svkDSCQuantify.h

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/*
 *  Copyright © 2009-2014 The Regents of the University of California.
 *  All Rights Reserved.
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 *      "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.
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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_DSC_QUANTIFY_H
#define SVK_DSC_QUANTIFY_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 svkDSCQuantify: public svkImageAlgorithm
{

    public:

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

        vtkstd::vector< svkMriImageData* >*                 GetDSCMaps();
        vtkstd::vector< vtkstd::vector< vtkstd::string > >  GetRegionNameVector();
        int                                                 GetIntFromString(vtkstd::string stringVal ); 
        float                                               GetFloatFromString(vtkstd::string stringVal ); 

    protected:

        svkDSCQuantify();
        ~svkDSCQuantify();

        virtual int             RequestInformation(
                                    vtkInformation* request,
                                    vtkInformationVector** inputVector,
                                    vtkInformationVector* outputVector
                                );
        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:
        virtual void                        UpdateProvenance();
        void                                Quantify();
        void                                GenerateDSCMaps();
        void                                GenerateNormalizedMaps(); 
        string                              ReplaceSlashesAndWhiteSpace( vtkstd::string inString); 
        void                                GetNumeratorAndDenominatorImages( 
                                                vtkXMLDataElement* ratioXML, 
                                                svkImageData* numeratorImage, 
                                                svkImageData* denominatorImage
                                            ); 


        //  Members:
        bool                                isVerbose; 
        vtkstd::vector< svkMriImageData* >  dscMapVector; 


        //  map of regions: region name, peak (ppm) and peak width (ppm)
        vtkstd::vector < vtkstd::vector< vtkstd::string > >  regionVector;

};


}   //svk


#endif //SVK_DSC_QUANTIFY_H