Changeset 1050

Timestamp:

May 6, 2009, 11:11:59 AM (14 years ago)

Author:

Jari Häkkinen

Message:

Addresses #118. Non-logged input values are expected, geometric mean is used for averaging.

File:

• plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc (modified) (3 diffs)

plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc

@@ -43 +43 @@
 using namespace theplu::yat::utility;
 
+
 void create_target_and_fix_nans(std::vector<double>&, MatrixWeighted&);
 void create_target_and_fix_nans(std::vector<double>&, MatrixWeighted&,
                                 const std::string&);
+
+void exp_numbers(MatrixWeighted&);
+template<typename Iterator> void log_numbers(Iterator first, Iterator last);
+void log_numbers(MatrixWeighted&);
+
 /**
    writes the data values in the matrix ignoring the weights, i.e.,
@@ -102 +108 @@
   ( assay.present() ? create_target_and_fix_nans(target,m,assay.value()) :
                       create_target_and_fix_nans(target,m) );
+  log_numbers(target.begin(),target.end());
+  log_numbers(m);
   qQuantileNormalizer qqn(target.begin(), target.end(), 100);
   ColumnNormalizer<qQuantileNormalizer> cn(qqn);
   MatrixWeighted result(m.rows(),m.columns());
   cn(m,result);
+  exp_numbers(result);
 
   std::ofstream* outfile=NULL;
@@ -186 +195 @@
 
 
+void exp_numbers(MatrixWeighted& m)
+{
+  MatrixWeighted::iterator i=m.begin();
+  while (i!=m.end()) {
+    i->data() =std::exp(i->data());
+    ++i;
+  }
+}
+
+
+template<typename Iterator> void log_numbers(Iterator i, Iterator last)
+{
+  while (i!=last) {
+    *i=std::log(*i);
+    ++i;
+  }
+}
+
+
+void log_numbers(MatrixWeighted& m)
+{
+  MatrixWeighted::iterator i=m.begin();
+  while (i!=m.end()) {
+    i->data() =std::log(i->data());
+    ++i;
+  }
+}
+
+
 std::ostream& operator<< (std::ostream& s, const MatrixWeighted& m)
 {