source: trunk/test/normalization_test.cc @ 1521

// $Id: normalization_test.cc 1521 2008-09-21 17:54:19Z peter $

/*
  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 "Suite.h"

#include "yat/normalizer/Centralizer.h"
#include "yat/normalizer/ColumnNormalizer.h"
#include "yat/utility/DataIterator.h"
#include "yat/normalizer/QuantileNormalizer.h"
#include "yat/normalizer/RowNormalizer.h"
#include "yat/normalizer/Spearman.h"
#include "yat/normalizer/Zscore.h"

#include "yat/utility/DataIterator.h"
#include "yat/utility/Matrix.h"
#include "yat/utility/MatrixWeighted.h"
#include "yat/utility/WeightIterator.h"

#include <limits>
#include <vector>

using namespace theplu::yat;
void test_centralizer(test::Suite&);
void test_column_normalize(test::Suite&);
void test_quantile_normalize(test::Suite&);
void test_row_normalize(test::Suite&);
void test_spearman(test::Suite&);
void test_spearman_weighted(test::Suite&);
void test_z_score(test::Suite&);

int main(int argc, char* argv[])
{  
  test::Suite suite(argc, argv);
  suite.err() << "testing normalizations ... " << std::endl;

  test_centralizer(suite);
  test_column_normalize(suite);
  test_quantile_normalize(suite);
  test_row_normalize(suite);
  test_spearman(suite);
  test_z_score(suite);

  return suite.return_value();
}


void test_centralizer(test::Suite& suite)
{
  suite.err() << "Testing Centralizer\n";
  std::vector<double> vec;
  vec.push_back(1);
  vec.push_back(2);
  vec.push_back(3);
  normalizer::Centralizer<> c;
  c(vec.begin(), vec.end(), vec.begin());
  for (size_t i=0; i<vec.size(); ++i)
    suite.add(suite.equal(vec[i], static_cast<double>(i)-1.0));
}


void test_column_normalize(test::Suite& suite)
{
  using namespace normalizer;
  suite.err() << "Testing ColumnNormalizer\n";
  
  utility::Matrix m(2,2);
  m(0,0) = 0;
  m(0,1) = 10;
  m(1,0) = 2;
  m(1,1) = 4;
  ColumnNormalizer<Centralizer<> > qn;
  qn(m, m);
  suite.err() << "Testing m(0,0)\n";
  suite.add(suite.equal(m(0,0), -1));
  suite.err() << "Testing m(0,1)\n";
  suite.add(suite.equal(m(0,1), 3));
  suite.err() << "Testing m(1,0)\n";
  suite.add(suite.equal(m(1,0), 1));
  suite.err() << "Testing m(1,1)\n";
  suite.add(suite.equal(m(1,1), -3));
}

void test_quantile_normalize(test::Suite& suite)
{
  suite.err() << "Testing QuantileNormalizer\n";
  
  utility::Matrix m(2,2);
  m(0,0) = 0;
  m(0,1) = 10;
  m(1,0) = 2;
  m(1,1) = 4;
  normalizer::QuantileNormalizer qn;
  qn(m, m);
  suite.err() << "Testing m(0,0)\n";
  suite.add(suite.equal(m(0,0), 2));
  suite.err() << "Testing m(0,1)\n";
  suite.add(suite.equal(m(0,1), 6));
  suite.err() << "Testing m(1,0)\n";
  suite.add(suite.equal(m(1,0), 6));
  suite.err() << "Testing m(1,1)\n";
  suite.add(suite.equal(m(1,1), 2));
}

void test_row_normalize(test::Suite& suite)
{
  using namespace normalizer;
  suite.err() << "Testing RowNormalizer\n";
  
  utility::Matrix m(2,3);
  m(0,0) = 0;
  m(0,1) = 10;
  m(1,0) = 2;
  m(1,1) = 4;
  utility::Matrix m2(m);
  m2.transpose();
  ColumnNormalizer<Centralizer<> > cn;
  RowNormalizer<Centralizer<> > rn;
  cn(m, m);
  rn(m2, m2);
  m2.transpose();
  suite.equal_range(m.begin(), m.end(), m2.begin());
}

void test_spearman(test::Suite& suite)
{
  suite.err() << "Testing Spearman\n";
  normalizer::Spearman spearman;
  std::vector<double> vec;
  vec.push_back(0);
  vec.push_back(2);
  vec.push_back(3);
  vec.push_back(1);
  spearman(vec.begin(), vec.end(), vec.begin());
  std::vector<double> correct;
  correct.push_back(1.0/8);
  correct.push_back(5.0/8);
  correct.push_back(7.0/8);
  correct.push_back(3.0/8);
  suite.add(suite.equal_range(vec.begin(), vec.end(), correct.begin()));
  suite.err() << "Testing Spearman with ties\n";
  vec[1]=vec[2];
  correct[1] = correct[2] = (correct[1]+correct[2])/2;
  spearman(vec.begin(), vec.end(), vec.begin());
  suite.add(suite.equal_range(vec.begin(), vec.end(), correct.begin()));
  test_spearman_weighted(suite);
}


void test_spearman_weighted(test::Suite& suite)
{
  suite.err() << "Testing Weighted Spearman\n";
  normalizer::Spearman spearman;

  suite.err() << "Testing that unity weights reproduces unweighted case\n";
  utility::MatrixWeighted m(1,4,0,1);
  utility::MatrixWeighted res(m.rows(), m.columns(),3.14,0);
  m(0,0).data()=0;
  m(0,1).data()=2;
  m(0,2).data()=3;
  m(0,3).data()=1;
  std::vector<double> correct(m.columns());
  std::vector<double> correct_w(m.columns(), 1.0);
  std::copy(utility::data_iterator(m.begin_row(0)),
            utility::data_iterator(m.end_row(0)),
            correct.begin());
  spearman(correct.begin(), correct.end(), correct.begin());
  spearman(m.begin_row(0), m.end_row(0), res.begin_row(0));

  using utility::data_iterator;
  suite.add(suite.equal_range(data_iterator(res.begin_row(0)),
                               data_iterator(res.end_row(0)),
                               correct.begin()));
  using utility::weight_iterator;
  suite.add(suite.equal_range(weight_iterator(res.begin_row(0)),
                               weight_iterator(res.end_row(0)),
                               correct_w.begin()));

  suite.err() << "Testing rescaling of weights\n";
  for (size_t i=0; i<m.columns(); ++i) {
    m(0,i).weight() *= 2;
    correct_w[i] *= 2;
  }   
  spearman(m.begin_row(0), m.end_row(0), res.begin_row(0));
  suite.add(suite.equal_range(data_iterator(res.begin_row(0)),
                               data_iterator(res.end_row(0)),
                               correct.begin()));
  suite.add(suite.equal_range(weight_iterator(res.begin_row(0)),
                               weight_iterator(res.end_row(0)),
                               correct_w.begin()));

  
  suite.err() << "Testing case with a zero weight\n";
  m(0,1).data() = std::numeric_limits<double>::quiet_NaN();
  m(0,1).weight() = 0.0;
  spearman(m.begin_row(0), m.end_row(0), res.begin_row(0));
  suite.add(suite.equal(res(0,0).data(), 0.5/3)); 
  suite.add(suite.equal(res(0,2).data(), 2.5/3)); 
  suite.add(suite.equal(res(0,3).data(), 1.5/3)); 

  suite.err() << "Testing case with ties\n";
  m(0,0).data() = m(0,2).data();
  spearman(m.begin_row(0), m.end_row(0), res.begin_row(0));
  suite.add(suite.equal(res(0,0).data(), 2.0/3)); 
  suite.add(suite.equal(res(0,2).data(), 2.0/3)); 
  suite.add(suite.equal(res(0,3).data(), 0.5/3)); 
}

void test_z_score(test::Suite& suite)
{
  suite.err() << "Testing Zscore\n";
  std::vector<double> vec;
  vec.push_back(0);
  vec.push_back(3.14);
  normalizer::Zscore zscore;
  zscore(vec.begin(), vec.end(), vec.begin());
  for (size_t i=0; i<vec.size(); ++i)
    suite.add(suite.equal(vec[i], 2.0*i-1.0));
}