@fideus-labs/ngff-zarr 0.0.1 → 0.2.0

package/script/mod.d.ts

@@ -1,17 +1,24 @@
 export * from "./types/units.js";
 export * from "./types/methods.js";
-export * from "./types/lazy_array.js";
+export * from "./types/array_interface.js";
 export * from "./types/zarr_metadata.js";
 export * from "./types/ngff_image.js";
 export * from "./types/multiscales.js";
+export * from "./types/rfc4.js";
+export * from "./types/hcs.js";
 export * from "./schemas/units.js";
 export * from "./schemas/methods.js";
-export * from "./schemas/lazy_array.js";
 export * from "./schemas/zarr_metadata.js";
 export * from "./schemas/ngff_image.js";
 export * from "./schemas/multiscales.js";
 export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
 export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
+export { getMethodMetadata } from "./utils/method_metadata.js";
 export * from "./io/from_ngff_zarr.js";
 export * from "./io/to_ngff_zarr.js";
+export * from "./io/to_multiscales.js";
+export type { MemoryStore } from "./io/from_ngff_zarr.js";
+export * from "./io/itk_image_to_ngff_image.js";
+export * from "./io/ngff_image_to_itk_image.js";
+export * from "./io/hcs.js";
 //# sourceMappingURL=mod.d.ts.map

package/script/mod.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"mod.d.ts","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAEA,cAAc,kBAAkB,CAAC;AACjC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAE/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,sBAAsB,CAAC;AACrC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAE/D,cAAc,wBAAwB,CAAC;AACvC,cAAc,sBAAsB,CAAC;AACrC,cAAc,wBAAwB,CAAC;AACvC,YAAY,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAC1D,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAChD,cAAc,aAAa,CAAC"}

package/script/mod.js

@@ -14,16 +14,19 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createNgffImage = exports.createMultiscales = exports.createMetadata = exports.createDataset = exports.createAxis = exports.validateMetadata = exports.isValidUnit = exports.isValidDimension = void 0;
+exports.getMethodMetadata = exports.createNgffImage = exports.createMultiscales = exports.createMetadata = exports.createDataset = exports.createAxis = exports.validateMetadata = exports.isValidUnit = exports.isValidDimension = void 0;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
 __exportStar(require("./types/units.js"), exports);
 __exportStar(require("./types/methods.js"), exports);
-__exportStar(require("./types/lazy_array.js"), exports);
+__exportStar(require("./types/array_interface.js"), exports);
 __exportStar(require("./types/zarr_metadata.js"), exports);
 __exportStar(require("./types/ngff_image.js"), exports);
 __exportStar(require("./types/multiscales.js"), exports);
+__exportStar(require("./types/rfc4.js"), exports);
+__exportStar(require("./types/hcs.js"), exports);
 __exportStar(require("./schemas/units.js"), exports);
 __exportStar(require("./schemas/methods.js"), exports);
-__exportStar(require("./schemas/lazy_array.js"), exports);
 __exportStar(require("./schemas/zarr_metadata.js"), exports);
 __exportStar(require("./schemas/ngff_image.js"), exports);
 __exportStar(require("./schemas/multiscales.js"), exports);
@@ -37,5 +40,11 @@ Object.defineProperty(exports, "createDataset", { enumerable: true, get: functio
 Object.defineProperty(exports, "createMetadata", { enumerable: true, get: function () { return factory_js_1.createMetadata; } });
 Object.defineProperty(exports, "createMultiscales", { enumerable: true, get: function () { return factory_js_1.createMultiscales; } });
 Object.defineProperty(exports, "createNgffImage", { enumerable: true, get: function () { return factory_js_1.createNgffImage; } });
+var method_metadata_js_1 = require("./utils/method_metadata.js");
+Object.defineProperty(exports, "getMethodMetadata", { enumerable: true, get: function () { return method_metadata_js_1.getMethodMetadata; } });
 __exportStar(require("./io/from_ngff_zarr.js"), exports);
 __exportStar(require("./io/to_ngff_zarr.js"), exports);
+__exportStar(require("./io/to_multiscales.js"), exports);
+__exportStar(require("./io/itk_image_to_ngff_image.js"), exports);
+__exportStar(require("./io/ngff_image_to_itk_image.js"), exports);
+__exportStar(require("./io/hcs.js"), exports);

package/script/schemas/coordinate_systems.d.ts

@@ -0,0 +1,251 @@
+import { z } from "zod";
+export declare const CoordinateSystemSchema: z.ZodObject<{
+    name: z.ZodString;
+    axes: z.ZodArray<z.ZodUnion<readonly [z.ZodObject<{
+        name: z.ZodLiteral<"c">;
+        type: z.ZodLiteral<"channel">;
+    }, z.core.$strip>, z.ZodObject<{
+        name: z.ZodEnum<{
+            x: "x";
+            y: "y";
+            z: "z";
+        }>;
+        type: z.ZodLiteral<"space">;
+        unit: z.ZodEnum<{
+            angstrom: "angstrom";
+            attometer: "attometer";
+            centimeter: "centimeter";
+            decimeter: "decimeter";
+            exameter: "exameter";
+            femtometer: "femtometer";
+            foot: "foot";
+            gigameter: "gigameter";
+            hectometer: "hectometer";
+            inch: "inch";
+            kilometer: "kilometer";
+            megameter: "megameter";
+            meter: "meter";
+            micrometer: "micrometer";
+            mile: "mile";
+            millimeter: "millimeter";
+            nanometer: "nanometer";
+            parsec: "parsec";
+            petameter: "petameter";
+            picometer: "picometer";
+            terameter: "terameter";
+            yard: "yard";
+            yoctometer: "yoctometer";
+            yottameter: "yottameter";
+            zeptometer: "zeptometer";
+            zettameter: "zettameter";
+        }>;
+        orientation: z.ZodOptional<z.ZodUnion<readonly [z.ZodType<{
+            type: "anatomical";
+            value: "left-to-right" | "right-to-left" | "anterior-to-posterior" | "posterior-to-anterior" | "inferior-to-superior" | "superior-to-inferior" | "dorsal-to-ventral" | "ventral-to-dorsal" | "dorsal-to-palmar" | "palmar-to-dorsal" | "dorsal-to-plantar" | "plantar-to-dorsal" | "rostral-to-caudal" | "caudal-to-rostral" | "cranial-to-caudal" | "caudal-to-cranial" | "proximal-to-distal" | "distal-to-proximal";
+        }, unknown, z.core.$ZodTypeInternals<{
+            type: "anatomical";
+            value: "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";
+        }, unknown>>, z.ZodNull]>>;
+    }, z.core.$strip>, z.ZodObject<{
+        name: z.ZodLiteral<"t">;
+        type: z.ZodLiteral<"time">;
+        unit: z.ZodEnum<{
+            attosecond: "attosecond";
+            centisecond: "centisecond";
+            day: "day";
+            decisecond: "decisecond";
+            exasecond: "exasecond";
+            femtosecond: "femtosecond";
+            gigasecond: "gigasecond";
+            hectosecond: "hectosecond";
+            hour: "hour";
+            kilosecond: "kilosecond";
+            megasecond: "megasecond";
+            microsecond: "microsecond";
+            millisecond: "millisecond";
+            minute: "minute";
+            nanosecond: "nanosecond";
+            petasecond: "petasecond";
+            picosecond: "picosecond";
+            second: "second";
+            terasecond: "terasecond";
+            yoctosecond: "yoctosecond";
+            yottasecond: "yottasecond";
+            zeptosecond: "zeptosecond";
+            zettasecond: "zettasecond";
+        }>;
+    }, z.core.$strip>]>>;
+}, z.core.$strip>;
+export declare const IdentityTransformationSchema: z.ZodType<{
+    type: "identity";
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const MapAxisTransformationSchema: z.ZodType<{
+    type: "mapAxis";
+    mapAxis: Record<string, string>;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const TranslationTransformationSchema: z.ZodType<{
+    type: "translation";
+    translation?: number[] | undefined;
+    path?: string | undefined;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const ScaleTransformationSchema: z.ZodType<{
+    type: "scale";
+    scale?: number[] | undefined;
+    path?: string | undefined;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const AffineTransformationSchema: z.ZodType<{
+    type: "affine";
+    affine?: number[][] | undefined;
+    path?: string | undefined;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const RotationTransformationSchema: z.ZodType<{
+    type: "rotation";
+    rotation?: number[] | undefined;
+    path?: string | undefined;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+type BaseCoordinateTransformation = {
+    type: "identity" | "mapAxis" | "translation" | "scale" | "affine" | "rotation";
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+    mapAxis?: Record<string, string> | undefined;
+    translation?: number[] | undefined;
+    path?: string | undefined;
+    scale?: number[] | undefined;
+    affine?: number[][] | undefined;
+    rotation?: number[] | undefined;
+};
+export declare const SequenceTransformationSchema: z.ZodType<{
+    type: "sequence";
+    transformations: BaseCoordinateTransformation[];
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const InverseTransformationSchema: z.ZodType<{
+    type: "inverseOf";
+    transformation: BaseCoordinateTransformation;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const BijectionTransformationSchema: z.ZodType<{
+    type: "bijection";
+    forward: BaseCoordinateTransformation;
+    inverse: BaseCoordinateTransformation;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const ByDimensionTransformationSchema: z.ZodType<{
+    type: "byDimension";
+    transformations: BaseCoordinateTransformation[];
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const CoordinateTransformationSchema: z.ZodType<{
+    type: "identity";
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+} | {
+    type: "mapAxis";
+    mapAxis: Record<string, string>;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+} | {
+    type: "translation";
+    translation?: number[] | undefined;
+    path?: string | undefined;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+} | {
+    type: "scale";
+    scale?: number[] | undefined;
+    path?: string | undefined;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+} | {
+    type: "affine";
+    affine?: number[][] | undefined;
+    path?: string | undefined;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+} | {
+    type: "rotation";
+    rotation?: number[] | undefined;
+    path?: string | undefined;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+} | {
+    type: "sequence";
+    transformations: BaseCoordinateTransformation[];
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+} | {
+    type: "inverseOf";
+    transformation: BaseCoordinateTransformation;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+} | {
+    type: "bijection";
+    forward: BaseCoordinateTransformation;
+    inverse: BaseCoordinateTransformation;
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+} | {
+    type: "byDimension";
+    transformations: BaseCoordinateTransformation[];
+    input?: string | string[] | undefined;
+    output?: string | string[] | undefined;
+    name?: string | undefined;
+}>;
+export declare const ArrayCoordinateSystemSchema: z.ZodObject<{
+    name: z.ZodString;
+    axes: z.ZodArray<z.ZodObject<{
+        name: z.ZodString;
+        type: z.ZodLiteral<"array">;
+    }, z.core.$strip>>;
+}, z.core.$strip>;
+export type CoordinateSystem = z.infer<typeof CoordinateSystemSchema>;
+export type IdentityTransformation = z.infer<typeof IdentityTransformationSchema>;
+export type MapAxisTransformation = z.infer<typeof MapAxisTransformationSchema>;
+export type TranslationTransformation = z.infer<typeof TranslationTransformationSchema>;
+export type ScaleTransformation = z.infer<typeof ScaleTransformationSchema>;
+export type AffineTransformation = z.infer<typeof AffineTransformationSchema>;
+export type RotationTransformation = z.infer<typeof RotationTransformationSchema>;
+export type SequenceTransformation = z.infer<typeof SequenceTransformationSchema>;
+export type InverseTransformation = z.infer<typeof InverseTransformationSchema>;
+export type BijectionTransformation = z.infer<typeof BijectionTransformationSchema>;
+export type ByDimensionTransformation = z.infer<typeof ByDimensionTransformationSchema>;
+export type CoordinateTransformation = z.infer<typeof CoordinateTransformationSchema>;
+export type ArrayCoordinateSystem = z.infer<typeof ArrayCoordinateSystemSchema>;
+export {};
+//# sourceMappingURL=coordinate_systems.d.ts.map

package/script/schemas/coordinate_systems.d.ts.map

@@ -0,0 +1 @@
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package/script/schemas/coordinate_systems.js

@@ -0,0 +1,142 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ArrayCoordinateSystemSchema = exports.CoordinateTransformationSchema = exports.ByDimensionTransformationSchema = exports.BijectionTransformationSchema = exports.InverseTransformationSchema = exports.SequenceTransformationSchema = exports.RotationTransformationSchema = exports.AffineTransformationSchema = exports.ScaleTransformationSchema = exports.TranslationTransformationSchema = exports.MapAxisTransformationSchema = exports.IdentityTransformationSchema = exports.CoordinateSystemSchema = void 0;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+const zod_1 = require("zod");
+const rfc4_js_1 = require("./rfc4.js");
+// RFC5: Coordinate Systems and Transformations
+// Coordinate System schema
+exports.CoordinateSystemSchema = zod_1.z.object({
+    name: zod_1.z.string().min(1), // MUST be non-empty and unique
+    axes: zod_1.z.array(rfc4_js_1.AxisSchema), // Array of axes that define the coordinate system
+});
+// Identity transformation
+exports.IdentityTransformationSchema = zod_1.z.object({
+    type: zod_1.z.literal("identity"),
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+});
+// Map Axis transformation (axis permutation)
+exports.MapAxisTransformationSchema = zod_1.z.object({
+    type: zod_1.z.literal("mapAxis"),
+    mapAxis: zod_1.z.record(zod_1.z.string(), zod_1.z.string()), // Dictionary mapping axis names
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+});
+// Translation transformation
+exports.TranslationTransformationSchema = zod_1.z
+    .object({
+    type: zod_1.z.literal("translation"),
+    translation: zod_1.z.array(zod_1.z.number()).optional(),
+    path: zod_1.z.string().optional(), // For binary data
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+})
+    .refine((data) => data.translation !== undefined || data.path !== undefined, {
+    message: "Either translation array or path must be provided",
+});
+// Scale transformation
+exports.ScaleTransformationSchema = zod_1.z
+    .object({
+    type: zod_1.z.literal("scale"),
+    scale: zod_1.z.array(zod_1.z.number()).optional(),
+    path: zod_1.z.string().optional(), // For binary data
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+})
+    .refine((data) => data.scale !== undefined || data.path !== undefined, {
+    message: "Either scale array or path must be provided",
+});
+// Affine transformation
+exports.AffineTransformationSchema = zod_1.z
+    .object({
+    type: zod_1.z.literal("affine"),
+    affine: zod_1.z.array(zod_1.z.array(zod_1.z.number())).optional(), // 2D array for matrix
+    path: zod_1.z.string().optional(), // For binary data
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+})
+    .refine((data) => data.affine !== undefined || data.path !== undefined, {
+    message: "Either affine matrix or path must be provided",
+});
+// Rotation transformation
+exports.RotationTransformationSchema = zod_1.z
+    .object({
+    type: zod_1.z.literal("rotation"),
+    rotation: zod_1.z.array(zod_1.z.number()).optional(),
+    path: zod_1.z.string().optional(), // For binary data
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+})
+    .refine((data) => data.rotation !== undefined || data.path !== undefined, {
+    message: "Either rotation array or path must be provided",
+});
+const BaseCoordinateTransformationSchema = zod_1.z.union([
+    exports.IdentityTransformationSchema,
+    exports.MapAxisTransformationSchema,
+    exports.TranslationTransformationSchema,
+    exports.ScaleTransformationSchema,
+    exports.AffineTransformationSchema,
+    exports.RotationTransformationSchema,
+]);
+// Sequence transformation (for chaining transformations)
+exports.SequenceTransformationSchema = zod_1.z.object({
+    type: zod_1.z.literal("sequence"),
+    transformations: zod_1.z.array(BaseCoordinateTransformationSchema),
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+});
+// Inverse transformation
+exports.InverseTransformationSchema = zod_1.z.object({
+    type: zod_1.z.literal("inverseOf"),
+    transformation: BaseCoordinateTransformationSchema,
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+});
+// Bijection transformation (forward and inverse)
+exports.BijectionTransformationSchema = zod_1.z.object({
+    type: zod_1.z.literal("bijection"),
+    forward: BaseCoordinateTransformationSchema,
+    inverse: BaseCoordinateTransformationSchema,
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+});
+// By dimension transformation
+exports.ByDimensionTransformationSchema = zod_1.z.object({
+    type: zod_1.z.literal("byDimension"),
+    transformations: zod_1.z.array(BaseCoordinateTransformationSchema),
+    input: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    output: zod_1.z.union([zod_1.z.string(), zod_1.z.array(zod_1.z.string())]).optional(),
+    name: zod_1.z.string().optional(),
+});
+// Complete coordinate transformation schema (union of all types)
+exports.CoordinateTransformationSchema = zod_1.z.union([
+    exports.IdentityTransformationSchema,
+    exports.MapAxisTransformationSchema,
+    exports.TranslationTransformationSchema,
+    exports.ScaleTransformationSchema,
+    exports.AffineTransformationSchema,
+    exports.RotationTransformationSchema,
+    exports.SequenceTransformationSchema,
+    exports.InverseTransformationSchema,
+    exports.BijectionTransformationSchema,
+    exports.ByDimensionTransformationSchema,
+]);
+// Array coordinate system schema
+exports.ArrayCoordinateSystemSchema = zod_1.z.object({
+    name: zod_1.z.string().min(1),
+    axes: zod_1.z.array(zod_1.z.object({
+        name: zod_1.z.string(),
+        type: zod_1.z.literal("array"),
+    })),
+});

package/script/schemas/index.d.ts

@@ -0,0 +1,9 @@
+export * from "./units.js";
+export * from "./methods.js";
+export { type AnatomicalOrientation, AnatomicalOrientationSchema, type AnatomicalOrientationValues, AnatomicalOrientationValuesSchema, type Axes as RFC4Axes, type AxesNames, AxesNamesSchema, AxesSchema as RFC4AxesSchema, type Axis as RFC4Axis, AxisSchema as RFC4AxisSchema, type AxisType, AxisTypeSchema, type BaseAxis, BaseAxisSchema, type ChannelAxis, ChannelAxisSchema, type Orientation, OrientationSchema, type SpaceAxesNames, SpaceAxesNamesSchema, type SpaceAxis, SpaceAxisSchema, type SpaceUnit, SpaceUnitSchema, type TimeAxis, TimeAxisSchema, type TimeUnit, TimeUnitSchema, } from "./rfc4.js";
+export * from "./coordinate_systems.js";
+export { AxisSchema, DatasetSchema, IdentitySchema, MetadataSchema, OmeroChannelSchema, OmeroSchema, OmeroWindowSchema, ScaleSchema, TransformSchema, TranslationSchema, } from "./zarr_metadata.js";
+export { AxisSchemaV05, type AxisV05, type CoordinateTransformation as OmeZarrCoordinateTransformation, DatasetSchemaV01, DatasetSchemaV05, type DatasetV01, type DatasetV05, type Image, ImageSchema, ImageSchemaV01, ImageSchemaV05, type ImageV01, type ImageV05, type LabelColor, LabelColorSchema, type LabelProperty, LabelPropertySchema, LabelSchemaV04, type LabelV04, type Multiscales, MultiscalesSchema, MultiscalesSchemaV01, MultiscalesSchemaV05, type MultiscalesV01, type MultiscalesV05, type OmeMetadata, OmeMetadataSchema, type Omero as OmeZarrOmero, type OmeroChannel as OmeZarrOmeroChannel, OmeroChannelSchema as OmeZarrOmeroChannelSchema, OmeroSchema as OmeZarrOmeroSchema, type OmeroWindow as OmeZarrOmeroWindow, OmeroWindowSchema as OmeZarrOmeroWindowSchema, type OmeSeries, OmeSeriesSchema, OmeZarrCoordinateTransformationSchema, type OmeZarrMetadata, OmeZarrMetadataSchema, type OmeZarrVersion, OmeZarrVersion01Schema, OmeZarrVersion02Schema, OmeZarrVersion03Schema, OmeZarrVersion04Schema, OmeZarrVersion05Schema, OmeZarrVersionSchema, type PlateAcquisition, PlateAcquisitionSchema, type PlateColumn, PlateColumnSchema, type PlateRow, PlateRowSchema, PlateSchemaV05, type PlateV05, type PlateWell, PlateWellSchema, type WellImage, WellImageSchema, WellSchemaV05, type WellV05, } from "./ome_zarr.js";
+export * from "./ngff_image.js";
+export * from "./multiscales.js";
+//# sourceMappingURL=index.d.ts.map

package/script/schemas/index.d.ts.map

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package/script/schemas/index.js

@@ -0,0 +1,101 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.PlateAcquisitionSchema = exports.OmeZarrVersionSchema = exports.OmeZarrVersion05Schema = exports.OmeZarrVersion04Schema = exports.OmeZarrVersion03Schema = exports.OmeZarrVersion02Schema = exports.OmeZarrVersion01Schema = exports.OmeZarrMetadataSchema = exports.OmeZarrCoordinateTransformationSchema = exports.OmeSeriesSchema = exports.OmeZarrOmeroWindowSchema = exports.OmeZarrOmeroSchema = exports.OmeZarrOmeroChannelSchema = exports.OmeMetadataSchema = exports.MultiscalesSchemaV05 = exports.MultiscalesSchemaV01 = exports.MultiscalesSchema = exports.LabelSchemaV04 = exports.LabelPropertySchema = exports.LabelColorSchema = exports.ImageSchemaV05 = exports.ImageSchemaV01 = exports.ImageSchema = exports.DatasetSchemaV05 = exports.DatasetSchemaV01 = exports.AxisSchemaV05 = exports.TranslationSchema = exports.TransformSchema = exports.ScaleSchema = exports.OmeroWindowSchema = exports.OmeroSchema = exports.OmeroChannelSchema = exports.MetadataSchema = exports.IdentitySchema = exports.DatasetSchema = exports.AxisSchema = exports.TimeUnitSchema = exports.TimeAxisSchema = exports.SpaceUnitSchema = exports.SpaceAxisSchema = exports.SpaceAxesNamesSchema = exports.OrientationSchema = exports.ChannelAxisSchema = exports.BaseAxisSchema = exports.AxisTypeSchema = exports.RFC4AxisSchema = exports.RFC4AxesSchema = exports.AxesNamesSchema = exports.AnatomicalOrientationValuesSchema = exports.AnatomicalOrientationSchema = void 0;
+exports.WellSchemaV05 = exports.WellImageSchema = exports.PlateWellSchema = exports.PlateSchemaV05 = exports.PlateRowSchema = exports.PlateColumnSchema = void 0;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+// Re-export all schemas with explicit naming to avoid conflicts
+__exportStar(require("./units.js"), exports);
+__exportStar(require("./methods.js"), exports);
+// RFC4 schemas
+var rfc4_js_1 = require("./rfc4.js");
+Object.defineProperty(exports, "AnatomicalOrientationSchema", { enumerable: true, get: function () { return rfc4_js_1.AnatomicalOrientationSchema; } });
+Object.defineProperty(exports, "AnatomicalOrientationValuesSchema", { enumerable: true, get: function () { return rfc4_js_1.AnatomicalOrientationValuesSchema; } });
+Object.defineProperty(exports, "AxesNamesSchema", { enumerable: true, get: function () { return rfc4_js_1.AxesNamesSchema; } });
+Object.defineProperty(exports, "RFC4AxesSchema", { enumerable: true, get: function () { return rfc4_js_1.AxesSchema; } });
+Object.defineProperty(exports, "RFC4AxisSchema", { enumerable: true, get: function () { return rfc4_js_1.AxisSchema; } });
+Object.defineProperty(exports, "AxisTypeSchema", { enumerable: true, get: function () { return rfc4_js_1.AxisTypeSchema; } });
+Object.defineProperty(exports, "BaseAxisSchema", { enumerable: true, get: function () { return rfc4_js_1.BaseAxisSchema; } });
+Object.defineProperty(exports, "ChannelAxisSchema", { enumerable: true, get: function () { return rfc4_js_1.ChannelAxisSchema; } });
+Object.defineProperty(exports, "OrientationSchema", { enumerable: true, get: function () { return rfc4_js_1.OrientationSchema; } });
+Object.defineProperty(exports, "SpaceAxesNamesSchema", { enumerable: true, get: function () { return rfc4_js_1.SpaceAxesNamesSchema; } });
+Object.defineProperty(exports, "SpaceAxisSchema", { enumerable: true, get: function () { return rfc4_js_1.SpaceAxisSchema; } });
+Object.defineProperty(exports, "SpaceUnitSchema", { enumerable: true, get: function () { return rfc4_js_1.SpaceUnitSchema; } });
+Object.defineProperty(exports, "TimeAxisSchema", { enumerable: true, get: function () { return rfc4_js_1.TimeAxisSchema; } });
+Object.defineProperty(exports, "TimeUnitSchema", { enumerable: true, get: function () { return rfc4_js_1.TimeUnitSchema; } });
+// Coordinate systems (RFC5)
+__exportStar(require("./coordinate_systems.js"), exports);
+// Zarr metadata schemas (with RFC4 integration)
+var zarr_metadata_js_1 = require("./zarr_metadata.js");
+Object.defineProperty(exports, "AxisSchema", { enumerable: true, get: function () { return zarr_metadata_js_1.AxisSchema; } });
+Object.defineProperty(exports, "DatasetSchema", { enumerable: true, get: function () { return zarr_metadata_js_1.DatasetSchema; } });
+Object.defineProperty(exports, "IdentitySchema", { enumerable: true, get: function () { return zarr_metadata_js_1.IdentitySchema; } });
+Object.defineProperty(exports, "MetadataSchema", { enumerable: true, get: function () { return zarr_metadata_js_1.MetadataSchema; } });
+Object.defineProperty(exports, "OmeroChannelSchema", { enumerable: true, get: function () { return zarr_metadata_js_1.OmeroChannelSchema; } });
+Object.defineProperty(exports, "OmeroSchema", { enumerable: true, get: function () { return zarr_metadata_js_1.OmeroSchema; } });
+Object.defineProperty(exports, "OmeroWindowSchema", { enumerable: true, get: function () { return zarr_metadata_js_1.OmeroWindowSchema; } });
+Object.defineProperty(exports, "ScaleSchema", { enumerable: true, get: function () { return zarr_metadata_js_1.ScaleSchema; } });
+Object.defineProperty(exports, "TransformSchema", { enumerable: true, get: function () { return zarr_metadata_js_1.TransformSchema; } });
+Object.defineProperty(exports, "TranslationSchema", { enumerable: true, get: function () { return zarr_metadata_js_1.TranslationSchema; } });
+// OME-Zarr specification schemas
+var ome_zarr_js_1 = require("./ome_zarr.js");
+// Axis schemas
+Object.defineProperty(exports, "AxisSchemaV05", { enumerable: true, get: function () { return ome_zarr_js_1.AxisSchemaV05; } });
+// Dataset schemas
+Object.defineProperty(exports, "DatasetSchemaV01", { enumerable: true, get: function () { return ome_zarr_js_1.DatasetSchemaV01; } });
+Object.defineProperty(exports, "DatasetSchemaV05", { enumerable: true, get: function () { return ome_zarr_js_1.DatasetSchemaV05; } });
+Object.defineProperty(exports, "ImageSchema", { enumerable: true, get: function () { return ome_zarr_js_1.ImageSchema; } });
+// Image schemas
+Object.defineProperty(exports, "ImageSchemaV01", { enumerable: true, get: function () { return ome_zarr_js_1.ImageSchemaV01; } });
+Object.defineProperty(exports, "ImageSchemaV05", { enumerable: true, get: function () { return ome_zarr_js_1.ImageSchemaV05; } });
+// Label schemas
+Object.defineProperty(exports, "LabelColorSchema", { enumerable: true, get: function () { return ome_zarr_js_1.LabelColorSchema; } });
+Object.defineProperty(exports, "LabelPropertySchema", { enumerable: true, get: function () { return ome_zarr_js_1.LabelPropertySchema; } });
+Object.defineProperty(exports, "LabelSchemaV04", { enumerable: true, get: function () { return ome_zarr_js_1.LabelSchemaV04; } });
+Object.defineProperty(exports, "MultiscalesSchema", { enumerable: true, get: function () { return ome_zarr_js_1.MultiscalesSchema; } });
+// Multiscales schemas
+Object.defineProperty(exports, "MultiscalesSchemaV01", { enumerable: true, get: function () { return ome_zarr_js_1.MultiscalesSchemaV01; } });
+Object.defineProperty(exports, "MultiscalesSchemaV05", { enumerable: true, get: function () { return ome_zarr_js_1.MultiscalesSchemaV05; } });
+Object.defineProperty(exports, "OmeMetadataSchema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeMetadataSchema; } });
+Object.defineProperty(exports, "OmeZarrOmeroChannelSchema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeroChannelSchema; } });
+Object.defineProperty(exports, "OmeZarrOmeroSchema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeroSchema; } });
+// Core schemas
+Object.defineProperty(exports, "OmeZarrOmeroWindowSchema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeroWindowSchema; } });
+// OME metadata schemas
+Object.defineProperty(exports, "OmeSeriesSchema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeSeriesSchema; } });
+Object.defineProperty(exports, "OmeZarrCoordinateTransformationSchema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeZarrCoordinateTransformationSchema; } });
+// Comprehensive schema
+Object.defineProperty(exports, "OmeZarrMetadataSchema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeZarrMetadataSchema; } });
+Object.defineProperty(exports, "OmeZarrVersion01Schema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeZarrVersion01Schema; } });
+Object.defineProperty(exports, "OmeZarrVersion02Schema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeZarrVersion02Schema; } });
+Object.defineProperty(exports, "OmeZarrVersion03Schema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeZarrVersion03Schema; } });
+Object.defineProperty(exports, "OmeZarrVersion04Schema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeZarrVersion04Schema; } });
+Object.defineProperty(exports, "OmeZarrVersion05Schema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeZarrVersion05Schema; } });
+// Version schemas
+Object.defineProperty(exports, "OmeZarrVersionSchema", { enumerable: true, get: function () { return ome_zarr_js_1.OmeZarrVersionSchema; } });
+// Plate schemas
+Object.defineProperty(exports, "PlateAcquisitionSchema", { enumerable: true, get: function () { return ome_zarr_js_1.PlateAcquisitionSchema; } });
+Object.defineProperty(exports, "PlateColumnSchema", { enumerable: true, get: function () { return ome_zarr_js_1.PlateColumnSchema; } });
+Object.defineProperty(exports, "PlateRowSchema", { enumerable: true, get: function () { return ome_zarr_js_1.PlateRowSchema; } });
+Object.defineProperty(exports, "PlateSchemaV05", { enumerable: true, get: function () { return ome_zarr_js_1.PlateSchemaV05; } });
+Object.defineProperty(exports, "PlateWellSchema", { enumerable: true, get: function () { return ome_zarr_js_1.PlateWellSchema; } });
+// Well schemas
+Object.defineProperty(exports, "WellImageSchema", { enumerable: true, get: function () { return ome_zarr_js_1.WellImageSchema; } });
+Object.defineProperty(exports, "WellSchemaV05", { enumerable: true, get: function () { return ome_zarr_js_1.WellSchemaV05; } });
+// NGFF Image and Multiscales
+__exportStar(require("./ngff_image.js"), exports);
+__exportStar(require("./multiscales.js"), exports);

package/script/schemas/methods.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"methods.d.ts","sourceRoot":"","sources":["../../src/schemas/methods.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,eAAO,MAAM,aAAa,EAAE,CAAC,CAAC,UAI5B,CAAC"}
+{"version":3,"file":"methods.d.ts","sourceRoot":"","sources":["../../src/schemas/methods.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,eAAO,MAAM,aAAa,EAAE,CAAC,CAAC,UAI5B,CAAC"}

package/script/schemas/methods.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MethodsSchema = void 0;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
 const zod_1 = require("zod");
 exports.MethodsSchema = zod_1.z.enum([
     "itkwasm_gaussian",

package/script/schemas/multiscales.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"multiscales.d.ts","sourceRoot":"","sources":["../../src/schemas/multiscales.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAKxB,eAAO,MAAM,eAAe,EAAE,CAAC,CAAC,UAK9B,CAAC;AAEH,eAAO,MAAM,wBAAwB,EAAE,CAAC,CAAC,UAQvC,CAAC"}
+{"version":3,"file":"multiscales.d.ts","sourceRoot":"","sources":["../../src/schemas/multiscales.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAKxB,eAAO,MAAM,eAAe,EAAE,CAAC,CAAC,UAK9B,CAAC;AAEH,eAAO,MAAM,wBAAwB,EAAE,CAAC,CAAC,UAQvC,CAAC"}

package/script/schemas/multiscales.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MultiscalesOptionsSchema = exports.ChunkSpecSchema = void 0;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
 const zod_1 = require("zod");
 const ngff_image_js_1 = require("./ngff_image.js");
 const zarr_metadata_js_1 = require("./zarr_metadata.js");