@fideus-labs/ngff-zarr 0.2.4 → 0.2.5

package/script/schemas/rfc4.js

@@ -1,132 +0,0 @@
-"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

@@ -1,78 +0,0 @@
-import { z } from "zod";
-export declare const SupportedDimsSchema: z.ZodEnum<{
-    c: "c";
-    x: "x";
-    y: "y";
-    z: "z";
-    t: "t";
-}>;
-export declare const SpatialDimsSchema: z.ZodEnum<{
-    x: "x";
-    y: "y";
-    z: "z";
-}>;
-export declare const AxesTypeSchema: z.ZodEnum<{
-    time: "time";
-    space: "space";
-    channel: "channel";
-}>;
-export declare const SpaceUnitsSchema: 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";
-}>;
-export declare const TimeUnitsSchema: 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";
-}>;
-export declare const UnitsSchema: z.ZodUnion<[
-    typeof SpaceUnitsSchema,
-    typeof TimeUnitsSchema
-]>;
-export declare const dimensionValidator: z.ZodTypeAny;
-export declare const unitValidator: z.ZodTypeAny;
-//# sourceMappingURL=units.d.ts.map

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

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

@@ -1,70 +0,0 @@
-"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(["c", "x", "y", "z", "t"]);
-exports.SpatialDimsSchema = zod_1.z.enum(["x", "y", "z"]);
-exports.AxesTypeSchema = zod_1.z.enum(["time", "space", "channel"]);
-exports.SpaceUnitsSchema = 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",
-]);
-exports.TimeUnitsSchema = 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",
-]);
-exports.UnitsSchema = zod_1.z.union([exports.SpaceUnitsSchema, exports.TimeUnitsSchema]);
-exports.dimensionValidator = zod_1.z
-    .string()
-    .refine((dim) => units_js_1.supportedDims.includes(dim), { message: "Dimension must be one of: c, x, y, z, t" });
-exports.unitValidator = zod_1.z
-    .string()
-    .refine((unit) => [...units_js_1.timeUnits, ...units_js_1.spaceUnits].includes(unit), { message: "Unit must be a valid time or space unit" });

package/script/schemas/zarr_metadata.d.ts

@@ -1,55 +0,0 @@
-import { z } from "zod";
-import { AxesTypeSchema, SupportedDimsSchema, UnitsSchema } from "./units.js";
-import { AnatomicalOrientationSchema } from "./rfc4.js";
-export declare const AxisSchema: z.ZodObject<{
-    name: typeof SupportedDimsSchema;
-    type: typeof AxesTypeSchema;
-    unit: z.ZodOptional<typeof UnitsSchema>;
-    orientation: z.ZodOptional<typeof AnatomicalOrientationSchema>;
-}>;
-export declare const IdentitySchema: z.ZodObject<{
-    type: z.ZodLiteral<"identity">;
-}>;
-export declare const ScaleSchema: z.ZodObject<{
-    scale: z.ZodArray<z.ZodNumber>;
-    type: z.ZodLiteral<"scale">;
-}>;
-export declare const TranslationSchema: z.ZodObject<{
-    translation: z.ZodArray<z.ZodNumber>;
-    type: z.ZodLiteral<"translation">;
-}>;
-export declare const TransformSchema: z.ZodType<unknown>;
-export declare const DatasetSchema: z.ZodObject<{
-    path: z.ZodString;
-    coordinateTransformations: z.ZodArray<typeof TransformSchema>;
-}>;
-export declare const OmeroWindowSchema: z.ZodObject<{
-    min: z.ZodNumber;
-    max: z.ZodNumber;
-    start: z.ZodNumber;
-    end: z.ZodNumber;
-}>;
-export declare const OmeroChannelSchema: z.ZodObject<{
-    color: z.ZodString;
-    window: typeof OmeroWindowSchema;
-    label: z.ZodOptional<z.ZodString>;
-}>;
-export declare const OmeroSchema: z.ZodObject<{
-    channels: z.ZodArray<typeof OmeroChannelSchema>;
-}>;
-export declare const MethodMetadataSchema: z.ZodType<{
-    description: string;
-    method: string;
-    version: string;
-}>;
-export declare const MetadataSchema: z.ZodObject<{
-    axes: z.ZodArray<typeof AxisSchema>;
-    datasets: z.ZodArray<typeof DatasetSchema>;
-    coordinateTransformations: z.ZodOptional<z.ZodArray<typeof TransformSchema>>;
-    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

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

@@ -1,71 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-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"),
-});
-exports.ScaleSchema = zod_1.z.object({
-    scale: zod_1.z.array(zod_1.z.number()),
-    type: zod_1.z.literal("scale"),
-});
-exports.TranslationSchema = zod_1.z.object({
-    translation: zod_1.z.array(zod_1.z.number()),
-    type: zod_1.z.literal("translation"),
-});
-// 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),
-});
-exports.OmeroWindowSchema = zod_1.z.object({
-    min: zod_1.z.number(),
-    max: zod_1.z.number(),
-    start: zod_1.z.number(),
-    end: zod_1.z.number(),
-});
-exports.OmeroChannelSchema = zod_1.z.object({
-    color: zod_1.z.string().regex(/^[0-9A-Fa-f]{6}$/, {
-        message: "Color must be 6 hex digits",
-    }),
-    window: exports.OmeroWindowSchema,
-    label: zod_1.z.string().optional(),
-});
-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),
-    coordinateTransformations: zod_1.z.array(exports.TransformSchema).optional(),
-    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

@@ -1,7 +0,0 @@
-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

@@ -1 +0,0 @@
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package/script/types/array_interface.js

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

package/script/types/hcs.d.ts

@@ -1,70 +0,0 @@
-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

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