Merge pull request #717 from HumanBrainProject/feat_julichBrainV118

feat: added JulichBrain v1.18

src/atlasViewer/atlasViewer.component.ts

@@ -123,7 +123,7 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
     map(arr => arr.map(item => {
       const overwrittenName = item['@version'] && item['@version']['name']
       return overwrittenName
-        ? { ...item, name: overwrittenName }
+        ? { ...item, displayName: overwrittenName }
         : item
     }))
   )

src/atlasViewer/atlasViewer.history.service.spec.ts

@@ -65,7 +65,7 @@ describe('atlasviewer.history.service.ts', () => {
       })
       
       const expected = cold('(a)', {
-        a: 'templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Cytoarchitectonic+Maps'
+        a: 'templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Cytoarchitectonic+Maps+-+v2.4'
       })
       
       expect(effect.currentStateSearchParam$).toBeObservable(expected)

src/atlasViewer/atlasViewer.urlUtil.spec.ts

@@ -28,7 +28,7 @@ const fetchedTemplateRootState = {
 }
 
 // TODO finish writing tests
-describe('atlasViewer.urlService.service.ts', () => {
+describe('atlasViewer.urlUtil.ts', () => {
   describe('cvtSearchParamToState', () => {
 
     it('> convert empty search param to empty state', () => {
@@ -176,9 +176,9 @@ describe('atlasViewer.urlService.service.ts', () => {
     })
   })
 
-  describe('cvtStateToSearchParam', () => {
+  describe('> cvtStateToSearchParam', () => {
 
-    it('should convert template selected', () => {
+    it('> should convert template selected', () => {
       const { viewerState } = defaultRootState
       const searchParam = cvtStateToSearchParam({
         ...defaultRootState,
@@ -191,7 +191,7 @@ describe('atlasViewer.urlService.service.ts', () => {
       const stringified = searchParam.toString()
       expect(stringified).toBe('templateSelected=Big+Brain+%28Histology%29')
     })
-    it('should convert template selected and parcellation selected', () => {
+    it('> should convert template selected and parcellation selected', () => {
   
       const { viewerState } = defaultRootState
       const searchParam = cvtStateToSearchParam({
@@ -204,7 +204,7 @@ describe('atlasViewer.urlService.service.ts', () => {
       })
   
       const stringified = searchParam.toString()
-      expect(stringified).toBe('templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Cytoarchitectonic+Maps')
+      expect(stringified).toBe('templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Cytoarchitectonic+Maps+-+v2.4')
     })
   })
 })

src/res/ext/atlas/atlas_multiLevelHuman.json

@@ -12,6 +12,10 @@
           "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
           "name": "Cytoarchitectonic maps"
         },
+        {
+          "@id": "juelich/iav/atlas/v1.0.0/8",
+          "name": "Cytoarchitectonic Maps - v1.18"
+        },
         {
           "name": "Long Bundle",
           "@id": "juelich/iav/atlas/v1.0.0/5"
@@ -50,6 +54,10 @@
         {
           "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
           "name": "Cytoarchitectonic maps"
+        },
+        {
+          "@id": "juelich/iav/atlas/v1.0.0/8",
+          "name": "Cytoarchitectonic Maps - v1.18"
         }
       ]
     },
@@ -73,14 +81,41 @@
     }
   ],
   "parcellations": [
+    {
+      "@id": "juelich/iav/atlas/v1.0.0/8",
+      "name": "Cytoarchitectonic Maps - v1.18",
+      "baseLayer": true,
+      "@version": {
+        "@next": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+        "this": "juelich/iav/atlas/v1.0.0/8",
+        "name": "v1.18",
+        "@previous": null
+      },
+      "availableIn": [
+        {
+          "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+          "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+          "originalDatasetFormats": [{
+            "name": "probability map"
+          }]
+        },
+        {
+          "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
+          "name": "MNI Colin 27",
+          "originalDatasetFormats": [{
+            "name": "probability map"
+          }]
+        }
+      ]
+    },
     {
       "@id": "juelich/iav/atlas/v1.0.0/7",
-      "name": "Cytoarchitectonic maps",
+      "name": "Cytoarchitectonic maps - v2.4",
       "baseLayer": true,
       "@version": {
         "@next": null,
         "this": "juelich/iav/atlas/v1.0.0/7",
-        "name": "v2.4",
+        "name": "current",
         "@previous": null
       },
       "availableIn": [
@@ -98,7 +133,7 @@
         "@next": null,
         "this": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
         "name": "v2.4",
-        "@previous": null
+        "@previous": "juelich/iav/atlas/v1.0.0/8"
       },
       "availableIn": [
         {

src/res/ext/bigbrain.json

@@ -17,7 +17,8 @@
     {
       "@id": "juelich/iav/atlas/v1.0.0/7",
       "fullId": "juelich/iav/atlas/v1.0.0/7",
-      "name": "Cytoarchitectonic Maps",
+      "name": "Cytoarchitectonic Maps - v2.4",
+      "displayName": "Cytoarchitectonic Maps",
       "properties": {
         "name": "Cytoarchitectonic Maps",
         "description": "This dataset contains cytoarchitectonic maps of brain regions in the BigBrain space [Amunts et al. 2013]. The mappings were created using the semi-automatic method presented in Schleicher et al. 1999, based on coronal histological sections on 1 micron resolution. Mappings are available on approximately every 100th section for each region. They were then transformed to the sections of the 3D reconstructed BigBrain space using the transformations used in Amunts et al. 2013, which were provided by Claude Lepage (McGill). Only a few cytoarchitectonic maps in the Big Brain are currently **fully mapped**, based on a workflow that automatically fills in missing sections based on expert annotations. Other 3D maps are available in a preliminary version, in which the expert annotations in the Big Brain space were simply **interpolated**."

src/res/ext/colinNehubaConfig.json

@@ -154,6 +154,68 @@
           "_": {
             "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20200926_JulichBrain-V2_4-Colin_MPM_mesh/raw/745a37f64b6995a661f5a61287b4067df01687cb/output/nehuba-ui/right_config.json"
           }
+        },
+        "jubrain colin v18 left": {
+          "type": "segmentation",
+          "visible": true,
+          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/colin27/left",
+          "transform": [
+            [
+              1,
+              0,
+              0,
+              -128500000
+            ],
+            [
+              0,
+              1,
+              0,
+              -148500000
+            ],
+            [
+              0,
+              0,
+              1,
+              -110500000
+            ],
+            [
+              0,
+              0,
+              0,
+              1
+            ]
+          ]
+        },
+        "jubrain colin v18 right": {
+          "type": "segmentation",
+          "visible": true,
+          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/colin27/right",
+          "transform": [
+            [
+              1,
+              0,
+              0,
+              -128500000
+            ],
+            [
+              0,
+              1,
+              0,
+              -148500000
+            ],
+            [
+              0,
+              0,
+              1,
+              -110500000
+            ],
+            [
+              0,
+              0,
+              0,
+              1
+            ]
+          ]
         }
       },
       "navigation": {

src/ui/nehubaContainer/splashScreen/splashScreen.component.ts

@@ -77,6 +77,9 @@ export class SplashScreen implements AfterViewInit {
      * if yes, it is interpreted as a click
      * if no, user may want to select a text
      */
+    /**
+     * TODO change to onclick listener
+     */
     this.subscriptions.push(
       fromEvent(this.parentContainer.nativeElement, 'mousedown').pipe(
         filter((ev: MouseEvent) => ev.which === 1),