+                ortho_sgs.forEach(sg => sg.stacks
+                    .filter(s => s.relation === 'view')
+                    .forEach(s => manager.addStackID(s.id)));
+                this.managers.set(stack.id, manager);
+              }
+
+              return manager;
+            });
+      }
+
+      return Promise.resolve(manager);
+    }
+  }
+
+  CATMAID.LabelAnnotations = new LabelAnnotations();
+
+  CATMAID.Init.on(CATMAID.Init.EVENT_PROJECT_CHANGED, CATMAID.LabelAnnotations.clear, CATMAID.LabelAnnotations);
+
+
+  const LABEL_FILTER_KEY = 'Object Label Color Map';
+
+  const SPECIAL_LABELS = {
+    background: 0,
+  };
+
+  class LabelStackAnnotations {
+    constructor(
+      primaryStack
+    ) {
+      this.primaryStack = primaryStack;
+      this.stackIDs = new Set([this.primaryStack.id]);
+      this.activeLabelID = undefined;
+
+      this.specialLabels = Object.assign({}, SPECIAL_LABELS, this.primaryStack.labelMetadata());
+      this.stackLayerFilters = new Map();
+
+      project.on(CATMAID.Project.EVENT_STACKVIEW_ADDED,
+          this.registerStackViewerLayers, this);
+      CATMAID.StackViewer.on(CATMAID.StackViewer.EVENT_STACK_LAYER_ADDED,
+          this.registerStackLayer, this);
+      CATMAID.StackViewer.on(CATMAID.StackViewer.EVENT_STACK_LAYER_REMOVED,
+          this.unregisterStackLayer, this);
+
+      this.registerAllStackLayers();
+    }
+
+    addStackID(stackID) {
+      this.stackIDs.add(stackID);
+    }
+
+    unregister() {
+      project.off(CATMAID.Project.EVENT_STACKVIEW_ADDED,
+          this.registerStackViewerLayers, this);
+      CATMAID.StackViewer.off(CATMAID.StackViewer.EVENT_STACK_LAYER_ADDED,
+          this.registerStackLayer, this);
+      CATMAID.StackViewer.off(CATMAID.StackViewer.EVENT_STACK_LAYER_REMOVED,
+          this.unregisterStackLayer, this);
+      this.stackLayerFilters.clear();
+    }
+
+    activateLabel(labelID) {
+      this.activeLabelID = labelID;
+
+      for (const [stackLayer, filter] of this.stackLayerFilters.entries()) {
+        this.updateFilter(filter);
+        stackLayer.redraw();
+        stackLayer.stackViewer.layercontrol.refresh();
+      }
+    }
+
+    registerAllStackLayers() {
+      for (const stackViewer of project.getStackViewers()) {
+        this.registerStackViewerLayers(stackViewer);
+      }
+    }
+
+    registerStackViewerLayers(stackViewer) {
+      for (const stackLayer of stackViewer.getLayersOfType(CATMAID.StackLayer)) {
+        this.registerStackLayer(stackLayer, stackViewer);
+      }
+    }
+
+    registerStackLayer(stackLayer, stackViewer) {
+      if (!this.stackIDs.has(stackLayer.stack.id)) return;
+
+      let layerFilters = stackLayer.getAvailableFilters ? stackLayer.getAvailableFilters() : [];
+      if (LABEL_FILTER_KEY in layerFilters && !this.stackLayerFilters.has(stackLayer)) {
+        stackLayer.setBlendMode('add');
+        stackLayer.setInterpolationMode(CATMAID.StackLayer.INTERPOLATION_MODES.NEAREST);
+        stackLayer.isHideable = true;
+        let filter = new (layerFilters[LABEL_FILTER_KEY])();
+        this.updateFilter(filter);
+        stackLayer.addFilter(filter);
+        this.stackLayerFilters.set(stackLayer, filter);
+
+        // TODO: coupling state refresh with stack viewer.
+        stackLayer.redraw();
+        stackViewer.layercontrol.refresh();
+      }
+    }
+
+    unregisterStackLayer(stackLayer, stackViewer) {
+      if (!this.stackIDs.has(stackLayer.stack.id)) return;
+
+      this.stackLayerFilters.delete(stackLayer);
+    }
+
+    updateFilter(filter) {
+      filter.pixiFilter.backgroundLabel = CATMAID.PixiLayer.Filters.int2arr(
+        this.specialLabels.background);
+      filter.pixiFilter.unknownLabel = typeof this.activeLabelID === 'undefined' ?
+        [-1, -1, -1, -1] :
+        CATMAID.PixiLayer.Filters.int2arr(this.activeLabelID);
+    }
+  }
+
+  CATMAID.LabelStackAnnotations = LabelStackAnnotations;
+
+})(CATMAID);

django/applications/catmaid/static/js/layers/layer-control.js

@@ -14,7 +14,7 @@
     this.view = document.createElement( "div" );
     this.view.className = "LayerControl";
     this.view.id = "LayerControl" + stackViewer.id;
-    this.view.style.zIndex = 8;
+    this.view.style.zIndex = 6;
 
     stackViewer.getView().appendChild( this.view );
   };