@jax-data-science/sci-image-visualizer 0.12.1 → 0.14.0

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

@@ -1,5 +1,5 @@
 import { EventEmitter, NgZone, OnInit } from '@angular/core';
-import { IVisualizer, ISpatialControls } from '../contracts/visualizer.contract';
+import { IVisualizer, ISpatialControls, RoiSelectionMode } from '../contracts/visualizer.contract';
 import { SpatialDataset } from '../contracts/spatial-dataset.contract';
 import { ColormapNode, SpatialViewState } from '../contracts/display-types';
 import { PanelOption, parseGeneGroups } from '../spatial/spatial-panel-model';
@@ -81,6 +81,12 @@ export declare class SpatialControlsComponent implements OnInit {
     /** An ROI selection that matched nothing, so the UI can say so rather than
      *  looking like the button did nothing. */
     protected selectionMissed: boolean;
+    /** The mode of the selection that {@link selectionMissed}: what it found nothing inside. */
+    protected missedMode: RoiSelectionMode;
+    /** The region classes picked in the Region Editor: in 3D, "Select from ROIs" selects inside them. */
+    protected pickedClasses: readonly string[];
+    /** While "Select from ROIs" reads the picked classes' outlines. */
+    protected selectingFromRegions: boolean;
     /**
      * Whether the Distribution section is expanded. Collapsed by default: the
      * panel's primary job is the colour controls, and the chart roughly doubles
@@ -106,8 +112,13 @@ export declare class SpatialControlsComponent implements OnInit {
     onGeneFilter(query: string): Promise<void>;
     /** A gene dropdown opened — see {@link GenePickerModel.ensureList}. */
     ensureGeneList(): Promise<void>;
-    /** Select every observation inside the drawn regions (their union). */
-    protected selectFromRegions(): void;
+    /** Select every observation inside the drawn regions (their union) — in 3D, inside the
+     *  picked classes' volumes. */
+    protected selectFromRegions(): Promise<void>;
+    /** In 3D with classes picked, "Select from ROIs" selects inside their volumes. */
+    protected get selectsClassVolumes(): boolean;
+    /** How "Select from ROIs" selects now: the controls' own rule, the one the selection runs by. */
+    private get roiSelectionMode();
     /** Legend click: select one category. Clicking the active row clears it, so a
      *  second click is an undo rather than a no-op. */
     protected selectCategory(index: number): Promise<void>;

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/region-selection.d.ts

@@ -10,18 +10,29 @@ interface HasId {
  * owner calls {@link sync} once the region array it projects onto is final,
  * which prunes ids that no longer exist and emits {@link indices$} only when
  * the index set changed.
+ *
+ * A selection made by picking classes (the class tree, a surface in 3D) also
+ * holds those classes: a class is a volume through the whole stack, whether or
+ * not it has a region on the slice. Any other selection drops them; an edit
+ * ({@link retain}, {@link sync}) keeps them.
  */
 export declare class RegionSelection {
     private selected;
+    private picked;
     private readonly indicesSubject;
+    private readonly classesSubject;
     /** The selected regions' current array indices (emits on change only). */
     readonly indices$: Observable<number[]>;
+    /** The classes the selection was picked as ([] for any other selection; emits on change only). */
+    readonly classes$: Observable<readonly string[]>;
+    /** The classes the selection was picked as, as last emitted by {@link sync}. */
+    get classes(): readonly string[];
     /** The selected indices as last projected by {@link sync}. */
     get indices(): number[];
     /** The selected ids, in selection order. */
     get ids(): readonly number[];
-    /** Replace the selected ids (no emit until {@link sync}). */
-    replace(ids: number[]): void;
+    /** Replace the selected ids, picked as `classes` if they were (no emit until {@link sync}). */
+    replace(ids: number[], classes?: readonly string[]): void;
     /** Keep only the ids `keep` accepts (no emit until {@link sync}). */
     retain(keep: (id: number) => boolean): void;
     /**
@@ -30,7 +41,7 @@ export declare class RegionSelection {
      */
     selectIndices(indices: number[], regions: readonly HasId[]): void;
     /** Project the selected ids onto `regions`, pruning ids it no longer holds,
-     *  and emit if the index set changed. */
+     *  and emit if the index set (or the picked classes) changed. */
     sync(regions: readonly HasId[]): void;
 }
 export {};

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

@@ -377,9 +377,22 @@ export declare class RegionStore implements IRegionStore, IRegionEditApi, IRegio
     /**
      * Select every region of these classes on the slice — the regions', and the region source's,
      * which are taken into the regions (at most {@link SELECT_CLASSES_LIMIT} of them). Added to the
-     * selection with `additive`. Resolves the selected region ids.
+     * selection with `additive`. The selection holds the classes too (see {@link getPickedClasses}).
+     * Resolves the selected region ids.
      */
     selectClasses(classes: readonly string[], additive?: boolean): Promise<number[]>;
+    /**
+     * The classes the selection was picked as by {@link selectClasses} (a class tree node with its
+     * subclasses, a surface clicked in 3D); [] once anything else selected. Each is a volume through
+     * the whole stack, whether or not it has a region on the slice.
+     */
+    getPickedClasses(): readonly string[];
+    getPickedClasses$(): Observable<readonly string[]>;
+    /**
+     * Every slice's exact outlines of these classes, the region sources' and the regions' (as the
+     * 3D reconstruction reads them at the stack's own resolution): what is inside their volume.
+     */
+    classSliceOutlines(classes: readonly string[]): Promise<SliceOutlines[]>;
     /**
      * The 3D reconstruction of each group of classes over every slice of the stack (an atlas
      * structure with its substructures, say): the outlines of the regions of those classes on every

package/lib/store/spatial-selection.service.d.ts

@@ -11,6 +11,14 @@ import * as i0 from "@angular/core";
  */
 export declare class SpatialSelectionStore {
     private readonly selection$;
+    /** Bumped by every write, a clear of nothing included (see {@link revision}). */
+    private writes;
+    /**
+     * How many times the selection was written (set or cleared, by any writer). A selection
+     * computed asynchronously compares it before publishing: a newer write — a Clear, a legend
+     * click, a linked chart's brush — supersedes it.
+     */
+    revision(): number;
     /** Emits on every change, including a clear. */
     getSelection$(): Observable<SpatialSelectionMask>;
     /** Synchronous read, for a renderer building its first frame. */

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": "0.12.1",
+  "version": "0.14.0",
   "engines": {
     "node": ">=20.9.0"
   },