@fideus-labs/ngff-zarr 0.2.8 → 0.3.0

package/esm/io/rfc9_zip.js

@@ -0,0 +1,337 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * 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
+ */
+import { zipSync } from "fflate";
+/**
+ * Check if a path refers to a .ozx file.
+ *
+ * @param path - Path to check
+ * @returns True if path ends with .ozx extension
+ */
+export function isOzxPath(path) {
+    return path.endsWith(".ozx");
+}
+/**
+ * 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 function orderFilesForRfc9(keys) {
+    const zarrJsons = keys.filter((k) => k.endsWith("zarr.json"));
+    const others = keys.filter((k) => !k.endsWith("zarr.json"));
+    // Root zarr.json first
+    const rootIdx = zarrJsons.indexOf("zarr.json");
+    if (rootIdx > 0) {
+        zarrJsons.splice(rootIdx, 1);
+        zarrJsons.unshift("zarr.json");
+    }
+    // Sort by depth for breadth-first order
+    zarrJsons.sort((a, b) => {
+        if (a === "zarr.json")
+            return -1;
+        if (b === "zarr.json")
+            return 1;
+        return a.split("/").length - b.split("/").length;
+    });
+    return [...zarrJsons, ...others.sort()];
+}
+/**
+ * Add a ZIP comment to existing ZIP data.
+ *
+ * fflate doesn't support ZIP comments natively, so we manually
+ * modify the End of Central Directory (EOCD) record to add one.
+ *
+ * @param zipData - Original ZIP data
+ * @param comment - Comment string to add (UTF-8)
+ * @returns New ZIP data with comment
+ */
+function addZipComment(zipData, comment) {
+    const commentBytes = new TextEncoder().encode(comment);
+    if (commentBytes.length > 65535) {
+        throw new Error("ZIP comment too long (max 65535 bytes)");
+    }
+    // Find EOCD signature (0x06054b50) searching from end
+    // EOCD is at least 22 bytes, so start searching from length - 22
+    let eocdOffset = -1;
+    for (let i = zipData.length - 22; i >= 0; i--) {
+        if (zipData[i] === 0x50 &&
+            zipData[i + 1] === 0x4b &&
+            zipData[i + 2] === 0x05 &&
+            zipData[i + 3] === 0x06) {
+            eocdOffset = i;
+            break;
+        }
+    }
+    if (eocdOffset === -1) {
+        throw new Error("Invalid ZIP: End of Central Directory not found");
+    }
+    // Note: We could read current comment length at EOCD + 20, but we
+    // always replace any existing comment, so we just need the EOCD position.
+    // Calculate the size of ZIP without the current comment
+    const zipWithoutComment = eocdOffset + 22;
+    // Create new array: ZIP without old comment + new comment
+    const result = new Uint8Array(zipWithoutComment + commentBytes.length);
+    // Copy ZIP data up to and including EOCD (excluding old comment)
+    result.set(zipData.subarray(0, zipWithoutComment));
+    // Update comment length field (little-endian at EOCD + 20)
+    result[eocdOffset + 20] = commentBytes.length & 0xff;
+    result[eocdOffset + 21] = (commentBytes.length >> 8) & 0xff;
+    // Append new comment
+    result.set(commentBytes, zipWithoutComment);
+    return result;
+}
+/**
+ * Read the OME-Zarr version from ZIP comment.
+ *
+ * @param zipData - ZIP file data
+ * @returns OME-Zarr version string if found, null otherwise
+ */
+export function readOzxVersion(zipData) {
+    // Find EOCD signature searching from end
+    let eocdOffset = -1;
+    for (let i = zipData.length - 22; i >= 0; i--) {
+        if (zipData[i] === 0x50 &&
+            zipData[i + 1] === 0x4b &&
+            zipData[i + 2] === 0x05 &&
+            zipData[i + 3] === 0x06) {
+            eocdOffset = i;
+            break;
+        }
+    }
+    if (eocdOffset === -1) {
+        return null;
+    }
+    // Get comment length (little-endian uint16 at EOCD + 20)
+    const commentLength = zipData[eocdOffset + 20] |
+        (zipData[eocdOffset + 21] << 8);
+    if (commentLength === 0) {
+        return null;
+    }
+    // Extract comment bytes
+    const commentStart = eocdOffset + 22;
+    const commentBytes = zipData.subarray(commentStart, commentStart + commentLength);
+    try {
+        const commentStr = new TextDecoder("utf-8").decode(commentBytes);
+        const commentObj = JSON.parse(commentStr);
+        if (commentObj?.ome?.version) {
+            return commentObj.ome.version;
+        }
+    }
+    catch {
+        // Invalid JSON or encoding
+    }
+    return 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 function readOzxJsonFirst(zipData) {
+    // Find EOCD signature searching from end
+    let eocdOffset = -1;
+    for (let i = zipData.length - 22; i >= 0; i--) {
+        if (zipData[i] === 0x50 &&
+            zipData[i + 1] === 0x4b &&
+            zipData[i + 2] === 0x05 &&
+            zipData[i + 3] === 0x06) {
+            eocdOffset = i;
+            break;
+        }
+    }
+    if (eocdOffset === -1) {
+        return false;
+    }
+    // Get comment length (little-endian uint16 at EOCD + 20)
+    const commentLength = zipData[eocdOffset + 20] |
+        (zipData[eocdOffset + 21] << 8);
+    if (commentLength === 0) {
+        return false;
+    }
+    // Extract comment bytes
+    const commentStart = eocdOffset + 22;
+    const commentBytes = zipData.subarray(commentStart, commentStart + commentLength);
+    try {
+        const commentStr = new TextDecoder("utf-8").decode(commentBytes);
+        const commentObj = JSON.parse(commentStr);
+        if (commentObj?.ome?.zipFile?.centralDirectory?.jsonFirst === true) {
+            return true;
+        }
+    }
+    catch {
+        // Invalid JSON or encoding
+    }
+    return false;
+}
+/**
+ * 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 function getZipFileCompressionMethod(zipData, filename) {
+    // Search for local file header with matching filename
+    const filenameBytes = new TextEncoder().encode(filename);
+    let offset = 0;
+    while (offset < zipData.length - 30) {
+        // Check for local file header signature (0x04034b50)
+        if (zipData[offset] === 0x50 &&
+            zipData[offset + 1] === 0x4b &&
+            zipData[offset + 2] === 0x03 &&
+            zipData[offset + 3] === 0x04) {
+            // Get filename length (little-endian at offset + 26)
+            const nameLength = zipData[offset + 26] | (zipData[offset + 27] << 8);
+            // Get extra field length (little-endian at offset + 28)
+            const extraLength = zipData[offset + 28] | (zipData[offset + 29] << 8);
+            // Extract filename
+            const nameStart = offset + 30;
+            const nameEnd = nameStart + nameLength;
+            if (nameEnd <= zipData.length) {
+                const nameBytes = zipData.subarray(nameStart, nameEnd);
+                // Compare filenames
+                if (nameBytes.length === filenameBytes.length &&
+                    nameBytes.every((b, i) => b === filenameBytes[i])) {
+                    // Found the file, return compression method (at offset + 8)
+                    return zipData[offset + 8] | (zipData[offset + 9] << 8);
+                }
+            }
+            // Get compressed size to skip to next header
+            const compressedSize = zipData[offset + 18] |
+                (zipData[offset + 19] << 8) |
+                (zipData[offset + 20] << 16) |
+                (zipData[offset + 21] << 24);
+            offset = nameEnd + extraLength + compressedSize;
+        }
+        else {
+            offset++;
+        }
+    }
+    return 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 function getZipFileList(zipData) {
+    const files = [];
+    // Find EOCD to get central directory location
+    let eocdOffset = -1;
+    for (let i = zipData.length - 22; i >= 0; i--) {
+        if (zipData[i] === 0x50 &&
+            zipData[i + 1] === 0x4b &&
+            zipData[i + 2] === 0x05 &&
+            zipData[i + 3] === 0x06) {
+            eocdOffset = i;
+            break;
+        }
+    }
+    if (eocdOffset === -1) {
+        return files;
+    }
+    // Get central directory offset (little-endian uint32 at EOCD + 16)
+    let cdOffset = zipData[eocdOffset + 16] |
+        (zipData[eocdOffset + 17] << 8) |
+        (zipData[eocdOffset + 18] << 16) |
+        (zipData[eocdOffset + 19] << 24);
+    // Get number of entries (little-endian uint16 at EOCD + 10)
+    const numEntries = zipData[eocdOffset + 10] | (zipData[eocdOffset + 11] << 8);
+    // Parse central directory entries
+    for (let i = 0; i < numEntries && cdOffset < eocdOffset; i++) {
+        // Check for central directory file header signature (0x02014b50)
+        if (zipData[cdOffset] !== 0x50 ||
+            zipData[cdOffset + 1] !== 0x4b ||
+            zipData[cdOffset + 2] !== 0x01 ||
+            zipData[cdOffset + 3] !== 0x02) {
+            break;
+        }
+        // Get filename length (little-endian at offset + 28)
+        const nameLength = zipData[cdOffset + 28] | (zipData[cdOffset + 29] << 8);
+        // Get extra field length (little-endian at offset + 30)
+        const extraLength = zipData[cdOffset + 30] | (zipData[cdOffset + 31] << 8);
+        // Get comment length (little-endian at offset + 32)
+        const commentLength = zipData[cdOffset + 32] |
+            (zipData[cdOffset + 33] << 8);
+        // Extract filename
+        const nameStart = cdOffset + 46;
+        const nameEnd = nameStart + nameLength;
+        if (nameEnd <= zipData.length) {
+            const filename = new TextDecoder("utf-8").decode(zipData.subarray(nameStart, nameEnd));
+            files.push(filename);
+        }
+        // Move to next entry
+        cdOffset = nameEnd + extraLength + commentLength;
+    }
+    return files;
+}
+/**
+ * Normalize a store key by removing leading slashes.
+ * zarrita uses leading slashes (e.g., "/zarr.json") but ZIP files
+ * should use relative paths (e.g., "zarr.json").
+ */
+function normalizeKey(key) {
+    return key.startsWith("/") ? key.slice(1) : key;
+}
+/**
+ * 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 function memoryStoreToZip(store, options = {}) {
+    const version = options.version ?? "0.5";
+    // Get all keys, normalize them (remove leading slashes from zarrita),
+    // and order them for RFC-9 compliance
+    const keys = Array.from(store.keys()).map(normalizeKey);
+    const orderedKeys = orderFilesForRfc9(keys);
+    // Build files object in the correct order
+    // Note: JavaScript objects maintain insertion order for string keys
+    const files = {};
+    for (const key of orderedKeys) {
+        // Try both normalized and original key (with leading slash) for lookup
+        const data = store.get(key) ?? store.get("/" + key);
+        if (data) {
+            files[key] = data;
+        }
+    }
+    // Create ZIP with no compression (level: 0 = ZIP_STORED equivalent)
+    const zipData = zipSync(files, { level: 0 });
+    // Add OME-Zarr version comment as per RFC-9
+    // Include jsonFirst flag to indicate zarr.json files are ordered
+    // breadth-first and precede other content
+    const comment = JSON.stringify({
+        ome: {
+            version,
+            zipFile: { centralDirectory: { jsonFirst: true } },
+        },
+    });
+    const zipWithComment = addZipComment(zipData, comment);
+    return zipWithComment;
+}
+//# sourceMappingURL=rfc9_zip.js.map

package/esm/io/rfc9_zip.js.map

@@ -0,0 +1 @@
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package/esm/io/to_ngff_zarr-browser.d.ts

@@ -1,15 +1,41 @@
 import * as zarr from "zarrita";
 import type { Multiscales } from "../types/multiscales.js";
 import type { MemoryStore } from "./from_ngff_zarr-browser.js";
+export { isOzxPath } from "./rfc9_zip.js";
 export interface ToNgffZarrOptions {
     overwrite?: boolean;
     version?: "0.4" | "0.5";
     chunksPerShard?: number | number[] | Record<string, number>;
 }
+/**
+ * Options for writing to .ozx (RFC-9) format.
+ * Note: chunksPerShard is NOT supported for .ozx files and will throw an error.
+ */
+export interface ToNgffZarrOzxOptions {
+    /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
+    enabledRfcs?: number[] | undefined;
+}
 /**
  * Browser-compatible version of toNgffZarr.
  * Only supports MemoryStore (Map) for writing.
  * Does NOT support local file paths or HTTP URLs (use the full version in Node.js/Deno).
  */
 export declare function toNgffZarr(store: string | MemoryStore | zarr.FetchStore, multiscales: Multiscales, options?: ToNgffZarrOptions): Promise<void>;
+/**
+ * Create OME-Zarr .ozx ZIP data (RFC-9) - Browser version.
+ *
+ * This function creates an OME-Zarr hierarchy in memory and returns
+ * the ZIP data as a Uint8Array. This is the browser-compatible version
+ * that returns the raw ZIP data for download or further processing.
+ *
+ * Note: Sharding is NOT supported because zarrita does not currently
+ * support writing shards. If you need sharding, use the Python implementation.
+ *
+ * @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 declare function toNgffZarrOzx(multiscales: Multiscales, _options?: ToNgffZarrOzxOptions): Promise<Uint8Array>;
 //# sourceMappingURL=to_ngff_zarr-browser.d.ts.map

package/esm/io/to_ngff_zarr-browser.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"to_ngff_zarr-browser.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr-browser.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAE3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAC;AAI/D,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAE1C,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7D;AAED;;;GAGG;AACH,MAAM,WAAW,oBAAoB;IACnC,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;CACpC;AAED;;;;GAIG;AACH,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,WAAW,EACxB,OAAO,GAAE,iBAAsB,GAC9B,OAAO,CAAC,IAAI,CAAC,CAyFf;AAsVD;;;;;;;;;;;;;;;GAeG;AACH,wBAAsB,aAAa,CACjC,WAAW,EAAE,WAAW,EACxB,QAAQ,GAAE,oBAAyB,GAClC,OAAO,CAAC,UAAU,CAAC,CAkBrB"}

package/esm/io/to_ngff_zarr-browser.js

@@ -4,6 +4,9 @@
 // (which contains Node.js-specific modules like node:fs, node:buffer, node:path)
 import * as zarr from "zarrita";
 import { createQueue } from "../utils/create_queue.js";
+import { memoryStoreToZip } from "./rfc9_zip.js";
+import { writeMultiscalesToMemoryStore } from "./to_ngff_zarr_ozx_common.js";
+export { isOzxPath } from "./rfc9_zip.js";
 /**
  * Browser-compatible version of toNgffZarr.
  * Only supports MemoryStore (Map) for writing.
@@ -47,22 +50,24 @@ 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++) {
@@ -321,4 +326,30 @@ function calculateChunkStride(chunkShape) {
     }
     return stride;
 }
+/**
+ * Create OME-Zarr .ozx ZIP data (RFC-9) - Browser version.
+ *
+ * This function creates an OME-Zarr hierarchy in memory and returns
+ * the ZIP data as a Uint8Array. This is the browser-compatible version
+ * that returns the raw ZIP data for download or further processing.
+ *
+ * Note: Sharding is NOT supported because zarrita does not currently
+ * support writing shards. If you need sharding, use the Python implementation.
+ *
+ * @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 toNgffZarrOzx(multiscales, _options = {}) {
+    const enabledRfcs = _options.enabledRfcs;
+    // Create a memory store to hold the zarr data
+    const memoryStore = new Map();
+    // Use the shared write function
+    await writeMultiscalesToMemoryStore(memoryStore, multiscales, enabledRfcs, _writeImage);
+    // Convert the memory store to ZIP data
+    const zipData = memoryStoreToZip(memoryStore, { version: "0.5" });
+    return zipData;
+}
 //# sourceMappingURL=to_ngff_zarr-browser.js.map

package/esm/io/to_ngff_zarr-browser.js.map

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package/esm/io/to_ngff_zarr.d.ts

@@ -3,8 +3,84 @@ import type { Multiscales } from "../types/multiscales.js";
 import type { MemoryStore } from "./from_ngff_zarr.js";
 export interface ToNgffZarrOptions {
     overwrite?: boolean;
+    /**
+     * OME-Zarr version to write. Defaults to "0.4" for regular Zarr files.
+     * For .ozx files (RFC-9), this must be version 0.5. If omitted for .ozx files,
+     * it defaults to 0.5. If explicitly set to any other value for .ozx files,
+     * an error will be thrown.
+     */
     version?: "0.4" | "0.5";
     chunksPerShard?: number | number[] | Record<string, number>;
+    /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
+    enabledRfcs?: number[];
 }
+/**
+ * Options for writing to .ozx (RFC-9) format.
+ * Note: chunksPerShard is NOT supported for .ozx files and will throw an error.
+ */
+export interface ToNgffZarrOzxOptions {
+    /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
+    enabledRfcs?: number[] | undefined;
+}
+/**
+ * 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 declare function toNgffZarr(store: string | MemoryStore | zarr.FetchStore, multiscales: Multiscales, options?: ToNgffZarrOptions): Promise<void>;
+/**
+ * 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 declare function toNgffZarrOzx(path: string, multiscales: Multiscales, options?: ToNgffZarrOzxOptions): Promise<void>;
+/**
+ * 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 declare function toNgffZarrOzxData(multiscales: Multiscales, options?: ToNgffZarrOzxOptions): Promise<Uint8Array>;
 //# sourceMappingURL=to_ngff_zarr.d.ts.map

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

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