diff --git a/deploy/nehubaConfig/index.js b/deploy/nehubaConfig/index.js
index 9b000cbb9003e4d37e7bc82c7f3eff22199e9f66..1ae4c77b9b2107eb570a731b6bef29cd2ba06711 100644
--- a/deploy/nehubaConfig/index.js
+++ b/deploy/nehubaConfig/index.js
@@ -1,21 +1,20 @@
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', `${configId}.json`)
- fs.readFile(configFilePath, 'utf-8', (error, data) => {
- if (error)
- return next({
- code: 500,
- error,
- trace: 'fetching config'
- })
- res.status(200).send(data)
- })
+ console.log('nehubaconfigrouter')
+ getTemplateNehubaConfig(configId)
+ .then(data => res.status(200).send(data))
+ .catch(error => next({
+ code: 500,
+ error,
+ trace: 'nehubaConfigRouter#getTemplateNehubaConfig'
+ }))
})
module.exports = nehubaConfigRouter
\ No newline at end of file
diff --git a/deploy/nehubaConfig/query.js b/deploy/nehubaConfig/query.js
new file mode 100644
index 0000000000000000000000000000000000000000..972c3d59633cd3748d3678a636f8bcecdf7ed0d9
--- /dev/null
+++ b/deploy/nehubaConfig/query.js
@@ -0,0 +1,15 @@
+const fs = require('fs')
+const path = require('path')
+
+exports.getTemplateNehubaConfig = (configId) => new Promise((resolve, reject) => {
+ let filepath
+ if (process.env.NODE_ENV === 'production') {
+ filepath = path.join(__dirname, '..', 'res', `${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
diff --git a/src/atlasViewer/atlasViewer.urlService.service.ts b/src/atlasViewer/atlasViewer.urlService.service.ts
index c707eb3c7a63a345ec5ab435d262e2278201503f..225cf6af97a909b8bb693c34abd3f9e0322c180f 100644
--- a/src/atlasViewer/atlasViewer.urlService.service.ts
+++ b/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)
})
}
}
diff --git a/src/res/ext/bigbrain.json b/src/res/ext/bigbrain.json
index 98a8fa262adcfac87b78f8363ce05a793bc236d4..8e85d5eb3d16b045008fe5fbbe2abddf063e44c0 100644
--- a/src/res/ext/bigbrain.json
+++ b/src/res/ext/bigbrain.json
@@ -1 +1 @@
-{"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
diff --git a/src/res/ext/bigbrainNehubaConfig.json b/src/res/ext/bigbrainNehubaConfig.json
index bb88d61ad3751766fa6c0723eb7aae6bbdcb4c97..9309e0c78b79d1e3cbd3ba3598f15b7796a1ee85 100644
--- a/src/res/ext/bigbrainNehubaConfig.json
+++ b/src/res/ext/bigbrainNehubaConfig.json
@@ -1 +1 @@
-{"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
diff --git a/src/ui/signinBanner/signinBanner.components.ts b/src/ui/signinBanner/signinBanner.components.ts
index d155395cb5bddb9763eb516e48919ae648f033a2..ac2005a420b308164eab1d230a892cbc12e4152b 100644
--- a/src/ui/signinBanner/signinBanner.components.ts
+++ b/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 }){