bugfix: allow selection of parcellation

bugfix: nehubaconfig in dev mode
chore: filter selected Region

deploy/nehubaConfig/index.js

 const express = require('express')
 const path = require('path')
 const fs = require('fs')
+const { getTemplateNehubaConfig } = require('./query')
 
 const nehubaConfigRouter = express.Router()
 
 nehubaConfigRouter.get('/:configId', (req, res, next) => {
   const { configId } = req.params
-  const configFilePath = path.join(__dirname, '..', 'res', `${configId}.json`)
-  fs.readFile(configFilePath, 'utf-8', (error, data) => {
-    if (error) 
-      return next({
-        code: 500,
-        error,
-        trace: 'fetching config'
-      })
-    res.status(200).send(data)
-  })
+  console.log('nehubaconfigrouter')
+  getTemplateNehubaConfig(configId)
+    .then(data => res.status(200).send(data))
+    .catch(error => next({
+      code: 500,
+      error,
+      trace: 'nehubaConfigRouter#getTemplateNehubaConfig'
+    }))
 })
 
 module.exports = nehubaConfigRouter
\ No newline at end of file

deploy/nehubaConfig/query.js

+const fs = require('fs')
+const path = require('path')
+
+exports.getTemplateNehubaConfig = (configId) => new Promise((resolve, reject) => {
+  let filepath
+  if (process.env.NODE_ENV === 'production') {
+    filepath = path.join(__dirname, '..', 'res', `${configId}.json`)
+  } else {
+    filepath = path.join(__dirname, '..', '..', 'src', 'res', 'ext', `${configId}.json`)
+  }
+  fs.readFile(filepath, 'utf-8', (err, data) => {
+    if (err) return reject(err)
+    resolve(data)
+  })
+})
\ No newline at end of file

src/atlasViewer/atlasViewer.urlService.service.ts

@@ -82,6 +82,12 @@ export class AtlasViewerURLService{
       take(1),
       map(ft => ft.filter(t => t !== null))
     ).subscribe(fetchedTemplates=>{
+
+      /**
+       * TODO
+       * consider what to do when we have ill formed search params
+       * param validation?
+       */
       const searchparams = new URLSearchParams(window.location.search)
  
       /* first, check if any template and parcellations are to be loaded */
@@ -107,7 +113,7 @@ export class AtlasViewerURLService{
         )
         const urlString = window.location.href
         /**
-         * TODO think of better way of doing this
+         * TODO think of better way of doing this... maybe pushstate?
          */
         history.replaceState(null, '', urlString.split('?')[0])
         return
@@ -143,7 +149,9 @@ export class AtlasViewerURLService{
         if(selectedRegions){
           this.store.dispatch({
             type : SELECT_REGIONS,
-            selectRegions : selectedRegions.split('_').map(labelIndex=>labelIndexMap.get(Number(labelIndex)))
+            selectRegions : selectedRegions.split('_')
+              .map(labelIndex=>labelIndexMap.get(Number(labelIndex)))
+              .filter(region => !!region)
           })
         }
       }

src/res/ext/bigbrain.json

-{"name":"Big Brain (Histology)","type":"template","species":"Human","useTheme":"light","nehubaId":" grey value: ","nehubaConfigURL":"res/json/bigbrainNehubaConfig.json","parcellations":[{"name":"Grey/White matter","type":"parcellation","ngData":null,"ngId":" tissue type: ","regions":[{"name":"Grey matter","labelIndex":100,"rgb":[200,200,200],"children":[]},{"name":"White matter","labelIndex":200,"rgb":[255,255,255],"children":[]}]}],"properties":{"name":"Big Brain (Histology)","description":"An ultrahigh resolution 3D model of a complete human brain (20 micron isotropic resolution), developed in a collaborative effort between the teams of Dr. Katrin Amunts and Dr. Karl Zilles (Forschungszentrum Jülich) and Dr. Alan Evans (Montreal Neurological Institute). Based on 7404 digitized histological brain sections, this so far unique reconstruction provides unprecedented neuroanatomical insight. The dataset contains a complete gray and white matter classification with corresponding surface reconstructions","publications":[{"doi":"https://doi.org/10.1126/science.1235381","citation":"K. Amunts, A. Evans et al.: BigBrain: An Ultrahigh-Resolution 3D Human Brain Model. Science 2013"},{"doi":"http://bigbrain.loris.ca","citation":"http://bigbrain.loris.ca"}]}}
\ No newline at end of file
+{"name":"Big Brain (Histology)","type":"template","species":"Human","useTheme":"light","nehubaId":" grey value: ","nehubaConfigURL":"nehubaConfig/bigbrainNehubaConfig","parcellations":[{"name":"Grey/White matter","type":"parcellation","ngData":null,"ngId":" tissue type: ","regions":[{"name":"Grey matter","labelIndex":100,"rgb":[200,200,200],"children":[]},{"name":"White matter","labelIndex":200,"rgb":[255,255,255],"children":[]}]},{"name":"Area V1","type":"parcellation","visible":false,"ngData":true,"ngId":"v1","regions":[{"name":"V1 - Root","labelIndex":null,"children":[{"name":"V1 - Area","rgb":[255,255,0],"labelIndex":1,"children":[]}]}]}],"properties":{"name":"Big Brain (Histology)","description":"An ultrahigh resolution 3D model of a complete human brain (20 micron isotropic resolution), developed in a collaborative effort between the teams of Dr. Katrin Amunts and Dr. Karl Zilles (Forschungszentrum Jülich) and Dr. Alan Evans (Montreal Neurological Institute). Based on 7404 digitized histological brain sections, this so far unique reconstruction provides unprecedented neuroanatomical insight. The dataset contains a complete gray and white matter classification with corresponding surface reconstructions","publications":[{"doi":"https://doi.org/10.1126/science.1235381","citation":"K. Amunts, A. Evans et al.: BigBrain: An Ultrahigh-Resolution 3D Human Brain Model. Science 2013"},{"doi":"http://bigbrain.loris.ca","citation":"http://bigbrain.loris.ca"}]}}
\ No newline at end of file

src/res/ext/bigbrainNehubaConfig.json

-{"configName":"BigBrain","globals":{"hideNullImageValues":true,"useNehubaLayout":{"keepDefaultLayouts":false},"useNehubaMeshLayer":true,"rightClickWithCtrlGlobal":false,"zoomWithoutCtrlGlobal":false,"useCustomSegmentColors":true},"zoomWithoutCtrl":true,"hideNeuroglancerUI":true,"rightClickWithCtrl":true,"rotateAtViewCentre":true,"enableMeshLoadingControl":true,"zoomAtViewCentre":true,"restrictUserNavigation":true,"disableSegmentSelection":true,"dataset":{"imageBackground":[1,1,1,1],"initialNgState":{"showDefaultAnnotations":false,"layers":{" grey value: ":{"type":"image","source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/8bit","transform":[[1,0,0,-70677184],[0,1,0,-70010000],[0,0,1,-58788284],[0,0,0,1]]}," tissue type: ":{"type":"segmentation","source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/classif","segments":["0"],"selectedAlpha":0,"notSelectedAlpha":0,"transform":[[1,0,0,-70666600],[0,1,0,-72910000],[0,0,1,-58777700],[0,0,0,1]]}},"navigation":{"pose":{"position":{"voxelSize":[21166.666015625,20000,21166.666015625],"voxelCoordinates":[-21.8844051361084,16.288618087768555,28.418994903564453]}},"zoomFactor":350000},"perspectiveOrientation":[0.3140767216682434,-0.7418519854545593,0.4988985061645508,-0.3195493221282959],"perspectiveZoom":1922235.5293810747}},"layout":{"views":"hbp-neuro","planarSlicesBackground":[1,1,1,1],"useNehubaPerspective":{"enableShiftDrag":false,"doNotRestrictUserNavigation":false,"perspectiveSlicesBackground":[1,1,1,1],"removePerspectiveSlicesBackground":{"color":[1,1,1,1],"mode":"=="},"perspectiveBackground":[1,1,1,1],"fixedZoomPerspectiveSlices":{"sliceViewportWidth":300,"sliceViewportHeight":300,"sliceZoom":563818.3562426177,"sliceViewportSizeMultiplier":2},"mesh":{"backFaceColor":[1,1,1,1],"removeBasedOnNavigation":true,"flipRemovedOctant":true},"centerToOrigin":true,"drawSubstrates":{"color":[0,0,0.5,0.15]},"drawZoomLevels":{"cutOff":200000,"color":[0.5,0,0,0.15]},"hideImages":false,"waitForMesh":true,"restrictZoomLevel":{"minZoom":1200000,"maxZoom":3500000}}}}
\ No newline at end of file
+{"configName":"","globals":{"hideNullImageValues":true,"useNehubaLayout":{"keepDefaultLayouts":false},"useNehubaMeshLayer":true,"rightClickWithCtrlGlobal":false,"zoomWithoutCtrlGlobal":false,"useCustomSegmentColors":true},"zoomWithoutCtrl":true,"hideNeuroglancerUI":true,"rightClickWithCtrl":true,"rotateAtViewCentre":true,"enableMeshLoadingControl":true,"zoomAtViewCentre":true,"restrictUserNavigation":true,"disableSegmentSelection":false,"dataset":{"imageBackground":[1,1,1,1],"initialNgState":{"showDefaultAnnotations":false,"layers":{" grey value: ":{"type":"image","source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/8bit","transform":[[1,0,0,-70677184],[0,1,0,-70010000],[0,0,1,-58788284],[0,0,0,1]]}," tissue type: ":{"type":"segmentation","source":"precomputed://https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/classif","segments":["0"],"selectedAlpha":0,"notSelectedAlpha":0,"transform":[[1,0,0,-70666600],[0,1,0,-72910000],[0,0,1,-58777700],[0,0,0,1]]},"v1":{"type":"segmentation","source":"precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/BigBrainRelease.2015/2019_05_01_v1","segments":["0"],"selectedAlpha":0.45,"notSelectedAlpha":0,"transform":[[1,0,0,-70677184],[0,1,0,-69410000],[0,0,1,-58788284],[0,0,0,1]]}},"navigation":{"pose":{"position":{"voxelSize":[21166.666015625,20000,21166.666015625],"voxelCoordinates":[-21.8844051361084,16.288618087768555,28.418994903564453]}},"zoomFactor":350000},"perspectiveOrientation":[0.3140767216682434,-0.7418519854545593,0.4988985061645508,-0.3195493221282959],"perspectiveZoom":1922235.5293810747}},"layout":{"views":"hbp-neuro","planarSlicesBackground":[1,1,1,1],"useNehubaPerspective":{"enableShiftDrag":false,"doNotRestrictUserNavigation":false,"perspectiveSlicesBackground":[1,1,1,1],"removePerspectiveSlicesBackground":{"color":[1,1,1,1],"mode":"=="},"perspectiveBackground":[1,1,1,1],"fixedZoomPerspectiveSlices":{"sliceViewportWidth":300,"sliceViewportHeight":300,"sliceZoom":563818.3562426177,"sliceViewportSizeMultiplier":2},"mesh":{"backFaceColor":[1,1,1,1],"removeBasedOnNavigation":true,"flipRemovedOctant":true},"centerToOrigin":true,"drawSubstrates":{"color":[0,0,0.5,0.15]},"drawZoomLevels":{"cutOff":200000,"color":[0.5,0,0,0.15]},"hideImages":false,"waitForMesh":true,"restrictZoomLevel":{"minZoom":1200000,"maxZoom":3500000}}}}
\ No newline at end of file

src/ui/signinBanner/signinBanner.components.ts

@@ -4,7 +4,7 @@ import { AuthService, User } from "src/services/auth.service";
 import { Store, select } from "@ngrx/store";
 import { ViewerConfiguration } from "src/services/state/viewerConfig.store";
 import { Subscription, Observable } from "rxjs";
-import { safeFilter, isDefined, NEWVIEWER, SELECT_REGIONS } from "src/services/stateStore.service";
+import { safeFilter, isDefined, NEWVIEWER, SELECT_REGIONS, SELECT_PARCELLATION } from "src/services/stateStore.service";
 import { map, filter, distinctUntilChanged } from "rxjs/operators";
 import { regionFlattener } from "src/util/regionFlattener";
 
@@ -84,7 +84,14 @@ export class SigninBanner implements OnInit, OnDestroy{
   }
 
   changeParcellation({ current, previous }){
-
+    const { ngId: prevNgId} = previous
+    const { ngId: currNgId} = current
+    if (prevNgId === currNgId)
+      return
+    this.store.dispatch({
+      type: SELECT_PARCELLATION,
+      selectParcellation: current
+    })
   }
 
   handleRegionClick({ mode = 'single', region }){