Merge pull request #217 from HumanBrainProject/staging

hotfixes

deploy/datasets/query.js

@@ -64,11 +64,6 @@ const getPublicDs = () => Promise.race([
   fetchDatasetFromKg().then(cacheData)
 ])
 
-
-const getDs = ({ user }) => user
-  ? fetchDatasetFromKg({ user }).then(({results}) => results)
-  : getPublicDs()
-
 /**
  * Needed by filter by parcellation
  */
@@ -94,31 +89,54 @@ const readConfigFile = (filename) => new Promise((resolve, reject) => {
   })
 })
 
-let juBrain = null
-let shortBundle = null
-let longBundle = null
-let waxholm = null
-let allen = null
+const parcellationNameToFlattenedRegion = new Map()
+
+const appendMap = (parcellation) => {
+  const { name, regions } = parcellation
+  parcellationNameToFlattenedRegion.set(name, flattenArray(regions))
+}
+
+readConfigFile('bigbrain.json')
+  .then(data => JSON.parse(data))
+  .then(json => {
+    const p = json.parcellations.find(p => p.name === 'Cytoarchitectonic Maps')
+    if (p) {
+      appendMap(p)
+    }
+  })
+  .catch(console.error)
 
 readConfigFile('colin.json')
   .then(data => JSON.parse(data))
   .then(json => {
-    juBrain = flattenArray(json.parcellations[0].regions)
+    const p = json.parcellations.find(p => p.name === 'JuBrain Cytoarchitectonic Atlas')
+    if (p) {
+      appendMap(p)
+    }
   })
   .catch(console.error)
 
 readConfigFile('MNI152.json')
   .then(data => JSON.parse(data))
   .then(json => {
-    longBundle = flattenArray(json.parcellations[0].regions)
-    shortBundle = flattenArray(json.parcellations[1].regions)
+    const p1 = json.parcellations.find(p => p.name === 'fibre bundle long')
+    if (p1) {
+      appendMap(p1)
+    }
+    const p2 = json.parcellations.find(p => p.name === 'fibre bundle short')
+    if (p2) {
+      appendMap(p2)
+    }
   })
   .catch(console.error)
 
 readConfigFile('waxholmRatV2_0.json')
   .then(data => JSON.parse(data))
   .then(json => {
-    waxholm = flattenArray(json.parcellations[0].regions)
+    const p = json.parcellations.find(p => p.name === 'Waxholm Space rat brain atlas v.2.0')
+    if (p) {
+      appendMap(p)
+    }
   })
   .catch(console.error)
 
@@ -135,7 +153,7 @@ const filterByPRs = (prs, atlasPr) => atlasPr
 const manualFilter = require('./supplements/parcellation')
 
 
-const filter = (datasets = [], {templateName, parcellationName}) => datasets
+const filterDataset = (datasets = [], {templateName, parcellationName}) => datasets
   .filter(ds => commonSenseDsFilter({ds, templateName, parcellationName }))
   .filter(ds => {
     if (/infant/.test(ds.name))
@@ -147,18 +165,14 @@ const filter = (datasets = [], {templateName, parcellationName}) => datasets
       if (parcellationName === 'Fibre Bundle Atlas - Long Bundle'){
         return manualFilterDWM(ds)
       }
-      return ds.parcellationRegion.length > 0
-        ? filterByPRs(
-            ds.parcellationRegion, 
-            parcellationName === 'JuBrain Cytoarchitectonic Atlas' && juBrain
-              ? juBrain
-              : parcellationName === 'Fibre Bundle Atlas - Short Bundle' && shortBundle
-                ? shortBundle
-                : parcellationName === 'Waxholm Space rat brain atlas v.2.0'
-                  ? waxholm
-                  : null
-          )
-        : false
+      if (ds.parcellationRegion.length > 0) {
+        const flattenedRegions = parcellationNameToFlattenedRegion.get(parcellationName)
+        if (flattenedRegions) {
+          return filterByPRs(ds.parcellationRegion, flattenedRegions)
+        }
+      } else {
+        return false
+      }
     }
 
     return false
@@ -186,8 +200,10 @@ exports.init = async () => {
   cachedData = results
 }
 
-exports.getDatasets = ({ templateName, parcellationName, user }) => getDs({ user })
-    .then(json => filter(json, {templateName, parcellationName}))
+exports.getDatasets = ({ templateName, parcellationName, user }) => (user
+  ? fetchDatasetFromKg({ user }).then(({results}) => results)
+  : getPublicDs())
+    .then(json => filterDataset(json, {templateName, parcellationName}))
 
 exports.getPreview = ({ datasetName, templateSelected }) => getPreviewFile({ datasetName, templateSelected })
 

deploy/datasets/supplements/commonSense.js

@@ -11,7 +11,8 @@ const humanParcellationSet = new Set([
   'Area V2',
   'JuBrain Cytoarchitectonic Atlas',
   'Fibre Bundle Atlas - Short Bundle',
-  'Fibre Bundle Atlas - Long Bundle'
+  'Fibre Bundle Atlas - Long Bundle',
+  'Cytoarchitectonic Maps'
 ])
 
 const ratTemplateSet = new Set([

deploy/plugins/index.js

@@ -5,15 +5,14 @@
 
 const express = require('express')
 const router = express.Router()
-const PLUGIN_URLS = process.env.PLUGIN_URLS && JSON.stringify(process.env.PLUGIN_URLS.split(';'))
+const PLUGIN_URLS = (process.env.PLUGIN_URLS && process.env.PLUGIN_URLS.split(';')) || []
+const STAGING_PLUGIN_URLS = (process.env.STAGING_PLUGIN_URLS && process.env.STAGING_PLUGIN_URLS.split(';')) || []
 
 router.get('', (_req, res) => {
-
-  if (PLUGIN_URLS) {
-    return res.status(200).send(PLUGIN_URLS)
-  } else {
-    return res.status(200).send('[]')
-  }
+  return res.status(200).json([
+    ...PLUGIN_URLS,
+    ...STAGING_PLUGIN_URLS
+  ])
 })
 
 module.exports = router
\ No newline at end of file

src/res/ext/MNI152NehubaConfig.json

-{"globals":{"hideNullImageValues":true,"useNehubaLayout":true,"useNehubaMeshLayer":true,"useCustomSegmentColors":true},"zoomWithoutCtrl":true,"hideNeuroglancerUI":true,"rightClickWithCtrl":true,"rotateAtViewCentre":true,"zoomAtViewCentre":true,"enableMeshLoadingControl":true,"layout":{"useNehubaPerspective":{"fixedZoomPerspectiveSlices":{"sliceViewportWidth":300,"sliceViewportHeight":300,"sliceZoom":724698.1843689409,"sliceViewportSizeMultiplier":2},"centerToOrigin":true,"mesh":{"removeBasedOnNavigation":true,"flipRemovedOctant":true,"surfaceParcellation":false},"removePerspectiveSlicesBackground":{"mode":"<","color":[0.1,0.1,0.1,1]},"waitForMesh":false,"drawSubstrates":{"color":[0.5,0.5,1,0.2]},"drawZoomLevels":{"cutOff":150000},"restrictZoomLevel":{"minZoom":2500000,"maxZoom":3500000}}},"dataset":{"imageBackground":[0,0,0,1],"initialNgState":{"showDefaultAnnotations":false,"layers":{"mni152":{"type":"image","visible":true,"source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/Fiber_Bundle/mni_icbm152_t1_tal_nlin_asym_09c_masked","transform":[[1,0,0,-96500000],[0,1,0,-132500000],[0,0,1,-78500000],[0,0,0,1]]},"jubrain v17 left":{"type":"segmentation","visible":true,"source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/17/icbm152casym/left","transform":[[1,0,0,-96500000],[0,1,0,-132500000],[0,0,1,-78500000],[0,0,0,1]]},"jubrain v17 right":{"type":"segmentation","visible":true,"source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/17/icbm152casym/right","transform":[[1,0,0,-96500000],[0,1,0,-132500000],[0,0,1,-78500000],[0,0,0,1]]},"fibre bundle long":{"type":"segmentation","source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/Fiber_Bundle/long-bundles_maxprob","transform":[[1,0,0,-96500000],[0,1,0,-132500000],[0,0,1,-78500000],[0,0,0,1]]},"fibre bundle short":{"visible":false,"type":"segmentation","source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/Fiber_Bundle/short-bundles_maxprob","transform":[[1,0,0,-96500000],[0,1,0,-132500000],[0,0,1,-78500000],[0,0,0,1]]}},"navigation":{"pose":{"position":{"voxelSize":[1000000,1000000,1000000],"voxelCoordinates":[0,-32,0]}},"zoomFactor":450000},"perspectiveOrientation":[-0.2753947079181671,0.6631333827972412,-0.6360703706741333,0.2825356423854828],"perspectiveZoom":3000000}}}
\ No newline at end of file
+{
+  "globals": {
+    "hideNullImageValues": true,
+    "useNehubaLayout": true,
+    "useNehubaMeshLayer": true,
+    "useCustomSegmentColors": true
+  },
+  "zoomWithoutCtrl": true,
+  "hideNeuroglancerUI": true,
+  "rightClickWithCtrl": true,
+  "rotateAtViewCentre": true,
+  "zoomAtViewCentre": true,
+  "enableMeshLoadingControl": true,
+  "layout": {
+    "useNehubaPerspective": {
+      "fixedZoomPerspectiveSlices": {
+        "sliceViewportWidth": 300,
+        "sliceViewportHeight": 300,
+        "sliceZoom": 724698.1843689409,
+        "sliceViewportSizeMultiplier": 2
+      },
+      "centerToOrigin": true,
+      "mesh": {
+        "removeBasedOnNavigation": true,
+        "flipRemovedOctant": true,
+        "surfaceParcellation": false
+      },
+      "removePerspectiveSlicesBackground": {
+        "mode": "<",
+        "color": [
+          0.1,
+          0.1,
+          0.1,
+          1
+        ]
+      },
+      "waitForMesh": false,
+      "drawSubstrates": {
+        "color": [
+          0.5,
+          0.5,
+          1,
+          0.2
+        ]
+      },
+      "drawZoomLevels": {
+        "cutOff": 150000
+      },
+      "restrictZoomLevel": {
+        "minZoom": 2500000,
+        "maxZoom": 3500000
+      }
+    }
+  },
+  "dataset": {
+    "imageBackground": [
+      0,
+      0,
+      0,
+      1
+    ],
+    "initialNgState": {
+      "showDefaultAnnotations": false,
+      "layers": {
+        "mni152": {
+          "type": "image",
+          "visible": true,
+          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/Fiber_Bundle/mni_icbm152_t1_tal_nlin_asym_09c_masked",
+          "transform": [
+            [
+              1,
+              0,
+              0,
+              -96500000
+            ],
+            [
+              0,
+              1,
+              0,
+              -132500000
+            ],
+            [
+              0,
+              0,
+              1,
+              -78500000
+            ],
+            [
+              0,
+              0,
+              0,
+              1
+            ]
+          ]
+        },
+        "jubrain mni152 v18 left": {
+          "type": "segmentation",
+          "visible": true,
+          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/icbm152casym/left",
+          "transform": [
+            [
+              1,
+              0,
+              0,
+              -96500000
+            ],
+            [
+              0,
+              1,
+              0,
+              -132500000
+            ],
+            [
+              0,
+              0,
+              1,
+              -78500000
+            ],
+            [
+              0,
+              0,
+              0,
+              1
+            ]
+          ]
+        },
+        "jubrain mni152 v18 right": {
+          "type": "segmentation",
+          "visible": true,
+          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/icbm152casym/right",
+          "transform": [
+            [
+              1,
+              0,
+              0,
+              -96500000
+            ],
+            [
+              0,
+              1,
+              0,
+              -132500000
+            ],
+            [
+              0,
+              0,
+              1,
+              -78500000
+            ],
+            [
+              0,
+              0,
+              0,
+              1
+            ]
+          ]
+        },
+        "fibre bundle long": {
+          "type": "segmentation",
+          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/Fiber_Bundle/long-bundles_maxprob",
+          "transform": [
+            [
+              1,
+              0,
+              0,
+              -96500000
+            ],
+            [
+              0,
+              1,
+              0,
+              -132500000
+            ],
+            [
+              0,
+              0,
+              1,
+              -78500000
+            ],
+            [
+              0,
+              0,
+              0,
+              1
+            ]
+          ]
+        },
+        "fibre bundle short": {
+          "visible": false,
+          "type": "segmentation",
+          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/Fiber_Bundle/short-bundles_maxprob",
+          "transform": [
+            [
+              1,
+              0,
+              0,
+              -96500000
+            ],
+            [
+              0,
+              1,
+              0,
+              -132500000
+            ],
+            [
+              0,
+              0,
+              1,
+              -78500000
+            ],
+            [
+              0,
+              0,
+              0,
+              1
+            ]
+          ]
+        }
+      },
+      "navigation": {
+        "pose": {
+          "position": {
+            "voxelSize": [
+              1000000,
+              1000000,
+              1000000
+            ],
+            "voxelCoordinates": [
+              0,
+              -32,
+              0
+            ]
+          }
+        },
+        "zoomFactor": 450000
+      },
+      "perspectiveOrientation": [
+        -0.2753947079181671,
+        0.6631333827972412,
+        -0.6360703706741333,
+        0.2825356423854828
+      ],
+      "perspectiveZoom": 3000000
+    }
+  }
+}
\ No newline at end of file

src/res/ext/colinNehubaConfig.json

-{"globals":{"hideNullImageValues":true,"useNehubaLayout":true,"useNehubaMeshLayer":true,"useCustomSegmentColors":true},"zoomWithoutCtrl":true,"hideNeuroglancerUI":true,"rightClickWithCtrl":true,"rotateAtViewCentre":true,"zoomAtViewCentre":true,"enableMeshLoadingControl":true,"layout":{"useNehubaPerspective":{"fixedZoomPerspectiveSlices":{"sliceViewportWidth":300,"sliceViewportHeight":300,"sliceZoom":724698.1843689409,"sliceViewportSizeMultiplier":2},"centerToOrigin":true,"mesh":{"removeBasedOnNavigation":true,"flipRemovedOctant":true,"surfaceParcellation":false},"removePerspectiveSlicesBackground":{"mode":"=="},"waitForMesh":false,"drawSubstrates":{"color":[0.5,0.5,1,0.2]},"drawZoomLevels":{"cutOff":150000},"restrictZoomLevel":{"minZoom":2500000,"maxZoom":3500000}}},"dataset":{"imageBackground":[0,0,0,1],"initialNgState":{"showDefaultAnnotations":false,"layers":{"colin":{"type":"image","visible":true,"source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/v2.2c/colin27_seg","transform":[[1,0,0,-75500000],[0,1,0,-111500000],[0,0,1,-67500000],[0,0,0,1]]},"jubrain v2_2c":{"type":"segmentation","source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/v2.2c/MPM","transform":[[1,0,0,-75500000],[0,1,0,-111500000],[0,0,1,-67500000],[0,0,0,1]]},"jubrain colin v17 left":{"type":"segmentation","visible":true,"source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/17/colin27/left","transform":[[1,0,0,-128500000],[0,1,0,-148500000],[0,0,1,-110500000],[0,0,0,1]]},"jubrain colin v17 right":{"type":"segmentation","visible":true,"source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/17/colin27/right","transform":[[1,0,0,-128500000],[0,1,0,-148500000],[0,0,1,-110500000],[0,0,0,1]]}},"navigation":{"pose":{"position":{"voxelSize":[1000000,1000000,1000000],"voxelCoordinates":[0,-32,0]}},"zoomFactor":1000000},"perspectiveOrientation":[-0.2753947079181671,0.6631333827972412,-0.6360703706741333,0.2825356423854828],"perspectiveZoom":3000000}}}
\ No newline at end of file
+{
+  "globals": {
+    "hideNullImageValues": true,
+    "useNehubaLayout": true,
+    "useNehubaMeshLayer": true,
+    "useCustomSegmentColors": true
+  },
+  "zoomWithoutCtrl": true,
+  "hideNeuroglancerUI": true,
+  "rightClickWithCtrl": true,
+  "rotateAtViewCentre": true,
+  "zoomAtViewCentre": true,
+  "enableMeshLoadingControl": true,
+  "layout": {
+    "useNehubaPerspective": {
+      "fixedZoomPerspectiveSlices": {
+        "sliceViewportWidth": 300,
+        "sliceViewportHeight": 300,
+        "sliceZoom": 724698.1843689409,
+        "sliceViewportSizeMultiplier": 2
+      },
+      "centerToOrigin": true,
+      "mesh": {
+        "removeBasedOnNavigation": true,
+        "flipRemovedOctant": true,
+        "surfaceParcellation": false
+      },
+      "removePerspectiveSlicesBackground": {
+        "mode": "=="
+      },
+      "waitForMesh": false,
+      "drawSubstrates": {
+        "color": [
+          0.5,
+          0.5,
+          1,
+          0.2
+        ]
+      },
+      "drawZoomLevels": {
+        "cutOff": 150000
+      },
+      "restrictZoomLevel": {
+        "minZoom": 2500000,
+        "maxZoom": 3500000
+      }
+    }
+  },
+  "dataset": {
+    "imageBackground": [
+      0,
+      0,
+      0,
+      1
+    ],
+    "initialNgState": {
+      "showDefaultAnnotations": false,
+      "layers": {
+        "colin": {
+          "type": "image",
+          "visible": true,
+          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/v2.2c/colin27_seg",
+          "transform": [
+            [
+              1,
+              0,
+              0,
+              -75500000
+            ],
+            [
+              0,
+              1,
+              0,
+              -111500000
+            ],
+            [
+              0,
+              0,
+              1,
+              -67500000
+            ],
+            [
+              0,
+              0,
+              0,
+              1
+            ]
+          ]
+        },
+        "jubrain v2_2c": {
+          "type": "segmentation",
+          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/v2.2c/MPM",
+          "transform": [
+            [
+              1,
+              0,
+              0,
+              -75500000
+            ],
+            [
+              0,
+              1,
+              0,
+              -111500000
+            ],
+            [
+              0,
+              0,
+              1,
+              -67500000
+            ],
+            [
+              0,
+              0,
+              0,
+              1
+            ]
+          ]
+        },
+        "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": {
+        "pose": {
+          "position": {
+            "voxelSize": [
+              1000000,
+              1000000,
+              1000000
+            ],
+            "voxelCoordinates": [
+              0,
+              -32,
+              0
+            ]
+          }
+        },
+        "zoomFactor": 1000000
+      },
+      "perspectiveOrientation": [
+        -0.2753947079181671,
+        0.6631333827972412,
+        -0.6360703706741333,
+        0.2825356423854828
+      ],
+      "perspectiveZoom": 3000000
+    }
+  }
+}
\ No newline at end of file

src/services/effect/effect.ts

 import { Injectable, OnDestroy } from "@angular/core";
 import { Effect, Actions, ofType } from "@ngrx/effects";
-import { Observable, Subscription, merge, fromEvent, combineLatest } from "rxjs";
-import { SHOW_KG_TOS } from "../state/uiState.store";
-import { withLatestFrom, map, tap, switchMap, filter } from "rxjs/operators";
+import { Subscription, merge, fromEvent, combineLatest } from "rxjs";
+import { withLatestFrom, map, filter } from "rxjs/operators";
 import { Store, select } from "@ngrx/store";
 import { SELECT_PARCELLATION, SELECT_REGIONS, NEWVIEWER, UPDATE_PARCELLATION, SELECT_REGIONS_WITH_ID } from "../state/viewerState.store";
 import { worker } from 'src/atlasViewer/atlasViewer.workerService.service'
@@ -62,9 +61,12 @@ export class UseEffects implements OnDestroy{
    * older versions of atlas viewer may only have labelIndex as region identifier
    */
   @Effect()
-  onSelectRegionWithId = this.actions$.pipe(
-    ofType(SELECT_REGIONS_WITH_ID),
-    withLatestFrom(this.updatedParcellation$),
+  onSelectRegionWithId = combineLatest(
+    this.actions$.pipe(
+      ofType(SELECT_REGIONS_WITH_ID)
+    ),
+    this.updatedParcellation$
+  ).pipe(
     map(([action, parcellation]) => {
       const { selectRegionIds } = action
       const { ngId: defaultNgId } = parcellation