@fideus-labs/ngff-zarr 0.7.5 → 0.9.0

package/esm/utils/omero_worker_rpc.js

@@ -0,0 +1,156 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+// Local typed array constructor lookup (avoids depending on fizarrita internals
+// from the main thread — the worker uses fizarrita's version)
+function get_ctr(data_type) {
+    const ctr = {
+        int8: Int8Array,
+        int16: Int16Array,
+        int32: Int32Array,
+        int64: globalThis.BigInt64Array,
+        uint8: Uint8Array,
+        uint16: Uint16Array,
+        uint32: Uint32Array,
+        uint64: globalThis.BigUint64Array,
+        float32: Float32Array,
+        float64: Float64Array,
+    }[data_type];
+    if (!ctr) {
+        throw new Error(`Unsupported data_type for worker codec: ${data_type}`);
+    }
+    return ctr;
+}
+class WorkerDispatcher {
+    worker;
+    pending = new Map();
+    /** Tracks which metaIds have been sent to this worker. */
+    sentMetas = new Set();
+    constructor(worker) {
+        this.worker = worker;
+        worker.addEventListener("message", this.onMessage);
+        worker.addEventListener("error", this.onError);
+    }
+    onMessage = (event) => {
+        const { id } = event.data;
+        const req = this.pending.get(id);
+        if (!req)
+            return;
+        this.pending.delete(id);
+        if (event.data.error) {
+            req.reject(new Error(event.data.error));
+        }
+        else {
+            req.resolve(event.data);
+        }
+    };
+    onError = (err) => {
+        const error = new Error(err.message ?? "Worker error");
+        for (const req of this.pending.values()) {
+            req.reject(error);
+        }
+        this.pending.clear();
+    };
+    send(id, message, transfer) {
+        return new Promise((resolve, reject) => {
+            this.pending.set(id, { resolve, reject });
+            this.worker.postMessage(message, transfer);
+        });
+    }
+    hasMeta(metaId) {
+        return this.sentMetas.has(metaId);
+    }
+    markMeta(metaId) {
+        this.sentMetas.add(metaId);
+    }
+}
+/** Map from Worker to its dispatcher. WeakMap so dispatchers are GC'd with workers. */
+const dispatchers = new WeakMap();
+function getDispatcher(worker) {
+    let d = dispatchers.get(worker);
+    if (!d) {
+        d = new WorkerDispatcher(worker);
+        dispatchers.set(worker, d);
+    }
+    return d;
+}
+// ---------------------------------------------------------------------------
+// Meta ID registry — assigns stable IDs to unique codec metadata
+// ---------------------------------------------------------------------------
+let nextMetaId = 0;
+const metaKeyToId = new Map();
+const metaIdToMeta = new Map();
+/**
+ * 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 function getMetaId(meta) {
+    const key = JSON.stringify(meta);
+    let id = metaKeyToId.get(key);
+    if (id === undefined) {
+        id = nextMetaId++;
+        metaKeyToId.set(key, id);
+        metaIdToMeta.set(id, meta);
+    }
+    return id;
+}
+// ---------------------------------------------------------------------------
+// Request ID
+// ---------------------------------------------------------------------------
+let nextRequestId = 0;
+// ---------------------------------------------------------------------------
+// Buffer transfer helpers
+// ---------------------------------------------------------------------------
+function prepareTransferBuffer(buffer, byteOffset, byteLength) {
+    // Always copy: store-fetched bytes may be cached/shared
+    return buffer.slice(byteOffset, byteOffset + byteLength);
+}
+// ---------------------------------------------------------------------------
+// Ensure meta is initialized on the worker
+// ---------------------------------------------------------------------------
+async function ensureMeta(dispatcher, metaId) {
+    if (dispatcher.hasMeta(metaId))
+        return;
+    const meta = metaIdToMeta.get(metaId);
+    const id = nextRequestId++;
+    await dispatcher.send(id, { type: "init", id, metaId, meta }, []);
+    dispatcher.markMeta(metaId);
+}
+/**
+ * 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 async function workerDecodeAndStats(worker, bytes, metaId, meta, nChannels, cIndex, actualChunkShape) {
+    const dispatcher = getDispatcher(worker);
+    await ensureMeta(dispatcher, metaId);
+    const id = nextRequestId++;
+    const transferBuffer = prepareTransferBuffer(bytes.buffer, bytes.byteOffset, bytes.byteLength);
+    const response = (await dispatcher.send(id, {
+        type: "decode_and_stats",
+        id,
+        bytes: transferBuffer,
+        metaId,
+        actualChunkShape,
+        nChannels,
+        cIndex,
+    }, [transferBuffer]));
+    // Reconstruct the TypedArray from the transferred buffer
+    const Ctr = get_ctr(meta.data_type);
+    const data = new Ctr(response.data, 0, response.data.byteLength / Ctr.BYTES_PER_ELEMENT);
+    const chunk = {
+        data,
+        shape: response.shape,
+        stride: response.stride,
+    };
+    return { chunk, accumulators: response.accumulators };
+}
+//# sourceMappingURL=omero_worker_rpc.js.map

package/esm/utils/omero_worker_rpc.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"omero_worker_rpc.js","sourceRoot":"","sources":["../../src/utils/omero_worker_rpc.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAiB/B,gFAAgF;AAChF,8DAA8D;AAC9D,SAAS,OAAO,CACd,SAAY;IAEZ,MAAM,GAAG,GAA0C;QACjD,IAAI,EAAE,SAAS;QACf,KAAK,EAAE,UAAU;QACjB,KAAK,EAAE,UAAU;QACjB,KAAK,EAAE,UAAU,CAAC,aAAa;QAC/B,KAAK,EAAE,UAAU;QACjB,MAAM,EAAE,WAAW;QACnB,MAAM,EAAE,WAAW;QACnB,MAAM,EAAE,UAAU,CAAC,cAAc;QACjC,OAAO,EAAE,YAAY;QACrB,OAAO,EAAE,YAAY;KACM,CAAC,SAAmB,CAEpC,CAAC;IACd,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,MAAM,IAAI,KAAK,CAAC,2CAA2C,SAAS,EAAE,CAAC,CAAC;IAC1E,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAWD,MAAM,gBAAgB;IAKA;IAJZ,OAAO,GAAG,IAAI,GAAG,EAA0B,CAAC;IACpD,0DAA0D;IAClD,SAAS,GAAG,IAAI,GAAG,EAAU,CAAC;IAEtC,YAAoB,MAAc;QAAd,WAAM,GAAN,MAAM,CAAQ;QAChC,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC;QACnD,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IACjD,CAAC;IAEO,SAAS,GAAG,CAAC,KAAmB,EAAQ,EAAE;QAChD,MAAM,EAAE,EAAE,EAAE,GAAG,KAAK,CAAC,IAAI,CAAC;QAC1B,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACjC,IAAI,CAAC,GAAG;YAAE,OAAO;QACjB,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;QAExB,IAAI,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YACrB,GAAG,CAAC,MAAM,CAAC,IAAI,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;QAC1C,CAAC;aAAM,CAAC;YACN,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QAC1B,CAAC;IACH,CAAC,CAAC;IAEM,OAAO,GAAG,CAAC,GAAe,EAAQ,EAAE;QAC1C,MAAM,KAAK,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,OAAO,IAAI,cAAc,CAAC,CAAC;QACvD,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;YACxC,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QACpB,CAAC;QACD,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;IACvB,CAAC,CAAC;IAEF,IAAI,CACF,EAAU,EACV,OAAgB,EAChB,QAAwB;QAExB,OAAO,IAAI,OAAO,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;YACrC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,CAAC;YAC1C,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC;QAC7C,CAAC,CAAC,CAAC;IACL,CAAC;IAED,OAAO,CAAC,MAAc;QACpB,OAAO,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACpC,CAAC;IAED,QAAQ,CAAC,MAAc;QACrB,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAC7B,CAAC;CACF;AAED,uFAAuF;AACvF,MAAM,WAAW,GAAG,IAAI,OAAO,EAA4B,CAAC;AAE5D,SAAS,aAAa,CAAC,MAAc;IACnC,IAAI,CAAC,GAAG,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAChC,IAAI,CAAC,CAAC,EAAE,CAAC;QACP,CAAC,GAAG,IAAI,gBAAgB,CAAC,MAAM,CAAC,CAAC;QACjC,WAAW,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC;IAC7B,CAAC;IACD,OAAO,CAAC,CAAC;AACX,CAAC;AAED,8EAA8E;AAC9E,iEAAiE;AACjE,8EAA8E;AAE9E,IAAI,UAAU,GAAG,CAAC,CAAC;AACnB,MAAM,WAAW,GAAG,IAAI,GAAG,EAAkB,CAAC;AAC9C,MAAM,YAAY,GAAG,IAAI,GAAG,EAA0B,CAAC;AAEvD;;;GAGG;AACH,MAAM,UAAU,SAAS,CAAC,IAAoB;IAC5C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;IACjC,IAAI,EAAE,GAAG,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;IAC9B,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;QACrB,EAAE,GAAG,UAAU,EAAE,CAAC;QAClB,WAAW,CAAC,GAAG,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC;QACzB,YAAY,CAAC,GAAG,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC;IAC7B,CAAC;IACD,OAAO,EAAE,CAAC;AACZ,CAAC;AAED,8EAA8E;AAC9E,aAAa;AACb,8EAA8E;AAE9E,IAAI,aAAa,GAAG,CAAC,CAAC;AAEtB,8EAA8E;AAC9E,0BAA0B;AAC1B,8EAA8E;AAE9E,SAAS,qBAAqB,CAC5B,MAAmB,EACnB,UAAkB,EAClB,UAAkB;IAElB,wDAAwD;IACxD,OAAO,MAAM,CAAC,KAAK,CAAC,UAAU,EAAE,UAAU,GAAG,UAAU,CAAC,CAAC;AAC3D,CAAC;AAED,8EAA8E;AAC9E,2CAA2C;AAC3C,8EAA8E;AAE9E,KAAK,UAAU,UAAU,CACvB,UAA4B,EAC5B,MAAc;IAEd,IAAI,UAAU,CAAC,OAAO,CAAC,MAAM,CAAC;QAAE,OAAO;IACvC,MAAM,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,MAAM,CAAE,CAAC;IACvC,MAAM,EAAE,GAAG,aAAa,EAAE,CAAC;IAC3B,MAAM,UAAU,CAAC,IAAI,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC;IAClE,UAAU,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;AAC9B,CAAC;AAaD;;;;;;;;;;;;;GAaG;AACH,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,MAAc,EACd,KAAiB,EACjB,MAAc,EACd,IAAoB,EACpB,SAAiB,EACjB,MAAc,EACd,gBAA2B;IAK3B,MAAM,UAAU,GAAG,aAAa,CAAC,MAAM,CAAC,CAAC;IACzC,MAAM,UAAU,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC;IAErC,MAAM,EAAE,GAAG,aAAa,EAAE,CAAC;IAC3B,MAAM,cAAc,GAAG,qBAAqB,CAC1C,KAAK,CAAC,MAAqB,EAC3B,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAC;IAEF,MAAM,QAAQ,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CACrC,EAAE,EACF;QACE,IAAI,EAAE,kBAAkB;QACxB,EAAE;QACF,KAAK,EAAE,cAAc;QACrB,MAAM;QACN,gBAAgB;QAChB,SAAS;QACT,MAAM;KACP,EACD,CAAC,cAAc,CAAC,CACjB,CAA2B,CAAC;IAE7B,yDAAyD;IACzD,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,SAAS,CAOjC,CAAC;IACF,MAAM,IAAI,GAAG,IAAI,GAAG,CAClB,QAAQ,CAAC,IAAI,EACb,CAAC,EACD,QAAQ,CAAC,IAAI,CAAC,UAAU,GAAG,GAAG,CAAC,iBAAiB,CACjD,CAAC;IACF,MAAM,KAAK,GAAa;QACtB,IAAI;QACJ,KAAK,EAAE,QAAQ,CAAC,KAAK;QACrB,MAAM,EAAE,QAAQ,CAAC,MAAM;KACxB,CAAC;IAEF,OAAO,EAAE,KAAK,EAAE,YAAY,EAAE,QAAQ,CAAC,YAAY,EAAE,CAAC;AACxD,CAAC"}

package/esm/workers/omero_codec_worker.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=omero_codec_worker.d.ts.map

package/esm/workers/omero_codec_worker.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"omero_codec_worker.d.ts","sourceRoot":"","sources":["../../src/workers/omero_codec_worker.ts"],"names":[],"mappings":""}

package/esm/workers/omero_codec_worker.js

@@ -0,0 +1,215 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * Custom Web Worker that extends fizarrita's codec worker with OMERO
+ * statistics computation.
+ *
+ * Handles all standard fizarrita codec messages (init, decode, decode_into,
+ * encode) PLUS a new `decode_and_stats` message that decodes a chunk AND
+ * computes per-channel statistics in a single round-trip.
+ *
+ * Message protocol (superset of fizarrita's codec-worker):
+ *   init:             → init_ok              (register codec pipeline metadata)
+ *   decode:           → decoded              (decode raw bytes, return chunk)
+ *   decode_into:      → decode_into_ok       (decode into SharedArrayBuffer)
+ *   encode:           → encoded              (encode chunk data)
+ *   decode_and_stats: → decoded_and_stats    (decode + compute channel stats)
+ */
+// fizarrita internals for codec pipeline
+import { create_codec_pipeline } from "@fideus-labs/fizarrita/internals/codec-pipeline";
+import { compat_chunk, set_from_chunk_binary, } from "@fideus-labs/fizarrita/internals/setter";
+import { get_ctr, get_strides } from "@fideus-labs/fizarrita/internals/util";
+// ngff-zarr stats functions
+import { createAccumulator, extractChannel, updateAccumulator, } from "../utils/compute_omero-shared.js";
+// Use typeof self for cross-environment compatibility (Deno, Node.js, Browser workers)
+// deno-lint-ignore no-explicit-any
+const ctx = self;
+// ---------------------------------------------------------------------------
+// Edge chunk shape correction (same as fizarrita's codec-worker)
+// ---------------------------------------------------------------------------
+function fixEdgeChunkShapeStride(chunk, actualChunkShape) {
+    if (actualChunkShape) {
+        const expectedElements = actualChunkShape.reduce((a, b) => a * b, 1);
+        const actualElements = chunk.data.length;
+        if (actualElements === expectedElements) {
+            return {
+                data: chunk.data,
+                shape: actualChunkShape,
+                stride: get_strides(actualChunkShape, "C"),
+            };
+        }
+    }
+    return chunk;
+}
+// ---------------------------------------------------------------------------
+// Codec pipeline cache — keyed by metaId
+// ---------------------------------------------------------------------------
+const pipelineByMetaId = new Map();
+const metaByMetaId = new Map();
+const pipelineByKey = new Map();
+function getPipeline(metaId) {
+    const pipeline = pipelineByMetaId.get(metaId);
+    if (!pipeline) {
+        throw new Error(`No pipeline for metaId ${metaId}. Send an 'init' message first.`);
+    }
+    return pipeline;
+}
+function getOrCreatePipelineLegacy(meta) {
+    const key = JSON.stringify(meta);
+    let pipeline = pipelineByKey.get(key);
+    if (!pipeline) {
+        pipeline = create_codec_pipeline({
+            data_type: meta.data_type,
+            shape: meta.chunk_shape,
+            codecs: meta.codecs,
+        });
+        pipelineByKey.set(key, pipeline);
+    }
+    return pipeline;
+}
+ctx.addEventListener("message", async (event) => {
+    const msg = event.data;
+    try {
+        if (msg.type === "init") {
+            metaByMetaId.set(msg.metaId, msg.meta);
+            const pipeline = create_codec_pipeline({
+                data_type: msg.meta.data_type,
+                shape: msg.meta.chunk_shape,
+                codecs: msg.meta.codecs,
+            });
+            pipelineByMetaId.set(msg.metaId, pipeline);
+            ctx.postMessage({ type: "init_ok", id: msg.id });
+            return;
+        }
+        if (msg.type === "decode") {
+            const pipeline = msg.metaId !== undefined && pipelineByMetaId.has(msg.metaId)
+                ? getPipeline(msg.metaId)
+                : getOrCreatePipelineLegacy(msg.meta);
+            const bytes = new Uint8Array(msg.bytes);
+            let chunk = (await pipeline.decode(bytes));
+            chunk = fixEdgeChunkShapeStride(chunk, msg.actualChunkShape);
+            const dataView = chunk.data;
+            const buffer = dataView.buffer;
+            const byteOffset = dataView.byteOffset;
+            const byteLength = dataView.byteLength;
+            let transferBuffer;
+            if (byteOffset === 0 && byteLength === buffer.byteLength) {
+                transferBuffer = buffer;
+            }
+            else {
+                transferBuffer = buffer.slice(byteOffset, byteOffset + byteLength);
+            }
+            ctx.postMessage({
+                type: "decoded",
+                id: msg.id,
+                data: transferBuffer,
+                shape: chunk.shape,
+                stride: chunk.stride,
+            }, [transferBuffer]);
+        }
+        else if (msg.type === "decode_into") {
+            const pipeline = getPipeline(msg.metaId);
+            const bytes = new Uint8Array(msg.bytes);
+            let chunk = (await pipeline.decode(bytes));
+            chunk = fixEdgeChunkShapeStride(chunk, msg.actualChunkShape);
+            const destView = new Uint8Array(msg.output, 0, msg.outputByteLength);
+            // deno-lint-ignore no-explicit-any
+            const src = compat_chunk(chunk);
+            set_from_chunk_binary({ data: destView, stride: msg.outputStride }, src, msg.bytesPerElement, msg.projections);
+            ctx.postMessage({ type: "decode_into_ok", id: msg.id });
+        }
+        else if (msg.type === "encode") {
+            let pipeline;
+            let meta;
+            if (msg.metaId !== undefined && pipelineByMetaId.has(msg.metaId)) {
+                pipeline = getPipeline(msg.metaId);
+                meta = metaByMetaId.get(msg.metaId);
+            }
+            else {
+                meta = msg.meta;
+                pipeline = getOrCreatePipelineLegacy(meta);
+            }
+            const Ctr = get_ctr(meta.data_type);
+            const data = new Ctr(msg.data, 0, msg.data.byteLength / Ctr.BYTES_PER_ELEMENT);
+            const shape = meta.chunk_shape;
+            const stride = get_strides(shape, "C");
+            const chunk = { data, shape, stride };
+            // deno-lint-ignore no-explicit-any
+            const encoded = await pipeline.encode(chunk);
+            const transferBuffer = encoded.byteOffset === 0 &&
+                encoded.byteLength === encoded.buffer.byteLength
+                ? encoded.buffer
+                : encoded.buffer.slice(encoded.byteOffset, encoded.byteOffset + encoded.byteLength);
+            ctx.postMessage({
+                type: "encoded",
+                id: msg.id,
+                bytes: transferBuffer,
+            }, [transferBuffer]);
+        }
+        else if (msg.type === "decode_and_stats") {
+            // NEW: Decode chunk AND compute per-channel statistics in one pass
+            const pipeline = getPipeline(msg.metaId);
+            const bytes = new Uint8Array(msg.bytes);
+            let chunk = (await pipeline.decode(bytes));
+            chunk = fixEdgeChunkShapeStride(chunk, msg.actualChunkShape);
+            const chunkData = chunk.data;
+            const chunkShape = chunk.shape;
+            const { nChannels, cIndex } = msg;
+            // Compute per-channel statistics
+            const accumulators = [];
+            if (cIndex >= 0) {
+                // Multi-channel: extract each channel and compute stats
+                for (let ch = 0; ch < nChannels; ch++) {
+                    const channelData = extractChannel(chunkData, chunkShape, ch, cIndex);
+                    const acc = createAccumulator();
+                    updateAccumulator(acc, channelData);
+                    accumulators.push(acc);
+                }
+            }
+            else {
+                // Single channel: compute stats on full chunk data
+                const acc = createAccumulator();
+                updateAccumulator(acc, chunkData);
+                accumulators.push(acc);
+            }
+            // Transfer the decoded data buffer back for caching
+            const dataView = chunk.data;
+            const buffer = dataView.buffer;
+            const byteOffset = dataView.byteOffset;
+            const byteLength = dataView.byteLength;
+            let transferBuffer;
+            if (byteOffset === 0 && byteLength === buffer.byteLength) {
+                transferBuffer = buffer;
+            }
+            else {
+                transferBuffer = buffer.slice(byteOffset, byteOffset + byteLength);
+            }
+            ctx.postMessage({
+                type: "decoded_and_stats",
+                id: msg.id,
+                data: transferBuffer,
+                shape: chunk.shape,
+                stride: chunk.stride,
+                accumulators,
+            }, [transferBuffer]);
+        }
+    }
+    catch (error) {
+        // Send error back to main thread
+        const errorType = msg.type === "decode"
+            ? "decoded"
+            : msg.type === "encode"
+                ? "encoded"
+                : msg.type === "decode_into"
+                    ? "decode_into_ok"
+                    : msg.type === "decode_and_stats"
+                        ? "decoded_and_stats"
+                        : "init_ok";
+        ctx.postMessage({
+            type: errorType,
+            id: msg.id,
+            error: error instanceof Error ? error.message : String(error),
+        });
+    }
+});
+//# sourceMappingURL=omero_codec_worker.js.map

package/esm/workers/omero_codec_worker.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"omero_codec_worker.js","sourceRoot":"","sources":["../../src/workers/omero_codec_worker.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAE/B;;;;;;;;;;;;;;GAcG;AAEH,yCAAyC;AACzC,OAAO,EAAE,qBAAqB,EAAE,MAAM,iDAAiD,CAAC;AACxF,OAAO,EACL,YAAY,EACZ,qBAAqB,GACtB,MAAM,yCAAyC,CAAC;AACjD,OAAO,EAAE,OAAO,EAAE,WAAW,EAAE,MAAM,uCAAuC,CAAC;AAa7E,4BAA4B;AAC5B,OAAO,EACL,iBAAiB,EACjB,cAAc,EACd,iBAAiB,GAClB,MAAM,kCAAkC,CAAC;AAE1C,uFAAuF;AACvF,mCAAmC;AACnC,MAAM,GAAG,GAAG,IAAW,CAAC;AAExB,8EAA8E;AAC9E,iEAAiE;AACjE,8EAA8E;AAE9E,SAAS,uBAAuB,CAC9B,KAAe,EACf,gBAA2B;IAE3B,IAAI,gBAAgB,EAAE,CAAC;QACrB,MAAM,gBAAgB,GAAG,gBAAgB,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC;QACrE,MAAM,cAAc,GAAI,KAAK,CAAC,IAAsC,CAAC,MAAM,CAAC;QAC5E,IAAI,cAAc,KAAK,gBAAgB,EAAE,CAAC;YACxC,OAAO;gBACL,IAAI,EAAE,KAAK,CAAC,IAAI;gBAChB,KAAK,EAAE,gBAAgB;gBACvB,MAAM,EAAE,WAAW,CAAC,gBAAgB,EAAE,GAAG,CAAC;aAC3C,CAAC;QACJ,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,8EAA8E;AAC9E,yCAAyC;AACzC,8EAA8E;AAE9E,MAAM,gBAAgB,GAAG,IAAI,GAAG,EAG7B,CAAC;AAEJ,MAAM,YAAY,GAAG,IAAI,GAAG,EAA0B,CAAC;AAEvD,MAAM,aAAa,GAAG,IAAI,GAAG,EAG1B,CAAC;AAEJ,SAAS,WAAW,CAClB,MAAc;IAEd,MAAM,QAAQ,GAAG,gBAAgB,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAC9C,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CACb,0BAA0B,MAAM,iCAAiC,CAClE,CAAC;IACJ,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,yBAAyB,CAAC,IAAoB;IACrD,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;IACjC,IAAI,QAAQ,GAAG,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,QAAQ,GAAG,qBAAqB,CAAC;YAC/B,SAAS,EAAE,IAAI,CAAC,SAAS;YACzB,KAAK,EAAE,IAAI,CAAC,WAAW;YACvB,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CAAC,CAAC;QACH,aAAa,CAAC,GAAG,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;IACnC,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AA6DD,GAAG,CAAC,gBAAgB,CAClB,SAAS,EACT,KAAK,EAAE,KAAkC,EAAE,EAAE;IAC3C,MAAM,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC;IAEvB,IAAI,CAAC;QACH,IAAI,GAAG,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;YACxB,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC;YACvC,MAAM,QAAQ,GAAG,qBAAqB,CAAC;gBACrC,SAAS,EAAE,GAAG,CAAC,IAAI,CAAC,SAAS;gBAC7B,KAAK,EAAE,GAAG,CAAC,IAAI,CAAC,WAAW;gBAC3B,MAAM,EAAE,GAAG,CAAC,IAAI,CAAC,MAAM;aACxB,CAAC,CAAC;YACH,gBAAgB,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;YAC3C,GAAG,CAAC,WAAW,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC;YACjD,OAAO;QACT,CAAC;QAED,IAAI,GAAG,CAAC,IAAI,KAAK,QAAQ,EAAE,CAAC;YAC1B,MAAM,QAAQ,GACZ,GAAG,CAAC,MAAM,KAAK,SAAS,IAAI,gBAAgB,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC;gBAC1D,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC;gBACzB,CAAC,CAAC,yBAAyB,CAAC,GAAG,CAAC,IAAK,CAAC,CAAC;YAE3C,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;YACxC,IAAI,KAAK,GAAG,CAAC,MAAM,QAAQ,CAAC,MAAM,CAAC,KAAK,CAAC,CAAoB,CAAC;YAC9D,KAAK,GAAG,uBAAuB,CAAC,KAAK,EAAE,GAAG,CAAC,gBAAgB,CAAC,CAAC;YAE7D,MAAM,QAAQ,GAAG,KAAK,CAAC,IAItB,CAAC;YACF,MAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC;YAC/B,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,CAAC;YACvC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,CAAC;YAEvC,IAAI,cAA2B,CAAC;YAChC,IAAI,UAAU,KAAK,CAAC,IAAI,UAAU,KAAK,MAAM,CAAC,UAAU,EAAE,CAAC;gBACzD,cAAc,GAAG,MAAM,CAAC;YAC1B,CAAC;iBAAM,CAAC;gBACN,cAAc,GAAG,MAAM,CAAC,KAAK,CAAC,UAAU,EAAE,UAAU,GAAG,UAAU,CAAC,CAAC;YACrE,CAAC;YAED,GAAG,CAAC,WAAW,CACb;gBACE,IAAI,EAAE,SAAkB;gBACxB,EAAE,EAAE,GAAG,CAAC,EAAE;gBACV,IAAI,EAAE,cAAc;gBACpB,KAAK,EAAE,KAAK,CAAC,KAAK;gBAClB,MAAM,EAAE,KAAK,CAAC,MAAM;aACrB,EACD,CAAC,cAAc,CAAC,CACjB,CAAC;QACJ,CAAC;aAAM,IAAI,GAAG,CAAC,IAAI,KAAK,aAAa,EAAE,CAAC;YACtC,MAAM,QAAQ,GAAG,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;YACzC,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;YACxC,IAAI,KAAK,GAAG,CAAC,MAAM,QAAQ,CAAC,MAAM,CAAC,KAAK,CAAC,CAAoB,CAAC;YAC9D,KAAK,GAAG,uBAAuB,CAAC,KAAK,EAAE,GAAG,CAAC,gBAAgB,CAAC,CAAC;YAE7D,MAAM,QAAQ,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,GAAG,CAAC,gBAAgB,CAAC,CAAC;YACrE,mCAAmC;YACnC,MAAM,GAAG,GAAG,YAAY,CAAC,KAAY,CAAC,CAAC;YAEvC,qBAAqB,CACnB,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,CAAC,YAAY,EAAE,EAC5C,GAAG,EACH,GAAG,CAAC,eAAe,EACnB,GAAG,CAAC,WAAW,CAChB,CAAC;YAEF,GAAG,CAAC,WAAW,CAAC,EAAE,IAAI,EAAE,gBAAgB,EAAE,EAAE,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC;QAC1D,CAAC;aAAM,IAAI,GAAG,CAAC,IAAI,KAAK,QAAQ,EAAE,CAAC;YACjC,IAAI,QAAkD,CAAC;YACvD,IAAI,IAAoB,CAAC;YACzB,IACE,GAAG,CAAC,MAAM,KAAK,SAAS,IAAI,gBAAgB,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,EAC5D,CAAC;gBACD,QAAQ,GAAG,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;gBACnC,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAE,CAAC;YACvC,CAAC;iBAAM,CAAC;gBACN,IAAI,GAAG,GAAG,CAAC,IAAK,CAAC;gBACjB,QAAQ,GAAG,yBAAyB,CAAC,IAAI,CAAC,CAAC;YAC7C,CAAC;YAED,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,SAAS,CAGjC,CAAC;YACF,MAAM,IAAI,GAAG,IAAI,GAAG,CAClB,GAAG,CAAC,IAAI,EACR,CAAC,EACD,GAAG,CAAC,IAAI,CAAC,UAAU,GAAG,GAAG,CAAC,iBAAiB,CAC5C,CAAC;YACF,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,CAAC;YAC/B,MAAM,MAAM,GAAG,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;YAEvC,MAAM,KAAK,GAAG,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAqB,CAAC;YACzD,mCAAmC;YACnC,MAAM,OAAO,GAAG,MAAM,QAAQ,CAAC,MAAM,CAAC,KAAY,CAAC,CAAC;YAEpD,MAAM,cAAc,GAAG,OAAO,CAAC,UAAU,KAAK,CAAC;gBAC3C,OAAO,CAAC,UAAU,KAAK,OAAO,CAAC,MAAM,CAAC,UAAU;gBAClD,CAAC,CAAE,OAAO,CAAC,MAAsB;gBACjC,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK,CACpB,OAAO,CAAC,UAAU,EAClB,OAAO,CAAC,UAAU,GAAG,OAAO,CAAC,UAAU,CACxC,CAAC;YAEJ,GAAG,CAAC,WAAW,CACb;gBACE,IAAI,EAAE,SAAkB;gBACxB,EAAE,EAAE,GAAG,CAAC,EAAE;gBACV,KAAK,EAAE,cAAc;aACtB,EACD,CAAC,cAAc,CAAC,CACjB,CAAC;QACJ,CAAC;aAAM,IAAI,GAAG,CAAC,IAAI,KAAK,kBAAkB,EAAE,CAAC;YAC3C,mEAAmE;YACnE,MAAM,QAAQ,GAAG,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;YACzC,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;YACxC,IAAI,KAAK,GAAG,CAAC,MAAM,QAAQ,CAAC,MAAM,CAAC,KAAK,CAAC,CAAoB,CAAC;YAC9D,KAAK,GAAG,uBAAuB,CAAC,KAAK,EAAE,GAAG,CAAC,gBAAgB,CAAC,CAAC;YAE7D,MAAM,SAAS,GAAG,KAAK,CAAC,IAAoC,CAAC;YAC7D,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAC;YAC/B,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,GAAG,CAAC;YAElC,iCAAiC;YACjC,MAAM,YAAY,GAA4B,EAAE,CAAC;YACjD,IAAI,MAAM,IAAI,CAAC,EAAE,CAAC;gBAChB,wDAAwD;gBACxD,KAAK,IAAI,EAAE,GAAG,CAAC,EAAE,EAAE,GAAG,SAAS,EAAE,EAAE,EAAE,EAAE,CAAC;oBACtC,MAAM,WAAW,GAAG,cAAc,CAChC,SAAS,EACT,UAAU,EACV,EAAE,EACF,MAAM,CACP,CAAC;oBACF,MAAM,GAAG,GAAG,iBAAiB,EAAE,CAAC;oBAChC,iBAAiB,CAAC,GAAG,EAAE,WAAW,CAAC,CAAC;oBACpC,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;gBACzB,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,mDAAmD;gBACnD,MAAM,GAAG,GAAG,iBAAiB,EAAE,CAAC;gBAChC,iBAAiB,CAAC,GAAG,EAAE,SAAS,CAAC,CAAC;gBAClC,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACzB,CAAC;YAED,oDAAoD;YACpD,MAAM,QAAQ,GAAG,KAAK,CAAC,IAItB,CAAC;YACF,MAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC;YAC/B,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,CAAC;YACvC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,CAAC;YAEvC,IAAI,cAA2B,CAAC;YAChC,IAAI,UAAU,KAAK,CAAC,IAAI,UAAU,KAAK,MAAM,CAAC,UAAU,EAAE,CAAC;gBACzD,cAAc,GAAG,MAAM,CAAC;YAC1B,CAAC;iBAAM,CAAC;gBACN,cAAc,GAAG,MAAM,CAAC,KAAK,CAAC,UAAU,EAAE,UAAU,GAAG,UAAU,CAAC,CAAC;YACrE,CAAC;YAED,GAAG,CAAC,WAAW,CACb;gBACE,IAAI,EAAE,mBAA4B;gBAClC,EAAE,EAAE,GAAG,CAAC,EAAE;gBACV,IAAI,EAAE,cAAc;gBACpB,KAAK,EAAE,KAAK,CAAC,KAAK;gBAClB,MAAM,EAAE,KAAK,CAAC,MAAM;gBACpB,YAAY;aACb,EACD,CAAC,cAAc,CAAC,CACjB,CAAC;QACJ,CAAC;IACH,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,iCAAiC;QACjC,MAAM,SAAS,GAAG,GAAG,CAAC,IAAI,KAAK,QAAQ;YACrC,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,GAAG,CAAC,IAAI,KAAK,QAAQ;gBACvB,CAAC,CAAC,SAAS;gBACX,CAAC,CAAC,GAAG,CAAC,IAAI,KAAK,aAAa;oBAC5B,CAAC,CAAC,gBAAgB;oBAClB,CAAC,CAAC,GAAG,CAAC,IAAI,KAAK,kBAAkB;wBACjC,CAAC,CAAC,mBAAmB;wBACrB,CAAC,CAAC,SAAS,CAAC;QACd,GAAG,CAAC,WAAW,CAAC;YACd,IAAI,EAAE,SAAS;YACf,EAAE,EAAE,GAAG,CAAC,EAAE;YACV,KAAK,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC;SAC9D,CAAC,CAAC;IACL,CAAC;AACH,CAAC,CACF,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fideus-labs/ngff-zarr",
-  "version": "0.7.5",
+  "version": "0.9.0",
   "description": "TypeScript implementation of ngff-zarr for reading and writing OME-Zarr files",
   "license": "MIT",
   "type": "module",
@@ -69,10 +69,9 @@
     "LICENSE.txt"
   ],
   "dependencies": {
-    "@fideus-labs/fizarrita": "^1.2.0",
+    "@fideus-labs/fizarrita": "^1.3.0",
     "@fideus-labs/worker-pool": "^1.0.0",
     "@itk-wasm/downsample": "^1.8.1",
-    "comlink": "^4.4.2",
     "itk-wasm": "^1.0.0-b.196",
     "@zarrita/storage": "^0.1.4",
     "zod": "^4.0.2",

package/esm/utils/compute_omero-browser.d.ts

@@ -1,45 +0,0 @@
-import type { NgffImage } from "../types/ngff_image.js";
-import type { Multiscales } from "../types/multiscales.js";
-import type { Omero } from "../types/zarr_metadata.js";
-import { type ComputeOmeroFromMultiscalesOptions, type ComputeOmeroOptions } from "./compute_omero-shared.js";
-export { type ComputeOmeroFromMultiscalesOptions, type ComputeOmeroOptions, getDefaultColors, GLASBEY_COLORS, } from "./compute_omero-shared.js";
-/**
- * Compute OMERO metadata from an NgffImage using WebWorker.
- *
- * 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.
- *
- * The computation is performed in a WebWorker to avoid blocking the main thread.
- * If WebWorkers are not available, falls back to main thread computation.
- *
- * @param image - The NgffImage to compute metadata for
- * @param options - Optional configuration for quantiles, colors, and labels
- * @returns Promise resolving to Omero metadata with computed window parameters
- */
-export declare function computeOmeroFromNgffImage(image: NgffImage, options?: ComputeOmeroOptions): Promise<Omero>;
-/**
- * Compute OMERO metadata from a Multiscales object using WebWorker.
- *
- * This is a convenience function that computes OMERO metadata from the
- * highest or lowest resolution image in a multiscales pyramid.
- *
- * @param multiscales - The Multiscales object to compute metadata for
- * @param options - Optional configuration for quantiles, colors, labels, and resolution
- * @returns Promise resolving to Omero metadata with computed window parameters
- */
-export declare function computeOmeroFromMultiscales(multiscales: Multiscales, options?: ComputeOmeroFromMultiscalesOptions): Promise<Omero>;
-/**
- * Terminate the OMERO computation worker and release resources.
- * Call this when you're done with OMERO computations to free memory.
- */
-export declare function terminateOmeroWorker(): void;
-/**
- * Check if the OMERO computation will use a WebWorker.
- * Useful for testing or conditional logic.
- */
-export declare function isUsingWorker(): boolean;
-//# sourceMappingURL=compute_omero-browser.d.ts.map

package/esm/utils/compute_omero-browser.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"compute_omero-browser.d.ts","sourceRoot":"","sources":["../../src/utils/compute_omero-browser.ts"],"names":[],"mappings":"AAgBA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACxD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,2BAA2B,CAAC;AAEvD,OAAO,EAEL,KAAK,kCAAkC,EACvC,KAAK,mBAAmB,EAKzB,MAAM,2BAA2B,CAAC;AAInC,OAAO,EACL,KAAK,kCAAkC,EACvC,KAAK,mBAAmB,EACxB,gBAAgB,EAChB,cAAc,GACf,MAAM,2BAA2B,CAAC;AAsHnC;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,yBAAyB,CAC7C,KAAK,EAAE,SAAS,EAChB,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,KAAK,CAAC,CA0FhB;AAED;;;;;;;;;GASG;AACH,wBAAsB,2BAA2B,CAC/C,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,kCAAuC,GAC/C,OAAO,CAAC,KAAK,CAAC,CAwBhB;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAa3C;AAED;;;GAGG;AACH,wBAAgB,aAAa,IAAI,OAAO,CAEvC"}