@fideus-labs/ngff-zarr 0.2.4 → 0.2.6

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 @@
-{"version":3,"file":"itk_image_to_ngff_image.d.ts","sourceRoot":"","sources":["../../src/io/itk_image_to_ngff_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AAEtC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAOnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,wBAAwB,CAAC,EAAE,OAAO,CAAC;IAEnC;;;OAGG;IACH,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,KAAK,EACf,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,SAAS,CAAC,CAmHpB"}

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,
-    });
-}

package/script/io/ngff_image_to_itk_image.d.ts

@@ -1,30 +0,0 @@
-/**
- * Convert NgffImage to ITK-Wasm Image
- */
-import type { Image } from "itk-wasm";
-import { NgffImage } from "../types/ngff_image.js";
-export interface NgffImageToItkImageOptions {
-    /**
-     * Extract a specific time index from a time-series image
-     * If specified and 't' dimension exists, extracts the slice at this time index
-     */
-    tIndex?: number;
-    /**
-     * Extract a specific channel index from a multi-channel image
-     * If specified and 'c' dimension exists, extracts the slice at this channel index
-     */
-    cIndex?: number;
-}
-/**
- * Convert an NgffImage to an ITK-Wasm Image, preserving spatial metadata.
- *
- * This function converts NgffImage objects to ITK-Wasm Image format while
- * preserving spatial information like spacing, origin, and direction matrix.
- * Optionally extracts specific time or channel slices.
- *
- * @param ngffImage - The NgffImage to convert
- * @param options - Conversion options
- * @returns Promise resolving to ITK-Wasm Image
- */
-export declare function ngffImageToItkImage(ngffImage: NgffImage, options?: NgffImageToItkImageOptions): Promise<Image>;
-//# sourceMappingURL=ngff_image_to_itk_image.d.ts.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"ngff_image_to_itk_image.d.ts","sourceRoot":"","sources":["../../src/io/ngff_image_to_itk_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAEV,KAAK,EAKN,MAAM,UAAU,CAAC;AAElB,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAEnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;IAEhB;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAsED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,SAAS,EAAE,SAAS,EACpB,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,KAAK,CAAC,CAmMhB"}

package/script/io/ngff_image_to_itk_image.js

@@ -1,244 +0,0 @@
-"use strict";
-// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
-// SPDX-License-Identifier: MIT
-/**
- * Convert NgffImage to ITK-Wasm Image
- */
-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.ngffImageToItkImage = ngffImageToItkImage;
-const zarr = __importStar(require("zarrita"));
-const ngff_image_js_1 = require("../types/ngff_image.js");
-/**
- * Convert the data type from zarr DataType to ITK-Wasm component type
- */
-function dataTypeToComponentType(dataType) {
-    switch (dataType) {
-        case "uint8":
-            return "uint8";
-        case "int8":
-            return "int8";
-        case "uint16":
-            return "uint16";
-        case "int16":
-            return "int16";
-        case "uint32":
-            return "uint32";
-        case "int32":
-            return "int32";
-        case "uint64":
-            return "uint64";
-        case "int64":
-            return "int64";
-        case "float32":
-            return "float32";
-        case "float64":
-            return "float64";
-        default:
-            throw new Error(`Unsupported data type: ${dataType}`);
-    }
-}
-/**
- * Move the channel dimension to the end (last position) if it exists
- * This follows the ITK convention where vector/RGB components are the last dimension
- */
-function moveChannelDimToLast(ngffImage) {
-    const dims = ngffImage.dims;
-    const cIndex = dims.indexOf("c");
-    if (cIndex === -1 || cIndex === dims.length - 1) {
-        // No channel dimension or already at the end
-        return ngffImage;
-    }
-    // Reorder dimensions to move 'c' to the end
-    const newDims = [...dims];
-    const cDim = newDims.splice(cIndex, 1)[0];
-    newDims.push(cDim);
-    // Note: We would need to transpose the zarr array data here
-    // For now, we'll assume the data is already in the correct order
-    // In a full implementation, you'd transpose the zarr array
-    return new ngff_image_js_1.NgffImage({
-        data: ngffImage.data, // TODO: transpose if needed
-        dims: newDims,
-        scale: ngffImage.scale,
-        translation: ngffImage.translation,
-        name: ngffImage.name,
-        axesUnits: ngffImage.axesUnits,
-        axesOrientations: ngffImage.axesOrientations,
-        computedCallbacks: ngffImage.computedCallbacks,
-    });
-}
-/**
- * Convert an NgffImage to an ITK-Wasm Image, preserving spatial metadata.
- *
- * This function converts NgffImage objects to ITK-Wasm Image format while
- * preserving spatial information like spacing, origin, and direction matrix.
- * Optionally extracts specific time or channel slices.
- *
- * @param ngffImage - The NgffImage to convert
- * @param options - Conversion options
- * @returns Promise resolving to ITK-Wasm Image
- */
-async function ngffImageToItkImage(ngffImage, options = {}) {
-    const { tIndex, cIndex } = options;
-    let workingImage = ngffImage;
-    // Extract time slice if requested
-    if (tIndex !== undefined && workingImage.dims.includes("t")) {
-        const tDimIndex = workingImage.dims.indexOf("t");
-        const newDims = workingImage.dims.filter((dim) => dim !== "t");
-        const newScale = Object.fromEntries(Object.entries(workingImage.scale).filter(([dim]) => dim !== "t"));
-        const newTranslation = Object.fromEntries(Object.entries(workingImage.translation).filter(([dim]) => dim !== "t"));
-        // Extract the time slice from zarr array
-        const selection = new Array(workingImage.data.shape.length).fill(null);
-        selection[tDimIndex] = tIndex;
-        const sliceData = await zarr.get(workingImage.data, selection);
-        // Create new zarr array with reduced dimensions
-        const store = new Map();
-        const root = zarr.root(store);
-        const newShape = workingImage.data.shape.filter((_, i) => i !== tDimIndex);
-        const chunkShape = newShape.map((s) => Math.min(s, 256));
-        const newArray = await zarr.create(root.resolve("slice"), {
-            shape: newShape,
-            chunk_shape: chunkShape,
-            data_type: workingImage.data.dtype,
-            fill_value: 0,
-        });
-        // Write the slice data
-        const fullSelection = new Array(newShape.length).fill(null);
-        await zarr.set(newArray, fullSelection, sliceData);
-        workingImage = new ngff_image_js_1.NgffImage({
-            data: newArray,
-            dims: newDims,
-            scale: newScale,
-            translation: newTranslation,
-            name: workingImage.name,
-            axesUnits: workingImage.axesUnits
-                ? Object.fromEntries(Object.entries(workingImage.axesUnits).filter(([dim]) => dim !== "t"))
-                : undefined,
-            axesOrientations: workingImage.axesOrientations
-                ? Object.fromEntries(Object.entries(workingImage.axesOrientations).filter(([dim]) => dim !== "t"))
-                : undefined,
-            computedCallbacks: workingImage.computedCallbacks,
-        });
-    }
-    // Extract channel slice if requested
-    if (cIndex !== undefined && workingImage.dims.includes("c")) {
-        const cDimIndex = workingImage.dims.indexOf("c");
-        const newDims = workingImage.dims.filter((dim) => dim !== "c");
-        const newScale = Object.fromEntries(Object.entries(workingImage.scale).filter(([dim]) => dim !== "c"));
-        const newTranslation = Object.fromEntries(Object.entries(workingImage.translation).filter(([dim]) => dim !== "c"));
-        // Extract the channel slice from zarr array
-        const selection = new Array(workingImage.data.shape.length).fill(null);
-        selection[cDimIndex] = cIndex;
-        const sliceData = await zarr.get(workingImage.data, selection);
-        // Create new zarr array with reduced dimensions
-        const store = new Map();
-        const root = zarr.root(store);
-        const newShape = workingImage.data.shape.filter((_, i) => i !== cDimIndex);
-        const chunkShape = newShape.map((s) => Math.min(s, 256));
-        const newArray = await zarr.create(root.resolve("slice"), {
-            shape: newShape,
-            chunk_shape: chunkShape,
-            data_type: workingImage.data.dtype,
-            fill_value: 0,
-        });
-        // Write the slice data
-        const fullSelection = new Array(newShape.length).fill(null);
-        await zarr.set(newArray, fullSelection, sliceData);
-        workingImage = new ngff_image_js_1.NgffImage({
-            data: newArray,
-            dims: newDims,
-            scale: newScale,
-            translation: newTranslation,
-            name: workingImage.name,
-            axesUnits: workingImage.axesUnits
-                ? Object.fromEntries(Object.entries(workingImage.axesUnits).filter(([dim]) => dim !== "c"))
-                : undefined,
-            axesOrientations: workingImage.axesOrientations
-                ? Object.fromEntries(Object.entries(workingImage.axesOrientations).filter(([dim]) => dim !== "c"))
-                : undefined,
-            computedCallbacks: workingImage.computedCallbacks,
-        });
-    }
-    // Move channel dimension to last position (ITK convention)
-    workingImage = moveChannelDimToLast(workingImage);
-    const dims = workingImage.dims;
-    const data = workingImage.data;
-    // Identify ITK spatial dimensions
-    const itkDimensionNames = new Set(["x", "y", "z", "t"]);
-    const itkDims = dims.filter((dim) => itkDimensionNames.has(dim));
-    // Sort ITK dimensions: spatial first (x, y, z), then time
-    const sortedItkDims = itkDims.sort((a, b) => {
-        const order = ["x", "y", "z", "t"];
-        return order.indexOf(a) - order.indexOf(b);
-    });
-    // Create ITK spacing, origin, and size arrays
-    // sortedItkDims is already in physical space order [x, y, z]
-    // Mapping from dims extracts the correct values from NGFF's array order [z, y, x]
-    const spacing = sortedItkDims.map((dim) => workingImage.scale[dim] || 1.0);
-    const origin = sortedItkDims.map((dim) => workingImage.translation[dim] || 0.0);
-    const size = sortedItkDims.map((dim) => data.shape[dims.indexOf(dim)]);
-    const dimension = sortedItkDims.length;
-    // Determine component type and pixel type
-    const componentType = dataTypeToComponentType(data.dtype);
-    let components = 1;
-    let pixelType = "Scalar";
-    if (dims.includes("c")) {
-        components = data.shape[dims.indexOf("c")];
-        if (components === 3 && componentType === "uint8") {
-            pixelType = "RGB";
-        }
-        else {
-            pixelType =
-                "VariableLengthVector";
-        }
-    }
-    // Create ImageType
-    const imageType = {
-        dimension,
-        componentType,
-        pixelType,
-        components,
-    };
-    // Read all data from zarr array
-    const selection = new Array(data.shape.length).fill(null);
-    const dataChunk = await zarr.get(data, selection);
-    // Create direction matrix (identity for now)
-    const direction = new Float64Array(dimension * dimension);
-    for (let i = 0; i < dimension; i++) {
-        direction[i * dimension + i] = 1.0;
-    }
-    // Create ITK-Wasm Image
-    const itkImage = {
-        imageType,
-        name: workingImage.name || "image",
-        origin,
-        spacing,
-        direction,
-        size,
-        metadata: new Map(),
-        data: dataChunk.data, // Cast to handle zarrita's data type
-    };
-    return itkImage;
-}

package/script/io/to_ngff_image.d.ts

@@ -1,17 +0,0 @@
-import { NgffImage } from "../types/ngff_image.js";
-export interface ToNgffImageOptions {
-    dims?: string[];
-    scale?: Record<string, number>;
-    translation?: Record<string, number>;
-    name?: string;
-    shape?: number[];
-}
-/**
- * Convert array data to NgffImage
- *
- * @param data - Input data as typed array or regular array
- * @param options - Configuration options for NgffImage creation
- * @returns NgffImage instance
- */
-export declare function toNgffImage(data: ArrayLike<number> | number[][] | number[][][], options?: ToNgffImageOptions): Promise<NgffImage>;
-//# sourceMappingURL=to_ngff_image.d.ts.map

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

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

@@ -1,162 +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.toNgffImage = toNgffImage;
-const zarr = __importStar(require("zarrita"));
-const ngff_image_js_1 = require("../types/ngff_image.js");
-/**
- * Convert array data to NgffImage
- *
- * @param data - Input data as typed array or regular array
- * @param options - Configuration options for NgffImage creation
- * @returns NgffImage instance
- */
-async function toNgffImage(data, options = {}) {
-    const { dims = ["y", "x"], scale = {}, translation = {}, name = "image", shape: explicitShape, } = options;
-    // Determine data shape and create typed array
-    let typedData;
-    let shape;
-    if (Array.isArray(data)) {
-        // Handle multi-dimensional arrays
-        if (Array.isArray(data[0])) {
-            if (Array.isArray(data[0][0])) {
-                // 3D array
-                const d3 = data;
-                shape = [d3.length, d3[0].length, d3[0][0].length];
-                typedData = new Float32Array(shape[0] * shape[1] * shape[2]);
-                let idx = 0;
-                for (let i = 0; i < shape[0]; i++) {
-                    for (let j = 0; j < shape[1]; j++) {
-                        for (let k = 0; k < shape[2]; k++) {
-                            typedData[idx++] = d3[i][j][k];
-                        }
-                    }
-                }
-            }
-            else {
-                // 2D array
-                const d2 = data;
-                shape = [d2.length, d2[0].length];
-                typedData = new Float32Array(shape[0] * shape[1]);
-                let idx = 0;
-                for (let i = 0; i < shape[0]; i++) {
-                    for (let j = 0; j < shape[1]; j++) {
-                        typedData[idx++] = d2[i][j];
-                    }
-                }
-            }
-        }
-        else {
-            // 1D array
-            const d1 = data;
-            shape = [d1.length];
-            typedData = new Float32Array(d1);
-        }
-    }
-    else {
-        // ArrayLike (already a typed array)
-        // Use explicit shape if provided, otherwise infer from data length and dims
-        if (explicitShape) {
-            shape = [...explicitShape];
-        }
-        else {
-            // Try to infer shape - this is a best guess
-            shape = [data.length];
-        }
-        // Preserve the original typed array type
-        if (data instanceof Uint8Array) {
-            typedData = data;
-        }
-        else if (data instanceof Uint16Array) {
-            typedData = data;
-        }
-        else {
-            typedData = new Float32Array(data);
-        }
-    }
-    // Adjust shape to match dims length if not explicitly provided
-    if (!explicitShape) {
-        while (shape.length < dims.length) {
-            shape.unshift(1);
-        }
-    }
-    if (shape.length !== dims.length) {
-        throw new Error(`Shape dimensionality (${shape.length}) must match dims length (${dims.length})`);
-    }
-    // Create in-memory zarr store and array
-    const store = new Map();
-    const root = zarr.root(store);
-    // Calculate appropriate chunk size
-    const chunkShape = shape.map((dim) => Math.min(dim, 256));
-    const zarrArray = await zarr.create(root.resolve("data"), {
-        shape,
-        chunk_shape: chunkShape,
-        data_type: "float32",
-        fill_value: 0,
-    });
-    // Write data to zarr array
-    await zarr.set(zarrArray, [], {
-        data: typedData,
-        shape,
-        stride: calculateStride(shape),
-    });
-    // Create scale and translation records with defaults
-    const fullScale = {};
-    const fullTranslation = {};
-    const spatialDims = new Set(["x", "y", "z"]);
-    for (const dim of dims) {
-        // Only set defaults for spatial dimensions
-        if (spatialDims.has(dim)) {
-            fullScale[dim] = scale[dim] ?? 1.0;
-            fullTranslation[dim] = translation[dim] ?? 0.0;
-        }
-        else {
-            // For non-spatial dimensions, only include if explicitly provided
-            if (scale[dim] !== undefined) {
-                fullScale[dim] = scale[dim];
-            }
-            if (translation[dim] !== undefined) {
-                fullTranslation[dim] = translation[dim];
-            }
-        }
-    }
-    return new ngff_image_js_1.NgffImage({
-        data: zarrArray,
-        dims,
-        scale: fullScale,
-        translation: fullTranslation,
-        name,
-        axesUnits: undefined,
-        computedCallbacks: undefined,
-    });
-}
-function calculateStride(shape) {
-    const stride = new Array(shape.length);
-    stride[shape.length - 1] = 1;
-    for (let i = shape.length - 2; i >= 0; i--) {
-        stride[i] = stride[i + 1] * shape[i + 1];
-    }
-    return stride;
-}

package/script/io/to_ngff_zarr.d.ts

@@ -1,10 +0,0 @@
-import * as zarr from "zarrita";
-import type { Multiscales } from "../types/multiscales.js";
-import type { MemoryStore } from "./from_ngff_zarr.js";
-export interface ToNgffZarrOptions {
-    overwrite?: boolean;
-    version?: "0.4" | "0.5";
-    chunksPerShard?: number | number[] | Record<string, number>;
-}
-export declare function toNgffZarr(store: string | MemoryStore | zarr.FetchStore, multiscales: Multiscales, options?: ToNgffZarrOptions): Promise<void>;
-//# sourceMappingURL=to_ngff_zarr.d.ts.map

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

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