@fideus-labs/ngff-zarr 0.2.8 → 0.3.0

package/esm/methods/itkwasm-node.js

@@ -12,7 +12,7 @@
 import { downsampleBinShrinkNode as downsampleBinShrink, downsampleLabelImageNode as downsampleLabelImage, downsampleNode as downsample, } from "@itk-wasm/downsample";
 import * as zarr from "zarrita";
 import { NgffImage } from "../types/ngff_image.js";
-import { dimScaleFactors, itkImageToZarr, nextScaleMetadata, SPATIAL_DIMS, updatePreviousDimFactors, zarrToItkImage, } from "./itkwasm-shared.js";
+import { dimScaleFactors, itkImageToZarr, MAX_VECTOR_COMPONENTS, nextScaleMetadata, SPATIAL_DIMS, updatePreviousDimFactors, zarrToItkImage, } from "./itkwasm-shared.js";
 /**
  * Perform Gaussian downsampling using ITK-Wasm (browser version)
  */
@@ -97,7 +97,93 @@ async function downsampleGaussian(image, dimFactors, spatialDims) {
             computedCallbacks: image.computedCallbacks,
         });
     }
-    const isVector = image.dims.includes("c");
+    // Determine if we should use vector mode for multi-channel images.
+    // Only use vector mode for small channel counts (≤ MAX_VECTOR_COMPONENTS)
+    // to avoid itkwasm limitations with VariableLengthVector images.
+    const cIndex = image.dims.indexOf("c");
+    const hasChannels = cIndex !== -1;
+    const numChannels = hasChannels ? image.data.shape[cIndex] : 1;
+    const isVector = hasChannels && numChannels <= MAX_VECTOR_COMPONENTS;
+    // Handle channel dimension by processing each channel independently when not using vector mode
+    if (hasChannels && !isVector) {
+        const cDimIndex = cIndex;
+        const cSize = numChannels;
+        const newDims = image.dims.filter((dim) => dim !== "c");
+        // Downsample each channel
+        const downsampledSlices = [];
+        for (let c = 0; c < cSize; c++) {
+            // Extract channel slice
+            const selection = new Array(image.data.shape.length).fill(null);
+            selection[cDimIndex] = c;
+            const sliceData = await zarr.get(image.data, selection);
+            // Create temporary zarr array for this slice
+            const sliceStore = new Map();
+            const sliceRoot = zarr.root(sliceStore);
+            const sliceShape = image.data.shape.filter((_, i) => i !== cDimIndex);
+            const sliceChunkShape = sliceShape.map((s) => Math.min(s, 256));
+            const sliceArray = await zarr.create(sliceRoot.resolve("slice"), {
+                shape: sliceShape,
+                chunk_shape: sliceChunkShape,
+                data_type: image.data.dtype,
+                fill_value: 0,
+            });
+            const fullSelection = new Array(sliceShape.length).fill(null);
+            await zarr.set(sliceArray, fullSelection, sliceData);
+            // Create NgffImage for this slice (without 'c' dimension)
+            const sliceImage = new NgffImage({
+                data: sliceArray,
+                dims: newDims,
+                scale: Object.fromEntries(Object.entries(image.scale).filter(([dim]) => dim !== "c")),
+                translation: Object.fromEntries(Object.entries(image.translation).filter(([dim]) => dim !== "c")),
+                name: image.name,
+                axesUnits: image.axesUnits
+                    ? Object.fromEntries(Object.entries(image.axesUnits).filter(([dim]) => dim !== "c"))
+                    : undefined,
+                computedCallbacks: image.computedCallbacks,
+            });
+            // Recursively downsample this slice (without 'c', so no infinite loop)
+            const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims);
+            downsampledSlices.push(downsampledSlice.data);
+        }
+        // Combine downsampled slices back into a single array with 'c' dimension
+        const firstSlice = downsampledSlices[0];
+        const combinedShape = [...image.data.shape];
+        combinedShape[cDimIndex] = cSize;
+        // Update spatial dimensions based on downsampled size
+        for (let i = 0; i < image.dims.length; i++) {
+            if (i !== cDimIndex) {
+                const sliceIndex = i < cDimIndex ? i : i - 1;
+                combinedShape[i] = firstSlice.shape[sliceIndex];
+            }
+        }
+        // Create combined array
+        const combinedStore = new Map();
+        const combinedRoot = zarr.root(combinedStore);
+        const combinedArray = await zarr.create(combinedRoot.resolve("combined"), {
+            shape: combinedShape,
+            chunk_shape: combinedShape.map((s) => Math.min(s, 256)),
+            data_type: image.data.dtype,
+            fill_value: 0,
+        });
+        // Copy each downsampled slice into the combined array
+        for (let c = 0; c < cSize; c++) {
+            const sliceData = await zarr.get(downsampledSlices[c]);
+            const targetSelection = new Array(combinedShape.length).fill(null);
+            targetSelection[cDimIndex] = c;
+            await zarr.set(combinedArray, targetSelection, sliceData);
+        }
+        // Compute new metadata (channel dimension unchanged, spatial dimensions downsampled)
+        const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
+        return new NgffImage({
+            data: combinedArray,
+            dims: image.dims,
+            scale: { ...image.scale, ...scale },
+            translation: { ...image.translation, ...translation },
+            name: image.name,
+            axesUnits: image.axesUnits,
+            computedCallbacks: image.computedCallbacks,
+        });
+    }
     // Convert to ITK-Wasm format
     const itkImage = await zarrToItkImage(image.data, image.dims, isVector);
     // Prepare shrink factors - need to be for ALL dimensions in ITK order (reversed)
@@ -215,7 +301,93 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims) {
             computedCallbacks: image.computedCallbacks,
         });
     }
-    const isVector = image.dims.includes("c");
+    // Determine if we should use vector mode for multi-channel images.
+    // Only use vector mode for small channel counts (≤ MAX_VECTOR_COMPONENTS)
+    // to avoid itkwasm limitations with VariableLengthVector images.
+    const cIndex = image.dims.indexOf("c");
+    const hasChannels = cIndex !== -1;
+    const numChannels = hasChannels ? image.data.shape[cIndex] : 1;
+    const isVector = hasChannels && numChannels <= MAX_VECTOR_COMPONENTS;
+    // Handle channel dimension by processing each channel independently when not using vector mode
+    if (hasChannels && !isVector) {
+        const cDimIndex = cIndex;
+        const cSize = numChannels;
+        const newDims = image.dims.filter((dim) => dim !== "c");
+        // Downsample each channel
+        const downsampledSlices = [];
+        for (let c = 0; c < cSize; c++) {
+            // Extract channel slice
+            const selection = new Array(image.data.shape.length).fill(null);
+            selection[cDimIndex] = c;
+            const sliceData = await zarr.get(image.data, selection);
+            // Create temporary zarr array for this slice
+            const sliceStore = new Map();
+            const sliceRoot = zarr.root(sliceStore);
+            const sliceShape = image.data.shape.filter((_, i) => i !== cDimIndex);
+            const sliceChunkShape = sliceShape.map((s) => Math.min(s, 256));
+            const sliceArray = await zarr.create(sliceRoot.resolve("slice"), {
+                shape: sliceShape,
+                chunk_shape: sliceChunkShape,
+                data_type: image.data.dtype,
+                fill_value: 0,
+            });
+            const fullSelection = new Array(sliceShape.length).fill(null);
+            await zarr.set(sliceArray, fullSelection, sliceData);
+            // Create NgffImage for this slice (without 'c' dimension)
+            const sliceImage = new NgffImage({
+                data: sliceArray,
+                dims: newDims,
+                scale: Object.fromEntries(Object.entries(image.scale).filter(([dim]) => dim !== "c")),
+                translation: Object.fromEntries(Object.entries(image.translation).filter(([dim]) => dim !== "c")),
+                name: image.name,
+                axesUnits: image.axesUnits
+                    ? Object.fromEntries(Object.entries(image.axesUnits).filter(([dim]) => dim !== "c"))
+                    : undefined,
+                computedCallbacks: image.computedCallbacks,
+            });
+            // Recursively downsample this slice (without 'c', so no infinite loop)
+            const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims);
+            downsampledSlices.push(downsampledSlice.data);
+        }
+        // Combine downsampled slices back into a single array with 'c' dimension
+        const firstSlice = downsampledSlices[0];
+        const combinedShape = [...image.data.shape];
+        combinedShape[cDimIndex] = cSize;
+        // Update spatial dimensions based on downsampled size
+        for (let i = 0; i < image.dims.length; i++) {
+            if (i !== cDimIndex) {
+                const sliceIndex = i < cDimIndex ? i : i - 1;
+                combinedShape[i] = firstSlice.shape[sliceIndex];
+            }
+        }
+        // Create combined array
+        const combinedStore = new Map();
+        const combinedRoot = zarr.root(combinedStore);
+        const combinedArray = await zarr.create(combinedRoot.resolve("combined"), {
+            shape: combinedShape,
+            chunk_shape: combinedShape.map((s) => Math.min(s, 256)),
+            data_type: image.data.dtype,
+            fill_value: 0,
+        });
+        // Copy each downsampled slice into the combined array
+        for (let c = 0; c < cSize; c++) {
+            const sliceData = await zarr.get(downsampledSlices[c]);
+            const targetSelection = new Array(combinedShape.length).fill(null);
+            targetSelection[cDimIndex] = c;
+            await zarr.set(combinedArray, targetSelection, sliceData);
+        }
+        // Compute new metadata (channel dimension unchanged, spatial dimensions downsampled)
+        const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
+        return new NgffImage({
+            data: combinedArray,
+            dims: image.dims,
+            scale: { ...image.scale, ...scale },
+            translation: { ...image.translation, ...translation },
+            name: image.name,
+            axesUnits: image.axesUnits,
+            computedCallbacks: image.computedCallbacks,
+        });
+    }
     // Convert to ITK-Wasm format
     const itkImage = await zarrToItkImage(image.data, image.dims, isVector);
     // Prepare shrink factors - only for spatial dimensions in ITK order (reversed)
@@ -330,7 +502,93 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims) {
             computedCallbacks: image.computedCallbacks,
         });
     }
-    const isVector = image.dims.includes("c");
+    // Determine if we should use vector mode for multi-channel images.
+    // Only use vector mode for small channel counts (≤ MAX_VECTOR_COMPONENTS)
+    // to avoid itkwasm limitations with VariableLengthVector images.
+    const cIndex = image.dims.indexOf("c");
+    const hasChannels = cIndex !== -1;
+    const numChannels = hasChannels ? image.data.shape[cIndex] : 1;
+    const isVector = hasChannels && numChannels <= MAX_VECTOR_COMPONENTS;
+    // Handle channel dimension by processing each channel independently when not using vector mode
+    if (hasChannels && !isVector) {
+        const cDimIndex = cIndex;
+        const cSize = numChannels;
+        const newDims = image.dims.filter((dim) => dim !== "c");
+        // Downsample each channel
+        const downsampledSlices = [];
+        for (let c = 0; c < cSize; c++) {
+            // Extract channel slice
+            const selection = new Array(image.data.shape.length).fill(null);
+            selection[cDimIndex] = c;
+            const sliceData = await zarr.get(image.data, selection);
+            // Create temporary zarr array for this slice
+            const sliceStore = new Map();
+            const sliceRoot = zarr.root(sliceStore);
+            const sliceShape = image.data.shape.filter((_, i) => i !== cDimIndex);
+            const sliceChunkShape = sliceShape.map((s) => Math.min(s, 256));
+            const sliceArray = await zarr.create(sliceRoot.resolve("slice"), {
+                shape: sliceShape,
+                chunk_shape: sliceChunkShape,
+                data_type: image.data.dtype,
+                fill_value: 0,
+            });
+            const fullSelection = new Array(sliceShape.length).fill(null);
+            await zarr.set(sliceArray, fullSelection, sliceData);
+            // Create NgffImage for this slice (without 'c' dimension)
+            const sliceImage = new NgffImage({
+                data: sliceArray,
+                dims: newDims,
+                scale: Object.fromEntries(Object.entries(image.scale).filter(([dim]) => dim !== "c")),
+                translation: Object.fromEntries(Object.entries(image.translation).filter(([dim]) => dim !== "c")),
+                name: image.name,
+                axesUnits: image.axesUnits
+                    ? Object.fromEntries(Object.entries(image.axesUnits).filter(([dim]) => dim !== "c"))
+                    : undefined,
+                computedCallbacks: image.computedCallbacks,
+            });
+            // Recursively downsample this slice (without 'c', so no infinite loop)
+            const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims);
+            downsampledSlices.push(downsampledSlice.data);
+        }
+        // Combine downsampled slices back into a single array with 'c' dimension
+        const firstSlice = downsampledSlices[0];
+        const combinedShape = [...image.data.shape];
+        combinedShape[cDimIndex] = cSize;
+        // Update spatial dimensions based on downsampled size
+        for (let i = 0; i < image.dims.length; i++) {
+            if (i !== cDimIndex) {
+                const sliceIndex = i < cDimIndex ? i : i - 1;
+                combinedShape[i] = firstSlice.shape[sliceIndex];
+            }
+        }
+        // Create combined array
+        const combinedStore = new Map();
+        const combinedRoot = zarr.root(combinedStore);
+        const combinedArray = await zarr.create(combinedRoot.resolve("combined"), {
+            shape: combinedShape,
+            chunk_shape: combinedShape.map((s) => Math.min(s, 256)),
+            data_type: image.data.dtype,
+            fill_value: 0,
+        });
+        // Copy each downsampled slice into the combined array
+        for (let c = 0; c < cSize; c++) {
+            const sliceData = await zarr.get(downsampledSlices[c]);
+            const targetSelection = new Array(combinedShape.length).fill(null);
+            targetSelection[cDimIndex] = c;
+            await zarr.set(combinedArray, targetSelection, sliceData);
+        }
+        // Compute new metadata (channel dimension unchanged, spatial dimensions downsampled)
+        const [translation, scale] = nextScaleMetadata(image, dimFactors, spatialDims);
+        return new NgffImage({
+            data: combinedArray,
+            dims: image.dims,
+            scale: { ...image.scale, ...scale },
+            translation: { ...image.translation, ...translation },
+            name: image.name,
+            axesUnits: image.axesUnits,
+            computedCallbacks: image.computedCallbacks,
+        });
+    }
     // Convert to ITK-Wasm format
     const itkImage = await zarrToItkImage(image.data, image.dims, isVector);
     // Prepare shrink factors - need to be for ALL dimensions in ITK order (reversed)

package/esm/methods/itkwasm-node.js.map

@@ -1 +1 @@
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package/esm/methods/itkwasm-shared.d.ts

@@ -6,6 +6,12 @@ import type { Image } from "itk-wasm";
 import * as zarr from "zarrita";
 import { NgffImage } from "../types/ngff_image.js";
 export declare const SPATIAL_DIMS: string[];
+/**
+ * Maximum number of components to use vector mode for itkwasm downsampling.
+ * Images with more components will iterate over channels individually to avoid
+ * itkwasm limitations with VariableLengthVector images.
+ */
+export declare const MAX_VECTOR_COMPONENTS = 8;
 export interface DimFactors {
     [key: string]: number;
 }

package/esm/methods/itkwasm-shared.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"itkwasm-shared.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm-shared.ts"],"names":[],"mappings":"AAGA;;;GAGG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AACtC,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAEnD,eAAO,MAAM,YAAY,UAAkB,CAAC;AAE5C;;;;GAIG;AACH,eAAO,MAAM,qBAAqB,IAAI,CAAC;AAEvC,MAAM,WAAW,UAAU;IACzB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAAC;CACvB;AAED;;;GAGG;AACH,wBAAgB,0BAA0B,CACxC,YAAY,EAAE,MAAM,EACpB,UAAU,EAAE,MAAM,GACjB,MAAM,CAsBR;AAED;;;;;;;;GAQG;AACH,wBAAgB,eAAe,CAC7B,IAAI,EAAE,MAAM,EAAE,EACd,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,EAC5C,kBAAkB,EAAE,UAAU,EAC9B,aAAa,CAAC,EAAE,SAAS,EACzB,aAAa,CAAC,EAAE,SAAS,GACxB,UAAU,CAqEZ;AAED;;GAEG;AACH,wBAAgB,wBAAwB,CACtC,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,EAC5C,WAAW,EAAE,MAAM,EAAE,EACrB,kBAAkB,EAAE,UAAU,GAC7B,UAAU,CAcZ;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAC/B,KAAK,EAAE,SAAS,EAChB,UAAU,EAAE,UAAU,EACtB,WAAW,EAAE,MAAM,EAAE,GACpB,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAkBlD;AAsCD;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,IAAI,EAAE,OAAO,GAEX,OAAO,GACP,MAAM,GACN,QAAQ,GACR,OAAO,GACP,QAAQ,GACR,OAAO,GACP,SAAS,GACT,SAAS,CASZ;AAED;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,SAAS,EAAE,MAAM,GAAG,YAAY,CAMpE;AAcD;;GAEG;AACH,wBAAgB,cAAc,CAC5B,IAAI,EAAE,OAAO,EACb,KAAK,EAAE,MAAM,EAAE,EACf,WAAW,EAAE,MAAM,EAAE,EACrB,aAAa,EACT,OAAO,GACP,MAAM,GACN,QAAQ,GACR,OAAO,GACP,QAAQ,GACR,OAAO,GACP,SAAS,GACT,SAAS,GAEX,YAAY,GACZ,YAAY,GACZ,UAAU,GACV,SAAS,GACT,WAAW,GACX,UAAU,GACV,WAAW,GACX,UAAU,CAqFb;AAED;;;GAGG;AACH,wBAAsB,cAAc,CAClC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,EAC/C,IAAI,EAAE,MAAM,EAAE,EACd,QAAQ,UAAQ,GACf,OAAO,CAAC,KAAK,CAAC,CAqFhB;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAsB,cAAc,CAClC,QAAQ,EAAE,KAAK,EACf,KAAK,EAAE,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,EAC9B,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,MAAM,EAAE,EACpB,UAAU,CAAC,EAAE,MAAM,EAAE,GACpB,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,CAAC,CAoJnD"}

package/esm/methods/itkwasm-shared.js

@@ -2,6 +2,12 @@
 // SPDX-License-Identifier: MIT
 import * as zarr from "zarrita";
 export const SPATIAL_DIMS = ["x", "y", "z"];
+/**
+ * Maximum number of components to use vector mode for itkwasm downsampling.
+ * Images with more components will iterate over channels individually to avoid
+ * itkwasm limitations with VariableLengthVector images.
+ */
+export const MAX_VECTOR_COMPONENTS = 8;
 /**
  * Calculate the incremental factor needed to reach the target size from the previous size.
  * This ensures exact target sizes when downsampling incrementally.

package/esm/methods/itkwasm-shared.js.map

@@ -1 +1 @@
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package/esm/mod.d.ts

@@ -6,6 +6,7 @@ export * from "./types/ngff_image.js";
 export * from "./types/multiscales.js";
 export * from "./types/rfc4.js";
 export * from "./types/hcs.js";
+export * from "./types/supported_versions.js";
 export * from "./schemas/units.js";
 export * from "./schemas/methods.js";
 export * from "./schemas/zarr_metadata.js";
@@ -14,6 +15,8 @@ export * from "./schemas/multiscales.js";
 export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
 export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
 export { getMethodMetadata } from "./utils/method_metadata.js";
+export { detectVersion, extractMethodMetadata, parseOmero, } from "./utils/parse_metadata.js";
+export { fromZarrAttrsV04, fromZarrAttrsV05 } from "./utils/from_zarr_attrs.js";
 export * from "./io/from_ngff_zarr.js";
 export * from "./io/to_ngff_zarr.js";
 export * from "./process/to_multiscales-node.js";
@@ -21,4 +24,6 @@ export type { MemoryStore } from "./io/from_ngff_zarr.js";
 export * from "./io/itk_image_to_ngff_image.js";
 export * from "./io/ngff_image_to_itk_image.js";
 export * from "./io/hcs.js";
+export { getZipFileCompressionMethod, getZipFileList, isOzxPath, memoryStoreToZip, orderFilesForRfc9, readOzxJsonFirst, readOzxVersion, } from "./io/rfc9_zip.js";
+export type { MemoryStoreToZipOptions } from "./io/rfc9_zip.js";
 //# sourceMappingURL=mod.d.ts.map

package/esm/mod.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"mod.d.ts","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAEA,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAE/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAE/D,cAAc,wBAAwB,CAAC;AACvC,cAAc,sBAAsB,CAAC;AACrC,cAAc,kCAAkC,CAAC;AACjD,YAAY,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAC1D,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAChD,cAAc,aAAa,CAAC"}
+{"version":3,"file":"mod.d.ts","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAEA,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,+BAA+B,CAAC;AAE9C,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,aAAa,EACb,qBAAqB,EACrB,UAAU,GACX,MAAM,2BAA2B,CAAC;AACnC,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAEhF,cAAc,wBAAwB,CAAC;AACvC,cAAc,sBAAsB,CAAC;AACrC,cAAc,kCAAkC,CAAC;AACjD,YAAY,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAC1D,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAChD,cAAc,aAAa,CAAC;AAG5B,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,SAAS,EACT,gBAAgB,EAChB,iBAAiB,EACjB,gBAAgB,EAChB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC"}

package/esm/mod.js

@@ -8,6 +8,7 @@ export * from "./types/ngff_image.js";
 export * from "./types/multiscales.js";
 export * from "./types/rfc4.js";
 export * from "./types/hcs.js";
+export * from "./types/supported_versions.js";
 export * from "./schemas/units.js";
 export * from "./schemas/methods.js";
 export * from "./schemas/zarr_metadata.js";
@@ -16,10 +17,14 @@ export * from "./schemas/multiscales.js";
 export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
 export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
 export { getMethodMetadata } from "./utils/method_metadata.js";
+export { detectVersion, extractMethodMetadata, parseOmero, } from "./utils/parse_metadata.js";
+export { fromZarrAttrsV04, fromZarrAttrsV05 } from "./utils/from_zarr_attrs.js";
 export * from "./io/from_ngff_zarr.js";
 export * from "./io/to_ngff_zarr.js";
 export * from "./process/to_multiscales-node.js";
 export * from "./io/itk_image_to_ngff_image.js";
 export * from "./io/ngff_image_to_itk_image.js";
 export * from "./io/hcs.js";
+// RFC-9 exports
+export { getZipFileCompressionMethod, getZipFileList, isOzxPath, memoryStoreToZip, orderFilesForRfc9, readOzxJsonFirst, readOzxVersion, } from "./io/rfc9_zip.js";
 //# sourceMappingURL=mod.js.map

package/esm/mod.js.map

@@ -1 +1 @@
-{"version":3,"file":"mod.js","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAE/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAE/D,cAAc,wBAAwB,CAAC;AACvC,cAAc,sBAAsB,CAAC;AACrC,cAAc,kCAAkC,CAAC;AAEjD,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAChD,cAAc,aAAa,CAAC"}
+{"version":3,"file":"mod.js","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,+BAA+B,CAAC;AAE9C,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,aAAa,EACb,qBAAqB,EACrB,UAAU,GACX,MAAM,2BAA2B,CAAC;AACnC,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAEhF,cAAc,wBAAwB,CAAC;AACvC,cAAc,sBAAsB,CAAC;AACrC,cAAc,kCAAkC,CAAC;AAEjD,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAChD,cAAc,aAAa,CAAC;AAE5B,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,SAAS,EACT,gBAAgB,EAChB,iBAAiB,EACjB,gBAAgB,EAChB,cAAc,GACf,MAAM,kBAAkB,CAAC"}

package/esm/process/to_multiscales-shared.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"to_multiscales-shared.d.ts","sourceRoot":"","sources":["../../src/process/to_multiscales-shared.ts"],"names":[],"mappings":"AAGA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAS9C,MAAM,WAAW,oBAAoB;IACnC,YAAY,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,CAAC;IACnD,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CACrD;AAED;;GAEG;AACH,MAAM,MAAM,kBAAkB,GAAG,CAC/B,KAAK,EAAE,SAAS,EAChB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,KACjD,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC;AAE1B;;;;;;;;GAQG;AACH,wBAAsB,iBAAiB,CACrC,KAAK,EAAE,SAAS,EAChB,OAAO,EAAE,oBAAoB,EAC7B,iBAAiB,EAAE,kBAAkB,GACpC,OAAO,CAAC,WAAW,CAAC,CAqEtB"}
+{"version":3,"file":"to_multiscales-shared.d.ts","sourceRoot":"","sources":["../../src/process/to_multiscales-shared.ts"],"names":[],"mappings":"AAGA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAS9C,MAAM,WAAW,oBAAoB;IACnC,YAAY,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,CAAC;IACnD,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CACrD;AAED;;GAEG;AACH,MAAM,MAAM,kBAAkB,GAAG,CAC/B,KAAK,EAAE,SAAS,EAChB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,KACjD,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC;AAE1B;;;;;;;;GAQG;AACH,wBAAsB,iBAAiB,CACrC,KAAK,EAAE,SAAS,EAChB,OAAO,EAAE,oBAAoB,EAC7B,iBAAiB,EAAE,kBAAkB,GACpC,OAAO,CAAC,WAAW,CAAC,CAuEtB"}

package/esm/process/to_multiscales-shared.js

@@ -31,10 +31,11 @@ export async function toMultiscalesCore(image, options, downsampleItkWasm) {
         // Fallback: create only the base image (no actual downsampling)
         images = [image];
     }
-    // Create axes from image dimensions
+    // Create axes from image dimensions, including orientation if present
     const axes = image.dims.map((dim) => {
         if (dim === "x" || dim === "y" || dim === "z") {
-            return createAxis(dim, "space", image.axesUnits?.[dim]);
+            const orientation = image.axesOrientations?.[dim];
+            return createAxis(dim, "space", image.axesUnits?.[dim], orientation);
         }
         else if (dim === "c") {
             return createAxis(dim, "channel");