improve performance when reading a large Newick tree

Use vtkTreeDFSIterator when calculating the node weights of a tree
ready by vtkNewickTreeReader.  For a sample tree with 63498 vertices,
this change improves read time from 70.47s to 4.14s

Change-Id: I0e35ff89ce207657a958cf606a85984aa8ee3de0

Filters/StatisticsGnuR/vtkRAdapter.cxx

@@ -774,25 +774,28 @@ vtkTree* vtkRAdapter::RToVTKTree(SEXP variable)
     trueWeights->SetNumberOfTuples(tree->GetNumberOfVertices());
 
     double maxWeight = 0.0;
-    for (vtkIdType vertex = 0; vertex < tree->GetNumberOfVertices(); ++vertex)
-      {
-        double weight = 0.0;
-        vtkIdType node = vertex;
-        vtkIdType parent = tree->GetParent(node);
-        while (parent != -1)
-          {
-          weight += weights->GetValue(tree->GetEdgeId(parent, node));
-          node = parent;
-          parent = tree->GetParent(node);
-          }
+    vtkNew<vtkTreeDFSIterator> treeIterator;
+    treeIterator->SetStartVertex(tree->GetRoot());
+    treeIterator->SetTree(tree);
+    while (treeIterator->HasNext())
+      {
+      vtkIdType vertex = treeIterator->Next();
+      vtkIdType parent = tree->GetParent(vertex);
+      double weight = 0.0;
+      if (parent >= 0)
+        {
+        weight = weights->GetValue(tree->GetEdgeId(parent, vertex));
+        }
+      weight += nodeWeights->GetValue(parent);
 
-        if (weight > maxWeight)
-          {
-          maxWeight = weight;
-          }
-        nodeWeights->SetValue(vertex, weight);
-        trueWeights->SetValue(vertex, weight);
+      if (weight > maxWeight)
+        {
+        maxWeight = weight;
+        }
+      nodeWeights->SetValue(vertex, weight);
+      trueWeights->SetValue(vertex, weight);
       }
+
     for (vtkIdType vertex = 0; vertex < tree->GetNumberOfVertices(); ++vertex)
       {
       if (tree->IsLeaf(vertex))
@@ -800,7 +803,6 @@ vtkTree* vtkRAdapter::RToVTKTree(SEXP variable)
         nodeWeights->SetValue(vertex, maxWeight);
         }
       }
-
     nodeWeights->SetName("node weight");
     tree->GetVertexData()->AddArray(nodeWeights.GetPointer());
 

IO/Infovis/vtkNewickTreeReader.cxx

@@ -21,6 +21,7 @@
 #include "vtkFieldData.h"
 #include "vtkNew.h"
 #include "vtkTree.h"
+#include "vtkTreeDFSIterator.h"
 #include "vtkInformation.h"
 #include "vtkInformationVector.h"
 #include "vtkMutableDirectedGraph.h"
@@ -140,25 +141,28 @@ int vtkNewickTreeReader:: ReadNewickTree(  char * const buffer, vtkTree & tree)
 
   //set node weights
   double maxWeight = 0.0;
-  for (vtkIdType vertex = 0; vertex < tree.GetNumberOfVertices(); ++vertex)
+  vtkNew<vtkTreeDFSIterator> treeIterator;
+  treeIterator->SetStartVertex(tree.GetRoot());
+  treeIterator->SetTree(&tree);
+  while (treeIterator->HasNext())
     {
-      double weight = 0.0;
-      vtkIdType node = vertex;
-      vtkIdType parent = tree.GetParent(node);
-      while (parent != -1)
-        {
-        weight += weights->GetValue(tree.GetEdgeId(parent, node));
-        node = parent;
-        parent = tree.GetParent(node);
-        }
-
-      if (weight > maxWeight)
-        {
-        maxWeight = weight;
-        }
-      nodeWeights->SetValue(vertex, weight);
-      trueWeights->SetValue(vertex, weight);
+    vtkIdType vertex = treeIterator->Next();
+    vtkIdType parent = tree.GetParent(vertex);
+    double weight = 0.0;
+    if (parent >= 0)
+      {
+      weight = weights->GetValue(tree.GetEdgeId(parent, vertex));
+      }
+    weight += nodeWeights->GetValue(parent);
+
+    if (weight > maxWeight)
+      {
+      maxWeight = weight;
+      }
+    nodeWeights->SetValue(vertex, weight);
+    trueWeights->SetValue(vertex, weight);
     }
+
   for (vtkIdType vertex = 0; vertex < tree.GetNumberOfVertices(); ++vertex)
     {
     if (tree.IsLeaf(vertex))