csm.hh

Go to the documentation of this file.

#ifndef CSM_H
#define CSM_H

#include <openmodeller/om.hh>
#include <gsl/gsl_matrix.h>





class Csm : public AlgorithmImpl
{
    public:
        Csm(AlgMetadata const* metadata);
        ~Csm();

        

        //
        // Methods used to build the model
        //


        virtual int initialize();

        int iterate();

        int done() const;

        //
        // Methods used to project the model
        //


        Scalar getValue( const Sample& x ) const;

        int getConvergence( Scalar * const val ) const;



    private:

    protected:  
        int SamplerToMatrix();


        bool csm1();

        int calculateMeanAndSd( gsl_matrix * theMatrix, 
                gsl_vector * theMeanVector,
                gsl_vector * theStdDevVector);

        int center();

        virtual int discardComponents()=0;



        void displayVector(const gsl_vector * v, const char * name,const  bool roundFlag=true) const;

        void displayMatrix(const gsl_matrix * m, const char * name, const bool roundFlag=true) const;
        gsl_matrix * transpose (gsl_matrix * m);

        double product (gsl_vector * va, gsl_vector * vb) const;

        gsl_matrix * product (gsl_matrix * a, gsl_matrix * b) const;

        gsl_matrix * autoCovariance(gsl_matrix * m);

        virtual void _getConfiguration( ConfigurationPtr& config ) const;

        virtual void _setConfiguration( const ConstConfigurationPtr& config );


        int _initialized;
        int _done;
        gsl_matrix * _gsl_environment_matrix;
        gsl_matrix * _gsl_covariance_matrix;
        gsl_vector * _gsl_avg_vector;
        gsl_vector * _gsl_stddev_vector;
        gsl_vector * _gsl_eigenvalue_vector;
        gsl_matrix * _gsl_eigenvector_matrix;
        int _layer_count; 
        int _retained_components_count;
        int _localityCount; 
        
        int minComponentsInt;
        bool verboseDebuggingBool;

};

#endif