@fideus-labs/ngff-zarr 0.2.4 → 0.2.6

package/script/types/units.js

@@ -1,66 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.timeUnits = exports.spaceUnits = exports.supportedDims = void 0;
-exports.isDimensionSupported = isDimensionSupported;
-exports.isUnitSupported = isUnitSupported;
-exports.supportedDims = ["x", "y", "z", "c", "t"];
-exports.spaceUnits = [
-    "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.timeUnits = [
-    "attosecond",
-    "centisecond",
-    "day",
-    "decisecond",
-    "exasecond",
-    "femtosecond",
-    "gigasecond",
-    "hectosecond",
-    "hour",
-    "kilosecond",
-    "megasecond",
-    "microsecond",
-    "millisecond",
-    "minute",
-    "nanosecond",
-    "petasecond",
-    "picosecond",
-    "second",
-    "terasecond",
-    "yoctosecond",
-    "yottasecond",
-    "zeptosecond",
-    "zettasecond",
-];
-function isDimensionSupported(dim) {
-    return exports.supportedDims.includes(dim);
-}
-function isUnitSupported(unit) {
-    return (exports.timeUnits.includes(unit) ||
-        exports.spaceUnits.includes(unit));
-}

package/script/types/zarr_metadata.d.ts

@@ -1,58 +0,0 @@
-import type { AxesType, SupportedDims, Units } from "./units.js";
-export interface Axis {
-    name: SupportedDims;
-    type: AxesType;
-    unit: Units | undefined;
-}
-export interface Identity {
-    type: "identity";
-}
-export interface Scale {
-    scale: number[];
-    type: "scale";
-}
-export interface Translation {
-    translation: number[];
-    type: "translation";
-}
-export type Transform = Scale | Translation;
-export interface Dataset {
-    path: string;
-    coordinateTransformations: Transform[];
-}
-export interface OmeroWindow {
-    min?: number;
-    max?: number;
-    start?: number;
-    end?: number;
-}
-export interface OmeroChannel {
-    color: string;
-    window: OmeroWindow;
-    label?: string;
-    active?: boolean;
-}
-export interface Omero {
-    channels: OmeroChannel[];
-    version?: string;
-}
-export interface MethodMetadata {
-    description: string;
-    method: string;
-    version: string;
-}
-export interface Metadata {
-    axes: Axis[];
-    datasets: Dataset[];
-    coordinateTransformations: Transform[] | undefined;
-    omero: Omero | undefined;
-    name: string;
-    version: string;
-    type?: string;
-    metadata?: MethodMetadata;
-}
-export declare function validateColor(color: string): void;
-export declare function createScale(scale: number[]): Scale;
-export declare function createTranslation(translation: number[]): Translation;
-export declare function createIdentity(): Identity;
-//# sourceMappingURL=zarr_metadata.d.ts.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"zarr_metadata.d.ts","sourceRoot":"","sources":["../../src/types/zarr_metadata.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AAEjE,MAAM,WAAW,IAAI;IACnB,IAAI,EAAE,aAAa,CAAC;IACpB,IAAI,EAAE,QAAQ,CAAC;IACf,IAAI,EAAE,KAAK,GAAG,SAAS,CAAC;CACzB;AAED,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,UAAU,CAAC;CAClB;AAED,MAAM,WAAW,KAAK;IACpB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,IAAI,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,WAAW;IAC1B,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,IAAI,EAAE,aAAa,CAAC;CACrB;AAED,MAAM,MAAM,SAAS,GAAG,KAAK,GAAG,WAAW,CAAC;AAE5C,MAAM,WAAW,OAAO;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,yBAAyB,EAAE,SAAS,EAAE,CAAC;CACxC;AAED,MAAM,WAAW,WAAW;IAC1B,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,WAAW,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,KAAK;IACpB,QAAQ,EAAE,YAAY,EAAE,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,cAAc;IAC7B,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,IAAI,EAAE,CAAC;IACb,QAAQ,EAAE,OAAO,EAAE,CAAC;IACpB,yBAAyB,EAAE,SAAS,EAAE,GAAG,SAAS,CAAC;IACnD,KAAK,EAAE,KAAK,GAAG,SAAS,CAAC;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,cAAc,CAAC;CAC3B;AAED,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAIjD;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,KAAK,CAElD;AAED,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,WAAW,CAEpE;AAED,wBAAgB,cAAc,IAAI,QAAQ,CAEzC"}

package/script/types/zarr_metadata.js

@@ -1,20 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.validateColor = validateColor;
-exports.createScale = createScale;
-exports.createTranslation = createTranslation;
-exports.createIdentity = createIdentity;
-function validateColor(color) {
-    if (!/^[0-9A-Fa-f]{6}$/.test(color)) {
-        throw new Error(`Invalid color '${color}'. Must be 6 hex digits.`);
-    }
-}
-function createScale(scale) {
-    return { scale: [...scale], type: "scale" };
-}
-function createTranslation(translation) {
-    return { translation: [...translation], type: "translation" };
-}
-function createIdentity() {
-    return { type: "identity" };
-}

package/script/utils/create_queue.d.ts

@@ -1,6 +0,0 @@
-export type ChunkQueue = {
-    add(fn: () => Promise<void>): void;
-    onIdle(): Promise<void>;
-};
-export declare function createQueue(): ChunkQueue;
-//# sourceMappingURL=create_queue.d.ts.map

package/script/utils/create_queue.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"create_queue.d.ts","sourceRoot":"","sources":["../../src/utils/create_queue.ts"],"names":[],"mappings":"AAIA,MAAM,MAAM,UAAU,GAAG;IACvB,GAAG,CAAC,EAAE,EAAE,MAAM,OAAO,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC;IACnC,MAAM,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC;CACzB,CAAC;AAEF,wBAAgB,WAAW,IAAI,UAAU,CAOxC"}

package/script/utils/create_queue.js

@@ -1,17 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.createQueue = createQueue;
-// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
-// SPDX-License-Identifier: MIT
-const p_queue_1 = __importDefault(require("p-queue"));
-function createQueue() {
-    const concurrency = Math.min(navigator?.hardwareConcurrency || 4, 128);
-    const queue = new p_queue_1.default({ concurrency });
-    return {
-        add: (fn) => queue.add(fn),
-        onIdle: queue.onIdle.bind(queue),
-    };
-}

package/script/utils/factory.d.ts

@@ -1,13 +0,0 @@
-import { NgffImage } from "../types/ngff_image.js";
-import { Multiscales } from "../types/multiscales.js";
-import type { Axis, Dataset, Metadata, Scale, Translation } from "../types/zarr_metadata.js";
-import type { AxesType, SupportedDims, Units } from "../types/units.js";
-import type { Methods } from "../types/methods.js";
-export declare function createNgffImage(_data: ArrayBuffer | number[], shape: number[], dtype: string, dims: string[], scale: Record<string, number>, translation: Record<string, number>, name?: string): Promise<NgffImage>;
-export declare function createAxis(name: SupportedDims, type: AxesType, unit?: Units): Axis;
-export declare function createScale(scale: number[]): Scale;
-export declare function createTranslation(translation: number[]): Translation;
-export declare function createDataset(path: string, scale: number[], translation: number[]): Dataset;
-export declare function createMetadata(axes: Axis[], datasets: Dataset[], name?: string, version?: string): Metadata;
-export declare function createMultiscales(images: NgffImage[], metadata: Metadata, scaleFactors?: (Record<string, number> | number)[], method?: Methods): Multiscales;
-//# sourceMappingURL=factory.d.ts.map

package/script/utils/factory.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"factory.d.ts","sourceRoot":"","sources":["../../src/utils/factory.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,KAAK,EACV,IAAI,EACJ,OAAO,EACP,QAAQ,EACR,KAAK,EACL,WAAW,EACZ,MAAM,2BAA2B,CAAC;AACnC,OAAO,KAAK,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,MAAM,mBAAmB,CAAC;AACxE,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAsBnD,wBAAsB,eAAe,CACnC,KAAK,EAAE,WAAW,GAAG,MAAM,EAAE,EAC7B,KAAK,EAAE,MAAM,EAAE,EACf,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,MAAM,EAAE,EACd,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EAC7B,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACnC,IAAI,SAAU,GACb,OAAO,CAAC,SAAS,CAAC,CAYpB;AAED,wBAAgB,UAAU,CACxB,IAAI,EAAE,aAAa,EACnB,IAAI,EAAE,QAAQ,EACd,IAAI,CAAC,EAAE,KAAK,GACX,IAAI,CAMN;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,KAAK,CAKlD;AAED,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,WAAW,CAKpE;AAED,wBAAgB,aAAa,CAC3B,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EAAE,EACf,WAAW,EAAE,MAAM,EAAE,GACpB,OAAO,CAQT;AAED,wBAAgB,cAAc,CAC5B,IAAI,EAAE,IAAI,EAAE,EACZ,QAAQ,EAAE,OAAO,EAAE,EACnB,IAAI,SAAU,EACd,OAAO,SAAQ,GACd,QAAQ,CASV;AAED,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,SAAS,EAAE,EACnB,QAAQ,EAAE,QAAQ,EAClB,YAAY,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EAClD,MAAM,CAAC,EAAE,OAAO,GACf,WAAW,CAQb"}

package/script/utils/factory.js

@@ -1,108 +0,0 @@
-"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 __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.createNgffImage = createNgffImage;
-exports.createAxis = createAxis;
-exports.createScale = createScale;
-exports.createTranslation = createTranslation;
-exports.createDataset = createDataset;
-exports.createMetadata = createMetadata;
-exports.createMultiscales = createMultiscales;
-// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
-// SPDX-License-Identifier: MIT
-const zarr = __importStar(require("zarrita"));
-const ngff_image_js_1 = require("../types/ngff_image.js");
-const multiscales_js_1 = require("../types/multiscales.js");
-// Create a zarr.Array for testing using an in-memory store
-async function createTestZarrArray(shape, dtype, chunks, name) {
-    const store = new Map();
-    const root = zarr.root(store);
-    // Create the array using zarrita with correct options
-    const array = await zarr.create(root.resolve(name), {
-        shape,
-        chunk_shape: chunks,
-        data_type: dtype,
-    });
-    return array;
-}
-async function createNgffImage(_data, shape, dtype, dims, scale, translation, name = "image") {
-    const zarrArray = await createTestZarrArray(shape, dtype, shape, name);
-    return new ngff_image_js_1.NgffImage({
-        data: zarrArray,
-        dims,
-        scale,
-        translation,
-        name,
-        axesUnits: undefined,
-        computedCallbacks: undefined,
-    });
-}
-function createAxis(name, type, unit) {
-    return {
-        name,
-        type,
-        unit: unit || undefined,
-    };
-}
-function createScale(scale) {
-    return {
-        scale: [...scale],
-        type: "scale",
-    };
-}
-function createTranslation(translation) {
-    return {
-        translation: [...translation],
-        type: "translation",
-    };
-}
-function createDataset(path, scale, translation) {
-    return {
-        path,
-        coordinateTransformations: [
-            createScale(scale),
-            createTranslation(translation),
-        ],
-    };
-}
-function createMetadata(axes, datasets, name = "image", version = "0.4") {
-    return {
-        axes: [...axes],
-        datasets: [...datasets],
-        coordinateTransformations: undefined,
-        omero: undefined,
-        name,
-        version,
-    };
-}
-function createMultiscales(images, metadata, scaleFactors, method) {
-    return new multiscales_js_1.Multiscales({
-        images: [...images],
-        metadata,
-        scaleFactors: scaleFactors || undefined,
-        method: method || undefined,
-        chunks: undefined,
-    });
-}

package/script/utils/method_metadata.d.ts

@@ -1,10 +0,0 @@
-import type { Methods } from "../types/methods.js";
-import type { MethodMetadata } from "../types/zarr_metadata.js";
-/**
- * Get metadata information for a given downsampling method.
- *
- * @param method - The downsampling method enum
- * @returns MethodMetadata with description, method (package.function), and version
- */
-export declare function getMethodMetadata(method: Methods): MethodMetadata | undefined;
-//# sourceMappingURL=method_metadata.d.ts.map

package/script/utils/method_metadata.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"method_metadata.d.ts","sourceRoot":"","sources":["../../src/utils/method_metadata.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AA6BhE;;;;;GAKG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,OAAO,GAAG,cAAc,GAAG,SAAS,CAe7E"}

package/script/utils/method_metadata.js

@@ -1,40 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getMethodMetadata = getMethodMetadata;
-const METHOD_INFO = {
-    itkwasm_gaussian: {
-        description: "Smoothed with a discrete gaussian filter to generate a scale space, ideal for intensity images. ITK-Wasm implementation is extremely portable and SIMD accelerated.",
-        package: "itkwasm-downsample",
-        method: "itkwasm_downsample.downsample",
-    },
-    itkwasm_bin_shrink: {
-        description: "Uses the local mean for the output value. WebAssembly build. Fast but generates more artifacts than gaussian-based methods. Appropriate for intensity images.",
-        package: "itkwasm-downsample",
-        method: "itkwasm_downsample.downsample_bin_shrink",
-    },
-    itkwasm_label_image: {
-        description: "A sample is the mode of the linearly weighted local labels in the image. Fast and minimal artifacts. For label images.",
-        package: "itkwasm-downsample",
-        method: "itkwasm_downsample.downsample_label_image",
-    },
-};
-/**
- * Get metadata information for a given downsampling method.
- *
- * @param method - The downsampling method enum
- * @returns MethodMetadata with description, method (package.function), and version
- */
-function getMethodMetadata(method) {
-    const methodInfo = METHOD_INFO[method];
-    if (!methodInfo) {
-        return undefined;
-    }
-    // TODO: Determine package version dynamically if possible,
-    // For now use a placeholder
-    const version = "unknown";
-    return {
-        description: methodInfo.description,
-        method: methodInfo.method,
-        version,
-    };
-}

package/script/utils/validation.d.ts

@@ -1,6 +0,0 @@
-import type { Metadata } from "../types/zarr_metadata.js";
-export declare function validateMetadata(metadata: unknown): Metadata;
-export declare function validateColor(color: string): void;
-export declare function isValidDimension(dim: string): boolean;
-export declare function isValidUnit(unit: string): boolean;
-//# sourceMappingURL=validation.d.ts.map

package/script/utils/validation.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"validation.d.ts","sourceRoot":"","sources":["../../src/utils/validation.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAC;AAG1D,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,OAAO,GAAG,QAAQ,CAQ5D;AAED,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAIjD;AAED,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAErD;AAED,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAyDjD"}

package/script/utils/validation.js

@@ -1,78 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.validateMetadata = validateMetadata;
-exports.validateColor = validateColor;
-exports.isValidDimension = isValidDimension;
-exports.isValidUnit = isValidUnit;
-const zarr_metadata_js_1 = require("../schemas/zarr_metadata.js");
-function validateMetadata(metadata) {
-    const result = zarr_metadata_js_1.MetadataSchema.safeParse(metadata);
-    if (!result.success) {
-        throw new Error(`Invalid metadata: ${result.error.message}`);
-    }
-    return result.data;
-}
-function validateColor(color) {
-    if (!/^[0-9A-Fa-f]{6}$/.test(color)) {
-        throw new Error(`Invalid color '${color}'. Must be 6 hex digits.`);
-    }
-}
-function isValidDimension(dim) {
-    return ["c", "x", "y", "z", "t"].includes(dim);
-}
-function isValidUnit(unit) {
-    const timeUnits = [
-        "attosecond",
-        "centisecond",
-        "day",
-        "decisecond",
-        "exasecond",
-        "femtosecond",
-        "gigasecond",
-        "hectosecond",
-        "hour",
-        "kilosecond",
-        "megasecond",
-        "microsecond",
-        "millisecond",
-        "minute",
-        "nanosecond",
-        "petasecond",
-        "picosecond",
-        "second",
-        "terasecond",
-        "yoctosecond",
-        "yottasecond",
-        "zeptosecond",
-        "zettasecond",
-    ];
-    const spaceUnits = [
-        "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",
-    ];
-    return timeUnits.includes(unit) || spaceUnits.includes(unit);
-}