From 2369b09905193cd5efe3edecac400d215fa41ec2 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Tue, 28 Jun 2022 10:19:48 +0200
Subject: [PATCH] bugfix: hiding meshes when multiple seg maps exist bugfix:
circular imports bugfix: catch annotation svc undefined reference chore:
added transform backend to csp
---
deploy/csp/index.js | 8 +-
.../annotations/annotation.service.ts | 3 +-
src/viewerModule/nehuba/constants.ts | 2 +
.../layerCtrl.service/layerCtrl.effects.ts | 8 +-
.../layerCtrl.service/layerCtrl.service.ts | 7 +-
.../nehuba/mesh.service/mesh.service.spec.ts | 133 ++++++++++++++----
.../nehuba/mesh.service/mesh.service.ts | 55 +++++---
7 files changed, 154 insertions(+), 62 deletions(-)
diff --git a/deploy/csp/index.js b/deploy/csp/index.js
index 7273c69b4..898228ce8 100644
--- a/deploy/csp/index.js
+++ b/deploy/csp/index.js
@@ -54,7 +54,9 @@ const connectSrc = [
'object.cscs.ch',
// required for dataset previews
- 'hbp-kg-dataset-previewer.apps.hbp.eu/v2/',
+
+ // spatial transform
+ "hbp-spatial-backend.apps.hbp.eu",
// injected by env var
...CSP_CONNECT_SRC
@@ -102,7 +104,6 @@ module.exports = {
],
imgSrc: [
"'self'",
- "hbp-kg-dataset-previewer.apps.hbp.eu/v2/"
],
scriptSrc:[
"'self'",
@@ -118,6 +119,9 @@ module.exports = {
...WHITE_LIST_SRC,
...defaultAllowedSites
],
+ frameSrc: [
+ "*"
+ ],
reportUri: CSP_REPORT_URI || '/report-violation'
},
reportOnly
diff --git a/src/atlasComponents/annotations/annotation.service.ts b/src/atlasComponents/annotations/annotation.service.ts
index ec352e5fb..fd67601ee 100644
--- a/src/atlasComponents/annotations/annotation.service.ts
+++ b/src/atlasComponents/annotations/annotation.service.ts
@@ -146,7 +146,8 @@ export class AnnotationLayer {
}
}
updateAnnotation(spec: AnnotationSpec) {
- const localAnnotations = this.nglayer.layer.localAnnotations
+ const localAnnotations = this.nglayer?.layer?.localAnnotations
+ if (!localAnnotations) return
const ref = localAnnotations.references.get(spec.id)
const _spec = this.parseNgSpecType(spec)
if (ref) {
diff --git a/src/viewerModule/nehuba/constants.ts b/src/viewerModule/nehuba/constants.ts
index 6537a7aef..ca5ae4be8 100644
--- a/src/viewerModule/nehuba/constants.ts
+++ b/src/viewerModule/nehuba/constants.ts
@@ -64,3 +64,5 @@ export interface IMeshesToLoad {
}
export const SET_MESHES_TO_LOAD = new InjectionToken<Observable<IMeshesToLoad>>('SET_MESHES_TO_LOAD')
+
+export const PMAP_LAYER_NAME = 'regional-pmap'
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
index 6f6d70887..579f7fb79 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
@@ -11,7 +11,7 @@ import { EnumColorMapName } from "src/util/colorMaps";
import { getShader } from "src/util/constants";
import { getNgLayersFromVolumesATP, getRegionLabelIndex } from "../config.service";
import { ParcVolumeSpec } from "../store/util";
-import { NehubaLayerControlService } from "./layerCtrl.service";
+import { PMAP_LAYER_NAME } from "../constants";
@Injectable()
export class LayerCtrlEffects {
@@ -22,7 +22,7 @@ export class LayerCtrlEffects {
),
mapTo(
atlasAppearance.actions.removeCustomLayer({
- id: NehubaLayerControlService.PMAP_LAYER_NAME
+ id: PMAP_LAYER_NAME
})
)
))
@@ -42,7 +42,7 @@ export class LayerCtrlEffects {
atlasAppearance.actions.addCustomLayer({
customLayer: {
clType: "customlayer/nglayer",
- id: NehubaLayerControlService.PMAP_LAYER_NAME,
+ id: PMAP_LAYER_NAME,
source: `nifti://${sapiRegion.getMapUrl(template["@id"])}`,
shader: getShader({
colormap: EnumColorMapName.VIRIDIS,
@@ -55,7 +55,7 @@ export class LayerCtrlEffects {
),
catchError(() => of(
atlasAppearance.actions.removeCustomLayer({
- id: NehubaLayerControlService.PMAP_LAYER_NAME
+ id: PMAP_LAYER_NAME
})
))
)
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
index ba8b1d0ad..5980c76d6 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
@@ -13,6 +13,7 @@ import { arrayEqual } from "src/util/array";
import { ColorMapCustomLayer } from "src/state/atlasAppearance";
import { SapiRegionModel } from "src/atlasComponents/sapi";
import { AnnotationLayer } from "src/atlasComponents/annotations";
+import { PMAP_LAYER_NAME } from "../constants"
export const BACKUP_COLOR = {
red: 255,
@@ -25,8 +26,6 @@ export const BACKUP_COLOR = {
})
export class NehubaLayerControlService implements OnDestroy{
- static PMAP_LAYER_NAME = 'regional-pmap'
-
private selectedRegion$ = this.store$.pipe(
select(atlasSelection.selectors.selectedRegions),
shareReplay(1),
@@ -367,7 +366,7 @@ export class NehubaLayerControlService implements OnDestroy{
*/
return customLayers
.map(l => l.id)
- .filter(name => name !== NehubaLayerControlService.PMAP_LAYER_NAME)
+ .filter(name => name !== PMAP_LAYER_NAME)
})
),
this.customLayers$.pipe(
@@ -378,7 +377,7 @@ export class NehubaLayerControlService implements OnDestroy{
}),
distinctUntilChanged(),
map(flag => flag
- ? [ NehubaLayerControlService.PMAP_LAYER_NAME ]
+ ? [ PMAP_LAYER_NAME ]
: []
)
)
diff --git a/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts b/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
index 62a4ce09e..ef3ac5332 100644
--- a/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
+++ b/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
@@ -7,7 +7,7 @@ import { SapiRegionModel } from "src/atlasComponents/sapi"
import * as configSvc from "../config.service"
import { LayerCtrlEffects } from "../layerCtrl.service/layerCtrl.effects"
import { NEVER, of, pipe } from "rxjs"
-import { mapTo } from "rxjs/operators"
+import { mapTo, take } from "rxjs/operators"
import { selectorAuxMeshes } from "../store"
@@ -51,6 +51,12 @@ describe('> mesh.service.ts', () => {
)
)
})
+
+ afterEach(() => {
+ getParcNgIdSpy.calls.reset()
+ getRegionLabelIndexSpy.calls.reset()
+ getATPSpy.calls.reset()
+ })
describe('> NehubaMeshService', () => {
beforeEach(() => {
TestBed.configureTestingModule({
@@ -72,37 +78,106 @@ describe('> mesh.service.ts', () => {
expect(service).toBeTruthy()
})
- it('> mixes in auxillaryMeshIndices', () => {
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(atlasSelection.selectors.selectedRegions, [ fits1 ])
- mockStore.overrideSelector(atlasSelection.selectors.selectedParcAllRegions, [])
- mockStore.overrideSelector(selectorAuxMeshes, [auxMesh])
+ describe("> loadMeshes$", () => {
- const ngId = 'blabla'
- const labelIndex = 12
- getParcNgIdSpy.and.returnValue(ngId)
- getRegionLabelIndexSpy.and.returnValue(labelIndex)
+ describe("> auxMesh defined", () => {
+
+ const ngId = 'blabla'
+ const labelIndex = 12
+
+ beforeEach(() => {
+
+ const mockStore = TestBed.inject(MockStore)
+ mockStore.overrideSelector(atlasSelection.selectors.selectedRegions, [ fits1 ])
+ mockStore.overrideSelector(atlasSelection.selectors.selectedParcAllRegions, [])
+ mockStore.overrideSelector(selectorAuxMeshes, [auxMesh])
+
+ getParcNgIdSpy.and.returnValue(ngId)
+ getRegionLabelIndexSpy.and.returnValue(labelIndex)
- const service = TestBed.inject(NehubaMeshService)
-
- expect(
- service.loadMeshes$
- ).toBeObservable(
- hot('(ab)', {
- a: {
- layer: {
- name: ngId
- },
- labelIndicies: [ labelIndex ]
- },
- b: {
- layer: {
- name: auxMesh.ngId,
- },
- labelIndicies: auxMesh.labelIndicies
- }
})
- )
+
+ it("> auxMesh ngId labelIndex emitted", () => {
+
+ const service = TestBed.inject(NehubaMeshService)
+ expect(
+ service.loadMeshes$
+ ).toBeObservable(
+ hot('(ab)', {
+ a: {
+ layer: {
+ name: ngId
+ },
+ labelIndicies: [ labelIndex ]
+ },
+ b: {
+ layer: {
+ name: auxMesh.ngId,
+ },
+ labelIndicies: auxMesh.labelIndicies
+ }
+ })
+ )
+ })
+ })
+
+ describe("> if multiple ngid and labelindicies are present", () => {
+
+ const ngId1 = 'blabla'
+ const labelIndex1 = 12
+
+ const ngId2 = 'foobar'
+ const labelIndex2 = 13
+
+ beforeEach(() => {
+
+ const mockStore = TestBed.inject(MockStore)
+ mockStore.overrideSelector(atlasSelection.selectors.selectedRegions, [ fits1 ])
+ mockStore.overrideSelector(atlasSelection.selectors.selectedParcAllRegions, [fits1, fits1])
+ mockStore.overrideSelector(selectorAuxMeshes, [])
+
+ getParcNgIdSpy.and.returnValues(ngId1, ngId2, ngId2)
+ getRegionLabelIndexSpy.and.returnValues(labelIndex1, labelIndex2, labelIndex2)
+ })
+
+ it('> should call getParcNgIdSpy and getRegionLabelIndexSpy thrice', () => {
+ const service = TestBed.inject(NehubaMeshService)
+ service.loadMeshes$.pipe(
+ take(1)
+ ).subscribe(() => {
+
+ expect(getParcNgIdSpy).toHaveBeenCalledTimes(3)
+ expect(getRegionLabelIndexSpy).toHaveBeenCalledTimes(3)
+ })
+ })
+
+ /**
+ * in the case of julich brain 2.9 in colin 27, we expect selecting a region will hide meshes from all relevant ngIds (both left and right)
+ */
+ it('> expect the emitted value to be incl all ngIds', () => {
+ const service = TestBed.inject(NehubaMeshService)
+ expect(
+ service.loadMeshes$
+ ).toBeObservable(
+ hot('(ab)', {
+ a: {
+ layer: {
+ name: ngId1
+ },
+ labelIndicies: []
+ },
+ b: {
+ layer: {
+ name: ngId2
+ },
+ labelIndicies: [ labelIndex2 ]
+ }
+ })
+ )
+
+ })
+ })
+
})
})
})
diff --git a/src/viewerModule/nehuba/mesh.service/mesh.service.ts b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
index 2585f0022..d372ce460 100644
--- a/src/viewerModule/nehuba/mesh.service/mesh.service.ts
+++ b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
@@ -47,7 +47,40 @@ export class NehubaMeshService implements OnDestroy {
]).pipe(
switchMap(([{ atlas, template, parcellation }, regions, selectedRegions]) => {
const ngIdRecord: Record<string, number[]> = {}
+
+ const tree = new Tree(
+ regions,
+ (c, p) => (c.hasParent || []).some(_p => _p["@id"] === p["@id"])
+ )
+
+ for (const r of regions) {
+ const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
+ if (!regionLabelIndex) {
+ continue
+ }
+ if (
+ tree.someAncestor(r, anc => !!getRegionLabelIndex(atlas, template, parcellation, anc))
+ ) {
+ continue
+ }
+ const ngId = getParcNgId(atlas, template, parcellation, r)
+ if (!ngIdRecord[ngId]) {
+ ngIdRecord[ngId] = []
+ }
+ ngIdRecord[ngId].push(regionLabelIndex)
+ }
+
if (selectedRegions.length > 0) {
+ /**
+ * If regions are selected, reset the meshes
+ */
+ for (const key in ngIdRecord) {
+ ngIdRecord[key] = []
+ }
+
+ /**
+ * only show selected region
+ */
for (const r of selectedRegions) {
const ngId = getParcNgId(atlas, template, parcellation, r)
const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
@@ -56,28 +89,6 @@ export class NehubaMeshService implements OnDestroy {
}
ngIdRecord[ngId].push(regionLabelIndex)
}
- } else {
- const tree = new Tree(
- regions,
- (c, p) => (c.hasParent || []).some(_p => _p["@id"] === p["@id"])
- )
-
- for (const r of regions) {
- const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
- if (!regionLabelIndex) {
- continue
- }
- if (
- tree.someAncestor(r, (anc) => !!getRegionLabelIndex(atlas, template, parcellation, anc))
- ) {
- continue
- }
- const ngId = getParcNgId(atlas, template, parcellation, r)
- if (!ngIdRecord[ngId]) {
- ngIdRecord[ngId] = []
- }
- ngIdRecord[ngId].push(regionLabelIndex)
- }
}
const arr: IMeshesToLoad[] = []
--
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