@fideus-labs/ngff-zarr 0.2.4 → 0.2.5

package/esm/package.json

@@ -1,3 +0,0 @@
-{
-  "type": "module"
-}

package/script/_dnt.shims.d.ts

@@ -1,2 +0,0 @@
-export declare const dntGlobalThis: Omit<typeof globalThis, never>;
-//# sourceMappingURL=_dnt.shims.d.ts.map

package/script/_dnt.shims.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"_dnt.shims.d.ts","sourceRoot":"","sources":["../src/_dnt.shims.ts"],"names":[],"mappings":"AAEA,eAAO,MAAM,aAAa,gCAA2C,CAAC"}

package/script/_dnt.shims.js

@@ -1,60 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.dntGlobalThis = void 0;
-const dntGlobals = {};
-exports.dntGlobalThis = createMergeProxy(globalThis, dntGlobals);
-function createMergeProxy(baseObj, extObj) {
-    return new Proxy(baseObj, {
-        get(_target, prop, _receiver) {
-            if (prop in extObj) {
-                return extObj[prop];
-            }
-            else {
-                return baseObj[prop];
-            }
-        },
-        set(_target, prop, value) {
-            if (prop in extObj) {
-                delete extObj[prop];
-            }
-            baseObj[prop] = value;
-            return true;
-        },
-        deleteProperty(_target, prop) {
-            let success = false;
-            if (prop in extObj) {
-                delete extObj[prop];
-                success = true;
-            }
-            if (prop in baseObj) {
-                delete baseObj[prop];
-                success = true;
-            }
-            return success;
-        },
-        ownKeys(_target) {
-            const baseKeys = Reflect.ownKeys(baseObj);
-            const extKeys = Reflect.ownKeys(extObj);
-            const extKeysSet = new Set(extKeys);
-            return [...baseKeys.filter((k) => !extKeysSet.has(k)), ...extKeys];
-        },
-        defineProperty(_target, prop, desc) {
-            if (prop in extObj) {
-                delete extObj[prop];
-            }
-            Reflect.defineProperty(baseObj, prop, desc);
-            return true;
-        },
-        getOwnPropertyDescriptor(_target, prop) {
-            if (prop in extObj) {
-                return Reflect.getOwnPropertyDescriptor(extObj, prop);
-            }
-            else {
-                return Reflect.getOwnPropertyDescriptor(baseObj, prop);
-            }
-        },
-        has(_target, prop) {
-            return prop in extObj || prop in baseObj;
-        },
-    });
-}

package/script/browser-mod.d.ts

@@ -1,16 +0,0 @@
-export * from "./types/units.js";
-export * from "./types/methods.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 "./schemas/units.js";
-export * from "./schemas/methods.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 "./process/to_multiscales-browser.js";
-//# sourceMappingURL=browser-mod.d.ts.map

package/script/browser-mod.d.ts.map

@@ -1 +0,0 @@
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package/script/browser-mod.js

@@ -1,51 +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 __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.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
-// Browser-compatible module exports
-// This module excludes I/O functionality (from_ngff_zarr, to_ngff_zarr)
-// because those modules depend on Node.js/Deno-specific filesystem APIs
-// that are not available in browser environments.
-//
-// For browser use cases, the schemas, types, and validation utilities
-// are the most commonly needed functionality.
-__exportStar(require("./types/units.js"), exports);
-__exportStar(require("./types/methods.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("./schemas/units.js"), exports);
-__exportStar(require("./schemas/methods.js"), exports);
-__exportStar(require("./schemas/zarr_metadata.js"), exports);
-__exportStar(require("./schemas/ngff_image.js"), exports);
-__exportStar(require("./schemas/multiscales.js"), exports);
-var validation_js_1 = require("./utils/validation.js");
-Object.defineProperty(exports, "isValidDimension", { enumerable: true, get: function () { return validation_js_1.isValidDimension; } });
-Object.defineProperty(exports, "isValidUnit", { enumerable: true, get: function () { return validation_js_1.isValidUnit; } });
-Object.defineProperty(exports, "validateMetadata", { enumerable: true, get: function () { return validation_js_1.validateMetadata; } });
-var factory_js_1 = require("./utils/factory.js");
-Object.defineProperty(exports, "createAxis", { enumerable: true, get: function () { return factory_js_1.createAxis; } });
-Object.defineProperty(exports, "createDataset", { enumerable: true, get: function () { return factory_js_1.createDataset; } });
-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; } });
-// Browser-compatible processing modules
-__exportStar(require("./process/to_multiscales-browser.js"), exports);

package/script/io/from_ngff_zarr.d.ts

@@ -1,10 +0,0 @@
-import * as zarr from "zarrita";
-import { Multiscales } from "../types/multiscales.js";
-export interface FromNgffZarrOptions {
-    validate?: boolean;
-    version?: "0.4" | "0.5";
-}
-export type MemoryStore = Map<string, Uint8Array>;
-export declare function fromNgffZarr(store: string | MemoryStore | zarr.FetchStore, options?: FromNgffZarrOptions): Promise<Multiscales>;
-export declare function readArrayData(storePath: string, arrayPath: string, selection?: (number | null)[]): Promise<unknown>;
-//# sourceMappingURL=from_ngff_zarr.d.ts.map

package/script/io/from_ngff_zarr.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"from_ngff_zarr.d.ts","sourceRoot":"","sources":["../../src/io/from_ngff_zarr.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAMtD,MAAM,WAAW,mBAAmB;IAClC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;CACzB;AAED,MAAM,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;AAElD,wBAAsB,YAAY,CAEhC,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,WAAW,CAAC,CA6MtB;AAED,wBAAsB,aAAa,CACjC,SAAS,EAAE,MAAM,EACjB,SAAS,EAAE,MAAM,EACjB,SAAS,CAAC,EAAE,CAAC,MAAM,GAAG,IAAI,CAAC,EAAE,GAC5B,OAAO,CAAC,OAAO,CAAC,CAmClB"}

package/script/io/from_ngff_zarr.js

@@ -1,234 +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.fromNgffZarr = fromNgffZarr;
-exports.readArrayData = readArrayData;
-// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
-// SPDX-License-Identifier: MIT
-const dntShim = __importStar(require("../_dnt.shims.js"));
-const zarr = __importStar(require("zarrita"));
-const multiscales_js_1 = require("../types/multiscales.js");
-const ngff_image_js_1 = require("../types/ngff_image.js");
-const zarr_metadata_js_1 = require("../schemas/zarr_metadata.js");
-async function fromNgffZarr(
-// Also accepts FileSystemStore, ZipFileStore objects in Node.js/Deno
-store, options = {}) {
-    const validate = options.validate ?? false;
-    const version = options.version;
-    try {
-        // Determine the appropriate store type based on the path
-        let resolvedStore;
-        if (store instanceof Map || store instanceof zarr.FetchStore) {
-            resolvedStore = store;
-        }
-        else if (store.startsWith("http://") || store.startsWith("https://")) {
-            // Use FetchStore for HTTP/HTTPS URLs
-            resolvedStore = new zarr.FetchStore(store);
-        }
-        else {
-            // For local paths, check if we're in a browser environment
-            if (typeof dntShim.dntGlobalThis !== "undefined") {
-                throw new Error("Local file paths are not supported in browser environments. Use HTTP/HTTPS URLs instead.");
-            }
-            // Use dynamic import for FileSystemStore, ZipFileStore in Node.js/Deno environments
-            try {
-                const { FileSystemStore, ZipFileStore } = await Promise.resolve().then(() => __importStar(require("@zarrita/storage")));
-                // @ts-ignore: Node/Deno workaround
-                if (store instanceof FileSystemStore || store instanceof ZipFileStore) {
-                    // @ts-ignore: Node/Deno workaround
-                    resolvedStore = store;
-                }
-                else {
-                    // Normalize the path for cross-platform compatibility
-                    const normalizedPath = store.replace(/^\/([A-Za-z]:)/, "$1");
-                    // @ts-ignore: Node/Deno workaround
-                    resolvedStore = new FileSystemStore(normalizedPath);
-                }
-            }
-            catch (error) {
-                throw new Error(`Failed to load FileSystemStore: ${error}. Use HTTP/HTTPS URLs for browser compatibility.`);
-            }
-        }
-        // Try to use consolidated metadata for better performance
-        let optimizedStore;
-        try {
-            // @ts-ignore: tryWithConsolidated typing
-            optimizedStore = await zarr.tryWithConsolidated(resolvedStore);
-        }
-        catch {
-            optimizedStore = resolvedStore;
-        }
-        const root = await zarr.open(optimizedStore, {
-            kind: "group",
-        });
-        const attrs = root.attrs;
-        if (!attrs || !attrs.multiscales) {
-            throw new Error("No multiscales metadata found in Zarr store");
-        }
-        const multiscalesArray = attrs
-            .multiscales;
-        if (!Array.isArray(multiscalesArray) || multiscalesArray.length === 0) {
-            throw new Error("No multiscales metadata found in Zarr store");
-        }
-        const multiscalesMetadata = multiscalesArray[0];
-        if (validate) {
-            const result = zarr_metadata_js_1.MetadataSchema.safeParse(multiscalesMetadata);
-            if (!result.success) {
-                throw new Error(`Invalid OME-Zarr metadata: ${result.error.message}`);
-            }
-            // Check version compatibility if specified
-            if (version) {
-                const metadataWithVersion = multiscalesMetadata;
-                if (metadataWithVersion.version !== version) {
-                    throw new Error(`Expected OME-Zarr version ${version}, but found ${metadataWithVersion.version || "unknown"}`);
-                }
-            }
-        }
-        const metadata = multiscalesMetadata;
-        // Extract omero metadata from root attributes if present
-        if (attrs.omero) {
-            const omeroData = attrs.omero;
-            // Handle backward compatibility for OMERO window metadata
-            if (omeroData.channels && Array.isArray(omeroData.channels)) {
-                for (const channel of omeroData.channels) {
-                    if (channel.window && typeof channel.window === "object") {
-                        const window = channel.window;
-                        // Ensure both min/max and start/end are present for compatibility
-                        if (window.min !== undefined && window.max !== undefined) {
-                            // If only min/max present, use them for start/end
-                            if (window.start === undefined) {
-                                window.start = window.min;
-                            }
-                            if (window.end === undefined) {
-                                window.end = window.max;
-                            }
-                        }
-                        else if (window.start !== undefined && window.end !== undefined) {
-                            // If only start/end present, use them for min/max
-                            if (window.min === undefined) {
-                                window.min = window.start;
-                            }
-                            if (window.max === undefined) {
-                                window.max = window.end;
-                            }
-                        }
-                    }
-                }
-            }
-            metadata.omero = omeroData;
-        }
-        const images = [];
-        for (const dataset of metadata.datasets) {
-            const arrayPath = dataset.path;
-            const zarrArray = (await zarr.open(root.resolve(arrayPath), {
-                kind: "array",
-            }));
-            // Verify we have an array with the expected properties
-            if (!zarrArray ||
-                !("shape" in zarrArray) ||
-                !("dtype" in zarrArray) ||
-                !("chunks" in zarrArray)) {
-                throw new Error(`Invalid zarr array at path ${arrayPath}: missing shape property`);
-            }
-            const scale = {};
-            const translation = {};
-            for (const transform of dataset.coordinateTransformations) {
-                if (transform.type === "scale") {
-                    metadata.axes.forEach((axis, i) => {
-                        if (i < transform.scale.length) {
-                            scale[axis.name] = transform.scale[i];
-                        }
-                    });
-                }
-                else if (transform.type === "translation") {
-                    metadata.axes.forEach((axis, i) => {
-                        if (i < transform.translation.length) {
-                            translation[axis.name] = transform.translation[i];
-                        }
-                    });
-                }
-            }
-            const dims = metadata.axes.map((axis) => axis.name);
-            const axesUnits = metadata.axes.reduce((acc, axis) => {
-                if (axis.unit) {
-                    acc[axis.name] = axis.unit;
-                }
-                return acc;
-            }, {});
-            const ngffImage = new ngff_image_js_1.NgffImage({
-                data: zarrArray,
-                dims,
-                scale,
-                translation,
-                name: metadata.name,
-                axesUnits: Object.keys(axesUnits).length > 0 ? axesUnits : undefined,
-                computedCallbacks: undefined,
-            });
-            images.push(ngffImage);
-        }
-        return new multiscales_js_1.Multiscales({
-            images,
-            metadata,
-            scaleFactors: undefined,
-            method: undefined,
-            chunks: undefined,
-        });
-    }
-    catch (error) {
-        throw new Error(`Failed to read OME-Zarr: ${error instanceof Error ? error.message : String(error)}`);
-    }
-}
-async function readArrayData(storePath, arrayPath, selection) {
-    try {
-        const store = new zarr.FetchStore(storePath);
-        const root = zarr.root(store);
-        // Try to open as zarr v2 first, then v3 if that fails
-        let zarrArray;
-        try {
-            zarrArray = await zarr.open.v2(root.resolve(arrayPath), {
-                kind: "array",
-            });
-        }
-        catch (v2Error) {
-            try {
-                zarrArray = await zarr.open.v3(root.resolve(arrayPath), {
-                    kind: "array",
-                });
-            }
-            catch (v3Error) {
-                throw new Error(`Failed to open zarr array ${arrayPath} as either v2 or v3 format. v2 error: ${v2Error}. v3 error: ${v3Error}`);
-            }
-        }
-        if (selection) {
-            return await zarr.get(zarrArray, selection);
-        }
-        else {
-            return await zarr.get(zarrArray);
-        }
-    }
-    catch (error) {
-        throw new Error(`Failed to read array data: ${error instanceof Error ? error.message : String(error)}`);
-    }
-}

package/script/io/hcs.d.ts

@@ -1,18 +0,0 @@
-import type { HCSPlate } from "../types/hcs.js";
-export interface FromHcsZarrOptions {
-    validate?: boolean;
-    wellCacheSize?: number;
-    imageCacheSize?: number;
-}
-export interface ToHcsZarrOptions {
-    compressionLevel?: number;
-}
-/**
- * Read an HCS plate from an OME-Zarr NGFF store.
- */
-export declare function fromHcsZarr(store: string | object, options?: FromHcsZarrOptions): HCSPlate;
-/**
- * Write an HCS plate to an OME-Zarr NGFF store.
- */
-export declare function toHcsZarr(plate: HCSPlate, store: string | object, _options?: ToHcsZarrOptions): void;
-//# sourceMappingURL=hcs.d.ts.map

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

@@ -1 +0,0 @@
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package/script/io/hcs.js

@@ -1,55 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fromHcsZarr = fromHcsZarr;
-exports.toHcsZarr = toHcsZarr;
-const hcs_js_1 = require("../types/hcs.js");
-/**
- * Read an HCS plate from an OME-Zarr NGFF store.
- */
-function fromHcsZarr(store, options = {}) {
-    const { validate = false, wellCacheSize, imageCacheSize } = options;
-    if (validate) {
-        console.warn("HCS validation not yet implemented");
-    }
-    if (typeof store !== "string") {
-        throw new Error("Non-string store types not yet supported");
-    }
-    // For now, create a mock implementation
-    // This will be properly implemented when the zarrita API integration is complete
-    const plateMetadata = {
-        columns: [{ name: "1" }, { name: "2" }],
-        rows: [{ name: "A" }, { name: "B" }],
-        wells: [
-            { path: "A/1", rowIndex: 0, columnIndex: 0 },
-            { path: "A/2", rowIndex: 0, columnIndex: 1 },
-            { path: "B/1", rowIndex: 1, columnIndex: 0 },
-            { path: "B/2", rowIndex: 1, columnIndex: 1 },
-        ],
-        version: "0.4",
-        acquisitions: [{ id: 0, name: "Test Acquisition" }],
-        field_count: 2,
-        name: "Test Plate",
-    };
-    return new hcs_js_1.HCSPlate({
-        store,
-        metadata: plateMetadata,
-        wellCacheSize,
-        imageCacheSize,
-    });
-}
-/**
- * Write an HCS plate to an OME-Zarr NGFF store.
- */
-function toHcsZarr(plate, store, _options = {}) {
-    if (typeof store !== "string") {
-        throw new Error("Non-string store types not yet supported");
-    }
-    // Mock implementation for now
-    console.log(`HCS plate structure would be created at ${store}`);
-    console.log(`Plate: ${plate.name}`);
-    console.log(`Wells: ${plate.wells.length}`);
-    console.log(`Rows: ${plate.rows.length}, Columns: ${plate.columns.length}`);
-    if (plate.acquisitions) {
-        console.log(`Acquisitions: ${plate.acquisitions.length}`);
-    }
-}

package/script/io/itk_image_to_ngff_image.d.ts

@@ -1,30 +0,0 @@
-/**
- * Convert ITK-Wasm Image to NgffImage
- */
-import type { Image } from "itk-wasm";
-import { NgffImage } from "../types/ngff_image.js";
-export interface ItkImageToNgffImageOptions {
-    /**
-     * Whether to add anatomical orientation metadata based on ITK LPS coordinate system
-     * @default true
-     */
-    addAnatomicalOrientation?: boolean;
-    /**
-     * Path prefix for the zarr array (e.g., "scale0/", "scale1/")
-     * @default "image"
-     */
-    path?: string;
-}
-/**
- * Convert an ITK-Wasm Image to an NgffImage, preserving spatial metadata.
- *
- * This function converts ITK-Wasm Image objects to NgffImage format while
- * preserving spatial information like spacing, origin, and optionally
- * anatomical orientation based on the ITK LPS coordinate system.
- *
- * @param itkImage - The ITK-Wasm Image to convert
- * @param options - Conversion options
- * @returns Promise resolving to NgffImage
- */
-export declare function itkImageToNgffImage(itkImage: Image, options?: ItkImageToNgffImageOptions): Promise<NgffImage>;
-//# sourceMappingURL=itk_image_to_ngff_image.d.ts.map

package/script/io/itk_image_to_ngff_image.d.ts.map

@@ -1 +0,0 @@
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package/script/io/itk_image_to_ngff_image.js

@@ -1,153 +0,0 @@
-"use strict";
-// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
-// SPDX-License-Identifier: MIT
-/**
- * Convert ITK-Wasm Image to NgffImage
- */
-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.itkImageToNgffImage = itkImageToNgffImage;
-const zarr = __importStar(require("zarrita"));
-const ngff_image_js_1 = require("../types/ngff_image.js");
-const rfc4_js_1 = require("../types/rfc4.js");
-// Import the get_strides function from zarrita utilities
-const zarrita_1 = require("zarrita");
-/**
- * Convert an ITK-Wasm Image to an NgffImage, preserving spatial metadata.
- *
- * This function converts ITK-Wasm Image objects to NgffImage format while
- * preserving spatial information like spacing, origin, and optionally
- * anatomical orientation based on the ITK LPS coordinate system.
- *
- * @param itkImage - The ITK-Wasm Image to convert
- * @param options - Conversion options
- * @returns Promise resolving to NgffImage
- */
-async function itkImageToNgffImage(itkImage, options = {}) {
-    const { addAnatomicalOrientation = true, path = "image" } = options;
-    // Extract image properties from ITK-Wasm Image
-    const _data = itkImage.data;
-    // ITK stores size in physical space order [x, y, z], but the data buffer is in
-    // C-order (row-major) which means [z, y, x] indexing. Reverse to match data layout.
-    const shape = [...itkImage.size].reverse();
-    const spacing = itkImage.spacing;
-    const origin = itkImage.origin;
-    const ndim = shape.length;
-    // Determine dimension names based on shape and image type
-    // This logic matches the Python implementation
-    let dims;
-    // Check if this is a vector image (multi-component)
-    const imageType = itkImage.imageType;
-    const isVector = imageType.components > 1;
-    if (ndim === 3 && isVector) {
-        // 2D RGB/vector image: 2D spatial + components
-        dims = ["y", "x", "c"];
-    }
-    else if (ndim < 4) {
-        // Scalar images up to 3D: take the last ndim spatial dimensions
-        dims = ["z", "y", "x"].slice(-ndim);
-    }
-    else if (ndim < 5) {
-        // 3D RGB/vector or 4D scalar
-        if (isVector) {
-            dims = ["z", "y", "x", "c"];
-        }
-        else {
-            dims = ["t", "z", "y", "x"];
-        }
-    }
-    else if (ndim < 6) {
-        // 4D RGB/vector
-        dims = ["t", "z", "y", "x", "c"];
-    }
-    else {
-        throw new Error(`Unsupported number of dimensions: ${ndim}`);
-    }
-    // Identify spatial dimensions
-    const allSpatialDims = new Set(["x", "y", "z"]);
-    const spatialDims = dims.filter((dim) => allSpatialDims.has(dim));
-    // Create scale mapping from spacing
-    // ITK stores spacing/origin in physical space order (x, y, z),
-    // but we need to map them to array order (z, y, x).
-    // Reverse the arrays to convert from physical to array order, matching Python implementation.
-    const scale = {};
-    const reversedSpacing = spacing.slice().reverse();
-    spatialDims.forEach((dim, idx) => {
-        scale[dim] = reversedSpacing[idx];
-    });
-    // Create translation mapping from origin
-    const translation = {};
-    const reversedOrigin = origin.slice().reverse();
-    spatialDims.forEach((dim, idx) => {
-        translation[dim] = reversedOrigin[idx];
-    });
-    // Create Zarr array from ITK-Wasm data
-    const store = new Map();
-    const root = zarr.root(store);
-    // Determine appropriate chunk size
-    const chunkShape = shape.map((s) => Math.min(s, 256));
-    const zarrArray = await zarr.create(root.resolve(path), {
-        shape: shape,
-        chunk_shape: chunkShape,
-        data_type: imageType.componentType,
-        fill_value: 0,
-    });
-    // Write the ITK-Wasm data to the zarr array
-    // We use zarrita's set function to write the entire data efficiently
-    // Create a selection that covers the entire array (null means "all" for each dimension)
-    const selection = new Array(ndim).fill(null);
-    // Create a chunk object with the ITK-Wasm data in zarrita format
-    // ITK-Wasm stores data in column-major order with size [x, y, z],
-    // which has the same memory layout as C-order (row-major) with shape [z, y, x].
-    // We reversed the shape above, and now use C-order strides for that reversed shape.
-    const dataChunk = {
-        data: itkImage.data,
-        shape: shape,
-        stride: (0, zarrita_1._zarrita_internal_get_strides)(shape, "C"), // C-order strides for the reversed shape
-    };
-    // Write all data to the zarr array using zarrita's set function
-    // This handles chunking and encoding automatically
-    await zarr.set(zarrArray, selection, dataChunk); // Add anatomical orientation if requested
-    let axesOrientations;
-    if (addAnatomicalOrientation) {
-        axesOrientations = {};
-        for (const dim of spatialDims) {
-            const orientation = (0, rfc4_js_1.itkLpsToAnatomicalOrientation)(dim);
-            if (orientation !== undefined) {
-                axesOrientations[dim] = orientation;
-            }
-        }
-    }
-    return new ngff_image_js_1.NgffImage({
-        data: zarrArray,
-        dims,
-        scale,
-        translation,
-        name: "image",
-        axesUnits: undefined,
-        axesOrientations,
-        computedCallbacks: undefined,
-    });
-}