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Diffstat (limited to 'matching/include/phat/boundary_matrix.h')
| -rw-r--r-- | matching/include/phat/boundary_matrix.h | 343 |
1 files changed, 0 insertions, 343 deletions
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;
- }
- };
-}
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