source: trunk/yat/utility/utility.cc @ 1419

// $Id: utility.cc 1419 2008-08-20 12:01:12Z peter $

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

  This file is part of the yat library, http://trac.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 2 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 this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
  02111-1307, USA.
*/

#include "utility.h"

#include "Matrix.h"
#include "stl_utility.h"
#include "VectorConstView.h"
#include "yat/statistics/Averager.h"

#include <sstream>
#include <string>

namespace theplu {
namespace yat {
namespace utility {

  bool is_double(const std::string& s)
  {
    return is<double>(s);
  }
  

  bool is_equal(std::string s, std::string other)
  {
    std::stringstream ss(s);
    std::string s2;
    ss >> s2; // to trim surrounding whitespaces
    to_lower(s2);
    // Check that nothing is left on stream
    std::string s3;
    ss >> s3;
    if(s3.size())
      return false;
    return (other==s2);
  }


  bool is_float(const std::string& s)
  {
    return is<float>(s);
  }


  bool is_int(const std::string& s)
  {
    return is<int>(s);
  }

  bool is_nan(const std::string& s)
  {
    return is_equal(s, "nan");
  }


  void quantile_normalize(Matrix& data)
  {
    Matrix data_copy(data);
    
    // sort columns in copy
    for (size_t column=0; column<data_copy.columns(); ++column){
      std::sort(data_copy.begin_column(column), data_copy.end_column(column));
    }

    // calculate average of each row
    std::vector<yat::statistics::Averager> averager(data_copy.rows());
    for (size_t row=0; row<data_copy.rows(); ++row){
      add(averager[row], data_copy.begin_row(row), data_copy.end_row(row));
    }

    for (size_t column=0; column<data.columns(); ++column){
      std::vector<size_t> index;
      yat::utility::sort_index(index, data.column_const_view(column));
                               
      for (size_t row=0; row<data.rows(); ++row)
        data(index[row], column) = averager[row].mean();
    }
  }



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