diff --git a/deploy/csp/index.js b/deploy/csp/index.js
index 1d67da419baa8f3c60bb7e93893ce5939f9d5ee2..e976dd482d2845490dd24bebef212ea1ab0aeb17 100644
--- a/deploy/csp/index.js
+++ b/deploy/csp/index.js
@@ -115,7 +115,7 @@ module.exports = {
'https://unpkg.com/d3@6.2.0/', // required for preview component
'https://unpkg.com/mathjax@3.1.2/', // math jax
'https://unpkg.com/three-surfer@0.0.13/dist/bundle.js', // for threeSurfer (freesurfer support in browser)
- 'https://unpkg.com/ng-layer-tune@0.0.6/dist/ng-layer-tune/', // needed for ng layer control
+ 'https://unpkg.com/ng-layer-tune@0.0.12/dist/ng-layer-tune/', // needed for ng layer control
'https://unpkg.com/hbp-connectivity-component@0.6.6/', // needed for connectivity component
(req, res) => res.locals.nonce ? `'nonce-${res.locals.nonce}'` : null,
...SCRIPT_SRC,
diff --git a/docs/releases/v2.11.1.md b/docs/releases/v2.11.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..3c4b52dceda310dbf1790cef6ff3b245e5875ffa
--- /dev/null
+++ b/docs/releases/v2.11.1.md
@@ -0,0 +1,20 @@
+# v2.11.1
+
+## Feature
+
+- Allow point assignment result to be sorted
+- Allow point assignment result to be downloaded as csv
+- Informs user when atlas download should be occurring, and check popup blocker
+- Restores Julich Brain 2.9 in Colin 27 space full mesh view
+
+## Bugfixes
+
+- Fixed point assignment full table not showing
+- On template/parcellation/atlas change, clear currently selected feature
+
+## Behind the scenes
+
+- Bump siibra-api version dependency. Remove guard for feature type query restrictions
+- Removed unused components
+- Tweaked context menu, showing on hover effects
+- now also attempts to fetch `transform.json` when external layer is populated
diff --git a/mkdocs.yml b/mkdocs.yml
index 0f21368640d98f4d765b121fe151f77a45ad86c5..df2d3dcc9969d727dc219a4a2450f0da70533330 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -33,6 +33,7 @@ nav:
- Fetching datasets: 'advanced/datasets.md'
- Display non-atlas volumes: 'advanced/otherVolumes.md'
- Release notes:
+ - v2.11.1: 'releases/v2.11.1.md'
- v2.11.0: 'releases/v2.11.0.md'
- v2.10.3: 'releases/v2.10.3.md'
- v2.10.2: 'releases/v2.10.2.md'
diff --git a/package.json b/package.json
index 593c06d72221ece38464f61b65e29828639ff594..9719e8ac3d423f69b3e79bc3c266675522175327 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "siibra-explorer",
- "version": "2.11.0",
+ "version": "2.11.1",
"description": "siibra-explorer - explore brain atlases. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular",
"scripts": {
"lint": "eslint src --ext .ts",
diff --git a/src/atlas-download/atlas-download.directive.spec.ts b/src/atlas-download/atlas-download.directive.spec.ts
index e81fe2966b376e21eded2b6ec96a79a85faaf616..61c17884a4151cbf5d22cd056e8ca42fc9e242d6 100644
--- a/src/atlas-download/atlas-download.directive.spec.ts
+++ b/src/atlas-download/atlas-download.directive.spec.ts
@@ -3,7 +3,7 @@ import { AtlasDownloadDirective } from './atlas-download.directive';
describe('AtlasDownloadDirective', () => {
it('should create an instance', () => {
- const directive = new AtlasDownloadDirective(NEVER as any);
+ const directive = new AtlasDownloadDirective(NEVER as any, null);
expect(directive).toBeTruthy();
});
});
diff --git a/src/atlas-download/atlas-download.directive.ts b/src/atlas-download/atlas-download.directive.ts
index ce873301181fa39c1975848bd4a76de9b09adbf4..9b2ba98268b8f52cebec05803ca637a0d75e2353 100644
--- a/src/atlas-download/atlas-download.directive.ts
+++ b/src/atlas-download/atlas-download.directive.ts
@@ -1,4 +1,5 @@
import { Directive, HostListener } from '@angular/core';
+import { MatSnackBar } from '@angular/material/snack-bar';
import { Store, select } from '@ngrx/store';
import { Subject, concat, of } from 'rxjs';
import { distinctUntilChanged, shareReplay, take } from 'rxjs/operators';
@@ -70,6 +71,7 @@ export class AtlasDownloadDirective {
*/
window.open(`${endpoint}/atlas_download/${task_id}/download`, "_blank")
this.#busy$.next(false)
+ this.snackbar.open(`Download starting. If it has not, please check your browser's popup blocker.`, 'Dismiss')
} catch (e) {
this.#busy$.next(false)
this.#error$.next(e.toString())
@@ -89,6 +91,6 @@ export class AtlasDownloadDirective {
#error$ = new Subject<string>()
error$ = this.#error$.pipe()
- constructor(private store: Store<MainState>) { }
+ constructor(private store: Store<MainState>, private snackbar: MatSnackBar) { }
}
diff --git a/src/atlas-download/atlas-download.module.ts b/src/atlas-download/atlas-download.module.ts
index b4181a9cc0526254f2cabd6fbe1aa7b9894acfc8..910154cb4bce732b351da2a27738d85cab6a275a 100644
--- a/src/atlas-download/atlas-download.module.ts
+++ b/src/atlas-download/atlas-download.module.ts
@@ -1,6 +1,7 @@
import { NgModule } from '@angular/core';
import { CommonModule } from '@angular/common';
import { AtlasDownloadDirective } from './atlas-download.directive';
+import { MatSnackBarModule } from '@angular/material/snack-bar';
@NgModule({
@@ -9,6 +10,7 @@ import { AtlasDownloadDirective } from './atlas-download.directive';
],
imports: [
CommonModule,
+ MatSnackBarModule,
],
exports: [
AtlasDownloadDirective
diff --git a/src/atlasComponents/sapi/sapi.service.ts b/src/atlasComponents/sapi/sapi.service.ts
index faf55163bb5607a3b9214cee6e4b6089e75cfc40..7959d63fbd7715d7be672d626e02ffaa77d68100 100644
--- a/src/atlasComponents/sapi/sapi.service.ts
+++ b/src/atlasComponents/sapi/sapi.service.ts
@@ -22,7 +22,7 @@ export const useViewer = {
} as const
export const SIIBRA_API_VERSION_HEADER_KEY='x-siibra-api-version'
-export const EXPECTED_SIIBRA_API_VERSION = '0.3.3'
+export const EXPECTED_SIIBRA_API_VERSION = '0.3.4'
let BS_ENDPOINT_CACHED_VALUE: Observable<string> = null
@@ -515,11 +515,11 @@ export class SAPI{
const map = await this.getLabelledMap(parcellation, template)
for (const regionname in map.indices) {
- if (parcellation.id === IDS.PARCELLATION.CORTICAL_LAYERS) {
- if (regionname.includes("left") || regionname.includes("right")) {
- continue
- }
- }
+ // if (parcellation.id === IDS.PARCELLATION.CORTICAL_LAYERS) {
+ // if (regionname.includes("left") || regionname.includes("right")) {
+ // continue
+ // }
+ // }
for (const { volume: volumeIdx, fragment, label } of map.indices[regionname]) {
const { providedVolumes } = map.volumes[volumeIdx]
if (!("neuroglancer/precomputed" in providedVolumes)) {
diff --git a/src/atlasComponents/sapi/schemaV3.ts b/src/atlasComponents/sapi/schemaV3.ts
index de27935f67b5a381ef1d04069f41fad1733a6b6e..e73a25736e182902ac13528a75848ee3a6f44e3c 100644
--- a/src/atlasComponents/sapi/schemaV3.ts
+++ b/src/atlasComponents/sapi/schemaV3.ts
@@ -81,6 +81,10 @@ export interface paths {
/** Get Task Id */
get: operations["get_task_id_atlas_download__task_id__get"]
}
+ "/atlas_download/{task_id}/download": {
+ /** Get Task Id */
+ get: operations["get_task_id_atlas_download__task_id__download_get"]
+ }
"/feature/_types": {
/** Get All Feature Types */
get: operations["get_all_feature_types_feature__types_get"]
@@ -441,12 +445,6 @@ export interface components {
*/
versionIdentifier: string
}
- /**
- * ConnectivityTypes
- * @description An enumeration.
- * @enum {unknown}
- */
- ConnectivityTypes: "FunctionalConnectivity" | "StreamlineCounts" | "StreamlineLengths"
/** CoordinatePointModel */
CoordinatePointModel: {
/** @Type */
@@ -494,20 +492,14 @@ export interface components {
*/
year: string
}
- /**
- * CorticalProfileTypes
- * @description An enumeration.
- * @enum {unknown}
- */
- CorticalProfileTypes: "ReceptorDensityProfile" | "CellDensityProfile" | "BigBrainIntensityProfile"
/** DataFrameModel */
DataFrameModel: {
/** @Type */
"@type": string
/** Index */
- index: unknown[]
+ index: any[]
/** Columns */
- columns: unknown[]
+ columns: any[]
/** Ndim */
ndim: number
/** Data */
@@ -1749,6 +1741,28 @@ export interface operations {
}
}
}
+ get_task_id_atlas_download__task_id__download_get: {
+ /** Get Task Id */
+ parameters: {
+ path: {
+ task_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": Record<string, never>
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
get_all_feature_types_feature__types_get: {
/** Get All Feature Types */
parameters?: {
@@ -1777,7 +1791,7 @@ export interface operations {
parameters: {
query: {
parcellation_id: string
- type?: components["schemas"]["ConnectivityTypes"]
+ type?: string
page?: number
size?: number
}
@@ -1808,7 +1822,7 @@ export interface operations {
query: {
parcellation_id: string
subject?: string
- type?: components["schemas"]["ConnectivityTypes"]
+ type?: string
}
path: {
feature_id: string
@@ -1835,7 +1849,7 @@ export interface operations {
query: {
parcellation_id: string
region_id: string
- type?: components["schemas"]["CorticalProfileTypes"]
+ type?: string
page?: number
size?: number
}
@@ -1861,7 +1875,7 @@ export interface operations {
query: {
parcellation_id: string
region_id: string
- type?: components["schemas"]["CorticalProfileTypes"]
+ type?: string
}
path: {
feature_id: string
diff --git a/src/atlasComponents/sapi/translateV3.ts b/src/atlasComponents/sapi/translateV3.ts
index 79775ba84f4ca64aa8a03169373ed1049a487c92..e92c14d9fe61a46e14b7bb4be99a1541c8e39ec8 100644
--- a/src/atlasComponents/sapi/translateV3.ts
+++ b/src/atlasComponents/sapi/translateV3.ts
@@ -287,17 +287,7 @@ class TranslateV3 {
segLayerSpec.layer.labelIndicies.push(label)
segLayerSpec.region.push(region)
}
- const { ['@id']: mapId } = map
for (const regionname in map.indices) {
- /**
- * temporary fix
- * see https://github.com/FZJ-INM1-BDA/siibra-python/issues/317
- */
- if (mapId === "siibra-map-v0.0.1_bigbrain-cortical-labelled") {
- if (regionname.includes("left") || regionname.includes("right")) {
- continue
- }
- }
for (const index of map.indices[regionname]) {
const { volume:volumeIdx=0, fragment, label } = index
if (!label) {
diff --git a/src/atlasComponents/sapiViews/core/space/boundingBox.directive.ts b/src/atlasComponents/sapiViews/core/space/boundingBox.directive.ts
index 72d0e2e66fc7ff0b8da0d520a6ec4438432a88df..ed1aa7731dfeda9b771a64cdadfc82236bf9eec1 100644
--- a/src/atlasComponents/sapiViews/core/space/boundingBox.directive.ts
+++ b/src/atlasComponents/sapiViews/core/space/boundingBox.directive.ts
@@ -1,4 +1,4 @@
-import { Directive, Input, OnChanges } from "@angular/core";
+import { Directive, Input, OnChanges, Output } from "@angular/core";
import { BehaviorSubject, Observable } from "rxjs";
import { distinctUntilChanged } from "rxjs/operators";
import { BoundingBox, SxplrTemplate, SxplrAtlas } from "src/atlasComponents/sapi/sxplrTypes"
@@ -60,6 +60,7 @@ export class SapiViewsCoreSpaceBoundingBox implements OnChanges{
bbox: null
})
+ @Output('sxplr-sapiviews-core-space-boundingbox-changed')
public bbox$: Observable<{
atlas: SxplrAtlas
space: SxplrTemplate
diff --git a/src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.html b/src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.html
index 8fc0aa7b4411e39a46e1d30f200f45907eb8d1ee..57a9cf3d5031587bc37f7ac36e115319b396f500 100644
--- a/src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.html
+++ b/src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.html
@@ -1,7 +1,7 @@
<div class="sxplr-m-2" *ngIf="busy$ | async">
<spinner-cmp class="sxplr-d-inline-block"></spinner-cmp>
<span>
- Loading assignment ...
+ Performing probabilistic assignment ...
</span>
</div>
@@ -13,9 +13,14 @@
</button>
<!-- simple table -->
- <table mat-table [dataSource]="df | dfToDs" class="sxplr-w-100">
+ <table mat-table [dataSource]="df | dfToDs : simpleTblSort"
+ matSort
+ class="sxplr-w-100"
+ #simpleTblSort="matSort"
+ matSortActive="map value"
+ matSortDirection="desc">
<ng-container matColumnDef="region">
- <th mat-header-cell *matHeaderCellDef>
+ <th mat-header-cell *matHeaderCellDef mat-sort-header>
region
</th>
<td mat-cell *matCellDef="let element">
@@ -25,12 +30,12 @@
</button>
</td>
</ng-container>
- <ng-container matColumnDef="intersection over union">
- <th mat-header-cell *matHeaderCellDef>
- intersection over union
+ <ng-container matColumnDef="map value">
+ <th mat-header-cell *matHeaderCellDef mat-sort-header>
+ map value
</th>
<td mat-cell *matCellDef="let element">
- {{ element['intersection over union'] | prettyPresent }}
+ {{ element['map value'] | prettyPresent }}
</td>
</ng-container>
@@ -42,10 +47,14 @@
<ng-template #datatableTmpl>
<h2 mat-dialog-title>Assignment</h2>
<mat-dialog-content>
- <table mat-table [dataSource]="df$ | async | dfToDs">
+ <table mat-table [dataSource]="df$ | async | dfToDs : comphTableSort"
+ matSort
+ #comphTableSort="matSort"
+ matSortActive="map value"
+ matSortDirection="desc">
<ng-container *ngFor="let column of columns$ | async"
[matColumnDef]="column">
- <th mat-header-cell *matHeaderCellDef>
+ <th mat-header-cell *matHeaderCellDef mat-sort-header>
{{ column }}
</th>
<td mat-cell *matCellDef="let element">
@@ -58,6 +67,14 @@
</table>
</mat-dialog-content>
<mat-dialog-actions align="center">
+ <button mat-raised-button color="primary"
+ [zip-files-output]="zipfileConfig$ | async"
+ zip-files-output-zip-filename="pointassignment.zip">
+ <i class="fas fa-download"></i>
+ <span>
+ Download CSV
+ </span>
+ </button>
<button mat-button mat-dialog-close>Close</button>
- </mat-dialog-actions>
+ </mat-dialog-actions>
</ng-template>
diff --git a/src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.ts b/src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.ts
index 2bf281e7816015f0607b4f77122373d7097705c5..90cf9b9ed7aaca875eec919e4a718e6a6ef66898 100644
--- a/src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.ts
+++ b/src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.ts
@@ -1,12 +1,14 @@
-import { Component, Input, OnDestroy, Output, TemplateRef, EventEmitter } from '@angular/core';
+import { Component, Input, OnDestroy, Output, TemplateRef, EventEmitter, ViewChild, AfterViewInit } from '@angular/core';
import { MatDialog } from '@angular/material/dialog';
-import { BehaviorSubject, EMPTY, Subscription, combineLatest, concat, of } from 'rxjs';
+import { BehaviorSubject, EMPTY, Observable, Subscription, combineLatest, concat, of } from 'rxjs';
import { map, shareReplay, switchMap, tap } from 'rxjs/operators';
-import { SAPI } from 'src/atlasComponents/sapi/sapi.service';
+import { SAPI, EXPECTED_SIIBRA_API_VERSION } from 'src/atlasComponents/sapi/sapi.service';
import { SxplrParcellation, SxplrRegion, SxplrTemplate } from 'src/atlasComponents/sapi/sxplrTypes';
import { translateV3Entities } from 'src/atlasComponents/sapi/translateV3';
import { PathReturn } from 'src/atlasComponents/sapi/typeV3';
import { TSandsPoint } from 'src/util/types';
+import { TZipFileConfig } from "src/zipFilesOutput/type"
+import { environment } from "src/environments/environment"
@Component({
selector: 'sxplr-point-assignment',
@@ -17,7 +19,7 @@ export class PointAssignmentComponent implements OnDestroy {
SIMPLE_COLUMNS = [
"region",
- "intersection over union",
+ "map value",
]
#busy$ = new BehaviorSubject(false)
@@ -44,7 +46,7 @@ export class PointAssignmentComponent implements OnDestroy {
@Output()
clickOnRegion = new EventEmitter<{ target: SxplrRegion, event: MouseEvent }>()
- df$ = combineLatest([
+ df$: Observable<PathReturn<"/map/assign">> = combineLatest([
this.#point,
this.#parcellation,
this.#template,
@@ -66,15 +68,14 @@ export class PointAssignmentComponent implements OnDestroy {
parcellation_id: parcellation.id,
point: point.coordinates.map(v => `${v.value/1e6}mm`).join(','),
space_id: template.id,
- sigma_mm: 3.0
+ sigma_mm: 0
}
}).pipe(
tap(() => this.#busy$.next(false)),
)
- ).pipe(
- shareReplay(1),
)
- })
+ }),
+ shareReplay(1),
)
columns$ = this.df$.pipe(
@@ -95,4 +96,76 @@ export class PointAssignmentComponent implements OnDestroy {
const sxplrReg = await translateV3Entities.translateRegion(region)
this.clickOnRegion.emit({ target: sxplrReg, event })
}
+
+ zipfileConfig$: Observable<TZipFileConfig[]> = combineLatest([
+ this.#point,
+ this.#parcellation,
+ this.#template,
+ this.df$
+ ]).pipe(
+ map(([ pt, parc, tmpl, df ]) => {
+ return [{
+ filename: 'README.md',
+ filecontent: generateReadMe(pt, parc, tmpl)
+ }, {
+ filename: 'pointassignment.csv',
+ filecontent: generateCsv(df)
+ }] as TZipFileConfig[]
+ })
+ )
+}
+
+function generateReadMe(pt: TSandsPoint, parc: SxplrParcellation, tmpl: SxplrTemplate){
+ return `# Point assignment exporter
+
+Exported by siibra-explorer verison \`${environment.VERSION}\` hash: \`${environment.GIT_HASH}\`.
+
+On: ${new Date().toString()}
+
+Data retrieved through siibra-api version \`${EXPECTED_SIIBRA_API_VERSION}\`
+
+Retrieval parameters:
+
+Point
+- coord: ${pt.coordinates.map(v => v.value/1e6).join(',')} mm
+
+Parcellation
+- name: ${parc.name || parc.shortName}
+- id: ${parc.id}
+
+Space
+- name: ${tmpl.name || tmpl.shortName}
+- id: ${tmpl.id}
+`
+}
+
+function escapeFactory(chars: string[] = []){
+ const search = new RegExp(`[${chars.join('').replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}]`, 'g')
+ return function escape(s: string) {
+ return s.replace(search, s => `\\${s}`)
+ }
+}
+
+const escapeDoubleQuotes = escapeFactory(['"'])
+
+function processRow(v: unknown[]): string{
+ const returnValue: string[] = []
+ for (const item of v) {
+
+ // region
+ if (typeof item === "object" && item?.['@type'] === "siibra-0.4/region") {
+ returnValue.push(item['name'])
+ continue
+ }
+
+ returnValue.push(JSON.stringify(item))
+ }
+ return returnValue.map(escapeDoubleQuotes).map(v => `"${v}"`).join(",")
+}
+
+function generateCsv(df: PathReturn<"/map/assign">) {
+ return [
+ df.columns.map(escapeDoubleQuotes).map(v => `"${v}"`).join(","),
+ ...df.data.map(processRow)
+ ].join("\n")
}
diff --git a/src/atlasComponents/sapiViews/volumes/volumes.module.ts b/src/atlasComponents/sapiViews/volumes/volumes.module.ts
index eee2503b61afec1b5533c4d265ce178669ee492c..1a5a32d0f5cf07a536f3e559c29ad835ca1abb6f 100644
--- a/src/atlasComponents/sapiViews/volumes/volumes.module.ts
+++ b/src/atlasComponents/sapiViews/volumes/volumes.module.ts
@@ -6,6 +6,8 @@ import { UtilModule } from 'src/util';
import { SpinnerModule } from 'src/components/spinner';
import { MatDialogModule } from '@angular/material/dialog';
import { MatButtonModule } from '@angular/material/button';
+import { MatSortModule } from '@angular/material/sort';
+import { ZipFilesOutputModule } from 'src/zipFilesOutput/module';
@@ -20,6 +22,8 @@ import { MatButtonModule } from '@angular/material/button';
SpinnerModule,
MatDialogModule,
MatButtonModule,
+ MatSortModule,
+ ZipFilesOutputModule,
],
exports: [
PointAssignmentComponent
diff --git a/src/features/category-acc.directive.ts b/src/features/category-acc.directive.ts
index cddba9e69912494aa8a156eb802fe2b25f76ad1e..73156e7af17e6cf4e39e97fca101655eb02b07bb 100644
--- a/src/features/category-acc.directive.ts
+++ b/src/features/category-acc.directive.ts
@@ -118,7 +118,8 @@ export class CategoryAccDirective implements AfterContentInit, OnDestroy {
return this.datasource
}),
)
- })
+ }),
+ shareReplay(1),
)
constructor(){
diff --git a/src/features/connectivity/connectivityBrowser/connectivityBrowser.component.ts b/src/features/connectivity/connectivityBrowser/connectivityBrowser.component.ts
index dbc546a7ead3d44685043b5654767b8499debe28..f4a2c8e6231db8386047195264206516136d8577 100644
--- a/src/features/connectivity/connectivityBrowser/connectivityBrowser.component.ts
+++ b/src/features/connectivity/connectivityBrowser/connectivityBrowser.component.ts
@@ -156,13 +156,15 @@ export class ConnectivityBrowserComponent implements OnChanges, OnDestroy {
* on
* - accordion update
* - colormap change
- * - fetching matrix
+ * - fetching matrix flag is true
* remove custom layer
*/
merge(
this.#accordionExpanded$,
this.colormap$,
- this.#fetchingMatrix$,
+ this.#fetchingMatrix$.pipe(
+ filter(flag => !!flag)
+ ),
).subscribe(() => {
this.removeCustomLayer()
}),
@@ -207,6 +209,7 @@ export class ConnectivityBrowserComponent implements OnChanges, OnDestroy {
* on pure connection update, update logchecked box
*/
this.#pureConnections$.subscribe(v => {
+ if (!v) return
for (const val of Object.values(v)) {
if (val > 1) {
this.displayForm.get("logChecked").enable()
@@ -256,30 +259,32 @@ export class ConnectivityBrowserComponent implements OnChanges, OnDestroy {
}
const typedName = getType(selectedType.name)
- if (!guardType(typedName)) {
- throw new Error(`type ${typedName} is not in ${validTypes.join(',')}`)
- }
const query = {
parcellation_id: parc.id,
type: typedName
}
this.busy$.next(true)
- return this.sapi.v3Get(
- "/feature/RegionalConnectivity",
- { query }
- ).pipe(
- switchMap(resp =>
- this.sapi.iteratePages(
- resp,
- page => this.sapi.v3Get(
- "/feature/RegionalConnectivity",
- { query: { ...query, page } }
- )
- )
+ return concat(
+ of(
+ [] as PathReturn<"/feature/RegionalConnectivity/{feature_id}">[],
),
- finalize(() => {
- this.busy$.next(false)
- })
+ this.sapi.v3Get(
+ "/feature/RegionalConnectivity",
+ { query }
+ ).pipe(
+ switchMap(resp =>
+ this.sapi.iteratePages(
+ resp,
+ page => this.sapi.v3Get(
+ "/feature/RegionalConnectivity",
+ { query: { ...query, page } }
+ )
+ )
+ ),
+ finalize(() => {
+ this.busy$.next(false)
+ })
+ )
)
})
)),
@@ -328,7 +333,7 @@ export class ConnectivityBrowserComponent implements OnChanges, OnDestroy {
displaySubject$ = this.selectedDataset$.pipe(
distinctUntilChanged((o, n) => o?.id === n?.id),
map(ds => {
- return (idx: number) => ds.subjects[idx]
+ return (idx: number) => ds?.subjects?.[idx]
})
)
@@ -336,7 +341,7 @@ export class ConnectivityBrowserComponent implements OnChanges, OnDestroy {
map(ds => ds ? ds.datasets : [])
)
- #fetchingMatrix$ = new BehaviorSubject<boolean>(true)
+ #fetchingMatrix$ = new BehaviorSubject<boolean>(false)
#matrixInput$ = combineLatest([
this.parcellation$,
@@ -346,7 +351,8 @@ export class ConnectivityBrowserComponent implements OnChanges, OnDestroy {
map(([ parcellation, form, dss ]) => {
const {
selectedDatasetIndex: dsIdx,
- selectedSubjectIndex: subIdx
+ selectedSubjectIndex: subIdx,
+ selectedView
} = form
const ds = dss[dsIdx]
if (!ds) {
@@ -360,7 +366,8 @@ export class ConnectivityBrowserComponent implements OnChanges, OnDestroy {
return {
parcellation,
feature_id: ds.id,
- subject
+ subject,
+ selectedView
}
}),
shareReplay(1),
@@ -379,26 +386,33 @@ export class ConnectivityBrowserComponent implements OnChanges, OnDestroy {
{
query: {
parcellation_id: parcellation.id,
- subject,
+ ...(input.selectedView === "average"
+ ? {}
+ : { subject })
},
path: {
feature_id
}
}
+ ).pipe(
+ finalize(() => {
+ this.#fetchingMatrix$.next(false)
+ })
)
}),
- tap(() => this.#fetchingMatrix$.next(false)),
shareReplay(1),
)
#pureConnections$ = this.#matrixInput$.pipe(
- filter(v => !!v),
- switchMap(({ subject }) =>
+ switchMap(matrixInput =>
this.#selectedMatrix$.pipe(
- filter(v => !!v.matrices[subject]),
withLatestFrom(this.region$),
map(([ v, region ]) => {
- const b = v.matrices[subject]
+ const matrixKey = matrixInput?.selectedView === "average" ? "_average" : matrixInput?.subject
+ if (!v || !matrixInput || !v.matrices?.[matrixKey]) {
+ return null
+ }
+ const b = v.matrices[matrixKey]
const foundIdx = b.columns.findIndex(v => v['name'] === region.name)
if (typeof foundIdx !== 'number') {
return null
@@ -429,6 +443,7 @@ export class ConnectivityBrowserComponent implements OnChanges, OnDestroy {
distinctUntilChanged()
)
]).pipe(
+ filter(conn => !!conn),
map(([ conn, flag ]) => processProfile(conn, flag))
)
))
@@ -545,12 +560,6 @@ function getType(name: string) {
return name.split(".").slice(-1)[0]
}
-const validTypes = ["FunctionalConnectivity", "StreamlineCounts", "StreamlineLengths"]
-
-function guardType(name: unknown): name is "FunctionalConnectivity" | "StreamlineCounts" | "StreamlineLengths" {
- return typeof name === "string" && validTypes.includes(name)
-}
-
type ConnectedArea = {
color: {r: number, g: number, b: number}
name: string
diff --git a/src/features/connectivity/connectivityBrowser/connectivityBrowser.template.html b/src/features/connectivity/connectivityBrowser/connectivityBrowser.template.html
index a7061fe7a83fedfb63c776e39deb613d1c5008dd..416763f02dab74f3dd141ab7d954d7155739a5b7 100644
--- a/src/features/connectivity/connectivityBrowser/connectivityBrowser.template.html
+++ b/src/features/connectivity/connectivityBrowser/connectivityBrowser.template.html
@@ -16,29 +16,37 @@
</mat-select>
</mat-form-field>
- <mat-form-field *ngIf="!(busy$ | async) && (formValue$ | async | getProperty : 'selectedType')" class="flex-grow-1 flex-shrink-1 w-100">
- <mat-label>
- Cohort
- </mat-label>
- <mat-select formControlName="selectedCohort">
- <mat-option *ngFor="let cohort of cohorts$ | async"
- [value]="cohort">
- {{ cohort }}
- </mat-option>
- </mat-select>
- </mat-form-field>
- </div>
- </ng-template>
+ <ng-template [ngIf]="cohorts$ | async" let-cohorts>
+ <ng-template [ngIf]="cohorts.length > 0">
- <ng-template [ngIf]="formValue$ | async | getProperty : 'selectedCohort'">
- <mat-radio-group formControlName="selectedView">
- <mat-radio-button value="average" class="m-2" color="primary">
- Average
- </mat-radio-button>
- <mat-radio-button value="subject" class="m-2" color="primary">
- Subject
- </mat-radio-button>
- </mat-radio-group>
+ <mat-form-field class="flex-grow-1 flex-shrink-1 w-100">
+ <mat-label>
+ Cohort
+ </mat-label>
+ <mat-select formControlName="selectedCohort">
+ <mat-option *ngFor="let cohort of cohorts$ | async"
+ [value]="cohort">
+ {{ cohort }}
+ </mat-option>
+ </mat-select>
+ </mat-form-field>
+
+
+ <ng-template [ngIf]="formValue$ | async | getProperty : 'selectedCohort'">
+ <mat-radio-group formControlName="selectedView">
+ <mat-radio-button value="average" class="m-2" color="primary">
+ Average
+ </mat-radio-button>
+ <mat-radio-button value="subject" class="m-2" color="primary">
+ Subject
+ </mat-radio-button>
+ </mat-radio-group>
+ </ng-template>
+
+ </ng-template>
+ </ng-template>
+
+ </div>
</ng-template>
<ng-template [ngIf]="cohortDatasets$ | async" let-cohortDatasets>
@@ -84,7 +92,7 @@
<!-- loading spinner -->
<ng-template [ngIf]="view$ | async | getProperty : 'fetchingMatrix'"
[ngIfElse]="profileTmpl">
- <div class="d-flex justify-content-center" id = 'blabla'>
+ <div class="d-flex justify-content-center">
<mat-spinner></mat-spinner>
</div>
</ng-template>
@@ -92,7 +100,13 @@
<!-- profile -->
<!-- <pre>{{ view$ | async | json }}</pre> -->
<ng-template #profileTmpl>
- <ng-template [ngIf]="view$ | async | getProperty : 'connections'" let-conn>
+
+ <ng-template #noConnTmpl>
+ No connectivity Found
+ </ng-template>
+
+ <ng-template [ngIf]="view$ | async | getProperty : 'connections'" let-conn
+ [ngIfElse]="noConnTmpl">
<div class="d-flex align-items-center">
<form [formGroup]="displayForm">
<mat-checkbox
diff --git a/src/features/entry/entry.component.ts b/src/features/entry/entry.component.ts
index 979fea404ef798b8f0bfc510477bf423782938b0..722fd8e99735fb88a04ab0435c6a0bccaa760306 100644
--- a/src/features/entry/entry.component.ts
+++ b/src/features/entry/entry.component.ts
@@ -1,13 +1,13 @@
import { AfterViewInit, Component, OnDestroy, QueryList, ViewChildren } from '@angular/core';
import { select, Store } from '@ngrx/store';
-import { distinctUntilChanged, map, scan, shareReplay, switchMap, tap } from 'rxjs/operators';
+import { debounceTime, distinctUntilChanged, map, scan, shareReplay, switchMap, withLatestFrom } from 'rxjs/operators';
import { IDS, SAPI } from 'src/atlasComponents/sapi';
import { Feature } from 'src/atlasComponents/sapi/sxplrTypes';
import { FeatureBase } from '../base';
import * as userInteraction from "src/state/userInteraction"
import { atlasSelection } from 'src/state';
import { CategoryAccDirective } from "../category-acc.directive"
-import { BehaviorSubject, combineLatest, concat, merge, of, Subscription } from 'rxjs';
+import { combineLatest, concat, forkJoin, merge, of, Subject, Subscription } from 'rxjs';
import { DsExhausted, IsAlreadyPulling, PulledDataSource } from 'src/util/pullable';
import { TranslatedFeature } from '../list/list.directive';
@@ -33,56 +33,63 @@ const categoryAcc = <T extends Record<string, unknown>>(categories: T[]) => {
})
export class EntryComponent extends FeatureBase implements AfterViewInit, OnDestroy {
- private _features$ = new BehaviorSubject<TranslatedFeature[]>([])
- features$ = this._features$.pipe(
- shareReplay(1)
- )
-
@ViewChildren(CategoryAccDirective)
catAccDirs: QueryList<CategoryAccDirective>
- public busyTallying$ = new BehaviorSubject<boolean>(false)
- public totals$ = new BehaviorSubject<number>(null)
-
constructor(private sapi: SAPI, private store: Store) {
super()
}
#subscriptions: Subscription[] = []
+ #catAccDirs = new Subject<CategoryAccDirective[]>()
+ features$ = this.#catAccDirs.pipe(
+ switchMap(dirs => concat(
+ of([] as TranslatedFeature[]),
+ merge(...dirs.map((dir, idx) =>
+ dir.datasource$.pipe(
+ switchMap(ds => ds.data$),
+ map(val => ({ val, idx }))
+ ))
+ ).pipe(
+ map(({ idx, val }) => ({ [idx.toString()]: val })),
+ scan((acc, curr) => ({ ...acc, ...curr })),
+ map(record => Object.values(record).flatMap(v => v))
+ )
+ )),
+ shareReplay(1),
+ )
- private _busy$ = new BehaviorSubject<boolean>(false)
- busy$ = this._busy$.pipe(
+ busy$ = this.#catAccDirs.pipe(
+ switchMap(dirs => combineLatest(
+ dirs.map(dir => dir.isBusy$)
+ )),
+ map(flags => flags.some(flag => flag)),
+ distinctUntilChanged(),
shareReplay(1)
)
- ngOnDestroy(): void {
- while (this.#subscriptions.length > 0) this.#subscriptions.pop().unsubscribe()
- }
- ngAfterViewInit(): void {
- const catAccDirs$ = merge(
- of(null),
- this.catAccDirs.changes
- ).pipe(
- map(() => Array.from(this.catAccDirs))
- )
- this.#subscriptions.push(
- catAccDirs$.pipe(
- switchMap(dirs => combineLatest(
- dirs.map(dir => dir.isBusy$)
- )),
- map(flags => flags.some(flag => flag)),
- distinctUntilChanged(),
- ).subscribe(value => {
- this._busy$.next(value)
- }),
- catAccDirs$.pipe(
- tap(() => this.busyTallying$.next(true)),
- switchMap(catArrDirs => merge(
- ...catArrDirs.map((dir, idx) => dir.total$.pipe(
- map(val => ({ idx, val }))
- ))
- )),
-
+ public busyTallying$ = this.#catAccDirs.pipe(
+ switchMap(arr => concat(
+ of(true),
+ forkJoin(
+ arr.map(dir => dir.total$)
+ ).pipe(
+ map(() => false)
+ )
+ )),
+ shareReplay(1)
+ )
+
+ public totals$ = this.#catAccDirs.pipe(
+ switchMap(arr => concat(
+ of(0),
+ merge(
+ ...arr.map((dir, idx) =>
+ dir.total$.pipe(
+ map(val => ({ val, idx }))
+ )
+ )
+ ).pipe(
map(({ idx, val }) => ({ [idx.toString()]: val })),
scan((acc, curr) => ({ ...acc, ...curr })),
map(record => {
@@ -92,11 +99,47 @@ export class EntryComponent extends FeatureBase implements AfterViewInit, OnDest
}
return tally
}),
- tap(num => {
- this.busyTallying$.next(false)
- this.totals$.next(num)
- }),
- ).subscribe(),
+ )
+ ))
+ )
+
+ ngOnDestroy(): void {
+ while (this.#subscriptions.length > 0) this.#subscriptions.pop().unsubscribe()
+ }
+ ngAfterViewInit(): void {
+ this.#subscriptions.push(
+ merge(
+ of(null),
+ this.catAccDirs.changes
+ ).pipe(
+ map(() => Array.from(this.catAccDirs))
+ ).subscribe(dirs => this.#catAccDirs.next(dirs)),
+
+ this.#pullAll.pipe(
+ debounceTime(320),
+ withLatestFrom(this.#catAccDirs),
+ switchMap(([_, dirs]) => combineLatest(dirs.map(dir => dir.datasource$))),
+ ).subscribe(async dss => {
+ await Promise.all(
+ dss.map(async ds => {
+ // eslint-disable-next-line no-constant-condition
+ while (true) {
+ try {
+ await ds.pull()
+ } catch (e) {
+ if (e instanceof DsExhausted) {
+ console.log('exhausted')
+ break
+ }
+ if (e instanceof IsAlreadyPulling ) {
+ continue
+ }
+ throw e
+ }
+ }
+ })
+ )
+ })
)
}
@@ -167,28 +210,8 @@ export class EntryComponent extends FeatureBase implements AfterViewInit, OnDest
}
}
- async pullAll(){
- const dss = Array.from(this.catAccDirs).map(catAcc => catAcc.datasource)
-
- this._features$.next([])
- await Promise.all(
- dss.map(async ds => {
- // eslint-disable-next-line no-constant-condition
- while (true) {
- try {
- await ds.pull()
- } catch (e) {
- if (e instanceof DsExhausted) {
- break
- }
- if (e instanceof IsAlreadyPulling ) {
- continue
- }
- throw e
- }
- }
- })
- )
- this._features$.next(dss.flatMap(ds => ds.finalValue))
+ #pullAll = new Subject()
+ pullAll(){
+ this.#pullAll.next(null)
}
}
diff --git a/src/features/voi-bbox.directive.ts b/src/features/voi-bbox.directive.ts
index d6ed2e0aac4ca11816b5f214699ed9c07cc8a47d..f150225b9cf66f5ce2f68f26c7a936f1c30f6576 100644
--- a/src/features/voi-bbox.directive.ts
+++ b/src/features/voi-bbox.directive.ts
@@ -47,7 +47,7 @@ export class VoiBboxDirective implements OnDestroy {
@Input()
set features(feats: Feature[]){
- this.#voiFeatures = feats.filter(isVoiData)
+ this.#voiFeatures = (feats || []).filter(isVoiData)
this.#features$.next(this.#voiFeatures)
}
get features(): VoiFeature[]{
diff --git a/src/index.html b/src/index.html
index 0f009f4f2d5ab33219754015cfc136a5c8758899..c1cef937495c9ed9218e6ec90326307b07a8816e 100644
--- a/src/index.html
+++ b/src/index.html
@@ -14,7 +14,7 @@
<script src="extra_js.js"></script>
<script src="https://unpkg.com/kg-dataset-previewer@1.2.0/dist/kg-dataset-previewer/kg-dataset-previewer.js" defer></script>
<script src="https://unpkg.com/three-surfer@0.0.13/dist/bundle.js" defer></script>
- <script type="module" src="https://unpkg.com/ng-layer-tune@0.0.6/dist/ng-layer-tune/ng-layer-tune.esm.js"></script>
+ <script type="module" src="https://unpkg.com/ng-layer-tune@0.0.12/dist/ng-layer-tune/ng-layer-tune.esm.js"></script>
<script type="module" src="https://unpkg.com/hbp-connectivity-component@0.6.6/dist/connectivity-component/connectivity-component.js" ></script>
<script defer src="https://unpkg.com/mathjax@3.1.2/es5/tex-svg.js"></script>
<script defer src="https://unpkg.com/d3@6.2.0/dist/d3.min.js"></script>
diff --git a/src/overwrite.scss b/src/overwrite.scss
index 9fd0bb0b88e2fc3039a03040dfa659a2ec341cf8..5b17076e66aca6d569e24b3e6f5d0b6ab4c65f32 100644
--- a/src/overwrite.scss
+++ b/src/overwrite.scss
@@ -289,3 +289,38 @@ a[mat-raised-button]
{
pointer-events: none!important;
}
+
+// list like button
+$llb: "#{$nsp}-list-like-button";
+button.#{$llb}
+{
+ width: 100%;
+
+ > .mat-button-wrapper
+ {
+ display: flex;
+
+ > .#{$llb}-icon
+ {
+ width: 2rem;
+ flex: 0 0 auto;
+ margin: auto;
+ font-size: 150%;
+ }
+
+ > .#{$llb}-body
+ {
+ flex: 1 1 0px;
+ display: flex;
+ flex-direction: column;
+ margin:1rem;
+
+ .#{$llb}-body-line
+ {
+ flex: 0 0 0px;
+ text-align: start;
+ line-height: 1.5rem;
+ }
+ }
+ }
+}
diff --git a/src/state/atlasSelection/util.ts b/src/state/atlasSelection/util.ts
index a76fd1f9f2e8fc45335a5b3695c65bb68322dfef..525df7f1fdc00f7528bdfbbc210a547db3b738ac 100644
--- a/src/state/atlasSelection/util.ts
+++ b/src/state/atlasSelection/util.ts
@@ -1,8 +1,6 @@
import { createSelector, select } from "@ngrx/store";
-import { forkJoin, of, pipe } from "rxjs";
-import { distinctUntilChanged, map, switchMap } from "rxjs/operators";
-import { SAPI } from "src/atlasComponents/sapi";
-import { translateV3Entities } from "src/atlasComponents/sapi/translateV3"
+import { pipe } from "rxjs";
+import { distinctUntilChanged, map } from "rxjs/operators";
import { SxplrAtlas, SxplrParcellation, SxplrTemplate } from "src/atlasComponents/sapi/sxplrTypes";
import { jsonEqual } from "src/util/json";
import * as selectors from "./selectors"
diff --git a/src/state/index.ts b/src/state/index.ts
index 40e84c234c4bca8d7eb7fece2c2c999ab249629f..12adc4b974fb893cef495e9310a5b990966478d4 100644
--- a/src/state/index.ts
+++ b/src/state/index.ts
@@ -71,6 +71,7 @@ export function getStoreEffects() {
plugins.Effects,
atlasSelection.Effect,
userInterface.Effects,
+ userInteraction.Effect,
]
}
diff --git a/src/state/userInteraction/effects.ts b/src/state/userInteraction/effects.ts
index 5d4986ad5965117705e6d1aa869407fabdbd8a65..7fd81d8ae1252522deba3c4f589eda32d61513e7 100644
--- a/src/state/userInteraction/effects.ts
+++ b/src/state/userInteraction/effects.ts
@@ -1,17 +1,33 @@
import { Injectable } from "@angular/core";
import { Actions, createEffect, ofType } from "@ngrx/effects";
-import * as atlasSelectionActions from "../atlasSelection/actions"
import * as userInterface from "../userInterface"
-import { mapTo } from "rxjs/operators";
+import * as atlasSelection from "../atlasSelection"
+import * as actions from "./actions"
+import { filter, map, mapTo, skip } from "rxjs/operators";
+import { Store } from "@ngrx/store";
@Injectable()
export class Effect {
onStandAloneVolumesExistCloseMatDrawer = createEffect(() => this.action.pipe(
- ofType(atlasSelectionActions.clearStandAloneVolumes),
+ ofType(atlasSelection.actions.clearStandAloneVolumes),
mapTo(userInterface.actions.closeSidePanel())
))
- constructor(private action: Actions){
+ #distinctATP$ = this.store.pipe(
+ atlasSelection.fromRootStore.distinctATP(),
+ )
+
+ onATPUpdateUnselectFeature = createEffect(() => this.#distinctATP$.pipe(
+ filter(v => !!v.atlas && !!v.parcellation && !!v.template),
+ /**
+ * First non empty emit would be from selecting atlas.
+ * So ignore it.
+ */
+ skip(1),
+ map(() => actions.clearShownFeature())
+ ))
+
+ constructor(private action: Actions, private store: Store){
}
-}
\ No newline at end of file
+}
diff --git a/src/ui/topMenu/topMenuCmp/topMenu.components.ts b/src/ui/topMenu/topMenuCmp/topMenu.components.ts
index cf6922a353a041bd18b136ac7c1876dbc6e74c05..688da21160db6fef1fd93c1e95e17423cb627cbf 100644
--- a/src/ui/topMenu/topMenuCmp/topMenu.components.ts
+++ b/src/ui/topMenu/topMenuCmp/topMenu.components.ts
@@ -3,7 +3,6 @@ import {
Component,
Input,
TemplateRef,
- ViewChild,
} from "@angular/core";
import { Observable } from "rxjs";
import { map } from "rxjs/operators";
diff --git a/src/ui/topMenu/topMenuCmp/topMenu.template.html b/src/ui/topMenu/topMenuCmp/topMenu.template.html
index a33377a72f41a7126bd272754e3862651fd8b86a..c64c0dcee48ba00781195e882d4ffe17cd84e72d 100644
--- a/src/ui/topMenu/topMenuCmp/topMenu.template.html
+++ b/src/ui/topMenu/topMenuCmp/topMenu.template.html
@@ -22,7 +22,7 @@
<!-- pinned dataset -->
<div iav-fab-speed-dial-child>
- <ng-container *ngTemplateOutlet="pinnedDatasetBtnTmpl">
+ <ng-container *ngTemplateOutlet="downloadAllTmpl">
</ng-container>
</div>
@@ -53,7 +53,7 @@
</ng-container>
<!-- pinned dataset -->
- <ng-container *ngTemplateOutlet="pinnedDatasetBtnTmpl">
+ <ng-container *ngTemplateOutlet="downloadAllTmpl">
</ng-container>
<!-- help one pager -->
@@ -100,7 +100,7 @@
</ng-template>
<!-- pinned dataset btn -->
-<ng-template #pinnedDatasetBtnTmpl>
+<ng-template #downloadAllTmpl>
<div class="btnWrapper"
[matTooltip]="(atlasDlDct.busy$| async) ? busyTxt : idleTxt"
quick-tour
diff --git a/src/ui/ui.module.ts b/src/ui/ui.module.ts
index a657e32cc68916a0b63a485f226dbdd7a05e948e..1d9c79d562f70331b06637468450d964b6d733b4 100644
--- a/src/ui/ui.module.ts
+++ b/src/ui/ui.module.ts
@@ -10,7 +10,6 @@ import { DownloadDirective } from "../util/directives/download.directive";
import { MobileOverlay } from "./nehubaContainer/mobileOverlay/mobileOverlay.component";
import { HumanReadableFileSizePipe } from "src/util/pipes/humanReadableFileSize.pipe";
import { ReorderPanelIndexPipe } from "./nehubaContainer/reorderPanelIndex.pipe";
-import { FixedMouseContextualContainerDirective } from "src/util/directives/FixedMouseContextualContainerDirective.directive";
import { ShareModule } from "src/share";
import { AuthModule } from "src/auth";
import { ActionDialog } from "./actionDialog/actionDialog.component";
@@ -41,7 +40,6 @@ import { HANDLE_SCREENSHOT_PROMISE, TypeHandleScrnShotPromise } from "../screens
ReorderPanelIndexPipe,
/* directive */
DownloadDirective,
- FixedMouseContextualContainerDirective,
],
providers: [
{
@@ -104,7 +102,6 @@ import { HANDLE_SCREENSHOT_PROMISE, TypeHandleScrnShotPromise } from "../screens
// NehubaContainer,
MobileOverlay,
// StatusCardComponent,
- FixedMouseContextualContainerDirective,
]
})
diff --git a/src/util/df-to-ds.pipe.ts b/src/util/df-to-ds.pipe.ts
index 612b8b48220cb6463458d21bd63f5f5c2eb60e7b..f50be028d82a3522df9277be89ef75b59accd33d 100644
--- a/src/util/df-to-ds.pipe.ts
+++ b/src/util/df-to-ds.pipe.ts
@@ -1,5 +1,7 @@
import { CdkTableDataSourceInput } from '@angular/cdk/table';
import { Pipe, PipeTransform } from '@angular/core';
+import { MatSort } from '@angular/material/sort';
+import { MatTableDataSource } from '@angular/material/table';
import { components } from "src/atlasComponents/sapi/schemaV3"
type DF = components["schemas"]["DataFrameModel"]
@@ -19,11 +21,11 @@ function isDf(val: object): val is DF {
})
export class DfToDsPipe implements PipeTransform {
- transform(df: object): CdkTableDataSourceInput<unknown> {
+ transform(df: object, sort: MatSort): CdkTableDataSourceInput<unknown> {
if (!isDf(df)) {
return null
}
- return df.data.map((arr, idx) => {
+ const v = df.data.map((arr, idx) => {
const val = df.index[idx] as any
const returnVal: Record<string, string|number|number[]> = {
index: val,
@@ -37,6 +39,9 @@ export class DfToDsPipe implements PipeTransform {
})
return returnVal
})
+ const ds = new MatTableDataSource(v)
+ ds.sort = sort
+ return ds
}
}
diff --git a/src/util/directives/FixedMouseContextualContainerDirective.directive.spec.ts b/src/util/directives/FixedMouseContextualContainerDirective.directive.spec.ts
deleted file mode 100644
index 0cf11aeb387d08a01a89f616e7095cc716fb63c5..0000000000000000000000000000000000000000
--- a/src/util/directives/FixedMouseContextualContainerDirective.directive.spec.ts
+++ /dev/null
@@ -1,131 +0,0 @@
-import { Component, ViewChild } from "@angular/core";
-import { TestBed } from "@angular/core/testing";
-import { FixedMouseContextualContainerDirective } from "./FixedMouseContextualContainerDirective.directive";
-import { By } from "@angular/platform-browser";
-
-@Component({
- template: ''
-})
-
-class TestCmp{
- @ViewChild(FixedMouseContextualContainerDirective) directive: FixedMouseContextualContainerDirective
-}
-
-describe('FixedMouseContextualContainerDirective', () => {
- beforeEach(() => {
- TestBed.configureTestingModule({
- imports: [
-
- ],
- declarations: [
- TestCmp,
- FixedMouseContextualContainerDirective
- ]
- })
- })
-
- it('> can instantiate directive properly', () => {
- TestBed.overrideComponent(TestCmp, {
- set: {
- template: `
- <div fixedMouseContextualContainerDirective>
- </div>
- `
- }
- }).compileComponents()
-
- const fixture = TestBed.createComponent(TestCmp)
- fixture.detectChanges()
- const directive = fixture.debugElement.query( By.directive(FixedMouseContextualContainerDirective) )
- expect(directive).toBeTruthy()
-
- expect(fixture.componentInstance.directive).toBeTruthy()
- })
-
- describe('> hides if no content', () => {
- it('> on #show, if content exists, isShown will be true', () => {
-
- TestBed.overrideComponent(TestCmp, {
- set: {
- template: `
- <div fixedMouseContextualContainerDirective>
- <span>Hello World</span>
- </div>
- `
- }
- }).compileComponents()
-
- const fixture = TestBed.createComponent(TestCmp)
- fixture.detectChanges()
-
- const cmp = fixture.componentInstance
- cmp.directive.show()
- fixture.detectChanges()
- expect(cmp.directive.isShown).toBeTrue()
- })
-
- it('> on #show, if only comment exists, isShown will be false', () => {
-
- TestBed.overrideComponent(TestCmp, {
- set: {
- template: `
- <div fixedMouseContextualContainerDirective>
- <!-- hello world -->
- </div>
- `
- }
- }).compileComponents()
-
- const fixture = TestBed.createComponent(TestCmp)
- fixture.detectChanges()
-
- const cmp = fixture.componentInstance
- cmp.directive.show()
- fixture.detectChanges()
- expect(cmp.directive.isShown).toBeFalse()
- })
-
- it('> on #show, if only text exists, isShown will be false', () => {
-
- TestBed.overrideComponent(TestCmp, {
- set: {
- template: `
- <div fixedMouseContextualContainerDirective>
- hello world
- </div>
- `
- }
- }).compileComponents()
-
- const fixture = TestBed.createComponent(TestCmp)
- fixture.detectChanges()
-
- const cmp = fixture.componentInstance
- cmp.directive.show()
- fixture.detectChanges()
- expect(cmp.directive.isShown).toBeFalse()
- })
-
- it('> on #show, if nothing exists, isShown will be false', () => {
-
- TestBed.overrideComponent(TestCmp, {
- set: {
- template: `
- <div fixedMouseContextualContainerDirective>
- </div>
- `
- }
- }).compileComponents()
-
- const fixture = TestBed.createComponent(TestCmp)
- fixture.detectChanges()
-
- const cmp = fixture.componentInstance
- cmp.directive.show()
- fixture.detectChanges()
- expect(cmp.directive.isShown).toBeFalse()
- })
- })
-
- // TODO complete tests for FixedMouseContextualContainerDirective
-})
\ No newline at end of file
diff --git a/src/util/directives/FixedMouseContextualContainerDirective.directive.ts b/src/util/directives/FixedMouseContextualContainerDirective.directive.ts
deleted file mode 100644
index d7fbf0905efa08166e8f864f45cf375a97950102..0000000000000000000000000000000000000000
--- a/src/util/directives/FixedMouseContextualContainerDirective.directive.ts
+++ /dev/null
@@ -1,72 +0,0 @@
-import { Directive, ElementRef, EventEmitter, HostBinding, Input, Output, AfterContentChecked, ChangeDetectorRef, AfterViewInit } from "@angular/core";
-
-@Directive({
- selector: '[fixedMouseContextualContainerDirective]',
- exportAs: 'iavFixedMouseCtxContainer'
-})
-
-export class FixedMouseContextualContainerDirective implements AfterContentChecked {
-
- private defaultPos: [number, number] = [-1e3, -1e3]
- public isShown: boolean = false
-
- @Input()
- public mousePos: [number, number] = this.defaultPos
-
- @Output()
- public onShow: EventEmitter<null> = new EventEmitter()
-
- @Output()
- public onHide: EventEmitter<null> = new EventEmitter()
-
- constructor(
- public el: ElementRef,
- private cdr: ChangeDetectorRef,
- ) {
- }
-
- public recalculatePosition(){
- const clientWidth = this.el.nativeElement.clientWidth
- const clientHeight = this.el.nativeElement.clientHeight
-
- const windowInnerWidth = window.innerWidth
- const windowInnerHeight = window.innerHeight
- if (windowInnerHeight - this.mousePos[1] < clientHeight) {
- this.mousePos[1] = windowInnerHeight - clientHeight
- }
-
- if ((windowInnerWidth - this.mousePos[0]) < clientWidth) {
- this.mousePos[0] = windowInnerWidth - clientWidth
- }
-
- this.transform = `translate(${this.mousePos.map(v => v.toString() + 'px').join(', ')})`
- }
-
- ngAfterContentChecked(){
- if (this.el.nativeElement.childElementCount === 0) {
- this.hide()
- }
- this.recalculatePosition()
- this.cdr.markForCheck()
- }
-
- public show() {
- this.styleDisplay = 'inline-block'
- this.isShown = true
- this.onShow.emit()
- }
-
- public hide() {
- this.transform = `translate(${this.defaultPos.map(v => v.toString() + 'px').join(', ')})`
- this.styleDisplay = 'none'
- this.isShown = false
- this.onHide.emit()
- }
-
- @HostBinding('style.display')
- public styleDisplay = `none`
-
- @HostBinding('style.transform')
- public transform = `translate(${this.mousePos.map(v => v.toString() + 'px').join(', ')})`
-
-}
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
index f68170be4a59e2610000d997b852084512529dc4..be87e8eeec2a8fad91596feadac14a1dde29da3f 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
@@ -46,13 +46,16 @@ export class NehubaLayerControlService implements OnDestroy{
combineLatest([
this.completeNgIdLabelRegionMap$,
this.customLayers$,
+ this.selectedRegion$,
]).pipe(
- map(([record, layers]) => {
+ map(([record, layers, selectedRegions]) => {
const returnVal: IColorMap = {}
const cmCustomLayers = layers.filter(l => l.clType === "customlayer/colormap") as atlasAppearance.const.ColorMapCustomLayer[]
const cmBaseLayers = layers.filter(l => l.clType === "baselayer/colormap") as atlasAppearance.const.ColorMapCustomLayer[]
+ const usingCustomCM = cmCustomLayers.length > 0
+
const useCm = (() => {
/**
* if custom layer exist, use the last custom layer
@@ -72,11 +75,20 @@ export class NehubaLayerControlService implements OnDestroy{
get: (r: SxplrRegion) => r.color
}
})()
+
+ const selectedRegionNameSet = new Set(selectedRegions.map(v => v.name))
for (const [ngId, labelRecord] of Object.entries(record)) {
for (const [label, region] of Object.entries(labelRecord)) {
if (!region.color) continue
- const [ red, green, blue ] = useCm.get(region) || [200, 200, 200]
+ /**
+ * if custom color map is used, do *not* selectively paint selected region
+ * custom color map can choose to subscribe to selected regions, and update the color map accordingly,
+ * if they wish to respect the selected regions
+ */
+ const [ red, green, blue ] = usingCustomCM || selectedRegionNameSet.size === 0 || selectedRegionNameSet.has(region.name)
+ ? useCm.get(region) || [200, 200, 200]
+ : [255, 255, 255]
if (!returnVal[ngId]) {
returnVal[ngId] = {}
}
diff --git a/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts b/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
index 051d366a882a44f75f782e10fe58ccd25314869e..7db5392a46b74554df8c9e2db2ab8d5e221ab44b 100644
--- a/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
+++ b/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
@@ -196,6 +196,8 @@ describe('> mesh.service.ts', () => {
beforeEach(() => {
const mockStore = TestBed.inject(MockStore)
mockStore.overrideSelector(atlasSelection.selectors.selectedRegions, [])
+ mockStore.overrideSelector(atlasSelection.selectors.selectedTemplate, {} as any)
+ mockStore.overrideSelector(atlasSelection.selectors.selectedParcellation, {} as any)
})
it("> load all meshes", () => {
@@ -226,6 +228,8 @@ describe('> mesh.service.ts', () => {
beforeEach(() => {
const mockStore = TestBed.inject(MockStore)
mockStore.overrideSelector(atlasSelection.selectors.selectedRegions, [fits1])
+ mockStore.overrideSelector(atlasSelection.selectors.selectedTemplate, {} as any)
+ mockStore.overrideSelector(atlasSelection.selectors.selectedParcellation, {} as any)
})
it("> load only selected mesh", () => {
diff --git a/src/viewerModule/nehuba/mesh.service/mesh.service.ts b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
index 29a40e94c6882b6022033b2d55103627d3d9b8cf..d46e128f4a84d082272101b67a215bf75d5165c3 100644
--- a/src/viewerModule/nehuba/mesh.service/mesh.service.ts
+++ b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
@@ -7,6 +7,7 @@ import { selectorAuxMeshes } from "../store";
import { LayerCtrlEffects } from "../layerCtrl.service/layerCtrl.effects";
import { atlasSelection } from "src/state";
import { BaseService } from "../base.service/base.service";
+import { IDS } from "src/atlasComponents/sapi"
/**
* control mesh loading etc
@@ -126,8 +127,21 @@ export class NehubaMeshService implements OnDestroy {
this.#allSegmentMeshes$,
this.#selectedSegmentMeshes$,
this.#auxMesh$,
+ this.store$.pipe(
+ select(atlasSelection.selectors.selectedTemplate)
+ ),
+ this.store$.pipe(
+ select(atlasSelection.selectors.selectedParcellation)
+ )
]).pipe(
- switchMap(([ allSegMesh, selectedSegMesh, auxmesh ]) => {
+ switchMap(([ allSegMesh, selectedSegMesh, auxmesh, selectedTemplate, selectedParcellation ]) => {
+ /**
+ * TODO monkey patching jba29 in colin to show all meshes
+ *
+ */
+ if (selectedParcellation.id === IDS.PARCELLATION.JBA29 && selectedTemplate.id === IDS.TEMPLATES.COLIN27) {
+ return of(...allSegMesh)
+ }
const hasSegSelected = selectedSegMesh.some(v => v.labelIndicies.length !== 0)
const hasAuxMesh = auxmesh.length > 0
const meshesToLoad: IMeshesToLoad[] = []
diff --git a/src/viewerModule/nehuba/userLayers/service.ts b/src/viewerModule/nehuba/userLayers/service.ts
index 042cc54851be1e31cf457926d81768dfcbc2a5a8..3fe9d0a7db656354ed6217ebd13a0fd0354deae4 100644
--- a/src/viewerModule/nehuba/userLayers/service.ts
+++ b/src/viewerModule/nehuba/userLayers/service.ts
@@ -1,8 +1,8 @@
import { Injectable, OnDestroy } from "@angular/core"
import { MatDialog } from "@angular/material/dialog"
import { select, Store } from "@ngrx/store"
-import { concat, of, Subscription } from "rxjs"
-import { pairwise } from "rxjs/operators"
+import { concat, from, of, Subscription } from "rxjs"
+import { catchError, map, pairwise, switchMap } from "rxjs/operators"
import {
linearTransform,
TVALID_LINEAR_XFORM_DST,
@@ -198,29 +198,48 @@ export class UserLayerService implements OnDestroy {
) {
this.#subscription.push(
concat(
- of(null),
- this.routerSvc.customRoute$.pipe(select((v) => v[OVERLAY_LAYER_KEY]))
- )
- .pipe(pairwise())
- .subscribe(([prev, curr]) => {
- if (prev) {
- this.removeUserLayer(prev)
+ of(null as string),
+ this.routerSvc.customRoute$.pipe(
+ select(v => v[OVERLAY_LAYER_KEY])
+ )
+ ).pipe(
+ pairwise(),
+ switchMap(([prev, curr]) => {
+ /**
+ * for precomputed sources, check if transform.json exists.
+ * if so, try to fetch it, and set it as transform
+ */
+ if (!curr) {
+ return of([prev, curr, null])
}
- if (curr) {
- this.addUserLayer(
- curr,
- {
- filename: curr,
- message: `Overlay layer populated in URL`,
- },
- {
- shader: getShader({
- colormap: EnumColorMapName.MAGMA,
- }),
- }
- )
+ if (!curr.startsWith("precomputed://")) {
+ return of([prev, curr, null])
}
+ return from(fetch(`${curr.replace('precomputed://', '')}/transform.json`).then(res => res.json())).pipe(
+ catchError(() => of([prev, curr, null])),
+ map(transform => [prev, curr, transform])
+ )
})
+ ).subscribe(([prev, curr, transform]) => {
+ if (prev) {
+ this.removeUserLayer(prev)
+ }
+ if (curr) {
+ this.addUserLayer(
+ curr,
+ {
+ filename: curr,
+ message: `Overlay layer populated in URL`,
+ },
+ {
+ shader: getShader({
+ colormap: EnumColorMapName.MAGMA,
+ }),
+ transform
+ }
+ )
+ }
+ })
)
}
diff --git a/src/viewerModule/viewerCmp/viewerCmp.component.ts b/src/viewerModule/viewerCmp/viewerCmp.component.ts
index 136f0baf82166534a9e0d7480159e0dce58edc32..2dbd534dbd0a309ec23fcf1f6545a88bfe1b5a18 100644
--- a/src/viewerModule/viewerCmp/viewerCmp.component.ts
+++ b/src/viewerModule/viewerCmp/viewerCmp.component.ts
@@ -14,6 +14,7 @@ import { atlasAppearance, atlasSelection, userInteraction } from "src/state";
import { SxplrTemplate } from "src/atlasComponents/sapi/sxplrTypes";
import { EntryComponent } from "src/features/entry/entry.component";
import { TFace, TSandsPoint, getCoord } from "src/util/types";
+import { wait } from "src/util/fn";
@Component({
selector: 'iav-cmp-viewer-container',
@@ -438,4 +439,14 @@ export class ViewerCmp implements OnDestroy {
})
)
}
+
+ @ViewChild('voiFeatureEntryCmp')
+ voiFeatureEntryCmp: EntryComponent
+
+ async pullAllVoi(){
+ if (this.voiFeatureEntryCmp){
+ await wait(320)
+ this.voiFeatureEntryCmp.pullAll()
+ }
+ }
}
diff --git a/src/viewerModule/viewerCmp/viewerCmp.template.html b/src/viewerModule/viewerCmp/viewerCmp.template.html
index 0c80076b1593496a3f94cfb7892f312d192cad22..459fb19e841d22944af9cf5a8bca36512bcb6d0c 100644
--- a/src/viewerModule/viewerCmp/viewerCmp.template.html
+++ b/src/viewerModule/viewerCmp/viewerCmp.template.html
@@ -905,62 +905,69 @@
<ng-template #viewerStatusCtxMenu let-data>
<ng-template [ngIf]="data.context" let-context>
- <mat-list>
+ <!-- ref space & position -->
+ <ng-container [ngSwitch]="context.viewerType">
- <!-- ref space & position -->
- <ng-container [ngSwitch]="context.viewerType">
-
- <!-- volumetric i.e. nehuba -->
- <ng-container *ngSwitchCase="'nehuba'">
- <mat-list-item mat-ripple
- (click)="selectPoint({ point: context.payload.mouse.real }, data.metadata.template)">
- <div mat-list-icon>
- <i class="fas fa-map"></i>
- </div>
-
- <div mat-line>
+ <!-- volumetric i.e. nehuba -->
+ <ng-container *ngSwitchCase="'nehuba'">
+ <button mat-button class="sxplr-list-like-button"
+ (click)="selectPoint({ point: context.payload.mouse.real }, data.metadata.template)">
+
+ <div class="sxplr-list-like-button-icon">
+ <i class="fas fa-map"></i>
+ </div>
+
+ <div class="sxplr-list-like-button-body">
+
+ <span class="sxplr-list-like-button-body-line">
{{ context.payload.mouse.real | nmToMm | numbers | addUnitAndJoin : '' }} (mm)
- </div>
- <div mat-line class="text-muted">
+ </span>
+ <span class="sxplr-list-like-button-body-line text-muted">
Point
- </div>
- <div mat-line class="text-muted">
+ </span>
+ <span class="sxplr-list-like-button-body-line text-muted">
{{ data.metadata.template.name }}
- </div>
- </mat-list-item>
- </ng-container>
-
- <ng-container *ngSwitchCase="'threeSurfer'">
-
- <ng-template [ngIf]="context.payload?.faceIndex" let-faceIndex>
- <ng-template [ngIf]="context.payload?.vertexIndices" let-vertexIndices>
- <mat-list-item mat-ripple
- (click)="selectPoint({ face: faceIndex, vertices: vertexIndices }, data.metadata.template)">
-
- <div mat-list-icon>
- <i class="fas fa-map"></i>
- </div>
-
- <div mat-line>
+ </span>
+ </div>
+
+ </button>
+ </ng-container>
+
+ <ng-container *ngSwitchCase="'threeSurfer'">
+
+ <ng-template [ngIf]="context.payload?.faceIndex" let-faceIndex>
+ <ng-template [ngIf]="context.payload?.vertexIndices" let-vertexIndices>
+ <button mat-button class="sxplr-list-like-button"
+ (click)="selectPoint({ face: faceIndex, vertices: vertexIndices }, data.metadata.template)">
+
+ <div class="sxplr-list-like-button-icon">
+ <i class="fas fa-map"></i>
+ </div>
+
+ <div class="sxplr-list-like-button-body">
+
+ <span class="sxplr-list-like-button-body-line">
Face Index: {{ faceIndex }}, Vertices Index: {{ vertexIndices | addUnitAndJoin : '' }}
- </div>
- <div mat-line class="text-muted">
+ </span>
+ <span class="sxplr-list-like-button-body-line text-muted">
Mesh Face
- </div>
- <div mat-line class="text-muted">
+ </span>
+ <span class="sxplr-list-like-button-body-line text-muted">
{{ data.metadata.template.name }}
- </div>
- </mat-list-item>
- </ng-template>
+ </span>
+ </div>
+
+ </button>
+
</ng-template>
-
- </ng-container>
-
- <ng-container *ngSwitchDefault>
- DEFAULT
- </ng-container>
+ </ng-template>
+
+ </ng-container>
+
+ <ng-container *ngSwitchDefault>
+ DEFAULT
</ng-container>
- </mat-list>
+ </ng-container>
</ng-template>
</ng-template>
@@ -968,41 +975,32 @@
<!-- viewer state hover ctx menu -->
<ng-template #viewerStatusRegionCtxMenu let-data>
<!-- hovered ROIs -->
- <mat-list>
- <ng-template ngFor [ngForOf]="data.metadata.hoveredRegions"
- let-region
- let-first="first">
+ <ng-template ngFor [ngForOf]="data.metadata.hoveredRegions"
+ let-region
+ let-first="first">
- <mat-divider class="top-0" *ngIf="!first"></mat-divider>
+ <mat-divider class="top-0" *ngIf="!first"></mat-divider>
- <mat-list-item mat-ripple
- class="cursor-default"
- (click)="$event.ctrlKey ? toggleRoi(region) : selectRoi(region)">
+ <button mat-button
+ (click)="$event.ctrlKey ? toggleRoi(region) : selectRoi(region)"
+ class="sxplr-list-like-button">
+
+ <div class="sxplr-list-like-button-icon">
+ <i class="fas fa-brain"></i>
+ </div>
- <div mat-list-icon>
- <i class="fas fa-brain"></i>
- </div>
+ <div class="sxplr-list-like-button-body">
- <span mat-line>
+ <span class="sxplr-list-like-button-body-line">
{{ region.name }}
</span>
- <span mat-line class="text-muted">
- <span>
- Brain region
- </span>
+ <span class="sxplr-list-like-button-body-line text-muted">
+ Brain region
</span>
-
- <!-- lookup region -->
- <!-- <button mat-icon-button
- (click)="selectRoi(region)"
- ctx-menu-dismiss>
- <i class="fas fa-search"></i>
- </button> -->
- </mat-list-item>
-
+ </div>
+ </button>
- </ng-template>
- </mat-list>
+ </ng-template>
</ng-template>
<!-- feature tmpls -->
@@ -1126,6 +1124,7 @@
class="sxplr-pe-all mat-elevation-z8"
[template]="view.selectedTemplate"
[bbox]="bbox.bbox$ | async | getProperty : 'bbox'"
+ [attr.data-feature-length]="((voiFeatureEntryCmp.features$ | async) || []).length"
#voiFeatureEntryCmp="featureEntryCmp">
</sxplr-feature-entry>
@@ -1143,7 +1142,7 @@
iav-switch
[iav-switch-state]="false"
#voiSwitch="iavSwitch"
- (iav-switch-event)="$event && voiFeatureEntryCmp.pullAll()"
+ (iav-switch-event)="$event && pullAllVoi()"
(click)="voiSwitch.toggle()">
<ng-template [ngIf]="voiSwitch.switchState$ | async" [ngIfElse]="chevronCollapseTmpl">
@@ -1175,6 +1174,7 @@
<div
sxplr-sapiviews-core-space-boundingbox
+ (sxplr-sapiviews-core-space-boundingbox-changed)="pullAllVoi()"
[sxplr-sapiviews-core-space-boundingbox-atlas]="selectedAtlas$ | async"
[sxplr-sapiviews-core-space-boundingbox-space]="templateSelected$ | async"
[sxplr-sapiviews-core-space-boundingbox-spec]="viewerCtx$ | async | nehubaVCtxToBbox"