Create 3D Volume From Series of 2D Images

Synopsis

Create a 3D volume from a series of 2D images.

Results

Note

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Code

C++

#include "itkImage.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"
#include "itkNumericSeriesFileNames.h"

int
main(int argc, char * argv[])
{
  // Verify the number of parameters in the command line
  if (argc < 5)
  {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << " pattern firstSliceValue lastSliceValue outputImageFile" << std::endl;
    return EXIT_FAILURE;
  }

  using PixelType = unsigned char;
  constexpr unsigned int Dimension = 3;

  using ImageType = itk::Image<PixelType, Dimension>;
  using ReaderType = itk::ImageSeriesReader<ImageType>;
  using WriterType = itk::ImageFileWriter<ImageType>;

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();

  const unsigned int first = std::stoi(argv[2]);
  const unsigned int last = std::stoi(argv[3]);

  const char * outputFilename = argv[4];

  using NameGeneratorType = itk::NumericSeriesFileNames;

  NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();

  nameGenerator->SetSeriesFormat(argv[1]);

  nameGenerator->SetStartIndex(first);
  nameGenerator->SetEndIndex(last);
  nameGenerator->SetIncrementIndex(1);
  std::vector<std::string> names = nameGenerator->GetFileNames();

  // List the files
  //
  std::vector<std::string>::iterator nit;
  for (nit = names.begin(); nit != names.end(); nit++)
  {
    std::cout << "File: " << (*nit).c_str() << std::endl;
  }

  reader->SetFileNames(names);

  writer->SetFileName(outputFilename);
  writer->SetInput(reader->GetOutput());
  try
  {
    writer->Update();
  }
  catch (itk::ExceptionObject & err)
  {
    std::cerr << "ExceptionObject caught !" << std::endl;
    std::cerr << err << std::endl;
    return EXIT_FAILURE;
  }
  return EXIT_SUCCESS;
}

Classes demonstrated

template<typename TOutputImage>
class ImageSeriesReader : public itk::ImageSource<TOutputImage>

Data source that reads image data from a series of disk files.

This class builds an n-dimension image from multiple n-1 dimension image files. The files stored in a vector of strings are read using the ImageFileReader. File format may vary between the files, but the image data must have the same Size for all dimensions.

See

GDCMSeriesFileNames

See

NumericSeriesFileNames

See itk::ImageSeriesReader for additional documentation.