svkMRSZeroOrderPhaseCostFunction.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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/*
 *  $URL$
 *  $Rev$
 *  $Author$
 *  $Date$
 *
 *  Authors:
 *      Jason C. Crane, Ph.D.
 *      Beck Olson,
 */

#ifndef SVK_MRS_ZERO_ORDER_PHASE_COST_FUNCTION_H
#define SVK_MRS_ZERO_ORDER_PHASE_COST_FUNCTION_H


#include <svkPhaseCostFunction.h>
#include <svkMRSPeakPick.h>
#include <svkMetaboliteMap.h>


using namespace svk;


/*
 *  Cost function for ITK optimizer: 
 */
class svkMRSZeroOrderPhaseCostFunction : public svkPhaseCostFunction
{

    public:

        typedef svkMRSZeroOrderPhaseCostFunction            Self;
        typedef svkPhaseCostFunction                        Superclass;
        typedef itk::SmartPointer<Self>                     Pointer;
        typedef itk::SmartPointer<const Self>               ConstPointer;


        itkTypeMacro( svkMRSZeroOrderPhaseCostFunction, svkPhaseCostFunction);

        itkNewMacro( Self );


        svkMRSZeroOrderPhaseCostFunction() {
            this->zeroOrderPhasePeak = 0;  
        }


        MeasureType  GetZeroOrderPhaseCost_2( const ParametersType& parameters) const
        {

            double phi0 = parameters[0];
        
            double intensity = 0; 
            float cmplxPt[2];
            double tmp; 

            //  Get the sum of the peak hits for picked peaks: 
            //  maximize positive peak height (minimize negative peak ht) 
            for ( int peakNum = 0; peakNum < this->peaks->GetNumPeaks(); peakNum++ ) {

                int startPt;     
                int endPt;     
                int peakPt;     
                this->peaks->GetPeakDefinition( peakNum, &startPt, &peakPt, &endPt ); 

                // apply zero order phase to data in window, then get peak ht:  
                for ( int freq = startPt; freq <= endPt; freq++) {
                    this->copySpectrum->GetTupleValue(freq, cmplxPt);
                    svk::svkPhaseSpec::ZeroOrderPhase(phi0, cmplxPt);
                    this->copySpectrum->SetTuple(freq, cmplxPt); 
                }
                float peakHt = svkMetaboliteMap::GetPeakHt( 
                        static_cast<float*>(this->copySpectrum->GetVoidPointer(4)), 
                        startPt, 
                        endPt 
                ); 
                cout << "PEAK HT: " << peakHt << " @ " << phi0 * 180. / vtkMath::Pi() << endl;
                intensity += (-1 * peakHt); 
            } 

            MeasureType measure = intensity; 
            return measure;
        }


        /*  
         *  returns the cost function for the current param values: 
         *  typedef double MeasureType
         */
        virtual MeasureType  GetValue( const ParametersType & parameters ) const
        { 

            double cost;  

            // make a member variable (copy)
            //cout << "copy spectrum" << endl;
            this->copySpectrum->DeepCopy(this->spectrum); 
            cost = GetZeroOrderPhaseCost_2( parameters ); 

            MeasureType measure = cost; 
            //cout << "                          cost: " << measure << endl; 
            return measure;
        }


        /*
         *
         */  
        virtual unsigned int GetNumberOfParameters(void) const
        {
            return 1; 
        }
        

        void SetPeakPicker( svkMRSPeakPick* peaks )  
        {
            this->peaks = peaks;
        }


        /*
         *
         */
        void SetZeroOrderPhasePeak( int peakNum)
        {
            this->zeroOrderPhasePeak = peakNum;
        }

        
        /*
         *
         */
        int GetZeroOrderPhasePeak( )
        {
            return this->zeroOrderPhasePeak;
        }

        
        


    private: 
        svkMRSPeakPick*                 peaks;
        int                             zeroOrderPhasePeak;

};



#endif// SVK_MRS_ZERO_ORDER_PHASE_COST_FUNCTION_H