testITKDicomReader.cpp

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#include <iostream>
#include "DGtal/base/Common.h"
#include "ConfigTest.h"
#include "DGtalCatch.h"
#include "DGtal/helpers/StdDefs.h"
#include "DGtal/images/ImageContainerBySTLVector.h"
#include "DGtal/images/ImageContainerByITKImage.h"
#include "DGtal/io/readers/ITKDicomReader.h"
// Required ITK files to read series DICOM files
// DGtal must be compiled with " -DDGTAL_WITH_ITK=true" option
#if defined(__clang__)
#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Wdocumentation"
#endif
#include <itkGDCMSeriesFileNames.h>
#if defined(__clang__)
#pragma clang diagnostic pop
#endif
 

 
using namespace std;
using namespace DGtal;

// Functions for testing class ITKReader.
 
std::vector<std::string>
getFirstDicomSerieFileNames(const std::string &path)
{
  typedef itk::GDCMSeriesFileNames NamesGeneratorType;
  NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
  nameGenerator->SetUseSeriesDetails( true );
  nameGenerator->SetDirectory( path );
 
  typedef itk::GDCMSeriesFileNames::SeriesUIDContainerType SeriesIdContainer;
  const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
 
  if (! seriesUID.empty() )
  {
    return nameGenerator->GetFileNames( *(seriesUID.begin()) );
  }
  return std::vector<std::string>();
}
 
 
template <typename Image>
void
testImportDICOM()
{
  std::vector<std::string> fileNames = getFirstDicomSerieFileNames( testPath + "samples/dicomSample" );
 
  Image image = ITKDicomReader<Image>::importDICOM( fileNames );
 
  unsigned int nbVal=0, nbPos = 0;
  typename Image::ConstRange r = image.constRange();
  for ( typename Image::ConstRange::ConstIterator it=r.begin(), itend=r.end() ; it != itend ; ++it )
    {
      ++nbVal;
      if ( (*it) > 0 ) ++nbPos;
    }
 
  REQUIRE( ( nbVal==2130048 && nbPos==296030 ) );
}
 
template <typename PixelType>
void testSpatialInformation()
{
  std::vector<std::string> fileNames = getFirstDicomSerieFileNames( testPath + "samples/dicomSample" );
 
  typedef ImageContainerByITKImage<Z3i::Domain, PixelType> DGtalImage;
  DGtalImage img = ITKDicomReader<DGtalImage>::importDICOM( fileNames );
  typename DGtalImage::ITKImagePointer dgtal_itk = img.getITKImagePointer();
 
  typedef itk::Image<PixelType, 3> ItkImage;
  typedef itk::ImageSeriesReader<ItkImage> ItkReader;
  typename ItkReader::Pointer reader = ItkReader::New();
  reader->SetFileNames( fileNames );
 
  reader->Update();
 
  typename ItkImage::Pointer itk = reader->GetOutput();
 
  INFO( "Checking spacing" )
  REQUIRE( dgtal_itk->GetSpacing() == itk->GetSpacing() );
  INFO( "Checking origin" )
  REQUIRE( dgtal_itk->GetOrigin() == itk->GetOrigin() );
  INFO( "Checking direction" )
  REQUIRE( dgtal_itk->GetDirection() == itk->GetDirection() );
}
 
 
 
 
 
TEST_CASE( "Testing ITKReader" )
{
  // Default image selector = STLVector
 
  SECTION(
  "Testing ITKDicomReader with 8 bits ImageContainerBySTLVector images" )
  {
    typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char> Image;
    testImportDICOM<Image>();
  }
 
  SECTION(
  "Testing ITKDicomReader with 8 bits ImageContainerByITKImage images" )
  {
    typedef ImageContainerByITKImage<Z3i::Domain, unsigned char> Image;
    testImportDICOM<Image>();
  }
 
  SECTION(
  "Testing ITKDicomReader with 16 bits ImageContainerBySTLVector images" )
  {
    typedef ImageContainerBySTLVector<Z3i::Domain, uint16_t> Image;
    testImportDICOM<Image>();
  }
 
  SECTION(
  "Testing ITKDicomReader with 16 bits ImageContainerByITKImage images" )
  {
    typedef ImageContainerByITKImage<Z3i::Domain, uint16_t> Image;
    testImportDICOM<Image>();
  }
 
 
 
  SECTION(
  "Testing behavior of ITKDicomReader on empty filenames vector" )
  {
    typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char> Image;
    std::vector<std::string> filenames;
    bool caughtException = false;
    try
    {
      Image im = ITKDicomReader<Image>::importDICOM(filenames);
    }
    catch(exception &)
    {
      caughtException = true;
      trace.info() <<"Exception was correctly caught" << std::endl;
    }
    REQUIRE( caughtException == true);
  }
 
  SECTION(
  "Testing ITKDicomReader with 8 bits ImageContainerByITKImage images keeps spatial information" )
  {
    testSpatialInformation<unsigned char>();
  }
 
  SECTION(
  "Testing ITKDicomReader with 16 bits ImageContainerByITKImage images keeps spatial information" )
  {
    testSpatialInformation<int16_t>();
  }
 
 
}