diff --git a/deploy/bkwdCompat/urlState.js b/deploy/bkwdCompat/urlState.js
index dd5331e3e9967e85eb07778d4f56edfe5a4dde0c..66f92c3dc4f6b375fcfe0c70f16a685b43c30e0d 100644
--- a/deploy/bkwdCompat/urlState.js
+++ b/deploy/bkwdCompat/urlState.js
@@ -42,7 +42,10 @@ const templateMap = {
id: 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588',
parc: {
'Cytoarchitectonic Maps - v2.4': {
- id: 'juelich/iav/atlas/v1.0.0/7'
+ id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290',
+ },
+ 'Cytoarchitectonic Maps': {
+ id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290',
},
'Cortical Layers Segmentation': {
id: 'juelich/iav/atlas/v1.0.0/3'
@@ -64,7 +67,7 @@ const templateMap = {
id: 'juelich/iav/atlas/v1.0.0/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c'
},
'Cytoarchitectonic maps - v1.18': {
- id: 'juelich/iav/atlas/v1.0.0/8'
+ id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
},
'Long Bundle': {
id: 'juelich/iav/atlas/v1.0.0/5'
@@ -94,7 +97,7 @@ const templateMap = {
id: 'minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992',
parc: {
'Cytoarchitectonic Maps - v1.18': {
- id: 'juelich/iav/atlas/v1.0.0/8'
+ id: 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579'
}
}
},
diff --git a/docs/releases/v2.4.1.md b/docs/releases/v2.4.1.md
index da64e9b3cbb0d49a953218160fd5231cd60b85f5..4768d30acb00b7b73b5472fbb48c86800739152a 100644
--- a/docs/releases/v2.4.1.md
+++ b/docs/releases/v2.4.1.md
@@ -2,4 +2,4 @@
## Bugfixes
-- fix JulichBrain v2.5.0 URL redirection
\ No newline at end of file
+- fix JulichBrain v2.5.0/v1.18 URL redirection
\ No newline at end of file
diff --git a/docs/releases/v2.4.3.md b/docs/releases/v2.4.3.md
new file mode 100644
index 0000000000000000000000000000000000000000..ede740c0394d101dc0fdf1074816c325bffbcbeb
--- /dev/null
+++ b/docs/releases/v2.4.3.md
@@ -0,0 +1,5 @@
+# v2.4.3
+
+## Bugfixes
+
+- fix some of the big brain maps
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index fdcc03b3df60b34d1ccefae2152ad01529a712ac..4b7828389a6ab6f4dd0d9e155493cd9dac4bd128 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -40,6 +40,7 @@ pages:
- Fetching datasets: 'advanced/datasets.md'
- Display non-atlas volumes: 'advanced/otherVolumes.md'
- Release notes:
+ - v2.4.3: 'releases/v2.4.3.md'
- v2.4.2: 'releases/v2.4.2.md'
- v2.4.1: 'releases/v2.4.1.md'
- v2.4.0: 'releases/v2.4.0.md'
diff --git a/package.json b/package.json
index 092b4973a467dfdd8e4332df9da4c4da5895a9d7..71b66c9ed2319db8b479ff6408733b10eaabdc61 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "interactive-viewer",
- "version": "2.4.2",
+ "version": "2.4.3",
"description": "HBP interactive atlas viewer. Integrating KG query, dataset previews & more. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular",
"scripts": {
"build-aot": "PRODUCTION=true GIT_HASH=`node -e 'console.log(require(\"./package.json\").version)'` webpack --config ./webpack/webpack.aot.js && node ./third_party/matomo/processMatomo.js",
diff --git a/src/atlasComponents/parcellationRegion/region.base.ts b/src/atlasComponents/parcellationRegion/region.base.ts
index c69a2f94658760f599f896f16affca4a70ab277c..29f4073df696e30dda71e2216f20947f9f12dd1b 100644
--- a/src/atlasComponents/parcellationRegion/region.base.ts
+++ b/src/atlasComponents/parcellationRegion/region.base.ts
@@ -284,7 +284,7 @@ export const regionInOtherTemplateSelector = createSelector(
const otherTemplates = fetchedTemplates
.filter(({ ['@id']: id }) => id !== regionOfInterest.context.template['@id']
&& atlasTemplateSpacesIds.includes(id)
- && regionOfInterest.availableIn.map(ai => ai.id).includes(id))
+ && (regionOfInterest.availableIn || []).map(ai => ai.id).includes(id))
for (const template of otherTemplates) {
const parcellation = template.parcellations.find(p => p['@id'] === regionOfInterest.context.parcellation['@id'])
diff --git a/src/util/fn.ts b/src/util/fn.ts
index db3ad47ce6e43a8065bef6acc0459be9a72d5d99..23ec5adeec3f09a0573bbb4fe4824f10ae73a84c 100644
--- a/src/util/fn.ts
+++ b/src/util/fn.ts
@@ -287,14 +287,41 @@ export class MultiDimMap{
}
}
-export function recursiveMutate<T>(arr: T[], getChildren: (obj: T) => T[], mutateFn: (obj: T) => void){
+export function mutateDeepMerge(toObj: any, fromObj: any){
+ if (typeof toObj !== 'object') throw new Error(`toObj needs to be object`)
+ if (typeof fromObj !== 'object') throw new Error(`fromObj needs to be object`)
+
+ for (const key in fromObj) {
+ if (!toObj[key]) {
+ toObj[key] = fromObj[key]
+ continue
+ }
+ if (Array.isArray(toObj[key])) {
+ const objToAppend = Array.isArray(fromObj[key])
+ ? fromObj[key]
+ : [fromObj[key]]
+ toObj[key].push(...objToAppend)
+ continue
+ }
+ if (typeof toObj[key] === typeof fromObj[key] && typeof toObj[key] === 'object') {
+ mutateDeepMerge(toObj[key], fromObj[key])
+ continue
+ }
+ throw new Error(`cannot mutate ${key} typeof ${typeof fromObj[key]}`)
+ }
+
+ return toObj
+}
+
+export function recursiveMutate<T>(arr: T[], getChildren: (obj: T) => T[], mutateFn: (obj: T) => void, depthFirst = false){
for (const obj of arr) {
- mutateFn(obj)
+ if (!depthFirst) mutateFn(obj)
recursiveMutate(
getChildren(obj),
getChildren,
mutateFn
)
+ if (depthFirst) mutateFn(obj)
}
}
diff --git a/src/util/patchPureConstants.ts b/src/util/patchPureConstants.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a97fe7ec66ec36fb149df93b0beee112f69eace2
--- /dev/null
+++ b/src/util/patchPureConstants.ts
@@ -0,0 +1,193 @@
+/**
+ * README: the purpose of this file is to monkey patch discrepency between siibra-api
+ * backend and original backend.
+ *
+ * In principle, these should be built into siibra-python, and this file should become obsolete.
+ */
+
+import { IHasId } from "./interfaces";
+import { TRegion } from "./siibraApiConstants/types";
+
+type TAppend = {
+ parent: IHasId | { name: string }
+ '@type': 'julich/siibra/append-region/v0.0.1'
+}
+
+type TPatch = {
+ target: IHasId | { name: string }
+ '@type': 'julich/siibra/patch-region/v0.0.1'
+}
+
+type TPatchRegion = {
+ '@id': string
+ targetSpace: IHasId[] | '*'
+ targetParcellation: IHasId[] | '*'
+ payload: Partial<TRegion>
+} & (TAppend | TPatch)
+
+const encoder = new TextEncoder()
+async function getShaDigest(input: string){
+ const digest = await crypto.subtle.digest('SHA-1', encoder.encode(input))
+ const array = Array.from(new Uint8Array(digest))
+ const hex = array.map(v => v.toString(16)).join('')
+ return hex
+}
+async function getInterpolatedPatchObj(targetName: string, labelIndex: number){
+ const returnObj: TPatchRegion = {
+ '@id': '',
+ "@type": 'julich/siibra/patch-region/v0.0.1',
+ "target": {
+ "name": targetName
+ },
+ "targetParcellation": [{
+ "@id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290'
+ }],
+ "targetSpace": [{
+ '@id': 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588'
+ }],
+ "payload": {
+ "volumeSrc": {
+ 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588': {
+ "collect": [{
+ "@type": "fzj/tmp/volume_type/v0.0.1" as "fzj/tmp/volume_type/v0.0.1",
+ "@id": "fzj/tmp/volume_type/v0.0.1/interpolated",
+ "name": "Julich Brain v2.5 interpolated map",
+ "volume_type": "neuroglancer/precomputed" as "neuroglancer/precomputed",
+ "url": "https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/2019_05_22_interpolated_areas",
+ "detail": {
+ "neuroglancer/precomputed": {
+ "labelIndex": labelIndex,
+ "transform": [[1,0,0,-70677184],[0,1,0,-51990000],[0,0,1,-58788284],[0,0,0,1]]
+ }
+ }
+ }]
+ }
+ }
+ }
+ }
+ const hex = await getShaDigest(JSON.stringify(returnObj))
+ return {
+ ...returnObj,
+ '@id': hex
+ }
+}
+
+async function getIndividualMap(parentName: string, regionName: string, url: string, transform: number[][], labelIndex: number){
+ const volumeId = await getShaDigest(url)
+ const returnObj: TPatchRegion = {
+ '@id': '',
+ "@type": 'julich/siibra/append-region/v0.0.1',
+ "parent": {
+ "name": parentName
+ },
+ "targetParcellation": [{
+ "@id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290'
+ }],
+ "targetSpace": [{
+ '@id': 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588'
+ }],
+ "payload": {
+ "name": regionName,
+ "volumeSrc": {
+ 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588': {
+ "collect": [{
+ "@type": "fzj/tmp/volume_type/v0.0.1" as "fzj/tmp/volume_type/v0.0.1",
+ "@id": `fzj/tmp/volume_type/v0.0.1/${volumeId}`,
+ "name": "Julich Brain v2.5 detailed map",
+ "volume_type": "neuroglancer/precomputed" as "neuroglancer/precomputed",
+ "url": url,
+ "detail": {
+ "neuroglancer/precomputed": {
+ "labelIndex": labelIndex,
+ "transform": transform
+ }
+ }
+ }]
+ }
+ }
+ }
+ }
+ const hex = await getShaDigest(JSON.stringify(returnObj))
+ return {
+ ...returnObj,
+ '@id': hex
+ }
+}
+
+const bigBrainRegions: Promise<TPatchRegion>[] = [
+ getInterpolatedPatchObj('Area IFJ1 (IFS,PreCS)', 9),
+ getInterpolatedPatchObj('Area IFJ2 (IFS,PreCS)', 10),
+ getInterpolatedPatchObj('Area IFS1 (IFS)', 11),
+ getInterpolatedPatchObj('Area IFS2 (IFS)', 12),
+ getInterpolatedPatchObj('Area IFS3 (IFS)', 13),
+ getInterpolatedPatchObj('Area IFS4 (IFS)', 14),
+
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam1 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam1/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam2 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam2/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam3 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam3/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam4 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam4/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam5 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam5/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'lateral geniculate body',
+ 'LGB-lam6 (CGL, Metathalamus)',
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2020_11_11_LGB-lam/LGB-lam6/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+
+ getIndividualMap(
+ 'medial geniculate body',
+ "MGB-MGBd (CGM, Metathalamus)",
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2021_04_27_mgb/2021_04_27_MGBd/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'medial geniculate body',
+ "MGB-MGBm (CGM, Metathalamus)",
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2021_04_27_mgb/2021_04_27_MGBm/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+ getIndividualMap(
+ 'medial geniculate body',
+ "MGB-MGBv (CGM, Metathalamus)",
+ "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2021_04_27_mgb/2021_04_27_MGBv/",
+ [[1,0,0,-70677184.0],[0,1,0,-7290000.0],[0,0,1,-58788284.0],[0,0,0,1]],
+ 1
+ ),
+]
+
+export const patchRegions = [
+ ...bigBrainRegions
+]
diff --git a/src/util/pureConstant.service.ts b/src/util/pureConstant.service.ts
index 0e6a9bc9ebaf706e78bb28fb4e04274449cd09db..6dce026c96ade1309808cad26c096774f04cce72 100644
--- a/src/util/pureConstant.service.ts
+++ b/src/util/pureConstant.service.ts
@@ -1,6 +1,6 @@
import { Inject, Injectable, OnDestroy } from "@angular/core";
import { Store, select } from "@ngrx/store";
-import { Observable, Subscription, of, forkJoin, fromEvent, combineLatest } from "rxjs";
+import { Observable, Subscription, of, forkJoin, fromEvent, combineLatest, from } from "rxjs";
import { viewerConfigSelectorUseMobileUi } from "src/services/state/viewerConfig.store.helper";
import { shareReplay, tap, scan, catchError, filter, switchMap, map, take, distinctUntilChanged, mapTo } from "rxjs/operators";
import { HttpClient } from "@angular/common/http";
@@ -11,7 +11,8 @@ import { viewerStateFetchedAtlasesSelector, viewerStateSelectedTemplateSelector
import { BS_ENDPOINT } from "src/util/constants";
import { flattenReducer } from 'common/util'
import { TAtlas, TId, TParc, TRegion, TRegionDetail, TSpaceFull, TSpaceSummary } from "./siibraApiConstants/types";
-import { MultiDimMap, recursiveMutate } from "./fn";
+import { MultiDimMap, mutateDeepMerge, recursiveMutate } from "./fn";
+import { patchRegions } from './patchPureConstants'
function getNgId(atlasId: string, tmplId: string, parcId: string, regionKey: string){
const proxyId = MultiDimMap.GetProxyKeyMatch(atlasId, tmplId, parcId, regionKey)
@@ -206,6 +207,12 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
)
}
+ private patchRegions$ = forkJoin(
+ patchRegions.map(patch => from(patch))
+ ).pipe(
+ shareReplay(1)
+ )
+
private getRegions(atlasId: string, parcId: string, spaceId: string){
return this.http.get<TRegion[]>(
`${this.bsEndpoint}/atlases/${encodeURIComponent(atlasId)}/parcellations/${encodeURIComponent(parcId)}/regions`,
@@ -215,6 +222,53 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
},
responseType: 'json'
}
+ ).pipe(
+ switchMap(regions => this.patchRegions$.pipe(
+ map(patchRegions => {
+ for (const p of patchRegions) {
+ if (
+ p.targetParcellation !== '*'
+ && Array.isArray(p.targetParcellation)
+ && p.targetParcellation.every(p => p["@id"] !== parcId)
+ ) {
+ continue
+ }
+ if (
+ p.targetSpace !== '*'
+ && Array.isArray(p.targetSpace)
+ && p.targetSpace.every(sp => sp['@id'] !== spaceId)
+ ) {
+ continue
+ }
+
+ recursiveMutate(
+ regions,
+ r => r.children || [],
+ region => {
+
+ if (p["@type"] === 'julich/siibra/append-region/v0.0.1') {
+ if (p.parent['name'] === region.name) {
+ if (!region.children) region.children = []
+ region.children.push(
+ p.payload as TRegion
+ )
+ }
+ }
+ if (p['@type'] === 'julich/siibra/patch-region/v0.0.1') {
+ if (p.target['name'] === region.name) {
+ mutateDeepMerge(
+ region,
+ p.payload
+ )
+ }
+ }
+ },
+ true
+ )
+ }
+ return regions
+ })
+ ))
)
}
diff --git a/src/util/siibraApiConstants/types.ts b/src/util/siibraApiConstants/types.ts
index da56c848a3e80b39b6f709373096be1e27e297be..db9dab33fa992ee91c8870420172e081f60b53ed 100644
--- a/src/util/siibraApiConstants/types.ts
+++ b/src/util/siibraApiConstants/types.ts
@@ -18,6 +18,7 @@ interface IVolumeTypeDetail {
'nii': null
'neuroglancer/precomputed': {
'neuroglancer/precomputed': {
+ 'labelIndex': number
'transform': TNgTransform
}
}