diff --git a/common/constants.js b/common/constants.js
index e30caaa6ac365ed3e0ad5780d93070a2357776f6..5734896dff5a3729ddd0a0c244af30df0ce8a0c4 100644
--- a/common/constants.js
+++ b/common/constants.js
@@ -69,6 +69,12 @@
TEMPLATE_NOT_FOUND: `Template not found. Maybe it is still loading. Try again in a few seconds?`,
PARC_NOT_FOUND: ``,
- PINNED_DATASETS_BADGE_DESC: `Number of pinned datasets`
+ PINNED_DATASETS_BADGE_DESC: `Number of pinned datasets`,
+
+ GDPR_TEXT: `This dataset is currently reviewed by the EBRAINS Data Protection Office regarding GDPR compliance. Therefore the atlas does not provide access to the underlying data files yet. The data will be available after this review.`,
+
+ RECEPTOR_FP_CAPTION: `The receptor densities are visualized as fingerprints (fp), which provide the mean density and standard deviation for each of the analyzed receptor types, averaged across samples.`,
+ RECEPTOR_PR_CAPTION: `For a single tissue sample, an exemplary density distribution for a single receptor from the pial surface to the border between layer VI and the white matter.`,
+ RECEPTOR_AR_CAPTION: `An exemplary density distribution of a single receptor for one laminar cross-section in a single tissue sample.`,
}
})(typeof exports === 'undefined' ? module.exports : exports)
diff --git a/package.json b/package.json
index 81cd549b87d5e2ec833087f961ea921c153b79d6..aa5a9d92d5c9578622a44e5e9e81cb46f7fdb146 100644
--- a/package.json
+++ b/package.json
@@ -87,7 +87,7 @@
"@ngrx/effects": "^9.1.1",
"@ngrx/store": "^9.1.1",
"@types/node": "12.12.39",
- "export-nehuba": "0.0.2",
+ "export-nehuba": "0.0.4",
"hbp-connectivity-component": "^0.3.18",
"zone.js": "^0.10.2"
}
diff --git a/src/atlasViewer/atlasViewer.apiService.service.ts b/src/atlasViewer/atlasViewer.apiService.service.ts
index d4872bb8221e35bd018b7d6e906c54979f788a25..75c5e5a231f25784773cb95a2941ed4692b2c834 100644
--- a/src/atlasViewer/atlasViewer.apiService.service.ts
+++ b/src/atlasViewer/atlasViewer.apiService.service.ts
@@ -1,5 +1,6 @@
/* eslint-disable @typescript-eslint/no-empty-function */
import {Injectable, NgZone, Optional, Inject, OnDestroy, InjectionToken} from "@angular/core";
+import { MatSnackBar } from "@angular/material/snack-bar";
import { select, Store } from "@ngrx/store";
import { Observable, Subject, Subscription, from, race, of, } from "rxjs";
import { distinctUntilChanged, map, filter, startWith, switchMap, catchError, mapTo, take } from "rxjs/operators";
@@ -12,6 +13,7 @@ import {
IavRootStoreInterface,
safeFilter
} from "src/services/stateStore.service";
+import { FRAGMENT_EMIT_RED } from "src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component";
import { ClickInterceptor, CLICK_INTERCEPTOR_INJECTOR } from "src/util";
import { ModalHandler } from "../util/pluginHandlerClasses/modalHandler";
import { ToastHandler } from "../util/pluginHandlerClasses/toastHandler";
@@ -35,12 +37,21 @@ interface IGetUserSelectRegionPr{
export const CANCELLABLE_DIALOG = 'CANCELLABLE_DIALOG'
export const GET_TOAST_HANDLER_TOKEN = 'GET_TOAST_HANDLER_TOKEN'
+export interface ILoadMesh {
+ type: 'VTK'
+ id: string
+ url: string
+}
+export const LOAD_MESH_TOKEN = new InjectionToken<(loadMeshParam: ILoadMesh) => void>('LOAD_MESH_TOKEN')
+
@Injectable({
- providedIn : 'root',
+ providedIn : 'root'
})
export class AtlasViewerAPIServices implements OnDestroy{
+ public loadMesh$ = new Subject<ILoadMesh>()
+
private onDestoryCb: Function[] = []
private loadedTemplates$: Observable<any>
private selectParcellation$: Observable<any>
@@ -146,6 +157,7 @@ export class AtlasViewerAPIServices implements OnDestroy{
constructor(
private store: Store<IavRootStoreInterface>,
private dialogService: DialogService,
+ private snackbar: MatSnackBar,
private zone: NgZone,
private pluginService: PluginServices,
@Optional() @Inject(CANCELLABLE_DIALOG) openCancellableDialog: (message: string, options: any) => () => void,
@@ -367,6 +379,21 @@ export class AtlasViewerAPIServices implements OnDestroy{
this.interactiveViewer.metadata.regionsLabelIndexMap = getLabelIndexMap(parcellation.regions)
this.interactiveViewer.metadata.layersRegionLabelIndexMap = getMultiNgIdsRegionsLabelIndexMap(parcellation)
})
+
+ this.s.push(
+ this.loadMesh$.subscribe(({ url, id, type }) => {
+ if (!this.interactiveViewer.viewerHandle) {
+ this.snackbar.open('No atlas loaded! Loading mesh failed!', 'Dismiss')
+ }
+ this.interactiveViewer.viewerHandle?.loadLayer({
+ [id]: {
+ type: 'mesh',
+ source: `vtk://${url}`,
+ shader: `void main(){${FRAGMENT_EMIT_RED};}`
+ }
+ })
+ })
+ )
}
ngOnDestroy(){
diff --git a/src/atlasViewer/atlasViewer.constantService.service.ts b/src/atlasViewer/atlasViewer.constantService.service.ts
index f435d07bed178da1c42a14bb1af88ca84818a4ed..b6e8358f72470566bf4350d61a78860038edf30c 100644
--- a/src/atlasViewer/atlasViewer.constantService.service.ts
+++ b/src/atlasViewer/atlasViewer.constantService.service.ts
@@ -73,8 +73,6 @@ export class AtlasViewerConstantsServices implements OnDestroy {
public spatialResultsPerPage = 10
public spatialWidth = 600
- public landmarkFlatProjection: boolean = false
-
public chartBaseStyle = {
fill : 'origin',
}
diff --git a/src/atlasViewer/atlasViewer.workerService.service.ts b/src/atlasViewer/atlasViewer.workerService.service.ts
index c5e222480facb343ec0d02b1ad8bca75ce486abb..17204cb05224dc78887f74cdae74ab9699ba6ec8 100644
--- a/src/atlasViewer/atlasViewer.workerService.service.ts
+++ b/src/atlasViewer/atlasViewer.workerService.service.ts
@@ -1,4 +1,6 @@
import { Injectable } from "@angular/core";
+import { fromEvent } from "rxjs";
+import { filter, take } from "rxjs/operators";
/* telling webpack to pack the worker file */
import '../util/worker.js'
@@ -8,10 +10,32 @@ import '../util/worker.js'
*/
export const worker = new Worker('worker.js')
+interface IWorkerMessage {
+ method: string
+ param: any
+}
+
@Injectable({
providedIn: 'root',
})
export class AtlasWorkerService {
public worker = worker
+
+ async sendMessage(data: IWorkerMessage){
+
+ const newUuid = crypto.getRandomValues(new Uint32Array(1))[0].toString(16)
+ this.worker.postMessage({
+ id: newUuid,
+ ...data
+ })
+ const message = await fromEvent(this.worker, 'message').pipe(
+ filter((message: MessageEvent) => message.data.id && message.data.id === newUuid),
+ take(1)
+ ).toPromise()
+
+ const { data: returnData } = message as MessageEvent
+ const { id, ...rest } = returnData
+ return rest
+ }
}
diff --git a/src/atlasViewer/pluginUnit/atlasViewer.pluginService.service.ts b/src/atlasViewer/pluginUnit/atlasViewer.pluginService.service.ts
index ff1264528a849463487777f6445d63b90335e132..dff1231817ccc94cd2e8f59b0f5ed5fcd1765179 100644
--- a/src/atlasViewer/pluginUnit/atlasViewer.pluginService.service.ts
+++ b/src/atlasViewer/pluginUnit/atlasViewer.pluginService.service.ts
@@ -1,10 +1,10 @@
import { HttpClient } from '@angular/common/http'
-import { ComponentFactory, ComponentFactoryResolver, Injectable, ViewContainerRef, Inject } from "@angular/core";
+import { ComponentFactory, ComponentFactoryResolver, Injectable, ViewContainerRef, Inject, InjectionToken } from "@angular/core";
import { PLUGINSTORE_ACTION_TYPES } from "src/services/state/pluginState.store";
import { IavRootStoreInterface, isDefined } from 'src/services/stateStore.service'
import { PluginUnit } from "./pluginUnit.component";
import { select, Store } from "@ngrx/store";
-import { BehaviorSubject, merge, Observable, of, zip } from "rxjs";
+import { BehaviorSubject, merge, Observable, of, Subject, zip } from "rxjs";
import { filter, map, shareReplay, switchMap, catchError } from "rxjs/operators";
import { LoggingService } from 'src/logging';
import { PluginHandler } from 'src/util/pluginHandler';
diff --git a/src/main.module.ts b/src/main.module.ts
index 3cc29399b3f96f5f9a7784197c66c8f62e436886..a87d7e6d8fa662263b04876717cbcd98a0c480b0 100644
--- a/src/main.module.ts
+++ b/src/main.module.ts
@@ -1,6 +1,6 @@
import { DragDropModule } from '@angular/cdk/drag-drop'
import { CommonModule } from "@angular/common";
-import { CUSTOM_ELEMENTS_SCHEMA, NgModule } from "@angular/core";
+import { CUSTOM_ELEMENTS_SCHEMA, InjectionToken, NgModule } from "@angular/core";
import { FormsModule } from "@angular/forms";
import { StoreModule, ActionReducer } from "@ngrx/store";
import { AngularMaterialModule } from 'src/ui/sharedModules/angularMaterial.module'
@@ -14,7 +14,7 @@ import { GetNamesPipe } from "./util/pipes/getNames.pipe";
import { HttpClientModule } from "@angular/common/http";
import { EffectsModule } from "@ngrx/effects";
-import { AtlasViewerAPIServices, CANCELLABLE_DIALOG, GET_TOAST_HANDLER_TOKEN, API_SERVICE_SET_VIEWER_HANDLE_TOKEN, setViewerHandleFactory } from "./atlasViewer/atlasViewer.apiService.service";
+import { AtlasViewerAPIServices, CANCELLABLE_DIALOG, GET_TOAST_HANDLER_TOKEN, API_SERVICE_SET_VIEWER_HANDLE_TOKEN, setViewerHandleFactory, LOAD_MESH_TOKEN, ILoadMesh } from "./atlasViewer/atlasViewer.apiService.service";
import { AtlasWorkerService } from "./atlasViewer/atlasViewer.workerService.service";
import { ModalUnit } from "./atlasViewer/modalUnit/modalUnit.component";
import { TransformOnhoverSegmentPipe } from "./atlasViewer/onhoverSegment.pipe";
@@ -242,6 +242,15 @@ export function debug(reducer: ActionReducer<any>): ActionReducer<any> {
deps: [
ClickInterceptorService
]
+ },
+ {
+ provide: LOAD_MESH_TOKEN,
+ useFactory: (apiService: AtlasViewerAPIServices) => {
+ return (loadMeshParam: ILoadMesh) => apiService.loadMesh$.next(loadMeshParam)
+ },
+ deps: [
+ AtlasViewerAPIServices
+ ]
}
],
bootstrap : [
diff --git a/src/messaging/module.ts b/src/messaging/module.ts
index ac8e266a422deb02734662b51bcfb402e99c1971..9e5152f3d6c62c9aa8442aab8362ab1d964f4bb6 100644
--- a/src/messaging/module.ts
+++ b/src/messaging/module.ts
@@ -1,6 +1,9 @@
-import { NgModule, Optional } from "@angular/core";
+import { Inject, NgModule, Optional } from "@angular/core";
import { MatDialog } from "@angular/material/dialog";
+import { MatSnackBar } from "@angular/material/snack-bar";
import { AtlasViewerAPIServices } from "src/atlasViewer/atlasViewer.apiService.service";
+import { AtlasWorkerService } from "src/atlasViewer/atlasViewer.workerService.service";
+import { LOAD_MESH_TOKEN, ILoadMesh } from "src/atlasViewer/atlasViewer.apiService.service";
import { ComponentsModule } from "src/components";
import { ConfirmDialogComponent } from "src/components/confirmDialog/confirmDialog.component";
import { AngularMaterialModule } from "src/ui/sharedModules/angularMaterial.module";
@@ -21,7 +24,10 @@ export class MesssagingModule{
constructor(
private dialog: MatDialog,
- @Optional() private apiService: AtlasViewerAPIServices
+ private snackbar: MatSnackBar,
+ private worker: AtlasWorkerService,
+ @Optional() private apiService: AtlasViewerAPIServices,
+ @Optional() @Inject(LOAD_MESH_TOKEN) private loadMesh: (loadMeshParam: ILoadMesh) => void
){
window.addEventListener('message', async ({ data, origin, source }) => {
@@ -83,7 +89,6 @@ export class MesssagingModule{
}
async processMessage({ method, param }){
- console.log({ method, param })
if (method === 'dummyMethod') {
return 'OK'
@@ -99,6 +104,27 @@ export class MesssagingModule{
return 'OK'
}
+ if (method === '_tmp:plotly') {
+ const isLoadingSnack = this.snackbar.open(`Loading plotly mesh ...`)
+ const resp = await this.worker.sendMessage({
+ method: `PROCESS_PLOTLY`,
+ param
+ })
+ isLoadingSnack?.dismiss()
+ const meshId = 'bobby'
+ if (this.loadMesh) {
+ const { objectUrl } = resp.result || {}
+ this.loadMesh({
+ type: 'VTK',
+ id: meshId,
+ url: objectUrl
+ })
+ } else {
+ this.snackbar.open(`Error: loadMesh method not injected.`)
+ }
+ return 'OK'
+ }
+
throw ({ code: 404, message: 'Method not found' })
}
diff --git a/src/res/css/extra_styles.css b/src/res/css/extra_styles.css
index e6e394ac82a97772f934c078c3d065e96dae846c..081fa25ea672331dbdb2509fcaf98e891028bbf8 100644
--- a/src/res/css/extra_styles.css
+++ b/src/res/css/extra_styles.css
@@ -530,6 +530,11 @@ markdown-dom pre code
background: none!important;
}
+.bg-50-grey-20
+{
+ background-color: rgba(128,128,128, 0.2);
+}
+
.dot
{
width: 0.5rem;
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index f1fd5865935f3a9920e951ff9c6f794a8deba195..4ff6635b1263ae0cf56f78c00f762747e866dda6 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -9,6 +9,15508 @@
"ngId": "mni152",
"nehubaConfigURL": "nehubaConfig/MNI152NehubaConfig",
"parcellations": [
+ {
+ "fullId": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25-1",
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25-1",
+ "name": "Cytoarchitectonic Maps - v2.5.1",
+ "auxillaryMeshIndices": [
+ 65535
+ ],
+ "hasAdditionalViewMode": [],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "5249afa7-5e04-4ffd-8039-c3a9231f717c"
+ }
+ ],
+ "properties": {
+ "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI ICBM 2009c Asymmetric as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "publications": [
+ {
+ "doi": "https://doi.org/10.1038/nrn2776",
+ "citation": "Zilles K, Amunts K (2010) Centenary of Brodmann’s map – conception and fate. Nature Reviews Neuroscience 11(2): 139-145 "
+ },
+ {
+ "doi": "https://doi.org/10.1016/j.neuroimage.2007.02.037",
+ "citation": "Amunts K, Schleicher A, Zilles K (2007) Cytoarchitecture of the cerebral cortex – more than localization. Neuroimage 37: 1061-1065"
+ },
+ {
+ "doi": "http://dx.doi.org/10.1016/B978-012693019-1/50023-X",
+ "citation": "Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) Quantitative analysis of cyto- and receptor architecture of the human brain. In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602."
+ }
+ ]
+ },
+ "regions": [
+ {
+ "name": "telencephalon",
+ "children": [
+ {
+ "name": "cerebral nuclei",
+ "children": [
+ {
+ "name": "basal forebrain",
+ "children": [
+ {
+ "name": "magnocellular group within septum",
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "left hemisphere",
+ "labelIndex": 62,
+ "ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "gray": "79"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ }
+ },
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "right hemisphere",
+ "labelIndex": 62,
+ "ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "gray": "79"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "arealabel": "Ch-123",
+ "status": "publicP",
+ "labelIndex": "286",
+ "doi": "https://doi.org/10.25493/7SEP-P2V",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ]
+ },
+ {
+ "name": "sublenticular part of basal forebrain",
+ "children": [
+ {
+ "name": "Ch 4 (Basal Forebrain)",
+ "children": [
+ {
+ "name": "Ch 4 (Basal Forebrain)",
+ "status": "left hemisphere",
+ "labelIndex": 97,
+ "ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 4 (Basal Forebrain)",
+ "gray": "13"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 4 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "791a14c8-b899-414f-b237-27574a4cce7e"
+ }
+ ],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
+ }
+ }
+ },
+ {
+ "name": "Ch 4 (Basal Forebrain)",
+ "status": "right hemisphere",
+ "labelIndex": 97,
+ "ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 4 (Basal Forebrain)",
+ "gray": "13"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 4 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "791a14c8-b899-414f-b237-27574a4cce7e"
+ }
+ ],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Ch 4 (Basal Forebrain)",
+ "arealabel": "Ch-4",
+ "status": "publicP",
+ "labelIndex": "264",
+ "doi": "https://doi.org/10.25493/VZJ5-8WJ",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ]
+ },
+ {
+ "name": "magnocellular group within horizontal limb of diagnoal band",
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "left hemisphere",
+ "labelIndex": 62,
+ "ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "gray": "79"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ }
+ },
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "right hemisphere",
+ "labelIndex": 62,
+ "ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "gray": "79"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "arealabel": "Ch-123",
+ "status": "publicP",
+ "labelIndex": "286",
+ "doi": "https://doi.org/10.25493/7SEP-P2V",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ]
+ }
+ ]
+ },
+ {
+ "name": "amygdala",
+ "children": [
+ {
+ "name": "laterobasal group",
+ "children": [
+ {
+ "name": "LB (Amygdala)",
+ "children": [
+ {
+ "name": "LB (Amygdala)",
+ "status": "left hemisphere",
+ "labelIndex": 41,
+ "ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
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+ "gray": "53"
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+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Entorhinal Cortex",
+ "arealabel": "Entorhinal-Cortex",
+ "status": "publicP",
+ "labelIndex": "60",
+ "doi": "https://doi.org/10.25493/KNXY-B1Z",
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+ "_": {
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+ "name": "CA3 (Hippocampus)",
+ "arealabel": "CA3",
+ "status": "publicP",
+ "labelIndex": "59",
+ "doi": "https://doi.org/10.1007%2Fs00429-019-02022-4",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
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+ "children": [
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+ "labelIndex": 87,
+ "ngId": "ICBM152_V25_LEFT_NG",
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+ ],
+ "_": {
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+ "arealabel": "HC-Transsubiculum",
+ "status": "publicP",
+ "labelIndex": "305",
+ "doi": "https://doi.org/10.1007%2Fs00429-019-02022-4",
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+ "labelIndex": 63,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
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+ "name": "HC-Subiculum (Hippocampus)",
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+ }
+ }
+ },
+ {
+ "name": "HC-Subiculum (Hippocampus)",
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+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
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+ "gray": "63"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
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+ "arealabel": "HC-Subiculum",
+ "status": "publicP",
+ "labelIndex": "67",
+ "doi": "https://doi.org/10.1007%2Fs00429-019-02022-4",
+ "synonyms": [],
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+ },
+ {
+ "name": "HC-Prosubiculum (Hippocampus)",
+ "children": [
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+ "name": "HC-Prosubiculum (Hippocampus)",
+ "labelIndex": 49,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "HC-Prosubiculum (Hippocampus)",
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+ }
+ }
+ },
+ {
+ "name": "HC-Prosubiculum (Hippocampus)",
+ "labelIndex": 48,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "HC-Prosubiculum (Hippocampus)",
+ "gray": "48"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "HC-Prosubiculum (Hippocampus)",
+ "arealabel": "HC-Prosubiculum",
+ "status": "publicP",
+ "labelIndex": "64",
+ "doi": "https://doi.org/10.1007%2Fs00429-019-02022-4",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "HC-Parasubiculum (Hippocampus)",
+ "children": [
+ {
+ "name": "HC-Parasubiculum (Hippocampus)",
+ "labelIndex": 60,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "HC-Parasubiculum (Hippocampus)",
+ "gray": "60"
+ }
+ }
+ },
+ {
+ "name": "HC-Parasubiculum (Hippocampus)",
+ "labelIndex": 59,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "HC-Parasubiculum (Hippocampus)",
+ "gray": "59"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "HC-Parasubiculum (Hippocampus)",
+ "arealabel": "HC-Parasubiculum",
+ "status": "publicP",
+ "labelIndex": "62",
+ "doi": "https://doi.org/10.1007%2Fs00429-019-02022-4",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "DG (Hippocampus)",
+ "children": [
+ {
+ "name": "DG (Hippocampus)",
+ "labelIndex": 22,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "DG (Hippocampus)",
+ "gray": "22"
+ }
+ }
+ },
+ {
+ "name": "DG (Hippocampus)",
+ "labelIndex": 22,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "DG (Hippocampus)",
+ "gray": "22"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "DG (Hippocampus)",
+ "arealabel": "DG",
+ "status": "publicP",
+ "labelIndex": "61",
+ "doi": "https://doi.org/10.25493/M8JP-XQT",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "CA2 (Hippocampus)",
+ "children": [
+ {
+ "name": "CA2 (Hippocampus)",
+ "labelIndex": 51,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "CA2 (Hippocampus)",
+ "gray": "51"
+ }
+ }
+ },
+ {
+ "name": "CA2 (Hippocampus)",
+ "labelIndex": 51,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "CA2 (Hippocampus)",
+ "gray": "51"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "CA2 (Hippocampus)",
+ "arealabel": "CA2",
+ "status": "publicP",
+ "labelIndex": "58",
+ "doi": "https://doi.org/10.1007%2Fs00429-019-02022-4",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "CA1 (Hippocampus)",
+ "children": [
+ {
+ "name": "CA1 (Hippocampus)",
+ "labelIndex": 56,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "CA1 (Hippocampus)",
+ "gray": "56"
+ }
+ }
+ },
+ {
+ "name": "CA1 (Hippocampus)",
+ "labelIndex": 57,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "CA1 (Hippocampus)",
+ "gray": "57"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "CA1 (Hippocampus)",
+ "arealabel": "CA1",
+ "status": "publicP",
+ "labelIndex": "66",
+ "doi": "https://doi.org/10.1007%2Fs00429-019-02022-4",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "hippocampal formation",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "limbic lobe",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "cerebral cortex",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "telencephalon",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "metencephalon",
+ "children": [
+ {
+ "name": "cerebellum",
+ "children": [
+ {
+ "name": "cerebellar nuclei",
+ "children": [
+ {
+ "name": "globose nucleus",
+ "children": [
+ {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "children": [
+ {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "labelIndex": 109,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "gray": "109"
+ }
+ }
+ },
+ {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "labelIndex": 109,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "gray": "109"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "arealabel": "Interposed-Nucleus",
+ "status": "publicP",
+ "labelIndex": "251",
+ "doi": "https://doi.org/10.25493/8PTB-JDH",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "globose nucleus",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "dentate nucleus",
+ "children": [
+ {
+ "name": "Dorsal Dentate Nucleus (Cerebellum)",
+ "children": [
+ {
+ "name": "Dorsal Dentate Nucleus (Cerebellum)",
+ "labelIndex": 16,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "Dorsal Dentate Nucleus (Cerebellum)",
+ "gray": "16"
+ }
+ }
+ },
+ {
+ "name": "Dorsal Dentate Nucleus (Cerebellum)",
+ "labelIndex": 18,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "Dorsal Dentate Nucleus (Cerebellum)",
+ "gray": "18"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Dorsal Dentate Nucleus (Cerebellum)",
+ "arealabel": "Dorsal-Dentate-Nucleus",
+ "status": "publicP",
+ "labelIndex": "240",
+ "doi": "https://doi.org/10.25493/M5QG-SHH",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "children": [
+ {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "labelIndex": 66,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "gray": "66"
+ }
+ }
+ },
+ {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "labelIndex": 65,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "gray": "65"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "arealabel": "Ventral-Dentate-Nucleus",
+ "status": "publicP",
+ "labelIndex": "241",
+ "doi": "https://doi.org/10.25493/FQE5-5QR",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "dentate nucleus",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "fastigial nucleus",
+ "children": [
+ {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "children": [
+ {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "labelIndex": 102,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "gray": "102"
+ }
+ }
+ },
+ {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "labelIndex": 102,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "gray": "102"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "arealabel": "Fastigial-Nucleus",
+ "status": "publicP",
+ "labelIndex": "219",
+ "doi": "https://doi.org/10.25493/3YJ9-S6G",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "fastigial nucleus",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "emboliform nucleus",
+ "children": [
+ {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "children": [
+ {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "labelIndex": 109,
+ "ngId": "ICBM152_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "gray": "109"
+ }
+ }
+ },
+ {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "labelIndex": 109,
+ "ngId": "ICBM152_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "gray": "109"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "arealabel": "Interposed-Nucleus",
+ "status": "publicP",
+ "labelIndex": "251",
+ "doi": "https://doi.org/10.25493/8PTB-JDH",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "emboliform nucleus",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "cerebellar nuclei",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "cerebellum",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "metencephalon",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20201202_JulichBrainHierarchy/src/07a76da90bdbd35e56a01de817befbe6c12f91da/output/nehubaUI/icbm_regions.json"
+ }
+ },
{
"fullId": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
"@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
diff --git a/src/res/ext/MNI152NehubaConfig.json b/src/res/ext/MNI152NehubaConfig.json
index 20f685aeaf022076f14029c38f69ca59acf91330..a19a6ba72d7a8e02e32f1326b7bd080ef89401cf 100644
--- a/src/res/ext/MNI152NehubaConfig.json
+++ b/src/res/ext/MNI152NehubaConfig.json
@@ -23,7 +23,7 @@
"mesh": {
"removeBasedOnNavigation": true,
"flipRemovedOctant": true,
- "surfaceParcellation": false
+ "surfaceParcellation": true
},
"removePerspectiveSlicesBackground": {
"mode": "<",
@@ -217,6 +217,130 @@
]
]
},
+ "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201204_JulichBrainV3_0_hemisphereSplit/precomputed/JuBrain_Map_icbm_v30_r",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -96500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -132500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -78500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
+ },
+ "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201204_JulichBrainV3_0_hemisphereSplit/precomputed/JuBrain_Map_icbm_v30_l",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -96500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -132500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -78500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
+ },
+ "ICBM152_V25_LEFT_NG": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201202_JulichBrainV2_5_colin_MPM/precomputed/JulichBrain_MPMAtlas_l_N10_nlin2Stdicbm152asym2009c_publicDOI_3f5ec6016bc2242769c41befdbc1b2e0",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -96500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -132500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -78500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
+ },
+ "ICBM152_V25_RIGHT_NG": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201202_JulichBrainV2_5_colin_MPM/precomputed/JulichBrain_MPMAtlas_r_N10_nlin2Stdicbm152asym2009c_publicDOI_453c4c95827e38dcce5372b200065cba",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -96500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -132500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -78500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
+ },
"ICBM152_V24_LEFT_NG": {
"type": "segmentation",
"visible": true,
diff --git a/src/res/ext/atlas/atlas_multiLevelHuman.json b/src/res/ext/atlas/atlas_multiLevelHuman.json
index 9f2c680338253486a3dd1f26a3c7ed552b2780ba..54b1f28a76d67dfbff51f45162f06c0b33b1f78b 100644
--- a/src/res/ext/atlas/atlas_multiLevelHuman.json
+++ b/src/res/ext/atlas/atlas_multiLevelHuman.json
@@ -8,9 +8,17 @@
"name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
"displayName": "ICBM 152 2009c Nonlinear Asymmetric",
"availableIn": [
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25-1",
+ "name": "Cytoarchitectonic maps - v2.5.1"
+ },
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25",
+ "name": "Cytoarchitectonic maps - v2.5"
+ },
{
"@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
- "name": "Cytoarchitectonic maps"
+ "name": "Cytoarchitectonic maps - v2.4"
},
{
"@id": "juelich/iav/atlas/v1.0.0/8",
@@ -55,9 +63,17 @@
"@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
"name": "MNI Colin 27",
"availableIn": [
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25-1",
+ "name": "Cytoarchitectonic maps - v2.5.1"
+ },
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25",
+ "name": "Cytoarchitectonic maps - v2.5"
+ },
{
"@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
- "name": "Cytoarchitectonic maps"
+ "name": "Cytoarchitectonic maps - v2.4"
},
{
"@id": "juelich/iav/atlas/v1.0.0/8",
@@ -130,11 +146,65 @@
]
},
{
- "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25-1",
"name": "Cytoarchitectonic maps",
"baseLayer": true,
"@version": {
"@next": null,
+ "@this": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25-1",
+ "name": "v2.5.1",
+ "@previous": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25"
+ },
+ "availableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+ "originalDatasetFormats": [{
+ "name": "probability map"
+ }]
+ },
+ {
+ "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
+ "name": "MNI Colin 27",
+ "originalDatasetFormats": [{
+ "name": "probability map"
+ }]
+ }
+ ]
+ },
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25",
+ "name": "Cytoarchitectonic maps",
+ "baseLayer": true,
+ "@version": {
+ "@next": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25-1",
+ "@this": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25",
+ "name": "v2.5",
+ "@previous": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579"
+ },
+ "availableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+ "originalDatasetFormats": [{
+ "name": "probability map"
+ }]
+ },
+ {
+ "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
+ "name": "MNI Colin 27",
+ "originalDatasetFormats": [{
+ "name": "probability map"
+ }]
+ }
+ ]
+ },
+ {
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "name": "Cytoarchitectonic maps",
+ "baseLayer": true,
+ "@version": {
+ "@next": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25",
"@this": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
"name": "v2.4",
"@previous": "juelich/iav/atlas/v1.0.0/8"
diff --git a/src/res/ext/colin.json b/src/res/ext/colin.json
index 4fab4579d34c4bcd6507f3273d04c6ce8c88d9d9..615812921d7a5b3b043375cdfa774b9cc287134b 100644
--- a/src/res/ext/colin.json
+++ b/src/res/ext/colin.json
@@ -8,6 +8,15508 @@
"ngId": "colin",
"nehubaConfigURL": "nehubaConfig/colinNehubaConfig",
"parcellations": [
+ {
+ "fullId": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25-1",
+ "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25-1",
+ "name": "Cytoarchitectonic Maps - v2.5.1",
+ "auxillaryMeshIndices": [
+ 65535
+ ],
+ "hasAdditionalViewMode": [],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "5249afa7-5e04-4ffd-8039-c3a9231f717c"
+ }
+ ],
+ "properties": {
+ "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI ICBM 2009c Asymmetric as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "publications": [
+ {
+ "doi": "https://doi.org/10.1038/nrn2776",
+ "citation": "Zilles K, Amunts K (2010) Centenary of Brodmann’s map – conception and fate. Nature Reviews Neuroscience 11(2): 139-145 "
+ },
+ {
+ "doi": "https://doi.org/10.1016/j.neuroimage.2007.02.037",
+ "citation": "Amunts K, Schleicher A, Zilles K (2007) Cytoarchitecture of the cerebral cortex – more than localization. Neuroimage 37: 1061-1065"
+ },
+ {
+ "doi": "http://dx.doi.org/10.1016/B978-012693019-1/50023-X",
+ "citation": "Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) Quantitative analysis of cyto- and receptor architecture of the human brain. In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602."
+ }
+ ]
+ },
+ "regions": [
+ {
+ "name": "telencephalon",
+ "children": [
+ {
+ "name": "cerebral nuclei",
+ "children": [
+ {
+ "name": "basal forebrain",
+ "children": [
+ {
+ "name": "magnocellular group within septum",
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "left hemisphere",
+ "labelIndex": 62,
+ "ngId": "COLIN_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "gray": "79"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, Colin 27, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ }
+ },
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "right hemisphere",
+ "labelIndex": 62,
+ "ngId": "COLIN_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "gray": "79"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, Colin 27, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
+ "rgb": [
+ 200,
+ 200,
+ 200
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "arealabel": "Ch-123",
+ "status": "publicP",
+ "labelIndex": "286",
+ "doi": "https://doi.org/10.25493/7SEP-P2V",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ]
+ },
+ {
+ "name": "sublenticular part of basal forebrain",
+ "children": [
+ {
+ "name": "Ch 4 (Basal Forebrain)",
+ "children": [
+ {
+ "name": "Ch 4 (Basal Forebrain)",
+ "status": "left hemisphere",
+ "labelIndex": 97,
+ "ngId": "COLIN_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 4 (Basal Forebrain)",
+ "gray": "13"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 4 (Basal Forebrain) [v4.2, Colin 27, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "791a14c8-b899-414f-b237-27574a4cce7e"
+ }
+ ],
+ "rgb": [
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+ "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
+ }
+ }
+ },
+ {
+ "name": "Ch 4 (Basal Forebrain)",
+ "status": "right hemisphere",
+ "labelIndex": 97,
+ "ngId": "COLIN_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 4 (Basal Forebrain)",
+ "gray": "13"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 4 (Basal Forebrain) [v4.2, Colin 27, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
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+ "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Ch 4 (Basal Forebrain)",
+ "arealabel": "Ch-4",
+ "status": "publicP",
+ "labelIndex": "264",
+ "doi": "https://doi.org/10.25493/VZJ5-8WJ",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ]
+ },
+ {
+ "name": "magnocellular group within horizontal limb of diagnoal band",
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "left hemisphere",
+ "labelIndex": 62,
+ "ngId": "COLIN_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "gray": "79"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, Colin 27, left hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
+ "rgb": [
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+ "fullId": {
+ "kg": {
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+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ }
+ },
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "status": "right hemisphere",
+ "labelIndex": 62,
+ "ngId": "COLIN_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "gray": "79"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "Ch 123 (Basal Forebrain) [v4.2, Colin 27, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "147aaab9-d5f2-48db-80f3-95adc9e7e8a6"
+ }
+ ],
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+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Ch 123 (Basal Forebrain)",
+ "arealabel": "Ch-123",
+ "status": "publicP",
+ "labelIndex": "286",
+ "doi": "https://doi.org/10.25493/7SEP-P2V",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ]
+ }
+ ]
+ },
+ {
+ "name": "amygdala",
+ "children": [
+ {
+ "name": "laterobasal group",
+ "children": [
+ {
+ "name": "LB (Amygdala)",
+ "children": [
+ {
+ "name": "LB (Amygdala)",
+ "status": "left hemisphere",
+ "labelIndex": 41,
+ "ngId": "COLIN_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "LB (Amygdala)",
+ "gray": "94"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "LB (Amygdala) [v8.0, Colin 27, left hemisphere]",
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+ "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
+ }
+ }
+ },
+ {
+ "name": "LB (Amygdala)",
+ "status": "right hemisphere",
+ "labelIndex": 41,
+ "ngId": "COLIN_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "LB (Amygdala)",
+ "gray": "94"
+ }
+ },
+ "originDatasets": [
+ {
+ "filename": "LB (Amygdala) [v8.0, Colin 27, right hemisphere]",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "fa4cab6a-1cec-4cec-b481-90aa0cc7d96c"
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+ "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "LB (Amygdala)",
+ "arealabel": "LB",
+ "status": "publicP",
+ "labelIndex": "187",
+ "doi": "https://doi.org/10.25493/C3X0-NV3",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ]
+ },
+ {
+ "name": "superficial group",
+ "children": [
+ {
+ "name": "CM (Amygdala)",
+ "children": [
+ {
+ "name": "CM (Amygdala)",
+ "status": "left hemisphere",
+ "labelIndex": 85,
+ "ngId": "COLIN_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "CM (Amygdala)",
+ "gray": "44"
+ }
+ },
+ "originDatasets": [
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+ }
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+ "status": "right hemisphere",
+ "labelIndex": 85,
+ "ngId": "COLIN_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "CM (Amygdala)",
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+ }
+ },
+ "originDatasets": [
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+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
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+ "arealabel": "CM",
+ "status": "publicP",
+ "labelIndex": "290",
+ "doi": "https://doi.org/10.25493/36FR-C95",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "SF (Amygdala)",
+ "children": [
+ {
+ "name": "SF (Amygdala)",
+ "status": "left hemisphere",
+ "labelIndex": 5,
+ "ngId": "COLIN_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "SF (Amygdala)",
+ "gray": "110"
+ }
+ },
+ "originDatasets": [
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+ "filename": "SF (Amygdala) [v8.0, Colin 27, left hemisphere]",
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+ {
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+ "status": "right hemisphere",
+ "labelIndex": 5,
+ "ngId": "COLIN_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "SF (Amygdala)",
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+ }
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+ "originDatasets": [
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+ "_": {
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+ "arealabel": "SF",
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+ "doi": "https://doi.org/10.25493/WD31-SEA",
+ "synonyms": [],
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+ }
+ ]
+ },
+ {
+ "name": "fiber masses",
+ "children": [
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+ "name": "VTM (Amygdala)",
+ "children": [
+ {
+ "name": "VTM (Amygdala)",
+ "status": "left hemisphere",
+ "labelIndex": 109,
+ "ngId": "COLIN_V25_LEFT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "VTM (Amygdala)",
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+ }
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+ }
+ }
+ },
+ {
+ "name": "VTM (Amygdala)",
+ "status": "right hemisphere",
+ "labelIndex": 109,
+ "ngId": "COLIN_V25_RIGHT_NG_SPLIT_HEMISPHERE",
+ "_": {
+ "xml": {
+ "name": "VTM (Amygdala)",
+ "gray": "83"
+ }
+ },
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+ }
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+ }
+ ],
+ "_": {
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+ "labelIndex": "228",
+ "doi": "https://doi.org/10.25493/99HN-XRE",
+ "synonyms": [],
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+ }
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+ "_": {
+ "xml": {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "gray": "65"
+ }
+ }
+ },
+ {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "labelIndex": 65,
+ "ngId": "COLIN_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "gray": "65"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Ventral Dentate Nucleus (Cerebellum)",
+ "arealabel": "Ventral-Dentate-Nucleus",
+ "status": "publicP",
+ "labelIndex": "241",
+ "doi": "https://doi.org/10.25493/FQE5-5QR",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "dentate nucleus",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "fastigial nucleus",
+ "children": [
+ {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "children": [
+ {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "labelIndex": 103,
+ "ngId": "COLIN_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "gray": "103"
+ }
+ }
+ },
+ {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "labelIndex": 102,
+ "ngId": "COLIN_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "gray": "102"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Fastigial Nucleus (Cerebellum)",
+ "arealabel": "Fastigial-Nucleus",
+ "status": "publicP",
+ "labelIndex": "219",
+ "doi": "https://doi.org/10.25493/3YJ9-S6G",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "fastigial nucleus",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ },
+ {
+ "name": "emboliform nucleus",
+ "children": [
+ {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "children": [
+ {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "labelIndex": 109,
+ "ngId": "COLIN_V25_LEFT_NG",
+ "_": {
+ "xml": {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "gray": "109"
+ }
+ }
+ },
+ {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "labelIndex": 109,
+ "ngId": "COLIN_V25_RIGHT_NG",
+ "_": {
+ "xml": {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "gray": "109"
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "Interposed Nucleus (Cerebellum)",
+ "arealabel": "Interposed-Nucleus",
+ "status": "publicP",
+ "labelIndex": "251",
+ "doi": "https://doi.org/10.25493/8PTB-JDH",
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "emboliform nucleus",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "cerebellar nuclei",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "cerebellum",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "julichbrain-ontology_25.json": {
+ "name": "metencephalon",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null
+ }
+ }
+ }
+ ],
+ "_": {
+ "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20201202_JulichBrainHierarchy/src/07a76da90bdbd35e56a01de817befbe6c12f91da/output/nehubaUI/colin_regions.json"
+ }
+ },
{
"fullId": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
"@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
diff --git a/src/res/ext/colinNehubaConfig.json b/src/res/ext/colinNehubaConfig.json
index 92a712d78d90aa5c7bd8c09f08e1651a7ea2a87d..d6c850ca8473d7f0e56bbfee24ef063111595830 100644
--- a/src/res/ext/colinNehubaConfig.json
+++ b/src/res/ext/colinNehubaConfig.json
@@ -87,6 +87,136 @@
]
]
},
+ "COLIN_V25_RIGHT_NG_SPLIT_HEMISPHERE": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201204_JulichBrainV3_0_hemisphereSplit/precomputed/JuBrain_Map_colin_v30_r_fixed",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -90500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -126500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -72500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
+ },
+ "COLIN_V25_LEFT_NG_SPLIT_HEMISPHERE": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201204_JulichBrainV3_0_hemisphereSplit/precomputed/JuBrain_Map_colin_v30_l_fixed",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -90500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -126500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -72500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
+ },
+ "COLIN_V25_LEFT_NG": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201202_JulichBrainV2_5_colin_MPM/precomputed/JulichBrain_MPMAtlas_l_N10_nlin2Stdcolin27_publicDOI_37fdd19c7ce06ca709a34e21d8ec0886",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -128500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -148500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -110500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ],
+ "_": {
+ "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20200926_JulichBrain-V2_4-Colin_MPM_mesh/raw/745a37f64b6995a661f5a61287b4067df01687cb/output/nehuba-ui/left_config.json"
+ }
+ },
+ "COLIN_V25_RIGHT_NG": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201202_JulichBrainV2_5_colin_MPM/precomputed/JulichBrain_MPMAtlas_r_N10_nlin2Stdcolin27_publicDOI_387941812ac0807aa1c7050b109ce623",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -128500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -148500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -110500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ],
+ "_": {
+ "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20200926_JulichBrain-V2_4-Colin_MPM_mesh/raw/745a37f64b6995a661f5a61287b4067df01687cb/output/nehuba-ui/right_config.json"
+ }
+ },
"COLIN_V24_LEFT_NG": {
"type": "segmentation",
"visible": true,
diff --git a/src/services/effect/effect.spec.ts b/src/services/effect/effect.spec.ts
index 9d36abbe0971ad7a2c2029652372cf557be3376a..a65e40146f7f9be14f93f6cd7a780d806aca00c5 100644
--- a/src/services/effect/effect.spec.ts
+++ b/src/services/effect/effect.spec.ts
@@ -11,6 +11,7 @@ import { defaultRootState } from '../stateStore.service'
const colinsJson = require('!json-loader!../../res/ext/colin.json')
const COLIN_JULICHBRAIN_LAYER_NAME = `COLIN_V24_LEFT_NG`
+const COLIN_V24_ID = 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
describe('effect.ts', () => {
describe('getGetRegionFromLabelIndexId', () => {
@@ -18,7 +19,7 @@ describe('effect.ts', () => {
const getRegionFromlabelIndexId = getGetRegionFromLabelIndexId({
parcellation: {
- ...colinsJson.parcellations[0],
+ ...colinsJson.parcellations.find(p => p['@id'] === COLIN_V24_ID),
updated: true,
},
})
diff --git a/src/services/state/dataStore.store.ts b/src/services/state/dataStore.store.ts
index aae960f5f7a6dcb032793dfdb80c1033f6e860d1..42e389fcf2d4f1d6e462e583337c09e958005de1 100644
--- a/src/services/state/dataStore.store.ts
+++ b/src/services/state/dataStore.store.ts
@@ -6,6 +6,7 @@ import { Action } from '@ngrx/store'
import { GENERAL_ACTION_TYPES } from '../stateStore.service'
import { LOCAL_STORAGE_CONST } from 'src/util/constants'
import { datastateActionUpdateFavDataset } from './dataState/actions'
+import { IHasId } from 'src/util/interfaces'
/**
* TODO merge with databrowser.usereffect.ts
@@ -114,7 +115,7 @@ export interface IDataEntry {
referenceSpaces: IReferenceSpace[]
files: File[]
publications: IPublication[]
- embargoStatus: string[]
+ embargoStatus: IHasId[]
methods: string[]
protocols: string[]
diff --git a/src/ui/databrowserModule/constants.ts b/src/ui/databrowserModule/constants.ts
index aaed7658f9b1a6bd79d2f56b0932c7319abafe79..45de86bd2ccec91d890921b5d2c0516936ef354a 100644
--- a/src/ui/databrowserModule/constants.ts
+++ b/src/ui/databrowserModule/constants.ts
@@ -1,6 +1,11 @@
import { InjectionToken } from "@angular/core";
import { LOCAL_STORAGE_CONST } from "src/util/constants";
import { Observable } from "rxjs";
+import { IHasId } from "src/util/interfaces";
+
+export const UNDER_REVIEW = {
+ ['@id']: "https://nexus.humanbrainproject.org/v0/data/minds/core/embargostatus/v1.0.0/1d726b76-b176-47ed-96f0-b4f2e17d5f19"
+}
export const OVERRIDE_IAV_DATASET_PREVIEW_DATASET_FN = new InjectionToken<(file: any, dataset: any) => void>('OVERRIDE_IAV_DATASET_PREVIEW_DATASET_FN')
export const DATASTORE_DEFAULT_STATE = {
@@ -74,7 +79,7 @@ export interface IKgDataEntry {
referenceSpaces: IKgReferenceSpace[]
files: File[]
publications: IKgPublication[]
- embargoStatus: string[]
+ embargoStatus: IHasId[]
methods: string[]
protocols: string[]
diff --git a/src/ui/databrowserModule/preview/previewCard/previewCard.template.html b/src/ui/databrowserModule/preview/previewCard/previewCard.template.html
index 51c3b7a79e00f0dbe0dd127b9d36b842ca19d1d1..697ef4010d189ef662977b2c2716363b6d4e53fe 100644
--- a/src/ui/databrowserModule/preview/previewCard/previewCard.template.html
+++ b/src/ui/databrowserModule/preview/previewCard/previewCard.template.html
@@ -1,5 +1,5 @@
<mat-card class="mat-elevation-z4">
- <div class="header-container">
+ <div class="header-container bg-50-grey-20">
<mat-card-title>
{{ singleDsView?.name || file.name || filename }}
</mat-card-title>
@@ -41,25 +41,51 @@
</mat-card-subtitle>
</div>
-</mat-card>
-<mat-card class="mt-4">
- <single-dataset-view [fullId]="datasetId"
- [hideTitle]="true"
- [hidePreview]="true"
- [hideExplore]="true"
- [hidePinBtn]="true"
- [hideDownloadBtn]="true"
- #singleDsView="singleDatasetView">
+ <mat-card-content class="mt-2 ml-15px-n mr-15px-n pb-4">
+ <mat-accordion>
+ <mat-expansion-panel hideToggle
+ [expanded]="true">
+
+ <mat-expansion-panel-header>
+ <mat-panel-title>
+ Description
+ </mat-panel-title>
+ </mat-expansion-panel-header>
+
+ <ng-template matExpansionPanelContent>
+ <single-dataset-view [fullId]="datasetId"
+ [hideTitle]="true"
+ [hidePreview]="true"
+ [hideExplore]="true"
+ [hidePinBtn]="true"
+ [hideDownloadBtn]="true"
+ #singleDsView="singleDatasetView">
+
+ </single-dataset-view>
+ </ng-template>
+ </mat-expansion-panel>
- </single-dataset-view>
-</mat-card>
-<!-- TODO -->
-<!-- this is not exactly right -->
-<div class="mt-4">
- <layer-browser></layer-browser>
-</div>
+ <mat-expansion-panel hideToggle>
+
+ <mat-expansion-panel-header>
+ <mat-panel-title>
+ Registered Volumes
+ </mat-panel-title>
+ </mat-expansion-panel-header>
+
+ <ng-template matExpansionPanelContent>
+ <!-- TODO -->
+ <!-- this is not exactly right -->
+ <layer-browser class="ml-24px-n mr-24px-n"></layer-browser>
+ </ng-template>
+
+ </mat-expansion-panel>
+ </mat-accordion>
+
+ </mat-card-content>
+</mat-card>
<!-- templates -->
<ng-template #favDatasetBtn let-singleDataset="singleDataset">
@@ -76,3 +102,14 @@
</button>
</ng-template>
</ng-template>
+
+<single-dataset-view [fullId]="datasetId"
+ [hidden]="true"
+ [hideTitle]="true"
+ [hidePreview]="true"
+ [hideExplore]="true"
+ [hidePinBtn]="true"
+ [hideDownloadBtn]="true"
+ #singleDsView="singleDatasetView">
+
+</single-dataset-view>
\ No newline at end of file
diff --git a/src/ui/databrowserModule/singleDataset/sideNavView/sDsSideNavView.component.ts b/src/ui/databrowserModule/singleDataset/sideNavView/sDsSideNavView.component.ts
index ca11f4955796b127e928fe8f29426cf52070c31a..d3de2c8a8805192414a4f4ec2f93c04348563853 100644
--- a/src/ui/databrowserModule/singleDataset/sideNavView/sDsSideNavView.component.ts
+++ b/src/ui/databrowserModule/singleDataset/sideNavView/sDsSideNavView.component.ts
@@ -5,7 +5,7 @@ import { REGION_OF_INTEREST, TRegionOfInterest } from "src/util/interfaces";
import { DatabrowserService } from "../../databrowser.service";
import { KgSingleDatasetService } from "../../kgSingleDatasetService.service";
import { SingleDatasetBase } from "../singleDataset.base";
-
+import { CONST } from 'common/constants'
@Component({
selector: 'single-dataset-sidenav-view',
@@ -21,6 +21,8 @@ export class SingleDatasetSideNavView extends SingleDatasetBase implements OnCha
@Output()
clear: EventEmitter<null> = new EventEmitter()
+ public GDPR_TEXT = CONST.GDPR_TEXT
+
constructor(
dbService: DatabrowserService,
sDsService: KgSingleDatasetService,
diff --git a/src/ui/databrowserModule/singleDataset/sideNavView/sDsSideNavView.template.html b/src/ui/databrowserModule/singleDataset/sideNavView/sDsSideNavView.template.html
index 0a64ef91df8cf25d0f2c594298dd7f0511078285..7ad003e91beeeb352324596cc8b645c8b881bfcb 100644
--- a/src/ui/databrowserModule/singleDataset/sideNavView/sDsSideNavView.template.html
+++ b/src/ui/databrowserModule/singleDataset/sideNavView/sDsSideNavView.template.html
@@ -8,8 +8,7 @@
</button>
<mat-card class="mat-elevation-z4">
- <div class="header-container"
- [style.backgroundColor]="'rgba(128,128,128, 0.2)'">
+ <div class="header-container bg-50-grey-20">
<mat-card-title>
<ng-content select="[region-of-interest]"></ng-content>
<div *ngIf="!fetchFlag; else isLoadingTmpl">
@@ -23,6 +22,12 @@
Dataset
</span>
+ <button *ngIf="isGdprProtected"
+ [matTooltip]="GDPR_TEXT"
+ mat-icon-button color="warn">
+ <i class="fas fa-exclamation-triangle"></i>
+ </button>
+
<mat-divider [vertical]="true" class="ml-2 h-2rem"></mat-divider>
<!-- explore btn -->
@@ -53,12 +58,11 @@
</mat-card-subtitle>
</div>
- <mat-card-content class="mt-2 ml-15px-n mr-15px-n">
+ <mat-card-content class="mt-2 ml-15px-n mr-15px-n pb-4">
<mat-accordion>
<!-- Description -->
- <mat-expansion-panel hideToggle
- [expanded]="true">
+ <mat-expansion-panel>
<mat-expansion-panel-header>
<mat-panel-title>
Description
@@ -120,8 +124,7 @@
<!-- feature tmpl -->
<ng-template #featureTmpl>
<ng-container *ngFor="let feature of (rfGetAllFeatures.features | filterRegionFeaturesById : fullId)">
- <mat-expansion-panel hideToggle
- #matExpansionPanel>
+ <mat-expansion-panel #matExpansionPanel>
<mat-expansion-panel-header>
<mat-panel-title>
{{ feature.type }}
diff --git a/src/ui/databrowserModule/singleDataset/singleDataset.base.ts b/src/ui/databrowserModule/singleDataset/singleDataset.base.ts
index 93367c8ae2283dd216c7d861f9b05b82198af5be..4db7d45dd6d32450ae35f27434c8970b611157e7 100644
--- a/src/ui/databrowserModule/singleDataset/singleDataset.base.ts
+++ b/src/ui/databrowserModule/singleDataset/singleDataset.base.ts
@@ -12,6 +12,7 @@ import { MatSnackBar } from "@angular/material/snack-bar";
import { ARIA_LABELS } from 'common/constants'
import { switchMap, distinctUntilChanged, filter } from "rxjs/operators";
import { IContributor } from "../contributor";
+import { UNDER_REVIEW } from "../constants";
const getDirectLinkToKg = (dataset: { fullId: string, id: string }) => {
const { id } = dataset
@@ -96,6 +97,8 @@ export class SingleDatasetBase implements OnChanges, OnDestroy {
public DS_PREVIEW_URL = DS_PREVIEW_URL
public strictLocal: boolean = STRICT_LOCAL
+ public isGdprProtected: boolean = false
+
/**
* sic!
*/
@@ -144,7 +147,7 @@ export class SingleDatasetBase implements OnChanges, OnDestroy {
const { kgSchema, kgId } = this
- const { name, description, publications, fullId, kgReference, files, contributors, ...rest } = dataset
+ const { name, description, publications, fullId, kgReference, files, contributors, embargoStatus, ...rest } = dataset
this.name = name
this.description = description
this.publications = publications
@@ -152,6 +155,8 @@ export class SingleDatasetBase implements OnChanges, OnDestroy {
this.files = files
this.fullId = fullId
+ this.isGdprProtected = embargoStatus.some(s => s['@id'] === UNDER_REVIEW['@id'])
+
this.kgReference = kgReference
this.directLinkToKg = getDirectLinkToKg(dataset)
diff --git a/src/ui/nehubaContainer/2dLandmarks/landmark.base.ts b/src/ui/nehubaContainer/2dLandmarks/landmark.base.ts
new file mode 100644
index 0000000000000000000000000000000000000000..52144fb7a41476a6387914067062fd6af99a3653
--- /dev/null
+++ b/src/ui/nehubaContainer/2dLandmarks/landmark.base.ts
@@ -0,0 +1,7 @@
+import { Input } from "@angular/core"
+
+export class LandmarkUnitBase{
+ @Input() public positionX: number = 0
+ @Input() public positionY: number = 0
+ @Input() public positionZ: number = 0
+}
diff --git a/src/ui/nehubaContainer/landmarkUnit/landmarkUnit.component.spec.ts b/src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.component.spec.ts
similarity index 94%
rename from src/ui/nehubaContainer/landmarkUnit/landmarkUnit.component.spec.ts
rename to src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.component.spec.ts
index 582f3f183379b5c8d65e5de6bac52f09e32a986d..b1861a32ae1f874b8a42bbc1ca94e94e6f3a9168 100644
--- a/src/ui/nehubaContainer/landmarkUnit/landmarkUnit.component.spec.ts
+++ b/src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.component.spec.ts
@@ -1,6 +1,6 @@
import { Component, ViewChild } from "@angular/core"
import { async, TestBed } from "@angular/core/testing"
-import { SafeStylePipe } from "src/util/pipes/safeStyle.pipe"
+import { Landmark2DModule } from "../module"
import { HOVER_COLOR, LandmarkUnit, NORMAL_COLOR } from "./landmarkUnit.component"
@@ -27,15 +27,16 @@ describe('> landmarkUnit.component.ts', () => {
describe('> LandmarkUnit', () => {
beforeEach(async(() => {
TestBed.configureTestingModule({
+ imports: [
+ Landmark2DModule
+ ],
declarations: [
- DummyCmp,
- LandmarkUnit,
- SafeStylePipe
+ DummyCmp
]
}).overrideComponent(DummyCmp, {
set: {
template: `
- <nehuba-2dlandmark-unit
+ <landmark-2d-stalk-cmp
[positionX]="positionX"
[positionY]="positionY"
[positionZ]="positionZ"
@@ -44,7 +45,7 @@ describe('> landmarkUnit.component.ts', () => {
[flatProjection]="flatProjection"
[fasClass]="fasClass"
>
- </nehuba-2dlandmark-unit>
+ </landmark-2d-stalk-cmp>
`
}
}).compileComponents()
@@ -121,4 +122,4 @@ describe('> landmarkUnit.component.ts', () => {
})
})
})
-})
\ No newline at end of file
+})
diff --git a/src/ui/nehubaContainer/landmarkUnit/landmarkUnit.component.ts b/src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.component.ts
similarity index 93%
rename from src/ui/nehubaContainer/landmarkUnit/landmarkUnit.component.ts
rename to src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.component.ts
index 5a9880a066b96a7f7d5f6a0ea26e62c739937460..e072f64328efe9bd2c4c5992d8b817db5d230a8d 100644
--- a/src/ui/nehubaContainer/landmarkUnit/landmarkUnit.component.ts
+++ b/src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.component.ts
@@ -1,7 +1,8 @@
import { ChangeDetectionStrategy, Component, HostBinding, Input, OnChanges, SimpleChanges } from "@angular/core";
+import { LandmarkUnitBase } from "../landmark.base";
@Component({
- selector : 'nehuba-2dlandmark-unit',
+ selector : 'landmark-2d-stalk-cmp',
templateUrl : './landmarkUnit.template.html',
styleUrls : [
`./landmarkUnit.style.css`,
@@ -9,15 +10,12 @@ import { ChangeDetectionStrategy, Component, HostBinding, Input, OnChanges, Simp
changeDetection : ChangeDetectionStrategy.OnPush,
})
-export class LandmarkUnit implements OnChanges {
- @Input() public positionX: number = 0
- @Input() public positionY: number = 0
- @Input() public positionZ: number = 0
+export class LandmarkUnit extends LandmarkUnitBase implements OnChanges {
@Input() public color: [number, number, number]
@Input() public highlight: boolean = false
- @Input() public flatProjection: boolean = false
+ @Input() public flatProjection: boolean = true
@Input() public fasClass: string = 'fa-map-marker'
@@ -136,6 +134,10 @@ export class LandmarkUnit implements OnChanges {
}
}
}
+
+ constructor(){
+ super()
+ }
}
export const NORMAL_COLOR: number[] = [201,54,38]
diff --git a/src/ui/nehubaContainer/landmarkUnit/landmarkUnit.style.css b/src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.style.css
similarity index 99%
rename from src/ui/nehubaContainer/landmarkUnit/landmarkUnit.style.css
rename to src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.style.css
index 6a09196fe028c971d28eb6f22ac3e87d385dafb7..b7285126604a52e78cf55a954275d59d605925be 100644
--- a/src/ui/nehubaContainer/landmarkUnit/landmarkUnit.style.css
+++ b/src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.style.css
@@ -88,4 +88,4 @@ div[landmarkContainer]
rgb(0, 0, 0) 0px 1px,
rgb(0, 0, 0) 1px 0px,
rgb(0, 0, 0) 0px -1px;
-}
\ No newline at end of file
+}
diff --git a/src/ui/nehubaContainer/landmarkUnit/landmarkUnit.template.html b/src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.template.html
similarity index 99%
rename from src/ui/nehubaContainer/landmarkUnit/landmarkUnit.template.html
rename to src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.template.html
index b28146e8fd8f3543897d90897f4fa6e7540cccc9..2caadee1b9554127752b2f491862cce8f335d8d7 100644
--- a/src/ui/nehubaContainer/landmarkUnit/landmarkUnit.template.html
+++ b/src/ui/nehubaContainer/2dLandmarks/landmarkUnit/landmarkUnit.template.html
@@ -37,4 +37,4 @@
class="pos-shadow">
</div>
-</div>
\ No newline at end of file
+</div>
diff --git a/src/ui/nehubaContainer/2dLandmarks/landmarkUnitMkII/flatLm.component.ts b/src/ui/nehubaContainer/2dLandmarks/landmarkUnitMkII/flatLm.component.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e425aca205c81b4e644508a769f280e65c6abcc0
--- /dev/null
+++ b/src/ui/nehubaContainer/2dLandmarks/landmarkUnitMkII/flatLm.component.ts
@@ -0,0 +1,50 @@
+import { ChangeDetectionStrategy, ChangeDetectorRef, Component, HostBinding, OnChanges, SimpleChanges } from "@angular/core";
+import { LandmarkUnitBase } from "../landmark.base";
+
+@Component({
+ selector: 'landmark-2d-flat-cmp',
+ templateUrl: './flatLm.template.html',
+ styleUrls: [
+ './flatLm.style.css'
+ ],
+ changeDetection: ChangeDetectionStrategy.OnPush
+})
+
+export class FlatLMCmp extends LandmarkUnitBase implements OnChanges{
+
+ @HostBinding('style.transform')
+ transform = `translate(0px, 0px)`
+
+ @HostBinding('style.opacity')
+ opacity = 1.0
+
+ @HostBinding('style.text-shadow')
+ textShadow = null
+
+ private scale: number = 1
+
+ constructor(private cdr: ChangeDetectorRef){
+ super()
+ this.cdr.detach()
+ }
+
+ ngOnChanges(){
+
+ const zModifier = Math.tanh(this.positionZ/10)
+ if (this.positionZ >= 0) {
+ const shadowLength = zModifier * 4
+ this.textShadow = `0 ${shadowLength}px ${shadowLength}px black`
+ this.opacity = 1.0
+ } else {
+ this.textShadow = null
+ /**
+ * assert(zModifier < 0)
+ */
+ this.opacity = 1.0 + (zModifier * 0.8)
+ }
+
+ this.transform = `translate(${this.positionX}px, ${this.positionY - (zModifier >= 0 ? zModifier * 4 : 0) }px)`
+ }
+}
+
+export const NORMAL_COLOR: number[] = [201,54,38]
diff --git a/src/ui/nehubaContainer/2dLandmarks/landmarkUnitMkII/flatLm.style.css b/src/ui/nehubaContainer/2dLandmarks/landmarkUnitMkII/flatLm.style.css
new file mode 100644
index 0000000000000000000000000000000000000000..462b4c7efcef86358db18579f078dc9043c37fab
--- /dev/null
+++ b/src/ui/nehubaContainer/2dLandmarks/landmarkUnitMkII/flatLm.style.css
@@ -0,0 +1,10 @@
+:host
+{
+ position: absolute;
+ color: rgba(201, 54, 38, 1.0)
+}
+
+:host > div
+{
+ transform: translate(-50%, -50%);
+}
diff --git a/src/ui/nehubaContainer/2dLandmarks/landmarkUnitMkII/flatLm.template.html b/src/ui/nehubaContainer/2dLandmarks/landmarkUnitMkII/flatLm.template.html
new file mode 100644
index 0000000000000000000000000000000000000000..a28b3899ac23b46084447e6104158475ca30f932
--- /dev/null
+++ b/src/ui/nehubaContainer/2dLandmarks/landmarkUnitMkII/flatLm.template.html
@@ -0,0 +1,3 @@
+<div class="pe-all">
+ <i class="fas fa-circle"></i>
+</div>
diff --git a/src/ui/nehubaContainer/2dLandmarks/module.ts b/src/ui/nehubaContainer/2dLandmarks/module.ts
new file mode 100644
index 0000000000000000000000000000000000000000..210aad4f4084c3045cea7cf203bd97ef206000c9
--- /dev/null
+++ b/src/ui/nehubaContainer/2dLandmarks/module.ts
@@ -0,0 +1,26 @@
+import { CommonModule } from "@angular/common";
+import { NgModule } from "@angular/core";
+import { LandmarkUnit } from "./landmarkUnit/landmarkUnit.component";
+import { FlatLMCmp } from "./landmarkUnitMkII/flatLm.component";
+import { SafeStylePipe } from "./safeStyle.pipe";
+
+@NgModule({
+ imports: [
+ CommonModule,
+ ],
+ declarations: [
+ LandmarkUnit,
+ FlatLMCmp,
+
+ /**
+ * pipes
+ */
+ SafeStylePipe,
+ ],
+ exports: [
+ LandmarkUnit,
+ FlatLMCmp,
+ ]
+})
+
+export class Landmark2DModule{}
diff --git a/src/util/pipes/safeStyle.pipe.ts b/src/ui/nehubaContainer/2dLandmarks/safeStyle.pipe.ts
similarity index 100%
rename from src/util/pipes/safeStyle.pipe.ts
rename to src/ui/nehubaContainer/2dLandmarks/safeStyle.pipe.ts
diff --git a/src/ui/nehubaContainer/nehubaContainer.component.spec.ts b/src/ui/nehubaContainer/nehubaContainer.component.spec.ts
index f14ef99c49fe88828f14cfb3bb25c39dcc2f744b..6feb8bf6185716a5e374a3588a8e498da519ce49 100644
--- a/src/ui/nehubaContainer/nehubaContainer.component.spec.ts
+++ b/src/ui/nehubaContainer/nehubaContainer.component.spec.ts
@@ -6,7 +6,6 @@ import { defaultRootState } from 'src/services/stateStore.service'
import { AngularMaterialModule } from "../sharedModules/angularMaterial.module"
import { TouchSideClass } from "./touchSideClass.directive"
import { MaximmisePanelButton } from "./maximisePanelButton/maximisePanelButton.component"
-import { LandmarkUnit } from './landmarkUnit/landmarkUnit.component'
import { LayoutModule } from 'src/layouts/layout.module'
import { PureContantService, UtilModule } from "src/util"
import { AtlasLayerSelector } from "../atlasLayerSelector/atlasLayerSelector.component"
@@ -21,7 +20,6 @@ import { RegionDirective } from 'src/ui/parcellationRegion/region.directive'
import { RegionTextSearchAutocomplete } from "../viewerStateController/regionSearch/regionSearch.component"
import { MobileControlNubStylePipe } from './pipes/mobileControlNubStyle.pipe'
import { ReorderPanelIndexPipe } from './reorderPanelIndex.pipe'
-import { SafeStylePipe } from 'src/util/pipes/safeStyle.pipe'
import { AuthModule } from 'src/auth'
import { StateModule } from 'src/state'
import { ReactiveFormsModule, FormsModule } from '@angular/forms'
@@ -30,7 +28,7 @@ import { WidgetModule } from 'src/widget'
import { NehubaModule } from './nehuba.module'
import { CommonModule } from '@angular/common'
import { IMPORT_NEHUBA_INJECT_TOKEN } from './nehubaViewer/nehubaViewer.component'
-import { viewerStateHelperStoreName } from 'src/services/state/viewerState.store.helper'
+import { viewerStateCustomLandmarkSelector, viewerStateHelperStoreName } from 'src/services/state/viewerState.store.helper'
import { RenderViewOriginDatasetLabelPipe } from '../parcellationRegion/region.base'
import { By } from '@angular/platform-browser'
import { ARIA_LABELS } from 'common/constants'
@@ -38,9 +36,10 @@ import { NoopAnimationsModule } from '@angular/platform-browser/animations'
import { RegionAccordionTooltipTextPipe } from '../util'
import { hot } from 'jasmine-marbles'
import { HttpClientTestingModule } from '@angular/common/http/testing'
-import { ngViewerSelectorPanelMode, ngViewerSelectorPanelOrder } from 'src/services/state/ngViewerState/selectors'
+import { ngViewerSelectorOctantRemoval, ngViewerSelectorPanelMode, ngViewerSelectorPanelOrder } from 'src/services/state/ngViewerState/selectors'
import { PANELS } from 'src/services/state/ngViewerState/constants'
import { RegionalFeaturesModule } from '../regionalFeatures'
+import { Landmark2DModule } from './2dLandmarks/module'
const {
TOGGLE_SIDE_PANEL,
@@ -88,12 +87,12 @@ describe('> nehubaContainer.component.ts', () => {
* so and so components needs to be compiled first. make sure you call compileComponents
*/
HttpClientTestingModule,
+ Landmark2DModule,
],
declarations: [
NehubaContainer,
TouchSideClass,
MaximmisePanelButton,
- LandmarkUnit,
AtlasLayerSelector,
StatusCardComponent,
NehubaViewerTouchDirective,
@@ -107,7 +106,6 @@ describe('> nehubaContainer.component.ts', () => {
// pipes
MobileControlNubStylePipe,
ReorderPanelIndexPipe,
- SafeStylePipe,
RenderViewOriginDatasetLabelPipe,
RegionAccordionTooltipTextPipe,
],
@@ -636,5 +634,66 @@ describe('> nehubaContainer.component.ts', () => {
})
})
+
+ describe('> on userLandmarks change', () => {
+ const lm1 = {
+ id: 'test-1',
+ position: [0, 0, 0]
+ }
+ const lm2 = {
+ id: 'test-2',
+ position: [1, 1,1 ]
+ }
+ it('> calls nehubaViewer.updateUserLandmarks', () => {
+ const fixture = TestBed.createComponent(NehubaContainer)
+
+ fixture.componentInstance.nehubaViewer = {
+ updateUserLandmarks: () => {}
+ } as any
+
+ const updateUserLandmarksSpy = spyOn(
+ fixture.componentInstance.nehubaViewer,
+ 'updateUserLandmarks'
+ )
+
+ const mockStore = TestBed.inject(MockStore)
+ mockStore.overrideSelector(viewerStateCustomLandmarkSelector, [
+ lm1,
+ lm2
+ ])
+ fixture.detectChanges()
+ expect(
+ updateUserLandmarksSpy
+ ).toHaveBeenCalledWith([
+ lm1, lm2
+ ])
+ })
+
+ it('> calls togglecotantREmoval', () => {
+
+ const fixture = TestBed.createComponent(NehubaContainer)
+
+ fixture.componentInstance.nehubaContainerDirective = {
+ toggleOctantRemoval: () => {},
+ clear: () => {}
+ } as any
+
+ const toggleOctantRemovalSpy = spyOn(
+ fixture.componentInstance.nehubaContainerDirective,
+ 'toggleOctantRemoval'
+ )
+
+ const mockStore = TestBed.inject(MockStore)
+ mockStore.overrideSelector(viewerStateCustomLandmarkSelector, [
+ lm1,
+ lm2
+ ])
+ mockStore.overrideSelector(ngViewerSelectorOctantRemoval, true)
+ fixture.detectChanges()
+ expect(
+ toggleOctantRemovalSpy
+ ).toHaveBeenCalledWith(false)
+ })
+ })
})
})
diff --git a/src/ui/nehubaContainer/nehubaContainer.component.ts b/src/ui/nehubaContainer/nehubaContainer.component.ts
index 43f30390e593e7452225b7516434e7039885a39a..3447e5160185d227687fd00fb1e16986698d3728 100644
--- a/src/ui/nehubaContainer/nehubaContainer.component.ts
+++ b/src/ui/nehubaContainer/nehubaContainer.component.ts
@@ -189,6 +189,11 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
@Output()
public nehubaViewerLoaded: EventEmitter<boolean> = new EventEmitter()
+ @Output()
+ public forceUI$: Observable<{ target: 'perspective:octantRemoval', mode: boolean, message?: string }>
+
+ public disableOctantRemoval$: Observable<{ message?: string, mode: boolean }>
+
public handleViewerLoadedEvent(flag: boolean){
this.viewerLoaded = flag
this.nehubaViewerLoaded.emit(flag)
@@ -364,6 +369,30 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
distinctUntilChanged(),
)
+ /**
+ * in future, perhaps add other force UI optinos here
+ */
+ this.forceUI$ = this.userLandmarks$.pipe(
+ map(lm => {
+ if (lm.length > 0) {
+ return {
+ target: 'perspective:octantRemoval',
+ mode: false,
+ message: `octant control disabled: showing landmarks.`
+ }
+ } else {
+ return {
+ target: 'perspective:octantRemoval',
+ mode: null
+ }
+ }
+ })
+ )
+
+ this.disableOctantRemoval$ = this.forceUI$.pipe(
+ filter(({ target }) => target === 'perspective:octantRemoval'),
+ )
+
this.sliceRenderEvent$ = fromEvent(this.elementRef.nativeElement, 'sliceRenderEvent').pipe(
map(ev => ev as CustomEvent)
)
@@ -407,7 +436,8 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
}),
distinctUntilChanged(),
startWith('Loading ...'),
- throttleTime(100, asyncScheduler, { leading: true, trailing: true })
+ throttleTime(100, asyncScheduler, { leading: true, trailing: true }),
+ shareReplay(1),
))
)
@@ -553,6 +583,9 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
}),
)
+ /**
+ * TODO deprecate, but document the method
+ */
this.subscriptions.push(
combineLatest(
this.fetchedSpatialDatasets$,
@@ -585,7 +618,16 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
)
this.subscriptions.push(
- this.userLandmarks$.subscribe(landmarks => {
+ this.userLandmarks$.pipe(
+ withLatestFrom(
+ this.nehubaViewerPerspectiveOctantRemoval$
+ )
+ ).subscribe(([landmarks, flag]) => {
+ if (this.nehubaContainerDirective) {
+ this.nehubaContainerDirective.toggleOctantRemoval(
+ landmarks.length > 0 ? false : flag
+ )
+ }
if (this.nehubaViewer) {
this.nehubaViewer.updateUserLandmarks(landmarks)
}
diff --git a/src/ui/nehubaContainer/nehubaContainer.template.html b/src/ui/nehubaContainer/nehubaContainer.template.html
index 499f5c3bb03e8588de34016681b512a7f2f74255..e071b93515a1814be2a96530418f53ccf697230d 100644
--- a/src/ui/nehubaContainer/nehubaContainer.template.html
+++ b/src/ui/nehubaContainer/nehubaContainer.template.html
@@ -20,16 +20,16 @@
<current-layout *ngIf="viewerLoaded" class="position-absolute w-100 h-100 d-block pe-none">
<div class="w-100 h-100 position-relative" cell-i>
- <ng-content *ngTemplateOutlet="ngPanelOverlayTmpl; context: { panelIndex: 0 }"></ng-content>
+ <ng-content *ngTemplateOutlet="ngPanelOverlayTmpl; context: { panelIndex: panelOrder$ | async | getNthElement : 0 | parseAsNumber }"></ng-content>
</div>
<div class="w-100 h-100 position-relative" cell-ii>
- <ng-content *ngTemplateOutlet="ngPanelOverlayTmpl; context: { panelIndex: 1 }"></ng-content>
+ <ng-content *ngTemplateOutlet="ngPanelOverlayTmpl; context: { panelIndex: panelOrder$ | async | getNthElement : 1 | parseAsNumber }"></ng-content>
</div>
<div class="w-100 h-100 position-relative" cell-iii>
- <ng-content *ngTemplateOutlet="ngPanelOverlayTmpl; context: { panelIndex: 2 }"></ng-content>
+ <ng-content *ngTemplateOutlet="ngPanelOverlayTmpl; context: { panelIndex: panelOrder$ | async | getNthElement : 2 | parseAsNumber }"></ng-content>
</div>
<div class="w-100 h-100 position-relative" cell-iv>
- <ng-content *ngTemplateOutlet="overlayPerspectiveTmpl"></ng-content>
+ <ng-content *ngTemplateOutlet="ngPanelOverlayTmpl; context: { panelIndex: panelOrder$ | async | getNthElement : 3 | parseAsNumber }"></ng-content>
</div>
</current-layout>
@@ -344,7 +344,7 @@
let-iconTooltip="iconTooltip"
let-iavNgIf="iavNgIf"
let-content="content">
- <mat-expansion-panel class="mt-1 mb-1"
+ <mat-expansion-panel
[attr.data-opened]="expansionPanel.expanded"
[attr.data-mat-expansion-title]="title"
hideToggle
@@ -563,93 +563,93 @@
}">
</ng-container>
+ <div class="w-0 h-0"
+ iav-counter
+ #connectedCounterDir="iavCounter">
+
+ <hbp-connectivity-matrix-row *ngIf="region && region.name" [region]="region.name"
+ (connectivityDataReceived)="connectedCounterDir.value = $event.detail.length"
+ class="invisible d-block h-0 w-0"
+ loadurl="https://connectivity-query-v1-1-connectivity.apps-dev.hbp.eu/v1.1/studies/1345998a08539dc24bda8817c7d5804558d83b1c">
+ </hbp-connectivity-matrix-row>
+ </div>
</mat-accordion>
- <div class="w-0 h-0"
- iav-counter
- #connectedCounterDir="iavCounter">
-
- <hbp-connectivity-matrix-row *ngIf="region && region.name" [region]="region.name"
- (connectivityDataReceived)="connectedCounterDir.value = $event.detail.length"
- class="invisible d-block h-0 w-0"
- loadurl="https://connectivity-query-v1-1-connectivity.apps-dev.hbp.eu/v1.1/studies/1345998a08539dc24bda8817c7d5804558d83b1c">
- </hbp-connectivity-matrix-row>
- </div>
</ng-template>
<!-- overlay templates -->
-<!-- perspective view tmpl -->
-<ng-template #overlayPerspectiveTmpl>
- <layout-floating-container class="tmp" landmarkContainer>
-
- <div class="d-flex flex-column justify-content-center align-items-center w-100 h-100 position-absolute opacity-crossfade screen-overlay pe-none"
- [ngClass]="{onHover: !!(showPerpsectiveScreen$ | async)}"
- [attr.id]="ID_MESH_LOADING_STATUS"
- role="status">
+<!-- slice view overlay tmpl -->
+<ng-template #ngPanelOverlayTmpl let-panelIndex="panelIndex">
- <spinner-cmp *ngIf="showPerpsectiveScreen$ | async">
- </spinner-cmp>
-
- <mat-list>
- <mat-list-item>
- {{ showPerpsectiveScreen$ | async }}
- </mat-list-item>
- </mat-list>
- </div>
+ <!-- perspective view tmpl -->
+ <ng-template #overlayPerspectiveTmpl>
+ <layout-floating-container class="tmp" landmarkContainer>
+
+ <div class="d-flex flex-column justify-content-center align-items-center w-100 h-100 position-absolute opacity-crossfade screen-overlay pe-none"
+ [ngClass]="{onHover: !!(showPerpsectiveScreen$ | async)}"
+ [attr.id]="ID_MESH_LOADING_STATUS"
+ role="status">
+
+ <spinner-cmp *ngIf="showPerpsectiveScreen$ | async">
+ </spinner-cmp>
+
+ <mat-list>
+ <mat-list-item>
+ {{ showPerpsectiveScreen$ | async }}
+ </mat-list-item>
+ </mat-list>
+ </div>
- <!-- maximise/minimise button -->
- <ng-container *ngTemplateOutlet="panelCtrlTmpl; context: {
- panelIndex: panelOrder$ | async | getNthElement : 3 | parseAsNumber,
- visible: (panelOrder$ | async | reorderPanelIndexPipe : ( hoveredPanelIndices$ | async )) === 3
- }">
- </ng-container>
+ <!-- maximise/minimise button -->
+ <ng-container *ngTemplateOutlet="panelCtrlTmpl; context: {
+ panelIndex: panelIndex,
+ visible: (hoveredPanelIndices$ | async) === panelIndex
+ }">
+ </ng-container>
- <!-- mesh loading is still weird -->
- <!-- if the precomputed server does not have the necessary fragment file, then the numberws will not collate -->
- <div *ngIf="false && (perspectiveViewLoading$ | async)" class="loadingIndicator">
- <spinner-cmp></spinner-cmp>
+ <!-- mesh loading is still weird -->
+ <!-- if the precomputed server does not have the necessary fragment file, then the numberws will not collate -->
+ <div *ngIf="false && (perspectiveViewLoading$ | async)" class="loadingIndicator">
+ <spinner-cmp></spinner-cmp>
- <div *ngIf="false" perspectiveLoadingText>
- {{ perspectiveViewLoading$ | async }}
+ <div *ngIf="false" perspectiveLoadingText>
+ {{ perspectiveViewLoading$ | async }}
+ </div>
</div>
- </div>
- </layout-floating-container>
-</ng-template>
-
-<!-- slice view overlay tmpl -->
-<ng-template #ngPanelOverlayTmpl let-panelIndex="panelIndex">
+ </layout-floating-container>
+ </ng-template>
<!-- nb this slice view is not suitable for perspective view! -->
- <layout-floating-container *ngIf="panelIndex < 3" landmarkContainer>
+ <layout-floating-container *ngIf="panelIndex < 3; else overlayPerspectiveTmpl"
+ landmarkContainer
+ class="overflow-hidden">
<!-- customLandmarks -->
- <nehuba-2dlandmark-unit *ngFor="let lm of (customLandmarks$ | async | filterByProperty : 'showInSliceView')"
+ <landmark-2d-flat-cmp *ngFor="let lm of (customLandmarks$ | async | filterByProperty : 'showInSliceView')"
(mouseenter)="handleMouseEnterCustomLandmark(lm)"
(mouseleave)="handleMouseLeaveCustomLandmark(lm)"
- fasClass="fa-chevron-down"
[color]="lm.color || [255, 255, 255]"
[positionX]="getPositionX(panelIndex, lm)"
[positionY]="getPositionY(panelIndex, lm)"
[positionZ]="getPositionZ(panelIndex, lm)">
- </nehuba-2dlandmark-unit>
+ </landmark-2d-flat-cmp>
<!-- only show landmarks in slice views -->
- <nehuba-2dlandmark-unit *ngFor="let spatialData of (selectedPtLandmarks$ | async)"
+ <landmark-2d-flat-cmp *ngFor="let spatialData of (selectedPtLandmarks$ | async)"
(mouseenter)="handleMouseEnterLandmark(spatialData)"
(mouseleave)="handleMouseLeaveLandmark(spatialData)"
[highlight]="spatialData.highlight ? spatialData.highlight : false"
- [fasClass]="spatialData.type === 'userLandmark' ? 'fa-chevron-down' : 'fa-map-marker'"
[positionX]="getPositionX(panelIndex, spatialData)"
[positionY]="getPositionY(panelIndex, spatialData)"
[positionZ]="getPositionZ(panelIndex, spatialData)">
- </nehuba-2dlandmark-unit>
+ </landmark-2d-flat-cmp>
<!-- maximise/minimise button -->
<ng-container *ngTemplateOutlet="panelCtrlTmpl; context: {
- panelIndex: panelOrder$ | async | getNthElement : panelIndex | parseAsNumber,
- visible: (panelOrder$ | async | reorderPanelIndexPipe : ( hoveredPanelIndices$ | async )) === panelIndex
+ panelIndex: panelIndex,
+ visible: (hoveredPanelIndices$ | async) === panelIndex
}">
</ng-container>
@@ -657,6 +657,7 @@
<spinner-cmp></spinner-cmp>
</div>
</layout-floating-container>
+
</ng-template>
<!-- panel control template -->
@@ -672,7 +673,10 @@
<!-- perspective specific control -->
<ng-container *ngIf="panelIndex === 3">
- <ng-container *ngTemplateOutlet="perspectiveOctantRemovalTmpl; context: { state: (nehubaViewerPerspectiveOctantRemoval$ | async) }">
+ <ng-container *ngTemplateOutlet="perspectiveOctantRemovalTmpl; context: {
+ state: (nehubaViewerPerspectiveOctantRemoval$ | async),
+ disableOctantRemoval: disableOctantRemoval$ | async
+ }">
</ng-container>
</ng-container>
@@ -700,23 +704,27 @@
</ng-template>
-<ng-template #perspectiveOctantRemovalTmpl let-state="state">
- <button
- (click)="setOctantRemoval(!state)"
- mat-icon-button
- [attr.aria-label]="ARIA_LABEL_TOGGLE_FRONTAL_OCTANT"
- color="primary">
+<ng-template #perspectiveOctantRemovalTmpl let-state="state" let-disableOctantRemoval="disableOctantRemoval">
+ <div class="d-inline-block"
+ [matTooltip]="disableOctantRemoval?.mode !== null ? disableOctantRemoval.message : null">
+ <button
+ (click)="setOctantRemoval(!state)"
+ mat-icon-button
+ [disabled]="disableOctantRemoval?.mode !== null"
+ [attr.aria-label]="ARIA_LABEL_TOGGLE_FRONTAL_OCTANT"
+ color="primary">
- <!-- octant removal is true -->
- <ng-template [ngIf]="nehubaViewerPerspectiveOctantRemoval$ | async" [ngIfElse]="octantRemovalOffTmpl">
- <i class="fas fa-eye-slash"></i>
- </ng-template>
+ <!-- octant removal is true -->
+ <ng-template [ngIf]="disableOctantRemoval?.mode !== null ? disableOctantRemoval.mode : state" [ngIfElse]="octantRemovalOffTmpl">
+ <i class="fas fa-eye-slash"></i>
+ </ng-template>
- <!-- octant removal is false -->
- <ng-template #octantRemovalOffTmpl>
- <i class="fas fa-eye"></i>
- </ng-template>
- </button>
+ <!-- octant removal is false -->
+ <ng-template #octantRemovalOffTmpl>
+ <i class="fas fa-eye"></i>
+ </ng-template>
+ </button>
+ </div>
</ng-template>
diff --git a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
index 8393b9980d03f4aae65fe64dd28961c23ea1dc74..d1edab5e0f9fa80aa6347906b43c5d4ccceef803 100644
--- a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
+++ b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
@@ -250,7 +250,19 @@ export class NehubaViewerUnit implements OnInit, OnDestroy {
/**
* url may be null if user removes all landmarks
*/
- if (!url) { return }
+ if (!url) {
+ /**
+ * remove transparency from meshes in current layer(s)
+ */
+ for (const layerKey of this.multiNgIdsLabelIndexMap.keys()) {
+ const layer = this.nehubaViewer.ngviewer.layerManager.getLayerByName(layerKey)
+ if (layer) {
+ layer.layer.displayState.objectAlpha.restoreState(1.0)
+ }
+ }
+
+ return
+ }
const _ = {}
_[NG_USER_LANDMARK_LAYER_NAME] = {
type: 'mesh',
@@ -258,6 +270,16 @@ export class NehubaViewerUnit implements OnInit, OnDestroy {
shader: this.userLandmarkShader,
}
this.loadLayer(_)
+
+ /**
+ * adding transparency to meshes in current layer(s)
+ */
+ for (const layerKey of this.multiNgIdsLabelIndexMap.keys()) {
+ const layer = this.nehubaViewer.ngviewer.layerManager.getLayerByName(layerKey)
+ if (layer) {
+ layer.layer.displayState.objectAlpha.restoreState(0.2)
+ }
+ }
}),
)
}
diff --git a/src/ui/nehubaContainer/nehubaViewerInterface/nehubaViewerInterface.directive.ts b/src/ui/nehubaContainer/nehubaViewerInterface/nehubaViewerInterface.directive.ts
index cb3f929af8b4724dbbf97d1e649932a06a77bc15..f4a1973ae240f4235f441159dc0892456c381f2f 100644
--- a/src/ui/nehubaContainer/nehubaViewerInterface/nehubaViewerInterface.directive.ts
+++ b/src/ui/nehubaContainer/nehubaViewerInterface/nehubaViewerInterface.directive.ts
@@ -313,11 +313,7 @@ export class NehubaViewerContainerDirective implements OnInit, OnDestroy{
this.nehubaViewerPerspectiveOctantRemoval$.pipe(
distinctUntilChanged()
).subscribe(flag =>{
- const showPerspectiveSliceViews = this.nehubaViewerInstance?.nehubaViewer?.ngviewer?.showPerspectiveSliceViews
- if (showPerspectiveSliceViews) showPerspectiveSliceViews.restoreState(flag)
- else {
- this.log && this.log.warn(`showPerspectiveSliceViews not defined`)
- }
+ this.toggleOctantRemoval(flag)
})
)
@@ -374,6 +370,14 @@ export class NehubaViewerContainerDirective implements OnInit, OnDestroy{
}
}
+ public toggleOctantRemoval(flag: boolean){
+ const showPerspectiveSliceViews = this.nehubaViewerInstance?.nehubaViewer?.ngviewer?.showPerspectiveSliceViews
+ if (showPerspectiveSliceViews) showPerspectiveSliceViews.restoreState(flag)
+ else {
+ this.log && this.log.warn(`showPerspectiveSliceViews not defined`)
+ }
+ }
+
createNehubaInstance(template: any, lifeCycle: INehubaLifecycleHook = {}){
this.clear()
this.iavNehubaViewerContainerViewerLoading.emit(true)
diff --git a/src/ui/parcellationRegion/region.base.ts b/src/ui/parcellationRegion/region.base.ts
index 2d341de8eb904b8ac23eace486ef5ac2a9e720a5..473a830af001bb96e532fb38d2f516afb92390b7 100644
--- a/src/ui/parcellationRegion/region.base.ts
+++ b/src/ui/parcellationRegion/region.base.ts
@@ -33,7 +33,7 @@ export class RegionBase {
set region(val) {
this._region = val
this.region$.next(this._region)
- this.position = val.position
+ this.position = val && val.position
if (!this._region) return
const rgb = this._region.rgb || (this._region.labelIndex && intToRgb(Number(this._region.labelIndex))) || [255, 200, 200]
@@ -90,19 +90,31 @@ export class RegionBase {
const filteredRsInOtherTmpls = []
for (const bundledObj of regionsInOtherTemplates) {
const { template, parcellation, region } = bundledObj
- const idx = filteredRsInOtherTmpls.findIndex(({ template: _template, region: _region }) => {
+
+ /**
+ * trying to find duplicate region
+ * with same templateId, and same hemisphere
+ */
+ const sameEntityIdx = filteredRsInOtherTmpls.findIndex(({ template: _template, region: _region }) => {
return _template['@id'] === template['@id']
- && getRegionHemisphere(_region) !== getRegionHemisphere(region)
+ && getRegionHemisphere(_region) === getRegionHemisphere(region)
})
- if ( idx < 0 ) {
+ /**
+ * if doesn't exist, just push to output
+ */
+ if ( sameEntityIdx < 0 ) {
filteredRsInOtherTmpls.push(bundledObj)
} else {
- const { parcellation: currentParc } = filteredRsInOtherTmpls[idx]
+
+ /**
+ * if exists, only append the latest version
+ */
+ const { parcellation: currentParc } = filteredRsInOtherTmpls[sameEntityIdx]
/**
* if the new element is newer than existing item
*/
if (isNewerThan(parcellations, parcellation, currentParc)) {
- filteredRsInOtherTmpls.splice(idx, 1)
+ filteredRsInOtherTmpls.splice(sameEntityIdx, 1)
filteredRsInOtherTmpls.push(bundledObj)
}
}
diff --git a/src/ui/parcellationRegion/regionMenu/regionMenu.component.spec.ts b/src/ui/parcellationRegion/regionMenu/regionMenu.component.spec.ts
index fceeb0c7046afe38195967825e12cbd82097dde2..3c7f395eece740396746c2e452f9f9061490736b 100644
--- a/src/ui/parcellationRegion/regionMenu/regionMenu.component.spec.ts
+++ b/src/ui/parcellationRegion/regionMenu/regionMenu.component.spec.ts
@@ -112,161 +112,5 @@ describe('> regionMenu.component.ts', () => {
const fixture = TestBed.createComponent(RegionMenuComponent)
expect(fixture).toBeTruthy()
})
-
- describe('> regionInOtherTemplatesTmpl', () => {
- beforeEach(() => {
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(
- viewerStateGetSelectedAtlas,
- { parcellations: [] }
- )
- })
-
- it('> if selector returns empty array, data-available-in-tmpl-count == 0', () => {
-
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(
- regionInOtherTemplateSelector,
- []
- )
-
- const fixture = TestBed.createComponent(RegionMenuComponent)
- fixture.componentInstance.region = mr1
- fixture.detectChanges()
-
- const toggleBtn = fixture.debugElement.query( By.css(`[aria-label="${ARIA_LABELS.AVAILABILITY_IN_OTHER_REF_SPACE}"]`) )
- expect(toggleBtn.attributes['data-available-in-tmpl-count']).toEqual('0')
- })
-
- it('> if selector returns non empty array, data-available-in-tmpl-count == array.length', () => {
-
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(
- regionInOtherTemplateSelector,
- nohemisphereHrms
- )
-
- const fixture = TestBed.createComponent(RegionMenuComponent)
- fixture.componentInstance.region = mr1
- fixture.detectChanges()
-
- const toggleBtn = fixture.debugElement.query( By.css(`[aria-label="${ARIA_LABELS.AVAILABILITY_IN_OTHER_REF_SPACE}"]`) )
- expect(toggleBtn.attributes['data-available-in-tmpl-count']).toEqual('2')
- })
-
- it('> if showRegionInOtherTmpl is set to false, toggle btn will not be shown', () => {
-
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(
- regionInOtherTemplateSelector,
- nohemisphereHrms
- )
-
- const fixture = TestBed.createComponent(RegionMenuComponent)
- fixture.componentInstance.region = mr1
- fixture.componentInstance.showRegionInOtherTmpl = false
- fixture.detectChanges()
-
- const toggleBtn = fixture.debugElement.query( By.css(`[aria-label="${ARIA_LABELS.SHOW_IN_OTHER_REF_SPACE}"]`) )
- expect(toggleBtn).toBeFalsy()
- })
-
- it('> even if toggleBtn exists, list should be hidden by default', () => {
-
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(
- regionInOtherTemplateSelector,
- nohemisphereHrms
- )
-
- const fixture = TestBed.createComponent(RegionMenuComponent)
- fixture.componentInstance.region = mr1
- fixture.detectChanges()
-
- const listContainer = fixture.debugElement.query( By.css(`[aria-label="${ARIA_LABELS.SHOW_IN_OTHER_REF_SPACE}"]`) )
- expect(listContainer).toBeFalsy()
- })
-
- it('> on click of toggle btn, list to become visible', () => {
-
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(
- regionInOtherTemplateSelector,
- nohemisphereHrms
- )
-
- const fixture = TestBed.createComponent(RegionMenuComponent)
- fixture.componentInstance.region = mr1
- fixture.detectChanges()
- const toggleBtn = fixture.debugElement.query( By.css(`[aria-label="${ARIA_LABELS.AVAILABILITY_IN_OTHER_REF_SPACE}"]`) )
- toggleBtn.triggerEventHandler('click', null)
- fixture.detectChanges()
- const listContainer = fixture.debugElement.query( By.css(`[aria-label="${ARIA_LABELS.SHOW_IN_OTHER_REF_SPACE}"]`) )
- expect(listContainer).toBeTruthy()
- })
-
- it('> once list becomes available, there should be 2 items on the list', () => {
-
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(
- regionInOtherTemplateSelector,
- nohemisphereHrms
- )
-
- const fixture = TestBed.createComponent(RegionMenuComponent)
- fixture.componentInstance.region = mr1
- fixture.detectChanges()
- const toggleBtn = fixture.debugElement.query( By.css(`[aria-label="${ARIA_LABELS.AVAILABILITY_IN_OTHER_REF_SPACE}"]`) )
- toggleBtn.triggerEventHandler('click', null)
- fixture.detectChanges()
- const listContainer = fixture.debugElement.queryAll( By.css(`[aria-label="${ARIA_LABELS.SHOW_IN_OTHER_REF_SPACE}"] [role="button"]`) )
- expect(listContainer.length).toEqual(2)
- })
-
- it('> the text (no hemisphere metadata) on the list is as expected', () => {
-
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(
- regionInOtherTemplateSelector,
- nohemisphereHrms
- )
-
- const fixture = TestBed.createComponent(RegionMenuComponent)
- fixture.componentInstance.region = mr1
- fixture.detectChanges()
- const toggleBtn = fixture.debugElement.query( By.css(`[aria-label="${ARIA_LABELS.AVAILABILITY_IN_OTHER_REF_SPACE}"]`) )
- toggleBtn.triggerEventHandler('click', null)
- fixture.detectChanges()
- const listContainer = fixture.debugElement.queryAll( By.css(`[aria-label="${ARIA_LABELS.SHOW_IN_OTHER_REF_SPACE}"] [role="button"]`) )
-
- // trim white spaces before and after
-
- const texts = listContainer.map(c => c.nativeElement.textContent.replace(/^\s+/, '').replace(/\s+$/, ''))
- expect(texts).toContain(mt0.name)
- expect(texts).toContain(mt1.name)
- })
-
- it('> the text (with hemisphere metadata) on the list is as expected', () => {
-
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(
- regionInOtherTemplateSelector,
- hemisphereMrms
- )
-
- const fixture = TestBed.createComponent(RegionMenuComponent)
- fixture.componentInstance.region = mr1
- fixture.detectChanges()
- const toggleBtn = fixture.debugElement.query( By.css(`[aria-label="${ARIA_LABELS.AVAILABILITY_IN_OTHER_REF_SPACE}"]`) )
- toggleBtn.triggerEventHandler('click', null)
- fixture.detectChanges()
- const listContainer = fixture.debugElement.queryAll( By.css(`[aria-label="${ARIA_LABELS.SHOW_IN_OTHER_REF_SPACE}"] [role="button"]`) )
-
- // trim white spaces before and after, and middle white spaces into a single white space
- const texts = listContainer.map(c => c.nativeElement.textContent.replace(/^\s+/, '').replace(/\s+$/, '').replace(/\s+/g, ' '))
- expect(texts).toContain(`${mt0.name} (left hemisphere)`)
- expect(texts).toContain(`${mt1.name} (left hemisphere)`)
- })
- })
})
})
\ No newline at end of file
diff --git a/src/ui/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.component.ts b/src/ui/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.component.ts
index 800249b0ece08fdce51e5185985fcdda780de3b9..37c0fdc07a32a9d479d8f1fa85c804f8ad6b2f5b 100644
--- a/src/ui/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.component.ts
+++ b/src/ui/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.component.ts
@@ -1,6 +1,8 @@
import { Component, Inject, Optional, EventEmitter } from "@angular/core";
+import { Store } from "@ngrx/store";
import { merge, Subject, Subscription } from "rxjs";
import { debounceTime, map, scan, take } from "rxjs/operators";
+import { viewerStateChangeNavigation } from "src/services/state/viewerState/actions";
import { RegionalFeaturesService } from "src/ui/regionalFeatures/regionalFeature.service";
import { ClickInterceptor, CLICK_INTERCEPTOR_INJECTOR } from "src/util";
import { IHasId } from "src/util/interfaces";
@@ -23,6 +25,7 @@ export class IEEGRecordingsCmp extends RegionFeatureBase implements ISingleFeatu
constructor(
private regionFeatureService: RegionalFeaturesService,
+ private store: Store<any>,
@Optional() @Inject(CLICK_INTERCEPTOR_INJECTOR) private regClickIntp: ClickInterceptor,
){
super(regionFeatureService)
@@ -101,6 +104,19 @@ export class IEEGRecordingsCmp extends RegionFeatureBase implements ISingleFeatu
while(this.sub.length > 0) this.sub.pop().unsubscribe()
}
+ handleContactPtClk(contactPt: IHasId & { position: number[] }){
+ const { position } = contactPt
+ this.store.dispatch(
+ viewerStateChangeNavigation({
+ navigation: {
+ position: position.map(v => v * 1e6),
+ positionReal: true,
+ animation: {}
+ },
+ })
+ )
+ }
+
handleDatumExpansion(electrodeId: string, open: boolean){
/**
* TODO either debounce call here, or later down stream
diff --git a/src/ui/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.template.html b/src/ui/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.template.html
index 64e66983c69b605a34b4a1fa918ed532cfc31fb1..8d5cd968e4803219c7f8dca22ba3438c4321644b 100644
--- a/src/ui/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.template.html
+++ b/src/ui/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.template.html
@@ -35,8 +35,11 @@
<section class="d-flex align-items-center mt-1">
<section id="contact-points-list" class="flex-grow-1 flex-shrink-1 overflow-x-auto">
<div role="list" class="ws-no-wrap">
- <mat-chip *ngFor="let contactPt of datum['contactPoints']" class="ml-1">
- {{ contactPt.position | addUnitAndJoin : '' }}
+ <mat-chip *ngFor="let contactPt of datum['contactPoints']"
+ [matTooltip]="contactPt['position']"
+ (click)="handleContactPtClk(contactPt)"
+ class="ml-1">
+ {{ contactPt['@id'] }}
</mat-chip>
</div>
</section>
diff --git a/src/ui/regionalFeatures/singleFeatures/receptorDensity/getUrl.pipe.ts b/src/ui/regionalFeatures/singleFeatures/receptorDensity/getUrl.pipe.ts
new file mode 100644
index 0000000000000000000000000000000000000000..f4fdfab5613c225aa293a05b45c9d0ab8be666ab
--- /dev/null
+++ b/src/ui/regionalFeatures/singleFeatures/receptorDensity/getUrl.pipe.ts
@@ -0,0 +1,45 @@
+import { Pipe, PipeTransform } from "@angular/core";
+import { IHasId } from "src/util/interfaces";
+
+interface IReceptorDatum extends IHasId{
+ ['@context']: {
+ [key: string]: string
+ }
+ filename: string
+ mimetype: string
+ url: string | {
+ url: string
+ ['receptors.tsv']: string
+ }
+}
+
+interface IHRef{
+ url: string
+ filename: string
+}
+
+@Pipe({
+ name: 'getUrls',
+ pure: true
+})
+
+export class GetUrlsPipe implements PipeTransform{
+ public transform(input: IReceptorDatum): IHRef[]{
+ const output: IHRef[] = []
+ let _url = typeof input.url === 'string'
+ ? input.url
+ : input.url.url
+
+ for (const key in (input['@context'] || {})) {
+ _url = _url.replace(`${key}:`, input['@context'][key])
+ }
+
+ const match = /\/([\w-.]+)$/.exec(_url)
+ output.push({
+ url: _url,
+ filename: match ? match[1] : 'download'
+ })
+ return output
+ }
+}
+
diff --git a/src/ui/regionalFeatures/singleFeatures/receptorDensity/module.ts b/src/ui/regionalFeatures/singleFeatures/receptorDensity/module.ts
index b090a287314d4371c393a45b6102251a99122880..e75a9049402245140516abdb08107b9033c08838 100644
--- a/src/ui/regionalFeatures/singleFeatures/receptorDensity/module.ts
+++ b/src/ui/regionalFeatures/singleFeatures/receptorDensity/module.ts
@@ -5,6 +5,7 @@ import { RegionalFeaturesService } from "../../regionalFeature.service";
import { FilterReceptorByType } from "./filterReceptorBytype.pipe";
import { GetAllReceptorsPipe } from "./getAllReceptors.pipe";
import { GetIdPipe } from "./getId.pipe";
+import { GetUrlsPipe } from "./getUrl.pipe";
import { ReceptorDensityFeatureCmp } from "./receptorDensity/receptorDensity.component";
@NgModule({
@@ -17,6 +18,7 @@ import { ReceptorDensityFeatureCmp } from "./receptorDensity/receptorDensity.com
FilterReceptorByType,
GetIdPipe,
GetAllReceptorsPipe,
+ GetUrlsPipe,
],
schemas: [
CUSTOM_ELEMENTS_SCHEMA
diff --git a/src/ui/regionalFeatures/singleFeatures/receptorDensity/receptorDensity/receptorDensity.component.ts b/src/ui/regionalFeatures/singleFeatures/receptorDensity/receptorDensity/receptorDensity.component.ts
index b375fa6c94fc299b29e7c401d9a5441083e61381..1ecf5f8d6c8b1f60bcb2520039666fe0b4a3f17d 100644
--- a/src/ui/regionalFeatures/singleFeatures/receptorDensity/receptorDensity/receptorDensity.component.ts
+++ b/src/ui/regionalFeatures/singleFeatures/receptorDensity/receptorDensity/receptorDensity.component.ts
@@ -4,7 +4,13 @@ import { RegionalFeaturesService } from "src/ui/regionalFeatures/regionalFeature
import { PureContantService } from "src/util";
import { RegionFeatureBase } from "../../base/regionFeature.base";
import { ISingleFeature } from "../../interfaces";
+import { CONST } from 'common/constants'
+const {
+ RECEPTOR_FP_CAPTION,
+ RECEPTOR_PR_CAPTION,
+ RECEPTOR_AR_CAPTION,
+} = CONST
@Component({
templateUrl: './receptorDensity.template.html',
styleUrls: [
@@ -13,6 +19,11 @@ import { ISingleFeature } from "../../interfaces";
})
export class ReceptorDensityFeatureCmp extends RegionFeatureBase implements ISingleFeature, OnDestroy{
+
+ public RECEPTOR_FP_CAPTION = RECEPTOR_FP_CAPTION
+ public RECEPTOR_PR_CAPTION = RECEPTOR_PR_CAPTION
+ public RECEPTOR_AR_CAPTION = RECEPTOR_AR_CAPTION
+
public DS_PREVIEW_URL = DATASET_PREVIEW_URL
viewChanged: EventEmitter<null> = new EventEmitter()
diff --git a/src/ui/regionalFeatures/singleFeatures/receptorDensity/receptorDensity/receptorDensity.template.html b/src/ui/regionalFeatures/singleFeatures/receptorDensity/receptorDensity/receptorDensity.template.html
index 63da533879908ef0a59b8cd9691411e192de6f41..55bebd6798509e8aff576185ee53fe3f65e71748 100644
--- a/src/ui/regionalFeatures/singleFeatures/receptorDensity/receptorDensity/receptorDensity.template.html
+++ b/src/ui/regionalFeatures/singleFeatures/receptorDensity/receptorDensity/receptorDensity.template.html
@@ -3,15 +3,25 @@
</label>
<ng-container *ngFor="let datum of (data$ | async | filterReceptorByType : '_fp_')">
+
+ <ng-container *ngTemplateOutlet="labelTmpl; context: {
+ for: 'fingerprint-cmp',
+ label: RECEPTOR_FP_CAPTION
+ }">
+ </ng-container>
+
<ng-container *ngTemplateOutlet="datasetPreviewTmpl; context: {
id: 'fingerprint-cmp',
kgId: (feature['@id'] | getId),
- filename: datum['@id']
+ filename: datum['@id'],
+ datum: datum
}">
-
</ng-container>
+
</ng-container>
+<mat-divider></mat-divider>
+
<ng-container *ngIf="data$ | async | getAllReceptors as allReceptors; else selectPlaceHolderTmpl">
<mat-form-field class="mt-2 w-100" *ngIf="allReceptors.length > 0; else selectPlaceHolderTmpl">
@@ -49,16 +59,42 @@
</label>
</ng-template>
+ <ng-container *ngTemplateOutlet="labelTmpl; context: {
+ for: label + '-cmp',
+ label: 'Autoradiograph' ? RECEPTOR_AR_CAPTION : RECEPTOR_PR_CAPTION
+ }">
+ </ng-container>
+
<ng-container *ngTemplateOutlet="datasetPreviewTmpl; context: {
id: label + '-cmp',
kgId: (feature['@id'] | getId),
- filename: datum['@id']
+ filename: datum['@id'],
+ datum: datum
}">
</ng-container>
+
</ng-container>
</ng-template>
-<ng-template #datasetPreviewTmpl let-id="id" let-kgId="kgId" let-filename="filename">
+
+<!-- display preview tmpl -->
+<ng-template #datasetPreviewTmpl
+ let-id="id"
+ let-kgId="kgId"
+ let-filename="filename"
+ let-datum="datum">
+
+ <!-- download btns -->
+ <ng-container *ngFor="let urlObj of datum | getUrls">
+ <ng-container *ngTemplateOutlet="downloadBtnTmpl; context: {
+ url: urlObj.url,
+ filename: urlObj.filename,
+ tooltip: 'download ' + urlObj.filename
+ }">
+ </ng-container>
+ </ng-container>
+
+ <!-- render preview -->
<kg-ds-prv-regional-feature-view
*ngIf="depScriptLoaded$ | async; else fallbackTmpl"
[attr.id]="id"
@@ -78,4 +114,25 @@
[filename]="filename">
</kg-dataset-previewer>
</ng-template>
+</ng-template>
+
+<ng-template #downloadBtnTmpl
+ let-url="url"
+ let-filename="filename"
+ let-tooltip="tooltip">
+ <a [href]="url"
+ [download]="filename"
+ [matTooltip]="tooltip">
+ <button mat-icon-button>
+ <i class="fas fa-download"></i>
+ </button>
+ </a>
+</ng-template>
+
+<ng-template #labelTmpl let-label="label" let-for="for">
+ <label [attr.for]="for" class="text-muted">
+ <span>
+ {{ label }}
+ </span>
+ </label>
</ng-template>
\ No newline at end of file
diff --git a/src/ui/ui.module.ts b/src/ui/ui.module.ts
index 0e09814462b7d34fe606b8872d771623af78b0cf..0c116696a290cd9e622c8f18d6ec4ce740ce429c 100644
--- a/src/ui/ui.module.ts
+++ b/src/ui/ui.module.ts
@@ -11,12 +11,10 @@ import { FilterRegionDataEntries } from "src/util/pipes/filterRegionDataEntries.
import { GroupDatasetByRegion } from "src/util/pipes/groupDataEntriesByRegion.pipe";
import { GetLayerNameFromDatasets } from "../util/pipes/getLayerNamePipe.pipe";
-import { SafeStylePipe } from "../util/pipes/safeStyle.pipe";
import { SortDataEntriesToRegion } from "../util/pipes/sortDataEntriesIntoRegion.pipe";
import { CitationsContainer } from "./citation/citations.component";
import { KgEntryViewer } from "./kgEntryViewer/kgentry.component";
import { SubjectViewer } from "./kgEntryViewer/subjectViewer/subjectViewer.component";
-import { LandmarkUnit } from "./nehubaContainer/landmarkUnit/landmarkUnit.component";
import { PluginBannerUI } from "./pluginBanner/pluginBanner.component";
import { ScrollingModule } from "@angular/cdk/scrolling"
@@ -86,6 +84,7 @@ import { RenderViewOriginDatasetLabelPipe } from "./parcellationRegion/region.ba
import { RegionAccordionTooltipTextPipe } from './util'
import { HelpOnePager } from "./helpOnePager/helpOnePager.component";
import { RegionalFeaturesModule } from "./regionalFeatures";
+import { Landmark2DModule } from "./nehubaContainer/2dLandmarks/module";
@NgModule({
imports : [
@@ -105,12 +104,12 @@ import { RegionalFeaturesModule } from "./regionalFeatures";
AuthModule,
FabSpeedDialModule,
RegionalFeaturesModule,
+ Landmark2DModule,
],
declarations : [
NehubaContainer,
SplashScreen,
- LandmarkUnit,
PluginBannerUI,
CitationsContainer,
KgEntryViewer,
@@ -151,7 +150,6 @@ import { RegionalFeaturesModule } from "./regionalFeatures";
GroupDatasetByRegion,
FilterRegionDataEntries,
FlatmapArrayPipe,
- SafeStylePipe,
GetLayerNameFromDatasets,
SortDataEntriesToRegion,
SpatialLandmarksToDataBrowserItemPipe,
diff --git a/src/util/worker.js b/src/util/worker.js
index a46c50fccc19223a9f2fadd1c317eddea9b2d141..9ca462de1c0e246c9fa36df94b315c742d78d373 100644
--- a/src/util/worker.js
+++ b/src/util/worker.js
@@ -5,6 +5,14 @@ const validTypes = [
'PROPAGATE_PARC_REGION_ATTR'
]
+const VALID_METHOD = {
+ PROCESS_PLOTLY: `PROCESS_PLOTLY`
+}
+
+const VALID_METHODS = [
+ VALID_METHOD.PROCESS_PLOTLY
+]
+
const validOutType = [
'ASSEMBLED_LANDMARKS_VTK',
'ASSEMBLED_USERLANDMARKS_VTK',
@@ -91,8 +99,7 @@ const parseLmToVtk = (landmarks, scale) => {
const reduce = landmarks.reduce((acc,curr,idx) => {
//curr : null | [number,number,number] | [ [number,number,number], [number,number,number], [number,number,number] ][]
- if(curr === null)
- return acc
+ if(curr === null) return acc
if(!isNaN(curr[0]))
/**
* point primitive, render icosahedron
@@ -162,12 +169,10 @@ const getLandmarksVtk = (action) => {
const vtk = parseLmToVtk(landmarks, scale)
- if(!vtk)
- return
+ if(!vtk) return
// when new set of landmarks are to be displayed, the old landmarks will be discarded
- if(landmarkVtkUrl)
- URL.revokeObjectURL(landmarkVtkUrl)
+ if(landmarkVtkUrl) URL.revokeObjectURL(landmarkVtkUrl)
landmarkVtkUrl = URL.createObjectURL(new Blob( [encoder.encode(vtk)], {type : 'application/octet-stream'} ))
postMessage({
@@ -201,8 +206,7 @@ const getuserLandmarksVtk = (action) => {
}
const vtk = parseLmToVtk(landmarks, scale)
- if(!vtk)
- return
+ if(!vtk) return
if(userLandmarkVtkUrl)
URL.revokeObjectURL(userLandmarkVtkUrl)
@@ -288,7 +292,55 @@ const processParcRegionAttr = (payload) => {
})
}
+let plotyVtkUrl
+
onmessage = (message) => {
+ if (message.data.method && VALID_METHODS.indexOf(message.data.method) >= 0) {
+ const { id } = message.data
+ if (message.data.method === VALID_METHOD.PROCESS_PLOTLY) {
+ /**
+ * units in mm --> convert to nm
+ */
+ const plotyMultiple=1e6
+ try {
+ const { data: plotlyData } = message.data.param
+ const { x, y, z } = plotlyData.traces[0]
+ const lm = []
+ for (const idx in x) {
+ if (typeof x !== 'undefined' && x !== null) {
+ lm.push([x[idx]*plotyMultiple, y[idx]*plotyMultiple, z[idx]*plotyMultiple])
+ }
+ }
+ if (plotyVtkUrl) URL.revokeObjectURL(plotyVtkUrl)
+ const vtkString = parseLmToVtk(lm, 3e-2)
+ plotyVtkUrl = URL.createObjectURL(
+ new Blob([ encoder.encode(vtkString) ], { type: 'application/octet-stream' })
+ )
+ postMessage({
+ id,
+ result: {
+ objectUrl: plotyVtkUrl
+ }
+ })
+ } catch (e) {
+ postMessage({
+ id,
+ error: {
+ code: 401,
+ message: `malformed plotly param: ${e.toString()}`
+ }
+ })
+ }
+ }
+ postMessage({
+ id,
+ error: {
+ code: 404,
+ message: `worker method not found`
+ }
+ })
+ return
+ }
if(validTypes.findIndex(type => type === message.data.type) >= 0){
switch(message.data.type){