@fideus-labs/ngff-zarr 0.2.7 → 0.3.0

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 @@
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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

package/esm/utils/rfc4_validation.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"rfc4_validation.js","sourceRoot":"","sources":["../../src/utils/rfc4_validation.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B;;;;GAIG;AAEH,OAAO,EAAE,iCAAiC,EAAE,MAAM,oBAAoB,CAAC;AAEvE,0CAA0C;AAC1C,MAAM,wBAAwB,GAAG,IAAI,GAAG,CAAC;IACvC,eAAe;IACf,eAAe;IACf,uBAAuB;IACvB,uBAAuB;IACvB,sBAAsB;IACtB,sBAAsB;IACtB,mBAAmB;IACnB,mBAAmB;IACnB,kBAAkB;IAClB,kBAAkB;IAClB,mBAAmB;IACnB,mBAAmB;IACnB,mBAAmB;IACnB,mBAAmB;IACnB,mBAAmB;IACnB,mBAAmB;IACnB,oBAAoB;IACpB,oBAAoB;CACrB,CAAC,CAAC;AAEH;;;;;GAKG;AACH,MAAM,UAAU,0BAA0B,CACxC,IAAoC;IAEpC,KAAK,MAAM,IAAI,IAAI,IAAI,EAAE,CAAC;QACxB,IACE,OAAO,IAAI,KAAK,QAAQ;YACxB,IAAI,KAAK,IAAI;YACb,IAAI,CAAC,IAAI,KAAK,OAAO;YACrB,aAAa,IAAI,IAAI,EACrB,CAAC;YACD,OAAO,IAAI,CAAC;QACd,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,uBAAuB,CACrC,IAAoC;IAEpC,IAAI,cAAc,GAAG,KAAK,CAAC;IAC3B,IAAI,eAAe,GAAkB,IAAI,CAAC;IAC1C,MAAM,0BAA0B,GAAa,EAAE,CAAC;IAChD,MAAM,6BAA6B,GAAa,EAAE,CAAC;IAEnD,KAAK,MAAM,IAAI,IAAI,IAAI,EAAE,CAAC;QACxB,IAAI,OAAO,IAAI,KAAK,QAAQ,IAAI,IAAI,KAAK,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,OAAO,EAAE,CAAC;YACvE,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,IAAI,SAAS,CAAC,CAAC;YAEhD,IAAI,aAAa,IAAI,IAAI,IAAI,IAAI,CAAC,WAAW,KAAK,IAAI,EAAE,CAAC;gBACvD,cAAc,GAAG,IAAI,CAAC;gBACtB,0BAA0B,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBAE1C,MAAM,WAAW,GAAG,IAAI,CAAC,WAAsC,CAAC;gBAEhE,iDAAiD;gBACjD,MAAM,WAAW,GAAG,WAAW,CAAC,IAA0B,CAAC;gBAC3D,IAAI,eAAe,KAAK,IAAI,EAAE,CAAC;oBAC7B,eAAe,GAAG,WAAW,IAAI,IAAI,CAAC;gBACxC,CAAC;qBAAM,IAAI,WAAW,KAAK,eAAe,EAAE,CAAC;oBAC3C,MAAM,IAAI,KAAK,CACb,yDAAyD;wBACvD,gBAAgB,eAAe,QAAQ,WAAW,EAAE,CACvD,CAAC;gBACJ,CAAC;gBAED,kDAAkD;gBAClD,MAAM,gBAAgB,GAAG,WAAW,CAAC,KAA2B,CAAC;gBACjE,IAAI,gBAAgB,KAAK,SAAS,EAAE,CAAC;oBACnC,MAAM,MAAM,GAAG,iCAAiC,CAAC,SAAS,CACxD,gBAAgB,CACjB,CAAC;oBACF,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC;wBACpB,MAAM,IAAI,KAAK,CACb,8BAA8B,gBAAgB,eAAe,QAAQ,KAAK;4BACxE,qBACE,CAAC,GAAG,wBAAwB,CAAC,CAAC,IAAI,EAAE,CAAC,IAAI,CAAC,IAAI,CAChD,EAAE,CACL,CAAC;oBACJ,CAAC;gBACH,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,6BAA6B,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;YAC/C,CAAC;QACH,CAAC;IACH,CAAC;IAED,qEAAqE;IACrE,0CAA0C;IAC1C,IAAI,cAAc,IAAI,6BAA6B,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC/D,MAAM,IAAI,KAAK,CACb,sEAAsE;YACpE,2CAA2C;YAC3C,0BAA0B,0BAA0B,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI;YACnE,6BAA6B,6BAA6B,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAC1E,CAAC;IACJ,CAAC;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fideus-labs/ngff-zarr",
-  "version": "0.2.7",
+  "version": "0.3.0",
   "description": "TypeScript implementation of ngff-zarr for reading and writing OME-Zarr files",
   "license": "MIT",
   "type": "module",
@@ -72,7 +72,7 @@
     "@itk-wasm/downsample": "^1.8.1",
     "itk-wasm": "^1.0.0-b.196",
     "p-queue": "^8.1.0",
-    "@zarrita/storage": "^0.1.1",
+    "@zarrita/storage": "^0.1.4",
     "zod": "^4.0.2",
     "zarrita": "^0.5.2"
   },