svkMRSAutoPhase.h

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/*
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 *      "The Regents of the University of California," or the names of any of its 
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 *      software without specific prior written permission.
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 *  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_MRS_AUTO_PHASE_H
#define SVK_MRS_AUTO_PHASE_H

#define SWARM

#include <itkPowellOptimizer.h>
#include <itkParticleSwarmOptimizer.h>

#include <vtkObject.h>
#include <vtkObjectFactory.h>
#include <vtkInformation.h>

#include <svkImageData.h>
#include <svkMrsImageData.h>
#include <vtkStreamingDemandDrivenPipeline.h>
#include <svkThreadedImageAlgorithm.h>

#include <complex>
#include <svkDcmHeader.h>

#include <math.h>
#include <stdio.h>
#include <string.h>


namespace svk {


using namespace std;


class svkMRSAutoPhase : public svkThreadedImageAlgorithm
{

    public:

        vtkTypeMacro( svkMRSAutoPhase, svkThreadedImageAlgorithm);
        //static          svkMRSAutoPhase* New();
        

        //  _0 are zero order models
        //      MAX_PEAK_HTS_0 maximizes the peak height of a specified peak
        //  _1 are first order models
        typedef enum {
            UNDEFINED_PHASE_MODEL   = 0, 
            FIRST_POINT_0           = 1, 
            MAX_PEAK_HTS_0          = 2, 
            MAX_PEAK_HT_ONE_PEAK_0  = 3, 
            //MAX_GLOBAL_PEAK_HT_0, 
            //MIN_DIFF_FROM_MAG_0, 
            //MAX_PEAK_HT_0_ONE_PEAK, 
            //MIN_DIFF_FROM_MAG_0_ONE_PEAK, 
            //LAST_ZERO_ORDER_MODEL, 
            //MAX_PEAK_HTS_1, 
            //MIN_DIFF_FROM_MAG_1, 
            //MAX_PEAK_HTS_01,       
            LAST_MODEL 
        } PhasingModel;

        //void   SetPhasingModel(svkMRSAutoPhase::phasingModel model); 
        void                    OnlyUseSelectionBox(); 
        
        virtual svkImageData*   GetOutput(int port); 



    protected:

        svkMRSAutoPhase();
        ~svkMRSAutoPhase();

        virtual int     RequestInformation(
                            vtkInformation* request,
                            vtkInformationVector** inputVector,
                            vtkInformationVector* outputVector
                        );

        virtual int     RequestData( 
                            vtkInformation* request, 
                            vtkInformationVector** inputVector, 
                            vtkInformationVector* outputVector 
                        );

        int             SVKRequestDataPreExec( 
                            vtkInformation* request, 
                            vtkInformationVector** inputVector, 
                            vtkInformationVector* outputVector 
                        );
        int             SVKRequestDataPostExec( 
                            vtkInformation* request, 
                            vtkInformationVector** inputVector, 
                            vtkInformationVector* outputVector 
                        );

        virtual void    ThreadedRequestData(
                            vtkInformation* request,
                            vtkInformationVector** inputVector,
                            vtkInformationVector* outputVector,
                            vtkImageData*** inData,
                            vtkImageData** outData,
                            int extent[6],
                            int threadId
                        );

        virtual void    ValidateInput(); 


        virtual int     FillInputPortInformation( int vtkNotUsed(port), vtkInformation* info );
        virtual int     FillOutputPortInformation( int vtkNotUsed(port), vtkInformation* info ); 

        void            ZeroData(); 
        virtual void    UpdateProvenance();

        void            AutoPhaseExecute(int* outExt, int id); 
        virtual void    AutoPhaseSpectrum( int cellID );
        virtual void    FitPhase( int cellID ) = 0; 
        virtual void    PrePhaseSetup() = 0;
        virtual void    PostPhaseCleanup() = 0; 
        void            SyncPointsFromCells(); 
        virtual void    SetMapSeriesDescription( ); 


        static int*     progress;


#ifdef SWARM
        virtual void    InitOptimizer( int cellID, itk::ParticleSwarmOptimizer::Pointer itkOptimizer ) = 0; 
#else
        virtual void    InitOptimizer( int cellID, itk::PowellOptimizer::Pointer itkOptimizer ) = 0; 
#endif

        int                             numTimePoints;
        svkMRSAutoPhase::PhasingModel   phaseModelType; 
        bool                            onlyUseSelectionBox; 
        short*                          selectionBoxMask;
        bool                            isSpectralFFTRequired; 
        string                          seriesDescription; 
        vtkDataArray*                   mapArrayZeroOrderPhase; 

};


}   //svk


#endif //SVK_MRS_AUTO_PHASE_H