npm - @fideus-labs/ngff-zarr - Versions diffs - 0.7.2 → 0.7.4 - Mend

@fideus-labs/ngff-zarr 0.7.2 → 0.7.4

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.

Files changed (36) hide show

package/esm/browser-mod.d.ts +1 -1
package/esm/browser-mod.d.ts.map +1 -1
package/esm/browser-mod.js.map +1 -1
package/esm/io/from_ngff_zarr-browser.d.ts +12 -0
package/esm/io/from_ngff_zarr-browser.d.ts.map +1 -1
package/esm/io/from_ngff_zarr-browser.js.map +1 -1
package/esm/io/from_ngff_zarr.d.ts +12 -0
package/esm/io/from_ngff_zarr.d.ts.map +1 -1
package/esm/io/from_ngff_zarr.js.map +1 -1
package/esm/io/itk_image_to_ngff_image.js +2 -2
package/esm/io/itk_image_to_ngff_image.js.map +1 -1
package/esm/io/ngff_image_to_itk_image.js +3 -3
package/esm/io/ngff_image_to_itk_image.js.map +1 -1
package/esm/io/to_ngff_image.js +2 -2
package/esm/io/to_ngff_image.js.map +1 -1
package/esm/io/to_ngff_zarr-browser.js +2 -2
package/esm/io/to_ngff_zarr-browser.js.map +1 -1
package/esm/io/to_ngff_zarr.js +2 -2
package/esm/io/to_ngff_zarr.js.map +1 -1
package/esm/methods/itkwasm-browser.js +13 -13
package/esm/methods/itkwasm-browser.js.map +1 -1
package/esm/methods/itkwasm-node.js +13 -13
package/esm/methods/itkwasm-node.js.map +1 -1
package/esm/methods/itkwasm-shared.js +2 -2
package/esm/methods/itkwasm-shared.js.map +1 -1
package/esm/utils/codecs.d.ts +34 -13
package/esm/utils/codecs.d.ts.map +1 -1
package/esm/utils/codecs.js +46 -8
package/esm/utils/codecs.js.map +1 -1
package/esm/utils/compute_omero-browser.js +17 -1
package/esm/utils/factory.js +2 -2
package/esm/utils/factory.js.map +1 -1
package/esm/utils/worker_pool.d.ts +1 -1
package/esm/utils/worker_pool.d.ts.map +1 -1
package/esm/utils/worker_pool.js.map +1 -1
package/package.json +2 -2

package/esm/browser-mod.d.ts CHANGED Viewed

@@ -17,7 +17,7 @@ export type { ComputeOmeroFromMultiscalesOptions, ComputeOmeroOptions, } from ".
 export { buildOmeroFromAccumulators, computeChannelStatistics, createAccumulator, extractChannel, finalizeStatistics, QUANTILE_SAMPLE_SIZE, updateAccumulator, validateQuantiles, } from "./utils/compute_omero-shared.js";
 export type { ChannelStatisticsAccumulator } from "./utils/compute_omero-shared.js";
 export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
-export { fromNgffZarr, type FromNgffZarrOptions, type MemoryStore, } from "./io/from_ngff_zarr-browser.js";
+export { type ChunkCache, fromNgffZarr, type FromNgffZarrOptions, type MemoryStore, } from "./io/from_ngff_zarr-browser.js";
 export { isOzxPath, toNgffZarr, type ToNgffZarrOptions, toNgffZarrOzx, type ToNgffZarrOzxOptions, } from "./io/to_ngff_zarr-browser.js";
 export { getZipFileCompressionMethod, getZipFileList, memoryStoreToZip, orderFilesForRfc9, readOzxVersion, } from "./io/rfc9_zip.js";
 export type { MemoryStoreToZipOptions } from "./io/rfc9_zip.js";

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package/esm/browser-mod.js.map CHANGED Viewed

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package/esm/io/from_ngff_zarr-browser.d.ts CHANGED Viewed

@@ -1,8 +1,20 @@
 import * as zarr from "zarrita";
 import { Multiscales } from "../types/multiscales.js";
+export type { ChunkCache } from "../utils/worker_pool.js";
 export interface FromNgffZarrOptions {
+    /** Enable schema validation of OME-Zarr metadata. */
     validate?: boolean;
+    /** Expected OME-Zarr version. */
     version?: "0.4" | "0.5";
+    /**
+     * Optional decoded-chunk cache passed to `zarrGet` calls.
+     *
+     * Any object with `get(key)` and `set(key, value)` works — a plain `Map`
+     * is the simplest option. For bounded memory use an LRU cache.
+     *
+     * @see {@link https://github.com/fideus-labs/worker-pool/tree/main/fizarrita#chunk-caching}
+     */
+    cache?: import("../utils/worker_pool.js").ChunkCache;
 }
 export type MemoryStore = Map<string, Uint8Array>;
 /**

package/esm/io/from_ngff_zarr-browser.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/io/from_ngff_zarr-browser.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/esm/io/from_ngff_zarr.d.ts CHANGED Viewed

@@ -1,8 +1,20 @@
 import * as zarr from "zarrita";
 import { Multiscales } from "../types/multiscales.js";
+export type { ChunkCache } from "../utils/worker_pool.js";
 export interface FromNgffZarrOptions {
+    /** Enable schema validation of OME-Zarr metadata. */
     validate?: boolean;
+    /** Expected OME-Zarr version. */
     version?: "0.4" | "0.5";
+    /**
+     * Optional decoded-chunk cache passed to `zarrGet` calls.
+     *
+     * Any object with `get(key)` and `set(key, value)` works — a plain `Map`
+     * is the simplest option. For bounded memory use an LRU cache.
+     *
+     * @see {@link https://github.com/fideus-labs/worker-pool/tree/main/fizarrita#chunk-caching}
+     */
+    cache?: import("../utils/worker_pool.js").ChunkCache;
 }
 export type MemoryStore = Map<string, Uint8Array>;
 export declare function fromNgffZarr(store: string | MemoryStore | zarr.FetchStore, options?: FromNgffZarrOptions): Promise<Multiscales>;

package/esm/io/from_ngff_zarr.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/io/from_ngff_zarr.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/io/itk_image_to_ngff_image.js CHANGED Viewed

@@ -4,7 +4,7 @@
  * Convert ITK-Wasm Image to NgffImage
  */
 import * as zarr from "zarrita";
-import { DEFAULT_CODECS } from "../utils/codecs.js";
+import { defaultCodecs } from "../utils/codecs.js";
 import { NgffImage } from "../types/ngff_image.js";
 import { itkLpsToAnatomicalOrientation } from "../types/rfc4.js";
 import { zarrSet } from "../utils/worker_pool.js";
@@ -91,7 +91,7 @@ export async function itkImageToNgffImage(itkImage, options = {}) {
         chunk_shape: chunkShape,
         data_type: imageType.componentType,
         fill_value: 0,
-        codecs: [...DEFAULT_CODECS],
+        codecs: defaultCodecs(imageType.componentType),
     });
     // Write the ITK-Wasm data to the zarr array
     // We use zarrita's set function to write the entire data efficiently

package/esm/io/itk_image_to_ngff_image.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/io/ngff_image_to_itk_image.js CHANGED Viewed

@@ -4,7 +4,7 @@
  * Convert NgffImage to ITK-Wasm Image
  */
 import * as zarr from "zarrita";
-import { DEFAULT_CODECS } from "../utils/codecs.js";
+import { defaultCodecs } from "../utils/codecs.js";
 import { NgffImage } from "../types/ngff_image.js";
 import { zarrGet, zarrSet } from "../utils/worker_pool.js";
 /**
@@ -99,7 +99,7 @@ export async function ngffImageToItkImage(ngffImage, options = {}) {
             chunk_shape: chunkShape,
             data_type: workingImage.data.dtype,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(workingImage.data.dtype),
         });
         // Write the slice data
         const fullSelection = new Array(newShape.length).fill(null);
@@ -139,7 +139,7 @@ export async function ngffImageToItkImage(ngffImage, options = {}) {
             chunk_shape: chunkShape,
             data_type: workingImage.data.dtype,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(workingImage.data.dtype),
         });
         // Write the slice data
         const fullSelection = new Array(newShape.length).fill(null);

package/esm/io/ngff_image_to_itk_image.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/io/to_ngff_image.js CHANGED Viewed

@@ -1,5 +1,5 @@
 import * as zarr from "zarrita";
-import { DEFAULT_CODECS } from "../utils/codecs.js";
+import { defaultCodecs } from "../utils/codecs.js";
 import { NgffImage } from "../types/ngff_image.js";
 import { zarrSet } from "../utils/worker_pool.js";
 /**
@@ -91,7 +91,7 @@ export async function toNgffImage(data, options = {}) {
         chunk_shape: chunkShape,
         data_type: "float32",
         fill_value: 0,
-        codecs: [...DEFAULT_CODECS],
+        codecs: defaultCodecs("float32"),
     });
     // Write data to zarr array
     await zarrSet(zarrArray, [], {

package/esm/io/to_ngff_image.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/io/to_ngff_zarr-browser.js CHANGED Viewed

@@ -4,7 +4,7 @@
 // (which contains Node.js-specific modules like node:fs, node:buffer, node:path)
 import * as zarr from "zarrita";
 import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
-import { DEFAULT_CODECS } from "../utils/codecs.js";
+import { defaultCodecs } from "../utils/codecs.js";
 import { memoryStoreToZip } from "./rfc9_zip.js";
 import { writeMultiscalesToMemoryStore } from "./to_ngff_zarr_ozx_common.js";
 export { isOzxPath } from "./rfc9_zip.js";
@@ -154,7 +154,7 @@ async function _writeImage(group, image, arrayPath) {
             data_type: zarrDataType,
             chunk_shape: chunks,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(zarrDataType),
         });
         await _writeArrayData(zarrArray, image);
     }

package/esm/io/to_ngff_zarr-browser.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/io/to_ngff_zarr.js CHANGED Viewed

@@ -2,7 +2,7 @@
 // SPDX-License-Identifier: MIT
 import * as zarr from "zarrita";
 import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
-import { DEFAULT_CODECS } from "../utils/codecs.js";
+import { defaultCodecs } from "../utils/codecs.js";
 import { isOzxPath, memoryStoreToZip } from "./rfc9_zip.js";
 import { processAxesForRfcs, writeMultiscalesToMemoryStore, } from "./to_ngff_zarr_ozx_common.js";
 /**
@@ -205,7 +205,7 @@ async function _writeImage(group, image, arrayPath) {
             data_type: zarrDataType,
             chunk_shape: chunks,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(zarrDataType),
         });
         await _writeArrayData(zarrArray, image);
     }

package/esm/io/to_ngff_zarr.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/methods/itkwasm-browser.js CHANGED Viewed

@@ -7,7 +7,7 @@
 import { downsample, downsampleBinShrink, downsampleLabelImage, } from "@itk-wasm/downsample";
 import * as zarr from "zarrita";
 import { zarrGet, zarrSet } from "../utils/worker_pool.js";
-import { DEFAULT_CODECS } from "../utils/codecs.js";
+import { defaultCodecs } from "../utils/codecs.js";
 import { NgffImage } from "../types/ngff_image.js";
 import { dimScaleFactors, itkImageToZarr, MAX_VECTOR_COMPONENTS, nextScaleMetadata, SPATIAL_DIMS, updatePreviousDimFactors, zarrToItkImage, } from "./itkwasm-shared.js";
 /**
@@ -62,7 +62,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: [...DEFAULT_CODECS],
+                codecs: defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -101,7 +101,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let t = 0; t < tSize; t++) {
@@ -154,7 +154,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: [...DEFAULT_CODECS],
+                codecs: defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -193,7 +193,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let c = 0; c < cSize; c++) {
@@ -278,7 +278,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: [...DEFAULT_CODECS],
+                codecs: defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -317,7 +317,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let t = 0; t < tSize; t++) {
@@ -370,7 +370,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: [...DEFAULT_CODECS],
+                codecs: defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -409,7 +409,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let c = 0; c < cSize; c++) {
@@ -491,7 +491,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: [...DEFAULT_CODECS],
+                codecs: defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -530,7 +530,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let t = 0; t < tSize; t++) {
@@ -583,7 +583,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: [...DEFAULT_CODECS],
+                codecs: defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -622,7 +622,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: [...DEFAULT_CODECS],
+            codecs: defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let c = 0; c < cSize; c++) {