new block_spectral_sequence_reduction

git-svn-id: https://phat.googlecode.com/svn/trunk@134 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d

3 files changed, 22 insertions, 6 deletions

diff --git a/src/benchmark.cpp b/src/benchmark.cpp
index 59b5f32..ca2497c 100644
--- a/src/benchmark.cpp
+++ b/src/benchmark.cpp
@@ -29,6 +29,7 @@
 #include <phat/algorithms/standard_reduction.h>

 #include <phat/algorithms/row_reduction.h>

 #include <phat/algorithms/chunk_reduction.h>

+#include <phat/algorithms/block_spectral_sequence_reduction.h>

 

 #include <phat/helpers/dualize.h>

 

@@ -37,7 +38,7 @@
 

 

 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};

+enum Algorithm_type  {STANDARD, TWIST, ROW, CHUNK, CHUNK_SEQUENTIAL, BLOCK_SPECTRAL_SEQUENCE};

 enum Ansatz_type  {PRIMAL, DUAL};

 

 void print_help() {

@@ -51,7 +52,7 @@ void print_help() {
     std::cerr << "--dualize   --  use only dualization approach" << std::endl;

     std::cerr << "--primal   --  use only primal approach" << std::endl;

     std::cerr << "--vector_vector, --vector_set, --vector_list, --full_pivot_column, --sparse_pivot_column, --bit_tree_pivot_column  --  use only a subset of representation data structures for boundary matrices" << std::endl;

-    std::cerr << "--standard, --twist, --chunk, --chunk_sequential, --row  --  use only a subset of reduction algorithms" << std::endl;

+    std::cerr << "--standard, --twist, --chunk, --chunk_sequential, --block_spectral_sequence, --row  --  use only a subset of reduction algorithms" << std::endl;

 }

 

 void print_help_and_exit() {

@@ -80,6 +81,7 @@ void parse_command_line( int argc, char** argv, bool& use_binary, std::vector< R
             else if( argument == "--twist" ) algorithms.push_back( TWIST );

             else if( argument == "--row" ) algorithms.push_back( ROW );

             else if( argument == "--chunk_sequential" ) algorithms.push_back( CHUNK_SEQUENTIAL );

+            else if( argument == "--block_spectral_sequence" ) algorithms.push_back( BLOCK_SPECTRAL_SEQUENCE );

             else if( argument == "--chunk" ) algorithms.push_back( CHUNK );

             else if( argument == "--primal" ) ansaetze.push_back( PRIMAL );

             else if( argument == "--dual" ) ansaetze.push_back( DUAL );

@@ -153,6 +155,7 @@ void benchmark( std::string input_filename, bool use_binary, Ansatz_type ansatz
     case TWIST: std::cout << " twist,"; benchmark< phat::Representation, phat::twist_reduction >( input_filename, use_binary, ansatz ); break; \

     case ROW: std::cout << " row,"; benchmark< phat::Representation, phat::row_reduction >( input_filename, use_binary, ansatz ); break; \

     case CHUNK: std::cout << " chunk,"; benchmark< phat::Representation, phat::chunk_reduction >( input_filename, use_binary, ansatz ); break; \

+    case BLOCK_SPECTRAL_SEQUENCE: std::cout << " block spectral sequence,"; benchmark< phat::Representation, phat::block_spectral_sequence_reduction >( input_filename, use_binary, ansatz ); break; \

     case CHUNK_SEQUENTIAL: std::cout << " chunk_sequential,"; \

                            int num_threads = omp_get_max_threads(); \

                            omp_set_num_threads( 1 ); \

diff --git a/src/phat.cpp b/src/phat.cpp
index c19aea8..1cc5ebb 100644
--- a/src/phat.cpp
+++ b/src/phat.cpp
@@ -29,11 +29,12 @@
 #include <phat/algorithms/standard_reduction.h>

 #include <phat/algorithms/row_reduction.h>

 #include <phat/algorithms/chunk_reduction.h>

+#include <phat/algorithms/block_spectral_sequence_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 };

+enum Algorithm_type  {STANDARD, TWIST, ROW, CHUNK, CHUNK_SEQUENTIAL, BLOCK_SPECTRAL_SEQUENCE };

 

 void print_help() {

     std::cerr << "Usage: " << "phat " << "[options] input_filename output_filename" << std::endl;

@@ -46,7 +47,7 @@ void print_help() {
     std::cerr << "--verbose --  verbose output" << std::endl;

     std::cerr << "--dualize   --  use dualization approach" << std::endl;

     std::cerr << "--vector_vector, --vector_set, --vector_list, --full_pivot_column, --sparse_pivot_column, --bit_tree_pivot_column  --  selects a representation data structure for boundary matrices (default is '--bit_tree_pivot_column')" << std::endl;

-    std::cerr << "--standard, --twist, --chunk, --chunk_sequential, --row  --  selects a reduction algorithm (default is '--twist')" << std::endl;

+    std::cerr << "--standard, --twist, --chunk, --chunk_sequential, --block_spectral_sequence, --row  --  selects a reduction algorithm (default is '--twist')" << std::endl;

 }

 

 void print_help_and_exit() {

@@ -79,6 +80,7 @@ void parse_command_line( int argc, char** argv, bool& use_binary, Representation
         else if( option == "--row" ) algorithm = ROW;

         else if( option == "--chunk" ) algorithm = CHUNK;

         else if( option == "--chunk_sequential" ) algorithm = CHUNK_SEQUENTIAL;

+        else if( option == "--block_spectral_sequence" ) algorithm = BLOCK_SPECTRAL_SEQUENCE;

         else if( option == "--verbose" ) verbose = true;

         else if( option == "--help" ) print_help_and_exit();

         else print_help_and_exit();

@@ -150,6 +152,7 @@ void compute_pairing( std::string input_filename, std::string output_filename, b
     case STANDARD: compute_pairing< phat::Representation, phat::standard_reduction> ( input_filename, output_filename, use_binary, verbose, dualize ); break; \

     case TWIST: compute_pairing< phat::Representation, phat::twist_reduction> ( input_filename, output_filename, use_binary, verbose, dualize ); break; \

     case ROW: compute_pairing< phat::Representation, phat::row_reduction >( input_filename, output_filename, use_binary, verbose, dualize ); break; \

+    case BLOCK_SPECTRAL_SEQUENCE: compute_pairing< phat::Representation, phat::block_spectral_sequence_reduction >( input_filename, output_filename, use_binary, verbose, dualize ); break; \

     case CHUNK: compute_pairing< phat::Representation, phat::chunk_reduction >( input_filename, output_filename, use_binary, verbose, dualize ); break; \

     case CHUNK_SEQUENTIAL: int num_threads = omp_get_max_threads(); \

                            omp_set_num_threads( 1 ); \

diff --git a/src/self_test.cpp b/src/self_test.cpp
index e3aaa32..cfecd0e 100644
--- a/src/self_test.cpp
+++ b/src/self_test.cpp
@@ -29,6 +29,7 @@
 #include <phat/algorithms/standard_reduction.h>

 #include <phat/algorithms/row_reduction.h>

 #include <phat/algorithms/chunk_reduction.h>

+#include <phat/algorithms/block_spectral_sequence_reduction.h>

 

 int main( int argc, char** argv )

 {

@@ -132,6 +133,11 @@ int main( int argc, char** argv )
         phat::boundary_matrix< BitTree > row_boundary_matrix = boundary_matrix;

         phat::compute_persistence_pairs< phat::row_reduction >( row_pairs, row_boundary_matrix );

 

+        std::cout << "Running Block spectral sequence - BitTree ..." << std::endl;

+        phat::persistence_pairs ss_pairs;

+        phat::boundary_matrix< BitTree > ss_boundary_matrix = boundary_matrix;

+        phat::compute_persistence_pairs< phat::block_spectral_sequence_reduction >( ss_pairs, ss_boundary_matrix );

+

         if( twist_pairs != std_pairs ) {

             std::cerr << "Error: twist and standard differ!" << std::endl;

             error = true;

@@ -144,8 +150,12 @@ int main( int argc, char** argv )
             std::cerr << "Error: chunk and row differ!" << std::endl;

             error = true;

         }

-        if( row_pairs != twist_pairs ) {

-            std::cerr << "Error: row and twist differ!" << std::endl;

+        if( row_pairs != ss_pairs ) {

+            std::cerr << "Error: row and block spectral sequence differ!" << std::endl;

+            error = true;

+        }

+        if( ss_pairs != twist_pairs ) {

+            std::cerr << "Error: block spectral sequence and twist differ!" << std::endl;

             error = true;

         }