Merge pull request #1092 from FZJ-INM1-BDA/dev_fix_hide_annotations

Do not hide annotations with parcellation

angular.json

 {
   "$schema": "./node_modules/@angular/cli/lib/config/schema.json",
+  "cli": {
+    "analytics": false
+  },
   "version": 1,
   "newProjectRoot": "projects",
   "projects": {

e2e/checklist.md

@@ -48,4 +48,11 @@
     - [ ] high res hoc1, hoc2, hoc3, lam1-6 are visible
 - [ ] Waxholm
   - [ ] v4 are visible
-  - [ ] on hover, show correct region name(s)
\ No newline at end of file
+  - [ ] on hover, show correct region name(s)
+
+## saneURL
+- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/bigbrainGreyWhite) redirects to big brain
+- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/julichbrain) redirects to julich brain (colin 27)
+- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/whs4) redirects to waxholm v4
+- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/allen2017) redirects to allen 2017
+- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/mebrains) redirects to monkey

src/util/pureConstant.service.ts

@@ -56,6 +56,20 @@ type TIAVAtlas = {
   } & THasId)[]
 } & THasId
 
+type TNehubaConfig = Record<string, {
+  source: string
+  transform: number[][]
+  type: 'segmentation' | 'image'
+}>
+
+type TViewerConfig = TNehubaConfig
+
+/**
+ * key value pair of
+ * atlasId -> templateId -> viewerConfig
+ */
+type TAtlasTmplViewerConfig = Record<string, Record<string, TViewerConfig>>
+
 export const spaceMiscInfoMap = new Map([
   ['minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588', {
     name: 'bigbrain',
@@ -515,12 +529,20 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
     shareReplay(1)
   )
 
+  private atlasTmplConfig: TAtlasTmplViewerConfig = {}
+
+  async getViewerConfig(atlasId: string, templateId: string, parcId: string) {
+    const atlasLayers = this.atlasTmplConfig[atlasId]
+    const templateLayers = atlasLayers && atlasLayers[templateId]
+    return templateLayers || {}
+  }
+
   public initFetchTemplate$ = this.fetchedAtlases$.pipe(
     switchMap(atlases => {
       return forkJoin(
         atlases.map(atlas => this.getSpacesAndParc(atlas['@id']).pipe(
           switchMap(({ templateSpaces, parcellations }) => {
-            const ngLayerObj = {}
+            this.atlasTmplConfig[atlas["@id"]] = {}
             return forkJoin(
               templateSpaces.map(
                 tmpl => {
@@ -535,7 +557,7 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
                       name: 'Julich-Brain Probabilistic Cytoarchitectonic Maps (v2.9)'
                     })
                   }
-                  ngLayerObj[tmpl.id] = {}
+                  this.atlasTmplConfig[atlas["@id"]][tmpl.id] = {}
                   return tmpl.availableParcellations.map(
                     parc => this.getRegions(atlas['@id'], parc.id, tmpl.id).pipe(
                       tap(regions => {
@@ -558,7 +580,7 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
                               const ngId = getNgId(atlas['@id'], tmpl.id, parc.id, dedicatedMap[0]['@id'])
                               region['ngId'] = ngId
                               region['labelIndex'] = dedicatedMap[0].detail['neuroglancer/precomputed'].labelIndex
-                              ngLayerObj[tmpl.id][ngId] = {
+                              this.atlasTmplConfig[atlas["@id"]][tmpl.id][ngId] = {
                                 source: `precomputed://${dedicatedMap[0].url}`,
                                 type: "segmentation",
                                 transform: dedicatedMap[0].detail['neuroglancer/precomputed'].transform
@@ -622,7 +644,7 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
                             const key = 'whole brain'
 
                             const ngIdKey = getNgId(atlas['@id'], tmpl.id, parseId(parc.id), key)
-                            ngLayerObj[tmpl.id][ngIdKey] = {
+                            this.atlasTmplConfig[atlas["@id"]][tmpl.id][ngIdKey] = {
                               source: `precomputed://${vol.url}`,
                               type: "segmentation",
                               transform: vol.detail['neuroglancer/precomputed'].transform
@@ -639,7 +661,7 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
                             }]
                             for (const { key, mapIndex } of mapIndexKey) {
                               const ngIdKey = getNgId(atlas['@id'], tmpl.id, parseId(parc.id), key)
-                              ngLayerObj[tmpl.id][ngIdKey] = {
+                              this.atlasTmplConfig[atlas["@id"]][tmpl.id][ngIdKey] = {
                                 source: `precomputed://${precomputedVols[mapIndex].url}`,
                                 type: "segmentation",
                                 transform: precomputedVols[mapIndex].detail['neuroglancer/precomputed'].transform
@@ -660,7 +682,7 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
                 }
               ).reduce(flattenReducer, [])
             ).pipe(
-              mapTo({ templateSpaces, parcellations, ngLayerObj })
+              mapTo({ templateSpaces, parcellations, ngLayerObj: this.atlasTmplConfig })
             )
           }),
           map(({ templateSpaces, parcellations, ngLayerObj }) => {
@@ -796,8 +818,8 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
                 }
               }
 
-              for (const key in (ngLayerObj[tmpl.id] || {})) {
-                initialLayers[key] = ngLayerObj[tmpl.id][key]
+              for (const key in (ngLayerObj[atlas["@id"]][tmpl.id] || {})) {
+                initialLayers[key] = ngLayerObj[atlas["@id"]][tmpl.id][key]
               }
 
               return {

src/viewerModule/nehuba/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.component.spec.ts

@@ -7,7 +7,7 @@ import { ComponentsModule } from "src/components"
 import { ngViewerSelectorOctantRemoval } from "src/services/state/ngViewerState.store.helper"
 import { viewerStateCustomLandmarkSelector, viewerStateSelectedTemplatePureSelector } from "src/services/state/viewerState/selectors"
 import { AngularMaterialModule } from "src/sharedModules"
-import { UtilModule } from "src/util"
+import {PureContantService, UtilModule} from "src/util"
 import { actionSetAuxMeshes, selectorAuxMeshes } from "../../store"
 import { NEHUBA_INSTANCE_INJTKN } from "../../util"
 import { ViewerCtrlCmp } from "./viewerCtrlCmp.component"
@@ -20,12 +20,31 @@ describe('> viewerCtrlCmp.component.ts', () => {
     let fixture: ComponentFixture<ViewerCtrlCmp>
     let loader: HarnessLoader
     let mockStore: MockStore
+
     let mockNehubaViewer = {
-      updateUserLandmarks: jasmine.createSpy()
+      updateUserLandmarks: jasmine.createSpy(),
+      nehubaViewer: {
+        ngviewer: {
+          layerManager: {
+            getLayerByName: jasmine.createSpy('getLayerByName'),
+            get managedLayers() {
+              return []
+            },
+            set managedLayers(val) {
+              return
+            }
+          },
+          display: {
+            scheduleRedraw: jasmine.createSpy('scheduleRedraw')
+          }
+        }
+      }
     }
 
     afterEach(() => {
       mockNehubaViewer.updateUserLandmarks.calls.reset()
+      mockNehubaViewer.nehubaViewer.ngviewer.layerManager.getLayerByName.calls.reset()
+      mockNehubaViewer.nehubaViewer.ngviewer.display.scheduleRedraw.calls.reset()
     })
 
     beforeEach( async () => {
@@ -43,7 +62,17 @@ describe('> viewerCtrlCmp.component.ts', () => {
           provideMockStore(),
           {
             provide: NEHUBA_INSTANCE_INJTKN,
-            useValue: new BehaviorSubject(mockNehubaViewer)
+            useFactory: () => {
+              return new BehaviorSubject(mockNehubaViewer).asObservable()
+            }
+          },
+          {
+            provide: PureContantService,
+            useFactory: () => {
+              return {
+                getViewerConfig: jasmine.createSpy('getViewerConfig')
+              }
+            }
           }
         ]
       }).compileComponents()
@@ -54,12 +83,12 @@ describe('> viewerCtrlCmp.component.ts', () => {
       mockStore.overrideSelector(viewerStateSelectedTemplatePureSelector, {})
       mockStore.overrideSelector(ngViewerSelectorOctantRemoval, true)
       mockStore.overrideSelector(viewerStateCustomLandmarkSelector, [])
+      mockStore.overrideSelector(selectorAuxMeshes, [])
     })
 
     describe('> can be init', () => {
 
       beforeEach(() => {
-        mockStore.overrideSelector(selectorAuxMeshes, [])
         fixture = TestBed.createComponent(ViewerCtrlCmp)
         fixture.detectChanges()
         loader = TestbedHarnessEnvironment.loader(fixture)
@@ -207,5 +236,120 @@ describe('> viewerCtrlCmp.component.ts', () => {
         )
       })
     })
+
+    describe('> flagDelin', () => {
+      let toggleParcVsblSpy: jasmine.Spy
+      beforeEach(() => {
+        fixture = TestBed.createComponent(ViewerCtrlCmp)
+        toggleParcVsblSpy = spyOn(fixture.componentInstance as any, 'toggleParcVsbl')
+        fixture.detectChanges()
+      })
+      it('> calls toggleParcVsbl', () => {
+        toggleParcVsblSpy.and.callFake(() => {})
+        fixture.componentInstance.flagDelin = false
+        expect(toggleParcVsblSpy).toHaveBeenCalled()
+      })
+    })
+    describe('> toggleParcVsbl', () => {
+      let getViewerConfigSpy: jasmine.Spy
+      let getLayerByNameSpy: jasmine.Spy
+      beforeEach(() => {
+        const pureCstSvc = TestBed.inject(PureContantService)
+        getLayerByNameSpy = mockNehubaViewer.nehubaViewer.ngviewer.layerManager.getLayerByName
+        getViewerConfigSpy = pureCstSvc.getViewerConfig as jasmine.Spy
+        fixture = TestBed.createComponent(ViewerCtrlCmp)
+        fixture.detectChanges()
+      })
+
+      it('> calls pureSvc.getViewerConfig', async () => {
+        getViewerConfigSpy.and.returnValue({})
+        await fixture.componentInstance['toggleParcVsbl']()
+        expect(getViewerConfigSpy).toHaveBeenCalled()
+      })
+
+      describe('> if _flagDelin is true', () => {
+        beforeEach(() => {
+          fixture.componentInstance['_flagDelin'] = true
+          fixture.componentInstance['hiddenLayerNames'] = [
+            'foo',
+            'bar',
+            'baz'
+          ]
+        })
+        it('> go through all hideen layer names and set them to true', async () => {
+          const setVisibleSpy = jasmine.createSpy('setVisible')
+          getLayerByNameSpy.and.returnValue({
+            setVisible: setVisibleSpy
+          })
+          await fixture.componentInstance['toggleParcVsbl']()
+          expect(getLayerByNameSpy).toHaveBeenCalledTimes(3)
+          for (const arg of ['foo', 'bar', 'baz']) {
+            expect(getLayerByNameSpy).toHaveBeenCalledWith(arg)
+          }
+          expect(setVisibleSpy).toHaveBeenCalledTimes(3)
+          expect(setVisibleSpy).toHaveBeenCalledWith(true)
+          expect(setVisibleSpy).not.toHaveBeenCalledWith(false)
+        })
+        it('> hiddenLayerNames resets', async () => {
+          await fixture.componentInstance['toggleParcVsbl']()
+          expect(fixture.componentInstance['hiddenLayerNames']).toEqual([])
+        })
+      })
+
+      describe('> if _flagDelin is false', () => {
+        let managedLayerSpyProp: jasmine.Spy
+        let setVisibleSpy: jasmine.Spy
+        beforeEach(() => {
+          fixture.componentInstance['_flagDelin'] = false
+          setVisibleSpy = jasmine.createSpy('setVisible')
+          getLayerByNameSpy.and.returnValue({
+            setVisible: setVisibleSpy
+          })
+          getViewerConfigSpy.and.resolveTo({
+            'foo': {},
+            'bar': {},
+            'baz': {}
+          })
+          managedLayerSpyProp = spyOnProperty(mockNehubaViewer.nehubaViewer.ngviewer.layerManager, 'managedLayers')
+          managedLayerSpyProp.and.returnValue([{
+            visible: true,
+            name: 'foo'
+          }, {
+            visible: false,
+            name: 'bar'
+          }, {
+            visible: true,
+            name: 'baz'
+          }])
+        })
+
+        afterEach(() => {
+          managedLayerSpyProp.calls.reset()
+        })
+
+        it('> calls schedulRedraw', async () => {
+          await fixture.componentInstance['toggleParcVsbl']()
+          await new Promise(rs => requestAnimationFrame(rs))
+          expect(mockNehubaViewer.nehubaViewer.ngviewer.display.scheduleRedraw).toHaveBeenCalled()
+        })
+
+        it('> only calls setVisible false on visible layers', async () => {
+          await fixture.componentInstance['toggleParcVsbl']()
+          expect(getLayerByNameSpy).toHaveBeenCalledTimes(2)
+          
+          for (const arg of ['foo', 'baz']) {
+            expect(getLayerByNameSpy).toHaveBeenCalledWith(arg)
+          }
+          expect(setVisibleSpy).toHaveBeenCalledTimes(2)
+          expect(setVisibleSpy).toHaveBeenCalledWith(false)
+          expect(setVisibleSpy).not.toHaveBeenCalledWith(true)
+        })
+
+        it('> sets hiddenLayerNames correctly', async () => {
+          await fixture.componentInstance['toggleParcVsbl']()
+          expect(fixture.componentInstance['hiddenLayerNames']).toEqual(['foo', 'baz'])
+        })
+      })
+    })
   })
 })

src/viewerModule/nehuba/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.component.ts

 import { Component, HostBinding, Inject, Optional } from "@angular/core";
 import { select, Store } from "@ngrx/store";
 import { combineLatest, merge, Observable, of, Subscription } from "rxjs";
-import { filter, map, pairwise, withLatestFrom } from "rxjs/operators";
+import {filter, map, pairwise, withLatestFrom} from "rxjs/operators";
 import { ngViewerActionSetPerspOctantRemoval } from "src/services/state/ngViewerState/actions";
 import { ngViewerSelectorOctantRemoval } from "src/services/state/ngViewerState/selectors";
-import { viewerStateCustomLandmarkSelector, viewerStateSelectedTemplatePureSelector } from "src/services/state/viewerState/selectors";
+import { viewerStateCustomLandmarkSelector, viewerStateGetSelectedAtlas, viewerStateSelectedTemplatePureSelector } from "src/services/state/viewerState/selectors";
 import { NehubaViewerUnit } from "src/viewerModule/nehuba";
 import { NEHUBA_INSTANCE_INJTKN } from "src/viewerModule/nehuba/util";
 import { ARIA_LABELS } from 'common/constants'
 import { actionSetAuxMeshes, selectorAuxMeshes } from "../../store";
 import { FormBuilder, FormControl, FormGroup } from "@angular/forms";
+import {PureContantService} from "src/util";
 
 @Component({
   selector: 'viewer-ctrl-component',
@@ -27,6 +28,9 @@ export class ViewerCtrlCmp{
   @HostBinding('attr.darktheme')
   darktheme = false
 
+  private selectedAtlasId: string
+  private selectedTemplateId: string
+
   private _flagDelin = true
   get flagDelin(){
     return this._flagDelin
@@ -68,9 +72,16 @@ export class ViewerCtrlCmp{
     select(selectorAuxMeshes),
   )
 
+  private nehubaInst: NehubaViewerUnit
+
+  get ngViewer() {
+    return this.nehubaInst?.nehubaViewer.ngviewer || (window as any).viewer
+  }
+
   constructor(
     private store$: Store<any>,
     formBuilder: FormBuilder,
+    private pureConstantService: PureContantService,
     @Optional() @Inject(NEHUBA_INSTANCE_INJTKN) private nehubaInst$: Observable<NehubaViewerUnit>,
   ){
 
@@ -83,20 +94,25 @@ export class ViewerCtrlCmp{
           this.customLandmarks$,
           this.nehubaInst$,
         ]).pipe(
-          filter(([_, neubaInst]) => !!neubaInst),
+          filter(([_, nehubaInst]) => !!nehubaInst),
         ).subscribe(([landmarks, nehubainst]) => {
           this.setOctantRemoval(landmarks.length === 0)
           nehubainst.updateUserLandmarks(landmarks)
-        })
+        }),
+        this.nehubaInst$.subscribe(nehubaInst => this.nehubaInst = nehubaInst)
       )
     } else {
       console.warn(`NEHUBA_INSTANCE_INJTKN not provided`)
     }
 
     this.sub.push(
+      this.store$.select(viewerStateGetSelectedAtlas)
+        .pipe(filter(a => !!a))
+        .subscribe(sa => this.selectedAtlasId = sa['@id']),
       this.store$.pipe(
         select(viewerStateSelectedTemplatePureSelector)
       ).subscribe(tmpl => {
+        this.selectedTemplateId = tmpl['@id']
         const { useTheme } = tmpl || {}
         this.darktheme = useTheme === 'dark'
       }),
@@ -152,29 +168,32 @@ export class ViewerCtrlCmp{
     )
   }
 
-  private toggleParcVsbl(){
-    const visibleParcLayers = ((window as any).viewer.layerManager.managedLayers)
-      .slice(1)
-      .filter(({ visible }) => visible)
-      .filter(layer => !this.auxMeshesNamesSet.has(layer.name))
+  private async toggleParcVsbl(){
+    const viewerConfig = await this.pureConstantService.getViewerConfig(this.selectedAtlasId, this.selectedTemplateId, null)
 
     if (this.flagDelin) {
       for (const name of this.hiddenLayerNames) {
-        const l = (window as any).viewer.layerManager.getLayerByName(name)
+        const l = this.ngViewer.layerManager.getLayerByName(name)
         l && l.setVisible(true)
       }
       this.hiddenLayerNames = []
     } else {
       this.hiddenLayerNames = []
-      for (const { name } of visibleParcLayers) {
-        const l = (window as any).viewer.layerManager.getLayerByName(name)
+      const segLayerNames: string[] = []
+      for (const layer of this.ngViewer.layerManager.managedLayers) {
+        if (layer.visible && layer.name in viewerConfig) {
+          segLayerNames.push(layer.name)
+        }
+      }
+      for (const name of segLayerNames) {
+        const l = this.ngViewer.layerManager.getLayerByName(name)
         l && l.setVisible(false)
         this.hiddenLayerNames.push( name )
       }
     }
-    
-    setTimeout(() => {
-      (window as any).viewer.display.scheduleRedraw()
+
+    requestAnimationFrame(() => {
+      this.ngViewer.display.scheduleRedraw()
     })
   }