@fideus-labs/fidnii 0.1.0 → 0.3.0

package/dist/BufferManager.d.ts

@@ -5,6 +5,18 @@ import type { TypedArray, ZarrDtype } from "./types.js";
  * The buffer is resized to match the fetched data dimensions exactly.
  * Memory is reused when possible to avoid unnecessary allocations.
  *
+ * For multi-component images (RGB/RGBA), `componentsPerVoxel` controls
+ * how many scalar elements each spatial voxel occupies. The buffer is
+ * sized to hold `spatialPixels * componentsPerVoxel` elements, and the
+ * typed array view spans all of them. Spatial dimensions (`[z, y, x]`)
+ * track only the spatial extent; the component count is a fixed
+ * multiplier on the element count.
+ *
+ * When the source dtype is not uint8 and `componentsPerVoxel > 1`
+ * (non-uint8 RGB/RGBA), the buffer stores **uint8** data because NiiVue
+ * only supports `DT_RGB24` / `DT_RGBA32` (uint8-per-channel). The raw
+ * data is normalized to uint8 externally before being written here.
+ *
  * Memory reuse strategy:
  * - Reuse buffer if newSize <= currentCapacity
  * - Reallocate if newSize > currentCapacity OR newSize < 25% of currentCapacity
@@ -16,13 +28,27 @@ export declare class BufferManager {
     private readonly TypedArrayCtor;
     private readonly bytesPerPixel;
     private readonly dtype;
+    /**
+     * Number of scalar components per spatial voxel.
+     * 1 for scalar images, 3 for RGB, 4 for RGBA.
+     */
+    readonly componentsPerVoxel: number;
+    /**
+     * Whether this buffer stores normalized uint8 data for a non-uint8
+     * RGB/RGBA source. When `true`, {@link getTypedArray} returns a
+     * `Uint8Array` and `bytesPerPixel` is 1, regardless of the source
+     * dtype.
+     */
+    readonly isNormalizedRGB: boolean;
     /**
      * Create a new BufferManager.
      *
      * @param maxPixels - Maximum number of pixels allowed (budget)
      * @param dtype - Data type for the buffer
+     * @param componentsPerVoxel - Number of components per spatial voxel
+     *   (default: 1; pass 3 for RGB, 4 for RGBA)
      */
-    constructor(maxPixels: number, dtype: ZarrDtype);
+    constructor(maxPixels: number, dtype: ZarrDtype, componentsPerVoxel?: number);
     /**
      * Resize the buffer to fit the given dimensions.
      *
@@ -44,7 +70,8 @@ export declare class BufferManager {
     /**
      * Get a typed array view over the current buffer region.
      *
-     * The view is sized to match currentDimensions, not the full buffer capacity.
+     * The view is sized to match `spatialPixels × componentsPerVoxel`,
+     * not the full buffer capacity.
      */
     getTypedArray(): TypedArray;
     /**
@@ -52,11 +79,17 @@ export declare class BufferManager {
      */
     getDimensions(): [number, number, number];
     /**
-     * Get the total number of pixels in the current buffer region.
+     * Get the total number of spatial pixels in the current buffer region.
+     * This does NOT include the component multiplier.
      */
     getPixelCount(): number;
     /**
-     * Get the buffer capacity in pixels.
+     * Get the total number of scalar elements in the current buffer region.
+     * For multi-component images, this is `spatialPixels × componentsPerVoxel`.
+     */
+    getElementCount(): number;
+    /**
+     * Get the buffer capacity in scalar elements.
      */
     getCapacity(): number;
     /**

package/dist/BufferManager.d.ts.map

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package/dist/BufferManager.js

@@ -7,6 +7,18 @@ import { getBytesPerPixel, getTypedArrayConstructor } from "./types.js";
  * The buffer is resized to match the fetched data dimensions exactly.
  * Memory is reused when possible to avoid unnecessary allocations.
  *
+ * For multi-component images (RGB/RGBA), `componentsPerVoxel` controls
+ * how many scalar elements each spatial voxel occupies. The buffer is
+ * sized to hold `spatialPixels * componentsPerVoxel` elements, and the
+ * typed array view spans all of them. Spatial dimensions (`[z, y, x]`)
+ * track only the spatial extent; the component count is a fixed
+ * multiplier on the element count.
+ *
+ * When the source dtype is not uint8 and `componentsPerVoxel > 1`
+ * (non-uint8 RGB/RGBA), the buffer stores **uint8** data because NiiVue
+ * only supports `DT_RGB24` / `DT_RGBA32` (uint8-per-channel). The raw
+ * data is normalized to uint8 externally before being written here.
+ *
  * Memory reuse strategy:
  * - Reuse buffer if newSize <= currentCapacity
  * - Reallocate if newSize > currentCapacity OR newSize < 25% of currentCapacity
@@ -18,17 +30,41 @@ export class BufferManager {
     TypedArrayCtor;
     bytesPerPixel;
     dtype;
+    /**
+     * Number of scalar components per spatial voxel.
+     * 1 for scalar images, 3 for RGB, 4 for RGBA.
+     */
+    componentsPerVoxel;
+    /**
+     * Whether this buffer stores normalized uint8 data for a non-uint8
+     * RGB/RGBA source. When `true`, {@link getTypedArray} returns a
+     * `Uint8Array` and `bytesPerPixel` is 1, regardless of the source
+     * dtype.
+     */
+    isNormalizedRGB;
     /**
      * Create a new BufferManager.
      *
      * @param maxPixels - Maximum number of pixels allowed (budget)
      * @param dtype - Data type for the buffer
+     * @param componentsPerVoxel - Number of components per spatial voxel
+     *   (default: 1; pass 3 for RGB, 4 for RGBA)
      */
-    constructor(maxPixels, dtype) {
+    constructor(maxPixels, dtype, componentsPerVoxel = 1) {
         this.maxPixels = maxPixels;
         this.dtype = dtype;
-        this.TypedArrayCtor = getTypedArrayConstructor(dtype);
-        this.bytesPerPixel = getBytesPerPixel(dtype);
+        this.componentsPerVoxel = componentsPerVoxel;
+        // Non-uint8 RGB/RGBA: the output buffer stores normalized uint8 data
+        // because NiiVue only supports uint8-per-channel color rendering.
+        this.isNormalizedRGB = componentsPerVoxel > 1 && dtype !== "uint8";
+        if (this.isNormalizedRGB) {
+            this.TypedArrayCtor = Uint8Array;
+            this.bytesPerPixel = 1;
+        }
+        else {
+            this.TypedArrayCtor = getTypedArrayConstructor(dtype);
+            this.bytesPerPixel = getBytesPerPixel(dtype);
+        }
         // Initialize with empty buffer - will be allocated on first resize
         this.currentDimensions = [0, 0, 0];
         this.buffer = new ArrayBuffer(0);
@@ -47,20 +83,20 @@ export class BufferManager {
      * @returns TypedArray view over the (possibly new) buffer
      */
     resize(dimensions) {
-        const requiredPixels = dimensions[0] * dimensions[1] * dimensions[2];
-        if (requiredPixels > this.maxPixels) {
-            console.warn(`[fidnii] BufferManager: Requested dimensions [${dimensions.join(", ")}] = ${requiredPixels} pixels exceeds maxPixels (${this.maxPixels}). ` +
+        const spatialPixels = dimensions[0] * dimensions[1] * dimensions[2];
+        if (spatialPixels > this.maxPixels) {
+            console.warn(`[fidnii] BufferManager: Requested dimensions [${dimensions.join(", ")}] = ${spatialPixels} pixels exceeds maxPixels (${this.maxPixels}). ` +
                 `Proceeding anyway (likely at lowest resolution).`);
         }
-        const currentCapacityPixels = this.buffer.byteLength / this.bytesPerPixel;
-        const utilizationRatio = currentCapacityPixels > 0
-            ? requiredPixels / currentCapacityPixels
+        // Total elements = spatial pixels × components per voxel
+        const requiredElements = spatialPixels * this.componentsPerVoxel;
+        const currentCapacityElements = this.buffer.byteLength / this.bytesPerPixel;
+        const utilizationRatio = currentCapacityElements > 0
+            ? requiredElements / currentCapacityElements
             : 0;
-        const needsReallocation = requiredPixels > currentCapacityPixels ||
-            utilizationRatio < 0.25;
+        const needsReallocation = requiredElements > currentCapacityElements || utilizationRatio < 0.25;
         if (needsReallocation) {
-            // Allocate new buffer
-            const newByteLength = requiredPixels * this.bytesPerPixel;
+            const newByteLength = requiredElements * this.bytesPerPixel;
             this.buffer = new ArrayBuffer(newByteLength);
         }
         this.currentDimensions = [...dimensions];
@@ -75,13 +111,14 @@ export class BufferManager {
     /**
      * Get a typed array view over the current buffer region.
      *
-     * The view is sized to match currentDimensions, not the full buffer capacity.
+     * The view is sized to match `spatialPixels × componentsPerVoxel`,
+     * not the full buffer capacity.
      */
     getTypedArray() {
-        const pixelCount = this.currentDimensions[0] *
+        const spatialPixels = this.currentDimensions[0] *
             this.currentDimensions[1] *
             this.currentDimensions[2];
-        return new this.TypedArrayCtor(this.buffer, 0, pixelCount);
+        return new this.TypedArrayCtor(this.buffer, 0, spatialPixels * this.componentsPerVoxel);
     }
     /**
      * Get the current buffer dimensions [z, y, x].
@@ -90,7 +127,8 @@ export class BufferManager {
         return [...this.currentDimensions];
     }
     /**
-     * Get the total number of pixels in the current buffer region.
+     * Get the total number of spatial pixels in the current buffer region.
+     * This does NOT include the component multiplier.
      */
     getPixelCount() {
         return (this.currentDimensions[0] *
@@ -98,7 +136,14 @@ export class BufferManager {
             this.currentDimensions[2]);
     }
     /**
-     * Get the buffer capacity in pixels.
+     * Get the total number of scalar elements in the current buffer region.
+     * For multi-component images, this is `spatialPixels × componentsPerVoxel`.
+     */
+    getElementCount() {
+        return this.getPixelCount() * this.componentsPerVoxel;
+    }
+    /**
+     * Get the buffer capacity in scalar elements.
      */
     getCapacity() {
         return this.buffer.byteLength / this.bytesPerPixel;
@@ -125,9 +170,9 @@ export class BufferManager {
      * Clear the current buffer region to zeros.
      */
     clear() {
-        const pixelCount = this.getPixelCount();
-        if (pixelCount > 0) {
-            const view = new Uint8Array(this.buffer, 0, pixelCount * this.bytesPerPixel);
+        const elementCount = this.getElementCount();
+        if (elementCount > 0) {
+            const view = new Uint8Array(this.buffer, 0, elementCount * this.bytesPerPixel);
             view.fill(0);
         }
     }
@@ -138,9 +183,9 @@ export class BufferManager {
      * @returns True if current buffer can fit the dimensions
      */
     canAccommodate(dimensions) {
-        const requiredPixels = dimensions[0] * dimensions[1] * dimensions[2];
-        const currentCapacityPixels = this.buffer.byteLength / this.bytesPerPixel;
-        return requiredPixels <= currentCapacityPixels;
+        const requiredElements = dimensions[0] * dimensions[1] * dimensions[2] * this.componentsPerVoxel;
+        const currentCapacityElements = this.buffer.byteLength / this.bytesPerPixel;
+        return requiredElements <= currentCapacityElements;
     }
 }
 //# sourceMappingURL=BufferManager.js.map

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package/dist/ClipPlanes.d.ts.map

@@ -1 +1 @@
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package/dist/ClipPlanes.js

@@ -1,7 +1,7 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
-import { pixelToWorld, worldToPixel } from "./utils/coordinates.js";
 import { getChunkShape, getVolumeShape } from "./ResolutionSelector.js";
+import { pixelToWorld, worldToPixel } from "./utils/coordinates.js";
 /** Maximum number of clip planes supported by NiiVue */
 export const MAX_CLIP_PLANES = 6;
 /**
@@ -276,7 +276,9 @@ export function clipPlanesToBoundingBox(clipPlanes, volumeBounds) {
                 maxX = Math.min(maxX, point[0]);
             }
         }
-        else if (absNy > 1 - tolerance && absNx < tolerance && absNz < tolerance) {
+        else if (absNy > 1 - tolerance &&
+            absNx < tolerance &&
+            absNz < tolerance) {
             // Y-aligned plane
             if (normal[1] > 0) {
                 minY = Math.max(minY, point[1]);
@@ -285,7 +287,9 @@ export function clipPlanesToBoundingBox(clipPlanes, volumeBounds) {
                 maxY = Math.min(maxY, point[1]);
             }
         }
-        else if (absNz > 1 - tolerance && absNx < tolerance && absNy < tolerance) {
+        else if (absNz > 1 - tolerance &&
+            absNx < tolerance &&
+            absNy < tolerance) {
             // Z-aligned plane
             if (normal[2] > 0) {
                 minZ = Math.max(minZ, point[2]);
@@ -323,16 +327,8 @@ export function clipPlanesToBoundingBox(clipPlanes, volumeBounds) {
     }
     // Ensure valid bounds (min <= max)
     return {
-        min: [
-            Math.min(minX, maxX),
-            Math.min(minY, maxY),
-            Math.min(minZ, maxZ),
-        ],
-        max: [
-            Math.max(minX, maxX),
-            Math.max(minY, maxY),
-            Math.max(minZ, maxZ),
-        ],
+        min: [Math.min(minX, maxX), Math.min(minY, maxY), Math.min(minZ, maxZ)],
+        max: [Math.max(minX, maxX), Math.max(minY, maxY), Math.max(minZ, maxZ)],
     };
 }
 /**
@@ -494,13 +490,13 @@ export function validateClipPlanes(clipPlanes) {
         // Check point is valid
         if (!Array.isArray(plane.point) ||
             plane.point.length !== 3 ||
-            plane.point.some((v) => typeof v !== "number" || !isFinite(v))) {
+            plane.point.some((v) => typeof v !== "number" || !Number.isFinite(v))) {
             throw new Error(`Invalid point in clip plane ${i}`);
         }
         // Check normal is valid
         if (!Array.isArray(plane.normal) ||
             plane.normal.length !== 3 ||
-            plane.normal.some((v) => typeof v !== "number" || !isFinite(v))) {
+            plane.normal.some((v) => typeof v !== "number" || !Number.isFinite(v))) {
             throw new Error(`Invalid normal in clip plane ${i}`);
         }
         // Check normal is not zero

package/dist/ClipPlanes.js.map

@@ -1 +1 @@
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package/dist/OMEZarrNVImage.d.ts

@@ -1,8 +1,8 @@
-import { NVImage } from "@niivue/niivue";
-import type { Niivue } from "@niivue/niivue";
 import type { Multiscales, Omero } from "@fideus-labs/ngff-zarr";
+import type { Niivue } from "@niivue/niivue";
+import { NVImage } from "@niivue/niivue";
+import { type OMEZarrNVImageEventListener, type OMEZarrNVImageEventListenerOptions, type OMEZarrNVImageEventMap, type PopulateTrigger } from "./events.js";
 import type { ClipPlane, ClipPlanes, OMEZarrNVImageOptions, SlabBufferState, SlabSliceType, VolumeBounds } from "./types.js";
-import { OMEZarrNVImageEventListener, OMEZarrNVImageEventListenerOptions, OMEZarrNVImageEventMap, PopulateTrigger } from "./events.js";
 /**
  * OMEZarrNVImage extends NVImage to support rendering OME-Zarr images in NiiVue.
  *
@@ -18,6 +18,14 @@ export declare class OMEZarrNVImage extends NVImage {
     readonly multiscales: Multiscales;
     /** Maximum number of pixels to use */
     readonly maxPixels: number;
+    /**
+     * True when `multiscales.method` is `Methods.ITKWASM_LABEL_IMAGE`.
+     *
+     * Label images are rendered with a discrete colormap
+     * (`setColormapLabel()`) instead of a continuous colormap, and
+     * OMERO intensity windowing is skipped.
+     */
+    readonly isLabelImage: boolean;
     /** Reference to NiiVue instance */
     private readonly niivue;
     /** Buffer manager for dynamically-sized pixel data */
@@ -36,6 +44,21 @@ export declare class OMEZarrNVImage extends NVImage {
     private isLoading;
     /** Data type of the volume */
     private readonly dtype;
+    /**
+     * Channel dimension info, or `null` for scalar (single-component) images.
+     * When non-null, the image has a `"c"` dimension and is treated as
+     * multi-component (RGB/RGBA) data.
+     */
+    private readonly _channelInfo;
+    /**
+     * Whether the image is 2D (no `"z"` dimension).
+     */
+    private readonly _is2D;
+    /**
+     * Whether to negate the y-scale in the NIfTI affine for 2D images
+     * so that NiiVue renders them right-side up.
+     */
+    private readonly _flipY2D;
     /** Full volume bounds in world space */
     private readonly _volumeBounds;
     /** Current buffer bounds in world space (may differ from full volume when clipped) */
@@ -177,6 +200,17 @@ export declare class OMEZarrNVImage extends NVImage {
      * This sets the display intensity range for NiiVue rendering.
      */
     private applyOmeroToHeader;
+    /**
+     * Build and apply a discrete NiiVue label colormap to an NVImage.
+     *
+     * Scans the pixel data for unique integer values and assigns each a
+     * distinct color from the Glasbey palette (via `@fideus-labs/ngff-zarr`).
+     * Label 0 is treated as background (fully transparent).
+     *
+     * @param nvImage - The NVImage to apply the label colormap to
+     * @param data - The pixel data to scan for unique labels
+     */
+    private _applyLabelColormap;
     /**
      * Ensure OMERO metadata is available and applied.
      *
@@ -191,6 +225,17 @@ export declare class OMEZarrNVImage extends NVImage {
      * @param levelIndex - The resolution level index
      */
     private ensureOmeroMetadata;
+    /**
+     * Get per-channel normalization windows for non-uint8 RGB/RGBA.
+     *
+     * Uses OMERO `window.start`/`window.end` (or `window.min`/`window.max`)
+     * when available. Falls back to computing min/max from the raw data.
+     *
+     * @param data - Raw multi-component data from the zarr fetch
+     * @param components - Number of components per voxel (3 or 4)
+     * @returns Per-channel windows for normalization to uint8
+     */
+    private _getChannelWindows;
     /**
      * Handle clip plane change from NiiVue.
      * This is called when the user interacts with clip planes in NiiVue.
@@ -260,6 +305,17 @@ export declare class OMEZarrNVImage extends NVImage {
      * Get the number of resolution levels.
      */
     getNumLevels(): number;
+    /**
+     * Load a specific resolution level.
+     *
+     * Overrides the automatic `maxPixels`-based level selection and loads the
+     * requested level directly.  The preview step is skipped because the caller
+     * has explicitly chosen a level.
+     *
+     * @param levelIndex - Zero-based resolution level (0 = highest resolution)
+     * @throws If `levelIndex` is out of range
+     */
+    loadLevel(levelIndex: number): Promise<void>;
     /**
      * Get the volume bounds in world space.
      */

package/dist/OMEZarrNVImage.d.ts.map

@@ -1 +1 @@
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