diff --git a/common/util.js b/common/util.js
index 4120e4c2744b0661cfdf34293a66ae9bc072068a..118d3079a160b1da15de10f84e9bcf22f008f510 100644
--- a/common/util.js
+++ b/common/util.js
@@ -80,6 +80,27 @@
return `${kgSchema}/${kgId}`
}
+ const getIdsObj = fullId => {
+ const returnArray = []
+ if (!fullId) return returnArray
+ const legacyFullId = getIdObj(fullId)
+ if (legacyFullId) returnArray.push(`${legacyFullId['kgSchema']}/${legacyFullId['kgId']}`)
+
+ const { ['minds/core/parcellationregion/v1.0.0']: uniMindsParcRegScheIds} = fullId
+ for (const key in uniMindsParcRegScheIds || {}) {
+ returnArray.push(`minds/core/parcellationregion/v1.0.0/${key}`)
+ }
+ return returnArray
+ }
+
+ exports.getStringIdsFromRegion = region => {
+ const { fullId } = region
+ /**
+ * other ways of getting id?
+ */
+ return getIdsObj(fullId)
+ }
+
const defaultConfig = {
timeout: 5000,
retries: 3
@@ -108,6 +129,8 @@
exports.flattenRegions = flattenRegions
+ exports.flattenReducer = (acc, curr) => acc.concat(curr)
+
exports.getRandomHex = (digit = 1024 * 1024 * 1024 * 1024) => Math.round(Math.random() * digit).toString(16)
/**
diff --git a/deploy/assets/images/atlas-selection/short-bundle-hcp.png b/deploy/assets/images/atlas-selection/short-bundle-hcp.png
new file mode 100644
index 0000000000000000000000000000000000000000..0204752305a93284af053ff9210266e30f288001
Binary files /dev/null and b/deploy/assets/images/atlas-selection/short-bundle-hcp.png differ
diff --git a/deploy/atlas/index.js b/deploy/atlas/index.js
index 92ff4f851d80f5762ad6b9a8bdc045bb9738afb9..08d79085e0bdde4e6c8db147853d297d4cc1fad7 100644
--- a/deploy/atlas/index.js
+++ b/deploy/atlas/index.js
@@ -54,6 +54,7 @@ const previewImageFIleNameMap = new Map([
['minds/core/parcellationatlas/v1.0.0/ebb923ba-b4d5-4b82-8088-fa9215c2e1fe', 'waxholm-v3.png'],
['minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d', 'waxholm-v2.png'],
['minds/core/parcellationatlas/v1.0.0/11017b35-7056-4593-baad-3934d211daba', 'waxholm-v1.png'],
+ ['juelich/iav/atlas/v1.0.0/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c', 'short-bundle-hcp.png'],
])
router.get('/preview', (req, res) => {
diff --git a/deploy/datasets/util.js b/deploy/datasets/util.js
index e473e3299f69c0b4a12bc5617be5b4d0e4a849b6..f394dad852746c26996d4fea857a98795cf492b7 100644
--- a/deploy/datasets/util.js
+++ b/deploy/datasets/util.js
@@ -3,7 +3,7 @@ const { getCommonSenseDsFilter } = require('./supplements/commonSense')
const { hasPreview } = require('./supplements/previewFile')
const path = require('path')
const fs = require('fs')
-const { getIdFromFullId, retry, flattenRegions, getUniqueRegionId } = require('../../common/util')
+const { getIdFromFullId, retry, flattenRegions, getUniqueRegionId, getStringIdsFromRegion, flattenReducer } = require('../../common/util')
let getPublicAccessToken
@@ -87,34 +87,28 @@ const regionMap = new Map()
const getParseRegion = (template, parcellation) => {
- const getRegionIdFromRegion = region => {
- return region.fullId
- ? getIdFromFullId(region.fullId)
- : getUniqueRegionId(template, parcellation, region)
+ const getRegionIdsFromRegion = region => {
+ return [
+ ...getStringIdsFromRegion(region),
+ getUniqueRegionId(template, parcellation, region)
+ ]
}
const parseRegion = (region, parent) => {
- const regionId = getRegionIdFromRegion(region)
+ const regionIds = getRegionIdsFromRegion(region)
+ const regionId = regionIds[0]
const { children, relatedAreas } = region
- const childrenIds = [
- ...(children || []).map(getRegionIdFromRegion)
- ]
-
- const alternateIds = [
- ...(relatedAreas || []).map(getRegionIdFromRegion)
- ]
+ const childrenIds = (children || []).map(getRegionIdsFromRegion).reduce(flattenReducer, [])
+ const alternateIds = (relatedAreas || []).map(getRegionIdsFromRegion).reduce(flattenReducer, [])
- regionMap.set(regionId, {
+ const regionObj = {
parent,
- self: [ regionId, ...alternateIds ],
+ self: [ ...regionIds, ...alternateIds ],
children: childrenIds
- })
+ }
+ regionMap.set(regionId, regionObj)
for (const altId of alternateIds) {
- regionMap.set(altId, {
- parent,
- self: [ regionId, ...alternateIds ],
- children: childrenIds
- })
+ regionMap.set(altId, regionObj)
}
for (const c of (children || [])) {
parseRegion(c, regionId)
@@ -284,6 +278,7 @@ const traverseRegionMap = regionSchemaId => {
}
const filterDatasetsByRegion = async (datasets = [], regionSchemaId) => {
+ await Promise.all(initPrArray)
const allRelevantSchemaSet = new Set(traverseRegionMap(regionSchemaId))
return datasets.filter(ds => ds['parcellationRegion'].some(pr => allRelevantSchemaSet.has(getIdFromFullId(pr.fullId))))
}
diff --git a/docs/releases/v2.3.0.md b/docs/releases/v2.3.0.md
index 168e0384fb236945f7766bd619d092035e351136..4d6fc0859d24b48fd83fd7329d4dfd88fe88a7f1 100644
--- a/docs/releases/v2.3.0.md
+++ b/docs/releases/v2.3.0.md
@@ -12,6 +12,7 @@
- tweaked mesh loading strategies. Now it will wait for all image chunks to be loaded before loading any meshes
- showing contributors to a regional feature/dataset if publications are not available
- added the ability to customize preview origin dataset to labels other to `View probability map`
+- Added short bundle HCP to the supported atlas
- **experimental** : previewing of curated regional features: iEEG coordinates
## Bugfixes:
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index a318f81ef075e6bbfb957b55184ab1ad11c87958..b0835340cfe7991e80842bef20f5280a45114585 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -13839,6 +13839,17145 @@
"_": {
"@src": "https://gin.g-node.org/FZJ-INM1-BDA/20201002_JulichBrain-V2_4-ICBM152_ontology/src/fdfca63e85a1fbea4df916cb604b8b1bc2ab0a28/output/nehuba-ui/julich-brain-v2_4-icbm152.json"
}
+ },{
+ "@id": "juelich/iav/atlas/v1.0.0/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c",
+ "ngId": "superficial-white-bundle-HCP",
+ "auxillaryMeshIndices": [
+ 65535
+ ],
+ "name": "Short Fiber Bundles - HCP",
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "6a7e07ad-303c-4b1d-b444-ded9ee782225"
+ }
+ ],
+ "regions": [
+ {
+ "name": "left hemisphere",
+ "children": [
+ {
+ "name": "lh_CAC-CAC_1",
+ "labelIndex": 1001,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-CAC_1",
+ "nameOfLocation": "lh_CAC-CAC_1",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-CAC_2",
+ "labelIndex": 1002,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-CAC_2",
+ "nameOfLocation": "lh_CAC-CAC_2",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-MOF_1",
+ "labelIndex": 1003,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-MOF_1",
+ "nameOfLocation": "lh_CAC-MOF_1",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ },
+ "6c52c49a-7495-4126-8a72-dd057e4f27f0": {
+ "name": "Middle orbitofrontal division"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-PoCi_1",
+ "labelIndex": 1004,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-PoCi_1",
+ "nameOfLocation": "lh_CAC-PoCi_1",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ },
+ "d9a8560f-9b80-4870-a99a-fca38f8b3d89": {
+ "name": "Posterior cingulate division"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-PrCu_1",
+ "labelIndex": 1005,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-PrCu_1",
+ "nameOfLocation": "lh_CAC-PrCu_1",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ },
+ "4fa33640-3ef7-4f7d-a69a-553cade7a233": {
+ "name": "Precuneus cortex"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-RAC_1",
+ "labelIndex": 1006,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-RAC_1",
+ "nameOfLocation": "lh_CAC-RAC_1",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ },
+ "fb573be5-64b8-4990-8d7e-9c25455d98dd": {
+ "name": "Rostral anterior cingulate division"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-SF_1",
+ "labelIndex": 1007,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-SF_1",
+ "nameOfLocation": "lh_CAC-SF_1",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ },
+ "9ff67049-fdcd-4474-a6cb-c67a4d8323d7": {
+ "name": "Superior frontal gyrus"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-SF_2",
+ "labelIndex": 1008,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-SF_2",
+ "nameOfLocation": "lh_CAC-SF_2",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ },
+ "9ff67049-fdcd-4474-a6cb-c67a4d8323d7": {
+ "name": "Superior frontal gyrus"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-SF_3",
+ "labelIndex": 1009,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-SF_3",
+ "nameOfLocation": "lh_CAC-SF_3",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ },
+ "9ff67049-fdcd-4474-a6cb-c67a4d8323d7": {
+ "name": "Superior frontal gyrus"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-SF_4",
+ "labelIndex": 1010,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-SF_4",
+ "nameOfLocation": "lh_CAC-SF_4",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ },
+ "9ff67049-fdcd-4474-a6cb-c67a4d8323d7": {
+ "name": "Superior frontal gyrus"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CAC-SF_5",
+ "labelIndex": 1011,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-lh_CAC-SF_5",
+ "nameOfLocation": "lh_CAC-SF_5",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-left-hemisphere",
+ "nameOfLocation": "Left hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "1b74b2d0-c8d5-4a99-9e99-e2be63e92016": {
+ "name": "Caudal anterior cingulate division"
+ },
+ "9ff67049-fdcd-4474-a6cb-c67a4d8323d7": {
+ "name": "Superior frontal gyrus"
+ }
+ }
+ }
+ },
+ {
+ "name": "lh_CMF-CMF_1",
+ "labelIndex": 1012,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
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+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-rh_Tr-Ins_1_1",
+ "nameOfLocation": "rh_Tr-Ins_1_1",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-right-hemisphere",
+ "nameOfLocation": "Right hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "bd978cc2-8546-4b7b-bd48-f4216943ba8b": {
+ "name": "Pars triangularis"
+ },
+ "c1d72383-7c59-469d-889e-52123f005b85": {
+ "name": "Insula"
+ }
+ }
+ }
+ },
+ {
+ "name": "rh_Tr-Ins_2",
+ "labelIndex": 2306,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-rh_Tr-Ins_2",
+ "nameOfLocation": "rh_Tr-Ins_2",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-right-hemisphere",
+ "nameOfLocation": "Right hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "bd978cc2-8546-4b7b-bd48-f4216943ba8b": {
+ "name": "Pars triangularis"
+ },
+ "c1d72383-7c59-469d-889e-52123f005b85": {
+ "name": "Insula"
+ }
+ }
+ }
+ },
+ {
+ "name": "rh_Tr-Tr_1",
+ "labelIndex": 2307,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-rh_Tr-Tr_1",
+ "nameOfLocation": "rh_Tr-Tr_1",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-right-hemisphere",
+ "nameOfLocation": "Right hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "bd978cc2-8546-4b7b-bd48-f4216943ba8b": {
+ "name": "Pars triangularis"
+ }
+ }
+ }
+ },
+ {
+ "name": "rh_Tr-Tr_2",
+ "labelIndex": 2308,
+ "children": [],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-rh_Tr-Tr_2",
+ "nameOfLocation": "rh_Tr-Tr_2",
+ "parentStructure": {
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-right-hemisphere",
+ "nameOfLocation": "Right hemisphere"
+ }
+ }
+ },
+ "minds/core/parcellationregion/v1.0.0": {
+ "bd978cc2-8546-4b7b-bd48-f4216943ba8b": {
+ "name": "Pars triangularis"
+ }
+ }
+ }
+ }
+ ],
+ "fullId": {
+ "sands": {
+ "d2912956684aa38c46a72ca2b357d248866e2242": {
+ "$schema": "https://github.com/HumanBrainProject/SANDS/raw/d2912956684aa38c46a72ca2b357d248866e2242/v0.1/core/anatomicalEntity.schema.json",
+ "@type": "https://schema.hbp.eu/sands/AnatomicalEntity",
+ "@id": "sands/v0.1/core/anatomicalEntity/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c-right-hemisphere",
+ "nameOfLocation": "Right hemisphere"
+ }
+ }
+ }
+ }
+ ],
+ "_": {
+ "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20201005-superficial-white-matter-HCP/raw/master/output/nehubaUI/short-bundle-hcp.json"
+ }
},{
"@id": "juelich/iav/atlas/v1.0.0/8",
"fullId": "juelich/iav/atlas/v1.0.0/8",
diff --git a/src/res/ext/MNI152NehubaConfig.json b/src/res/ext/MNI152NehubaConfig.json
index b155b9172f98d720ddc07f7cb46e614044c42057..20f685aeaf022076f14029c38f69ca59acf91330 100644
--- a/src/res/ext/MNI152NehubaConfig.json
+++ b/src/res/ext/MNI152NehubaConfig.json
@@ -158,7 +158,7 @@
"julich brain mni152 v22 left": {
"type": "segmentation",
"visible": false,
- "source": "precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/data-repo/20200807_julich_brain_v2_mni152_left/precomputed",
+ "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/data-repo/20200807_julich_brain_v2_mni152_left/precomputed",
"transform": [
[
1,
@@ -189,7 +189,7 @@
"julich brain mni152 v22 right": {
"type": "segmentation",
"visible": false,
- "source": "precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/data-repo/20200807_julich_brain_v2_mni152_right/precomputed",
+ "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/data-repo/20200807_julich_brain_v2_mni152_right/precomputed",
"transform": [
[
1,
@@ -346,6 +346,39 @@
]
]
},
+ "superficial-white-bundle-HCP": {
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -96500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -132500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -78500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ],
+ "type": "segmentation",
+ "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201111-superficial-whitematter-ng-volume/precomputed",
+ "_": {
+ "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20201111-superficial-whitematter-ng-volume/src/6bcd8428556cce104b646de1fe8ef14aa9009728/output/nehuba-ui/nehuba-ui-config-prettified.json"
+ }
+ },
"DiFuMo Atlas (64 dimensions)": {
"type": "segmentation",
"visible": false,
diff --git a/src/res/ext/atlas/atlas_multiLevelHuman.json b/src/res/ext/atlas/atlas_multiLevelHuman.json
index fdbb4afc693d56c5f4dfcdb902b4d72b6243630f..9f2c680338253486a3dd1f26a3c7ed552b2780ba 100644
--- a/src/res/ext/atlas/atlas_multiLevelHuman.json
+++ b/src/res/ext/atlas/atlas_multiLevelHuman.json
@@ -25,6 +25,10 @@
"name": "Short Bundle",
"@id": "juelich/iav/atlas/v1.0.0/6"
},
+ {
+ "ngId": "superficial-white-bundle-HCP",
+ "@id": "juelich/iav/atlas/v1.0.0/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c"
+ },
{
"name": "64 dimensions",
"@id": "minds/core/parcellationatlas/v1.0.0/d80fbab2-ce7f-4901-a3a2-3c8ef8a3b721"
@@ -201,6 +205,20 @@
}
]
},
+ {
+ "ngId": "superficial-white-bundle-HCP",
+ "@id": "juelich/iav/atlas/v1.0.0/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c",
+ "groupName": "Fibre tracts",
+ "availableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+ "originalDatasetFormats": [{
+ "name": "probability map"
+ }]
+ }
+ ]
+ },
{
"name": "64 dimensions",
"@id": "minds/core/parcellationatlas/v1.0.0/d80fbab2-ce7f-4901-a3a2-3c8ef8a3b721",
diff --git a/src/ui/databrowserModule/databrowser.service.ts b/src/ui/databrowserModule/databrowser.service.ts
index fb1c8cc099a9121d61057e368e8c69017c079a5c..7c8ccc1dfc1d9b1de747ded340616cf1bc3cae5f 100644
--- a/src/ui/databrowserModule/databrowser.service.ts
+++ b/src/ui/databrowserModule/databrowser.service.ts
@@ -17,7 +17,7 @@ import { NO_METHODS } from "./util/filterDataEntriesByMethods.pipe";
import { FilterDataEntriesByRegion } from "./util/filterDataEntriesByRegion.pipe";
import { datastateActionToggleFav, datastateActionUnfavDataset, datastateActionFavDataset } from "src/services/state/dataState/actions";
-import { getIdFromFullId } from 'common/util'
+import { getStringIdsFromRegion } from 'common/util'
import { viewerStateSelectorNavigation } from "src/services/state/viewerState/selectors";
const noMethodDisplayName = 'No methods described'
@@ -271,21 +271,34 @@ export class DatabrowserService implements OnDestroy {
public fetchingFlag: boolean = false
private mostRecentFetchToken: any
- private memoizedDatasetByRegion = new Map<string, Observable<IDataEntry>>()
- private getDatasetsByRegion(region: { fullId: string }){
- const fullId = getIdFromFullId(region.fullId)
- if (this.memoizedDatasetByRegion.has(fullId)) return this.memoizedDatasetByRegion.get(fullId)
- const obs$ = this.http.get<IDataEntry>(
- `${this.constantService.backendUrl}datasets/byRegion/${encodeURIComponent(fullId)}`,
- {
- headers: this.constantService.getHttpHeader(),
- responseType: 'json'
+ private memoizedDatasetByRegion = new Map<string, Observable<IDataEntry[]>>()
+ private getDatasetsByRegion(region: { fullId: any }){
+ const fullIds = getStringIdsFromRegion(region) as string[]
+
+ for (const fullId of fullIds) {
+ if (!this.memoizedDatasetByRegion.has(fullId)) {
+ const obs$ = this.http.get<IDataEntry[]>(
+ `${this.constantService.backendUrl}datasets/byRegion/${encodeURIComponent(fullId)}`,
+ {
+ headers: this.constantService.getHttpHeader(),
+ responseType: 'json'
+ }
+ ).pipe(
+ shareReplay(1),
+ )
+ this.memoizedDatasetByRegion.set(fullId, obs$)
}
+ }
+
+ return forkJoin(
+ fullIds.map(fullId => this.memoizedDatasetByRegion.get(fullId))
).pipe(
- shareReplay(1),
+ map(array => array.reduce((acc, currArr) => {
+ return acc.concat(
+ currArr.filter(ds => !new Set(acc.map(ds => ds['fullId'])).has(ds['fullId']))
+ )
+ }, []))
)
- this.memoizedDatasetByRegion.set(fullId, obs$)
- return obs$
}
private lowLevelQuery(templateName: string, parcellationName: string): Promise<IDataEntry[]> {
diff --git a/src/ui/databrowserModule/databrowser/databrowser.base.ts b/src/ui/databrowserModule/databrowser/databrowser.base.ts
index a3ec2a4fc14a666b57f166b8bd23dfbb7e85d7f3..c2c8279a94419ca203a44a2a011aa6c9c5b098d3 100644
--- a/src/ui/databrowserModule/databrowser/databrowser.base.ts
+++ b/src/ui/databrowserModule/databrowser/databrowser.base.ts
@@ -3,8 +3,9 @@ import { LoggingService } from "src/logging"
import { DatabrowserService } from "../singleDataset/singleDataset.base"
import { Observable, Subject, Subscription } from "rxjs"
import { IDataEntry } from "src/services/stateStore.service"
-import { getIdFromFullId, setsEql } from 'common/util'
+import { setsEql } from 'common/util'
import { switchMap, tap } from "rxjs/operators"
+import { getStringIdsFromRegion, flattenReducer } from 'common/util'
export class DatabrowserBase implements OnDestroy{
@@ -21,10 +22,10 @@ export class DatabrowserBase implements OnDestroy{
}
@Input()
set regions(arr: any[]){
- const currentSet = new Set(this._regions.map(r => getIdFromFullId(r.fullId)))
- const newSet = new Set(arr.map(r => getIdFromFullId(r.fullId)).filter(v => !!v))
+ const currentSet = new Set(this._regions.map(r => getStringIdsFromRegion(r)).reduce(flattenReducer, []))
+ const newSet = new Set(arr.map(r => getStringIdsFromRegion(r)).reduce(flattenReducer, []).filter(v => !!v))
if (setsEql(newSet, currentSet)) return
- this._regions = arr.filter(r => !!getIdFromFullId(r.fullId))
+ this._regions = arr.filter(r => !getStringIdsFromRegion(r).every(id => !id))
this.regions$.next(this._regions)
}
diff --git a/src/ui/regionalFeatures/regionalFeature.service.ts b/src/ui/regionalFeatures/regionalFeature.service.ts
index faa71b067870bdcaf85f4f39443a6b0d3fd800dd..8e47bfeb5b62c14e243bb2df909d2af5e4030ba0 100644
--- a/src/ui/regionalFeatures/regionalFeature.service.ts
+++ b/src/ui/regionalFeatures/regionalFeature.service.ts
@@ -1,9 +1,9 @@
import { HttpClient } from "@angular/common/http";
import { Injectable, OnDestroy } from "@angular/core";
import { PureContantService } from "src/util";
-import { getIdFromFullId, getRegionHemisphere } from 'common/util'
+import { getIdFromFullId, getRegionHemisphere, getStringIdsFromRegion, flattenReducer } from 'common/util'
import { forkJoin, Subject, Subscription } from "rxjs";
-import { switchMap } from "rxjs/operators";
+import { map, switchMap } from "rxjs/operators";
import { IHasId } from "src/util/interfaces";
import { select, Store } from "@ngrx/store";
import { viewerStateSelectedTemplateSelector } from "src/services/state/viewerState/selectors";
@@ -47,7 +47,7 @@ export class RegionalFeaturesService implements OnDestroy{
public getAllFeaturesByRegion(region: {['fullId']: string}){
if (!region.fullId) throw new Error(`getAllFeaturesByRegion - region does not have fullId defined`)
const regionFullId = getIdFromFullId(region.fullId)
-
+ const regionFullIds = getStringIdsFromRegion(region)
const hemisphereObj = (() => {
const hemisphere = getRegionHemisphere(region)
return hemisphere ? { hemisphere } : {}
@@ -56,31 +56,35 @@ export class RegionalFeaturesService implements OnDestroy{
const refSpaceObj = this.templateSelected && this.templateSelected.fullId
? { referenceSpaceId: getIdFromFullId(this.templateSelected.fullId) }
: {}
-
- return this.http.get<{features: IHasId[]}>(
- `${this.pureConstantService.backendUrl}regionalFeatures/byRegion/${encodeURIComponent( regionFullId )}`,
- {
- params: {
- ...hemisphereObj,
- ...refSpaceObj,
- },
- responseType: 'json'
- }
- ).pipe(
- switchMap(({ features }) => forkJoin(
- features.map(({ ['@id']: featureId }) =>
- this.http.get<IFeature>(
- `${this.pureConstantService.backendUrl}regionalFeatures/byRegion/${encodeURIComponent( regionFullId )}/${encodeURIComponent( featureId )}`,
- {
- params: {
- ...hemisphereObj,
- ...refSpaceObj,
- },
- responseType: 'json'
- }
+
+ return forkJoin(
+ regionFullIds.map(regionFullId => this.http.get<{features: IHasId[]}>(
+ `${this.pureConstantService.backendUrl}regionalFeatures/byRegion/${encodeURIComponent( regionFullId )}`,
+ {
+ params: {
+ ...hemisphereObj,
+ ...refSpaceObj,
+ },
+ responseType: 'json'
+ }
+ ).pipe(
+ switchMap(({ features }) => forkJoin(
+ features.map(({ ['@id']: featureId }) =>
+ this.http.get<IFeature>(
+ `${this.pureConstantService.backendUrl}regionalFeatures/byRegion/${encodeURIComponent( regionFullId )}/${encodeURIComponent( featureId )}`,
+ {
+ params: {
+ ...hemisphereObj,
+ ...refSpaceObj,
+ },
+ responseType: 'json'
+ }
+ )
)
- )
- )),
+ )),
+ ))
+ ).pipe(
+ map((arr: IFeature[][]) => arr.reduce(flattenReducer, []))
)
}