Dicom Series Reader

Overview

This example illustrates how to read a DICOM series into a 3D volume. Additional actions include printing some information, writing the image and possibly displaying it using the default display program via the SimpleITK Show function. The program makes several assumptions: the given directory contains at least one DICOM series, if there is more than one series the first series is read, and the default SimpleITK external viewer is installed.

Code

using System;
using System.Diagnostics;
using itk.simple;
using sitk = itk.simple.SimpleITK;


namespace itk.simple.examples {
    class DicomSeriesReader {

static void Main(string[] args) {
  try {
    if (args.Length < 2) {
      Console.WriteLine( "Usage: DicomSeriesReader <input_directory> <output_file>" );
      return;
    }

    Console.WriteLine( "Reading Dicom directory: " + args[0] );
    ImageSeriesReader reader = new ImageSeriesReader();

    VectorString dicom_names = ImageSeriesReader.GetGDCMSeriesFileNames( args[0] );
    reader.SetFileNames( dicom_names );

    Image image = reader.Execute();

    VectorUInt32 size = image.GetSize();
    Console.WriteLine( "Image size: " + size[0] + " " + size[1] + " " + size[2] );

    Console.WriteLine( "Writing image: " + args[1] );
    ImageFileWriter writer = new ImageFileWriter();
    writer.SetFileName( args[1] );
    writer.Execute( image );

    if (Environment.GetEnvironmentVariable("SITK_NOSHOW") == null)
      SimpleITK.Show( image, "Dicom Series" );


  } catch (Exception ex) {
    Console.WriteLine( "Usage: DicomSeriesReader <input_directory> <output_file>" );
    Console.WriteLine( ex );
  }
}

    }
}

// This one header will include all SimpleITK filters and external
// objects.
#include <SimpleITK.h>
#include <iostream>
#include <stdlib.h>


// create convenient namespace alias
namespace sitk = itk::simple;

int
main(int argc, char * argv[])
{

  if (argc < 3)
  {
    std::cerr << "Usage: " << argv[0] << " <input_directory> <output_file>\n";
    return 1;
  }

  std::cout << "Reading Dicom directory: " << argv[1] << std::endl;

  // Read the Dicom image series
  sitk::ImageSeriesReader reader;
  auto                    dicom_names = sitk::ImageSeriesReader::GetGDCMSeriesFileNames(argv[1]);
  reader.SetFileNames(dicom_names);

  sitk::Image image = reader.Execute();

  std::vector<unsigned int> size = image.GetSize();
  std::cout << "Image size: " << size[0] << " " << size[1] << " " << size[2] << std::endl;

  std::cout << "Writing " << argv[2] << std::endl;

  sitk::WriteImage(image, argv[2]);

  if (getenv("SITK_NOSHOW") == NULL)
    sitk::Show(image, "Hello World: C++", true);

  return 0;
}

import org.itk.simple.*;

public class DicomSeriesReader {
  public static void main(String[] args) {

    if (args.length < 2) {
      System.out.println("Usage: DicomSeriesReader <input_directory> <output_file>");
      System.exit(1);
    }

    System.out.println("Reading Dicom directory: " + args[0]);

    ImageSeriesReader imageSeriesReader = new ImageSeriesReader();
    final VectorString dicomNames = ImageSeriesReader.getGDCMSeriesFileNames(args[0]);
    imageSeriesReader.setFileNames(dicomNames);

    Image image = imageSeriesReader.execute();

    VectorUInt32 size = image.getSize();
    System.out.println("Image size: " + size.get(0) + " " + size.get(1) + " " + size.get(2));

    System.out.println("Writing " + args[1]);

    SimpleITK.writeImage(image, args[1]);

    if (System.getenv("SITK_NOSHOW") == null) {
      SimpleITK.show( image, "Hello World: Java", true );
    }

  }
}

require "SimpleITK"

if #arg < 2 then
  print ( "Usage: DicomSeriesReader <input_directory> <output_file>" )
  os.exit ( 1 )
end

print( "Reading Dicom directory:", arg[1] )
reader = SimpleITK.ImageSeriesReader()

dicom_names = SimpleITK.ImageSeriesReader.GetGDCMSeriesFileNames( arg[1] )
reader:SetFileNames ( dicom_names )

image = reader:Execute();

size = image:GetSize();
print("Image size:", size[0], size[1], size[2]);

print( "Writing image:", arg[2] )
SimpleITK.WriteImage( image, arg[2] )

if os.getenv("SITK_NOSHOW") == nil then
    sitk.Show( image, "Hello World: Lua", true )
end

#!/usr/bin/env python

import sys
import os
import SimpleITK as sitk

if len(sys.argv) < 3:
    print("Usage: DicomSeriesReader <input_directory> <output_file>")
    sys.exit(1)

print("Reading Dicom directory:", sys.argv[1])
reader = sitk.ImageSeriesReader()

dicom_names = reader.GetGDCMSeriesFileNames(sys.argv[1])
reader.SetFileNames(dicom_names)

image = reader.Execute()

size = image.GetSize()
print("Image size:", size[0], size[1], size[2])

print("Writing image:", sys.argv[2])

sitk.WriteImage(image, sys.argv[2])

if "SITK_NOSHOW" not in os.environ:
    sitk.Show(image, "Dicom Series")

library(SimpleITK)

args <- commandArgs( TRUE )

if (length(args) <  2) {
   write("Usage arguments: <input_directory> <output_file>", stderr())
   quit(1)
}


cat( "Reading Dicom directory:", args[[1]] )

reader <- ImageSeriesReader()

dicomNames <- ImageSeriesReader_GetGDCMSeriesFileNames(args[[1]])
reader$SetFileNames(dicomNames)

image <- reader$Execute()

size <- image$GetSize()

cat ("Image size:", size[1], size[2], size[3])

cat("Writing image:", args[[2]])

WriteImage(image, args[[2]])

if(Sys.getenv("SITK_NOSHOW") == "") {
    Show(image, "Hello World: R", debugOn=TRUE)
}