svkMRSNoise.h

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/*
 *  Copyright © 2009-2014 The Regents of the University of California.
 *  All Rights Reserved.
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 *  Redistribution and use in source and binary forms, with or without 
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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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 *  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_MRS_NOISE_H
#define SVK_MRS_NOISE_H


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

#include <svkImageInPlaceFilter.h>
#include <svkSpecUtils.h>


namespace svk {


using namespace std;



class svkMRSNoise : public svkImageInPlaceFilter
{

    public:

        static svkMRSNoise* New();
        vtkTypeMacro( svkMRSNoise, svkImageInPlaceFilter);

        float           GetNoiseSD(); 
        float           GetMagnitudeNoiseSD(); 
        float           GetMeanBaseline(); 
        float           GetMagnitudeMeanBaseline(); 
        void            OnlyUseSelectionBox();
        vtkFloatArray*  GetAverageMagnitudeSpectrum(); 
        virtual void    PrintSelf( ostream &os, vtkIndent indent );
        int             GetNoiseStartPoint(); 
        int             GetNoiseEndPoint(); 


    protected:

        svkMRSNoise();
        ~svkMRSNoise();

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


        //  Methods:
        virtual int     RequestInformation(
                            vtkInformation* request, 
                            vtkInformationVector** inputVector,
                            vtkInformationVector* outputVector
                        );
        virtual int     RequestData(
                            vtkInformation* request, 
                            vtkInformationVector** inputVector,
                            vtkInformationVector* outputVector
                        );


    private:
        
        void            InitAverageSpectrum(); 
        void            FindNoiseWindow();
        void            CalculateNoiseSD(); 
        float           CalcWindowSD( vtkFloatArray* spectrum, float mean, int startPt, int endPt ); 
        float           CalcWindowMean( vtkFloatArray* spectrum, int startPt, int endPt ); 


        //  Members:
        float           noiseSD;
        float           magnitudeNoiseSD;
        float           noiseWindowMean;
        float           magnitudeNoiseWindowMean;
        int                     onlyUseSelectionBox;
        short*          selectionBoxMask;
        vtkFloatArray*  averageSpectrum; 
        int             noiseWindowStartPt; 
        int             noiseWindowEndPt; 
        float           noiseWindowPercent;



};


}   //svk


#endif //SVK_MRS_NOISE_H