new representation type heap_pivot_column

git-svn-id: https://phat.googlecode.com/svn/trunk@147 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d

4 files changed, 130 insertions, 6 deletions

diff --git a/include/phat/representations/heap_pivot_column.h b/include/phat/representations/heap_pivot_column.h
new file mode 100644
index 0000000..f2bf845
--- /dev/null
+++ b/include/phat/representations/heap_pivot_column.h
@@ -0,0 +1,107 @@
+/*  Copyright 2013 IST Austria

+    Contributed by: Ulrich Bauer, Michael Kerber, Jan Reininghaus

+

+    This file is part of PHAT.

+

+    PHAT is free software: you can redistribute it and/or modify

+    it under the terms of the GNU Lesser General Public License as published by

+    the Free Software Foundation, either version 3 of the License, or

+    (at your option) any later version.

+

+    PHAT is distributed in the hope that it will be useful,

+    but WITHOUT ANY WARRANTY; without even the implied warranty of

+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

+    GNU Lesser General Public License for more details.

+

+    You should have received a copy of the GNU Lesser General Public License

+    along with PHAT.  If not, see <http://www.gnu.org/licenses/>. */

+

+#pragma once

+

+#include <phat/helpers/misc.h>

+#include <phat/representations/abstract_pivot_column.h>

+

+namespace phat {

+    class heap_column {

+

+    protected:

+        std::priority_queue< index > data;

+

+        void add_index( const index idx ) {

+            data.push( idx );

+        }

+

+    public:

+        void init( const index total_size ) {

+            clear();

+        }

+

+        void add_col( const column& col ) {

+            for( index idx = 0; idx < (index) col.size(); idx++ )

+                add_index( col[ idx ] );

+        }

+

+        index get_max_index() {

+            if( data.empty() )

+                return -1;

+            else {

+                index max_element = data.top();

+                data.pop();

+                while( !data.empty() && data.top() == max_element ) {

+                    data.pop();

+                    if( data.empty() )

+                        return -1;

+                    else {

+                        max_element = data.top();

+                        data.pop();

+                    }

+                }

+

+                data.push( max_element );

+                return max_element;

+            }

+        }

+

+        void get_col_and_clear( column& col ) {

+            col.clear();

+            while( !data.empty() ) {

+                index max_element = data.top();

+                data.pop();

+                if( data.empty() )

+                    col.push_back( max_element );

+                else {

+                    if( data.top() != max_element )

+                        col.push_back( max_element );

+                    else

+                        data.pop();

+                }

+            }

+            std::reverse( col.begin(), col.end() );

+        }

+

+        bool is_empty() {

+            return data.empty();

+        }

+

+		void clear() {

+			while( !data.empty() )

+                data.pop();

+		}

+

+		void remove_max() {

+            add_index( get_max_index() );

+        }

+

+        void set_col( const column& col  ) {

+            clear();

+            add_col( col );

+        }

+

+        void get_col( column& col  ) {

+            get_col_and_clear( col );

+            add_col( col );

+        }

+    };

+

+    typedef abstract_pivot_column< heap_column > heap_pivot_column;

+}

diff --git a/src/benchmark.cpp b/src/benchmark.cpp
index ca2497c..6a75bfe 100644
--- a/src/benchmark.cpp
+++ b/src/benchmark.cpp
@@ -22,6 +22,7 @@
 #include <phat/representations/vector_set.h>

 #include <phat/representations/vector_list.h>

 #include <phat/representations/sparse_pivot_column.h>

+#include <phat/representations/heap_pivot_column.h>

 #include <phat/representations/full_pivot_column.h>

 #include <phat/representations/bit_tree_pivot_column.h>

 

@@ -37,7 +38,7 @@
 #include <iomanip>

 

 

-enum Representation_type  {VECTOR_VECTOR, VECTOR_SET, SPARSE_PIVOT_COLUMN, FULL_PIVOT_COLUMN, BIT_TREE_PIVOT_COLUMN, VECTOR_LIST};

+enum Representation_type  {VECTOR_VECTOR, VECTOR_SET, SPARSE_PIVOT_COLUMN, HEAP_PIVOT_COLUMN, FULL_PIVOT_COLUMN, BIT_TREE_PIVOT_COLUMN, VECTOR_LIST};

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

 enum Ansatz_type  {PRIMAL, DUAL};

 

@@ -51,7 +52,7 @@ void print_help() {
     std::cerr << "--help    --  prints this screen" << std::endl;

     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 << "--vector_vector, --vector_set, --vector_list, --full_pivot_column, --sparse_pivot_column, --heap_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, --block_spectral_sequence, --row  --  use only a subset of reduction algorithms" << std::endl;

 }

 

@@ -77,6 +78,7 @@ void parse_command_line( int argc, char** argv, bool& use_binary, std::vector< R
             else if( argument == "--full_pivot_column" )  representations.push_back( FULL_PIVOT_COLUMN );

             else if( argument == "--bit_tree_pivot_column" )  representations.push_back( BIT_TREE_PIVOT_COLUMN );

             else if( argument == "--sparse_pivot_column" ) representations.push_back( SPARSE_PIVOT_COLUMN );

+            else if( argument == "--heap_pivot_column" ) representations.push_back( HEAP_PIVOT_COLUMN );

             else if( argument == "--standard" ) algorithms.push_back( STANDARD );

             else if( argument == "--twist" ) algorithms.push_back( TWIST );

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

@@ -191,6 +193,7 @@ int main( int argc, char** argv )
                     case FULL_PIVOT_COLUMN: COMPUTE(full_pivot_column) break;

                     case BIT_TREE_PIVOT_COLUMN: COMPUTE(bit_tree_pivot_column) break;

                     case SPARSE_PIVOT_COLUMN: COMPUTE(sparse_pivot_column) break;

+                    case HEAP_PIVOT_COLUMN: COMPUTE(heap_pivot_column) break;

                     }

                 }

             }

diff --git a/src/phat.cpp b/src/phat.cpp
index 1cc5ebb..7f994db 100644
--- a/src/phat.cpp
+++ b/src/phat.cpp
@@ -22,6 +22,7 @@
 #include <phat/representations/vector_set.h>

 #include <phat/representations/vector_list.h>

 #include <phat/representations/sparse_pivot_column.h>

+#include <phat/representations/heap_pivot_column.h>

 #include <phat/representations/full_pivot_column.h>

 #include <phat/representations/bit_tree_pivot_column.h>

 

@@ -33,7 +34,7 @@
 

 #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 Representation_type  {VECTOR_VECTOR, VECTOR_SET, SPARSE_PIVOT_COLUMN, FULL_PIVOT_COLUMN, BIT_TREE_PIVOT_COLUMN, VECTOR_LIST, HEAP_PIVOT_COLUMN};

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

 

 void print_help() {

@@ -46,7 +47,7 @@ void print_help() {
     std::cerr << "--help    --  prints this screen" << std::endl;

     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 << "--vector_vector, --vector_set, --vector_list, --full_pivot_column, --sparse_pivot_column, --heap_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, --block_spectral_sequence, --row  --  selects a reduction algorithm (default is '--twist')" << std::endl;

 }

 

@@ -75,6 +76,7 @@ void parse_command_line( int argc, char** argv, bool& use_binary, Representation
         else if( option == "--full_pivot_column" )  representation = FULL_PIVOT_COLUMN;

         else if( option == "--bit_tree_pivot_column" )  representation = BIT_TREE_PIVOT_COLUMN;

         else if( option == "--sparse_pivot_column" ) representation = SPARSE_PIVOT_COLUMN;

+        else if( option == "--heap_pivot_column" ) representation = HEAP_PIVOT_COLUMN;

         else if( option == "--standard" ) algorithm = STANDARD;

         else if( option == "--twist" ) algorithm = TWIST;

         else if( option == "--row" ) algorithm = ROW;

@@ -180,5 +182,6 @@ int main( int argc, char** argv )
     case FULL_PIVOT_COLUMN: COMPUTE_PAIRING(full_pivot_column) break;

     case BIT_TREE_PIVOT_COLUMN: COMPUTE_PAIRING(bit_tree_pivot_column) break;

     case SPARSE_PIVOT_COLUMN: COMPUTE_PAIRING(sparse_pivot_column) break;

+    case HEAP_PIVOT_COLUMN: COMPUTE_PAIRING(heap_pivot_column) break;

     }

 }

diff --git a/src/self_test.cpp b/src/self_test.cpp
index cfecd0e..21bb3bc 100644
--- a/src/self_test.cpp
+++ b/src/self_test.cpp
@@ -22,6 +22,7 @@
 #include <phat/representations/vector_set.h>

 #include <phat/representations/vector_list.h>

 #include <phat/representations/sparse_pivot_column.h>

+#include <phat/representations/heap_pivot_column.h>

 #include <phat/representations/full_pivot_column.h>

 #include <phat/representations/bit_tree_pivot_column.h>

 

@@ -36,6 +37,7 @@ int main( int argc, char** argv )
     std::string test_data = argc > 1 ? argv[ 1 ] : "examples/torus.bin";

 

     typedef phat::sparse_pivot_column Sparse;

+    typedef phat::heap_pivot_column Heap;

     typedef phat::full_pivot_column Full;

     typedef phat::bit_tree_pivot_column BitTree;

     typedef phat::vector_vector Vec_vec;

@@ -57,6 +59,11 @@ int main( int argc, char** argv )
         phat::boundary_matrix< Sparse > sparse_boundary_matrix = boundary_matrix;

         phat::compute_persistence_pairs< phat::chunk_reduction >( sparse_pairs, sparse_boundary_matrix );

 

+        std::cout << "Running Chunk - Heap ..." << std::endl;

+        phat::persistence_pairs heap_pairs;

+        phat::boundary_matrix< Heap > heap_boundary_matrix = boundary_matrix;

+        phat::compute_persistence_pairs< phat::chunk_reduction >( heap_pairs, heap_boundary_matrix );

+

         std::cout << "Running Chunk - Full ..." << std::endl;

         phat::persistence_pairs full_pairs;

         phat::boundary_matrix< Full > full_boundary_matrix = boundary_matrix;

@@ -82,8 +89,12 @@ int main( int argc, char** argv )
         phat::boundary_matrix< Vec_list > vec_list_boundary_matrix = boundary_matrix;

         phat::compute_persistence_pairs< phat::chunk_reduction >( vec_list_pairs, vec_list_boundary_matrix );

 

-        if( sparse_pairs != full_pairs ) {

-            std::cerr << "Error: sparse and full differ!" << std::endl;

+        if( sparse_pairs != heap_pairs ) {

+            std::cerr << "Error: sparse and heap differ!" << std::endl;

+            error = true;

+        }

+        if( heap_pairs != full_pairs ) {

+            std::cerr << "Error: heap and full differ!" << std::endl;

             error = true;

         }

         if( full_pairs != vec_vec_pairs ) {