@fideus-labs/ngff-zarr 0.1.0 → 0.2.1

package/script/methods/itkwasm-shared.js

@@ -0,0 +1,524 @@
+"use strict";
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+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.SPATIAL_DIMS = void 0;
+exports.calculateIncrementalFactor = calculateIncrementalFactor;
+exports.dimScaleFactors = dimScaleFactors;
+exports.updatePreviousDimFactors = updatePreviousDimFactors;
+exports.nextScaleMetadata = nextScaleMetadata;
+exports.getItkComponentType = getItkComponentType;
+exports.createIdentityMatrix = createIdentityMatrix;
+exports.transposeArray = transposeArray;
+exports.zarrToItkImage = zarrToItkImage;
+exports.itkImageToZarr = itkImageToZarr;
+const zarr = __importStar(require("zarrita"));
+exports.SPATIAL_DIMS = ["x", "y", "z"];
+/**
+ * Calculate the incremental factor needed to reach the target size from the previous size.
+ * This ensures exact target sizes when downsampling incrementally.
+ */
+function calculateIncrementalFactor(previousSize, targetSize) {
+    if (targetSize <= 0) {
+        return 1;
+    }
+    // Start with the theoretical factor
+    let factor = Math.floor(Math.ceil(previousSize / (targetSize + 0.5)));
+    // Verify this gives us the right size
+    let actualSize = Math.floor(previousSize / factor);
+    if (actualSize !== targetSize) {
+        // Adjust factor to get exact target
+        factor = Math.max(1, Math.floor(previousSize / targetSize));
+        actualSize = Math.floor(previousSize / factor);
+        // If still not exact, try ceil
+        if (actualSize !== targetSize) {
+            factor = Math.max(1, Math.ceil(previousSize / targetSize));
+        }
+    }
+    return Math.max(1, factor);
+}
+/**
+ * Convert dimension scale factors to ITK-Wasm format
+ * This computes the incremental scale factor relative to the previous scale,
+ * not the absolute scale factor from the original image.
+ *
+ * When originalImage and previousImage are provided, calculates the exact
+ * incremental factor needed to reach the target size from the previous size.
+ * This ensures we get exact 1x, 2x, 3x, 4x sizes even with incremental downsampling.
+ */
+function dimScaleFactors(dims, scaleFactor, previousDimFactors, originalImage, previousImage) {
+    const dimFactors = {};
+    if (typeof scaleFactor === "number") {
+        if (originalImage !== undefined && previousImage !== undefined) {
+            // Calculate target size: floor(original_size / scale_factor)
+            // Then calculate incremental factor from previous size to target size
+            for (const dim of dims) {
+                if (exports.SPATIAL_DIMS.includes(dim)) {
+                    const dimIndex = originalImage.dims.indexOf(dim);
+                    const originalSize = originalImage.data.shape[dimIndex];
+                    const targetSize = Math.floor(originalSize / scaleFactor);
+                    const prevDimIndex = previousImage.dims.indexOf(dim);
+                    const previousSize = previousImage.data.shape[prevDimIndex];
+                    dimFactors[dim] = calculateIncrementalFactor(previousSize, targetSize);
+                }
+                else {
+                    dimFactors[dim] = 1;
+                }
+            }
+        }
+        else {
+            // Fallback to old behavior when images not provided
+            for (const dim of dims) {
+                if (exports.SPATIAL_DIMS.includes(dim)) {
+                    // Divide by previous factor to get incremental scaling
+                    // Use Math.floor to truncate (matching Python's int() behavior)
+                    const incrementalFactor = scaleFactor /
+                        (previousDimFactors[dim] || 1);
+                    dimFactors[dim] = Math.max(1, Math.floor(incrementalFactor));
+                }
+                else {
+                    dimFactors[dim] = previousDimFactors[dim] || 1;
+                }
+            }
+        }
+    }
+    else {
+        if (originalImage !== undefined && previousImage !== undefined) {
+            for (const dim in scaleFactor) {
+                const dimIndex = originalImage.dims.indexOf(dim);
+                const originalSize = originalImage.data.shape[dimIndex];
+                const targetSize = Math.floor(originalSize / scaleFactor[dim]);
+                const prevDimIndex = previousImage.dims.indexOf(dim);
+                const previousSize = previousImage.data.shape[prevDimIndex];
+                dimFactors[dim] = calculateIncrementalFactor(previousSize, targetSize);
+            }
+        }
+        else {
+            // Fallback to old behavior when images not provided
+            for (const dim in scaleFactor) {
+                // Divide by previous factor to get incremental scaling
+                // Use Math.floor to truncate (matching Python's int() behavior)
+                const incrementalFactor = scaleFactor[dim] /
+                    (previousDimFactors[dim] || 1);
+                dimFactors[dim] = Math.max(1, Math.floor(incrementalFactor));
+            }
+        }
+        // Add dims not in scale_factor with factor of 1
+        for (const dim of dims) {
+            if (!(dim in dimFactors)) {
+                dimFactors[dim] = 1;
+            }
+        }
+    }
+    return dimFactors;
+}
+/**
+ * Update previous dimension factors
+ */
+function updatePreviousDimFactors(scaleFactor, spatialDims, previousDimFactors) {
+    const updated = { ...previousDimFactors };
+    if (typeof scaleFactor === "number") {
+        for (const dim of spatialDims) {
+            updated[dim] = scaleFactor;
+        }
+    }
+    else {
+        for (const dim in scaleFactor) {
+            updated[dim] = scaleFactor[dim];
+        }
+    }
+    return updated;
+}
+/**
+ * Compute next scale metadata
+ */
+function nextScaleMetadata(image, dimFactors, spatialDims) {
+    const translation = {};
+    const scale = {};
+    for (const dim of image.dims) {
+        if (spatialDims.includes(dim)) {
+            const factor = dimFactors[dim];
+            scale[dim] = image.scale[dim] * factor;
+            // Add offset to account for pixel center shift when downsampling
+            translation[dim] = image.translation[dim] +
+                0.5 * (factor - 1) * image.scale[dim];
+        }
+        else {
+            scale[dim] = image.scale[dim];
+            translation[dim] = image.translation[dim];
+        }
+    }
+    return [translation, scale];
+}
+/**
+ * Copy typed array to appropriate type
+ */
+function copyTypedArray(data) {
+    if (data instanceof Float32Array) {
+        return new Float32Array(data);
+    }
+    else if (data instanceof Float64Array) {
+        return new Float64Array(data);
+    }
+    else if (data instanceof Uint8Array) {
+        return new Uint8Array(data);
+    }
+    else if (data instanceof Int8Array) {
+        return new Int8Array(data);
+    }
+    else if (data instanceof Uint16Array) {
+        return new Uint16Array(data);
+    }
+    else if (data instanceof Int16Array) {
+        return new Int16Array(data);
+    }
+    else if (data instanceof Uint32Array) {
+        return new Uint32Array(data);
+    }
+    else if (data instanceof Int32Array) {
+        return new Int32Array(data);
+    }
+    else {
+        // Convert to Float32Array as fallback
+        return new Float32Array(data);
+    }
+}
+/**
+ * Get ITK component type from typed array
+ */
+function getItkComponentType(data) {
+    if (data instanceof Uint8Array)
+        return "uint8";
+    if (data instanceof Int8Array)
+        return "int8";
+    if (data instanceof Uint16Array)
+        return "uint16";
+    if (data instanceof Int16Array)
+        return "int16";
+    if (data instanceof Uint32Array)
+        return "uint32";
+    if (data instanceof Int32Array)
+        return "int32";
+    if (data instanceof Float64Array)
+        return "float64";
+    return "float32";
+}
+/**
+ * Create identity matrix for ITK direction
+ */
+function createIdentityMatrix(dimension) {
+    const matrix = new Float64Array(dimension * dimension);
+    for (let i = 0; i < dimension * dimension; i++) {
+        matrix[i] = i % (dimension + 1) === 0 ? 1 : 0;
+    }
+    return matrix;
+}
+/**
+ * Calculate stride for array
+ */
+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;
+}
+/**
+ * Transpose array data according to permutation
+ */
+function transposeArray(data, shape, permutation, componentType) {
+    const typedData = data;
+    // Create output array of same type
+    let output;
+    const totalSize = typedData.length;
+    switch (componentType) {
+        case "uint8":
+            output = new Uint8Array(totalSize);
+            break;
+        case "int8":
+            output = new Int8Array(totalSize);
+            break;
+        case "uint16":
+            output = new Uint16Array(totalSize);
+            break;
+        case "int16":
+            output = new Int16Array(totalSize);
+            break;
+        case "uint32":
+            output = new Uint32Array(totalSize);
+            break;
+        case "int32":
+            output = new Int32Array(totalSize);
+            break;
+        case "float64":
+            output = new Float64Array(totalSize);
+            break;
+        case "float32":
+        default:
+            output = new Float32Array(totalSize);
+            break;
+    }
+    // Calculate strides for source
+    const sourceStride = calculateStride(shape);
+    // Calculate new shape after permutation
+    const newShape = permutation.map((i) => shape[i]);
+    const targetStride = calculateStride(newShape);
+    // Perform transpose
+    const indices = new Array(shape.length).fill(0);
+    for (let i = 0; i < totalSize; i++) {
+        // Calculate source index from multi-dimensional indices
+        let sourceIdx = 0;
+        for (let j = 0; j < shape.length; j++) {
+            sourceIdx += indices[j] * sourceStride[j];
+        }
+        // Calculate target index with permuted dimensions
+        let targetIdx = 0;
+        for (let j = 0; j < permutation.length; j++) {
+            targetIdx += indices[permutation[j]] * targetStride[j];
+        }
+        output[targetIdx] = typedData[sourceIdx];
+        // Increment indices
+        for (let j = shape.length - 1; j >= 0; j--) {
+            indices[j]++;
+            if (indices[j] < shape[j])
+                break;
+            indices[j] = 0;
+        }
+    }
+    return output;
+}
+/**
+ * Convert zarr array to ITK-Wasm Image format
+ * If isVector is true, ensures "c" dimension is last by transposing if needed
+ */
+async function zarrToItkImage(array, dims, isVector = false) {
+    // Read the full array data
+    const result = await zarr.get(array);
+    // Ensure we have the data
+    if (!result.data || result.data.length === 0) {
+        throw new Error("Zarr array data is empty");
+    }
+    let data;
+    let shape = result.shape;
+    let _finalDims = dims;
+    // If vector image, ensure "c" is last dimension
+    if (isVector) {
+        const cIndex = dims.indexOf("c");
+        if (cIndex !== -1 && cIndex !== dims.length - 1) {
+            // Need to transpose to move "c" to the end
+            const permutation = dims.map((_, i) => i).filter((i) => i !== cIndex);
+            permutation.push(cIndex);
+            // Reorder dims
+            _finalDims = permutation.map((i) => dims[i]);
+            // Reorder shape
+            shape = permutation.map((i) => result.shape[i]);
+            // Transpose the data
+            data = transposeArray(result.data, result.shape, permutation, getItkComponentType(result.data));
+        }
+        else {
+            // "c" already at end or not present, just copy data
+            data = copyTypedArray(result.data);
+        }
+    }
+    else {
+        // Not a vector image, just copy data
+        data = copyTypedArray(result.data);
+    }
+    // For vector images, the last dimension is the component count, not a spatial dimension
+    const spatialShape = isVector ? shape.slice(0, -1) : shape;
+    const components = isVector ? shape[shape.length - 1] : 1;
+    // ITK expects size in physical space order [x, y, z], but spatialShape is in array order [z, y, x]
+    // So we need to reverse it
+    const itkSize = [...spatialShape].reverse();
+    // Create ITK-Wasm image
+    const itkImage = {
+        imageType: {
+            dimension: spatialShape.length,
+            componentType: getItkComponentType(data),
+            pixelType: isVector ? "VariableLengthVector" : "Scalar",
+            components,
+        },
+        name: "image",
+        origin: spatialShape.map(() => 0),
+        spacing: spatialShape.map(() => 1),
+        direction: createIdentityMatrix(spatialShape.length),
+        size: itkSize,
+        data: data,
+        metadata: new Map(),
+    };
+    return itkImage;
+}
+/**
+ * Convert ITK-Wasm Image back to zarr array
+ * Uses the provided store instead of creating a new one
+ *
+ * Important: ITK-Wasm stores size in physical space order [x, y, z], but data in
+ * column-major order (x contiguous). This column-major layout with size [x, y, z]
+ * is equivalent to C-order (row-major) with shape [z, y, x]. We reverse the size
+ * to get the zarr shape and use C-order strides for that reversed shape.
+ *
+ * @param itkImage - The ITK-Wasm image to convert
+ * @param store - The zarr store to write to
+ * @param path - The path within the store
+ * @param chunkShape - The chunk shape (in spatial dimension order, will be adjusted for components)
+ * @param targetDims - The target dimension order (e.g., ["c", "z", "y", "x"])
+ */
+async function itkImageToZarr(itkImage, store, path, chunkShape, targetDims) {
+    const root = zarr.root(store);
+    if (!itkImage.data) {
+        throw new Error("ITK image data is null or undefined");
+    }
+    // Determine data type - support all ITK TypedArray types
+    let dataType;
+    if (itkImage.data instanceof Uint8Array) {
+        dataType = "uint8";
+    }
+    else if (itkImage.data instanceof Int8Array) {
+        dataType = "int8";
+    }
+    else if (itkImage.data instanceof Uint16Array) {
+        dataType = "uint16";
+    }
+    else if (itkImage.data instanceof Int16Array) {
+        dataType = "int16";
+    }
+    else if (itkImage.data instanceof Uint32Array) {
+        dataType = "uint32";
+    }
+    else if (itkImage.data instanceof Int32Array) {
+        dataType = "int32";
+    }
+    else if (itkImage.data instanceof Float32Array) {
+        dataType = "float32";
+    }
+    else if (itkImage.data instanceof Float64Array) {
+        dataType = "float64";
+    }
+    else {
+        throw new Error(`Unsupported data type: ${itkImage.data.constructor.name}`);
+    }
+    // ITK stores size/spacing/origin in physical space order [x, y, z],
+    // but the data buffer is in C-order (row-major) which means [z, y, x] indexing.
+    // We need to reverse the size to match the data layout, just like we do for spacing/origin.
+    const shape = [...itkImage.size].reverse();
+    // For vector images, the components are stored in the data but not in the size
+    // The actual data length includes components
+    const components = itkImage.imageType.components || 1;
+    const isVector = components > 1;
+    // Validate data length matches expected shape (including components for vector images)
+    const spatialElements = shape.reduce((a, b) => a * b, 1);
+    const expectedLength = spatialElements * components;
+    if (itkImage.data.length !== expectedLength) {
+        console.error(`[ERROR] Data length mismatch in itkImageToZarr:`);
+        console.error(`  ITK image size (physical order):`, itkImage.size);
+        console.error(`  Shape (reversed):`, shape);
+        console.error(`  Components:`, components);
+        console.error(`  Expected data length:`, expectedLength);
+        console.error(`  Actual data length:`, itkImage.data.length);
+        throw new Error(`Data length (${itkImage.data.length}) doesn't match expected shape ${shape} with ${components} components (${expectedLength} elements)`);
+    }
+    // Determine the final shape and whether we need to transpose
+    // ITK image data has shape [...spatialDimsReversed, components] (with c at end)
+    // If targetDims is provided, we need to match that order
+    let zarrShape;
+    let zarrChunkShape;
+    let finalData = itkImage.data;
+    if (isVector && targetDims) {
+        // Find where "c" should be in targetDims
+        const cIndex = targetDims.indexOf("c");
+        if (cIndex === -1) {
+            throw new Error("Vector image but 'c' not found in targetDims");
+        }
+        // Current shape is [z, y, x, c] (spatial reversed + c at end)
+        // Target shape should match targetDims order
+        const currentShape = [...shape, components];
+        // Build target shape based on targetDims
+        zarrShape = new Array(targetDims.length);
+        const spatialDims = shape.slice(); // [z, y, x]
+        let spatialIdx = 0;
+        for (let i = 0; i < targetDims.length; i++) {
+            if (targetDims[i] === "c") {
+                zarrShape[i] = components;
+            }
+            else {
+                zarrShape[i] = spatialDims[spatialIdx++];
+            }
+        }
+        // If c is not at the end, we need to transpose
+        if (cIndex !== targetDims.length - 1) {
+            // Build permutation: where does each target dim come from in current shape?
+            const permutation = [];
+            spatialIdx = 0;
+            for (let i = 0; i < targetDims.length; i++) {
+                if (targetDims[i] === "c") {
+                    permutation.push(currentShape.length - 1); // c is at end of current
+                }
+                else {
+                    permutation.push(spatialIdx++);
+                }
+            }
+            // Transpose the data
+            finalData = transposeArray(itkImage.data, currentShape, permutation, getItkComponentType(itkImage.data));
+        }
+        // Chunk shape should match zarrShape
+        zarrChunkShape = new Array(zarrShape.length);
+        spatialIdx = 0;
+        for (let i = 0; i < targetDims.length; i++) {
+            if (targetDims[i] === "c") {
+                zarrChunkShape[i] = components;
+            }
+            else {
+                zarrChunkShape[i] = chunkShape[spatialIdx++];
+            }
+        }
+    }
+    else {
+        // No targetDims or not a vector - use default behavior
+        zarrShape = isVector ? [...shape, components] : shape;
+        zarrChunkShape = isVector ? [...chunkShape, components] : chunkShape;
+    }
+    // Chunk shape should match the dimensionality of zarrShape
+    if (zarrChunkShape.length !== zarrShape.length) {
+        throw new Error(`chunkShape length (${zarrChunkShape.length}) must match shape length (${zarrShape.length})`);
+    }
+    const array = await zarr.create(root.resolve(path), {
+        shape: zarrShape,
+        chunk_shape: zarrChunkShape,
+        data_type: dataType,
+        fill_value: 0,
+    });
+    // Write data - preserve the actual data type, don't cast to Float32Array
+    // Shape and stride should match the ITK image size order
+    // Use null for each dimension to select the entire array
+    const selection = zarrShape.map(() => null);
+    await zarr.set(array, selection, {
+        data: finalData,
+        shape: zarrShape,
+        stride: calculateStride(zarrShape),
+    });
+    return array;
+}

package/script/methods/itkwasm.d.ts

@@ -1,6 +1,14 @@
-import { NgffImage } from "../types/ngff_image.js";
 /**
- * Main downsampling function for ITK-Wasm
+ * ITK-Wasm downsampling support for multiscale generation
+ *
+ * This module provides conditional exports for browser and Node environments.
+ * The actual implementation is delegated to environment-specific modules:
+ * - itkwasm-browser.ts: Uses WebWorker-based functions for browser environments
+ * - itkwasm-node.ts: Uses native WASM functions for Node/Deno environments
+ *
+ * For Deno runtime, we default to the node implementation.
+ * For browser bundlers, they should use conditional exports in package.json
+ * to resolve to the browser implementation.
  */
-export declare function downsampleItkWasm(ngffImage: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image"): Promise<NgffImage[]>;
+export { downsampleItkWasm } from "./itkwasm-node.js";
 //# sourceMappingURL=itkwasm.d.ts.map

package/script/methods/itkwasm.d.ts.map

@@ -1 +1 @@
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