/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis 
 * Copyright (c) Leipzig, Madrid 1999-2016 Gert Wollny
 *
 * MIA is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with MIA; if not, see <http://www.gnu.org/licenses/>.
 *
 */


#include <mia/core/gsl_pca.hh>
#include <algorithm>
#include <cassert>
#include <vector>

#include <gsl/gsl_eigen.h>

namespace gsl {

using std::pair; 
using std::sort; 
using std::vector; 

PCA::PCA(unsigned max_pc, double energy_thresh_ratio):
        m_max_pc(max_pc), 
        m_energy_thresh_ratio(energy_thresh_ratio), 
        m_eval_min(1e-9)
{
        assert(max_pc > 0  || 
               (m_energy_thresh_ratio >= 0.0 || m_energy_thresh_ratio <= 1.0)); 
}

void PCA::set_eigenvalue_minimum(double min)
{
        assert(m_eval_min >= 0); 
        m_eval_min = min; 
}

PCA::Result PCA::analyze(const Matrix& signal) const
{
        auto  covariance_matrix = signal.row_covariance();

        // evaluate eigen-decomposition of covariance matrix 

	CSymmvEvalEvec see(covariance_matrix); 
	 

	double ev_energy = 0.0; 
	for (unsigned i = 0; i < see.eval.size(); ++i) {
		ev_energy += see.eval[i];
	}
	
	gsl_eigen_symmv_sort (see.eval, see.evec, GSL_EIGEN_SORT_ABS_DESC);
             
        unsigned max_useful_eigen = 0; 
        if (m_max_pc < 1) {
                // automatic number based on culmulative energy threshold 
		double ev_part_energy = 0.0;
		double ev_part_thresh = m_energy_thresh_ratio * ev_energy;
		
		while ((ev_part_energy < ev_part_thresh) && 
		       (max_useful_eigen < see.eval.size())) {
			ev_part_energy += see.eval[max_useful_eigen]; 
			++max_useful_eigen;
		}
	} else { 
                // fixed number of PC/IC
		while ((see.eval[max_useful_eigen] > m_eval_min) && 
		       (max_useful_eigen < see.eval.size()) && 
		       (max_useful_eigen < m_max_pc))
			++max_useful_eigen; 
	}
        
        PCA::Result result;
        if (max_useful_eigen >= 1) {
                // copy the useful eigenvalues and eigenvectors over 
                result.eval = Vector(max_useful_eigen, false); 
                result.evec.reset(covariance_matrix.rows(), max_useful_eigen, false); 
                
                for (unsigned i = 0; i < max_useful_eigen; ++i) {
                        result.eval[i] = see.eval[i]; 
                        auto in_col = gsl_matrix_column (see.evec, i);
                        auto out_col = gsl_matrix_column (result.evec, i); 
                        gsl_vector_memcpy (&out_col.vector, &in_col.vector); 
                }
        }
        return result; 
}

}
