From 8afecf944f76e52fd0668eb106a717fe64e1341c Mon Sep 17 00:00:00 2001 From: "jan.reininghaus" Date: Fri, 3 May 2013 09:30:12 +0000 Subject: ignore list git-svn-id: https://phat.googlecode.com/svn/trunk@56 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d --- README | 8 ++++---- addons/alpha_3.cpp | 6 ++++-- build/Visual Studio/VisualStudio2008.sln | 19 +++++++++++++++++++ build/Visual Studio/VisualStudio2012.sln | 10 ++++++++++ build/Visual Studio/benchmark/benchmark.vcxproj | 2 +- include/phat/representations/vector_vector.h | 2 +- 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::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 @@ X64 - Full + MaxSpeed true $(SolutionDir)\..\..\include;%(AdditionalIncludeDirectories) WIN32;NDEBUG;_CONSOLE;%(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) -- cgit v1.2.3