@fideus-labs/ngff-zarr 0.1.0 → 0.2.0

package/README.md

@@ -45,6 +45,7 @@ The main Python package provides:
 - [Sharded Zarr] stores
 - Optional writing via zarr-python 2, zarr-python 3, [tensorstore] or zarrita (TypeScript)
 - [Anatomical orientation metadata](./docs/rfc4.md) (RFC-4)
+- **OME-Zarr Zip (.ozx) file support** for single-file OME-Zarr datasets (RFC-9)
 - **High Content Screening (HCS) support** for plate and well data
 - **Model Context Protocol (MCP) server** for AI agent integration
 

package/esm/io/itk_image_to_ngff_image.d.ts

@@ -9,6 +9,11 @@ export interface ItkImageToNgffImageOptions {
      * @default true
      */
     addAnatomicalOrientation?: boolean;
+    /**
+     * Path prefix for the zarr array (e.g., "scale0/", "scale1/")
+     * @default "image"
+     */
+    path?: string;
 }
 /**
  * Convert an ITK-Wasm Image to an NgffImage, preserving spatial metadata.

package/esm/io/itk_image_to_ngff_image.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"itk_image_to_ngff_image.d.ts","sourceRoot":"","sources":["../../src/io/itk_image_to_ngff_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AAEtC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAOnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,wBAAwB,CAAC,EAAE,OAAO,CAAC;CACpC;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,KAAK,EACf,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,SAAS,CAAC,CAmHpB"}
+{"version":3,"file":"itk_image_to_ngff_image.d.ts","sourceRoot":"","sources":["../../src/io/itk_image_to_ngff_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AAEtC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAOnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,wBAAwB,CAAC,EAAE,OAAO,CAAC;IAEnC;;;OAGG;IACH,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,KAAK,EACf,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,SAAS,CAAC,CAmHpB"}

package/esm/io/itk_image_to_ngff_image.js

@@ -20,10 +20,12 @@ import { _zarrita_internal_get_strides as getStrides } from "zarrita";
  * @returns Promise resolving to NgffImage
  */
 export async function itkImageToNgffImage(itkImage, options = {}) {
-    const { addAnatomicalOrientation = true } = options;
+    const { addAnatomicalOrientation = true, path = "image" } = options;
     // Extract image properties from ITK-Wasm Image
     const _data = itkImage.data;
-    const shape = itkImage.size;
+    // ITK stores size in physical space order [x, y, z], but the data buffer is in
+    // C-order (row-major) which means [z, y, x] indexing. Reverse to match data layout.
+    const shape = [...itkImage.size].reverse();
     const spacing = itkImage.spacing;
     const origin = itkImage.origin;
     const ndim = shape.length;
@@ -60,32 +62,27 @@ export async function itkImageToNgffImage(itkImage, options = {}) {
     // Identify spatial dimensions
     const allSpatialDims = new Set(["x", "y", "z"]);
     const spatialDims = dims.filter((dim) => allSpatialDims.has(dim));
-    // Create scale mapping from spacing (ITK order: [z, y, x] for 3D, [y, x] for 2D)
+    // Create scale mapping from spacing
+    // ITK stores spacing/origin in physical space order (x, y, z),
+    // but we need to map them to array order (z, y, x).
+    // Reverse the arrays to convert from physical to array order, matching Python implementation.
     const scale = {};
-    // Define canonical ITK spatial order for up to 3D
-    const itkSpatialOrder = ["z", "y", "x"].slice(-spatialDims.length);
-    spatialDims.forEach((dim) => {
-        const spatialIndex = itkSpatialOrder.indexOf(dim);
-        if (spatialIndex === -1) {
-            throw new Error(`Unknown spatial dimension: ${dim}`);
-        }
-        scale[dim] = spacing[spatialIndex];
+    const reversedSpacing = spacing.slice().reverse();
+    spatialDims.forEach((dim, idx) => {
+        scale[dim] = reversedSpacing[idx];
     });
-    // Create translation mapping from origin (ITK order: [z, y, x] for 3D, [y, x] for 2D)
+    // Create translation mapping from origin
     const translation = {};
-    spatialDims.forEach((dim) => {
-        const spatialIndex = itkSpatialOrder.indexOf(dim);
-        if (spatialIndex === -1) {
-            throw new Error(`Unknown spatial dimension: ${dim}`);
-        }
-        translation[dim] = origin[spatialIndex];
+    const reversedOrigin = origin.slice().reverse();
+    spatialDims.forEach((dim, idx) => {
+        translation[dim] = reversedOrigin[idx];
     });
     // Create Zarr array from ITK-Wasm data
     const store = new Map();
     const root = zarr.root(store);
     // Determine appropriate chunk size
     const chunkShape = shape.map((s) => Math.min(s, 256));
-    const zarrArray = await zarr.create(root.resolve("image"), {
+    const zarrArray = await zarr.create(root.resolve(path), {
         shape: shape,
         chunk_shape: chunkShape,
         data_type: imageType.componentType,
@@ -96,10 +93,13 @@ export async function itkImageToNgffImage(itkImage, options = {}) {
     // Create a selection that covers the entire array (null means "all" for each dimension)
     const selection = new Array(ndim).fill(null);
     // Create a chunk object with the ITK-Wasm data in zarrita format
+    // ITK-Wasm stores data in column-major order with size [x, y, z],
+    // which has the same memory layout as C-order (row-major) with shape [z, y, x].
+    // We reversed the shape above, and now use C-order strides for that reversed shape.
     const dataChunk = {
         data: itkImage.data,
         shape: shape,
-        stride: getStrides(shape, "C"), // C-order (row-major) strides for compatibility
+        stride: getStrides(shape, "C"), // C-order strides for the reversed shape
     };
     // Write all data to the zarr array using zarrita's set function
     // This handles chunking and encoding automatically

package/esm/io/ngff_image_to_itk_image.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ngff_image_to_itk_image.d.ts","sourceRoot":"","sources":["../../src/io/ngff_image_to_itk_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAEV,KAAK,EAKN,MAAM,UAAU,CAAC;AAElB,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAEnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;IAEhB;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAsED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,SAAS,EAAE,SAAS,EACpB,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,KAAK,CAAC,CAiMhB"}
+{"version":3,"file":"ngff_image_to_itk_image.d.ts","sourceRoot":"","sources":["../../src/io/ngff_image_to_itk_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAEV,KAAK,EAKN,MAAM,UAAU,CAAC;AAElB,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAEnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;IAEhB;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAsED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,SAAS,EAAE,SAAS,EACpB,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,KAAK,CAAC,CAmMhB"}

package/esm/io/ngff_image_to_itk_image.js

@@ -168,6 +168,8 @@ export async function ngffImageToItkImage(ngffImage, options = {}) {
         return order.indexOf(a) - order.indexOf(b);
     });
     // Create ITK spacing, origin, and size arrays
+    // sortedItkDims is already in physical space order [x, y, z]
+    // Mapping from dims extracts the correct values from NGFF's array order [z, y, x]
     const spacing = sortedItkDims.map((dim) => workingImage.scale[dim] || 1.0);
     const origin = sortedItkDims.map((dim) => workingImage.translation[dim] || 0.0);
     const size = sortedItkDims.map((dim) => data.shape[dims.indexOf(dim)]);

package/esm/io/to_multiscales.js

@@ -47,7 +47,7 @@ export async function toMultiscales(image, options = {}) {
     });
     // Create datasets for all images
     const datasets = images.map((img, index) => {
-        return createDataset(`${index}`, img.dims.map((dim) => img.scale[dim]), img.dims.map((dim) => img.translation[dim]));
+        return createDataset(`scale${index}`, img.dims.map((dim) => img.scale[dim]), img.dims.map((dim) => img.translation[dim]));
     });
     // Create metadata with method information
     const methodMetadata = getMethodMetadata(method);

package/esm/io/to_ngff_zarr.js

@@ -194,6 +194,22 @@ async function writeChunkWithGet(zarrArray, image, chunkIndex) {
     // Convert chunk data to target type
     const targetTypedArrayConstructor = getTypedArrayConstructor(zarrArray.dtype);
     const chunkTargetData = convertChunkToTargetType(chunkSourceData, zarrArray.dtype, targetTypedArrayConstructor);
+    // Validate chunk data size
+    const expectedSize = chunkShape.reduce((a, b) => a * b, 1);
+    const actualSize = chunkTargetData.byteLength /
+        (chunkTargetData
+            .BYTES_PER_ELEMENT || 1);
+    if (actualSize !== expectedSize) {
+        console.error(`[writeChunkWithGet] Chunk data size mismatch!`);
+        console.error(`  Image shape:`, shape);
+        console.error(`  Chunk index:`, chunkIndex);
+        console.error(`  Chunk start:`, chunkStart);
+        console.error(`  Chunk end:`, chunkEnd);
+        console.error(`  Chunk shape:`, chunkShape);
+        console.error(`  Expected size:`, expectedSize);
+        console.error(`  Actual size:`, actualSize);
+        throw new Error(`Chunk data size mismatch: expected ${expectedSize} elements, got ${actualSize}`);
+    }
     // Create the selection for writing to the target zarr array
     const targetSelection = chunkStart.map((start, dim) => zarr.slice(start, chunkEnd[dim]));
     // Write the chunk using zarrita's set function

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

@@ -1 +1 @@
-{"version":3,"file":"itkwasm.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm.ts"],"names":[],"mappings":"AAeA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAohCnD;;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,GACnD,OAAO,CAAC,SAAS,EAAE,CAAC,CA+CtB"}
+{"version":3,"file":"itkwasm.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm.ts"],"names":[],"mappings":"AAcA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAknCnD;;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,GACnD,OAAO,CAAC,SAAS,EAAE,CAAC,CA8HtB"}