From 204f8ace0554cb8290a7f8cfca947d4a1251f985 Mon Sep 17 00:00:00 2001
From: "ulrich.bauer@gmail.com"
 <ulrich.bauer@gmail.com@8e3bb3c2-eed4-f18f-5264-0b6c94e6926d>
Date: Tue, 30 Apr 2013 09:19:22 +0000
Subject: alpha shape creation update

git-svn-id: https://phat.googlecode.com/svn/trunk@50 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d
---
 CMakeLists.txt                           | 22 ++++++++++++++++++++++
 addons/alpha_3.cpp                       | 21 +++++++++------------
 include/phat/compute_persistence_pairs.h | 16 ++++++++++++++++
 3 files changed, 47 insertions(+), 12 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 98ffc17..923a069 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -5,6 +5,7 @@ set(CMAKE_BUILD_TYPE "Release")
 INCLUDE(CheckCXXSourceCompiles)
 
 include_directories (include)
+include_directories (/opt/local/include)
 
 FIND_PACKAGE(OpenMP)
 
@@ -38,3 +39,24 @@ endif()
 add_executable (simple_example src/simple_example.cpp)
 add_executable (self_test src/self_test.cpp)
 add_executable (phat src/phat.cpp)
+add_executable (reduction_test reduction_test.cpp)
+add_executable (benchmark src/benchmark.cpp)
+
+
+set(CMAKE_MODULE_PATH "modules")
+set(CGAL_DIR "/opt/local/lib/cmake")
+
+FIND_PACKAGE(CGAL)
+
+if ( CGAL_FOUND )
+
+  include( ${CGAL_USE_FILE} )
+else()
+  
+    message(STATUS "This program requires the CGAL library, and will not be compiled.")
+  
+endif()
+
+FIND_PACKAGE(Boost)
+
+add_executable (alpha_3 addons/alpha_3.cpp)
diff --git a/addons/alpha_3.cpp b/addons/alpha_3.cpp
index 548500a..7616e27 100644
--- a/addons/alpha_3.cpp
+++ b/addons/alpha_3.cpp
@@ -229,8 +229,7 @@ int main(int argc, char** argv)
 
     std::cerr << "Filtration of size " << circumradii.size() << std::endl;
 
-    Matrix M;
-    Dim_container dim_container;
+    phat::boundary_matrix< phat::vector_vector > boundary_matrix;
 
     Vertex_handle v;
     Edge e;
@@ -257,13 +256,13 @@ int main(int argc, char** argv)
 
         if(CGAL::assign(v,obj)) {
             //std::cout << "Vertex " << it->second << std::endl;
-            dim_container.push_back(0);
+            boundary_matrix.set_dim(curr_index, 0);
             v->info().set_index(curr_index);
-            M.push_back(col);
+            boundary_matrix.set_col(curr_index, col);
         }
         if(CGAL::assign(e,obj)) {
             //std::cout << "Edge " << it->second << std::endl;
-            dim_container.push_back(1);
+            boundary_matrix.set_dim(curr_index, 1);
             Vertex_handle v1 = e.first->vertex(e.second);
             CGAL_assertion(v1->info().has_index());
             Vertex_handle v2 = e.first->vertex(e.third);
@@ -276,12 +275,12 @@ int main(int argc, char** argv)
             }
             col.push_back(i1);
             col.push_back(i2);
-            M.push_back(col);
+            boundary_matrix.set_col(curr_index, col);
             set_index_of_edge(dt,e,curr_index);
         }
         if(CGAL::assign(f,obj)) {
             //std::cout << "Facet " << it->second << std::endl;
-            dim_container.push_back(2);
+            boundary_matrix.set_dim(curr_index, 2);
 
             Index i1= f.first->info().edge_index( (f.second+1)%4, (f.second+2)%4 );
             col.push_back(i1);
@@ -290,25 +289,23 @@ int main(int argc, char** argv)
             Index i3= f.first->info().edge_index( (f.second+2)%4, (f.second+3)%4 );
             col.push_back(i3);
             std::sort(col.begin(),col.end());
-            M.push_back(col);
+            boundary_matrix.set_col(curr_index, col);
             set_index_of_facet(dt,f,curr_index);
 
         }
         if(CGAL::assign(c,obj)) {
             //std::cout << "Cell " << it->second << std::endl;
-            dim_container.push_back(3);
+            boundary_matrix.set_dim(curr_index, 3);
             col.push_back(c->info().facet_index(0));
             col.push_back(c->info().facet_index(1));
             col.push_back(c->info().facet_index(2));
             col.push_back(c->info().facet_index(3));
             std::sort(col.begin(),col.end());
-            M.push_back(col);
+            boundary_matrix.set_col(curr_index, col);
         }
         curr_index++;
     }
 
-    phat::boundary_matrix< phat::vector_vector > boundary_matrix;
-    boundary_matrix.init(M, dim_container);
     boundary_matrix.save_binary("alpha_filtration.bin");
     
     //phat::write(std::cout,M,dim_container);
diff --git a/include/phat/compute_persistence_pairs.h b/include/phat/compute_persistence_pairs.h
index e782bd7..ca46ac0 100644
--- a/include/phat/compute_persistence_pairs.h
+++ b/include/phat/compute_persistence_pairs.h
@@ -43,8 +43,24 @@ namespace phat {
     void compute_persistence_pairs_dualized( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) {
         ReductionAlgorithm reduce;
         const index nr_columns = boundary_matrix.get_num_cols();
+        
+        double start;
+        
+        start= omp_get_wtime();
+        std::clog << "Dualize ... " << std::endl;
+
         dualize( boundary_matrix );
+        
+        std::clog <<  omp_get_wtime() - start <<"s" << std::endl;
+
+        start= omp_get_wtime();
+        std::clog << "Reduce ... " << std::endl;
+        
         reduce( boundary_matrix );
+        
+        std::clog <<  omp_get_wtime() - start <<"s" << std::endl;
+
+        
         pairs.clear();
         for( index idx = 0; idx < nr_columns; idx++ ) {
             if( !boundary_matrix.is_empty( idx ) ) {
-- 
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