WikiExamples/DICOM/ResampleDICOM.cxx

// Resample a DICOM study
//   Usage: ResampleDICOM InputDirectory OutputDirectory
//                        xSpacing ySpacing zSpacing
//
//   Example: ResampleDICOM CT CTResample 0 0 1.5
//            will read a series from the CT directory and create a
//            new series in the CTResample directory. The new series
//            will have the same x,y spacing as the input series, but
//            will have a z-spacing of 1.5.
//
// Description:
// ResampleDICOM resamples a DICOM series with user-specified
// spacing. The program outputs a new DICOM series with a series
// number set to 1001. All non-private DICOM tags are moved from the input
// series to the output series. The Image Position Patient is adjusted
// for each slice to reflect the z-spacing. The number of slices in
// the output series may be larger or smaller due to changes in the
// z-spacing. To retain the spacing for a given dimension, specify 0.
//
// The program progresses as follows:
// 1) Read the input series
// 2) Resample the series according to the user specified x-y-z
//    spacing.
// 3) Create a MetaDataDictionary for each slice.
// 4) Shift data to undo the effect of a rescale intercept by the
//    DICOM reader (only for ITK < 4.6)
// 5) Write the new DICOM series
//

#include "itkVersion.h"

#include "itkImage.h"
#include "itkMinimumMaximumImageFilter.h"

#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkNumericSeriesFileNames.h"

#include "itkImageSeriesReader.h"
#include "itkImageSeriesWriter.h"

#include "itkResampleImageFilter.h"

#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
#include "itkShiftScaleImageFilter.h"
#endif

#include "itkIdentityTransform.h"
#include "itkLinearInterpolateImageFunction.h"

#include <itksys/SystemTools.hxx>

#if ITK_VERSION_MAJOR >= 4
#include "gdcmUIDGenerator.h"
#else
#include "gdcm/src/gdcmFile.h"
#include "gdcm/src/gdcmUtil.h"
#endif

#include <string>
#include <sstream>

static void CopyDictionary (itk::MetaDataDictionary &fromDict,
                     itk::MetaDataDictionary &toDict);


int main( int argc, char* argv[] )
{
  // Validate input parameters
  if( argc < 4 )
    {
    std::cerr << "Usage: "
              << argv[0]
              << " InputDicomDirectory OutputDicomDirectory spacing_x spacing_y spacing_z"
              << std::endl;
    return EXIT_FAILURE;
    }

  constexpr unsigned int InputDimension = 3;
  constexpr unsigned int OutputDimension = 2;

  using PixelType = signed short;

  using InputImageType = itk::Image< PixelType, InputDimension >;
  using OutputImageType = itk::Image< PixelType, OutputDimension >;
  using ReaderType = itk::ImageSeriesReader< InputImageType >;
  using ImageIOType = itk::GDCMImageIO;
  using InputNamesGeneratorType = itk::GDCMSeriesFileNames;
  using OutputNamesGeneratorType = itk::NumericSeriesFileNames;
  using TransformType = itk::IdentityTransform< double, InputDimension >;
  using InterpolatorType = itk::LinearInterpolateImageFunction< InputImageType, double >;
  using ResampleFilterType = itk::ResampleImageFilter< InputImageType, InputImageType >;
#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
  using ShiftScaleType = itk::ShiftScaleImageFilter< InputImageType, InputImageType >;
#endif
  using SeriesWriterType = itk::ImageSeriesWriter< InputImageType, OutputImageType >;

// 1) Read the input series

  ImageIOType::Pointer gdcmIO = ImageIOType::New();
  InputNamesGeneratorType::Pointer inputNames = InputNamesGeneratorType::New();
  inputNames->SetInputDirectory( argv[1] );

  const ReaderType::FileNamesContainer & filenames =
                            inputNames->GetInputFileNames();

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

  reader->SetImageIO( gdcmIO );
  reader->SetFileNames( filenames );
  try
    {
    reader->Update();
    }
  catch (itk::ExceptionObject &excp)
    {
    std::cerr << "Exception thrown while reading the series" << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }

// 2) Resample the series
  InterpolatorType::Pointer interpolator = InterpolatorType::New();

  TransformType::Pointer transform = TransformType::New();
  transform->SetIdentity();

  const InputImageType::SpacingType& inputSpacing =
    reader->GetOutput()->GetSpacing();
  const InputImageType::RegionType& inputRegion =
    reader->GetOutput()->GetLargestPossibleRegion();
  const InputImageType::SizeType& inputSize =
    inputRegion.GetSize();

  std::cout << "The input series in directory " << argv[1]
            << " has " << filenames.size() << " files with spacing "
            << inputSpacing
            << std::endl;

  // Compute the size of the output. The user specifies a spacing on
  // the command line. If the spacing is 0, the input spacing will be
  // used. The size (# of pixels) in the output is recomputed using
  // the ratio of the input and output sizes.
  InputImageType::SpacingType outputSpacing;
  outputSpacing[0] = atof(argv[3]);
  outputSpacing[1] = atof(argv[4]);
  outputSpacing[2] = atof(argv[5]);

  bool changeInSpacing = false;
  for (unsigned int i = 0; i < 3; i++)
    {
    if (outputSpacing[i] == 0.0)
      {
      outputSpacing[i] = inputSpacing[i];
      }
    else
      {
      changeInSpacing = true;
      }
    }
  InputImageType::SizeType   outputSize;
  using SizeValueType = InputImageType::SizeType::SizeValueType;
  outputSize[0] = static_cast<SizeValueType>(inputSize[0] * inputSpacing[0] / outputSpacing[0] + .5);
  outputSize[1] = static_cast<SizeValueType>(inputSize[1] * inputSpacing[1] / outputSpacing[1] + .5);
  outputSize[2] = static_cast<SizeValueType>(inputSize[2] * inputSpacing[2] / outputSpacing[2] + .5);

  ResampleFilterType::Pointer resampler = ResampleFilterType::New();
  resampler->SetInput( reader->GetOutput() );
  resampler->SetTransform( transform );
  resampler->SetInterpolator( interpolator );
  resampler->SetOutputOrigin ( reader->GetOutput()->GetOrigin());
  resampler->SetOutputSpacing ( outputSpacing );
  resampler->SetOutputDirection ( reader->GetOutput()->GetDirection());
  resampler->SetSize ( outputSize );
  resampler->Update ();


// 3) Create a MetaDataDictionary for each slice.

  // Copy the dictionary from the first image and override slice
  // specific fields
  ReaderType::DictionaryRawPointer inputDict = (*(reader->GetMetaDataDictionaryArray()))[0];
  ReaderType::DictionaryArrayType outputArray;

  // To keep the new series in the same study as the original we need
  // to keep the same study UID. But we need new series and frame of
  // reference UID's.
#if ITK_VERSION_MAJOR >= 4
  gdcm::UIDGenerator suid;
  std::string seriesUID = suid.Generate();
  gdcm::UIDGenerator fuid;
  std::string frameOfReferenceUID = fuid.Generate();
#else
  std::string seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
  std::string frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
#endif
  std::string studyUID;
  std::string sopClassUID;
  itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
  itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
  gdcmIO->KeepOriginalUIDOn();

  for (unsigned int f = 0; f < outputSize[2]; f++)
    {
    // Create a new dictionary for this slice
    auto dict = new ReaderType::DictionaryType;

    // Copy the dictionary from the first slice
    CopyDictionary (*inputDict, *dict);

    // Set the UID's for the study, series, SOP  and frame of reference
    itk::EncapsulateMetaData<std::string>(*dict,"0020|000d", studyUID);
    itk::EncapsulateMetaData<std::string>(*dict,"0020|000e", seriesUID);
    itk::EncapsulateMetaData<std::string>(*dict,"0020|0052", frameOfReferenceUID);

#if ITK_VERSION_MAJOR >= 4
    gdcm::UIDGenerator sopuid;
    std::string sopInstanceUID = sopuid.Generate();
#else
    std::string sopInstanceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
#endif
    itk::EncapsulateMetaData<std::string>(*dict,"0008|0018", sopInstanceUID);
    itk::EncapsulateMetaData<std::string>(*dict,"0002|0003", sopInstanceUID);

    // Change fields that are slice specific
    std::ostringstream value;
    value.str("");
    value << f + 1;

    // Image Number
    itk::EncapsulateMetaData<std::string>(*dict,"0020|0013", value.str());

    // Series Description - Append new description to current series
    // description
    std::string oldSeriesDesc;
    itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);

    value.str("");
    value << oldSeriesDesc
          << ": Resampled with pixel spacing "
          << outputSpacing[0] << ", "
          << outputSpacing[1] << ", "
          << outputSpacing[2];
    // This is an long string and there is a 64 character limit in the
    // standard
    unsigned lengthDesc = value.str().length();

    std::string seriesDesc( value.str(), 0,
                            lengthDesc > 64 ? 64
                            : lengthDesc);
    itk::EncapsulateMetaData<std::string>(*dict,"0008|103e", seriesDesc);

    // Series Number
    value.str("");
    value << 1001;
    itk::EncapsulateMetaData<std::string>(*dict,"0020|0011", value.str());

    // Derivation Description - How this image was derived
    value.str("");
    for (int i = 0; i < argc; i++)
      {
      value << argv[i] << " ";
      }
    value << ": " << ITK_SOURCE_VERSION;

    lengthDesc = value.str().length();
    std::string derivationDesc( value.str(), 0,
                                lengthDesc > 1024 ? 1024
                                : lengthDesc);
    itk::EncapsulateMetaData<std::string>(*dict,"0008|2111", derivationDesc);

    // Image Position Patient: This is calculated by computing the
    // physical coordinate of the first pixel in each slice.
    InputImageType::PointType position;
    InputImageType::IndexType index;
    index[0] = 0;
    index[1] = 0;
    index[2] = f;
    resampler->GetOutput()->TransformIndexToPhysicalPoint(index, position);

    value.str("");
    value << position[0] << "\\" << position[1] << "\\" << position[2];
    itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str());
    // Slice Location: For now, we store the z component of the Image
    // Position Patient.
    value.str("");
    value << position[2];
    itk::EncapsulateMetaData<std::string>(*dict,"0020|1041", value.str());

    if (changeInSpacing)
      {
      // Slice Thickness: For now, we store the z spacing
      value.str("");
      value << outputSpacing[2];
      itk::EncapsulateMetaData<std::string>(*dict,"0018|0050",
                                            value.str());
      // Spacing Between Slices
      itk::EncapsulateMetaData<std::string>(*dict,"0018|0088",
                                            value.str());
      }

    // Save the dictionary
    outputArray.push_back(dict);
    }

#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
// 4) Shift data to undo the effect of a rescale intercept by the
//    DICOM reader
  std::string interceptTag("0028|1052");
  using MetaDataStringType = itk::MetaDataObject< std::string >;
  itk::MetaDataObjectBase::Pointer entry = (*inputDict)[interceptTag];

  MetaDataStringType::ConstPointer interceptValue =
    dynamic_cast<const MetaDataStringType *>( entry.GetPointer() );

  int interceptShift = 0;
  if( interceptValue )
    {
    std::string tagValue = interceptValue->GetMetaDataObjectValue();
    interceptShift = -atoi ( tagValue.c_str() );
    }

  ShiftScaleType::Pointer shiftScale = ShiftScaleType::New();
  shiftScale->SetInput( resampler->GetOutput());
  shiftScale->SetShift( interceptShift );
#endif

// 5) Write the new DICOM series

  // Make the output directory and generate the file names.
  itksys::SystemTools::MakeDirectory( argv[2] );

  // Generate the file names
  OutputNamesGeneratorType::Pointer outputNames = OutputNamesGeneratorType::New();
  std::string seriesFormat(argv[2]);
  seriesFormat = seriesFormat + "/" + "IM%d.dcm";
  outputNames->SetSeriesFormat (seriesFormat.c_str());
  outputNames->SetStartIndex (1);
  outputNames->SetEndIndex (outputSize[2]);

  SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
  seriesWriter->SetInput( shiftScale->GetOutput() );
#else
  seriesWriter->SetInput( resampler->GetOutput() );
#endif
    seriesWriter->SetImageIO( gdcmIO );
    seriesWriter->SetFileNames( outputNames->GetFileNames() );
    seriesWriter->SetMetaDataDictionaryArray( &outputArray );
  try
    {
    seriesWriter->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown while writing the series " << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }
  std::cout << "The output series in directory " << argv[2]
            << " has " << outputSize[2] << " files with spacing "
            << outputSpacing
            << std::endl;
  return EXIT_SUCCESS;
}

void CopyDictionary (itk::MetaDataDictionary &fromDict, itk::MetaDataDictionary &toDict)
{
  using DictionaryType = itk::MetaDataDictionary;

  DictionaryType::ConstIterator itr = fromDict.Begin();
  DictionaryType::ConstIterator end = fromDict.End();
  using MetaDataStringType = itk::MetaDataObject< std::string >;

  while( itr != end )
    {
    itk::MetaDataObjectBase::Pointer  entry = itr->second;

    MetaDataStringType::Pointer entryvalue =
      dynamic_cast<MetaDataStringType *>( entry.GetPointer() );
    if( entryvalue )
      {
      std::string tagkey   = itr->first;
      std::string tagvalue = entryvalue->GetMetaDataObjectValue();
      itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
      }
    ++itr;
    }
}