diff --git a/src/atlasViewer/atlasViewer.dataService.service.ts b/src/atlasViewer/atlasViewer.dataService.service.ts
index 74d8f5d243aa6b38ebdc717900df675a3f82b52f..38c2ed3a7f2c9409d9efa50799edecf1fdb40dae 100644
--- a/src/atlasViewer/atlasViewer.dataService.service.ts
+++ b/src/atlasViewer/atlasViewer.dataService.service.ts
@@ -93,7 +93,6 @@ export class AtlasViewerDataService implements OnDestroy{
this.store.dispatch({
type : FETCHED_SPATIAL_DATA,
fetchedDataEntries : arr.reduce((acc,curr) => acc.concat(curr.map(obj => Object.assign({}, obj, {
- position : obj.position.map(pos => pos/1e6),
properties : {}
}))), [])
})
@@ -103,6 +102,20 @@ export class AtlasViewerDataService implements OnDestroy{
})
})
.catch(console.error)
+ }else if (templateSpace === 'Allen Mouse'){
+ return fetch('res/json/allenTestPlane.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/cvtPtsToSpatial.js b/src/res/cvtPtsToSpatial.js
index b232bfdb9b479f08650c9cecafc70a3412ff2e8e..6765f731841cfbdbdb78313cf9824ab8d8b2fd71 100644
--- a/src/res/cvtPtsToSpatial.js
+++ b/src/res/cvtPtsToSpatial.js
@@ -21,11 +21,16 @@ filenames.map(filename => {
return {
type : 'iEEG Recording Site',
name : filename.replace('_MNI.pts', '').concat(`_${name.replace(/^.p/g,(s) => s.slice(0,1).concat('\''))}`),
- position : [
- Number(x) * 1e6,
- Number(y) * 1e6,
- Number(z) * 1e6
- ],
+ templateSpace : 'MNI 152 ICBM 2009c Nonlinear Asymmetric',
+ geometry : {
+ type : 'point',
+ space : 'real',
+ position : [
+ Number(x),
+ Number(y),
+ Number(z)
+ ],
+ },
properties : {
description : descContactPts,
publications : []
diff --git a/src/res/ext/allenTestPlane.json b/src/res/ext/allenTestPlane.json
new file mode 100644
index 0000000000000000000000000000000000000000..bbf92f741739b54173dfcaf95b85d21162898f88
--- /dev/null
+++ b/src/res/ext/allenTestPlane.json
@@ -0,0 +1 @@
+[{"type":"Test Allen plane spatial anchor","name":"Plane 01","templateSpace":"Allen Mouse","geometry":{"type":"plane","corners":[[2.689,-0.8875,3.3125],[2.689,-5.2675,2.8925],[-1.711,-5.2675,2.8925],[-1.711,-0.8875,3.3125]]},"properties":{"description":"This spatial plane represent an observation plane of the mouse.","publications":[]},"files":[{"filename":"DATA1/DATA1_FILE1","name":"DATA1_FILE1","mimetype":"application/raw","url":"http://about:blank","properties":{"description":"This is the description for the DATA1 FILE1","publications":[]}},{"filename":"DATA1/DATA1_FILE2","name":"DATA1 FILE2","mimetype":"application/raw","url":"http://about:blank","properties":{"description":"This is the description for the DATA1 FILE2","publications":[]}},{"filename":"DATA2/DATA2_FILE1","name":"DATA2_FILE1","mimetype":"application/raw","url":"http://about:blank","properties":{"description":"This is the description for the DATA2 FILE1","publications":[]}},{"filename":"DATA2/DATA2_FILE2","name":"DATA2_FILE2","mimetype":"application/raw","url":"http://about:blank","properties":{"description":"This is the description for the DATA2 FILE2","publications":[]}}],"originalJson":{"reference_atlas":"CCF v3","name":"hbp-00552_GCaMP6.json","HBP_Storage_path":"bp00sp01/Pavone_SGA1_1.3.2/hbp-00552/GCaMP6/","Primary region(s)":"Anterior cingulate area, dorsal part; Anterolateral visual area; Posteromedial visual area; Primary motor area; Primary somatosensory area, barrel field; Primary somatosensory area, lower limb; Primary somatosensory area, nose; Primary somatosensory area, trunk; Primary somatosensory area, unassigned; Primary somatosensory area, upper limb; Primary visual area; Retrosplenial area, dorsal part; Retrosplenial area, lateral agranular part; Retrosplenial area, ventral part; Rostrolateral area; Secondary motor area","Landmarks":[{"name":"upper left corner","x":230,"y":294,"z":322.5},{"name":"upper right corner","x":54.8,"y":277.2,"z":322.5},{"name":"lower right corner","x":54.8,"y":277.2,"z":146.5},{"name":"lower left corner","x":230,"y":294,"z":146.5}]},"processedData":{"transformedCorners":[[230,294,322.5],[54.8,277.2,322.5],[54.8,277.2,146.5],[230,294,146.5]]}}]
\ No newline at end of file
diff --git a/src/services/stateStore.service.ts b/src/services/stateStore.service.ts
index 6c45c411ba6837dcb7f0784ba02e7f2f4d3d2cca..7d49498576165b98c3e70426ccfd0a67519c1f41 100644
--- a/src/services/stateStore.service.ts
+++ b/src/services/stateStore.service.ts
@@ -446,6 +446,30 @@ export interface UIAction extends Action{
focusedSidePanel? : string
}
+export interface Landmark{
+ type : string //e.g. sEEG recording site, etc
+ name : string
+ templateSpace : string // possibily inherited from LandmarkBundle (?)
+ geometry : PointLandmarkGeometry | PlaneLandmarkGeometry
+ properties : Property
+ files : File[]
+}
+
+export interface LandmarkGeometry{
+ type : 'point' | 'plane'
+ space? : 'voxel' | 'real'
+}
+
+export interface PointLandmarkGeometry extends LandmarkGeometry{
+ position : [number, number, number]
+}
+
+export interface PlaneLandmarkGeometry extends LandmarkGeometry{
+ // corners have to be CW or CCW (no zigzag)
+ corners : [[number, number, number],[number, number, number],[number, number, number],[number, number, number]]
+}
+
+
export function isDefined(obj){
return typeof obj !== 'undefined' && obj !== null
}
\ No newline at end of file
diff --git a/src/ui/nehubaContainer/nehubaContainer.component.ts b/src/ui/nehubaContainer/nehubaContainer.component.ts
index aa71ad7a408349d93c67690b93f1dca2c5ca4eca..e83f390949bdd867c51e77bd8cb87a4f35cd5e65 100644
--- a/src/ui/nehubaContainer/nehubaContainer.component.ts
+++ b/src/ui/nehubaContainer/nehubaContainer.component.ts
@@ -1,15 +1,13 @@
import { Component, ViewChild, ViewContainerRef, ComponentFactoryResolver, ComponentFactory, ComponentRef, OnInit, OnDestroy, ElementRef, Injector } from "@angular/core";
import { NehubaViewerUnit } from "./nehubaViewer/nehubaViewer.component";
import { Store, select } from "@ngrx/store";
-import { ViewerStateInterface, safeFilter, SELECT_REGIONS, getLabelIndexMap, DataEntry, CHANGE_NAVIGATION, isDefined, MOUSE_OVER_SEGMENT, USER_LANDMARKS, ADD_NG_LAYER, REMOVE_NG_LAYER, SHOW_NG_LAYER, NgViewerStateInterface, HIDE_NG_LAYER, MOUSE_OVER_LANDMARK, SELECT_LANDMARKS } from "../../services/stateStore.service";
+import { ViewerStateInterface, safeFilter, SELECT_REGIONS, getLabelIndexMap, DataEntry, CHANGE_NAVIGATION, isDefined, MOUSE_OVER_SEGMENT, USER_LANDMARKS, ADD_NG_LAYER, REMOVE_NG_LAYER, SHOW_NG_LAYER, NgViewerStateInterface, HIDE_NG_LAYER, MOUSE_OVER_LANDMARK, SELECT_LANDMARKS, Landmark, PointLandmarkGeometry, PlaneLandmarkGeometry } from "../../services/stateStore.service";
import { Observable, Subscription, fromEvent, combineLatest, merge, of } from "rxjs";
import { filter,map, take, scan, debounceTime, distinctUntilChanged, switchMap, skip, withLatestFrom, buffer } from "rxjs/operators";
import { AtlasViewerAPIServices, UserLandmark } from "../../atlasViewer/atlasViewer.apiService.service";
import { timedValues } from "../../util/generator";
import { AtlasViewerDataService } from "../../atlasViewer/atlasViewer.dataService.service";
import { AtlasViewerConstantsServices } from "../../atlasViewer/atlasViewer.constantService.service";
-import { DatasetViewerComponent } from "../datasetViewer/datasetViewer.component";
-import { WidgetServices } from "../../atlasViewer/widgetUnit/widgetService.service";
@Component({
selector : 'ui-nehuba-container',
@@ -28,7 +26,6 @@ export class NehubaContainer implements OnInit, OnDestroy{
@ViewChild('[pos11]',{read:ElementRef}) bottomright : ElementRef
private nehubaViewerFactory : ComponentFactory<NehubaViewerUnit>
- private datasetViewerFactory : ComponentFactory<DatasetViewerComponent>
public viewerLoaded : boolean = false
@@ -43,7 +40,7 @@ export class NehubaContainer implements OnInit, OnDestroy{
private selectedLandmarks$ : Observable<any[]>
private hideSegmentations$ : Observable<boolean>
- private fetchedSpatialDatasets$ : Observable<any[]>
+ private fetchedSpatialDatasets$ : Observable<Landmark[]>
private userLandmarks$ : Observable<UserLandmark[]>
public onHoverSegmentName$ : Observable<string>
public onHoverSegment$ : Observable<any>
@@ -55,7 +52,7 @@ export class NehubaContainer implements OnInit, OnDestroy{
private selectedTemplate : any | null
private selectedRegionIndexSet : Set<number> = new Set()
- public fetchedSpatialData : DataEntry[] = []
+ public fetchedSpatialData : Landmark[] = []
private ngLayersRegister : NgViewerStateInterface = {layers : [], forceShowSegment: null}
private ngLayers$ : Observable<NgViewerStateInterface>
@@ -86,7 +83,6 @@ export class NehubaContainer implements OnInit, OnDestroy{
private elementRef : ElementRef
){
this.nehubaViewerFactory = this.csf.resolveComponentFactory(NehubaViewerUnit)
- this.datasetViewerFactory = this.csf.resolveComponentFactory(DatasetViewerComponent)
this.newViewer$ = this.store.pipe(
select('viewerState'),
@@ -117,10 +113,10 @@ export class NehubaContainer implements OnInit, OnDestroy{
this.fetchedSpatialDatasets$ = this.store.pipe(
select('dataStore'),
- debounceTime(300),
safeFilter('fetchedSpatialData'),
map(state => state.fetchedSpatialData),
- distinctUntilChanged(this.constantService.testLandmarksChanged)
+ distinctUntilChanged(this.constantService.testLandmarksChanged),
+ debounceTime(300),
)
this.navigationChanges$ = this.store.pipe(
@@ -290,12 +286,12 @@ export class NehubaContainer implements OnInit, OnDestroy{
)
.pipe(
map(([datas,visible, ...rest]) => visible ? datas : []),
- map(arr => arr.map(v => Object.assign({}, v, {type : 'spatialSearchLandmark'})))
+ // map(arr => arr.map(v => Object.assign({}, v, {type : 'spatialSearchLandmark'})))
),
this.userLandmarks$.pipe(
- map(arr => arr.map(v => Object.assign({}, v, {type : 'userLandmark'})))
+ // map(arr => arr.map(v => Object.assign({}, v, {type : 'userLandmark'})))
)
- ).pipe(map(arr => arr[0].concat(arr[1])))
+ ).pipe(map(arr => [...arr[0], ...arr[1]]))
this.ngLayers$ = this.store.pipe(
select('ngViewerState')
@@ -324,10 +320,21 @@ export class NehubaContainer implements OnInit, OnDestroy{
).subscribe(([fetchedSpatialData,visible])=>{
this.fetchedSpatialData = fetchedSpatialData
- if(visible)
- this.nehubaViewer.addSpatialSearch3DLandmarks(this.fetchedSpatialData.map((data:any)=>data.position))
- else
+ if(visible && this.fetchedSpatialData && this.fetchedSpatialData.length > 0){
+ this.nehubaViewer.addSpatialSearch3DLandmarks(
+ this.fetchedSpatialData
+ .map(data=> data.geometry.type === 'point'
+ ? (data.geometry as PointLandmarkGeometry).position
+ : data.geometry.type === 'plane'
+ ? [
+ (data.geometry as PlaneLandmarkGeometry).corners,
+ [[0,1,2], [0,2,3]]
+ ]
+ : null)
+ )
+ }else{
this.nehubaViewer.removeSpatialSearch3DLandmarks()
+ }
})
)
diff --git a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
index 10492466bce64367f726d6b7e80a71a7bc9b53ab..a07f85932460235dc138339c9aa64414d31817da 100644
--- a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
+++ b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
@@ -72,7 +72,7 @@ export class NehubaViewerUnit implements AfterViewInit,OnDestroy{
// console.error('worker response message.data is undefined', message.data)
return false
}
- if(message.data.type !== 'ASSEMBLED_LANDMARK_VTK'){
+ if(message.data.type !== 'ASSEMBLED_LANDMARKS_VTK'){
/* worker responded with not assembled landmark, no need to act */
return false
}
@@ -307,10 +307,17 @@ export class NehubaViewerUnit implements AfterViewInit,OnDestroy{
}
//pos in mm
- public addSpatialSearch3DLandmarks(poss:[number,number,number][],scale?:number,type?:'icosahedron'){
+ public addSpatialSearch3DLandmarks(geometries: any[],scale?:number,type?:'icosahedron'){
this.workerService.worker.postMessage({
- type : 'GET_LANDMARK_VTK',
- landmarks : poss.map(pos => pos.map(v => v * 1e6))
+ type : 'GET_LANDMARKS_VTK',
+ landmarks : geometries.map(geometry =>
+ geometry === null
+ ? null
+ //gemoetry : [number,number,number] | [ [number,number,number][], [number,number,number][] ]
+ : isNaN(geometry[0])
+ ? [geometry[0].map(triplets => triplets.map(coord => (console.log(coord), coord * 1e6))), geometry[1]]
+ : geometry.map(coord => coord * 1e6)
+ )
})
}
diff --git a/src/util/pipes/spatialLandmarksToDatabrowserItem.pipe.ts b/src/util/pipes/spatialLandmarksToDatabrowserItem.pipe.ts
index 9ba40df5d61678179817ee66ac7007fed8c63d64..4b5316976e9eefe521d571c28999ee09eef8a9d4 100644
--- a/src/util/pipes/spatialLandmarksToDatabrowserItem.pipe.ts
+++ b/src/util/pipes/spatialLandmarksToDatabrowserItem.pipe.ts
@@ -1,5 +1,5 @@
import { Pipe, PipeTransform } from "@angular/core";
-import { DataEntry } from "../../services/stateStore.service";
+import { DataEntry, Landmark, PointLandmarkGeometry, PlaneLandmarkGeometry } from "../../services/stateStore.service";
@Pipe({
@@ -7,12 +7,19 @@ import { DataEntry } from "../../services/stateStore.service";
})
export class SpatialLandmarksToDataBrowserItemPipe implements PipeTransform{
- public transform(landmarks:any[]):{region:any, searchResults:Partial<DataEntry>[]}[]{
+ public transform(landmarks:Landmark[]):{region:any, searchResults:Partial<DataEntry>[]}[]{
return landmarks.map(landmark => ({
region : Object.assign({}, landmark, {
- position : landmark.position.map(v => v*1e6),
spatialLandmark : true
- }),
+ }, landmark.geometry.type === 'point'
+ ? {
+ position : (landmark.geometry as PointLandmarkGeometry).position.map(v => v*1e6),
+ }
+ : landmark.geometry.type === 'plane'
+ ? {
+ POIs : (landmark.geometry as PlaneLandmarkGeometry).corners.map(corner => corner.map(coord => coord * 1e6))
+ }
+ : {}),
searchResults : [{
name : 'Associated dataset',
type : 'Associated dataset',
diff --git a/src/util/worker.js b/src/util/worker.js
index c167cd81e9eb7cc72455558fa288c33bb6b375a8..4f92bfc1f78a624fb5ebbda9907201cfafa64dfb 100644
--- a/src/util/worker.js
+++ b/src/util/worker.js
@@ -1,5 +1,5 @@
-const validTypes = ['CHECK_MESHES', 'GET_LANDMARK_VTK']
-const validOutType = ['CHECKED_MESH', 'ASSEMBLED_LANDMARK_VTK']
+const validTypes = ['CHECK_MESHES', 'GET_LANDMARKS_VTK']
+const validOutType = ['CHECKED_MESH', 'ASSEMBLED_LANDMARKS_VTK']
const checkMeshes = (action) => {
@@ -38,11 +38,11 @@ Created by worker thread at https://github.com/HumanBrainProject/interactive-vie
ASCII
DATASET POLYDATA`
-const getVertexHeader = (numLandmarks) => `POINTS ${12 * numLandmarks} float`
+const getVertexHeader = (numVertex) => `POINTS ${numVertex} float`
-const getPolyHeader = (numLandmarks) => `POLYGONS ${20 * numLandmarks} ${80 * numLandmarks}`
+const getPolyHeader = (numPoly) => `POLYGONS ${numPoly} ${4 * numPoly}`
-const getLabelHeader = (numLandmarks) => `POINT_DATA ${numLandmarks * 12}
+const getLabelHeader = (numVertex) => `POINT_DATA ${numVertex}
SCALARS label unsigned_char 1
LOOKUP_TABLE none`
@@ -68,7 +68,8 @@ const getIcoVertex = (pos, scale) => `-525731.0 0.0 850651.0
)
.join('\n')
-const getIcoPoly = (idx2) => `3 1 4 0
+
+const getIcoPoly = (startingIdx) => `3 1 4 0
3 4 9 0
3 4 5 9
3 8 5 4
@@ -92,79 +93,90 @@ const getIcoPoly = (idx2) => `3 1 4 0
.map((line) =>
line
.split(' ')
- .map((v,idx) => idx === 0 ? v : (Number(v) + idx2 * 12).toString() )
+ .map((v,idx) => idx === 0 ? v : (Number(v) + startingIdx).toString() )
.join(' ')
)
.join('\n')
-const getLabelScalar = (idx) => [...Array(12)].map(() => idx.toString()).join('\n')
-
-const ICOSAHEDRON = `# vtk DataFile Version 2.0
-Converted using https://github.com/HumanBrainProject/neuroglancer-scripts
-ASCII
-DATASET POLYDATA
-POINTS 12 float
--525731.0 0.0 850651.0
-525731.0 0.0 850651.0
--525731.0 0.0 -850651.0
-525731.0 0.0 -850651.0
-0.0 850651.0 525731.0
-0.0 850651.0 -525731.0
-0.0 -850651.0 525731.0
-0.0 -850651.0 -525731.0
-850651.0 525731.0 0.0
--850651.0 525731.0 0.0
-850651.0 -525731.0 0.0
--850651.0 -525731.0 0.0
-POLYGONS 20 80
-3 1 4 0
-3 4 9 0
-3 4 5 9
-3 8 5 4
-3 1 8 4
-3 1 10 8
-3 10 3 8
-3 8 3 5
-3 3 2 5
-3 3 7 2
-3 3 10 7
-3 10 6 7
-3 6 11 7
-3 6 0 11
-3 6 1 0
-3 10 1 6
-3 11 0 9
-3 2 11 9
-3 5 2 9
-3 11 2 7`
+const getMeshVertex = (vertices) => (console.log(vertices), vertices.map(vertex => vertex.join(' ')).join('\n'))
+const getMeshPoly = (polyIndices, currentIdx) => polyIndices.map(triplet =>
+ '3 '.concat(triplet.map(index =>
+ index + currentIdx
+ ).join(' '))
+).join('\n')
let landmarkVtkUrl
const encoder = new TextEncoder()
-const getLandmarkVtk = (action) => {
+const getLandmarksVtk = (action) => {
+ console.log('getin vtk')
// landmarks are array of triples in nm (array of array of numbers)
const landmarks = action.landmarks
+
+ console.log({landmarks})
+
+ const reduce = landmarks.reduce((acc,curr,idx) => {
+ //curr : null | [number,number,number] | [ [number,number,number], [number,number,number], [number,number,number] ][]
+ if(curr === null)
+ return acc
+ if(!isNaN(curr[0]))
+ return {
+ currentVertexIndex : acc.currentVertexIndex + 12,
+ vertexString : acc.vertexString.concat(getIcoVertex(curr, 2.8)),
+ polyCount : acc.polyCount + 20,
+ polyString : acc.polyString.concat(getIcoPoly(acc.currentVertexIndex)),
+ labelString : acc.labelString.concat(Array(12).fill(idx.toString()).join('\n'))
+ }
+ else{
+ //curr[0] : [number,number,number][] vertices
+ //curr[1] : [number,number,number][] indices for the vertices that poly forms
+
+ const vertices = curr[0]
+ const polyIndices = curr[1]
+
+ return {
+ currentVertexIndex : acc.currentVertexIndex + vertices.length,
+ vertexString : acc.vertexString.concat(getMeshVertex(vertices)),
+ polyCount : acc.currentVertexIndex + polyIndices.length,
+ polyString : acc.polyString.concat(getMeshPoly(polyIndices, acc.currentVertexIndex)),
+ labelString : acc.labelString.concat(Array(vertices.length).fill(idx.toString()).join('\n'))
+ }
+ }
+ }, {
+ currentVertexIndex : 0,
+ vertexString : [],
+ polyCount : 0,
+ polyString: [],
+ labelString : [],
+ })
+
+ // if no vertices are been rendered, do not replace old
+ if(reduce.currentVertexIndex === 0)
+ return
+
const vtk = vtkHeader
.concat('\n')
- .concat(getVertexHeader(landmarks.length))
+ .concat(getVertexHeader(reduce.currentVertexIndex))
.concat('\n')
- .concat(landmarks.map(landmark => getIcoVertex(landmark, 2.8)).join('\n'))
+ .concat(reduce.vertexString.join('\n'))
.concat('\n')
- .concat(getPolyHeader(landmarks.length))
+ .concat(getPolyHeader(reduce.polyCount))
.concat('\n')
- .concat(landmarks.map((_, idx) => getIcoPoly(idx)).join('\n'))
+ .concat(reduce.polyString.join('\n'))
.concat('\n')
- .concat(getLabelHeader(landmarks.length))
+ .concat(getLabelHeader(reduce.currentVertexIndex))
.concat('\n')
- .concat(landmarks.map((_, idx) => getLabelScalar(idx)).join('\n'))
+ .concat(reduce.labelString.join('\n'))
+ console.log({vtk})
// when new set of landmarks are to be displayed, the old landmarks will be discarded
if(landmarkVtkUrl)
URL.revokeObjectURL(landmarkVtkUrl)
+
landmarkVtkUrl = URL.createObjectURL(new Blob( [encoder.encode(vtk)], {type : 'application/octet-stream'} ))
postMessage({
- type : 'ASSEMBLED_LANDMARK_VTK',
+ type : 'ASSEMBLED_LANDMARKS_VTK',
url : landmarkVtkUrl
})
}
@@ -175,12 +187,12 @@ onmessage = (message) => {
switch(message.data.type){
case 'CHECK_MESHES':
checkMeshes(message.data)
- return;
- case 'GET_LANDMARK_VTK':
- getLandmarkVtk(message.data)
- return;
+ return
+ case 'GET_LANDMARKS_VTK':
+ getLandmarksVtk(message.data)
+ return
default:
- console.warn('unhandled worker action')
+ console.warn('unhandled worker action', message)
}
}
}