@jax-data-science/sci-image-visualizer 0.13.0 → 0.15.0

package/lib/spatial-controls/spatial-gene-style/spatial-gene-style.component.d.ts

@@ -0,0 +1,30 @@
+import { EventEmitter } from '@angular/core';
+import { TranscriptGlyphName } from '../../contracts/display-types';
+import * as i0 from "@angular/core";
+/**
+ * One gene's icon and colour: the icon grid, a colour picker with its hex value, presets, and
+ * a reset — the content of a popover its host opens on the gene's swatch. Writes nothing itself:
+ * it reports the choice, and the host stores it where it belongs.
+ */
+export declare class SpatialGeneStyleComponent {
+    /** The gene, for the controls' labels. */
+    gene: string;
+    /** What the icons and colour are of ("Observation", "Transcript"), for the titles. */
+    what: string;
+    /** The gene's colour, `#rrggbb`. */
+    color: string;
+    /** The gene's icon. */
+    glyph: TranscriptGlyphName;
+    /** A note under the icons, e.g. where they show; none when null. */
+    iconHint: string | null;
+    readonly colorChange: EventEmitter<string>;
+    readonly glyphChange: EventEmitter<TranscriptGlyphName>;
+    /** Back to the gene's default icon and colour. */
+    readonly resetStyle: EventEmitter<void>;
+    protected readonly glyphOptions: import("../../spatial/spatial-panel-model").GlyphOption[];
+    protected readonly colorPresets: string[];
+    /** A typed hex colour, accepted as `#rrggbb` or `rrggbb`; anything else is ignored. */
+    protected onHex(text: string): void;
+    static ɵfac: i0.ɵɵFactoryDeclaration<SpatialGeneStyleComponent, never>;
+    static ɵcmp: i0.ɵɵComponentDeclaration<SpatialGeneStyleComponent, "spatial-gene-style", never, { "gene": { "alias": "gene"; "required": false; }; "what": { "alias": "what"; "required": false; }; "color": { "alias": "color"; "required": false; }; "glyph": { "alias": "glyph"; "required": false; }; "iconHint": { "alias": "iconHint"; "required": false; }; }, { "colorChange": "colorChange"; "glyphChange": "glyphChange"; "resetStyle": "resetStyle"; }, never, never, true, never>;
+}

package/lib/spatial-controls/spatial-gene-tree/spatial-gene-tree.component.d.ts

@@ -13,11 +13,21 @@ interface GeneRowView {
     /** Transcripts in view, or null before the renderer reports any. */
     count: number | null;
 }
+/** One row of the all-genes list. */
+interface AllGeneRowView {
+    gene: string;
+    shown: boolean;
+    /** Its colour when coloured by gene, or null when the dataset's code order is unknown. */
+    swatch: string | null;
+    count: number | null;
+}
 /**
  * The selected transcript genes as Xenium Explorer's tree: the gene groups, then the
  * ungrouped genes, each row with an eye that hides it without deselecting it, its marker
  * in its colour (opening one icon-and-colour picker per gene), and its transcript count in
- * view.
+ * view. With "All genes" on, the root eye hides or shows every transcript and the root
+ * expands to every gene of the dataset, each with its eye when the dataset lists its genes
+ * in code order (`transcriptTiles.genes`), filtered by name past a few hundred.
  *
  * Writes only through `controls.setViewState`.
  */
@@ -34,9 +44,7 @@ export declare class SpatialGeneTreeComponent implements OnChanges {
     geneCounts: Record<string, number> | null;
     /** Real genes in the panel — the tree's denominator. */
     geneTotal: number;
-    protected readonly glyphOptions: import("../../spatial/spatial-panel-model").GlyphOption[];
     /** Swatches in the picker: the categorical palette genes are coloured from by default. */
-    protected readonly colorPresets: string[];
     /** The tree, rebuilt when the view changes — never per change-detection pass. */
     protected geneTree: GeneTreeNode[];
     /** Per gene: its eye, swatch, glyph and count — rebuilt with the inputs (and when the
@@ -47,6 +55,18 @@ export declare class SpatialGeneTreeComponent implements OnChanges {
     protected rootShown: boolean;
     protected collapsedGeneGroups: Set<string>;
     protected geneTreeOpen: boolean;
+    /** The all-genes list starts closed: it can run to thousands of genes. */
+    protected allGenesOpen: boolean;
+    /** The genes "All genes" lists, or null when the dataset names none. */
+    protected allGeneList: readonly string[] | null;
+    /** Whether a gene of "All genes" can be hidden: the dataset lists its genes in code order. */
+    protected canHideAllGenes: boolean;
+    protected allGenesFilter: string;
+    /** The list's rows matching the filter, at most {@link ALL_GENES_ROWS}. */
+    protected allRows: AllGeneRowView[];
+    /** How many genes match the filter, for the "showing n of m" line. */
+    protected allGenesMatched: number;
+    protected readonly allGenesRowCap = 200;
     /** The gene the open picker edits. */
     protected styleGene: string | null;
     /** Colours of the cells' groups, by name — what a cluster of the same name is drawn in. */
@@ -58,13 +78,26 @@ export declare class SpatialGeneTreeComponent implements OnChanges {
     constructor(zone: NgZone, cdr: ChangeDetectorRef);
     ngOnChanges(changes: SimpleChanges): void;
     private rebuildRows;
+    /**
+     * The all-genes list's rows: the genes matching the filter, up to the cap. Built only while
+     * the list is open: the counts in view change with every pan, and the list can be thousands.
+     */
+    private rebuildAllRows;
+    /** Whether "All genes" draws anything: not switched off whole, nor every listed gene hidden. */
+    private anyOfAllGenesShown;
+    /** A gene of "All genes" in its colour by gene: its chosen one, else the palette's by code. */
+    private allGeneColorOf;
+    protected toggleAllGenesOpen(): void;
+    protected onAllGenesFilter(text: string): void;
     protected toggleGeneGroup(name: string): void;
     protected isGeneShown(gene: string): boolean;
     protected areGenesShown(genes: string[]): boolean;
     /** The eye toggle: hide or show genes without removing them from the selection. */
     protected onGenesShown(genes: string[], on: boolean): void;
-    /** The root eye while every gene is shown: back to the chosen list. */
-    protected onToggleAllGenes(): void;
+    /** The root eye while every gene is drawn: hide or show them all (the '±' leaves "All genes"). */
+    protected onAllGenesShown(on: boolean): void;
+    /** One gene's eye in the all-genes list. Showing one while all are off shows it alone. */
+    protected onAllGeneShown(gene: string, on: boolean): void;
     protected onGeneColor(gene: string, hex: string): void;
     protected openGeneStyle(event: Event, gene: string, panel: {
         toggle(e: Event): void;
@@ -75,8 +108,6 @@ export declare class SpatialGeneTreeComponent implements OnChanges {
     protected glyphPoints(glyph: TranscriptGlyphName): string;
     protected glyphOf(gene: string, slot: number): TranscriptGlyphName;
     protected onGlyph(gene: string, glyph: TranscriptGlyphName): void;
-    /** A typed hex colour, accepted as `#rrggbb` or `rrggbb`; anything else is ignored. */
-    protected onGeneHex(gene: string, text: string): void;
     /** Back to the gene's default icon and colour (by its position in the list). */
     protected resetGeneStyle(gene: string): void;
     /** The colour gene `slot` is drawn in when transcripts are coloured by gene. */
@@ -89,6 +120,7 @@ export declare class SpatialGeneTreeComponent implements OnChanges {
         name: string | null;
     }) => string;
     protected trackByLabelString: (_i: number, s: string) => string;
+    protected trackByAllRow: (_i: number, row: AllGeneRowView) => string;
     /**
      * The cluster colours, rebuilt only when what they come from changes. The template asks
      * once per gene row per change-detection pass, and rebuilding per call made that O(G²).

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

@@ -33,6 +33,10 @@ export declare class VisualizerStore {
     private defaultChannelStates;
     /** The image the current channel states were derived for (see setImageMeta). */
     private channelImageKey;
+    /** The channel info the host gave with the image (see setImageMeta), apart from what a tile
+     *  descriptor added since: each adoption merges against this, so a later descriptor can change
+     *  or clear what an earlier one put in. */
+    private hostChannelInfo;
     private readonly grayscale$;
     private readonly invert$;
     private presetSet;
@@ -76,6 +80,20 @@ 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. Each adoption replaces the last
+     * one's names, tints and groups: only the host's own count as overrides.
+     */
+    adoptChannelInfo(info: ReadonlyArray<{
+        name?: string;
+        color?: string;
+        group?: string[] | null;
+    }> | null | undefined): void;
     /**
      * Publish the current image's metadata and derive its channels.
      *
@@ -90,6 +108,7 @@ 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": "0.15.0",
   "engines": {
     "node": ">=20.9.0"
   },