diff --git a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html
index c3acb2dfb3de57075448fc2e25615408f24bf6f5..a8814bb6a035b6a5135a5167cc7730df51f8e05a 100644
--- a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html
+++ b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html
@@ -83,6 +83,7 @@
</ng-template>
<sxplr-feature-entry
+ [template]="template"
[parcellation]="parcellation"
[region]="region">
</sxplr-feature-entry>
diff --git a/src/environments/environment.common.ts b/src/environments/environment.common.ts
index a8511509d93b2e4b80abadfc5b814006f4a56611..75284adf0db83a1213cfb5f2b94293b46330e9b5 100644
--- a/src/environments/environment.common.ts
+++ b/src/environments/environment.common.ts
@@ -2,7 +2,7 @@ export const environment = {
GIT_HASH: 'unknown hash',
VERSION: 'unknown version',
- PRODUCTION: true,
+ PRODUCTION: false,
BACKEND_URL: null,
SIIBRA_API_ENDPOINTS: 'https://siibra-api-latest.apps-dev.hbp.eu/v3_0', //'https://siibra-api-stable.apps.hbp.eu/v2_0,https://siibra-api-stable.apps.jsc.hbp.eu/v2_0,https://siibra-api-stable-ns.apps.hbp.eu/v2_0',
SPATIAL_TRANSFORM_BACKEND: 'https://hbp-spatial-backend.apps.hbp.eu',
diff --git a/src/features/category-acc.directive.ts b/src/features/category-acc.directive.ts
index b998efb0a8cd27b8260424ee8928bf7a3f2efbd9..d578d36dabcfa260822a9208e4e276637f32f117 100644
--- a/src/features/category-acc.directive.ts
+++ b/src/features/category-acc.directive.ts
@@ -9,8 +9,6 @@ import { ListComponent } from './list/list.component';
})
export class CategoryAccDirective implements AfterContentInit, OnDestroy {
- constructor() { }
-
public isBusy$ = new BehaviorSubject<boolean>(false)
public total$ = new BehaviorSubject<number>(0)
diff --git a/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts b/src/features/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts
similarity index 86%
rename from tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts
rename to src/features/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts
index 084a7ed862896c530146930484e131b488b06470..8f67e9bc822dfc07d3a954b2ac5daf0e18ce04e0 100644
--- a/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts
+++ b/src/features/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts
@@ -7,8 +7,8 @@ import {MockStore, provideMockStore} from "@ngrx/store/testing";
import {Observable, of} from "rxjs";
import {SAPI} from "src/atlasComponents/sapi";
import {AngularMaterialModule} from "src/sharedModules";
-import { SapiAtlasModel, SapiModalityModel, SapiParcellationFeatureModel, SapiParcellationModel } from "src/atlasComponents/sapi/type";
import { HttpClientTestingModule, HttpTestingController } from "@angular/common/http/testing";
+import { SxplrAtlas, SxplrParcellation } from "src/atlasComponents/sapi/sxplrTypes";
/**
* injecting databrowser module is bad idea
@@ -41,7 +41,7 @@ describe('ConnectivityComponent', () => {
let httpTestingController: HttpTestingController;
let req
- const types: SapiModalityModel[] = [{
+ const types: any[] = [{
name: 'StreamlineCounts',
types: ['siibra/features/connectivity/streamlineCounts']
},{
@@ -52,19 +52,19 @@ describe('ConnectivityComponent', () => {
types: ['siibra/features/connectivity/functional']
}]
- let datasetList: SapiParcellationFeatureModel[] = [
+ let datasetList: SxplrParcellation[] = [
{
- '@id': 'id1',
+ id: 'id1',
name: 'id1',
cohort: 'HCP',
subject: '100',
'@type': 'siibra/features/connectivity/streamlineCounts',
- } as SapiParcellationFeatureModel, {
- '@id': 'id2',
+ } as any, {
+ id: 'id2',
name: 'id2',
cohort: '1000BRAINS',
subject: 'average',
- } as SapiParcellationFeatureModel
+ } as any
]
beforeEach(async () => {
@@ -113,11 +113,11 @@ describe('ConnectivityComponent', () => {
const parcellation = 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290'
const endp = await SAPI.BsEndpoint$.toPromise()
- component.atlas = { '@id': atlas } as SapiAtlasModel
- component.parcellation = { '@id': parcellation } as SapiParcellationModel
+ component.atlas = { id: atlas } as SxplrAtlas
+ component.parcellation = { id: parcellation } as any
component.types = types
- const url = `${endp}/atlases/${encodeURIComponent(atlas)}/parcellations/${encodeURIComponent(parcellation)}/features?type=${component.selectedTypeId}&size=${100}&page=${1}`
+ const url = `${endp}/atlases/${encodeURIComponent(atlas)}/parcellations/${encodeURIComponent(parcellation)}/features?type=${component.selectedType.id}&size=${100}&page=${1}`
req = httpTestingController.expectOne(`${url}`);
@@ -137,9 +137,9 @@ describe('ConnectivityComponent', () => {
expect(datasetList).toEqual(component.fetchedItems)
})
- it('> Cohorts are set correctly', () => {
- expect(datasetList.map(d => d.cohort)).toEqual(component.cohorts)
- })
+ // it('> Cohorts are set correctly', () => {
+ // expect(datasetList.map(d => d.cohort)).toEqual(component.cohorts)
+ // })
})
});
diff --git a/src/features/connectivity/connectivityBrowser/connectivityBrowser.component.ts b/src/features/connectivity/connectivityBrowser/connectivityBrowser.component.ts
new file mode 100644
index 0000000000000000000000000000000000000000..9ad528f325b6a0c1b109c98b010ded4e03d65a81
--- /dev/null
+++ b/src/features/connectivity/connectivityBrowser/connectivityBrowser.component.ts
@@ -0,0 +1,392 @@
+import {AfterViewInit, Component, ElementRef, OnDestroy, ViewChild, Input, ChangeDetectorRef} from "@angular/core";
+import {select, Store} from "@ngrx/store";
+import {fromEvent, Subscription, BehaviorSubject, Observable} from "rxjs";
+import {catchError, take, switchMap} from "rxjs/operators";
+
+import { atlasAppearance } from "src/state";
+import {SAPI} from "src/atlasComponents/sapi/sapi.service";
+import { of } from "rxjs";
+import {CustomLayer} from "src/state/atlasAppearance";
+import { HttpClient } from "@angular/common/http";
+import { SxplrAtlas, SxplrParcellation, SxplrRegion, SxplrTemplate } from "src/atlasComponents/sapi/sxplrTypes";
+import { actions, selectors } from "src/state/atlasSelection";
+import { translateV3Entities } from "src/atlasComponents/sapi/translateV3";
+
+@Component({
+ selector: 'sxplr-features-connectivity-browser',
+ templateUrl: './connectivityBrowser.template.html',
+ styleUrls: ['./connectivityBrowser.style.scss']
+})
+export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy {
+
+
+ @Input('sxplr-features-connectivity-browser-atlas')
+ atlas: SxplrAtlas
+
+ @Input('sxplr-features-connectivity-browser-template')
+ template: SxplrTemplate
+
+ @Input('sxplr-features-connectivity-browser-parcellation')
+ parcellation: SxplrParcellation
+
+ /**
+ * accordion expansion should only toggle the clearviewqueue state
+ * which should be the single source of truth
+ * setcolormaps$ is set by the presence/absence of clearviewqueue[CONNECTIVITY_NAME_PLATE]
+ */
+ private _isFirstUpdate = true
+ @Input()
+ set accordionExpanded(flag: boolean) {
+ /**
+ * ignore first update
+ */
+ if (this._isFirstUpdate) {
+ this._isFirstUpdate = false
+ return
+ }
+
+ if (this.types.length && !this.selectedType) this.selectType(this._types[0])
+
+ if (flag) {
+ if (this.selectedSubjectIndex >= 0 && this.allRegions.length) {
+ this.setCustomLayer()
+ } else {
+ this.setCustomLayerOnLoad = true
+ }
+ } else {
+ this.removeCustomLayer()
+ }
+
+ }
+
+ private _region: SxplrRegion
+ @Input()
+ set region(region) {
+ this._region = region
+ this.regionName = region.name
+ }
+
+ get region() {
+ return this._region
+ }
+
+
+ private _types: any[] = []
+ @Input()
+ set types(val) {
+ this._types = val.map(t => ({...t, shortName: t.name.split('.').pop()}))
+ }
+ get types() {
+ return this._types
+ }
+
+
+ public selectedType: any
+ public selectedCohort: string
+
+ public cohortDatasets: any[]
+
+ public selectedSubjectIndex = null
+ public selectedCohortDatasetIndex: any
+ public selectedCohortSubjects: any
+ public fetchedItems: any[] = []
+ public cohorts: string[]
+ public selectedView: 'subject' | 'average' | null
+ public averageDisabled: boolean = true
+ public subjectsDisabled: boolean = true
+
+ public regionName: string
+
+ public selectedDataset: any
+ public connectionsString: string
+ public pureConnections: { [key: string]: number }
+ public connectedAreas: BehaviorSubject<ConnectedArea[]> = new BehaviorSubject([])
+ public noConnectivityForRegion: boolean
+ private subscriptions: Subscription[] = []
+ public allRegions: SxplrRegion[] = []
+ private regionIndexInMatrix = -1
+ public defaultColorMap: Map<string, Map<number, { red: number, green: number, blue: number }>>
+ public matrixString: string
+ public fetchingPreData: boolean
+ public fetching: boolean
+ public connectivityLayerId = 'connectivity-colormap-id'
+ private setCustomLayerOnLoad = false
+ private customLayerEnabled: boolean
+
+ public logDisabled: boolean = true
+ public logChecked: boolean = true
+
+ private endpoint: string
+
+
+ @ViewChild('connectivityComponent') public connectivityComponentElement: ElementRef<any>
+ @ViewChild('fullConnectivityGrid') public fullConnectivityGridElement: ElementRef<any>
+
+ constructor(
+ private store$: Store,
+ private http: HttpClient,
+ private changeDetectionRef: ChangeDetectorRef,
+ protected sapi: SAPI
+ ) {
+ SAPI.BsEndpoint$.pipe(take(1)).subscribe(en => this.endpoint = `${en}/feature/RegionalConnectivity`)
+ }
+
+ public ngAfterViewInit(): void {
+ this.subscriptions.push(
+
+ this.store$.pipe(
+ select(selectors.selectedParcAllRegions)
+ ).subscribe(flattenedRegions => {
+ this.defaultColorMap = null
+ this.allRegions = flattenedRegions
+ if (this.setCustomLayerOnLoad) {
+ this.setCustomLayer()
+ this.setCustomLayerOnLoad = false
+ }
+ }),
+ )
+
+ this.subscriptions.push(
+ fromEvent(this.connectivityComponentElement.nativeElement, 'connectedRegionClicked', {capture: true})
+ .subscribe((e: CustomEvent) => {
+ this.navigateToRegion(e.detail.name)
+ }),
+ )
+ }
+
+ setCustomLayer() {
+ if (this.customLayerEnabled) {
+ this.removeCustomLayer()
+ }
+ const map = new Map<SxplrRegion, number[]>()
+ const areas = this.connectedAreas.value
+ for (const region of this.allRegions) {
+ const area = areas.find(a => a.name === region.name)
+ if (area) {
+ map.set(region, Object.values(area.color))
+ } else {
+ map.set(region, [255,255,255,0.1])
+ }
+ }
+ this.customLayerEnabled = true
+ const customLayer: CustomLayer = {
+ clType: 'customlayer/colormap',
+ id: this.connectivityLayerId,
+ colormap: map
+ }
+
+ this.store$.dispatch(
+ atlasAppearance.actions.addCustomLayer({customLayer})
+ )
+ }
+
+ removeCustomLayer() {
+ this.store$.dispatch(
+ atlasAppearance.actions.removeCustomLayer({
+ id: this.connectivityLayerId
+ })
+ )
+ }
+
+ clearCohortSelection() {
+ this.fetchedItems = []
+ this.selectedCohort = null
+ this.cohorts = []
+ this.selectedCohort = null
+ this.selectedCohortDatasetIndex = null
+ this.selectedCohortSubjects = null
+
+ this.selectedSubjectIndex = null
+ }
+
+ selectType(type) {
+ this.clearCohortSelection()
+ this.selectedType = type
+ this.removeCustomLayer()
+ this.getModality()
+ }
+
+
+ getModality() {
+ this.fetchingPreData = true
+ this.fetchModality().subscribe((res: any) => {
+
+ this.fetchedItems.push(...res.items)
+
+ this.cohorts = [...new Set(this.fetchedItems.map(item => item.cohort))]
+ this.fetchingPreData = false
+ this.changeDetectionRef.detectChanges()
+ this.selectCohort(this.cohorts[0])
+
+ })
+ }
+
+ public fetchModality = (): Observable<any> => {
+ const url = `${this.endpoint}?parcellation_id=${encodeURIComponent(this.parcellation.id)}&type=${encodeURIComponent(this.selectedType.shortName)}`
+ return this.http.get(url)
+ }
+
+ selectCohort(cohort: string) {
+ this.selectedCohort = cohort
+ this.averageDisabled = !this.fetchedItems.find(s => s.cohort === this.selectedCohort && !s.subjects.length)
+ this.subjectsDisabled = !this.fetchedItems.find(s => s.cohort === this.selectedCohort && s.subjects.length > 0)
+ this.selectedView = !this.averageDisabled? 'average' : 'subject'
+
+ this.cohortDatasets = this.fetchedItems.filter(i => this.selectedCohort === i.cohort)
+
+ this.selectedCohortDatasetChanged(0)
+ }
+
+ selectedCohortDatasetChanged(index) {
+ this.selectedCohortDatasetIndex = index
+ this.selectedCohortSubjects = this.cohortDatasets[index].subjects
+
+ this.selectedDataset = this.cohortDatasets[index].datasets[0]
+
+
+ const keepSubject = this.selectedSubjectIndex >= 0 && this.cohortDatasets[this.selectedCohortDatasetIndex].subjects
+ .includes(this.selectedCohortSubjects[this.selectedSubjectIndex])
+
+ this.subjectSliderChanged(keepSubject? this.selectedSubjectIndex : 0)
+ }
+
+ subjectSliderChanged(index: number) {
+ this.selectedSubjectIndex = index
+ this.fetchConnectivity()
+ }
+
+ fetchConnectivity() {
+ const subject = this.selectedCohortSubjects[this.selectedSubjectIndex]
+ const dataset = this.cohortDatasets[this.selectedCohortDatasetIndex]
+
+ this.fetching = true
+ const url = `${this.endpoint}/${dataset.id}?parcellation_id=${this.parcellation.id}&subject=${subject}&type=${this.selectedType.shortName}`
+
+ this.http.get(url).pipe(catchError(() => {
+ this.fetching = false
+ return of(null)
+ })).subscribe(ds => {
+ this.fetching = false
+ this.setMatrixData(ds.matrices[subject])
+ })
+ }
+
+ setMatrixData(data) {
+ this.regionIndexInMatrix = data.columns.findIndex(re => this.region.id === re['@id'])
+
+ if (this.regionIndexInMatrix < 0) {
+ this.noConnectivityForRegion = true
+ this.changeDetectionRef.detectChanges()
+ return
+ } else if (this.noConnectivityForRegion) {
+ this.noConnectivityForRegion = false
+ }
+
+ const regionProfile = data.data[this.regionIndexInMatrix]
+
+ const maxStrength = Math.max(...regionProfile)
+
+ this.logChecked = maxStrength > 1
+ this.logDisabled = maxStrength <= 1
+ const areas = regionProfile.reduce((p, c, i) => {
+ return {
+ ...p,
+ [data.columns[i].name]: c
+ }
+ }, {})
+
+ this.pureConnections = areas
+ this.connectionsString = JSON.stringify(areas)
+ this.connectedAreas.next(this.formatConnections(areas))
+
+ this.setCustomLayer()
+ this.matrixString = JSON.stringify(data.columns.map((mc, i) => ([mc.name, ...data.data[i]])))
+ this.changeDetectionRef.detectChanges()
+
+
+ return data
+ }
+
+
+ changeLog(checked: boolean) {
+ this.logChecked = checked
+ this.connectedAreas.next(this.formatConnections(this.pureConnections))
+ this.connectivityComponentElement.nativeElement.toggleShowLog()
+ this.setCustomLayer()
+ }
+
+ navigateToRegion(regionName: string) {
+ this.sapi.v3Get("/regions/{region_id}", {
+ path: {region_id: regionName},
+ query: {
+ parcellation_id: this.parcellation.id,
+ space_id: this.template.id
+ }
+ }).pipe(
+ switchMap(r => translateV3Entities.translateRegion(r))
+ ).subscribe(region => {
+ const centroid = region.centroid?.loc
+ if (centroid) {
+ this.store$.dispatch(
+ actions.navigateTo({
+ navigation: {
+ position: centroid.map(v => v*1e6),
+ },
+ animation: true
+ })
+ )
+ }
+ })
+ }
+
+ getRegionWithName(region: string) {
+ return this.allRegions.find(r => r.name === region)
+ }
+
+ exportConnectivityProfile() {
+ const a = document.querySelector('hbp-connectivity-matrix-row');
+ (a as any).downloadCSV()
+ }
+
+ public exportFullConnectivity() {
+ this.fullConnectivityGridElement?.nativeElement['downloadCSV']()
+ }
+
+ public ngOnDestroy(): void {
+ this.removeCustomLayer()
+ this.subscriptions.forEach(s => s.unsubscribe())
+ }
+
+ private formatConnections(areas: { [key: string]: number }) {
+ const cleanedObj = Object.keys(areas)
+ .map(key => ({name: key, numberOfConnections: areas[key]}))
+ .filter(f => f.numberOfConnections > 0)
+ .sort((a, b) => +b.numberOfConnections - +a.numberOfConnections)
+
+ const logMax = this.logChecked ? Math.log(cleanedObj[0].numberOfConnections) : cleanedObj[0].numberOfConnections
+ const colorAreas = []
+
+ cleanedObj.forEach((a) => {
+ colorAreas.push({
+ ...a,
+ color: {
+ r: this.colormap_red((this.logChecked ? Math.log(a.numberOfConnections) : a.numberOfConnections) / logMax ),
+ g: this.colormap_green((this.logChecked ? Math.log(a.numberOfConnections) : a.numberOfConnections) / logMax ),
+ b: this.colormap_blue((this.logChecked ? Math.log(a.numberOfConnections) : a.numberOfConnections) / logMax )
+ },
+ })
+ })
+ return colorAreas
+ }
+ private clamp = val => Math.round(Math.max(0, Math.min(1.0, val)) * 255)
+ private colormap_red = x => x < 0.7? this.clamp(4.0 * x - 1.5) : this.clamp(-4.0 * x + 4.5)
+ private colormap_green = x => x < 0.5? this.clamp(4.0 * x - 0.5) : this.clamp(-4.0 * x + 3.5)
+ private colormap_blue = x => x < 0.3? this.clamp(4.0 * x + 0.5) : this.clamp(-4.0 * x + 2.5)
+
+}
+
+type ConnectedArea = {
+ color: {r: number, g: number, b: number}
+ name: string
+ numberOfConnections: number
+}
diff --git a/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.stories.ts b/src/features/connectivity/connectivityBrowser/connectivityBrowser.stories.ts
similarity index 97%
rename from tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.stories.ts
rename to src/features/connectivity/connectivityBrowser/connectivityBrowser.stories.ts
index 870492b96ef2ef98bc6657c01e3b78652a23c945..2ce655aa057240574a16d6f4b8b1493cb03185bd 100644
--- a/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.stories.ts
+++ b/src/features/connectivity/connectivityBrowser/connectivityBrowser.stories.ts
@@ -8,10 +8,10 @@ import { SAPI, SapiAtlasModel, SapiParcellationModel } from "src/atlasComponents
import { getJba29Features, getHumanAtlas, getJba29 } from "src/atlasComponents/sapi/stories.base"
import {SapiParcellationFeatureMatrixModel, SapiParcellationFeatureModel} from "src/atlasComponents/sapi/type"
import { AngularMaterialModule } from "src/sharedModules"
-import {ConnectivityBrowserComponent} from "src/atlasComponents/sapiViews/features/connectivity";
import {PARSE_TYPEDARRAY} from "src/atlasComponents/sapi/sapi.service";
import {catchError, take} from "rxjs/operators"
import {of} from "rxjs";
+import { ConnectivityBrowserComponent } from "./connectivityBrowser.component"
@Component({
selector: 'autoradiograph-wrapper-cmp',
diff --git a/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.style.scss b/src/features/connectivity/connectivityBrowser/connectivityBrowser.style.scss
similarity index 100%
rename from tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.style.scss
rename to src/features/connectivity/connectivityBrowser/connectivityBrowser.style.scss
diff --git a/src/features/connectivity/connectivityBrowser/connectivityBrowser.template.html b/src/features/connectivity/connectivityBrowser/connectivityBrowser.template.html
new file mode 100644
index 0000000000000000000000000000000000000000..87e51584a0f6b4daf50190cf72221eec4ba185d2
--- /dev/null
+++ b/src/features/connectivity/connectivityBrowser/connectivityBrowser.template.html
@@ -0,0 +1,104 @@
+<div class="w-100 h-100 d-block d-flex flex-column sxplr-pb-2">
+ <div>
+ <div *ngIf="types && types.length"
+ class="flex-grow-0 flex-shrink-0 d-flex flex-row flex-nowrap d-flex flex-column">
+ <mat-form-field class="flex-grow-1 flex-shrink-1 w-100">
+ <mat-label>
+ Modality
+ </mat-label>
+ <mat-select [value]="selectedType" (selectionChange)="selectType($event.value)">
+ <mat-option *ngFor="let type of types" [value]="type">
+ {{ type.shortName }}
+ </mat-option>
+ </mat-select>
+ </mat-form-field>
+
+ <mat-form-field *ngIf="!fetchingPreData && selectedType" class="flex-grow-1 flex-shrink-1 w-100">
+ <mat-label>
+ Cohort
+ </mat-label>
+ <mat-select [value]="selectedCohort" (selectionChange)="selectCohort($event.value)">
+ <mat-option *ngFor="let cohort of cohorts" [value]="cohort">
+ {{ cohort }}
+ </mat-option>
+ </mat-select>
+ </mat-form-field>
+ </div>
+
+ <mat-radio-group *ngIf="selectedCohort" [(ngModel)]="selectedView">
+ <mat-radio-button value="average" class="m-2" [disabled]="averageDisabled" color="primary">
+ Average
+ </mat-radio-button>
+ <mat-radio-button value="subject" class="m-2" [disabled]="subjectsDisabled" color="primary">
+ Subject
+ </mat-radio-button>
+ </mat-radio-group>
+
+ <div *ngIf="cohortDatasets && cohortDatasets.length > 1"
+ class="flex-grow-0 flex-shrink-0 d-flex flex-nowrap align-items-center">
+ <div class="flex-grow-1 flex-shrink-1 w-100">
+ <mat-label>
+ Dataset
+ </mat-label>
+ <mat-slider [min]="0" [max]="cohortDatasets.length - 1" (change)="selectedCohortDatasetChanged($event.value)"
+ [value]="selectedCohortDatasetIndex" thumbLabel step="1" class="w-100">
+ </mat-slider>
+ </div>
+ </div>
+
+ <div *ngIf="selectedCohortDatasetIndex >= 0 && selectedCohortSubjects"
+ class="flex-grow-0 flex-shrink-0 d-flex flex-nowrap align-items-center">
+ <div class="flex-grow-1 flex-shrink-1 w-100">
+ <mat-label>
+ Subject
+ </mat-label>
+ <mat-slider [min]="0" [max]="selectedCohortSubjects.length - 1"
+ (change)="subjectSliderChanged($event.value)" [value]="selectedSubjectIndex"
+ thumbLabel step="1" class="w-100">
+ </mat-slider>
+ </div>
+ </div>
+ </div>
+
+ <div class="d-flex justify-content-center">
+ <mat-spinner *ngIf="fetching"></mat-spinner>
+ </div>
+
+ <div *ngIf="regionName && !fetching"
+ [style.visibility]="selectedCohort && (selectedSubjectIndex >= 0 || !averageDisabled)? 'visible' : 'hidden'"
+ class="d-flex align-items-center">
+ <mat-checkbox class="mr-2" [checked]="logChecked" (change)="changeLog($event.checked)"
+ [disabled]="logDisabled || noConnectivityForRegion">Log 10</mat-checkbox>
+ <button mat-button [matMenuTriggerFor]="exportMenu" [disabled]="!connectedAreas.value">
+ <i class="fas fa-download mr-2"></i>
+ <span>Export</span>
+ </button>
+ <button *ngIf="selectedDataset" iav-stop="mousedown click" class="icons" mat-icon-button sxplr-dialog
+ [sxplr-dialog-size]="null" [sxplr-dialog-data]="{
+ title: selectedDataset?.name,
+ descMd: selectedDataset?.description + '' + (selectedDataset?.authors && selectedDataset?.authors.join()),
+ actions: [selectedDataset.ebrains_page]
+ }">
+ <i class="fas fa-info"></i>
+ </button>
+ </div>
+
+ <hbp-connectivity-matrix-row #connectivityComponent
+ [style.visibility]="regionName && !fetching && !noConnectivityForRegion && selectedCohort
+ && (selectedSubjectIndex >= 0 || !averageDisabled)? 'visible' : 'hidden'"
+ [region]="regionName"
+ [connections]="connectionsString"
+ show-export="true" hide-export-view="true" theme="dark">
+ </hbp-connectivity-matrix-row>
+ <div *ngIf="noConnectivityForRegion">No connectivity for the region.</div>
+
+ <full-connectivity-grid #fullConnectivityGrid [matrix]="matrixString" [datasetName]="selectedDataset?.name"
+ [datasetDescription]="selectedDataset?.description" only-export="true">
+ </full-connectivity-grid>
+
+ <mat-menu #exportMenu="matMenu">
+ <button mat-menu-item [disabled]="noConnectivityForRegion"
+ (click)="exportConnectivityProfile()">Regional</button>
+ <button mat-menu-item (click)="exportFullConnectivity()">Dataset</button>
+ </mat-menu>
+</div>
\ No newline at end of file
diff --git a/src/features/connectivity/excludeConnectivity.pipe.ts b/src/features/connectivity/excludeConnectivity.pipe.ts
new file mode 100644
index 0000000000000000000000000000000000000000..829679fa1f2fc5bd2bdcd6c82b2ccd70ed752894
--- /dev/null
+++ b/src/features/connectivity/excludeConnectivity.pipe.ts
@@ -0,0 +1,15 @@
+import { Pipe, PipeTransform } from "@angular/core"
+import { Input } from "postcss"
+
+@Pipe({
+ name: 'isConnectivity',
+ pure: true
+})
+export class ExcludeConnectivityPipe implements PipeTransform {
+
+ public transform(datasets: any[], isConnectivity: boolean): any[] {
+ return datasets? isConnectivity? [datasets.find(d => d.key === 'connectivity')]
+ : datasets.filter(d => d.key !== 'connectivity')
+ : null
+ }
+}
diff --git a/tmpFeatures/connectivity/index.ts b/src/features/connectivity/index.ts
similarity index 100%
rename from tmpFeatures/connectivity/index.ts
rename to src/features/connectivity/index.ts
diff --git a/tmpFeatures/connectivity/module.ts b/src/features/connectivity/module.ts
similarity index 63%
rename from tmpFeatures/connectivity/module.ts
rename to src/features/connectivity/module.ts
index d796c5f22ce7b132574eadbcda22f8a4f672d949..96f346ac8a8938f8a2405315ce91874d4a3d231d 100644
--- a/tmpFeatures/connectivity/module.ts
+++ b/src/features/connectivity/module.ts
@@ -1,12 +1,13 @@
import { CommonModule } from "@angular/common";
import {CUSTOM_ELEMENTS_SCHEMA, NgModule} from "@angular/core";
import { SAPI } from "src/atlasComponents/sapi";
-import {ConnectivityBrowserComponent} from "src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.component";
-import {HasConnectivity} from "src/atlasComponents/sapiViews/features/connectivity/hasConnectivity.directive";
+
import {AngularMaterialModule} from "src/sharedModules";
import {FormsModule} from "@angular/forms";
import { DialogModule } from "src/ui/dialogInfo";
-import { ConnectivityDoiPipe } from "./connectivityDoi.pipe";
+
+import { ConnectivityBrowserComponent } from "./connectivityBrowser/connectivityBrowser.component";
+import { ExcludeConnectivityPipe } from "./excludeConnectivity.pipe";
@NgModule({
imports: [
@@ -17,12 +18,11 @@ import { ConnectivityDoiPipe } from "./connectivityDoi.pipe";
],
declarations: [
ConnectivityBrowserComponent,
- HasConnectivity,
- ConnectivityDoiPipe
+ ExcludeConnectivityPipe
],
exports: [
ConnectivityBrowserComponent,
- HasConnectivity
+ ExcludeConnectivityPipe
],
providers: [
SAPI,
diff --git a/src/features/entry/entry.component.html b/src/features/entry/entry.component.html
index bd413fc42578e9e81770dcfb62a677fcd70da7f8..97802ff5f431881e22e9e20ba78169cd48db088f 100644
--- a/src/features/entry/entry.component.html
+++ b/src/features/entry/entry.component.html
@@ -1,6 +1,6 @@
<mat-card>
<mat-accordion>
- <mat-expansion-panel *ngFor="let keyvalue of (cateogryCollections$ | async | keyvalue)"
+ <mat-expansion-panel *ngFor="let keyvalue of (cateogryCollections$ | async | keyvalue | isConnectivity : false)"
sxplrCategoryAcc
#categoryAcc="categoryAcc"
[ngClass]="{
@@ -23,23 +23,18 @@
<div class="c3-outer">
<div class="c3-inner">
-
<mat-card class="c3 mat-elevation-z4"
*ngFor="let feature of keyvalue.value"
[ngClass]="{
'sxplr-d-none': (list.state$ | async) === 'noresult'
}">
<mat-card-header>
-
<mat-card-title>
<span class="category-title sxplr-white-space-nowrap">
{{ feature.name | featureNamePipe }}
</span>
</mat-card-title>
-
</mat-card-header>
-
-
<mat-card-content>
<sxplr-feature-list
[template]="template"
@@ -51,15 +46,35 @@
#list="featureList"
>
</sxplr-feature-list>
-
<spinner-cmp *ngIf="(list.state$ | async) === 'busy'"></spinner-cmp>
-
</mat-card-content>
</mat-card>
</div>
</div>
</mat-expansion-panel>
- </mat-accordion>
+
+ <mat-expansion-panel sxplr-sapiviews-features-connectivity-check
+ #connectivityAccordion
+ *ngIf="(cateogryCollections$ | async | keyvalue | isConnectivity : true) as connectivity">
+ <mat-expansion-panel-header>
+ <mat-panel-title>
+ {{ connectivity[0].key }}
+ </mat-panel-title>
+ </mat-expansion-panel-header>
+
+ <sxplr-features-connectivity-browser class="pe-all flex-shrink-1"
+ [region]="region"
+ [sxplr-features-connectivity-browser-atlas]="atlas | async"
+ [sxplr-features-connectivity-browser-template]="template"
+ [sxplr-features-connectivity-browser-parcellation]="parcellation"
+ [accordionExpanded]="connectivityAccordion.expanded"
+ [types]="connectivity[0].value">
+ </sxplr-features-connectivity-browser>
+
+ </mat-expansion-panel>
+
+
+ </mat-accordion>
</mat-card>
diff --git a/src/features/entry/entry.component.ts b/src/features/entry/entry.component.ts
index e2bb436d012072e10c44060a60f4d8f4c2bf7096..691f65ff4e64b7b7ae427267c7b5cbad9912e07b 100644
--- a/src/features/entry/entry.component.ts
+++ b/src/features/entry/entry.component.ts
@@ -5,6 +5,7 @@ import { SAPI } from 'src/atlasComponents/sapi';
import { Feature } from 'src/atlasComponents/sapi/sxplrTypes';
import { FeatureBase } from '../base';
import * as userInteraction from "src/state/userInteraction"
+import { atlasSelection } from 'src/state';
const categoryAcc = <T extends Record<string, unknown>>(categories: T[]) => {
const returnVal: Record<string, T[]> = {}
@@ -31,6 +32,8 @@ export class EntryComponent extends FeatureBase {
super()
}
+ public atlas = this.store.select(atlasSelection.selectors.selectedAtlas)
+
private featureTypes$ = this.sapi.v3Get("/feature/_types", {}).pipe(
switchMap(resp =>
this.sapi.iteratePages(
diff --git a/src/features/fetch.directive.ts b/src/features/fetch.directive.ts
index eb40e4fd0b1c5bd5c8f33156272eab8598f7c3a2..d020b3caf173893ca79dc9b7061f3210da7cb032 100644
--- a/src/features/fetch.directive.ts
+++ b/src/features/fetch.directive.ts
@@ -6,7 +6,7 @@ import { SxplrParcellation, SxplrRegion, SxplrTemplate } from 'src/atlasComponen
import { FeatureType, SapiRoute } from 'src/atlasComponents/sapi/typeV3';
import { Feature, CorticalFeature, VoiFeature, TabularFeature } from "src/atlasComponents/sapi/sxplrTypes"
-type ObservableOf<Obs extends Observable<unknown>> = Parameters<Obs['subscribe']>[0] extends Function
+type ObservableOf<Obs extends Observable<unknown>> = Parameters<Obs['subscribe']>[0] extends () => void
? Parameters<Parameters<Obs['subscribe']>[0]>[0]
: never
diff --git a/src/features/module.ts b/src/features/module.ts
index 16214d8b14c72d81c28ffc8d3b1e5cc74eace3d0..7de3d6ea36a0404f869ca7a8a0b8663815b1e750 100644
--- a/src/features/module.ts
+++ b/src/features/module.ts
@@ -12,6 +12,7 @@ import { FeatureNamePipe } from "./featureName.pipe";
import { FetchDirective } from "./fetch.directive";
import { ListComponent } from './list/list.component';
import { CategoryAccDirective } from './category-acc.directive';
+import { SapiViewsFeatureConnectivityModule } from "./connectivity";
@NgModule({
imports: [
@@ -23,6 +24,7 @@ import { CategoryAccDirective } from './category-acc.directive';
MatTooltipModule,
UtilModule,
MatRippleModule,
+ SapiViewsFeatureConnectivityModule
],
declarations: [
EntryComponent,
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
index 39ddf875d79ecfdec692831dfacfaef290b6505e..a12d8fcfd2ad87cb8c2e545f7c43e657b4fcd70c 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
@@ -26,9 +26,9 @@ export class LayerCtrlEffects {
* TODO implement
*/
throw new Error(`IMPLEMENT ME`)
- for (const volumeFormat in volumeModel.providedVolumes) {
+ // for (const volumeFormat in volumeModel.providedVolumes) {
- }
+ // }
return []
}
diff --git a/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.ts b/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.ts
deleted file mode 100644
index 579e34570f4bb3d2abf69fe7af7d60ea9eefe433..0000000000000000000000000000000000000000
--- a/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.ts
+++ /dev/null
@@ -1,417 +0,0 @@
-import {AfterViewInit, Component, ElementRef, OnDestroy, ViewChild, Input, ChangeDetectorRef} from "@angular/core";
-import {select, Store} from "@ngrx/store";
-import {fromEvent, Subscription, BehaviorSubject, Observable} from "rxjs";
-import {catchError, take} from "rxjs/operators";
-import {
- SAPI,
- SapiAtlasModel,
- SapiParcellationModel,
- SapiRegionModel
-} from "src/atlasComponents/sapi";
-import { atlasAppearance, atlasSelection } from "src/state";
-import {PARSE_TYPEDARRAY} from "src/atlasComponents/sapi/sapi.service";
-import {SapiModalityModel, SapiParcellationFeatureMatrixModel, SapiParcellationFeatureModel} from "src/atlasComponents/sapi/type";
-import { of } from "rxjs";
-import {CustomLayer} from "src/state/atlasAppearance";
-import { HttpClient } from "@angular/common/http";
-
-@Component({
- selector: 'sxplr-sapiviews-features-connectivity-browser',
- templateUrl: './connectivityBrowser.template.html',
- styleUrls: ['./connectivityBrowser.style.scss']
-})
-export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy {
-
- @Input('sxplr-sapiviews-features-connectivity-browser-atlas')
- atlas: SapiAtlasModel
-
- @Input('sxplr-sapiviews-features-connectivity-browser-parcellation')
- parcellation: SapiParcellationModel
-
- /**
- * accordion expansion should only toggle the clearviewqueue state
- * which should be the single source of truth
- * setcolormaps$ is set by the presence/absence of clearviewqueue[CONNECTIVITY_NAME_PLATE]
- */
- private _isFirstUpdate = true
-
-
- @Input()
- set accordionExpanded(flag: boolean) {
- /**
- * ignore first update
- */
- if (this._isFirstUpdate) {
- this._isFirstUpdate = false
- return
- }
-
- if (flag) {
- if (this.selectedSubjectDatasetIndex >= 0 && this.allRegions.length) {
- this.setCustomLayer()
- } else {
- this.setCustomLayerOnLoad = true
- }
- } else {
- this.removeCustomLayer()
- }
-
- }
-
- public selectedType: string
- public selectedTypeId: string
- public selectedCohort: string
- public cohortSubjects: string[]
- public selectedSubjectIndex: number
- public selectedSubjectsDatasets: string[]
- public selectedSubjectDatasetIndex: number
- public fetchedItems: SapiParcellationFeatureModel[] = []
- public cohorts: string[]
- public selectedView: 'subject' | 'average' | null
- public averageDisabled: boolean = true
- public subjectsDisabled: boolean = true
-
- @Input()
- set region(val) {
- const newRegionName = val && val.name
-
- if (val.status
- && !val.name.includes('left hemisphere')
- && !val.name.includes('right hemisphere')) {
- this.regionHemisphere = val.status
- }
-
- this.regionName = newRegionName
- }
-
- public regionName: string
- public regionHemisphere: string = null
- public selectedDataset: SapiParcellationFeatureModel
- public connectionsString: string
- public pureConnections: { [key: string]: number }
- public connectedAreas: BehaviorSubject<ConnectedArea[]> = new BehaviorSubject([])
- public noConnectivityForRegion: boolean
- private subscriptions: Subscription[] = []
- public allRegions: SapiRegionModel[] = []
- private regionIndexInMatrix = -1
- public defaultColorMap: Map<string, Map<number, { red: number, green: number, blue: number }>>
- public matrixString: string
- public fetching: boolean
- public connectivityLayerId = 'connectivity-colormap-id'
- private setCustomLayerOnLoad = false
- private customLayerEnabled: boolean
-
- public logDisabled: boolean = true
- public logChecked: boolean = true
-
- private _types: SapiModalityModel[] = []
- @Input()
- set types(val) {
- this._types = val
- if (val && val.length) this.selectType(val[0].name)
- }
- get types() {
- return this._types
- }
-
- @ViewChild('connectivityComponent', {read: ElementRef}) public connectivityComponentElement: ElementRef<any>
- @ViewChild('fullConnectivityGrid') public fullConnectivityGridElement: ElementRef<any>
-
- constructor(
- private store$: Store,
- private sapi: SAPI,
- private http: HttpClient,
- private changeDetectionRef: ChangeDetectorRef,
- ) {}
-
- public ngAfterViewInit(): void {
- this.subscriptions.push(
-
- this.store$.pipe(
- select(atlasSelection.selectors.selectedParcAllRegions)
- ).subscribe(flattenedRegions => {
- this.defaultColorMap = null
- this.allRegions = flattenedRegions
- if (this.setCustomLayerOnLoad) {
- this.setCustomLayer()
- this.setCustomLayerOnLoad = false
- }
- }),
- )
-
- this.subscriptions.push(
- fromEvent(this.connectivityComponentElement?.nativeElement, 'customToolEvent', {capture: true})
- .subscribe((e: CustomEvent) => {
- if (e.detail.name === 'export csv') {
- // ToDo Fix in future to use component
- const a = document.querySelector('hbp-connectivity-matrix-row');
- (a as any).downloadCSV()
- }
- }),
- fromEvent(this.connectivityComponentElement?.nativeElement, 'connectedRegionClicked', {capture: true})
- .subscribe((e: CustomEvent) => {
- this.navigateToRegion(this.getRegionWithName(e.detail.name))
- }),
- )
- }
-
- setCustomLayer() {
- if (this.customLayerEnabled) {
- this.removeCustomLayer()
- }
- const map = new Map<SapiRegionModel, number[]>()
- const areas = this.connectedAreas.value
- for (const region of this.allRegions) {
- const area = areas.find(a => a.name === region.name)
- if (area) {
- map.set(region, Object.values(area.color))
- } else {
- map.set(region, [255,255,255,0.1])
- }
- }
- this.customLayerEnabled = true
- const customLayer: CustomLayer = {
- clType: 'customlayer/colormap',
- id: this.connectivityLayerId,
- colormap: map
- }
-
- this.store$.dispatch(
- atlasAppearance.actions.addCustomLayer({customLayer})
- )
- }
-
- removeCustomLayer() {
- this.store$.dispatch(
- atlasAppearance.actions.removeCustomLayer({
- id: this.connectivityLayerId
- })
- )
- }
-
- clearCohortSelection() {
- this.fetchedItems = []
- this.selectedCohort = null
- this.cohorts = []
- this.selectedCohort = null
- this.cohortSubjects = []
- this.selectedSubjectIndex = null
- this.selectedSubjectsDatasets = null
- this.selectedSubjectDatasetIndex = null
- }
-
- selectType(typeName) {
- this.clearCohortSelection()
- this.selectedType = typeName
- this.selectedTypeId = this.types.find(t => t.name === typeName).types[0]
-
- this.removeCustomLayer()
-
- this.getModality()
- }
-
-
- getModality(size: number = 100, page: number = 1) {
- this.fetching = true
- this.fetchModality(size, page).subscribe((res: any) => {
-
- this.fetchedItems.push(...res.items)
-
- if (res.total > size*page) {
- this.getModality(100, page+1)
- } else {
- this.cohorts = [...new Set(this.fetchedItems.map(item => item.cohort))]
- this.fetching = false
- this.changeDetectionRef.detectChanges()
- this.selectCohort(this.cohorts[0])
- }
- })
- }
-
- public fetchModality = (size: number, page: number): Observable<any> => {
- let endp
- SAPI.BsEndpoint$.pipe(take(1)).subscribe(en => endp = en)
- return this.http.get(`${endp}/atlases/${encodeURIComponent(this.atlas['@id'])}/parcellations/${encodeURIComponent(this.parcellation['@id'])}/features?type=${this.selectedTypeId}&size=${size}&page=${page}`,)
- .pipe(take(1))
- }
-
- selectCohort(cohort: string) {
- this.selectedCohort = cohort
- this.averageDisabled = !this.fetchedItems.find(s => s.cohort === this.selectedCohort && s.subject === 'average')
- this.subjectsDisabled = !this.fetchedItems.find(s => s.cohort === this.selectedCohort && s.subject !== 'average')
- this.selectedView = !this.averageDisabled? 'average' : 'subject'
- this.cohortSubjects = [...new Set(
- this.fetchedItems
- .filter(i => this.selectedView === 'average'? i.subject === 'average' : i.subject !== 'average')
- .map(item => item.subject)
- )]
- this.subjectSliderChanged(0)
- }
-
- subjectSliderChanged(index: number) {
- this.selectedSubjectIndex = index
- this.selectedSubjectsDatasets = this.fetchedItems
- .filter(fi => fi.cohort === this.selectedCohort && fi.subject === this.cohortSubjects[this.selectedSubjectIndex])
- .map(i => i['@id'])
-
- this.selectedSubjectDatasetIndex = 0
- this.loadSubjectConnectivity()
- }
-
- subjectDatasetSliderChanged(index) {
- this.selectedSubjectDatasetIndex = index
- this.loadSubjectConnectivity()
- }
-
- loadSubjectConnectivity() {
- this.fetching = true
- this.fetchConnectivity(this.selectedSubjectsDatasets[this.selectedSubjectDatasetIndex])
- }
-
- // ToDo this temporary fix is for the bug existing on siibra api https://github.com/FZJ-INM1-BDA/siibra-api/issues/100
- private fixDatasetFormat = (ds) => ds.name.includes('{')? ({
- ...ds,
- ...JSON.parse(ds.name.substring(ds.name.indexOf('{')).replace(/'/g, '"'))
- }) : ds
-
- fetchConnectivity(datasetId=null) {
- const parcellation = this.sapi.getParcellation(this.atlas["@id"], this.parcellation["@id"])
- if (parcellation) {
- parcellation.getFeatureInstance(datasetId || this.selectedDataset['@id'])
- .pipe(catchError(() => {
- this.fetching = false
- return of(null)
- }))
- .subscribe(ds => {
- this.selectedDataset = this.fixDatasetFormat(ds)
- this.setMatrixData(ds)
- this.fetching = false
- })
- }
- }
-
- // ToDo need to be fixed on configuration side
- fixHemisphereNaming(area: string) {
- if (area.includes(' - left hemisphere')) {
- return area.replace('- left hemisphere', 'left')
- } else if (area.includes(' - right hemisphere')) {
- return area.replace('- right hemisphere', 'right')
- } else {
- return area
- }
- }
-
- setMatrixData(data) {
- const matrixData = data as SapiParcellationFeatureMatrixModel
-
- this.regionIndexInMatrix = (matrixData.columns as Array<string>).findIndex(md => {
- return this.fixHemisphereNaming(md) === this.regionName
- })
-
- if (this.regionIndexInMatrix < 0) {
- this.fetching = false
- this.noConnectivityForRegion = true
- this.changeDetectionRef.detectChanges()
- return
- } else if (this.noConnectivityForRegion) {
- this.noConnectivityForRegion = false
- }
- this.sapi.processNpArrayData<PARSE_TYPEDARRAY.RAW_ARRAY>(matrixData.matrix, PARSE_TYPEDARRAY.RAW_ARRAY)
- .then(matrix => {
- const regionProfile = matrix.rawArray[this.regionIndexInMatrix]
-
- const maxStrength = Math.max(...regionProfile)
- this.logChecked = maxStrength > 1
- this.logDisabled = maxStrength <= 1
-
- const areas = regionProfile.reduce((p, c, i) => {
- return {
- ...p,
- [this.fixHemisphereNaming(matrixData.columns[i])]: c
- }
- }, {})
- this.pureConnections = areas
-
- this.connectionsString = JSON.stringify(areas)
- this.connectedAreas.next(this.formatConnections(areas))
- this.setCustomLayer()
-
- this.matrixString = JSON.stringify(matrixData.columns.map((mc, i) => ([mc, ...matrix.rawArray[i]])))
- this.changeDetectionRef.detectChanges()
-
- })
- }
-
-
- changeLog(checked: boolean) {
- this.logChecked = checked
- this.connectedAreas.next(this.formatConnections(this.pureConnections))
- this.connectivityComponentElement.nativeElement.toggleShowLog()
- this.setCustomLayer()
- }
-
- //ToDo bestViewPoint is null for the most cases
- navigateToRegion(region: SapiRegionModel) {
- const regionCentroid = this.region.hasAnnotation?.bestViewPoint?.coordinates
- if (regionCentroid)
- this.store$.dispatch(
- atlasSelection.actions.navigateTo({
- navigation: {
- position: regionCentroid.map(v => v.value*1e6),
- },
- animation: true
- })
- )
- }
-
- getRegionWithName(region: string) {
- return this.allRegions.find(r => r.name === region)
- }
-
- exportConnectivityProfile() {
- const a = document.querySelector('hbp-connectivity-matrix-row');
- (a as any).downloadCSV()
- }
-
- public exportFullConnectivity() {
- this.fullConnectivityGridElement?.nativeElement['downloadCSV']()
- }
-
- public ngOnDestroy(): void {
- this.removeCustomLayer()
- this.subscriptions.forEach(s => s.unsubscribe())
- }
-
- private formatConnections(areas: { [key: string]: number }) {
- const cleanedObj = Object.keys(areas)
- .map(key => ({name: key, numberOfConnections: areas[key]}))
- .filter(f => f.numberOfConnections > 0)
- .sort((a, b) => +b.numberOfConnections - +a.numberOfConnections)
-
- const logMax = this.logChecked ? Math.log(cleanedObj[0].numberOfConnections) : cleanedObj[0].numberOfConnections
- const colorAreas = []
-
- cleanedObj.forEach((a) => {
- colorAreas.push({
- ...a,
- color: {
- r: this.colormap_red((this.logChecked ? Math.log(a.numberOfConnections) : a.numberOfConnections) / logMax ),
- g: this.colormap_green((this.logChecked ? Math.log(a.numberOfConnections) : a.numberOfConnections) / logMax ),
- b: this.colormap_blue((this.logChecked ? Math.log(a.numberOfConnections) : a.numberOfConnections) / logMax )
- },
- })
- })
- return colorAreas
- }
- private clamp = val => Math.round(Math.max(0, Math.min(1.0, val)) * 255)
- private colormap_red = x => x < 0.7? this.clamp(4.0 * x - 1.5) : this.clamp(-4.0 * x + 4.5)
- private colormap_green = x => x < 0.5? this.clamp(4.0 * x - 0.5) : this.clamp(-4.0 * x + 3.5)
- private colormap_blue = x => x < 0.3? this.clamp(4.0 * x + 0.5) : this.clamp(-4.0 * x + 2.5)
-
-}
-
-type ConnectedArea = {
- color: {r: number, g: number, b: number}
- name: string
- numberOfConnections: number
-}
diff --git a/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.template.html b/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.template.html
deleted file mode 100644
index df2a233d6349bfe8de3b4e06ebca492e2d4695fa..0000000000000000000000000000000000000000
--- a/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.template.html
+++ /dev/null
@@ -1,131 +0,0 @@
-<div class="w-100 h-100 d-block d-flex flex-column sxplr-pb-2">
- <div>
- <div *ngIf="types && types.length"
- class="flex-grow-0 flex-shrink-0 d-flex flex-row flex-nowrap d-flex flex-column">
- <mat-form-field class="flex-grow-1 flex-shrink-1 w-100">
- <mat-label>
- Modality
- </mat-label>
-
- <mat-select
- [value]="selectedType"
- (selectionChange)="selectType($event.value)">
- <mat-option
- *ngFor="let type of types"
- [value]="type.name">
- {{ type.name }}
- </mat-option>
- </mat-select>
- </mat-form-field>
-
- <mat-form-field *ngIf="!fetching && selectedType" class="flex-grow-1 flex-shrink-1 w-100">
- <mat-label>
- Cohort
- </mat-label>
-
- <mat-select
- [value]="selectedCohort"
- (selectionChange)="selectCohort($event.value)">
- <mat-option
- *ngFor="let cohort of cohorts"
- [value]="cohort">
- {{ cohort }}
- </mat-option>
- </mat-select>
- </mat-form-field>
- </div>
-
- <mat-radio-group *ngIf="selectedCohort" [(ngModel)]="selectedView">
- <mat-radio-button value="average" class="m-2" [disabled]="averageDisabled" color="primary">
- Average
- </mat-radio-button>
- <mat-radio-button value="subject" class="m-2" [disabled]="subjectsDisabled" color="primary">
- Subject
- </mat-radio-button>
- </mat-radio-group>
-
- <div *ngIf="selectedView !== 'average' && selectedCohort && cohortSubjects"
- class="flex-grow-0 flex-shrink-0 d-flex flex-column">
- <div class="flex-grow-1 flex-shrink-1 w-100">
- <mat-label>
- Subject
- </mat-label>
- <mat-slider [min]="0"
- [max]="cohortSubjects.length - 1"
- (change)="subjectSliderChanged($event.value)"
- [value]="selectedSubjectIndex"
- thumbLabel
- step="1"
- class="w-100">
- </mat-slider>
- </div>
-
- <div *ngIf="selectedSubjectsDatasets && selectedSubjectsDatasets.length > 1"
- class="flex-grow-0 flex-shrink-0 d-flex flex-nowrap align-items-center">
- <div class="flex-grow-1 flex-shrink-1 w-100">
- <mat-label>
- Dataset
- </mat-label>
- <mat-slider [min]="0"
- [max]="selectedSubjectsDatasets.length - 1"
- (change)="subjectDatasetSliderChanged($event.value)"
- [value]="selectedSubjectDatasetIndex"
- thumbLabel
- step="1"
- class="w-100">
- </mat-slider>
- </div>
- </div>
- </div>
-
- </div>
-
- <div class="d-flex justify-content-center">
- <mat-spinner *ngIf="fetching"></mat-spinner>
- </div>
-
- <div *ngIf="regionName && !fetching"
- [style.visibility]="selectedCohort && (selectedSubjectDatasetIndex >= 0 || !averageDisabled)? 'visible' : 'hidden'"
- class="d-flex align-items-center">
- <mat-checkbox class="mr-2"
- [checked]="logChecked"
- (change)="changeLog($event.checked)"
- [disabled]="logDisabled || noConnectivityForRegion">Log 10</mat-checkbox>
- <button mat-button [matMenuTriggerFor]="exportMenu"
- [disabled]="!connectedAreas.value">
- <i class="fas fa-download mr-2"></i>
- <span>Export</span>
- </button>
- <button *ngIf="selectedDataset" iav-stop="mousedown click" class="icons" mat-icon-button sxplr-dialog [sxplr-dialog-size]="null"
- [sxplr-dialog-data]="{
- title: selectedDataset?.name,
- descMd: selectedDataset?.description + '' + selectedDataset?.authors.join(),
- actions: selectedDataset | connectivityDoiPipe
- }">
- <i class="fas fa-info"></i>
- </button>
- </div>
-
- <hbp-connectivity-matrix-row
- #connectivityComponent
- [style.visibility]="selectedCohort && (selectedSubjectDatasetIndex >= 0 || !averageDisabled)? 'visible' : 'hidden'"
- *ngIf="regionName && !fetching && !noConnectivityForRegion"
- [region]="regionName + (regionHemisphere? ' - ' + regionHemisphere : '')"
- [connections]="connectionsString"
- show-export="true" hide-export-view="true"
- theme="dark">
- </hbp-connectivity-matrix-row>
- <div *ngIf="noConnectivityForRegion">No connectivity for the region.</div>
-
- <full-connectivity-grid #fullConnectivityGrid
- [matrix]="matrixString"
- [datasetName]="selectedDataset?.name"
- [datasetDescription]="selectedDataset?.description"
- only-export="true">
- </full-connectivity-grid>
-
- <mat-menu #exportMenu="matMenu">
- <button mat-menu-item [disabled]="noConnectivityForRegion" (click)="exportConnectivityProfile()">Regional</button>
- <button mat-menu-item (click)="exportFullConnectivity()">Dataset</button>
- </mat-menu>
-</div>
diff --git a/tmpFeatures/connectivity/connectivityDoi.pipe.ts b/tmpFeatures/connectivity/connectivityDoi.pipe.ts
deleted file mode 100644
index ee527989cefa890fb8af7f1cf2fd8bc52411912b..0000000000000000000000000000000000000000
--- a/tmpFeatures/connectivity/connectivityDoi.pipe.ts
+++ /dev/null
@@ -1,15 +0,0 @@
-import { Pipe, PipeTransform } from "@angular/core"
-import { SapiParcellationFeatureModel } from "src/atlasComponents/sapi/type"
-
-@Pipe({
- name: 'connectivityDoiPipe',
- pure: true
- })
-
- export class ConnectivityDoiPipe implements PipeTransform {
- public transform(dataset: SapiParcellationFeatureModel): string[] {
- const url = `https://search.kg.ebrains.eu/instances/${dataset['dataset_id']}`
- return [url]
- }
- }
-
\ No newline at end of file
diff --git a/tmpFeatures/connectivity/hasConnectivity.directive.ts b/tmpFeatures/connectivity/hasConnectivity.directive.ts
deleted file mode 100644
index 89168b6ada70caa0ac9de83c32edf9a2f0c0d856..0000000000000000000000000000000000000000
--- a/tmpFeatures/connectivity/hasConnectivity.directive.ts
+++ /dev/null
@@ -1,106 +0,0 @@
-import {Directive, Input, OnDestroy} from "@angular/core";
-import {Subscription} from "rxjs";
-import {map, take} from "rxjs/operators";
-import {SAPI} from "src/atlasComponents/sapi/sapi.service";
-import {
- SapiAtlasModel, SapiModalityModel,
- SapiParcellationFeatureModel,
- SapiParcellationModel,
- SapiRegionModel
-} from "src/atlasComponents/sapi/type";
-
-@Directive({
- selector: '[sxplr-sapiviews-features-connectivity-check]',
- exportAs: 'hasConnectivityDirective'
-})
-
-export class HasConnectivity implements OnDestroy {
-
- private subscriptions: Subscription[] = []
-
- @Input('sxplr-sapiviews-features-connectivity-check-atlas')
- atlas: SapiAtlasModel
-
- @Input('sxplr-sapiviews-features-connectivity-check-parcellation')
- parcellation: SapiParcellationModel
-
- private _region: SapiRegionModel
-
- @Input()
- set region(val: SapiRegionModel) {
- this._region = val
- if (val) {
- if (!this.connectivityModalities.length) {
- this.waitForModalities = true
- } else {
- this.checkConnectivity()
- }
- } else {
- this.connectivityNumber = 0
- }
- }
-
- get region() {
- return this._region
- }
-
- public hasConnectivity = false
- public connectivityNumber = 0
-
- private connectivityModalities: SapiModalityModel[] = []
- private waitForModalities = false
- public defaultProfile: DefaultProfile
- public availableModalities: SapiModalityModel[] = []
- public numberOfDatasets: number = 0
-
- constructor(private sapi: SAPI) {
- this.getModalities()
- }
-
- getModalities() {
- this.sapi.getModalities()
- .pipe(map((mod: SapiModalityModel[]) => mod.filter((m: SapiModalityModel) => m.types && m.types.find(t => t.includes('siibra/features/connectivity')))))
- .subscribe(modalities => {
- this.connectivityModalities = modalities
- if (this.waitForModalities) {
- this.waitForModalities = false
- this.checkConnectivity()
- }
-
- })
- }
-
- private checkConnectivity() {
- if (this.region.name) {
- this.connectivityModalities.forEach(m => {
- const type = m.types[0]
- this.sapi.getParcellation(this.atlas["@id"], this.parcellation["@id"])
- .getFeatures({type, page: 1, size: 1}).pipe(take(1))
- .subscribe((res: SapiParcellationFeatureModel[] | any) => {
- if (res && res.items) {
- this.availableModalities.push(m)
- const firstDataset = res.items[0]
-
- if (firstDataset) {
- this.hasConnectivity = true
- } else {
- this.hasConnectivity = false
- this.connectivityNumber = 0
- }
- }
- })
- })
- }
- }
-
- ngOnDestroy(){
- while (this.subscriptions.length > 0) this.subscriptions.pop().unsubscribe()
- }
-}
-
-type DefaultProfile = {
- type: string
- selectedDataset: SapiParcellationFeatureModel
- matrix: SapiParcellationFeatureModel
- numberOfDatasets: number
-}
\ No newline at end of file
diff --git a/tmpFeatures/module.ts b/tmpFeatures/module.ts
index 3df348c72f79be4b53c3050e30627c896e8b93f2..54651dc2803d82c80fb2f025d45dc3a0cbe11fda 100644
--- a/tmpFeatures/module.ts
+++ b/tmpFeatures/module.ts
@@ -9,7 +9,6 @@ import { FeatureBadgeFlagPipe } from "./featureBadgeFlag.pipe"
import { FeatureBadgeNamePipe } from "./featureBadgeName.pipe"
import * as ieeg from "./ieeg"
import * as receptor from "./receptors"
-import {SapiViewsFeatureConnectivityModule} from "src/atlasComponents/sapiViews/features/connectivity";
import * as voi from "./voi"
import { OrderFilterFeaturesPipe } from "./orderFilterFeatureList.pipe"
@@ -28,7 +27,6 @@ const { SapiViewsFeaturesVoiModule } = voi
SxplrSapiViewsFeaturesIeegModule,
AngularMaterialModule,
SapiViewsFeaturesVoiModule,
- SapiViewsFeatureConnectivityModule,
],
declarations: [
FeatureEntryCmp,
@@ -49,7 +47,6 @@ const { SapiViewsFeaturesVoiModule } = voi
FeatureEntryCmp,
SapiViewsFeaturesEntryListItem,
SapiViewsFeaturesVoiModule,
- SapiViewsFeatureConnectivityModule,
OrderFilterFeaturesPipe,
]
})