Changeset 3320 for trunk/yat/classifier/IGP.h

Timestamp:

Sep 19, 2014, 8:15:58 AM (9 years ago)

Author:

Peter

Message:

speedup. assume Distance is symmetric. closes #814

File:

• trunk/yat/classifier/IGP.h (modified) (4 diffs)

trunk/yat/classifier/IGP.h

@@ -28 +28 @@
 #include "Target.h"
 #include "yat/utility/concept_check.h"
+#include "yat/utility/Matrix.h"
 #include "yat/utility/Vector.h"
 #include "yat/utility/yat_assert.h"
@@ -53 +54 @@
      http://biostatistics.oxfordjournals.org/cgi/content/abstract/kxj029v1">
      Kapp and Tibshirani, Biostatistics (2006)</a>.
+
+     \note Distance must be symmetric, i.e., Distance(x,y) == Distance(y,x).
   */
   template <typename Distance>
@@ -126 +129 @@
 
     // Calculate IGP for each class
-    igp_ = utility::Vector(target_.nof_classes());
+    igp_.resize(target_.nof_classes(), 0.0);
 
+    // calculate distances
+    utility::Matrix dist(matrix_.columns(), matrix_.columns());
+    for (size_t i=0; i<dist.rows(); ++i)
+      for (size_t j=i+1; j<dist.rows(); ++j) {
+        dist(i,j) = dist(j,i) = distance_(matrix_.begin_column(i),
+                                          matrix_.end_column(i),
+                                          matrix_.begin_column(j));
+      }
+
+    // find nearest neigbour for each sample
     for(size_t i=0; i<target_.size(); i++) {
       size_t neighbor=i;
@@ -134 +147 @@
         if (i==j) // avoid self-self comparison
           continue;
-        double dist = distance_(matrix_.begin_column(i), matrix_.end_column(i),
-                                matrix_.begin_column(j));
-        if(dist<mindist) {
-          mindist=dist;
+        if(dist(i,j)<mindist) {
+          mindist=dist(i,j);
           neighbor=j;
         }