From 8fa5020a3710161bb0ddfda1b9003a369b3b2174 Mon Sep 17 00:00:00 2001
From: "ulrich.bauer@gmail.com"
 <ulrich.bauer@gmail.com@8e3bb3c2-eed4-f18f-5264-0b6c94e6926d>
Date: Thu, 16 May 2013 15:34:15 +0000
Subject: dualization timing in phat binary, explicit function for dualizing
 persistence pairs

git-svn-id: https://phat.googlecode.com/svn/trunk@87 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d
---
 include/phat/compute_persistence_pairs.h | 14 +++-----------
 include/phat/helpers/dualize.h           |  9 +++++++++
 include/phat/persistence_pairs.h         |  4 ++++
 src/phat.cpp                             | 22 +++++++++++++++++-----
 4 files changed, 33 insertions(+), 16 deletions(-)

diff --git a/include/phat/compute_persistence_pairs.h b/include/phat/compute_persistence_pairs.h
index e782bd7..d3e61dd 100644
--- a/include/phat/compute_persistence_pairs.h
+++ b/include/phat/compute_persistence_pairs.h
@@ -41,18 +41,10 @@ namespace phat {
     
     template< typename ReductionAlgorithm, typename Representation >
     void compute_persistence_pairs_dualized( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) {
-        ReductionAlgorithm reduce;
-        const index nr_columns = boundary_matrix.get_num_cols();
+
         dualize( boundary_matrix );
-        reduce( boundary_matrix );
-        pairs.clear();
-        for( index idx = 0; idx < nr_columns; idx++ ) {
-            if( !boundary_matrix.is_empty( idx ) ) {
-                index death = nr_columns - 1 - boundary_matrix.get_max_index( idx );
-                index birth = nr_columns - 1 - idx;
-                pairs.append_pair( birth, death );
-            }
-        }
+        compute_persistence_pairs( pairs, boundary_matrix );
+        dualize_persistence_pairs( pairs, boundary_matrix.get_num_cols() );
     }
     
     template< typename Representation >
diff --git a/include/phat/helpers/dualize.h b/include/phat/helpers/dualize.h
index 5a9baf7..e3ae9ed 100644
--- a/include/phat/helpers/dualize.h
+++ b/include/phat/helpers/dualize.h
@@ -20,6 +20,8 @@
 
 #include <phat/helpers/misc.h>
 #include <phat/boundary_matrix.h>
+#include <phat/persistence_pairs.h>
+
 
 namespace phat {
     template< typename Representation >
@@ -60,4 +62,11 @@ namespace phat {
 
         boundary_matrix.load_vector_vector( dual_matrix, dual_dims );
     }
+    
+    void dualize_persistence_pairs( persistence_pairs& pairs, const index n ) {
+        for (index i = 0; i < pairs.get_num_pairs(); ++i) {
+            std::pair< index, index > pair = pairs.get_pair( i );
+            pairs.set_pair( i , n - 1 - pair.second, n - 1 - pair.first);
+        }
+    }
 }
diff --git a/include/phat/persistence_pairs.h b/include/phat/persistence_pairs.h
index b808a28..eafc638 100644
--- a/include/phat/persistence_pairs.h
+++ b/include/phat/persistence_pairs.h
@@ -39,6 +39,10 @@ namespace phat {
             return pairs[ idx ];
         }
 
+        void set_pair( index idx, index birth, index death )  {
+            pairs[ idx ] = std::make_pair( birth, death );
+        }
+        
         void clear() {
             pairs.clear();
         }
diff --git a/src/phat.cpp b/src/phat.cpp
index a955b54..c19aea8 100644
--- a/src/phat.cpp
+++ b/src/phat.cpp
@@ -30,6 +30,7 @@
 #include <phat/algorithms/row_reduction.h>
 #include <phat/algorithms/chunk_reduction.h>
 
+#include <phat/helpers/dualize.h>
 
 enum Representation_type  {VECTOR_VECTOR, VECTOR_SET, SPARSE_PIVOT_COLUMN, FULL_PIVOT_COLUMN, BIT_TREE_PIVOT_COLUMN, VECTOR_LIST};
 enum Algorithm_type  {STANDARD, TWIST, ROW, CHUNK, CHUNK_SEQUENTIAL };
@@ -108,17 +109,28 @@ void compute_pairing( std::string input_filename, std::string output_filename, b
         std::cerr << "Error opening file " << input_filename << std::endl;
         print_help_and_exit();
     }
-
+    
+    phat::index num_cols = matrix.get_num_cols();
+
+    if( dualize ) {
+        double dualize_timer = omp_get_wtime();
+        LOG( "Dualizing ..." )
+        phat::dualize ( matrix );
+        double dualize_time = omp_get_wtime() - dualize_timer;
+        double dualize_time_rounded = floor( dualize_time * 10.0 + 0.5 ) / 10.0;
+        LOG( "Dualizing took " << setiosflags( std::ios::fixed ) << setiosflags( std::ios::showpoint ) << std::setprecision( 1 ) << dualize_time_rounded <<"s" )
+    }
+        
     double pairs_timer = omp_get_wtime();
     phat::persistence_pairs pairs;
     LOG( "Computing persistence pairs ..." )
-    if( dualize )
-        phat::compute_persistence_pairs_dualized< Algorithm > ( pairs, matrix );
-    else
-        phat::compute_persistence_pairs < Algorithm > ( pairs, matrix );
+    phat::compute_persistence_pairs < Algorithm > ( pairs, matrix );
     double pairs_time = omp_get_wtime() - pairs_timer;
     double pairs_time_rounded = floor( pairs_time * 10.0 + 0.5 ) / 10.0;
     LOG( "Computing persistence pairs took " << setiosflags( std::ios::fixed ) << setiosflags( std::ios::showpoint ) << std::setprecision( 1 ) << pairs_time_rounded <<"s" )
+    
+    if( dualize ) dualize_persistence_pairs( pairs, num_cols );
+    
 
     double write_timer = omp_get_wtime();
     if( use_binary ) {
-- 
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