From 899132a9523ce90d14d2d5104ff302d525b80d16 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Tue, 4 May 2021 14:36:39 +0200
Subject: [PATCH] exmpt MVP use siibra-api for template/parc/region
Co-authored-by: Xiao Gui <xgui3783@gmail.com>
Co-authored-by: Daviti Gogshelidze <daviti1@mail.com>
---
.../regionalFeatures/bsFeatures/constants.ts | 3 +-
.../regionalFeatures/bsFeatures/module.ts | 5 -
.../splashScreen/splashScreen.component.ts | 5 -
.../atlasViewer.constantService.service.ts | 11 +-
src/main.module.ts | 7 +-
src/util/constants.ts | 1 +
src/util/fn.ts | 37 ++
src/util/pureConstant.service.ts | 528 +++++++++++++++---
src/util/siibraApiConstants/types.ts | 140 +++++
.../layerCtrl.service/layerCtrl.service.ts | 2 +-
10 files changed, 631 insertions(+), 108 deletions(-)
create mode 100644 src/util/siibraApiConstants/types.ts
diff --git a/src/atlasComponents/regionalFeatures/bsFeatures/constants.ts b/src/atlasComponents/regionalFeatures/bsFeatures/constants.ts
index 4bbc8df0f..1d2f42a5c 100644
--- a/src/atlasComponents/regionalFeatures/bsFeatures/constants.ts
+++ b/src/atlasComponents/regionalFeatures/bsFeatures/constants.ts
@@ -2,8 +2,7 @@ import { InjectionToken } from "@angular/core";
import { Observable } from "rxjs";
import { IHasId } from "src/util/interfaces";
import { TBSDetail, TBSSummary } from "./receptor/type";
-
-export const BS_ENDPOINT = new InjectionToken<string>('BS_ENDPOINT')
+export { BS_ENDPOINT } from 'src/util/constants'
export type TRegion = {
name: string
diff --git a/src/atlasComponents/regionalFeatures/bsFeatures/module.ts b/src/atlasComponents/regionalFeatures/bsFeatures/module.ts
index f4f16b8fa..185a3387c 100644
--- a/src/atlasComponents/regionalFeatures/bsFeatures/module.ts
+++ b/src/atlasComponents/regionalFeatures/bsFeatures/module.ts
@@ -1,6 +1,5 @@
import { CommonModule } from "@angular/common";
import { NgModule } from "@angular/core";
-import { BS_ENDPOINT } from "./constants";
import { BSFeatureReceptorModule } from "./receptor";
import { BsFeatureService } from "./service";
@@ -10,10 +9,6 @@ import { BsFeatureService } from "./service";
BSFeatureReceptorModule,
],
providers: [
- {
- provide: BS_ENDPOINT,
- useValue: BS_REST_URL || `https://brainscapes.apps-dev.hbp.eu`
- },
BsFeatureService
],
exports: [
diff --git a/src/atlasComponents/splashScreen/splashScreen/splashScreen.component.ts b/src/atlasComponents/splashScreen/splashScreen/splashScreen.component.ts
index d70b2ba32..b734cf054 100644
--- a/src/atlasComponents/splashScreen/splashScreen/splashScreen.component.ts
+++ b/src/atlasComponents/splashScreen/splashScreen/splashScreen.component.ts
@@ -30,7 +30,6 @@ export class SplashScreen implements AfterViewInit {
constructor(
private store: Store<IavRootStoreInterface>,
- private constanceService: AtlasViewerConstantsServices,
private pureConstantService: PureContantService
) {
this.loadedTemplate$ = this.store.pipe(
@@ -91,10 +90,6 @@ export class SplashScreen implements AfterViewInit {
})
)
}
-
- get totalTemplates() {
- return this.constanceService.templateUrls.length
- }
}
@Pipe({
diff --git a/src/atlasViewer/atlasViewer.constantService.service.ts b/src/atlasViewer/atlasViewer.constantService.service.ts
index b9484fd0f..bf9b870c4 100644
--- a/src/atlasViewer/atlasViewer.constantService.service.ts
+++ b/src/atlasViewer/atlasViewer.constantService.service.ts
@@ -26,12 +26,6 @@ export class AtlasViewerConstantsServices implements OnDestroy {
// instead of using window.location.href, which includes query param etc
public backendUrl = (BACKEND_URL && `${BACKEND_URL}/`.replace(/\/\/$/, '/')) || `${window.location.origin}${window.location.pathname}`
- public totalTemplates = null
-
- public getTemplateEndpoint$ = this.http.get(`${this.backendUrl}templates`, { responseType: 'json' }).pipe(
- shareReplay(1)
- )
-
public templateUrls = Array(100)
/* to be provided by KG in future */
@@ -217,10 +211,7 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
this.dissmissUserLayerSnackbarMessage = this.dissmissUserLayerSnackbarMessageDesktop
}
}),
- ),
- this.pureConstantService.getTemplateEndpoint$.subscribe(arr => {
- this.totalTemplates = arr.length
- })
+ )
}
private subscriptions: Subscription[] = []
diff --git a/src/main.module.ts b/src/main.module.ts
index f4a8fcaa0..887448d74 100644
--- a/src/main.module.ts
+++ b/src/main.module.ts
@@ -62,6 +62,7 @@ import { KgTosModule } from './ui/kgtos/module';
import { MouseoverModule } from './mouseoverModule/mouseover.module';
import { AtlasViewerRouterModule } from './routerModule';
import { MessagingGlue } from './messagingGlue';
+import { BS_ENDPOINT } from './util/constants';
export function debug(reducer: ActionReducer<any>): ActionReducer<any> {
return function(state, action) {
@@ -254,7 +255,11 @@ export function debug(reducer: ActionReducer<any>): ActionReducer<any> {
{
provide: WINDOW_MESSAGING_HANDLER_TOKEN,
useClass: MessagingGlue
- }
+ },
+ {
+ provide: BS_ENDPOINT,
+ useValue: (BS_REST_URL || `https://brainscapes.apps-dev.hbp.eu`).replace(/\/$/, '')
+ },
],
bootstrap : [
AtlasViewer,
diff --git a/src/util/constants.ts b/src/util/constants.ts
index 0236f4e41..773b99b8b 100644
--- a/src/util/constants.ts
+++ b/src/util/constants.ts
@@ -115,3 +115,4 @@ export const compareLandmarksChanged: (prevLandmarks: any[], newLandmarks: any[]
}
export const CYCLE_PANEL_MESSAGE = `[spacebar] to cycle through views`
+export const BS_ENDPOINT = new InjectionToken<string>('BS_ENDPOINT')
diff --git a/src/util/fn.ts b/src/util/fn.ts
index 4f673a08e..96369e7dd 100644
--- a/src/util/fn.ts
+++ b/src/util/fn.ts
@@ -83,3 +83,40 @@ export function switchMapWaitFor(opts: ISwitchMapWaitFor){
mapTo(arg)
)
}
+
+export class MultiDimMap{
+
+ private map = new Map()
+
+ static GetKey(...arg: any[]){
+ let mapKey = ``
+ for (let i = 0; i < arg.length; i++) {
+ mapKey += arg[i]
+ }
+ return mapKey
+ }
+
+ set(...arg: any[]) {
+ const mapKey = MultiDimMap.GetKey(...(arg.slice(0, -1)))
+ this.map.set(mapKey, arg[arg.length - 1])
+ }
+ get(...arg: any[]) {
+ const mapKey = MultiDimMap.GetKey(...arg)
+ return this.map.get(mapKey)
+ }
+ delete(...arg: any[]) {
+ const mapKey = MultiDimMap.GetKey(...arg)
+ return this.map.delete(mapKey)
+ }
+}
+
+export function recursiveMutate<T>(arr: T[], getChildren: (obj: T) => T[], mutateFn: (obj: T) => void){
+ for (const obj of arr) {
+ mutateFn(obj)
+ recursiveMutate(
+ getChildren(obj),
+ getChildren,
+ mutateFn
+ )
+ }
+}
diff --git a/src/util/pureConstant.service.ts b/src/util/pureConstant.service.ts
index 6bd40e68d..7224fd7f9 100644
--- a/src/util/pureConstant.service.ts
+++ b/src/util/pureConstant.service.ts
@@ -1,15 +1,142 @@
-import { Injectable, OnDestroy } from "@angular/core";
+import { Inject, Injectable, OnDestroy } from "@angular/core";
import { Store, select } from "@ngrx/store";
import { Observable, merge, Subscription, of, forkJoin, fromEvent, combineLatest, timer } from "rxjs";
import { viewerConfigSelectorUseMobileUi } from "src/services/state/viewerConfig.store.helper";
-import { shareReplay, tap, scan, catchError, filter, switchMap, map, take, distinctUntilChanged } from "rxjs/operators";
+import { shareReplay, tap, scan, catchError, filter, switchMap, map, take, distinctUntilChanged, mapTo } from "rxjs/operators";
import { HttpClient } from "@angular/common/http";
import { viewerStateFetchedTemplatesSelector, viewerStateSetFetchedAtlases } from "src/services/state/viewerState.store.helper";
import { AtlasWorkerService } from "src/atlasViewer/atlasViewer.workerService.service";
import { LoggingService } from "src/logging";
import { viewerStateFetchedAtlasesSelector } from "src/services/state/viewerState/selectors";
+import { BS_ENDPOINT } from "src/util/constants";
+import { flattenReducer } from 'common/util'
+import { TAtlas, TId, TParc, TRegion, TSpaceFull, TSpaceSummary } from "./siibraApiConstants/types";
+import { MultiDimMap, recursiveMutate } from "./fn";
-const getUniqueId = () => Math.round(Math.random() * 1e16).toString(16)
+function parseId(id: TId){
+ if (typeof id === 'string') return id
+ return `${id.kg.kgSchema}/${id.kg.kgId}`
+}
+
+type THasId = {
+ ['@id']: string
+ name: string
+}
+
+type TIAVAtlas = {
+ templateSpaces: ({ availableIn: THasId[] } & THasId)[]
+ parcellations: ({
+ availableIn: THasId[]
+ baseLayer: boolean
+ '@version': {
+ name: string
+ '@next': string
+ '@previous': string
+ '@this': string
+ }
+ } & THasId)[]
+} & THasId
+
+function getNehubaConfig(darkTheme: boolean) {
+ const backgrd = darkTheme
+ ? [0,0,0,1]
+ : [1,1,1,1]
+
+ const rmPsp = darkTheme
+ ? {"mode":"<","color":[0.1,0.1,0.1,1]}
+ :{"color":[1,1,1,1],"mode":"=="}
+ const drawSubstrates = darkTheme
+ ? {"color":[0.5,0.5,1,0.2]}
+ : {"color":[0,0,0.5,0.15]}
+ const drawZoomLevels = darkTheme
+ ? {"cutOff":150000}
+ : {"cutOff":200000,"color":[0.5,0,0,0.15] }
+
+ return {
+ "configName": "",
+ "globals": {
+ "hideNullImageValues": true,
+ "useNehubaLayout": {
+ "keepDefaultLayouts": false
+ },
+ "useNehubaMeshLayer": true,
+ "rightClickWithCtrlGlobal": false,
+ "zoomWithoutCtrlGlobal": false,
+ "useCustomSegmentColors": true
+ },
+ "zoomWithoutCtrl": true,
+ "hideNeuroglancerUI": true,
+ "rightClickWithCtrl": true,
+ "rotateAtViewCentre": true,
+ "enableMeshLoadingControl": true,
+ "zoomAtViewCentre": true,
+ "restrictUserNavigation": true,
+ "disableSegmentSelection": false,
+ "dataset": {
+ "imageBackground": backgrd,
+ "initialNgState": {
+ "showDefaultAnnotations": false,
+ "layers": {},
+ // "navigation": {
+ // "pose": {
+ // "position": {
+ // "voxelSize": [
+ // 21166.666015625,
+ // 20000,
+ // 21166.666015625
+ // ],
+ // "voxelCoordinates": [
+ // -21.8844051361084,
+ // 16.288618087768555,
+ // 28.418994903564453
+ // ]
+ // }
+ // },
+ // "zoomFactor": 350000
+ // },
+ "perspectiveOrientation": [
+ 0.3140767216682434,
+ -0.7418519854545593,
+ 0.4988985061645508,
+ -0.3195493221282959
+ ],
+ "perspectiveZoom": 1922235.5293810747
+ }
+ },
+ "layout": {
+ "views": "hbp-neuro",
+ "planarSlicesBackground": backgrd,
+ "useNehubaPerspective": {
+ "enableShiftDrag": false,
+ "doNotRestrictUserNavigation": false,
+ "perspectiveSlicesBackground": backgrd,
+ "removePerspectiveSlicesBackground": rmPsp,
+ "perspectiveBackground": backgrd,
+ "fixedZoomPerspectiveSlices": {
+ "sliceViewportWidth": 300,
+ "sliceViewportHeight": 300,
+ "sliceZoom": 563818.3562426177,
+ "sliceViewportSizeMultiplier": 2
+ },
+ "mesh": {
+ "backFaceColor": backgrd,
+ "removeBasedOnNavigation": true,
+ "flipRemovedOctant": true
+ },
+ "centerToOrigin": true,
+ "drawSubstrates": drawSubstrates,
+ "drawZoomLevels": drawZoomLevels,
+ "hideImages": false,
+ "waitForMesh": true,
+ "restrictZoomLevel": {
+ "minZoom": 1200000,
+ "maxZoom": 3500000
+ }
+ }
+ }
+ }
+
+}
@Injectable({
providedIn: 'root'
@@ -17,96 +144,103 @@ const getUniqueId = () => Math.round(Math.random() * 1e16).toString(16)
export class PureContantService implements OnDestroy{
+ private subscriptions: Subscription[] = []
public useTouchUI$: Observable<boolean>
- public fetchedAtlases$: Observable<any>
public darktheme$: Observable<boolean>
public totalAtlasesLength: number
public allFetchingReady$: Observable<boolean>
- public backendUrl = (BACKEND_URL && `${BACKEND_URL}/`.replace(/\/\/$/, '/')) || `${window.location.origin}${window.location.pathname}`
+ private atlasParcSpcRegionMap = new MultiDimMap()
+
+ private _backendUrl = (BACKEND_URL && `${BACKEND_URL}/`.replace(/\/\/$/, '/')) || `${window.location.origin}${window.location.pathname}`
+ get backendUrl() {
+ console.warn(`something is using backendUrl`)
+ return this._backendUrl
+ }
+ /**
+ * TODO remove
+ * when removing, also remove relevant worker code
+ */
private workerUpdateParcellation$ = fromEvent(this.workerService.worker, 'message').pipe(
filter((message: MessageEvent) => message && message.data && message.data.type === 'UPDATE_PARCELLATION_REGIONS'),
map(({ data }) => data)
)
- private fetchTemplate = (templateUrl) => this.http.get(`${this.backendUrl}${templateUrl}`, { responseType: 'json' }).pipe(
- switchMap((template: any) => {
- if (template.nehubaConfig) {
- return of(template)
- }
- if (template.nehubaConfigURL) {
- return this.http.get(`${this.backendUrl}${template.nehubaConfigURL}`, { responseType: 'json' }).pipe(
- map(nehubaConfig => {
- return {
- ...template,
- nehubaConfig,
- }
- }),
- )
+ private getRegions(atlasId: string, parcId: string, spaceId: string){
+ return this.http.get<TRegion[]>(
+ `${this.bsEndpoint}/atlases/${encodeURIComponent(atlasId)}/parcellations/${encodeURIComponent(parcId)}/regions`,
+ {
+ params: {
+ space_id: spaceId
+ },
+ responseType: 'json'
}
- return of(template)
- }),
- )
+ )
+ }
- private processTemplate = template => forkJoin(
- template.parcellations.map(parcellation => {
+ private getParcs(atlasId: string){
+ return this.http.get<TParc[]>(
+ `${this.bsEndpoint}/atlases/${encodeURIComponent(atlasId)}/parcellations`,
+ { responseType: 'json' }
+ )
+ }
- const id = getUniqueId()
+ private getParcDetail(atlasId: string, parcId: string) {
+ return this.http.get<TParc>(
+ `${this.bsEndpoint}/atlases/${encodeURIComponent(atlasId)}/parcellations/${encodeURIComponent(parcId)}`,
+ { responseType: 'json' }
+ )
+ }
- this.workerService.worker.postMessage({
- type: 'PROPAGATE_PARC_REGION_ATTR',
- parcellation,
- inheritAttrsOpts: {
- ngId: (parcellation as any ).ngId,
- relatedAreas: [],
- fullId: null
- },
- id
- })
+ private getSpaces(atlasId: string){
+ return this.http.get<TSpaceSummary[]>(
+ `${this.bsEndpoint}/atlases/${encodeURIComponent(atlasId)}/spaces`,
+ { responseType: 'json' }
+ )
+ }
- return this.workerUpdateParcellation$.pipe(
- filter(({ id: returnedId }) => id === returnedId),
- take(1),
- map(({ parcellation }) => parcellation)
- )
- })
- )
+ private getSpaceDetail(atlasId: string, spaceId: string) {
+ return this.http.get<TSpaceFull>(
+ `${this.bsEndpoint}/atlases/${encodeURIComponent(atlasId)}/spaces/${encodeURIComponent(spaceId)}`,
+ { responseType: 'json' }
+ )
+ }
- public getTemplateEndpoint$ = this.http.get<any[]>(`${this.backendUrl}templates`, { responseType: 'json' }).pipe(
- catchError(() => {
- this.log.warn(`fetching root /tempaltes error`)
- return of([])
- }),
- shareReplay(),
- )
+ private getSpacesAndParc(atlasId: string) {
+ const spaces$ = this.getSpaces(atlasId).pipe(
+ switchMap(spaces => forkJoin(
+ spaces.map(space => this.getSpaceDetail(atlasId, parseId(space.id)))
+ ))
+ )
+ const parcs$ = this.getParcs(atlasId).pipe(
+ // need not to get full parc data. first level gets all data
+ // switchMap(parcs => forkJoin(
+ // parcs.map(parc => this.getParcDetail(atlasId, parseId(parc.id)))
+ // ))
+ )
+ return forkJoin([
+ spaces$,
+ parcs$,
+ ]).pipe(
+ map(([ templateSpaces, parcellations ]) => {
+ return { templateSpaces, parcellations }
+ })
+ )
+ }
- public initFetchTemplate$ = this.getTemplateEndpoint$.pipe(
- switchMap((templates: string[]) => merge(
- ...templates.map(templateName => this.fetchTemplate(templateName).pipe(
- switchMap(template => this.processTemplate(template).pipe(
- map(parcellations => {
- return {
- ...template,
- parcellations
- }
- })
- ))
- )),
- )),
- catchError((err) => {
- this.log.warn(`fetching templates error`, err)
- return of(null)
- }),
- )
+ private getFullRegions(atlasId: string, parcId: string, spaceId: string) {
+
+ }
constructor(
private store: Store<any>,
private http: HttpClient,
private log: LoggingService,
private workerService: AtlasWorkerService,
+ @Inject(BS_ENDPOINT) private bsEndpoint: string,
){
this.darktheme$ = this.store.pipe(
select(state => state?.viewerState?.templateSelected?.useTheme === 'dark')
@@ -117,21 +251,6 @@ export class PureContantService implements OnDestroy{
shareReplay(1)
)
- this.fetchedAtlases$ = this.http.get(`${this.backendUrl.replace(/\/$/, '')}/atlases/`, { responseType: 'json' }).pipe(
- catchError((err, obs) => of(null)),
- filter(v => !!v),
- tap((arr: any[]) => this.totalAtlasesLength = arr.length),
- switchMap(atlases => merge(
- ...atlases.map(({ url }) => this.http.get(
- /^http/.test(url)
- ? url
- : `${this.backendUrl.replace(/\/$/, '')}/${url}`,
- { responseType: 'json' }))
- )),
- scan((acc, curr) => acc.concat(curr).sort((a, b) => (a.order || 1000) - (b.order || 1001)), []),
- shareReplay(1)
- )
-
this.subscriptions.push(
this.fetchedAtlases$.subscribe(fetchedAtlases =>
this.store.dispatch(
@@ -141,7 +260,8 @@ export class PureContantService implements OnDestroy{
)
this.allFetchingReady$ = combineLatest([
- this.getTemplateEndpoint$.pipe(
+ this.initFetchTemplate$.pipe(
+ filter(v => !!v),
map(arr => arr.length),
),
this.store.pipe(
@@ -161,7 +281,247 @@ export class PureContantService implements OnDestroy{
)
}
- private subscriptions: Subscription[] = []
+ private getAtlases$ = this.http.get<TAtlas[]>(
+ `${this.bsEndpoint}/atlases`,
+ {
+ responseType: 'json'
+ }
+ ).pipe(
+ shareReplay(1)
+ )
+
+ public fetchedAtlases$: Observable<TIAVAtlas[]> = this.getAtlases$.pipe(
+ switchMap(atlases => {
+ return forkJoin(
+ atlases.map(
+ atlas => this.getSpacesAndParc(atlas.id).pipe(
+ map(({ templateSpaces, parcellations }) => {
+ return {
+ '@id': atlas.id,
+ name: atlas.name,
+ templateSpaces: templateSpaces.map(tmpl => {
+ return {
+ '@id': tmpl.id,
+ name: tmpl.name,
+ availableIn: tmpl.availableParcellations.map(parc => {
+ return {
+ '@id': parc.id,
+ name: parc.name
+ }
+ })
+ }
+ }),
+ parcellations: parcellations.map(parc => {
+ return {
+ '@id': parseId(parc.id),
+ name: parc.name,
+ baseLayer: parc.modality === 'cytoarchitecture',
+ '@version': {
+ '@next': parc.version?.next,
+ '@previous': parc.version?.prev,
+ 'name': parc.version?.name,
+ '@this': parseId(parc.id)
+ },
+ availableIn: parc.availableSpaces.map(space => {
+ return {
+ '@id': space.id,
+ name: space.name,
+ /**
+ * TODO need original data format
+ */
+ // originalDatasetFormats: [{
+ // name: "probability map"
+ // }]
+ }
+ })
+ }
+ })
+ }
+ })
+ )
+ )
+ )
+ }),
+ catchError((err, obs) => of([])),
+ tap((arr: any[]) => this.totalAtlasesLength = arr.length),
+ scan((acc, curr) => acc.concat(curr).sort((a, b) => (a.order || 1000) - (b.order || 1001)), []),
+ shareReplay(1)
+ )
+
+ public initFetchTemplate$ = this.fetchedAtlases$.pipe(
+ switchMap(atlases => {
+ return forkJoin(
+ atlases.map(atlas => this.getSpacesAndParc(atlas['@id']).pipe(
+ switchMap(({ templateSpaces, parcellations }) => {
+ const ngLayerObj = {}
+ return forkJoin(
+ templateSpaces.map(
+ tmpl => {
+ ngLayerObj[tmpl.id] = {}
+ return tmpl.availableParcellations.map(
+ parc => this.getRegions(atlas['@id'], parc.id, tmpl.id).pipe(
+ tap(regions => {
+ recursiveMutate(
+ regions,
+ region => region.children,
+ region => {
+ /**
+ * individual map(s)
+ * this should work for both fully mapped and interpolated
+ * in the case of interpolated, it sucks that the ngLayerObj will be set multiple times
+ */
+ if (
+ tmpl.id in region.volumeSrc
+ && 'collect' in region.volumeSrc[tmpl.id]
+ ) {
+ const dedicatedMap = region.volumeSrc[tmpl.id]['collect'].filter(v => v.volume_type === 'neuroglancer/precomputed')
+ if (dedicatedMap.length === 1) {
+ const ngId = MultiDimMap.GetKey(atlas['@id'], tmpl.id, parc.id, dedicatedMap[0].id)
+ region['ngId'] = ngId
+ region['labelIndex'] = dedicatedMap[0].detail['neuroglancer/precomputed'].labelIndex
+ ngLayerObj[tmpl.id][ngId] = {
+ source: `precomputed://${dedicatedMap[0].url}`,
+ type: "segmentation",
+ transform: dedicatedMap[0].detail['neuroglancer/precomputed'].transform
+ }
+ }
+ }
+
+ /**
+ * if label index is defined
+ */
+ if (!!region.labelIndex) {
+ const hemisphereKey = /left hemisphere/.test(region.name)
+ // these two keys are, unfortunately, more or less hardcoded
+ // which is less than ideal
+ ? 'left hemisphere'
+ : /right hemisphere/.test(region.name)
+ ? 'right hemisphere'
+ : 'whole brain'
+
+ /**
+ * TODO fix in siibra-api
+ */
+ if (
+ tmpl.id !== 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588'
+ && parc.id === 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25'
+ && hemisphereKey === 'whole brain'
+ ) {
+ region.labelIndex = null
+ return
+ }
+
+ const hemispheredNgId = MultiDimMap.GetKey(atlas['@id'], tmpl.id, parc.id, hemisphereKey)
+ region['ngId'] = hemispheredNgId
+ }
+ }
+ )
+ this.atlasParcSpcRegionMap.set(
+ atlas['@id'], tmpl.id, parc.id, regions
+ )
+
+ /**
+ * populate maps for parc
+ */
+ for (const parc of parcellations) {
+ if (tmpl.id in (parc.volumeSrc || {})) {
+ // key: 'left hemisphere' | 'right hemisphere' | 'whole brain'
+ for (const key in parc.volumeSrc[tmpl.id]) {
+ for (const vol of parc.volumeSrc[tmpl.id][key]) {
+ if (vol.volume_type === 'neuroglancer/precomputed') {
+ const ngIdKey = MultiDimMap.GetKey(atlas['@id'], tmpl.id, parseId(parc.id), key)
+ ngLayerObj[tmpl.id][ngIdKey] = {
+ source: `precomputed://${vol.url}`,
+ type: "segmentation",
+ transform: vol.detail['neuroglancer/precomputed'].transform
+ }
+ }
+ }
+ }
+ }
+ }
+ })
+ )
+ )
+ }
+ ).reduce(flattenReducer, [])
+ ).pipe(
+ mapTo({ templateSpaces, parcellations, ngLayerObj })
+ )
+ }),
+ map(({ templateSpaces, ngLayerObj }) => {
+ return templateSpaces.map(tmpl => {
+ const darkTheme = tmpl.src_volume_type === 'mri'
+ const nehubaConfig = getNehubaConfig(darkTheme)
+ const initialLayers = nehubaConfig.dataset.initialNgState.layers
+
+ const tmplNgId = tmpl.name
+ const tmplAuxMesh = `${tmpl.name} auxmesh`
+
+ const precomputed = tmpl.volume_src.find(src => src.volume_type === 'neuroglancer/precomputed')
+ if (precomputed) {
+ initialLayers[tmplNgId] = {
+ type: "image",
+ source: `precomputed://${precomputed.url}`,
+ transform: precomputed.detail['neuroglancer/precomputed'].transform
+ }
+ }
+
+ const precompmesh = tmpl.volume_src.find(src => src.volume_type === 'neuroglancer/precompmesh')
+ const auxMeshes = []
+ if (precompmesh){
+ initialLayers[tmplAuxMesh] = {
+ source: `precompmesh://${precompmesh.url}`,
+ type: "segmentation",
+ transform: precompmesh.detail['neuroglancer/precompmesh'].transform
+ }
+ for (const auxMesh of precompmesh.detail['neuroglancer/precompmesh'].auxMeshes) {
+
+ auxMeshes.push({
+ ...auxMesh,
+ ngId: tmplAuxMesh,
+ '@id': `${tmplAuxMesh} ${auxMesh.name}`,
+ visible: true
+ })
+ }
+ }
+
+ for (const key in (ngLayerObj[tmpl.id] || {})) {
+ initialLayers[key] = ngLayerObj[tmpl.id][key]
+ }
+
+ return {
+ name: tmpl.name,
+ '@id': tmpl.id,
+ fullId: tmpl.id,
+ useTheme: darkTheme ? 'dark' : 'light',
+ ngId: tmplNgId,
+ nehubaConfig,
+ auxMeshes,
+ parcellations: tmpl.availableParcellations.map(parc => {
+ const regions = this.atlasParcSpcRegionMap.get(atlas['@id'], tmpl.id, parc.id) || []
+ return {
+ fullId: parc.id,
+ '@id': parc.id,
+ name: parc.name,
+ regions
+ }
+ })
+ }
+ })
+ })
+ ))
+ )
+ }),
+ map(arr => {
+ return arr.reduce(flattenReducer, [])
+ }),
+ catchError((err) => {
+ this.log.warn(`fetching templates error`, err)
+ return of(null)
+ }),
+ shareReplay(1),
+ )
ngOnDestroy(){
while(this.subscriptions.length > 0) this.subscriptions.pop().unsubscribe()
diff --git a/src/util/siibraApiConstants/types.ts b/src/util/siibraApiConstants/types.ts
new file mode 100644
index 000000000..4510e27ee
--- /dev/null
+++ b/src/util/siibraApiConstants/types.ts
@@ -0,0 +1,140 @@
+type THref = {
+ href: string
+}
+
+type TSpaceType = 'mri' | 'histology'
+
+type TNgTransform = number[][]
+
+type TVolumeType = 'nii' | 'neuroglancer/precomputed' | 'neuroglancer/precompmesh' | 'detailed maps'
+type TParcModality = 'cytoarchitecture'
+
+type TAuxMesh = {
+ name: string
+ labelIndicies: number[]
+}
+
+interface IVolumeTypeDetail {
+ 'nii': null
+ 'neuroglancer/precomputed': {
+ 'neuroglancer/precomputed': {
+ 'transform': TNgTransform
+ }
+ }
+ 'neuroglancer/precompmesh': {
+ 'neuroglancer/precompmesh': {
+ 'auxMeshes': TAuxMesh[]
+ 'transform': TNgTransform
+ }
+ }
+ 'detailed maps': null
+}
+
+type TVolumeSrc<VolumeType extends keyof IVolumeTypeDetail> = {
+ id: string
+ name: string
+ url: string
+ volume_type: TVolumeType
+ detail: IVolumeTypeDetail[VolumeType]
+}
+
+type TKgIdentifier = {
+ kgSchema: string
+ kgId: string
+}
+
+type TVersion = {
+ name: string
+ prev: string | null
+ next: string | null
+}
+
+export type TId = string | { kg: TKgIdentifier }
+
+export type TAtlas = {
+ id: string
+ name: string
+ links: {
+ parcellations: THref
+ spaces: THref
+ }
+}
+
+export type TSpaceSummary = {
+ id: {
+ kg: TKgIdentifier
+ },
+ name: string
+ links: {
+ self: THref
+ }
+}
+
+export type TParcSummary = {
+ id: string
+ name: string
+}
+
+export type TSpaceFull = {
+ id: string
+ name: string
+ key: string //???
+ type: string //???
+ url: string //???
+ ziptarget: string //???
+ src_volume_type: TSpaceType
+ volume_src: TVolumeSrc<keyof IVolumeTypeDetail>[]
+ availableParcellations: TParcSummary[]
+ links: {
+ templates: THref
+ parcellation_maps: THref
+ }
+}
+
+export type TParc = {
+ id: {
+ kg: TKgIdentifier
+ }
+ name: string
+ availableSpaces: {
+ id: string
+ name: string
+ }[]
+ links: {
+ self: THref
+ }
+ regions: THref
+ modality: TParcModality
+ version: TVersion
+ volumeSrc: {
+ [key: string]: {
+ [key: string]: TVolumeSrc<keyof IVolumeTypeDetail>[]
+ }
+ }
+}
+
+export type TRegion = {
+ name: string
+ children: TRegion[]
+ volumeSrc: {
+ [key: string]: {
+ [key: string]: TVolumeSrc<keyof IVolumeTypeDetail>[]
+ }
+ }
+
+ labelIndex?: number
+ rgb?: number[]
+ id?: {
+ kg: TKgIdentifier
+ }
+
+ /**
+ * missing
+ */
+
+ originDatasets?: ({
+ filename: string
+ } & TKgIdentifier) []
+
+ position?: number[]
+}
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
index 7a338c72e..194681b36 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
@@ -10,7 +10,7 @@ import { IAuxMesh } from '../store'
export function getAuxMeshesAndReturnIColor(auxMeshes: IAuxMesh[]): IColorMap{
const returnVal: IColorMap = {}
for (const auxMesh of auxMeshes as IAuxMesh[]) {
- const { ngId, labelIndicies, rgb } = auxMesh
+ const { ngId, labelIndicies, rgb = [255, 255, 255] } = auxMesh
const auxMeshColorMap = returnVal[ngId] || {}
for (const lblIdx of labelIndicies) {
auxMeshColorMap[lblIdx as number] = {
--
GitLab