@fideus-labs/ngff-zarr 0.7.5 → 0.9.0

package/esm/utils/compute_omero.js

@@ -1,136 +1,386 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
-import { zarrGet } from "./worker_pool.js";
+/**
+ * Unified OMERO metadata computation using @fideus-labs/worker-pool.
+ *
+ * Works in Node.js, Deno, and browser environments. Each zarr chunk is
+ * decoded and its per-channel statistics computed in parallel via a
+ * WorkerPool. Decoded chunks are cached so that a subsequent zarrGet()
+ * with the same cache avoids redundant decompression.
+ */
+import { WorkerPool } from "@fideus-labs/worker-pool";
+import { createCacheKey, readArrayMetadata } from "@fideus-labs/fizarrita";
+import { buildOmeroFromAccumulators, createAccumulator, extractChannel, mergeAccumulators, updateAccumulator, validateColor, validateQuantiles, } from "./compute_omero-shared.js";
+import { getMetaId, workerDecodeAndStats } from "./omero_worker_rpc.js";
 // Re-export shared utilities for backward compatibility
 export { computeChannelStatistics, extractChannel, getDefaultColors, GLASBEY_COLORS, QUANTILE_SAMPLE_SIZE, validateColor, validateQuantiles, } from "./compute_omero-shared.js";
-// Import for internal use
-import { computeChannelStatistics, extractChannel, getDefaultColors, validateColor, validateQuantiles, } from "./compute_omero-shared.js";
+// ---------------------------------------------------------------------------
+// Worker pool for omero computation
+// ---------------------------------------------------------------------------
+/** Pool size for the omero worker pool. */
+const POOL_SIZE = Math.min(typeof navigator !== "undefined" ? (navigator?.hardwareConcurrency || 4) : 4, 128);
+/** Blob URL used by inlined browser builds — set by inline_worker.ts. */
+let workerBlobUrl = null;
+let _omeroPool = null;
+function getOmeroPool() {
+    if (!_omeroPool) {
+        _omeroPool = new WorkerPool(POOL_SIZE);
+    }
+    return _omeroPool;
+}
+/** Create a new omero codec worker instance. */
+function createOmeroWorker() {
+    return new Worker(new URL("../workers/omero_codec_worker.js", import.meta.url), { type: "module" });
+}
+/**
+ * Terminate the omero computation worker pool and release resources.
+ * Call this when you're done with OMERO computations to free memory.
+ */
+export function terminateOmeroWorkerPool() {
+    if (_omeroPool) {
+        _omeroPool.terminateWorkers();
+        _omeroPool = null;
+    }
+    if (workerBlobUrl) {
+        URL.revokeObjectURL(workerBlobUrl);
+        workerBlobUrl = null;
+    }
+}
+// ---------------------------------------------------------------------------
+// Chunk coordinate enumeration
+// ---------------------------------------------------------------------------
+/**
+ * Enumerate all chunk coordinates for a given array shape and chunk shape.
+ * Returns an array of coordinate tuples.
+ */
+function enumerateChunkCoords(shape, chunkShape) {
+    const gridDims = shape.map((s, i) => Math.ceil(s / chunkShape[i]));
+    const coords = [];
+    const ndim = gridDims.length;
+    // Recursive enumeration of all grid coordinates
+    function enumerate(dim, current) {
+        if (dim === ndim) {
+            coords.push([...current]);
+            return;
+        }
+        for (let i = 0; i < gridDims[dim]; i++) {
+            current[dim] = i;
+            enumerate(dim + 1, current);
+        }
+    }
+    enumerate(0, new Array(ndim).fill(0));
+    return coords;
+}
+// ---------------------------------------------------------------------------
+// Shared TextDecoder for metadata reading
+// ---------------------------------------------------------------------------
+const _textDecoder = new TextDecoder();
+// ---------------------------------------------------------------------------
+// Codec detection — skip workers for unsupported codecs
+// ---------------------------------------------------------------------------
+const UNSUPPORTED_CODEC_NAMES = new Set(["sharding_indexed"]);
+// deno-lint-ignore no-explicit-any
+const _codecCheckCache = new WeakMap();
+async function hasUnsupportedCodecs(arr) {
+    let pathMap = _codecCheckCache.get(arr.store);
+    if (pathMap?.has(arr.path)) {
+        return pathMap.get(arr.path);
+    }
+    const zarrJsonPath = (arr.path === "/" ? "/zarr.json" : `${arr.path}/zarr.json`);
+    const bytes = await arr.store.get(zarrJsonPath);
+    let result = false;
+    if (bytes) {
+        try {
+            const meta = JSON.parse(_textDecoder.decode(bytes));
+            const codecs = meta.codecs ?? [];
+            result = codecs.some((c) => UNSUPPORTED_CODEC_NAMES.has(c.name));
+        }
+        catch {
+            result = false;
+        }
+    }
+    if (!pathMap) {
+        pathMap = new Map();
+        _codecCheckCache.set(arr.store, pathMap);
+    }
+    pathMap.set(arr.path, result);
+    return result;
+}
+// ---------------------------------------------------------------------------
+// Chunk key encoding (local fallback for when fizarrita metadata isn't usable)
+// ---------------------------------------------------------------------------
+function createChunkKeyEncoder(metadata, isV2) {
+    if (isV2) {
+        const separator = metadata.dimension_separator ?? ".";
+        return (chunk_coords) => chunk_coords.join(separator) || "0";
+    }
+    const encoding = metadata.chunk_key_encoding ?? { name: "default" };
+    if (encoding.name === "default") {
+        const separator = encoding.configuration?.separator ?? "/";
+        return (chunk_coords) => ["c", ...chunk_coords].join(separator);
+    }
+    if (encoding.name === "v2") {
+        const separator = encoding.configuration?.separator ?? ".";
+        return (chunk_coords) => chunk_coords.join(separator) || "0";
+    }
+    throw new Error(`Unknown chunk key encoding: ${encoding.name}`);
+}
+async function readLocalArrayMetadata(arr) {
+    const store = arr.store;
+    // Try v3 first: read zarr.json
+    const v3Path = (arr.path === "/" ? "/zarr.json" : `${arr.path}/zarr.json`);
+    const v3Bytes = await store.get(v3Path);
+    if (v3Bytes) {
+        const metadata = JSON.parse(_textDecoder.decode(v3Bytes));
+        return {
+            codecMeta: {
+                data_type: metadata.data_type,
+                chunk_shape: metadata.chunk_grid.configuration.chunk_shape,
+                codecs: metadata.codecs,
+            },
+            encodeChunkKey: createChunkKeyEncoder(metadata, false),
+        };
+    }
+    // Try v2: read .zarray
+    const v2Path = (arr.path === "/" ? "/.zarray" : `${arr.path}/.zarray`);
+    const v2Bytes = await store.get(v2Path);
+    if (v2Bytes) {
+        const metadata = JSON.parse(_textDecoder.decode(v2Bytes));
+        const codecs = [];
+        if (metadata.order === "F") {
+            codecs.push({ name: "transpose", configuration: { order: "F" } });
+        }
+        if (metadata.compressor) {
+            const { id, ...configuration } = metadata.compressor;
+            codecs.push({ name: id, configuration });
+        }
+        for (const { id, ...configuration } of metadata.filters ?? []) {
+            codecs.push({ name: id, configuration });
+        }
+        return {
+            codecMeta: {
+                data_type: arr.dtype,
+                chunk_shape: arr.chunks,
+                codecs: codecs.length > 0
+                    ? codecs
+                    : [{ name: "bytes", configuration: { endian: "little" } }],
+            },
+            encodeChunkKey: createChunkKeyEncoder(metadata, true),
+        };
+    }
+    // Fallback
+    return {
+        codecMeta: {
+            data_type: arr.dtype,
+            chunk_shape: arr.chunks,
+            codecs: [{ name: "bytes", configuration: { endian: "little" } }],
+        },
+        encodeChunkKey: createChunkKeyEncoder({
+            chunk_key_encoding: { name: "default" },
+        }, false),
+    };
+}
+// ---------------------------------------------------------------------------
+// Main-thread fallback for stats computation from a cached/decoded chunk
+// ---------------------------------------------------------------------------
+function computeStatsFromDecodedChunk(chunkData, chunkShape, nChannels, cIndex) {
+    const accumulators = [];
+    if (cIndex >= 0) {
+        for (let ch = 0; ch < nChannels; ch++) {
+            const channelData = extractChannel(chunkData, chunkShape, ch, cIndex);
+            const acc = createAccumulator();
+            updateAccumulator(acc, channelData);
+            accumulators.push(acc);
+        }
+    }
+    else {
+        const acc = createAccumulator();
+        updateAccumulator(acc, chunkData);
+        accumulators.push(acc);
+    }
+    return accumulators;
+}
+// ---------------------------------------------------------------------------
+// Main-thread fallback for full computation (unsupported codecs)
+// ---------------------------------------------------------------------------
+async function computeOmeroMainThread(image, options = {}) {
+    // Lazy import to avoid circular dependency
+    const { zarrGet } = await import("./worker_pool.js");
+    const quantiles = options.quantiles ?? [0.02, 0.98];
+    validateQuantiles(quantiles);
+    const dims = image.dims;
+    const shape = image.data.shape;
+    const cIndex = dims.indexOf("c");
+    const hasChannelDim = cIndex !== -1;
+    const nChannels = hasChannelDim ? shape[cIndex] : 1;
+    const result = await zarrGet(image.data);
+    const fullData = result.data;
+    const accumulators = Array.from({ length: nChannels }, () => createAccumulator());
+    if (hasChannelDim) {
+        for (let chIdx = 0; chIdx < nChannels; chIdx++) {
+            const channelData = extractChannel(fullData, shape, chIdx, cIndex);
+            updateAccumulator(accumulators[chIdx], channelData);
+        }
+    }
+    else {
+        updateAccumulator(accumulators[0], fullData);
+    }
+    return buildOmeroFromAccumulators(accumulators, quantiles, options.colors, options.labels);
+}
+// ---------------------------------------------------------------------------
+// Public API: computeOmeroFromNgffImage
+// ---------------------------------------------------------------------------
 /**
  * Compute OMERO metadata from an NgffImage.
  *
- * This function computes visualization parameters (OMERO metadata) from image data:
- * - min/max: The actual data range
- * - start/end: Display window based on quantiles (default 2% and 98%)
- *
- * For multi-channel images (with 'c' dimension), statistics are computed
- * separately for each channel, resulting in per-channel OMERO windows.
- *
- * Memory requirements: This function loads the entire image data into memory
- * for statistics computation. For large images, use the lowest resolution
- * image from a multiscales pyramid.
- *
- * Edge cases:
- * - If all values in a channel are NaN, the statistics will be NaN.
- * - If a channel has constant values, min/max/start/end will all be the same.
+ * Each zarr chunk is decoded and its per-channel statistics computed in
+ * parallel via a WorkerPool. Decoded chunks are optionally cached so that
+ * a subsequent zarrGet() with the same cache avoids redundant decompression.
  *
  * @param image - The NgffImage to compute metadata for
- * @param options - Optional configuration for quantiles, colors, and labels
- *   - quantiles: Tuple of (low, high) quantile values. Must be between 0 and 1,
- *                with low < high. Default is [0.02, 0.98] for 2% and 98% quantiles.
- *   - colors: List of hex color strings (without #) for each channel.
- *             Must be 6-digit hexadecimal strings (e.g., "FF0000" for red).
- *             If not provided, uses white for single channel or Glasbey
- *             progression for multi-channel.
- *   - labels: List of label strings for each channel.
- *             If not provided, uses empty strings.
+ * @param options - Optional configuration for quantiles, colors, labels, and cache
  * @returns Promise resolving to Omero metadata with computed window parameters
- * @throws {Error} If quantiles are invalid, colors are invalid format,
- *                 or not enough colors/labels provided.
- *
- * @example
- * ```ts
- * const omero = await computeOmeroFromNgffImage(image);
- * multiscales.metadata.omero = omero;
- * ```
  */
 export async function computeOmeroFromNgffImage(image, options = {}) {
     const quantiles = options.quantiles ?? [0.02, 0.98];
-    // Validate quantiles
     validateQuantiles(quantiles);
     const dims = image.dims;
     const shape = image.data.shape;
-    // Check if there's a channel dimension
-    const hasChannelDim = dims.includes("c");
-    const cIndex = hasChannelDim ? dims.indexOf("c") : -1;
+    const cIndex = dims.indexOf("c");
+    const hasChannelDim = cIndex !== -1;
     const nChannels = hasChannelDim ? shape[cIndex] : 1;
-    // Get colors
-    let channelColors;
+    // Validate colors
     if (options.colors !== undefined) {
         if (options.colors.length < nChannels) {
             throw new Error(`Not enough colors provided. Got ${options.colors.length}, need ${nChannels}.`);
         }
-        // Validate each color
         for (const color of options.colors.slice(0, nChannels)) {
             validateColor(color);
         }
-        channelColors = options.colors.slice(0, nChannels);
-    }
-    else {
-        channelColors = getDefaultColors(nChannels);
     }
-    // Get labels
-    let channelLabels;
+    // Validate labels
     if (options.labels !== undefined) {
         if (options.labels.length < nChannels) {
             throw new Error(`Not enough labels provided. Got ${options.labels.length}, need ${nChannels}.`);
         }
-        channelLabels = options.labels.slice(0, nChannels);
     }
-    else {
-        channelLabels = Array(nChannels).fill("");
+    // Fall back to main-thread for unsupported codecs (e.g. sharding)
+    if (await hasUnsupportedCodecs(image.data)) {
+        return computeOmeroMainThread(image, options);
     }
-    // Read all data from the zarr array
-    const result = await zarrGet(image.data);
-    const fullData = result.data;
-    // Compute statistics for each channel
-    const channels = [];
-    for (let chIdx = 0; chIdx < nChannels; chIdx++) {
-        let channelData;
-        if (hasChannelDim) {
-            // Extract this channel's data
-            channelData = extractChannel(fullData, shape, chIdx, cIndex);
+    // Read array metadata for codec pipeline + chunk key encoding
+    let codecMeta;
+    let encodeChunkKey;
+    try {
+        const metadata = await readArrayMetadata(image.data);
+        codecMeta = metadata.codecMeta;
+        encodeChunkKey = metadata.encodeChunkKey;
+    }
+    catch {
+        // Fall back to local metadata reading if fizarrita's version fails
+        const localMeta = await readLocalArrayMetadata(image.data);
+        codecMeta = localMeta.codecMeta;
+        encodeChunkKey = localMeta.encodeChunkKey;
+    }
+    const chunkShape = codecMeta.chunk_shape;
+    const metaId = getMetaId(codecMeta);
+    // Optional cache for decoded chunks
+    const cache = options.cache;
+    // Enumerate all chunk coordinates
+    const allChunkCoords = enumerateChunkCoords(shape, chunkShape);
+    // Build worker pool tasks — one per chunk
+    const pool = getOmeroPool();
+    const tasks = [];
+    for (const chunk_coords of allChunkCoords) {
+        const chunkKey = encodeChunkKey(chunk_coords);
+        const chunkPath = image.data.resolve(chunkKey).path;
+        // Compute edge chunk shape
+        const edgeChunkShape = chunk_coords.map((coord, dim) => Math.min(chunkShape[dim], shape[dim] - coord * chunkShape[dim]));
+        // Check cache before building the task
+        const cacheKey = cache
+            ? createCacheKey(image.data, encodeChunkKey, chunk_coords)
+            : "";
+        if (cache) {
+            const cachedChunk = cache.get(cacheKey);
+            if (cachedChunk) {
+                // Cache hit — compute stats from cached decoded chunk on main thread
+                const accs = computeStatsFromDecodedChunk(cachedChunk.data, cachedChunk.shape, nChannels, cIndex);
+                // No worker needed — return the slot directly for pool management.
+                // For cached results, we use the provided workerSlot if available,
+                // or create a worker to satisfy the type contract.
+                tasks.push((workerSlot) => {
+                    const worker = workerSlot ?? createOmeroWorker();
+                    return Promise.resolve({
+                        worker,
+                        result: accs,
+                    });
+                });
+                continue;
+            }
         }
-        else {
-            channelData = fullData;
+        tasks.push(async (workerSlot) => {
+            const worker = workerSlot ?? createOmeroWorker();
+            // Fetch raw bytes from store on main thread
+            const rawBytes = await image.data.store.get(chunkPath);
+            if (!rawBytes) {
+                // Missing chunk — fill with zeros, compute trivial stats
+                const accs = [];
+                for (let ch = 0; ch < nChannels; ch++) {
+                    accs.push(createAccumulator());
+                }
+                return { worker, result: accs };
+            }
+            // Send to worker: decode + compute stats in one round-trip
+            const { chunk, accumulators } = await workerDecodeAndStats(worker, rawBytes, metaId, codecMeta, nChannels, cIndex, edgeChunkShape);
+            // Cache decoded chunk for future zarrGet reuse.
+            // Cast needed: jsr:zarrita vs npm:zarrita Chunk types are structurally
+            // identical but TypeScript sees differing #private class fields.
+            if (cache) {
+                // deno-lint-ignore no-explicit-any
+                cache.set(cacheKey, chunk);
+            }
+            return { worker, result: accumulators };
+        });
+    }
+    // Execute all tasks with bounded concurrency
+    let allAccumulators;
+    if (tasks.length > 0) {
+        const { promise } = pool.runTasks(tasks);
+        allAccumulators = await promise;
+    }
+    else {
+        allAccumulators = [];
+    }
+    // Merge partial accumulators across all chunks
+    const mergedAccumulators = Array.from({ length: nChannels }, () => createAccumulator());
+    for (const chunkAccs of allAccumulators) {
+        for (let ch = 0; ch < nChannels; ch++) {
+            if (chunkAccs[ch]) {
+                mergedAccumulators[ch] = mergeAccumulators(mergedAccumulators[ch], chunkAccs[ch]);
+            }
         }
-        // Compute statistics
-        const stats = computeChannelStatistics(channelData, quantiles);
-        // Create OMERO window
-        const window = {
-            min: stats.min,
-            max: stats.max,
-            start: stats.qLow,
-            end: stats.qHigh,
-        };
-        // Create channel metadata
-        const channel = {
-            color: channelColors[chIdx],
-            window,
-            label: channelLabels[chIdx],
-        };
-        channels.push(channel);
     }
-    return { channels };
+    return buildOmeroFromAccumulators(mergedAccumulators, quantiles, options.colors, options.labels);
 }
+// ---------------------------------------------------------------------------
+// Public API: computeOmeroFromMultiscales
+// ---------------------------------------------------------------------------
 /**
  * Compute OMERO metadata from a Multiscales object.
  *
  * This is a convenience function that computes OMERO metadata from the
- * highest or lowest resolution image in a multiscales pyramid.
+ * highest resolution image in a multiscales pyramid for accurate statistics.
  *
  * @param multiscales - The Multiscales object to compute metadata for
- * @param options - Optional configuration for quantiles, colors, labels, and resolution
+ * @param options - Optional configuration for quantiles, colors, and labels
  * @returns Promise resolving to Omero metadata with computed window parameters
  */
 export async function computeOmeroFromMultiscales(multiscales, options = {}) {
     if (!multiscales.images || multiscales.images.length === 0) {
         throw new Error("Multiscales has no images");
     }
-    const useLowestResolution = options.useLowestResolution ?? true;
-    // Select which image to use based on resolution preference
-    const image = useLowestResolution
-        ? multiscales.images[multiscales.images.length - 1] // Last image (lowest resolution)
-        : multiscales.images[0]; // First image (highest resolution)
+    // Always use the highest resolution (first) image for accurate statistics
+    const image = multiscales.images[0];
     const computeOptions = {};
     if (options.quantiles !== undefined) {
         computeOptions.quantiles = options.quantiles;

package/esm/utils/compute_omero.js.map

@@ -1 +1 @@
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package/esm/utils/omero_worker_rpc.d.ts

@@ -0,0 +1,37 @@
+/**
+ * Main-thread RPC helpers for communicating with the omero codec worker.
+ *
+ * Follows the same persistent-dispatcher pattern as fizarrita's worker-rpc.ts:
+ *   - One message listener per worker, routed by request ID
+ *   - Meta-init protocol: codec metadata sent once per worker per array config
+ *   - Zero-copy buffer transfer where possible
+ *
+ * Adds the `workerDecodeAndStats` function for the decode_and_stats message.
+ */
+import type { Chunk, DataType } from "zarrita";
+import type { CodecChunkMeta } from "@fideus-labs/fizarrita";
+import type { ChannelStatisticsAccumulator } from "./compute_omero-shared.js";
+/**
+ * Get or create a stable metaId for the given codec metadata.
+ * Uses JSON.stringify as the dedup key — called once per unique array config.
+ */
+export declare function getMetaId(meta: CodecChunkMeta): number;
+/**
+ * Send raw bytes to the omero codec worker for decoding AND per-channel
+ * statistics computation. Returns both the decoded chunk (for caching)
+ * and partial accumulators (for merging).
+ *
+ * @param worker - The Web Worker to send the message to
+ * @param bytes - Raw encoded chunk bytes from the store
+ * @param metaId - Stable ID for the codec metadata
+ * @param meta - Codec metadata for this array
+ * @param nChannels - Number of channels in the image
+ * @param cIndex - Index of the channel dimension (-1 if no channel dim)
+ * @param actualChunkShape - Edge chunk shape correction (optional)
+ * @returns The decoded chunk and per-channel accumulators
+ */
+export declare function workerDecodeAndStats<D extends DataType>(worker: Worker, bytes: Uint8Array, metaId: number, meta: CodecChunkMeta, nChannels: number, cIndex: number, actualChunkShape?: number[]): Promise<{
+    chunk: Chunk<D>;
+    accumulators: ChannelStatisticsAccumulator[];
+}>;
+//# sourceMappingURL=omero_worker_rpc.d.ts.map

package/esm/utils/omero_worker_rpc.d.ts.map

@@ -0,0 +1 @@
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