source: branches/0.12-stable/yat/normalizer/QuantileNormalizer.cc @ 3321

// $Id: QuantileNormalizer.cc 3321 2014-09-19 06:59:59Z peter $

/*
  Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér
  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
  Copyright (C) 2012, 2014 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 <config.h>

#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.columns());
    for (size_t column=0; column<data.columns(); ++column) {
      assert(column<index.size());
      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) {
        assert(column<index.size());
        assert(rank<index[column].size());
        a.add(data(index[column][rank], column));
      }
      double mean = a.mean();
      for (size_t column=0; column<data.columns(); ++column) {
        assert(column<index.size());
        result(index[column][rank], column) = mean;
      }
    }
  }



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