@jax-data-science/sci-image-visualizer 0.1.0

package/lib/implementations/osd/osd-region-overlay.d.ts

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+import { IRegionStore } from '../../contracts/visualizer.contract';
+import { IRegionEditApi } from '../../contracts/region-store.contract';
+import { IRegionOverlay, RegionToolMode } from '../../contracts/region-overlay.contract';
+/**
+ * The shared region store as the overlay needs it: the cross-backend
+ * {@link IRegionStore} (read regions, selection, colours) plus the Region-native
+ * {@link IRegionEditApi} (add/move/resize/vertex edits). The shared RegionStore
+ * satisfies both. The overlay edits through these typed operations on the
+ * neutral Region model — it never touches a backend's own shape representation
+ * (e.g. Plotly's `x0/y0/x1/y1` / `M…L…Z` dicts).
+ */
+export type RegionEditStore = IRegionStore & IRegionEditApi;
+/**
+ * OpenSeadragon implementation of {@link IRegionOverlay}.
+ *
+ * - Renders the store's regions (rect/polygon) in image-pixel space, kept
+ *   aligned on every pan/zoom via the OSD viewport API.
+ * - Draws new rectangle and polygon regions (committed to the shared store).
+ * - Click-to-select in 'select' mode.
+ *
+ * Reads/writes the shared {@link IRegionStore}, so regions stay in sync with the
+ * Region Editor and the Plotly backend. The wand, vertex-eraser and zoom-to-box
+ * tools are NOT handled here — they're owned by OpenSeadragonVisualizerService
+ * (which binds them to OSD via the shared coordinate transform + viewport pixel
+ * readback), the same singleton tool services the Plotly backend uses.
+ */
+export declare class OsdRegionOverlay implements IRegionOverlay {
+    private viewer;
+    private store;
+    private readonly svg;
+    private readonly subs;
+    private readonly osd;
+    private selected;
+    private mode;
+    private tracker;
+    private rectStart;
+    private rectCurrent;
+    private polyPoints;
+    /** True while dragging a freehand path (freeform / polyline). */
+    private freehandDragging;
+    /** True while placing a click-to-add polygon ('drawpolygon' mode). */
+    private drawingPolygon;
+    /** Last element-pixel point appended, to thin the freehand path. */
+    private lastFreehandPx;
+    /**
+     * In-progress edit of the selected region:
+     *  - kind 'bounds' — rectangle resize/move or whole-region move (uses `zone`);
+     *  - kind 'vertex' — dragging a single polygon vertex (uses `vertexIndex`).
+     */
+    private edit;
+    private editDragged;
+    /** Rubber-band (marquee) multi-select in 'select' mode: press on empty space
+     *  and drag to select every region the band intersects. Image coords. */
+    private bandStart;
+    private bandCurrent;
+    private bandDragged;
+    private readonly redrawHandler;
+    constructor(viewer: any, store: RegionEditStore);
+    /** Switch drawing/selection mode; toggles OSD navigation accordingly. */
+    setMode(mode: RegionToolMode): void;
+    /** Drive OSD zoom from the wheel while any tool owns the pointer.
+     *
+     * OSD's native scroll-zoom is part of mouse-nav, so `setMouseNavEnabled(false)`
+     * (used by every region tool and by the wand/brush/eraser/SAM tools) disables
+     * it. The covering-canvas tools also sit above the OSD canvas and swallow the
+     * wheel outright. This listener is bound once to the viewer element — an
+     * ancestor of both the OSD canvas and the tool overlays — and forwards the
+     * wheel to a cursor-centred zoom whenever mouse-nav is off. When nav is on (no
+     * tool active) it does nothing and OSD zooms natively. (jit-ui#94) */
+    private readonly wheelZoomHandler;
+    /** Cursor feedback per mode (crosshair while drawing; pointer over a region
+     *  in select mode). */
+    private updateCursor;
+    /** Whether the selected region's vertices/handles should be drawn. Shown
+     *  whenever a region is selected — including `none` (display) mode and while
+     *  another tool (wand, brush, SAM…) is active — so a selection always reveals
+     *  its vertices. Suppressed only while actively drawing a brand-new shape,
+     *  where stray handles would be noise. */
+    private get showsSelectedVertices();
+    destroy(): void;
+    /** Image-pixel point -> element pixel point. */
+    private toPx;
+    /** Element pixel point (from a MouseTracker event) -> image-pixel point. */
+    private toImage;
+    redraw(): void;
+    /** A small vertex handle (filled for an emphasised marker, hollow otherwise).
+     *  Colour defaults to the global shape colour (used by the in-progress draw
+     *  preview); selected-region handles pass the region's own colour. */
+    private vertexMarker;
+    private buildRegionEl;
+    /** Marquee rectangle for rubber-band multi-select (dashed outline + faint fill). */
+    private selectionBand;
+    private rectPreview;
+    private polyPreview;
+    /** SVG path `d` (element-pixel coords) for a straight-edged ring/polyline. */
+    private straightPathD;
+    /** SVG path `d` (element-pixel coords) for the smooth cubic bezier through a
+     *  polygon's anchors — the paper.js-equivalent curve. */
+    private bezierPathD;
+    /** SVG cubic-bezier path `d` (element px) for any ring (exterior or hole). Uses the stored
+     *  per-vertex handle offsets when present, else the Catmull-Rom default (resolveHandles). */
+    private ringBezierPathD;
+    /**
+     * Draw the bezier editing handles for the selected region, paper.js-style:
+     * each anchor as a small square, with tangent lines out to its two control
+     * points (drawn as small circles).
+     */
+    private drawBezierHandles;
+    /** A tangent line from an anchor to a control point, with a circle at the end. */
+    private drawHandle;
+    /** A filled-white anchor square (the editable vertex). */
+    private anchorSquare;
+    private rgba;
+    private get isFreehand();
+    private onPress;
+    /** Begin an edit gesture (move/resize or single-vertex drag) and open a store
+     *  batch so the live drag emits once on release. */
+    private startEdit;
+    private onDrag;
+    private onRelease;
+    private onClick;
+    /**
+     * Click-to-place polygon ('drawpolygon'): the first click starts the
+     * polygon, each subsequent click adds a vertex, and clicking near the first
+     * vertex (with at least 3 placed) closes and commits it.
+     */
+    private onDrawPolygonClick;
+    /**
+     * Hover feedback in select mode: move/resize cursors over the selected
+     * region's body/edges/corners, a pointer over any other region.
+     */
+    private onMove;
+    /**
+     * The move/resize zone under the cursor for the currently-selected region
+     * (rectangles get edge/corner handles + body; polygons get body-move only),
+     * or null if the cursor isn't over the selected region.
+     */
+    private editZoneAt;
+    /** The currently-selected region (the last one selected), or null. */
+    private selectedRegionInfo;
+    /** The vertex of the selected polygon under the cursor (screen-pixel
+     *  tolerance), or null. Rectangles have no editable vertices. */
+    private hitVertex;
+    /** The bezier control handle of the selected region under the cursor (which
+     *  anchor, and whether the in- or out-handle), or null. */
+    private hitBezierHandle;
+    /** The edge of `region`'s polygon nearest the cursor (within tolerance), with
+     *  the clicked point in image coords as the insertion position, or null. */
+    private hitEdge;
+    /** Classify a screen point against a screen-space rectangle into a zone. */
+    private rectZone;
+    /** Snapshot the selected region's geometry at the start of an edit. */
+    private snapshot;
+    /**
+     * Apply the in-progress move/resize to the region, live, through the
+     * Region-native edit API. Recomputed absolutely from the gesture-start
+     * snapshot (`orig`) + the total delta, so each frame is idempotent.
+     */
+    private applyEdit;
+    private selectAt;
+    /** Indices of every region whose bounding box intersects the image-space
+     *  rectangle [x0,y0]–[x1,y1] (rubber-band multi-select). */
+    private regionsInRect;
+    /** Axis-aligned bounding box of a region in image coords, or null if empty. */
+    private regionBBox;
+    /** Index of the topmost region under a point, or -1. */
+    private regionIndexAt;
+    private containsPoint;
+    /** Point-in-closed-polygon (image coords) honouring interior rings (holes):
+     *  inside the exterior AND outside every hole (even-odd). */
+    private closedPolygonContains;
+    /** Shortest distance from point p to segment a–b, all in screen pixels. */
+    private distToSegmentPx;
+    private resetInProgress;
+    private commitRectangle;
+    private commitPolygon;
+    /**
+     * Add a freshly-drawn region to the shared store and redraw immediately. The
+     * store mints the id, selects the new region (so it renders solid/highlighted
+     * rather than as a dashed in-progress shape) and emits the full region list to
+     * the Region Editor — we still redraw locally rather than relying solely on
+     * the store's update event, which can be swallowed when Plotly isn't active.
+     */
+    private commitRegion;
+    /**
+     * Convert the selected region(s) to/from a bezier curve (toBezier = true /
+     * toPolygon = false). One-shot; the anchors are unchanged,
+     * only the smooth-curve rendering is toggled.
+     */
+    setSelectedBezier(bezier: boolean): void;
+}

package/lib/implementations/osd/osd-scale-bar.d.ts

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+/**
+ * A physical scale bar drawn over an OpenSeadragon viewer. Recomputes on every
+ * pan/zoom from the viewport's image→screen scale and the image's µm/pixel
+ * (`mppX`, from Bio-Formats). Hidden when the image has no physical pixel size.
+ */
+export declare class OsdScaleBar {
+    private viewer;
+    private mppX;
+    private readonly osd;
+    private readonly bar;
+    private readonly line;
+    private readonly label;
+    private readonly redrawHandler;
+    constructor(viewer: any, mppX: number);
+    private update;
+    destroy(): void;
+}

package/lib/implementations/osd/slice-cache.d.ts

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+/**
+ * Stack-slice cache for the OpenSeadragon backend (refactoring plan, Step 3 —
+ * a pure move of the cache cluster out of the visualizer service).
+ *
+ * Scrubbing the z-slider used to viewer.open() a fresh tile source per slice,
+ * which destroys the current tiled image (and its decoded+recolored tiles), so
+ * revisiting a slice re-fetched everything. Instead we keep each visited slice
+ * as its own tiled image in the world and just toggle opacity — a revisited
+ * slice is instant (no network, no re-decode, no re-recolor). Bounded by an
+ * LRU so deep stacks don't grow without limit. Multichannel slices cache one
+ * TiledImage per channel (additively composited); composite slices cache one.
+ * A background loader pre-fills the rest of the stack, one slice at a time,
+ * yielding to the visible slice so on-screen tiles always win the connection.
+ */
+/** What the cache needs from the visualizer service. All accessors are live
+ *  (called at use time, never captured) so the cache always sees the current
+ *  viewer/descriptor/z — matching the field reads it replaced. */
+export interface SliceCacheHost {
+    /** The mounted viewer, or null. */
+    viewer(): any | null;
+    /** True when a viewer, descriptor and infoB64 are all present. */
+    hasImage(): boolean;
+    /** Stack depth (descriptor.z, 1 for single images). */
+    sliceCount(): number;
+    /** The currently displayed z-slice. */
+    currentZ(): number;
+    /** Per-channel rendering (multichannel fluorescence) vs composite. */
+    isMultiChannel(): boolean;
+    /** Channel count for a multichannel group add. */
+    channelCount(): number;
+    /** Channel visibility (drives group reveal opacity). */
+    channelVisible(c: number): boolean;
+    /** Tile source for slice z (optionally one channel). */
+    buildTileSource(z: number, channel?: number): any;
+    /** A composite slice landed in the world — the service samples its window. */
+    onCompositeSliceAdded(z: number): void;
+}
+export declare class SliceCache {
+    private host;
+    /** z-slice → its TiledImage in the viewer world (composite path). */
+    private sliceItems;
+    /** Multichannel per-slice cache: z → the N channel TiledImages for that slice
+     *  (additively composited by OSD; index = channel). Only the active slice's
+     *  visible channels have opacity > 0. */
+    private channelSliceItems;
+    /** Cached multichannel slices whose tiles were tinted before the latest
+     *  display change; re-tinted lazily when next revealed by z-scrub. */
+    private staleSlices;
+    /** Most-recently-shown z last; drives LRU eviction. */
+    private sliceLru;
+    /** z-slices whose tiled image is being added (dedupe rapid scrubbing). */
+    private slicesLoading;
+    /** Bumped whenever the loaded image changes; in-flight background slice adds
+     *  captured under an older token are dropped (cancelled image switch). */
+    private sliceLoadToken;
+    /** The slice the background loader is currently waiting on (its tiles are
+     *  still streaming): addTiledImage 'success' fires on add, not on tile load,
+     *  so we gate the next slice on getFullyLoaded(). */
+    private bgLoadingZ;
+    /** When bgLoadingZ started loading — a fallback so a slow/stuck slice can't
+     *  stall the whole background pass forever. */
+    private bgLoadingSince;
+    /** Slices the background loader has already attempted (no tight retry loop). */
+    private bgAttempted;
+    /** Max cached slice tiled images kept resident before LRU eviction. */
+    private maxCachedSlices;
+    /** Upper bound on resident slices, regardless of stack depth (memory guard). */
+    private readonly MAX_CACHED_SLICES_CAP;
+    /** Fit-view tile budget above which background preloading is skipped: a huge
+     *  no-pyramid stack would preload every slice at full resolution and
+     *  flood/timeout. Normal stacks stay below it and KEEP the flicker-free
+     *  pre-cache. */
+    private readonly MAX_PREFETCH_FIT_TILES;
+    /** True only for stacks too large to background-preload. */
+    private skipSlicePrefetch;
+    private prefetchTimer;
+    constructor(host: SliceCacheHost);
+    /** Size the cache for the loaded image: keep the whole stack resident
+     *  (capped) so the background loader fills every slice without evicting
+     *  itself; skip preloading entirely when even the coarsest level's tile
+     *  grid is too large (its slices only exist at full resolution). */
+    configure(stackDepth: number, coarseFitTiles: number): void;
+    /** Current LRU cap (the viewer sizes its tile cache from it). */
+    maxSlices(): number;
+    /** Drop the per-channel groups (on a fresh plot). */
+    clearChannelGroups(): void;
+    /** Seed the cache with the just-opened composite slice (world item 0), so
+     *  scrubbing back to it later is an instant opacity toggle, not a re-open. */
+    seedComposite(z: number, item: any): void;
+    /** Show slice z: reveal it instantly when cached (re-tinting a stale
+     *  multichannel group), otherwise add it once. The current slice stays
+     *  visible until the new one is in — no white-flicker. */
+    showSlice(z: number): void;
+    /** Add a never-seen slice as a hidden tiled image, then reveal it once loaded
+     *  (composite path; multichannel routes to addChannelSlice). */
+    private addSlice;
+    /**
+     * Add slice z's channel group: one additively-composited ('lighter' = Fiji
+     * "Composite") TiledImage per channel, hidden (opacity 0) until revealed.
+     * Each is preloaded so the background loader can pre-fill every slice.
+     * Cached so a revisit is an instant opacity toggle — no re-fetch, no
+     * white-flicker. Mirrors addSlice for the composite path.
+     */
+    addChannelSlice(z: number): void;
+    /** Reveal slice z's channel group (each visible channel → opacity 1) and
+     *  hide every other cached slice's group. Instant; no fetch/decode. */
+    revealChannelSlice(z: number): void;
+    /** Show the given composite slice (opacity 1) and hide all other cached slices. */
+    private showOnlySlice;
+    /** Re-tint after a display change: invalidate ONLY the visible slice's
+     *  channel images — invalidating the whole world would re-process every
+     *  hidden/preloaded slice's tiles (hundreds), flooding OSD and wasting work
+     *  on tiles that aren't on screen. The other cached slices are marked stale
+     *  and re-tinted lazily when revealed. */
+    invalidateChannelDisplay(z: number): void;
+    /** Invalidate (restore + re-recolor) just the channel images of one cached
+     *  slice. A shared timestamp batches the per-image invalidations into one
+     *  processing pass (OSD dedupes tiles already stamped at >= tStamp). */
+    private invalidateSlice;
+    /** Debounce so a burst of viewport/slice events coalesces, then advance the
+     *  background stack loader by one slice. */
+    schedulePrefetch(): void;
+    /**
+     * Background-load the whole stack: add each not-yet-cached slice as a
+     * hidden, preloaded tiled image, one at a time, working outward from the
+     * current slice — and never blocking the visible slice (it yields while the
+     * current view is still streaming tiles; only one slice is in flight at a
+     * time so the on-screen tiles always win the connection).
+     */
+    private loadNextBackgroundSlice;
+    /** The not-yet-cached slice closest to the current one (load nearest first),
+     *  skipping any already attempted so a failed/slow one isn't retried in a loop. */
+    private nearestUncachedSlice;
+    /**
+     * Stop background stack preloading and invalidate any in-flight slice add.
+     * Called when a different image is selected so the previous stack stops
+     * loading immediately instead of finishing in the background.
+     */
+    cancelBackgroundLoad(): void;
+    /** Remove every cached slice except the currently displayed one, aborting
+     *  their in-flight tile requests. */
+    private dropHiddenSlices;
+    /** Whether slice z is in the active cache (composite single image, or the
+     *  multichannel per-channel group). */
+    private sliceCacheHas;
+    /** The cached TiledImage(s) for slice z (0–1 for composite, N for multichannel). */
+    private sliceGroup;
+    /** Whether slice z's tiles are still streaming (any cached image not fully loaded). */
+    private sliceTilesLoading;
+    /** Remove slice z's cached image(s) from the world and the active cache. */
+    private removeCachedSlice;
+    /** Is the tiled image still in the world (not evicted)? */
+    private sliceInWorld;
+    /** Mark z as most-recently-used. */
+    private touchSliceLru;
+    /** Drop the least-recently-used cached slices beyond the cap (never the
+     *  current one), removing their tiled images so memory stays bounded. */
+    private evictSliceLru;
+    /** Clear the cache (on teardown / image switch). */
+    reset(): void;
+}

package/lib/implementations/osd/tile-client.d.ts

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+import { HttpClient } from '@angular/common/http';
+/**
+ * Single source of truth for jit-service `/tile` access from the OSD backend
+ * (refactoring plan, Step 2). Before this module the tile URL was string-built
+ * in four places and the fetch→decode pipeline copy-pasted in three — every
+ * query-param change had to be repeated per site.
+ *
+ * Error handling is deliberately left to the CALL SITES: these helpers
+ * propagate failures so each caller keeps its own tagged catch
+ * (`[viz:histogram]`, `[viz:window]`, `[viz:export]`) and its own
+ * skip/fallback semantics.
+ */
+/** Tile coordinates for one `/tile` request. `channel == null` (or omitted)
+ *  requests the server-composited tile; an index (including 0) requests that
+ *  single channel as grayscale. */
+export interface TileCoords {
+    res: number;
+    col: number;
+    row: number;
+    z: number;
+    tileSize: number;
+    channel?: number | null;
+}
+/** Build the `/tile` request URL — the one place its query shape lives. */
+export declare function buildTileUrl(api: string, infoB64: string, c: TileCoords): string;
+/** Fetch a tile PNG and decode it to an ImageBitmap. The caller owns the
+ *  bitmap (call `close()` when done). Throws on network/decode failure. */
+export declare function fetchTileBitmap(http: HttpClient, url: string, timeoutMs: number): Promise<ImageBitmap>;
+/** Fetch a tile and read its pixels back as RGBA ImageData (via an offscreen
+ *  canvas). Returns null only when a 2d context can't be created; throws on
+ *  network/decode failure (the caller's tagged catch handles it). */
+export declare function fetchTileRgba(http: HttpClient, url: string, timeoutMs: number): Promise<ImageData | null>;

package/lib/implementations/plotly/plotly-coordinate-transform.d.ts

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+import { ICoordinateTransform } from '../../contracts/coordinate-transform.contract';
+/**
+ * Plotly implementation of {@link ICoordinateTransform}. Wraps the axis objects
+ * on the plot's `_fullLayout`. This is the exact math the wand / vertex-eraser
+ * used inline before they were decoupled — lifted here verbatim so Plotly
+ * behaviour is unchanged.
+ */
+export declare class PlotlyCoordinateTransform implements ICoordinateTransform {
+    private getGraphDiv;
+    private getContainer;
+    constructor(getGraphDiv: () => any, getContainer: () => HTMLElement | null);
+    private axes;
+    isReady(): boolean;
+    clientToData(clientX: number, clientY: number): {
+        x: number;
+        y: number;
+    };
+    dataLengthToScreen(dataLength: number): number;
+}

package/lib/implementations/plotly/plotly-region-overlay.d.ts

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+import { PlotlyService } from './plotly.service';
+import { IRegionOverlay, RegionToolMode } from '../../contracts/region-overlay.contract';
+/**
+ * Plotly implementation of {@link IRegionOverlay}.
+ *
+ * Plotly renders region shapes natively in its plot layout and edits them via
+ * its own drag modes, so this adapter is thin: it maps the neutral
+ * {@link RegionToolMode} onto Plotly drag modes and lets Plotly draw. `redraw`
+ * is a no-op because Plotly re-renders its shapes itself on relayout.
+ *
+ * It is the symmetric counterpart to {@link OsdRegionOverlay}: both render the
+ * same shared `IRegionStore`, each onto its own backend's canvas.
+ */
+export declare class PlotlyRegionOverlay implements IRegionOverlay {
+    private plotly;
+    constructor(plotly: PlotlyService);
+    setMode(mode: RegionToolMode): void;
+    redraw(): void;
+    /** Bezier regions are an OpenSeadragon-only feature (Plotly has no native
+     *  curved-shape rendering), so this is a no-op here. */
+    setSelectedBezier(_bezier: boolean): void;
+    destroy(): void;
+}

package/lib/implementations/plotly/plotly-trace-builders.d.ts

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+import { PlotType } from '../../contracts/plot-type';
+/**
+ * Pluggable Plotly trace builders for the plot types added on top of the
+ * original HEATMAP / SURFACE / RGB-image renderers.
+ *
+ * DESIGN / EXTRACTION ALIGNMENT
+ * -----------------------------
+ * Every function here is **pure** — it takes a `TraceBuildInput` and returns
+ * Plotly trace dicts. There is no Angular, no RxJS, no host-state coupling
+ * (`MainState`, `FilesService`, …). That keeps the module relocatable into the
+ * future `@jax-data-science/image-visualization` library core (see the
+ * `sketch/jit-plotting-extraction` SOW) without port surgery.
+ *
+ * Layout building stays in `PlotlyService` (it needs live service state such
+ * as screen height, scale ratio and the current shapes); only TRACE building
+ * is pluggable here. To add a new plot type: write a builder, register it in
+ * `PLOTLY_PLOT_TYPE_IMPLS`, and add a descriptor in `contracts/plot-type.ts`.
+ *
+ * The original HEATMAP/SURFACE/RGB types intentionally keep their dedicated
+ * renderers in `PlotlyService` (they are also reused by the high-def zoom
+ * re-fetch path), so they are NOT registered here.
+ */
+/** Normalised input for a trace builder. Frames are per-z-plane matrices:
+ *  grayscale cells are scalars, RGB cells are `[r, g, b]`. */
+export interface TraceBuildInput {
+    frames: any[];
+    width: number;
+    height: number;
+    /** [xRatio, yRatio] — data units per pixel. */
+    ratios: number[];
+    /** [x0, x1, y0, y1] — true image extent in data units. */
+    trueImageSize: number[];
+    isGrayscale: boolean;
+    /** Plotly colorscale value (e.g. from the active colormap). */
+    colorscale: any;
+    reversescale: boolean;
+    /** Region polygons in data coords, for region-sourced plots (SCATTER). */
+    regions: {
+        xpoints: number[];
+        ypoints: number[];
+    }[];
+    /** Default marker/line colour for derived (non-image-LUT) traces. */
+    shapeColor: string;
+    /** ISOSURFACE intensity bounds (0–255): surfaces are drawn for values in
+     *  [isoMin, isoMax], mapped straight onto Plotly's isomin/isomax. */
+    isoMin: number;
+    isoMax: number;
+}
+export type TraceBuilder = (input: TraceBuildInput) => any[];
+export type PlotLayoutKind = '2d-image' | '2d-overlay' | '2d-chart' | '3d-volume';
+export interface PlotlyPlotTypeImpl {
+    buildTraces: TraceBuilder;
+    /** Which layout `PlotlyService` should build for this type. */
+    layoutKind: PlotLayoutKind;
+    /** True for scene-based (3D) traces — picks the 3D Plotly config. */
+    threeD: boolean;
+}
+/** Registry of the pluggable (non-original) plot types. */
+export declare const PLOTLY_PLOT_TYPE_IMPLS: Partial<Record<PlotType, PlotlyPlotTypeImpl>>;
+export declare function getPlotTypeImpl(type: PlotType): PlotlyPlotTypeImpl | undefined;