@fideus-labs/ngff-zarr 0.20.0 → 0.22.0

package/README.md

@@ -14,7 +14,7 @@ compatible with Deno, Node.js, and the browser.
 - 🦕 **Deno-first**: Built for Deno with first-class TypeScript support
 - 📦 **npm compatible**: Automatically builds npm packages using @deno/dnt
 - 🔍 **Type-safe**: Full TypeScript support with Zod schema validation
-- 🗂️ **OME-Zarr support**: Read and write OME-Zarr files using zarrita
+- 🗂️ **OME-Zarr support**: Read and write OME-Zarr v0.4, v0.5, and v0.6 using zarrita
 - 🧪 **Well-tested**: Comprehensive test suite using @std/assert
 - 🏗️ **Mirrors Python API**: TypeScript classes and types mirror the Python
   dataclasses

package/esm/io/from_ngff_zarr-browser.d.ts

@@ -5,7 +5,7 @@ export interface FromOmeZarrOptions {
     /** Enable schema validation of OME-Zarr metadata. */
     validate?: boolean;
     /** Expected OME-Zarr version. */
-    version?: "0.4" | "0.5";
+    version?: "0.4" | "0.5" | "0.6";
     /**
      * Optional decoded-chunk cache passed to `zarrGet` calls.
      *

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

@@ -1 +1 @@
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+{"version":3,"file":"from_ngff_zarr-browser.d.ts","sourceRoot":"","sources":["../../src/io/from_ngff_zarr-browser.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAGhC,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAQ1D,YAAY,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAE1D,MAAM,WAAW,kBAAkB;IACjC,qDAAqD;IACrD,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iCAAiC;IACjC,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,GAAG,KAAK,CAAC;IAChC;;;;;;;OAOG;IACH,KAAK,CAAC,EAAE,OAAO,yBAAyB,EAAE,UAAU,CAAC;CACtD;AAED,0DAA0D;AAC1D,MAAM,MAAM,mBAAmB,GAAG,kBAAkB,CAAC;AAErD,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD;;;;;GAKG;AACH,wBAAsB,WAAW,CAC/B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EAC7D,OAAO,GAAE,kBAAuB,GAC/B,OAAO,CAAC,eAAe,CAAC,CAkR1B;AAED,mDAAmD;AACnD,eAAO,MAAM,YAAY,oBAAc,CAAC"}

package/esm/io/from_ngff_zarr-browser.js

@@ -7,6 +7,8 @@ import { MetadataSchema } from "../schemas/zarr_metadata.js";
 import { NgffMultiscales } from "../types/multiscales.js";
 import { NgffImage } from "../types/ngff_image.js";
 import { extractMethodMetadata } from "../utils/parse_metadata.js";
+import { fromZarrAttrsV06 } from "../utils/from_zarr_attrs.js";
+import { isV06Version } from "../types/supported_versions.js";
 /**
  * Browser-compatible version of fromOmeZarr.
  * Supports HTTP/HTTPS URLs, MemoryStore (Map), FetchStore, and any
@@ -51,6 +53,37 @@ export async function fromOmeZarr(store, options = {}) {
             kind: "group",
         });
         const attrs = root.attrs;
+        // OME-Zarr v0.6 (RFC 5) uses a different on-disk shape (coordinateSystems +
+        // per-dataset sequence transforms) than the inline v0.4/v0.5 parser below,
+        // so delegate to the shared, environment-agnostic v0.6 reader.
+        const rootAttrsForVersion = attrs;
+        const omeForVersion = rootAttrsForVersion.ome;
+        if (omeForVersion && typeof omeForVersion.version === "string" &&
+            isV06Version(omeForVersion.version)) {
+            // Gate the requested-version mismatch behind `validate`, matching the node
+            // reader and the v0.4/v0.5 path below; otherwise behavior diverges by
+            // version and environment. The v0.6 family (`0.6` and draft `0.6.dev4`)
+            // is treated as equivalent.
+            if (validate && version && !isV06Version(version)) {
+                throw new Error(`Expected OME-Zarr version ${version}, but found ${omeForVersion.version}`);
+            }
+            const result = await fromZarrAttrsV06(rootAttrsForVersion, resolvedStore, validate);
+            const entry = omeForVersion.multiscales[0];
+            const { method, methodType, methodMetadata } = extractMethodMetadata(entry);
+            if (methodType) {
+                result.metadata.type = methodType;
+            }
+            if (methodMetadata) {
+                result.metadata.metadata = methodMetadata;
+            }
+            return new NgffMultiscales({
+                images: result.images,
+                metadata: result.metadata,
+                scaleFactors: undefined,
+                method,
+                chunks: undefined,
+            });
+        }
         // Handle both 0.4 (multiscales at root) and 0.5 (multiscales under ome) formats
         let multiscalesArray;
         let detectedVersion;

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

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

@@ -5,7 +5,7 @@ export interface FromOmeZarrOptions {
     /** Enable schema validation of OME-Zarr metadata. */
     validate?: boolean;
     /** Expected OME-Zarr version. */
-    version?: "0.4" | "0.5";
+    version?: "0.4" | "0.5" | "0.6";
     /**
      * Optional decoded-chunk cache passed to `zarrGet` calls.
      *

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

@@ -1 +1 @@
-{"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;AAEhC,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAY1D,YAAY,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAE1D,MAAM,WAAW,kBAAkB;IACjC,qDAAqD;IACrD,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iCAAiC;IACjC,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB;;;;;;;OAOG;IACH,KAAK,CAAC,EAAE,OAAO,yBAAyB,EAAE,UAAU,CAAC;CACtD;AAED,0DAA0D;AAC1D,MAAM,MAAM,mBAAmB,GAAG,kBAAkB,CAAC;AAErD,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD,wBAAsB,WAAW,CAE/B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EAC7D,OAAO,GAAE,kBAAuB,GAC/B,OAAO,CAAC,eAAe,CAAC,CAqI1B;AAED,mDAAmD;AACnD,eAAO,MAAM,YAAY,oBAAc,CAAC;AAExC,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"}
+{"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;AAEhC,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAa1D,YAAY,EAAE,UAAU,EAAE,MAAM,yBAAyB,CAAC;AAE1D,MAAM,WAAW,kBAAkB;IACjC,qDAAqD;IACrD,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iCAAiC;IACjC,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,GAAG,KAAK,CAAC;IAChC;;;;;;;OAOG;IACH,KAAK,CAAC,EAAE,OAAO,yBAAyB,EAAE,UAAU,CAAC;CACtD;AAED,0DAA0D;AAC1D,MAAM,MAAM,mBAAmB,GAAG,kBAAkB,CAAC;AAErD,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD,wBAAsB,WAAW,CAE/B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EAC7D,OAAO,GAAE,kBAAuB,GAC/B,OAAO,CAAC,eAAe,CAAC,CA4I1B;AAED,mDAAmD;AACnD,eAAO,MAAM,YAAY,oBAAc,CAAC;AAExC,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

@@ -2,8 +2,8 @@
 // SPDX-License-Identifier: MIT
 import * as zarr from "zarrita";
 import { NgffMultiscales } from "../types/multiscales.js";
-import { NgffVersion } from "../types/supported_versions.js";
-import { fromZarrAttrsV04, fromZarrAttrsV05, } from "../utils/from_zarr_attrs.js";
+import { isV06Version, NgffVersion } from "../types/supported_versions.js";
+import { fromZarrAttrsV04, fromZarrAttrsV05, fromZarrAttrsV06, } from "../utils/from_zarr_attrs.js";
 import { detectVersion, extractMethodMetadata, } from "../utils/parse_metadata.js";
 import { zarrGet } from "../utils/worker_pool.js";
 export async function fromOmeZarr(
@@ -76,15 +76,23 @@ store, options = {}) {
         }
         // Detect version from attributes
         const detectedVersion = detectVersion(rootAttrs);
-        // Validate version if requested
+        // Validate version if requested. Treat the v0.6 family as equivalent so a
+        // store tagged `0.6.dev4` on disk satisfies a requested version of `"0.6"`
+        // (and vice versa).
         if (validate && requestedVersion) {
-            if (detectedVersion !== requestedVersion) {
+            const versionsMatch = detectedVersion === requestedVersion ||
+                (isV06Version(detectedVersion) && isV06Version(requestedVersion));
+            if (!versionsMatch) {
                 throw new Error(`Expected OME-Zarr version ${requestedVersion}, but found ${detectedVersion}`);
             }
         }
-        // Parse metadata using version-specific function
+        // Parse metadata using version-specific function. The v0.6 reader handles
+        // both `0.6` and the draft `0.6.dev4` on-disk version strings.
         let result;
-        if (detectedVersion === NgffVersion.V05) {
+        if (isV06Version(detectedVersion)) {
+            result = await fromZarrAttrsV06(rootAttrs, resolvedStore, validate);
+        }
+        else if (detectedVersion === NgffVersion.V05) {
             result = await fromZarrAttrsV05(rootAttrs, resolvedStore, validate);
         }
         else {

package/esm/io/from_ngff_zarr.js.map

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

@@ -5,10 +5,8 @@ import type { MemoryStore } from "./from_ngff_zarr-browser.js";
 export { isOzxPath } from "./rfc9_zip.js";
 export interface ToOmeZarrOptions {
     overwrite?: boolean;
-    version?: "0.4" | "0.5";
+    version?: "0.4" | "0.5" | "0.6";
     chunksPerShard?: number | number[] | Record<string, number>;
-    /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
-    enabledRfcs?: number[];
     /**
      * Custom codec pipeline for array compression. When omitted the default
      * ``blosc(zstd)`` pipeline from {@link defaultCodecs} is used. Use
@@ -23,8 +21,6 @@ export type ToNgffZarrOptions = ToOmeZarrOptions;
  * Note: chunksPerShard is NOT supported for .ozx files and will throw an error.
  */
 export interface ToOmeZarrOzxOptions {
-    /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
-    enabledRfcs?: number[] | undefined;
     /**
      * Optional progress callback invoked after each chunk is written.
      * Reports cumulative progress across all scale levels.

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

@@ -1 +1 @@
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package/esm/io/to_ngff_zarr-browser.js

@@ -5,8 +5,10 @@
 import * as zarr from "zarrita";
 import { defaultCodecs } from "../utils/codecs.js";
 import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
+import { V06_ONDISK_VERSION } from "../types/supported_versions.js";
 import { memoryStoreToZip } from "./rfc9_zip.js";
-import { processAxesForRfcs, writeNgffMultiscalesToMemoryStore, } from "./to_ngff_zarr_ozx_common.js";
+import { processAxes, writeNgffMultiscalesToMemoryStore, } from "./to_ngff_zarr_ozx_common.js";
+import { buildV06MultiscalesEntry, legacyTopLevelTransforms, } from "../utils/v06_metadata.js";
 export { isOzxPath } from "./rfc9_zip.js";
 /**
  * Browser-compatible version of toOmeZarr.
@@ -16,7 +18,6 @@ export { isOzxPath } from "./rfc9_zip.js";
 export async function toOmeZarr(store, multiscales, options = {}) {
     const _overwrite = options.overwrite ?? true;
     const _version = options.version ?? "0.4";
-    const enabledRfcs = options.enabledRfcs;
     try {
         // Determine the appropriate store type based on the path
         let _resolvedStore;
@@ -35,43 +36,64 @@ export async function toOmeZarr(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: 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 the root group with OME-Zarr metadata
-        // 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"
-            ? {
+        // Process axes (orientation included when present)
+        const processedAxes = processAxes(multiscales.metadata.axes);
+        // Create the root group with OME-Zarr metadata.
+        // - v0.6 (RFC 5): coordinate systems + per-dataset sequence transforms,
+        //   wrapped under the "ome" property.
+        // - v0.5: axes carried directly, wrapped under "ome".
+        // - v0.4: axes carried directly, placed at the root.
+        let attributes;
+        if (_version === "0.6") {
+            const v06Entry = buildV06MultiscalesEntry(multiscales.metadata, processedAxes);
+            attributes = {
                 ome: {
-                    version: _version,
-                    multiscales: [multiscalesMetadata],
+                    // The v0.6 spec is still a draft; tag the store with the development
+                    // version `0.6.dev4` even though the requested version is `"0.6"`.
+                    version: V06_ONDISK_VERSION,
+                    multiscales: [v06Entry],
                     ...(multiscales.metadata.omero && {
                         omero: multiscales.metadata.omero,
                     }),
                 },
-            }
-            : {
-                multiscales: [multiscalesMetadata],
-                ...(multiscales.metadata.omero && {
-                    omero: multiscales.metadata.omero,
+            };
+        }
+        else {
+            // v0.4/v0.5 only support the simple scale/translation subset of top-level
+            // transformations; drop richer v0.6 transforms when downgrading.
+            const legacyTransforms = legacyTopLevelTransforms(multiscales.metadata.coordinateTransformations);
+            const multiscalesMetadata = {
+                version: _version,
+                name: multiscales.metadata.name,
+                axes: processedAxes,
+                datasets: multiscales.metadata.datasets,
+                ...(legacyTransforms && {
+                    coordinateTransformations: legacyTransforms,
+                }),
+                ...(multiscales.metadata.type && {
+                    type: multiscales.metadata.type,
+                }),
+                ...(multiscales.metadata.metadata && {
+                    metadata: multiscales.metadata.metadata,
                 }),
             };
+            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,
+                    }),
+                };
+        }
         const rootGroup = await zarr.create(root, { attributes });
         // Write each image in the multiscales
         for (let i = 0; i < multiscales.images.length; i++) {
@@ -351,11 +373,10 @@ function calculateChunkStride(chunkShape) {
  * @see https://ngff.openmicroscopy.org/rfc/9/index.html
  */
 export async function toOmeZarrOzx(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 writeNgffMultiscalesToMemoryStore(memoryStore, multiscales, enabledRfcs, _writeImage, _options.onProgress ?? null);
+    await writeNgffMultiscalesToMemoryStore(memoryStore, multiscales, _writeImage, _options.onProgress ?? null);
     // Convert the memory store to ZIP data
     const zipData = memoryStoreToZip(memoryStore, { version: "0.5" });
     return zipData;

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

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package/esm/io/to_ngff_zarr.d.ts

@@ -6,14 +6,13 @@ export interface ToOmeZarrOptions {
     overwrite?: boolean;
     /**
      * OME-Zarr version to write. Defaults to "0.5" for regular Zarr files.
+     * Version "0.6" writes RFC 5 coordinate systems and transformations.
      * 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";
+    version?: "0.4" | "0.5" | "0.6";
     chunksPerShard?: number | number[] | Record<string, number>;
-    /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
-    enabledRfcs?: number[];
     /**
      * Custom codec pipeline for array compression. When omitted the default
      * ``blosc(zstd)`` pipeline from {@link defaultCodecs} is used. Use
@@ -28,8 +27,6 @@ export type ToNgffZarrOptions = ToOmeZarrOptions;
  * Note: chunksPerShard is NOT supported for .ozx files and will throw an error.
  */
 export interface ToOmeZarrOzxOptions {
-    /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
-    enabledRfcs?: number[] | undefined;
     /**
      * Optional progress callback invoked after each chunk is written.
      * Reports cumulative progress across all scale levels.

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

@@ -1 +1 @@
-{"version":3,"file":"to_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAE/D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAGpD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAOvD,MAAM,WAAW,gBAAgB;IAC/B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB;;;;;OAKG;IACH,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC5D,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB;;;;OAIG;IACH,MAAM,CAAC,EAAE,SAAS,EAAE,CAAC;CACtB;AAED,wDAAwD;AACxD,MAAM,MAAM,iBAAiB,GAAG,gBAAgB,CAAC;AAEjD;;;GAGG;AACH,MAAM,WAAW,mBAAmB;IAClC,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACnC;;;;;;OAMG;IACH,UAAU,CAAC,EACP,CAAC,CAAC,eAAe,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,KAAK,IAAI,CAAC,GACxD,SAAS,CAAC;CACf;AAED,2DAA2D;AAC3D,MAAM,MAAM,oBAAoB,GAAG,mBAAmB,CAAC;AAEvD;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AACH,wBAAsB,SAAS,CAC7B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,eAAe,EAC5B,OAAO,GAAE,gBAAqB,GAC7B,OAAO,CAAC,IAAI,CAAC,CA0If;AAED,iDAAiD;AACjD,eAAO,MAAM,UAAU,kBAAY,CAAC;AA2VpC;;;;;;;;;;;;;;;;;;;GAmBG;AACH,wBAAsB,YAAY,CAChC,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,eAAe,EAC5B,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,IAAI,CAAC,CAyBf;AAED,oDAAoD;AACpD,eAAO,MAAM,aAAa,qBAAe,CAAC;AAE1C;;;;;;;;;;;;GAYG;AACH,wBAAsB,gBAAgB,CACpC,WAAW,EAAE,eAAe,EAC5B,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,UAAU,CAAC,CAoBrB;AAED,wDAAwD;AACxD,eAAO,MAAM,iBAAiB,yBAAmB,CAAC"}
+{"version":3,"file":"to_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAE/D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAGpD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAYvD,MAAM,WAAW,gBAAgB;IAC/B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB;;;;;;OAMG;IACH,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,GAAG,KAAK,CAAC;IAChC,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC5D;;;;OAIG;IACH,MAAM,CAAC,EAAE,SAAS,EAAE,CAAC;CACtB;AAED,wDAAwD;AACxD,MAAM,MAAM,iBAAiB,GAAG,gBAAgB,CAAC;AAEjD;;;GAGG;AACH,MAAM,WAAW,mBAAmB;IAClC;;;;;;OAMG;IACH,UAAU,CAAC,EACP,CAAC,CAAC,eAAe,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,KAAK,IAAI,CAAC,GACxD,SAAS,CAAC;CACf;AAED,2DAA2D;AAC3D,MAAM,MAAM,oBAAoB,GAAG,mBAAmB,CAAC;AAEvD;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AACH,wBAAsB,SAAS,CAC7B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,eAAe,EAC5B,OAAO,GAAE,gBAAqB,GAC7B,OAAO,CAAC,IAAI,CAAC,CA8Jf;AAED,iDAAiD;AACjD,eAAO,MAAM,UAAU,kBAAY,CAAC;AA2VpC;;;;;;;;;;;;;;;;;;;GAmBG;AACH,wBAAsB,YAAY,CAChC,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,eAAe,EAC5B,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,IAAI,CAAC,CAyBf;AAED,oDAAoD;AACpD,eAAO,MAAM,aAAa,qBAAe,CAAC;AAE1C;;;;;;;;;;;;GAYG;AACH,wBAAsB,gBAAgB,CACpC,WAAW,EAAE,eAAe,EAC5B,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,UAAU,CAAC,CAiBrB;AAED,wDAAwD;AACxD,eAAO,MAAM,iBAAiB,yBAAmB,CAAC"}

package/esm/io/to_ngff_zarr.js

@@ -3,8 +3,10 @@
 import * as zarr from "zarrita";
 import { defaultCodecs } from "../utils/codecs.js";
 import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
+import { V06_ONDISK_VERSION } from "../types/supported_versions.js";
 import { isOzxPath, memoryStoreToZip } from "./rfc9_zip.js";
-import { processAxesForRfcs, writeNgffMultiscalesToMemoryStore, } from "./to_ngff_zarr_ozx_common.js";
+import { processAxes, writeNgffMultiscalesToMemoryStore, } from "./to_ngff_zarr_ozx_common.js";
+import { buildV06MultiscalesEntry, legacyTopLevelTransforms, } from "../utils/v06_metadata.js";
 /**
  * Write multiscales data to an OME-Zarr store.
  *
@@ -33,7 +35,6 @@ import { processAxesForRfcs, writeNgffMultiscalesToMemoryStore, } from "./to_ngf
 export async function toOmeZarr(store, multiscales, options = {}) {
     const _overwrite = options.overwrite ?? true;
     const _version = options.version ?? "0.5";
-    const enabledRfcs = options.enabledRfcs;
     // Handle .ozx paths (RFC-9)
     if (typeof store === "string" && isOzxPath(store)) {
         // Validate version - RFC-9 requires version 0.5
@@ -50,7 +51,7 @@ export async function toOmeZarr(store, multiscales, options = {}) {
                 "zarrita does not currently support writing shards.");
         }
         // Delegate to toOmeZarrOzx (which always uses version 0.5)
-        await toOmeZarrOzx(store, multiscales, { enabledRfcs });
+        await toOmeZarrOzx(store, multiscales);
         return;
     }
     try {
@@ -83,43 +84,64 @@ export async function toOmeZarr(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: 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 the root group with OME-Zarr metadata
-        // 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"
-            ? {
+        // Process axes (orientation included when present)
+        const processedAxes = processAxes(multiscales.metadata.axes);
+        // Create the root group with OME-Zarr metadata.
+        // - v0.6 (RFC 5): coordinate systems + per-dataset sequence transforms,
+        //   wrapped under the "ome" property.
+        // - v0.5: axes carried directly, wrapped under "ome".
+        // - v0.4: axes carried directly, placed at the root.
+        let attributes;
+        if (_version === "0.6") {
+            const v06Entry = buildV06MultiscalesEntry(multiscales.metadata, processedAxes);
+            attributes = {
                 ome: {
-                    version: _version,
-                    multiscales: [multiscalesMetadata],
+                    // The v0.6 spec is still a draft; tag the store with the development
+                    // version `0.6.dev4` even though the requested version is `"0.6"`.
+                    version: V06_ONDISK_VERSION,
+                    multiscales: [v06Entry],
                     ...(multiscales.metadata.omero && {
                         omero: multiscales.metadata.omero,
                     }),
                 },
-            }
-            : {
-                multiscales: [multiscalesMetadata],
-                ...(multiscales.metadata.omero && {
-                    omero: multiscales.metadata.omero,
+            };
+        }
+        else {
+            // v0.4/v0.5 only support the simple scale/translation subset of top-level
+            // transformations; drop richer v0.6 transforms when downgrading.
+            const legacyTransforms = legacyTopLevelTransforms(multiscales.metadata.coordinateTransformations);
+            const multiscalesMetadata = {
+                version: _version,
+                name: multiscales.metadata.name,
+                axes: processedAxes,
+                datasets: multiscales.metadata.datasets,
+                ...(legacyTransforms && {
+                    coordinateTransformations: legacyTransforms,
+                }),
+                ...(multiscales.metadata.type && {
+                    type: multiscales.metadata.type,
+                }),
+                ...(multiscales.metadata.metadata && {
+                    metadata: multiscales.metadata.metadata,
                 }),
             };
+            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,
+                    }),
+                };
+        }
         const rootGroup = await zarr.create(root, { attributes });
         // Write each image in the multiscales
         for (let i = 0; i < multiscales.images.length; i++) {
@@ -437,13 +459,12 @@ export const toNgffZarrOzx = toOmeZarrOzx;
  * @see https://ngff.openmicroscopy.org/rfc/9/index.html
  */
 export async function toOmeZarrOzxData(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 toOmeZarr logic
     // but we need to inline the core logic since toOmeZarr would
     // try to detect .ozx again
-    await _writeToMemoryStore(memoryStore, multiscales, enabledRfcs, options.onProgress ?? null);
+    await _writeToMemoryStore(memoryStore, multiscales, options.onProgress ?? null);
     // Convert the memory store to ZIP data
     const zipData = memoryStoreToZip(memoryStore, { version: "0.5" });
     return zipData;
@@ -454,7 +475,7 @@ export const toNgffZarrOzxData = toOmeZarrOzxData;
  * Internal function to write multiscales to a memory store.
  * Used by toOmeZarrOzxData to avoid recursion with toOmeZarr.
  */
-async function _writeToMemoryStore(store, multiscales, enabledRfcs, onProgress) {
-    await writeNgffMultiscalesToMemoryStore(store, multiscales, enabledRfcs, _writeImage, onProgress);
+async function _writeToMemoryStore(store, multiscales, onProgress) {
+    await writeNgffMultiscalesToMemoryStore(store, multiscales, _writeImage, onProgress);
 }
 //# sourceMappingURL=to_ngff_zarr.js.map