diff --git a/common/constants.js b/common/constants.js
index d3f6f24546090062459459f82f8652db30691244..fb5a018be88f017fb2b1767e07a7305288fb7b03 100644
--- a/common/constants.js
+++ b/common/constants.js
@@ -108,7 +108,7 @@ These outlines are based on the authoritative Terms and Conditions are found <ht
If you do not accept the Terms & Conditions you are not permitted to access or use the KG to search for, to submit, to post, or to download any materials found there-in.
`,
- NEHUBA_DRAG_DROP_TEXT: `Drag and drop any .nii.gz, .nii or .swc files.`,
+ NEHUBA_DRAG_DROP_TEXT: `Drag and drop any .nii.gz, .nii, .json or .swc files.`,
LOADING_TXT: `Loading ...`,
diff --git a/src/atlasComponents/annotations/annotation.service.ts b/src/atlasComponents/annotations/annotation.service.ts
index 776fb7848761df1bc48e99403ded8b3607cdba0a..be1b3fe8ed9f57747c9ec1c27788c37173524edf 100644
--- a/src/atlasComponents/annotations/annotation.service.ts
+++ b/src/atlasComponents/annotations/annotation.service.ts
@@ -61,6 +61,13 @@ interface NgAnnotationLayer {
visible: boolean
}
+export const ID_AFFINE = [
+ [1, 0, 0, 0],
+ [0, 1, 0, 0],
+ [0, 0, 1, 0],
+ [0, 0, 0, 1],
+]
+
export class AnnotationLayer {
static Map = new Map<string, AnnotationLayer>()
static Get(name: string, color: string){
@@ -79,7 +86,8 @@ export class AnnotationLayer {
private idset = new Set<string>()
constructor(
private name: string = getUuid(),
- private color="#ffffff"
+ private color="#ffffff",
+ affine=ID_AFFINE,
){
const layerSpec = this.viewer.layerSpecification.getLayer(
this.name,
@@ -88,12 +96,7 @@ export class AnnotationLayer {
"annotationColor": this.color,
"annotations": [],
name: this.name,
- transform: [
- [1, 0, 0, 0],
- [0, 1, 0, 0],
- [0, 0, 1, 0],
- [0, 0, 0, 1],
- ]
+ transform: affine,
}
)
this.nglayer = this.viewer.layerManager.addManagedLayer(layerSpec)
@@ -134,19 +137,35 @@ export class AnnotationLayer {
}
}
- async addAnnotation(spec: AnnotationSpec){
+ /**
+ * Unsafe method. Caller should ensure this.nglayer.isReady()
+ *
+ * @param spec
+ */
+ #addSingleAnn(spec: AnnotationSpec) {
+ const localAnnotations = this.nglayer.layer.localAnnotations
+ this.idset.add(spec.id)
+ const annSpec = this.parseNgSpecType(spec)
+ localAnnotations.add(
+ annSpec
+ )
+ }
+
+ async addAnnotation(spec: AnnotationSpec|AnnotationSpec[]){
if (!this.nglayer) {
throw new Error(`layer has already been disposed`)
}
PeriodicSvc.AddToQueue(() => {
if (this.nglayer.isReady()) {
- const localAnnotations = this.nglayer.layer.localAnnotations
- this.idset.add(spec.id)
- const annSpec = this.parseNgSpecType(spec)
- localAnnotations.add(
- annSpec
- )
+ if (Array.isArray(spec)) {
+ for (const item of spec) {
+ this.#addSingleAnn(item)
+ }
+ } else {
+ this.#addSingleAnn(spec)
+ }
+
return true
}
return false
@@ -162,8 +181,13 @@ export class AnnotationLayer {
localAnnotations.references.delete(spec.id)
}
}
- async updateAnnotation(spec: AnnotationSpec) {
- await waitFor(() => !!this.nglayer?.layer?.localAnnotations)
+
+ /**
+ * Unsafe method. Caller should ensure this.nglayer.layer is defined
+ *
+ * @param spec
+ */
+ #updateSingleAnn(spec: AnnotationSpec) {
const { localAnnotations } = this.nglayer.layer
const ref = localAnnotations.references.get(spec.id)
const _spec = this.parseNgSpecType(spec)
@@ -178,6 +202,17 @@ export class AnnotationLayer {
}
}
+ async updateAnnotation(spec: AnnotationSpec|AnnotationSpec[]) {
+ await waitFor(() => !!this.nglayer?.layer?.localAnnotations)
+ if (Array.isArray(spec)) {
+ for (const item of spec){
+ this.#updateSingleAnn(item)
+ }
+ return
+ }
+ this.#updateSingleAnn(spec)
+ }
+
private get viewer() {
if ((window as any).viewer) return (window as any).viewer
throw new Error(`window.viewer not defined`)
diff --git a/src/atlasComponents/sapi/core/space/interspaceLinearXform.ts b/src/atlasComponents/sapi/core/space/interspaceLinearXform.ts
index 44c93c74186567e3967d2224cb4937ee391de215..74bf8078cb9ae9765684ec78e5b038d02d4b3c15 100644
--- a/src/atlasComponents/sapi/core/space/interspaceLinearXform.ts
+++ b/src/atlasComponents/sapi/core/space/interspaceLinearXform.ts
@@ -1,29 +1,33 @@
-export const VALID_LINEAR_XFORM_SRC = {
- CCF: "Allen Common Coordination Framework"
-}
-
-export const VALID_LINEAR_XFORM_DST = {
- NEHUBA: "nehuba"
-}
+const VALID_XFORM_SRC = ["CCF_V2_5", "QUICKNII"] as const
+const VALID_XFORM_DST = ["NEHUBA"] as const
-export type TVALID_LINEAR_XFORM_SRC = keyof typeof VALID_LINEAR_XFORM_SRC
-export type TVALID_LINEAR_XFORM_DST = keyof typeof VALID_LINEAR_XFORM_DST
+export type TVALID_LINEAR_XFORM_SRC = typeof VALID_XFORM_SRC[number]
+export type TVALID_LINEAR_XFORM_DST = typeof VALID_XFORM_DST[number]
type TLinearXform = number[][]
const _linearXformDict: Record<
- keyof typeof VALID_LINEAR_XFORM_SRC,
+ TVALID_LINEAR_XFORM_SRC,
Record<
- keyof typeof VALID_LINEAR_XFORM_DST,
+ TVALID_LINEAR_XFORM_DST,
TLinearXform
>> = {
- CCF: {
+ CCF_V2_5: {
NEHUBA: [
[-1e3, 0, 0, 11400000 - 5737500], //
[0, 0, -1e3, 13200000 - 6637500], //
[0, -1e3, 0, 8000000 - 4037500], //
[0, 0, 0, 1],
]
+ },
+ // see https://www.nitrc.org/plugins/mwiki/index.php?title=quicknii:Coordinate_systems
+ QUICKNII: {
+ NEHUBA: [
+ [2.5e4, 0, 0, -5737500], //
+ [0, 2.5e4, 0, -6637500], //
+ [0, 0, 2.5e4, -4037500], //
+ [0, 0, 0, 1],
+ ]
}
}
@@ -48,13 +52,13 @@ export const linearXformDict = getProxyXform(_linearXformDict, (value: Record<st
return defaultXform
})
}) as Record<
- keyof typeof VALID_LINEAR_XFORM_SRC,
+TVALID_LINEAR_XFORM_SRC,
Record<
- keyof typeof VALID_LINEAR_XFORM_DST,
+ TVALID_LINEAR_XFORM_DST,
TLinearXform
>>
-export const linearTransform = async (srcTmplName: keyof typeof VALID_LINEAR_XFORM_SRC, targetTmplName: keyof typeof VALID_LINEAR_XFORM_DST) => {
+export const linearTransform = async (srcTmplName: TVALID_LINEAR_XFORM_SRC, targetTmplName: TVALID_LINEAR_XFORM_DST) => {
return linearXformDict[srcTmplName][targetTmplName]
}
diff --git a/src/atlasComponents/userAnnotations/tools/line.ts b/src/atlasComponents/userAnnotations/tools/line.ts
index 9223b1d989aacccab83e470f9145aca1b81674a9..37299eb4e820d2696e7ed6e61b510c1b3cd7af1f 100644
--- a/src/atlasComponents/userAnnotations/tools/line.ts
+++ b/src/atlasComponents/userAnnotations/tools/line.ts
@@ -23,7 +23,6 @@ export type TLineJsonSpec = {
} & TBaseAnnotationGeomtrySpec
export class Line extends IAnnotationGeometry{
- public id: string
public annotationType = 'Line'
public points: Point[] = []
diff --git a/src/atlasComponents/userAnnotations/tools/point.ts b/src/atlasComponents/userAnnotations/tools/point.ts
index 5086a30459665423439da1b8ee6cbb2fe51d35df..dea8847d747aec28f0f8d852dcdf6c030de8c6c1 100644
--- a/src/atlasComponents/userAnnotations/tools/point.ts
+++ b/src/atlasComponents/userAnnotations/tools/point.ts
@@ -11,7 +11,6 @@ export type TPointJsonSpec = {
} & TBaseAnnotationGeomtrySpec
export class Point extends IAnnotationGeometry {
- id: string
x: number
y: number
z: number
diff --git a/src/atlasComponents/userAnnotations/tools/poly.ts b/src/atlasComponents/userAnnotations/tools/poly.ts
index 4bc86182aa6849161b384923cabd24d76534f502..01dada57995f76dd898547980faa8c9dd9cefb10 100644
--- a/src/atlasComponents/userAnnotations/tools/poly.ts
+++ b/src/atlasComponents/userAnnotations/tools/poly.ts
@@ -12,7 +12,6 @@ export type TPolyJsonSpec = {
} & TBaseAnnotationGeomtrySpec
export class Polygon extends IAnnotationGeometry{
- public id: string
public annotationType = 'Polygon'
public points: Point[] = []
diff --git a/src/viewerModule/nehuba/userLayers/service.ts b/src/viewerModule/nehuba/userLayers/service.ts
index 5937a106ed53e1fa3682f2900446bba171ffcdb5..0a960972f7f7b2770826ae1bdd970fa250e6ef3d 100644
--- a/src/viewerModule/nehuba/userLayers/service.ts
+++ b/src/viewerModule/nehuba/userLayers/service.ts
@@ -1,5 +1,5 @@
import { Injectable, OnDestroy } from "@angular/core"
-import { MatDialog } from "@angular/material/dialog"
+import { MatDialog, MatDialogRef } from "@angular/material/dialog"
import { select, Store } from "@ngrx/store"
import { forkJoin, from, Subscription } from "rxjs"
import { distinctUntilChanged, filter } from "rxjs/operators"
@@ -17,6 +17,8 @@ import { getExportNehuba, getUuid } from "src/util/fn"
import { UserLayerInfoCmp } from "./userlayerInfo/userlayerInfo.component"
import { translateV3Entities } from "src/atlasComponents/sapi/translateV3"
import { MetaV1Schema } from "src/atlasComponents/sapi/typeV3"
+import { AnnotationLayer } from "src/atlasComponents/annotations"
+import { rgbToHex } from 'common/util'
type OmitKeys = "clType" | "id" | "source"
type LayerOption = Omit<atlasAppearance.const.NgLayerCustomLayer, OmitKeys>
@@ -32,9 +34,9 @@ const SUPPORTED_PREFIX = ["nifti://", "precomputed://", "swc://", "deepzoom://"]
type ValidProtocol = typeof SUPPORTED_PREFIX[number]
type ValidInputTypes = File|string
-type ProcessorOutput = {option: LayerOption, url: string, protocol: ValidProtocol, meta: Meta, cleanup: () => void}
+type ProcessorOutput = {option?: LayerOption, url?: string, protocol?: ValidProtocol, meta: Meta, cleanup: () => void}
type ProcessResource = {
- matcher: (input: ValidInputTypes) => boolean
+ matcher: (input: ValidInputTypes) => Promise<boolean>
processor: (input: ValidInputTypes) => Promise<ProcessorOutput>
}
@@ -52,6 +54,7 @@ function RegisterSource(matcher: ProcessResource['matcher']) {
@Injectable()
export class UserLayerService implements OnDestroy {
#idToCleanup = new Map<string, () => void>()
+ #dialogRef: MatDialogRef<unknown>
static VerifyUrl(source: string) {
for (const prefix of SUPPORTED_PREFIX) {
@@ -63,7 +66,7 @@ export class UserLayerService implements OnDestroy {
}
@RegisterSource(
- input => input instanceof File && input.name.endsWith(".swc")
+ async input => input instanceof File && input.name.endsWith(".swc")
)
async processSwc(file: File): ReturnType<ProcessResource['processor']> {
let message = `The swc rendering is experimental. Please contact us on any feedbacks. `
@@ -71,7 +74,7 @@ export class UserLayerService implements OnDestroy {
let src: TVALID_LINEAR_XFORM_SRC
const dst: TVALID_LINEAR_XFORM_DST = "NEHUBA"
if (/ccf/i.test(swcText)) {
- src = "CCF"
+ src = "CCF_V2_5"
message += `CCF detected, applying known transformation.`
}
if (!src) {
@@ -123,7 +126,7 @@ export class UserLayerService implements OnDestroy {
}
@RegisterSource(
- input => input instanceof File && input.name.endsWith(".nii")
+ async input => input instanceof File && input.name.endsWith(".nii")
)
async processNifti(file: File){
const buf = await file.arrayBuffer()
@@ -131,7 +134,7 @@ export class UserLayerService implements OnDestroy {
}
@RegisterSource(
- input => input instanceof File && input.name.endsWith(".nii.gz")
+ async input => input instanceof File && input.name.endsWith(".nii.gz")
)
async processNiiGz(file: File) {
const buf = await file.arrayBuffer()
@@ -146,7 +149,7 @@ export class UserLayerService implements OnDestroy {
}
@RegisterSource(
- input => typeof input === "string" && input.startsWith(OVERLAY_LAYER_PROTOCOL)
+ async input => typeof input === "string" && input.startsWith(OVERLAY_LAYER_PROTOCOL)
)
async processOverlayPath(source: string) {
const strippedSrc = source.replace(OVERLAY_LAYER_PROTOCOL, "")
@@ -161,7 +164,7 @@ export class UserLayerService implements OnDestroy {
}
@RegisterSource(
- input => typeof input === "string" && input.startsWith("precomputed://")
+ async input => typeof input === "string" && input.startsWith("precomputed://")
)
async processPrecomputed(source: string): Promise<ProcessorOutput>{
const url = source.replace("precomputed://", "")
@@ -190,7 +193,7 @@ export class UserLayerService implements OnDestroy {
}
@RegisterSource(
- input => typeof input === "string" && input.startsWith("deepzoom://")
+ async input => typeof input === "string" && input.startsWith("deepzoom://")
)
async processDzi(source: string): Promise<ProcessorOutput> {
const url = source.replace("deepzoom://", "")
@@ -214,13 +217,82 @@ export class UserLayerService implements OnDestroy {
}
}
+ @RegisterSource(async input => {
+ if (input instanceof File && input.name.endsWith(".json")) {
+ const JSON_KEYS = [
+ // "b",
+ // "count",
+ // "g",
+ // "idx",
+ // "name",
+ // "r",
+ "triplets"
+ ]
+ const text = await input.text()
+ const arr = JSON.parse(text)
+
+ // must be array
+ if (!Array.isArray(arr)) {
+ return false
+ }
+ // can only deal with length 1 for now
+ if (arr.length !== 1) {
+ return false
+ }
+ const item = arr[0]
+ for (const key of JSON_KEYS) {
+ if (!item[key]) {
+ console.log(`Parsing PCJson failed. ${key} does not exist`)
+ return false
+ }
+ }
+ return true
+ }
+ return false
+ })
+ async processPCJson(file: File): Promise<ProcessorOutput>{
+ const arr = JSON.parse(await file.text())
+ const item = arr[0]
+ const { r, g, b } = item
+
+ const rgbString = [r, g, b].every(v => Number.isInteger(v))
+ ? rgbToHex([r, g, b])
+ : "#ff0000"
+
+ const id = getUuid()
+ const src = "QUICKNII"
+ const dst = "NEHUBA"
+ const xform = await linearTransform(src, dst)
+ const layer = new AnnotationLayer(id, rgbString, xform)
+
+ const triplets: number[][] = [item.triplets.slice(0, 3)]
+ for (const num of item.triplets as number[]) {
+ if (triplets.at(-1).length === 3) {
+ triplets.push([num])
+ continue
+ }
+ triplets.at(-1).push(num)
+ }
+
+ layer.addAnnotation(triplets.map((triplet, idx) => ({
+ id: `${id}-${idx}`,
+ type: 'point',
+ point: triplet.map(v => v) as [number, number, number]
+ })))
+ return {
+ cleanup: () => layer.dispose(),
+ meta: {
+ filename: file.name,
+ }
+ }
+ }
+
async #processInput(input: ValidInputTypes): Promise<ProcessorOutput> {
for (const { matcher, processor } of SOURCE_PROCESSOR) {
- if (matcher(input)) {
+ if (await matcher(input)) {
return await processor.apply(this, [input])
}
}
- debugger
const inputStr = input instanceof File
? input.name
: input
@@ -236,7 +308,7 @@ export class UserLayerService implements OnDestroy {
this.#idToCleanup.set(id, cleanup)
this.addUserLayer(
id,
- `${protocol}${url}`,
+ protocol && url &&`${protocol}${url}`,
meta,
option,
)
@@ -245,24 +317,30 @@ export class UserLayerService implements OnDestroy {
addUserLayer(
id: string,
- source: string,
+ source: string|null|undefined,
meta: Meta,
options: LayerOption = {}
) {
- UserLayerService.VerifyUrl(source)
- const layer = {
- id,
- clType: "customlayer/nglayer" as const,
- source,
- ...options,
+ if (source) {
+ UserLayerService.VerifyUrl(source)
+ const layer = {
+ id,
+ clType: "customlayer/nglayer" as const,
+ source,
+ ...options,
+ }
+ this.store$.dispatch(
+ atlasAppearance.actions.addCustomLayer({
+ customLayer: layer,
+ })
+ )
}
- this.store$.dispatch(
- atlasAppearance.actions.addCustomLayer({
- customLayer: layer,
- })
- )
- this.dialog.open(UserLayerInfoCmp, {
+ if (this.#dialogRef) {
+ this.#dialogRef.close()
+ this.#dialogRef = null
+ }
+ this.#dialogRef = this.dialog.open(UserLayerInfoCmp, {
data: {
layerName: id,
filename: meta.filename,
@@ -276,15 +354,16 @@ export class UserLayerService implements OnDestroy {
autoFocus: false,
panelClass: ["no-padding-dialog", "w-100"],
})
- .afterClosed()
- .subscribe(() => {
- this.store$.dispatch(atlasAppearance.actions.removeCustomLayer({ id }))
+
+ this.#dialogRef.afterClosed().subscribe(() => {
const cleanup = this.#idToCleanup.get(id)
- if (!cleanup) {
- console.warn(`idToCleanup ${id} could not be found! ${meta.filename}`)
- return
+ cleanup && cleanup()
+ if (source) {
+ this.store$.dispatch(
+ atlasAppearance.actions.removeCustomLayer({ id })
+ )
}
- cleanup()
+ this.#idToCleanup.delete(id)
})
}
diff --git a/tsconfig.json b/tsconfig.json
index bfd3effbebe1bbe4804212fd1188169c72d3937e..77502016e3320cade026e538bf74cf842a976c72 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -3,8 +3,9 @@
"experimentalDecorators": true,
"emitDecoratorMetadata": true,
"moduleResolution": "node",
+ "useDefineForClassFields": false,
"module": "esnext",
- "target": "es2020",
+ "target": "es2022",
"sourceMap": false,
"baseUrl": ".",
"paths": {
@@ -25,4 +26,4 @@
"annotateForClosureCompiler" : true,
"strictTemplates": true
}
-}
\ No newline at end of file
+}