diff options
| author | Gard Spreemann <gspr@nonempty.org> | 2020-06-03 10:05:46 +0200 |
|---|---|---|
| committer | Gard Spreemann <gspr@nonempty.org> | 2020-06-03 10:05:46 +0200 |
| commit | 069338dfb03b4d04c1410b3e24b762b18db5c233 (patch) | |
| tree | e9b53324fe48f2a71f10b2ccea8784ae537659f2 | |
| parent | 803fd45bc77103813895ac045a278157554fd39a (diff) | |
Delete bundled copy of PHAT.
20 files changed, 0 insertions, 2345 deletions
diff --git a/matching/include/phat/algorithms/chunk_reduction.h b/matching/include/phat/algorithms/chunk_reduction.h deleted file mode 100644 index 1797023..0000000 --- a/matching/include/phat/algorithms/chunk_reduction.h +++ /dev/null @@ -1,223 +0,0 @@ -/* 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/boundary_matrix.h>
-
-namespace phat {
- class chunk_reduction {
- public:
- enum column_type { GLOBAL
- , LOCAL_POSITIVE
- , LOCAL_NEGATIVE };
-
- public:
- template< typename Representation >
- void operator() ( boundary_matrix< Representation >& boundary_matrix ) {
-
-
- const index nr_columns = boundary_matrix.get_num_cols();
- if( omp_get_max_threads( ) > nr_columns )
- omp_set_num_threads( 1 );
-
- const dimension max_dim = boundary_matrix.get_max_dim();
-
- std::vector< index > lowest_one_lookup( nr_columns, -1 );
- std::vector < column_type > column_type( nr_columns, GLOBAL );
- std::vector< char > is_active( nr_columns, false );
-
- const index chunk_size = omp_get_max_threads() == 1 ? (index)sqrt( (double)nr_columns ) : nr_columns / omp_get_max_threads();
-
- std::vector< index > chunk_boundaries;
- for( index cur_boundary = 0; cur_boundary < nr_columns; cur_boundary += chunk_size )
- chunk_boundaries.push_back( cur_boundary );
- chunk_boundaries.push_back( nr_columns );
-
- for( dimension cur_dim = max_dim; cur_dim >= 1; cur_dim-- ) {
- // Phase 1: Reduce chunks locally -- 1st pass
- #pragma omp parallel for schedule( guided, 1 )
- for( index chunk_id = 0; chunk_id < (index)chunk_boundaries.size() - 1; chunk_id++ )
- _local_chunk_reduction( boundary_matrix, lowest_one_lookup, column_type, cur_dim,
- chunk_boundaries[ chunk_id ], chunk_boundaries[ chunk_id + 1 ], chunk_boundaries[ chunk_id ] );
- boundary_matrix.sync();
-
- // Phase 1: Reduce chunks locally -- 2nd pass
- #pragma omp parallel for schedule( guided, 1 )
- for( index chunk_id = 1; chunk_id < (index)chunk_boundaries.size( ) - 1; chunk_id++ )
- _local_chunk_reduction( boundary_matrix, lowest_one_lookup, column_type, cur_dim,
- chunk_boundaries[ chunk_id ], chunk_boundaries[ chunk_id + 1 ], chunk_boundaries[ chunk_id - 1 ] );
- boundary_matrix.sync( );
- }
-
- // get global columns
- std::vector< index > global_columns;
- for( index cur_col_idx = 0; cur_col_idx < nr_columns; cur_col_idx++ )
- if( column_type[ cur_col_idx ] == GLOBAL )
- global_columns.push_back( cur_col_idx );
-
- // get active columns
- #pragma omp parallel for
- for( index idx = 0; idx < (index)global_columns.size(); idx++ )
- is_active[ global_columns[ idx ] ] = true;
- _get_active_columns( boundary_matrix, lowest_one_lookup, column_type, global_columns, is_active );
-
- // Phase 2+3: Simplify columns and reduce them
- for( dimension cur_dim = max_dim; cur_dim >= 1; cur_dim-- ) {
- // Phase 2: Simplify columns
- std::vector< index > temp_col;
- #pragma omp parallel for schedule( guided, 1 ), private( temp_col )
- for( index idx = 0; idx < (index)global_columns.size(); idx++ )
- if( boundary_matrix.get_dim( global_columns[ idx ] ) == cur_dim )
- _global_column_simplification( global_columns[ idx ], boundary_matrix, lowest_one_lookup, column_type, is_active, temp_col );
- boundary_matrix.sync();
-
- // Phase 3: Reduce columns
- for( index idx = 0; idx < (index)global_columns.size(); idx++ ) {
- index cur_col = global_columns[ idx ];
- if( boundary_matrix.get_dim( cur_col ) == cur_dim && column_type[ cur_col ] == GLOBAL ) {
- index lowest_one = boundary_matrix.get_max_index( cur_col );
- while( lowest_one != -1 && lowest_one_lookup[ lowest_one ] != -1 ) {
- boundary_matrix.add_to( lowest_one_lookup[ lowest_one ], cur_col );
- lowest_one = boundary_matrix.get_max_index( cur_col );
- }
- if( lowest_one != -1 ) {
- lowest_one_lookup[ lowest_one ] = cur_col;
- boundary_matrix.clear( lowest_one );
- }
- boundary_matrix.finalize( cur_col );
- }
- }
- }
-
- boundary_matrix.sync();
- }
-
- protected:
- template< typename Representation >
- void _local_chunk_reduction( boundary_matrix< Representation >& boundary_matrix
- , std::vector<index>& lowest_one_lookup
- , std::vector< column_type >& column_type
- , const dimension cur_dim
- , const index chunk_begin
- , const index chunk_end
- , const index row_begin ) {
-
- for( index cur_col = chunk_begin; cur_col < chunk_end; cur_col++ ) {
- if( column_type[ cur_col ] == GLOBAL && boundary_matrix.get_dim( cur_col ) == cur_dim ) {
- index lowest_one = boundary_matrix.get_max_index( cur_col );
- while( lowest_one != -1 && lowest_one >= row_begin && lowest_one_lookup[ lowest_one ] != -1 ) {
- boundary_matrix.add_to( lowest_one_lookup[ lowest_one ], cur_col );
- lowest_one = boundary_matrix.get_max_index( cur_col );
- }
- if( lowest_one >= row_begin ) {
- lowest_one_lookup[ lowest_one ] = cur_col;
- column_type[ cur_col ] = LOCAL_NEGATIVE;
- column_type[ lowest_one ] = LOCAL_POSITIVE;
- boundary_matrix.clear( lowest_one );
- boundary_matrix.finalize( cur_col );
- }
- }
- }
- }
-
- template< typename Representation >
- void _get_active_columns( const boundary_matrix< Representation >& boundary_matrix
- , const std::vector< index >& lowest_one_lookup
- , const std::vector< column_type >& column_type
- , const std::vector< index >& global_columns
- , std::vector< char >& is_active ) {
-
- const index nr_columns = boundary_matrix.get_num_cols();
- std::vector< char > finished( nr_columns, false );
-
- std::vector< std::pair < index, index > > stack;
- std::vector< index > cur_col_values;
- #pragma omp parallel for schedule( guided, 1 ), private( stack, cur_col_values )
- for( index idx = 0; idx < (index)global_columns.size(); idx++ ) {
- bool pop_next = false;
- index start_col = global_columns[ idx ];
- stack.push_back( std::pair< index, index >( start_col, -1 ) );
- while( !stack.empty() ) {
- index cur_col = stack.back().first;
- index prev_col = stack.back().second;
- if( pop_next ) {
- stack.pop_back();
- pop_next = false;
- if( prev_col != -1 ) {
- if( is_active[ cur_col ] ) {
- is_active[ prev_col ] = true;
- }
- if( prev_col == stack.back().first ) {
- finished[ prev_col ] = true;
- pop_next = true;
- }
- }
- } else {
- pop_next = true;
- boundary_matrix.get_col( cur_col, cur_col_values );
- for( index idx = 0; idx < (index) cur_col_values.size(); idx++ ) {
- index cur_row = cur_col_values[ idx ];
- if( ( column_type[ cur_row ] == GLOBAL ) ) {
- is_active[ cur_col ] = true;
- } else if( column_type[ cur_row ] == LOCAL_POSITIVE ) {
- index next_col = lowest_one_lookup[ cur_row ];
- if( next_col != cur_col && !finished[ cur_col ] ) {
- stack.push_back( std::make_pair( next_col, cur_col ) );
- pop_next = false;
- }
- }
- }
- }
- }
- }
- }
-
- template< typename Representation >
- void _global_column_simplification( const index col_idx
- , boundary_matrix< Representation >& boundary_matrix
- , const std::vector< index >& lowest_one_lookup
- , const std::vector< column_type >& column_type
- , const std::vector< char >& is_active
- , std::vector< index >& temp_col )
- {
- temp_col.clear();
- while( !boundary_matrix.is_empty( col_idx ) ) {
- index cur_row = boundary_matrix.get_max_index( col_idx );
- switch( column_type[ cur_row ] ) {
- case GLOBAL:
- temp_col.push_back( cur_row );
- boundary_matrix.remove_max( col_idx );
- break;
- case LOCAL_NEGATIVE:
- boundary_matrix.remove_max( col_idx );
- break;
- case LOCAL_POSITIVE:
- if( is_active[ lowest_one_lookup[ cur_row ] ] )
- boundary_matrix.add_to( lowest_one_lookup[ cur_row ], col_idx );
- else
- boundary_matrix.remove_max( col_idx );
- break;
- }
- }
- std::reverse( temp_col.begin(), temp_col.end() );
- boundary_matrix.set_col( col_idx, temp_col );
- }
- };
-}
diff --git a/matching/include/phat/algorithms/row_reduction.h b/matching/include/phat/algorithms/row_reduction.h deleted file mode 100644 index cdd1a8f..0000000 --- a/matching/include/phat/algorithms/row_reduction.h +++ /dev/null @@ -1,56 +0,0 @@ -/* 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/boundary_matrix.h>
-
-namespace phat {
- class row_reduction {
- public:
- template< typename Representation >
- void operator() ( boundary_matrix< Representation >& boundary_matrix ) {
-
- const index nr_columns = boundary_matrix.get_num_cols();
- std::vector< std::vector< index > > lowest_one_lookup( nr_columns );
-
- for( index cur_col = nr_columns - 1; cur_col >= 0; cur_col-- ) {
- if( !boundary_matrix.is_empty( cur_col ) )
- lowest_one_lookup[ boundary_matrix.get_max_index( cur_col ) ].push_back( cur_col );
-
- if( !lowest_one_lookup[ cur_col ].empty() ) {
- boundary_matrix.clear( cur_col );
- boundary_matrix.finalize( cur_col );
- std::vector< index >& cols_with_cur_lowest = lowest_one_lookup[ cur_col ];
- index source = *min_element( cols_with_cur_lowest.begin(), cols_with_cur_lowest.end() );
- for( index idx = 0; idx < (index)cols_with_cur_lowest.size(); idx++ ) {
- index target = cols_with_cur_lowest[ idx ];
- if( target != source && !boundary_matrix.is_empty( target ) ) {
- boundary_matrix.add_to( source, target );
- if( !boundary_matrix.is_empty( target ) ) {
- index lowest_one_of_target = boundary_matrix.get_max_index( target );
- lowest_one_lookup[ lowest_one_of_target ].push_back( target );
- }
- }
- }
- }
- }
- }
- };
-}
\ No newline at end of file diff --git a/matching/include/phat/algorithms/spectral_sequence_reduction.h b/matching/include/phat/algorithms/spectral_sequence_reduction.h deleted file mode 100644 index bf442e6..0000000 --- a/matching/include/phat/algorithms/spectral_sequence_reduction.h +++ /dev/null @@ -1,80 +0,0 @@ -/* Copyright 2013 IST Austria
- Contributed by: 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/boundary_matrix.h>
-
-namespace phat {
- class spectral_sequence_reduction {
- public:
- template< typename Representation >
- void operator () ( boundary_matrix< Representation >& boundary_matrix ) {
-
- const index nr_columns = boundary_matrix.get_num_cols();
- std::vector< index > lowest_one_lookup( nr_columns, -1 );
-
- //const index num_stripes = (index) sqrt( (double)nr_columns );
- const index num_stripes = omp_get_max_threads();
-
- index block_size = ( nr_columns % num_stripes == 0 ) ? nr_columns / num_stripes : block_size = nr_columns / num_stripes + 1;
-
- std::vector< std::vector< index > > unreduced_cols_cur_pass( num_stripes );
- std::vector< std::vector< index > > unreduced_cols_next_pass( num_stripes );
-
- for( index cur_dim = boundary_matrix.get_max_dim(); cur_dim >= 1 ; cur_dim-- ) {
- #pragma omp parallel for schedule( guided, 1 )
- for( index cur_stripe = 0; cur_stripe < num_stripes; cur_stripe++ ) {
- index col_begin = cur_stripe * block_size;
- index col_end = std::min( (cur_stripe+1) * block_size, nr_columns );
- for( index cur_col = col_begin; cur_col < col_end; cur_col++ )
- if( boundary_matrix.get_dim( cur_col ) == cur_dim && boundary_matrix.get_max_index( cur_col ) != -1 )
- unreduced_cols_cur_pass[ cur_stripe ].push_back( cur_col );
- }
- for( index cur_pass = 0; cur_pass < num_stripes; cur_pass++ ) {
- boundary_matrix.sync();
- #pragma omp parallel for schedule( guided, 1 )
- for( int cur_stripe = 0; cur_stripe < num_stripes; cur_stripe++ ) {
- index row_begin = (cur_stripe - cur_pass) * block_size;
- index row_end = row_begin + block_size;
- unreduced_cols_next_pass[ cur_stripe ].clear();
- for( index idx = 0; idx < (index)unreduced_cols_cur_pass[ cur_stripe ].size(); idx++ ) {
- index cur_col = unreduced_cols_cur_pass[ cur_stripe ][ idx ];
- index lowest_one = boundary_matrix.get_max_index( cur_col );
- while( lowest_one != -1 && lowest_one >= row_begin && lowest_one < row_end && lowest_one_lookup[ lowest_one ] != -1 ) {
- boundary_matrix.add_to( lowest_one_lookup[ lowest_one ], cur_col );
- lowest_one = boundary_matrix.get_max_index( cur_col );
- }
- if( lowest_one != -1 ) {
- if( lowest_one >= row_begin && lowest_one < row_end ) {
- lowest_one_lookup[ lowest_one ] = cur_col;
- boundary_matrix.clear( lowest_one );
- boundary_matrix.finalize( cur_col );
- } else {
- unreduced_cols_next_pass[ cur_stripe ].push_back( cur_col );
- }
- }
- }
- unreduced_cols_next_pass[ cur_stripe ].swap( unreduced_cols_cur_pass[ cur_stripe ] );
- }
- }
- }
- }
- };
-}
diff --git a/matching/include/phat/algorithms/standard_reduction.h b/matching/include/phat/algorithms/standard_reduction.h deleted file mode 100644 index e490a5e..0000000 --- a/matching/include/phat/algorithms/standard_reduction.h +++ /dev/null @@ -1,47 +0,0 @@ -/* 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/boundary_matrix.h>
-
-namespace phat {
- class standard_reduction {
- public:
- template< typename Representation >
- void operator() ( boundary_matrix< Representation >& boundary_matrix ) {
-
- const index nr_columns = boundary_matrix.get_num_cols();
- std::vector< index > lowest_one_lookup( nr_columns, -1 );
-
- for( index cur_col = 0; cur_col < nr_columns; cur_col++ ) {
- index lowest_one = boundary_matrix.get_max_index( cur_col );
- while( lowest_one != -1 && lowest_one_lookup[ lowest_one ] != -1 ) {
- boundary_matrix.add_to( lowest_one_lookup[ lowest_one ], cur_col );
- lowest_one = boundary_matrix.get_max_index( cur_col );
- }
- if( lowest_one != -1 ) {
- lowest_one_lookup[ lowest_one ] = cur_col;
- }
- boundary_matrix.finalize( cur_col );
- }
- }
- };
-}
-
diff --git a/matching/include/phat/algorithms/twist_reduction.h b/matching/include/phat/algorithms/twist_reduction.h deleted file mode 100644 index 2357df0..0000000 --- a/matching/include/phat/algorithms/twist_reduction.h +++ /dev/null @@ -1,51 +0,0 @@ -/* 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/boundary_matrix.h>
-
-namespace phat {
- class twist_reduction {
- public:
- template< typename Representation >
- void operator () ( boundary_matrix< Representation >& boundary_matrix ) {
-
- const index nr_columns = boundary_matrix.get_num_cols();
- std::vector< index > lowest_one_lookup( nr_columns, -1 );
-
- for( index cur_dim = boundary_matrix.get_max_dim(); cur_dim >= 1 ; cur_dim-- ) {
- for( index cur_col = 0; cur_col < nr_columns; cur_col++ ) {
- if( boundary_matrix.get_dim( cur_col ) == cur_dim ) {
- index lowest_one = boundary_matrix.get_max_index( cur_col );
- while( lowest_one != -1 && lowest_one_lookup[ lowest_one ] != -1 ) {
- boundary_matrix.add_to( lowest_one_lookup[ lowest_one ], cur_col );
- lowest_one = boundary_matrix.get_max_index( cur_col );
- }
- if( lowest_one != -1 ) {
- lowest_one_lookup[ lowest_one ] = cur_col;
- boundary_matrix.clear( lowest_one );
- }
- boundary_matrix.finalize( cur_col );
- }
- }
- }
- }
- };
-}
diff --git a/matching/include/phat/boundary_matrix.h b/matching/include/phat/boundary_matrix.h deleted file mode 100644 index 10c66cc..0000000 --- a/matching/include/phat/boundary_matrix.h +++ /dev/null @@ -1,343 +0,0 @@ -/* 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/bit_tree_pivot_column.h>
-
-// interface class for the main data structure -- implementations of the interface can be found in ./representations
-namespace phat {
- template< class Representation = bit_tree_pivot_column >
- class boundary_matrix
- {
-
- protected:
- Representation rep;
-
- // interface functions -- actual implementation and complexity depends on chosen @Representation template
- public:
- // get overall number of columns in boundary_matrix
- index get_num_cols() const { return rep._get_num_cols(); }
-
- // set overall number of columns in boundary_matrix
- void set_num_cols( index nr_of_columns ) { rep._set_num_cols( nr_of_columns ); }
-
- // get dimension of given index
- dimension get_dim( index idx ) const { return rep._get_dim( idx ); }
-
- // set dimension of given index
- void set_dim( index idx, dimension dim ) { rep._set_dim( idx, dim ); }
-
- // replaces content of @col with boundary of given index
- void get_col( index idx, column& col ) const { col.clear(); rep._get_col( idx, col ); }
-
- // set column @idx to the values contained in @col
- void set_col( index idx, const column& col ) { rep._set_col( idx, col ); }
-
- // true iff boundary of given column is empty
- bool is_empty( index idx ) const { return rep._is_empty( idx ); }
-
- // largest index of given column (new name for lowestOne()) -- NOT thread-safe
- index get_max_index( index idx ) const { return rep._get_max_index( idx ); }
-
- // removes maximal index from given column
- void remove_max( index idx ) { rep._remove_max( idx ); }
-
- // adds column @source to column @target'
- void add_to( index source, index target ) { rep._add_to( source, target ); }
-
- // clears given column
- void clear( index idx ) { rep._clear( idx ); }
-
- // finalizes given column
- void finalize( index idx ) { rep._finalize( idx ); }
-
- // syncronizes all internal data structures -- has to be called before and after any multithreaded access!
- void sync() { rep._sync(); }
-
- // info functions -- independent of chosen 'Representation'
- public:
- // maximal dimension
- dimension get_max_dim() const {
- dimension cur_max_dim = 0;
- for( index idx = 0; idx < get_num_cols(); idx++ )
- cur_max_dim = get_dim( idx ) > cur_max_dim ? get_dim( idx ) : cur_max_dim;
- return cur_max_dim;
- }
-
- // number of nonzero rows for given column @idx
- index get_num_rows( index idx ) const {
- column cur_col;
- get_col( idx, cur_col );
- return cur_col.size();
- }
-
- // maximal number of nonzero rows of all columns
- index get_max_col_entries() const {
- index max_col_entries = -1;
- const index nr_of_columns = get_num_cols();
- for( index idx = 0; idx < nr_of_columns; idx++ )
- max_col_entries = get_num_rows( idx ) > max_col_entries ? get_num_rows( idx ) : max_col_entries;
- return max_col_entries;
- }
-
- // maximal number of nonzero cols of all rows
- index get_max_row_entries() const {
- size_t max_row_entries = 0;
- const index nr_of_columns = get_num_cols();
- std::vector< std::vector< index > > transposed_matrix( nr_of_columns );
- column temp_col;
- for( index cur_col = 0; cur_col < nr_of_columns; cur_col++ ) {
- get_col( cur_col, temp_col );
- for( index idx = 0; idx < (index)temp_col.size(); idx++)
- transposed_matrix[ temp_col[ idx ] ].push_back( cur_col );
- }
- for( index idx = 0; idx < nr_of_columns; idx++ )
- max_row_entries = transposed_matrix[ idx ].size() > max_row_entries ? transposed_matrix[ idx ].size() : max_row_entries;
- return max_row_entries;
- }
-
- // overall number of entries in the matrix
- index get_num_entries() const {
- index number_of_nonzero_entries = 0;
- const index nr_of_columns = get_num_cols();
- for( index idx = 0; idx < nr_of_columns; idx++ )
- number_of_nonzero_entries += get_num_rows( idx );
- return number_of_nonzero_entries;
- }
-
- // operators / constructors
- public:
- boundary_matrix() {};
-
- template< class OtherRepresentation >
- boundary_matrix( const boundary_matrix< OtherRepresentation >& other ) {
- *this = other;
- }
-
- template< typename OtherRepresentation >
- bool operator==( const boundary_matrix< OtherRepresentation >& other_boundary_matrix ) const {
- const index number_of_columns = this->get_num_cols();
-
- if( number_of_columns != other_boundary_matrix.get_num_cols() )
- return false;
-
- column temp_col;
- column other_temp_col;
- for( index idx = 0; idx < number_of_columns; idx++ ) {
- this->get_col( idx, temp_col );
- other_boundary_matrix.get_col( idx, other_temp_col );
- if( temp_col != other_temp_col || this->get_dim( idx ) != other_boundary_matrix.get_dim( idx ) )
- return false;
- }
- return true;
- }
-
- template< typename OtherRepresentation >
- bool operator!=( const boundary_matrix< OtherRepresentation >& other_boundary_matrix ) const {
- return !( *this == other_boundary_matrix );
- }
-
- template< typename OtherRepresentation >
- boundary_matrix< Representation >& operator=( const boundary_matrix< OtherRepresentation >& other )
- {
- const index nr_of_columns = other.get_num_cols();
- this->set_num_cols( nr_of_columns );
- column temp_col;
- for( index cur_col = 0; cur_col < nr_of_columns; cur_col++ ) {
- this->set_dim( cur_col, other.get_dim( cur_col ) );
- other.get_col( cur_col, temp_col );
- this->set_col( cur_col, temp_col );
- }
-
- // by convention, always return *this
- return *this;
- }
-
- // I/O -- independent of chosen 'Representation'
- public:
-
- // initializes boundary_matrix from (vector<vector>, vector) pair -- untested
- template< typename index_type, typename dimemsion_type >
- void load_vector_vector( const std::vector< std::vector< index_type > >& input_matrix, const std::vector< dimemsion_type >& input_dims ) {
- const index nr_of_columns = (index)input_matrix.size();
- this->set_num_cols( nr_of_columns );
- column temp_col;
- #pragma omp parallel for private( temp_col )
- for( index cur_col = 0; cur_col < nr_of_columns; cur_col++ ) {
- this->set_dim( cur_col, (dimension)input_dims[ cur_col ] );
-
- index num_rows = input_matrix[ cur_col ].size();
- temp_col.resize( num_rows );
- for( index cur_row = 0; cur_row < num_rows; cur_row++ )
- temp_col[ cur_row ] = (index)input_matrix[ cur_col ][ cur_row ];
- this->set_col( cur_col, temp_col );
- }
- }
-
- template< typename index_type, typename dimemsion_type >
- void save_vector_vector( std::vector< std::vector< index_type > >& output_matrix, std::vector< dimemsion_type >& output_dims ) {
- const index nr_of_columns = get_num_cols();
- output_matrix.resize( nr_of_columns );
- output_dims.resize( nr_of_columns );
- column temp_col;
- for( index cur_col = 0; cur_col < nr_of_columns; cur_col++ ) {
- output_dims[ cur_col ] = (dimemsion_type)get_dim( cur_col );
- get_col( cur_col, temp_col );
- index num_rows = temp_col.size();
- output_matrix[ cur_col ].clear();
- output_matrix[ cur_col ].resize( num_rows );
- for( index cur_row = 0; cur_row < num_rows; cur_row++ )
- output_matrix[ cur_col ][ cur_row ] = (index_type)temp_col[ cur_row ];
- }
- }
-
-
- // Loads the boundary_matrix from given file in ascii format
- // Format: each line represents a column, first number is dimension, other numbers are the content of the column.
- // Ignores empty lines and lines starting with a '#'.
- bool load_ascii( std::string filename ) {
- // first count number of columns:
- std::string cur_line;
- std::ifstream dummy( filename .c_str() );
- if( dummy.fail() )
- return false;
-
- index number_of_columns = 0;
- while( getline( dummy, cur_line ) ) {
- cur_line.erase(cur_line.find_last_not_of(" \t\n\r\f\v") + 1);
- if( cur_line != "" && cur_line[ 0 ] != '#' )
- number_of_columns++;
-
- }
- this->set_num_cols( number_of_columns );
- dummy.close();
-
- std::ifstream input_stream( filename.c_str() );
- if( input_stream.fail() )
- return false;
-
- column temp_col;
- index cur_col = -1;
- while( getline( input_stream, cur_line ) ) {
- cur_line.erase(cur_line.find_last_not_of(" \t\n\r\f\v") + 1);
- if( cur_line != "" && cur_line[ 0 ] != '#' ) {
- cur_col++;
- std::stringstream ss( cur_line );
-
- int64_t temp_dim;
- ss >> temp_dim;
- this->set_dim( cur_col, (dimension) temp_dim );
-
- int64_t temp_index;
- temp_col.clear();
- while( ss.good() ) {
- ss >> temp_index;
- temp_col.push_back( (index)temp_index );
- }
- std::sort( temp_col.begin(), temp_col.end() );
- this->set_col( cur_col, temp_col );
- }
- }
-
- input_stream.close();
- return true;
- }
-
- // Saves the boundary_matrix to given file in ascii format
- // Format: each line represents a column, first number is dimension, other numbers are the content of the column
- bool save_ascii( std::string filename ) {
- std::ofstream output_stream( filename.c_str() );
- if( output_stream.fail() )
- return false;
-
- const index nr_columns = this->get_num_cols();
- column tempCol;
- for( index cur_col = 0; cur_col < nr_columns; cur_col++ ) {
- output_stream << (int64_t)this->get_dim( cur_col );
- this->get_col( cur_col, tempCol );
- for( index cur_row_idx = 0; cur_row_idx < (index)tempCol.size(); cur_row_idx++ )
- output_stream << " " << tempCol[ cur_row_idx ];
- output_stream << std::endl;
- }
-
- output_stream.close();
- return true;
- }
-
- // Loads boundary_matrix from given file
- // Format: nr_columns % dim1 % N1 % row1 row2 % ...% rowN1 % dim2 % N2 % ...
- bool load_binary( std::string filename )
- {
- std::ifstream input_stream( filename.c_str( ), std::ios_base::binary | std::ios_base::in );
- if( input_stream.fail( ) )
- return false;
-
- int64_t nr_columns;
- input_stream.read( (char*)&nr_columns, sizeof( int64_t ) );
- this->set_num_cols( (index)nr_columns );
-
- column temp_col;
- for( index cur_col = 0; cur_col < nr_columns; cur_col++ ) {
- int64_t cur_dim;
- input_stream.read( (char*)&cur_dim, sizeof( int64_t ) );
- this->set_dim( cur_col, (dimension)cur_dim );
- int64_t nr_rows;
- input_stream.read( (char*)&nr_rows, sizeof( int64_t ) );
- temp_col.resize( ( std::size_t )nr_rows );
- for( index idx = 0; idx < nr_rows; idx++ ) {
- int64_t cur_row;
- input_stream.read( (char*)&cur_row, sizeof( int64_t ) );
- temp_col[ idx ] = (index)cur_row;
- }
- this->set_col( cur_col, temp_col );
- }
-
- input_stream.close( );
- return true;
- }
-
- // Saves the boundary_matrix to given file in binary format
- // Format: nr_columns % dim1 % N1 % row1 row2 % ...% rowN1 % dim2 % N2 % ...
- bool save_binary( std::string filename )
- {
- std::ofstream output_stream( filename.c_str( ), std::ios_base::binary | std::ios_base::out );
- if( output_stream.fail( ) )
- return false;
-
- const int64_t nr_columns = this->get_num_cols( );
- output_stream.write( (char*)&nr_columns, sizeof( int64_t ) );
- column tempCol;
- for( index cur_col = 0; cur_col < nr_columns; cur_col++ ) {
- int64_t cur_dim = this->get_dim( cur_col );
- output_stream.write( (char*)&cur_dim, sizeof( int64_t ) );
- this->get_col( cur_col, tempCol );
- int64_t cur_nr_rows = tempCol.size( );
- output_stream.write( (char*)&cur_nr_rows, sizeof( int64_t ) );
- for( index cur_row_idx = 0; cur_row_idx < (index)tempCol.size( ); cur_row_idx++ ) {
- int64_t cur_row = tempCol[ cur_row_idx ];
- output_stream.write( (char*)&cur_row, sizeof( int64_t ) );
- }
- }
-
- output_stream.close( );
- return true;
- }
- };
-}
diff --git a/matching/include/phat/compute_persistence_pairs.h b/matching/include/phat/compute_persistence_pairs.h deleted file mode 100644 index 06f5372..0000000 --- a/matching/include/phat/compute_persistence_pairs.h +++ /dev/null @@ -1,137 +0,0 @@ -/* 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/persistence_pairs.h> -#include <phat/boundary_matrix.h> -#include <phat/helpers/dualize.h> -#include <phat/algorithms/twist_reduction.h> - -namespace phat { - // Extracts persistence pairs in separate dimensions from a reduced - // boundary matrix representing ``double`` filtration. The pairs - // give persistent relative homology of the pair of filtrations. - // TODO: Use it with standard reduction algorithm (no template option). - template< typename ReductionAlgorithm, typename Representation > - void compute_relative_persistence_pairs(std::vector<persistence_pairs>& pairs, boundary_matrix<Representation>& boundary_matrix, const std::map<int, int>& L) { - ReductionAlgorithm reduce; - reduce(boundary_matrix); - std::map<int, bool> free; - std::map<int, int> invL; - for (std::map<int, int>::const_iterator it = L.begin(); it != L.end(); ++it) { invL[it->second] = it->first; } - for (std::vector<persistence_pairs>::iterator it = pairs.begin(); it != pairs.end(); ++it) { it->clear(); } - for (index idx = 0; idx < boundary_matrix.get_num_cols(); ++idx) { - int dimension = boundary_matrix.get_dim(idx); - if (L.find(idx) != L.end()) { ++dimension; } - free[idx] = true; - if (!boundary_matrix.is_empty(idx)) { - index birth = boundary_matrix.get_max_index(idx); - index death = idx; - pairs[dimension-1].append_pair(birth, death); - free[birth] = false; - free[death] = false; - } else { - // This is an L-simplex and a (dimension+1)-dimensional cycle - if (L.find(idx) != L.end()) { - assert(dimension < pairs.size()); - pairs[dimension].append_pair(idx, -1); - } - } - } - for (std::map<int, bool>::iterator it = free.begin(); it != free.end(); ++it) { - if (it->second) { - int dimension = boundary_matrix.get_dim(it->first); - if (invL.find(it->first) == invL.end() && L.find(it->first) == L.end()) { - assert(dimension < pairs.size()); - pairs[dimension].append_pair(it->first, -1); - } - } - } - } - - // Extracts persistence pairs in separate dimensions; expects a d-dimensional vector of persistent_pairs - template< typename ReductionAlgorithm, typename Representation > - void compute_persistence_pairs(std::vector<persistence_pairs>& pairs, boundary_matrix<Representation>& boundary_matrix) { - ReductionAlgorithm reduce; - reduce(boundary_matrix); - std::map<int, bool> free; - for (std::vector<persistence_pairs>::iterator it = pairs.begin(); it != pairs.end(); ++it) { it->clear(); } - for (index idx = 0; idx < boundary_matrix.get_num_cols(); ++idx) { - int dimension = boundary_matrix.get_dim(idx); - free[idx] = true; - if (!boundary_matrix.is_empty(idx)) { - index birth = boundary_matrix.get_max_index(idx); - index death = idx; - pairs[dimension-1].append_pair(birth, death); - // Cannot be of the form (a, infinity) - free[birth] = false; - free[death] = false; - } - } - for (std::map<int, bool>::iterator it = free.begin(); it != free.end(); ++it) { - if (it->second) { - int dimension = boundary_matrix.get_dim(it->first); - pairs[dimension].append_pair(it->first, -1); - } - } - } - - template< typename ReductionAlgorithm, typename Representation > - void compute_persistence_pairs( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) { - ReductionAlgorithm reduce; - reduce( boundary_matrix ); - pairs.clear(); - std::set<index> max_indices; - // finite pairs - for( index idx = 0; idx < boundary_matrix.get_num_cols(); idx++ ) { - if( !boundary_matrix.is_empty( idx ) ) { - index birth = boundary_matrix.get_max_index( idx ); - max_indices.insert(birth); - index death = idx; - pairs.append_pair( birth, death ); - } - } - // infinite pairs: column idx is 0, and row idx does not contain a lowest one - for( index idx = 0; idx < boundary_matrix.get_num_cols(); idx++ ) { - if(boundary_matrix.is_empty(idx) && max_indices.count(idx) == 0 ) { - pairs.append_pair( idx, k_infinity_index); - } - } - } - - template< typename ReductionAlgorithm, typename Representation > - void compute_persistence_pairs_dualized( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) { - - dualize( boundary_matrix ); - compute_persistence_pairs< ReductionAlgorithm >( pairs, boundary_matrix ); - dualize_persistence_pairs( pairs, boundary_matrix.get_num_cols() ); - } - - template< typename Representation > - void compute_persistence_pairs( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) { - phat::compute_persistence_pairs< twist_reduction >( pairs, boundary_matrix ); - } - - - template< typename Representation > - void compute_persistence_pairs_dualized( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) { - compute_persistence_pairs_dualized< twist_reduction >( pairs, boundary_matrix ); - } - -} diff --git a/matching/include/phat/helpers/dualize.h b/matching/include/phat/helpers/dualize.h deleted file mode 100644 index 5731408..0000000 --- a/matching/include/phat/helpers/dualize.h +++ /dev/null @@ -1,74 +0,0 @@ -/* 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/boundary_matrix.h>
-#include <phat/persistence_pairs.h>
-
-
-namespace phat {
- template< typename Representation >
- void dualize( boundary_matrix< Representation >& boundary_matrix ) {
-
- std::vector< dimension > dual_dims;
- std::vector< std::vector< index > > dual_matrix;
-
- index nr_of_columns = boundary_matrix.get_num_cols();
- dual_matrix.resize( nr_of_columns );
- dual_dims.resize( nr_of_columns );
-
- std::vector< index > dual_sizes( nr_of_columns, 0 );
-
- column temp_col;
- for( index cur_col = 0; cur_col < nr_of_columns; cur_col++ ) {
- boundary_matrix.get_col( cur_col, temp_col );
- for( index idx = 0; idx < (index)temp_col.size(); idx++)
- dual_sizes[ nr_of_columns - 1 - temp_col[ idx ] ]++;
- }
-
- #pragma omp parallel for
- for( index cur_col = 0; cur_col < nr_of_columns; cur_col++ )
- dual_matrix[cur_col].reserve(dual_sizes[cur_col]);
-
- for( index cur_col = 0; cur_col < nr_of_columns; cur_col++ ) {
- boundary_matrix.get_col( cur_col, temp_col );
- for( index idx = 0; idx < (index)temp_col.size(); idx++)
- dual_matrix[ nr_of_columns - 1 - temp_col[ idx ] ].push_back( nr_of_columns - 1 - cur_col );
- }
-
- const dimension max_dim = boundary_matrix.get_max_dim();
- #pragma omp parallel for
- for( index cur_col = 0; cur_col < nr_of_columns; cur_col++ )
- dual_dims[ nr_of_columns - 1 - cur_col ] = max_dim - boundary_matrix.get_dim( cur_col );
-
- #pragma omp parallel for
- for( index cur_col = 0; cur_col < nr_of_columns; cur_col++ )
- std::reverse( dual_matrix[ cur_col ].begin(), dual_matrix[ cur_col ].end() );
-
- boundary_matrix.load_vector_vector( dual_matrix, dual_dims );
- }
-
- inline 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/matching/include/phat/helpers/misc.h b/matching/include/phat/helpers/misc.h deleted file mode 100644 index 5a5c682..0000000 --- a/matching/include/phat/helpers/misc.h +++ /dev/null @@ -1,78 +0,0 @@ -/* 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
-
-// STL includes
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <vector>
-#include <set>
-#include <list>
-#include <map>
-#include <algorithm>
-#include <queue>
-#include <cassert>
-#include <sstream>
-#include <algorithm>
-#include <iomanip>
-#include <cmath>
-#include <cstdlib>
-#include <iterator>
-#include <limits>
-
-// VS2008 and below unfortunately do not support stdint.h
-#if defined(_MSC_VER)&& _MSC_VER < 1600
- typedef __int8 int8_t;
- typedef unsigned __int8 uint8_t;
- typedef __int16 int16_t;
- typedef unsigned __int16 uint16_t;
- typedef __int32 int32_t;
- typedef unsigned __int32 uint32_t;
- typedef __int64 int64_t;
- typedef unsigned __int64 uint64_t;
-#else
- #include <stdint.h>
-#endif
-
-// basic types. index can be changed to int32_t to save memory on small instances
-namespace phat {
- typedef int64_t index;
- typedef int8_t dimension;
- typedef std::vector< index > column;
-
- constexpr index k_infinity_index = std::numeric_limits<index>::max();
-}
-
-// OpenMP (proxy) functions
-#if defined _OPENMP
- #include <omp.h>
-#else
- #define omp_get_thread_num() 0
- #define omp_get_max_threads() 1
- #define omp_get_num_threads() 1
- inline void omp_set_num_threads( int ) {};
- #include <time.h>
- #define omp_get_wtime() (float)clock() / (float)CLOCKS_PER_SEC
-#endif
-
-#include <phat/helpers/thread_local_storage.h>
-
-
-
diff --git a/matching/include/phat/helpers/thread_local_storage.h b/matching/include/phat/helpers/thread_local_storage.h deleted file mode 100644 index d0b5332..0000000 --- a/matching/include/phat/helpers/thread_local_storage.h +++ /dev/null @@ -1,52 +0,0 @@ -/* 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>
-
-// should ideally be equal to the cache line size of the CPU
-#define PHAT_TLS_SPACING_FACTOR 64
-
-// ThreadLocalStorage with some spacing to avoid "false sharing" (see wikipedia)
-template< typename T >
-class thread_local_storage
-{
-public:
-
- thread_local_storage() : per_thread_storage( omp_get_max_threads() * PHAT_TLS_SPACING_FACTOR ) {};
-
- T& operator()() {
- return per_thread_storage[ omp_get_thread_num() * PHAT_TLS_SPACING_FACTOR ];
- }
-
- const T& operator()() const {
- return per_thread_storage[ omp_get_thread_num() * PHAT_TLS_SPACING_FACTOR ];
- }
-
- T& operator[]( int tid ) {
- return per_thread_storage[ tid * PHAT_TLS_SPACING_FACTOR ];
- }
-
- const T& operator[]( int tid ) const {
- return per_thread_storage[ tid * PHAT_TLS_SPACING_FACTOR ];
- }
-
-protected:
- std::vector< T > per_thread_storage;
-};
diff --git a/matching/include/phat/persistence_pairs.h b/matching/include/phat/persistence_pairs.h deleted file mode 100644 index eafc638..0000000 --- a/matching/include/phat/persistence_pairs.h +++ /dev/null @@ -1,155 +0,0 @@ -/* 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>
-
-namespace phat {
- class persistence_pairs {
-
- protected:
- std::vector< std::pair< index, index > > pairs;
-
- public:
- index get_num_pairs() const {
- return (index)pairs.size();
- }
-
- void append_pair( index birth, index death ) {
- pairs.push_back( std::make_pair( birth, death ) );
- }
-
- std::pair< index, index > get_pair( index idx ) const {
- return pairs[ idx ];
- }
-
- void set_pair( index idx, index birth, index death ) {
- pairs[ idx ] = std::make_pair( birth, death );
- }
-
- void clear() {
- pairs.clear();
- }
-
- void sort() {
- std::sort( pairs.begin(), pairs.end() );
- }
-
- // Loads the persistence pairs from given file in asci format
- // Format: nr_pairs % newline % birth1 % death1 % newline % birth2 % death2 % newline ...
- bool load_ascii( std::string filename ) {
- std::ifstream input_stream( filename.c_str() );
- if( input_stream.fail() )
- return false;
-
- int64_t nr_pairs;
- input_stream >> nr_pairs;
- pairs.clear();
- for( index idx = 0; idx < nr_pairs; idx++ ) {
- int64_t birth;
- input_stream >> birth;
- int64_t death;
- input_stream >> death;
- append_pair( (index)birth, (index)death );
- }
-
- input_stream.close();
- return true;
- }
-
- // Saves the persistence pairs to given file in binary format
- // Format: nr_pairs % newline % birth1 % death1 % newline % birth2 % death2 % newline ...
- bool save_ascii( std::string filename ) {
- std::ofstream output_stream( filename.c_str() );
- if( output_stream.fail() )
- return false;
-
- this->sort();
- output_stream << get_num_pairs() << std::endl;
- for( std::size_t idx = 0; idx < pairs.size(); idx++ ) {
- output_stream << pairs[idx].first << " " << pairs[idx].second << std::endl;
- }
-
- output_stream.close();
- return true;
- }
-
- // Loads the persistence pairs from given file in binary format
- // Format: nr_pairs % birth1 % death1 % birth2 % death2 ...
- bool load_binary( std::string filename ) {
- std::ifstream input_stream( filename.c_str(), std::ios_base::binary | std::ios_base::in );
- if( input_stream.fail() )
- return false;
-
- int64_t nr_pairs;
- input_stream.read( (char*)&nr_pairs, sizeof( int64_t ) );
- for( index idx = 0; idx < nr_pairs; idx++ ) {
- int64_t birth;
- input_stream.read( (char*)&birth, sizeof( int64_t ) );
- int64_t death;
- input_stream.read( (char*)&death, sizeof( int64_t ) );
- append_pair( (index)birth, (index)death );
- }
-
- input_stream.close();
- return true;
- }
-
- // Saves the persistence pairs to given file in binary format
- // Format: nr_pairs % birth1 % death1 % birth2 % death2 ...
- bool save_binary( std::string filename ) {
- std::ofstream output_stream( filename.c_str(), std::ios_base::binary | std::ios_base::out );
- if( output_stream.fail() )
- return false;
-
- this->sort();
- int64_t nr_pairs = get_num_pairs();
- output_stream.write( (char*)&nr_pairs, sizeof( int64_t ) );
- for( std::size_t idx = 0; idx < pairs.size(); idx++ ) {
- int64_t birth = pairs[ idx ].first;
- output_stream.write( (char*)&birth, sizeof( int64_t ) );
- int64_t death = pairs[ idx ].second;
- output_stream.write( (char*)&death, sizeof( int64_t ) );
- }
-
- output_stream.close();
- return true;
- }
-
- bool operator==( persistence_pairs& other_pairs ) {
- this->sort();
- other_pairs.sort();
- if( pairs.size() != (std::size_t)other_pairs.get_num_pairs() )
- return false;
-
- for( index idx = 0; idx < (index)pairs.size(); idx++ )
- if( get_pair( idx ) != other_pairs.get_pair( idx ) )
- return false;
-
- return true;
- }
-
- bool operator!=( persistence_pairs& other_pairs ) {
- return !( *this == other_pairs );
- }
- };
-
-
-
-}
diff --git a/matching/include/phat/representations/abstract_pivot_column.h b/matching/include/phat/representations/abstract_pivot_column.h deleted file mode 100644 index e16d7a5..0000000 --- a/matching/include/phat/representations/abstract_pivot_column.h +++ /dev/null @@ -1,102 +0,0 @@ -/* 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/vector_vector.h>
-
-namespace phat {
-
- // Note: We could even make the rep generic in the underlying Const representation
- // But I cannot imagine that anything else than vector<vector<index>> would
- // make sense
- template< typename PivotColumn >
- class abstract_pivot_column : public vector_vector {
-
- protected:
- typedef vector_vector Base;
- typedef PivotColumn pivot_col;
-
- // For parallization purposes, it could be more than one full column
- mutable thread_local_storage< pivot_col > pivot_cols;
- mutable thread_local_storage< index > idx_of_pivot_cols;
-
- pivot_col& get_pivot_col() const {
- return pivot_cols();
- }
-
- bool is_pivot_col( index idx ) const {
- return idx_of_pivot_cols() == idx;
- }
-
- void release_pivot_col() {
- index idx = idx_of_pivot_cols();
- if( idx != -1 ) {
- this->matrix[ idx ].clear();
- pivot_cols().get_col_and_clear( this->matrix[ idx ] );
- }
- idx_of_pivot_cols() = -1;
- }
-
- void make_pivot_col( index idx ) {
- release_pivot_col();
- idx_of_pivot_cols() = idx;
- get_pivot_col().add_col( matrix[ idx ] );
- }
-
- public:
-
- void _set_num_cols( index nr_of_cols ) {
- #pragma omp parallel for
- for( int tid = 0; tid < omp_get_num_threads(); tid++ ) {
- pivot_cols[ tid ].init( nr_of_cols );
- idx_of_pivot_cols[ tid ] = -1;
- }
- Base::_set_num_cols( nr_of_cols );
- }
-
- void _add_to( index source, index target ) {
- if( !is_pivot_col( target ) )
- make_pivot_col( target );
- get_pivot_col().add_col( matrix[source] );
- }
-
- void _sync() {
- #pragma omp parallel for
- for( int tid = 0; tid < omp_get_num_threads(); tid++ )
- release_pivot_col();
- }
-
- void _get_col( index idx, column& col ) const { is_pivot_col( idx ) ? get_pivot_col().get_col( col ) : Base::_get_col( idx, col ); }
-
- bool _is_empty( index idx ) const { return is_pivot_col( idx ) ? get_pivot_col().is_empty() : Base::_is_empty( idx ); }
-
- index _get_max_index( index idx ) const { return is_pivot_col( idx ) ? get_pivot_col().get_max_index() : Base::_get_max_index( idx ); }
-
- void _clear( index idx ) { is_pivot_col( idx ) ? get_pivot_col().clear() : Base::_clear( idx ); }
-
- void _set_col( index idx, const column& col ) { is_pivot_col( idx ) ? get_pivot_col().set_col( col ) : Base::_set_col( idx, col ); }
-
- void _remove_max( index idx ) { is_pivot_col( idx ) ? get_pivot_col().remove_max() : Base::_remove_max( idx ); }
-
- void finalize( index idx ) { Base::_finalize( idx ); }
- };
-}
-
-
diff --git a/matching/include/phat/representations/bit_tree_pivot_column.h b/matching/include/phat/representations/bit_tree_pivot_column.h deleted file mode 100644 index 4d48e88..0000000 --- a/matching/include/phat/representations/bit_tree_pivot_column.h +++ /dev/null @@ -1,165 +0,0 @@ -/* Copyright 2013 IST Austria
- Contributed by: Hubert Wagner
-
- 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 {
-
- // This is a bitset indexed with a 64-ary tree. Each node in the index
- // has 64 bits; i-th bit says that the i-th subtree is non-empty.
- // Supports practically O(1), inplace, zero-allocation: insert, remove, max_element
- // and clear in O(number of ones in the bitset).
- // 'add_index' is still the real bottleneck in practice.
- class bit_tree_column
- {
- protected:
-
- size_t offset; // data[i + offset] = ith block of the data-bitset
- typedef uint64_t block_type;
- std::vector< block_type > data;
-
-
- size_t debrujin_magic_table[ 64 ];
-
- enum { block_size_in_bits = 64 };
- enum { block_shift = 6 };
-
- // Some magic: http://graphics.stanford.edu/~seander/bithacks.html
- // Gets the position of the rightmost bit of 'x'. 0 means the most significant bit.
- // (-x)&x isolates the rightmost bit.
- // The whole method is much faster than calling log2i, and very comparable to using ScanBitForward/Reverse intrinsic,
- // which should be one CPU instruction, but is not portable.
- size_t rightmost_pos( const block_type value ) const {
- return 64 - 1 - debrujin_magic_table[ ( (value & (-(int64_t)value) ) * 0x07EDD5E59A4E28C2 ) >> 58 ];
- }
-
- public:
-
- void init( index num_cols ) {
- int64_t n = 1; // in case of overflow
- int64_t bottom_blocks_needed = ( num_cols + block_size_in_bits - 1 ) / block_size_in_bits;
- int64_t upper_blocks = 1;
-
- // How many blocks/nodes of index needed to index the whole bitset?
- while( n * block_size_in_bits < bottom_blocks_needed ) {
- n *= block_size_in_bits;
- upper_blocks += n;
- }
-
- offset = upper_blocks;
- data.resize( upper_blocks + bottom_blocks_needed, 0 );
-
- std::size_t temp_array[ 64 ] = {
- 63, 0, 58, 1, 59, 47, 53, 2,
- 60, 39, 48, 27, 54, 33, 42, 3,
- 61, 51, 37, 40, 49, 18, 28, 20,
- 55, 30, 34, 11, 43, 14, 22, 4,
- 62, 57, 46, 52, 38, 26, 32, 41,
- 50, 36, 17, 19, 29, 10, 13, 21,
- 56, 45, 25, 31, 35, 16, 9, 12,
- 44, 24, 15, 8, 23, 7, 6, 5 };
-
- std::copy( &temp_array[ 0 ], &temp_array[ 64 ], &debrujin_magic_table[ 0 ] );
- }
-
- index get_max_index() const {
- if( !data[ 0 ] )
- return -1;
-
- size_t n = 0;
- size_t newn = 0;
- size_t index = 0;
- while( newn < data.size() ) {
- n = newn;
- index = rightmost_pos( data[ n ] );
- newn = ( n << block_shift ) + index + 1;
- }
-
- return ( ( n - offset ) << block_shift ) + index;
- }
-
- bool is_empty() const {
- return data[ 0 ] == 0;
- }
-
- void add_index( const size_t entry ) {
- const block_type ONE = 1;
- const block_type block_modulo_mask = ( ONE << block_shift ) - 1;
- size_t index_in_level = entry >> block_shift;
- size_t address = index_in_level + offset;
- size_t index_in_block = entry & block_modulo_mask;
-
- block_type mask = ( ONE << ( block_size_in_bits - index_in_block - 1 ) );
-
- data[ address ] ^= mask;
-
- // Check if we reached the root. Also, if anyone else was in this block, we don't need to update the path up.
- while( address && !( data[ address ] & ~mask ) ) {
- index_in_block = index_in_level & block_modulo_mask;
- index_in_level >>= block_shift;
- --address;
- address >>= block_shift;
- mask = ( ONE << ( block_size_in_bits - index_in_block - 1 ) );
- data[ address ] ^= mask;
- }
- }
-
- void get_col_and_clear( column &out ) {
- index mx = this->get_max_index();
- while( mx != -1 ) {
- out.push_back( mx );
- add_index( mx );
- mx = this->get_max_index();
- }
-
- std::reverse( out.begin(), out.end() );
- }
-
- void add_col(const column &col) {
- for( size_t i = 0; i < col.size(); ++i )
- add_index(col[i]);
- }
-
- void clear() {
- index mx = this->get_max_index();
- while( mx != -1 ) {
- add_index( mx );
- mx = this->get_max_index();
- }
- }
-
- 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<bit_tree_column> bit_tree_pivot_column;
-}
diff --git a/matching/include/phat/representations/full_pivot_column.h b/matching/include/phat/representations/full_pivot_column.h deleted file mode 100644 index c2e9e3c..0000000 --- a/matching/include/phat/representations/full_pivot_column.h +++ /dev/null @@ -1,100 +0,0 @@ -/* 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 full_column {
-
- protected:
- std::priority_queue< index > history;
- std::vector< char > is_in_history;
- std::vector< char > col_bit_field;
-
- public:
- void init( const index total_size ) {
- col_bit_field.resize( total_size, false );
- is_in_history.resize( total_size, false );
- }
-
- void add_col( const column& col ) {
- for( index idx = 0; idx < (index) col.size(); idx++ ) {
- add_index( col[ idx ] );
- }
- }
-
- void add_index( const index idx ) {
- if( !is_in_history[ idx ] ) {
- history.push( idx );
- is_in_history[ idx ] = true;
- }
-
- col_bit_field[ idx ] = !col_bit_field[ idx ];
- }
-
- index get_max_index() {
- while( history.size() > 0 ) {
- index topIndex = history.top();
- if( col_bit_field[ topIndex ] ) {
- return topIndex;
- } else {
- history.pop();
- is_in_history[ topIndex ] = false;
- }
- }
-
- return -1;
- }
-
- void get_col_and_clear( column& col ) {
- while( !is_empty() ) {
- col.push_back( get_max_index() );
- add_index( get_max_index() );
- }
- std::reverse( col.begin(), col.end() );
- }
-
- bool is_empty() {
- return (get_max_index() == -1);
- }
-
- void clear() {
- while( !is_empty() )
- add_index( get_max_index() );
- }
-
- 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< full_column > full_pivot_column;
-}
diff --git a/matching/include/phat/representations/heap_pivot_column.h b/matching/include/phat/representations/heap_pivot_column.h deleted file mode 100644 index 33cd07b..0000000 --- a/matching/include/phat/representations/heap_pivot_column.h +++ /dev/null @@ -1,126 +0,0 @@ -/* 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;
-
- column temp_col;
- index inserts_since_last_prune;
-
- void prune()
- {
- temp_col.clear( );
- index max_index = pop_max_index( );
- while( max_index != -1 ) {
- temp_col.push_back( max_index );
- max_index = pop_max_index( );
- }
-
- for( index idx = 0; idx < (index)temp_col.size( ); idx++ )
- data.push( temp_col[ idx ] );
-
- inserts_since_last_prune = 0;
- }
-
- index pop_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( );
- }
- }
- return max_element;
- }
- }
-
- public:
- void init( const index total_size ) {
- inserts_since_last_prune = 0;
- clear();
- }
-
- void add_col( const column& col ) {
- for( index idx = 0; idx < (index) col.size(); idx++ )
- data.push( col[ idx ] );
- inserts_since_last_prune += col.size( );
- if( 2 * inserts_since_last_prune >( index ) data.size( ) )
- prune();
- }
-
- index get_max_index() {
- index max_element = pop_max_index( );
- if( max_element == -1 )
- return -1;
- else {
- data.push( max_element );
- return max_element;
- }
- }
-
- void get_col_and_clear( column& col ) {
- col.clear();
- index max_index = pop_max_index( );
- while( max_index != -1 ) {
- col.push_back( max_index );
- max_index = pop_max_index( );
- }
- std::reverse( col.begin(), col.end() );
- }
-
- bool is_empty() {
- return get_max_index() == -1;
- }
-
- void clear() {
- data = std::priority_queue< index >();
- }
-
- void remove_max() {
- pop_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/matching/include/phat/representations/sparse_pivot_column.h b/matching/include/phat/representations/sparse_pivot_column.h deleted file mode 100644 index 390fd91..0000000 --- a/matching/include/phat/representations/sparse_pivot_column.h +++ /dev/null @@ -1,79 +0,0 @@ -/* 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 sparse_column {
-
- protected:
- std::set< index > data;
-
- void add_index( const index idx ) {
- std::pair< std::set< index >::iterator, bool > result = data.insert( idx );
- if( result.second == false )
- data.erase( result.first );
- }
-
- public:
- void init( const index total_size ) {
- data.clear();
- }
-
- void add_col( const column& col ) {
- for( index idx = 0; idx < (index) col.size(); idx++ )
- add_index( col[ idx ] );
- }
-
- index get_max_index() {
- return data.empty() ? -1 : *data.rbegin();
- }
-
- void get_col_and_clear( column& col ) {
- col.assign( data.begin(), data.end() );
- data.clear();
- }
-
- bool is_empty() {
- return data.empty();
- }
-
- void clear() {
- data.clear();
- }
-
- 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< sparse_column > sparse_pivot_column;
-}
diff --git a/matching/include/phat/representations/vector_heap.h b/matching/include/phat/representations/vector_heap.h deleted file mode 100644 index db0420f..0000000 --- a/matching/include/phat/representations/vector_heap.h +++ /dev/null @@ -1,170 +0,0 @@ -/* Copyright 2013 IST Austria
-Contributed by: 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>
-
-namespace phat {
- class vector_heap {
-
- protected:
- std::vector< dimension > dims;
- std::vector< column > matrix;
-
- std::vector< index > inserts_since_last_prune;
-
- mutable thread_local_storage< column > temp_column_buffer;
-
- protected:
- void _prune( index idx )
- {
- column& col = matrix[ idx ];
- column& temp_col = temp_column_buffer();
- temp_col.clear();
- index max_index = _pop_max_index( col );
- while( max_index != -1 ) {
- temp_col.push_back( max_index );
- max_index = _pop_max_index( col );
- }
- col = temp_col;
- std::reverse( col.begin( ), col.end( ) );
- std::make_heap( col.begin( ), col.end( ) );
- inserts_since_last_prune[ idx ] = 0;
- }
-
- index _pop_max_index( index idx )
- {
- return _pop_max_index( matrix[ idx ] );
- }
-
- index _pop_max_index( column& col ) const
- {
- if( col.empty( ) )
- return -1;
- else {
- index max_element = col.front( );
- std::pop_heap( col.begin( ), col.end( ) );
- col.pop_back( );
- while( !col.empty( ) && col.front( ) == max_element ) {
- std::pop_heap( col.begin( ), col.end( ) );
- col.pop_back( );
- if( col.empty( ) )
- return -1;
- else {
- max_element = col.front( );
- std::pop_heap( col.begin( ), col.end( ) );
- col.pop_back( );
- }
- }
- return max_element;
- }
- }
-
- public:
- // overall number of cells in boundary_matrix
- index _get_num_cols( ) const
- {
- return (index)matrix.size( );
- }
- void _set_num_cols( index nr_of_columns )
- {
- dims.resize( nr_of_columns );
- matrix.resize( nr_of_columns );
- inserts_since_last_prune.assign( nr_of_columns, 0 );
- }
-
- // dimension of given index
- dimension _get_dim( index idx ) const
- {
- return dims[ idx ];
- }
- void _set_dim( index idx, dimension dim )
- {
- dims[ idx ] = dim;
- }
-
- // replaces(!) content of 'col' with boundary of given index
- void _get_col( index idx, column& col ) const
- {
- temp_column_buffer( ) = matrix[ idx ];
-
- index max_index = _pop_max_index( temp_column_buffer() );
- while( max_index != -1 ) {
- col.push_back( max_index );
- max_index = _pop_max_index( temp_column_buffer( ) );
- }
- std::reverse( col.begin( ), col.end( ) );
- }
- void _set_col( index idx, const column& col )
- {
- matrix[ idx ] = col;
- std::make_heap( matrix[ idx ].begin( ), matrix[ idx ].end( ) );
- }
-
- // true iff boundary of given idx is empty
- bool _is_empty( index idx ) const
- {
- return _get_max_index( idx ) == -1;
- }
-
- // largest row index of given column idx (new name for lowestOne())
- index _get_max_index( index idx ) const
- {
- column& col = const_cast< column& >( matrix[ idx ] );
- index max_element = _pop_max_index( col );
- col.push_back( max_element );
- std::push_heap( col.begin( ), col.end( ) );
- return max_element;
- }
-
- // removes the maximal index of a column
- void _remove_max( index idx )
- {
- _pop_max_index( idx );
- }
-
- // clears given column
- void _clear( index idx )
- {
- matrix[ idx ].clear( );
- }
-
- // syncronizes all data structures (essential for openmp stuff)
- void _sync( ) {}
-
- // adds column 'source' to column 'target'
- void _add_to( index source, index target )
- {
- for( index idx = 0; idx < (index)matrix[ source ].size( ); idx++ ) {
- matrix[ target ].push_back( matrix[ source ][ idx ] );
- std::push_heap( matrix[ target ].begin(), matrix[ target ].end() );
- }
- inserts_since_last_prune[ target ] += matrix[ source ].size();
-
- if( 2 * inserts_since_last_prune[ target ] > ( index )matrix[ target ].size() )
- _prune( target );
- }
-
- // finalizes given column
- void _finalize( index idx ) {
- _prune( idx );
- }
-
- };
-}
diff --git a/matching/include/phat/representations/vector_list.h b/matching/include/phat/representations/vector_list.h deleted file mode 100644 index ca0b5b8..0000000 --- a/matching/include/phat/representations/vector_list.h +++ /dev/null @@ -1,101 +0,0 @@ -/* Copyright 2013 IST Austria
- Contributed by: 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>
-
-namespace phat {
- class vector_list {
-
- protected:
- std::vector< dimension > dims;
- std::vector< std::list< index > > matrix;
-
- public:
- // overall number of cells in boundary_matrix
- index _get_num_cols() const {
- return (index)matrix.size();
- }
- void _set_num_cols( index nr_of_columns ) {
- dims.resize( nr_of_columns );
- matrix.resize( nr_of_columns );
- }
-
- // dimension of given index
- dimension _get_dim( index idx ) const {
- return dims[ idx ];
- }
- void _set_dim( index idx, dimension dim ) {
- dims[ idx ] = dim;
- }
-
- // replaces(!) content of 'col' with boundary of given index
- void _get_col( index idx, column& col ) const {
- col.clear();
- col.reserve( matrix[idx].size() );
- std::copy (matrix[idx].begin(), matrix[idx].end(), std::back_inserter(col) );
- }
-
- void _set_col( index idx, const column& col ) {
- matrix[ idx ].clear();
- matrix[ idx ].resize( col.size() );
- std::copy (col.begin(), col.end(), matrix[ idx ].begin() );
- }
-
- // true iff boundary of given idx is empty
- bool _is_empty( index idx ) const {
- return matrix[ idx ].empty();
- }
-
- // largest row index of given column idx (new name for lowestOne())
- index _get_max_index( index idx ) const {
- return matrix[ idx ].empty() ? -1 : *matrix[ idx ].rbegin();
- }
-
- // removes the maximal index of a column
- void _remove_max( index idx ) {
- std::list< index >::iterator it = matrix[ idx ].end();
- it--;
- matrix[ idx ].erase( it );
- }
-
- // clears given column
- void _clear( index idx ) {
- matrix[ idx ].clear();
- }
-
- // syncronizes all data structures (essential for openmp stuff)
- void _sync() {}
-
- // adds column 'source' to column 'target'
- void _add_to( index source, index target ) {
- std::list< index >& source_col = matrix[ source ];
- std::list< index >& target_col = matrix[ target ];
- std::list< index > temp_col;
- target_col.swap( temp_col );
- std::set_symmetric_difference( temp_col.begin(), temp_col.end(),
- source_col.begin(), source_col.end(),
- std::back_inserter( target_col ) );
- }
-
- // finalizes given column
- void _finalize( index idx ) {
- }
- };
-}
diff --git a/matching/include/phat/representations/vector_set.h b/matching/include/phat/representations/vector_set.h deleted file mode 100644 index 6878a27..0000000 --- a/matching/include/phat/representations/vector_set.h +++ /dev/null @@ -1,99 +0,0 @@ -/* 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> - -namespace phat { - class vector_set { - - protected: - std::vector< dimension > dims; - std::vector< std::set< index > > matrix; - - public: - // overall number of cells in boundary_matrix - index _get_num_cols() const { - return (index)matrix.size(); - } - void _set_num_cols( index nr_of_columns ) { - dims.resize( nr_of_columns ); - matrix.resize( nr_of_columns ); - } - - // dimension of given index - dimension _get_dim( index idx ) const { - return dims[ idx ]; - } - void _set_dim( index idx, dimension dim ) { - dims[ idx ] = dim; - } - - // replaces(!) content of 'col' with boundary of given index - void _get_col( index idx, column& col ) const { - col.clear(); - col.reserve( matrix[idx].size() ); - std::copy (matrix[idx].begin(), matrix[idx].end(), std::back_inserter(col) ); - } - void _set_col( index idx, const column& col ) { - matrix[ idx ].clear(); - matrix[ idx ].insert( col.begin(), col.end() ); - } - - // true iff boundary of given idx is empty - bool _is_empty( index idx ) const { - return matrix[ idx ].empty(); - } - - // largest row index of given column idx (new name for lowestOne()) - index _get_max_index( index idx ) const { - return matrix[ idx ].empty() ? -1 : *matrix[ idx ].rbegin(); - } - - // removes the maximal index of a column - void _remove_max( index idx ) { - std::set< index >::iterator it = matrix[ idx ].end(); - it--; - matrix[ idx ].erase( it ); - } - - // clears given column - void _clear( index idx ) { - matrix[ idx ].clear(); - } - - // syncronizes all data structures (essential for openmp stuff) - void _sync() {} - - // adds column 'source' to column 'target' - void _add_to( index source, index target ) { - for( std::set< index >::iterator it = matrix[ source ].begin(); it != matrix[ source ].end(); it++ ) { - std::set< index >& col = matrix[ target ]; - std::pair< std::set< index >::iterator, bool > result = col.insert( *it ); - if( !result.second ) - col.erase( result.first ); - } - } - - // finalizes given column - void _finalize( index idx ) { - } - - }; -} diff --git a/matching/include/phat/representations/vector_vector.h b/matching/include/phat/representations/vector_vector.h deleted file mode 100644 index f111d6b..0000000 --- a/matching/include/phat/representations/vector_vector.h +++ /dev/null @@ -1,107 +0,0 @@ -/* 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>
-
-namespace phat {
- class vector_vector {
-
- protected:
- std::vector< dimension > dims;
- std::vector< column > matrix;
-
- thread_local_storage< column > temp_column_buffer;
-
- public:
- // overall number of cells in boundary_matrix
- index _get_num_cols() const {
- return (index)matrix.size();
- }
- void _set_num_cols( index nr_of_columns ) {
- dims.resize( nr_of_columns );
- matrix.resize( nr_of_columns );
- }
-
- // dimension of given index
- dimension _get_dim( index idx ) const {
- return dims[ idx ];
- }
- void _set_dim( index idx, dimension dim ) {
- dims[ idx ] = dim;
- }
-
- // replaces(!) content of 'col' with boundary of given index
- void _get_col( index idx, column& col ) const {
- col = matrix[ idx ];
- }
- void _set_col( index idx, const column& col ) {
- matrix[ idx ] = col;
- }
-
- // true iff boundary of given idx is empty
- bool _is_empty( index idx ) const {
- return matrix[ idx ].empty();
- }
-
- // largest row index of given column idx (new name for lowestOne())
- index _get_max_index( index idx ) const {
- return matrix[ idx ].empty() ? -1 : matrix[ idx ].back();
- }
-
- // removes the maximal index of a column
- void _remove_max( index idx ) {
- matrix[ idx ].pop_back();
- }
-
- // clears given column
- void _clear( index idx ) {
- matrix[ idx ].clear();
- }
-
- // syncronizes all data structures (essential for openmp stuff)
- void _sync() {}
-
- // adds column 'source' to column 'target'
- void _add_to( index source, index target ) {
- column& source_col = matrix[ source ];
- column& target_col = matrix[ target ];
- column& temp_col = temp_column_buffer();
-
-
- size_t new_size = source_col.size() + target_col.size();
-
- if (new_size > temp_col.size()) temp_col.resize(new_size);
-
- std::vector<index>::iterator col_end = std::set_symmetric_difference( target_col.begin(), target_col.end(),
- source_col.begin(), source_col.end(),
- temp_col.begin() );
- temp_col.erase(col_end, temp_col.end());
-
-
- target_col.swap(temp_col);
- }
-
- // finalizes given column
- void _finalize( index idx ) {
- column& col = matrix[ idx ];
- column(col.begin(), col.end()).swap(col);
- }
- };
-}
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