Revision 78d7695e70694df479099377176af419ae0c1782 authored by Konrad Werys on 09 March 2019, 17:32:43 UTC, committed by Konrad Werys on 09 March 2019, 17:32:43 UTC
1 parent cd69cb0
Tomato.h
/*!
* \file Tomato.h
* \author Konrad Werys
* \date 2018/08/14
*/
#ifndef Tomato_Tomato_H
#define Tomato_Tomato_H
#include "CmakeConfigForTomato.h"
#ifdef USE_ITK
#include "TomatoOptions.h"
#include "TomatoColormap.h"
#include "itkReadFileListFilter.h"
#include "itkReadDirectoryFilter.h"
#include "itkSortInvTimesImageFilter.h"
#include "itkCalculatorT1ImageFilter.h"
#include "itkColorbar2DImageFilter.h"
#include "itkNShmolliSamplesUsedTo123ImageFilter.h"
#include "itkTimeProbe.h"
// for exporting
#include "gdcmUIDGenerator.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkMultiplyImageFilter.h"
#include "itkImageFileWriter.h"
#include "itkFileTools.h"
#include "itkAdaptImageFilter.h"
#ifdef USE_VTK
#include "QuickView.h"
#endif //USE_VTK
namespace Ox {
/**
* \class Tomato
* includes factories and methods needed for calculation
*/
template< typename MeasureType >
class Tomato {
public:
// typedefs primitive data types
typedef MeasureType InputPixelType;
typedef int16_t OutputPixelType; // int does not work with some dicom viewers, be sure to use short (int16)
// typedefs image data types
typedef itk::Image<InputPixelType, 3> ImageType3D;
typedef itk::Image<InputPixelType, 2> ImageType2D;
typedef itk::Image<OutputPixelType, 2> OutputImageType;
typedef itk::ReadFileListFilter<ImageType3D> ReadFileListFilterType;
typedef itk::ReadDirectoryFilter<ImageType3D> ReadDirectoryFilterType;
typedef itk::SortInvTimesImageFilter<ImageType3D, ImageType3D> SortInvTimesImageFilterType;
typedef itk::CalculatorT1ImageFilter<ImageType3D, ImageType2D> CalculatorT1ImageFilterType;
typedef itk::MetaDataDictionary DictionaryType;
// member variables
TomatoOptions<InputPixelType> *_opts;
InputPixelType *_invTimes;
InputPixelType *_echoTimes;
int _nSamples;
typename ImageType3D::Pointer _imageMag;
typename ImageType3D::Pointer _imagePha;
typename CalculatorT1ImageFilterType::Pointer _imageCalculatorItk;
//SortInvTimesImageFilterType::Pointer _sorterMag;
//SortInvTimesImageFilterType::Pointer _sorterPha;
DictionaryType _dictionaryInput;
/**
* readAndSort
* @return success/failure
*/
int readAndSort();
/**
* calculate
* @return success/failure
*/
int calculate();
/**
* visualise
* @return success/failure
*/
int visualise();
/**
* method so long and ugly, that I put it in a separate file
* @return success/failure
*/
int exportToDicom();
/**
* constructor
* @param inputFileName
*/
Tomato(std::string inputFileName);
/**
* \brief do not forget about the virtual destructor, see
* https://stackoverflow.com/questions/461203/when-to-use-virtual-destructors
*/
virtual ~Tomato();
private:
/**
* We do not want the default constructor, so let's make it private.
* I cant delete it to be compatible with c++98
*/
Tomato(){};
/**
* readAndSortInputFileList
* @return success/failure
*/
int readAndSortInputFileList();
/**
* readAndSortInputDirs
* @return success/failure
*/
int readAndSortInputDirs();
};
} // namespace Ox
#include "Tomato.hxx"
#include "Tomato_export.hxx"
#endif
#endif //Tomato_Tomato_H
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