@fideus-labs/ngff-zarr 0.8.0 → 0.10.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/esm/browser-mod.d.ts +2 -2
- package/esm/browser-mod.d.ts.map +1 -1
- package/esm/browser-mod.js +2 -2
- package/esm/browser-mod.js.map +1 -1
- package/esm/io/from_ngff_zarr-browser.d.ts +3 -2
- package/esm/io/from_ngff_zarr-browser.d.ts.map +1 -1
- package/esm/io/from_ngff_zarr-browser.js +14 -4
- package/esm/io/from_ngff_zarr-browser.js.map +1 -1
- package/esm/io/from_ngff_zarr.d.ts +1 -1
- package/esm/io/from_ngff_zarr.d.ts.map +1 -1
- package/esm/io/from_ngff_zarr.js +16 -9
- package/esm/io/from_ngff_zarr.js.map +1 -1
- package/esm/mod.d.ts +1 -1
- package/esm/mod.d.ts.map +1 -1
- package/esm/mod.js +1 -1
- package/esm/mod.js.map +1 -1
- package/esm/utils/compute_omero-shared.d.ts +12 -0
- package/esm/utils/compute_omero-shared.d.ts.map +1 -1
- package/esm/utils/compute_omero-shared.js +28 -0
- package/esm/utils/compute_omero-shared.js.map +1 -1
- package/esm/utils/compute_omero.d.ts +10 -38
- package/esm/utils/compute_omero.d.ts.map +1 -1
- package/esm/utils/compute_omero.js +383 -79
- package/esm/utils/compute_omero.js.map +1 -1
- package/esm/utils/omero_worker_rpc.d.ts +37 -0
- package/esm/utils/omero_worker_rpc.d.ts.map +1 -0
- package/esm/utils/omero_worker_rpc.js +156 -0
- package/esm/utils/omero_worker_rpc.js.map +1 -0
- package/esm/workers/omero_codec_worker.d.ts +2 -0
- package/esm/workers/omero_codec_worker.d.ts.map +1 -0
- package/esm/workers/omero_codec_worker.js +215 -0
- package/esm/workers/omero_codec_worker.js.map +1 -0
- package/package.json +2 -3
- package/esm/utils/compute_omero-browser.d.ts +0 -45
- package/esm/utils/compute_omero-browser.d.ts.map +0 -1
- package/esm/utils/compute_omero-browser.js +0 -250
- package/esm/utils/compute_omero-browser.js.map +0 -1
- package/esm/workers/compute_omero_worker.d.ts +0 -47
- package/esm/workers/compute_omero_worker.d.ts.map +0 -1
- package/esm/workers/compute_omero_worker.js +0 -113
- package/esm/workers/compute_omero_worker.js.map +0 -1
package/esm/browser-mod.d.ts
CHANGED
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@@ -12,8 +12,8 @@ export * from "./schemas/multiscales.js";
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export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
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export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
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export { getMethodMetadata } from "./utils/method_metadata.js";
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export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS,
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export type { ComputeOmeroFromMultiscalesOptions, ComputeOmeroOptions, } from "./utils/compute_omero
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export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
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export type { ComputeOmeroFromMultiscalesOptions, ComputeOmeroOptions, } from "./utils/compute_omero.js";
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export { buildOmeroFromAccumulators, computeChannelStatistics, createAccumulator, extractChannel, finalizeStatistics, QUANTILE_SAMPLE_SIZE, updateAccumulator, validateQuantiles, } from "./utils/compute_omero-shared.js";
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export type { ChannelStatisticsAccumulator } from "./utils/compute_omero-shared.js";
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export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
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package/esm/browser-mod.d.ts.map
CHANGED
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@@ -1 +1 @@
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-
{"version":3,"file":"browser-mod.d.ts","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAOA,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAE/D,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,
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{"version":3,"file":"browser-mod.d.ts","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAOA,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAE/D,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAClC,YAAY,EACV,kCAAkC,EAClC,mBAAmB,GACpB,MAAM,0BAA0B,CAAC;AAGlC,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AACzC,YAAY,EAAE,4BAA4B,EAAE,MAAM,iCAAiC,CAAC;AACpF,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAK/E,OAAO,EACL,KAAK,UAAU,EACf,YAAY,EACZ,KAAK,mBAAmB,EACxB,KAAK,WAAW,GACjB,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,SAAS,EACT,UAAU,EACV,KAAK,iBAAiB,EACtB,aAAa,EACb,KAAK,oBAAoB,GAC1B,MAAM,8BAA8B,CAAC;AAGtC,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC;AAGhE,cAAc,qCAAqC,CAAC;AAGpD,OAAO,EACL,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC"}
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package/esm/browser-mod.js
CHANGED
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@@ -19,8 +19,8 @@ export * from "./schemas/multiscales.js";
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export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
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export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
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export { getMethodMetadata } from "./utils/method_metadata.js";
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//
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export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS,
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// OMERO computation with WorkerPool
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export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
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// Shared OMERO computation functions for benchmarking and direct use
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export { buildOmeroFromAccumulators, computeChannelStatistics, createAccumulator, extractChannel, finalizeStatistics, QUANTILE_SAMPLE_SIZE, updateAccumulator, validateQuantiles, } from "./utils/compute_omero-shared.js";
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export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
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package/esm/browser-mod.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"browser-mod.js","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,oCAAoC;AACpC,wEAAwE;AACxE,EAAE;AACF,kFAAkF;AAClF,yEAAyE;AACzE,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,
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{"version":3,"file":"browser-mod.js","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,oCAAoC;AACpC,wEAAwE;AACxE,EAAE;AACF,kFAAkF;AAClF,yEAAyE;AACzE,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,oCAAoC;AACpC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAMlC,qEAAqE;AACrE,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AAEzC,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAE/E,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EAEL,YAAY,GAGb,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,SAAS,EACT,UAAU,EAEV,aAAa,GAEd,MAAM,8BAA8B,CAAC;AAEtC,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAG1B,wCAAwC;AACxC,cAAc,qCAAqC,CAAC;AAEpD,gCAAgC;AAChC,OAAO,EACL,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC"}
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@@ -19,8 +19,9 @@ export interface FromNgffZarrOptions {
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export type MemoryStore = Map<string, Uint8Array>;
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/**
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* Browser-compatible version of fromNgffZarr.
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* Supports HTTP/HTTPS URLs, MemoryStore (Map), and
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* Supports HTTP/HTTPS URLs, MemoryStore (Map), FetchStore, and any
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* zarrita-compatible Readable store (e.g. TiffStore from @fideus-labs/fiff).
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* Does NOT support local file paths (use the full version in Node.js/Deno).
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*/
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export declare function fromNgffZarr(store: string | MemoryStore | zarr.FetchStore, options?: FromNgffZarrOptions): Promise<Multiscales>;
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export declare function fromNgffZarr(store: string | MemoryStore | zarr.FetchStore | zarr.Readable, options?: FromNgffZarrOptions): Promise<Multiscales>;
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//# sourceMappingURL=from_ngff_zarr-browser.d.ts.map
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{"version":3,"file":"from_ngff_zarr-browser.d.ts","sourceRoot":"","sources":["../../src/io/from_ngff_zarr-browser.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAGhC,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAMtD,YAAY,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAE1D,MAAM,WAAW,mBAAmB;IAClC,qDAAqD;IACrD,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iCAAiC;IACjC,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB;;;;;;;OAOG;IACH,KAAK,CAAC,EAAE,OAAO,yBAAyB,EAAE,UAAU,CAAC;CACtD;AAED,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD
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{"version":3,"file":"from_ngff_zarr-browser.d.ts","sourceRoot":"","sources":["../../src/io/from_ngff_zarr-browser.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAGhC,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAMtD,YAAY,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAE1D,MAAM,WAAW,mBAAmB;IAClC,qDAAqD;IACrD,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iCAAiC;IACjC,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB;;;;;;;OAOG;IACH,KAAK,CAAC,EAAE,OAAO,yBAAyB,EAAE,UAAU,CAAC;CACtD;AAED,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD;;;;;GAKG;AACH,wBAAsB,YAAY,CAChC,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EAC7D,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,WAAW,CAAC,CAmOtB"}
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@@ -9,7 +9,8 @@ import { NgffImage } from "../types/ngff_image.js";
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import { extractMethodMetadata } from "../utils/parse_metadata.js";
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/**
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* Browser-compatible version of fromNgffZarr.
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* Supports HTTP/HTTPS URLs, MemoryStore (Map), and
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* Supports HTTP/HTTPS URLs, MemoryStore (Map), FetchStore, and any
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* zarrita-compatible Readable store (e.g. TiffStore from @fideus-labs/fiff).
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*/
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export async function fromNgffZarr(store, options = {}) {
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try {
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// Determine the appropriate store type based on the path
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let resolvedStore;
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if (
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if (typeof store === "object" &&
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store !== null &&
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"get" in store &&
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typeof store.get === "function") {
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// Duck-type check for zarrita Readable stores (e.g. TiffStore, FetchStore, MemoryStore)
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resolvedStore = store;
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}
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else if (store
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else if (store instanceof Map || store instanceof zarr.FetchStore) {
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// Defensive fallback for Map/FetchStore (normally caught by duck-type check above)
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resolvedStore = store;
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}
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else if (typeof store === "string" &&
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}
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else {
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// Local file paths are not supported in browser environments
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throw new Error("Local file paths are not supported in browser environments. Use HTTP/HTTPS URLs or
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throw new Error("Local file paths are not supported in browser environments. Use HTTP/HTTPS URLs, MemoryStore, or a Readable store instead.");
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}
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// Try to use consolidated metadata for better performance
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{"version":3,"file":"from_ngff_zarr-browser.js","sourceRoot":"","sources":["../../src/io/from_ngff_zarr-browser.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,oFAAoF;AACpF,iFAAiF;AACjF,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAC7D,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAGnD,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AAsBnE
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|
+
{"version":3,"file":"from_ngff_zarr-browser.js","sourceRoot":"","sources":["../../src/io/from_ngff_zarr-browser.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,oFAAoF;AACpF,iFAAiF;AACjF,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAC7D,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAGnD,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AAsBnE;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,YAAY,CAChC,KAA6D,EAC7D,UAA+B,EAAE;IAEjC,MAAM,QAAQ,GAAG,OAAO,CAAC,QAAQ,IAAI,KAAK,CAAC;IAC3C,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC;IAEhC,IAAI,CAAC;QACH,yDAAyD;QACzD,IAAI,aAA4D,CAAC;QACjE,IACE,OAAO,KAAK,KAAK,QAAQ;YACzB,KAAK,KAAK,IAAI;YACd,KAAK,IAAI,KAAK;YACd,OAAQ,KAAuB,CAAC,GAAG,KAAK,UAAU,EAClD,CAAC;YACD,wFAAwF;YACxF,aAAa,GAAG,KAAsB,CAAC;QACzC,CAAC;aAAM,IAAI,KAAK,YAAY,GAAG,IAAI,KAAK,YAAY,IAAI,CAAC,UAAU,EAAE,CAAC;YACpE,mFAAmF;YACnF,aAAa,GAAG,KAAK,CAAC;QACxB,CAAC;aAAM,IACL,OAAO,KAAK,KAAK,QAAQ;YACzB,CAAC,KAAK,CAAC,UAAU,CAAC,SAAS,CAAC,IAAI,KAAK,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC,EAC7D,CAAC;YACD,qCAAqC;YACrC,aAAa,GAAG,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;QAC7C,CAAC;aAAM,CAAC;YACN,6DAA6D;YAC7D,MAAM,IAAI,KAAK,CACb,4HAA4H,CAC7H,CAAC;QACJ,CAAC;QAED,0DAA0D;QAC1D,IAAI,cAA4D,CAAC;QACjE,IAAI,CAAC;YACH,cAAc,GAAG,MAAM,IAAI,CAAC,mBAAmB,CAC7C,aAA8B,CAC/B,CAAC;QACJ,CAAC;QAAC,MAAM,CAAC;YACP,cAAc,GAAG,aAA8B,CAAC;QAClD,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,cAA+B,EAAE;YAC5D,IAAI,EAAE,OAAO;SACd,CAAC,CAAC;QACH,MAAM,KAAK,GAAG,IAAI,CAAC,KAAgB,CAAC;QAEpC,gFAAgF;QAChF,IAAI,gBAA2B,CAAC;QAChC,IAAI,eAAmC,CAAC;QAExC,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,IAAI,KAAK,EAAE,CAAC;YACzD,4DAA4D;YAC5D,MAAM,QAAQ,GAAI,KAAiC,CAAC,GAGnD,CAAC;YACF,IAAI,CAAC,QAAQ,IAAI,CAAC,QAAQ,CAAC,WAAW,EAAE,CAAC;gBACvC,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;YACzE,CAAC;YACD,gBAAgB,GAAG,QAAQ,CAAC,WAAwB,CAAC;YACrD,eAAe,GAAG,QAAQ,CAAC,OAA6B,CAAC;QAC3D,CAAC;aAAM,IAAI,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,aAAa,IAAI,KAAK,EAAE,CAAC;YACxE,2CAA2C;YAC3C,gBAAgB,GAAI,KAAiC;iBAClD,WAAwB,CAAC;QAC9B,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,6CAA6C,CAAC,CAAC;QACjE,CAAC;QAED,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,gBAAgB,CAAC,IAAI,gBAAgB,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACtE,MAAM,IAAI,KAAK,CAAC,6CAA6C,CAAC,CAAC;QACjE,CAAC;QACD,MAAM,mBAAmB,GAAG,gBAAgB,CAAC,CAAC,CAAY,CAAC;QAE3D,IAAI,QAAQ,EAAE,CAAC;YACb,MAAM,MAAM,GAAG,cAAc,CAAC,SAAS,CAAC,mBAAmB,CAAC,CAAC;YAC7D,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC;gBACpB,MAAM,IAAI,KAAK,CAAC,8BAA8B,MAAM,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC;YACxE,CAAC;YAED,2CAA2C;YAC3C,IAAI,OAAO,EAAE,CAAC;gBACZ,MAAM,mBAAmB,GAAG,mBAA2C,CAAC;gBACxE,MAAM,aAAa,GAAG,mBAAmB,CAAC,OAAO,IAAI,eAAe,CAAC;gBACrE,IAAI,aAAa,KAAK,OAAO,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CACb,6BAA6B,OAAO,eAClC,aAAa,IAAI,SACnB,EAAE,CACH,CAAC;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,QAAQ,GAAG,mBAA+B,CAAC;QAEjD,yDAAyD;QACzD,IAAK,KAAiC,CAAC,KAAK,EAAE,CAAC;YAC7C,MAAM,SAAS,GAAI,KAAiC,CAAC,KAGpD,CAAC;YAEF,0DAA0D;YAC1D,IAAI,SAAS,CAAC,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC;gBAC5D,KACE,MAAM,OAAO,IAAI,SAAS,CAAC,QAE1B,EACD,CAAC;oBACD,IAAI,OAAO,CAAC,MAAM,IAAI,OAAO,OAAO,CAAC,MAAM,KAAK,QAAQ,EAAE,CAAC;wBACzD,MAAM,MAAM,GAAG,OAAO,CAAC,MAA4C,CAAC;wBAEpE,kEAAkE;wBAClE,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;4BACzD,kDAAkD;4BAClD,IAAI,MAAM,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;gCAC/B,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,GAAG,CAAC;4BAC5B,CAAC;4BACD,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;gCAC7B,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC;4BAC1B,CAAC;wBACH,CAAC;6BAAM,IAAI,MAAM,CAAC,KAAK,KAAK,SAAS,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;4BAClE,kDAAkD;4BAClD,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;gCAC7B,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC;4BAC5B,CAAC;4BACD,IAAI,MAAM,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;gCAC7B,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC;4BAC1B,CAAC;wBACH,CAAC;oBACH,CAAC;gBACH,CAAC;YACH,CAAC;YAED,QAAQ,CAAC,KAAK,GAAG,SAA6B,CAAC;QACjD,CAAC;QAED,MAAM,MAAM,GAAgB,EAAE,CAAC;QAE/B,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,QAAQ,EAAE,CAAC;YACxC,MAAM,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC;YAE/B,MAAM,SAAS,GAAG,CAAC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE;gBAC1D,IAAI,EAAE,OAAO;aACd,CAAC,CAA6C,CAAC;YAEhD,uDAAuD;YACvD,IACE,CAAC,SAAS;gBACV,CAAC,CAAC,OAAO,IAAI,SAAS,CAAC;gBACvB,CAAC,CAAC,OAAO,IAAI,SAAS,CAAC;gBACvB,CAAC,CAAC,QAAQ,IAAI,SAAS,CAAC,EACxB,CAAC;gBACD,MAAM,IAAI,KAAK,CACb,8BAA8B,SAAS,0BAA0B,CAClE,CAAC;YACJ,CAAC;YAED,MAAM,KAAK,GAA2B,EAAE,CAAC;YACzC,MAAM,WAAW,GAA2B,EAAE,CAAC;YAE/C,KAAK,MAAM,SAAS,IAAI,OAAO,CAAC,yBAAyB,EAAE,CAAC;gBAC1D,IAAI,SAAS,CAAC,IAAI,KAAK,OAAO,EAAE,CAAC;oBAC/B,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,EAAE;wBAChC,IAAI,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;4BAC/B,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;wBACxC,CAAC;oBACH,CAAC,CAAC,CAAC;gBACL,CAAC;qBAAM,IAAI,SAAS,CAAC,IAAI,KAAK,aAAa,EAAE,CAAC;oBAC5C,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,EAAE;wBAChC,IAAI,CAAC,GAAG,SAAS,CAAC,WAAW,CAAC,MAAM,EAAE,CAAC;4BACrC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;wBACpD,CAAC;oBACH,CAAC,CAAC,CAAC;gBACL,CAAC;YACH,CAAC;YAED,MAAM,IAAI,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACpD,MAAM,SAAS,GAAG,QAAQ,CAAC,IAAI,CAAC,MAAM,CACpC,CAAC,GAAG,EAAE,IAAI,EAAE,EAAE;gBACZ,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;oBACd,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC;gBAC7B,CAAC;gBACD,OAAO,GAAG,CAAC;YACb,CAAC,EACD,EAA2B,CAC5B,CAAC;YAEF,MAAM,SAAS,GAAG,IAAI,SAAS,CAAC;gBAC9B,IAAI,EAAE,SAAS;gBACf,IAAI;gBACJ,KAAK;gBACL,WAAW;gBACX,IAAI,EAAE,QAAQ,CAAC,IAAI;gBACnB,SAAS,EAAE,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS;gBACpE,iBAAiB,EAAE,SAAS;aAC7B,CAAC,CAAC;YAEH,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;QACzB,CAAC;QAED,mFAAmF;QACnF,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,cAAc,EAAE,GAAG,qBAAqB,CAClE,mBAA8C,CAC/C,CAAC;QACF,IAAI,UAAU,EAAE,CAAC;YACf,QAAQ,CAAC,IAAI,GAAG,UAAU,CAAC;QAC7B,CAAC;QACD,IAAI,cAAc,EAAE,CAAC;YACnB,QAAQ,CAAC,QAAQ,GAAG,cAAc,CAAC;QACrC,CAAC;QAED,OAAO,IAAI,WAAW,CAAC;YACrB,MAAM;YACN,QAAQ;YACR,YAAY,EAAE,SAAS;YACvB,MAAM;YACN,MAAM,EAAE,SAAS;SAClB,CAAC,CAAC;IACL,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,IAAI,KAAK,CACb,4BACE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CACvD,EAAE,CACH,CAAC;IACJ,CAAC;AACH,CAAC"}
|
|
@@ -17,6 +17,6 @@ export interface FromNgffZarrOptions {
|
|
|
17
17
|
cache?: import("../utils/worker_pool.js").ChunkCache;
|
|
18
18
|
}
|
|
19
19
|
export type MemoryStore = Map<string, Uint8Array>;
|
|
20
|
-
export declare function fromNgffZarr(store: string | MemoryStore | zarr.FetchStore, options?: FromNgffZarrOptions): Promise<Multiscales>;
|
|
20
|
+
export declare function fromNgffZarr(store: string | MemoryStore | zarr.FetchStore | zarr.Readable, options?: FromNgffZarrOptions): Promise<Multiscales>;
|
|
21
21
|
export declare function readArrayData(storePath: string, arrayPath: string, selection?: (number | null)[]): Promise<unknown>;
|
|
22
22
|
//# sourceMappingURL=from_ngff_zarr.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"from_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/from_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;
|
|
1
|
+
{"version":3,"file":"from_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/from_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAYtD,YAAY,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAE1D,MAAM,WAAW,mBAAmB;IAClC,qDAAqD;IACrD,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iCAAiC;IACjC,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB;;;;;;;OAOG;IACH,KAAK,CAAC,EAAE,OAAO,yBAAyB,EAAE,UAAU,CAAC;CACtD;AAED,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD,wBAAsB,YAAY,CAEhC,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EAC7D,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,WAAW,CAAC,CAqItB;AAED,wBAAsB,aAAa,CACjC,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,EACjB,SAAS,CAAC,EAAE,CAAC,MAAM,GAAG,IAAI,CAAC,EAAE,GAC5B,OAAO,CAAC,OAAO,CAAC,CAmClB"}
|
package/esm/io/from_ngff_zarr.js
CHANGED
|
@@ -3,25 +3,36 @@
|
|
|
3
3
|
import * as zarr from "zarrita";
|
|
4
4
|
import { Multiscales } from "../types/multiscales.js";
|
|
5
5
|
import { NgffVersion } from "../types/supported_versions.js";
|
|
6
|
-
import { detectVersion, extractMethodMetadata, } from "../utils/parse_metadata.js";
|
|
7
6
|
import { fromZarrAttrsV04, fromZarrAttrsV05, } from "../utils/from_zarr_attrs.js";
|
|
7
|
+
import { detectVersion, extractMethodMetadata, } from "../utils/parse_metadata.js";
|
|
8
8
|
import { zarrGet } from "../utils/worker_pool.js";
|
|
9
9
|
export async function fromNgffZarr(
|
|
10
|
-
// Also accepts FileSystemStore, ZipFileStore
|
|
10
|
+
// Also accepts FileSystemStore, ZipFileStore, or any zarrita Readable store
|
|
11
11
|
store, options = {}) {
|
|
12
12
|
const validate = options.validate ?? false;
|
|
13
13
|
const requestedVersion = options.version;
|
|
14
14
|
try {
|
|
15
15
|
// Determine the appropriate store type based on the path
|
|
16
16
|
let resolvedStore;
|
|
17
|
-
if (
|
|
17
|
+
if (typeof store === "object" &&
|
|
18
|
+
store !== null &&
|
|
19
|
+
"get" in store &&
|
|
20
|
+
typeof store.get === "function") {
|
|
21
|
+
// Duck-type check for zarrita Readable stores (e.g. TiffStore, FetchStore, MemoryStore)
|
|
22
|
+
resolvedStore = store;
|
|
23
|
+
}
|
|
24
|
+
else if (store instanceof Map || store instanceof zarr.FetchStore) {
|
|
25
|
+
// Defensive fallback for Map/FetchStore (normally caught by duck-type check above)
|
|
18
26
|
resolvedStore = store;
|
|
19
27
|
}
|
|
20
|
-
else if (store
|
|
28
|
+
else if (typeof store === "string" &&
|
|
29
|
+
(store.startsWith("http://") || store.startsWith("https://"))) {
|
|
21
30
|
// Use FetchStore for HTTP/HTTPS URLs
|
|
22
31
|
resolvedStore = new zarr.FetchStore(store);
|
|
23
32
|
}
|
|
24
33
|
else {
|
|
34
|
+
// Only strings (local paths) reach this branch
|
|
35
|
+
const storePath = store;
|
|
25
36
|
// For local paths, check if we're in a browser environment
|
|
26
37
|
if (typeof window !== "undefined") {
|
|
27
38
|
throw new Error("Local file paths are not supported in browser environments. Use HTTP/HTTPS URLs instead.");
|
|
@@ -29,15 +40,12 @@ store, options = {}) {
|
|
|
29
40
|
// Use dynamic import for FileSystemStore, ZipFileStore in Node.js/Deno environments
|
|
30
41
|
try {
|
|
31
42
|
const { FileSystemStore, ZipFileStore } = await import("@zarrita/storage");
|
|
32
|
-
// @ts-ignore: Node/Deno workaround
|
|
33
43
|
if (store instanceof FileSystemStore || store instanceof ZipFileStore) {
|
|
34
|
-
// @ts-ignore: Node/Deno workaround
|
|
35
44
|
resolvedStore = store;
|
|
36
45
|
}
|
|
37
46
|
else {
|
|
38
47
|
// Normalize the path for cross-platform compatibility
|
|
39
|
-
const normalizedPath =
|
|
40
|
-
// @ts-ignore: Node/Deno workaround
|
|
48
|
+
const normalizedPath = storePath.replace(/^\/([A-Za-z]:)/, "$1");
|
|
41
49
|
resolvedStore = new FileSystemStore(normalizedPath);
|
|
42
50
|
}
|
|
43
51
|
}
|
|
@@ -48,7 +56,6 @@ store, options = {}) {
|
|
|
48
56
|
// Try to use consolidated metadata for better performance
|
|
49
57
|
let optimizedStore;
|
|
50
58
|
try {
|
|
51
|
-
// @ts-ignore: tryWithConsolidated typing
|
|
52
59
|
optimizedStore = await zarr.tryWithConsolidated(resolvedStore);
|
|
53
60
|
}
|
|
54
61
|
catch {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"from_ngff_zarr.js","sourceRoot":"","sources":["../../src/io/from_ngff_zarr.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;
|
|
1
|
+
{"version":3,"file":"from_ngff_zarr.js","sourceRoot":"","sources":["../../src/io/from_ngff_zarr.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,EAAE,WAAW,EAAE,MAAM,gCAAgC,CAAC;AAC7D,OAAO,EACL,gBAAgB,EAChB,gBAAgB,GACjB,MAAM,6BAA6B,CAAC;AACrC,OAAO,EACL,aAAa,EACb,qBAAqB,GACtB,MAAM,4BAA4B,CAAC;AACpC,OAAO,EAAE,OAAO,EAAE,MAAM,yBAAyB,CAAC;AAsBlD,MAAM,CAAC,KAAK,UAAU,YAAY;AAChC,4EAA4E;AAC5E,KAA6D,EAC7D,UAA+B,EAAE;IAEjC,MAAM,QAAQ,GAAG,OAAO,CAAC,QAAQ,IAAI,KAAK,CAAC;IAC3C,MAAM,gBAAgB,GAAG,OAAO,CAAC,OAAO,CAAC;IAEzC,IAAI,CAAC;QACH,yDAAyD;QACzD,IAAI,aAA4D,CAAC;QACjE,IACE,OAAO,KAAK,KAAK,QAAQ;YACzB,KAAK,KAAK,IAAI;YACd,KAAK,IAAI,KAAK;YACd,OAAQ,KAAuB,CAAC,GAAG,KAAK,UAAU,EAClD,CAAC;YACD,wFAAwF;YACxF,aAAa,GAAG,KAAsB,CAAC;QACzC,CAAC;aAAM,IAAI,KAAK,YAAY,GAAG,IAAI,KAAK,YAAY,IAAI,CAAC,UAAU,EAAE,CAAC;YACpE,mFAAmF;YACnF,aAAa,GAAG,KAAK,CAAC;QACxB,CAAC;aAAM,IACL,OAAO,KAAK,KAAK,QAAQ;YACzB,CAAC,KAAK,CAAC,UAAU,CAAC,SAAS,CAAC,IAAI,KAAK,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC,EAC7D,CAAC;YACD,qCAAqC;YACrC,aAAa,GAAG,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;QAC7C,CAAC;aAAM,CAAC;YACN,+CAA+C;YAC/C,MAAM,SAAS,GAAG,KAAe,CAAC;YAElC,2DAA2D;YAC3D,IAAI,OAAO,MAAM,KAAK,WAAW,EAAE,CAAC;gBAClC,MAAM,IAAI,KAAK,CACb,0FAA0F,CAC3F,CAAC;YACJ,CAAC;YAED,oFAAoF;YACpF,IAAI,CAAC;gBACH,MAAM,EAAE,eAAe,EAAE,YAAY,EAAE,GAAG,MAAM,MAAM,CACpD,kBAAkB,CACnB,CAAC;gBACF,IAAI,KAAK,YAAY,eAAe,IAAI,KAAK,YAAY,YAAY,EAAE,CAAC;oBACtE,aAAa,GAAG,KAAiC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,sDAAsD;oBACtD,MAAM,cAAc,GAAG,SAAS,CAAC,OAAO,CAAC,gBAAgB,EAAE,IAAI,CAAC,CAAC;oBACjE,aAAa,GAAG,IAAI,eAAe,CACjC,cAAc,CACa,CAAC;gBAChC,CAAC;YACH,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,mCAAmC,KAAK,kDAAkD,CAC3F,CAAC;YACJ,CAAC;QACH,CAAC;QAED,0DAA0D;QAC1D,IAAI,cAA4D,CAAC;QACjE,IAAI,CAAC;YACH,cAAc,GAAG,MAAM,IAAI,CAAC,mBAAmB,CAC7C,aAA8B,CAC/B,CAAC;QACJ,CAAC;QAAC,MAAM,CAAC;YACP,cAAc,GAAG,aAA8B,CAAC;QAClD,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,cAA+B,EAAE;YAC5D,IAAI,EAAE,OAAO;SACd,CAAC,CAAC;QACH,MAAM,KAAK,GAAG,IAAI,CAAC,KAAgB,CAAC;QACpC,MAAM,SAAS,GAAG,KAAgC,CAAC;QAEnD,4EAA4E;QAC5E,MAAM,aAAa,GAAG,KAAK,IAAI,SAAS,CAAC;QACzC,MAAM,iBAAiB,GAAG,aAAa;YACrC,CAAC,CAAE,SAAS,CAAC,GAA+B;YAC5C,CAAC,CAAC,SAAS,CAAC;QAEd,IAAI,CAAC,iBAAiB,CAAC,WAAW,EAAE,CAAC;YACnC,MAAM,IAAI,KAAK,CAAC,6CAA6C,CAAC,CAAC;QACjE,CAAC;QAED,iCAAiC;QACjC,MAAM,eAAe,GAAG,aAAa,CAAC,SAAS,CAAC,CAAC;QAEjD,gCAAgC;QAChC,IAAI,QAAQ,IAAI,gBAAgB,EAAE,CAAC;YACjC,IAAI,eAAe,KAAK,gBAAgB,EAAE,CAAC;gBACzC,MAAM,IAAI,KAAK,CACb,6BAA6B,gBAAgB,eAAe,eAAe,EAAE,CAC9E,CAAC;YACJ,CAAC;QACH,CAAC;QAED,iDAAiD;QACjD,IAAI,MAAM,CAAC;QACX,IAAI,eAAe,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;YACxC,MAAM,GAAG,MAAM,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,QAAQ,CAAC,CAAC;QACtE,CAAC;aAAM,CAAC;YACN,MAAM,GAAG,MAAM,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,QAAQ,CAAC,CAAC;QACtE,CAAC;QAED,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC;QAEpC,wDAAwD;QACxD,MAAM,gBAAgB,GAAG,iBAAiB,CAAC,WAAwB,CAAC;QACpE,MAAM,mBAAmB,GAAG,gBAAgB,CAAC,CAAC,CAA4B,CAAC;QAC3E,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,cAAc,EAAE,GAAG,qBAAqB,CAClE,mBAAmB,CACpB,CAAC;QAEF,0CAA0C;QAC1C,IAAI,UAAU,EAAE,CAAC;YACf,QAAQ,CAAC,IAAI,GAAG,UAAU,CAAC;QAC7B,CAAC;QACD,IAAI,cAAc,EAAE,CAAC;YACnB,QAAQ,CAAC,QAAQ,GAAG,cAAc,CAAC;QACrC,CAAC;QAED,OAAO,IAAI,WAAW,CAAC;YACrB,MAAM;YACN,QAAQ;YACR,YAAY,EAAE,SAAS;YACvB,MAAM;YACN,MAAM,EAAE,SAAS;SAClB,CAAC,CAAC;IACL,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,IAAI,KAAK,CACb,4BACE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CACvD,EAAE,CACH,CAAC;IACJ,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,SAAiB,EACjB,SAAiB,EACjB,SAA6B;IAE7B,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,IAAI,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC,CAAC;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QAE9B,sDAAsD;QACtD,IAAI,SAAS,CAAC;QACd,IAAI,CAAC;YACH,SAAS,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE;gBACtD,IAAI,EAAE,OAAO;aACd,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,OAAO,EAAE,CAAC;YACjB,IAAI,CAAC;gBACH,SAAS,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE;oBACtD,IAAI,EAAE,OAAO;iBACd,CAAC,CAAC;YACL,CAAC;YAAC,OAAO,OAAO,EAAE,CAAC;gBACjB,MAAM,IAAI,KAAK,CACb,6BAA6B,SAAS,yCAAyC,OAAO,eAAe,OAAO,EAAE,CAC/G,CAAC;YACJ,CAAC;QACH,CAAC;QAED,IAAI,SAAS,EAAE,CAAC;YACd,OAAO,MAAM,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAC;QAC7C,CAAC;aAAM,CAAC;YACN,OAAO,MAAM,OAAO,CAAC,SAAS,CAAC,CAAC;QAClC,CAAC;IACH,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,IAAI,KAAK,CACb,8BACE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CACvD,EAAE,CACH,CAAC;IACJ,CAAC;AACH,CAAC"}
|
package/esm/mod.d.ts
CHANGED
|
@@ -16,7 +16,7 @@ export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/valida
|
|
|
16
16
|
export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
|
|
17
17
|
export { getMethodMetadata } from "./utils/method_metadata.js";
|
|
18
18
|
export { detectVersion, extractMethodMetadata, parseOmero, } from "./utils/parse_metadata.js";
|
|
19
|
-
export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, } from "./utils/compute_omero.js";
|
|
19
|
+
export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
|
|
20
20
|
export type { ComputeOmeroFromMultiscalesOptions, ComputeOmeroOptions, } from "./utils/compute_omero.js";
|
|
21
21
|
export { fromZarrAttrsV04, fromZarrAttrsV05 } from "./utils/from_zarr_attrs.js";
|
|
22
22
|
export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
|
package/esm/mod.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"mod.d.ts","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAEA,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,+BAA+B,CAAC;AAE9C,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,aAAa,EACb,qBAAqB,EACrB,UAAU,GACX,MAAM,2BAA2B,CAAC;AACnC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,
|
|
1
|
+
{"version":3,"file":"mod.d.ts","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAEA,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,+BAA+B,CAAC;AAE9C,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,aAAa,EACb,qBAAqB,EACrB,UAAU,GACX,MAAM,2BAA2B,CAAC;AACnC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAClC,YAAY,EACV,kCAAkC,EAClC,mBAAmB,GACpB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAChF,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAE/E,cAAc,wBAAwB,CAAC;AACvC,cAAc,sBAAsB,CAAC;AACrC,cAAc,kCAAkC,CAAC;AACjD,YAAY,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAC1D,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAChD,cAAc,aAAa,CAAC;AAG5B,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,SAAS,EACT,gBAAgB,EAChB,iBAAiB,EACjB,gBAAgB,EAChB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC"}
|
package/esm/mod.js
CHANGED
|
@@ -18,7 +18,7 @@ export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/valida
|
|
|
18
18
|
export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
|
|
19
19
|
export { getMethodMetadata } from "./utils/method_metadata.js";
|
|
20
20
|
export { detectVersion, extractMethodMetadata, parseOmero, } from "./utils/parse_metadata.js";
|
|
21
|
-
export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, } from "./utils/compute_omero.js";
|
|
21
|
+
export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
|
|
22
22
|
export { fromZarrAttrsV04, fromZarrAttrsV05 } from "./utils/from_zarr_attrs.js";
|
|
23
23
|
export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
|
|
24
24
|
export * from "./io/from_ngff_zarr.js";
|
package/esm/mod.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"mod.js","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,+BAA+B,CAAC;AAE9C,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,aAAa,EACb,qBAAqB,EACrB,UAAU,GACX,MAAM,2BAA2B,CAAC;AACnC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,
|
|
1
|
+
{"version":3,"file":"mod.js","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,+BAA+B,CAAC;AAE9C,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,aAAa,EACb,qBAAqB,EACrB,UAAU,GACX,MAAM,2BAA2B,CAAC;AACnC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAKlC,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAChF,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAE/E,cAAc,wBAAwB,CAAC;AACvC,cAAc,sBAAsB,CAAC;AACrC,cAAc,kCAAkC,CAAC;AAEjD,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAChD,cAAc,aAAa,CAAC;AAE5B,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,SAAS,EACT,gBAAgB,EAChB,iBAAiB,EACjB,gBAAgB,EAChB,cAAc,GACf,MAAM,kBAAkB,CAAC"}
|
|
@@ -63,6 +63,11 @@ export declare function finalizeStatistics(acc: ChannelStatisticsAccumulator, qu
|
|
|
63
63
|
qLow: number;
|
|
64
64
|
qHigh: number;
|
|
65
65
|
};
|
|
66
|
+
/**
|
|
67
|
+
* Merge two channel statistics accumulators.
|
|
68
|
+
* Used to combine partial results from parallel per-chunk workers.
|
|
69
|
+
*/
|
|
70
|
+
export declare function mergeAccumulators(a: ChannelStatisticsAccumulator, b: ChannelStatisticsAccumulator): ChannelStatisticsAccumulator;
|
|
66
71
|
/**
|
|
67
72
|
* Compute channel statistics from array data (non-streaming version).
|
|
68
73
|
* For datasets larger than QUANTILE_SAMPLE_SIZE, uses reservoir sampling.
|
|
@@ -87,6 +92,13 @@ export interface ComputeOmeroOptions {
|
|
|
87
92
|
colors?: string[] | undefined;
|
|
88
93
|
/** Optional list of label strings for each channel. */
|
|
89
94
|
labels?: string[] | undefined;
|
|
95
|
+
/**
|
|
96
|
+
* Optional decoded-chunk cache. When provided, decoded chunks are cached
|
|
97
|
+
* during omero computation so that subsequent zarrGet() calls with the
|
|
98
|
+
* same cache get cache hits (no re-decode). Any object with get(key)
|
|
99
|
+
* and set(key, value) works — a plain Map is the simplest option.
|
|
100
|
+
*/
|
|
101
|
+
cache?: import("@fideus-labs/fizarrita").ChunkCache | undefined;
|
|
90
102
|
}
|
|
91
103
|
/**
|
|
92
104
|
* Options for computing OMERO metadata from multiscales.
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
|
@@ -378,6 +378,34 @@ export function finalizeStatistics(acc, quantiles) {
|
|
|
378
378
|
const qHigh = computeQuantile(acc.sample, quantiles[1]);
|
|
379
379
|
return { min: acc.min, max: acc.max, qLow, qHigh };
|
|
380
380
|
}
|
|
381
|
+
/**
|
|
382
|
+
* Merge two channel statistics accumulators.
|
|
383
|
+
* Used to combine partial results from parallel per-chunk workers.
|
|
384
|
+
*/
|
|
385
|
+
export function mergeAccumulators(a, b) {
|
|
386
|
+
const merged = {
|
|
387
|
+
min: Math.min(a.min, b.min),
|
|
388
|
+
max: Math.max(a.max, b.max),
|
|
389
|
+
count: a.count + b.count,
|
|
390
|
+
sample: [...a.sample, ...b.sample],
|
|
391
|
+
};
|
|
392
|
+
// Downsample if combined reservoir exceeds limit
|
|
393
|
+
if (merged.sample.length > QUANTILE_SAMPLE_SIZE) {
|
|
394
|
+
// Use reservoir sampling over the concatenated sample for unbiased downsampling
|
|
395
|
+
const k = QUANTILE_SAMPLE_SIZE;
|
|
396
|
+
const n = merged.sample.length;
|
|
397
|
+
// Treat the first k elements as the initial reservoir and
|
|
398
|
+
// stream the remaining elements, applying the reservoir update rule.
|
|
399
|
+
for (let i = k; i < n; i++) {
|
|
400
|
+
const j = Math.floor(Math.random() * (i + 1));
|
|
401
|
+
if (j < k) {
|
|
402
|
+
merged.sample[j] = merged.sample[i];
|
|
403
|
+
}
|
|
404
|
+
}
|
|
405
|
+
merged.sample.length = k;
|
|
406
|
+
}
|
|
407
|
+
return merged;
|
|
408
|
+
}
|
|
381
409
|
/**
|
|
382
410
|
* Compute channel statistics from array data (non-streaming version).
|
|
383
411
|
* For datasets larger than QUANTILE_SAMPLE_SIZE, uses reservoir sampling.
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
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@@ -1,51 +1,23 @@
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/**
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* Compute OMERO metadata from NgffImage data.
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*
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* This is the main-thread (Node.js/Deno) implementation.
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* For browser environments with WebWorker support, see compute_omero-browser.ts.
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*/
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import type { NgffImage } from "../types/ngff_image.js";
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import type { Multiscales } from "../types/multiscales.js";
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import type { Omero } from "../types/zarr_metadata.js";
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export { computeChannelStatistics, type ComputeOmeroFromMultiscalesOptions, type ComputeOmeroOptions, extractChannel, getDefaultColors, GLASBEY_COLORS, QUANTILE_SAMPLE_SIZE, validateColor, validateQuantiles, } from "./compute_omero-shared.js";
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import { type ComputeOmeroFromMultiscalesOptions, type ComputeOmeroOptions } from "./compute_omero-shared.js";
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export { computeChannelStatistics, type ComputeOmeroFromMultiscalesOptions, type ComputeOmeroOptions, extractChannel, getDefaultColors, GLASBEY_COLORS, QUANTILE_SAMPLE_SIZE, validateColor, validateQuantiles, } from "./compute_omero-shared.js";
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/**
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* Terminate the omero computation worker pool and release resources.
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* Call this when you're done with OMERO computations to free memory.
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*/
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export declare function terminateOmeroWorkerPool(): void;
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/**
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12
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* Compute OMERO metadata from an NgffImage.
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*
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*
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*
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*
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*
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* For multi-channel images (with 'c' dimension), statistics are computed
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* separately for each channel, resulting in per-channel OMERO windows.
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*
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* Memory requirements: This function loads the entire image data into memory
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23
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* for statistics computation. For large images, use the lowest resolution
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* image from a multiscales pyramid.
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*
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* Edge cases:
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* - If all values in a channel are NaN, the statistics will be NaN.
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* - If a channel has constant values, min/max/start/end will all be the same.
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14
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+
* Each zarr chunk is decoded and its per-channel statistics computed in
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15
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+
* parallel via a WorkerPool. Decoded chunks are optionally cached so that
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16
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+
* a subsequent zarrGet() with the same cache avoids redundant decompression.
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17
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*
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18
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* @param image - The NgffImage to compute metadata for
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* @param options - Optional configuration for quantiles, colors, and
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* - quantiles: Tuple of (low, high) quantile values. Must be between 0 and 1,
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* with low < high. Default is [0.02, 0.98] for 2% and 98% quantiles.
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* - colors: List of hex color strings (without #) for each channel.
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35
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* Must be 6-digit hexadecimal strings (e.g., "FF0000" for red).
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36
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-
* If not provided, uses white for single channel or Glasbey
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* progression for multi-channel.
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38
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* - labels: List of label strings for each channel.
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39
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* If not provided, uses empty strings.
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19
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+
* @param options - Optional configuration for quantiles, colors, labels, and cache
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20
|
* @returns Promise resolving to Omero metadata with computed window parameters
|
|
41
|
-
* @throws {Error} If quantiles are invalid, colors are invalid format,
|
|
42
|
-
* or not enough colors/labels provided.
|
|
43
|
-
*
|
|
44
|
-
* @example
|
|
45
|
-
* ```ts
|
|
46
|
-
* const omero = await computeOmeroFromNgffImage(image);
|
|
47
|
-
* multiscales.metadata.omero = omero;
|
|
48
|
-
* ```
|
|
49
21
|
*/
|
|
50
22
|
export declare function computeOmeroFromNgffImage(image: NgffImage, options?: ComputeOmeroOptions): Promise<Omero>;
|
|
51
23
|
/**
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"compute_omero.d.ts","sourceRoot":"","sources":["../../src/utils/compute_omero.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"compute_omero.d.ts","sourceRoot":"","sources":["../../src/utils/compute_omero.ts"],"names":[],"mappings":"AAmBA,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,EAGL,KAAK,kCAAkC,EACvC,KAAK,mBAAmB,EAOzB,MAAM,2BAA2B,CAAC;AAKnC,OAAO,EACL,wBAAwB,EACxB,KAAK,kCAAkC,EACvC,KAAK,mBAAmB,EACxB,cAAc,EACd,gBAAgB,EAChB,cAAc,EACd,oBAAoB,EACpB,aAAa,EACb,iBAAiB,GAClB,MAAM,2BAA2B,CAAC;AAuCnC;;;GAGG;AACH,wBAAgB,wBAAwB,IAAI,IAAI,CAS/C;AAoQD;;;;;;;;;;GAUG;AACH,wBAAsB,yBAAyB,CAC7C,KAAK,EAAE,SAAS,EAChB,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,KAAK,CAAC,CA0KhB;AAMD;;;;;;;;;GASG;AACH,wBAAsB,2BAA2B,CAC/C,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,kCAAuC,GAC/C,OAAO,CAAC,KAAK,CAAC,CAoBhB"}
|