Resample and Convert DICOM to Common Image Formats

Overview

This example illustrates the use of SimpleITK for converting a set of DICOM images to other file formats (tif, jpg, png,…). The output file format is specified by the user, and the output image width can also be specified by the user (height is determined from the width as resulting pixel sizes are required to be isotropic). Grayscale images with high dynamic range are rescaled to [0,255] before conversion to the new format. Output is written in the same location as the input image, or to a user specified output directory. An additional csv file mapping between original and converted file names is also written, either to the specified output directory or to the current working directory.

Code

C#C++JavaPythonR

// A SimpleITK example demonstrating how to convert and resize DICOM files to common image types.

using System;
using System.Collections.Generic;
using System.IO;
using itk.simple;

namespace itk.simple.examples
{
    public class DicomConvert
    {
        public static void Main(string[] args)
        {
            if (args.Length < 2)
            {
                Console.WriteLine("Usage: DicomConvert <root_of_data_directory> <output_file_extension> [--w width] [--od output_directory]");
                return;
            }
            string rootDir = args[0];
            string outputExt = args[1];
            int? width = null;
            string outDir = null;
            for (int i = 2; i < args.Length; ++i)
            {
                if (args[i] == "--w" && i + 1 < args.Length)
                {
                    width = int.Parse(args[++i]);
                }
                else if (args[i] == "--od" && i + 1 < args.Length)
                {
                    outDir = args[++i];
                }
            }
            var inputFiles = new List<string>();
            WalkDir(new DirectoryInfo(rootDir), inputFiles);
            var fileNames = new List<string>();
            if (outDir != null)
            {
                for (int i = 0; i < inputFiles.Count; ++i)
                {
                    fileNames.Add(Path.Combine(outDir, i.ToString()));
                }
            }
            else
            {
                fileNames.AddRange(inputFiles);
            }
            var outputFiles = new List<string>();
            foreach (var f in fileNames)
            {
                outputFiles.Add(f + "." + outputExt);
            }
            var res = new List<bool>();
            for (int i = 0; i < inputFiles.Count; ++i)
            {
                res.Add(ConvertImage(inputFiles[i], outputFiles[i], width));
            }
            var filteredInput = new List<string>();
            var filteredOutput = new List<string>();
            for (int i = 0; i < res.Count; ++i)
            {
                if (res[i])
                {
                    filteredInput.Add(inputFiles[i]);
                    filteredOutput.Add(outputFiles[i]);
                }
            }
            string csvDir = outDir ?? Directory.GetCurrentDirectory();
            using (var writer = new StreamWriter(Path.Combine(csvDir, "file_names.csv")))
            {
                writer.WriteLine("input file name,output file name");
                for (int i = 0; i < filteredInput.Count; ++i)
                {
                    writer.WriteLine(filteredInput[i] + ","+ filteredOutput[i]);
                }
            }
        }

        static void WalkDir(DirectoryInfo dir, List<string> files)
        {
            foreach (var f in dir.GetFileSystemInfos())
            {
                if ((f.Attributes & FileAttributes.Directory) == FileAttributes.Directory)
                {
                    WalkDir((DirectoryInfo)f, files);
                }
                else
                {
                    files.Add(f.FullName);
                }
            }
        }

        static bool ConvertImage(string inputFile, string outputFile, int? newWidth)
        {
            try
            {
                var reader = new ImageFileReader();
                // Only read DICOM images
                reader.SetImageIO("GDCMImageIO");
                reader.SetFileName(inputFile);
                var image = reader.Execute();
                var imageSize = image.GetSize();
                // If 3D image with single slice, treat as 2D
                if (imageSize.Count == 3 && imageSize[2] == 1) {
                  ExtractImageFilter extractFilter = new ExtractImageFilter();
                  extractFilter.SetIndex(new VectorInt32( new int[] { 0, 0, 0 }));
                  imageSize[2] = 0;
                  extractFilter.SetSize(imageSize);
                  image = extractFilter.Execute(image);
                }
                // Resample if new width is specified
                if (newWidth.HasValue)
                {
                    var originalSize = image.GetSize();
                    var originalSpacing = image.GetSpacing();
                    double newSpacing = ((originalSize[0] - 1) * originalSpacing[0]) / (newWidth.Value - 1);
                    long newHeight = (long)(((originalSize[1] - 1) * originalSpacing[1]) / newSpacing);
                    image = SimpleITK.Resample(image, new VectorUInt32(new long[] { newWidth.Value, newHeight }), new Transform(), InterpolatorEnum.sitkLinear,
                        image.GetOrigin(), new VectorDouble(new double[] { newSpacing, newSpacing }), image.GetDirection(), 0, image.GetPixelID());
                }
                // If a single channel image, rescale to [0,255] and cast to UInt8.
                if (image.GetNumberOfComponentsPerPixel() == 1)
                {
                    image = SimpleITK.RescaleIntensity(image, 0, 255);
                    image = SimpleITK.Cast(image, PixelIDValueEnum.sitkUInt8);
                }
                SimpleITK.WriteImage(image, outputFile);
                return true;
            }
            catch
            {
                return false;
            }
        }
    }
}