From 7fdbff0f0baf73965bff9df3f075a76b84991b54 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Fri, 6 May 2022 09:27:37 +0200
Subject: [PATCH] bugfix: jba29 in bigbrain
---
src/atlasComponents/sapi/constants.ts | 9 ++
src/atlasComponents/sapi/core/sapiRegion.ts | 16 ++-
src/atlasComponents/sapi/index.ts | 4 +
src/atlasComponents/sapi/schema.ts | 100 +++++++++++---
src/atlasComponents/sapi/type.ts | 6 +
.../features/voi/voiQuery.directive.ts | 8 +-
.../util/parcellationSupportedInSpace.pipe.ts | 7 +-
.../routeStateTransform.service.ts | 47 +++----
.../nehuba/config.service/type.ts | 1 -
.../nehuba/config.service/util.ts | 69 ++++++----
.../layerCtrl.service/layerCtrl.effects.ts | 128 +++++++++++++-----
.../nehubaViewerGlue.component.ts | 9 +-
src/viewerModule/nehuba/store/util.ts | 8 +-
13 files changed, 297 insertions(+), 115 deletions(-)
create mode 100644 src/atlasComponents/sapi/constants.ts
diff --git a/src/atlasComponents/sapi/constants.ts b/src/atlasComponents/sapi/constants.ts
new file mode 100644
index 000000000..40011a86a
--- /dev/null
+++ b/src/atlasComponents/sapi/constants.ts
@@ -0,0 +1,9 @@
+export const IDS = {
+ TEMPLATES: {
+ BIG_BRAIN: "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
+ MNI152: "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+ },
+ PARCELLATION: {
+ JBA29: "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290"
+ }
+}
diff --git a/src/atlasComponents/sapi/core/sapiRegion.ts b/src/atlasComponents/sapi/core/sapiRegion.ts
index afadc4929..1787145e8 100644
--- a/src/atlasComponents/sapi/core/sapiRegion.ts
+++ b/src/atlasComponents/sapi/core/sapiRegion.ts
@@ -1,5 +1,5 @@
import { SAPI } from "..";
-import { SapiRegionalFeatureModel, SapiRegionMapInfoModel, SapiRegionModel, cleanIeegSessionDatasets, SapiIeegSessionModel, CleanedIeegDataset } from "../type";
+import { SapiRegionalFeatureModel, SapiRegionMapInfoModel, SapiRegionModel, cleanIeegSessionDatasets, SapiIeegSessionModel, CleanedIeegDataset, SapiVolumeModel, PaginatedResponse } from "../type";
import { strToRgb, hexToRgb } from 'common/util'
import { forkJoin, Observable, of } from "rxjs";
import { catchError, map } from "rxjs/operators";
@@ -80,6 +80,20 @@ export class SAPIRegion{
return `${this.prefix}/regional_map/map?space_id=${encodeURI(spaceId)}`
}
+ getVolumes(): Observable<PaginatedResponse<SapiVolumeModel>>{
+ const url = `${this.prefix}/volumes`
+ return this.sapi.httpGet<PaginatedResponse<SapiVolumeModel>>(
+ url
+ )
+ }
+
+ getVolumeInstance(volumeId: string): Observable<SapiVolumeModel> {
+ const url = `${this.prefix}/volumes/${encodeURIComponent(volumeId)}`
+ return this.sapi.httpGet<SapiVolumeModel>(
+ url
+ )
+ }
+
getDetail(spaceId: string): Observable<SapiRegionModel> {
const url = `${this.prefix}/${encodeURIComponent(this.id)}`
return this.sapi.httpGet<SapiRegionModel>(
diff --git a/src/atlasComponents/sapi/index.ts b/src/atlasComponents/sapi/index.ts
index 2c223648d..e5d8afd20 100644
--- a/src/atlasComponents/sapi/index.ts
+++ b/src/atlasComponents/sapi/index.ts
@@ -24,3 +24,7 @@ export {
SAPIParcellation,
SAPIRegion
} from "./core"
+
+export {
+ IDS
+} from "./constants"
\ No newline at end of file
diff --git a/src/atlasComponents/sapi/schema.ts b/src/atlasComponents/sapi/schema.ts
index 3eb4599d5..a54de84de 100644
--- a/src/atlasComponents/sapi/schema.ts
+++ b/src/atlasComponents/sapi/schema.ts
@@ -24,6 +24,9 @@ export interface paths {
/** Returns a regional map for given region name. */
get: operations["get_regional_map_file_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__regional_map_map_get"]
}
+ "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/volumes": {
+ get: operations["get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes_get"]
+ }
"/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}": {
get: operations["get_single_region_detail_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__get"]
}
@@ -104,7 +107,7 @@ export interface paths {
* :param space_id:
* :param parcellation_id:
* :param region_id:
- * :return: UnionRegionalFeatureModels
+ * :return: FeatureModels
*/
get: operations["get_feature_details_features__feature_id__get"]
}
@@ -235,11 +238,24 @@ export interface components {
/** Urls */
urls: components["schemas"]["Url"][]
/** Cells */
- cells: string
+ cells?: components["schemas"]["CorticalCellModel"][]
/** Section */
- section: string
+ section?: string
/** Patch */
- patch: string
+ patch?: string
+ }
+ /** CorticalCellModel */
+ CorticalCellModel: {
+ /** X */
+ x: number
+ /** Y */
+ y: number
+ /** Area */
+ area: number
+ /** Layer */
+ layer: number
+ /** Instance Label */
+ "instance label": number
}
/** DatasetJsonModel */
DatasetJsonModel: {
@@ -420,6 +436,29 @@ export interface components {
/** Content */
content: string
}
+ /** Page[Union[siibra.features.connectivity.ConnectivityMatrixDataModel, app.models.SerializationErrorModel]] */
+ "Page_Union_siibra.features.connectivity.ConnectivityMatrixDataModel__app.models.SerializationErrorModel__": {
+ /** Items */
+ items: (Partial<components["schemas"]["ConnectivityMatrixDataModel"]> &
+ Partial<components["schemas"]["SerializationErrorModel"]>)[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ }
+ /** Page[VolumeModel] */
+ Page_VolumeModel_: {
+ /** Items */
+ items: components["schemas"]["VolumeModel"][]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ }
/** ProfileDataModel */
ProfileDataModel: {
density: components["schemas"]["NpArrayDataModel"]
@@ -787,7 +826,7 @@ export interface components {
/** ValidationError */
ValidationError: {
/** Location */
- loc: string[]
+ loc: (Partial<string> & Partial<number>)[]
/** Message */
msg: string
/** Error Type */
@@ -822,11 +861,8 @@ export interface components {
VolumeModel: {
/** @Id */
"@id": string
- /**
- * @Type
- * @constant
- */
- "@type"?: "https://openminds.ebrains.eu/core/DatasetVersion"
+ /** @Type */
+ "@type": string
metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
/** Urls */
urls: components["schemas"]["Url"][]
@@ -1491,6 +1527,35 @@ export interface operations {
}
}
}
+ get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes_get: {
+ parameters: {
+ path: {
+ atlas_id: string
+ parcellation_id: string
+ region_id: string
+ }
+ query: {
+ space_id?: string
+ type?: string
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_VolumeModel_"]
+ }
+ }
+ /** Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
get_single_region_detail_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__get: {
parameters: {
path: {
@@ -1575,18 +1640,15 @@ export interface operations {
}
query: {
type?: string
- per_page?: number
page?: number
+ size?: number
}
}
responses: {
/** Successful Response */
200: {
content: {
- "application/json": (Partial<
- components["schemas"]["ConnectivityMatrixDataModel"]
- > &
- Partial<components["schemas"]["SerializationErrorModel"]>)[]
+ "application/json": components["schemas"]["Page_Union_siibra.features.connectivity.ConnectivityMatrixDataModel__app.models.SerializationErrorModel__"]
}
}
/** Validation Error */
@@ -1889,7 +1951,7 @@ export interface operations {
* :param space_id:
* :param parcellation_id:
* :param region_id:
- * :return: UnionRegionalFeatureModels
+ * :return: FeatureModels
*/
get_feature_details_features__feature_id__get: {
parameters: {
@@ -1911,7 +1973,11 @@ export interface operations {
components["schemas"]["ReceptorDatasetModel"]
> &
Partial<components["schemas"]["BaseDatasetJsonModel"]> &
- Partial<components["schemas"]["CorticalCellDistributionModel"]>
+ Partial<components["schemas"]["CorticalCellDistributionModel"]> &
+ Partial<components["schemas"]["IEEGSessionModel"]> &
+ Partial<components["schemas"]["VOIDataModel"]> &
+ Partial<components["schemas"]["ConnectivityMatrixDataModel"]> &
+ Partial<components["schemas"]["SerializationErrorModel"]>
}
}
/** Validation Error */
diff --git a/src/atlasComponents/sapi/type.ts b/src/atlasComponents/sapi/type.ts
index 1796c54d0..3eb47a670 100644
--- a/src/atlasComponents/sapi/type.ts
+++ b/src/atlasComponents/sapi/type.ts
@@ -34,6 +34,12 @@ export type SapiIeegSessionModel = components["schemas"]["IEEGSessionModel"]
* utility types
*/
type PathReturn<T extends keyof paths> = Required<paths[T]["get"]["responses"][200]["content"]["application/json"]>
+export type PaginatedResponse<T> = {
+ items: T[]
+ total: number
+ page: number
+ size: number
+}
/**
* serialization error type
diff --git a/src/atlasComponents/sapiViews/features/voi/voiQuery.directive.ts b/src/atlasComponents/sapiViews/features/voi/voiQuery.directive.ts
index e70d1ab45..623011d89 100644
--- a/src/atlasComponents/sapiViews/features/voi/voiQuery.directive.ts
+++ b/src/atlasComponents/sapiViews/features/voi/voiQuery.directive.ts
@@ -1,10 +1,11 @@
import { Directive, EventEmitter, Inject, Input, OnChanges, OnDestroy, Optional, Output, SimpleChanges } from "@angular/core";
import { interval, merge, Observable, of, Subject, Subscription } from "rxjs";
-import { debounce, debounceTime, filter, pairwise, shareReplay, startWith, switchMap, take, tap } from "rxjs/operators";
+import { debounce, debounceTime, distinctUntilChanged, filter, pairwise, shareReplay, startWith, switchMap, take, tap } from "rxjs/operators";
import { AnnotationLayer, TNgAnnotationPoint, TNgAnnotationAABBox } from "src/atlasComponents/annotations";
import { SAPI } from "src/atlasComponents/sapi/sapi.service";
import { BoundingBoxConcept, SapiAtlasModel, SapiSpaceModel, SapiVOIDataResponse, OpenMINDSCoordinatePoint } from "src/atlasComponents/sapi/type";
import { ClickInterceptor, CLICK_INTERCEPTOR_INJECTOR } from "src/util";
+import { arrayEqual } from "src/util/array";
@Directive({
selector: '[sxplr-sapiviews-features-voi-query]',
@@ -130,14 +131,15 @@ export class SapiViewsFeaturesVoiQuery implements OnChanges, OnDestroy{
clickInterceptor.register(handle)
this.subscription.push(
this.features$.pipe(
+ startWith([] as SapiVOIDataResponse[]),
+ distinctUntilChanged(arrayEqual((o, n) => o["@id"] === n["@id"])),
+ pairwise(),
debounce(() =>
interval(16).pipe(
filter(() => !!this.voiBBoxSvc),
take(1),
)
),
- startWith([] as SapiVOIDataResponse[]),
- pairwise()
).subscribe(([ prev, curr ]) => {
for (const v of prev) {
const box = this.pointsToAABB(v.location.maxpoint, v.location.minpoint)
diff --git a/src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe.ts b/src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe.ts
index aaafaf90f..f16e6a0a8 100644
--- a/src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe.ts
+++ b/src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe.ts
@@ -1,5 +1,5 @@
import { Pipe, PipeTransform } from "@angular/core";
-import { Observable } from "rxjs";
+import { Observable, of } from "rxjs";
import { map } from "rxjs/operators";
import { SAPIParcellation } from "src/atlasComponents/sapi/core";
import { SAPI } from "src/atlasComponents/sapi/sapi.service";
@@ -35,6 +35,11 @@ export class ParcellationSupportedInSpacePipe implements PipeTransform{
const tmplId = typeof tmpl === "string"
? tmpl
: tmpl["@id"]
+ for (const key in knownExceptions.supported) {
+ if (key === parcId && knownExceptions.supported[key].indexOf(tmplId) >= 0) {
+ return of(true)
+ }
+ }
return this.sapi.registry.get<SAPIParcellation>(parcId).getVolumes().pipe(
map(volumes => volumes.some(v => v.data.space["@id"] === tmplId))
)
diff --git a/src/routerModule/routeStateTransform.service.ts b/src/routerModule/routeStateTransform.service.ts
index d7deecf51..10f003638 100644
--- a/src/routerModule/routeStateTransform.service.ts
+++ b/src/routerModule/routeStateTransform.service.ts
@@ -1,7 +1,7 @@
import { Injectable } from "@angular/core";
import { UrlSegment, UrlTree } from "@angular/router";
import { map } from "rxjs/operators";
-import { SAPI } from "src/atlasComponents/sapi";
+import { SAPI, SapiRegionModel } from "src/atlasComponents/sapi";
import { atlasSelection, defaultState, MainState, plugins, userInteraction } from "src/state";
import { getParcNgId, getRegionLabelIndex } from "src/viewerModule/nehuba/config.service";
import { decodeToNumber, encodeNumber, encodeURIFull, separator } from "./cipher";
@@ -43,16 +43,21 @@ export class RouteStateTransformSvc {
this.sapi.getParcRegions(selectedAtlasId, selectedParcellationId, selectedTemplateId, { priority: 10 }).toPromise(),
])
- const latNgIdMap = ["left hemisphere", "right hemisphere", "whole brain"].map(lat => {
- let regex: RegExp = /./
- if (lat === "left hemisphere") regex = /left/i
- if (lat === "right hemisphere") regex = /right/i
- return {
- lat,
- regex,
- ngId: getParcNgId(selectedAtlas, selectedTemplate, selectedParcellation, lat)
+ const ngIdToRegionMap: Map<string, Map<number, SapiRegionModel[]>> = new Map()
+
+ for (const region of allParcellationRegions) {
+ const ngId = getParcNgId(selectedAtlas, selectedTemplate, selectedParcellation, region)
+ if (!ngIdToRegionMap.has(ngId)) {
+ ngIdToRegionMap.set(ngId, new Map())
}
- })
+ const map = ngIdToRegionMap.get(ngId)
+
+ const idx = getRegionLabelIndex(selectedAtlas, selectedTemplate, selectedParcellation, region)
+ if (!map.has(idx)) {
+ map.set(idx, [])
+ }
+ map.get(idx).push(region)
+ }
const selectedRegions = (() => {
if (!selectedRegionIds) return []
@@ -63,12 +68,12 @@ export class RouteStateTransformSvc {
const json = { [selectedRegionIds[0]]: selectedRegionIds[1] }
for (const ngId in json) {
- const matchingMap = latNgIdMap.find(ngIdMap => ngIdMap.ngId === ngId)
- if (!matchingMap) {
+ if (!ngIdToRegionMap.has(ngId)) {
console.error(`could not find matching map for ${ngId}`)
continue
}
- const filteredRegions = allParcellationRegions.filter(r => matchingMap.regex.test(r.name))
+
+ const map = ngIdToRegionMap.get(ngId)
const val = json[ngId]
const labelIndicies = val.split(separator).map(n => {
@@ -81,20 +86,8 @@ export class RouteStateTransformSvc {
return null
}
}).filter(v => !!v)
-
- for (const labelIndex of labelIndicies) {
- /**
- * currently, only 1 region is expected to be selected at max
- * this method probably out performs creating a map
- * but with 2+ regions, creating a map would consistently be faster
- */
- for (const r of filteredRegions) {
- const idx = getRegionLabelIndex(selectedAtlas, selectedTemplate, selectedParcellation, r)
- if (idx === labelIndex) {
- return [ r ]
- }
- }
- }
+
+ return labelIndicies.map(idx => map.get(idx) || []).flatMap(v => v)
}
return []
})()
diff --git a/src/viewerModule/nehuba/config.service/type.ts b/src/viewerModule/nehuba/config.service/type.ts
index c0e963ecb..c8154dd44 100644
--- a/src/viewerModule/nehuba/config.service/type.ts
+++ b/src/viewerModule/nehuba/config.service/type.ts
@@ -112,5 +112,4 @@ export type NgPrecompMeshSpec = {
export type NgSegLayerSpec = {
labelIndicies: number[]
- laterality: 'left hemisphere' | 'right hemisphere' | 'whole brain'
} & NgLayerSpec
diff --git a/src/viewerModule/nehuba/config.service/util.ts b/src/viewerModule/nehuba/config.service/util.ts
index a89599f60..6cd2b0c35 100644
--- a/src/viewerModule/nehuba/config.service/util.ts
+++ b/src/viewerModule/nehuba/config.service/util.ts
@@ -1,5 +1,5 @@
import { SapiParcellationModel, SapiSpaceModel, SapiAtlasModel, SapiRegionModel } from 'src/atlasComponents/sapi'
-import { SapiVolumeModel } from 'src/atlasComponents/sapi/type'
+import { SapiVolumeModel, IDS } from 'src/atlasComponents/sapi'
import { atlasSelection } from 'src/state'
import { MultiDimMap } from 'src/util/fn'
import { ParcVolumeSpec } from "../store/util"
@@ -14,7 +14,7 @@ import {
// fsaverage uses threesurfer, which, whilst do not use ngId, uses 'left' and 'right' as keys
const fsAverageKeyVal = {
- "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290": {
+ [IDS.PARCELLATION.JBA29]: {
"left hemisphere": "left",
"right hemisphere": "right"
}
@@ -29,7 +29,7 @@ const BACKCOMAP_KEY_DICT = {
// human multi level
'juelich/iav/atlas/v1.0.0/1': {
// icbm152
- 'minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2': {
+ [IDS.TEMPLATES.MNI152]: {
// julich brain v2.6
'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-26': {
'left hemisphere': 'MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE',
@@ -186,15 +186,23 @@ export function getTmplAuxNgLayer(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, s
}
}
-export function getParcNgId(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, parc: SapiParcellationModel, _laterality: string | SapiRegionModel): string {
- let laterality: string
- if (typeof _laterality === "string") {
- laterality = _laterality
- } else {
- laterality = "whole brain"
- if (_laterality.name.indexOf("left") >= 0) laterality = "left hemisphere"
- if (_laterality.name.indexOf("right") >= 0) laterality = "right hemisphere"
+export function getParcNgId(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, parc: SapiParcellationModel, region: SapiRegionModel): string {
+
+ let laterality: string = "whole brain"
+ if (region.name.indexOf("left") >= 0) laterality = "left hemisphere"
+ if (region.name.indexOf("right") >= 0) laterality = "right hemisphere"
+
+ /**
+ * for JBA29 in big brain, there exist several volumes. (e.g. v1, v2, v5, interpolated, etc)
+ */
+ if (tmpl['@id'] === IDS.TEMPLATES.BIG_BRAIN && parc['@id'] === IDS.PARCELLATION.JBA29) {
+ laterality = region.hasAnnotation.visualizedIn?.['@id']
}
+
+ if (!laterality) {
+ return null
+ }
+
let ngId = BACKCOMAP_KEY_DICT[atlas["@id"]]?.[tmpl["@id"]]?.[parc["@id"]]?.[laterality]
if (!ngId) {
ngId = `_${MultiDimMap.GetKey(atlas["@id"], tmpl["@id"], parc["@id"], laterality)}`
@@ -202,18 +210,37 @@ export function getParcNgId(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, parc: S
return ngId
}
+const labelIdxRegex = /siibra_python_ng_precomputed_labelindex:\/\/(.*?)#([0-9]+)$/
+
+export function getRegionLabelIndex(_atlas: SapiAtlasModel, _tmpl: SapiSpaceModel, _parc: SapiParcellationModel, region: SapiRegionModel): number {
+ const overwriteLabelIndex = region.hasAnnotation.inspiredBy.map(({ "@id": id }) => labelIdxRegex.exec(id)).filter(v => !!v)
+ if (overwriteLabelIndex.length > 0) {
+ const match = overwriteLabelIndex[0]
+ const volumeId = match[1]
+ const labelIndex = match[2]
+ const _labelIndex = Number(labelIndex)
+ if (!isNaN(_labelIndex)) return _labelIndex
+ }
+ const lblIdx = Number(region?.hasAnnotation?.internalIdentifier)
+ if (isNaN(lblIdx)) return null
+ return lblIdx
+}
+
export function getParcNgLayers(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, parc: SapiParcellationModel, parcVolumes: { volume: SapiVolumeModel, volumeMetadata: ParcVolumeSpec }[]): Record<string, NgSegLayerSpec>{
const returnVal: Record<string, NgSegLayerSpec> = {}
for (const parcVol of parcVolumes) {
const { volume, volumeMetadata } = parcVol
- const { laterality, labelIndicies } = volumeMetadata
- const ngId = getParcNgId(atlas, tmpl, parc, laterality)
+ const { regions } = volumeMetadata
+ if (regions.length === 0) {
+ console.warn(`parc volume with no associated region`)
+ continue
+ }
+ const ngId = getParcNgId(atlas, tmpl, parc, regions[0].region)
returnVal[ngId] = {
source: `precomputed://${volume.data.url.replace(/^precomputed:\/\//, '')}`,
- labelIndicies,
- laterality,
- transform: (volume.data.detail["neuroglancer/precomputed"] as any).transform
+ transform: (volume.data.detail["neuroglancer/precomputed"] as any).transform,
+ labelIndicies: regions.map(v => v.labelIndex)
}
}
return returnVal
@@ -240,12 +267,6 @@ export const getNgLayersFromVolumesATP = (volumes: CongregatedVolume, ATP: { atl
}
}
-export function getRegionLabelIndex(_atlas: SapiAtlasModel, _tmpl: SapiSpaceModel, _parc: SapiParcellationModel, region: SapiRegionModel): number {
- const lblIdx = Number(region?.hasAnnotation?.internalIdentifier)
- if (isNaN(lblIdx)) return null
- return lblIdx
-}
-
export const defaultNehubaConfig: NehubaConfig = {
"configName": "",
"globals": {
@@ -318,11 +339,11 @@ export const defaultNehubaConfig: NehubaConfig = {
}
export const spaceMiscInfoMap = new Map([
- ['minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588', {
+ [IDS.TEMPLATES.BIG_BRAIN, {
name: 'bigbrain',
scale: 1,
}],
- ['minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2', {
+ [IDS.TEMPLATES.MNI152, {
name: 'icbm2009c',
scale: 1,
}],
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
index 314049276..6f6d70887 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
@@ -3,8 +3,8 @@ import { createEffect } from "@ngrx/effects";
import { select, Store } from "@ngrx/store";
import { forkJoin, of } from "rxjs";
import { mapTo, switchMap, withLatestFrom, filter, catchError, map, debounceTime, shareReplay, distinctUntilChanged, startWith, pairwise } from "rxjs/operators";
-import { SAPI, SapiAtlasModel, SapiFeatureModel, SapiParcellationModel, SapiSpaceModel } from "src/atlasComponents/sapi";
-import { SapiVOIDataResponse } from "src/atlasComponents/sapi/type";
+import { SAPI, SapiAtlasModel, SapiFeatureModel, SapiParcellationModel, SapiSpaceModel, SapiRegionModel } from "src/atlasComponents/sapi";
+import { SapiVOIDataResponse, SapiVolumeModel } from "src/atlasComponents/sapi/type";
import { atlasAppearance, atlasSelection, userInteraction } from "src/state";
import { arrayEqual } from "src/util/array";
import { EnumColorMapName } from "src/util/colorMaps";
@@ -146,51 +146,115 @@ export class LayerCtrlEffects {
throw new Error(`parcellation defined, but template not defined!`)
}
+ /**
+ * some labelled maps (such as julich brain in big brain) do not have the volumes defined on the parcellation level.
+ * While we have the URLs of these volumes (the method we use is also kind of hacky), and in theory, we could construct a volume object directly
+ * It is probably better to fetch the correct volume object to begin with
+ */
const parcVolumes$ = !parcellation
- ? of([])
+ ? of([] as {volume: SapiVolumeModel, volumeMetadata: ParcVolumeSpec}[])
: forkJoin([
this.sapi.getParcellation(atlas["@id"], parcellation["@id"]).getRegions(template["@id"]).pipe(
map(regions => {
- const returnArr: ParcVolumeSpec[] = []
+ const volumeIdToRegionMap = new Map<string, {
+ labelIndex: number
+ region: SapiRegionModel
+ }[]>()
+
for (const r of regions) {
- const source = r?.hasAnnotation?.visualizedIn?.["@id"]
- if (!source) continue
- if (source.indexOf("precomputed://") < 0) continue
+ const volumeId = r?.hasAnnotation?.visualizedIn?.["@id"]
+ if (!volumeId) continue
+
const labelIndex = getRegionLabelIndex(atlas, template, parcellation, r)
if (!labelIndex) continue
-
- const found = returnArr.find(v => v.volumeSrc === source)
- if (found) {
- found.labelIndicies.push(labelIndex)
- continue
- }
- let laterality: "left hemisphere" | "right hemisphere" | "whole brain" = "whole brain"
- if (r.name.indexOf("left") >= 0) laterality = "left hemisphere"
- if (r.name.indexOf("right") >= 0) laterality = "right hemisphere"
- returnArr.push({
- volumeSrc: source,
- labelIndicies: [labelIndex],
- parcellation,
- laterality,
+ if (!volumeIdToRegionMap.has(volumeId)) {
+ volumeIdToRegionMap.set(volumeId, [])
+ }
+ volumeIdToRegionMap.get(volumeId).push({
+ labelIndex,
+ region: r
})
}
- return returnArr
+ return volumeIdToRegionMap
})
),
this.sapi.getParcellation(atlas["@id"], parcellation["@id"]).getVolumes()
]).pipe(
- map(([ volumeSrcs, volumes ]) => {
- return volumes.map(
- v => {
- const found = volumeSrcs.find(volSrc => volSrc.volumeSrc.indexOf(v.data.url) >= 0)
- return {
- volume: v,
- volumeMetadata: found,
+ switchMap(([ volumeIdToRegionMap, volumes ]) => {
+ const missingVolumeIds = Array.from(volumeIdToRegionMap.keys()).filter(id => volumes.map(v => v["@id"]).indexOf(id) < 0)
+
+ const volumesFromParc: {volume: SapiVolumeModel, volumeMetadata: ParcVolumeSpec}[] = volumes.map(
+ volume => {
+ const found = volumeIdToRegionMap.get(volume["@id"])
+ if (!found) return null
+
+ try {
+
+ const volumeMetadata: ParcVolumeSpec = {
+ regions: found,
+ parcellation,
+ volumeSrc: volume.data.url
+ }
+ return {
+ volume,
+ volumeMetadata,
+ }
+ } catch (e) {
+ console.error(e)
+ return null
}
- }).filter(
- v => !!v.volumeMetadata?.labelIndicies
+ }
+ ).filter(v => v?.volumeMetadata?.regions)
+
+ if (missingVolumeIds.length === 0) return of([...volumesFromParc])
+ return forkJoin(
+ missingVolumeIds.map(missingId => {
+ if (!volumeIdToRegionMap.has(missingId)) {
+ console.warn(`volumeIdToRegionMap does not have volume with id ${missingId}`)
+ return of(null as SapiVolumeModel)
+ }
+ const { region } = volumeIdToRegionMap.get(missingId)[0]
+ return this.sapi.getRegion(atlas["@id"], parcellation["@id"], region.name).getVolumeInstance(missingId).pipe(
+ catchError((err, obs) => of(null as SapiVolumeModel))
+ )
+ })
+ ).pipe(
+ map((missingVolumes: SapiVolumeModel[]) => {
+
+ const volumesFromRegion: { volume: SapiVolumeModel, volumeMetadata: ParcVolumeSpec }[] = missingVolumes.map(
+ volume => {
+ if (!volume || !volumeIdToRegionMap.has(volume['@id'])) {
+ return null
+ }
+
+ try {
+
+ const found = volumeIdToRegionMap.get(volume['@id'])
+ const volumeMetadata: ParcVolumeSpec = {
+ regions: found,
+ parcellation,
+ volumeSrc: volume.data.url
+ }
+ return {
+ volume,
+ volumeMetadata
+ }
+ } catch (e) {
+ console.error(`volume from region error`, e)
+ return null
+ }
+ }
+ ).filter(
+ v => !!v
+ )
+
+ return [
+ ...volumesFromParc,
+ ...volumesFromRegion
+ ]
+ })
)
})
)
@@ -199,7 +263,7 @@ export class LayerCtrlEffects {
? this.sapi.getSpace(atlas["@id"], template["@id"]).getVolumes().pipe(
shareReplay(1),
)
- : of([])
+ : of([] as SapiVolumeModel[])
return forkJoin({
tmplVolumes: spaceVols$.pipe(
diff --git a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
index c719c98ce..0c7b084eb 100644
--- a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
@@ -187,11 +187,6 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnDestroy, AfterViewIni
private layerCtrlService: NehubaLayerControlService,
@Optional() @Inject(CLICK_INTERCEPTOR_INJECTOR) clickInterceptor: ClickInterceptor,
){
- /**
- * This **massively** improve the performance of the viewer
- * TODO investigate why, and perhaps eventually remove the cdr.detach()
- */
- // this.cdr.detach()
/**
* define onclick behaviour
@@ -215,10 +210,12 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnDestroy, AfterViewIni
this.multiNgIdsRegionsLabelIndexMap.clear()
for (const r of regions) {
const ngId = getParcNgId(atlas, template, parcellation, r)
- const labelIndex = getRegionLabelIndex(atlas, template, parcellation, r)
+ if (!ngId) continue
if (!this.multiNgIdsRegionsLabelIndexMap.has(ngId)) {
this.multiNgIdsRegionsLabelIndexMap.set(ngId, new Map())
}
+ const labelIndex = getRegionLabelIndex(atlas, template, parcellation, r)
+ if (!labelIndex) continue
this.multiNgIdsRegionsLabelIndexMap.get(ngId).set(labelIndex, r)
}
})
diff --git a/src/viewerModule/nehuba/store/util.ts b/src/viewerModule/nehuba/store/util.ts
index cc59b9f00..14a59dc1d 100644
--- a/src/viewerModule/nehuba/store/util.ts
+++ b/src/viewerModule/nehuba/store/util.ts
@@ -1,8 +1,10 @@
-import { SapiParcellationModel } from "src/atlasComponents/sapi";
+import { SapiParcellationModel, SapiRegionModel } from "src/atlasComponents/sapi";
export type ParcVolumeSpec = {
volumeSrc: string
- labelIndicies: number[]
parcellation: SapiParcellationModel
- laterality: 'left hemisphere' | 'right hemisphere' | 'whole brain'
+ regions: {
+ labelIndex: number
+ region: SapiRegionModel
+ }[]
}
--
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