svkGEPFileMapperUCSFfidcsiDev0.h

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/*
 *  Copyright © 2009-2014 The Regents of the University of California.
 *  All Rights Reserved.
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 *  modification, are permitted provided that the following conditions are met:
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 *      "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.
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 *  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_GE_PFILE_MAPPER_UCSF_FIDCSI_DEV0_H
#define SVK_GE_PFILE_MAPPER_UCSF_FIDCSI_DEV0_H


#include <svkGEPFileMapperUCSF.h>


namespace svk {


class svkGEPFileMapperUCSFfidcsiDev0 : public svkGEPFileMapperUCSF 
{

    public:

        vtkTypeMacro( svkGEPFileMapperUCSFfidcsiDev0, svkGEPFileMapperUCSF );
        static svkGEPFileMapperUCSFfidcsiDev0* New();

        virtual void    ReadData(vtkStringArray* pFileNames, svkImageData* data); 
        static void     RedimensionData( svkImageData* data, 
                                         int* numVoxelsOriginal, 
                                         int* numVoxelsReordered, 
                                         int numFreqPts ); 


    protected:

        svkGEPFileMapperUCSFfidcsiDev0();
        ~svkGEPFileMapperUCSFfidcsiDev0();
  
        virtual vtkstd::string  GetVolumeLocalizationTechnique(); 
        virtual void            GetSelBoxCenter( float selBoxCenter[3] );
        virtual void            GetSelBoxSize( float selBoxSize[3] );
        virtual void            GetCenterFromRawFile( double* center ); 
        virtual bool            IsChopOn(); 
        void                    ModifyForPatientEntry( svkImageData* data ); 
        void                    InitMRSpectroscopyModule(); 
        float                   GetPPMRef(); 



    private: 

        void                    ReorderEPSIData( svkImageData* data ); 
        void                    EPSIPhaseCorrection( 
                                    svkImageData* data, 
                                    int* numVoxels, 
                                    int numRead, 
                                    int epsiAxis
                                ); 
        void                    ZeroFill( svkImageData* data ); 
        void                    FlipAxis( svkImageData* data, int axis, int lobe = -1 ); 
        void                    FFTShift( svkImageData* data ); 
        void                    ResampleRamps( svkImageData* data, int deltaT, int plateauTime, int rampTime, int epsiAxis ); 
        virtual void            GetWaveFormIntegral( float* waveFormIntegral, int deltaT, int plateauTime, int rampTime ); 
        void                    GetKaiserBesselValues( 
                                    vtkstd::vector<float>* u, 
                                    float width, 
                                    float beta,
                                    vtkstd::vector<float>* kbVals 
                                    ); 
        double                  GetBessel0Term( float arg, int index);
        double                  GetBessel0( float arg);
        double                  GetModifiedBessel0( float arg ); 
        void                    GetRolloffCorrection( int gridSize, float width, float beta, float* apodCor); 
        void                    AddReorderedTimePoint(
                                    svkMrsImageData* dynamicImage, 
                                    svkImageData* tmpImage, 
                                    int timePt, 
                                    int numTimePts
                                ); 
        void                    PrintSpecPts( 
                                    svkImageData* data, 
                                    int numFreqPts, 
                                    svkDcmHeader::DimensionVector* dimensionVector, 
                                    svkDcmHeader::DimensionVector* loopIndex, 
                                    vtkstd::string comment 
                                ); 
        void                    CombineLobes(svkImageData* data);




}; 

}   //svk

#endif //SVK_GE_PFILE_MAPPER_UCSF_FIDCSI_DEV0_H