@fideus-labs/ngff-zarr 0.20.0 → 0.22.0

package/esm/types/zarr_metadata.d.ts

@@ -2,6 +2,12 @@ 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";
+/**
+ * Name of the implicit coordinate system generated for a multiscale image,
+ * matching the Python port. Datasets map their array index space into this
+ * system via a scale + translation sequence.
+ */
+export declare const INTRINSIC_COORDINATE_SYSTEM_NAME = "intrinsic";
 /**
  * Orientation metadata for spatial axes (RFC 4).
  * This interface represents the serialized form in the zarr metadata.
@@ -16,18 +22,81 @@ export interface Axis {
     unit: Units | undefined;
     orientation?: AxisOrientation | AnatomicalOrientation | undefined;
 }
+/**
+ * RFC 5 / OME-Zarr v0.6 coordinate-system reference used by the `input` and
+ * `output` fields of a transformation. Mirrors the Python
+ * `CoordinateSystemIdentifier` dataclass and the spec `inputOutput` object: a
+ * transformation references either a coordinate system by `name` or a dataset
+ * array by `path`.
+ */
+export interface CoordinateSystemIdentifier {
+    path?: string;
+    name?: string;
+}
+/**
+ * RFC 5 / OME-Zarr v0.6 coordinate system: a named set of axes. The implicit
+ * "intrinsic" coordinate system is generated for the multiscale image.
+ */
+export interface CoordinateSystem {
+    name: string;
+    axes: Axis[];
+}
 export interface Identity {
     type: "identity";
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
 }
 export interface Scale {
     scale: number[];
     type: "scale";
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
 }
 export interface Translation {
     translation: number[];
     type: "translation";
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
+}
+/** RFC 5 rotation transformation (v0.6). */
+export interface Rotation {
+    rotation: number[][];
+    type: "rotation";
+    path?: string;
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
 }
+/** RFC 5 affine transformation (v0.6). */
+export interface Affine {
+    affine: number[][];
+    type: "affine";
+    path?: string;
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
+}
+/** RFC 5 sequence transformation, chaining sub-transformations (v0.6). */
+export interface TransformSequence {
+    transformations: V06Transform[];
+    type: "sequence";
+    input?: CoordinateSystemIdentifier;
+    output?: CoordinateSystemIdentifier;
+    name?: string;
+}
+/**
+ * Simple per-dataset transform used by the v0.4/v0.5 in-memory model and as the
+ * extracted scale/translation of a v0.6 dataset.
+ */
 export type Transform = Scale | Translation;
+/**
+ * Full RFC 5 / v0.6 transformation union. Used for top-level multiscale
+ * `coordinateTransformations` and the per-dataset `sequence` on the wire.
+ */
+export type V06Transform = Identity | Scale | Translation | Rotation | Affine | TransformSequence;
 export interface Dataset {
     path: string;
     coordinateTransformations: Transform[];
@@ -59,7 +128,18 @@ export interface MethodMetadata {
 export interface MetadataInterface {
     axes: Axis[];
     datasets: Dataset[];
-    coordinateTransformations: Transform[] | undefined;
+    /**
+     * Top-level multiscale transformations. For v0.4/v0.5 these are simple
+     * {@link Transform}s; for RFC 5 / v0.6 they may be any {@link V06Transform}
+     * (rotation, affine, sequence, ...) referencing coordinate systems.
+     */
+    coordinateTransformations: V06Transform[] | undefined;
+    /**
+     * RFC 5 / OME-Zarr v0.6 coordinate systems. Populated when reading a v0.6
+     * store and by `toMultiscales` (the implicit "intrinsic" system). Unused when
+     * serializing v0.4/v0.5, where axes live on the multiscale entry directly.
+     */
+    coordinateSystems?: CoordinateSystem[];
     omero: Omero | undefined;
     name: string;
     version: string;
@@ -105,4 +185,8 @@ export declare function validateColor(color: string): void;
 export declare function createScale(scale: number[]): Scale;
 export declare function createTranslation(translation: number[]): Translation;
 export declare function createIdentity(): Identity;
+export declare function createRotation(rotation: number[][]): Rotation;
+export declare function createAffine(affine: number[][]): Affine;
+export declare function createTransformSequence(transformations: V06Transform[]): TransformSequence;
+export declare function createCoordinateSystem(name: string, axes: Axis[]): CoordinateSystem;
 //# sourceMappingURL=zarr_metadata.d.ts.map

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

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package/esm/types/zarr_metadata.js

@@ -1,4 +1,10 @@
 import { NgffVersion } from "./supported_versions.js";
+/**
+ * Name of the implicit coordinate system generated for a multiscale image,
+ * matching the Python port. Datasets map their array index space into this
+ * system via a scale + translation sequence.
+ */
+export const INTRINSIC_COORDINATE_SYSTEM_NAME = "intrinsic";
 /**
  * Supported dimension names for backward compatibility
  */
@@ -28,6 +34,18 @@ export function createMetadataWithVersion(metadata, targetVersion) {
             version: "0.5",
         };
     }
+    else if (version === NgffVersion.V06) {
+        // The in-memory model is version-agnostic (axes + per-dataset scale and
+        // translation); v0.6 additionally exposes coordinate systems. Synthesize
+        // the implicit "intrinsic" system from the axes when one is not present, so
+        // a value converted to v0.6 carries the field the writer expects.
+        return {
+            ...metadata,
+            version: "0.6",
+            coordinateSystems: metadata.coordinateSystems ??
+                [{ name: INTRINSIC_COORDINATE_SYSTEM_NAME, axes: metadata.axes }],
+        };
+    }
     else {
         throw new Error(`Unsupported version conversion: ${metadata.version} -> ${version}`);
     }
@@ -52,4 +70,16 @@ export function createTranslation(translation) {
 export function createIdentity() {
     return { type: "identity" };
 }
+export function createRotation(rotation) {
+    return { rotation: rotation.map((row) => [...row]), type: "rotation" };
+}
+export function createAffine(affine) {
+    return { affine: affine.map((row) => [...row]), type: "affine" };
+}
+export function createTransformSequence(transformations) {
+    return { transformations: [...transformations], type: "sequence" };
+}
+export function createCoordinateSystem(name, axes) {
+    return { name, axes: [...axes] };
+}
 //# sourceMappingURL=zarr_metadata.js.map

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;AAItD;;;;GAIG;AACH,MAAM,CAAC,MAAM,gCAAgC,GAAG,WAAW,CAAC;AA+L5D;;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,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QACvC,wEAAwE;QACxE,yEAAyE;QACzE,4EAA4E;QAC5E,kEAAkE;QAClE,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;YACd,iBAAiB,EAAE,QAAQ,CAAC,iBAAiB;gBAC3C,CAAC,EAAE,IAAI,EAAE,gCAAgC,EAAE,IAAI,EAAE,QAAQ,CAAC,IAAI,EAAE,CAAC;SACpE,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;AAED,MAAM,UAAU,cAAc,CAAC,QAAoB;IACjD,OAAO,EAAE,QAAQ,EAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;AACzE,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,MAAkB;IAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;AACnE,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,eAA+B;IAE/B,OAAO,EAAE,eAAe,EAAE,CAAC,GAAG,eAAe,CAAC,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;AACrE,CAAC;AAED,MAAM,UAAU,sBAAsB,CACpC,IAAY,EACZ,IAAY;IAEZ,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,EAAE,CAAC;AACnC,CAAC"}

package/esm/utils/from_zarr_attrs.d.ts

@@ -18,4 +18,16 @@ export declare function fromZarrAttrsV04(rootAttrs: Record<string, unknown>, sto
  * 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>;
+/**
+ * Parse Metadata and NgffImages from OME-Zarr v0.6 (RFC 5) root attributes.
+ *
+ * Unlike v0.4/v0.5, a v0.6 multiscale entry carries `coordinateSystems` instead
+ * of a top-level `axes` list, and maps each dataset's array index space into the
+ * implicit "intrinsic" system through a `sequence` of scale + translation. This
+ * reader recovers the version-agnostic in-memory model (axes + per-dataset scale
+ * and translation) while preserving the coordinate systems and any top-level
+ * transformations for round-tripping. Mirrors the Python
+ * `v06.zarr_metadata.Metadata._from_zarr_attrs`.
+ */
+export declare function fromZarrAttrsV06(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

@@ -1 +1 @@
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+{"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,EAIV,mBAAmB,EAOpB,MAAM,2BAA2B,CAAC;AAMnC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AA4H3D;;;;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,CAkU9B;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,CAuC9B;AAED;;;;;;;;;;GAUG;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,CAmO9B"}

package/esm/utils/from_zarr_attrs.js

@@ -5,6 +5,7 @@
  */
 import * as zarr from "zarrita";
 import { SUPPORTED_DIMS } from "../types/zarr_metadata.js";
+import { extractScaleTranslation, parseV06Transforms } from "./v06_metadata.js";
 import { NgffImage } from "../types/ngff_image.js";
 import { parseOmero } from "./parse_metadata.js";
 import { hasRfc4OrientationMetadata, validateRfc4Orientation, } from "./rfc4_validation.js";
@@ -417,4 +418,185 @@ export async function fromZarrAttrsV05(rootAttrs, store, validate = false) {
     result.metadata.version = "0.5";
     return result;
 }
+/**
+ * Parse Metadata and NgffImages from OME-Zarr v0.6 (RFC 5) root attributes.
+ *
+ * Unlike v0.4/v0.5, a v0.6 multiscale entry carries `coordinateSystems` instead
+ * of a top-level `axes` list, and maps each dataset's array index space into the
+ * implicit "intrinsic" system through a `sequence` of scale + translation. This
+ * reader recovers the version-agnostic in-memory model (axes + per-dataset scale
+ * and translation) while preserving the coordinate systems and any top-level
+ * transformations for round-tripping. Mirrors the Python
+ * `v06.zarr_metadata.Metadata._from_zarr_attrs`.
+ */
+export async function fromZarrAttrsV06(rootAttrs, store, validate = false) {
+    // v0.6 wraps the multiscales under the "ome" key; tolerate a root-level
+    // layout for symmetry with the v0.5 reader.
+    const omeData = rootAttrs.ome;
+    let entry;
+    let omeroRaw;
+    if (omeData && "multiscales" in omeData) {
+        const multiscales = omeData.multiscales;
+        if (!Array.isArray(multiscales) || multiscales.length === 0) {
+            throw new Error("No multiscales metadata found in root attributes");
+        }
+        entry = multiscales[0];
+        omeroRaw = omeData.omero ?? rootAttrs.omero;
+    }
+    else if ("multiscales" in rootAttrs) {
+        const multiscales = rootAttrs.multiscales;
+        if (!Array.isArray(multiscales) || multiscales.length === 0) {
+            throw new Error("No multiscales metadata found in root attributes");
+        }
+        entry = multiscales[0];
+        omeroRaw = rootAttrs.omero;
+    }
+    else {
+        throw new Error("No multiscales metadata found in root attributes for v0.6 format");
+    }
+    const coordinateSystemsRaw = entry.coordinateSystems;
+    if (!Array.isArray(coordinateSystemsRaw) || coordinateSystemsRaw.length === 0) {
+        throw new Error("Invalid OME-Zarr v0.6 metadata: missing 'coordinateSystems' in " +
+            "multiscales metadata.");
+    }
+    const coordinateSystems = coordinateSystemsRaw.map((cs, csIndex) => {
+        // Guard the untrusted-input boundary: a missing/non-array `axes` would
+        // otherwise surface as a generic `.map` TypeError rather than a clear
+        // metadata error. (Per-axis name/type are still coerced, mirroring the
+        // v0.4 reader's tolerance.)
+        if (!Array.isArray(cs.axes)) {
+            throw new Error("Invalid OME-Zarr v0.6 metadata: " +
+                `coordinateSystems[${csIndex}].axes must be an array.`);
+        }
+        return {
+            name: String(cs.name),
+            axes: cs.axes.map((axis) => ({
+                name: String(axis.name),
+                type: String(axis.type),
+                unit: axis.unit,
+                ...(axis.orientation !== undefined && axis.orientation !== null
+                    ? { orientation: axis.orientation }
+                    : {}),
+            })),
+        };
+    });
+    const coordinateSystemNames = coordinateSystems.map((cs) => cs.name);
+    // The intrinsic coordinate system (the first one) backs the multiscale image
+    // dimensions, units, and anatomical orientations.
+    const intrinsic = coordinateSystems[0];
+    const intrinsicRawAxes = coordinateSystemsRaw[0].axes;
+    const dims = intrinsic.axes.map((axis) => String(axis.name));
+    const units = {};
+    for (const axis of intrinsic.axes) {
+        if (axis.unit !== undefined && axis.unit !== null) {
+            units[axis.name] = axis.unit;
+        }
+    }
+    const axesOrientations = extractOrientationsFromAxes(intrinsicRawAxes);
+    // RFC 4 anatomical-orientation validation, mirroring the v0.4 reader.
+    if (validate) {
+        const axesDicts = intrinsicRawAxes.filter((axis) => typeof axis === "object" && axis !== null);
+        if (axesDicts.length > 0 && hasRfc4OrientationMetadata(axesDicts)) {
+            validateRfc4Orientation(axesDicts);
+        }
+    }
+    // Open root group for array access (reuse consolidated metadata if present).
+    let optimizedStore;
+    try {
+        const tryWithConsolidated = zarr.tryWithConsolidated;
+        optimizedStore = tryWithConsolidated
+            ? (await tryWithConsolidated(store))
+            : store;
+    }
+    catch {
+        optimizedStore = store;
+    }
+    const root = await zarr.open(optimizedStore, {
+        kind: "group",
+    });
+    const datasetsData = entry.datasets;
+    if (!Array.isArray(datasetsData) || datasetsData.length === 0) {
+        throw new Error("Invalid OME-Zarr metadata: 'datasets' must be a non-empty array");
+    }
+    const images = [];
+    const datasets = [];
+    for (const dataset of datasetsData) {
+        const path = String(dataset.path);
+        const zarrArray = (await zarr.open(root.resolve(path), {
+            kind: "array",
+        }));
+        let scaleValues = dims.map(() => 1.0);
+        let translationValues = dims.map(() => 0.0);
+        if ("coordinateTransformations" in dataset) {
+            if (!Array.isArray(dataset.coordinateTransformations)) {
+                throw new Error("Invalid OME-Zarr v0.6 metadata: " +
+                    `dataset '${path}' coordinateTransformations must be an array.`);
+            }
+            const parsed = parseV06Transforms(dataset.coordinateTransformations, coordinateSystemNames);
+            const extracted = extractScaleTranslation(parsed, dims);
+            scaleValues = extracted.scale;
+            translationValues = extracted.translation;
+        }
+        const scale = {};
+        const translation = {};
+        dims.forEach((dim, i) => {
+            scale[dim] = i < scaleValues.length ? scaleValues[i] : 1.0;
+            translation[dim] = i < translationValues.length
+                ? translationValues[i]
+                : 0.0;
+        });
+        datasets.push({
+            path,
+            coordinateTransformations: [
+                { type: "scale", scale: scaleValues },
+                { type: "translation", translation: translationValues },
+            ],
+        });
+        images.push(new NgffImage({
+            data: zarrArray,
+            dims,
+            scale,
+            translation,
+            name: entry.name ?? "image",
+            axesUnits: Object.keys(units).length > 0 ? units : undefined,
+            axesOrientations,
+            computedCallbacks: undefined,
+        }));
+    }
+    let coordinateTransformations;
+    if ("coordinateTransformations" in entry) {
+        if (!Array.isArray(entry.coordinateTransformations)) {
+            throw new Error("Invalid OME-Zarr v0.6 metadata: multiscales " +
+                "coordinateTransformations must be an array.");
+        }
+        coordinateTransformations = parseV06Transforms(entry.coordinateTransformations, coordinateSystemNames);
+    }
+    const omero = parseOmero(omeroRaw);
+    const metadata = {
+        axes: intrinsic.axes,
+        datasets,
+        coordinateSystems,
+        coordinateTransformations,
+        name: entry.name ?? "image",
+        version: "0.6",
+        omero,
+        ...(entry.type !== undefined && entry.type !== null
+            ? { type: String(entry.type) }
+            : {}),
+        ...(entry.metadata !== undefined && entry.metadata !== null
+            ? {
+                metadata: entry.metadata,
+            }
+            : {}),
+    };
+    // Run the structural pass against the normalized metadata (axes + per-dataset
+    // scale/translation), matching the v0.4/v0.5 readers. The metadata is
+    // reconstructed into the same shape, so the same rules apply. Full RFC-5 wire
+    // validation (coordinate-system graphs, arbitrary transform chains) remains
+    // deferred.
+    if (validate) {
+        validateStructural(metadata, { level: ValidationLevel.Strict });
+    }
+    return { metadata, images };
+}
 //# sourceMappingURL=from_zarr_attrs.js.map

package/esm/utils/from_zarr_attrs.js.map

@@ -1 +1 @@
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package/esm/utils/parse_metadata.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"parse_metadata.d.ts","sourceRoot":"","sources":["../../src/utils/parse_metadata.ts"],"names":[],"mappings":"AAGA;;GAEG;AAEH,OAAO,EAEL,WAAW,EACZ,MAAM,gCAAgC,CAAC;AACxC,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAEnD,OAAO,KAAK,EACV,cAAc,EACd,KAAK,EAGN,MAAM,2BAA2B,CAAC;AAEnC;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,MAAM,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5B,UAAU,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B,cAAc,EAAE,cAAc,GAAG,SAAS,CAAC;CAC5C;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CACnC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GACpC,oBAAoB,CA4BtB;AAED;;GAEG;AACH,wBAAgB,UAAU,CACxB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,SAAS,GAAG,IAAI,GACpD,KAAK,GAAG,SAAS,CAmFnB;AAED;;GAEG;AACH,wBAAgB,aAAa,CAC3B,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GACjC,WAAW,CA0Bb"}
+{"version":3,"file":"parse_metadata.d.ts","sourceRoot":"","sources":["../../src/utils/parse_metadata.ts"],"names":[],"mappings":"AAGA;;GAEG;AAEH,OAAO,EAGL,WAAW,EACZ,MAAM,gCAAgC,CAAC;AACxC,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAEnD,OAAO,KAAK,EACV,cAAc,EACd,KAAK,EAGN,MAAM,2BAA2B,CAAC;AAEnC;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,MAAM,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5B,UAAU,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B,cAAc,EAAE,cAAc,GAAG,SAAS,CAAC;CAC5C;AAED;;GAEG;AACH,wBAAgB,qBAAqB,CACnC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GACpC,oBAAoB,CA4BtB;AAED;;GAEG;AACH,wBAAgB,UAAU,CACxB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,SAAS,GAAG,IAAI,GACpD,KAAK,GAAG,SAAS,CAmFnB;AAED;;GAEG;AACH,wBAAgB,aAAa,CAC3B,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GACjC,WAAW,CAiCb"}

package/esm/utils/parse_metadata.js

@@ -3,7 +3,7 @@
 /**
  * Utilities for parsing OME-Zarr metadata from zarr attributes.
  */
-import { isSupportedVersion, } from "../types/supported_versions.js";
+import { isSupportedVersion, isV06Version, NgffVersion, } from "../types/supported_versions.js";
 import { methodsValues } from "../types/methods.js";
 /**
  * Extract method type and convert to Methods enum.
@@ -130,6 +130,12 @@ export function detectVersion(rootAttrs) {
     if (versionStr === undefined) {
         throw new Error("Could not detect NGFF version from root attributes.");
     }
+    // Any 0.6-family version, including draft development tags such as
+    // `0.6.dev4`, is read as v0.6. Mirrors the Python port's
+    // `version.startswith("0.6")` read check so dev releases remain readable.
+    if (isV06Version(versionStr)) {
+        return NgffVersion.V06;
+    }
     if (!isSupportedVersion(versionStr)) {
         throw new Error(`Unsupported NGFF version: ${versionStr}`);
     }

package/esm/utils/parse_metadata.js.map

@@ -1 +1 @@
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package/esm/utils/rfc4_validation.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"rfc4_validation.d.ts","sourceRoot":"","sources":["../../src/utils/rfc4_validation.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AAiCH;;;;;GAKG;AACH,wBAAgB,0BAA0B,CACxC,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GACnC,OAAO,CAYT;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,uBAAuB,CACrC,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GACnC,IAAI,CA4DN"}
+{"version":3,"file":"rfc4_validation.d.ts","sourceRoot":"","sources":["../../src/utils/rfc4_validation.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AAiCH;;;;;GAKG;AACH,wBAAgB,0BAA0B,CACxC,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GACnC,OAAO,CAgBT;AAeD;;;;;;;;;;;;;GAaG;AACH,wBAAgB,uBAAuB,CACrC,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GACnC,IAAI,CA4DN"}

package/esm/utils/rfc4_validation.js

@@ -45,12 +45,28 @@ export function hasRfc4OrientationMetadata(axes) {
         if (typeof axis === "object" &&
             axis !== null &&
             axis.type === "space" &&
-            "orientation" in axis) {
+            "orientation" in axis &&
+            // Orientation value has to be non-empty for it to count as orientation
+            // metadata, mirroring the Python `if axis['orientation']:` guard (null,
+            // {}, and "" are all treated as "no orientation").
+            isNonEmptyOrientation(axis.orientation)) {
             return true;
         }
     }
     return false;
 }
+function isNonEmptyOrientation(orientation) {
+    if (orientation === null || orientation === undefined) {
+        return false;
+    }
+    if (typeof orientation === "object") {
+        return Object.keys(orientation).length > 0;
+    }
+    if (typeof orientation === "string") {
+        return orientation.length > 0;
+    }
+    return Boolean(orientation);
+}
 /**
  * Validate RFC 4 anatomical orientation metadata.
  *

package/esm/utils/rfc4_validation.js.map

@@ -1 +1 @@
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