diff --git a/src/atlasComponents/sapi/core/space/interspaceLinearXform.ts b/src/atlasComponents/sapi/core/space/interspaceLinearXform.ts
new file mode 100644
index 0000000000000000000000000000000000000000..44c93c74186567e3967d2224cb4937ee391de215
--- /dev/null
+++ b/src/atlasComponents/sapi/core/space/interspaceLinearXform.ts
@@ -0,0 +1,60 @@
+export const VALID_LINEAR_XFORM_SRC = {
+ CCF: "Allen Common Coordination Framework"
+}
+
+export const VALID_LINEAR_XFORM_DST = {
+ NEHUBA: "nehuba"
+}
+
+export type TVALID_LINEAR_XFORM_SRC = keyof typeof VALID_LINEAR_XFORM_SRC
+export type TVALID_LINEAR_XFORM_DST = keyof typeof VALID_LINEAR_XFORM_DST
+
+type TLinearXform = number[][]
+
+const _linearXformDict: Record<
+ keyof typeof VALID_LINEAR_XFORM_SRC,
+ Record<
+ keyof typeof VALID_LINEAR_XFORM_DST,
+ TLinearXform
+ >> = {
+ CCF: {
+ NEHUBA: [
+ [-1e3, 0, 0, 11400000 - 5737500], //
+ [0, 0, -1e3, 13200000 - 6637500], //
+ [0, -1e3, 0, 8000000 - 4037500], //
+ [0, 0, 0, 1],
+ ]
+ }
+ }
+
+const defaultXform = [
+ [1e3, 0, 0, 0],
+ [0, 1e3, 0, 0],
+ [0, 0, 1e3, 0],
+ [0, 0, 0, 1],
+]
+
+
+const getProxyXform = <T>(obj: Record<string, T>, cb: (value: T) => T) => new Proxy({}, {
+ get: (_target, prop: string, _receiver) => {
+ return cb(obj[prop])
+ }
+})
+
+export const linearXformDict = getProxyXform(_linearXformDict, (value: Record<string, TLinearXform>) => {
+ if (!value) return getProxyXform({}, () => defaultXform)
+ return getProxyXform(value, (v: TLinearXform) => {
+ if (v) return v
+ return defaultXform
+ })
+}) as Record<
+ keyof typeof VALID_LINEAR_XFORM_SRC,
+ Record<
+ keyof typeof VALID_LINEAR_XFORM_DST,
+ TLinearXform
+ >>
+
+
+export const linearTransform = async (srcTmplName: keyof typeof VALID_LINEAR_XFORM_SRC, targetTmplName: keyof typeof VALID_LINEAR_XFORM_DST) => {
+ return linearXformDict[srcTmplName][targetTmplName]
+}
diff --git a/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts b/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts
index fb6500281577a0791f6c82b7d53ce6b7aef636a6..d339398c0a55865d2a4fce6e2feb9246e4a5606b 100644
--- a/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts
+++ b/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts
@@ -14,7 +14,7 @@ export class FilterAnnotationsBySpace implements PipeTransform{
public transform(annotations: IAnnotationGeometry[], space: { '@id': string }, opts?: TOpts): IAnnotationGeometry[]{
const { reverse = false } = opts || {}
return reverse
- ? annotations.filter(ann => ann.space["@id"] !== space["@id"])
- : annotations.filter(ann => ann.space["@id"] === space["@id"])
+ ? annotations.filter(ann => ann.space?.["@id"] !== space?.["@id"])
+ : annotations.filter(ann => ann.space?.["@id"] === space?.["@id"])
}
-}
\ No newline at end of file
+}
diff --git a/src/viewerModule/nehuba/config.service/util.ts b/src/viewerModule/nehuba/config.service/util.ts
index 7233d0f26bb2bda42bfe3b0141c9c9b64a377c77..8f2b0de2dc144f287815a503dd95e35c741e82fb 100644
--- a/src/viewerModule/nehuba/config.service/util.ts
+++ b/src/viewerModule/nehuba/config.service/util.ts
@@ -409,6 +409,11 @@ export function getNehubaConfig(space: SapiSpaceModel): NehubaConfig {
"layers": {},
"navigation": {
"zoomFactor": 350000 * scale,
+ pose: {
+ position: {
+ voxelSize: [1, 1, 1]
+ }
+ }
},
"perspectiveOrientation": [
0.3140767216682434,
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
index 136c0d0a314394628ddccdcd91010e85420f7524..da9855ecb93b0344c2239776590f0625dd20117a 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
@@ -176,14 +176,23 @@ export class NehubaLayerControlService implements OnDestroy{
* on custom landmarks loaded, set mesh transparency
*/
this.sub.push(
- this.store$.pipe(
- select(annotation.selectors.annotations),
+ merge(
+ this.store$.pipe(
+ select(annotation.selectors.annotations),
+ map(landmarks => landmarks.length > 0),
+ ),
+ this.store$.pipe(
+ select(atlasAppearance.selectors.customLayers),
+ map(customLayers => customLayers.filter(l => l.clType === "customlayer/nglayer" && /^swc:\/\//.test(l.source)).length > 0),
+ )
+ ).pipe(
+ startWith(false),
withLatestFrom(this.defaultNgLayers$)
- ).subscribe(([landmarks, { tmplAuxNgLayers }]) => {
+ ).subscribe(([flag, { tmplAuxNgLayers }]) => {
const payload: {
[key: string]: number
} = {}
- const alpha = landmarks.length > 0
+ const alpha = flag
? 0.2
: 1.0
for (const ngId in tmplAuxNgLayers) {
diff --git a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
index fea1911266af6a410bdd339c805c4aeb3129f20c..5c16b0a065f1f5b2d14be81d724230ed30b7b301 100644
--- a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
@@ -20,6 +20,7 @@ import { SapiRegionModel } from "src/atlasComponents/sapi";
import { NehubaConfig, getParcNgId, getRegionLabelIndex } from "../config.service";
import { SET_MESHES_TO_LOAD } from "../constants";
import { annotation, atlasAppearance, atlasSelection, userInteraction } from "src/state";
+import { linearTransform, TVALID_LINEAR_XFORM_DST, TVALID_LINEAR_XFORM_SRC } from "src/atlasComponents/sapi/core/space/interspaceLinearXform";
export const INVALID_FILE_INPUT = `Exactly one (1) nifti file is required!`
@@ -287,6 +288,20 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnDestroy, AfterViewIni
this.dismissAllAddedLayers()
if (/\.swc$/i.test(file.name)) {
+ let message = `The swc rendering is experimental. Please contact us on any feedbacks. `
+ const swcText = await file.text()
+ let src: TVALID_LINEAR_XFORM_SRC
+ const dst: TVALID_LINEAR_XFORM_DST = "NEHUBA"
+ if (/ccf/i.test(swcText)) {
+ src = "CCF"
+ message += `CCF detected, applying known transformation.`
+ }
+ if (!src) {
+ message += `no known space detected. Applying default transformation.`
+ }
+
+ const xform = await linearTransform(src, dst)
+
const url = URL.createObjectURL(file)
this.droppedLayerNames.push({
layerName: randomUuid,
@@ -298,16 +313,14 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnDestroy, AfterViewIni
id: randomUuid,
source: `swc://${url}`,
segments: ["1"],
- transform: [
- [1e3, 0, 0, 0],
- [0, 1e3, 0, 0],
- [0, 0, 1e3, 0],
- [0, 0, 0, 1],
- ],
+ transform: xform,
clType: 'customlayer/nglayer' as const
}
})
)
+ this.snackbar.open(message, "Dismiss", {
+ duration: 10000
+ })
return
}