diff --git a/src/atlasViewer/atlasViewer.component.ts b/src/atlasViewer/atlasViewer.component.ts
index c897c231df9f6256bee9abed0629ea797da7d1f2..4bbf3551b57b593832bf7ecb3960948f0b78052b 100644
--- a/src/atlasViewer/atlasViewer.component.ts
+++ b/src/atlasViewer/atlasViewer.component.ts
@@ -64,6 +64,9 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
private subscriptions: Subscription[] = []
/* handlers for nglayer */
+ /**
+ * TODO make untangle nglayernames and its dependency on ng
+ */
public ngLayerNames$ : Observable<any>
public ngLayers : NgLayerInterface[]
private disposeHandler : any
diff --git a/src/atlasViewer/atlasViewer.dataService.service.ts b/src/atlasViewer/atlasViewer.dataService.service.ts
index 7dad5e9b1113ce2c159952ea8de6b2c30e045f02..a152b1647c0b24bd65e07228db1798dfec87b7dc 100644
--- a/src/atlasViewer/atlasViewer.dataService.service.ts
+++ b/src/atlasViewer/atlasViewer.dataService.service.ts
@@ -80,10 +80,8 @@ export class AtlasViewerDataService implements OnDestroy{
templateSpace == 'Waxholm Rat V2.0' ?
'datapath:metadata/OSLO_sp_data_rev.json' :
null
-
- if(filterTemplateSpace){
- url.searchParams.append('fq',filterTemplateSpace)
- }else if (templateSpace === 'MNI 152 ICBM 2009c Nonlinear Asymmetric'){
+
+ if (templateSpace === 'MNI 152 ICBM 2009c Nonlinear Asymmetric'){
return Promise.all([
fetch('res/json/***REMOVED***.json').then(res=>res.json()),
fetch('res/json/***REMOVED***.json').then(res=>res.json())
@@ -115,6 +113,20 @@ export class AtlasViewerDataService implements OnDestroy{
})
})
.catch(console.error)
+ }else if (templateSpace === 'Waxholm Rat V2.0'){
+ return fetch('res/json/camillaWaxholmPointsAggregatedData.json')
+ .then(res => res.json())
+ .then(arr => {
+ this.store.dispatch({
+ type : FETCHED_SPATIAL_DATA,
+ fetchedDataEntries : arr.map(item => Object.assign({}, item, { properties : {} }))
+ })
+ this.store.dispatch({
+ type : UPDATE_SPATIAL_DATA,
+ totalResults : arr.length
+ })
+ })
+ .catch(console.error)
}else{
return
}
diff --git a/src/res/ext/camillaWaxholmPointsAggregatedData.json b/src/res/ext/camillaWaxholmPointsAggregatedData.json
new file mode 100644
index 0000000000000000000000000000000000000000..0e33aa15b19d357ead67bf38e0dea3e107d19c24
--- /dev/null
+++ b/src/res/ext/camillaWaxholmPointsAggregatedData.json
@@ -0,0 +1,478 @@
+[
+ {
+ "name": "Channel 1",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -1.7382810000000006,
+ 5.371094500000002,
+ 5.566406499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 1",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 2",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -1.8164060000000006,
+ 2.4804695000000017,
+ 6.191406499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 2",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 3",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 1.8164064999999994,
+ 5.410157000000002,
+ 5.566406499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 3",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 4",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 1.5429689999999994,
+ 2.5585945000000017,
+ 6.347656499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 4",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 5",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -4.746093500000001,
+ -0.33203049999999834,
+ 6.113281499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 5",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 6",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -1.8554685000000006,
+ -0.25390549999999834,
+ 6.855468999999999
+ ],
+ "properties": {
+ "description": "Description of Channel 6",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 7",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 1.4257814999999994,
+ -0.17578049999999834,
+ 7.011718999999999
+ ],
+ "properties": {
+ "description": "Description of Channel 7",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 8",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 4.433593999999999,
+ -0.17578049999999834,
+ 6.269531499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 8",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 9",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -4.941406000000001,
+ -3.1054679999999983,
+ 6.621093999999999
+ ],
+ "properties": {
+ "description": "Description of Channel 9",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 10",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -2.0507810000000006,
+ -2.9882804999999983,
+ 7.128906499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 10",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 11",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 1.5039064999999994,
+ -2.9492179999999983,
+ 7.324218999999999
+ ],
+ "properties": {
+ "description": "Description of Channel 11",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 12",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 4.355468999999999,
+ -2.9101554999999983,
+ 6.894531499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 12",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 13",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -5.058593500000001,
+ -6.152342999999998,
+ 6.464843999999999
+ ],
+ "properties": {
+ "description": "Description of Channel 13",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 14",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -1.9335935000000006,
+ -5.996092999999998,
+ 7.441406499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 14",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 15",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 1.3867189999999994,
+ -5.957030499999998,
+ 7.480468999999999
+ ],
+ "properties": {
+ "description": "Description of Channel 15",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Channel 16",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 4.550781499999999,
+ -5.957030499999998,
+ 6.894531499999999
+ ],
+ "properties": {
+ "description": "Description of Channel 16",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "Ground",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -0.05859350000000063,
+ -9.550780499999998,
+ 7.089843999999999
+ ],
+ "properties": {
+ "description": "Description of Ground",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "hbp-00941_ERP_j10_hippo-histo",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 2.0976564999999994,
+ -2.5273429999999983,
+ 3.5234377499999994
+ ],
+ "properties": {
+ "description": "Description of hbp-00941_ERP_j10_hippo-histo",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "hbp-00941_ERP_j10_histo-M2_nr1",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -1.0781247500000006,
+ 4.984375750000002,
+ 4.996093999999999
+ ],
+ "properties": {
+ "description": "Description of hbp-00941_ERP_j10_histo-M2_nr1",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "hbp-00941_ERP_j10_histo-M2_nr2",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -1.4804685000000006,
+ 4.957032000000002,
+ 5.007812749999999
+ ],
+ "properties": {
+ "description": "Description of hbp-00941_ERP_j10_histo-M2_nr2",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "hbp-00941_ERP_j11_hippo-histo",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ 2.9921877499999994,
+ -2.9257804999999983,
+ 4.039062749999999
+ ],
+ "properties": {
+ "description": "Description of hbp-00941_ERP_j11_hippo-histo",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "hbp-00941_ERP_j11_histo-M2_nr1",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -1.3242185000000006,
+ 4.507813250000002,
+ 5.148437749999999
+ ],
+ "properties": {
+ "description": "Description of hbp-00941_ERP_j11_histo-M2_nr1",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "hbp-00941_ERP_j11_histo-M2_nr2",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -1.6445310000000006,
+ 4.523438250000002,
+ 5.187500249999999
+ ],
+ "properties": {
+ "description": "Description of hbp-00941_ERP_j11_histo-M2_nr2",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "S1BFsurface",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -5.378906000000001,
+ -2.3906242499999983,
+ 6.375000249999999
+ ],
+ "properties": {
+ "description": "Description of S1BFsurface",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "dorsal HPC CA1 surface",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -2.5898435000000006,
+ -2.5820304999999983,
+ 7.027343999999999
+ ],
+ "properties": {
+ "description": "Description of dorsal HPC CA1 surface",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "V1Msurface",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -3.4843747500000006,
+ -5.167967999999998,
+ 7.160156499999999
+ ],
+ "properties": {
+ "description": "Description of V1Msurface",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "PHR surface",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -5.480468500000001,
+ -4.261717999999998,
+ 6.480468999999999
+ ],
+ "properties": {
+ "description": "Description of PHR surface",
+ "publications": []
+ }
+ }
+ },
+ {
+ "name": "PHRborder",
+ "templateSpace": "Waxholm Rat V2.0",
+ "geometry": {
+ "type": "point",
+ "space": "real",
+ "position": [
+ -6.980468500000001,
+ -5.613280499999998,
+ 1.6289064999999994
+ ],
+ "properties": {
+ "description": "Description of PHRborder",
+ "publications": []
+ }
+ }
+ }
+]
\ No newline at end of file
diff --git a/src/ui/layerbrowser/layerbrowser.component.ts b/src/ui/layerbrowser/layerbrowser.component.ts
index b144220b66e0ce2e5727436fd85244732540e8dd..5de054dc184ff7b15058974344c54513e4105183 100644
--- a/src/ui/layerbrowser/layerbrowser.component.ts
+++ b/src/ui/layerbrowser/layerbrowser.component.ts
@@ -13,6 +13,9 @@ import { filter, distinctUntilChanged, map, delay } from "rxjs/operators";
export class LayerBrowser implements OnDestroy{
+ /**
+ * TODO make untangle nglayernames and its dependency on ng
+ */
ngLayers : NgLayerInterface[] = []
lockedLayers : string[] = []
diff --git a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
index d9218a9458fcd19e1e506aa643aa2519a1edc326..c2506a5511be0c22d0a84d44df972e67d1f9e56d 100644
--- a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
+++ b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
@@ -28,8 +28,13 @@ export class NehubaViewerUnit implements OnDestroy{
initNiftiLayers : any[] = []
config : any
-
nehubaViewer : any
+ private _dim: [number, number, number]
+ get dim(){
+ return this._dim
+ ? this._dim
+ : [1.5e9, 1.5e9, 1.5e9]
+ }
_s1$ : any
_s2$ : any
@@ -75,6 +80,19 @@ export class NehubaViewerUnit implements OnDestroy{
this.constantService.loadExportNehubaPromise
.then(() => {
+ const layers = this.config.dataset.initialNgState.layers
+ const key = Object.keys(layers)[0]
+ const regex = /http.*$/.exec(layers[key].source)
+ if(regex[0]){
+ fetch(`${regex[0]}/info`)
+ .then(res => res.json())
+ .then(json => {
+ const {resolution, size} = json.scales[0]
+ this._dim = resolution.map((v, idx) => v * size[idx])
+ })
+ .catch(e => this.errorEmitter.emit(e))
+ }
+
this.patchNG()
this.loadNehuba()
})
@@ -456,6 +474,7 @@ export class NehubaViewerUnit implements OnDestroy{
return
this.workerService.worker.postMessage({
type : 'GET_USERLANDMARKS_VTK',
+ scale: Math.min(...this.dim.map(v => v * 2e-9)),
landmarks : landmarks.map(lm => lm.position.map(coord => coord * 1e6))
})
}
@@ -477,6 +496,7 @@ export class NehubaViewerUnit implements OnDestroy{
this.workerService.worker.postMessage({
type : 'GET_LANDMARKS_VTK',
template : this.templateId,
+ scale: Math.min(...this.dim.map(v => v * 1.4e-8)),
landmarks : geometries.map(geometry =>
geometry === null
? null
diff --git a/src/util/worker.js b/src/util/worker.js
index 8fd3f883eb71f7dff0a443fc675b50e4d1b2d02c..0ab35834b383d53c420d55cd85ecbb24b2c8483d 100644
--- a/src/util/worker.js
+++ b/src/util/worker.js
@@ -108,7 +108,7 @@ const getMeshPoly = (polyIndices, currentIdx) => polyIndices.map(triplet =>
const encoder = new TextEncoder()
-const parseLmToVtk = (landmarks) => {
+const parseLmToVtk = (landmarks, scale) => {
const reduce = landmarks.reduce((acc,curr,idx) => {
//curr : null | [number,number,number] | [ [number,number,number], [number,number,number], [number,number,number] ][]
@@ -117,7 +117,7 @@ const parseLmToVtk = (landmarks) => {
if(!isNaN(curr[0]))
return {
currentVertexIndex : acc.currentVertexIndex + 12,
- vertexString : acc.vertexString.concat(getIcoVertex(curr, 2.8)),
+ vertexString : acc.vertexString.concat(getIcoVertex(curr, scale)),
polyCount : acc.polyCount + 20,
polyString : acc.polyString.concat(getIcoPoly(acc.currentVertexIndex)),
labelString : acc.labelString.concat(Array(12).fill(idx.toString()).join('\n'))
@@ -171,8 +171,11 @@ const getLandmarksVtk = (action) => {
// landmarks are array of triples in nm (array of array of numbers)
const landmarks = action.landmarks
const template = action.template
+ const scale = action.scale
+ ? action.scale
+ : 2.8
- const vtk = parseLmToVtk(landmarks)
+ const vtk = parseLmToVtk(landmarks, scale)
if(!vtk)
return
@@ -193,7 +196,10 @@ let userLandmarkVtkUrl
const getuserLandmarksVtk = (action) => {
const landmarks = action.landmarks
- const vtk = parseLmToVtk(landmarks)
+ const scale = action.scale
+ ? action.scale
+ : 2.8
+ const vtk = parseLmToVtk(landmarks, scale)
if(!vtk)
return