@fideus-labs/ngff-zarr 0.2.3 → 0.2.5

package/package.json

@@ -1,7 +1,19 @@
 {
   "name": "@fideus-labs/ngff-zarr",
-  "version": "0.2.3",
+  "version": "0.2.5",
   "description": "TypeScript implementation of ngff-zarr for reading and writing OME-Zarr files",
+  "license": "MIT",
+  "type": "module",
+  "main": "./esm/mod.js",
+  "types": "./esm/mod.d.ts",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/thewtex/ngff-zarr.git"
+  },
+  "bugs": {
+    "url": "https://github.com/thewtex/ngff-zarr/issues"
+  },
+  "homepage": "https://github.com/thewtex/ngff-zarr#readme",
   "keywords": [
     "ome-zarr",
     "zarr",
@@ -12,58 +24,49 @@
     "deno"
   ],
   "author": "ngff-zarr contributors",
-  "homepage": "https://github.com/thewtex/ngff-zarr#readme",
-  "repository": {
-    "type": "git",
-    "url": "git+https://github.com/thewtex/ngff-zarr.git"
-  },
-  "license": "MIT",
-  "bugs": {
-    "url": "https://github.com/thewtex/ngff-zarr/issues"
-  },
-  "main": "./esm/mod.js",
-  "module": "./esm/mod.js",
-  "types": "./esm/mod.d.ts",
   "exports": {
     ".": {
       "types": "./esm/mod.d.ts",
       "browser": "./esm/browser-mod.js",
       "node": "./esm/mod.js",
       "import": "./esm/mod.js",
-      "require": "./script/mod.js",
       "default": "./esm/mod.js"
     },
     "./browser": {
-      "types": "./types/browser-mod.d.ts",
+      "types": "./esm/browser-mod.d.ts",
       "import": "./esm/browser-mod.js",
-      "require": "./script/browser-mod.js",
       "default": "./esm/browser-mod.js"
     },
     "./methods/itkwasm-browser": {
-      "types": "./types/methods/itkwasm-browser.d.ts",
+      "types": "./esm/methods/itkwasm-browser.d.ts",
       "import": "./esm/methods/itkwasm-browser.js",
-      "require": "./script/methods/itkwasm-browser.js",
       "default": "./esm/methods/itkwasm-browser.js"
     },
     "./methods/itkwasm-node": {
-      "types": "./types/methods/itkwasm-node.d.ts",
+      "types": "./esm/methods/itkwasm-node.d.ts",
       "import": "./esm/methods/itkwasm-node.js",
-      "require": "./script/methods/itkwasm-node.js",
       "default": "./esm/methods/itkwasm-node.js"
+    },
+    "./process/to_multiscales-browser": {
+      "types": "./esm/process/to_multiscales-browser.d.ts",
+      "import": "./esm/process/to_multiscales-browser.js",
+      "default": "./esm/process/to_multiscales-browser.js"
+    },
+    "./process/to_multiscales-node": {
+      "types": "./esm/process/to_multiscales-node.d.ts",
+      "import": "./esm/process/to_multiscales-node.js",
+      "default": "./esm/process/to_multiscales-node.js"
     }
   },
   "browser": {
     "./esm/methods/itkwasm.js": "./esm/methods/itkwasm-browser.js",
-    "./script/methods/itkwasm.js": "./script/methods/itkwasm-browser.js",
     "./esm/methods/itkwasm-node.js": "./esm/methods/itkwasm-browser.js",
-    "./script/methods/itkwasm-node.js": "./script/methods/itkwasm-browser.js"
+    "./esm/process/to_multiscales-node.js": "./esm/process/to_multiscales-browser.js"
   },
   "files": [
     "esm/",
-    "script/",
-    "types/",
     "README.md",
-    "LICENSE"
+    "LICENSE.txt"
   ],
   "dependencies": {
     "@itk-wasm/downsample": "^1.8.1",
@@ -74,7 +77,7 @@
     "zarrita": "^0.5.2"
   },
   "devDependencies": {
-    "@itk-wasm/image-io": "^1.6.0"
-  },
-  "_generatedBy": "dnt@dev"
+    "@itk-wasm/image-io": "^1.6.0",
+    "typescript": "^5.7.2"
+  }
 }

package/esm/_dnt.shims.d.ts

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

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

@@ -1 +0,0 @@
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package/esm/_dnt.shims.js

@@ -1,57 +0,0 @@
-const dntGlobals = {};
-export const 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/esm/io/to_multiscales.d.ts

@@ -1,18 +0,0 @@
-import { NgffImage } from "../types/ngff_image.js";
-import { Multiscales } from "../types/multiscales.js";
-import { Methods } from "../types/methods.js";
-export { toNgffImage, type ToNgffImageOptions } from "./to_ngff_image.js";
-export interface ToMultiscalesOptions {
-    scaleFactors?: (Record<string, number> | number)[];
-    method?: Methods;
-    chunks?: number | number[] | Record<string, number>;
-}
-/**
- * Generate multiple resolution scales for an NgffImage (simplified version for testing)
- *
- * @param image - Input NgffImage
- * @param options - Configuration options
- * @returns Multiscales object
- */
-export declare function toMultiscales(image: NgffImage, options?: ToMultiscalesOptions): Promise<Multiscales>;
-//# sourceMappingURL=to_multiscales.d.ts.map

package/esm/io/to_multiscales.d.ts.map

@@ -1 +0,0 @@
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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

@@ -1,14 +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";
-//# 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

@@ -1,48 +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.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; } });
-// Note: Excluding I/O modules for browser compatibility

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 @@
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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 @@
-{"version":3,"file":"hcs.d.ts","sourceRoot":"","sources":["../../src/io/hcs.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAiB,MAAM,iBAAiB,CAAC;AAG/D,MAAM,WAAW,kBAAkB;IACjC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED,MAAM,WAAW,gBAAgB;IAE/B,gBAAgB,CAAC,EAAE,MAAM,CAAC;CAC3B;AAED;;GAEG;AACH,wBAAgB,WAAW,CACzB,KAAK,EAAE,MAAM,GAAG,MAAM,EACtB,OAAO,GAAE,kBAAuB,GAC/B,QAAQ,CAkCV;AAED;;GAEG;AACH,wBAAgB,SAAS,CACvB,KAAK,EAAE,QAAQ,EACf,KAAK,EAAE,MAAM,GAAG,MAAM,EACtB,QAAQ,GAAE,gBAAqB,GAC9B,IAAI,CAaN"}

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}`);
-    }
-}