diff --git a/docs/releases/v2.13.3.md b/docs/releases/v2.13.3.md
index f1ed8b123c31772f17971b20e4fe1bcf9aeed334..0dfc54a1f9d26e39fca796ff29a9f08ecaa6d266 100644
--- a/docs/releases/v2.13.3.md
+++ b/docs/releases/v2.13.3.md
@@ -1,5 +1,9 @@
# v2.13.3
+## Feature
+
+- 1um section now does not move x,z position
+
## Behind the scene
- user added layer now sits on index 1
\ No newline at end of file
diff --git a/src/atlasComponents/sapi/sxplrTypes.ts b/src/atlasComponents/sapi/sxplrTypes.ts
index 25ac84c21cba44c1ad394de9c00ba0e657bb4c55..e8d44c8dbea30d2e1d992b6da54a83f54e5d0b6a 100644
--- a/src/atlasComponents/sapi/sxplrTypes.ts
+++ b/src/atlasComponents/sapi/sxplrTypes.ts
@@ -74,6 +74,7 @@ export {
} from "src/viewerModule/nehuba/config.service/type"
import { TThreeSurferMesh, TThreeMesh, TThreeMeshLabel } from "src/viewerModule/threeSurfer/types"
+import { MetaV1Schema } from "./typeV3"
export { TThreeSurferMesh, TThreeMesh, TThreeMeshLabel }
/**
@@ -108,6 +109,7 @@ export type VoiFeature = {
url: string
transform: number[][]
info: Record<string, any>
+ meta?: MetaV1Schema
}
} & Feature
diff --git a/src/atlasComponents/sapi/translateV3.ts b/src/atlasComponents/sapi/translateV3.ts
index 098aa6b4e26c07591a64f36d03e047f15d7b1712..dabec3badf48d08d9e8a739459ebe5b1a5985f97 100644
--- a/src/atlasComponents/sapi/translateV3.ts
+++ b/src/atlasComponents/sapi/translateV3.ts
@@ -1,12 +1,19 @@
import {
SxplrAtlas, SxplrParcellation, SxplrTemplate, SxplrRegion, NgLayerSpec, NgPrecompMeshSpec, NgSegLayerSpec, VoiFeature, Point, TThreeMesh, LabelledMap, CorticalFeature, Feature, GenericInfo, BoundingBox
} from "./sxplrTypes"
-import { PathReturn } from "./typeV3"
+import { PathReturn, MetaV1Schema } from "./typeV3"
import { hexToRgb } from 'common/util'
import { components } from "./schemaV3"
import { defaultdict } from "src/util/fn"
+const BIGBRAIN_XZ = [
+ [-70.677, 62.222],
+ [-70.677, -58.788],
+ [68.533, -58.788],
+ [68.533, 62.222],
+]
+
class TranslateV3 {
#atlasMap: Map<string, PathReturn<"/atlases/{atlas_id}">> = new Map()
@@ -118,20 +125,23 @@ class TranslateV3 {
url: string
transform: number[][]
info: Record<string, any>
+ meta?: MetaV1Schema
}> = {}
for (const key in input) {
if (key !== 'neuroglancer/precomputed') {
continue
}
const url = input[key]
- const [ transform, info ] = await Promise.all([
+ const [ transform, info, meta ] = await Promise.all([
this.cFetch(`${url}/transform.json`).then(res => res.json()) as Promise<number[][]>,
this.cFetch(`${url}/info`).then(res => res.json()) as Promise<Record<string, any>>,
+ this.fetchMeta(url),
])
returnObj[key] = {
url: input[key],
transform: transform,
info: info,
+ meta,
}
}
return returnObj
@@ -354,6 +364,41 @@ class TranslateV3 {
}
}
+ async fetchMeta(url: string): Promise<MetaV1Schema|null> {
+ const is1umRegisteredSlices = url.startsWith("https://1um.brainatlas.eu/registered_sections/bigbrain")
+ if (is1umRegisteredSlices) {
+ const found = /B20_([0-9]{4})/.exec(url)
+ if (found) {
+ const sectionId = parseInt(found[1])
+ const realYDis = (sectionId * 2e4 - 70010000) / 1e6
+ return {
+ version: 1,
+ preferredColormap: ["greyscale"],
+ bestViewPoints: [{
+ type: "enclosed",
+ points: BIGBRAIN_XZ.map(([x, z]) => ({
+ type: "point",
+ value: [x, realYDis, z]
+ }))
+ }]
+ }
+ }
+ }
+ /**
+ * TODO ensure all /meta endpoints are populated
+ */
+ // try{
+ // const resp = await this.cFetch(`${url}/meta`)
+ // if (resp.status === 200) {
+ // return resp.json()
+ // }
+ // } catch (e) {
+
+ // }
+
+ return null
+ }
+
async translateSpaceToAuxMesh(template: SxplrTemplate): Promise<NgPrecompMeshSpec[]>{
if (!template) return []
const space = this.retrieveTemplate(template)
diff --git a/src/atlasComponents/sapi/typeV3.ts b/src/atlasComponents/sapi/typeV3.ts
index 9be5ef62376b3f67a496268220b78a5ca7f53cc8..13d2d393b2cfee465f4927ed21522832b70726d9 100644
--- a/src/atlasComponents/sapi/typeV3.ts
+++ b/src/atlasComponents/sapi/typeV3.ts
@@ -52,3 +52,83 @@ export type PaginatedModel<T> = {
page: number
size: number
}
+
+type X4Affine = number[][]
+
+type ShaderEnum =
+ | "greyscale"
+ | "viridis"
+ | "plasma"
+ | "magma"
+ | "inferno"
+ | "jet"
+/**
+ * Preferred colormap in order of preference
+ */
+type PreferredColormap = ShaderEnum[]
+type X1Vector = [number, number, number]
+/**
+ * Best locations to view this volume.
+ */
+type BestViewPoints = (PointGeometry | PlaneGeometry | EnclosedROI)[]
+
+export interface MetaV1Schema {
+ version: 1
+ data?: GenericImage | SingleChannelImage | ThreeChannelImage
+ transform?: X4Affine
+ preferredColormap?: PreferredColormap
+ override?: Override
+ bestViewPoints?: BestViewPoints
+}
+/**
+ * Generic image, with arbitary dimensions.
+ */
+interface GenericImage {
+ type: "image"
+ range?: ValueRange[]
+}
+/**
+ * Describes the range of values
+ */
+interface ValueRange {
+ min?: number
+ max?: number
+}
+/**
+ * Describes an image with 1 dimension, e.g. used as greyscale image.
+ */
+interface SingleChannelImage {
+ type: "image/1d"
+ range?: [ValueRange]
+}
+/**
+ * Describes an image with 3 dimensions, mostly used as RGB image.
+ */
+interface ThreeChannelImage {
+ type: "image/3d"
+ range?: [ValueRange, ValueRange, ValueRange]
+}
+/**
+ * Overrides provide some low level/implementation hints. They are more prone to breaking, and thus should be used with the knowledge as such.
+ */
+interface Override {
+ /**
+ * Hints that client should use this shader for the volume in neuroglancer
+ */
+ shader?: string
+}
+interface PointGeometry {
+ type: "point"
+ value?: X1Vector
+}
+interface PlaneGeometry {
+ type: "plane"
+}
+interface EnclosedROI {
+ type: "enclosed"
+ points: PointGeometry[]
+}
+
+export function isEnclosed(v: BestViewPoints[number]): v is EnclosedROI {
+ return v.type === "enclosed"
+}
diff --git a/src/features/feature-view/feature-view.component.html b/src/features/feature-view/feature-view.component.html
index 41a18ab45fb8ec4dea3855ffdff863b80feafe36..26a02e48c3a15673db3878ebba79fc0748d795c0 100644
--- a/src/features/feature-view/feature-view.component.html
+++ b/src/features/feature-view/feature-view.component.html
@@ -97,6 +97,7 @@
[ng-layer-ctl-transform]="voi.ngVolume.transform"
[ng-layer-ctl-info]="voi.ngVolume.info"
[ng-layer-ctl-opacity]="1.0"
+ [ng-layer-ctl-meta]="voi.ngVolume.meta"
[ng-layer-ctrl-show]="true">
</ng-layer-ctl>
</mat-tab>
diff --git a/src/viewerModule/nehuba/ngLayerCtlModule/ngLayerCtl/ngLayerCtrl.component.ts b/src/viewerModule/nehuba/ngLayerCtlModule/ngLayerCtl/ngLayerCtrl.component.ts
index 71d2acd47818b95728595616c3a0d53c9efddf6f..9ddf114f71c86ee55bfbcf0c9b85d186bb7c496b 100644
--- a/src/viewerModule/nehuba/ngLayerCtlModule/ngLayerCtl/ngLayerCtrl.component.ts
+++ b/src/viewerModule/nehuba/ngLayerCtlModule/ngLayerCtl/ngLayerCtrl.component.ts
@@ -1,5 +1,5 @@
import { ChangeDetectionStrategy, Component, Inject, Input, OnChanges, OnDestroy } from "@angular/core";
-import { Store } from "@ngrx/store";
+import { Store, select } from "@ngrx/store";
import { isMat4 } from "common/util"
import { CONST } from "common/constants"
import { Observable } from "rxjs";
@@ -8,6 +8,7 @@ import { NehubaViewerUnit, NEHUBA_INSTANCE_INJTKN } from "src/viewerModule/nehub
import { getExportNehuba } from "src/util/fn";
import { getShader } from "src/util/constants";
import { EnumColorMapName } from "src/util/colorMaps";
+import { MetaV1Schema, isEnclosed } from "src/atlasComponents/sapi/typeV3";
type Vec4 = [number, number, number, number]
type Mat4 = [Vec4, Vec4, Vec4, Vec4]
@@ -50,6 +51,9 @@ export class NgLayerCtrlCmp implements OnChanges, OnDestroy{
@Input('ng-layer-ctl-shader')
shader: string
+ @Input("ng-layer-ctl-meta")
+ meta: MetaV1Schema
+
opacity: number = 1.0
@Input('ng-layer-ctl-opacity')
set _opacity(val: number | string) {
@@ -80,14 +84,21 @@ export class NgLayerCtrlCmp implements OnChanges, OnDestroy{
private viewer: NehubaViewerUnit
private exportNehuba: any
+ private currentPositionMm: number[]
constructor(
private store: Store<any>,
@Inject(NEHUBA_INSTANCE_INJTKN) nehubaViewer$: Observable<NehubaViewerUnit>
){
const sub = nehubaViewer$.subscribe(v => this.viewer = v)
+ const navSub = this.store.pipe(
+ select(atlasSelection.selectors.navigation)
+ ).subscribe(nav => {
+ this.currentPositionMm = nav?.position.map(v => v / 1e6)
+ })
this.onDestroyCb.push(
- () => sub.unsubscribe()
+ () => sub.unsubscribe(),
+ () => navSub.unsubscribe(),
)
getExportNehuba().then(exportNehuba => {
@@ -167,6 +178,28 @@ export class NgLayerCtrlCmp implements OnChanges, OnDestroy{
vec3.scale(final, final, 0.5)
position = Array.from(final)
}
+
+ const enclosed = this.meta?.bestViewPoints.filter(isEnclosed).find(v => v.points.length >= 3)
+ if (enclosed) {
+ const curr = vec3.fromValues(...this.currentPositionMm)
+ const pt1 = vec3.fromValues(...enclosed.points[0].value)
+ const pt0 = vec3.fromValues(...enclosed.points[1].value)
+ const pt2 = vec3.fromValues(...enclosed.points[2].value)
+ vec3.sub(pt1, pt1, pt0)
+ vec3.sub(pt2, pt2, pt0)
+ vec3.normalize(pt1, pt1)
+ vec3.normalize(pt2, pt2)
+
+ vec3.sub(curr, curr, pt0)
+
+ vec3.mul(pt1, pt1, curr)
+ vec3.mul(pt2, pt2, curr)
+
+ const resultant = vec3.add(vec3.create(), pt1, pt2)
+ vec3.add(resultant, resultant, pt0)
+ vec3.scale(resultant, resultant, 1e6)
+ position = Array.from(resultant)
+ }
this.store.dispatch(
diff --git a/src/viewerModule/viewerCmp/viewerCmp.template.html b/src/viewerModule/viewerCmp/viewerCmp.template.html
index dff8e4b55526b59147c566f195691a0d19746551..14259c7f42e1b25cb7455688129282dcee4a453d 100644
--- a/src/viewerModule/viewerCmp/viewerCmp.template.html
+++ b/src/viewerModule/viewerCmp/viewerCmp.template.html
@@ -1048,19 +1048,17 @@
</ng-template>
</ng-template>
-<!-- feature tmpls -->
-<ng-template #sapiBaseFeatureTmpl
- let-backCb="backCb"
- let-feature="feature">
-
+<!-- general feature tmpl -->
+<ng-template let-feature="feature" #selectedFeatureTmpl>
+ <!-- TODO differentiate between features (spatial, regional etc) -->
+
<sxplr-feature-view class="sxplr-z-2 mat-elevation-z2"
[feature]="feature">
<div header>
<!-- back btn -->
<button mat-button
- *ngIf="backCb"
- (click)="backCb()"
+ (click)="clearSelectedFeature()"
[attr.aria-label]="ARIA_LABELS.CLOSE"
class="sxplr-mb-2"
>
@@ -1072,28 +1070,6 @@
</div>
</sxplr-feature-view>
-
-</ng-template>
-
-<!-- general feature tmpl -->
-<ng-template let-feature="feature" #selectedFeatureTmpl>
- <!-- TODO differentiate between features (spatial, regional etc) -->
-
- <!-- spatial feature tmpl -->
- <ng-container *ngTemplateOutlet="sapiBaseFeatureTmpl; context: {
- backCb: clearSelectedFeature.bind(this),
- feature: feature
- }">
- </ng-container>
-
- <ng-layer-ctl *ngFor="let vol of feature.volumes"
- class="d-block"
- [ng-layer-ctl-name]="vol.metadata.fullName"
- [ng-layer-ctl-src]="vol.data.url"
- [ng-layer-ctl-transform]="vol.data | getProperty : 'detail' | getProperty: 'neuroglancer/precomputed' | getProperty : 'transform'">
- </ng-layer-ctl>
- <ng-template #sapiVOITmpl>
- </ng-template>
</ng-template>
<!-- general point tmpl -->