testITKReader.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/io/readers/ITKReader.h"
 
using namespace std;
using namespace DGtal;
 
// Functions for testing class ITKReader.
 
template <typename PixelType>
void testSpatialInformation(const std::string &filename)
{
  typedef DGtal::ImageContainerByITKImage < DGtal::Z3i::Domain, PixelType > DGtalImage;
 
  DGtalImage img = DGtal::ITKReader<DGtalImage>::importITK(filename);
 
  typename DGtalImage::ITKImagePointer dgtal_itk = img.getITKImagePointer();
 
  
  typedef itk::Image<PixelType, 3> ItkImage;
  typedef itk::ImageFileReader<ItkImage> ReaderType;
  typename ReaderType::Pointer reader = ReaderType::New();
  reader->SetFileName(filename);
 
  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
  typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char> Image3DUC;
  typedef ImageContainerBySTLVector<Z3i::Domain, uint16_t> Image3D16b;
  typedef ImageContainerBySTLVector<Z3i::Domain, double> Image3Dd;
 
  SECTION(
  "Testing feature io/readers of ITKReader with  16 bits (uint16) images" )
  {
    Image3D16b im = ITKReader<Image3D16b>::importITK(
    testPath + "samples/lobsterCroped16b.mhd" );
    REQUIRE( ( im( Z3i::Point( 35, 29, 3 ) ) == 60400 ) );
  }
 
  SECTION(
  "Testing feature io/readers of ITKReader with rescaled 16 bits (uint16) "
  "images" )
  {
    typedef DGtal::functors::Rescaling<uint16_t, unsigned char> RescalFCT;
    RescalFCT resc = RescalFCT( 0, 65535, 0, 255 );
    Image3DUC im   = ITKReader<Image3DUC>::importITK(
    testPath + "samples/lobsterCroped16b.mhd", resc );
    REQUIRE( ( im( Z3i::Point( 35, 29, 3 ) ) == resc( 60400 ) ) );
  }
  SECTION(
  "Testing behavior of ITKReader on non existent image file" )
  {
    bool caughtException = false;
    const std::string filename = testPath + "samples/null.mhd"; //non existent file
    try
    {
      Image3DUC im = ITKReader<Image3DUC>::importITK(filename);
    }
    catch(exception &)
    {
      caughtException = true;
      trace.info() <<"Exception was correctly caught" << std::endl;
    }
    REQUIRE( caughtException == true);
  }
 
  SECTION(
  "Checking spatial information when loading through DGtal" )
  {
    testSpatialInformation<int16_t>(testPath + "samples/lobsterCroped16b.mhd" );
    testSpatialInformation<int16_t>(testPath + "samples/lobsterCropedB16b.mhd" );
  }
 
  SECTION(
    "Checking import with/without shifted domain")
    
  {
    Image3Dd imShifted = ITKReader<Image3Dd>::importITK(testPath + "samples/lobsterCroped2.nii",
                                                        ITKIOTrait<Image3Dd::Value>::DefaultReadFunctor(), true );
 
    Image3Dd imNonShifted = ITKReader<Image3Dd>::importITK(testPath + "samples/lobsterCroped2.nii", false );
 
    REQUIRE( ( imShifted( Z3i::Point( 144, 100, 21 ) ) == 113 )  );
    REQUIRE( ( imNonShifted( Z3i::Point( 94, 50, 11 ) ) == 113 )  );
    Z3i::Point pTarget (95,76,7);
    auto i = 101*pTarget[1]+pTarget[0]+pTarget[2]*101*101;
    trace.info() << "value:"  << *(imNonShifted.range().begin()+i);
    REQUIRE( ( *(imNonShifted.range().begin()+i) == *(imShifted.range().begin()+i ) ));
    REQUIRE( ( *(imNonShifted.range().begin()+i) == 68  ));
  }
 
  
}