@abi-software/scaffoldvuer 1.20.1-beta.0 → 1.21.1-beta.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/scaffoldvuer",
-  "version": "1.20.1-beta.0",
+  "version": "1.21.1-beta.1",
   "license": "Apache-2.0",
   "engines": {
     "node": "^24.20.0"
@@ -56,7 +56,7 @@
     "simple-dropzone": "^0.8.3",
     "vue": "^3.5.41",
     "vue-router": "^5.2.0",
-    "zincjs": "^2.3.1-beta.1"
+    "zincjs": "^2.4.1-beta.0"
   },
   "devDependencies": {
     "@babel/eslint-parser": "^8.0.1",
@@ -77,9 +77,6 @@
     "vitepress": "^1.6.4",
     "vue-docgen-api": "^4.79.2"
   },
-  "overrides": {
-    "three": "^0.185.1"
-  },
   "optionalDependencies": {
     "@esbuild/darwin-arm64": "0.28.2",
     "@esbuild/linux-x64": "0.28.2",

package/src/App.vue

@@ -731,7 +731,7 @@ export default {
         "https://mapcore-bucket1.s3.us-west-2.amazonaws.com/digital_twins/080626-demo/downsample_phase_3.nii.gz",
         "https://mapcore-bucket1.s3.us-west-2.amazonaws.com/digital_twins/080626-demo/downsample_phase_5.nii.gz"
       ]
-      const newTexture = await this.$refs.scaffold.readNIFTIFromSource(urls, true, this.maskUrl, v1, options, true);
+      const newTexture = await this.$refs.scaffold.readNIFTIFromSource(urls, true, undefined, v1, options, true);
       newTexture.timeEnabled = true;
       newTexture.setIsPickable(false);
       const scene = this.$refs.scaffold.$module.scene;
@@ -771,9 +771,9 @@ export default {
       this.$refs.scaffold.search(term, true);
     },
     viewerMounted: function() {
-      this.selectedCoordinates =
-        this.$refs.scaffold.getDynamicSelectedCoordinates();
-      this.rendererInfo = this.$refs.scaffold.getRendererInfo();
+    //  this.selectedCoordinates =
+    //    this.$refs.scaffold.getDynamicSelectedCoordinates();
+    //  this.rendererInfo = this.$refs.scaffold.getRendererInfo();
     },
     PrintViewport: function() {
       const scene = this.$refs.scaffold.$module.scene;

package/src/components/ScaffoldTreeControls.vue

@@ -466,14 +466,16 @@ export default {
     },
     //Set this right at the beginning.
     setModule: function (moduleIn) {
-      this.module = markRaw(moduleIn);
-      this.nodeNumbers = 0;
-      const objects = this.module.scene.getRootRegion().getAllObjects(true);
-      objects.forEach((zincObject) => {
-        this.zincObjectAdded(zincObject);
-      });
-      this.module.addOrganPartAddedCallback(this.zincObjectAdded);
-      this.module.addOrganPartRemovedCallback(this.zincObjectRemoved);
+      if (!this.module && moduleIn?.scene) {
+        this.module = markRaw(moduleIn);
+        this.nodeNumbers = 0;
+        const objects = this.module.scene.getRootRegion().getAllObjects(true);
+        objects.forEach((zincObject) => {
+          this.zincObjectAdded(zincObject);
+        });
+        this.module.addOrganPartAddedCallback(this.zincObjectAdded);
+        this.module.addOrganPartRemovedCallback(this.zincObjectRemoved);
+      }
     },
     setColourField: function (treeData, nodeData = undefined) {
       treeData

package/src/components/ScaffoldVuer.vue

@@ -547,6 +547,14 @@ export default {
     return { annotator }
   },
   props: {
+    /**
+      * The option to edit annotation regardless of whether
+      * resources matches or not
+      */
+      annotationIgnoreResource: {
+      type: Boolean,
+      default: false,
+    },
     /**
       * The option to show annotation information in sidebar
       */
@@ -962,6 +970,11 @@ export default {
         isSearch: false,
       }),
       //checkedRegions: []
+      unwatchURL: null,
+      unwatchRegion: null,
+      unwatchState: null,
+      unwatchViewURL: null,
+      unwatchMarkerCluster: null,
     };
   },
   watch: {
@@ -971,6 +984,7 @@ export default {
       },
       immediate: true,
     },
+    /*
     url: {
       handler: function (newValue) {
         if (this.state === undefined || this.state.url === undefined)
@@ -997,6 +1011,13 @@ export default {
       },
       immediate: true,
     },
+    markerCluster: {
+      handler: function (val) {
+        this.$module.scene.enableMarkerCluster(val);
+      },
+      immediate: true,
+    },
+    */
     helpMode: function (newVal, oldVal) {
       if (newVal !== oldVal) {
         this.setHelpMode(newVal)
@@ -1037,12 +1058,6 @@ export default {
     render: function (val) {
       this.toggleRendering(val);
     },
-    markerCluster: {
-      handler: function (val) {
-        this.$module.scene.enableMarkerCluster(val);
-      },
-      immediate: true,
-    },
     markerLabels: function(labels) {
       for (const [key, value] of Object.entries(this.previousMarkerLabels)) {
         this.setMarkerModeForObjectsWithName(key, value, "off");
@@ -1062,16 +1077,15 @@ export default {
     this.availableBackground = ["white", "black", "lightskyblue"];
     this.$_searchIndex = new SearchIndex();
   },
-  mounted: function () {
+  mounted: async function () {
     this.openMapRef = shallowRef(this.$refs.openMapRef);
     this.backgroundIconRef = shallowRef(this.$refs.backgroundIconRef);
-    this.$refs.scaffoldTreeControls.setModule(this.$module);
     let eventNotifier = new EventNotifier();
     eventNotifier.subscribe(this, this.eventNotifierCallback);
     this.$module.addNotifier(eventNotifier);
     this.$module.addOrganPartAddedCallback(this.zincObjectAdded);
     this.$module.addOrganPartRemovedCallback(this.zincObjectRemoved);
-    this.$module.initialiseRenderer(this.$refs.display);
+    await this.$module.initialise(this.$refs.display);
     this.toggleRendering(this.render);
     this.clientHeight = this.$refs.scaffoldContainer.$el.clientHeight;
     this.ro = new ResizeObserver(this.adjustLayout).observe(
@@ -1086,8 +1100,62 @@ export default {
     this.$module.zincRenderer.addContextRestoredCallbackFunction(() => {
       this.backgroundChangeCallback(this.currentBackground);
     })
+    //Setup some watchers that depend on threejs init()
+    this.unwatchURL = this.$watch(
+      'url',
+      (newVal) => {
+        if (this.state === undefined || this.state.url === undefined) {
+          this.setURL(newVal);
+        }
+      },
+      { immediate: true } // Runs immediately after creation, if desired
+    );
+    this.unwatchRegion = this.$watch(
+      'region',
+      (region) => {
+        if (!(this.state || this.viewURL)) {
+          this.setFocusedRegion(region);
+        }
+      },
+      { immediate: true }
+    );
+    this.unwatchState = this.$watch(
+      'state',
+      (state) => {
+        this.setState(state);
+      },
+      {  deep: true, immediate: true }
+    );
+    this.unwatchViewURL = this.$watch(
+      'viewURL',
+      (viewURL) => {
+        this.updateViewURL(viewURL);
+      },
+      { immediate: true }
+    );
+    this.unwatchURL = this.$watch(
+      'url',
+      (newValue) => {
+        if (this.state === undefined || this.state.url === undefined) {
+          this.setURL(newValue);
+        }
+      },
+      { immediate: true }
+    );
+    this.unwatchMarkerCluster = this.$watch(
+      'markerCluster',
+      (val) => {
+        this.$module.scene.enableMarkerCluster(val);
+      },
+      { immediate: true }
+    );
   },
   beforeUnmount: function () {
+    if (this.unwatchURL) this.unwatchURL();
+    if (this.unwatchRegion) this.unwatchRegion();
+    if (this.unwatchState) this.unwatchState();
+    if (this.unwatchViewURL) this.unwatchViewURL();
+    if (this.unwatchMarkerCluster) this.unwatchMarkerCluster();
     if (this.ro) this.ro.disconnect();
     this.$module.destroy();
     this.$module = undefined;
@@ -1374,7 +1442,7 @@ export default {
         const found = this.offlineAnnotations.find((element) => {
           return element.group === annotation.group &&
             element.region === annotation.region &&
-            element.resource === annotation.resource &&
+            (this.annotationIgnoreResource || element.resource === annotation.resource) &&
             element.feature.geometry.type === annotation.feature.geometry.type;
         });
         if (found) {
@@ -1413,7 +1481,7 @@ export default {
         const found = this.offlineAnnotations.find((element) => {
           return element.group === oldName &&
                  element.region === annotation.region &&
-                 element.resource === annotation.resource &&
+                 (this.annotationIgnoreResource || element.resource === annotation.resource) &&
                  element.feature.geometry.type === annotation.feature.geometry.type;
         });
         if (found) {
@@ -1579,7 +1647,7 @@ export default {
               const found = this.offlineAnnotations.find((element) => {
                 return element.group === group &&
                       element.region === annotation.region &&
-                      element.resource === annotation.resource &&
+                      (this.annotationIgnoreResource || element.resource === annotation.resource) &&
                       element.feature.geometry.type === annotation.feature.geometry.type;
               });
               Object.assign(found, annotation);
@@ -1783,9 +1851,12 @@ export default {
             this.tData.x = 50;
             this.tData.y = 200;
             if (this._tempPoint) {
-              const positionAttribute = this._tempPoint.geometry.getAttribute( 'position' );
+              const positionAttribute = this._tempPoint.geometry.getAttribute( 'instancePosition' );
               positionAttribute.setXYZ(0, worldCoords[0], worldCoords[1], worldCoords[2]);
               positionAttribute.needsUpdate = true;
+              this._tempPoint.pointPositions[0] = worldCoords[0];
+              this._tempPoint.pointPositions[1] = worldCoords[1];
+              this._tempPoint.pointPositions[2] = worldCoords[2];
             } else {
               this._tempPoint = this.$module.scene.addTemporaryPoints(
                 [worldCoords], 0x00ffff);
@@ -2880,7 +2951,6 @@ export default {
         //this.$module.scene.enableAxisDisplay(true, true);
         this.isReady = true;
         this.calculateBoundingBox();
-        //console.log(`found ${foundNerves}`);
         this.$nextTick(() => {
           this.restoreSettings(options);
           this.$emit("on-ready");
@@ -3068,6 +3138,7 @@ export default {
           );
         }
         if (this.$module && this.$module.scene) {
+          this.$refs.scaffoldTreeControls.setModule(this.$module);
           this.$module.scene.displayMarkers = this.displayMarkers;
           this.$module.scene.forcePickableObjectsUpdate = true;
           this.$module.scene.displayMinimap = this.displayMinimap;

package/src/scripts/BaseModule.js

@@ -25,21 +25,6 @@ BaseModule.prototype.settingsChanged = function() {
   }
 }
 
-BaseModule.prototype.exportSettings = function() {
-  const settings = {};
-  settings.dialog = this.typeName;
-  settings.name = this.instanceName;
-  return settings;
-}
-
-BaseModule.prototype.importSettings = function(settings) {
-	if (settings.dialog == this.typeName) {
-		this.setName(settings.name);
-		return true;
-	}
-	return false;
-}
-
 BaseModule.prototype.publishChanges = function(annotations, eventType, zincObjects) {
   for (let i = 0; i < this.eventNotifiers.length; i++) {
     this.eventNotifiers[i].publish(this, eventType, annotations, zincObjects);
@@ -58,7 +43,7 @@ BaseModule.prototype.destroy = function() {
   }
 
   delete this;
-} 
+}
 
 BaseModule.prototype.addChangedCallback = function(callback) {
   if (this.onChangedCallbacks.includes(callback) == false)
@@ -70,7 +55,7 @@ BaseModule.prototype.removeChangedCallback = function(callback) {
   if (index > -1) {
     this.onChangedCallbacks.splice(index, 1);
   }
-} 
+}
 
 BaseModule.prototype.addNotifier = function(eventNotifier) {
   this.eventNotifiers.push(eventNotifier);