svkMetaboliteRatioZScores.h

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/*
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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_METABOLITE_RATIO_Z_SCORES_H
#define SVK_METABOLITE_RATIO_Z_SCORES_H


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

#include <svkImageData.h>
#include <svkMriImageData.h>
#include <svkMrsImageData.h>
#include <svkImageAlgorithm.h>
#include <svkDcmHeader.h>
#include <svkEnhancedMRIIOD.h>


namespace svk {


using namespace std;


class svkMetaboliteRatioZScores: public svkImageAlgorithm
{

    public:

        static svkMetaboliteRatioZScores* New();
        vtkTypeMacro( svkMetaboliteRatioZScores, svkImageAlgorithm);

        void                    SetSeriesDescription(vtkstd::string newSeriesDescription);
        void                    SetVerbose( bool isVerbose );     
        void                    LimitToSelectedVolume(float fraction = 0.5001);
        void                    LimitToSelectedVolume( short* selectedVolumeMask);
        void                    SetInputNumerator(vtkDataObject *in) { this->SetInputDataObject(0, in); }
        void                    SetInputDenominator(vtkDataObject *in) { this->SetInputDataObject(1, in); }
        void                    SetInputMrsData(vtkDataObject *in) { this->SetInputDataObject(2, in); }
        void                    SetZScoreThresholds( double lowerThreshold, double upperThreshold ); 


    protected:

        svkMetaboliteRatioZScores();
        ~svkMetaboliteRatioZScores();

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

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


    private:

        //  Methods:
        void                    ZeroData(); 
        void                    InitQuantificationMask(); 
        int                     GetTotalVoxels(); 
        void                    ComputeZScore(); 
        virtual void            UpdateProvenance();
        double                  GetMean( double* pixels, int numVoxels ); 
        double                  GetDistanceSD( double* pixels, int numVoxels); 
        double                  GetRegressionSlope( 
                                    double* numeratorPixels, 
                                    double* denominatorPixels, 
                                    double numeratorMean, 
                                    double denominatorMean, 
                                    int numVoxels 
                                ); 
        double                  GetRegressionSlopeZeroIntercept(
                                    double* numeratorPixels, 
                                    double* denominatorPixels, 
                                    int totalVoxels
                                ); 
        double                  GetRegressionIntercept(double slope, double numeratorMean, double denominatorMean); 
        void                    GetRegression(double& slope, double& intercept); 
        void                    GetDistanceFromRegression( double slope, double intercept ); 
        void                    GetZScores(double slope, double intercept); 
        int                     GetOutliers(); 


        //  Members:
        vtkstd::string          newSeriesDescription; 
        bool                    isVerbose; 
        float                   useSelectedVolumeFraction;
        short*                  quantificationMask;
        short*                  iterationMask;
        double                  zscoreLowerThreshold; 
        double                  zscoreUpperThreshold; 
        bool                    yInterceptZero;

};


}   //svk


#endif //SVK_METABOLITE_RATIO_Z_SCORES_H