svkVarianUCSFEPSI2DMapper.h

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/*
 *  Copyright © 2009-2014 The Regents of the University of California.
 *  All Rights Reserved.
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 *  Redistribution and use in source and binary forms, with or without 
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 *  •   None of the names of any campus of the University of California, the name 
 *      "The Regents of the University of California," or the names of any of its 
 *      contributors may be used to endorse or promote products derived from this 
 *      software without specific prior written permission.
 *  
 *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
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 *  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
 *  IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
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/*
 *  $URL$
 *  $Rev$
 *  $Author$
 *  $Date$
 *
 *  Authors:
 *      Jason C. Crane, Ph.D.
 *      Beck Olson
 */

#ifndef SVK_VARIAN_UCSF_EPSI_2D_MAPPER_H
#define SVK_VARIAN_UCSF_EPSI_2D_MAPPER_H


#include <vtkImageData.h>

#include <svkDcmHeader.h>
#include <svkMRSIOD.h>
#include <svkVarianFidMapper.h>
#include <svkImageData.h>
#include <map>
#include <string>
#include <vector>


namespace svk {


class svkVarianUCSFEPSI2DMapper : public svkVarianFidMapper
{

    public:

        vtkTypeMacro( svkVarianUCSFEPSI2DMapper, svkVarianFidMapper);
        static          svkVarianUCSFEPSI2DMapper* New();

        
    protected:

        svkVarianUCSFEPSI2DMapper();
        ~svkVarianUCSFEPSI2DMapper();

        virtual void    InitMRSpectroscopyPulseSequenceModule(); 
        virtual void    InitPixelMeasuresMacro(); 
        virtual void    InitPerFrameFunctionalGroupMacros(); 
        virtual void    InitMRSpectroscopyDataModule(); 
        virtual void    InitMRSpectroscopyModule(); 
        virtual void    InitMultiFrameFunctionalGroupsModule(); 
        virtual void    ReadFidFile( string fidFileName, svkImageData* data ); 
        void            ReorderEPSIData( svkImageData* data); 
        void            RemoveArrays( svkImageData* data ); 
        void            RedimensionData( 
                            svkImageData* data, 
                            int* numVoxelsOriginal, 
                            int* numVoxelsReordered, 
                            int numFreqPts 
                        );


        virtual void    SetCellSpectrum(vtkImageData* data, int x, int y, int z, int timePt, int coilNum); 



    private: 
        void            GetNumVoxels(int* numVoxels); 
        void            EPSIPhaseCorrection( svkImageData* data, int numRead, int epsiAxis); 


};


}   //svk

#endif //SVK_VARIAN_UCSF_EPSI_2D_MAPPER_H