diff --git a/package.json b/package.json
index d4b47cfb3001a96f0e61c254a7c174ee31cb965a..b05fd47fcb2775a0304ecef3bf84318a0891656c 100644
--- a/package.json
+++ b/package.json
@@ -15,7 +15,7 @@
"watch": "ng build --watch --configuration development",
"test": "ng test",
"test-ci": "ng test --progress false --watch false --browsers=ChromeHeadless",
- "sapi-schema": "npx openapi-typescript@5.1.1 http://localhost:5000/v1_0/openapi.json --output ./src/atlasComponents/sapi/schema.ts",
+ "sapi-schema": "npx openapi-typescript@5.1.1 http://localhost:5000/v1_0/openapi.json --output ./src/atlasComponents/sapi/schema.ts && eslint ./src/atlasComponents/sapi/schema.ts --no-ignore --fix",
"docs:json": "compodoc -p ./tsconfig.json -e json -d .",
"storybook": "npm run docs:json && start-storybook -p 6006",
"build-storybook": "npm run docs:json && build-storybook"
diff --git a/src/atlasComponents/annotations/annotation.service.ts b/src/atlasComponents/annotations/annotation.service.ts
new file mode 100644
index 0000000000000000000000000000000000000000..471e628bbff4e137d91d4bd5c3fb2633d25a6dd9
--- /dev/null
+++ b/src/atlasComponents/annotations/annotation.service.ts
@@ -0,0 +1,120 @@
+import { getUuid } from "src/util/fn";
+
+export type TNgAnnotationLine = {
+ type: 'line'
+ pointA: [number, number, number]
+ pointB: [number, number, number]
+ id: string
+ description?: string
+}
+
+export type TNgAnnotationPoint = {
+ type: 'point'
+ point: [number, number, number]
+ id: string
+ description?: string
+}
+
+export type AnnotationSpec = TNgAnnotationLine | TNgAnnotationPoint
+type _AnnotationSpec = Omit<AnnotationSpec, 'type'> & { type: number }
+type AnnotationRef = {}
+
+interface NgAnnotationLayer {
+ layer: {
+ localAnnotations: {
+ references: {
+ get(id: string): AnnotationRef
+ delete(id: string): void
+ }
+ update(ref: AnnotationRef, spec: _AnnotationSpec): void
+ add(spec: _AnnotationSpec): void
+ delete(spec: AnnotationRef):void
+ annotationMap: Map<string, _AnnotationSpec>
+ }
+ registerDisposer(fn: () => void): void
+ }
+ setVisible(flag: boolean): void
+}
+
+export class AnnotationLayer {
+ private nglayer: NgAnnotationLayer
+ constructor(
+ private name: string = getUuid(),
+ private color="#ffffff"
+ ){
+ const layerSpec = this.viewer.layerSpecification.getLayer(
+ this.name,
+ {
+ type: "annotation",
+ "annotationColor": this.color,
+ "annotations": [],
+ name: this.name,
+ transform: [
+ [1, 0, 0, 0],
+ [0, 1, 0, 0],
+ [0, 0, 1, 0],
+ [0, 0, 0, 1],
+ ]
+ }
+ )
+ this.nglayer = this.viewer.layerManager.addManagedLayer(layerSpec)
+ this.nglayer.layer.registerDisposer(() => {
+ this.nglayer = null
+ })
+ }
+ setVisible(flag: boolean){
+ this.nglayer.setVisible(flag)
+ }
+ dispose() {
+ try {
+ this.viewer.layerManager.removeManagedLayer(this.nglayer)
+ } catch (e) {
+
+ }
+ }
+
+ addAnnotation(spec: AnnotationSpec){
+ const localAnnotations = this.nglayer.layer.localAnnotations
+ const annSpec = this.parseNgSpecType(spec)
+ localAnnotations.add(
+ annSpec
+ )
+ }
+ removeAnnotation(spec: { id: string }) {
+ const { localAnnotations } = this.nglayer.layer
+ const ref = localAnnotations.references.get(spec.id)
+ if (ref) {
+ localAnnotations.delete(ref)
+ localAnnotations.references.delete(spec.id)
+ }
+ }
+ updateAnnotation(spec: AnnotationSpec) {
+ const localAnnotations = this.nglayer.layer.localAnnotations
+ const ref = localAnnotations.references.get(spec.id)
+ const _spec = this.parseNgSpecType(spec)
+ if (ref) {
+ localAnnotations.update(
+ ref,
+ _spec
+ )
+ } else {
+ localAnnotations.add(_spec)
+ }
+ }
+
+ private get viewer() {
+ if ((window as any).viewer) return (window as any).viewer
+ throw new Error(`window.viewer not defined`)
+ }
+
+ private parseNgSpecType(spec: AnnotationSpec): _AnnotationSpec{
+ let overwritingType = null
+ if (spec.type === 'point') overwritingType = 0
+ if (spec.type === 'line') overwritingType = 1
+ if (overwritingType === null) throw new Error(`overwrite type lookup failed for ${spec.type}`)
+ return {
+ ...spec,
+ type: overwritingType
+ }
+ }
+}
diff --git a/src/atlasComponents/annotations/index.ts b/src/atlasComponents/annotations/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..651584158e28cbeb2ea72a5f3cbb954e4e402310
--- /dev/null
+++ b/src/atlasComponents/annotations/index.ts
@@ -0,0 +1 @@
+export { AnnotationLayer, TNgAnnotationPoint } from "./annotation.service"
\ No newline at end of file
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegSession/ieegSession.style.css b/src/atlasComponents/annotations/module.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/ieeg/ieegSession/ieegSession.style.css
rename to src/atlasComponents/annotations/module.ts
diff --git a/src/atlasComponents/sapi/core/sapiParcellation.ts b/src/atlasComponents/sapi/core/sapiParcellation.ts
index e33e20de39edda831adc161e5e2d2acf1b3219d9..5f956620942b6f2edb19a0046eeea8d59a958b20 100644
--- a/src/atlasComponents/sapi/core/sapiParcellation.ts
+++ b/src/atlasComponents/sapi/core/sapiParcellation.ts
@@ -44,9 +44,9 @@ export class SAPIParcellation{
)
}
- getFeatureInstance(instanceId: string): Promise<SapiParcellationFeatureModel> {
+ getFeatureInstance(instanceId: string): Observable<SapiParcellationFeatureModel> {
return this.sapi.http.get<SapiParcellationFeatureModel>(
`${this.sapi.bsEndpoint}/atlases/${encodeURIComponent(this.atlasId)}/parcellations/${encodeURIComponent(this.id)}/features/${encodeURIComponent(instanceId)}`,
- ).toPromise()
+ )
}
}
diff --git a/src/atlasComponents/sapi/core/sapiRegion.ts b/src/atlasComponents/sapi/core/sapiRegion.ts
index 0b2c4fb68c1646edbc4a01abf2ec34bd39ccd9ba..afadc4929dc48394affa9daa5a246b301b914b1f 100644
--- a/src/atlasComponents/sapi/core/sapiRegion.ts
+++ b/src/atlasComponents/sapi/core/sapiRegion.ts
@@ -1,7 +1,8 @@
import { SAPI } from "..";
-import { SapiRegionalFeatureModel, SapiRegionMapInfoModel, SapiRegionModel } from "../type";
+import { SapiRegionalFeatureModel, SapiRegionMapInfoModel, SapiRegionModel, cleanIeegSessionDatasets, SapiIeegSessionModel, CleanedIeegDataset } from "../type";
import { strToRgb, hexToRgb } from 'common/util'
-import { Observable } from "rxjs";
+import { forkJoin, Observable, of } from "rxjs";
+import { catchError, map } from "rxjs/operators";
export class SAPIRegion{
@@ -26,29 +27,45 @@ export class SAPIRegion{
this.prefix = `${this.sapi.bsEndpoint}/atlases/${encodeURIComponent(this.atlasId)}/parcellations/${encodeURIComponent(this.parcId)}/regions/${encodeURIComponent(this.id)}`
}
- getFeatures(spaceId: string): Promise<SapiRegionalFeatureModel[]> {
- return this.sapi.http.get<SapiRegionalFeatureModel[]>(
- `${this.prefix}/features`,
- {
- params: {
+ getFeatures(spaceId: string): Observable<(SapiRegionalFeatureModel | CleanedIeegDataset)[]> {
+ return forkJoin({
+ regionalFeatures: this.sapi.httpGet<SapiRegionalFeatureModel[]>(
+ `${this.prefix}/features`,
+ {
space_id: spaceId
}
- }
- ).toPromise()
+ ).pipe(
+ catchError((err, obs) => of([]))
+ ),
+ spatialFeatures: spaceId
+ ? this.sapi.getSpace(this.atlasId, spaceId).getFeatures({ parcellationId: this.parcId, region: this.id }).pipe(
+ catchError((err, obs) => {
+ console.log('error caught')
+ return of([])
+ }),
+ map(feats => {
+ const ieegSessions: SapiIeegSessionModel[] = feats.filter(feat => feat["@type"] === "siibra/features/ieegSession")
+ return cleanIeegSessionDatasets(ieegSessions)
+ }),
+ )
+ : of([] as CleanedIeegDataset[])
+ }).pipe(
+ map(({ regionalFeatures, spatialFeatures }) => {
+ return [...spatialFeatures, ...regionalFeatures]
+ })
+ )
}
- getFeatureInstance(instanceId: string, spaceId: string = null): Promise<SapiRegionalFeatureModel> {
- return this.sapi.http.get<SapiRegionalFeatureModel>(
+ getFeatureInstance(instanceId: string, spaceId: string = null): Observable<SapiRegionalFeatureModel> {
+ return this.sapi.httpGet<SapiRegionalFeatureModel>(
`${this.prefix}/features/${encodeURIComponent(instanceId)}`,
{
- params: {
- space_id: spaceId
- }
+ space_id: spaceId
}
- ).toPromise()
+ )
}
- getMapInfo(spaceId: string): Promise<SapiRegionMapInfoModel> {
+ getMapInfo(spaceId: string): Observable<SapiRegionMapInfoModel> {
return this.sapi.http.get<SapiRegionMapInfoModel>(
`${this.prefix}/regional_map/info`,
{
@@ -56,7 +73,7 @@ export class SAPIRegion{
space_id: spaceId
}
}
- ).toPromise()
+ )
}
getMapUrl(spaceId: string): string {
diff --git a/src/atlasComponents/sapi/core/sapiSpace.ts b/src/atlasComponents/sapi/core/sapiSpace.ts
index bd33b4239601550338b500a49aa77292952e0045..3ed79e8a7c06be812fc56de29d83cd4d543f8fa4 100644
--- a/src/atlasComponents/sapi/core/sapiSpace.ts
+++ b/src/atlasComponents/sapi/core/sapiSpace.ts
@@ -32,13 +32,24 @@ export class SAPISpace{
)
}
- getFeatures(modalityId: string, opts: SpatialFeatureOpts): Observable<SapiSpatialFeatureModel[]> {
+ getFeatures(opts: SpatialFeatureOpts): Observable<SapiSpatialFeatureModel[]> {
const query: Record<string, string> = {}
for (const [key, value] of Object.entries(opts)) {
query[camelToSnake(key)] = value
}
return this.sapi.httpGet<SapiSpatialFeatureModel[]>(
- `${this.sapi.bsEndpoint}/atlases/${encodeURIComponent(this.atlasId)}/spaces/${encodeURIComponent(this.id)}/features/${encodeURIComponent(modalityId)}`,
+ `${this.sapi.bsEndpoint}/atlases/${encodeURIComponent(this.atlasId)}/spaces/${encodeURIComponent(this.id)}/features`,
+ query
+ )
+ }
+
+ getFeatureInstance(instanceId: string, opts: SpatialFeatureOpts): Observable<SapiSpatialFeatureModel> {
+ const query: Record<string, string> = {}
+ for (const [key, value] of Object.entries(opts)) {
+ query[camelToSnake(key)] = value
+ }
+ return this.sapi.httpGet<SapiSpatialFeatureModel>(
+ `${this.sapi.bsEndpoint}/atlases/${encodeURIComponent(this.atlasId)}/spaces/${encodeURIComponent(this.id)}/features/${encodeURIComponent(instanceId)}`,
query
)
}
diff --git a/src/atlasComponents/sapi/index.ts b/src/atlasComponents/sapi/index.ts
index b1bbb7c2313d3c88f505f59b4a4947bbb620c99d..7e00877e930cd38bd040751ccd4b5dadd5ee723b 100644
--- a/src/atlasComponents/sapi/index.ts
+++ b/src/atlasComponents/sapi/index.ts
@@ -12,6 +12,9 @@ export {
SapiSpatialFeatureModel,
SapiFeatureModel,
SapiParcellationFeatureModel,
+ CleanedIeegDataset,
+ SxplrCleanedFeatureModel,
+ CLEANED_IEEG_DATASET_TYPE,
} from "./type"
export { SAPI } from "./sapi.service"
diff --git a/src/atlasComponents/sapi/module.ts b/src/atlasComponents/sapi/module.ts
index 452d71f70804eedce57e4c5b051e3c3abdff4be4..32701a9c5e86af9becbcbcbf23261d796f754f4a 100644
--- a/src/atlasComponents/sapi/module.ts
+++ b/src/atlasComponents/sapi/module.ts
@@ -2,17 +2,15 @@ import { NgModule } from "@angular/core";
import { SAPI } from "./sapi.service";
import { SpatialFeatureBBox } from "./directives/spatialFeatureBBox.directive"
import { CommonModule } from "@angular/common";
-import { EffectsModule } from "@ngrx/effects";
-import { SapiEffects } from "./sapi.effects";
-import { HTTP_INTERCEPTORS } from "@angular/common/http";
+import { HttpClientModule, HTTP_INTERCEPTORS } from "@angular/common/http";
import { PriorityHttpInterceptor } from "src/util/priority";
+import { MatSnackBarModule } from "@angular/material/snack-bar";
@NgModule({
imports: [
CommonModule,
- EffectsModule.forFeature([
- SapiEffects
- ])
+ HttpClientModule,
+ MatSnackBarModule,
],
declarations: [
SpatialFeatureBBox,
diff --git a/src/atlasComponents/sapi/sapi.effects.ts b/src/atlasComponents/sapi/sapi.effects.ts
deleted file mode 100644
index c1cb06fb33676d803368afaac8f39bbd0c7887ef..0000000000000000000000000000000000000000
--- a/src/atlasComponents/sapi/sapi.effects.ts
+++ /dev/null
@@ -1,12 +0,0 @@
-import { Injectable } from "@angular/core";
-import { SAPI } from "./sapi.service"
-
-@Injectable()
-export class SapiEffects{
-
- constructor(
- private sapiSvc: SAPI
- ){
-
- }
-}
diff --git a/src/atlasComponents/sapi/sapi.service.ts b/src/atlasComponents/sapi/sapi.service.ts
index 86c05ee11654f9041900de8dba83be00dd26b0cf..de44e86da06479ad232478e98d05b52491303c7c 100644
--- a/src/atlasComponents/sapi/sapi.service.ts
+++ b/src/atlasComponents/sapi/sapi.service.ts
@@ -1,10 +1,9 @@
-import { Inject, Injectable } from "@angular/core";
+import { Injectable } from "@angular/core";
import { HttpClient } from '@angular/common/http';
-import { BS_ENDPOINT } from 'src/util/constants';
-import { map, shareReplay, take, tap } from "rxjs/operators";
+import { map, shareReplay, tap } from "rxjs/operators";
import { SAPIAtlas, SAPISpace } from './core'
-import { SapiAtlasModel, SapiParcellationModel, SapiQueryParam, SapiRegionalFeatureModel, SapiRegionModel, SapiSpaceModel, SpyNpArrayDataModel } from "./type";
-import { CachedFunction, getExportNehuba } from "src/util/fn";
+import { SapiAtlasModel, SapiParcellationModel, SapiQueryParam, SapiRegionalFeatureModel, SapiRegionModel, SapiSpaceModel, SpyNpArrayDataModel, SxplrCleanedFeatureModel } from "./type";
+import { getExportNehuba } from "src/util/fn";
import { SAPIParcellation } from "./core/sapiParcellation";
import { SAPIRegion } from "./core/sapiRegion"
import { MatSnackBar } from "@angular/material/snack-bar";
@@ -71,10 +70,7 @@ export class SAPI{
return parc.getRegions(spaceId, queryParam)
}
- @CachedFunction({
- serialization: (atlasId, parcId, spaceId, regionId, ...args) => `sapi::getRegions::${atlasId}::${parcId}::${spaceId}::${regionId}`
- })
- getRegionFeatures(atlasId: string, parcId: string, spaceId: string, regionId: string, priority = 0): Promise<SapiRegionalFeatureModel[]>{
+ getRegionFeatures(atlasId: string, parcId: string, spaceId: string, regionId: string, priority = 0): Observable<(SapiRegionalFeatureModel | SxplrCleanedFeatureModel)[]>{
const reg = this.getRegion(atlasId, parcId, regionId)
return reg.getFeatures(spaceId)
diff --git a/src/atlasComponents/sapi/schema.ts b/src/atlasComponents/sapi/schema.ts
index c6b5bbca49d58c286aa0381ce8752ce59b4071ac..483b4d62789e416bb058b676c31a728a52715b71 100644
--- a/src/atlasComponents/sapi/schema.ts
+++ b/src/atlasComponents/sapi/schema.ts
@@ -10,11 +10,11 @@ export interface paths {
}
"/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/features": {
/** Returns all regional features for a region. */
- get: operations["get_all_features_for_region_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features_get"]
+ get: operations["get_all_regional_features_for_region_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features_get"]
}
"/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/features/{feature_id}": {
/** Returns a feature for a region, as defined by by the modality and feature ID */
- get: operations["get_regional_modality_by_id_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features__feature_id__get"]
+ get: operations["get_single_detailed_regional_feature_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features__feature_id__get"]
}
"/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/regional_map/info": {
/** Returns information about a regional map for given region name. */
@@ -33,19 +33,19 @@ export interface paths {
}
"/atlases/{atlas_id}/parcellations/{parcellation_id}/features/{feature_id}": {
/** Returns a global feature for a specific modality id. */
- get: operations["get_single_global_feature_detail_atlases__atlas_id__parcellations__parcellation_id__features__feature_id__get"]
+ get: operations["get_single_detailed_global_feature_atlases__atlas_id__parcellations__parcellation_id__features__feature_id__get"]
}
"/atlases/{atlas_id}/parcellations/{parcellation_id}/features": {
/** Returns all global features for a parcellation. */
- get: operations["get_global_features_names_atlases__atlas_id__parcellations__parcellation_id__features_get"]
+ get: operations["get_all_global_features_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__features_get"]
}
"/atlases/{atlas_id}/parcellations/{parcellation_id}/volumes": {
/** Returns one parcellation for given id. */
- get: operations["get_volumes_by_id_atlases__atlas_id__parcellations__parcellation_id__volumes_get"]
+ get: operations["get_volumes_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__volumes_get"]
}
"/atlases/{atlas_id}/parcellations/{parcellation_id}": {
/** Returns one parcellation for given id. */
- get: operations["get_parcellation_by_id_atlases__atlas_id__parcellations__parcellation_id__get"]
+ get: operations["get_single_parcellation_detail_atlases__atlas_id__parcellations__parcellation_id__get"]
}
"/atlases/{atlas_id}/spaces": {
/** Returns all spaces that are defined in the siibra client. */
@@ -64,18 +64,18 @@ export interface paths {
* Get a detailed view on a single spatial feature.
* A parcellation id and region id can be provided optional to get more details.
*/
- get: operations["get_single_spatial_feature_detail_atlases__atlas_id__spaces__space_id__features__feature_id__get"]
+ get: operations["get_single_detailed_spatial_feature_atlases__atlas_id__spaces__space_id__features__feature_id__get"]
}
"/atlases/{atlas_id}/spaces/{space_id}/features": {
/** Return all possible feature names and links to get more details */
- get: operations["get_spatial_features_from_space_atlases__atlas_id__spaces__space_id__features_get"]
+ get: operations["get_all_spatial_features_for_space_atlases__atlas_id__spaces__space_id__features_get"]
}
"/atlases/{atlas_id}/spaces/{space_id}/volumes": {
- get: operations["get_one_space_volumes_atlases__atlas_id__spaces__space_id__volumes_get"]
+ get: operations["get_volumes_for_space_atlases__atlas_id__spaces__space_id__volumes_get"]
}
"/atlases/{atlas_id}/spaces/{space_id}": {
/** Returns one space for given id, with links to further resources */
- get: operations["get_one_space_by_id_atlases__atlas_id__spaces__space_id__get"]
+ get: operations["get_single_space_detail_atlases__atlas_id__spaces__space_id__get"]
}
"/atlases": {
/** Get all atlases known by siibra. */
@@ -153,10 +153,10 @@ export interface components {
/** @Id */
"@id": string
/**
- * Type
+ * @Type
* @constant
*/
- type?: "siibra/core/dataset"
+ "@type"?: "siibra/core/dataset"
metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
/** Urls */
urls: components["schemas"]["Url"][]
@@ -181,6 +181,8 @@ export interface components {
}
/** BoundingBoxModel */
BoundingBoxModel: {
+ /** @Type */
+ "@type": string
/** Space */
space: { [key: string]: string }
center: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
@@ -195,11 +197,8 @@ export interface components {
ConnectivityMatrixDataModel: {
/** @Id */
"@id": string
- /**
- * Type
- * @constant
- */
- type?: "siibra/features/connectivity"
+ /** @Type */
+ "@type": string
/** Name */
name: string
/** Parcellations */
@@ -213,10 +212,10 @@ export interface components {
/** @Id */
"@id": string
/**
- * Type
+ * @Type
* @constant
*/
- type?: "siibra/core/dataset"
+ "@type"?: "siibra/core/dataset"
metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
/** Urls */
urls: components["schemas"]["Url"][]
@@ -310,12 +309,16 @@ export interface components {
}
/** IEEGContactPointModel */
IEEGContactPointModel: {
+ /** Inroi */
+ inRoi?: boolean
/** Id */
id: string
point: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
}
/** IEEGElectrodeModel */
IEEGElectrodeModel: {
+ /** Inroi */
+ inRoi?: boolean
/** Electrode Id */
electrode_id: string
/** Contact Points */
@@ -325,13 +328,15 @@ export interface components {
}
/** IEEGSessionModel */
IEEGSessionModel: {
+ /** Inroi */
+ inRoi?: boolean
/** @Id */
"@id": string
/**
- * Type
+ * @Type
* @constant
*/
- type?: "siibra/features/ieegSession"
+ "@type"?: "siibra/features/ieegSession"
dataset: components["schemas"]["DatasetJsonModel"]
/** Sub Id */
sub_id: string
@@ -459,10 +464,10 @@ export interface components {
/** @Id */
"@id": string
/**
- * Type
+ * @Type
* @constant
*/
- type?: "siibra/features/receptor"
+ "@type"?: "siibra/features/receptor"
metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
/** Urls */
urls: components["schemas"]["Url"][]
@@ -734,10 +739,10 @@ export interface components {
/** @Id */
"@id": string
/**
- * Type
+ * @Type
* @constant
*/
- type?: "siibra/features/voi"
+ "@type"?: "siibra/features/voi"
metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
/** Urls */
urls: components["schemas"]["Url"][]
@@ -784,10 +789,10 @@ export interface components {
/** @Id */
"@id": string
/**
- * Type
+ * @Type
* @constant
*/
- type?: "siibra/core/dataset"
+ "@type"?: "siibra/core/dataset"
metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
/** Urls */
urls: components["schemas"]["Url"][]
@@ -1333,7 +1338,7 @@ export interface operations {
}
}
/** Returns all regional features for a region. */
- get_all_features_for_region_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features_get: {
+ get_all_regional_features_for_region_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features_get: {
parameters: {
path: {
atlas_id: string
@@ -1363,7 +1368,7 @@ export interface operations {
}
}
/** Returns a feature for a region, as defined by by the modality and feature ID */
- get_regional_modality_by_id_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features__feature_id__get: {
+ get_single_detailed_regional_feature_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features__feature_id__get: {
parameters: {
path: {
atlas_id: string
@@ -1498,7 +1503,7 @@ export interface operations {
}
}
/** Returns a global feature for a specific modality id. */
- get_single_global_feature_detail_atlases__atlas_id__parcellations__parcellation_id__features__feature_id__get: {
+ get_single_detailed_global_feature_atlases__atlas_id__parcellations__parcellation_id__features__feature_id__get: {
parameters: {
path: {
atlas_id: string
@@ -1525,7 +1530,7 @@ export interface operations {
}
}
/** Returns all global features for a parcellation. */
- get_global_features_names_atlases__atlas_id__parcellations__parcellation_id__features_get: {
+ get_all_global_features_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__features_get: {
parameters: {
path: {
atlas_id: string
@@ -1555,7 +1560,7 @@ export interface operations {
}
}
/** Returns one parcellation for given id. */
- get_volumes_by_id_atlases__atlas_id__parcellations__parcellation_id__volumes_get: {
+ get_volumes_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__volumes_get: {
parameters: {
path: {
atlas_id: string
@@ -1578,7 +1583,7 @@ export interface operations {
}
}
/** Returns one parcellation for given id. */
- get_parcellation_by_id_atlases__atlas_id__parcellations__parcellation_id__get: {
+ get_single_parcellation_detail_atlases__atlas_id__parcellations__parcellation_id__get: {
parameters: {
path: {
atlas_id: string
@@ -1674,7 +1679,7 @@ export interface operations {
* Get a detailed view on a single spatial feature.
* A parcellation id and region id can be provided optional to get more details.
*/
- get_single_spatial_feature_detail_atlases__atlas_id__spaces__space_id__features__feature_id__get: {
+ get_single_detailed_spatial_feature_atlases__atlas_id__spaces__space_id__features__feature_id__get: {
parameters: {
path: {
feature_id: string
@@ -1682,8 +1687,8 @@ export interface operations {
space_id: string
}
query: {
- parcellation_id: string
- region: string
+ parcellation_id?: string
+ region?: string
bbox?: string
}
}
@@ -1706,7 +1711,7 @@ export interface operations {
}
}
/** Return all possible feature names and links to get more details */
- get_spatial_features_from_space_atlases__atlas_id__spaces__space_id__features_get: {
+ get_all_spatial_features_for_space_atlases__atlas_id__spaces__space_id__features_get: {
parameters: {
path: {
atlas_id: string
@@ -1736,7 +1741,7 @@ export interface operations {
}
}
}
- get_one_space_volumes_atlases__atlas_id__spaces__space_id__volumes_get: {
+ get_volumes_for_space_atlases__atlas_id__spaces__space_id__volumes_get: {
parameters: {
path: {
atlas_id: string
@@ -1759,7 +1764,7 @@ export interface operations {
}
}
/** Returns one space for given id, with links to further resources */
- get_one_space_by_id_atlases__atlas_id__spaces__space_id__get: {
+ get_single_space_detail_atlases__atlas_id__spaces__space_id__get: {
parameters: {
path: {
atlas_id: string
diff --git a/src/atlasComponents/sapi/stories.base.ts b/src/atlasComponents/sapi/stories.base.ts
index f4162b72d80ec585472dbe40e77423336f0ec630..51fde4f0cd5695f6055398e8bd9ec39ed469c541 100644
--- a/src/atlasComponents/sapi/stories.base.ts
+++ b/src/atlasComponents/sapi/stories.base.ts
@@ -1,5 +1,5 @@
import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionalFeatureModel, SapiRegionModel, SapiSpaceModel } from "."
-import { SapiParcellationFeatureModel } from "./type"
+import { cleanIeegSessionDatasets, SapiParcellationFeatureModel, SapiSpatialFeatureModel, SxplrCleanedFeatureModel } from "./type"
import addons from '@storybook/addons';
import { DARKTHEME } from "src/util/injectionTokens";
import { APP_INITIALIZER, NgZone } from "@angular/core";
@@ -101,11 +101,11 @@ export async function getJba29Regions(): Promise<SapiRegionModel[]> {
return await getParcRegions(atlasId.human, parcId.human.jba29, spaceId.human.mni152)
}
-export async function getHoc1Left(spaceId=null): Promise<SapiRegionModel> {
+export async function getHoc1Right(spaceId=null): Promise<SapiRegionModel> {
if (!spaceId) {
- return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/regions/hoc1%20left`)).json()
+ return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/regions/hoc1%20right`)).json()
}
- return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/regions/hoc1%20left?space_id=${encodeURIComponent(spaceId)}`)).json()
+ return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/regions/hoc1%20right?space_id=${encodeURIComponent(spaceId)}`)).json()
}
export async function get44Left(spaceId=null): Promise<SapiRegionModel> {
@@ -115,14 +115,37 @@ export async function get44Left(spaceId=null): Promise<SapiRegionModel> {
return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/regions/area%2044%20left?space_id=${encodeURIComponent(spaceId)}`)).json()
}
-export async function getHoc1Features(): Promise<SapiRegionalFeatureModel[]> {
- return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/regions/hoc1%20left/features`)).json()
+export async function getHoc1RightSpatialFeatures(): Promise<SxplrCleanedFeatureModel[]> {
+ const json: SapiSpatialFeatureModel[] = await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/spaces/${spaceId.human.mni152}/features?parcellation_id=2.9®ion=hoc1%20right`)).json()
+ return cleanIeegSessionDatasets(json.filter(it => it['@type'] === "siibra/features/ieegSession"))
}
-export async function getHoc1FeatureDetail(featId: string): Promise<SapiRegionalFeatureModel>{
- return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/regions/hoc1%20left/features/${encodeURIComponent(featId)}`)).json()
+export async function getHoc1RightFeatures(): Promise<SapiRegionalFeatureModel[]> {
+ return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/regions/hoc1%20right/features`)).json()
+}
+
+export async function getHoc1RightFeatureDetail(featId: string): Promise<SapiRegionalFeatureModel>{
+ return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/regions/hoc1%20right/features/${encodeURIComponent(featId)}`)).json()
}
export async function getJba29Features(): Promise<SapiParcellationFeatureModel[]> {
return await (await fetch(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/parcellations/${parcId.human.jba29}/features`)).json()
}
+
+export async function getBigbrainSpatialFeatures(): Promise<SapiSpatialFeatureModel[]>{
+ const bbox = [
+ [-1000, -1000, -1000],
+ [1000, 1000, 1000]
+ ]
+ const url = new URL(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/spaces/${spaceId.human.bigbrain}/features`)
+ url.searchParams.set(`bbox`, JSON.stringify(bbox))
+ return await (await fetch(url.toString())).json()
+}
+
+export async function getMni152SpatialFeatureHoc1Right(): Promise<SapiSpatialFeatureModel[]>{
+
+ const url = new URL(`${SAPI.bsEndpoint}/atlases/${atlasId.human}/spaces/${spaceId.human.mni152}/features`)
+ url.searchParams.set(`parcellation_id`, parcId.human.jba29)
+ url.searchParams.set("region", 'hoc1 right')
+ return await (await fetch(url.toString())).json()
+}
diff --git a/src/atlasComponents/sapi/type.ts b/src/atlasComponents/sapi/type.ts
index 77a94d21f0ebc6ad92236fe2324642bf746615a2..97519d6fd6fcf91e68880e7f8e359f508897815b 100644
--- a/src/atlasComponents/sapi/type.ts
+++ b/src/atlasComponents/sapi/type.ts
@@ -1,6 +1,6 @@
import { OperatorFunction } from "rxjs"
import { map } from "rxjs/operators"
-import { components } from "./schema"
+import { components, operations, paths } from "./schema"
export type IdName = {
id: string
@@ -15,35 +15,17 @@ export type SapiAtlasModel = components["schemas"]["SapiAtlasModel"]
export type SapiSpaceModel = components["schemas"]["SapiSpaceModel"]
export type SapiParcellationModel = components["schemas"]["SapiParcellationModel"]
export type SapiRegionModel = components["schemas"]["siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Model"]
-export type SapiRegionMapInfoModel = components["schemas"]["NiiMetadataModel"]
-export type SapiSpatialFeatureModel = components["schemas"]["VOIDataModel"]
+export type SapiRegionMapInfoModel = components["schemas"]["NiiMetadataModel"]
export type SapiVOIDataResponse = components["schemas"]["VOIDataModel"]
-
export type SapiVolumeModel = components["schemas"]["VolumeModel"]
export type SapiDatasetModel = components["schemas"]["DatasetJsonModel"]
-
export type SpyNpArrayDataModel = components["schemas"]["NpArrayDataModel"]
-
-
-export function FeatureTypeGuard(input: SapiFeatureModel) {
- if (input.type === "siibra/core/dataset") {
- return input as SapiDatasetModel
- }
- if (input.type === "siibra/features/connectivity") {
- return input as SapiParcellationFeatureMatrixModel
- }
- if (input.type === "siibra/features/receptor") {
- return input as SapiRegionalFeatureReceptorModel
- }
- if (input.type === "siibra/features/voi") {
- return input as SapiVOIDataResponse
- }
- if (input.type === "spy/serialization-error") {
- return input as SapiSerializationErrorModel
- }
- throw new Error(`cannot parse type: ${input}`)
-}
+export type SapiIeegSessionModel = components["schemas"]["IEEGSessionModel"]
+/**
+ * utility types
+ */
+type PathReturn<T extends keyof paths> = Required<paths[T]["get"]["responses"][200]["content"]["application/json"]>
/**
* serialization error type
@@ -51,16 +33,53 @@ export function FeatureTypeGuard(input: SapiFeatureModel) {
export type SapiSerializationErrorModel = components["schemas"]["SerializationErrorModel"]
/**
- * datafeatures
+ * datafeatures from operations
*/
-export type SapiRegionalFeatureReceptorModel = components["schemas"]["ReceptorDatasetModel"]
-export type SapiRegionalFeatureModel = components["schemas"]["BaseDatasetJsonModel"] | SapiRegionalFeatureReceptorModel
-export type SapiParcellationFeatureMatrixModel = components["schemas"]["ConnectivityMatrixDataModel"]
-export type SapiParcellationFeatureModel = SapiParcellationFeatureMatrixModel | SapiSerializationErrorModel
+export type SapiRegionalFeatureModel = PathReturn<"/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/features/{feature_id}">
+export type SapiParcellationFeatureModel = PathReturn<"/atlases/{atlas_id}/parcellations/{parcellation_id}/features/{feature_id}">
+export type SapiSpatialFeatureModel = PathReturn<"/atlases/{atlas_id}/spaces/{space_id}/features/{feature_id}">
export type SapiFeatureModel = SapiRegionalFeatureModel | SapiSpatialFeatureModel | SapiParcellationFeatureModel
+/**
+ * specific data features
+ */
+
+export type SapiRegionalFeatureReceptorModel = components["schemas"]["ReceptorDatasetModel"]
+export type SapiParcellationFeatureMatrixModel = components["schemas"]["ConnectivityMatrixDataModel"]
+
+
+export const CLEANED_IEEG_DATASET_TYPE = 'sxplr/cleanedIeegDataset'
+export type CleanedIeegDataset = Required<
+ Omit<SapiDatasetModel, "@type"> & {
+ '@type': 'sxplr/cleanedIeegDataset'
+ sessions: Record<string, Omit<SapiIeegSessionModel, "dataset">>
+ }
+>
+
+export function cleanIeegSessionDatasets(ieegSessions: SapiIeegSessionModel[]): CleanedIeegDataset[]{
+ const returnArr: CleanedIeegDataset[] = []
+ for (const sess of ieegSessions) {
+ const { dataset, ...itemToAppend } = sess
+ const existing = returnArr.find(it => it["@id"] === dataset["@id"])
+ if (!existing) {
+ returnArr.push({
+ ...dataset,
+ '@type': CLEANED_IEEG_DATASET_TYPE,
+ sessions: {
+ [sess.sub_id]: itemToAppend
+ }
+ })
+ continue
+ }
+ existing.sessions[sess.sub_id] = itemToAppend
+ }
+ return returnArr
+}
+
+export type SxplrCleanedFeatureModel = CleanedIeegDataset
+
export function guardPipe<
InputType,
GuardType extends InputType
diff --git a/src/atlasComponents/sapiViews/core/atlas/module.ts b/src/atlasComponents/sapiViews/core/atlas/module.ts
index a41cdb25c60ea1255837923285522a32ca85dfcc..691d41303c80c52229423586c9243d27fc419479 100644
--- a/src/atlasComponents/sapiViews/core/atlas/module.ts
+++ b/src/atlasComponents/sapiViews/core/atlas/module.ts
@@ -7,6 +7,7 @@ import { SapiViewsUtilModule } from "../../util";
import { SapiViewsCoreParcellationModule } from "../parcellation";
import { SapiViewsCoreSpaceModule } from "../space";
import { SapiViewsCoreAtlasAtlasDropdownSelector } from "./dropdownAtlasSelector/dropdownAtlasSelector.component";
+import { SapiViewsCoreAtlasSplashScreen } from "./splashScreen/splashScreen.component";
import { SapiViewsCoreAtlasAtlasTmplParcSelector } from "./tmplParcSelector/tmplParcSelector.component";
@NgModule({
@@ -22,10 +23,12 @@ import { SapiViewsCoreAtlasAtlasTmplParcSelector } from "./tmplParcSelector/tmpl
declarations: [
SapiViewsCoreAtlasAtlasDropdownSelector,
SapiViewsCoreAtlasAtlasTmplParcSelector,
+ SapiViewsCoreAtlasSplashScreen,
],
exports: [
SapiViewsCoreAtlasAtlasDropdownSelector,
SapiViewsCoreAtlasAtlasTmplParcSelector,
+ SapiViewsCoreAtlasSplashScreen,
]
})
diff --git a/src/atlasComponents/splashScreen/splashScreen/splashScreen.component.ts b/src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.component.ts
similarity index 95%
rename from src/atlasComponents/splashScreen/splashScreen/splashScreen.component.ts
rename to src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.component.ts
index 775b1a486bc18ec333ce8aec1a32ccdcc8c14091..056e3660c4243ee41bff9e5090354bd6e6fb2deb 100644
--- a/src/atlasComponents/splashScreen/splashScreen/splashScreen.component.ts
+++ b/src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.component.ts
@@ -14,7 +14,7 @@ import { atlasSelection } from "src/state"
changeDetection: ChangeDetectionStrategy.OnPush,
})
-export class SplashScreen {
+export class SapiViewsCoreAtlasSplashScreen {
public finishedLoading: boolean = false
diff --git a/src/atlasComponents/splashScreen/splashScreen/splashScreen.style.css b/src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.style.css
similarity index 100%
rename from src/atlasComponents/splashScreen/splashScreen/splashScreen.style.css
rename to src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.style.css
diff --git a/src/atlasComponents/splashScreen/splashScreen/splashScreen.template.html b/src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.template.html
similarity index 100%
rename from src/atlasComponents/splashScreen/splashScreen/splashScreen.template.html
rename to src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.template.html
diff --git a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.stories.ts b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.stories.ts
index ff2a0406288b6db8a48c20e7de29f6b29edcb0a3..acec7a744768e383bdb511d15b4a8d537b9e0633 100644
--- a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.stories.ts
+++ b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.stories.ts
@@ -2,7 +2,7 @@ import { CommonModule } from "@angular/common"
import { HttpClientModule } from "@angular/common/http"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
import { SAPI } from "src/atlasComponents/sapi"
-import { getHoc1FeatureDetail, getHoc1Features, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
+import { getHoc1RightFeatureDetail, getHoc1RightFeatures, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
import { SapiViewsCoreDatasetModule } from ".."
import { DatasetView } from "./dataset.component"
@@ -35,9 +35,9 @@ const Template: Story<DatasetView> = (args: DatasetView, { loaded }) => {
}
const loadFeat = async () => {
- const features = await getHoc1Features()
- const receptorfeat = features.find(f => f.type === "siibra/core/dataset")
- const feature = await getHoc1FeatureDetail(receptorfeat["@id"])
+ const features = await getHoc1RightFeatures()
+ const receptorfeat = features.find(f => f['@type'] === "siibra/core/dataset")
+ const feature = await getHoc1RightFeatureDetail(receptorfeat["@id"])
return {
feature
}
diff --git a/src/atlasComponents/sapiViews/core/region/region/chip/region.chip.stories.ts b/src/atlasComponents/sapiViews/core/region/region/chip/region.chip.stories.ts
index 1fc06697565f11e974950f757052ead015238ed6..ec74e25aadf0b5f3d00ef164efd2ff19238259bb 100644
--- a/src/atlasComponents/sapiViews/core/region/region/chip/region.chip.stories.ts
+++ b/src/atlasComponents/sapiViews/core/region/region/chip/region.chip.stories.ts
@@ -1,8 +1,8 @@
import { CommonModule } from "@angular/common"
import { HttpClientModule } from "@angular/common/http"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
-import { SAPI, SapiParcellationModel } from "src/atlasComponents/sapi"
-import { atlasId, getAtlas, provideDarkTheme, getParc, getHumanAtlas, getJba29, getMni152, getHoc1Left, get44Left } from "src/atlasComponents/sapi/stories.base"
+import { SAPI } from "src/atlasComponents/sapi"
+import { provideDarkTheme, getHumanAtlas, getJba29, getMni152, getHoc1Right, get44Left } from "src/atlasComponents/sapi/stories.base"
import { AngularMaterialModule } from "src/sharedModules"
import { SapiViewsCoreRegionModule } from "../../module"
import { SapiViewsCoreRegionRegionChip } from "./region.chip.component"
@@ -72,7 +72,7 @@ Default.loaders = [
const atlas = await getHumanAtlas()
const parcellation = await getJba29()
const template = await getMni152()
- const region = await getHoc1Left()
+ const region = await getHoc1Right()
return {
atlas,
diff --git a/src/atlasComponents/sapiViews/core/region/region/listItem/region.listItem.stories.ts b/src/atlasComponents/sapiViews/core/region/region/listItem/region.listItem.stories.ts
index 900bd2e0a0f01a7ec5797aec22c19bb539aee4a7..abc0bef7a287e6f8e8d2f284d52d0bf0b99f9258 100644
--- a/src/atlasComponents/sapiViews/core/region/region/listItem/region.listItem.stories.ts
+++ b/src/atlasComponents/sapiViews/core/region/region/listItem/region.listItem.stories.ts
@@ -2,7 +2,7 @@ import { CommonModule } from "@angular/common"
import { HttpClientModule } from "@angular/common/http"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
import { SAPI } from "src/atlasComponents/sapi"
-import { getHoc1Left, getHumanAtlas, getJba29, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
+import { getHoc1Right, getHumanAtlas, getJba29, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
import { SapiViewsCoreRegionModule } from "../../module"
import { SapiViewsCoreRegionRegionListItem } from "./region.listItem.component"
@@ -55,7 +55,7 @@ const loadRegions = async () => {
const human = await getHumanAtlas()
const mni152 = await getMni152()
const jba29 = await getJba29()
- const hoc1left = await getHoc1Left(mni152["@id"])
+ const hoc1left = await getHoc1Right(mni152["@id"])
return {
human,
diff --git a/src/atlasComponents/sapiViews/core/region/region/region.features.directive.ts b/src/atlasComponents/sapiViews/core/region/region/region.features.directive.ts
index d542fc05dd988f4f599b292633b20445402f8dea..9c3cad17f525199cc4f91b21a890dff98c822235 100644
--- a/src/atlasComponents/sapiViews/core/region/region/region.features.directive.ts
+++ b/src/atlasComponents/sapiViews/core/region/region/region.features.directive.ts
@@ -2,6 +2,7 @@ import { Directive, OnChanges, SimpleChanges } from "@angular/core";
import { BehaviorSubject, merge, Observable } from "rxjs";
import { switchMap, filter, startWith, shareReplay, mapTo, delay, tap } from "rxjs/operators";
import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionalFeatureModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SxplrCleanedFeatureModel } from "src/atlasComponents/sapi/type";
import { SapiViewsCoreRegionRegionBase } from "./region.base.directive";
@Directive({
@@ -27,7 +28,7 @@ export class SapiViewsCoreRegionRegionalFeatureDirective extends SapiViewsCoreRe
super(sapi)
}
- private features$: Observable<SapiRegionalFeatureModel[]> = this.ATPR$.pipe(
+ private features$: Observable<(SapiRegionalFeatureModel|SxplrCleanedFeatureModel)[]> = this.ATPR$.pipe(
filter(arg => {
if (!arg) return false
const { atlas, parcellation, region, template } = arg
@@ -36,7 +37,7 @@ export class SapiViewsCoreRegionRegionalFeatureDirective extends SapiViewsCoreRe
switchMap(({ atlas, parcellation, region, template }) => this.sapi.getRegionFeatures(atlas["@id"], parcellation["@id"], template["@id"], region.name)),
)
- public listOfFeatures$: Observable<SapiRegionalFeatureModel[]> = this.features$.pipe(
+ public listOfFeatures$: Observable<(SapiRegionalFeatureModel|SxplrCleanedFeatureModel)[]> = this.features$.pipe(
startWith([]),
shareReplay(1),
)
diff --git a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.stories.ts b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.stories.ts
index 551ed5a081fb5536fc91ff2e2d4c2196aed3740f..6e9f8907cd68facc3c60f31b6e28cadbb4873573 100644
--- a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.stories.ts
+++ b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.stories.ts
@@ -2,7 +2,7 @@ import { CommonModule } from "@angular/common"
import { HttpClientModule } from "@angular/common/http"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
import { SAPI } from "src/atlasComponents/sapi"
-import { atlasId, getHoc1Left, getHumanAtlas, getJba29, getJba29Regions, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
+import { getHoc1Right, getHumanAtlas, getJba29, getJba29Regions, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
import { SapiViewsCoreRegionModule } from "../../module"
import { SapiViewsCoreRegionRegionRich } from "./region.rich.component"
import { action } from '@storybook/addon-actions';
@@ -61,7 +61,7 @@ const loadRegions = async () => {
const human = await getHumanAtlas()
const mni152 = await getMni152()
const jba29 = await getJba29()
- const hoc1left = await getHoc1Left(mni152["@id"])
+ const hoc1left = await getHoc1Right(mni152["@id"])
return {
human,
mni152,
diff --git a/src/atlasComponents/sapiViews/features/connectivity/connectivityMatrix/connectivityMatrix.component.ts b/src/atlasComponents/sapiViews/features/connectivity/connectivityMatrix/connectivityMatrix.component.ts
index 69cd8b70d89a6d9fc65be10e8448da65ff25ce88..44fa05d6623595e6100e4e86149f52c6fe5b4bf1 100644
--- a/src/atlasComponents/sapiViews/features/connectivity/connectivityMatrix/connectivityMatrix.component.ts
+++ b/src/atlasComponents/sapiViews/features/connectivity/connectivityMatrix/connectivityMatrix.component.ts
@@ -31,7 +31,7 @@ export class ConnectivityMatrixView implements OnChanges, AfterViewInit{
private async fetchMatrixData(){
this.matrixData = null
- const matrix = await this.sapi.getParcellation(this.atlas["@id"], this.parcellation["@id"]).getFeatureInstance(this.featureId)
+ const matrix = await this.sapi.getParcellation(this.atlas["@id"], this.parcellation["@id"]).getFeatureInstance(this.featureId).toPromise()
if ((matrix as SapiSerializationErrorModel)?.type === "spy/serialization-error") {
return
}
diff --git a/src/atlasComponents/sapiViews/features/entry/entry.component.ts b/src/atlasComponents/sapiViews/features/entry/entry.component.ts
index 79ee7640af146039fb2fc14d566c12daf7bef396..53b27fb3087946cb260a1a2087a93e1cacb776bb 100644
--- a/src/atlasComponents/sapiViews/features/entry/entry.component.ts
+++ b/src/atlasComponents/sapiViews/features/entry/entry.component.ts
@@ -1,5 +1,9 @@
-import { Component, Input } from "@angular/core";
-import { SapiFeatureModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { Component, Input, OnDestroy } from "@angular/core";
+import { Store } from "@ngrx/store";
+import { AnnotationLayer, TNgAnnotationPoint } from "src/atlasComponents/annotations";
+import { SapiFeatureModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel, CLEANED_IEEG_DATASET_TYPE } from "src/atlasComponents/sapi";
+import { IeegOnFocusEvent, ContactPoint, Electrode, Session, IeegOnDefocusEvent } from "../ieeg";
+import { atlasSelection, annotation, atlasAppearance } from "src/state"
@Component({
selector: 'sxplr-sapiviews-features-entry',
@@ -9,7 +13,7 @@ import { SapiFeatureModel, SapiParcellationModel, SapiRegionModel, SapiSpaceMode
]
})
-export class FeatureEntryCmp{
+export class FeatureEntryCmp implements OnDestroy{
/**
* in future, hopefully feature detail can be queried with just id,
@@ -31,6 +35,145 @@ export class FeatureEntryCmp{
feature: SapiFeatureModel
featureType = {
- receptor: "siibra/features/receptor"
+ receptor: "siibra/features/receptor",
+ ieeg: CLEANED_IEEG_DATASET_TYPE
+ }
+
+ static readonly IEEG_ANNOTATION_LAYER_RED = `ieeg-annotation-layer-red`
+ static readonly IEEG_ANNOTATION_LAYER_WHITE = `ieeg-annotation-layer-white`
+ private ieegRedAnnLayer: AnnotationLayer
+ private ieegWhiteAnnLayer: AnnotationLayer
+
+ ieegOnFocus(ev: IeegOnFocusEvent){
+ if (ev.contactPoint) {
+ /**
+ * navigate to the point
+ */
+ this.store.dispatch(
+ atlasSelection.actions.navigateTo({
+ navigation: {
+ position: ev.contactPoint.point.coordinates.map(v => v.value * 1e6)
+ },
+ animation: true
+ })
+ )
+ return
+ }
+ if (ev.session) {
+ /**
+ *
+ */
+ if (!this.ieegRedAnnLayer) {
+ this.ieegRedAnnLayer = new AnnotationLayer(FeatureEntryCmp.IEEG_ANNOTATION_LAYER_RED, "#ff0000")
+ }
+ if (!this.ieegWhiteAnnLayer) {
+ this.ieegWhiteAnnLayer = new AnnotationLayer(FeatureEntryCmp.IEEG_ANNOTATION_LAYER_WHITE, "#ffffff")
+ }
+ const allInRoiPoints: TNgAnnotationPoint[] = this.getPointsFromSession(ev.session, true)
+ const allNonInRoiPoints: TNgAnnotationPoint[] = this.getPointsFromSession(ev.session, false)
+ for (const pt of allInRoiPoints) {
+ this.ieegRedAnnLayer.addAnnotation(pt)
+ }
+ for (const pt of allNonInRoiPoints) {
+ this.ieegWhiteAnnLayer.addAnnotation(pt)
+ }
+ this.store.dispatch(
+ annotation.actions.addAnnotations({
+ annotations: [...allInRoiPoints, ...allNonInRoiPoints].map(p => {
+ return { "@id": p.id }
+ })
+ })
+ )
+ this.store.dispatch(
+ atlasAppearance.actions.setOctantRemoval({
+ flag: false
+ })
+ )
+ }
+ }
+ ieegOnDefocus(ev: IeegOnDefocusEvent){
+ if (ev.session) {
+ const allInRoiPoints: TNgAnnotationPoint[] = this.getPointsFromSession(ev.session, true)
+ const allNonInRoiPoints: TNgAnnotationPoint[] = this.getPointsFromSession(ev.session, false)
+
+ this.store.dispatch(
+ annotation.actions.rmAnnotations({
+ annotations: [...allInRoiPoints, ...allNonInRoiPoints].map(p => {
+ return { "@id": p.id }
+ })
+ })
+ )
+
+ this.store.dispatch(
+ atlasAppearance.actions.setOctantRemoval({
+ flag: true
+ })
+ )
+
+ if (this.ieegRedAnnLayer) {
+ for (const pt of allInRoiPoints) {
+ this.ieegRedAnnLayer.removeAnnotation(pt)
+ }
+ }
+
+ if (this.ieegWhiteAnnLayer) {
+ for (const pt of allNonInRoiPoints) {
+ this.ieegWhiteAnnLayer.removeAnnotation(pt)
+ }
+ }
+
+
+ }
+ }
+ ngOnDestroy(): void {
+ if (this.ieegRedAnnLayer) this.ieegRedAnnLayer.dispose()
+ if (this.ieegWhiteAnnLayer) this.ieegWhiteAnnLayer.dispose()
+ }
+
+ constructor(
+ private store: Store
+ ){
+
+ }
+
+ private getPointsFromSession(session: Session<string>, inRoi: boolean):TNgAnnotationPoint[]{
+ const allPoints: TNgAnnotationPoint[] = []
+ for (const electrodeKey in session.electrodes) {
+ const electrode = session.electrodes[electrodeKey]
+ const points = this.getPointsFromElectrode(electrode, inRoi)
+ allPoints.push(...points)
+ }
+ return allPoints.map(pt => {
+ return {
+ ...pt,
+ id: `${session.sub_id}:${pt.id}`
+ }
+ })
+ }
+
+ private getPointsFromElectrode(electrode: Electrode<string>, inRoi: boolean): TNgAnnotationPoint[] {
+ const allPoints: TNgAnnotationPoint[] = []
+ for (const ctptKey in electrode.contact_points) {
+ const ctpt = electrode.contact_points[ctptKey]
+ if (!inRoi !== !ctpt.inRoi) {
+ continue
+ }
+ const point = this.getPointFromCtPt(ctpt)
+ allPoints.push(point)
+ }
+ return allPoints.map(pt => {
+ return {
+ ...pt,
+ id: `${electrode.electrode_id}:${pt.id}`
+ }
+ })
+ }
+
+ private getPointFromCtPt(ctpt: ContactPoint<string>): TNgAnnotationPoint {
+ return {
+ id: ctpt.id,
+ point: ctpt.point.coordinates.map(coord => coord.value * 1e6 ) as [number, number, number],
+ type: 'point'
+ }
}
}
diff --git a/src/atlasComponents/sapiViews/features/entry/entry.template.html b/src/atlasComponents/sapiViews/features/entry/entry.template.html
index 0affeaa6282725139eb7fd7af2258061ff7d1b44..38a00def6eba0d9546e5c729431e4d53a05292bb 100644
--- a/src/atlasComponents/sapiViews/features/entry/entry.template.html
+++ b/src/atlasComponents/sapiViews/features/entry/entry.template.html
@@ -1,9 +1,22 @@
-<div [ngSwitch]="feature?.type">
- <sxplr-sapiviews-features-receptor-entry *ngSwitchCase="featureType.receptor"
+<div [ngSwitch]="feature?.['@type']">
+ <sxplr-sapiviews-features-receptor-entry
+ *ngSwitchCase="featureType.receptor"
[sxplr-sapiviews-features-receptor-atlas]="atlas"
[sxplr-sapiviews-features-receptor-parcellation]="parcellation"
[sxplr-sapiviews-features-receptor-template]="space"
[sxplr-sapiviews-features-receptor-region]="region"
[sxplr-sapiviews-features-receptor-featureid]="feature['@id']">
</sxplr-sapiviews-features-receptor-entry>
+ <sxplr-sapiviews-features-ieeg-ieegdataset
+ *ngSwitchCase="featureType.ieeg"
+ [sxplr-sapiviews-features-ieeg-ieegdataset-atlas]="atlas"
+ [sxplr-sapiviews-features-ieeg-ieegdataset-space]="space"
+ [sxplr-sapiviews-features-ieeg-ieegdataset-parcellation]="parcellation"
+ [sxplr-sapiviews-features-ieeg-ieegdataset-region]="region"
+ [sxplr-sapiviews-features-ieeg-ieegdataset-feature]="feature"
+ (sxplr-sapiviews-features-ieeg-ieegdataset-on-focus)="ieegOnFocus($event)"
+ (sxplr-sapiviews-features-ieeg-ieegdataset-on-defocus)="ieegOnDefocus($event)"
+ >
+
+ </sxplr-sapiviews-features-ieeg-ieegdataset>
</div>
diff --git a/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts b/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts
index d7fcb675825a2a3692e9acb8800f6181ff359627..6fb2e383091f37a59d814180e1fa208575b2af74 100644
--- a/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts
+++ b/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts
@@ -1,6 +1,6 @@
import { Component, Input } from "@angular/core";
import { SapiFeatureModel, SapiRegionalFeatureModel, SapiSpatialFeatureModel, SapiParcellationFeatureModel } from "src/atlasComponents/sapi";
-import { SapiDatasetModel, SapiParcellationFeatureMatrixModel, SapiRegionalFeatureReceptorModel, SapiSerializationErrorModel, SapiVOIDataResponse } from "src/atlasComponents/sapi/type";
+import { CleanedIeegDataset, CLEANED_IEEG_DATASET_TYPE, SapiDatasetModel, SapiParcellationFeatureMatrixModel, SapiRegionalFeatureReceptorModel, SapiSerializationErrorModel, SapiVOIDataResponse, SxplrCleanedFeatureModel } from "src/atlasComponents/sapi/type";
@Component({
selector: `sxplr-sapiviews-features-entry-list-item`,
@@ -12,23 +12,27 @@ import { SapiDatasetModel, SapiParcellationFeatureMatrixModel, SapiRegionalFeatu
export class SapiViewsFeaturesEntryListItem{
@Input('sxplr-sapiviews-features-entry-list-item-feature')
- feature: SapiFeatureModel
+ feature: SapiFeatureModel | SxplrCleanedFeatureModel
@Input('sxplr-sapiviews-features-entry-list-item-ripple')
ripple = true
get label(): string{
if (!this.feature) return null
- const { type } = this.feature
+ const { '@type': type } = this.feature
if (
type === "siibra/core/dataset" ||
type === "siibra/features/receptor" ||
- type === "siibra/features/voi"
+ type === "siibra/features/voi" ||
+ type === CLEANED_IEEG_DATASET_TYPE
) {
- return (this.feature as (SapiDatasetModel | SapiRegionalFeatureReceptorModel | SapiVOIDataResponse) ).metadata.fullName
+ return (this.feature as (SapiDatasetModel | SapiRegionalFeatureReceptorModel | SapiVOIDataResponse | CleanedIeegDataset) ).metadata.fullName
}
- if (type === "siibra/features/connectivity") {
+ if (
+ type === "siibra/features/connectivity" ||
+ type === "siibra/features/connectivity/streamlineCounts"
+ ) {
return (this.feature as SapiParcellationFeatureMatrixModel).name
}
if (type === "spy/serialization-error") {
diff --git a/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.template.html b/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.template.html
index 5bbc24ee23c600789b6c3000e4bcbe8d73a407e3..76f584328b3e46b5a240defb44e98e7cc2abe4a2 100644
--- a/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.template.html
+++ b/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.template.html
@@ -1,8 +1,10 @@
<div matRipple [matRippleDisabled]="!ripple"
class="sxplr-p-2">
- <mat-chip-list [ngSwitch]="feature.type" class="sxplr-scale-80 transform-origin-left-center">
- <mat-chip *ngSwitchCase="'siibra/features/receptor'"
+ <mat-chip-list
+ *ngIf="feature | featureBadgeFlag"
+ class="sxplr-scale-80 transform-origin-left-center">
+ <mat-chip
[color]="feature | featureBadgeColour"
selected>
{{ feature | featureBadgeName }}
diff --git a/src/atlasComponents/sapiViews/features/entryListItem/entryListitem.stories.ts b/src/atlasComponents/sapiViews/features/entryListItem/entryListitem.stories.ts
index 434fe9e1ec4fee2181e27077222441200d56dc3a..a93cd9816a00d9f29567b8a55ecfe481030e8c31 100644
--- a/src/atlasComponents/sapiViews/features/entryListItem/entryListitem.stories.ts
+++ b/src/atlasComponents/sapiViews/features/entryListItem/entryListitem.stories.ts
@@ -1,7 +1,7 @@
import { CommonModule } from "@angular/common"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
import { SapiFeatureModel } from "src/atlasComponents/sapi"
-import { getHoc1Features, getJba29Features, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
+import { getHoc1RightFeatures, getHoc1RightSpatialFeatures, getJba29Features, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
import { AngularMaterialModule } from "src/sharedModules"
import { SapiViewsFeaturesEntryListItem } from "./entryListItem.component"
import { Component, EventEmitter, Input, Output } from "@angular/core"
@@ -66,7 +66,10 @@ RegionalFeatures.args = {
}
RegionalFeatures.loaders = [
async () => {
- const features = await getHoc1Features()
+ const features = [
+ ...(await getHoc1RightSpatialFeatures()),
+ ...(await getHoc1RightFeatures())
+ ]
return {
features
}
diff --git a/src/atlasComponents/sapiViews/features/featureBadgeColor.pipe.ts b/src/atlasComponents/sapiViews/features/featureBadgeColor.pipe.ts
index 4e7704c1afe9cf250cf0e8417a05ef0ecb2b8486..474d6a2adfe72257c35a406abde767ab7054f143 100644
--- a/src/atlasComponents/sapiViews/features/featureBadgeColor.pipe.ts
+++ b/src/atlasComponents/sapiViews/features/featureBadgeColor.pipe.ts
@@ -1,5 +1,5 @@
import { Pipe, PipeTransform } from "@angular/core";
-import { SapiFeatureModel } from "src/atlasComponents/sapi";
+import { SapiFeatureModel, SxplrCleanedFeatureModel, CLEANED_IEEG_DATASET_TYPE } from "src/atlasComponents/sapi";
@Pipe({
name: 'featureBadgeColour',
@@ -7,10 +7,13 @@ import { SapiFeatureModel } from "src/atlasComponents/sapi";
})
export class FeatureBadgeColourPipe implements PipeTransform{
- public transform(regionalFeature: SapiFeatureModel) {
- if (regionalFeature.type === "siibra/features/receptor") {
+ public transform(regionalFeature: SapiFeatureModel|SxplrCleanedFeatureModel) {
+ if (regionalFeature['@type'] === "siibra/features/receptor") {
return "accent"
}
+ if (regionalFeature['@type'] === CLEANED_IEEG_DATASET_TYPE) {
+ return "primary"
+ }
return "default"
}
}
diff --git a/src/atlasComponents/sapiViews/features/featureBadgeFlag.pipe.ts b/src/atlasComponents/sapiViews/features/featureBadgeFlag.pipe.ts
new file mode 100644
index 0000000000000000000000000000000000000000..986edffac941e522ee27d76dd3ab626aa40b993d
--- /dev/null
+++ b/src/atlasComponents/sapiViews/features/featureBadgeFlag.pipe.ts
@@ -0,0 +1,14 @@
+import { Pipe, PipeTransform } from "@angular/core";
+import { SapiFeatureModel, SxplrCleanedFeatureModel, CLEANED_IEEG_DATASET_TYPE } from "src/atlasComponents/sapi";
+
+@Pipe({
+ name: 'featureBadgeFlag',
+ pure: true
+})
+
+export class FeatureBadgeFlagPipe implements PipeTransform{
+ public transform(regionalFeature: SapiFeatureModel|SxplrCleanedFeatureModel) {
+ return regionalFeature['@type'] === "siibra/features/receptor"
+ || regionalFeature['@type'] === CLEANED_IEEG_DATASET_TYPE
+ }
+}
diff --git a/src/atlasComponents/sapiViews/features/featureBadgeName.pipe.ts b/src/atlasComponents/sapiViews/features/featureBadgeName.pipe.ts
index 8072a85081587b7847123fafdbedcb355b0efcca..33570440c6aa4c0f601d7171cac61cce7c42e712 100644
--- a/src/atlasComponents/sapiViews/features/featureBadgeName.pipe.ts
+++ b/src/atlasComponents/sapiViews/features/featureBadgeName.pipe.ts
@@ -1,5 +1,5 @@
import { Pipe, PipeTransform } from "@angular/core";
-import { SapiFeatureModel } from "src/atlasComponents/sapi";
+import { SapiFeatureModel, SxplrCleanedFeatureModel, CLEANED_IEEG_DATASET_TYPE } from "src/atlasComponents/sapi";
@Pipe({
name: 'featureBadgeName',
@@ -7,10 +7,13 @@ import { SapiFeatureModel } from "src/atlasComponents/sapi";
})
export class FeatureBadgeNamePipe implements PipeTransform{
- public transform(regionalFeature: SapiFeatureModel) {
- if (regionalFeature.type === "siibra/features/receptor") {
+ public transform(regionalFeature: SapiFeatureModel|SxplrCleanedFeatureModel) {
+ if (regionalFeature['@type'] === "siibra/features/receptor") {
return "receptor density"
}
+ if (regionalFeature["@type"] === CLEANED_IEEG_DATASET_TYPE) {
+ return "IEEG dataset"
+ }
return null
}
}
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.component.ts b/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.component.ts
new file mode 100644
index 0000000000000000000000000000000000000000..de23194ff366b475d57954b3050aa2cf94cfb256
--- /dev/null
+++ b/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.component.ts
@@ -0,0 +1,113 @@
+import { Component, EventEmitter, Input, OnChanges, OnDestroy, Output, SimpleChanges } from "@angular/core";
+import { BehaviorSubject, forkJoin } from "rxjs";
+import { SAPI } from "src/atlasComponents/sapi/sapi.service";
+import { CleanedIeegDataset, cleanIeegSessionDatasets, SapiAtlasModel, SapiIeegSessionModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi/type";
+
+export type Session<SId extends string> = CleanedIeegDataset['sessions'][SId]
+export type Electrode<EId extends string> = Session<string>['electrodes'][EId]
+export type ContactPoint<CId extends string> = Electrode<string>['contact_points'][CId]
+
+export type IeegOnFocusEvent = {
+ contactPoint: ContactPoint<string>
+ electrode: Electrode<string>
+ session: Session<string>
+}
+
+export type IeegOnDefocusEvent = {
+ contactPoint: ContactPoint<string>
+ electrode: Electrode<string>
+ session: Session<string>
+}
+
+@Component({
+ selector: `sxplr-sapiviews-features-ieeg-ieegdataset`,
+ templateUrl: `./ieegDataset.template.html`,
+ styleUrls: [
+ `./ieegDataset.style.css`
+ ]
+})
+
+export class IEEGDatasetCmp implements OnChanges{
+
+ @Input('sxplr-sapiviews-features-ieeg-ieegdataset-atlas')
+ public atlas: SapiAtlasModel
+
+ @Input('sxplr-sapiviews-features-ieeg-ieegdataset-space')
+ public space: SapiSpaceModel
+
+ @Input('sxplr-sapiviews-features-ieeg-ieegdataset-parcellation')
+ public parcellation: SapiParcellationModel
+
+ @Input('sxplr-sapiviews-features-ieeg-ieegdataset-region')
+ public region: SapiRegionModel
+
+ /**
+ * we must assume that the passed feature does not have the detail flag on
+ * We need to fetch the
+ */
+ @Input('sxplr-sapiviews-features-ieeg-ieegdataset-feature')
+ public feature: CleanedIeegDataset
+ public detailedFeature: CleanedIeegDataset
+
+ @Output('sxplr-sapiviews-features-ieeg-ieegdataset-on-focus')
+ public onFocus = new EventEmitter<IeegOnFocusEvent>()
+
+ @Output('sxplr-sapiviews-features-ieeg-ieegdataset-on-defocus')
+ public onDefocus = new EventEmitter<IeegOnDefocusEvent>()
+
+ public busy$ = new BehaviorSubject<boolean>(false)
+
+ ngOnChanges(changes: SimpleChanges): void {
+ if (!this.feature) {
+ return
+ }
+ if (this.feature && this.feature["@type"] !== "sxplr/cleanedIeegDataset") {
+ throw new Error(`expected @type to be sxplr-cleaned-ieeg-dataset, but is ${this.feature['@type']}.`)
+ }
+ this.busy$.next(true)
+
+ forkJoin(
+ Object.entries(this.feature.sessions).map(([ key, session ]) => {
+ return this.sapi.getSpace(this.atlas["@id"], this.space["@id"]).getFeatureInstance(session["@id"], { parcellationId: this.parcellation["@id"], region: this.region.name })
+ })
+ ).subscribe(feats => {
+
+ const ieegSessions: SapiIeegSessionModel[] = feats.filter(feat => feat["@type"] === "siibra/features/ieegSession")
+ const features = cleanIeegSessionDatasets(ieegSessions)
+ const foundFeat = features.find(f => f["@id"] === this.feature["@id"])
+ if (foundFeat) {
+ this.detailedFeature = foundFeat
+ }
+ this.busy$.next(false)
+ })
+ }
+
+ public onContactPointClicked(cpt: ContactPoint<string>, ele: Electrode<string>, sess: Session<string>){
+ this.onFocus.emit({
+ contactPoint: cpt,
+ electrode: ele,
+ session: sess
+ })
+ }
+
+ public onPanelOpen(session: Session<string>){
+ this.onFocus.emit({
+ contactPoint: null,
+ electrode: null,
+ session: session
+ })
+ }
+
+ public onPanelClose(session: Session<string>){
+ this.onDefocus.emit({
+ contactPoint: null,
+ electrode: null,
+ session: session
+ })
+ }
+
+ constructor(private sapi: SAPI){
+
+ }
+
+}
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.stories.ts b/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.stories.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c9f08880e4525ab8c2d9f550abee83bf60c876fc
--- /dev/null
+++ b/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.stories.ts
@@ -0,0 +1,113 @@
+import { Meta, moduleMetadata, Story } from "@storybook/angular"
+import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi"
+import { getHoc1Right, getHumanAtlas, getJba29, getMni152, provideDarkTheme, getMni152SpatialFeatureHoc1Right } from "src/atlasComponents/sapi/stories.base"
+import { SxplrSapiViewsFeaturesIeegModule } from ".."
+import { Component } from "@angular/core"
+import { cleanIeegSessionDatasets, SapiSpatialFeatureModel } from "src/atlasComponents/sapi/type"
+import { action } from "@storybook/addon-actions"
+
+@Component({
+ selector: 'ieeg-entry-wrapper-cmp',
+ template: `
+ <sxplr-sapiviews-features-ieeg-ieegdataset
+ [sxplr-sapiviews-features-ieeg-ieegdataset-atlas]="atlas"
+ [sxplr-sapiviews-features-ieeg-ieegdataset-space]="template"
+ [sxplr-sapiviews-features-ieeg-ieegdataset-parcellation]="parcellation"
+ [sxplr-sapiviews-features-ieeg-ieegdataset-region]="region"
+ [sxplr-sapiviews-features-ieeg-ieegdataset-feature]="feature"
+ (sxplr-sapiviews-features-ieeg-ieegdataset-on-focus)="handleCtptClick($event)"
+ (sxplr-sapiviews-features-ieeg-ieegdataset-on-defocus)="handleOnDeFocus($event)"
+ >
+ </sxplr-sapiviews-features-ieeg-ieegdataset>
+ `,
+ styles: [
+ `
+ :host
+ {
+ display: block;
+ width: 20rem;
+ }
+ `
+ ]
+})
+class EntryWrappercls {
+ atlas: SapiAtlasModel
+ template: SapiSpaceModel
+ feature: SapiSpatialFeatureModel
+ parcellation: SapiParcellationModel
+ region: SapiRegionModel
+
+ handleOnFocus(cpt: unknown){}
+ handleOnDeFocus(cpt: unknown) {}
+}
+
+export default {
+ component: EntryWrappercls,
+ decorators: [
+ moduleMetadata({
+ imports: [
+ SxplrSapiViewsFeaturesIeegModule,
+ ],
+ providers: [
+ SAPI,
+ ...provideDarkTheme,
+ ],
+ declarations: [
+ EntryWrappercls
+ ]
+ })
+ ],
+} as Meta
+
+const Template: Story<EntryWrappercls> = (args: EntryWrappercls, { loaded }) => {
+ const { atlas, parc, space, region, feature } = loaded
+ return ({
+ props: {
+ ...args,
+ atlas: atlas,
+ parcellation: parc,
+ template: space,
+ region: region,
+ feature,
+ handleOnFocus: action('handleOnFocus'),
+ handleOnDeFocus: action('handleOnDeFocus')
+ },
+ })
+}
+
+const loadFeat = async () => {
+ const atlas = await getHumanAtlas()
+ const space = await getMni152()
+ const parc = await getJba29()
+ const region = await getHoc1Right()
+
+ const features = await getMni152SpatialFeatureHoc1Right()
+ const spatialFeats = features.filter(f => f["@type"] === "siibra/features/ieegSession")
+ const feature = cleanIeegSessionDatasets(spatialFeats)[0]
+ return {
+ atlas,
+ space,
+ parc,
+ region,
+ feature
+ }
+}
+
+export const Default = Template.bind({})
+Default.args = {
+
+}
+Default.loaders = [
+ async () => {
+ const {
+ atlas,
+ space,
+ feature,
+ parc,
+ region,
+ } = await loadFeat()
+ return {
+ atlas, space, feature, parc, region
+ }
+ }
+]
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.style.css b/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.style.css
new file mode 100644
index 0000000000000000000000000000000000000000..1c554eef70e8adae01cba4530c534a389ce6c93a
--- /dev/null
+++ b/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.style.css
@@ -0,0 +1,4 @@
+mat-form-field
+{
+ width: 100%;
+}
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.template.html b/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.template.html
new file mode 100644
index 0000000000000000000000000000000000000000..af7464f5e24b254d42985ef55766f755696c4909
--- /dev/null
+++ b/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.template.html
@@ -0,0 +1,112 @@
+<spinner-cmp *ngIf="busy$ | async; else resultTmpl">
+</spinner-cmp>
+
+<ng-template #resultTmpl>
+
+ <mat-accordion *ngIf="!!detailedFeature">
+ <ng-template
+ ngFor
+ [ngForOf]="detailedFeature.sessions | keyvalue"
+ let-sessionKeyVal>
+
+ <ng-template
+ [ngIf]="sessionKeyVal.value.inRoi"
+ [ngTemplateOutlet]="sessionTmpl"
+ [ngTemplateOutletContext]="{
+ $implicit: sessionKeyVal.value
+ }">
+
+ </ng-template>
+
+ </ng-template>
+ </mat-accordion>
+
+</ng-template>
+
+<!-- session template -->
+<ng-template #sessionTmpl let-session>
+ <mat-expansion-panel
+ (opened)="onPanelOpen(session)"
+ (closed)="onPanelClose(session)">
+ <mat-expansion-panel-header>
+ SessionID: {{ session.sub_id }}
+ </mat-expansion-panel-header>
+
+ <ng-template matExpansionPanelContent>
+ <ng-template
+ ngFor
+ [ngForOf]="session.electrodes | keyvalue | inRoi"
+ let-electrodeKeyVal>
+ <ng-template
+ [ngTemplateOutlet]="electrodeTmpl"
+ [ngTemplateOutletContext]="{
+ electrode: electrodeKeyVal.value,
+ session: session
+ }">
+
+ </ng-template>
+ </ng-template>
+
+ <mat-divider></mat-divider>
+ <ng-template
+ ngFor
+ [ngForOf]="session.electrodes | keyvalue | inRoi : false"
+ let-electrodeKeyVal>
+ <div class="sxplr-very-muted">
+ <ng-template
+ [ngTemplateOutlet]="electrodeTmpl"
+ [ngTemplateOutletContext]="{
+ electrode: electrodeKeyVal.value,
+ session: session
+ }">
+
+ </ng-template>
+ </div>
+ </ng-template>
+ </ng-template>
+ </mat-expansion-panel>
+</ng-template>
+
+<!-- electrode template -->
+<ng-template
+ #electrodeTmpl
+ let-electrode="electrode"
+ let-session="session">
+ <mat-form-field appearance="fill">
+ <mat-label>
+ ElectrodeID: {{ electrode.electrode_id }}
+ </mat-label>
+ <mat-chip-list>
+ <ng-template
+ ngFor
+ [ngForOf]="electrode.contact_points | keyvalue"
+ let-contactPointKeyVal>
+
+ <ng-template
+ [ngTemplateOutlet]="contactPointTmpl"
+ [ngTemplateOutletContext]="{
+ contactPointKey: contactPointKeyVal.key,
+ contactPoint: contactPointKeyVal.value,
+ electrode: electrode,
+ session: session
+ }">
+ </ng-template>
+ </ng-template>
+ </mat-chip-list>
+ </mat-form-field>
+</ng-template>
+
+<!-- contact point template -->
+<ng-template
+ #contactPointTmpl
+ let-contactPoint="contactPoint"
+ let-key="contactPointKey"
+ let-electrode="electrode"
+ let-session="session">
+ <mat-chip
+ (click)="onContactPointClicked(contactPoint, electrode, session)"
+ [color]="contactPoint.inRoi ? 'primary' : 'default'"
+ selected>
+ {{ key }}
+ </mat-chip>
+</ng-template>
\ No newline at end of file
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegSession/ieegSession.component.ts b/src/atlasComponents/sapiViews/features/ieeg/ieegSession/ieegSession.component.ts
deleted file mode 100644
index 9725ac61ea28969bf932c600e7b82521b9b0ab5f..0000000000000000000000000000000000000000
--- a/src/atlasComponents/sapiViews/features/ieeg/ieegSession/ieegSession.component.ts
+++ /dev/null
@@ -1,26 +0,0 @@
-import { Component } from "@angular/core";
-
-type Landmark = {} & {
- showInSliceView
-}
-
-@Component({
- templateUrl: `./ieegSession.template.html`,
- styleUrls: [
- `./ieegSession.style.css`
- ]
-})
-
-export class IEEGSessionCmp{
- private loadedLms: Landmark[]
-
- private unloadLandmarks(){}
- private loadlandmarks(lms: Landmark[]){}
- private handleDatumExpansion(dataset: any){
-
- }
- private handleContactPtClick(contactPt){
- // navigate there
-
- }
-}
\ No newline at end of file
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegSession/ieegSession.template.html b/src/atlasComponents/sapiViews/features/ieeg/ieegSession/ieegSession.template.html
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/src/atlasComponents/sapiViews/features/ieeg/inRoi.pipe.ts b/src/atlasComponents/sapiViews/features/ieeg/inRoi.pipe.ts
new file mode 100644
index 0000000000000000000000000000000000000000..4f215c8ccd96ff7af503abc521e3c6558383c234
--- /dev/null
+++ b/src/atlasComponents/sapiViews/features/ieeg/inRoi.pipe.ts
@@ -0,0 +1,19 @@
+import { Pipe, PipeTransform } from "@angular/core";
+
+interface InRoi {
+ key: string
+ value: {
+ inRoi: boolean
+ }
+}
+
+@Pipe({
+ name: 'inRoi',
+ pure: true
+})
+
+export class InRoiPipe implements PipeTransform{
+ public transform(list: InRoi[], inroi=true): InRoi[] {
+ return list.filter(it => it.value.inRoi === inroi)
+ }
+}
diff --git a/src/atlasComponents/sapiViews/features/ieeg/index.ts b/src/atlasComponents/sapiViews/features/ieeg/index.ts
index 663fabd8603621b891428afeb0d68e861690cfd4..757808e777ca4f96b83bba521ab6c71d3903cfaa 100644
--- a/src/atlasComponents/sapiViews/features/ieeg/index.ts
+++ b/src/atlasComponents/sapiViews/features/ieeg/index.ts
@@ -1 +1,2 @@
-export { IEEGSessionCmp } from "./ieegSession/ieegSession.component"
\ No newline at end of file
+export { IEEGDatasetCmp, IeegOnFocusEvent, IeegOnDefocusEvent, ContactPoint, Electrode, Session } from "./ieegDataset/ieegDataset.component"
+export { SxplrSapiViewsFeaturesIeegModule } from "./module"
\ No newline at end of file
diff --git a/src/atlasComponents/sapiViews/features/ieeg/module.ts b/src/atlasComponents/sapiViews/features/ieeg/module.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c91161eac8e261121aaa58e583265961b324c007
--- /dev/null
+++ b/src/atlasComponents/sapiViews/features/ieeg/module.ts
@@ -0,0 +1,33 @@
+import { CommonModule } from "@angular/common";
+import { NgModule } from "@angular/core";
+import { MatChipsModule } from "@angular/material/chips";
+import { MatDividerModule } from "@angular/material/divider";
+import { MatExpansionModule } from "@angular/material/expansion";
+import { MatFormFieldModule } from "@angular/material/form-field";
+import { BrowserAnimationsModule } from "@angular/platform-browser/animations";
+import { SAPIModule } from "src/atlasComponents/sapi/module";
+import { SpinnerModule } from "src/components/spinner";
+import { IEEGDatasetCmp } from "./ieegDataset/ieegDataset.component";
+import { InRoiPipe } from "./inRoi.pipe";
+
+@NgModule({
+ imports: [
+ CommonModule,
+ MatExpansionModule,
+ MatChipsModule,
+ MatFormFieldModule,
+ MatDividerModule,
+ BrowserAnimationsModule,
+ SpinnerModule,
+ SAPIModule,
+ ],
+ declarations: [
+ IEEGDatasetCmp,
+ InRoiPipe,
+ ],
+ exports: [
+ IEEGDatasetCmp,
+ ]
+})
+
+export class SxplrSapiViewsFeaturesIeegModule{}
\ No newline at end of file
diff --git a/src/atlasComponents/sapiViews/features/module.ts b/src/atlasComponents/sapiViews/features/module.ts
index 654d96c9ca9143516658b3505c9916a83df26858..6ee7b852c0400d3bb9b6af371f8f930c4bfb2ceb 100644
--- a/src/atlasComponents/sapiViews/features/module.ts
+++ b/src/atlasComponents/sapiViews/features/module.ts
@@ -5,12 +5,13 @@ import { appendScriptFactory, APPEND_SCRIPT_TOKEN } from "src/util/constants"
import { FeatureEntryCmp } from "./entry/entry.component"
import { SapiViewsFeaturesEntryListItem } from "./entryListItem/entryListItem.component"
import { FeatureBadgeColourPipe } from "./featureBadgeColor.pipe"
+import { FeatureBadgeFlagPipe } from "./featureBadgeFlag.pipe"
import { FeatureBadgeNamePipe } from "./featureBadgeName.pipe"
import * as ieeg from "./ieeg"
import * as receptor from "./receptors"
const {
- IEEGSessionCmp
+ SxplrSapiViewsFeaturesIeegModule
} = ieeg
const {
ReceptorViewModule
@@ -20,13 +21,14 @@ const {
imports: [
CommonModule,
ReceptorViewModule,
+ SxplrSapiViewsFeaturesIeegModule,
AngularMaterialModule,
],
declarations: [
- IEEGSessionCmp,
FeatureEntryCmp,
FeatureBadgeNamePipe,
FeatureBadgeColourPipe,
+ FeatureBadgeFlagPipe,
SapiViewsFeaturesEntryListItem,
],
providers: [
@@ -37,7 +39,6 @@ const {
}
],
exports: [
- IEEGSessionCmp,
FeatureEntryCmp,
SapiViewsFeaturesEntryListItem,
]
diff --git a/src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiograph.stories.ts b/src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiograph.stories.ts
index 5ebfdce9870f959574846ebd56383535d376fd4b..093ec6a110eaca060b0bf3e48204026ee5ed1946 100644
--- a/src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiograph.stories.ts
+++ b/src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiograph.stories.ts
@@ -5,7 +5,7 @@ import { FormsModule } from "@angular/forms"
import { BrowserAnimationsModule } from "@angular/platform-browser/animations"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi"
-import { getHoc1FeatureDetail, getHoc1Features, getHoc1Left, getHumanAtlas, getJba29, getMni152 } from "src/atlasComponents/sapi/stories.base"
+import { getHoc1RightFeatureDetail, getHoc1RightFeatures, getHoc1Right, getHumanAtlas, getJba29, getMni152 } from "src/atlasComponents/sapi/stories.base"
import { SapiRegionalFeatureReceptorModel } from "src/atlasComponents/sapi/type"
import { AngularMaterialModule } from "src/sharedModules"
import { Autoradiography } from "./autoradiography.component"
@@ -106,11 +106,11 @@ const Template: Story<AutoRadiographWrapperCls> = (args: AutoRadiographWrapperCl
const loadFeat = async () => {
const atlas = await getHumanAtlas()
const parc = await getJba29()
- const region = await getHoc1Left()
+ const region = await getHoc1Right()
const space = await getMni152()
- const features = await getHoc1Features()
- const receptorfeat = features.find(f => f.type === "siibra/features/receptor")
- const feature = await getHoc1FeatureDetail(receptorfeat["@id"])
+ const features = await getHoc1RightFeatures()
+ const receptorfeat = features.find(f => f['@type'] === "siibra/features/receptor")
+ const feature = await getHoc1RightFeatureDetail(receptorfeat["@id"])
return {
atlas,
parc,
diff --git a/src/atlasComponents/sapiViews/features/receptors/base.ts b/src/atlasComponents/sapiViews/features/receptors/base.ts
index b393969c20c50862e35eabe9b8efe49738bc57eb..cbcd75fc2460c847e907d4c312eb0eb9ea19b081 100644
--- a/src/atlasComponents/sapiViews/features/receptors/base.ts
+++ b/src/atlasComponents/sapiViews/features/receptors/base.ts
@@ -74,9 +74,9 @@ export abstract class BaseReceptor{
this.error = `featureId needs to be defined, but is not`
return
}
- const result = await this.sapi.getRegion(this.atlas["@id"], this.parcellation["@id"], this.region.name).getFeatureInstance(this.featureId, this.template["@id"])
- if (result.type !== "siibra/features/receptor") {
- throw new Error(`BaseReceptor Error. Expected .type to be "siibra/features/receptor", but was "${result.type}"`)
+ const result = await this.sapi.getRegion(this.atlas["@id"], this.parcellation["@id"], this.region.name).getFeatureInstance(this.featureId, this.template["@id"]).toPromise()
+ if (result["@type"] !== "siibra/features/receptor") {
+ throw new Error(`BaseReceptor Error. Expected .type to be "siibra/features/receptor", but was "${result['@type']}"`)
}
return result
}
diff --git a/src/atlasComponents/sapiViews/features/receptors/entry/entry.stories.ts b/src/atlasComponents/sapiViews/features/receptors/entry/entry.stories.ts
index 0c69f821626c7590721e6e91054d4e39633ea633..63f07ee1ef4f6dd57c402e07d08a4e9c5d742f01 100644
--- a/src/atlasComponents/sapiViews/features/receptors/entry/entry.stories.ts
+++ b/src/atlasComponents/sapiViews/features/receptors/entry/entry.stories.ts
@@ -1,10 +1,8 @@
import { CommonModule, DOCUMENT } from "@angular/common"
import { HttpClientModule } from "@angular/common/http"
-import { FormsModule } from "@angular/forms"
-import { BrowserAnimationsModule } from "@angular/platform-browser/animations"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi"
-import { getHoc1FeatureDetail, getHoc1Features, getHoc1Left, getHumanAtlas, getJba29, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
+import { getHoc1RightFeatureDetail, getHoc1RightFeatures, getHoc1Right, getHumanAtlas, getJba29, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
import { AngularMaterialModule } from "src/sharedModules"
import { Entry } from "./entry.component"
import { ReceptorViewModule } from ".."
@@ -89,11 +87,11 @@ const Template: Story<Entry> = (args: Entry, { loaded }) => {
const loadFeat = async () => {
const atlas = await getHumanAtlas()
const parc = await getJba29()
- const region = await getHoc1Left()
+ const region = await getHoc1Right()
const space = await getMni152()
- const features = await getHoc1Features()
- const receptorfeat = features.find(f => f.type === "siibra/features/receptor")
- const feature = await getHoc1FeatureDetail(receptorfeat["@id"])
+ const features = await getHoc1RightFeatures()
+ const receptorfeat = features.find(f => f['@type'] === "siibra/features/receptor")
+ const feature = await getHoc1RightFeatureDetail(receptorfeat["@id"])
return {
atlas,
parc,
diff --git a/src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.stories.ts b/src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.stories.ts
index 7c5da4f82f24a859db259439ce6fef8ec71e29c3..1c3327ac1470cc2a7d650aa3b5196f70958dbbe2 100644
--- a/src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.stories.ts
+++ b/src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.stories.ts
@@ -3,7 +3,7 @@ import { HttpClientModule } from "@angular/common/http"
import { Component, EventEmitter, Output } from "@angular/core"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi"
-import { getHoc1FeatureDetail, getHoc1Features, getHoc1Left, getHumanAtlas, getJba29, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
+import { getHoc1RightFeatureDetail, getHoc1RightFeatures, getHoc1Right, getHumanAtlas, getJba29, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
import { SapiRegionalFeatureReceptorModel } from "src/atlasComponents/sapi/type"
import { AngularMaterialModule } from "src/sharedModules"
import { appendScriptFactory, APPEND_SCRIPT_TOKEN } from "src/util/constants"
@@ -88,11 +88,11 @@ const Template: Story<FingerprintWrapperCls> = (args: FingerprintWrapperCls, { l
const loadFeat = async () => {
const atlas = await getHumanAtlas()
const parc = await getJba29()
- const region = await getHoc1Left()
+ const region = await getHoc1Right()
const space = await getMni152()
- const features = await getHoc1Features()
- const receptorfeat = features.find(f => f.type === "siibra/features/receptor")
- const feature = await getHoc1FeatureDetail(receptorfeat["@id"])
+ const features = await getHoc1RightFeatures()
+ const receptorfeat = features.find(f => f['@type'] === "siibra/features/receptor")
+ const feature = await getHoc1RightFeatureDetail(receptorfeat["@id"])
return {
atlas,
parc,
diff --git a/src/atlasComponents/sapiViews/features/receptors/profile/profile.stories.ts b/src/atlasComponents/sapiViews/features/receptors/profile/profile.stories.ts
index f4dc8b4bdaadb96aff3ca76ad0f69450c7a0aeef..83d309f52d008d14183329f0539cf179c0354867 100644
--- a/src/atlasComponents/sapiViews/features/receptors/profile/profile.stories.ts
+++ b/src/atlasComponents/sapiViews/features/receptors/profile/profile.stories.ts
@@ -6,7 +6,7 @@ import { BrowserAnimationsModule } from "@angular/platform-browser/animations"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
import { BehaviorSubject, Subject } from "rxjs"
import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi"
-import { addAddonEventListener, getHoc1FeatureDetail, getHoc1Features, getHoc1Left, getHumanAtlas, getJba29, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
+import { addAddonEventListener, getHoc1RightFeatureDetail, getHoc1RightFeatures, getHoc1Right, getHumanAtlas, getJba29, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
import { SapiRegionalFeatureReceptorModel } from "src/atlasComponents/sapi/type"
import { AngularMaterialModule } from "src/sharedModules"
import { appendScriptFactory, APPEND_SCRIPT_TOKEN } from "src/util/constants"
@@ -115,11 +115,11 @@ const Template: Story<ProfileWrapperCls> = (args: ProfileWrapperCls, { loaded })
const loadFeat = async () => {
const atlas = await getHumanAtlas()
const parc = await getJba29()
- const region = await getHoc1Left()
+ const region = await getHoc1Right()
const space = await getMni152()
- const features = await getHoc1Features()
- const receptorfeat = features.find(f => f.type === "siibra/features/receptor")
- const feature = await getHoc1FeatureDetail(receptorfeat["@id"])
+ const features = await getHoc1RightFeatures()
+ const receptorfeat = features.find(f => f['@type'] === "siibra/features/receptor")
+ const feature = await getHoc1RightFeatureDetail(receptorfeat["@id"])
return {
atlas,
parc,
diff --git a/src/atlasComponents/sapiViews/richDataset.stories.ts b/src/atlasComponents/sapiViews/richDataset.stories.ts
index c49035dbe93ff1d54764413660bea9afd4bbef9e..4904bf1d163283ab146de866abd5274bd2a19c29 100644
--- a/src/atlasComponents/sapiViews/richDataset.stories.ts
+++ b/src/atlasComponents/sapiViews/richDataset.stories.ts
@@ -3,9 +3,9 @@ import { HttpClientModule } from "@angular/common/http"
import { Component } from "@angular/core"
import { Meta, moduleMetadata, Story } from "@storybook/angular"
import { SAPI } from "src/atlasComponents/sapi"
-import { getHoc1FeatureDetail, getHoc1Features, getHoc1Left, getHumanAtlas, getJba29, getMni152, provideDarkTheme } from "src/atlasComponents/sapi/stories.base"
+import { getHoc1RightFeatureDetail, getHoc1RightFeatures, getHoc1Right, getHumanAtlas, getJba29, getMni152, provideDarkTheme, getMni152SpatialFeatureHoc1Right } from "src/atlasComponents/sapi/stories.base"
import { AngularMaterialModule } from "src/sharedModules"
-import { SapiAtlasModel, SapiFeatureModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "../sapi/type"
+import { cleanIeegSessionDatasets, SapiAtlasModel, SapiFeatureModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "../sapi/type"
import { SapiViewsCoreDatasetModule } from "./core/datasets"
import { SapiViewsFeaturesModule } from "./features"
@@ -88,7 +88,7 @@ const loadRegionMetadata = async () => {
const atlas = await getHumanAtlas()
const parcellation = await getJba29()
const template = await getMni152()
- const region = await getHoc1Left()
+ const region = await getHoc1Right()
return {
atlas,
parcellation,
@@ -98,7 +98,7 @@ const loadRegionMetadata = async () => {
}
const loadFeat = async () => {
- const features = await getHoc1Features()
+ const features = await getHoc1RightFeatures()
return { features }
}
@@ -112,10 +112,25 @@ ReceptorDataset.loaders = [
},
async () => {
const { features } = await loadFeat()
- const receptorfeat = features.find(f => f.type === "siibra/features/receptor")
- const feature = await getHoc1FeatureDetail(receptorfeat["@id"])
- return {
- feature
- }
+ const receptorfeat = features.find(f => f['@type'] === "siibra/features/receptor")
+ const feature = await getHoc1RightFeatureDetail(receptorfeat["@id"])
+ return { feature }
+ }
+]
+
+export const IeegDataset = Template.bind({})
+IeegDataset.args = {
+
+}
+IeegDataset.loaders = [
+ async () => {
+ return await loadRegionMetadata()
+ },
+ async () => {
+ const features = await getMni152SpatialFeatureHoc1Right()
+ const spatialFeats = features.filter(f => f["@type"] === "siibra/features/ieegSession")
+ const feature = cleanIeegSessionDatasets(spatialFeats)[0]
+
+ return { feature }
}
]
diff --git a/src/atlasComponents/splashScreen/index.ts b/src/atlasComponents/splashScreen/index.ts
deleted file mode 100644
index 0750a03038aaecc1a9de8097d87ecd240121e418..0000000000000000000000000000000000000000
--- a/src/atlasComponents/splashScreen/index.ts
+++ /dev/null
@@ -1,2 +0,0 @@
-export { SplashScreen } from "./splashScreen/splashScreen.component";
-export { SplashUiModule } from './module'
\ No newline at end of file
diff --git a/src/atlasComponents/splashScreen/module.ts b/src/atlasComponents/splashScreen/module.ts
deleted file mode 100644
index 587e1217dad6d50acbe9f78b7f9074b3c0e844c8..0000000000000000000000000000000000000000
--- a/src/atlasComponents/splashScreen/module.ts
+++ /dev/null
@@ -1,25 +0,0 @@
-import { CommonModule } from "@angular/common";
-import { NgModule } from "@angular/core";
-import { ComponentsModule } from "src/components";
-import { KgTosModule } from "src/ui/kgtos/module";
-import { AngularMaterialModule } from "src/sharedModules";
-import { UtilModule } from "src/util";
-import { SplashScreen } from "./splashScreen/splashScreen.component";
-
-@NgModule({
- imports: [
- AngularMaterialModule,
- CommonModule,
- UtilModule,
- KgTosModule,
- ComponentsModule,
- ],
- declarations: [
- SplashScreen,
- ],
- exports: [
- SplashScreen,
- ]
-})
-
-export class SplashUiModule{}
\ No newline at end of file
diff --git a/src/atlasComponents/userAnnotations/tools/service.ts b/src/atlasComponents/userAnnotations/tools/service.ts
index 546cd1238464c9830f8778d91bc38d1810c9c62c..1381520da9c9a7fae35e5203c9e40a5790c7aa07 100644
--- a/src/atlasComponents/userAnnotations/tools/service.ts
+++ b/src/atlasComponents/userAnnotations/tools/service.ts
@@ -16,6 +16,8 @@ import { retry } from 'common/util'
import { MatSnackBar } from "@angular/material/snack-bar";
import { actions } from "src/state/atlasSelection";
import { atlasSelection } from "src/state";
+import { SapiSpaceModel } from "src/atlasComponents/sapi";
+import { AnnotationLayer } from "src/atlasComponents/annotations";
const LOCAL_STORAGE_KEY = 'userAnnotationKey'
@@ -85,11 +87,11 @@ export class ModularUserAnnotationToolService implements OnDestroy{
private previewNgAnnIds: string[] = []
- private ngAnnotationLayer: any
+ private annotationLayer: AnnotationLayer
private activeToolName: string
private forcedAnnotationRefresh$ = new BehaviorSubject(null)
- private selectedTmpl: any
+ private selectedTmpl: SapiSpaceModel
private selectedTmpl$ = this.store.pipe(
select(atlasSelection.selectors.selectedTemplate),
)
@@ -321,7 +323,7 @@ export class ModularUserAnnotationToolService implements OnDestroy{
*/
this.subscription.push(
nehubaViewer$.subscribe(() => {
- this.ngAnnotationLayer = null
+ this.annotationLayer = null
})
)
@@ -411,23 +413,12 @@ export class ModularUserAnnotationToolService implements OnDestroy{
this.clearAllPreviewAnnotations()
}
for (let idx = 0; idx < previewNgAnnotation.length; idx ++) {
- const localAnnotations = this.ngAnnotationLayer.layer.localAnnotations
- const annSpec = {
- ...parseNgAnnotation(previewNgAnnotation[idx]),
+ const spec = {
+ ...previewNgAnnotation[idx],
id: `${ModularUserAnnotationToolService.TMP_PREVIEW_ANN_ID}_${idx}`
}
- const annRef = localAnnotations.references.get(annSpec.id)
- if (annRef) {
- localAnnotations.update(
- annRef,
- annSpec
- )
- } else {
- localAnnotations.add(
- annSpec
- )
- }
- this.previewNgAnnIds[idx] = annSpec.id
+ this.annotationLayer.updateAnnotation(spec)
+ this.previewNgAnnIds[idx] = spec.id
}
})
)
@@ -439,7 +430,7 @@ export class ModularUserAnnotationToolService implements OnDestroy{
this.forcedAnnotationRefresh$,
this.spaceFilteredManagedAnnotations$.pipe(
switchMap(switchMapWaitFor({
- condition: () => !!this.ngAnnotationLayer,
+ condition: () => !!this.annotationLayer,
leading: true
})),
)
@@ -479,20 +470,8 @@ export class ModularUserAnnotationToolService implements OnDestroy{
this.deleteNgAnnotationById(annotation.id)
continue
}
- if (!this.ngAnnotationLayer) continue
- const localAnnotations = this.ngAnnotationLayer.layer.localAnnotations
- const annRef = localAnnotations.references.get(annotation.id)
- const annSpec = parseNgAnnotation(annotation)
- if (annRef) {
- localAnnotations.update(
- annRef,
- annSpec
- )
- } else {
- localAnnotations.add(
- annSpec
- )
- }
+ if (!this.annotationLayer) continue
+ this.annotationLayer.updateAnnotation(annotation)
}
})
)
@@ -506,26 +485,18 @@ export class ModularUserAnnotationToolService implements OnDestroy{
).subscribe(viewerMode => {
this.currMode = viewerMode
if (viewerMode === ModularUserAnnotationToolService.VIEWER_MODE) {
- if (this.ngAnnotationLayer) this.ngAnnotationLayer.setVisible(true)
+ if (this.annotationLayer) this.annotationLayer.setVisible(true)
else {
const viewer = (window as any).viewer
- const voxelSize = IAV_VOXEL_SIZES_NM[this.selectedTmpl.fullId]
- if (!voxelSize) throw new Error(`voxelSize of ${this.selectedTmpl.fullId} cannot be found!`)
- const layer = viewer.layerSpecification.getLayer(
+ const voxelSize = IAV_VOXEL_SIZES_NM[this.selectedTmpl["@id"]]
+ if (!voxelSize) throw new Error(`voxelSize of ${this.selectedTmpl["@id"]} cannot be found!`)
+ if (this.annotationLayer) {
+ this.annotationLayer.dispose()
+ }
+ this.annotationLayer = new AnnotationLayer(
ModularUserAnnotationToolService.ANNOTATION_LAYER_NAME,
- {
- ...ModularUserAnnotationToolService.USER_ANNOTATION_LAYER_SPEC,
- // since voxel coordinates are no longer defined, so voxel size will always be 1/1/1
- transform: [
- [1, 0, 0, 0],
- [0, 1, 0, 0],
- [0, 0, 1, 0],
- [0, 0, 0, 1],
- ]
- }
+ ModularUserAnnotationToolService.USER_ANNOTATION_LAYER_SPEC.annotationColor
)
- this.ngAnnotationLayer = viewer.layerManager.addManagedLayer(layer)
-
/**
* on template changes, the layer gets lost
* force redraw annotations if layer needs to be recreated
@@ -533,7 +504,7 @@ export class ModularUserAnnotationToolService implements OnDestroy{
this.forcedAnnotationRefresh$.next(null)
}
} else {
- if (this.ngAnnotationLayer) this.ngAnnotationLayer.setVisible(false)
+ if (this.annotationLayer) this.annotationLayer.setVisible(false)
}
})
)
@@ -667,12 +638,7 @@ export class ModularUserAnnotationToolService implements OnDestroy{
}
private deleteNgAnnotationById(annId: string) {
- const localAnnotations = this.ngAnnotationLayer.layer.localAnnotations
- const annRef = localAnnotations.references.get(annId)
- if (annRef) {
- localAnnotations.delete(annRef)
- localAnnotations.references.delete(annId)
- }
+ this.annotationLayer.removeAnnotation({ id: annId })
}
public defaultTool: AbsToolClass<any>
@@ -750,7 +716,7 @@ export class ModularUserAnnotationToolService implements OnDestroy{
private currMode: string
switchAnnotationMode(mode: 'on' | 'off' | 'toggle' = 'toggle') {
- let payload = null
+ let payload: 'annotating' = null
if (mode === 'on') payload = ARIA_LABELS.VIEWER_MODE_ANNOTATING
if (mode === 'off') {
if (this.currMode === ARIA_LABELS.VIEWER_MODE_ANNOTATING) payload = null
@@ -763,7 +729,7 @@ export class ModularUserAnnotationToolService implements OnDestroy{
}
this.store.dispatch(
actions.setViewerMode({
- viewerMode: "annotating"
+ viewerMode: payload
})
)
}
diff --git a/src/components/flatHierarchy/treeView/treeControl.ts b/src/components/flatHierarchy/treeView/treeControl.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e664e5984ce4350f3e3f6d746a28fd2487ad0e34
--- /dev/null
+++ b/src/components/flatHierarchy/treeView/treeControl.ts
@@ -0,0 +1,100 @@
+
+type IsParent<T> = (child: T, parent: T) => boolean
+
+export class Tree<T extends object>{
+
+ private _nodes: T[] = []
+ protected set nodes(nodes: T[]) {
+ if (nodes === this._nodes) return
+ this._nodes = nodes
+ this.resetWeakMaps()
+ }
+ protected get nodes() {
+ return this._nodes
+ }
+
+ private _isParent: IsParent<T> = (c, p) => false
+ protected set isParent(fn: IsParent<T>){
+ if (fn === this._isParent) return
+ this._isParent = fn
+ this.resetWeakMaps()
+ }
+ protected get isParent(){
+ return this._isParent
+ }
+ public someAncestor(node: T, predicate: (anc: T) => boolean) {
+ const parent = this.getParent(node)
+ if (!parent) {
+ return false
+ }
+ if (predicate(parent)) {
+ return true
+ }
+ return this.someAncestor(parent, predicate)
+ }
+ public getParent(node: T): T {
+ if (!this.parentWeakMap.has(node)) {
+ for (const parentNode of this.nodes) {
+ if (this.isParent(node, parentNode)) {
+ this.parentWeakMap.set(node, parentNode)
+ break
+ }
+ }
+ }
+ return this.parentWeakMap.get(node)
+ }
+ public getChildren(node: T): T[] {
+ if (!this.childrenWeakMap.has(node)) {
+ const children = this.nodes.filter(childNode => this.isParent(childNode, node))
+ this.childrenWeakMap.set(node, children)
+ for (const c of children) {
+ this.parentWeakMap.set(c, node)
+ }
+ }
+ return this.childrenWeakMap.get(node)
+ }
+ public getLevel(node: T): number {
+ let level = -1, cursor = node
+ const maxLevel = 32
+ do {
+ if (level >= maxLevel) {
+ level = 0
+ break
+ }
+ level++
+ cursor = this.getParent(cursor)
+ } while (!!cursor)
+ return level
+ }
+ protected childrenWeakMap = new WeakMap<T, T[]>()
+ protected parentWeakMap = new WeakMap<T, T>()
+ protected nodeAncestorIsLast = new WeakMap<T, boolean[]>()
+
+ get rootNodes() {
+ const root = this.nodes.filter(node => !this.getParent(node))
+ for (const el of root) {
+ this.parentWeakMap.set(el, null)
+ this.nodeAncestorIsLast.set(el, [])
+ }
+ return root
+ }
+
+ constructor(
+ _nodes: T[] = [],
+ _isParent: IsParent<T> = (c, p) => false
+ ){
+ this._nodes = _nodes
+ this._isParent = _isParent
+ }
+
+ private resetWeakMaps() {
+
+ /**
+ * on new nodes passed, reset all maps
+ * otherwise, tree will show stale data and will not update
+ */
+ this.childrenWeakMap = new WeakMap()
+ this.parentWeakMap = new WeakMap()
+ this.nodeAncestorIsLast = new WeakMap()
+ }
+}
diff --git a/src/components/flatHierarchy/treeView/treeView.component.ts b/src/components/flatHierarchy/treeView/treeView.component.ts
index cab03376d07031cf42a1f2bc137edf8ef5c9a912..99d55b39dc6e811e495fca162b83db92e3d2bfb9 100644
--- a/src/components/flatHierarchy/treeView/treeView.component.ts
+++ b/src/components/flatHierarchy/treeView/treeView.component.ts
@@ -2,6 +2,7 @@ import { FlatTreeControl } from "@angular/cdk/tree";
import { MatTreeFlatDataSource, MatTreeFlattener } from "@angular/material/tree"
import { ChangeDetectionStrategy, Component, EventEmitter, HostBinding, Input, OnChanges, Output, SimpleChanges, TemplateRef } from "@angular/core";
import { TreeNode } from "../const"
+import { Tree } from "./treeControl"
@Component({
selector: `sxplr-flat-hierarchy-tree-view`,
@@ -13,15 +14,15 @@ import { TreeNode } from "../const"
exportAs: 'flatHierarchyTreeView'
})
-export class SxplrFlatHierarchyTreeView<T extends object> implements OnChanges{
+export class SxplrFlatHierarchyTreeView<T extends object> extends Tree<T> implements OnChanges{
@HostBinding('class')
class = 'sxplr-custom-cmp'
@Input('sxplr-flat-hierarchy-nodes')
- nodes: T[] = []
+ sxplrNodes: T[] = []
@Input('sxplr-flat-hierarchy-is-parent')
- isParent: (child: T, parent: T) => boolean
+ sxplrIsParent: (child: T, parent: T) => boolean
@Input('sxplr-flat-hierarchy-render-node-tmpl')
renderNodeTmplRef: TemplateRef<T>
@@ -42,57 +43,15 @@ export class SxplrFlatHierarchyTreeView<T extends object> implements OnChanges{
nodeClicked = new EventEmitter<T>()
ngOnChanges(changes: SimpleChanges): void {
- if (changes.nodes) {
-
- /**
- * on new nodes passed, reset all maps
- * otherwise, tree will show stale data and will not update
- */
- this.childrenWeakMap = new WeakMap()
- this.parentWeakMap = new WeakMap()
- this.nodeAncestorIsLast = new WeakMap()
-
- const root = this.nodes.filter(node => !this.getParent(node))
- for (const el of root) {
- this.parentWeakMap.set(el, null)
- this.nodeAncestorIsLast.set(el, [])
- }
- this.dataSource.data = root
+ if (changes.sxplrNodes || changes.sxplrIsParent) {
+ this.nodes = this.sxplrNodes
+ this.isParent = this.sxplrIsParent
+ this.dataSource.data = this.rootNodes
if (this.expandOnInit) {
this.treeControl.expandAll()
}
}
}
-
- private getLevel(node: T): number {
- let level = -1, cursor = node
- const maxLevel = 32
- do {
- if (level >= maxLevel) {
- level = 0
- break
- }
- level++
- cursor = this.getParent(cursor)
- } while (!!cursor)
- return level
- }
-
- private getParent(node: T): T {
- if (!this.parentWeakMap.has(node)) {
- for (const parentNode of this.nodes) {
- if (this.isParent(node, parentNode)) {
- this.parentWeakMap.set(node, parentNode)
- break
- }
- }
- }
- return this.parentWeakMap.get(node)
- }
-
- private childrenWeakMap = new WeakMap<T, T[]>()
- private parentWeakMap = new WeakMap<T, T>()
- private nodeAncestorIsLast = new WeakMap<T, boolean[]>()
private getNodeAncestorIsLast(node: T, visited = new WeakSet<T>() ): boolean[] {
if (!this.nodeAncestorIsLast.has(node)) {
@@ -115,16 +74,6 @@ export class SxplrFlatHierarchyTreeView<T extends object> implements OnChanges{
}
return this.nodeAncestorIsLast.get(node)
}
- private getChildren(node: T): T[] {
- if (!this.childrenWeakMap.has(node)) {
- const children = this.nodes.filter(childNode => this.isParent(childNode, node))
- this.childrenWeakMap.set(node, children)
- for (const c of children) {
- this.parentWeakMap.set(c, node)
- }
- }
- return this.childrenWeakMap.get(node)
- }
public treeControl = new FlatTreeControl<TreeNode<T>>(
({ level }) => level,
@@ -177,6 +126,6 @@ export class SxplrFlatHierarchyTreeView<T extends object> implements OnChanges{
}
constructor(){
-
+ super()
}
}
diff --git a/src/extra_styles.css b/src/extra_styles.css
index d7e99033c285ee0b2f3894cadd4dae90631098c3..c4cd571217731a53be10b0b21b9d9e9520757471 100644
--- a/src/extra_styles.css
+++ b/src/extra_styles.css
@@ -858,6 +858,12 @@ iav-cmp-viewer-container .mat-chip-list-wrapper
flex-wrap: nowrap;
}
+sxplr-sapiviews-features-ieeg-ieegdataset .mat-chip-list-wrapper
+{
+ overflow-y: hidden;
+ overflow-x: auto;
+}
+
iav-cmp-viewer-container poly-update-cmp .mat-chip-list-wrapper
{
flex-wrap: wrap;
diff --git a/src/routerModule/routeStateTransform.service.ts b/src/routerModule/routeStateTransform.service.ts
index 7bb2ae41a0c584bc69fae676ec90315c91a09067..3769be747cb1d2194df43637b6d043c445a59dda 100644
--- a/src/routerModule/routeStateTransform.service.ts
+++ b/src/routerModule/routeStateTransform.service.ts
@@ -104,6 +104,7 @@ export class RouteStateTransformSvc {
selectedTemplate,
selectedParcellation,
selectedRegions,
+ allParcellationRegions
}
}
@@ -180,11 +181,12 @@ export class RouteStateTransformSvc {
try {
- const { selectedAtlas, selectedParcellation, selectedRegions = [], selectedTemplate } = await this.getATPR(returnObj as TUrlPathObj<string[], TUrlAtlas<string[]>>)
+ const { selectedAtlas, selectedParcellation, selectedRegions = [], selectedTemplate, allParcellationRegions } = await this.getATPR(returnObj as TUrlPathObj<string[], TUrlAtlas<string[]>>)
returnState["[state.atlasSelection]"].selectedAtlas = selectedAtlas
returnState["[state.atlasSelection]"].selectedParcellation = selectedParcellation
returnState["[state.atlasSelection]"].selectedTemplate = selectedTemplate
- returnState["[state.atlasSelection]"].selectedRegions = selectedRegions
+ returnState["[state.atlasSelection]"].selectedRegions = selectedRegions || []
+ returnState["[state.atlasSelection]"].selectedParcellationAllRegions = allParcellationRegions || []
returnState["[state.atlasSelection]"].navigation = parsedNavObj
} catch (e) {
// if error, show error on UI?
@@ -193,7 +195,13 @@ export class RouteStateTransformSvc {
return returnState
}
- cvtStateToRoute(state: MainState) {
+ cvtStateToRoute(_state: MainState) {
+
+ /**
+ * need to create new references here
+ * or else, the memoized selector will spit out undefined
+ */
+ const state:MainState = JSON.parse(JSON.stringify(_state))
const selectedAtlas = atlasSelection.selectors.selectedAtlas(state)
const selectedParcellation = atlasSelection.selectors.selectedParcellation(state)
diff --git a/src/routerModule/router.service.ts b/src/routerModule/router.service.ts
index 3a05c6a11fab226f243d6331146fabec4dd1c27f..44f6983f90ef1eb95c3b701d2fc6f93f998b52ce 100644
--- a/src/routerModule/router.service.ts
+++ b/src/routerModule/router.service.ts
@@ -3,7 +3,7 @@ import { APP_BASE_HREF } from "@angular/common";
import { Inject } from "@angular/core";
import { NavigationEnd, Router } from '@angular/router'
import { Store } from "@ngrx/store";
-import { debounceTime, distinctUntilChanged, filter, map, mapTo, shareReplay, startWith, switchMap, switchMapTo, take, tap, withLatestFrom } from "rxjs/operators";
+import { debounceTime, distinctUntilChanged, filter, finalize, map, mapTo, shareReplay, startWith, switchMap, switchMapTo, take, tap, withLatestFrom } from "rxjs/operators";
import { encodeCustomState, decodeCustomState, verifyCustomState } from "./util";
import { BehaviorSubject, combineLatest, concat, EMPTY, merge, NEVER, Observable, of, timer } from 'rxjs'
import { scan } from 'rxjs/operators'
@@ -120,9 +120,19 @@ export class RouterService {
/**
* does work too well =(
*/
- navEnd$.pipe(
- map(navEv => navEv.urlAfterRedirects)
+ concat(
+ onload$.pipe(
+ mapTo(false)
+ ),
+ timer(160).pipe(
+ mapTo(false)
+ ),
+ ready$.pipe(
+ map(val => !!val)
+ )
).pipe(
+ switchMap(() => navEnd$),
+ map(navEv => navEv.urlAfterRedirects),
switchMap(url =>
routeToStateTransformSvc.cvtRouteToState(
router.parseUrl(
diff --git a/src/state/annotations/actions.ts b/src/state/annotations/actions.ts
index da4ad8edeb6f86d3f80a5d8d3a310d56dc353428..daaddd8ce723f92010ab287f01056314e5a6b838 100644
--- a/src/state/annotations/actions.ts
+++ b/src/state/annotations/actions.ts
@@ -2,18 +2,20 @@ import { createAction, props } from "@ngrx/store"
import { nameSpace } from "./const"
import { Annotation } from "./store"
-const clearAllAnnotations = createAction(
+export const clearAllAnnotations = createAction(
`${nameSpace} clearAllAnnotations`
)
-const rmAnnotations = createAction(
- `${nameSpace} rmAnnotation`,
+export const rmAnnotations = createAction(
+ `${nameSpace} rmAnnotations`,
props<{
annotations: Annotation[]
}>()
)
-export const actions = {
- clearAllAnnotations,
- rmAnnotations,
-}
+export const addAnnotations = createAction(
+ `${nameSpace} addAnnotations`,
+ props<{
+ annotations: Annotation[]
+ }>()
+)
diff --git a/src/state/annotations/index.ts b/src/state/annotations/index.ts
index 4071cad11b68b6473c88bb7d7374a4d1de77767d..4ad0f0680a29a2c7725e37ffa614f74122a0e152 100644
--- a/src/state/annotations/index.ts
+++ b/src/state/annotations/index.ts
@@ -1,4 +1,4 @@
-export { actions } from "./actions"
+export * as actions from "./actions"
export { Annotation, AnnotationState, reducer, defaultState } from "./store"
export { nameSpace } from "./const"
-export * as selectors from "./selectors"
\ No newline at end of file
+export * as selectors from "./selectors"
diff --git a/src/state/annotations/store.ts b/src/state/annotations/store.ts
index 2cb8146bfabd329d4a80b60bb3dff6c9a41663f8..113220b473143036be868d2479282d70bb2d33d7 100644
--- a/src/state/annotations/store.ts
+++ b/src/state/annotations/store.ts
@@ -1,4 +1,5 @@
-import { createReducer } from "@ngrx/store"
+import { createReducer, on } from "@ngrx/store"
+import * as actions from "./actions"
export type Annotation = {
"@id": string
@@ -13,7 +14,29 @@ export const defaultState: AnnotationState = {
}
const reducer = createReducer(
- defaultState
+ defaultState,
+ on(
+ actions.addAnnotations,
+ (state, { annotations }) => {
+ return {
+ ...state,
+ annotations: [
+ ...state.annotations,
+ ...annotations,
+ ]
+ }
+ }
+ ),
+ on(
+ actions.rmAnnotations,
+ (state, { annotations }) => {
+ const annIdToBeRemoved = annotations.map(ann => ann["@id"])
+ return {
+ ...state,
+ annotations: state.annotations.filter(ann => !annIdToBeRemoved.includes(ann["@id"]) )
+ }
+ }
+ )
)
export {
diff --git a/src/state/atlasSelection/actions.ts b/src/state/atlasSelection/actions.ts
index f96dd19ee44328028247e58bba9f0b14b30aac85..8787234b909287c331473dfe6d0cceb578375111 100644
--- a/src/state/atlasSelection/actions.ts
+++ b/src/state/atlasSelection/actions.ts
@@ -24,7 +24,7 @@ export const selectParcellation = createAction(
)
/**
- * setATP is called as a final step to (potentially) set:
+ * setAtlasSelectionState is called as a final step to (potentially) set:
* - selectedAtlas
* - selectedTemplate
* - selectedParcellation
@@ -36,13 +36,9 @@ export const selectParcellation = createAction(
* We may setup post hook for navigation adjustments/etc.
* Probably easier is simply subscribe to store and react to selectedTemplate selector
*/
-export const setATP = createAction(
- `${nameSpace} setATP`,
- props<{
- atlas?: SapiAtlasModel,
- template?: SapiSpaceModel,
- parcellation?: SapiParcellationModel,
- }>()
+export const setAtlasSelectionState = createAction(
+ `${nameSpace} setAtlasSelectionState`,
+ props<Partial<AtlasSelectionState>>()
)
export const setSelectedParcellationAllRegions = createAction(
diff --git a/src/state/atlasSelection/effects.ts b/src/state/atlasSelection/effects.ts
index ae69fa17c4345bd3e1f5d77873be1f37dd0cf4cb..6b988a8db2347fc1d0e3fe70cbb41b2cdba8744e 100644
--- a/src/state/atlasSelection/effects.ts
+++ b/src/state/atlasSelection/effects.ts
@@ -1,28 +1,62 @@
import { Injectable } from "@angular/core";
import { Actions, createEffect, ofType } from "@ngrx/effects";
-import { concat, forkJoin, merge, of } from "rxjs";
+import { concat, forkJoin, merge, Observable, of } from "rxjs";
import { filter, map, mapTo, switchMap, switchMapTo, take, tap, withLatestFrom } from "rxjs/operators";
-import { SAPI, SapiParcellationModel, SAPIRegion, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SAPI, SapiAtlasModel, SapiParcellationModel, SAPIRegion, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
import * as mainActions from "../actions"
import { select, Store } from "@ngrx/store";
import { selectors, actions } from '.'
import { fromRootStore } from "./util";
+import { AtlasSelectionState } from "./const"
import { ParcellationIsBaseLayer } from "src/atlasComponents/sapiViews/core/parcellation/parcellationIsBaseLayer.pipe";
import { OrderParcellationByVersionPipe } from "src/atlasComponents/sapiViews/core/parcellation/parcellationVersion.pipe";
-import { atlasAppearance, atlasSelection } from "..";
+import { atlasAppearance } from "..";
import { ParcellationSupportedInSpacePipe } from "src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe";
+type OnTmplParcHookArg = {
+ previous: {
+ atlas: SapiAtlasModel
+ template: SapiSpaceModel
+ parcellation: SapiParcellationModel
+ }
+ current: {
+ atlas: SapiAtlasModel
+ template: SapiSpaceModel
+ parcellation: SapiParcellationModel
+ }
+}
+
@Injectable()
export class Effect {
- parcSupportedInSpacePipe = new ParcellationSupportedInSpacePipe(this.sapiSvc)
+ onTemplateParcSelectionPostHook: ((arg: OnTmplParcHookArg) => Observable<Partial<AtlasSelectionState>>)[] = [
+ /**
+ * This hook gets the region associated with the selected parcellation and template,
+ * and then set selectedParcellationAllRegions to it
+ */
+ ({ current }) => {
+ const { atlas, parcellation, template } = current
+ return (
+ !!atlas && !!parcellation && !!template
+ ? this.sapiSvc.getParcRegions(atlas["@id"], parcellation["@id"], template["@id"])
+ : of([])
+ ).pipe(
+ map(regions => {
+ return {
+ selectedParcellationAllRegions: regions
+ }
+ })
+ )
+ }
+ ]
+ parcSupportedInSpacePipe = new ParcellationSupportedInSpacePipe(this.sapiSvc)
onTemplateParcSelection = createEffect(() => merge<{ template: SapiSpaceModel, parcellation: SapiParcellationModel }>(
this.action.pipe(
ofType(actions.selectTemplate),
map(({ template }) => {
return {
- template,
+ template,
parcellation: null
}
})
@@ -52,6 +86,7 @@ export class Effect {
*/
if (flag) {
return of({
+ atlas: currAtlas,
template: template || currTmpl,
parcellation: parcellation || currParc,
})
@@ -71,6 +106,7 @@ export class Effect {
take(1),
map(parcellation => {
return {
+ atlas: currAtlas,
template,
parcellation
}
@@ -89,6 +125,7 @@ export class Effect {
take(1),
map(template => {
return {
+ atlas: currAtlas,
template,
parcellation
}
@@ -97,15 +134,28 @@ export class Effect {
}
throw new Error(`neither template nor parcellation has been defined!`)
}),
- map(({ parcellation, template }) => {
- return actions.setATP({
- parcellation,
- template
- })
- })
+ switchMap(({ atlas, template, parcellation }) =>
+ forkJoin(
+ this.onTemplateParcSelectionPostHook.map(fn => fn({ previous: { atlas: currAtlas, template: currTmpl, parcellation: currParc }, current: { atlas, template, parcellation } }))
+ ).pipe(
+ map(partialStates => {
+ let returnState: Partial<AtlasSelectionState> = {
+ selectedAtlas: atlas,
+ selectedTemplate: template,
+ selectedParcellation: parcellation
+ }
+ for (const s of partialStates) {
+ returnState = {
+ ...returnState,
+ ...s,
+ }
+ }
+ return actions.setAtlasSelectionState(returnState)
+ })
+ )
+ )
)
- }),
-
+ })
))
onAtlasSelectionSelectTmplParc = createEffect(() => this.action.pipe(
@@ -131,35 +181,30 @@ export class Effect {
this.sapiSvc.getSpaceDetail(atlas["@id"], spaceId["@id"])
)
).pipe(
- map(spaces => {
+ switchMap(spaces => {
const selectedSpace = spaces.find(s => /152/.test(s.fullName)) || spaces[0]
- return actions.setATP({
- atlas,
- template: selectedSpace,
- parcellation
- })
- })
- )
- }),
- ))
+ return forkJoin(
+ this.onTemplateParcSelectionPostHook.map(fn => fn({ previous: null, current: { atlas, parcellation, template: selectedSpace } }))
+ ).pipe(
+ map(partialStates => {
- onATPSelectionGetAndSetAllRegions = createEffect(() => this.store.pipe(
- atlasSelection.fromRootStore.distinctATP(),
- switchMap(({ atlas, template, parcellation }) =>
- !!atlas && !!template && !!parcellation
- ? this.sapiSvc.getParcRegions(atlas["@id"], parcellation["@id"], template["@id"]).pipe(
- map(regions =>
- actions.setSelectedParcellationAllRegions({
- regions
+ let returnState: Partial<AtlasSelectionState> = {
+ selectedAtlas: atlas,
+ selectedTemplate: selectedSpace,
+ selectedParcellation: parcellation
+ }
+ for (const s of partialStates) {
+ returnState = {
+ ...returnState,
+ ...s,
+ }
+ }
+ return actions.setAtlasSelectionState(returnState)
})
)
- )
- : of(
- actions.setSelectedParcellationAllRegions({
- regions: []
})
)
- )
+ })
))
onATPSelectionClearBaseLayerColorMap = createEffect(() => this.store.pipe(
diff --git a/src/state/atlasSelection/store.ts b/src/state/atlasSelection/store.ts
index 45bc4f669ead58ed58c6af97e3cb45e2c601f14c..08848c1efa9b81e649bfc8d7c29d3cc6581f77ed 100644
--- a/src/state/atlasSelection/store.ts
+++ b/src/state/atlasSelection/store.ts
@@ -24,13 +24,11 @@ export const defaultState: AtlasSelectionState = {
const reducer = createReducer(
defaultState,
on(
- actions.setATP,
- (state, { atlas, parcellation, template }) => {
+ actions.setAtlasSelectionState,
+ (state, partialState) => {
return {
...state,
- selectedAtlas: atlas || state.selectedAtlas,
- selectedTemplate: template || state.selectedTemplate,
- selectedParcellation: parcellation || state.selectedParcellation,
+ ...partialState
}
}
),
@@ -116,6 +114,15 @@ const reducer = createReducer(
}
}
),
+ on(
+ actions.selectAtlas,
+ (state, { atlas }) => {
+ return {
+ ...state,
+ selectedAtlas: atlas
+ }
+ }
+ ),
on(
actions.dismissBreadCrumb,
(state, { id }) => {
diff --git a/src/state/index.ts b/src/state/index.ts
index d465bfb4a624ead5445fdf23388dd0e9bbedcc42..3eba9c31857ad2db855c3c9c8e4c461c8fd488ee 100644
--- a/src/state/index.ts
+++ b/src/state/index.ts
@@ -35,13 +35,11 @@ function generalApplyStateReducer(reducer: ActionReducer<MainState>): ActionRedu
return function(_state, action) {
let state = _state
if (action.type === generalApplyState.type) {
- state = {
- ...state,
- /**
- * typing is a bit scuffed, but works
- */
- ...(action as any).state
- }
+ state = JSON.parse(
+ JSON.stringify(
+ (action as any).state
+ )
+ )
}
return reducer(state, action)
}
diff --git a/src/viewerModule/module.ts b/src/viewerModule/module.ts
index a4d1fc05f373b2ca33076f7c8d690bfb9c8f7e1b..a485a115773c2953b3396c72a0d054d925fa85f6 100644
--- a/src/viewerModule/module.ts
+++ b/src/viewerModule/module.ts
@@ -1,7 +1,6 @@
import { CommonModule } from "@angular/common";
import { NgModule } from "@angular/core";
import { Observable } from "rxjs";
-import { SplashUiModule } from "src/atlasComponents/splashScreen";
import { ComponentsModule } from "src/components";
import { ContextMenuModule, ContextMenuService, TContextMenuReg } from "src/contextMenuModule";
import { LayoutModule } from "src/layouts/layout.module";
@@ -33,7 +32,6 @@ import { DialogModule } from "src/ui/dialogInfo/module";
ThreeSurferModule,
LayoutModule,
AngularMaterialModule,
- SplashUiModule,
TopMenuModule,
UtilModule,
ComponentsModule,
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
index e74aee0c302bdf627dbe60b1e7a0cd758ff705e5..934f5ba8d3147fba7292b51436c2bdc1357f8417 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
@@ -37,8 +37,8 @@ export class LayerCtrlEffects {
),
switchMap(([ regions, { atlas, parcellation, template } ]) => {
const sapiRegion = this.sapi.getRegion(atlas["@id"], parcellation["@id"], regions[0].name)
- return sapiRegion.getMapInfo(template["@id"])
- .then(val =>
+ return sapiRegion.getMapInfo(template["@id"]).pipe(
+ map(val =>
atlasAppearance.actions.addCustomLayer({
customLayer: {
clType: "customlayer/nglayer",
@@ -52,13 +52,14 @@ export class LayerCtrlEffects {
})
}
})
- )
+ ),
+ catchError((err, obs) => of(
+ atlasAppearance.actions.removeCustomLayer({
+ id: NehubaLayerControlService.PMAP_LAYER_NAME
+ })
+ ))
+ )
}),
- catchError((err, obs) => of(
- atlasAppearance.actions.removeCustomLayer({
- id: NehubaLayerControlService.PMAP_LAYER_NAME
- })
- ))
))
onATP$ = this.store.pipe(
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
index ad0528023661161f926a263545e72bc268f3c6d9..2f86c53b2a37395d57f7805a6df835025c018398 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
@@ -3,15 +3,13 @@ import { select, Store } from "@ngrx/store";
import { BehaviorSubject, combineLatest, merge, Observable, Subject, Subscription } from "rxjs";
import { debounceTime, distinctUntilChanged, filter, map, shareReplay, switchMap, tap, withLatestFrom } from "rxjs/operators";
import { IColorMap, INgLayerCtrl, TNgLayerCtrl } from "./layerCtrl.util";
-import { IAuxMesh } from '../store'
-import { IVolumeTypeDetail } from "src/util/siibraApiConstants/types";
-import { SAPI, SapiParcellationModel } from "src/atlasComponents/sapi";
-import { SAPISpace, SAPIRegion } from "src/atlasComponents/sapi/core";
+import { SAPIRegion } from "src/atlasComponents/sapi/core";
import { getParcNgId } from "../config.service"
import { getRegionLabelIndex } from "../config.service/util";
import { annotation, atlasAppearance, atlasSelection } from "src/state";
import { serializeSegment } from "../util";
import { LayerCtrlEffects } from "./layerCtrl.effects";
+import { arrayEqual } from "src/util/array";
export const BACKUP_COLOR = {
red: 255,
@@ -96,33 +94,6 @@ export class NehubaLayerControlService implements OnDestroy{
...cmAux
}))
)
-
- private auxMeshes$: Observable<IAuxMesh[]> = this.selectedATP$.pipe(
- map(({ template }) => template),
- switchMap(tmpl => this.sapiSvc.registry.get<SAPISpace>(tmpl["@id"]).getVolumes().pipe(
- map(
- tmplVolumes => {
- const auxMeshArr: IAuxMesh[] = []
- for (const vol of tmplVolumes) {
- if (vol.data.detail["neuroglancer/precompmesh"]) {
- const detail = vol.data.detail as IVolumeTypeDetail["neuroglancer/precompmesh"]
- for (const auxMesh of detail["neuroglancer/precompmesh"].auxMeshes) {
- auxMeshArr.push({
- "@id": `auxmesh-${tmpl["@id"]}-${auxMesh.name}`,
- labelIndicies: auxMesh.labelIndicies,
- name: auxMesh.name,
- ngId: '',
- rgb: [255, 255, 255],
- visible: auxMesh.name !== "Sulci"
- })
- }
- }
- }
- return auxMeshArr
- }
- )
- ))
- )
private sub: Subscription[] = []
@@ -132,7 +103,6 @@ export class NehubaLayerControlService implements OnDestroy{
constructor(
private store$: Store<any>,
- private sapiSvc: SAPI,
private layerEffects: LayerCtrlEffects,
){
@@ -166,43 +136,22 @@ export class NehubaLayerControlService implements OnDestroy{
})
)
- this.sub.push(
- this.store$.pipe(
- select(atlasAppearance.selectors.customLayers),
- map(cl => cl.filter(l => l.clType === "customlayer/colormap").length > 0),
- distinctUntilChanged()
- ).subscribe(flag => {
- const pmapLayer = this.ngLayersRegister.find(l => l.id === NehubaLayerControlService.PMAP_LAYER_NAME)
- if (!pmapLayer) return
- const payload = {
- type: 'update',
- payload: {
- [NehubaLayerControlService.PMAP_LAYER_NAME]: {
- visible: !flag
- }
- }
- } as TNgLayerCtrl<'update'>
- this.manualNgLayersControl$.next(payload)
- })
- )
-
/**
* on custom landmarks loaded, set mesh transparency
*/
this.sub.push(
this.store$.pipe(
select(annotation.selectors.annotations),
- withLatestFrom(this.auxMeshes$)
- ).subscribe(([landmarks, auxMeshes]) => {
-
+ withLatestFrom(this.defaultNgLayers$)
+ ).subscribe(([landmarks, { tmplAuxNgLayers }]) => {
const payload: {
[key: string]: number
} = {}
const alpha = landmarks.length > 0
? 0.2
: 1.0
- for (const auxMesh of auxMeshes) {
- payload[auxMesh.ngId] = alpha
+ for (const ngId in tmplAuxNgLayers) {
+ payload[ngId] = alpha
}
this.manualNgLayersControl$.next({
@@ -242,11 +191,28 @@ export class NehubaLayerControlService implements OnDestroy{
})
)
- public visibleLayer$: Observable<string[]> = this.expectedLayerNames$.pipe(
- map(expectedLayerNames => {
- const ngIdSet = new Set<string>([...expectedLayerNames])
- return Array.from(ngIdSet)
- })
+ public visibleLayer$: Observable<string[]> = combineLatest([
+ this.expectedLayerNames$.pipe(
+ map(expectedLayerNames => {
+ const ngIdSet = new Set<string>([...expectedLayerNames])
+ return Array.from(ngIdSet)
+ })
+ ),
+ this.store$.pipe(
+ select(atlasAppearance.selectors.customLayers),
+ map(cl => {
+ const otherColormapExist = cl.filter(l => l.clType === "customlayer/colormap").length > 0
+ const pmapExist = cl.filter(l => l.clType === "customlayer/nglayer").length > 0
+ return pmapExist && !otherColormapExist
+ }),
+ distinctUntilChanged(),
+ map(flag => flag
+ ? [ NehubaLayerControlService.PMAP_LAYER_NAME ]
+ : []
+ )
+ )
+ ]).pipe(
+ map(([ expectedLayerNames, pmapLayer ]) => [...expectedLayerNames, ...pmapLayer])
)
/**
@@ -303,6 +269,9 @@ export class NehubaLayerControlService implements OnDestroy{
private ngLayers$ = this.store$.pipe(
select(atlasAppearance.selectors.customLayers),
map(customLayers => customLayers.filter(l => l.clType === "customlayer/nglayer") as atlasAppearance.NgLayerCustomLayer[]),
+ distinctUntilChanged(
+ arrayEqual((o, n) => o.id === n.id)
+ ),
map(customLayers => {
const newLayers = customLayers.filter(l => {
const registeredLayerNames = this.ngLayersRegister.map(l => l.id)
diff --git a/src/viewerModule/nehuba/mesh.service/mesh.service.ts b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
index c1aadf90a5fdda983bc101105652574020317a58..6313ccba3200e4195fe17ae03dfa522daa5e7ef6 100644
--- a/src/viewerModule/nehuba/mesh.service/mesh.service.ts
+++ b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
@@ -1,10 +1,13 @@
import { Injectable, OnDestroy } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { merge, Observable, of } from "rxjs";
+import { combineLatest, merge, Observable, of } from "rxjs";
import { map, switchMap } from "rxjs/operators";
import { IMeshesToLoad } from '../constants'
import { selectorAuxMeshes } from "../store";
import { LayerCtrlEffects } from "../layerCtrl.service/layerCtrl.effects";
+import { atlasSelection } from "src/state";
+import { Tree } from "src/components/flatHierarchy/treeView/treeControl"
+import { getParcNgId, getRegionLabelIndex } from "../config.service";
/**
* control mesh loading etc
@@ -33,13 +36,55 @@ export class NehubaMeshService implements OnDestroy {
private ngLayers$ = this.effect.onATPDebounceNgLayers$
public loadMeshes$: Observable<IMeshesToLoad> = merge(
- this.ngLayers$.pipe(
- switchMap(ngLayers => {
+ combineLatest([
+ this.store$.pipe(
+ atlasSelection.fromRootStore.distinctATP(),
+ ),
+ this.store$.pipe(
+ select(atlasSelection.selectors.selectedParcAllRegions),
+ ),
+ this.store$.pipe(
+ select(atlasSelection.selectors.selectedRegions),
+ )
+ ]).pipe(
+ switchMap(([{ atlas, template, parcellation }, regions, selectedRegions]) => {
+ const tree = new Tree(
+ regions,
+ (c, p) => (c.hasParent || []).some(_p => _p["@id"] === p["@id"])
+ )
+
+ const ngIdRecord: Record<string, number[]> = {}
+ if (selectedRegions.length > 0) {
+ for (const r of selectedRegions) {
+ const ngId = getParcNgId(atlas, template, parcellation, r)
+ const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
+ if (!ngIdRecord[ngId]) {
+ ngIdRecord[ngId] = []
+ }
+ ngIdRecord[ngId].push(regionLabelIndex)
+ }
+ } else {
+ for (const r of regions) {
+ const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
+ if (!regionLabelIndex) {
+ continue
+ }
+ if (
+ tree.someAncestor(r, (anc) => !!getRegionLabelIndex(atlas, template, parcellation, anc))
+ ) {
+ continue
+ }
+ const ngId = getParcNgId(atlas, template, parcellation, r)
+ if (!ngIdRecord[ngId]) {
+ ngIdRecord[ngId] = []
+ }
+ ngIdRecord[ngId].push(regionLabelIndex)
+ }
+ }
const arr: IMeshesToLoad[] = []
- const { parcNgLayers } = ngLayers
- for (const ngId in parcNgLayers) {
- const {labelIndicies} = parcNgLayers[ngId]
+ for (const ngId in ngIdRecord) {
+ const labelIndicies = ngIdRecord[ngId]
arr.push({
labelIndicies,
layer: { name: ngId }
diff --git a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
index 964fdbb5646f7dd3edd385d6859e5ea22d3eba36..707a473bfe8a82b3ebb865bb4691639a0cdcc222 100644
--- a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
@@ -2,11 +2,10 @@ import { AfterViewInit, ChangeDetectionStrategy, ChangeDetectorRef, Component, E
import { select, Store } from "@ngrx/store";
import { Subject, Subscription } from "rxjs";
import { ClickInterceptor, CLICK_INTERCEPTOR_INJECTOR } from "src/util";
-import { debounceTime, distinctUntilChanged, filter, map, startWith, switchMap, take } from "rxjs/operators";
+import { distinctUntilChanged, startWith } from "rxjs/operators";
import { ARIA_LABELS } from 'common/constants'
import { LoggingService } from "src/logging";
import { EnumViewerEvt, IViewer, TViewerEvent } from "../../viewer.interface";
-import { NehubaViewerUnit } from "../nehubaViewer/nehubaViewer.component";
import { NehubaViewerContainerDirective, TMouseoverEvent } from "../nehubaViewerInterface/nehubaViewerInterface.directive";
import { API_SERVICE_SET_VIEWER_HANDLE_TOKEN, TSetViewerHandle } from "src/atlasViewer/atlasViewer.apiService.service";
import { NehubaMeshService } from "../mesh.service";
@@ -19,13 +18,10 @@ import { getShader } from "src/util/constants";
import { EnumColorMapName } from "src/util/colorMaps";
import { MatDialog } from "@angular/material/dialog";
import { AtlasWorkerService } from "src/atlasViewer/atlasViewer.workerService.service";
-import { SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
-import { NehubaConfig, getNehubaConfig, getParcNgId, getRegionLabelIndex } from "../config.service";
+import { SapiRegionModel } from "src/atlasComponents/sapi";
+import { NehubaConfig, getParcNgId, getRegionLabelIndex } from "../config.service";
import { SET_MESHES_TO_LOAD } from "../constants";
import { annotation, atlasAppearance, atlasSelection, userInteraction } from "src/state";
-import { NgLayerCustomLayer } from "src/state/atlasAppearance";
-import { arrayEqual } from "src/util/array";
-import { LayerCtrlEffects } from "../layerCtrl.service/layerCtrl.effects";
export const INVALID_FILE_INPUT = `Exactly one (1) nifti file is required!`
@@ -80,14 +76,10 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnDestroy, AfterViewIni
private onhoverSegments: SapiRegionModel[] = []
private onDestroyCb: (() => void)[] = []
- private viewerUnit: NehubaViewerUnit
private multiNgIdsRegionsLabelIndexMap = new Map<string, Map<number, SapiRegionModel>>()
public nehubaConfig: NehubaConfig
- private navigation: any
- private newViewer$ = new Subject()
-
public customLandmarks$ = this.store$.pipe(
select(annotation.selectors.annotations),
)
@@ -187,7 +179,6 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnDestroy, AfterViewIni
/**
* clear existing container
*/
- this.viewerUnit = null
this.nehubaContainerDirective && this.nehubaContainerDirective.clear()
}
@@ -256,14 +247,6 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnDestroy, AfterViewIni
if (setViewerHandle) {
console.warn(`NYI viewer handle is deprecated`)
}
-
- // listen to navigation change from store
- const navSub = this.store$.pipe(
- select(atlasSelection.selectors.navigation)
- ).subscribe(nav => {
- this.navigation = nav
- })
- this.onDestroyCb.push(() => navSub.unsubscribe())
}