@fideus-labs/ngff-zarr 0.2.7 → 0.3.0

package/esm/process/to_multiscales-shared.js.map

@@ -1 +1 @@
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package/esm/types/supported_versions.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Constants for ngff-zarr package.
+ */
+export declare enum NgffVersion {
+    V01 = "0.1",
+    V02 = "0.2",
+    V03 = "0.3",
+    V04 = "0.4",
+    V05 = "0.5",
+    LATEST = "0.5"
+}
+/**
+ * Supported NGFF specification versions
+ */
+export declare const SUPPORTED_VERSIONS: readonly NgffVersion[];
+/**
+ * Check if a version string is supported
+ */
+export declare function isSupportedVersion(version: string): version is NgffVersion;
+//# sourceMappingURL=supported_versions.d.ts.map

package/esm/types/supported_versions.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"supported_versions.d.ts","sourceRoot":"","sources":["../../src/types/supported_versions.ts"],"names":[],"mappings":"AAGA;;GAEG;AAEH,oBAAY,WAAW;IACrB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,MAAM,QAAQ;CACf;AAED;;GAEG;AACH,eAAO,MAAM,kBAAkB,EAAE,SAAS,WAAW,EAM3C,CAAC;AAEX;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,IAAI,WAAW,CAE1E"}

package/esm/types/supported_versions.js

@@ -0,0 +1,31 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * Constants for ngff-zarr package.
+ */
+export var NgffVersion;
+(function (NgffVersion) {
+    NgffVersion["V01"] = "0.1";
+    NgffVersion["V02"] = "0.2";
+    NgffVersion["V03"] = "0.3";
+    NgffVersion["V04"] = "0.4";
+    NgffVersion["V05"] = "0.5";
+    NgffVersion["LATEST"] = "0.5";
+})(NgffVersion || (NgffVersion = {}));
+/**
+ * Supported NGFF specification versions
+ */
+export const SUPPORTED_VERSIONS = [
+    NgffVersion.V01,
+    NgffVersion.V02,
+    NgffVersion.V03,
+    NgffVersion.V04,
+    NgffVersion.V05,
+];
+/**
+ * Check if a version string is supported
+ */
+export function isSupportedVersion(version) {
+    return Object.values(NgffVersion).includes(version);
+}
+//# sourceMappingURL=supported_versions.js.map

package/esm/types/supported_versions.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"supported_versions.js","sourceRoot":"","sources":["../../src/types/supported_versions.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAE/B;;GAEG;AAEH,MAAM,CAAN,IAAY,WAOX;AAPD,WAAY,WAAW;IACrB,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,0BAAW,CAAA;IACX,6BAAc,CAAA;AAChB,CAAC,EAPW,WAAW,KAAX,WAAW,QAOtB;AAED;;GAEG;AACH,MAAM,CAAC,MAAM,kBAAkB,GAA2B;IACxD,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;IACf,WAAW,CAAC,GAAG;CACP,CAAC;AAEX;;GAEG;AACH,MAAM,UAAU,kBAAkB,CAAC,OAAe;IAChD,OAAO,MAAM,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,OAAsB,CAAC,CAAC;AACrE,CAAC"}

package/esm/types/zarr_metadata.d.ts

@@ -1,8 +1,20 @@
 import type { AxesType, SupportedDims, Units } from "./units.js";
+import { NgffVersion } from "./supported_versions.js";
+import type { NgffImage } from "./ngff_image.js";
+import type { AnatomicalOrientation } from "./rfc4.js";
+/**
+ * Orientation metadata for spatial axes (RFC 4).
+ * This interface represents the serialized form in the zarr metadata.
+ */
+export interface AxisOrientation {
+    type: string;
+    value: string;
+}
 export interface Axis {
     name: SupportedDims;
     type: AxesType;
     unit: Units | undefined;
+    orientation?: AxisOrientation | AnatomicalOrientation | undefined;
 }
 export interface Identity {
     type: "identity";
@@ -41,7 +53,10 @@ export interface MethodMetadata {
     method: string;
     version: string;
 }
-export interface Metadata {
+/**
+ * OME-Zarr Metadata interface for data transfer
+ */
+export interface MetadataInterface {
     axes: Axis[];
     datasets: Dataset[];
     coordinateTransformations: Transform[] | undefined;
@@ -51,6 +66,33 @@ export interface Metadata {
     type?: string;
     metadata?: MethodMetadata;
 }
+/**
+ * Result from parsing zarr attributes
+ */
+export interface FromZarrAttrsResult {
+    metadata: MetadataInterface;
+    images: NgffImage[];
+}
+export type Metadata = MetadataInterface;
+/**
+ * Result from parsing zarr attributes
+ */
+export interface FromZarrAttrsResult {
+    metadata: MetadataInterface;
+    images: NgffImage[];
+}
+/**
+ * Supported dimension names for backward compatibility
+ */
+export declare const SUPPORTED_DIMS: readonly SupportedDims[];
+/**
+ * Create a Metadata object with the specified version
+ */
+export declare function createMetadataWithVersion(metadata: MetadataInterface, targetVersion: string | NgffVersion): MetadataInterface;
+/**
+ * Get dimension names from metadata axes
+ */
+export declare function getDimensionNames(metadata: MetadataInterface): string[];
 export declare function validateColor(color: string): void;
 export declare function createScale(scale: number[]): Scale;
 export declare function createTranslation(translation: number[]): Translation;

package/esm/types/zarr_metadata.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"zarr_metadata.d.ts","sourceRoot":"","sources":["../../src/types/zarr_metadata.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAC;AACjD,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,WAAW,CAAC;AAEvD;;;GAGG;AACH,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,IAAI;IACnB,IAAI,EAAE,aAAa,CAAC;IACpB,IAAI,EAAE,QAAQ,CAAC;IACf,IAAI,EAAE,KAAK,GAAG,SAAS,CAAC;IACxB,WAAW,CAAC,EAAE,eAAe,GAAG,qBAAqB,GAAG,SAAS,CAAC;CACnE;AAED,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,UAAU,CAAC;CAClB;AAED,MAAM,WAAW,KAAK;IACpB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,IAAI,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,WAAW;IAC1B,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,IAAI,EAAE,aAAa,CAAC;CACrB;AAED,MAAM,MAAM,SAAS,GAAG,KAAK,GAAG,WAAW,CAAC;AAE5C,MAAM,WAAW,OAAO;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,yBAAyB,EAAE,SAAS,EAAE,CAAC;CACxC;AAED,MAAM,WAAW,WAAW;IAC1B,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,WAAW,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,KAAK;IACpB,QAAQ,EAAE,YAAY,EAAE,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,cAAc;IAC7B,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,IAAI,EAAE,CAAC;IACb,QAAQ,EAAE,OAAO,EAAE,CAAC;IACpB,yBAAyB,EAAE,SAAS,EAAE,GAAG,SAAS,CAAC;IACnD,KAAK,EAAE,KAAK,GAAG,SAAS,CAAC;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,cAAc,CAAC;CAC3B;AAED;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,QAAQ,EAAE,iBAAiB,CAAC;IAC5B,MAAM,EAAE,SAAS,EAAE,CAAC;CACrB;AAGD,MAAM,MAAM,QAAQ,GAAG,iBAAiB,CAAC;AAEzC;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,QAAQ,EAAE,iBAAiB,CAAC;IAC5B,MAAM,EAAE,SAAS,EAAE,CAAC;CACrB;AAED;;GAEG;AACH,eAAO,MAAM,cAAc,EAAE,SAAS,aAAa,EAMzC,CAAC;AAEX;;GAEG;AACH,wBAAgB,yBAAyB,CACvC,QAAQ,EAAE,iBAAiB,EAC3B,aAAa,EAAE,MAAM,GAAG,WAAW,GAClC,iBAAiB,CAoBnB;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,iBAAiB,GAAG,MAAM,EAAE,CAEvE;AAED,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAIjD;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,KAAK,CAElD;AAED,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,WAAW,CAEpE;AAED,wBAAgB,cAAc,IAAI,QAAQ,CAEzC"}

package/esm/types/zarr_metadata.js

@@ -1,3 +1,43 @@
+import { NgffVersion } from "./supported_versions.js";
+/**
+ * Supported dimension names for backward compatibility
+ */
+export const SUPPORTED_DIMS = [
+    "t",
+    "c",
+    "z",
+    "y",
+    "x",
+];
+/**
+ * Create a Metadata object with the specified version
+ */
+export function createMetadataWithVersion(metadata, targetVersion) {
+    const version = typeof targetVersion === "string"
+        ? targetVersion
+        : targetVersion;
+    if (version === NgffVersion.V04) {
+        return {
+            ...metadata,
+            version: "0.4",
+        };
+    }
+    else if (version === NgffVersion.V05) {
+        return {
+            ...metadata,
+            version: "0.5",
+        };
+    }
+    else {
+        throw new Error(`Unsupported version conversion: ${metadata.version} -> ${version}`);
+    }
+}
+/**
+ * Get dimension names from metadata axes
+ */
+export function getDimensionNames(metadata) {
+    return metadata.axes.map((ax) => ax.name);
+}
 export function validateColor(color) {
     if (!/^[0-9A-Fa-f]{6}$/.test(color)) {
         throw new Error(`Invalid color '${color}'. Must be 6 hex digits.`);

package/esm/types/zarr_metadata.js.map

@@ -1 +1 @@
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+{"version":3,"file":"zarr_metadata.js","sourceRoot":"","sources":["../../src/types/zarr_metadata.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAmGtD;;GAEG;AACH,MAAM,CAAC,MAAM,cAAc,GAA6B;IACtD,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;CACK,CAAC;AAEX;;GAEG;AACH,MAAM,UAAU,yBAAyB,CACvC,QAA2B,EAC3B,aAAmC;IAEnC,MAAM,OAAO,GAAG,OAAO,aAAa,KAAK,QAAQ;QAC/C,CAAC,CAAE,aAA6B;QAChC,CAAC,CAAC,aAAa,CAAC;IAElB,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QAChC,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;SACf,CAAC;IACJ,CAAC;SAAM,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QACvC,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;SACf,CAAC;IACJ,CAAC;SAAM,CAAC;QACN,MAAM,IAAI,KAAK,CACb,mCAAmC,QAAQ,CAAC,OAAO,OAAO,OAAO,EAAE,CACpE,CAAC;IACJ,CAAC;AACH,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,iBAAiB,CAAC,QAA2B;IAC3D,OAAO,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC;AAC5C,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,KAAa;IACzC,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACpC,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,0BAA0B,CAAC,CAAC;IACrE,CAAC;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAe;IACzC,OAAO,EAAE,KAAK,EAAE,CAAC,GAAG,KAAK,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;AAC9C,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,WAAqB;IACrD,OAAO,EAAE,WAAW,EAAE,CAAC,GAAG,WAAW,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC;AAChE,CAAC;AAED,MAAM,UAAU,cAAc;IAC5B,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;AAC9B,CAAC"}

package/esm/utils/factory.d.ts

@@ -1,10 +1,11 @@
 import { NgffImage } from "../types/ngff_image.js";
 import { Multiscales } from "../types/multiscales.js";
-import type { Axis, Dataset, Metadata, Scale, Translation } from "../types/zarr_metadata.js";
+import type { Axis, AxisOrientation, Dataset, Metadata, Scale, Translation } from "../types/zarr_metadata.js";
 import type { AxesType, SupportedDims, Units } from "../types/units.js";
 import type { Methods } from "../types/methods.js";
+import type { AnatomicalOrientation } from "../types/rfc4.js";
 export declare function createNgffImage(_data: ArrayBuffer | number[], shape: number[], dtype: string, dims: string[], scale: Record<string, number>, translation: Record<string, number>, name?: string): Promise<NgffImage>;
-export declare function createAxis(name: SupportedDims, type: AxesType, unit?: Units): Axis;
+export declare function createAxis(name: SupportedDims, type: AxesType, unit?: Units, orientation?: AxisOrientation | AnatomicalOrientation): Axis;
 export declare function createScale(scale: number[]): Scale;
 export declare function createTranslation(translation: number[]): Translation;
 export declare function createDataset(path: string, scale: number[], translation: number[]): Dataset;

package/esm/utils/factory.d.ts.map

@@ -1 +1 @@
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package/esm/utils/factory.js

@@ -27,12 +27,16 @@ export async function createNgffImage(_data, shape, dtype, dims, scale, translat
         computedCallbacks: undefined,
     });
 }
-export function createAxis(name, type, unit) {
-    return {
+export function createAxis(name, type, unit, orientation) {
+    const axis = {
         name,
         type,
         unit: unit || undefined,
     };
+    if (orientation) {
+        axis.orientation = orientation;
+    }
+    return axis;
 }
 export function createScale(scale) {
     return {

package/esm/utils/factory.js.map

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package/esm/utils/from_zarr_attrs.d.ts

@@ -0,0 +1,21 @@
+/**
+ * Functions for parsing Metadata from zarr store attributes.
+ */
+import * as zarr from "zarrita";
+import type { FromZarrAttrsResult } from "../types/zarr_metadata.js";
+import type { MemoryStore } from "../io/from_ngff_zarr.js";
+/**
+ * Parse Metadata and NgffImages from OME-Zarr v0.4 root attributes.
+ *
+ * This mirrors the Python `Metadata._from_zarr_attrs` class method.
+ */
+export declare function fromZarrAttrsV04(rootAttrs: Record<string, unknown>, store: MemoryStore | zarr.FetchStore | zarr.Readable, validate?: boolean): Promise<FromZarrAttrsResult>;
+/**
+ * Parse Metadata and NgffImages from OME-Zarr v0.5 root attributes.
+ *
+ * The v0.5 format typically wraps multiscales under the "ome" key,
+ * but for compatibility we also handle the case where multiscales
+ * is at the root level (as written by toNgffZarr).
+ */
+export declare function fromZarrAttrsV05(rootAttrs: Record<string, unknown>, store: MemoryStore | zarr.FetchStore | zarr.Readable, validate?: boolean): Promise<FromZarrAttrsResult>;
+//# sourceMappingURL=from_zarr_attrs.d.ts.map

package/esm/utils/from_zarr_attrs.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"from_zarr_attrs.d.ts","sourceRoot":"","sources":["../../src/utils/from_zarr_attrs.ts"],"names":[],"mappings":"AAGA;;GAEG;AAEH,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAGV,mBAAmB,EAMpB,MAAM,2BAA2B,CAAC;AAKnC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAsE3D;;;;GAIG;AACH,wBAAsB,gBAAgB,CACpC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAClC,KAAK,EAAE,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EACpD,QAAQ,UAAQ,GACf,OAAO,CAAC,mBAAmB,CAAC,CA6R9B;AAED;;;;;;GAMG;AACH,wBAAsB,gBAAgB,CACpC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAClC,KAAK,EAAE,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EACpD,QAAQ,UAAQ,GACf,OAAO,CAAC,mBAAmB,CAAC,CA6B9B"}

package/esm/utils/from_zarr_attrs.js

@@ -0,0 +1,326 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * Functions for parsing Metadata from zarr store attributes.
+ */
+import * as zarr from "zarrita";
+import { SUPPORTED_DIMS } from "../types/zarr_metadata.js";
+import { NgffImage } from "../types/ngff_image.js";
+import { parseOmero } from "./parse_metadata.js";
+import { hasRfc4OrientationMetadata, validateRfc4Orientation, } from "./rfc4_validation.js";
+import { AnatomicalOrientationValues } from "../types/rfc4.js";
+/**
+ * Map string orientation values to enum values
+ */
+const ORIENTATION_VALUE_MAP = {
+    "left-to-right": AnatomicalOrientationValues.LeftToRight,
+    "right-to-left": AnatomicalOrientationValues.RightToLeft,
+    "anterior-to-posterior": AnatomicalOrientationValues.AnteriorToPosterior,
+    "posterior-to-anterior": AnatomicalOrientationValues.PosteriorToAnterior,
+    "inferior-to-superior": AnatomicalOrientationValues.InferiorToSuperior,
+    "superior-to-inferior": AnatomicalOrientationValues.SuperiorToInferior,
+    "dorsal-to-ventral": AnatomicalOrientationValues.DorsalToVentral,
+    "ventral-to-dorsal": AnatomicalOrientationValues.VentralToDorsal,
+    "dorsal-to-palmar": AnatomicalOrientationValues.DorsalToPalmar,
+    "palmar-to-dorsal": AnatomicalOrientationValues.PalmarToDorsal,
+    "dorsal-to-plantar": AnatomicalOrientationValues.DorsalToPlantar,
+    "plantar-to-dorsal": AnatomicalOrientationValues.PlantarToDorsal,
+    "rostral-to-caudal": AnatomicalOrientationValues.RostralToCaudal,
+    "caudal-to-rostral": AnatomicalOrientationValues.CaudalToRostral,
+    "cranial-to-caudal": AnatomicalOrientationValues.CranialToCaudal,
+    "caudal-to-cranial": AnatomicalOrientationValues.CaudalToCranial,
+    "proximal-to-distal": AnatomicalOrientationValues.ProximalToDistal,
+    "distal-to-proximal": AnatomicalOrientationValues.DistalToProximal,
+};
+/**
+ * Extract anatomical orientations from axes metadata.
+ * Returns a record mapping axis names to their orientations, or undefined if no orientations.
+ */
+function extractOrientationsFromAxes(axesData) {
+    const orientations = {};
+    let hasOrientation = false;
+    for (const axis of axesData) {
+        if (typeof axis === "object" && axis !== null) {
+            const axisObj = axis;
+            const name = axisObj.name;
+            const orientation = axisObj.orientation;
+            if (orientation &&
+                typeof orientation === "object" &&
+                orientation.type === "anatomical") {
+                const enumValue = ORIENTATION_VALUE_MAP[orientation.value];
+                if (enumValue) {
+                    orientations[name] = {
+                        type: "anatomical",
+                        value: enumValue,
+                    };
+                    hasOrientation = true;
+                }
+            }
+        }
+    }
+    return hasOrientation ? orientations : undefined;
+}
+/**
+ * Parse Metadata and NgffImages from OME-Zarr v0.4 root attributes.
+ *
+ * This mirrors the Python `Metadata._from_zarr_attrs` class method.
+ */
+export async function fromZarrAttrsV04(rootAttrs, store, validate = false) {
+    // Extract the multiscales metadata
+    const multiscalesArray = rootAttrs.multiscales;
+    if (!Array.isArray(multiscalesArray) || multiscalesArray.length === 0) {
+        throw new Error("No multiscales metadata found in root attributes");
+    }
+    const multiscalesMetadata = multiscalesArray[0];
+    // Validate the root attributes against the OME-Zarr v0.4 schema
+    if (validate) {
+        // Basic structural validation
+        if (!("multiscales" in rootAttrs)) {
+            throw new Error("Invalid OME-Zarr metadata: missing 'multiscales' key");
+        }
+        if (!Array.isArray(rootAttrs.multiscales) ||
+            rootAttrs.multiscales.length === 0) {
+            throw new Error("Invalid OME-Zarr metadata: 'multiscales' must be a non-empty array");
+        }
+        // Validate datasets exist
+        const datasets = multiscalesMetadata.datasets;
+        if (!Array.isArray(datasets) || datasets.length === 0) {
+            throw new Error("Invalid OME-Zarr metadata: 'datasets' must be a non-empty array");
+        }
+        // RFC 4 validation for anatomical orientation
+        if ("axes" in multiscalesMetadata &&
+            Array.isArray(multiscalesMetadata.axes)) {
+            const axesData = multiscalesMetadata.axes;
+            // Filter to only dict-style axes for RFC4 validation
+            const axesDicts = axesData.filter((axis) => typeof axis === "object" && axis !== null);
+            if (axesDicts.length > 0 && hasRfc4OrientationMetadata(axesDicts)) {
+                validateRfc4Orientation(axesDicts);
+            }
+        }
+    }
+    // Parse OMERO metadata
+    const omero = parseOmero(rootAttrs.omero);
+    // Handle backwards compatibility for version <= 0.3
+    let dims;
+    let axes;
+    let units;
+    if (!("axes" in multiscalesMetadata)) {
+        // Version <= 0.3 - use default dims
+        dims = [...SUPPORTED_DIMS].reverse();
+        axes = [
+            { name: "t", type: "time", unit: undefined },
+            {
+                name: "c",
+                type: "channel",
+                unit: undefined,
+            },
+            {
+                name: "z",
+                type: "space",
+                unit: undefined,
+            },
+            {
+                name: "y",
+                type: "space",
+                unit: undefined,
+            },
+            {
+                name: "x",
+                type: "space",
+                unit: undefined,
+            },
+        ];
+        units = Object.fromEntries(dims.map((d) => [d, undefined]));
+    }
+    else {
+        const axesData = multiscalesMetadata.axes;
+        dims = axesData.map((a) => typeof a === "object" && "name" in a ? String(a.name) : String(a));
+        // Check if axes have names (v0.4+) or are just strings (v0.3)
+        if (typeof axesData[0] === "object" && "name" in axesData[0]) {
+            axes = axesData.map((axis) => {
+                const axisObj = axis;
+                return {
+                    name: String(axisObj.name),
+                    type: String(axisObj.type),
+                    unit: axisObj.unit,
+                };
+            });
+        }
+        else {
+            // v0.3 - string axes
+            const typeDict = {
+                t: "time",
+                c: "channel",
+                z: "space",
+                y: "space",
+                x: "space",
+            };
+            axes = axesData.map((axis) => {
+                const name = String(axis);
+                return {
+                    name,
+                    type: typeDict[name] ?? "space",
+                    unit: undefined,
+                };
+            });
+        }
+        // Extract units from axes
+        units = Object.fromEntries(dims.map((d) => [d, undefined]));
+        for (const axis of axesData) {
+            if (typeof axis === "object") {
+                const axisObj = axis;
+                const name = axisObj.name;
+                const unit = axisObj.unit;
+                if (name !== undefined && unit !== undefined) {
+                    units[name] = unit;
+                }
+            }
+        }
+    }
+    // Extract anatomical orientations from axes (RFC 4)
+    let axesOrientations;
+    if ("axes" in multiscalesMetadata && Array.isArray(multiscalesMetadata.axes)) {
+        const axesData = multiscalesMetadata.axes;
+        axesOrientations = extractOrientationsFromAxes(axesData);
+    }
+    // Parse datasets and create NgffImages
+    const images = [];
+    const datasets = [];
+    const datasetsData = multiscalesMetadata.datasets;
+    // Open root group for array access
+    let optimizedStore;
+    try {
+        const tryWithConsolidated = zarr
+            .tryWithConsolidated;
+        if (tryWithConsolidated) {
+            optimizedStore = (await tryWithConsolidated(store));
+        }
+        else {
+            optimizedStore = store;
+        }
+    }
+    catch {
+        optimizedStore = store;
+    }
+    const root = await zarr.open(optimizedStore, {
+        kind: "group",
+    });
+    for (const dataset of datasetsData) {
+        const path = String(dataset.path);
+        // Open the zarr array
+        const zarrArray = (await zarr.open(root.resolve(path), {
+            kind: "array",
+        }));
+        // Parse coordinate transformations
+        const scale = Object.fromEntries(dims.map((d) => [d, 1.0]));
+        const translation = Object.fromEntries(dims.map((d) => [d, 0.0]));
+        const coordinateTransformations = [];
+        if ("coordinateTransformations" in dataset) {
+            const transforms = dataset.coordinateTransformations;
+            for (const transformation of transforms) {
+                if ("scale" in transformation) {
+                    const scaleValues = transformation.scale;
+                    dims.forEach((dim, i) => {
+                        if (i < scaleValues.length) {
+                            scale[dim] = scaleValues[i];
+                        }
+                    });
+                    coordinateTransformations.push({
+                        type: "scale",
+                        scale: scaleValues,
+                    });
+                }
+                else if ("translation" in transformation) {
+                    const translationValues = transformation.translation;
+                    dims.forEach((dim, i) => {
+                        if (i < translationValues.length) {
+                            translation[dim] = translationValues[i];
+                        }
+                    });
+                    coordinateTransformations.push({
+                        type: "translation",
+                        translation: translationValues,
+                    });
+                }
+            }
+        }
+        datasets.push({
+            path,
+            coordinateTransformations,
+        });
+        const filteredUnits = {};
+        for (const [axis, unit] of Object.entries(units)) {
+            if (unit !== undefined && unit !== null) {
+                filteredUnits[axis] = unit;
+            }
+        }
+        const ngffImage = new NgffImage({
+            data: zarrArray,
+            dims,
+            scale,
+            translation,
+            name: multiscalesMetadata.name ?? "image",
+            axesUnits: Object.keys(filteredUnits).length > 0
+                ? filteredUnits
+                : undefined,
+            axesOrientations,
+            computedCallbacks: undefined,
+        });
+        images.push(ngffImage);
+    }
+    // Build the metadata object - use spread to only include optional properties if defined
+    const metadata = {
+        axes,
+        datasets,
+        name: multiscalesMetadata.name ?? "image",
+        version: multiscalesMetadata.version ?? "0.4",
+        omero,
+        coordinateTransformations: multiscalesMetadata.coordinateTransformations ??
+            undefined,
+        ...(multiscalesMetadata.type !== undefined &&
+            multiscalesMetadata.type !== null
+            ? { type: String(multiscalesMetadata.type) }
+            : {}),
+        ...(multiscalesMetadata.metadata !== undefined &&
+            multiscalesMetadata.metadata !== null
+            ? {
+                metadata: multiscalesMetadata.metadata,
+            }
+            : {}),
+    };
+    return { metadata, images };
+}
+/**
+ * Parse Metadata and NgffImages from OME-Zarr v0.5 root attributes.
+ *
+ * The v0.5 format typically wraps multiscales under the "ome" key,
+ * but for compatibility we also handle the case where multiscales
+ * is at the root level (as written by toNgffZarr).
+ */
+export async function fromZarrAttrsV05(rootAttrs, store, validate = false) {
+    // v0.5 may wrap everything under "ome" key, or may have multiscales at root
+    const omeData = rootAttrs.ome;
+    let v04Attrs;
+    if (omeData && "multiscales" in omeData) {
+        // Standard v0.5 format with "ome" wrapper
+        v04Attrs = {
+            multiscales: omeData.multiscales,
+            omero: omeData.omero ?? rootAttrs.omero,
+        };
+    }
+    else if ("multiscales" in rootAttrs) {
+        // Compatibility mode: multiscales at root level (as written by toNgffZarr)
+        v04Attrs = {
+            multiscales: rootAttrs.multiscales,
+            omero: rootAttrs.omero,
+        };
+    }
+    else {
+        throw new Error("No multiscales metadata found in root attributes for v0.5 format");
+    }
+    const result = await fromZarrAttrsV04(v04Attrs, store, validate);
+    // Update version to 0.5
+    result.metadata.version = "0.5";
+    return result;
+}
+//# sourceMappingURL=from_zarr_attrs.js.map

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