Merge pull request #868 from HumanBrainProject/staging

v2.3.5
FZJ-INM1-BDA · Feb 9, 2021 · e621665 · e621665
2 parents 85a4eb2 + ec2ae62
commit e621665
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diff --git a/docs/releases/v2.3.5.md b/docs/releases/v2.3.5.md
@@ -0,0 +1,6 @@
+# v2.3.5
+
+## Under the hood stuff
+
+- Temporarily disable Colin 27 template.
+- Update to JulichBrain v2.5
diff --git 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:
+    - v2.3.5: 'releases/v2.3.5.md'
     - v2.3.4: 'releases/v2.3.4.md'
     - v2.3.3: 'releases/v2.3.3.md'
     - v2.3.2: 'releases/v2.3.2.md'

diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
diff --git a/src/res/ext/MNI152NehubaConfig.json b/src/res/ext/MNI152NehubaConfig.json
@@ -220,7 +220,7 @@
         "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE": {
           "type": "segmentation",
           "visible": true,
-          "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201204_JulichBrainV3_0_hemisphereSplit/precomputed/JuBrain_Map_icbm_v30_r",
+          "source": "precomputed://https://neuroglancer-dev.humanbrainproject.eu/precomputed/data-repo-ng-bot/JulichBrainV2_5_3/precomputed/JulichBrain_MPMAtlas_r_N10_nlin2Stdicbm152asym2009c_publicDOI_453c4c95827e38dcce5372b200065cba",
           "transform": [
             [
               1,
@@ -251,7 +251,7 @@
         "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE": {
           "type": "segmentation",
           "visible": true,
-          "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201204_JulichBrainV3_0_hemisphereSplit/precomputed/JuBrain_Map_icbm_v30_l",
+          "source": "precomputed://https://neuroglancer-dev.humanbrainproject.eu//precomputed/data-repo-ng-bot/JulichBrainV2_5_3/precomputed/JulichBrain_MPMAtlas_l_N10_nlin2Stdicbm152asym2009c_publicDOI_3f5ec6016bc2242769c41befdbc1b2e0",
           "transform": [
             [
               1,

diff --git a/src/res/ext/atlas/atlas_multiLevelHuman.json b/src/res/ext/atlas/atlas_multiLevelHuman.json
@@ -51,20 +51,6 @@
         }
       ]
     },
-    {
-      "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
-      "name": "MNI Colin 27",
-      "availableIn": [
-        {
-          "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25",
-          "name": "Cytoarchitectonic maps - v2.5"
-        },
-        {
-          "@id": "juelich/iav/atlas/v1.0.0/8",
-          "name": "Cytoarchitectonic Maps - v1.18"
-        }
-      ]
-    },
     {
       "@id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
       "name": "Big Brain (Histology)",
@@ -102,13 +88,6 @@
           "originalDatasetFormats": [{
             "name": "probability map"
           }]
-        },
-        {
-          "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
-          "name": "MNI Colin 27",
-          "originalDatasetFormats": [{
-            "name": "probability map"
-          }]
         }
       ]
     },
@@ -136,7 +115,7 @@
       "@version": {
         "@next": null,
         "@this": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25",
-        "name": "v2.5",
+        "name": "v2.6",
         "@previous": "juelich/iav/atlas/v1.0.0/8"
       },
       "availableIn": [
@@ -146,13 +125,6 @@
           "originalDatasetFormats": [{
             "name": "probability map"
           }]
-        },
-        {
-          "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
-          "name": "MNI Colin 27",
-          "originalDatasetFormats": [{
-            "name": "probability map"
-          }]
         }
       ]
     },

diff --git a/src/ui/parcellationRegion/region.base.spec.ts b/src/ui/parcellationRegion/region.base.spec.ts
@@ -328,16 +328,22 @@ const getRegionInOtherTemplateSelectorBundle = (version: EnumParcRegVersion) =>
 describe('> region.base.ts', () => {
   describe('> regionInOtherTemplateSelector', () => {
 
+    // TODO
+    it('> only selects region in the template specified by selected atlas')
+
     for (const enumKey of Object.keys(EnumParcRegVersion)) {
       describe(`> selector version for ${enumKey}`, () => {
 
         const { mockFetchedTemplates, mr0, mt2, mt0, mp0, mt1, mp1h, mr0lh, mt3, mr0rh } = getRegionInOtherTemplateSelectorBundle(enumKey as EnumParcRegVersion)
 
+        let selectedAtlas = {
+          templateSpaces: mockFetchedTemplates
+        }
         describe('> no hemisphere selected, simulates big brain cyto map', () => {
 
           let result: any[]
           beforeAll(() => {
-            result = regionInOtherTemplateSelector.projector(mockFetchedTemplates, mt0, { region: mr0 })
+            result = regionInOtherTemplateSelector.projector(selectedAtlas, mockFetchedTemplates, mt0, { region: mr0 })
           })
 
           it('> length checks out', () => {
@@ -409,7 +415,7 @@ describe('> region.base.ts', () => {
         describe('> hemisphere data selected (left hemisphere), simulates julich-brain in mni152', () => {
           let result
           beforeAll(() => {
-            result = regionInOtherTemplateSelector.projector(mockFetchedTemplates, mt2, { region: mr0lh })
+            result = regionInOtherTemplateSelector.projector(selectedAtlas, mockFetchedTemplates, mt2, { region: mr0lh })
           })
 
           it('> length checks out', () => {

diff --git a/src/ui/parcellationRegion/region.base.ts b/src/ui/parcellationRegion/region.base.ts
@@ -257,9 +257,11 @@ export class RenderViewOriginDatasetLabelPipe implements PipeTransform{
 }
 
 export const regionInOtherTemplateSelector = createSelector(
+  viewerStateGetSelectedAtlas,
   viewerStateFetchedTemplatesSelector,
   viewerStateSelectedTemplateSelector,
-  (fetchedTemplates, templateSelected, prop) => {
+  (atlas, fetchedTemplates, templateSelected, prop) => {
+    const atlasTemplateSpacesIds = atlas.templateSpaces.map(({ ['@id']: id, fullId }) => id || fullId)
     const { region: regionOfInterest } = prop
     const returnArr = []
 
@@ -268,7 +270,13 @@ export const regionInOtherTemplateSelector = createSelector(
     const regionOfInterestId = getIdFromFullId(regionOfInterest.fullId)
     if (!templateSelected) return []
     const selectedTemplateId = getIdFromFullId(templateSelected.fullId)
-    const otherTemplates = fetchedTemplates.filter(({ fullId }) => getIdFromFullId(fullId) !== selectedTemplateId)
+
+    // need to ensure that the templates are defined in atlas definition
+    // atlas is the single source of truth 
+
+    const otherTemplates = fetchedTemplates
+      .filter(({ fullId }) => getIdFromFullId(fullId) !== selectedTemplateId)
+      .filter(({ ['@id']: id, fullId }) => atlasTemplateSpacesIds.includes(id || fullId))
     for (const template of otherTemplates) {
       for (const parcellation of template.parcellations) {
         const flattenedRegions = flattenRegions(parcellation.regions)