@fideus-labs/ngff-zarr 0.10.0 → 0.12.0

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.
Files changed (59) hide show
  1. package/esm/browser-mod.d.ts +23 -20
  2. package/esm/browser-mod.d.ts.map +1 -1
  3. package/esm/browser-mod.js +24 -22
  4. package/esm/browser-mod.js.map +1 -1
  5. package/esm/io/itk_image_to_ngff_image.d.ts.map +1 -1
  6. package/esm/io/itk_image_to_ngff_image.js +63 -6
  7. package/esm/io/itk_image_to_ngff_image.js.map +1 -1
  8. package/esm/io/to_ngff_zarr-browser.d.ts +8 -0
  9. package/esm/io/to_ngff_zarr-browser.d.ts.map +1 -1
  10. package/esm/io/to_ngff_zarr-browser.js +6 -6
  11. package/esm/io/to_ngff_zarr-browser.js.map +1 -1
  12. package/esm/io/to_ngff_zarr.d.ts +8 -0
  13. package/esm/io/to_ngff_zarr.d.ts.map +1 -1
  14. package/esm/io/to_ngff_zarr.js +8 -8
  15. package/esm/io/to_ngff_zarr.js.map +1 -1
  16. package/esm/io/to_ngff_zarr_ozx_common.d.ts +3 -1
  17. package/esm/io/to_ngff_zarr_ozx_common.d.ts.map +1 -1
  18. package/esm/io/to_ngff_zarr_ozx_common.js +47 -2
  19. package/esm/io/to_ngff_zarr_ozx_common.js.map +1 -1
  20. package/esm/methods/itkwasm-browser.d.ts +2 -1
  21. package/esm/methods/itkwasm-browser.d.ts.map +1 -1
  22. package/esm/methods/itkwasm-browser.js +30 -30
  23. package/esm/methods/itkwasm-browser.js.map +1 -1
  24. package/esm/methods/itkwasm-node.d.ts +2 -1
  25. package/esm/methods/itkwasm-node.d.ts.map +1 -1
  26. package/esm/methods/itkwasm-node.js +30 -30
  27. package/esm/methods/itkwasm-node.js.map +1 -1
  28. package/esm/methods/itkwasm-shared.d.ts +3 -2
  29. package/esm/methods/itkwasm-shared.d.ts.map +1 -1
  30. package/esm/methods/itkwasm-shared.js +12 -2
  31. package/esm/methods/itkwasm-shared.js.map +1 -1
  32. package/esm/mod.d.ts +24 -23
  33. package/esm/mod.d.ts.map +1 -1
  34. package/esm/mod.js +22 -21
  35. package/esm/mod.js.map +1 -1
  36. package/esm/process/to_multiscales-shared.d.ts +16 -3
  37. package/esm/process/to_multiscales-shared.d.ts.map +1 -1
  38. package/esm/process/to_multiscales-shared.js +7 -2
  39. package/esm/process/to_multiscales-shared.js.map +1 -1
  40. package/esm/types/rfc4.d.ts +26 -0
  41. package/esm/types/rfc4.d.ts.map +1 -1
  42. package/esm/types/rfc4.js +84 -0
  43. package/esm/types/rfc4.js.map +1 -1
  44. package/esm/utils/codecs.d.ts +20 -0
  45. package/esm/utils/codecs.d.ts.map +1 -1
  46. package/esm/utils/codecs.js +12 -0
  47. package/esm/utils/codecs.js.map +1 -1
  48. package/esm/utils/compute_omero-shared.d.ts +7 -0
  49. package/esm/utils/compute_omero-shared.d.ts.map +1 -1
  50. package/esm/utils/compute_omero-shared.js.map +1 -1
  51. package/esm/utils/compute_omero.d.ts +1 -1
  52. package/esm/utils/compute_omero.d.ts.map +1 -1
  53. package/esm/utils/compute_omero.js +7 -63
  54. package/esm/utils/compute_omero.js.map +1 -1
  55. package/esm/utils/worker_pool.d.ts +15 -1
  56. package/esm/utils/worker_pool.d.ts.map +1 -1
  57. package/esm/utils/worker_pool.js +7 -18
  58. package/esm/utils/worker_pool.js.map +1 -1
  59. package/package.json +1 -1
package/esm/io/to_ngff_zarr_ozx_common.js CHANGED
@@ -73,6 +73,18 @@ export function prepareRfc9Metadata(multiscales, enabledRfcs) {
73
73
  }),
74
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  };
75
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  }
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+ /**
77
+ * Get chunks from an NgffImage, falling back to default chunk size if not specified.
78
+ *
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+ * @param image - NgffImage to get chunks from
80
+ * @returns Array of chunk sizes for each dimension
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+ */
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+ function getChunksFromImage(image) {
83
+ if (image.data.chunks && image.data.chunks.length > 0) {
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+ return image.data.chunks;
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+ }
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+ return image.data.shape.map((s) => Math.min(s, 1024));
87
+ }
76
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  /**
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  * Create root group attributes for RFC-9 export.
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  *
@@ -102,8 +114,10 @@ export function createRfc9RootAttributes(multiscalesMetadata, multiscales) {
102
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  * @param multiscales - Multiscales data to write
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  * @param enabledRfcs - Optional list of RFC numbers to enable
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  * @param writeImage - Function to write individual images
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+ * @param onProgress - Optional progress callback for cumulative chunk
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+ * progress across all scale levels
105
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  */
106
- export async function writeMultiscalesToMemoryStore(store, multiscales, enabledRfcs, writeImage) {
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+ export async function writeMultiscalesToMemoryStore(store, multiscales, enabledRfcs, writeImage, onProgress) {
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  // Validate version
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  validateRfc9Version(multiscales);
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  // Create root location and group with zarrita API
@@ -113,14 +127,45 @@ export async function writeMultiscalesToMemoryStore(store, multiscales, enabledR
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  // Create root attributes
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  const attributes = createRfc9RootAttributes(multiscalesMetadata, multiscales);
115
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  const rootGroup = await zarr.create(root, { attributes });
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+ // Pre-calculate total chunk count across all images for cumulative progress
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+ let totalChunks = 0;
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+ if (onProgress) {
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+ for (const image of multiscales.images) {
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+ const shape = image.data.shape;
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+ const chunks = getChunksFromImage(image);
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+ let imageChunks = 1;
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+ for (let d = 0; d < shape.length; d++) {
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+ imageChunks *= Math.ceil(shape[d] / chunks[d]);
139
+ }
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+ totalChunks += imageChunks;
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+ }
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+ }
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  // Write each image in the multiscales
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+ let completedChunks = 0;
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  for (let i = 0; i < multiscales.images.length; i++) {
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  const image = multiscales.images[i];
119
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  const dataset = multiscales.metadata.datasets[i];
120
148
  if (!dataset) {
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  throw new Error(`No dataset configuration found for image ${i}`);
122
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  }
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- await writeImage(rootGroup, image, dataset.path);
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+ // Create a per-image progress wrapper that reports cumulative progress
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+ const imageOffset = completedChunks;
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+ const imageProgress = onProgress
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+ ? (completed, _imageTotal) => {
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+ onProgress(imageOffset + completed, totalChunks);
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+ }
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+ : null;
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+ await writeImage(rootGroup, image, dataset.path, imageProgress);
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+ // Update cumulative offset for next image
160
+ if (onProgress) {
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+ const shape = image.data.shape;
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+ const chunks = getChunksFromImage(image);
163
+ let imageChunkCount = 1;
164
+ for (let d = 0; d < shape.length; d++) {
165
+ imageChunkCount *= Math.ceil(shape[d] / chunks[d]);
166
+ }
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+ completedChunks += imageChunkCount;
168
+ }
124
169
  }
125
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  }
126
171
  //# sourceMappingURL=to_ngff_zarr_ozx_common.js.map
package/esm/io/to_ngff_zarr_ozx_common.js.map CHANGED
@@ -1 +1 @@
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package/esm/methods/itkwasm-browser.d.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  import { NgffImage } from "../types/ngff_image.js";
2
+ import type { ZarrCodec } from "../utils/codecs.js";
2
3
  /**
3
4
  * Main downsampling function for ITK-Wasm (browser version)
4
5
  */
5
- export declare function downsampleItkWasm(ngffImage: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>): Promise<NgffImage[]>;
6
+ export declare function downsampleItkWasm(ngffImage: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>, codecs?: ZarrCodec[]): Promise<NgffImage[]>;
6
7
  //# sourceMappingURL=itkwasm-browser.d.ts.map
package/esm/methods/itkwasm-browser.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"itkwasm-browser.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm-browser.ts"],"names":[],"mappings":"AAgBA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AA86BnD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,EACpD,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAClD,OAAO,CAAC,SAAS,EAAE,CAAC,CAyHtB"}
1
+ {"version":3,"file":"itkwasm-browser.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm-browser.ts"],"names":[],"mappings":"AAeA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AA47BpD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,EACpD,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACnD,MAAM,CAAC,EAAE,SAAS,EAAE,GACnB,OAAO,CAAC,SAAS,EAAE,CAAC,CA4HtB"}
package/esm/methods/itkwasm-browser.js CHANGED
@@ -6,9 +6,9 @@
6
6
  */
7
7
  import { downsample, downsampleBinShrink, downsampleLabelImage, } from "@itk-wasm/downsample";
8
8
  import * as zarr from "zarrita";
9
- import { zarrGet, zarrSet } from "../utils/worker_pool.js";
10
- import { defaultCodecs } from "../utils/codecs.js";
11
9
  import { NgffImage } from "../types/ngff_image.js";
10
+ import { defaultCodecs } from "../utils/codecs.js";
11
+ import { zarrGet, zarrSet } from "../utils/worker_pool.js";
12
12
  import { dimScaleFactors, itkImageToZarr, MAX_VECTOR_COMPONENTS, nextScaleMetadata, SPATIAL_DIMS, updatePreviousDimFactors, zarrToItkImage, } from "./itkwasm-shared.js";
13
13
  /**
14
14
  * Compute chunk shape from configurable chunks option
@@ -36,7 +36,7 @@ function computeChunkShape(shape, chunks, dims, defaultChunk = 256) {
36
36
  /**
37
37
  * Perform Gaussian downsampling using ITK-Wasm (browser version)
38
38
  */
39
- async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
39
+ async function downsampleGaussian(image, dimFactors, spatialDims, chunks, codecs) {
40
40
  // Handle time dimension by processing each time slice independently
41
41
  if (image.dims.includes("t")) {
42
42
  const tDimIndex = image.dims.indexOf("t");
@@ -62,7 +62,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
62
62
  chunk_shape: sliceChunkShape,
63
63
  data_type: image.data.dtype,
64
64
  fill_value: 0,
65
- codecs: defaultCodecs(image.data.dtype),
65
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
66
66
  });
67
67
  const fullSelection = new Array(sliceShape.length).fill(null);
68
68
  await zarrSet(sliceArray, fullSelection, sliceData);
@@ -79,7 +79,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
79
79
  computedCallbacks: image.computedCallbacks,
80
80
  });
81
81
  // Recursively downsample this slice (without 't', so no infinite loop)
82
- const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims, sliceChunks);
82
+ const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
83
83
  downsampledSlices.push(downsampledSlice.data);
84
84
  }
85
85
  // Combine downsampled slices back into a single array with 't' dimension
@@ -101,7 +101,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
101
101
  chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
102
102
  data_type: image.data.dtype,
103
103
  fill_value: 0,
104
- codecs: defaultCodecs(image.data.dtype),
104
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
105
105
  });
106
106
  // Copy each downsampled slice into the combined array
107
107
  for (let t = 0; t < tSize; t++) {
@@ -154,7 +154,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
154
154
  chunk_shape: sliceChunkShape,
155
155
  data_type: image.data.dtype,
156
156
  fill_value: 0,
157
- codecs: defaultCodecs(image.data.dtype),
157
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
158
158
  });
159
159
  const fullSelection = new Array(sliceShape.length).fill(null);
160
160
  await zarrSet(sliceArray, fullSelection, sliceData);
@@ -171,7 +171,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
171
171
  computedCallbacks: image.computedCallbacks,
172
172
  });
173
173
  // Recursively downsample this slice (without 'c', so no infinite loop)
174
- const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims, sliceChunks);
174
+ const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
175
175
  downsampledSlices.push(downsampledSlice.data);
176
176
  }
177
177
  // Combine downsampled slices back into a single array with 'c' dimension
@@ -193,7 +193,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
193
193
  chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
194
194
  data_type: image.data.dtype,
195
195
  fill_value: 0,
196
- codecs: defaultCodecs(image.data.dtype),
196
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
197
197
  });
198
198
  // Copy each downsampled slice into the combined array
199
199
  for (let c = 0; c < cSize; c++) {
@@ -238,7 +238,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
238
238
  // downsampled.size is in ITK order [x, y, z], reverse to get array order [z, y, x]
239
239
  const reversedShape = [...downsampled.size].reverse();
240
240
  const chunkShape = computeChunkShape(reversedShape, chunks, image.dims);
241
- const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims);
241
+ const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims, codecs);
242
242
  return new NgffImage({
243
243
  data: array,
244
244
  dims: image.dims,
@@ -252,7 +252,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
252
252
  /**
253
253
  * Perform bin shrink downsampling using ITK-Wasm (browser version)
254
254
  */
255
- async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
255
+ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks, codecs) {
256
256
  // Handle time dimension by processing each time slice independently
257
257
  if (image.dims.includes("t")) {
258
258
  const tDimIndex = image.dims.indexOf("t");
@@ -278,7 +278,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
278
278
  chunk_shape: sliceChunkShape,
279
279
  data_type: image.data.dtype,
280
280
  fill_value: 0,
281
- codecs: defaultCodecs(image.data.dtype),
281
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
282
282
  });
283
283
  const fullSelection = new Array(sliceShape.length).fill(null);
284
284
  await zarrSet(sliceArray, fullSelection, sliceData);
@@ -295,7 +295,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
295
295
  computedCallbacks: image.computedCallbacks,
296
296
  });
297
297
  // Recursively downsample this slice
298
- const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims, sliceChunks);
298
+ const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
299
299
  downsampledSlices.push(downsampledSlice.data);
300
300
  }
301
301
  // Combine downsampled slices back into a single array with 't' dimension
@@ -317,7 +317,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
317
317
  chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
318
318
  data_type: image.data.dtype,
319
319
  fill_value: 0,
320
- codecs: defaultCodecs(image.data.dtype),
320
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
321
321
  });
322
322
  // Copy each downsampled slice into the combined array
323
323
  for (let t = 0; t < tSize; t++) {
@@ -370,7 +370,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
370
370
  chunk_shape: sliceChunkShape,
371
371
  data_type: image.data.dtype,
372
372
  fill_value: 0,
373
- codecs: defaultCodecs(image.data.dtype),
373
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
374
374
  });
375
375
  const fullSelection = new Array(sliceShape.length).fill(null);
376
376
  await zarrSet(sliceArray, fullSelection, sliceData);
@@ -387,7 +387,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
387
387
  computedCallbacks: image.computedCallbacks,
388
388
  });
389
389
  // Recursively downsample this slice (without 'c', so no infinite loop)
390
- const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims, sliceChunks);
390
+ const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
391
391
  downsampledSlices.push(downsampledSlice.data);
392
392
  }
393
393
  // Combine downsampled slices back into a single array with 'c' dimension
@@ -409,7 +409,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
409
409
  chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
410
410
  data_type: image.data.dtype,
411
411
  fill_value: 0,
412
- codecs: defaultCodecs(image.data.dtype),
412
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
413
413
  });
414
414
  // Copy each downsampled slice into the combined array
415
415
  for (let c = 0; c < cSize; c++) {
@@ -451,7 +451,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
451
451
  // downsampled.size is in ITK order [x, y, z], reverse to get array order [z, y, x]
452
452
  const reversedShape = [...downsampled.size].reverse();
453
453
  const chunkShape = computeChunkShape(reversedShape, chunks, image.dims);
454
- const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims);
454
+ const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims, codecs);
455
455
  return new NgffImage({
456
456
  data: array,
457
457
  dims: image.dims,
@@ -465,7 +465,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
465
465
  /**
466
466
  * Perform label image downsampling using ITK-Wasm (browser version)
467
467
  */
468
- async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks) {
468
+ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks, codecs) {
469
469
  // Handle time dimension by processing each time slice independently
470
470
  if (image.dims.includes("t")) {
471
471
  const tDimIndex = image.dims.indexOf("t");
@@ -491,7 +491,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
491
491
  chunk_shape: sliceChunkShape,
492
492
  data_type: image.data.dtype,
493
493
  fill_value: 0,
494
- codecs: defaultCodecs(image.data.dtype),
494
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
495
495
  });
496
496
  const fullSelection = new Array(sliceShape.length).fill(null);
497
497
  await zarrSet(sliceArray, fullSelection, sliceData);
@@ -508,7 +508,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
508
508
  computedCallbacks: image.computedCallbacks,
509
509
  });
510
510
  // Recursively downsample this slice
511
- const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims, sliceChunks);
511
+ const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
512
512
  downsampledSlices.push(downsampledSlice.data);
513
513
  }
514
514
  // Combine downsampled slices back into a single array with 't' dimension
@@ -530,7 +530,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
530
530
  chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
531
531
  data_type: image.data.dtype,
532
532
  fill_value: 0,
533
- codecs: defaultCodecs(image.data.dtype),
533
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
534
534
  });
535
535
  // Copy each downsampled slice into the combined array
536
536
  for (let t = 0; t < tSize; t++) {
@@ -583,7 +583,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
583
583
  chunk_shape: sliceChunkShape,
584
584
  data_type: image.data.dtype,
585
585
  fill_value: 0,
586
- codecs: defaultCodecs(image.data.dtype),
586
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
587
587
  });
588
588
  const fullSelection = new Array(sliceShape.length).fill(null);
589
589
  await zarrSet(sliceArray, fullSelection, sliceData);
@@ -600,7 +600,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
600
600
  computedCallbacks: image.computedCallbacks,
601
601
  });
602
602
  // Recursively downsample this slice (without 'c', so no infinite loop)
603
- const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims, sliceChunks);
603
+ const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
604
604
  downsampledSlices.push(downsampledSlice.data);
605
605
  }
606
606
  // Combine downsampled slices back into a single array with 'c' dimension
@@ -622,7 +622,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
622
622
  chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
623
623
  data_type: image.data.dtype,
624
624
  fill_value: 0,
625
- codecs: defaultCodecs(image.data.dtype),
625
+ codecs: codecs ?? defaultCodecs(image.data.dtype),
626
626
  });
627
627
  // Copy each downsampled slice into the combined array
628
628
  for (let c = 0; c < cSize; c++) {
@@ -670,7 +670,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
670
670
  // downsampled.size is in ITK order [x, y, z], reverse to get array order [z, y, x]
671
671
  const reversedShape = [...downsampled.size].reverse();
672
672
  const chunkShape = computeChunkShape(reversedShape, chunks, image.dims);
673
- const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims);
673
+ const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims, codecs);
674
674
  return new NgffImage({
675
675
  data: array,
676
676
  dims: image.dims,
@@ -684,7 +684,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
684
684
  /**
685
685
  * Main downsampling function for ITK-Wasm (browser version)
686
686
  */
687
- export async function downsampleItkWasm(ngffImage, scaleFactors, smoothing, chunks) {
687
+ export async function downsampleItkWasm(ngffImage, scaleFactors, smoothing, chunks, codecs) {
688
688
  const multiscales = [ngffImage];
689
689
  const dims = ngffImage.dims;
690
690
  const spatialDims = dims.filter((dim) => SPATIAL_DIMS.includes(dim));
@@ -748,13 +748,13 @@ export async function downsampleItkWasm(ngffImage, scaleFactors, smoothing, chun
748
748
  }
749
749
  let downsampled;
750
750
  if (smoothing === "gaussian") {
751
- downsampled = await downsampleGaussian(sourceImage, sourceDimFactors, spatialDims, chunks);
751
+ downsampled = await downsampleGaussian(sourceImage, sourceDimFactors, spatialDims, chunks, codecs);
752
752
  }
753
753
  else if (smoothing === "bin_shrink") {
754
- downsampled = await downsampleBinShrinkImpl(sourceImage, sourceDimFactors, spatialDims, chunks);
754
+ downsampled = await downsampleBinShrinkImpl(sourceImage, sourceDimFactors, spatialDims, chunks, codecs);
755
755
  }
756
756
  else if (smoothing === "label_image") {
757
- downsampled = await downsampleLabelImageImpl(sourceImage, sourceDimFactors, spatialDims, chunks);
757
+ downsampled = await downsampleLabelImageImpl(sourceImage, sourceDimFactors, spatialDims, chunks, codecs);
758
758
  }
759
759
  else {
760
760
  throw new Error(`Unknown smoothing method: ${smoothing}`);
package/esm/methods/itkwasm-browser.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/methods/itkwasm-node.d.ts CHANGED
@@ -1,6 +1,7 @@
1
1
  import { NgffImage } from "../types/ngff_image.js";
2
+ import type { ZarrCodec } from "../utils/codecs.js";
2
3
  /**
3
4
  * Main downsampling function for ITK-Wasm (Node version)
4
5
  */
5
- export declare function downsampleItkWasm(ngffImage: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>): Promise<NgffImage[]>;
6
+ export declare function downsampleItkWasm(ngffImage: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>, codecs?: ZarrCodec[]): Promise<NgffImage[]>;
6
7
  //# sourceMappingURL=itkwasm-node.d.ts.map
package/esm/methods/itkwasm-node.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"itkwasm-node.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm-node.ts"],"names":[],"mappings":"AAoBA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AA47BpD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,EACpD,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACnD,MAAM,CAAC,EAAE,SAAS,EAAE,GACnB,OAAO,CAAC,SAAS,EAAE,CAAC,CA4HtB"}