ignore list

git-svn-id: https://phat.googlecode.com/svn/trunk@56 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d

6 files changed, 39 insertions, 8 deletions

diff --git a/README b/README
index 82201e4..8a0ca31 100644
--- a/README
+++ b/README
@@ -38,9 +38,9 @@ algorithm. We provide the following choices of representation classes:
   * {{{vector_vector}}}: Each column is represented as a sorted {{{std::vector}}} of integers, containing the indices of the non-zero entries of the column. The matrix itself is a {{{std::vector}}} of such columns.
   * {{{vector_set}}}: Each column is a {{{std::set}}} of integers, with the same meaning as above. The matrix is stored as a {{{std::vector}}} of such columns.
   * {{{vector_list}}}: Each column is a sorted {{{std::list}}} of integers, with the same meaning as above. The matrix is stored as a {{{std::vector}}} of such columns.
-  * {{{sparse_pivot_column}}}: The matrix is stored as in the vector_vector representation. However, when a column is manipulated, it is first  converted into a {{{std::set}}}, using an extra data field called the "pivot column".  When another column is manipulated later, the pivot column is converted back to  the {{{std::vector}}} representation. This can lead to speed improvements when many columns  are added to a given pivot column consecutively. In a multicore setup, there is one pivot column per core.
+  * {{{sparse_pivot_column}}}: The matrix is stored as in the vector_vector representation. However, when a column is manipulated, it is first  converted into a {{{std::set}}}, using an extra data field called the "pivot column".  When another column is manipulated later, the pivot column is converted back to  the {{{std::vector}}} representation. This can lead to significant speed improvements when many columns  are added to a given pivot column consecutively. In a multicore setup, there is one pivot column per thread.
   * {{{full_pivot_column}}}: The same idea as in the sparse version. However, instead of a {{{std::set}}}, the pivot column is expanded into a bit vector of size n (the dimension of the matrix). To avoid costly initializations, the class remembers which entries have been manipulated for a pivot column and updates only those entries when another column becomes the pivot.
-  * {{{bit_tree_pivot_column}}} (default representation): Similar to the {{{full_pivot_column}}} but the implementation is more efficient. Internally it is a bit-set with fast iteration over present elements, and fast access to the maximum element. The structure is initialized before the reduction algorithm is started and reused.
+  * {{{bit_tree_pivot_column}}} (default representation): Similar to the {{{full_pivot_column}}} but the implementation is more efficient. Internally it is a bit-set with fast iteration over nonzero elements, and fast access to the maximal element. 
   
 There are two ways to interface with the library:
 
@@ -56,7 +56,7 @@ There are two ways to interface with the library:
     # include all headers found in {{{src/phat.cpp}}}
     # define a boundary matrix object, e.g. 
 {{{
-phat::boundary_matrix< full_pivot_column > boundary_matrix;
+phat::boundary_matrix< bit_tree_pivot_column > boundary_matrix;
 }}}
     # set the number of columns:
 {{{
@@ -73,7 +73,7 @@ phat::persistence_pairs pairs;
 }}}
     # run an algorithm like this:
 {{{
-phat::compute_persistence_pairs< phat::chunk_reduction >( pairs, boundary_matrix );
+phat::compute_persistence_pairs< phat::twist_reduction >( pairs, boundary_matrix );
 }}}
     # examine the result: 
 {{{
diff --git a/addons/alpha_3.cpp b/addons/alpha_3.cpp
index 7616e27..6df251c 100644
--- a/addons/alpha_3.cpp
+++ b/addons/alpha_3.cpp
@@ -176,7 +176,7 @@ int main(int argc, char** argv)
     std::string next_line;
     while( getline( is, next_line ) ) {
         if( next_line != "" && next_line[ 0 ] != '#' ) {
-            std::cerr << next_line;
+            //std::cerr << next_line;
             std::stringstream sstr(next_line);
             sstr >> p;
             lp.push_back(p);
@@ -239,12 +239,14 @@ int main(int argc, char** argv)
     std::size_t filtration_index = 0;
     std::size_t filtration_size = circumradii.size();
 
+    boundary_matrix.set_num_cols( filtration_size );
+
     Index curr_index = 0;
 
     for(std::vector<Triple>::const_iterator it = circumradii.begin();
         it != circumradii.end(); it++) {
 
-        if(filtration_index % 1000 == 0) {
+        if(filtration_index % 100000 == 0) {
             std::cerr << filtration_index << " of " << filtration_size
                       << std::endl;
         }
diff --git a/build/Visual Studio/VisualStudio2008.sln b/build/Visual Studio/VisualStudio2008.sln
index 10bc0b9..a7de81e 100644
--- a/build/Visual Studio/VisualStudio2008.sln
+++ b/build/Visual Studio/VisualStudio2008.sln
@@ -9,6 +9,10 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "simple_example", "simple_ex
 EndProject

 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "benchmark", "benchmark\benchmark.vcproj", "{41BD21B0-A6E5-4446-AF0A-D64BAF097341}"

 EndProject

+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "alpha_3", "alpha_3\alpha_3.vcproj", "{ABFB0956-E677-49BF-BDA3-68C69D79C37F}"

+EndProject

+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "rips", "rips\rips.vcproj", "{56999E92-DC5A-47CC-8044-B981E069F5B7}"

+EndProject

 Global

 	GlobalSection(SolutionConfigurationPlatforms) = preSolution

 		Debug|Win32 = Debug|Win32

@@ -46,6 +50,21 @@ Global
 		{41BD21B0-A6E5-4446-AF0A-D64BAF097341}.Release|Win32.Build.0 = Release|Win32

 		{41BD21B0-A6E5-4446-AF0A-D64BAF097341}.Release|x64.ActiveCfg = Release|x64

 		{41BD21B0-A6E5-4446-AF0A-D64BAF097341}.Release|x64.Build.0 = Release|x64

+		{ABFB0956-E677-49BF-BDA3-68C69D79C37F}.Debug|Win32.ActiveCfg = Debug|Win32

+		{ABFB0956-E677-49BF-BDA3-68C69D79C37F}.Debug|Win32.Build.0 = Debug|Win32

+		{ABFB0956-E677-49BF-BDA3-68C69D79C37F}.Debug|x64.ActiveCfg = Debug|Win32

+		{ABFB0956-E677-49BF-BDA3-68C69D79C37F}.Release|Win32.ActiveCfg = Release|Win32

+		{ABFB0956-E677-49BF-BDA3-68C69D79C37F}.Release|Win32.Build.0 = Release|Win32

+		{ABFB0956-E677-49BF-BDA3-68C69D79C37F}.Release|x64.ActiveCfg = Release|x64

+		{ABFB0956-E677-49BF-BDA3-68C69D79C37F}.Release|x64.Build.0 = Release|x64

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Debug|Win32.ActiveCfg = Debug|Win32

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Debug|Win32.Build.0 = Debug|Win32

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Debug|x64.ActiveCfg = Debug|x64

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Debug|x64.Build.0 = Debug|x64

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Release|Win32.ActiveCfg = Release|Win32

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Release|Win32.Build.0 = Release|Win32

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Release|x64.ActiveCfg = Release|x64

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Release|x64.Build.0 = Release|x64

 	EndGlobalSection

 	GlobalSection(SolutionProperties) = preSolution

 		HideSolutionNode = FALSE

diff --git a/build/Visual Studio/VisualStudio2012.sln b/build/Visual Studio/VisualStudio2012.sln
index 226005b..c11f45f 100644
--- a/build/Visual Studio/VisualStudio2012.sln
+++ b/build/Visual Studio/VisualStudio2012.sln
@@ -9,6 +9,8 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "simple_example", "simple_ex
 EndProject

 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "benchmark", "benchmark\benchmark.vcxproj", "{41BD21B0-A6E5-4446-AF0A-D64BAF097341}"

 EndProject

+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "rips", "rips\rips.vcxproj", "{56999E92-DC5A-47CC-8044-B981E069F5B7}"

+EndProject

 Global

 	GlobalSection(SolutionConfigurationPlatforms) = preSolution

 		Debug|Win32 = Debug|Win32

@@ -50,6 +52,14 @@ Global
 		{41BD21B0-A6E5-4446-AF0A-D64BAF097341}.Release|x64.ActiveCfg = Release|x64

 		{41BD21B0-A6E5-4446-AF0A-D64BAF097341}.Release|x64.Build.0 = Release|x64

 		{41BD21B0-A6E5-4446-AF0A-D64BAF097341}.Release|x64.Deploy.0 = Release|x64

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Debug|Win32.ActiveCfg = Debug|Win32

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Debug|Win32.Build.0 = Debug|Win32

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Debug|x64.ActiveCfg = Debug|x64

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Debug|x64.Build.0 = Debug|x64

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Release|Win32.ActiveCfg = Release|Win32

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Release|Win32.Build.0 = Release|Win32

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Release|x64.ActiveCfg = Release|x64

+		{56999E92-DC5A-47CC-8044-B981E069F5B7}.Release|x64.Build.0 = Release|x64

 	EndGlobalSection

 	GlobalSection(SolutionProperties) = preSolution

 		HideSolutionNode = FALSE

diff --git a/build/Visual Studio/benchmark/benchmark.vcxproj b/build/Visual Studio/benchmark/benchmark.vcxproj
index 5ae7842..334ef10 100644
--- a/build/Visual Studio/benchmark/benchmark.vcxproj
+++ b/build/Visual Studio/benchmark/benchmark.vcxproj
@@ -149,7 +149,7 @@
       <TargetEnvironment>X64</TargetEnvironment>

     </Midl>

     <ClCompile>

-      <Optimization>Full</Optimization>

+      <Optimization>MaxSpeed</Optimization>

       <IntrinsicFunctions>true</IntrinsicFunctions>

       <AdditionalIncludeDirectories>$(SolutionDir)\..\..\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>

       <PreprocessorDefinitions>WIN32;NDEBUG;_CONSOLE;%(PreprocessorDefinitions)</PreprocessorDefinitions>

diff --git a/include/phat/representations/vector_vector.h b/include/phat/representations/vector_vector.h
index 84609c2..06fd060 100644
--- a/include/phat/representations/vector_vector.h
+++ b/include/phat/representations/vector_vector.h
@@ -72,7 +72,7 @@ namespace phat {
 

         // clears given column

         void _clear( index idx ) { 

-            matrix[ idx ].clear(); 

+            matrix[ idx ].clear();

         }

 

         // syncronizes all data structures (essential for openmp stuff)