source: trunk/yat/normalizer/QuantileNormalizer.cc @ 1518

Last change on this file since 1518 was 1518, checked in by Peter, 13 years ago

changed implementation of a couple of normalizer so that operator() takes two matrices of which one is an input marix and one is a result matrix, i.e., the result does only depend on the input matrix and the result is only used as a receiver - I think this behaviour is more intuitive, although it is not as general as the previous one. We should probably document somewhere how we expect a 2Dnormalizer to behave (refs #425).

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 2.0 KB
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1// $Id: QuantileNormalizer.cc 1518 2008-09-21 04:07:45Z peter $
2
3/*
4  Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér
5  Copyright (C) 2007 Jari Häkkinen, Peter Johansson
6  Copyright (C) 2008 Peter Johansson
7
8  This file is part of the yat library, http://dev.thep.lu.se/yat
9
10  The yat library is free software; you can redistribute it and/or
11  modify it under the terms of the GNU General Public License as
12  published by the Free Software Foundation; either version 3 of the
13  License, or (at your option) any later version.
14
15  The yat library is distributed in the hope that it will be useful,
16  but WITHOUT ANY WARRANTY; without even the implied warranty of
17  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18  General Public License for more details.
19
20  You should have received a copy of the GNU General Public License
21  along with yat. If not, see <http://www.gnu.org/licenses/>.
22*/
23
24#include "QuantileNormalizer.h"
25
26#include "yat/statistics/Averager.h"
27
28#include "yat/utility/Matrix.h"
29#include "yat/utility/VectorConstView.h"
30
31#include <cassert>
32
33namespace theplu {
34namespace yat {
35namespace normalizer {
36
37  void QuantileNormalizer::operator()(const utility::Matrix& data,
38                                      utility::Matrix& result) const
39  {
40    assert(data.rows()==result.rows());
41    assert(data.columns()==result.columns());
42
43    // create a tmp copy
44    utility::Matrix data_copy(data);
45   
46    // sort columns in copy
47    for (size_t column=0; column<data_copy.columns(); ++column){
48      std::sort(data_copy.begin_column(column), data_copy.end_column(column));
49    }
50
51    // calculate average of each row
52    std::vector<yat::statistics::Averager> averager(data_copy.rows());
53    for (size_t row=0; row<result.rows(); ++row){
54      add(averager[row], data_copy.begin_row(row), data_copy.end_row(row));
55    }
56
57    for (size_t column=0; column<result.columns(); ++column){
58      std::vector<size_t> index;
59      utility::sort_index(index, data.column_const_view(column));
60                               
61      for (size_t row=0; row<data.rows(); ++row)
62        result(index[row], column) = averager[row].mean();
63    }
64  }
65
66
67
68}}} // end of namespace utility, yat and thep
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