diff --git a/package-lock.json b/package-lock.json
index ecb53104c7d5b6939da22d90b41344f8a82c2473..8e7f6b6a39ea268baf93a705910d5bae30c429ea 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -23,7 +23,7 @@
"@ngrx/effects": "^14.3.2",
"@ngrx/store": "^14.3.2",
"acorn": "^8.4.1",
- "export-nehuba": "^0.1.0-dev.7",
+ "export-nehuba": "^0.1.0-dev.8",
"file-loader": "^6.2.0",
"jszip": "^3.6.0",
"postcss": "^8.3.6",
@@ -26966,9 +26966,9 @@
"dev": true
},
"node_modules/export-nehuba": {
- "version": "0.1.0-dev.7",
- "resolved": "https://registry.npmjs.org/export-nehuba/-/export-nehuba-0.1.0-dev.7.tgz",
- "integrity": "sha512-hBDeOWo/OoThgfqa9RtRpYlPj0/5RwgBsoMjHKYMRqgsscoYglfPYaMSG57mANEIii4hxnsFiUUXOQTn2B2P+w==",
+ "version": "0.1.0-dev.8",
+ "resolved": "https://registry.npmjs.org/export-nehuba/-/export-nehuba-0.1.0-dev.8.tgz",
+ "integrity": "sha512-nSiGMclXztCG5N9tNL9xf1Q8Eq2WN2FwtjJpXEtUxsIj/rzVWdU0EkEHjv6APDNTbDA9kgU2Nc61HLqcWWdIgQ==",
"dependencies": {
"pako": "^1.0.6"
}
diff --git a/package.json b/package.json
index 70a41160d17071ee9886ea4490c35ad23d394980..e0c290ded11056934fb23cf9ec04454531840cf8 100644
--- a/package.json
+++ b/package.json
@@ -66,7 +66,7 @@
"@ngrx/effects": "^14.3.2",
"@ngrx/store": "^14.3.2",
"acorn": "^8.4.1",
- "export-nehuba": "^0.1.0-dev.7",
+ "export-nehuba": "^0.1.0-dev.8",
"file-loader": "^6.2.0",
"jszip": "^3.6.0",
"postcss": "^8.3.6",
diff --git a/src/atlasComponents/annotations/annotation.service.ts b/src/atlasComponents/annotations/annotation.service.ts
index 3969bc420cdea13c69fef90bbc765de4b047e0de..f0a63f7aa298c0cad46efcd96a1dfbe452f1098b 100644
--- a/src/atlasComponents/annotations/annotation.service.ts
+++ b/src/atlasComponents/annotations/annotation.service.ts
@@ -167,9 +167,6 @@ export class AnnotationLayer {
}
private parseNgSpecType(spec: AnnotationSpec): _AnnotationSpec{
- const voxelSize = this.viewer.navigationState.voxelSize.toJSON()
- const sanitizePoint = (p: [number, number, number]) => p.map((v, idx) => v / voxelSize[idx]) as [number, number, number]
- const needSanitizePosition = voxelSize[0] !== 1 || voxelSize[1] !== 1 || voxelSize[2] !== 1
const overwrite: Partial<_AnnotationSpec> = {}
switch (spec.type) {
case "point": {
@@ -187,15 +184,6 @@ export class AnnotationLayer {
default: throw new Error(`overwrite type lookup failed for ${(spec as any).type}`)
}
- /**
- * The unit of annotation(s) depends on voxel size. If it is 1,1,1 then it would be in um, but often it is not.
- * If not sanitized, the annotation can be miles off.
- */
- if (needSanitizePosition) {
- for (const key of ['point', 'pointA', 'pointB'] ) {
- if (!!spec[key]) overwrite[key] = sanitizePoint(spec[key])
- }
- }
return {
...spec,
...overwrite,
diff --git a/src/messagingGlue.ts b/src/messagingGlue.ts
index ae415e68cff96abaaf964e6606a2a93df8cbc782..994bf30d8aab393eccfa769dc1ac17f1c5fcf8ce 100644
--- a/src/messagingGlue.ts
+++ b/src/messagingGlue.ts
@@ -86,7 +86,8 @@ export class MessagingGlue implements IWindowMessaging, OnDestroy {
"1"
],
transform: transform,
- clType: 'customlayer/nglayer' as const
+ clType: 'customlayer/nglayer' as const,
+ type: 'segmentation',
}
this.store.dispatch(
diff --git a/src/util/periodic.service.ts b/src/util/periodic.service.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e3e280cbc541f9a891dc6d7fd36f54dbb5ef385d
--- /dev/null
+++ b/src/util/periodic.service.ts
@@ -0,0 +1,57 @@
+import { Injectable } from "@angular/core";
+import { Subject, combineLatest, interval, merge } from "rxjs";
+import { filter, map, scan } from "rxjs/operators";
+import { getUuid } from "./fn";
+
+type Queue = {
+ callback: () => boolean
+ uuid: string
+}
+
+@Injectable({
+ providedIn: 'root'
+})
+export class PeriodicSvc{
+ #queue$ = new Subject<Queue>()
+ #dequeue$ = new Subject<Queue>()
+ #scannedQueue$ = merge<{ queue?: Queue, dequeue?: Queue }>(
+ this.#queue$.pipe(
+ map(queue => ({ queue })),
+ ),
+ this.#dequeue$.pipe(
+ map(dequeue => ({ dequeue }))
+ )
+ ).pipe(
+ scan((acc, curr) => {
+ const { queue, dequeue } = curr
+ if (queue) {
+ return [...acc, queue]
+ }
+ if (dequeue) {
+ return acc.filter(q => q.uuid !== dequeue.uuid)
+ }
+ console.warn(`neither queue nor dequeue were defined!`)
+ return acc
+ }, [] as Queue[])
+ )
+
+ addToQueue(callback: () => boolean){
+ this.#queue$.next({ callback, uuid: getUuid() })
+ }
+ constructor(){
+ combineLatest([
+ this.#scannedQueue$,
+ interval(160)
+ ]).pipe(
+ map(([queues, _]) => queues),
+ filter(queues => queues.length > 0),
+ ).subscribe(queues => {
+ for (const queue of queues) {
+ const { callback } = queue
+ if (callback()) {
+ this.#dequeue$.next(queue)
+ }
+ }
+ })
+ }
+}
diff --git a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
index 073893847ad53cd310d9252333f7124a4031147d..1bdcedc1685bc6605bb95f56f9e881daebadf6f0 100644
--- a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
@@ -13,6 +13,7 @@ import { IColorMap, SET_COLORMAP_OBS, SET_LAYER_VISIBILITY } from "../layerCtrl.
*/
import { INgLayerCtrl, NG_LAYER_CONTROL, SET_SEGMENT_VISIBILITY, TNgLayerCtrl } from "../layerCtrl.service/layerCtrl.util";
import { NgCoordinateSpace, Unit } from "../types";
+import { PeriodicSvc } from "src/util/periodic.service";
function translateUnit(unit: Unit) {
if (unit === "m") {
@@ -118,6 +119,7 @@ export class NehubaViewerUnit implements OnDestroy {
constructor(
public elementRef: ElementRef,
private log: LoggingService,
+ private periodicSvc: PeriodicSvc,
@Inject(IMPORT_NEHUBA_INJECT_TOKEN) getImportNehubaPr: () => Promise<any>,
@Optional() @Inject(NEHUBA_INSTANCE_INJTKN) private nehubaViewer$: Subject<NehubaViewerUnit>,
@Optional() @Inject(SET_MESHES_TO_LOAD) private injSetMeshesToLoad$: Observable<IMeshesToLoad>,
@@ -475,6 +477,27 @@ export class NehubaViewerUnit implements OnDestroy {
/* if the layer exists, it will not be loaded */
!viewer.layerManager.getLayerByName(key))
.map(key => {
+ /**
+ * new implementation of neuroglancer treats swc as a mesh layer of segmentation layer
+ * But it cannot *directly* be accessed by nehuba's setMeshesToLoad, since it filters by
+ * UserSegmentationLayer.
+ *
+ * The below monkey patch sets the mesh to load, allow the SWC to be shown
+ */
+ const isSwc = layerObj[key]['source'].includes("swc://")
+ const hasSegment = (layerObj[key]["segments"] || []).length > 0
+ if (isSwc && hasSegment) {
+ this.periodicSvc.addToQueue(
+ () => {
+ const layer = viewer.layerManager.getLayerByName(key)
+ if (!(layer?.layer)) {
+ return false
+ }
+ layer.layer.displayState.visibleSegments.setMeshesToLoad([1])
+ return true
+ }
+ )
+ }
viewer.layerManager.addManagedLayer(
viewer.layerSpecification.getLayer(key, layerObj[key]))
diff --git a/src/viewerModule/nehuba/userLayers/service.ts b/src/viewerModule/nehuba/userLayers/service.ts
index 0bc5bb32e6dbf1a727144c32006856f8156e3911..41d16e71bc3e20aa74f717d11ec8a598d13b3c42 100644
--- a/src/viewerModule/nehuba/userLayers/service.ts
+++ b/src/viewerModule/nehuba/userLayers/service.ts
@@ -77,6 +77,7 @@ export class UserLayerService implements OnDestroy {
options: {
segments: ["1"],
transform: xform,
+ type: "segmentation"
},
}
}
diff --git a/third_party/vanilla.html b/third_party/vanilla.html
index 38206ec40b244a8b3011c6850dc46aa41f047b2f..be223e1e38ab861e649e4c4666e894d0a48c6f8c 100644
--- a/third_party/vanilla.html
+++ b/third_party/vanilla.html
@@ -8,6 +8,7 @@
<script src="main.bundle.js"></script>
<link rel="stylesheet" href="vanilla_styles.css">
+ <link rel="stylesheet" href="main.css">
</head>
<body>
<div id="neuroglancer-container"></div>