svkVarianCSFidMapper.h

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/*
 *  Copyright © 2009-2014 The Regents of the University of California.
 *  All Rights Reserved.
 *
 *  Redistribution and use in source and binary forms, with or without 
 *  modification, are permitted provided that the following conditions are met:
 *  •   Redistributions of source code must retain the above copyright notice, 
 *      this list of conditions and the following disclaimer.
 *  •   Redistributions in binary form must reproduce the above copyright notice, 
 *      this list of conditions and the following disclaimer in the documentation 
 *      and/or other materials provided with the distribution.
 *  •   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_CS_FID_MAPPER_H
#define SVK_VARIAN_CS_FID_MAPPER_H


#include <vtkImageData.h>
#include <svkVarianFidMapper.h>

#include <vector>


namespace svk {


class svkVarianCSFidMapper : public svkVarianFidMapper
{

    public:

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

        virtual void    ReadFidFile( string fidFileName, svkImageData* data );


    protected:

        svkVarianCSFidMapper();
        ~svkVarianCSFidMapper();
  
        virtual void    InitMultiFrameFunctionalGroupsModule();
        virtual void    InitAcquisitionContextModule();
        virtual void    InitPlaneOrientationMacro(); 
        virtual void    InitSharedFunctionalGroupMacros();
        virtual void    InitPerFrameFunctionalGroupMacros();
        virtual void    InitPixelMeasuresMacro();
        virtual void    InitMRReceiveCoilMacro();
        virtual void    InitMRSpectroscopyPulseSequenceModule();
        virtual void    InitMRSpectroscopyModule();
        virtual void    InitMRSpectroscopyFOVGeometryMacro();
        virtual void    InitMRSpectroscopyDataModule();

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

    private:

        float***            paddedData; 
        float****           rectilinearData; 
        void                ReOrderSamples( float* specDataReordered, int numberDataPointsInFIDFile ); 
        void                ReOrderFlyback(); 
        void                ZeroPadCompressedSensingData( int numberDataPointsInFIDFile ); 
        vector<int>         GetBlips(); 
        void                GetBlipString(string* blipString);

        int                 numXReordered; 
        int                 numYReordered; 
        int                 numZReordered; 
        int                 numTReordered; 

};


}   //svk

#endif //SVK_VARIAN_CS_FID_MAPPER_H