@fideus-labs/ngff-zarr 0.17.0 → 0.19.0
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 +6 -5
- package/esm/browser-mod.d.ts.map +1 -1
- package/esm/browser-mod.js +5 -4
- package/esm/browser-mod.js.map +1 -1
- package/esm/io/from_ngff_zarr-browser.d.ts +8 -4
- package/esm/io/from_ngff_zarr-browser.d.ts.map +1 -1
- package/esm/io/from_ngff_zarr-browser.js +6 -4
- package/esm/io/from_ngff_zarr-browser.js.map +1 -1
- package/esm/io/from_ngff_zarr.d.ts +7 -3
- package/esm/io/from_ngff_zarr.d.ts.map +1 -1
- package/esm/io/from_ngff_zarr.js +5 -3
- package/esm/io/from_ngff_zarr.js.map +1 -1
- package/esm/io/hcs.d.ts.map +1 -1
- package/esm/io/hcs.js +11 -3
- package/esm/io/hcs.js.map +1 -1
- package/esm/io/to_ngff_zarr-browser.d.ts +24 -7
- package/esm/io/to_ngff_zarr-browser.d.ts.map +1 -1
- package/esm/io/to_ngff_zarr-browser.js +18 -10
- package/esm/io/to_ngff_zarr-browser.js.map +1 -1
- package/esm/io/to_ngff_zarr.d.ts +30 -13
- package/esm/io/to_ngff_zarr.d.ts.map +1 -1
- package/esm/io/to_ngff_zarr.js +30 -23
- package/esm/io/to_ngff_zarr.js.map +1 -1
- package/esm/io/to_ngff_zarr_ozx_common.d.ts +8 -8
- package/esm/io/to_ngff_zarr_ozx_common.d.ts.map +1 -1
- package/esm/io/to_ngff_zarr_ozx_common.js +5 -5
- package/esm/io/to_ngff_zarr_ozx_common.js.map +1 -1
- package/esm/mod.d.ts +4 -3
- package/esm/mod.d.ts.map +1 -1
- package/esm/mod.js +3 -2
- package/esm/mod.js.map +1 -1
- package/esm/process/to_multiscales-browser.d.ts +3 -3
- package/esm/process/to_multiscales-browser.d.ts.map +1 -1
- package/esm/process/to_multiscales-browser.js +1 -1
- package/esm/process/to_multiscales-node.d.ts +3 -3
- package/esm/process/to_multiscales-node.d.ts.map +1 -1
- package/esm/process/to_multiscales-node.js +1 -1
- package/esm/process/to_multiscales-shared.d.ts +3 -3
- package/esm/process/to_multiscales-shared.d.ts.map +1 -1
- package/esm/process/to_multiscales-shared.js +3 -3
- package/esm/process/to_multiscales-shared.js.map +1 -1
- package/esm/schemas/multiscales.d.ts +2 -1
- package/esm/schemas/multiscales.d.ts.map +1 -1
- package/esm/schemas/multiscales.js +3 -1
- package/esm/schemas/multiscales.js.map +1 -1
- package/esm/types/hcs.d.ts +10 -3
- package/esm/types/hcs.d.ts.map +1 -1
- package/esm/types/hcs.js +19 -6
- package/esm/types/hcs.js.map +1 -1
- package/esm/types/multiscales.d.ts +6 -3
- package/esm/types/multiscales.d.ts.map +1 -1
- package/esm/types/multiscales.js +3 -2
- package/esm/types/multiscales.js.map +1 -1
- package/esm/utils/codecs.d.ts +27 -0
- package/esm/utils/codecs.d.ts.map +1 -1
- package/esm/utils/codecs.js +84 -0
- package/esm/utils/codecs.js.map +1 -1
- package/esm/utils/compute_omero.d.ts +4 -4
- package/esm/utils/compute_omero.d.ts.map +1 -1
- package/esm/utils/compute_omero.js +3 -3
- package/esm/utils/compute_omero.js.map +1 -1
- package/esm/utils/factory.d.ts +3 -2
- package/esm/utils/factory.d.ts.map +1 -1
- package/esm/utils/factory.js +5 -3
- package/esm/utils/factory.js.map +1 -1
- package/esm/utils/from_zarr_attrs.d.ts.map +1 -1
- package/esm/utils/from_zarr_attrs.js +40 -0
- package/esm/utils/from_zarr_attrs.js.map +1 -1
- package/esm/utils/py_format.d.ts +18 -0
- package/esm/utils/py_format.d.ts.map +1 -0
- package/esm/utils/py_format.js +22 -0
- package/esm/utils/py_format.js.map +1 -0
- package/esm/utils/rfc4_validation.d.ts +8 -0
- package/esm/utils/rfc4_validation.d.ts.map +1 -1
- package/esm/utils/rfc4_validation.js +13 -2
- package/esm/utils/rfc4_validation.js.map +1 -1
- package/esm/utils/structural_validation.d.ts +379 -0
- package/esm/utils/structural_validation.d.ts.map +1 -0
- package/esm/utils/structural_validation.js +739 -0
- package/esm/utils/structural_validation.js.map +1 -0
- package/package.json +1 -1
package/esm/browser-mod.d.ts
CHANGED
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@@ -1,10 +1,10 @@
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export { config, setWorkerPoolSize } from "./config.js";
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export { type ChunkCache, fromNgffZarr, type FromNgffZarrOptions, type MemoryStore, } from "./io/from_ngff_zarr-browser.js";
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export { type ChunkCache, fromNgffZarr, type FromNgffZarrOptions, fromOmeZarr, type FromOmeZarrOptions, type MemoryStore, } from "./io/from_ngff_zarr-browser.js";
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export { itkImageToNgffImage, type ItkImageToNgffImageOptions, } from "./io/itk_image_to_ngff_image.js";
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export { dataTypeToComponentType, ngffImageToItkImage, type NgffImageToItkImageOptions, } from "./io/ngff_image_to_itk_image.js";
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export type { MemoryStoreToZipOptions } from "./io/rfc9_zip.js";
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export { getZipFileCompressionMethod, getZipFileList, memoryStoreToZip, orderFilesForRfc9, readOzxVersion, } from "./io/rfc9_zip.js";
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export { isOzxPath, toNgffZarr, type ToNgffZarrOptions, toNgffZarrOzx, type ToNgffZarrOzxOptions, } from "./io/to_ngff_zarr-browser.js";
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export { isOzxPath, toNgffZarr, type ToNgffZarrOptions, toNgffZarrOzx, type ToNgffZarrOzxOptions, toOmeZarr, type ToOmeZarrOptions, toOmeZarrOzx, type ToOmeZarrOzxOptions, } from "./io/to_ngff_zarr-browser.js";
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export * from "./process/to_multiscales-browser.js";
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export * from "./schemas/methods.js";
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export * from "./schemas/multiscales.js";
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@@ -17,14 +17,15 @@ export * from "./types/multiscales.js";
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export * from "./types/ngff_image.js";
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export * from "./types/units.js";
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export * from "./types/zarr_metadata.js";
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export type { ZarrCodec } from "./utils/codecs.js";
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export { bytesOnlyCodecs, defaultCodecs } from "./utils/codecs.js";
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export type { CodecName, ZarrCodec } from "./utils/codecs.js";
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export { AVAILABLE_CODECS, bytesOnlyCodecs, codecFromName, defaultCodecs, } from "./utils/codecs.js";
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export type { ComputeOmeroFromMultiscalesOptions, ComputeOmeroOptions, } from "./utils/compute_omero.js";
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export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
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export type { ChannelStatisticsAccumulator } from "./utils/compute_omero-shared.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 { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
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export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, createNgffMultiscales, } from "./utils/factory.js";
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export { getMethodMetadata } from "./utils/method_metadata.js";
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export { SpecRule, type ValidateOptions, validatePlate, validateStructural, validateWell, ValidationError, ValidationLevel, } from "./utils/structural_validation.js";
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export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
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export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
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//# sourceMappingURL=browser-mod.d.ts.map
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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":"AAQA,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAIxD,OAAO,EACL,KAAK,UAAU,EACf,YAAY,EACZ,KAAK,mBAAmB,EACxB,KAAK,WAAW,GACjB,MAAM,gCAAgC,CAAC;AAExC,OAAO,EACL,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,uBAAuB,EACvB,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC;AAEhE,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,SAAS,EACT,UAAU,EACV,KAAK,iBAAiB,EACtB,aAAa,EACb,KAAK,oBAAoB,
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{"version":3,"file":"browser-mod.d.ts","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAIxD,OAAO,EACL,KAAK,UAAU,EACf,YAAY,EACZ,KAAK,mBAAmB,EACxB,WAAW,EACX,KAAK,kBAAkB,EACvB,KAAK,WAAW,GACjB,MAAM,gCAAgC,CAAC;AAExC,OAAO,EACL,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,uBAAuB,EACvB,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC;AAEhE,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,SAAS,EACT,UAAU,EACV,KAAK,iBAAiB,EACtB,aAAa,EACb,KAAK,oBAAoB,EACzB,SAAS,EACT,KAAK,gBAAgB,EACrB,YAAY,EACZ,KAAK,mBAAmB,GACzB,MAAM,8BAA8B,CAAC;AAEtC,cAAc,qCAAqC,CAAC;AACpD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AACzC,YAAY,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAC9D,OAAO,EACL,gBAAgB,EAChB,eAAe,EACf,aAAa,EACb,aAAa,GACd,MAAM,mBAAmB,CAAC;AAC3B,YAAY,EACV,kCAAkC,EAClC,mBAAmB,GACpB,MAAM,0BAA0B,CAAC;AAElC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAClC,YAAY,EAAE,4BAA4B,EAAE,MAAM,iCAAiC,CAAC;AAEpF,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,QAAQ,EACR,KAAK,eAAe,EACpB,aAAa,EACb,kBAAkB,EAClB,YAAY,EACZ,eAAe,EACf,eAAe,GAChB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}
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package/esm/browser-mod.js
CHANGED
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// Browser-compatible I/O modules
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// Note: Uses browser-specific versions that don't import @zarrita/storage
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// (which contains Node.js-specific modules like node:fs, node:buffer, node:path)
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export { fromNgffZarr, } from "./io/from_ngff_zarr-browser.js";
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export { fromNgffZarr, fromOmeZarr, } from "./io/from_ngff_zarr-browser.js";
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// ITK-Wasm conversion utilities
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export { itkImageToNgffImage, } from "./io/itk_image_to_ngff_image.js";
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export { dataTypeToComponentType, ngffImageToItkImage, } from "./io/ngff_image_to_itk_image.js";
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// RFC-9 exports
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export { getZipFileCompressionMethod, getZipFileList, memoryStoreToZip, orderFilesForRfc9, readOzxVersion, } from "./io/rfc9_zip.js";
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export { isOzxPath, toNgffZarr, toNgffZarrOzx, } from "./io/to_ngff_zarr-browser.js";
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export { isOzxPath, toNgffZarr, toNgffZarrOzx, toOmeZarr, toOmeZarrOzx, } from "./io/to_ngff_zarr-browser.js";
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// Browser-compatible processing modules
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export * from "./process/to_multiscales-browser.js";
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export * from "./schemas/methods.js";
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export * from "./types/ngff_image.js";
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export * from "./types/units.js";
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export * from "./types/zarr_metadata.js";
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export { bytesOnlyCodecs, defaultCodecs } from "./utils/codecs.js";
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export { AVAILABLE_CODECS, bytesOnlyCodecs, codecFromName, defaultCodecs, } from "./utils/codecs.js";
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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 { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
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export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, createNgffMultiscales, } from "./utils/factory.js";
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export { getMethodMetadata } from "./utils/method_metadata.js";
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export { SpecRule, validatePlate, validateStructural, validateWell, ValidationError, ValidationLevel, } from "./utils/structural_validation.js";
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export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
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export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
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//# sourceMappingURL=browser-mod.js.map
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package/esm/browser-mod.js.map
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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;AAEzE,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AACxD,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EAEL,YAAY,
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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;AAEzE,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AACxD,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EAEL,YAAY,EAEZ,WAAW,GAGZ,MAAM,gCAAgC,CAAC;AACxC,gCAAgC;AAChC,OAAO,EACL,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,uBAAuB,EACvB,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC;AAEzC,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,SAAS,EACT,UAAU,EAEV,aAAa,EAEb,SAAS,EAET,YAAY,GAEb,MAAM,8BAA8B,CAAC;AACtC,wCAAwC;AACxC,cAAc,qCAAqC,CAAC;AACpD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,eAAe,EACf,aAAa,EACb,aAAa,GACd,MAAM,mBAAmB,CAAC;AAK3B,oCAAoC;AACpC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAElC,qEAAqE;AACrE,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,QAAQ,EAER,aAAa,EACb,kBAAkB,EAClB,YAAY,EACZ,eAAe,EACf,eAAe,GAChB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}
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1
|
import * as zarr from "zarrita";
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-
import {
|
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2
|
+
import { NgffMultiscales } from "../types/multiscales.js";
|
|
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3
|
export type { ChunkCache } from "../utils/worker_pool.js";
|
|
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|
-
export interface
|
|
4
|
+
export interface FromOmeZarrOptions {
|
|
5
5
|
/** Enable schema validation of OME-Zarr metadata. */
|
|
6
6
|
validate?: boolean;
|
|
7
7
|
/** Expected OME-Zarr version. */
|
|
@@ -16,12 +16,16 @@ export interface FromNgffZarrOptions {
|
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|
16
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|
*/
|
|
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17
|
cache?: import("../utils/worker_pool.js").ChunkCache;
|
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|
}
|
|
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|
+
/** @deprecated Use {@link FromOmeZarrOptions} instead. */
|
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|
+
export type FromNgffZarrOptions = FromOmeZarrOptions;
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|
export type MemoryStore = Map<string, Uint8Array>;
|
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/**
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* Browser-compatible version of
|
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* Browser-compatible version of fromOmeZarr.
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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
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|
+
export declare function fromOmeZarr(store: string | MemoryStore | zarr.FetchStore | zarr.Readable, options?: FromOmeZarrOptions): Promise<NgffMultiscales>;
|
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29
|
+
/** @deprecated Use {@link fromOmeZarr} instead. */
|
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30
|
+
export declare const fromNgffZarr: typeof fromOmeZarr;
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|
//# sourceMappingURL=from_ngff_zarr-browser.d.ts.map
|
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@@ -1 +1 @@
|
|
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1
|
-
{"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,
|
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1
|
+
{"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,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAM1D,YAAY,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAE1D,MAAM,WAAW,kBAAkB;IACjC,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,0DAA0D;AAC1D,MAAM,MAAM,mBAAmB,GAAG,kBAAkB,CAAC;AAErD,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD;;;;;GAKG;AACH,wBAAsB,WAAW,CAC/B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EAC7D,OAAO,GAAE,kBAAuB,GAC/B,OAAO,CAAC,eAAe,CAAC,CAmO1B;AAED,mDAAmD;AACnD,eAAO,MAAM,YAAY,oBAAc,CAAC"}
|
|
@@ -4,16 +4,16 @@
|
|
|
4
4
|
// (which contains Node.js-specific modules like node:fs, node:buffer, node:path)
|
|
5
5
|
import * as zarr from "zarrita";
|
|
6
6
|
import { MetadataSchema } from "../schemas/zarr_metadata.js";
|
|
7
|
-
import {
|
|
7
|
+
import { NgffMultiscales } from "../types/multiscales.js";
|
|
8
8
|
import { NgffImage } from "../types/ngff_image.js";
|
|
9
9
|
import { extractMethodMetadata } from "../utils/parse_metadata.js";
|
|
10
10
|
/**
|
|
11
|
-
* Browser-compatible version of
|
|
11
|
+
* Browser-compatible version of fromOmeZarr.
|
|
12
12
|
* Supports HTTP/HTTPS URLs, MemoryStore (Map), FetchStore, and any
|
|
13
13
|
* zarrita-compatible Readable store (e.g. TiffStore from @fideus-labs/fiff).
|
|
14
14
|
* Does NOT support local file paths (use the full version in Node.js/Deno).
|
|
15
15
|
*/
|
|
16
|
-
export async function
|
|
16
|
+
export async function fromOmeZarr(store, options = {}) {
|
|
17
17
|
const validate = options.validate ?? false;
|
|
18
18
|
const version = options.version;
|
|
19
19
|
try {
|
|
@@ -179,7 +179,7 @@ export async function fromNgffZarr(store, options = {}) {
|
|
|
179
179
|
if (methodMetadata) {
|
|
180
180
|
metadata.metadata = methodMetadata;
|
|
181
181
|
}
|
|
182
|
-
return new
|
|
182
|
+
return new NgffMultiscales({
|
|
183
183
|
images,
|
|
184
184
|
metadata,
|
|
185
185
|
scaleFactors: undefined,
|
|
@@ -191,4 +191,6 @@ export async function fromNgffZarr(store, options = {}) {
|
|
|
191
191
|
throw new Error(`Failed to read OME-Zarr: ${error instanceof Error ? error.message : String(error)}`);
|
|
192
192
|
}
|
|
193
193
|
}
|
|
194
|
+
/** @deprecated Use {@link fromOmeZarr} instead. */
|
|
195
|
+
export const fromNgffZarr = fromOmeZarr;
|
|
194
196
|
//# sourceMappingURL=from_ngff_zarr-browser.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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,
|
|
1
|
+
{"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,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAC1D,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAGnD,OAAO,EAAE,qBAAqB,EAAE,MAAM,4BAA4B,CAAC;AAyBnE;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,KAA6D,EAC7D,UAA8B,EAAE;IAEhC,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,eAAe,CAAC;YACzB,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,mDAAmD;AACnD,MAAM,CAAC,MAAM,YAAY,GAAG,WAAW,CAAC"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import * as zarr from "zarrita";
|
|
2
|
-
import {
|
|
2
|
+
import { NgffMultiscales } from "../types/multiscales.js";
|
|
3
3
|
export type { ChunkCache } from "../utils/worker_pool.js";
|
|
4
|
-
export interface
|
|
4
|
+
export interface FromOmeZarrOptions {
|
|
5
5
|
/** Enable schema validation of OME-Zarr metadata. */
|
|
6
6
|
validate?: boolean;
|
|
7
7
|
/** Expected OME-Zarr version. */
|
|
@@ -16,7 +16,11 @@ export interface FromNgffZarrOptions {
|
|
|
16
16
|
*/
|
|
17
17
|
cache?: import("../utils/worker_pool.js").ChunkCache;
|
|
18
18
|
}
|
|
19
|
+
/** @deprecated Use {@link FromOmeZarrOptions} instead. */
|
|
20
|
+
export type FromNgffZarrOptions = FromOmeZarrOptions;
|
|
19
21
|
export type MemoryStore = Map<string, Uint8Array>;
|
|
20
|
-
export declare function
|
|
22
|
+
export declare function fromOmeZarr(store: string | MemoryStore | zarr.FetchStore | zarr.Readable, options?: FromOmeZarrOptions): Promise<NgffMultiscales>;
|
|
23
|
+
/** @deprecated Use {@link fromOmeZarr} instead. */
|
|
24
|
+
export declare const fromNgffZarr: typeof fromOmeZarr;
|
|
21
25
|
export declare function readArrayData(storePath: string, arrayPath: string, selection?: (number | null)[]): Promise<unknown>;
|
|
22
26
|
//# 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;AAEhC,OAAO,EAAE,
|
|
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,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAY1D,YAAY,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAE1D,MAAM,WAAW,kBAAkB;IACjC,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,0DAA0D;AAC1D,MAAM,MAAM,mBAAmB,GAAG,kBAAkB,CAAC;AAErD,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD,wBAAsB,WAAW,CAE/B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EAC7D,OAAO,GAAE,kBAAuB,GAC/B,OAAO,CAAC,eAAe,CAAC,CAqI1B;AAED,mDAAmD;AACnD,eAAO,MAAM,YAAY,oBAAc,CAAC;AAExC,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
|
@@ -1,12 +1,12 @@
|
|
|
1
1
|
// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
|
|
2
2
|
// SPDX-License-Identifier: MIT
|
|
3
3
|
import * as zarr from "zarrita";
|
|
4
|
-
import {
|
|
4
|
+
import { NgffMultiscales } from "../types/multiscales.js";
|
|
5
5
|
import { NgffVersion } from "../types/supported_versions.js";
|
|
6
6
|
import { fromZarrAttrsV04, fromZarrAttrsV05, } from "../utils/from_zarr_attrs.js";
|
|
7
7
|
import { detectVersion, extractMethodMetadata, } from "../utils/parse_metadata.js";
|
|
8
8
|
import { zarrGet } from "../utils/worker_pool.js";
|
|
9
|
-
export async function
|
|
9
|
+
export async function fromOmeZarr(
|
|
10
10
|
// Also accepts FileSystemStore, ZipFileStore, or any zarrita Readable store
|
|
11
11
|
store, options = {}) {
|
|
12
12
|
const validate = options.validate ?? false;
|
|
@@ -102,7 +102,7 @@ store, options = {}) {
|
|
|
102
102
|
if (methodMetadata) {
|
|
103
103
|
metadata.metadata = methodMetadata;
|
|
104
104
|
}
|
|
105
|
-
return new
|
|
105
|
+
return new NgffMultiscales({
|
|
106
106
|
images,
|
|
107
107
|
metadata,
|
|
108
108
|
scaleFactors: undefined,
|
|
@@ -114,6 +114,8 @@ store, options = {}) {
|
|
|
114
114
|
throw new Error(`Failed to read OME-Zarr: ${error instanceof Error ? error.message : String(error)}`);
|
|
115
115
|
}
|
|
116
116
|
}
|
|
117
|
+
/** @deprecated Use {@link fromOmeZarr} instead. */
|
|
118
|
+
export const fromNgffZarr = fromOmeZarr;
|
|
117
119
|
export async function readArrayData(storePath, arrayPath, selection) {
|
|
118
120
|
try {
|
|
119
121
|
const store = new zarr.FetchStore(storePath);
|
|
@@ -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;AAEhC,OAAO,EAAE,
|
|
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,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAC1D,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;AAyBlD,MAAM,CAAC,KAAK,UAAU,WAAW;AAC/B,4EAA4E;AAC5E,KAA6D,EAC7D,UAA8B,EAAE;IAEhC,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,eAAe,CAAC;YACzB,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,mDAAmD;AACnD,MAAM,CAAC,MAAM,YAAY,GAAG,WAAW,CAAC;AAExC,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/io/hcs.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"hcs.d.ts","sourceRoot":"","sources":["../../src/io/hcs.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAiB,MAAM,iBAAiB,CAAC;
|
|
1
|
+
{"version":3,"file":"hcs.d.ts","sourceRoot":"","sources":["../../src/io/hcs.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAiB,MAAM,iBAAiB,CAAC;AAO/D,MAAM,WAAW,kBAAkB;IACjC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED,MAAM,WAAW,gBAAgB;IAE/B,gBAAgB,CAAC,EAAE,MAAM,CAAC;CAC3B;AAED;;GAEG;AACH,wBAAgB,WAAW,CACzB,KAAK,EAAE,MAAM,GAAG,MAAM,EACtB,OAAO,GAAE,kBAAuB,GAC/B,QAAQ,CAyCV;AAED;;GAEG;AACH,wBAAgB,SAAS,CACvB,KAAK,EAAE,QAAQ,EACf,KAAK,EAAE,MAAM,GAAG,MAAM,EACtB,QAAQ,GAAE,gBAAqB,GAC9B,IAAI,CAaN"}
|
package/esm/io/hcs.js
CHANGED
|
@@ -1,12 +1,10 @@
|
|
|
1
1
|
import { HCSPlate as HCSPlateClass } from "../types/hcs.js";
|
|
2
|
+
import { validatePlate, ValidationLevel, } from "../utils/structural_validation.js";
|
|
2
3
|
/**
|
|
3
4
|
* Read an HCS plate from an OME-Zarr NGFF store.
|
|
4
5
|
*/
|
|
5
6
|
export function fromHcsZarr(store, options = {}) {
|
|
6
7
|
const { validate = false, wellCacheSize, imageCacheSize } = options;
|
|
7
|
-
if (validate) {
|
|
8
|
-
console.warn("HCS validation not yet implemented");
|
|
9
|
-
}
|
|
10
8
|
if (typeof store !== "string") {
|
|
11
9
|
throw new Error("Non-string store types not yet supported");
|
|
12
10
|
}
|
|
@@ -26,11 +24,21 @@ export function fromHcsZarr(store, options = {}) {
|
|
|
26
24
|
field_count: 2,
|
|
27
25
|
name: "Test Plate",
|
|
28
26
|
};
|
|
27
|
+
if (validate) {
|
|
28
|
+
// Strict structural validation of the parsed plate, layered after the
|
|
29
|
+
// schema pass (schema first, then structural -- mirrors the image reader).
|
|
30
|
+
// Per-well image rules run lazily in HCSPlate.getWell, where each well's
|
|
31
|
+
// own metadata is loaded. These plate/well rules are version-agnostic and
|
|
32
|
+
// the HCS reader handles only v0.4/v0.5 plates, so -- unlike the image
|
|
33
|
+
// reader's structural pass -- no >=0.4 version gate is required.
|
|
34
|
+
validatePlate(plateMetadata, { level: ValidationLevel.Strict });
|
|
35
|
+
}
|
|
29
36
|
return new HCSPlateClass({
|
|
30
37
|
store,
|
|
31
38
|
metadata: plateMetadata,
|
|
32
39
|
wellCacheSize,
|
|
33
40
|
imageCacheSize,
|
|
41
|
+
validate,
|
|
34
42
|
});
|
|
35
43
|
}
|
|
36
44
|
/**
|
package/esm/io/hcs.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"hcs.js","sourceRoot":"","sources":["../../src/io/hcs.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,QAAQ,IAAI,aAAa,EAAE,MAAM,iBAAiB,CAAC;
|
|
1
|
+
{"version":3,"file":"hcs.js","sourceRoot":"","sources":["../../src/io/hcs.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,QAAQ,IAAI,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAC5D,OAAO,EACL,aAAa,EACb,eAAe,GAChB,MAAM,mCAAmC,CAAC;AAa3C;;GAEG;AACH,MAAM,UAAU,WAAW,CACzB,KAAsB,EACtB,UAA8B,EAAE;IAEhC,MAAM,EAAE,QAAQ,GAAG,KAAK,EAAE,aAAa,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC;IAEpE,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAC;IAC9D,CAAC;IAED,wCAAwC;IACxC,iFAAiF;IACjF,MAAM,aAAa,GAAkB;QACnC,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;QACvC,IAAI,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;QACpC,KAAK,EAAE;YACL,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;YAC5C,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;YAC5C,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;YAC5C,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;SAC7C;QACD,OAAO,EAAE,KAAK;QACd,YAAY,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,IAAI,EAAE,kBAAkB,EAAE,CAAC;QACnD,WAAW,EAAE,CAAC;QACd,IAAI,EAAE,YAAY;KACnB,CAAC;IAEF,IAAI,QAAQ,EAAE,CAAC;QACb,sEAAsE;QACtE,2EAA2E;QAC3E,yEAAyE;QACzE,0EAA0E;QAC1E,uEAAuE;QACvE,iEAAiE;QACjE,aAAa,CAAC,aAAa,EAAE,EAAE,KAAK,EAAE,eAAe,CAAC,MAAM,EAAE,CAAC,CAAC;IAClE,CAAC;IAED,OAAO,IAAI,aAAa,CAAC;QACvB,KAAK;QACL,QAAQ,EAAE,aAAa;QACvB,aAAa;QACb,cAAc;QACd,QAAQ;KACT,CAAC,CAAC;AACL,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,SAAS,CACvB,KAAe,EACf,KAAsB,EACtB,WAA6B,EAAE;IAE/B,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAC;IAC9D,CAAC;IAED,8BAA8B;IAC9B,OAAO,CAAC,GAAG,CAAC,2CAA2C,KAAK,EAAE,CAAC,CAAC;IAChE,OAAO,CAAC,GAAG,CAAC,UAAU,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;IACpC,OAAO,CAAC,GAAG,CAAC,UAAU,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5C,OAAO,CAAC,GAAG,CAAC,SAAS,KAAK,CAAC,IAAI,CAAC,MAAM,cAAc,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5E,IAAI,KAAK,CAAC,YAAY,EAAE,CAAC;QACvB,OAAO,CAAC,GAAG,CAAC,iBAAiB,KAAK,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5D,CAAC;AACH,CAAC"}
|
|
@@ -1,17 +1,28 @@
|
|
|
1
1
|
import * as zarr from "zarrita";
|
|
2
|
-
import type {
|
|
2
|
+
import type { NgffMultiscales } from "../types/multiscales.js";
|
|
3
|
+
import type { ZarrCodec } from "../utils/codecs.js";
|
|
3
4
|
import type { MemoryStore } from "./from_ngff_zarr-browser.js";
|
|
4
5
|
export { isOzxPath } from "./rfc9_zip.js";
|
|
5
|
-
export interface
|
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+
export interface ToOmeZarrOptions {
|
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7
|
overwrite?: boolean;
|
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7
8
|
version?: "0.4" | "0.5";
|
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9
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chunksPerShard?: number | number[] | Record<string, number>;
|
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10
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+
/** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
|
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11
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+
enabledRfcs?: number[];
|
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12
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+
/**
|
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13
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+
* Custom codec pipeline for array compression. When omitted the default
|
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14
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+
* ``blosc(zstd)`` pipeline from {@link defaultCodecs} is used. Use
|
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+
* {@link codecFromName} or {@link bytesOnlyCodecs} to build common pipelines.
|
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+
*/
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+
codecs?: ZarrCodec[];
|
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9
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}
|
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+
/** @deprecated Use {@link ToOmeZarrOptions} instead. */
|
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+
export type ToNgffZarrOptions = ToOmeZarrOptions;
|
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|
/**
|
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11
22
|
* Options for writing to .ozx (RFC-9) format.
|
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* Note: chunksPerShard is NOT supported for .ozx files and will throw an error.
|
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|
*/
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|
-
export interface
|
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|
+
export interface ToOmeZarrOzxOptions {
|
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26
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/** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
|
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27
|
enabledRfcs?: number[] | undefined;
|
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/**
|
|
@@ -23,12 +34,16 @@ export interface ToNgffZarrOzxOptions {
|
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23
34
|
*/
|
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24
35
|
onProgress?: ((completedChunks: number, totalChunks: number) => void) | undefined;
|
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25
36
|
}
|
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37
|
+
/** @deprecated Use {@link ToOmeZarrOzxOptions} instead. */
|
|
38
|
+
export type ToNgffZarrOzxOptions = ToOmeZarrOzxOptions;
|
|
26
39
|
/**
|
|
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|
-
* Browser-compatible version of
|
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40
|
+
* Browser-compatible version of toOmeZarr.
|
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28
41
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* Only supports MemoryStore (Map) for writing.
|
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|
* Does NOT support local file paths or HTTP URLs (use the full version in Node.js/Deno).
|
|
30
43
|
*/
|
|
31
|
-
export declare function
|
|
44
|
+
export declare function toOmeZarr(store: string | MemoryStore | zarr.FetchStore, multiscales: NgffMultiscales, options?: ToOmeZarrOptions): Promise<void>;
|
|
45
|
+
/** @deprecated Use {@link toOmeZarr} instead. */
|
|
46
|
+
export declare const toNgffZarr: typeof toOmeZarr;
|
|
32
47
|
/**
|
|
33
48
|
* Create OME-Zarr .ozx ZIP data (RFC-9) - Browser version.
|
|
34
49
|
*
|
|
@@ -39,11 +54,13 @@ export declare function toNgffZarr(store: string | MemoryStore | zarr.FetchStore
|
|
|
39
54
|
* Note: Sharding is NOT supported because zarrita does not currently
|
|
40
55
|
* support writing shards. If you need sharding, use the Python implementation.
|
|
41
56
|
*
|
|
42
|
-
* @param multiscales -
|
|
57
|
+
* @param multiscales - NgffMultiscales data to write
|
|
43
58
|
* @param options - Options for writing
|
|
44
59
|
* @returns ZIP file data as Uint8Array
|
|
45
60
|
*
|
|
46
61
|
* @see https://ngff.openmicroscopy.org/rfc/9/index.html
|
|
47
62
|
*/
|
|
48
|
-
export declare function
|
|
63
|
+
export declare function toOmeZarrOzx(multiscales: NgffMultiscales, _options?: ToOmeZarrOzxOptions): Promise<Uint8Array>;
|
|
64
|
+
/** @deprecated Use {@link toOmeZarrOzx} instead. */
|
|
65
|
+
export declare const toNgffZarrOzx: typeof toOmeZarrOzx;
|
|
49
66
|
//# sourceMappingURL=to_ngff_zarr-browser.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"to_ngff_zarr-browser.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr-browser.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,KAAK,EAAE,
|
|
1
|
+
{"version":3,"file":"to_ngff_zarr-browser.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr-browser.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAE/D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAGpD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAC;AAO/D,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAE1C,MAAM,WAAW,gBAAgB;IAC/B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC5D,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB;;;;OAIG;IACH,MAAM,CAAC,EAAE,SAAS,EAAE,CAAC;CACtB;AAED,wDAAwD;AACxD,MAAM,MAAM,iBAAiB,GAAG,gBAAgB,CAAC;AAEjD;;;GAGG;AACH,MAAM,WAAW,mBAAmB;IAClC,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACnC;;;;;;OAMG;IACH,UAAU,CAAC,EACP,CAAC,CAAC,eAAe,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,KAAK,IAAI,CAAC,GACxD,SAAS,CAAC;CACf;AAED,2DAA2D;AAC3D,MAAM,MAAM,oBAAoB,GAAG,mBAAmB,CAAC;AAEvD;;;;GAIG;AACH,wBAAsB,SAAS,CAC7B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,eAAe,EAC5B,OAAO,GAAE,gBAAqB,GAC7B,OAAO,CAAC,IAAI,CAAC,CAkGf;AAED,iDAAiD;AACjD,eAAO,MAAM,UAAU,kBAAY,CAAC;AA2VpC;;;;;;;;;;;;;;;GAeG;AACH,wBAAsB,YAAY,CAChC,WAAW,EAAE,eAAe,EAC5B,QAAQ,GAAE,mBAAwB,GACjC,OAAO,CAAC,UAAU,CAAC,CAmBrB;AAED,oDAAoD;AACpD,eAAO,MAAM,aAAa,qBAAe,CAAC"}
|
|
@@ -6,16 +6,17 @@ import * as zarr from "zarrita";
|
|
|
6
6
|
import { defaultCodecs } from "../utils/codecs.js";
|
|
7
7
|
import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
|
|
8
8
|
import { memoryStoreToZip } from "./rfc9_zip.js";
|
|
9
|
-
import {
|
|
9
|
+
import { processAxesForRfcs, writeNgffMultiscalesToMemoryStore, } from "./to_ngff_zarr_ozx_common.js";
|
|
10
10
|
export { isOzxPath } from "./rfc9_zip.js";
|
|
11
11
|
/**
|
|
12
|
-
* Browser-compatible version of
|
|
12
|
+
* Browser-compatible version of toOmeZarr.
|
|
13
13
|
* Only supports MemoryStore (Map) for writing.
|
|
14
14
|
* Does NOT support local file paths or HTTP URLs (use the full version in Node.js/Deno).
|
|
15
15
|
*/
|
|
16
|
-
export async function
|
|
16
|
+
export async function toOmeZarr(store, multiscales, options = {}) {
|
|
17
17
|
const _overwrite = options.overwrite ?? true;
|
|
18
18
|
const _version = options.version ?? "0.4";
|
|
19
|
+
const enabledRfcs = options.enabledRfcs;
|
|
19
20
|
try {
|
|
20
21
|
// Determine the appropriate store type based on the path
|
|
21
22
|
let _resolvedStore;
|
|
@@ -34,11 +35,13 @@ export async function toNgffZarr(store, multiscales, options = {}) {
|
|
|
34
35
|
}
|
|
35
36
|
// Create root location and group with zarrita v0.5.2 API
|
|
36
37
|
const root = zarr.root(_resolvedStore);
|
|
38
|
+
// Process axes - filter orientation based on enabledRfcs
|
|
39
|
+
const processedAxes = processAxesForRfcs(multiscales.metadata.axes, enabledRfcs);
|
|
37
40
|
// Prepare multiscales metadata
|
|
38
41
|
const multiscalesMetadata = {
|
|
39
42
|
version: _version,
|
|
40
43
|
name: multiscales.metadata.name,
|
|
41
|
-
axes:
|
|
44
|
+
axes: processedAxes,
|
|
42
45
|
datasets: multiscales.metadata.datasets,
|
|
43
46
|
...(multiscales.metadata.coordinateTransformations && {
|
|
44
47
|
coordinateTransformations: multiscales.metadata.coordinateTransformations,
|
|
@@ -77,13 +80,16 @@ export async function toNgffZarr(store, multiscales, options = {}) {
|
|
|
77
80
|
if (!dataset) {
|
|
78
81
|
throw new Error(`No dataset configuration found for image ${i}`);
|
|
79
82
|
}
|
|
80
|
-
await _writeImage(rootGroup, image, dataset.path
|
|
83
|
+
await _writeImage(rootGroup, image, dataset.path, undefined, // onProgress
|
|
84
|
+
options.codecs);
|
|
81
85
|
}
|
|
82
86
|
}
|
|
83
87
|
catch (error) {
|
|
84
88
|
throw new Error(`Failed to write OME-Zarr: ${error instanceof Error ? error.message : String(error)}`);
|
|
85
89
|
}
|
|
86
90
|
}
|
|
91
|
+
/** @deprecated Use {@link toOmeZarr} instead. */
|
|
92
|
+
export const toNgffZarr = toOmeZarr;
|
|
87
93
|
function _convertDtypeToZarrType(dtype) {
|
|
88
94
|
// Map common numpy/LazyArray dtypes to zarrita data types
|
|
89
95
|
const dtypeMap = {
|
|
@@ -141,7 +147,7 @@ function getTypedArrayConstructor(dtype) {
|
|
|
141
147
|
throw new Error(`Unsupported data type for typed array: ${dtype}`);
|
|
142
148
|
}
|
|
143
149
|
}
|
|
144
|
-
async function _writeImage(group, image, arrayPath, onProgress) {
|
|
150
|
+
async function _writeImage(group, image, arrayPath, onProgress, codecs) {
|
|
145
151
|
try {
|
|
146
152
|
const chunks = getChunksFromImage(image);
|
|
147
153
|
// Convert LazyArray dtype to zarrita DataType
|
|
@@ -154,7 +160,7 @@ async function _writeImage(group, image, arrayPath, onProgress) {
|
|
|
154
160
|
data_type: zarrDataType,
|
|
155
161
|
chunk_shape: chunks,
|
|
156
162
|
fill_value: 0,
|
|
157
|
-
codecs: defaultCodecs(zarrDataType),
|
|
163
|
+
codecs: codecs ?? defaultCodecs(zarrDataType),
|
|
158
164
|
});
|
|
159
165
|
await _writeArrayData(zarrArray, image, onProgress);
|
|
160
166
|
}
|
|
@@ -338,20 +344,22 @@ function calculateChunkStride(chunkShape) {
|
|
|
338
344
|
* Note: Sharding is NOT supported because zarrita does not currently
|
|
339
345
|
* support writing shards. If you need sharding, use the Python implementation.
|
|
340
346
|
*
|
|
341
|
-
* @param multiscales -
|
|
347
|
+
* @param multiscales - NgffMultiscales data to write
|
|
342
348
|
* @param options - Options for writing
|
|
343
349
|
* @returns ZIP file data as Uint8Array
|
|
344
350
|
*
|
|
345
351
|
* @see https://ngff.openmicroscopy.org/rfc/9/index.html
|
|
346
352
|
*/
|
|
347
|
-
export async function
|
|
353
|
+
export async function toOmeZarrOzx(multiscales, _options = {}) {
|
|
348
354
|
const enabledRfcs = _options.enabledRfcs;
|
|
349
355
|
// Create a memory store to hold the zarr data
|
|
350
356
|
const memoryStore = new Map();
|
|
351
357
|
// Use the shared write function
|
|
352
|
-
await
|
|
358
|
+
await writeNgffMultiscalesToMemoryStore(memoryStore, multiscales, enabledRfcs, _writeImage, _options.onProgress ?? null);
|
|
353
359
|
// Convert the memory store to ZIP data
|
|
354
360
|
const zipData = memoryStoreToZip(memoryStore, { version: "0.5" });
|
|
355
361
|
return zipData;
|
|
356
362
|
}
|
|
363
|
+
/** @deprecated Use {@link toOmeZarrOzx} instead. */
|
|
364
|
+
export const toNgffZarrOzx = toOmeZarrOzx;
|
|
357
365
|
//# sourceMappingURL=to_ngff_zarr-browser.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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