fix: minimap in axial maximized view

feat: allow labelled nifti to be visualized

.helm/adhoc/configmap-siibra-explorer.yml

@@ -3,7 +3,7 @@ data:
   SIIBRA_CACHEDIR: /siibra-api-volume
   HBP_DISCOVERY_URL: "https://iam.ebrains.eu/auth/realms/hbp"
   REDIS_ADDR: "cache-redis-service"
-  V2_7_PLUGIN_URLS: "https://siibra-jugex.apps.tc.humanbrainproject.eu/viewer_plugin/manifest.json;https://neurogenpy.apps.ebrains.eu/viewer_plugin/manifest.json"
+  V2_7_PLUGIN_URLS: "https://siibra-jugex.apps.tc.humanbrainproject.eu/viewer_plugin/manifest.json;https://ngpy.apps.hbp.eu/viewer_plugin/manifest.json"
   LOGGER_DIR: "/sxplr-log"
   OVERWRITE_API_ENDPOINT: https://siibra-api-prod.apps.tc.humanbrainproject.eu/v3_0
   OVERWRITE_SPATIAL_ENDPOINT: 'https://siibra-spatial-backend.apps.tc.humanbrainproject.eu'

codemeta.json

@@ -46,7 +46,7 @@
         "python 3",
         "typescript"
     ],
-    "schema:releaseNotes": "# v2.14.13\n\n## Feature\n\n- Added an example of setting up a proxy for access-controlled content\n- Added free-mode (access via `?free=true`)\n- Added hint for drag-n-drop nifti file (in helper one pager and quick tour)\n\n## Bugfix\n\n- Fixed layout issues when user drag-n-dropped nifti has irregularities\n\n## Behind the scene\n\n- Added script to automatically create release metadata files\n",
+    "schema:releaseNotes": "# v2.14.13\n\n## Feature\n\n- Added an example of setting up a proxy for access-controlled content\n- Added free-mode (access via `?free=true`)\n- Added hint for drag-n-drop nifti file (in helper one pager and quick tour)\n- Allow nifti to be added as a labelled volume by using `.label.nii.gz` or `.label.nii` extension\n\n## Bugfix\n\n- Fixed layout issues when user drag-n-dropped nifti has irregularities\n- Fixed picture-in-picture minimap in maximized axial view\n\n## Behind the scene\n\n- Added script to automatically create release metadata files\n",
     "runtimePlatform": "docker",
     "version": "2.14.13",
     "contIntegration": "https://github.com/FZJ-INM1-BDA/siibra-explorer/actions",

common/helpOnePager.md

@@ -13,4 +13,4 @@
 
 You can enable the touch interface, which is selected per default on mobile devices, by selecting the user menu from the top right (👤), then choosing `Settings` and `Enable Mobile UI`.
 
-You can drag-and-drop NiFTi (`.nii` or `.nii.gz`) file on top of your desired template to co-visualize them.
+You can drag-and-drop NiFTi (`[.label].nii[.gz]`) file on top of your desired template to co-visualize them. Files with extension`.label.nii[.gz]` will be visualized as labelled volume.

docs/releases/v2.14.13.md

@@ -5,10 +5,12 @@
 - Added an example of setting up a proxy for access-controlled content
 - Added free-mode (access via `?free=true`)
 - Added hint for drag-n-drop nifti file (in helper one pager and quick tour)
+- Allow nifti to be added as a labelled volume by using `.label.nii.gz` or `.label.nii` extension
 
 ## Bugfix
 
 - Fixed layout issues when user drag-n-dropped nifti has irregularities
+- Fixed picture-in-picture minimap in maximized axial view
 
 ## Behind the scene
 

src/extra_styles.css

@@ -793,9 +793,9 @@ body::after
   gap: 0.2rem 0.2rem;
 }
 
-.grid > .grid-wide-3
+.grid > .grid-wide-4
 {
-  grid-column: 1 / 4;
+  grid-column: 1 / 5;
 }
 
 .v-center-text-span

src/index.html

@@ -13,7 +13,7 @@
   <link rel="icon" type="image/png" href="assets/favicons/favicon-128-light.png"/>
   <script src="extra_js.js"></script>
   <script src="https://unpkg.com/three-surfer@0.0.17/dist/bundle.js" defer></script>
-  <script type="module" src="https://unpkg.com/ng-layer-tune@0.0.26/dist/ng-layer-tune/ng-layer-tune.esm.js"></script>
+  <script type="module" src="https://unpkg.com/ng-layer-tune@0.0.28/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 src="https://cdn.plot.ly/plotly-2.24.1.min.js" charset="utf-8"></script>
   <script src="main.bundle.js" charset="utf-8"></script> <!-- export_nehuba -->

src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts

@@ -56,7 +56,7 @@ export class NehubaGlueCmp implements IViewer<'nehuba'>, OnDestroy {
   private onDestroyCb: (() => void)[] = []
 
   public nehubaConfig: NehubaConfig
-  public QUICKTOUR_DND_MD = `Drag and drop any \`.nii\` or \`.nii.gz\` on top of the template to co-visualize.`
+  public QUICKTOUR_DND_MD = `Drag and drop any \`[.label].nii[.gz]\` on top of the template to co-visualize.`
 
   ngOnDestroy(): void {
     while (this.onDestroyCb.length) this.onDestroyCb.pop()()

src/viewerModule/nehuba/userLayers/service.ts

@@ -113,12 +113,15 @@ export class UserLayerService implements OnDestroy {
     })
     const { buffer, meta } = result
     const url = URL.createObjectURL(new Blob([buffer]))
+    const type = file.name.includes(".label.nii")
+    ? 'segmentation'
+    : 'image'
     return {
       protocol: 'nifti://',
       url,
       option: {
         legacySpecFlag: "old",
-        type: 'image',
+        type,
         shader: getShader({
           colormap: EnumColorMapName.MAGMA,
           lowThreshold: meta.min || 0,

src/viewerModule/nehuba/userLayers/userlayerInfo/userlayerInfo.template.html

@@ -38,12 +38,12 @@
     </button>
 
     <div *ngIf="view.showMore || view.compact"
-      class="sxplr-custom-cmp darker-bg overflow-hidden grid-wide-3">
+      class="sxplr-custom-cmp darker-bg overflow-hidden grid-wide-4">
       <ng-template [ngTemplateOutlet]="ngLayerController" [ngTemplateOutletContext]="{ onlyOpacity: !view.showMore }">
       </ng-template>
     </div>
 
-    <ul class="grid-wide-3 sxplr-custom-cmp darker-bg" *ngIf="view.showMore">
+    <ul class="grid-wide-4 sxplr-custom-cmp darker-bg" *ngIf="view.showMore">
       <li *ngFor="let warn of data.warning">{{ warn }}</li>
     </ul>
 

src/viewerModule/nehuba/viewerCtrl/perspectiveViewSlider/perspectiveViewSlider.component.ts

@@ -2,7 +2,7 @@ import { Component, Inject, ViewChild, ChangeDetectionStrategy, inject, HostList
 import { FormControl } from "@angular/forms";
 import { select, Store } from "@ngrx/store";
 import { BehaviorSubject, combineLatest, concat, merge, NEVER, Observable, of, Subject } from "rxjs";
-import { switchMap, distinctUntilChanged, map, debounceTime, shareReplay, take, withLatestFrom, filter, takeUntil } from "rxjs/operators";
+import { switchMap, distinctUntilChanged, map, debounceTime, shareReplay, take, withLatestFrom, filter, takeUntil, tap } from "rxjs/operators";
 import { SxplrTemplate } from "src/atlasComponents/sapi/sxplrTypes"
 import { selectedTemplate } from "src/state/atlasSelection/selectors";
 import { panelMode, panelOrder } from "src/state/userInterface/selectors";
@@ -26,10 +26,10 @@ const anatOriToIdx: Record<AnatomicalOrientation, number> = {
   'ap': 1,
   'si': 2
 }
-const anaOriAltAxis: Record<AnatomicalOrientation, (tmplSize: [number, number, number], ratio: {x: number, y: number}) => {idx: number, value: number}> = {
-  'rl': (tmplSize, { y }) => ({ idx: 2, value: tmplSize[2] * (0.5 - y) }),
-  'ap': (tmplSize, { y }) => ({ idx: 2, value: tmplSize[2] * (0.5 - y) }),
-  'si': (tmplSize, { x }) => ({ idx: 2, value: tmplSize[0] * (0.5 - x) })
+const anaOriAltAxis: Record<AnatomicalOrientation, (templateInfo: TemplateInfo, ratio: {x: number, y: number}) => {idx: number, value: number}> = {
+  'rl': (templateInfo, { y }) => ({ idx: 2, value: templateInfo.real[0] * (0.5 - y) }),
+  'ap': (templateInfo, { y }) => ({ idx: 2, value: templateInfo.real[1] * (0.5 - y) }),
+  'si': (templateInfo, { y }) => ({ idx: 0, value: templateInfo.real[2] * (y - 0.5) })
 }
 
 function getDim(triplet: number[], view: EnumClassicalView) {
@@ -424,7 +424,7 @@ export class PerspectiveViewSlider {
             }
 
             if (!isNullish(xyRatio.x) && !isNullish(xyRatio.y)) {
-              const { idx, value } = anaOriAltAxis[anatomicalOrientation](currTmplSize.real, xyRatio)
+              const { idx, value } = anaOriAltAxis[anatomicalOrientation](currTmplSize, xyRatio)
               positionMod.push({
                 idx,
                 value