Tomato.h

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#ifndef Tomato_Tomato_H
#define Tomato_Tomato_H

#include "CmakeConfigForTomato.h"
#include "tomatolib_export.h"
#ifdef USE_ITK

#include "TomatoOptions.h"
#include "TomatoColormap.h"

#include "itkReadFileListFilter.h"
#include "itkSortInvTimesImageFilter.h"
#include "itkCalculatorT1ImageFilter.h"
#include "itkColorbar2DImageFilter.h"
#include "itkNShmolliSamplesUsedTo123ImageFilter.h"

#include "itkTimeProbe.h"

namespace Ox {

    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::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;

        int readAndSort();

        int calculate();

        int exportToDicom();

        Tomato(std::string inputFileName);

        virtual ~Tomato();

    private:
        Tomato(){};

        int exportT1ToDicom();

        int exportT1MagSignRecovToDicom();

        int exportT2ToDicom();

    };

} // namespace Ox

#ifndef TOMATOLIB_COMPILED
#include "Tomato.hxx"
#include "Tomato_exportT1.hxx"
#include "Tomato_exportT1_magSignRecov.hxx"
#include "Tomato_exportT2.hxx"
#endif // TOMATOLIB_COMPILED

#endif // USE_ITK

#endif // Tomato_Tomato_H