3 files changed, 0 insertions, 204 deletions
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; 
-};