@jax-data-science/sci-image-visualizer 0.13.0 → 0.14.0

package/lib/spatial-controls/spatial-observations-panel/spatial-observations-panel.component.d.ts

@@ -1,7 +1,8 @@
 import { EventEmitter, OnChanges, SimpleChanges } from '@angular/core';
+import { Observable } from 'rxjs';
 import type { ISpatialControls } from '../../contracts/visualizer.contract';
 import type { SpatialDataset } from '../../contracts/spatial-dataset.contract';
-import { ColormapNode, SpatialViewState } from '../../contracts/display-types';
+import { ColormapNode, SpatialViewState, TranscriptGlyphName } from '../../contracts/display-types';
 import { SpatialSelectionMask } from '../../spatial/spatial-selection';
 import { PanelOption } from '../../spatial/spatial-panel-model';
 import type { GenePickerModel } from '../spatial-gene-picker';
@@ -45,6 +46,8 @@ export declare class SpatialObservationsPanelComponent implements OnChanges {
     /** A legend row was clicked (see the key). */
     readonly categoryClicked: EventEmitter<number>;
     protected readonly clipOptions: PanelOption<[number, number]>[];
+    /** How several genes of the observation filter combine. */
+    protected readonly matchOptions: PanelOption<SpatialViewState['observationGenesMatch']>[];
     /** Virtual-scrolled only past this many options (see the cells panel's gene dropdown). */
     protected readonly geneVirtualScrollFrom = 200;
     /** Colour-by column choices — "None" plus every column the dataset declares. */
@@ -62,6 +65,35 @@ export declare class SpatialObservationsPanelComponent implements OnChanges {
     protected onColumn(name: string | null): void;
     /** A gene was picked; it supersedes any column selection. */
     protected onGene(name: string | null): void;
+    /** Genes picked for the observation filter; none draws every observation. */
+    protected onObservationGenes(genes: string[] | null): void;
+    protected onObservationGenesMatch(match: SpatialViewState['observationGenesMatch'] | null): void;
+    /** Whether the gene filter could not be applied (an expression read failed); one stream per
+     *  `controls`, so the template's async pipe keeps its subscription. */
+    protected geneFilterFailed$: Observable<boolean>;
+    /** Ask for the picked genes' expression again (a failed read is not cached). */
+    protected retryGeneFilter(): void;
+    protected onObservationGenesColorBy(on: boolean): void;
+    protected removeObservationGene(gene: string): void;
+    protected isObservationGene(gene: string): boolean;
+    protected trackByGene(_i: number, gene: string): string;
+    /** The gene the icon and colour picker is open for. */
+    protected styleGene: string | null;
+    protected geneColorOf(gene: string): string;
+    protected geneGlyphOf(gene: string): TranscriptGlyphName;
+    protected glyphPointsOf(gene: string): string;
+    /** Open the picker on the gene's swatch. Inside the genes dropdown the click must not also
+     *  reach the option, which would unpick the gene. */
+    protected openGeneStyle(event: Event, gene: string, panel: {
+        toggle(e: Event): void;
+        hide(): void;
+    }): void;
+    protected onGeneColor(gene: string, hex: string): void;
+    protected onGeneGlyph(gene: string, glyph: TranscriptGlyphName): void;
+    /** Back to the gene's default colour (its place in the list) and icon (a circle). */
+    protected resetGeneStyle(gene: string): void;
+    /** What the filter hides, in words. */
+    protected get geneFilterHint(): string;
     /** Cell outlines on offer, which changes what the circles mean. */
     protected get hasCells(): boolean;
     /** True while a selection is active — everything else renders muted. */

package/lib/spatial-controls/spatial-transcripts-panel/spatial-transcripts-panel.component.d.ts

@@ -54,7 +54,13 @@ export declare class SpatialTranscriptsPanelComponent implements OnChanges {
     readonly openChange: EventEmitter<boolean>;
     /** Virtual-scrolled only past this many options (see the cells panel's gene dropdown). */
     protected readonly geneVirtualScrollFrom = 200;
-    protected readonly transcriptColorOptions: PanelOption<SpatialViewState['transcriptColorBy']>[];
+    /**
+     * Colourings on offer: "Cell type" only for a dataset with cell types. Rebuilt only when that
+     * changes, for the same reason as {@link transcriptModeOptions}.
+     */
+    protected transcriptColorOptions: PanelOption<SpatialViewState['transcriptColorBy']>[];
+    /** Whether the dataset has a column naming each cell's type (see `cellTypeColumnFor`). */
+    protected hasCellTypes: boolean;
     protected readonly glyphOptions: import("../../spatial/spatial-panel-model").GlyphOption[];
     protected readonly budgetOptions: {
         label: string;
@@ -117,8 +123,14 @@ export declare class SpatialTranscriptsPanelComponent implements OnChanges {
      */
     protected onImportGeneGroups(input: HTMLInputElement): Promise<void>;
     protected get estimatePercent(): number;
+    /** Whether the Observations gene filter is on, which limits the transcripts drawn. */
+    protected get observationsFiltered(): boolean;
     protected get estimateOverMax(): boolean;
     protected onTranscriptBudget(n: number): void;
+    /** The colouring in use: "Cell type" without cell types colours by gene (as the markers do). */
+    protected get transcriptColorShown(): SpatialViewState['transcriptColorBy'];
+    /** Genes of "All genes" hidden one by one (not the whole set switched off). */
+    protected get allGenesSomeHidden(): boolean;
     protected onTranscriptColorBy(by: SpatialViewState['transcriptColorBy']): void;
     protected onTranscriptScale(value: number | undefined): void;
     protected onTranscriptOpacity(value: number | undefined): void;

package/lib/store/visualizer-store.service.d.ts

@@ -76,6 +76,18 @@ export declare class VisualizerStore {
      * Editor) show µm²/mm² instead of px². No-op when neither axis is positive.
      */
     setPhysicalPixelSize(mppX?: number, mppY?: number): void;
+    /**
+     * Fill in the channel names and tints the host's image meta left out, from the image's tile
+     * descriptor: the server reads them from the file (an OME-TIFF's channel names, such as Cytos's
+     * "Actin" or "Cell-Membrane"), where a host's metadata (jit-ui's `/metadata`) carries none, so
+     * the Channels pane showed "Channel 1", "Channel 2"… The host's own names and tints win; only a
+     * channel still showing its derived default takes the descriptor's, so an edit made in the pane
+     * stays. A no-op when the channel counts differ, or for RGB.
+     */
+    adoptChannelInfo(info: ReadonlyArray<{
+        name?: string;
+        color?: string;
+    }> | null | undefined): void;
     /**
      * Publish the current image's metadata and derive its channels.
      *
@@ -90,6 +102,7 @@ export declare class VisualizerStore {
      *   - RGB (rgbChannels ≥ 3) → Red/Green/Blue;
      *   - multichannel fluorescence (channelCount > 1) → one channel per band,
      *     named/tinted from the server `channelInfo` when present, else a palette;
+     *     only the first `DEFAULT_VISIBLE_CHANNELS` start visible (see `defaultChannelVisible`);
      *   - otherwise a single grayscale "Intensity" channel. */
     private deriveChannels;
     getChannelStates(): Observable<IChannelState[]>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jax-data-science/sci-image-visualizer",
-  "version": "0.13.0",
+  "version": "0.14.0",
   "engines": {
     "node": ">=20.9.0"
   },