@fideus-labs/ngff-zarr 0.2.8 → 0.4.0

package/esm/io/to_ngff_zarr.js

@@ -2,9 +2,56 @@
 // SPDX-License-Identifier: MIT
 import * as zarr from "zarrita";
 import { createQueue } from "../utils/create_queue.js";
+import { isOzxPath, memoryStoreToZip } from "./rfc9_zip.js";
+import { processAxesForRfcs, writeMultiscalesToMemoryStore, } from "./to_ngff_zarr_ozx_common.js";
+/**
+ * Write multiscales data to an OME-Zarr store.
+ *
+ * This function automatically detects .ozx paths (RFC-9 zipped OME-Zarr format)
+ * and handles them appropriately. For .ozx files:
+ * - Version 0.5 is always used when the version option is omitted (undefined)
+ * - Sharding (chunksPerShard) is not supported
+ * - An error is thrown if you explicitly specify a version other than "0.5"
+ *
+ * @param store - File path, MemoryStore, or FetchStore to write to
+ * @param multiscales - Multiscales data to write
+ * @param options - Writing options
+ *
+ * @example
+ * ```typescript
+ * // Writing to .ozx file - version 0.5 is used automatically
+ * await toNgffZarr("output.ozx", multiscales);
+ *
+ * // Writing to regular zarr with version 0.4 (default)
+ * await toNgffZarr("output.zarr", multiscales);
+ *
+ * // Writing to regular zarr with version 0.5
+ * await toNgffZarr("output.zarr", multiscales, { version: "0.5" });
+ * ```
+ */
 export async function toNgffZarr(store, multiscales, options = {}) {
     const _overwrite = options.overwrite ?? true;
     const _version = options.version ?? "0.4";
+    const enabledRfcs = options.enabledRfcs;
+    // Handle .ozx paths (RFC-9)
+    if (typeof store === "string" && isOzxPath(store)) {
+        // Validate version - RFC-9 requires version 0.5
+        // If no version is specified (undefined), we silently default to 0.5
+        // If a version is explicitly specified and it's not 0.5, throw an error
+        if (options.version !== undefined && options.version !== "0.5") {
+            throw new Error("RFC-9 (.ozx) requires OME-Zarr version 0.5. " +
+                `Got version "${options.version}". ` +
+                "For .ozx files, either omit the version option or explicitly set it to '0.5'.");
+        }
+        // Throw error if chunksPerShard is specified
+        if (options.chunksPerShard !== undefined) {
+            throw new Error("RFC-9 (.ozx) does not support sharding (chunksPerShard). " +
+                "zarrita does not currently support writing shards.");
+        }
+        // Delegate to toNgffZarrOzx (which always uses version 0.5)
+        await toNgffZarrOzx(store, multiscales, { enabledRfcs });
+        return;
+    }
     try {
         // Determine the appropriate store type based on the path
         let _resolvedStore; // Use unknown for FileSystemStore since we import it dynamically
@@ -35,11 +82,13 @@ export async function toNgffZarr(store, multiscales, options = {}) {
         }
         // Create root location and group with zarrita v0.5.2 API
         const root = zarr.root(_resolvedStore);
+        // Process axes - filter orientation based on enabledRfcs
+        const processedAxes = processAxesForRfcs(multiscales.metadata.axes, enabledRfcs);
         // Prepare multiscales metadata
         const multiscalesMetadata = {
             version: _version,
             name: multiscales.metadata.name,
-            axes: multiscales.metadata.axes,
+            axes: processedAxes,
             datasets: multiscales.metadata.datasets,
             ...(multiscales.metadata.coordinateTransformations && {
                 coordinateTransformations: multiscales.metadata.coordinateTransformations,
@@ -52,22 +101,24 @@ export async function toNgffZarr(store, multiscales, options = {}) {
             }),
         };
         // Create the root group with OME-Zarr metadata
-        // For version 0.5, wrap metadata under "ome" property
-        // For version 0.4, place multiscales directly at root
+        // For version 0.5, wrap metadata under "ome" property (including omero)
+        // For version 0.4, place multiscales and omero directly at root
         const attributes = _version === "0.5"
             ? {
                 ome: {
                     version: _version,
                     multiscales: [multiscalesMetadata],
+                    ...(multiscales.metadata.omero && {
+                        omero: multiscales.metadata.omero,
+                    }),
                 },
             }
             : {
                 multiscales: [multiscalesMetadata],
+                ...(multiscales.metadata.omero && {
+                    omero: multiscales.metadata.omero,
+                }),
             };
-        // Add OMERO metadata at root level if present (both versions)
-        if (multiscales.metadata.omero) {
-            attributes.omero = multiscales.metadata.omero;
-        }
         const rootGroup = await zarr.create(root, { attributes });
         // Write each image in the multiscales
         for (let i = 0; i < multiscales.images.length; i++) {
@@ -326,4 +377,75 @@ function calculateChunkStride(chunkShape) {
     }
     return stride;
 }
+/**
+ * Write OME-Zarr to .ozx ZIP file (RFC-9).
+ *
+ * This function creates an OME-Zarr hierarchy in memory and then writes it
+ * to a ZIP file following RFC-9 specification:
+ * - Root-level zarr.json is the first entry
+ * - Other zarr.json files follow in breadth-first order
+ * - ZIP-level compression is disabled (ZIP_STORED)
+ * - A comment with OME-Zarr version is added
+ *
+ * Note: Sharding is NOT supported because zarrita does not currently
+ * support writing shards. If you need sharding, use the Python implementation.
+ *
+ * @param path - Output .ozx file path
+ * @param multiscales - Multiscales data to write
+ * @param options - Options for writing
+ * @throws Error if called in a browser environment (use toNgffZarrOzxData instead)
+ *
+ * @see https://ngff.openmicroscopy.org/rfc/9/index.html
+ */
+export async function toNgffZarrOzx(path, multiscales, options = {}) {
+    // Check for browser environment
+    if (typeof window !== "undefined") {
+        throw new Error("toNgffZarrOzx cannot write files in browser environments. " +
+            "Use toNgffZarrOzxData to get the ZIP data as Uint8Array.");
+    }
+    // Get the ZIP data
+    const zipData = await toNgffZarrOzxData(multiscales, options);
+    // Write to file using fs module (works in both Node.js and Deno)
+    try {
+        // Use dynamic import for Node.js fs module
+        // Deno also supports node:fs/promises via its Node compatibility layer
+        const { writeFile } = await import("node:fs/promises");
+        await writeFile(path, zipData);
+    }
+    catch (error) {
+        throw new Error(`Failed to write .ozx file: ${error instanceof Error ? error.message : String(error)}`);
+    }
+}
+/**
+ * Create OME-Zarr .ozx ZIP data (RFC-9).
+ *
+ * This function creates an OME-Zarr hierarchy in memory and returns
+ * the ZIP data as a Uint8Array. Useful for browser environments or
+ * when you need the raw ZIP data.
+ *
+ * @param multiscales - Multiscales data to write
+ * @param options - Options for writing
+ * @returns ZIP file data as Uint8Array
+ *
+ * @see https://ngff.openmicroscopy.org/rfc/9/index.html
+ */
+export async function toNgffZarrOzxData(multiscales, options = {}) {
+    const enabledRfcs = options.enabledRfcs;
+    // Create a memory store to hold the zarr data
+    const memoryStore = new Map();
+    // Write to the memory store using existing toNgffZarr logic
+    // but we need to inline the core logic since toNgffZarr would
+    // try to detect .ozx again
+    await _writeToMemoryStore(memoryStore, multiscales, enabledRfcs);
+    // Convert the memory store to ZIP data
+    const zipData = memoryStoreToZip(memoryStore, { version: "0.5" });
+    return zipData;
+}
+/**
+ * Internal function to write multiscales to a memory store.
+ * Used by toNgffZarrOzxData to avoid recursion with toNgffZarr.
+ */
+async function _writeToMemoryStore(store, multiscales, enabledRfcs) {
+    await writeMultiscalesToMemoryStore(store, multiscales, enabledRfcs, _writeImage);
+}
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package/esm/io/to_ngff_zarr.js.map

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package/esm/io/to_ngff_zarr_ozx_common.d.ts

@@ -0,0 +1,51 @@
+/**
+ * Shared internal utilities for RFC-9 (.ozx) writing
+ * Used by both Node and browser implementations to avoid code duplication
+ */
+import * as zarr from "zarrita";
+import type { Multiscales } from "../types/multiscales.js";
+import type { NgffImage } from "../types/ngff_image.js";
+import type { Axis } from "../types/zarr_metadata.js";
+import type { MemoryStore } from "./rfc9_zip.js";
+/**
+ * Process axes for RFC enablement.
+ * If RFC 4 is enabled, include orientation metadata.
+ * If RFC 4 is not enabled, strip orientation from axes.
+ */
+export declare function processAxesForRfcs(axes: Axis[], enabledRfcs?: number[]): Record<string, unknown>[];
+/**
+ * Validate that the Multiscales metadata version is compatible with RFC-9.
+ * RFC-9 always uses version 0.5.
+ *
+ * @param multiscales - Multiscales object to validate
+ * @throws Error if metadata.version is defined and not "0.5"
+ */
+export declare function validateRfc9Version(multiscales: Multiscales): void;
+/**
+ * Prepare multiscales metadata for RFC-9 export.
+ * This includes processing axes for RFC enablement and setting version to 0.5.
+ *
+ * @param multiscales - Source multiscales data
+ * @param enabledRfcs - Optional list of RFC numbers to enable
+ * @returns Prepared metadata object
+ */
+export declare function prepareRfc9Metadata(multiscales: Multiscales, enabledRfcs?: number[]): Record<string, unknown>;
+/**
+ * Create root group attributes for RFC-9 export.
+ *
+ * @param multiscalesMetadata - Prepared multiscales metadata
+ * @param multiscales - Original multiscales (for OMERO metadata)
+ * @returns Attributes object for root group
+ */
+export declare function createRfc9RootAttributes(multiscalesMetadata: Record<string, unknown>, multiscales: Multiscales): Record<string, unknown>;
+/**
+ * Write multiscales data to a memory store for RFC-9 export.
+ * This is the shared implementation used by both Node and browser versions.
+ *
+ * @param store - Memory store to write to
+ * @param multiscales - Multiscales data to write
+ * @param enabledRfcs - Optional list of RFC numbers to enable
+ * @param writeImage - Function to write individual images
+ */
+export declare function writeMultiscalesToMemoryStore(store: MemoryStore, multiscales: Multiscales, enabledRfcs: number[] | undefined, writeImage: (group: zarr.Group<MemoryStore>, image: NgffImage, path: string) => Promise<void>): Promise<void>;
+//# sourceMappingURL=to_ngff_zarr_ozx_common.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"to_ngff_zarr_ozx_common.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr_ozx_common.ts"],"names":[],"mappings":"AAEA;;;GAGG;AAEH,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACxD,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,2BAA2B,CAAC;AACtD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAGjD;;;;GAIG;AACH,wBAAgB,kBAAkB,CAChC,IAAI,EAAE,IAAI,EAAE,EACZ,WAAW,CAAC,EAAE,MAAM,EAAE,GACrB,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,CAwB3B;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,EAAE,WAAW,GAAG,IAAI,CAOlE;AAED;;;;;;;GAOG;AACH,wBAAgB,mBAAmB,CACjC,WAAW,EAAE,WAAW,EACxB,WAAW,CAAC,EAAE,MAAM,EAAE,GACrB,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAwBzB;AAED;;;;;;GAMG;AACH,wBAAgB,wBAAwB,CACtC,mBAAmB,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC5C,WAAW,EAAE,WAAW,GACvB,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAgBzB;AAED;;;;;;;;GAQG;AACH,wBAAsB,6BAA6B,CACjD,KAAK,EAAE,WAAW,EAClB,WAAW,EAAE,WAAW,EACxB,WAAW,EAAE,MAAM,EAAE,GAAG,SAAS,EACjC,UAAU,EAAE,CACV,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,EAC9B,KAAK,EAAE,SAAS,EAChB,IAAI,EAAE,MAAM,KACT,OAAO,CAAC,IAAI,CAAC,GACjB,OAAO,CAAC,IAAI,CAAC,CA0Bf"}

package/esm/io/to_ngff_zarr_ozx_common.js

@@ -0,0 +1,126 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * Shared internal utilities for RFC-9 (.ozx) writing
+ * Used by both Node and browser implementations to avoid code duplication
+ */
+import * as zarr from "zarrita";
+import { isRfc4Enabled } from "../types/rfc4.js";
+/**
+ * Process axes for RFC enablement.
+ * If RFC 4 is enabled, include orientation metadata.
+ * If RFC 4 is not enabled, strip orientation from axes.
+ */
+export function processAxesForRfcs(axes, enabledRfcs) {
+    const rfc4Enabled = isRfc4Enabled(enabledRfcs);
+    return axes.map((axis) => {
+        const result = {
+            name: axis.name,
+            type: axis.type,
+        };
+        // Include unit if present
+        if (axis.unit !== undefined) {
+            result.unit = axis.unit;
+        }
+        // Include orientation only if RFC 4 is enabled and orientation exists
+        if (rfc4Enabled && axis.orientation) {
+            result.orientation = {
+                type: axis.orientation.type,
+                value: axis.orientation.value,
+            };
+        }
+        return result;
+    });
+}
+/**
+ * Validate that the Multiscales metadata version is compatible with RFC-9.
+ * RFC-9 always uses version 0.5.
+ *
+ * @param multiscales - Multiscales object to validate
+ * @throws Error if metadata.version is defined and not "0.5"
+ */
+export function validateRfc9Version(multiscales) {
+    const providedVersion = multiscales.metadata.version;
+    if (providedVersion !== undefined && providedVersion !== "0.5") {
+        throw new Error(`Inconsistent NGFF version in Multiscales metadata: expected "0.5" for RFC-9 OZX export, but got "${providedVersion}".`);
+    }
+}
+/**
+ * Prepare multiscales metadata for RFC-9 export.
+ * This includes processing axes for RFC enablement and setting version to 0.5.
+ *
+ * @param multiscales - Source multiscales data
+ * @param enabledRfcs - Optional list of RFC numbers to enable
+ * @returns Prepared metadata object
+ */
+export function prepareRfc9Metadata(multiscales, enabledRfcs) {
+    const _version = "0.5";
+    // Process axes - filter orientation based on enabledRfcs
+    const processedAxes = processAxesForRfcs(multiscales.metadata.axes, enabledRfcs);
+    return {
+        version: _version,
+        name: multiscales.metadata.name,
+        axes: processedAxes,
+        datasets: multiscales.metadata.datasets,
+        ...(multiscales.metadata.coordinateTransformations && {
+            coordinateTransformations: multiscales.metadata.coordinateTransformations,
+        }),
+        ...(multiscales.metadata.type && {
+            type: multiscales.metadata.type,
+        }),
+        ...(multiscales.metadata.metadata && {
+            metadata: multiscales.metadata.metadata,
+        }),
+    };
+}
+/**
+ * Create root group attributes for RFC-9 export.
+ *
+ * @param multiscalesMetadata - Prepared multiscales metadata
+ * @param multiscales - Original multiscales (for OMERO metadata)
+ * @returns Attributes object for root group
+ */
+export function createRfc9RootAttributes(multiscalesMetadata, multiscales) {
+    const _version = "0.5";
+    const attributes = {
+        ome: {
+            version: _version,
+            multiscales: [multiscalesMetadata],
+        },
+    };
+    // Add OMERO metadata at root level if present
+    if (multiscales.metadata.omero) {
+        attributes.omero = multiscales.metadata.omero;
+    }
+    return attributes;
+}
+/**
+ * Write multiscales data to a memory store for RFC-9 export.
+ * This is the shared implementation used by both Node and browser versions.
+ *
+ * @param store - Memory store to write to
+ * @param multiscales - Multiscales data to write
+ * @param enabledRfcs - Optional list of RFC numbers to enable
+ * @param writeImage - Function to write individual images
+ */
+export async function writeMultiscalesToMemoryStore(store, multiscales, enabledRfcs, writeImage) {
+    // Validate version
+    validateRfc9Version(multiscales);
+    // Create root location and group with zarrita API
+    const root = zarr.root(store);
+    // Prepare metadata
+    const multiscalesMetadata = prepareRfc9Metadata(multiscales, enabledRfcs);
+    // Create root attributes
+    const attributes = createRfc9RootAttributes(multiscalesMetadata, multiscales);
+    const rootGroup = await zarr.create(root, { attributes });
+    // Write each image in the multiscales
+    for (let i = 0; i < multiscales.images.length; i++) {
+        const image = multiscales.images[i];
+        const dataset = multiscales.metadata.datasets[i];
+        if (!dataset) {
+            throw new Error(`No dataset configuration found for image ${i}`);
+        }
+        await writeImage(rootGroup, image, dataset.path);
+    }
+}
+//# sourceMappingURL=to_ngff_zarr_ozx_common.js.map

package/esm/io/to_ngff_zarr_ozx_common.js.map

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