@fideus-labs/ngff-zarr 0.2.8 → 0.3.0

package/esm/browser-mod.d.ts

@@ -13,8 +13,8 @@ export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/valida
 export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
 export { getMethodMetadata } from "./utils/method_metadata.js";
 export { fromNgffZarr, type FromNgffZarrOptions, type MemoryStore, } from "./io/from_ngff_zarr-browser.js";
-export { toNgffZarr, type ToNgffZarrOptions, } from "./io/to_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";
 export * from "./process/to_multiscales-browser.js";
-export { ngffImageToItkImage } from "./io/ngff_image_to_itk_image.js";
-export { itkImageToNgffImage } from "./io/itk_image_to_ngff_image.js";
 //# sourceMappingURL=browser-mod.d.ts.map

package/esm/browser-mod.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"browser-mod.d.ts","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAOA,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,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;AAK/D,OAAO,EACL,YAAY,EACZ,KAAK,mBAAmB,EACxB,KAAK,WAAW,GACjB,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,SAAS,EACT,UAAU,EACV,KAAK,iBAAiB,EACtB,aAAa,EACb,KAAK,oBAAoB,GAC1B,MAAM,8BAA8B,CAAC;AAGtC,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC;AAGhE,cAAc,qCAAqC,CAAC"}

package/esm/browser-mod.js

@@ -23,10 +23,9 @@ export { getMethodMetadata } from "./utils/method_metadata.js";
 // Note: Uses browser-specific versions that don't import @zarrita/storage
 // (which contains Node.js-specific modules like node:fs, node:buffer, node:path)
 export { fromNgffZarr, } from "./io/from_ngff_zarr-browser.js";
-export { toNgffZarr, } from "./io/to_ngff_zarr-browser.js";
+export { isOzxPath, toNgffZarr, toNgffZarrOzx, } from "./io/to_ngff_zarr-browser.js";
+// RFC-9 exports
+export { getZipFileCompressionMethod, getZipFileList, memoryStoreToZip, orderFilesForRfc9, readOzxVersion, } from "./io/rfc9_zip.js";
 // Browser-compatible processing modules
 export * from "./process/to_multiscales-browser.js";
-// ITK conversions (browser-compatible)
-export { ngffImageToItkImage } from "./io/ngff_image_to_itk_image.js";
-export { itkImageToNgffImage } from "./io/itk_image_to_ngff_image.js";
 //# sourceMappingURL=browser-mod.js.map

package/esm/browser-mod.js.map

@@ -1 +1 @@
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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;AACzE,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,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,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EACL,YAAY,GAGb,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,SAAS,EACT,UAAU,EAEV,aAAa,GAEd,MAAM,8BAA8B,CAAC;AAEtC,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAG1B,wCAAwC;AACxC,cAAc,qCAAqC,CAAC"}

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

@@ -1 +1 @@
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+{"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;AAChC,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAWtD,MAAM,WAAW,mBAAmB;IAClC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;CACzB;AAED,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD,wBAAsB,YAAY,CAEhC,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,WAAW,CAAC,CAsHtB;AAED,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

@@ -2,13 +2,14 @@
 // SPDX-License-Identifier: MIT
 import * as zarr from "zarrita";
 import { Multiscales } from "../types/multiscales.js";
-import { NgffImage } from "../types/ngff_image.js";
-import { MetadataSchema } from "../schemas/zarr_metadata.js";
+import { NgffVersion } from "../types/supported_versions.js";
+import { detectVersion, extractMethodMetadata, } from "../utils/parse_metadata.js";
+import { fromZarrAttrsV04, fromZarrAttrsV05, } from "../utils/from_zarr_attrs.js";
 export async function fromNgffZarr(
 // Also accepts FileSystemStore, ZipFileStore objects in Node.js/Deno
 store, options = {}) {
     const validate = options.validate ?? false;
-    const version = options.version;
+    const requestedVersion = options.version;
     try {
         // Determine the appropriate store type based on the path
         let resolvedStore;
@@ -56,131 +57,48 @@ store, options = {}) {
             kind: "group",
         });
         const attrs = root.attrs;
-        // Handle both 0.4 (multiscales at root) and 0.5 (multiscales under ome) formats
-        let multiscalesArray;
-        let detectedVersion;
-        if (attrs && typeof attrs === "object" && "ome" in attrs) {
-            // OME-Zarr 0.5 format: metadata is under the 'ome' property
-            const omeAttrs = attrs.ome;
-            if (!omeAttrs || !omeAttrs.multiscales) {
-                throw new Error("No multiscales metadata found in OME-Zarr 0.5 store");
+        const rootAttrs = attrs;
+        // Handle both v0.4 (multiscales at root) and v0.5 (multiscales under "ome")
+        const hasOmeWrapper = "ome" in rootAttrs;
+        const multiscalesSource = hasOmeWrapper
+            ? rootAttrs.ome
+            : rootAttrs;
+        if (!multiscalesSource.multiscales) {
+            throw new Error("No multiscales metadata found in Zarr store");
+        }
+        // Detect version from attributes
+        const detectedVersion = detectVersion(rootAttrs);
+        // Validate version if requested
+        if (validate && requestedVersion) {
+            if (detectedVersion !== requestedVersion) {
+                throw new Error(`Expected OME-Zarr version ${requestedVersion}, but found ${detectedVersion}`);
             }
-            multiscalesArray = omeAttrs.multiscales;
-            detectedVersion = omeAttrs.version;
         }
-        else if (attrs && typeof attrs === "object" && "multiscales" in attrs) {
-            // OME-Zarr 0.4 format: metadata is at root
-            multiscalesArray = attrs
-                .multiscales;
+        // Parse metadata using version-specific function
+        let result;
+        if (detectedVersion === NgffVersion.V05) {
+            result = await fromZarrAttrsV05(rootAttrs, resolvedStore, validate);
         }
         else {
-            throw new Error("No multiscales metadata found in Zarr store");
-        }
-        if (!Array.isArray(multiscalesArray) || multiscalesArray.length === 0) {
-            throw new Error("No multiscales metadata found in Zarr store");
+            result = await fromZarrAttrsV04(rootAttrs, resolvedStore, validate);
         }
+        const { metadata, images } = result;
+        // Extract method metadata from the multiscales metadata
+        const multiscalesArray = multiscalesSource.multiscales;
         const multiscalesMetadata = multiscalesArray[0];
-        if (validate) {
-            const result = MetadataSchema.safeParse(multiscalesMetadata);
-            if (!result.success) {
-                throw new Error(`Invalid OME-Zarr metadata: ${result.error.message}`);
-            }
-            // Check version compatibility if specified
-            if (version) {
-                const metadataWithVersion = multiscalesMetadata;
-                const actualVersion = metadataWithVersion.version || detectedVersion;
-                if (actualVersion !== version) {
-                    throw new Error(`Expected OME-Zarr version ${version}, but found ${actualVersion || "unknown"}`);
-                }
-            }
-        }
-        const metadata = multiscalesMetadata;
-        // Extract omero metadata from root attributes if present
-        if (attrs.omero) {
-            const omeroData = attrs.omero;
-            // Handle backward compatibility for OMERO window metadata
-            if (omeroData.channels && Array.isArray(omeroData.channels)) {
-                for (const channel of omeroData.channels) {
-                    if (channel.window && typeof channel.window === "object") {
-                        const window = channel.window;
-                        // Ensure both min/max and start/end are present for compatibility
-                        if (window.min !== undefined && window.max !== undefined) {
-                            // If only min/max present, use them for start/end
-                            if (window.start === undefined) {
-                                window.start = window.min;
-                            }
-                            if (window.end === undefined) {
-                                window.end = window.max;
-                            }
-                        }
-                        else if (window.start !== undefined && window.end !== undefined) {
-                            // If only start/end present, use them for min/max
-                            if (window.min === undefined) {
-                                window.min = window.start;
-                            }
-                            if (window.max === undefined) {
-                                window.max = window.end;
-                            }
-                        }
-                    }
-                }
-            }
-            metadata.omero = omeroData;
+        const { method, methodType, methodMetadata } = extractMethodMetadata(multiscalesMetadata);
+        // Update metadata with method information
+        if (methodType) {
+            metadata.type = methodType;
         }
-        const images = [];
-        for (const dataset of metadata.datasets) {
-            const arrayPath = dataset.path;
-            const zarrArray = (await zarr.open(root.resolve(arrayPath), {
-                kind: "array",
-            }));
-            // Verify we have an array with the expected properties
-            if (!zarrArray ||
-                !("shape" in zarrArray) ||
-                !("dtype" in zarrArray) ||
-                !("chunks" in zarrArray)) {
-                throw new Error(`Invalid zarr array at path ${arrayPath}: missing shape property`);
-            }
-            const scale = {};
-            const translation = {};
-            for (const transform of dataset.coordinateTransformations) {
-                if (transform.type === "scale") {
-                    metadata.axes.forEach((axis, i) => {
-                        if (i < transform.scale.length) {
-                            scale[axis.name] = transform.scale[i];
-                        }
-                    });
-                }
-                else if (transform.type === "translation") {
-                    metadata.axes.forEach((axis, i) => {
-                        if (i < transform.translation.length) {
-                            translation[axis.name] = transform.translation[i];
-                        }
-                    });
-                }
-            }
-            const dims = metadata.axes.map((axis) => axis.name);
-            const axesUnits = metadata.axes.reduce((acc, axis) => {
-                if (axis.unit) {
-                    acc[axis.name] = axis.unit;
-                }
-                return acc;
-            }, {});
-            const ngffImage = new NgffImage({
-                data: zarrArray,
-                dims,
-                scale,
-                translation,
-                name: metadata.name,
-                axesUnits: Object.keys(axesUnits).length > 0 ? axesUnits : undefined,
-                computedCallbacks: undefined,
-            });
-            images.push(ngffImage);
+        if (methodMetadata) {
+            metadata.metadata = methodMetadata;
         }
         return new Multiscales({
             images,
             metadata,
             scaleFactors: undefined,
-            method: undefined,
+            method,
             chunks: undefined,
         });
     }

package/esm/io/from_ngff_zarr.js.map

@@ -1 +1 @@
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package/esm/io/rfc9_zip.d.ts

@@ -0,0 +1,80 @@
+/**
+ * RFC-9: Zipped OME-Zarr (.ozx) support
+ *
+ * This module provides utilities for writing OME-Zarr hierarchies
+ * to ZIP archives according to RFC-9 specification.
+ *
+ * @see https://ngff.openmicroscopy.org/rfc/9/index.html
+ */
+/** MemoryStore type for zarr data */
+export type MemoryStore = Map<string, Uint8Array>;
+/**
+ * Check if a path refers to a .ozx file.
+ *
+ * @param path - Path to check
+ * @returns True if path ends with .ozx extension
+ */
+export declare function isOzxPath(path: string): boolean;
+/**
+ * Order files for RFC-9 compliance.
+ *
+ * According to RFC-9:
+ * - Root-level zarr.json must be the first entry
+ * - Other zarr.json files should follow in breadth-first order
+ * - Data files come after all zarr.json files
+ *
+ * @param keys - Array of file paths from the store
+ * @returns Ordered array of file paths
+ */
+export declare function orderFilesForRfc9(keys: string[]): string[];
+/**
+ * Read the OME-Zarr version from ZIP comment.
+ *
+ * @param zipData - ZIP file data
+ * @returns OME-Zarr version string if found, null otherwise
+ */
+export declare function readOzxVersion(zipData: Uint8Array): string | null;
+/**
+ * Read the jsonFirst flag from ZIP comment.
+ *
+ * The jsonFirst flag indicates that zarr.json files are ordered
+ * breadth-first in the central directory and precede other content.
+ *
+ * @param zipData - ZIP file data
+ * @returns true if jsonFirst is set to true in the ZIP comment, false otherwise
+ */
+export declare function readOzxJsonFirst(zipData: Uint8Array): boolean;
+/**
+ * Check if a file in the ZIP uses compression.
+ *
+ * @param zipData - ZIP file data
+ * @param filename - Name of the file to check
+ * @returns Compression method (0 = stored, 8 = deflate, etc.)
+ */
+export declare function getZipFileCompressionMethod(zipData: Uint8Array, filename: string): number | null;
+/**
+ * Get the list of files in a ZIP archive in order.
+ *
+ * @param zipData - ZIP file data
+ * @returns Array of filenames in the order they appear in the central directory
+ */
+export declare function getZipFileList(zipData: Uint8Array): string[];
+export interface MemoryStoreToZipOptions {
+    /** OME-Zarr version string (default: "0.5") */
+    version?: string;
+}
+/**
+ * Convert a MemoryStore to ZIP data following RFC-9 specification.
+ *
+ * According to RFC-9:
+ * - Root-level zarr.json must be the first entry
+ * - Other zarr.json files should follow in breadth-first order
+ * - ZIP-level compression should be disabled (ZIP_STORED)
+ * - A comment with OME-Zarr version should be added
+ *
+ * @param store - MemoryStore containing zarr data
+ * @param options - Options for ZIP creation
+ * @returns ZIP file data as Uint8Array
+ */
+export declare function memoryStoreToZip(store: MemoryStore, options?: MemoryStoreToZipOptions): Uint8Array;
+//# sourceMappingURL=rfc9_zip.d.ts.map

package/esm/io/rfc9_zip.d.ts.map

@@ -0,0 +1 @@
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