enfa.hh

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#ifndef ENFA_H
#define ENFA_H

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





class Enfa : public AlgorithmImpl
{
public:
    Enfa();
    ~Enfa();

    //
    // 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();
    
    int BackgroundToMatrix();
    
    bool enfa1();
    
    int calculateMeanAndSd( gsl_matrix * theMatrix, 
          gsl_vector * theMeanVector,
          gsl_vector * theStdDevVector);
    
    int center(gsl_matrix * theMatrix,
         int spCount);
    
    gsl_matrix* sqrtm(gsl_matrix* original_matrix) const;
    
    gsl_matrix* inverse(gsl_matrix* _m) const;

    double getGeomean(gsl_vector* v) const;

    int discardComponents() const;
    
    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;
    
    void displayLoadings(const gsl_matrix * m, const int f) const;

    gsl_matrix * autoCovariance(gsl_matrix * m);
    
    virtual void _getConfiguration( ConfigurationPtr& ) const;
    
    virtual void _setConfiguration( const ConstConfigurationPtr& );
    
    
    int _initialized;
    int _done;
    gsl_matrix * _gsl_environment_matrix;
    /* Pointer to gsl matrix with environmental data for each locality 
       converted to factors using the enfa score matrix */
    gsl_matrix * _gsl_environment_factor_matrix;
    
    gsl_matrix * _gsl_background_matrix;
    
    gsl_matrix * _gsl_covariance_matrix;
    
    gsl_matrix * _gsl_covariance_background_matrix;
    
    gsl_vector * _gsl_avg_vector;
    gsl_vector * _gsl_stddev_vector;
    
    gsl_vector * _gsl_avg_background_vector;
    
    gsl_vector * _gsl_stddev_background_vector;
    
    gsl_vector * _gsl_eigenvalue_vector;
    gsl_matrix * _gsl_eigenvector_matrix;
    gsl_matrix * _gsl_score_matrix ;
    gsl_matrix * _gsl_covariance_matrix_root_inverse;
    gsl_matrix * _gsl_workspace_H;
    gsl_matrix * _gsl_workspace_W;
    gsl_matrix * _gsl_workspace_y;
    gsl_vector * _gsl_workspace_z;
    gsl_vector* _gsl_factor_weights_all_components;
    gsl_vector* _gsl_factor_weights;
    gsl_vector* _gsl_geomean_vector;
    
    int _layer_count; 
    int _retained_components_count;
    int _localityCount; 
    
    int _backgroundCount; 

    int _backgroundProvided; 
    
    int _discardMethod; 

    int _retainComponents; 

    double _retainVariation; 

    int minComponentsInt;
    
    int _verboseDebug; 

    int _displayLoadings; 

    int _gsl_vector_min;
    
    double _marginality;

    double _specialisation;

    int _numRetries;

    int _retryCount;


};

/* catch the case that generating an inverse fails
   gsl doesnt do this well, and we want to catch, 
   ignore and retry when this happens */
class InverseFailedException : public OmException {
public:
  InverseFailedException( const std::string& msg ) :
    OmException( msg )
  {}
};

#endif