@fideus-labs/ngff-zarr 0.2.8 → 0.4.0

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

package/esm/utils/from_zarr_attrs.js.map

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package/esm/utils/parse_metadata.d.ts

@@ -0,0 +1,27 @@
+/**
+ * Utilities for parsing OME-Zarr metadata from zarr attributes.
+ */
+import { NgffVersion } from "../types/supported_versions.js";
+import type { Methods } from "../types/methods.js";
+import type { MethodMetadata, Omero } from "../types/zarr_metadata.js";
+/**
+ * Result from extracting method metadata
+ */
+export interface MethodMetadataResult {
+    method: Methods | undefined;
+    methodType: string | undefined;
+    methodMetadata: MethodMetadata | undefined;
+}
+/**
+ * Extract method type and convert to Methods enum.
+ */
+export declare function extractMethodMetadata(metadataDict: Record<string, unknown>): MethodMetadataResult;
+/**
+ * Parse OMERO metadata dictionary into Omero interface.
+ */
+export declare function parseOmero(omeroData: Record<string, unknown> | undefined | null): Omero | undefined;
+/**
+ * Detect NGFF version from root attributes.
+ */
+export declare function detectVersion(rootAttrs: Record<string, unknown>): NgffVersion;
+//# sourceMappingURL=parse_metadata.d.ts.map

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

@@ -0,0 +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"}

package/esm/utils/parse_metadata.js

@@ -0,0 +1,138 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * Utilities for parsing OME-Zarr metadata from zarr attributes.
+ */
+import { isSupportedVersion, } from "../types/supported_versions.js";
+import { methodsValues } from "../types/methods.js";
+/**
+ * Extract method type and convert to Methods enum.
+ */
+export function extractMethodMetadata(metadataDict) {
+    let method = undefined;
+    let methodType = undefined;
+    let methodMetadata = undefined;
+    if (metadataDict && typeof metadataDict === "object") {
+        if ("type" in metadataDict && metadataDict.type !== null) {
+            methodType = metadataDict.type;
+            // Find the corresponding Methods enum
+            if (methodsValues.includes(methodType)) {
+                method = methodType;
+            }
+        }
+        // Extract method metadata if present
+        if ("metadata" in metadataDict && metadataDict.metadata !== null) {
+            const metadata = metadataDict.metadata;
+            if (metadata && typeof metadata === "object") {
+                methodMetadata = {
+                    description: String(metadata.description ?? ""),
+                    method: String(metadata.method ?? ""),
+                    version: String(metadata.version ?? ""),
+                };
+            }
+        }
+    }
+    return { method, methodType, methodMetadata };
+}
+/**
+ * Parse OMERO metadata dictionary into Omero interface.
+ */
+export function parseOmero(omeroData) {
+    if (!omeroData || typeof omeroData !== "object") {
+        return undefined;
+    }
+    if (!("channels" in omeroData) || !Array.isArray(omeroData.channels)) {
+        return undefined;
+    }
+    const channels = [];
+    for (const channel of omeroData.channels) {
+        if (!channel ||
+            typeof channel !== "object" ||
+            !("window" in channel) ||
+            !channel.window) {
+            continue;
+        }
+        const windowData = channel.window;
+        if (typeof windowData !== "object") {
+            continue;
+        }
+        // Handle backward compatibility for OMERO window metadata
+        // Prefer start/end format, fall back to min/max, use one as the other if needed
+        let start;
+        let end;
+        let minVal;
+        let maxVal;
+        if ("start" in windowData && "end" in windowData) {
+            // New format with start/end
+            start = Number(windowData.start);
+            end = Number(windowData.end);
+            // Use start/end as min/max if not present
+            minVal = ("min" in windowData) ? Number(windowData.min) : start;
+            maxVal = ("max" in windowData) ? Number(windowData.max) : end;
+        }
+        else if ("min" in windowData && "max" in windowData) {
+            // Old format with min/max only
+            minVal = Number(windowData.min);
+            maxVal = Number(windowData.max);
+            // Use min/max as start/end for backward compatibility
+            start = minVal;
+            end = maxVal;
+        }
+        else {
+            // Invalid window data, skip this channel
+            continue;
+        }
+        const window = {
+            min: minVal,
+            max: maxVal,
+            start: start,
+            end: end,
+        };
+        const omeroChannel = {
+            color: String(channel.color),
+            window,
+            ...(channel.label !== undefined && channel.label !== null
+                ? { label: String(channel.label) }
+                : {}),
+            ...(typeof channel.active === "boolean"
+                ? { active: channel.active }
+                : {}),
+        };
+        channels.push(omeroChannel);
+    }
+    if (channels.length === 0) {
+        return undefined;
+    }
+    return {
+        channels,
+        ...(typeof omeroData.version === "string"
+            ? { version: omeroData.version }
+            : {}),
+    };
+}
+/**
+ * Detect NGFF version from root attributes.
+ */
+export function detectVersion(rootAttrs) {
+    let versionStr = undefined;
+    if ("ome" in rootAttrs && rootAttrs.ome) {
+        const ome = rootAttrs.ome;
+        versionStr = ome.version;
+    }
+    // Fall back to multiscales if version not found in ome
+    if (versionStr === undefined) {
+        const multiscales = rootAttrs.multiscales;
+        if (multiscales && Array.isArray(multiscales) && multiscales.length > 0) {
+            const firstMultiscale = multiscales[0];
+            versionStr = firstMultiscale.version ?? "0.4";
+        }
+    }
+    if (versionStr === undefined) {
+        throw new Error("Could not detect NGFF version from root attributes.");
+    }
+    if (!isSupportedVersion(versionStr)) {
+        throw new Error(`Unsupported NGFF version: ${versionStr}`);
+    }
+    return versionStr;
+}
+//# sourceMappingURL=parse_metadata.js.map

package/esm/utils/parse_metadata.js.map

@@ -0,0 +1 @@
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package/esm/utils/rfc4_validation.d.ts

@@ -0,0 +1,20 @@
+/**
+ * RFC 4 validation for anatomical orientation in OME-NGFF.
+ *
+ * This module provides validation for RFC 4 anatomical orientation metadata.
+ */
+/**
+ * Check if the axes contain RFC 4 anatomical orientation metadata.
+ *
+ * @param axes - List of axis metadata objects
+ * @returns True if any spatial axis has orientation metadata
+ */
+export declare function hasRfc4OrientationMetadata(axes: Array<Record<string, unknown>>): boolean;
+/**
+ * Validate RFC 4 anatomical orientation metadata.
+ *
+ * @param axes - List of axis metadata dictionaries to validate
+ * @throws Error if the orientation metadata is invalid or inconsistent
+ */
+export declare function validateRfc4Orientation(axes: Array<Record<string, unknown>>): void;
+//# sourceMappingURL=rfc4_validation.d.ts.map

package/esm/utils/rfc4_validation.d.ts.map

@@ -0,0 +1 @@
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package/esm/utils/rfc4_validation.js

@@ -0,0 +1,98 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * RFC 4 validation for anatomical orientation in OME-NGFF.
+ *
+ * This module provides validation for RFC 4 anatomical orientation metadata.
+ */
+import { AnatomicalOrientationValuesSchema } from "../schemas/rfc4.js";
+/** Valid anatomical orientation values */
+const VALID_ORIENTATION_VALUES = new Set([
+    "left-to-right",
+    "right-to-left",
+    "anterior-to-posterior",
+    "posterior-to-anterior",
+    "inferior-to-superior",
+    "superior-to-inferior",
+    "dorsal-to-ventral",
+    "ventral-to-dorsal",
+    "dorsal-to-palmar",
+    "palmar-to-dorsal",
+    "dorsal-to-plantar",
+    "plantar-to-dorsal",
+    "rostral-to-caudal",
+    "caudal-to-rostral",
+    "cranial-to-caudal",
+    "caudal-to-cranial",
+    "proximal-to-distal",
+    "distal-to-proximal",
+]);
+/**
+ * Check if the axes contain RFC 4 anatomical orientation metadata.
+ *
+ * @param axes - List of axis metadata objects
+ * @returns True if any spatial axis has orientation metadata
+ */
+export function hasRfc4OrientationMetadata(axes) {
+    for (const axis of axes) {
+        if (typeof axis === "object" &&
+            axis !== null &&
+            axis.type === "space" &&
+            "orientation" in axis) {
+            return true;
+        }
+    }
+    return false;
+}
+/**
+ * Validate RFC 4 anatomical orientation metadata.
+ *
+ * @param axes - List of axis metadata dictionaries to validate
+ * @throws Error if the orientation metadata is invalid or inconsistent
+ */
+export function validateRfc4Orientation(axes) {
+    let hasOrientation = false;
+    let orientationType = null;
+    const spatialAxesWithOrientation = [];
+    const spatialAxesWithoutOrientation = [];
+    for (const axis of axes) {
+        if (typeof axis === "object" && axis !== null && axis.type === "space") {
+            const axisName = String(axis.name ?? "unknown");
+            if ("orientation" in axis && axis.orientation !== null) {
+                hasOrientation = true;
+                spatialAxesWithOrientation.push(axisName);
+                const orientation = axis.orientation;
+                // Check that all orientations have the same type
+                const currentType = orientation.type;
+                if (orientationType === null) {
+                    orientationType = currentType ?? null;
+                }
+                else if (currentType !== orientationType) {
+                    throw new Error(`All spatial axis orientations must have the same type. ` +
+                        `Found types: ${orientationType} and ${currentType}`);
+                }
+                // Validate the orientation value using the schema
+                const orientationValue = orientation.value;
+                if (orientationValue !== undefined) {
+                    const result = AnatomicalOrientationValuesSchema.safeParse(orientationValue);
+                    if (!result.success) {
+                        throw new Error(`Invalid orientation value '${orientationValue}' for axis '${axisName}'. ` +
+                            `Valid values are: ${[...VALID_ORIENTATION_VALUES].sort().join(", ")}`);
+                    }
+                }
+            }
+            else {
+                spatialAxesWithoutOrientation.push(axisName);
+            }
+        }
+    }
+    // RFC 4 requirement: if orientation is defined for one spatial axis,
+    // it must be defined for all spatial axes
+    if (hasOrientation && spatialAxesWithoutOrientation.length > 0) {
+        throw new Error(`RFC 4 requires that if orientation is defined for one spatial axis, ` +
+            `it must be defined for all spatial axes. ` +
+            `Axes with orientation: ${spatialAxesWithOrientation.join(", ")}, ` +
+            `axes without orientation: ${spatialAxesWithoutOrientation.join(", ")}`);
+    }
+}
+//# sourceMappingURL=rfc4_validation.js.map

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