Changeset 1432

Timestamp:

Aug 25, 2008, 3:54:18 PM (15 years ago)

Author:

Peter

Message:

refs #416 moving quantile normalizer to new dir. Also moved the algorithm to a class (rather than free function).

Location:

trunk

Files:

• test/Makefile.am (modified) (1 diff)
• test/Suite.h (modified) (1 diff)
• test/normalization_test.cc (added)
• test/utility_test.cc (modified) (3 diffs)
• yat/normalization/Makefile.am (modified) (1 diff)
• yat/normalization/QuantileNormalizer.cc (copied) (copied from trunk/yat/utility/utility.cc) (3 diffs)
• yat/normalization/QuantileNormalizer.h (added)
• yat/utility/utility.cc (modified) (1 diff)
• yat/utility/utility.h (modified) (1 diff)

trunk/test/Makefile.am

@@ -41 +41 @@
   knn_test matrix_lookup_test matrix_test \
   nbc_test \
-  ncc_test nni_test pca_test range_test regression_test rnd_test roc_test \
+  ncc_test nni_test normalization_test pca_test \
+  range_test regression_test rnd_test roc_test \
   score_test  smart_ptr_test    \
   statistics_test subset_generator_test svd_test svm_test target_test \

trunk/test/Suite.h

@@ -26 +26 @@
 
 #include <fstream>
+#include <iostream>
 #include <sstream>
 

trunk/test/utility_test.cc

@@ -37 +37 @@
 
 using namespace theplu::yat;
-void test_quantile_normalize(test::Suite&);
 void test_inverse(test::Suite&);
 
@@ -151 +150 @@
   }
 
-  test_quantile_normalize(suite);
   test_inverse(suite);
 
@@ -218 +216 @@
   
 }
-
-
-void test_quantile_normalize(test::Suite& suite)
-{
-  suite.err() << "Testing quantile normalization\n";
-  
-  utility::Matrix m(2,2);
-  m(0,0) = 0;
-  m(0,1) = 10;
-  m(1,0) = 2;
-  m(1,1) = 4;
-  utility::quantile_normalize(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));
-
-}

trunk/yat/normalization/Makefile.am

@@ -25 +25 @@
 
 noinst_LTLIBRARIES = libnormalization.la
-libnormalization_la_SOURCES = 
+libnormalization_la_SOURCES = QuantileNormalizer.cc
 
 include_normalizationdir = $(includedir)/yat/normalization
 
-include_normalization_HEADERS = 
+include_normalization_HEADERS = QuantileNormalizer.h

trunk/yat/normalization/QuantileNormalizer.cc

@@ -4 +4 @@
   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://trac.thep.lu.se/yat
+  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
@@ -23 +24 @@
 */
 
-#include "utility.h"
+#include "QuantileNormalizer.h"
 
-#include "Matrix.h"
-#include "stl_utility.h"
-#include "VectorConstView.h"
 #include "yat/statistics/Averager.h"
 
-#include <sstream>
-#include <string>
+#include "yat/utility/Matrix.h"
+#include "yat/utility/VectorConstView.h"
 
 namespace theplu {
 namespace yat {
-namespace utility {
+namespace normalization {
 
-  bool is_double(const std::string& s)
+  void QuantileNormalizer::operator()(utility::Matrix& data) const
   {
-    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);
+    utility::Matrix data_copy(data);
     
     // sort columns in copy
@@ -92 +52 @@
     for (size_t column=0; column<data.columns(); ++column){
       std::vector<size_t> index;
-      yat::utility::sort_index(index, data.column_const_view(column));
+      utility::sort_index(index, data.column_const_view(column));
                                
       for (size_t row=0; row<data.rows(); ++row)

trunk/yat/utility/utility.cc

@@ -75 +75 @@
 
 
-  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

trunk/yat/utility/utility.h

@@ -98 +98 @@
   bool is_nan(const std::string& s);
 
-  /**
-     \brief Perform quantile normalization
-
-     \since New in yat 0.5
-   */
-  void quantile_normalize(Matrix&);
-
   // template implementations
   template<typename T>