@idetik/core 0.40.0 → 0.40.2

package/dist/types/src/layers/image_layer.d.ts

@@ -1,4 +1,4 @@
-import { Layer, LayerProps } from "../core/layer";
+import { BlendMode, Layer } from "../core/layer";
 import { Viewport } from "../core/viewport";
 import type { IdetikContext } from "../idetik";
 import { Chunk, ChunkSource, SliceCoordinates } from "../data/chunk";
@@ -9,30 +9,61 @@ import { ChannelProps, ChannelsEnabled } from "../core/channel";
 import { EventContext } from "../core/event_dispatcher";
 import { vec3 } from "gl-matrix";
 import { PointPickingResult } from "./point_picking";
-/** @inline */
-export type ImageLayerProps = LayerProps & {
+/**
+ * Initialization properties for constructing an image layer.
+ */
+export type ImageLayerProps = {
+    /** The chunked image source to stream from. */
     source: ChunkSource;
+    /** The slice to display in world units. */
     sliceCoords: SliceCoordinates;
+    /** Streaming policy. Defaults to the exploration policy. */
     policy?: ImageSourcePolicy;
+    /** Slice plane orientation. Defaults to `"XY"`. */
     orientation?: SliceOrientation;
+    /** Per-channel appearance. Length must match the source. */
     channelProps?: ChannelProps[];
+    /** Called with the picked value when the layer is clicked. */
     onPickValue?: (info: PointPickingResult) => void;
+    /** Layer opacity in `[0, 1]`. Defaults to `1`. */
+    opacity?: number;
+    /** How the layer blends. Defaults to `"additive"`. */
+    blendMode?: BlendMode;
+    /** Hides content behind. Defaults to `true`. */
+    occludes?: boolean;
 };
 /**
- * A layer that renders a 2D slice of a chunked, multi-channel image source.
+ * A layer that renders a 2D slice of a chunked multi-channel image source.
+ *
+ * Image layer streams chunks from a source such as
+ * {@link OmeZarrImageSource} according to its streaming policy, which
+ * decides which resolution levels and chunks to load for the current view.
+ * Per-channel appearance is controlled with {@link ChannelProps} and the
+ * visible slice is selected with {@link SliceCoordinates}. The layer holds
+ * `sliceCoords` by reference, so mutating the object it was constructed
+ * with moves through the data.
  *
- * `ImageLayer` streams chunks from a `ChunkSource` (e.g.
- * {@link OmeZarrImageSource}) according to the supplied `ImageSourcePolicy`,
- * which decides which resolution levels and chunks to load for the current
- * view. Per-channel appearance (contrast limits,
- * color, visibility) is controlled via {@link ChannelProps}, and the visible
- * slice is selected with {@link SliceCoordinates}.
+ * ```ts
+ * const source = await OmeZarrImageSource.fromHttp({ url });
+ *
+ * const layer = new ImageLayer({
+ *   source,
+ *   sliceCoords: { t: 0, z: 0, c: [0, 1] },
+ *   channelProps: [
+ *     { color: Color.GREEN, contrastLimits: [0, 1024] },
+ *     { color: Color.MAGENTA, contrastLimits: [0, 1024] },
+ *   ],
+ * });
+ *
+ * viewport.addLayer(layer);
+ * ```
  *
  * @see {@link VolumeLayer} for 3D volume rendering of the same data.
  *
  * @group Layers
  */
 export declare class ImageLayer extends Layer implements ChannelsEnabled {
+    /** Identifies the layer type as `ImageLayer`. */
     readonly type = "ImageLayer";
     private readonly source_;
     private readonly sliceCoords_;
@@ -55,26 +86,61 @@ export declare class ImageLayer extends Layer implements ChannelsEnabled {
     private lastPresentationTimeStamp_?;
     private lastPresentationTimeCoord_?;
     private readonly wireframeColors_;
+    /**
+     * Creates an image layer for the given source and slice.
+     *
+     * @param props - Initialization properties.
+     */
     constructor({ source, sliceCoords, policy, orientation, channelProps, onPickValue, ...layerOptions }: ImageLayerProps);
+    /** @hidden */
     protected attach(context: IdetikContext): void;
+    /** @hidden */
     protected detach(_context: IdetikContext): void;
+    /**
+     * Streams chunks for the current view and refreshes the visible slice.
+     *
+     * @param viewport - The viewport being rendered.
+     */
     update(viewport?: Viewport): void;
+    /** The slice plane the layer displays. */
     get orientation(): SliceOrientation;
     /**
-     * Changes the slice orientation at runtime. Visible renderables are rebuilt
-     * for the new plane, chunks already resident in the shared cache are reused.
+     * Changes the slice orientation at runtime. Visible renderables are
+     * rebuilt for the new plane and chunks already resident in the shared
+     * cache are reused.
+     *
+     * @param orientation - The new slice plane.
      */
     setOrientation(orientation: SliceOrientation): void;
     private updateChunks;
     private rebuildRenderGroups;
+    /** The `t` coordinate of the most recently presented slice. */
     get lastPresentationTimeCoord(): number | undefined;
     private isPresentationStale;
+    /**
+     * Handles click picking for `onPickValue`. Called automatically for
+     * each pointer event.
+     *
+     * @param event - The event with clip and world coordinates attached.
+     */
     onEvent(event: EventContext): void;
     private pickAtRay;
+    /** The layer's chunk store view for diagnostic overlays. */
     get chunkStoreView(): ChunkStoreView | undefined;
+    /**
+     * The slice coordinates the layer displays. This is the object passed
+     * at construction and may be mutated to move through the data.
+     */
     get sliceCoords(): SliceCoordinates;
+    /** The chunked image source the layer streams from. */
     get source(): ChunkSource;
+    /**
+     * The streaming policy in effect. Assign a new policy to reschedule
+     * loading at runtime, for example when switching between exploration
+     * and playback.
+     */
     get imageSourcePolicy(): Readonly<ImageSourcePolicy>;
+    /** @param newPolicy - The policy to apply. */
     set imageSourcePolicy(newPolicy: ImageSourcePolicy);
     private getImageForChunk;
     private getChannelPropsForChunk;
@@ -82,14 +148,42 @@ export declare class ImageLayer extends Layer implements ChannelsEnabled {
     private updateSlicePosition;
     private sliceIndexForChunk;
     private updateImageChunk;
+    /**
+     * Reads the data value at a world position from the resident chunks.
+     * Prefers the current level of detail and falls back to other resident
+     * levels.
+     *
+     * @param world - The world-space position to sample.
+     * @returns The sampled value or `null` if no resident chunk covers it.
+     */
     getValueAtWorld(world: vec3): Promise<number | null>;
     private readValueFromChunk;
+    /** Whether chunk wireframes are drawn colored by level of detail. */
     get debugMode(): boolean;
+    /** @param debug - Whether to draw chunk wireframes. */
     set debugMode(debug: boolean);
+    /** The current per-channel appearance settings. */
     get channelProps(): ChannelProps[] | undefined;
+    /**
+     * Applies new per-channel appearance settings to all visible chunks
+     * and notifies channel change callbacks.
+     *
+     * @param channelProps - One entry per source channel.
+     */
     setChannelProps(channelProps: ChannelProps[]): void;
+    /** Restores the channel settings passed at construction. */
     resetChannelProps(): void;
+    /**
+     * Registers a callback invoked after every channel settings change.
+     *
+     * @param callback - The callback to add.
+     */
     addChannelChangeCallback(callback: () => void): void;
+    /**
+     * Removes a previously registered channel change callback.
+     *
+     * @param callback - The callback to remove.
+     */
     removeChannelChangeCallback(callback: () => void): void;
     private releaseAndRemoveChunks;
 }

package/dist/types/src/layers/image_layer.d.ts.map

@@ -1 +1 @@
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package/dist/types/src/layers/label_layer.d.ts

@@ -1,4 +1,4 @@
-import { Layer, LayerProps } from "../core/layer";
+import { BlendMode, Layer } from "../core/layer";
 import { Viewport } from "../core/viewport";
 import type { IdetikContext } from "../idetik";
 import { ChunkSource, SliceCoordinates } from "../data/chunk";
@@ -9,17 +9,61 @@ import { LabelColorMapProps, LabelColorMap } from "../objects/renderable/label_i
 import { EventContext } from "../core/event_dispatcher";
 import { vec3 } from "gl-matrix";
 import { PointPickingResult } from "./point_picking";
-export type LabelLayerProps = LayerProps & {
+/**
+ * Initialization properties for constructing a label layer.
+ */
+export type LabelLayerProps = {
+    /** The single-channel label source to stream from. */
     source: ChunkSource;
+    /** The slice to display in world units. */
     sliceCoords: SliceCoordinates;
+    /** Streaming policy. Defaults to the exploration policy. */
     policy?: ImageSourcePolicy;
+    /** Slice plane orientation. Defaults to `"XY"`. */
     orientation?: SliceOrientation;
+    /** Colors for label values. Defaults to a built-in cycle. */
     colorMap?: LabelColorMapProps;
+    /** Called with the picked label when the layer is clicked. */
     onPickValue?: (info: PointPickingResult) => void;
+    /** Outlines the picked label. Defaults to `false`. */
     outlineSelected?: boolean;
+    /** Layer opacity in `[0, 1]`. Defaults to `1`. */
+    opacity?: number;
+    /** How the layer blends. Defaults to `"none"`. */
+    blendMode?: BlendMode;
+    /** Hides content behind. Inferred from `blendMode`. */
+    occludes?: boolean;
 };
-/** @group Layers */
+/**
+ * A layer that renders a 2D slice of a single-channel label image.
+ *
+ * Label layer displays segmentation data where each pixel holds an
+ * integer label. Labels are colored by cycling through the color map's
+ * `cycle` with exact-value overrides in its `lookupTable`. Chunks stream
+ * through the same policy machinery as {@link ImageLayer} and the source
+ * must be single channel.
+ *
+ * Clicking the layer picks the label under the pointer. With
+ * `outlineSelected` the picked label is outlined, and `onPickValue`
+ * receives the world position and label value for custom handling such as
+ * highlighting through {@link setColorMap}.
+ *
+ * ```ts
+ * const labels = new LabelLayer({
+ *   source: labelSource,
+ *   sliceCoords: { z: 12, c: [0] },
+ *   opacity: 0.55,
+ *   blendMode: "normal",
+ *   onPickValue: ({ value }) => console.log(`label ${value}`),
+ * });
+ *
+ * viewport.addLayer(labels);
+ * ```
+ *
+ * @group Layers
+ */
 export declare class LabelLayer extends Layer {
+    /** Identifies the layer type as `LabelLayer`. */
     readonly type = "LabelLayer";
     private readonly source_;
     private readonly sliceCoords_;
@@ -39,29 +83,86 @@ export declare class LabelLayer extends Layer {
     private static readonly STALE_PRESENTATION_MS_;
     private lastPresentationTimeStamp_?;
     private lastPresentationTimeCoord_?;
+    /**
+     * Creates a label layer for the given source and slice.
+     *
+     * @param props - Initialization properties.
+     */
     constructor({ source, sliceCoords, policy, orientation, colorMap, onPickValue, outlineSelected, ...layerOptions }: LabelLayerProps);
+    /** @hidden */
     protected attach(context: IdetikContext): void;
+    /** @hidden */
     protected detach(_context: IdetikContext): void;
+    /**
+     * Streams chunks for the current view and refreshes the visible slice.
+     * Called automatically once per frame.
+     *
+     * @param viewport - The viewport being rendered.
+     */
     update(viewport?: Viewport): void;
+    /** The slice plane the layer displays. */
     get orientation(): SliceOrientation;
     /**
-     * Changes the slice orientation at runtime. Visible renderables are rebuilt
-     * for the new plane, chunks already resident in the shared cache are reused.
+     * Changes the slice orientation at runtime. Visible renderables are
+     * rebuilt for the new plane and chunks already resident in the shared
+     * cache are reused.
+     *
+     * @param orientation - The new slice plane.
      */
     setOrientation(orientation: SliceOrientation): void;
     private updateChunks;
     private isPresentationStale;
+    /**
+     * Handles click picking and selection outlining. Called automatically
+     * for each pointer event on the owning viewport.
+     *
+     * @param event - The event with clip and world coordinates attached.
+     */
     onEvent(event: EventContext): void;
     private pickAtRay;
+    /** The validated color map currently in effect. */
     get colorMap(): LabelColorMap;
+    /**
+     * Replaces the color map and recolors all visible chunks.
+     *
+     * @param colorMap - Colors for label values. Omitted fields fall back
+     *   to defaults.
+     */
     setColorMap(colorMap: LabelColorMapProps): void;
+    /**
+     * Sets the label value drawn as selected or `null` to clear the
+     * selection.
+     *
+     * @param value - The label value to select.
+     */
     setSelectedValue(value: number | null): void;
+    /**
+     * The slice coordinates the layer displays. This is the object passed
+     * at construction and may be mutated to move through the data.
+     */
     get sliceCoords(): SliceCoordinates;
+    /** The chunked label source the layer streams from. */
     get source(): ChunkSource;
+    /**
+     * The streaming policy in effect. Assign a new policy to reschedule
+     * loading at runtime, for example when switching between exploration
+     * and playback.
+     */
     get imageSourcePolicy(): Readonly<ImageSourcePolicy>;
+    /** @param newPolicy - The policy to apply. */
     set imageSourcePolicy(newPolicy: ImageSourcePolicy);
+    /** The layer's chunk store view for diagnostic overlays. */
     get chunkStoreView(): ChunkStoreView | undefined;
+    /** The `t` coordinate of the most recently presented slice. */
     get lastPresentationTimeCoord(): number | undefined;
+    /**
+     * Reads the label value at a world position from the resident chunks.
+     * Prefers the current level of detail and falls back to other resident
+     * levels.
+     *
+     * @param world - The world-space position to sample.
+     * @returns The label value or `null` if no resident chunk covers it.
+     */
     getValueAtWorld(world: vec3): Promise<number | null>;
     private readValueFromChunk;
     private getLabelForChunk;

package/dist/types/src/layers/label_layer.d.ts.map

@@ -1 +1 @@
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package/dist/types/src/layers/point_picking.d.ts

@@ -1,10 +1,15 @@
 import { EventContext } from "../core/event_dispatcher";
 import { Ray } from "../math/ray";
 import { vec2, vec3 } from "gl-matrix";
-export interface PointPickingResult {
+/**
+ * The result of picking a value from a layer with a click.
+ */
+export type PointPickingResult = {
+    /** The picked position in world units. */
     world: vec3;
+    /** The data value sampled at the position. */
     value: number;
-}
+};
 export declare function handlePointPickingEvent<T>(event: EventContext, pointerDownPos: vec2 | null, pickAtRay: (ray: Ray) => Promise<{
     world: vec3;
     value: T;

package/dist/types/src/layers/point_picking.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"point_picking.d.ts","sourceRoot":"","sources":["../../../../src/layers/point_picking.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AACxD,OAAO,EAAE,GAAG,EAAE,MAAM,aAAa,CAAC;AAElC,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAEvC;;GAEG;AACH,MAAM,MAAM,kBAAkB,GAAG;IAC/B,0CAA0C;IAC1C,KAAK,EAAE,IAAI,CAAC;IACZ,8CAA8C;IAC9C,KAAK,EAAE,MAAM,CAAC;CACf,CAAC;AAEF,wBAAgB,uBAAuB,CAAC,CAAC,EACvC,KAAK,EAAE,YAAY,EACnB,cAAc,EAAE,IAAI,GAAG,IAAI,EAC3B,SAAS,EAAE,CAAC,GAAG,EAAE,GAAG,KAAK,OAAO,CAAC;IAAE,KAAK,EAAE,IAAI,CAAC;IAAC,KAAK,EAAE,CAAC,CAAA;CAAE,GAAG,IAAI,CAAC,EAClE,WAAW,CAAC,EAAE,CAAC,IAAI,EAAE;IAAE,KAAK,EAAE,IAAI,CAAC;IAAC,KAAK,EAAE,CAAC,CAAA;CAAE,KAAK,IAAI,EACvD,aAAa,GAAE,MAAU,GACxB,IAAI,GAAG,IAAI,CAyCb"}

package/dist/types/src/layers/volume_layer.d.ts

@@ -4,15 +4,61 @@ import { Viewport } from "../core/viewport";
 import { IdetikContext } from "../idetik";
 import { ImageSourcePolicy } from "../core/image_source_policy";
 import { ChannelProps, ChannelsEnabled } from "../core/channel";
+/**
+ * Initialization properties for constructing a volume layer.
+ */
 export type VolumeLayerProps = {
+    /** The chunked image source to stream from. */
     source: ChunkSource;
+    /** Selects `t` and `c`. Spatial axes are ignored. */
     sliceCoords: SliceCoordinates;
+    /** Streaming policy. Defaults to the exploration policy. */
     policy?: ImageSourcePolicy;
+    /** Per-channel appearance. Length must match the source. */
     channelProps?: ChannelProps[];
 };
-/** @group Layers */
+/**
+ * A layer that renders a chunked multi-channel image source as a 3D
+ * volume.
+ *
+ * Volume layer ray marches the loaded chunks with premultiplied blending
+ * and composites all visible channels in a single pass. The volume renders
+ * at a single level of detail taken from the policy's `lod.min`, so pin
+ * one with the policy when constructing the layer. While the camera moves
+ * the ray march step size is doubled to keep interaction responsive.
+ *
+ * ```ts
+ * const source = await OmeZarrImageSource.fromHttp({ url });
+ *
+ * const layer = new VolumeLayer({
+ *   source,
+ *   sliceCoords: { t: 0, c: undefined },
+ *   policy: createExplorationPolicy({ lod: { min: 2, max: 2 } }),
+ *   channelProps: [
+ *     { color: "#00ffff", contrastLimits: [300, 1500] },
+ *     { color: "#ff00ff", contrastLimits: [75, 500] },
+ *   ],
+ * });
+ *
+ * viewport.addLayer(layer);
+ * ```
+ *
+ * @see {@link ImageLayer} for 2D slicing of the same data.
+ *
+ * @group Layers
+ */
 export declare class VolumeLayer extends Layer implements ChannelsEnabled {
+    /** Identifies the layer type as `VolumeLayer`. */
     readonly type = "VolumeLayer";
+    /** Highlights rays of zero length for debugging. Defaults to `false`. */
+    debugShowDegenerateRays: boolean;
+    /** Ray march step size relative to voxel size. Defaults to `1`. */
+    relativeStepSize: number;
+    /** Scales sample opacity during compositing. Defaults to `1`. */
+    opacityMultiplier: number;
+    /** Alpha where a ray stops early. Defaults to `0.99`. */
+    earlyTerminationAlpha: number;
+    /** Volume ray marching reads scene depth to composite with occluding layers. */
     protected requiresSceneDepth_: boolean;
     private readonly source_;
     private readonly sliceCoords_;
@@ -28,27 +74,63 @@ export declare class VolumeLayer extends Layer implements ChannelsEnabled {
     private lastNumRenderedChannelChunks_;
     private interactiveStepSizeScale_;
     private debugShowWireframes_;
-    debugShowDegenerateRays: boolean;
-    relativeStepSize: number;
-    opacityMultiplier: number;
-    earlyTerminationAlpha: number;
+    /** Whether chunk bounding wireframes are drawn for debugging. */
     get debugShowWireframes(): boolean;
+    /** @param value - Whether to draw chunk wireframes. */
     set debugShowWireframes(value: boolean);
+    /**
+     * Sets the streaming policy at runtime and reschedules loading. The
+     * volume renders the level of detail given by the policy's `lod.min`.
+     *
+     * @param newPolicy - The policy to apply.
+     */
     set imageSourcePolicy(newPolicy: ImageSourcePolicy);
+    /**
+     * Applies new per-channel appearance settings to all visible volumes
+     * and notifies channel change callbacks.
+     *
+     * @param channelProps - One entry per source channel.
+     */
     setChannelProps(channelProps: ChannelProps[]): void;
+    /** The current per-channel appearance settings. */
     get channelProps(): ChannelProps[] | undefined;
+    /** Restores the channel settings passed at construction. */
     resetChannelProps(): void;
+    /**
+     * Registers a callback invoked after every channel settings change.
+     *
+     * @param callback - The callback to add.
+     */
     addChannelChangeCallback(callback: () => void): void;
+    /**
+     * Removes a previously registered channel change callback.
+     *
+     * @param callback - The callback to remove.
+     */
     removeChannelChangeCallback(callback: () => void): void;
+    /**
+     * Creates a volume layer for the given source.
+     *
+     * @param props - Initialization properties.
+     */
     constructor({ source, sliceCoords, policy, channelProps }: VolumeLayerProps);
     private getOrCreateVolume;
+    /** @hidden */
     protected attach(context: IdetikContext): void;
+    /** @hidden */
     protected detach(_context: IdetikContext): void;
     private updateChunks;
     private updateVolumeTransform;
     private releaseAndRemoveVolume;
+    /**
+     * Streams chunks for the current view and rebuilds the volume set
+     * sorted front to back. Called automatically once per frame.
+     *
+     * @param viewport - The viewport being rendered.
+     */
     update(viewport?: Viewport): void;
     private rebuildObjects;
+    /** Returns the ray marching uniforms for this layer. */
     getUniforms(): Record<string, unknown>;
 }
 export declare function poolKeyForChunk(chunk: Chunk): string;

package/dist/types/src/layers/volume_layer.d.ts.map

@@ -1 +1 @@
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package/dist/types/src/math/axes.d.ts

@@ -6,6 +6,9 @@ export type SliceAxes = {
     w: SpatialAxis;
 };
 export declare const AxisComponent: Record<SpatialAxis, 0 | 1 | 2>;
+/**
+ * The plane a 2D slice lies on, named by its in-plane axes.
+ */
 export type SliceOrientation = "XY" | "XZ" | "YZ";
 export declare function sliceAxesFor(orientation: SliceOrientation): SliceAxes;
 export declare function orientationRotation(axes: SliceAxes): quat;

package/dist/types/src/math/axes.d.ts.map

@@ -1 +1 @@
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package/dist/types/src/math/box2.d.ts

@@ -1,19 +1,49 @@
 import { vec2 } from "gl-matrix";
+/**
+ * Axis-aligned bounding box defined by minimum and maximum corners.
+ *
+ * Box2 represents a 2D region bounded by two corners: `min` and `max`. It
+ * is used for view rectangles, viewport regions, and intersection checks.
+ * A default-constructed box is empty and intersection treats boxes
+ * as half-open intervals.
+ *
+ * @group Math
+ */
 export declare class Box2 {
+    /** Minimum corner of the box. */
     min: vec2;
+    /** Maximum corner of the box. */
     max: vec2;
     /**
-     * Initializes as an empty box if no values are provided using the
-     * "empty-by-sentinel" pattern: min = +Infinity, max = -Infinity.
-     * This allows expansion functions to work without special-casing
-     * the first element, and avoids biasing toward (0,0).
+     * Creates a box from optional corner points. The corners are cloned.
+     * When a corner is omitted the box starts empty.
+     *
+     * @param min - The minimum corner.
+     * @param max - The maximum corner.
      */
     constructor(min?: vec2, max?: vec2);
+    /** Returns a deep copy of the box. */
     clone(): Box2;
+    /** Returns `true` when the box encloses no area. */
     isEmpty(): boolean;
+    /**
+     * Tests whether two boxes overlap. Boxes are treated as half-open
+     * intervals so touching edges do not count as overlap.
+     *
+     * @param a - The first box.
+     * @param b - The second box.
+     */
     static intersects(a: Box2, b: Box2): boolean;
+    /**
+     * Tests whether two boxes have exactly equal corners.
+     *
+     * @param a - The first box.
+     * @param b - The second box.
+     */
     static equals(a: Box2, b: Box2): boolean;
+    /** Returns a copy with both corners floored componentwise. */
     floor(): Box2;
+    /** Converts the box to an `x, y, width, height` rectangle. */
     toRect(): {
         x: number;
         y: number;

package/dist/types/src/math/box2.d.ts.map

@@ -1 +1 @@
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