@fideus-labs/ngff-zarr 0.8.0 → 0.10.0

package/esm/utils/compute_omero-browser.js

@@ -1,250 +0,0 @@
-// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
-// SPDX-License-Identifier: MIT
-/**
- * Browser-specific OMERO metadata computation using WebWorker.
- * This module offloads CPU-intensive statistics computation to a WebWorker
- * to prevent blocking the main thread.
- *
- * Features:
- * - WebWorker-based computation via Comlink
- * - Chunked streaming for memory efficiency with large images
- * - Automatic fallback to main thread if WebWorker unavailable
- * - Inline worker code (bundled as Blob URL)
- */
-import * as Comlink from "comlink";
-import { buildOmeroFromAccumulators, createAccumulator, extractChannel, updateAccumulator, validateQuantiles, } from "./compute_omero-shared.js";
-import { zarrGet } from "./worker_pool.js";
-// Re-export shared utilities for convenience
-export { getDefaultColors, GLASBEY_COLORS, } from "./compute_omero-shared.js";
-// Worker state
-let worker = null;
-let workerProxy = null;
-let workerSupported = null;
-let workerBlobUrl = null;
-// Chunk size for streaming (256K elements = ~1MB for float32)
-const CHUNK_SIZE = 256 * 1024;
-/**
- * Check if WebWorkers are supported in this environment.
- */
-function isWorkerSupported() {
-    if (workerSupported === null) {
-        try {
-            workerSupported = typeof Worker !== "undefined" &&
-                typeof Blob !== "undefined" &&
-                typeof URL !== "undefined" &&
-                typeof URL.createObjectURL === "function";
-        }
-        catch {
-            workerSupported = false;
-        }
-    }
-    return workerSupported;
-}
-/**
- * Get or create the worker proxy.
- * Returns null if workers are not supported.
- */
-function getWorkerProxy() {
-    if (!isWorkerSupported()) {
-        return null;
-    }
-    if (!workerProxy) {
-        try {
-            // In bundled builds, the Worker constructor line below is replaced with
-            // inline Blob URL code that assigns workerBlobUrl. In non-bundled mode,
-            // we use a module URL and there's no Blob URL to clean up.
-            workerBlobUrl = null; // Will be overwritten in bundled mode
-            worker = (() => {
-    const workerCode = `var L=Symbol("Comlink.proxy"),q=Symbol("Comlink.endpoint"),v=Symbol("Comlink.releaseProxy"),y=Symbol("Comlink.finalizer"),B=Symbol("Comlink.thrown"),P=t=>typeof t=="object"&&t!==null||typeof t=="function",H={canHandle:t=>P(t)&&t[L],serialize(t){let{port1:e,port2:n}=new MessageChannel;return w(t,e),[n,[n]]},deserialize(t){return t.start(),j(t)}},\$={canHandle:t=>P(t)&&B in t,serialize({value:t}){let e;return t instanceof Error?e={isError:!0,value:{message:t.message,name:t.name,stack:t.stack}}:e={isError:!1,value:t},[e,[]]},deserialize(t){throw t.isError?Object.assign(new Error(t.value.message),t.value):t.value}},I=new Map([["proxy",H],["throw",\$]]);function U(t,e){for(let n of t)if(e===n||n==="*"||n instanceof RegExp&&n.test(e))return!0;return!1}function w(t,e=globalThis,n=["*"]){e.addEventListener("message",function o(r){if(!r||!r.data)return;if(!U(n,r.origin)){console.warn(\`Invalid origin '\${r.origin}' for comlink proxy\`);return}let{id:a,type:c,path:u}=Object.assign({path:[]},r.data),l=(r.data.argumentList||[]).map(E),i;try{let s=u.slice(0,-1).reduce((f,A)=>f[A],t),F=u.reduce((f,A)=>f[A],t);switch(c){case"GET":i=F;break;case"SET":s[u.slice(-1)[0]]=E(r.data.value),i=!0;break;case"APPLY":i=F.apply(s,l);break;case"CONSTRUCT":{let f=new F(...l);i=Z(f)}break;case"ENDPOINT":{let{port1:f,port2:A}=new MessageChannel;w(t,A),i=V(f,[f])}break;case"RELEASE":i=void 0;break;default:return}}catch(s){i={value:s,[B]:0}}Promise.resolve(i).catch(s=>({value:s,[B]:0})).then(s=>{let[F,f]=p(s);e.postMessage(Object.assign(Object.assign({},F),{id:a}),f),c==="RELEASE"&&(e.removeEventListener("message",o),T(e),y in t&&typeof t[y]=="function"&&t[y]())}).catch(s=>{let[F,f]=p({value:new TypeError("Unserializable return value"),[B]:0});e.postMessage(Object.assign(Object.assign({},F),{id:a}),f)})}),e.start&&e.start()}function G(t){return t.constructor.name==="MessagePort"}function T(t){G(t)&&t.close()}function j(t,e){let n=new Map;return t.addEventListener("message",function(r){let{data:a}=r;if(!a||!a.id)return;let c=n.get(a.id);if(c)try{c(a)}finally{n.delete(a.id)}}),x(t,n,[],e)}function h(t){if(t)throw new Error("Proxy has been released and is not useable")}function k(t){return m(t,new Map,{type:"RELEASE"}).then(()=>{T(t)})}var g=new WeakMap,d="FinalizationRegistry"in globalThis&&new FinalizationRegistry(t=>{let e=(g.get(t)||0)-1;g.set(t,e),e===0&&k(t)});function Q(t,e){let n=(g.get(e)||0)+1;g.set(e,n),d&&d.register(t,e,t)}function W(t){d&&d.unregister(t)}function x(t,e,n=[],o=function(){}){let r=!1,a=new Proxy(o,{get(c,u){if(h(r),u===v)return()=>{W(a),k(t),e.clear(),r=!0};if(u==="then"){if(n.length===0)return{then:()=>a};let l=m(t,e,{type:"GET",path:n.map(i=>i.toString())}).then(E);return l.then.bind(l)}return x(t,e,[...n,u])},set(c,u,l){h(r);let[i,s]=p(l);return m(t,e,{type:"SET",path:[...n,u].map(F=>F.toString()),value:i},s).then(E)},apply(c,u,l){h(r);let i=n[n.length-1];if(i===q)return 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K(t){return t===1?["FFFFFF"]:Array.from({length:t},(e,n)=>_[n%_.length])}function b(t){let[e,n]=t;if(!(e>=0&&e<=1))throw new Error(\`Low quantile must be between 0 and 1, got \${e}\`);if(!(n>=0&&n<=1))throw new Error(\`High quantile must be between 0 and 1, got \${n}\`);if(e>=n)throw new Error(\`Low quantile must be less than high quantile, got (\${e}, \${n})\`)}function tt(t){if(!/^[0-9A-Fa-f]{6}\$/.test(t))throw new Error(\`Color must be a 6-digit hexadecimal string without # prefix, got '\${t}'\`)}function R(t,e){if(t.length===0)return NaN;if(t.length===1)return t[0];let n=e*(t.length-1),o=Math.floor(n),r=Math.ceil(n),a=n-o;return o===r?t[o]:t[o]*(1-a)+t[r]*a}function N(){return{min:Number.POSITIVE_INFINITY,max:Number.NEGATIVE_INFINITY,sample:[],count:0}}function D(t,e){for(let n=0;n<e.length;n++){let o=e[n];if(!Number.isNaN(o)){if(o<t.min&&(t.min=o),o>t.max&&(t.max=o),t.sample.length<1e4)t.sample.push(o);else{let r=Math.floor(Math.random()*(t.count+1));r<1e4&&(t.sample[r]=o)}t.count++}}}function et(t,e){if(t.count===0)return{min:NaN,max:NaN,qLow:NaN,qHigh:NaN};t.sample.sort((r,a)=>r-a);let n=R(t.sample,e[0]),o=R(t.sample,e[1]);return{min:t.min,max:t.max,qLow:n,qHigh:o}}function S(t,e,n,o){let r=e[o],a=1;for(let s=o+1;s<e.length;s++)a*=e[s];let c=1;for(let s=0;s<o;s++)c*=e[s];let u=c*a,l=new Array(u),i=0;for(let s=0;s<c;s++){let f=s*r*a+n*a;for(let A=0;A<a;A++)l[i++]=t[f+A]}return l}function M(t,e,n,o){let r=t.length,a;if(n!==void 0){if(n.length<r)throw new Error(\`Not enough colors provided. Got \${n.length}, need \${r}.\`);for(let l of n.slice(0,r))tt(l);a=n.slice(0,r)}else a=K(r);let c;if(o!==void 0){if(o.length<r)throw new Error(\`Not enough labels provided. Got \${o.length}, need \${r}.\`);c=o.slice(0,r)}else c=Array(r).fill("");return{channels:t.map((l,i)=>{let s=et(l,e),F={min:s.min,max:s.max,start:s.qLow,end:s.qHigh};return{color:a[i],window:F,label:c[i]}})}}var C=null,nt={initializeComputation(t){b(t.quantiles);let e=t.dims.indexOf("c"),n=e!==-1?t.shape[e]:1;C={accumulators:Array.from({length:n},()=>N()),input:t}},processChunk(t){if(!C)throw new Error("Computation not initialized. Call initializeComputation first.");let{accumulators:e,input:n}=C,{shape:o,dims:r}=n,{chunkData:a}=t,c=r.indexOf("c");if(c!==-1)for(let l=0;l<e.length;l++){let i=S(a,o,l,c);D(e[l],i)}else D(e[0],a)},finalizeComputation(){if(!C)throw new Error("Computation not initialized. Call initializeComputation first.");let{accumulators:t,input:e}=C,n=M(t,e.quantiles,e.colors,e.labels);return C=null,n},computeOmero(t,e){b(e.quantiles);let{shape:n,dims:o,quantiles:r,colors:a,labels:c}=e,u=o.indexOf("c"),l=u!==-1,i=l?n[u]:1,s=Array.from({length:i},()=>N());if(l)for(let F=0;F<i;F++){let f=S(t,n,F,u);D(s[F],f)}else D(s[0],t);return M(s,r,a,c)},ping(){return"pong"}};w(nt);
-/*! Bundled license information:
-
-comlink/dist/esm/comlink.mjs:
-  (**
-   * @license
-   * Copyright 2019 Google LLC
-   * SPDX-License-Identifier: Apache-2.0
-   *)
-*/
-`;
-    const blob = new Blob([workerCode], { type: "application/javascript" });
-    const url = URL.createObjectURL(blob);
-    workerBlobUrl = url;
-    return new Worker(url, { type: "module" });
-  })();
-            workerProxy = Comlink.wrap(worker);
-        }
-        catch (e) {
-            // Worker creation failed, fall back to main thread
-            console.warn("Failed to create OMERO computation worker:", e);
-            workerSupported = false;
-            return null;
-        }
-    }
-    return workerProxy;
-}
-/**
- * Compute OMERO metadata on the main thread (fallback implementation).
- * Used when WebWorker is not available.
- */
-async function computeOmeroMainThread(image, options = {}) {
-    const quantiles = options.quantiles ?? [0.02, 0.98];
-    validateQuantiles(quantiles);
-    const dims = image.dims;
-    const shape = image.data.shape;
-    // Check if there's a channel dimension
-    const cIndex = dims.indexOf("c");
-    const hasChannelDim = cIndex !== -1;
-    const nChannels = hasChannelDim ? shape[cIndex] : 1;
-    // Read all data from the zarr array
-    const result = await zarrGet(image.data);
-    const fullData = result.data;
-    // Create accumulators for each channel
-    const accumulators = Array.from({ length: nChannels }, () => createAccumulator());
-    if (hasChannelDim) {
-        // Multi-channel: extract each channel and compute statistics
-        for (let chIdx = 0; chIdx < nChannels; chIdx++) {
-            const channelData = extractChannel(fullData, shape, chIdx, cIndex);
-            updateAccumulator(accumulators[chIdx], channelData);
-        }
-    }
-    else {
-        // Single channel: compute directly
-        updateAccumulator(accumulators[0], fullData);
-    }
-    return buildOmeroFromAccumulators(accumulators, quantiles, options.colors, options.labels);
-}
-/**
- * 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 async function computeOmeroFromNgffImage(image, options = {}) {
-    const api = getWorkerProxy();
-    // Fallback to main thread if worker unavailable
-    if (!api) {
-        return computeOmeroMainThread(image, options);
-    }
-    try {
-        const quantiles = options.quantiles ?? [0.02, 0.98];
-        const shape = image.data.shape;
-        const dims = image.dims;
-        // Read data from zarr array
-        const result = await zarrGet(image.data);
-        const fullData = result.data;
-        const totalSize = fullData.length;
-        // For small datasets, use single-call API
-        if (totalSize <= CHUNK_SIZE * 2) {
-            // Transfer the data buffer to the worker
-            const typedArray = fullData;
-            // Create a copy of the buffer that we can transfer
-            const buffer = new ArrayBuffer(typedArray.byteLength);
-            const view = new Uint8Array(buffer);
-            view.set(new Uint8Array(typedArray.buffer, typedArray.byteOffset, typedArray.byteLength));
-            const TypedArrayConstructor = typedArray.constructor;
-            return await api.computeOmero(Comlink.transfer(new TypedArrayConstructor(buffer), [buffer]), {
-                shape,
-                dims,
-                quantiles: quantiles,
-                colors: options.colors,
-                labels: options.labels,
-            });
-        }
-        // For large datasets, use streaming API
-        await api.initializeComputation({
-            shape,
-            dims,
-            quantiles: quantiles,
-            colors: options.colors,
-            labels: options.labels,
-        });
-        // Stream data in chunks
-        const typedArray = fullData;
-        for (let offset = 0; offset < totalSize; offset += CHUNK_SIZE) {
-            const end = Math.min(offset + CHUNK_SIZE, totalSize);
-            const chunk = typedArray.slice(offset, end);
-            // Create a copy of the chunk buffer that we can transfer
-            const chunkBuffer = new ArrayBuffer(chunk.byteLength);
-            const chunkView = new Uint8Array(chunkBuffer);
-            chunkView.set(new Uint8Array(chunk.buffer, chunk.byteOffset, chunk.byteLength));
-            const ChunkConstructor = chunk.constructor;
-            await api.processChunk({
-                chunkData: Comlink.transfer(new ChunkConstructor(chunkBuffer), [
-                    chunkBuffer,
-                ]),
-            });
-        }
-        // Finalize and return result
-        return await api.finalizeComputation();
-    }
-    catch (error) {
-        // Fallback to main thread on any error
-        console.warn("WebWorker OMERO computation failed, falling back to main thread:", error);
-        return computeOmeroMainThread(image, options);
-    }
-}
-/**
- * Compute OMERO metadata from a Multiscales object using WebWorker.
- *
- * This is a convenience function that computes OMERO metadata from the
- * 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, 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");
-    }
-    // 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;
-    }
-    if (options.colors !== undefined) {
-        computeOptions.colors = options.colors;
-    }
-    if (options.labels !== undefined) {
-        computeOptions.labels = options.labels;
-    }
-    return await computeOmeroFromNgffImage(image, computeOptions);
-}
-/**
- * Terminate the OMERO computation worker and release resources.
- * Call this when you're done with OMERO computations to free memory.
- */
-export function terminateOmeroWorker() {
-    if (workerProxy) {
-        workerProxy[Comlink.releaseProxy]();
-        workerProxy = null;
-    }
-    if (worker) {
-        worker.terminate();
-        worker = null;
-    }
-    if (workerBlobUrl) {
-        URL.revokeObjectURL(workerBlobUrl);
-        workerBlobUrl = null;
-    }
-}
-/**
- * Check if the OMERO computation will use a WebWorker.
- * Useful for testing or conditional logic.
- */
-export function isUsingWorker() {
-    return isWorkerSupported() && getWorkerProxy() !== null;
-}
-//# sourceMappingURL=compute_omero-browser.js.map

package/esm/utils/compute_omero-browser.js.map

@@ -1 +0,0 @@
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package/esm/workers/compute_omero_worker.d.ts

@@ -1,47 +0,0 @@
-import { type ComputeOmeroChunkInput, type ComputeOmeroWorkerInput } from "../utils/compute_omero-shared.js";
-import type { Omero } from "../types/zarr_metadata.js";
-/**
- * Worker API exposed via Comlink.
- *
- * IMPORTANT: This worker maintains global state and does not support
- * concurrent computations. Only one computation can be active at a time.
- * If initializeComputation is called while another computation is in
- * progress, the previous computation state will be lost.
- *
- * The typical workflow is:
- * 1. initializeComputation() - Start a new computation
- * 2. processChunk() - Call multiple times to stream data
- * 3. finalizeComputation() - Get results and reset state
- */
-declare const workerApi: {
-    /**
-     * Initialize a new OMERO computation.
-     * Must be called before processChunk.
-     *
-     * WARNING: This will overwrite any existing computation state.
-     * Do not call this if another computation is in progress.
-     */
-    initializeComputation(input: ComputeOmeroWorkerInput): void;
-    /**
-     * Process a chunk of data.
-     * Call this multiple times for streaming large datasets.
-     */
-    processChunk(chunkInput: ComputeOmeroChunkInput): void;
-    /**
-     * Finalize computation and return OMERO metadata.
-     * Resets state after returning.
-     */
-    finalizeComputation(): Omero;
-    /**
-     * Compute OMERO metadata in a single call (non-streaming).
-     * Useful for smaller datasets where streaming overhead isn't needed.
-     */
-    computeOmero(data: ArrayLike<number>, input: ComputeOmeroWorkerInput): Omero;
-    /**
-     * Check if worker is ready.
-     */
-    ping(): string;
-};
-export type ComputeOmeroWorkerApi = typeof workerApi;
-export {};
-//# sourceMappingURL=compute_omero_worker.d.ts.map

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

@@ -1 +0,0 @@
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package/esm/workers/compute_omero_worker.js

@@ -1,113 +0,0 @@
-// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
-// SPDX-License-Identifier: MIT
-/**
- * WebWorker for computing OMERO metadata.
- * This worker performs CPU-intensive statistics computation off the main thread.
- */
-import * as Comlink from "comlink";
-import { buildOmeroFromAccumulators, createAccumulator, extractChannel, updateAccumulator, validateQuantiles, } from "../utils/compute_omero-shared.js";
-let currentState = null;
-/**
- * Worker API exposed via Comlink.
- *
- * IMPORTANT: This worker maintains global state and does not support
- * concurrent computations. Only one computation can be active at a time.
- * If initializeComputation is called while another computation is in
- * progress, the previous computation state will be lost.
- *
- * The typical workflow is:
- * 1. initializeComputation() - Start a new computation
- * 2. processChunk() - Call multiple times to stream data
- * 3. finalizeComputation() - Get results and reset state
- */
-const workerApi = {
-    /**
-     * Initialize a new OMERO computation.
-     * Must be called before processChunk.
-     *
-     * WARNING: This will overwrite any existing computation state.
-     * Do not call this if another computation is in progress.
-     */
-    initializeComputation(input) {
-        validateQuantiles(input.quantiles);
-        const cIndex = input.dims.indexOf("c");
-        const nChannels = cIndex !== -1 ? input.shape[cIndex] : 1;
-        currentState = {
-            accumulators: Array.from({ length: nChannels }, () => createAccumulator()),
-            input,
-        };
-    },
-    /**
-     * Process a chunk of data.
-     * Call this multiple times for streaming large datasets.
-     */
-    processChunk(chunkInput) {
-        if (!currentState) {
-            throw new Error("Computation not initialized. Call initializeComputation first.");
-        }
-        const { accumulators, input } = currentState;
-        const { shape, dims } = input;
-        const { chunkData } = chunkInput;
-        const cIndex = dims.indexOf("c");
-        const hasChannelDim = cIndex !== -1;
-        if (hasChannelDim) {
-            // Multi-channel: extract each channel and update its accumulator
-            for (let chIdx = 0; chIdx < accumulators.length; chIdx++) {
-                const channelData = extractChannel(chunkData, shape, chIdx, cIndex);
-                updateAccumulator(accumulators[chIdx], channelData);
-            }
-        }
-        else {
-            // Single channel: update directly
-            updateAccumulator(accumulators[0], chunkData);
-        }
-    },
-    /**
-     * Finalize computation and return OMERO metadata.
-     * Resets state after returning.
-     */
-    finalizeComputation() {
-        if (!currentState) {
-            throw new Error("Computation not initialized. Call initializeComputation first.");
-        }
-        const { accumulators, input } = currentState;
-        const result = buildOmeroFromAccumulators(accumulators, input.quantiles, input.colors, input.labels);
-        // Reset state
-        currentState = null;
-        return result;
-    },
-    /**
-     * Compute OMERO metadata in a single call (non-streaming).
-     * Useful for smaller datasets where streaming overhead isn't needed.
-     */
-    computeOmero(data, input) {
-        validateQuantiles(input.quantiles);
-        const { shape, dims, quantiles, colors, labels } = input;
-        const cIndex = dims.indexOf("c");
-        const hasChannelDim = cIndex !== -1;
-        const nChannels = hasChannelDim ? shape[cIndex] : 1;
-        // Create accumulators for each channel
-        const accumulators = Array.from({ length: nChannels }, () => createAccumulator());
-        if (hasChannelDim) {
-            // Multi-channel: extract each channel and compute statistics
-            for (let chIdx = 0; chIdx < nChannels; chIdx++) {
-                const channelData = extractChannel(data, shape, chIdx, cIndex);
-                updateAccumulator(accumulators[chIdx], channelData);
-            }
-        }
-        else {
-            // Single channel: compute directly
-            updateAccumulator(accumulators[0], data);
-        }
-        return buildOmeroFromAccumulators(accumulators, quantiles, colors, labels);
-    },
-    /**
-     * Check if worker is ready.
-     */
-    ping() {
-        return "pong";
-    },
-};
-// Expose the API via Comlink
-Comlink.expose(workerApi);
-//# sourceMappingURL=compute_omero_worker.js.map

package/esm/workers/compute_omero_worker.js.map

@@ -1 +0,0 @@
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