svkQuantifyMetabolites.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 
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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_QUANTIFY_METABOLITES_H
#define SVK_QUANTIFY_METABOLITES_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>

#include "svkTypes.h"


namespace svk {


using namespace std;


class svkQuantifyMetabolites: public svkImageAlgorithm
{

    public:

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

        void                                                SetXMLFileName( vtkstd::string xmlFileName );     
        vtkstd::string                                      GetXMLFileName( );
        void                                                ClearXMLFile( );
        void                                                SetVerbose( bool isVerbose );     
        vtkstd::vector< svkMriImageData* >*                 GetMetMaps();
        void                                                LimitToSelectedVolume(float fraction = 0.5001); 
        vtkstd::vector< vtkstd::vector< vtkstd::string > >  GetRegionNameVector();
        int                                                 GetIntFromString(vtkstd::string stringVal ); 
        float                                               GetFloatFromString(vtkstd::string stringVal ); 
        void                                                ModifyRegion( int regionID, float peakPPM, float widthPPM ); 
        static void                                         WriteDefaultXMLTemplate( string fileName, bool clobber = false ); 
        static string                                       GetDefaultXMLFileName(); 
        void                                                SetAnatomyType( svkTypes::AnatomyType anatomyType);
        static bool                                         ShouldUpgradeXML(); 
        static string                                       GetOldVersionName(); 
        static void                                         SaveOldVersion(); 


    protected:

        svkQuantifyMetabolites();
        ~svkQuantifyMetabolites();

        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 ); 
        static void             GetCurrentXMLVersion(string* v1, string* v2, string* v3); 


    private:

        //  Methods:
        virtual void                        UpdateProvenance();
        void                                Quantify();
        void                                GenerateRegionMaps();
        void                                GenerateRatioMaps();
        void                                GenerateZScoreMaps();
        string                              ReplaceSlashesAndWhiteSpace( vtkstd::string inString); 
        void                                GetNumeratorAndDenominatorImages( 
                                                vtkXMLDataElement* ratioXML, 
                                                svkImageData* numeratorImage, 
                                                svkImageData* denominatorImage
                                            ); 


        //  Members:
        bool                                isVerbose; 
        vtkstd::string                      xmlFileName; 
        vtkstd::vector< svkMriImageData* >  metMapVector; 
        float                               useSelectedVolumeFraction;
        short*                              selectedVolumeMask;
        vtkXMLDataElement*                  mrsXML;
        vtkXMLDataElement*                  applicationXML;
        svkTypes::AnatomyType               anatomyType; 


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



};


}   //svk


#endif //SVK_QUANTIFY_METABOLITES_H