source: trunk/yat/normalizer/QuantileNormalizer.cc @ 1520

// $Id: QuantileNormalizer.cc 1519 2008-09-21 04:35:39Z peter $

/*
  Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér
  Copyright (C) 2007 Jari Häkkinen, Peter Johansson
  Copyright (C) 2008 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library 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.

  The yat library 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 yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include "QuantileNormalizer.h"

#include "yat/statistics/Averager.h"

#include "yat/utility/Matrix.h"
#include "yat/utility/VectorConstView.h"

#include <cassert>

namespace theplu {
namespace yat {
namespace normalizer {

  void QuantileNormalizer::operator()(const utility::Matrix& data,
                                      utility::Matrix& result) const
  {
    assert(data.rows()==result.rows());
    assert(data.columns()==result.columns());

    std::vector<std::vector<size_t> > index(data.rows());
    for (size_t column=0; column<data.columns(); ++column)
      utility::sort_index(index[column], data.column_const_view(column));
      
    for (size_t rank=0; rank<data.rows(); ++rank) {
      statistics::Averager a;
      for (size_t column=0; column<data.columns(); ++column)
        a.add(data(index[column][rank], column));
      double mean = a.mean();
      for (size_t column=0; column<data.columns(); ++column)
        result(index[column][rank], column) = mean;
    }
  }



}}} // end of namespace utility, yat and thep