@fideus-labs/ngff-zarr 0.0.1 → 0.1.0

package/script/schemas/rfc4.js

@@ -0,0 +1,132 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AxesSchema = exports.AxisSchema = exports.TimeAxisSchema = exports.SpaceAxisSchema = exports.ChannelAxisSchema = exports.BaseAxisSchema = exports.TimeUnitSchema = exports.SpaceUnitSchema = exports.AxisTypeSchema = exports.SpaceAxesNamesSchema = exports.AxesNamesSchema = exports.OrientationSchema = exports.OrientationTypeSchema = exports.AnatomicalOrientationSchema = exports.AnatomicalOrientationValuesSchema = void 0;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+const zod_1 = require("zod");
+// Anatomical Orientation Values based on RFC4
+exports.AnatomicalOrientationValuesSchema = zod_1.z.enum([
+    "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",
+]);
+// AnatomicalOrientation object schema
+exports.AnatomicalOrientationSchema = zod_1.z.object({
+    type: zod_1.z.literal("anatomical"),
+    value: exports.AnatomicalOrientationValuesSchema,
+});
+// Base Orientation schema (extensible for future orientation types)
+exports.OrientationTypeSchema = zod_1.z.enum(["anatomical"]);
+exports.OrientationSchema = zod_1.z.object({
+    type: exports.OrientationTypeSchema,
+    value: exports.AnatomicalOrientationValuesSchema,
+});
+// Axes Names enum
+exports.AxesNamesSchema = zod_1.z.enum(["t", "c", "z", "y", "x"]);
+// Space Axes Names enum (subset of AxesNames for spatial dimensions)
+exports.SpaceAxesNamesSchema = zod_1.z.enum(["z", "y", "x"]);
+// Axis Type enum
+exports.AxisTypeSchema = zod_1.z.enum(["channel", "space", "time"]);
+// Space Units enum
+exports.SpaceUnitSchema = zod_1.z.enum([
+    "angstrom",
+    "attometer",
+    "centimeter",
+    "decimeter",
+    "exameter",
+    "femtometer",
+    "foot",
+    "gigameter",
+    "hectometer",
+    "inch",
+    "kilometer",
+    "megameter",
+    "meter",
+    "micrometer",
+    "mile",
+    "millimeter",
+    "nanometer",
+    "parsec",
+    "petameter",
+    "picometer",
+    "terameter",
+    "yard",
+    "yoctometer",
+    "yottameter",
+    "zeptometer",
+    "zettameter",
+]);
+// Time Units enum
+exports.TimeUnitSchema = zod_1.z.enum([
+    "attosecond",
+    "centisecond",
+    "day",
+    "decisecond",
+    "exasecond",
+    "femtosecond",
+    "gigasecond",
+    "hectosecond",
+    "hour",
+    "kilosecond",
+    "megasecond",
+    "microsecond",
+    "millisecond",
+    "minute",
+    "nanosecond",
+    "petasecond",
+    "picosecond",
+    "second",
+    "terasecond",
+    "yoctosecond",
+    "yottasecond",
+    "zeptosecond",
+    "zettasecond",
+]);
+// Base Axis schema
+exports.BaseAxisSchema = zod_1.z.object({
+    name: zod_1.z.string(),
+    type: exports.AxisTypeSchema,
+});
+// Channel Axis schema
+exports.ChannelAxisSchema = zod_1.z.object({
+    name: zod_1.z.literal("c"),
+    type: zod_1.z.literal("channel"),
+});
+// Space Axis schema (includes orientation)
+exports.SpaceAxisSchema = zod_1.z.object({
+    name: exports.SpaceAxesNamesSchema,
+    type: zod_1.z.literal("space"),
+    unit: exports.SpaceUnitSchema,
+    orientation: zod_1.z.union([exports.AnatomicalOrientationSchema, zod_1.z.null()]).optional(),
+});
+// Time Axis schema
+exports.TimeAxisSchema = zod_1.z.object({
+    name: zod_1.z.literal("t"),
+    type: zod_1.z.literal("time"),
+    unit: exports.TimeUnitSchema,
+});
+// Union of all axis types
+exports.AxisSchema = zod_1.z.union([
+    exports.ChannelAxisSchema,
+    exports.SpaceAxisSchema,
+    exports.TimeAxisSchema,
+]);
+// Axes collection schema
+exports.AxesSchema = zod_1.z.object({
+    axes: zod_1.z.array(exports.AxisSchema).nullable().optional(),
+});

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

@@ -1 +1 @@
-{"version":3,"file":"units.d.ts","sourceRoot":"","sources":["../../src/schemas/units.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AASxB,eAAO,MAAM,mBAAmB,EAAE,CAAC,CAAC,UAMlC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,CAAC,CAAC,UAAoC,CAAC;AAEvE,eAAO,MAAM,cAAc,EAAE,CAAC,CAAC,UAI7B,CAAC;AAEH,eAAO,MAAM,gBAAgB,EAAE,CAAC,CAAC,UA2B/B,CAAC;AAEH,eAAO,MAAM,eAAe,EAAE,CAAC,CAAC,UAwB9B,CAAC;AAEH,eAAO,MAAM,WAAW,EAAE,CAAC,CAAC,QAAQ,CAClC;IAAC,OAAO,gBAAgB;IAAE,OAAO,eAAe;CAAC,CACH,CAAC;AAEjD,eAAO,MAAM,kBAAkB,EAAE,CAAC,CAAC,UAKhC,CAAC;AAEJ,eAAO,MAAM,aAAa,EAAE,CAAC,CAAC,UAM3B,CAAC"}
+{"version":3,"file":"units.d.ts","sourceRoot":"","sources":["../../src/schemas/units.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AASxB,eAAO,MAAM,mBAAmB,EAAE,CAAC,CAAC,UAMlC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,CAAC,CAAC,UAAoC,CAAC;AAEvE,eAAO,MAAM,cAAc,EAAE,CAAC,CAAC,UAO7B,CAAC;AAEH,eAAO,MAAM,gBAAgB,EAAE,CAAC,CAAC,UA2B/B,CAAC;AAEH,eAAO,MAAM,eAAe,EAAE,CAAC,CAAC,UAwB9B,CAAC;AAEH,eAAO,MAAM,WAAW,EAAE,CAAC,CAAC,QAAQ,CAClC;IAAC,OAAO,gBAAgB;IAAE,OAAO,eAAe;CAAC,CACH,CAAC;AAEjD,eAAO,MAAM,kBAAkB,EAAE,CAAC,CAAC,UAKhC,CAAC;AAEJ,eAAO,MAAM,aAAa,EAAE,CAAC,CAAC,UAM3B,CAAC"}

package/script/schemas/units.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.unitValidator = exports.dimensionValidator = exports.UnitsSchema = exports.TimeUnitsSchema = exports.SpaceUnitsSchema = exports.AxesTypeSchema = exports.SpatialDimsSchema = exports.SupportedDimsSchema = void 0;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
 const zod_1 = require("zod");
 const units_js_1 = require("../types/units.js");
 exports.SupportedDimsSchema = zod_1.z.enum([
@@ -15,6 +17,9 @@ exports.AxesTypeSchema = zod_1.z.enum([
     "time",
     "space",
     "channel",
+    "array",
+    "coordinate",
+    "displacement",
 ]);
 exports.SpaceUnitsSchema = zod_1.z.enum([
     "angstrom",

package/script/schemas/zarr_metadata.d.ts

@@ -1,10 +1,32 @@
 import { z } from "zod";
-import { AxesTypeSchema, SupportedDimsSchema, UnitsSchema } from "./units.js";
 export declare const AxisSchema: z.ZodObject<{
-    name: typeof SupportedDimsSchema;
-    type: typeof AxesTypeSchema;
-    unit: z.ZodOptional<typeof UnitsSchema>;
-}>;
+    name: z.ZodType<unknown, unknown, z.core.$ZodTypeInternals<unknown, unknown>>;
+    type: z.ZodType<unknown, unknown, z.core.$ZodTypeInternals<unknown, unknown>>;
+    unit: z.ZodOptional<z.ZodUnion<[z.ZodType<unknown, unknown, z.core.$ZodTypeInternals<unknown, unknown>>, z.ZodType<unknown, unknown, z.core.$ZodTypeInternals<unknown, unknown>>]>>;
+    orientation: z.ZodOptional<z.ZodObject<{
+        type: z.ZodLiteral<"anatomical">;
+        value: z.ZodEnum<{
+            "left-to-right": "left-to-right";
+            "right-to-left": "right-to-left";
+            "anterior-to-posterior": "anterior-to-posterior";
+            "posterior-to-anterior": "posterior-to-anterior";
+            "inferior-to-superior": "inferior-to-superior";
+            "superior-to-inferior": "superior-to-inferior";
+            "dorsal-to-ventral": "dorsal-to-ventral";
+            "ventral-to-dorsal": "ventral-to-dorsal";
+            "dorsal-to-palmar": "dorsal-to-palmar";
+            "palmar-to-dorsal": "palmar-to-dorsal";
+            "dorsal-to-plantar": "dorsal-to-plantar";
+            "plantar-to-dorsal": "plantar-to-dorsal";
+            "rostral-to-caudal": "rostral-to-caudal";
+            "caudal-to-rostral": "caudal-to-rostral";
+            "cranial-to-caudal": "cranial-to-caudal";
+            "caudal-to-cranial": "caudal-to-cranial";
+            "proximal-to-distal": "proximal-to-distal";
+            "distal-to-proximal": "distal-to-proximal";
+        }>;
+    }, z.core.$strip>>;
+}, z.core.$strip>;
 export declare const IdentitySchema: z.ZodObject<{
     type: z.ZodLiteral<"identity">;
 }>;
@@ -16,10 +38,274 @@ export declare const TranslationSchema: z.ZodObject<{
     translation: z.ZodArray<z.ZodNumber>;
     type: z.ZodLiteral<"translation">;
 }>;
-export declare const TransformSchema: z.ZodUnion<[
-    typeof ScaleSchema,
-    typeof TranslationSchema
-]>;
+export declare const TransformSchema: z.ZodUnion<readonly [z.ZodObject<{
+    scale: z.ZodArray<z.ZodNumber>;
+    type: z.ZodLiteral<"scale">;
+}, z.core.$strip>, z.ZodObject<{
+    translation: z.ZodArray<z.ZodNumber>;
+    type: z.ZodLiteral<"translation">;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"identity">;
+}, z.core.$strip>, z.ZodUnion<readonly [z.ZodObject<{
+    type: z.ZodLiteral<"identity">;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"mapAxis">;
+    mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"translation">;
+    translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+    path: z.ZodOptional<z.ZodString>;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"scale">;
+    scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+    path: z.ZodOptional<z.ZodString>;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"affine">;
+    affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
+    path: z.ZodOptional<z.ZodString>;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"rotation">;
+    rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+    path: z.ZodOptional<z.ZodString>;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"sequence">;
+    transformations: z.ZodArray<z.ZodUnion<readonly [z.ZodObject<{
+        type: z.ZodLiteral<"identity">;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"mapAxis">;
+        mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"translation">;
+        translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"scale">;
+        scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"affine">;
+        affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"rotation">;
+        rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>]>>;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"inverseOf">;
+    transformation: z.ZodUnion<readonly [z.ZodObject<{
+        type: z.ZodLiteral<"identity">;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"mapAxis">;
+        mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"translation">;
+        translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"scale">;
+        scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"affine">;
+        affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"rotation">;
+        rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>]>;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"bijection">;
+    forward: z.ZodUnion<readonly [z.ZodObject<{
+        type: z.ZodLiteral<"identity">;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"mapAxis">;
+        mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"translation">;
+        translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"scale">;
+        scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"affine">;
+        affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"rotation">;
+        rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>]>;
+    inverse: z.ZodUnion<readonly [z.ZodObject<{
+        type: z.ZodLiteral<"identity">;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"mapAxis">;
+        mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"translation">;
+        translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"scale">;
+        scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"affine">;
+        affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"rotation">;
+        rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>]>;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    type: z.ZodLiteral<"byDimension">;
+    transformations: z.ZodArray<z.ZodUnion<readonly [z.ZodObject<{
+        type: z.ZodLiteral<"identity">;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"mapAxis">;
+        mapAxis: z.ZodRecord<z.ZodString, z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"translation">;
+        translation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"scale">;
+        scale: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"affine">;
+        affine: z.ZodOptional<z.ZodArray<z.ZodArray<z.ZodNumber>>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        type: z.ZodLiteral<"rotation">;
+        rotation: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        path: z.ZodOptional<z.ZodString>;
+        input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+        name: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>]>>;
+    input: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    output: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>;
+    name: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>]>]>;
 export declare const DatasetSchema: z.ZodObject<{
     path: z.ZodString;
     coordinateTransformations: z.ZodArray<typeof TransformSchema>;
@@ -38,6 +324,11 @@ export declare const OmeroChannelSchema: z.ZodObject<{
 export declare const OmeroSchema: z.ZodObject<{
     channels: z.ZodArray<typeof OmeroChannelSchema>;
 }>;
+export declare const MethodMetadataSchema: z.ZodObject<{
+    description: z.ZodString;
+    method: z.ZodString;
+    version: z.ZodString;
+}, z.core.$strip>;
 export declare const MetadataSchema: z.ZodObject<{
     axes: z.ZodArray<typeof AxisSchema>;
     datasets: z.ZodArray<typeof DatasetSchema>;
@@ -45,5 +336,7 @@ export declare const MetadataSchema: z.ZodObject<{
     omero: z.ZodOptional<typeof OmeroSchema>;
     name: z.ZodDefault<z.ZodString>;
     version: z.ZodDefault<z.ZodString>;
+    type: z.ZodOptional<z.ZodString>;
+    metadata: z.ZodOptional<typeof MethodMetadataSchema>;
 }>;
 //# sourceMappingURL=zarr_metadata.d.ts.map

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

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+{"version":3,"file":"zarr_metadata.d.ts","sourceRoot":"","sources":["../../src/schemas/zarr_metadata.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAMxB,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAMrB,CAAC;AAGH,eAAO,MAAM,cAAc,EAAE,CAAC,CAAC,SAAS,CAAC;IACvC,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC;CAChC,CAEC,CAAC;AAEH,eAAO,MAAM,WAAW,EAAE,CAAC,CAAC,SAAS,CAAC;IACpC,KAAK,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAC/B,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC;CAC7B,CAGC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC1C,WAAW,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACrC,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,aAAa,CAAC,CAAC;CACnC,CAGC,CAAC;AAGH,eAAO,MAAM,eAAe;WAhBnB,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC;UACxB,CAAC,CAAC,UAAU,CAAC,OAAO,CAAC;;iBAOd,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC;UAC9B,CAAC,CAAC,UAAU,CAAC,aAAa,CAAC;;UAf3B,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBA2B9B,CAAC;AAEH,eAAO,MAAM,aAAa,EAAE,CAAC,CAAC,SAAS,CAAC;IACtC,IAAI,EAAE,CAAC,CAAC,SAAS,CAAC;IAClB,yBAAyB,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,eAAe,CAAC,CAAC;CAC/D,CAGC,CAAC;AAEH,eAAO,MAAM,iBAAiB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC1C,GAAG,EAAE,CAAC,CAAC,SAAS,CAAC;IACjB,GAAG,EAAE,CAAC,CAAC,SAAS,CAAC;IACjB,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC;IACnB,GAAG,EAAE,CAAC,CAAC,SAAS,CAAC;CAClB,CAKC,CAAC;AAEH,eAAO,MAAM,kBAAkB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC3C,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC;IACnB,MAAM,EAAE,OAAO,iBAAiB,CAAC;IACjC,KAAK,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;CACnC,CAMC,CAAC;AAEH,eAAO,MAAM,WAAW,EAAE,CAAC,CAAC,SAAS,CAAC;IACpC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,kBAAkB,CAAC,CAAC;CACjD,CAEC,CAAC;AAEH,eAAO,MAAM,oBAAoB;;;;iBAI/B,CAAC;AAEH,eAAO,MAAM,cAAc,EAAE,CAAC,CAAC,SAAS,CAAC;IACvC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,UAAU,CAAC,CAAC;IACpC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,OAAO,aAAa,CAAC,CAAC;IAC3C,yBAAyB,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,QAAQ,CAAC,OAAO,eAAe,CAAC,CAAC,CAAC;IAC7E,KAAK,EAAE,CAAC,CAAC,WAAW,CAAC,OAAO,WAAW,CAAC,CAAC;IACzC,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAChC,OAAO,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACnC,IAAI,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACjC,QAAQ,EAAE,CAAC,CAAC,WAAW,CAAC,OAAO,oBAAoB,CAAC,CAAC;CACtD,CASC,CAAC"}

package/script/schemas/zarr_metadata.js

@@ -1,13 +1,21 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MetadataSchema = exports.OmeroSchema = exports.OmeroChannelSchema = exports.OmeroWindowSchema = exports.DatasetSchema = exports.TransformSchema = exports.TranslationSchema = exports.ScaleSchema = exports.IdentitySchema = exports.AxisSchema = void 0;
+exports.MetadataSchema = exports.MethodMetadataSchema = exports.OmeroSchema = exports.OmeroChannelSchema = exports.OmeroWindowSchema = exports.DatasetSchema = exports.TransformSchema = exports.TranslationSchema = exports.ScaleSchema = exports.IdentitySchema = exports.AxisSchema = void 0;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
 const zod_1 = require("zod");
 const units_js_1 = require("./units.js");
+const rfc4_js_1 = require("./rfc4.js");
+const coordinate_systems_js_1 = require("./coordinate_systems.js");
+// Enhanced Axis schema that supports RFC4 orientation
 exports.AxisSchema = zod_1.z.object({
     name: units_js_1.SupportedDimsSchema,
     type: units_js_1.AxesTypeSchema,
     unit: units_js_1.UnitsSchema.optional(),
+    // RFC4: Optional orientation for space axes
+    orientation: rfc4_js_1.AnatomicalOrientationSchema.optional(),
 });
+// Legacy schemas for backward compatibility
 exports.IdentitySchema = zod_1.z.object({
     type: zod_1.z.literal("identity"),
 });
@@ -19,7 +27,13 @@ exports.TranslationSchema = zod_1.z.object({
     translation: zod_1.z.array(zod_1.z.number()),
     type: zod_1.z.literal("translation"),
 });
-exports.TransformSchema = zod_1.z.union([exports.ScaleSchema, exports.TranslationSchema]);
+// Enhanced transform schema that includes all RFC5 transformations
+exports.TransformSchema = zod_1.z.union([
+    exports.ScaleSchema,
+    exports.TranslationSchema,
+    exports.IdentitySchema,
+    coordinate_systems_js_1.CoordinateTransformationSchema,
+]);
 exports.DatasetSchema = zod_1.z.object({
     path: zod_1.z.string(),
     coordinateTransformations: zod_1.z.array(exports.TransformSchema),
@@ -40,6 +54,11 @@ exports.OmeroChannelSchema = zod_1.z.object({
 exports.OmeroSchema = zod_1.z.object({
     channels: zod_1.z.array(exports.OmeroChannelSchema),
 });
+exports.MethodMetadataSchema = zod_1.z.object({
+    description: zod_1.z.string(),
+    method: zod_1.z.string(),
+    version: zod_1.z.string(),
+});
 exports.MetadataSchema = zod_1.z.object({
     axes: zod_1.z.array(exports.AxisSchema),
     datasets: zod_1.z.array(exports.DatasetSchema),
@@ -47,4 +66,6 @@ exports.MetadataSchema = zod_1.z.object({
     omero: exports.OmeroSchema.optional(),
     name: zod_1.z.string().default("image"),
     version: zod_1.z.string().default("0.4"),
+    type: zod_1.z.string().optional(),
+    metadata: exports.MethodMetadataSchema.optional(),
 });

package/script/types/array_interface.d.ts

@@ -0,0 +1,7 @@
+export interface ArrayLike {
+    readonly shape: number[];
+    readonly dtype: string;
+    readonly chunks: number[];
+    readonly path?: string;
+}
+//# sourceMappingURL=array_interface.d.ts.map

package/script/types/array_interface.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"array_interface.d.ts","sourceRoot":"","sources":["../../src/types/array_interface.ts"],"names":[],"mappings":"AAGA,MAAM,WAAW,SAAS;IACxB,QAAQ,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC;IACzB,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC;IAC1B,QAAQ,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC;CACxB"}

package/script/types/array_interface.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/script/types/hcs.d.ts

@@ -0,0 +1,70 @@
+import type { Multiscales } from "./multiscales.js";
+import type { PlateAcquisition, PlateColumn, PlateRow, PlateWell, WellImage } from "../schemas/index.js";
+export interface LRUCacheOptions {
+    maxSize: number;
+}
+export declare class LRUCache<K, V> {
+    private cache;
+    private readonly maxSize;
+    constructor(options: LRUCacheOptions);
+    get(key: K): V | undefined;
+    set(key: K, value: V): void;
+    has(key: K): boolean;
+    clear(): void;
+}
+export interface PlateMetadata {
+    columns: PlateColumn[];
+    rows: PlateRow[];
+    wells: PlateWell[];
+    version: string;
+    acquisitions?: PlateAcquisition[] | undefined;
+    field_count?: number | undefined;
+    name?: string | undefined;
+}
+export interface WellMetadata {
+    images: WellImage[];
+    version: string;
+}
+export interface HCSPlateOptions {
+    store: string | object;
+    metadata: PlateMetadata;
+    wellCacheSize?: number | undefined;
+    imageCacheSize?: number | undefined;
+}
+export interface HCSWellOptions {
+    store: string | object;
+    wellPath: string;
+    plateMetadata: PlateWell;
+    wellGroupMetadata: WellMetadata;
+    imageCacheSize?: number | undefined;
+}
+export declare class HCSWell {
+    private readonly store;
+    readonly path: string;
+    readonly plateMetadata: PlateWell;
+    readonly metadata: WellMetadata;
+    private readonly _images;
+    constructor(options: HCSWellOptions);
+    get rowIndex(): number;
+    get columnIndex(): number;
+    get images(): WellImage[];
+    getImage(fieldIndex?: number): Promise<Multiscales | null>;
+    getImageByAcquisition(acquisitionId: number, fieldIndex?: number): Promise<Multiscales | null>;
+    static fromStore(store: string | object, wellPath: string, wellMetadata: PlateWell, imageCacheSize?: number | undefined): HCSWell;
+}
+export declare class HCSPlate {
+    private readonly store;
+    readonly metadata: PlateMetadata;
+    private readonly _wells;
+    private readonly imageCacheSize;
+    constructor(options: HCSPlateOptions);
+    get name(): string | undefined;
+    get rows(): PlateRow[];
+    get columns(): PlateColumn[];
+    get wells(): PlateWell[];
+    get acquisitions(): PlateAcquisition[] | undefined;
+    get fieldCount(): number | undefined;
+    getWell(rowName: string, columnName: string): HCSWell | null;
+    getWellByIndices(rowIndex: number, columnIndex: number): HCSWell | null;
+}
+//# sourceMappingURL=hcs.d.ts.map

package/script/types/hcs.d.ts.map

@@ -0,0 +1 @@
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