testITKDicomReader.cpp File Reference

#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"
#include <itkGDCMSeriesFileNames.h>

Go to the source code of this file.

Functions
std::vector< std::string >	getFirstDicomSerieFileNames (const std::string &path)
template<typename Image >
void	testImportDICOM ()
template<typename PixelType >
void	testSpatialInformation ()
	TEST_CASE ("Testing ITKReader")

Detailed Description

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Author

Boris Mansencal (boris.nosp@m..man.nosp@m.senca.nosp@m.l@la.nosp@m.bri.f.nosp@m.r ) LaBRI (CNRS, UMR 5800, University of Bordeaux, Bordeaux-INP), France

Date

2019/02/05

Functions for testing class ITKDicomReader.

This file is part of the DGtal library.

Definition in file testITKDicomReader.cpp.

Function Documentation

getFirstDicomSerieFileNames()

std::vector< std::string > getFirstDicomSerieFileNames

(

const std::string &

path

)

Definition at line 61 of file testITKDicomReader.cpp.

{
  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>();
}

Referenced by testImportDICOM(), and testSpatialInformation().

TEST_CASE()

TEST_CASE

(

"Testing ITKReader"

)

Definition at line 128 of file testITKDicomReader.cpp.

{
  // 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>();
  }
 
 
}

References DGtal::ITKDicomReader< TImage >::importDICOM(), DGtal::Trace::info(), REQUIRE(), SECTION(), and DGtal::trace.

testImportDICOM()

template<typename Image >

void testImportDICOM

(

)

Definition at line 81 of file testITKDicomReader.cpp.

{
  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 ) );
}

References getFirstDicomSerieFileNames(), DGtal::ITKDicomReader< TImage >::importDICOM(), and REQUIRE().

testSpatialInformation()

template<typename PixelType >

void testSpatialInformation

(

)

Definition at line 99 of file testITKDicomReader.cpp.

{
  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() );
}

References getFirstDicomSerieFileNames(), DGtal::ITKDicomReader< TImage >::importDICOM(), and REQUIRE().