diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c3c07d114df83ae2c2dc663da720cc5451914f31..78d9a7e7b59248e5b280835a47c7860b579061e2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -15,10 +15,10 @@ jobs:
steps:
- uses: actions/checkout@v2
- - name: Use Node.js 14.x for lint
+ - name: Use Node.js 16.x for lint
uses: actions/setup-node@v1
with:
- node-version: '14.x'
+ node-version: '16.x'
- run: npm i
- run: npm run lint
@@ -28,7 +28,7 @@ jobs:
strategy:
matrix:
- node-version: [12.x, 14.x, 16.x]
+ node-version: [16.x]
env:
NODE_ENV: test
@@ -47,7 +47,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
- node-version: [12.x, 14.x, 16.x]
+ node-version: [16.x]
env:
NODE_ENV: test
diff --git a/common/constants.js b/common/constants.js
index cf56106555a3b26559711671e22fcc0e06494e86..94a42b81abf59142a3d50f5a175d64208e02fbbd 100644
--- a/common/constants.js
+++ b/common/constants.js
@@ -108,6 +108,7 @@ If you do not accept the Terms & Conditions you are not permitted to access or u
CANNOT_DECIPHER_HEMISPHERE: 'Cannot decipher region hemisphere.',
DOES_NOT_SUPPORT_MULTI_REGION_SELECTION: `Please only select a single region.`,
MULTI_REGION_SELECTION: `Multi region selection`,
+ DESCRIPTION: 'Description',
REGIONAL_FEATURES: 'Regional features',
CONNECTIVITY: 'Connectivity',
NO_ADDIONTAL_INFO_AVAIL: `Currently, no additional information is linked to this region.`,
diff --git a/deploy/bkwdCompat/urlState.js b/deploy/bkwdCompat/urlState.js
index 66f92c3dc4f6b375fcfe0c70f16a685b43c30e0d..64093f9e035e19fc95c9ee8eea8b2caa2303912b 100644
--- a/deploy/bkwdCompat/urlState.js
+++ b/deploy/bkwdCompat/urlState.js
@@ -114,8 +114,12 @@ const WARNING_STRINGS = {
REGION_SELECT_ERROR: 'Region selected cannot be processed properly.',
TEMPLATE_ERROR: 'Template not found.',
}
-
+const pliPreviewUrl = `/a:juelich:iav:atlas:v1.0.0:1/t:minds:core:referencespace:v1.0.0:a1655b99-82f1-420f-a3c2-fe80fd4c8588/p:juelich:iav:atlas:v1.0.0:4/@:0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..7LIy..1qI1a.D31U~.i-Os~..HRE/f:siibra:features:voi:19c437087299dd62e7c507200f69aea6`
module.exports = (query, _warningCb) => {
+
+ const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
+ let redirectUrl = `${HOST_PATHNAME}/#`
+
const {
standaloneVolumes,
niftiLayers, // deprecating - check if anyone calls this url
@@ -163,7 +167,17 @@ module.exports = (query, _warningCb) => {
if (Array.isArray(parsedDsp)) {
if (parsedDsp.length === 1) {
const { datasetId, filename } = parsedDsp[0]
- dsp = `/dsp:${encodeId(datasetId)}::${encodeURI(filename)}`
+ if (datasetId === "minds/core/dataset/v1.0.0/b08a7dbc-7c75-4ce7-905b-690b2b1e8957") {
+ /**
+ * if preview pli link, return hardcoded link
+ */
+ return `${HOST_PATHNAME}/#${pliPreviewUrl}`
+ } else {
+ /**
+ * TODO deprecate dsp
+ */
+ dsp = `/dsp:${encodeId(datasetId)}::${encodeURI(filename)}`
+ }
} else {
searchParam.set(`previewingDatasetFiles`, previewingDatasetFiles)
}
@@ -206,8 +220,6 @@ module.exports = (query, _warningCb) => {
// ignore region selected and move on
}
}
- const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
- let redirectUrl = `${HOST_PATHNAME}/#`
if (standaloneVolumes) {
searchParam.set('standaloneVolumes', standaloneVolumes)
if (nav) redirectUrl += nav
diff --git a/deploy/csp/index.js b/deploy/csp/index.js
index 7273c69b4e841bc5e0be5aa85d68fb8c10b15e09..898228ce845b95c747d027704c08ab96f8196c30 100644
--- a/deploy/csp/index.js
+++ b/deploy/csp/index.js
@@ -54,7 +54,9 @@ const connectSrc = [
'object.cscs.ch',
// required for dataset previews
- 'hbp-kg-dataset-previewer.apps.hbp.eu/v2/',
+
+ // spatial transform
+ "hbp-spatial-backend.apps.hbp.eu",
// injected by env var
...CSP_CONNECT_SRC
@@ -102,7 +104,6 @@ module.exports = {
],
imgSrc: [
"'self'",
- "hbp-kg-dataset-previewer.apps.hbp.eu/v2/"
],
scriptSrc:[
"'self'",
@@ -118,6 +119,9 @@ module.exports = {
...WHITE_LIST_SRC,
...defaultAllowedSites
],
+ frameSrc: [
+ "*"
+ ],
reportUri: CSP_REPORT_URI || '/report-violation'
},
reportOnly
diff --git a/src/atlasComponents/annotations/annotation.service.ts b/src/atlasComponents/annotations/annotation.service.ts
index ec352e5fbd3707b63b4da42ca92e9157c36bfb0c..fd67601ee087cf32ddd230d7e42b3ca9fdaea421 100644
--- a/src/atlasComponents/annotations/annotation.service.ts
+++ b/src/atlasComponents/annotations/annotation.service.ts
@@ -146,7 +146,8 @@ export class AnnotationLayer {
}
}
updateAnnotation(spec: AnnotationSpec) {
- const localAnnotations = this.nglayer.layer.localAnnotations
+ const localAnnotations = this.nglayer?.layer?.localAnnotations
+ if (!localAnnotations) return
const ref = localAnnotations.references.get(spec.id)
const _spec = this.parseNgSpecType(spec)
if (ref) {
diff --git a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.component.ts b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.component.ts
index 08bdb9d55bd85a616914cae076797142f3ff1026..88614d6194880e18d3e802de65c1660f75557b13 100644
--- a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.component.ts
+++ b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.component.ts
@@ -1,5 +1,8 @@
-import { Component, Input } from "@angular/core";
+import { Component, Input, OnChanges, SimpleChanges } from "@angular/core";
import { SapiDatasetModel } from "src/atlasComponents/sapi";
+import { CONST } from "common/constants"
+
+const RESTRICTED_ACCESS_ID = "https://nexus.humanbrainproject.org/v0/data/minds/core/embargostatus/v1.0.0/3054f80d-96a8-4dce-9b92-55c68a8b5efd"
@Component({
selector: `sxplr-sapiviews-core-datasets-dataset`,
@@ -9,7 +12,17 @@ import { SapiDatasetModel } from "src/atlasComponents/sapi";
]
})
-export class DatasetView {
+export class DatasetView implements OnChanges{
@Input('sxplr-sapiviews-core-datasets-dataset-input')
dataset: SapiDatasetModel
+
+ public isRestricted = false
+ public CONST = CONST
+
+ ngOnChanges(changes: SimpleChanges): void {
+ const { dataset } = changes
+ if (dataset) {
+ this.isRestricted = (dataset.currentValue as SapiDatasetModel)?.metadata?.accessibility?.["@id"] === RESTRICTED_ACCESS_ID
+ }
+ }
}
diff --git a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.template.html b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.template.html
index 68ce4f9a8540b0c1154408328260ed2e00a07b5a..f9c37f9907d70750b2de1db334ac2c15949db7ca 100644
--- a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.template.html
+++ b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.template.html
@@ -24,6 +24,13 @@
<span class="sxplr-m-a">
EBRAINS dataset
</span>
+
+ <button *ngIf="isRestricted"
+ [matTooltip]="CONST.GDPR_TEXT"
+ mat-icon-button color="warn">
+ <i class="fas fa-exclamation-triangle"></i>
+ </button>
+
<mat-divider class="sxplr-pl-1" [vertical]="true"></mat-divider>
<a mat-icon-button *ngFor="let url of dataset.urls" [href]="url.doi | parseDoi" target="_blank">
diff --git a/src/atlasComponents/sapiViews/core/index.ts b/src/atlasComponents/sapiViews/core/index.ts
index 6db4628176e571f0a50adca091dc02c5d51801de..cb3d0ffce18ea93d534e44866392f0fc819b0ae8 100644
--- a/src/atlasComponents/sapiViews/core/index.ts
+++ b/src/atlasComponents/sapiViews/core/index.ts
@@ -1,3 +1,7 @@
export {
SapiViewsCoreModule
-} from "./module"
\ No newline at end of file
+} from "./module"
+
+export {
+ SapiViewsCoreSpaceBoundingBox
+} from "./space"
\ No newline at end of file
diff --git a/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.component.ts b/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.component.ts
index 541b428be133981a956008ca640e2b2a67a52cf1..27d4a53cc941a95164407b86f61825c01df1527f 100644
--- a/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.component.ts
+++ b/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.component.ts
@@ -1,5 +1,5 @@
-import { Component, EventEmitter, Input, OnChanges, Output } from "@angular/core";
-import { concat, Observable, of, timer } from "rxjs";
+import { Component, EventEmitter, Input, OnChanges, Output, SimpleChange, SimpleChanges } from "@angular/core";
+import { BehaviorSubject, concat, Observable, of, timer } from "rxjs";
import { SapiParcellationModel } from "src/atlasComponents/sapi/type";
import { ParcellationVisibilityService } from "../parcellationVis.service";
import { ARIA_LABELS } from "common/constants"
@@ -38,7 +38,11 @@ export class SapiViewsCoreParcellationParcellationSmartChip implements OnChanges
otherVersions: SapiParcellationModel[]
- ngOnChanges() {
+ ngOnChanges(changes: SimpleChanges) {
+ const { parcellation } = changes
+ if (parcellation) {
+ this.onDismissClicked$.next(false)
+ }
this.otherVersions = []
if (!this.parcellation) {
return
@@ -82,6 +86,8 @@ export class SapiViewsCoreParcellationParcellationSmartChip implements OnChanges
}
dismiss(){
+ if (this.onDismissClicked$.value) return
+ this.onDismissClicked$.next(true)
this.onDismiss.emit(this.parcellation)
}
@@ -93,4 +99,6 @@ export class SapiViewsCoreParcellationParcellationSmartChip implements OnChanges
trackByFn(parc: SapiParcellationModel){
return parc["@id"]
}
+
+ onDismissClicked$ = new BehaviorSubject<boolean>(false)
}
diff --git a/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.style.css b/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.style.css
index 93caeb8c21b229a9d3a4efb5a9219e9f604163d3..e8d0ca357ccbfe577e65a2f9d78c1589227cbf33 100644
--- a/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.style.css
+++ b/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.style.css
@@ -5,20 +5,6 @@
margin: 0.5rem;
}
-.otherversion-wrapper.loading > sxplr-sapiviews-core-parcellation-chip
-{
- animation: blink 500ms ease-in-out infinite alternate;
-}
-
-@keyframes blink {
- 0% {
- opacity: 0.8;
- }
- 100% {
- opacity: 0.5;
- }
-}
-
.otherversion-wrapper.loading > .spinner-container
{
position: absolute;
diff --git a/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.template.html b/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.template.html
index b21af3c775b330b100c4aa8c3e877fdc88237dfd..e56b6b69b9fc9405c4efb29900f9a448921839cf 100644
--- a/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.template.html
+++ b/src/atlasComponents/sapiViews/core/parcellation/smartChip/parcellation.smartChip.template.html
@@ -10,7 +10,10 @@
}">
- <sxplr-sapiviews-core-parcellation-chip
+ <sxplr-sapiviews-core-parcellation-chip
+ [ngClass]="{
+ 'sxplr-blink': (loadingParc$ | async) === parc
+ }"
[sxplr-sapiviews-core-parcellation-chip-parcellation]="parc"
[sxplr-sapiviews-core-parcellation-chip-color]="(parcellation | equality : parc : trackByFn) ? 'primary' : 'default'"
(sxplr-sapiviews-core-parcellation-chip-onclick)="selectParcellation(parc)">
@@ -28,7 +31,8 @@
<sxplr-sapiviews-core-parcellation-chip
[ngClass]="{
- 'sxplr-muted': !(parcellationVisibility$ | async)
+ 'sxplr-muted': !(parcellationVisibility$ | async),
+ 'sxplr-blink': onDismissClicked$ | async
}"
class="sxplr-d-inline-block"
[sxplr-sapiviews-core-parcellation-chip-parcellation]="parcellation"
@@ -63,7 +67,12 @@
color="primary"
iav-stop="mousedown click"
(click)="dismiss()">
- <i class="fas fa-times"></i>
+
+ <spinner-cmp class="sxplr-w-100 sxplr-h-100" *ngIf="onDismissClicked$ | async; else defaultDismissIcon"></spinner-cmp>
+ <ng-template #defaultDismissIcon>
+ <i class="fas fa-times"></i>
+ </ng-template>
+
</button>
</div>
</sxplr-sapiviews-core-parcellation-chip>
diff --git a/src/atlasComponents/sapiViews/core/region/module.ts b/src/atlasComponents/sapiViews/core/region/module.ts
index f0e19a9bc9a82c83dc8e3501ce3f2b99ff51b7bd..6c30611aa3b4ce8494f21bc60501da87089b9bb6 100644
--- a/src/atlasComponents/sapiViews/core/region/module.ts
+++ b/src/atlasComponents/sapiViews/core/region/module.ts
@@ -1,5 +1,6 @@
import { CommonModule } from "@angular/common";
import { NgModule } from "@angular/core";
+import { MarkdownModule } from "src/components/markdown";
import { SpinnerModule } from "src/components/spinner";
import { AngularMaterialModule } from "src/sharedModules";
import { SapiViewsFeaturesModule } from "../../features";
@@ -17,6 +18,7 @@ import { SapiViewsCoreRegionRegionRich } from "./region/rich/region.rich.compone
SapiViewsUtilModule,
SapiViewsFeaturesModule,
SpinnerModule,
+ MarkdownModule,
],
declarations: [
SapiViewsCoreRegionRegionListItem,
diff --git a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html
index 8884f0786d55340b4e389cd1b47ddaaec1d08f85..d4a9a79d17698288b49f115c83d895459327bd20 100644
--- a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html
+++ b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html
@@ -68,7 +68,7 @@
<spinner-cmp *ngIf="rfDir.busy$ | async"></spinner-cmp>
<sxplr-sapiviews-features-entry-list-item
- *ngFor="let feat of rfDir.listOfFeatures$ | async"
+ *ngFor="let feat of rfDir.listOfFeatures$ | async | orderFilterFeatures"
[sxplr-sapiviews-features-entry-list-item-feature]="feat"
(click)="handleRegionalFeatureClicked(feat)">
</sxplr-sapiviews-features-entry-list-item>
@@ -76,10 +76,23 @@
</ng-template>
+ <ng-template #regionDesc>
+ <markdown-dom class="sxplr-muted" [markdown]="region?.versionInnovation || 'No description provided.'">
+ </markdown-dom>
+ </ng-template>
+ <mat-accordion class="d-block mt-2">
+ <ng-container *ngTemplateOutlet="ngMatAccordionTmpl; context: {
+ title: CONST.DESCRIPTION,
+ iconClass: 'fas fa-info',
+ content: regionDesc,
+ desc: '',
+ iconTooltip: 'Description',
+ iavNgIf: !!region?.versionInnovation
+ }">
- <mat-accordion class="d-block mt-2">
+ </ng-container>
<ng-container *ngTemplateOutlet="ngMatAccordionTmpl; context: {
title: CONST.REGIONAL_FEATURES,
@@ -91,10 +104,6 @@
}">
</ng-container>
- </mat-accordion>
-
- <mat-accordion class="d-block mt-2">
-
<!-- connectivity -->
<ng-template #sxplrSapiviewsFeaturesConnectivityBrowser>
<sxplr-sapiviews-features-connectivity-browser
diff --git a/src/atlasComponents/sapiViews/core/space/index.ts b/src/atlasComponents/sapiViews/core/space/index.ts
index 46f783b69e03bdae2ef01144ba731e0b264c1c12..26c7eed07b1e454d4eac3bcbdf0c77bb9fe4f162 100644
--- a/src/atlasComponents/sapiViews/core/space/index.ts
+++ b/src/atlasComponents/sapiViews/core/space/index.ts
@@ -1 +1,4 @@
-export { SapiViewsCoreSpaceModule } from "./module"
\ No newline at end of file
+export { SapiViewsCoreSpaceModule } from "./module"
+export {
+ SapiViewsCoreSpaceBoundingBox
+} from "./boundingBox.directive"
\ No newline at end of file
diff --git a/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts b/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts
index 3b915ff248a21b0cf19d3dc5fbac8131b2d21643..8008affe34a6b783fd1b93ed14ee527279e36d04 100644
--- a/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts
+++ b/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts
@@ -1,4 +1,4 @@
-import { Component, Input } from "@angular/core";
+import { ChangeDetectionStrategy, Component, Input } from "@angular/core";
import { SapiFeatureModel } from "src/atlasComponents/sapi";
import { CleanedIeegDataset, CLEANED_IEEG_DATASET_TYPE, SapiDatasetModel, SapiParcellationFeatureMatrixModel, SapiRegionalFeatureReceptorModel, SapiSerializationErrorModel, SapiVOIDataResponse, SxplrCleanedFeatureModel } from "src/atlasComponents/sapi/type";
@@ -7,7 +7,8 @@ import { CleanedIeegDataset, CLEANED_IEEG_DATASET_TYPE, SapiDatasetModel, SapiPa
templateUrl: `./entryListItem.template.html`,
styleUrls: [
`./entryListItem.style.css`
- ]
+ ],
+ changeDetection: ChangeDetectionStrategy.OnPush,
})
export class SapiViewsFeaturesEntryListItem{
diff --git a/src/atlasComponents/sapiViews/features/index.ts b/src/atlasComponents/sapiViews/features/index.ts
index 19e30dcb1873aa37868be5e8944eaad3a9b0ce05..89e1fafbad8108576c708d401326b2d5f4137f6d 100644
--- a/src/atlasComponents/sapiViews/features/index.ts
+++ b/src/atlasComponents/sapiViews/features/index.ts
@@ -1,3 +1,7 @@
export {
SapiViewsFeaturesModule
-} from "./module"
\ No newline at end of file
+} from "./module"
+
+export {
+ SapiViewsFeaturesVoiQuery
+} from "./voi"
diff --git a/src/atlasComponents/sapiViews/features/module.ts b/src/atlasComponents/sapiViews/features/module.ts
index cbf7aeacaeccaf721bb6ca55108b01366f3fa685..3df348c72f79be4b53c3050e30627c896e8b93f2 100644
--- a/src/atlasComponents/sapiViews/features/module.ts
+++ b/src/atlasComponents/sapiViews/features/module.ts
@@ -11,6 +11,7 @@ import * as ieeg from "./ieeg"
import * as receptor from "./receptors"
import {SapiViewsFeatureConnectivityModule} from "src/atlasComponents/sapiViews/features/connectivity";
import * as voi from "./voi"
+import { OrderFilterFeaturesPipe } from "./orderFilterFeatureList.pipe"
const {
SxplrSapiViewsFeaturesIeegModule
@@ -35,6 +36,7 @@ const { SapiViewsFeaturesVoiModule } = voi
FeatureBadgeColourPipe,
FeatureBadgeFlagPipe,
SapiViewsFeaturesEntryListItem,
+ OrderFilterFeaturesPipe,
],
providers: [
{
@@ -48,6 +50,7 @@ const { SapiViewsFeaturesVoiModule } = voi
SapiViewsFeaturesEntryListItem,
SapiViewsFeaturesVoiModule,
SapiViewsFeatureConnectivityModule,
+ OrderFilterFeaturesPipe,
]
})
export class SapiViewsFeaturesModule{}
diff --git a/src/atlasComponents/sapiViews/features/orderFilterFeatureList.pipe.ts b/src/atlasComponents/sapiViews/features/orderFilterFeatureList.pipe.ts
new file mode 100644
index 0000000000000000000000000000000000000000..382862b0300f4bdaffadce20aeb4e28274a8bef6
--- /dev/null
+++ b/src/atlasComponents/sapiViews/features/orderFilterFeatureList.pipe.ts
@@ -0,0 +1,37 @@
+import { Pipe, PipeTransform } from "@angular/core";
+import { CLEANED_IEEG_DATASET_TYPE, SapiFeatureModel, SxplrCleanedFeatureModel } from "src/atlasComponents/sapi/type";
+import { environment } from "src/environments/environment"
+
+type PipableFeatureType = SapiFeatureModel | SxplrCleanedFeatureModel
+
+type ArrayOperation<T extends boolean | number> = (input: PipableFeatureType) => T
+
+const FILTER_FN: ArrayOperation<boolean> = feature => {
+ return feature["@type"] !== "siibra/features/cells"
+}
+
+const ORDER_LIST: ArrayOperation<number> = feature => {
+ if (feature["@type"] === "siibra/features/receptor") return -4
+ if (feature["@type"] === CLEANED_IEEG_DATASET_TYPE) return -3
+ if (feature['@type'] === "https://openminds.ebrains.eu/core/DatasetVersion") return 2
+ return 0
+}
+
+@Pipe({
+ name: 'orderFilterFeatures',
+ pure: true
+})
+
+export class OrderFilterFeaturesPipe implements PipeTransform{
+ public transform(inputFeatures: PipableFeatureType[]): PipableFeatureType[] {
+ return inputFeatures
+ .filter(f => {
+ /**
+ * if experimental flag is set, do not filter out anything
+ */
+ if (environment.EXPERIMENTAL_FEATURE_FLAG) return true
+ return FILTER_FN(f)
+ })
+ .sort((a, b) => ORDER_LIST(a) - ORDER_LIST(b))
+ }
+}
diff --git a/src/overwrite.scss b/src/overwrite.scss
index a6b3e9f55255d3080d58a94e7be6aedce47fc890..790e436d35acc4e970127548ec060fa796b6a650 100644
--- a/src/overwrite.scss
+++ b/src/overwrite.scss
@@ -264,4 +264,18 @@ $flex-directions: row,column;
.#{$nsp}-flex-static {
flex: 0 0 auto;
-}
\ No newline at end of file
+}
+
+.#{$nsp}-blink
+{
+ animation: blink 500ms ease-in-out infinite alternate;
+}
+
+@keyframes blink {
+ 0% {
+ opacity: 0.8;
+ }
+ 100% {
+ opacity: 0.5;
+ }
+}
diff --git a/src/viewerModule/nehuba/constants.ts b/src/viewerModule/nehuba/constants.ts
index 6537a7aef4ea762d6d38c85ac335011551b5767e..ca5ae4be810af998f93318a6348f751555fabff3 100644
--- a/src/viewerModule/nehuba/constants.ts
+++ b/src/viewerModule/nehuba/constants.ts
@@ -64,3 +64,5 @@ export interface IMeshesToLoad {
}
export const SET_MESHES_TO_LOAD = new InjectionToken<Observable<IMeshesToLoad>>('SET_MESHES_TO_LOAD')
+
+export const PMAP_LAYER_NAME = 'regional-pmap'
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
index 6f6d708876773bd84a484d73226fab01066f731a..579f7fb79ab3e65547cc420391f2097587eeff18 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
@@ -11,7 +11,7 @@ import { EnumColorMapName } from "src/util/colorMaps";
import { getShader } from "src/util/constants";
import { getNgLayersFromVolumesATP, getRegionLabelIndex } from "../config.service";
import { ParcVolumeSpec } from "../store/util";
-import { NehubaLayerControlService } from "./layerCtrl.service";
+import { PMAP_LAYER_NAME } from "../constants";
@Injectable()
export class LayerCtrlEffects {
@@ -22,7 +22,7 @@ export class LayerCtrlEffects {
),
mapTo(
atlasAppearance.actions.removeCustomLayer({
- id: NehubaLayerControlService.PMAP_LAYER_NAME
+ id: PMAP_LAYER_NAME
})
)
))
@@ -42,7 +42,7 @@ export class LayerCtrlEffects {
atlasAppearance.actions.addCustomLayer({
customLayer: {
clType: "customlayer/nglayer",
- id: NehubaLayerControlService.PMAP_LAYER_NAME,
+ id: PMAP_LAYER_NAME,
source: `nifti://${sapiRegion.getMapUrl(template["@id"])}`,
shader: getShader({
colormap: EnumColorMapName.VIRIDIS,
@@ -55,7 +55,7 @@ export class LayerCtrlEffects {
),
catchError(() => of(
atlasAppearance.actions.removeCustomLayer({
- id: NehubaLayerControlService.PMAP_LAYER_NAME
+ id: PMAP_LAYER_NAME
})
))
)
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
index ba8b1d0adbe40c1c00fb794cac66a0b1890c25ae..5980c76d634265b8d20acac43b548da7d0f293e6 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
@@ -13,6 +13,7 @@ import { arrayEqual } from "src/util/array";
import { ColorMapCustomLayer } from "src/state/atlasAppearance";
import { SapiRegionModel } from "src/atlasComponents/sapi";
import { AnnotationLayer } from "src/atlasComponents/annotations";
+import { PMAP_LAYER_NAME } from "../constants"
export const BACKUP_COLOR = {
red: 255,
@@ -25,8 +26,6 @@ export const BACKUP_COLOR = {
})
export class NehubaLayerControlService implements OnDestroy{
- static PMAP_LAYER_NAME = 'regional-pmap'
-
private selectedRegion$ = this.store$.pipe(
select(atlasSelection.selectors.selectedRegions),
shareReplay(1),
@@ -367,7 +366,7 @@ export class NehubaLayerControlService implements OnDestroy{
*/
return customLayers
.map(l => l.id)
- .filter(name => name !== NehubaLayerControlService.PMAP_LAYER_NAME)
+ .filter(name => name !== PMAP_LAYER_NAME)
})
),
this.customLayers$.pipe(
@@ -378,7 +377,7 @@ export class NehubaLayerControlService implements OnDestroy{
}),
distinctUntilChanged(),
map(flag => flag
- ? [ NehubaLayerControlService.PMAP_LAYER_NAME ]
+ ? [ PMAP_LAYER_NAME ]
: []
)
)
diff --git a/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts b/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
index 62a4ce09eb3d14682498812aee8e9e90dd01b253..ef3ac53320fbfa6ee86ec80ac140c105a2534af8 100644
--- a/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
+++ b/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
@@ -7,7 +7,7 @@ import { SapiRegionModel } from "src/atlasComponents/sapi"
import * as configSvc from "../config.service"
import { LayerCtrlEffects } from "../layerCtrl.service/layerCtrl.effects"
import { NEVER, of, pipe } from "rxjs"
-import { mapTo } from "rxjs/operators"
+import { mapTo, take } from "rxjs/operators"
import { selectorAuxMeshes } from "../store"
@@ -51,6 +51,12 @@ describe('> mesh.service.ts', () => {
)
)
})
+
+ afterEach(() => {
+ getParcNgIdSpy.calls.reset()
+ getRegionLabelIndexSpy.calls.reset()
+ getATPSpy.calls.reset()
+ })
describe('> NehubaMeshService', () => {
beforeEach(() => {
TestBed.configureTestingModule({
@@ -72,37 +78,106 @@ describe('> mesh.service.ts', () => {
expect(service).toBeTruthy()
})
- it('> mixes in auxillaryMeshIndices', () => {
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(atlasSelection.selectors.selectedRegions, [ fits1 ])
- mockStore.overrideSelector(atlasSelection.selectors.selectedParcAllRegions, [])
- mockStore.overrideSelector(selectorAuxMeshes, [auxMesh])
+ describe("> loadMeshes$", () => {
- const ngId = 'blabla'
- const labelIndex = 12
- getParcNgIdSpy.and.returnValue(ngId)
- getRegionLabelIndexSpy.and.returnValue(labelIndex)
+ describe("> auxMesh defined", () => {
+
+ const ngId = 'blabla'
+ const labelIndex = 12
+
+ beforeEach(() => {
+
+ const mockStore = TestBed.inject(MockStore)
+ mockStore.overrideSelector(atlasSelection.selectors.selectedRegions, [ fits1 ])
+ mockStore.overrideSelector(atlasSelection.selectors.selectedParcAllRegions, [])
+ mockStore.overrideSelector(selectorAuxMeshes, [auxMesh])
+
+ getParcNgIdSpy.and.returnValue(ngId)
+ getRegionLabelIndexSpy.and.returnValue(labelIndex)
- const service = TestBed.inject(NehubaMeshService)
-
- expect(
- service.loadMeshes$
- ).toBeObservable(
- hot('(ab)', {
- a: {
- layer: {
- name: ngId
- },
- labelIndicies: [ labelIndex ]
- },
- b: {
- layer: {
- name: auxMesh.ngId,
- },
- labelIndicies: auxMesh.labelIndicies
- }
})
- )
+
+ it("> auxMesh ngId labelIndex emitted", () => {
+
+ const service = TestBed.inject(NehubaMeshService)
+ expect(
+ service.loadMeshes$
+ ).toBeObservable(
+ hot('(ab)', {
+ a: {
+ layer: {
+ name: ngId
+ },
+ labelIndicies: [ labelIndex ]
+ },
+ b: {
+ layer: {
+ name: auxMesh.ngId,
+ },
+ labelIndicies: auxMesh.labelIndicies
+ }
+ })
+ )
+ })
+ })
+
+ describe("> if multiple ngid and labelindicies are present", () => {
+
+ const ngId1 = 'blabla'
+ const labelIndex1 = 12
+
+ const ngId2 = 'foobar'
+ const labelIndex2 = 13
+
+ beforeEach(() => {
+
+ const mockStore = TestBed.inject(MockStore)
+ mockStore.overrideSelector(atlasSelection.selectors.selectedRegions, [ fits1 ])
+ mockStore.overrideSelector(atlasSelection.selectors.selectedParcAllRegions, [fits1, fits1])
+ mockStore.overrideSelector(selectorAuxMeshes, [])
+
+ getParcNgIdSpy.and.returnValues(ngId1, ngId2, ngId2)
+ getRegionLabelIndexSpy.and.returnValues(labelIndex1, labelIndex2, labelIndex2)
+ })
+
+ it('> should call getParcNgIdSpy and getRegionLabelIndexSpy thrice', () => {
+ const service = TestBed.inject(NehubaMeshService)
+ service.loadMeshes$.pipe(
+ take(1)
+ ).subscribe(() => {
+
+ expect(getParcNgIdSpy).toHaveBeenCalledTimes(3)
+ expect(getRegionLabelIndexSpy).toHaveBeenCalledTimes(3)
+ })
+ })
+
+ /**
+ * in the case of julich brain 2.9 in colin 27, we expect selecting a region will hide meshes from all relevant ngIds (both left and right)
+ */
+ it('> expect the emitted value to be incl all ngIds', () => {
+ const service = TestBed.inject(NehubaMeshService)
+ expect(
+ service.loadMeshes$
+ ).toBeObservable(
+ hot('(ab)', {
+ a: {
+ layer: {
+ name: ngId1
+ },
+ labelIndicies: []
+ },
+ b: {
+ layer: {
+ name: ngId2
+ },
+ labelIndicies: [ labelIndex2 ]
+ }
+ })
+ )
+
+ })
+ })
+
})
})
})
diff --git a/src/viewerModule/nehuba/mesh.service/mesh.service.ts b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
index 2585f00224e8729a4434afa568e127a486e66fcb..d372ce460746d01c5cf560518e1532f38616b882 100644
--- a/src/viewerModule/nehuba/mesh.service/mesh.service.ts
+++ b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
@@ -47,7 +47,40 @@ export class NehubaMeshService implements OnDestroy {
]).pipe(
switchMap(([{ atlas, template, parcellation }, regions, selectedRegions]) => {
const ngIdRecord: Record<string, number[]> = {}
+
+ const tree = new Tree(
+ regions,
+ (c, p) => (c.hasParent || []).some(_p => _p["@id"] === p["@id"])
+ )
+
+ for (const r of regions) {
+ const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
+ if (!regionLabelIndex) {
+ continue
+ }
+ if (
+ tree.someAncestor(r, anc => !!getRegionLabelIndex(atlas, template, parcellation, anc))
+ ) {
+ continue
+ }
+ const ngId = getParcNgId(atlas, template, parcellation, r)
+ if (!ngIdRecord[ngId]) {
+ ngIdRecord[ngId] = []
+ }
+ ngIdRecord[ngId].push(regionLabelIndex)
+ }
+
if (selectedRegions.length > 0) {
+ /**
+ * If regions are selected, reset the meshes
+ */
+ for (const key in ngIdRecord) {
+ ngIdRecord[key] = []
+ }
+
+ /**
+ * only show selected region
+ */
for (const r of selectedRegions) {
const ngId = getParcNgId(atlas, template, parcellation, r)
const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
@@ -56,28 +89,6 @@ export class NehubaMeshService implements OnDestroy {
}
ngIdRecord[ngId].push(regionLabelIndex)
}
- } else {
- const tree = new Tree(
- regions,
- (c, p) => (c.hasParent || []).some(_p => _p["@id"] === p["@id"])
- )
-
- for (const r of regions) {
- const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
- if (!regionLabelIndex) {
- continue
- }
- if (
- tree.someAncestor(r, (anc) => !!getRegionLabelIndex(atlas, template, parcellation, anc))
- ) {
- continue
- }
- const ngId = getParcNgId(atlas, template, parcellation, r)
- if (!ngIdRecord[ngId]) {
- ngIdRecord[ngId] = []
- }
- ngIdRecord[ngId].push(regionLabelIndex)
- }
}
const arr: IMeshesToLoad[] = []
diff --git a/src/viewerModule/nehuba/ngLayerCtl/ngLayerCtrl.component.ts b/src/viewerModule/nehuba/ngLayerCtl/ngLayerCtrl.component.ts
index fd216151b9bbbf14d3b498eae8ffc98b2501ba05..f2e75e77f501517ac2f166f44a1b851042458489 100644
--- a/src/viewerModule/nehuba/ngLayerCtl/ngLayerCtrl.component.ts
+++ b/src/viewerModule/nehuba/ngLayerCtl/ngLayerCtrl.component.ts
@@ -54,6 +54,10 @@ export class NgLayerCtrlCmp implements OnChanges, OnDestroy{
private onDestroyCb: (() => void)[] = []
private removeLayer: () => void
+ public showOpacityCtrl = false
+ public hideNgTuneCtrl = 'lower_threshold,higher_threshold,brightness,contrast,colormap,hide-threshold-checkbox'
+ public defaultOpacity = 1
+
@Input('ng-layer-ctl-name')
name: string
diff --git a/src/viewerModule/nehuba/ngLayerCtl/ngLayerCtrl.template.html b/src/viewerModule/nehuba/ngLayerCtl/ngLayerCtrl.template.html
index 2188b17d9f57f496928a0b40f2ba78e3508be9d5..e3442c7b4323dac373e0b9110549b8c97a206a3e 100644
--- a/src/viewerModule/nehuba/ngLayerCtl/ngLayerCtrl.template.html
+++ b/src/viewerModule/nehuba/ngLayerCtl/ngLayerCtrl.template.html
@@ -7,4 +7,16 @@
<span>
{{ name }}
</span>
+
+ <button mat-icon-button (click)="showOpacityCtrl = !showOpacityCtrl">
+ <i class="fas fa-cog"></i>
+ </button>
+
+ <ng-template [ngIf]="showOpacityCtrl">
+ <ng-layer-tune
+ [ngLayerName]="name"
+ [hideCtrl]="hideNgTuneCtrl"
+ [opacity]="defaultOpacity">
+ </ng-layer-tune>
+ </ng-template>
</div>
diff --git a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
index a194176aa6d83027be793d3ebe1d098aa75f8c8d..f04ad6cc1b0a5b85875c6bc247150b737eb5605c 100644
--- a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
+++ b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
@@ -328,7 +328,8 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
* subscribe to main store and negotiate with relay to set camera
*/
const navSub = this.store$.pipe(
- select(atlasSelection.selectors.navigation)
+ select(atlasSelection.selectors.navigation),
+ filter(v => !!v),
).subscribe(nav => {
const { perspectiveOrientation, perspectiveZoom } = nav
this.mainStoreCameraNav = {
diff --git a/src/viewerModule/viewerCmp/viewerCmp.component.ts b/src/viewerModule/viewerCmp/viewerCmp.component.ts
index c01b335222d6ed39caf95183524d7d4c7aae2fac..f0b32efea3c8233a648e0277bfd38ddeaebe2074 100644
--- a/src/viewerModule/viewerCmp/viewerCmp.component.ts
+++ b/src/viewerModule/viewerCmp/viewerCmp.component.ts
@@ -12,6 +12,9 @@ import { SAPI, SapiRegionModel } from "src/atlasComponents/sapi";
import { atlasSelection, userInteraction, } from "src/state";
import { SapiSpatialFeatureModel, SapiFeatureModel, SapiParcellationModel, SapiSpaceModel } from "src/atlasComponents/sapi/type";
import { getUuid } from "src/util/fn";
+import { environment } from "src/environments/environment"
+import { SapiViewsFeaturesVoiQuery } from "src/atlasComponents/sapiViews/features";
+import { SapiViewsCoreSpaceBoundingBox } from "src/atlasComponents/sapiViews/core";
@Component({
selector: 'iav-cmp-viewer-container',
@@ -62,10 +65,17 @@ export class ViewerCmp implements OnDestroy {
public CONST = CONST
public ARIA_LABELS = ARIA_LABELS
+ public VOI_QUERY_FLAG = environment.EXPERIMENTAL_FEATURE_FLAG
@ViewChild('genericInfoVCR', { read: ViewContainerRef })
genericInfoVCR: ViewContainerRef
+ @ViewChild('voiFeatures', { read: SapiViewsFeaturesVoiQuery })
+ voiQueryDirective: SapiViewsFeaturesVoiQuery
+
+ @ViewChild('bbox', { read: SapiViewsCoreSpaceBoundingBox })
+ boundingBoxDirective: SapiViewsCoreSpaceBoundingBox
+
public quickTourRegionSearch: IQuickTourData = {
order: 7,
description: QUICKTOUR_DESC.REGION_SEARCH,
diff --git a/src/viewerModule/viewerCmp/viewerCmp.template.html b/src/viewerModule/viewerCmp/viewerCmp.template.html
index 2012afcff01d3121e46f30ddca9ceff8faebb46d..90d6d4a3810ecb35d68f616af533a3579493d78a 100644
--- a/src/viewerModule/viewerCmp/viewerCmp.template.html
+++ b/src/viewerModule/viewerCmp/viewerCmp.template.html
@@ -29,7 +29,7 @@
</mat-list-item>
- <ng-template [ngIf]="voiFeatures.onhover | async" let-feat>
+ <ng-template [ngIf]="voiQueryDirective && (voiQueryDirective.onhover | async)" let-feat>
<mat-list-item>
<mat-icon
fontSet="fas"
@@ -223,9 +223,11 @@
<ng-container *ngTemplateOutlet="autocompleteTmpl; context: { showTour: true }">
</ng-container>
- <div *ngIf="!((selectedRegions$ | async)[0])" class="sxplr-p-2 w-100">
- <ng-container *ngTemplateOutlet="spatialFeatureListViewTmpl"></ng-container>
- </div>
+ <ng-template [ngIf]="VOI_QUERY_FLAG">
+ <div *ngIf="!((selectedRegions$ | async)[0])" class="sxplr-p-2 w-100">
+ <ng-container *ngTemplateOutlet="spatialFeatureListViewTmpl"></ng-container>
+ </div>
+ </ng-template>
</div>
<!-- such a gross implementation -->
@@ -264,7 +266,7 @@
isOpen: minTrayVisSwitch.switchState$ | async,
regionSelected: selectedRegions$ | async,
click: minTrayVisSwitch.toggle.bind(minTrayVisSwitch),
- badge: (voiFeatures.features$ | async).length || null
+ badge: voiQueryDirective && (voiQueryDirective.features$ | async).length || null
}">
</ng-container>
</div>
@@ -983,18 +985,18 @@
</ng-template>
<ng-template #spatialFeatureListViewTmpl>
- <div *ngIf="voiFeatures.busy$ | async; else notBusyTmpl" class="fs-200">
+ <div *ngIf="voiQueryDirective && (voiQueryDirective.busy$ | async); else notBusyTmpl" class="fs-200">
<spinner-cmp></spinner-cmp>
</div>
<ng-template #notBusyTmpl>
- <mat-card *ngIf="(voiFeatures.features$ | async).length > 0" class="pe-all mat-elevation-z4">
+ <mat-card *ngIf="voiQueryDirective && (voiQueryDirective.features$ | async).length > 0" class="pe-all mat-elevation-z4">
<mat-card-title>
Volumes of interest
</mat-card-title>
<mat-card-subtitle class="overflow-hidden">
<!-- TODO in future, perhaps encapsulate this as a component? seems like a nature fit in sapiView/space/boundingbox -->
- <ng-template let-bbox [ngIf]="bbox.bbox$ | async | getProperty : 'bbox'" [ngIfElse]="bboxFallbackTmpl">
+ <ng-template let-bbox [ngIf]="boundingBoxDirective && (boundingBoxDirective.bbox$ | async | getProperty : 'bbox')" [ngIfElse]="bboxFallbackTmpl">
Bounding box: {{ bbox[0] | numbers | json }} - {{ bbox[1] | numbers | json }} mm
</ng-template>
<ng-template #bboxFallbackTmpl>
@@ -1005,17 +1007,21 @@
<mat-divider></mat-divider>
- <div *ngFor="let feature of voiFeatures.features$ | async"
- mat-ripple
- (click)="showDataset(feature)"
- class="sxplr-custom-cmp hoverable w-100 overflow-hidden text-overflow-ellipses">
- {{ feature.metadata.fullName }}
- </div>
+ <ng-template [ngIf]="voiQueryDirective">
+
+ <div *ngFor="let feature of voiQueryDirective.features$ | async"
+ mat-ripple
+ (click)="showDataset(feature)"
+ class="sxplr-custom-cmp hoverable w-100 overflow-hidden text-overflow-ellipses">
+ {{ feature.metadata.fullName }}
+ </div>
+ </ng-template>
</mat-card>
</ng-template>
</ng-template>
<div class="d-none"
+ *ngIf="VOI_QUERY_FLAG"
sxplr-sapiviews-core-space-boundingbox
[sxplr-sapiviews-core-space-boundingbox-atlas]="selectedAtlas$ | async"
[sxplr-sapiviews-core-space-boundingbox-space]="templateSelected$ | async"