3 files changed, 204 insertions, 0 deletions
diff --git a/matching/include/phat/helpers/dualize.h b/matching/include/phat/helpers/dualize.h
new file mode 100644
index 0000000..5731408
--- /dev/null
+++ b/matching/include/phat/helpers/dualize.h
@@ -0,0 +1,74 @@
+/*  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
new file mode 100644
index 0000000..5a5c682
--- /dev/null
+++ b/matching/include/phat/helpers/misc.h
@@ -0,0 +1,78 @@
+/*  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
new file mode 100644
index 0000000..d0b5332
--- /dev/null
+++ b/matching/include/phat/helpers/thread_local_storage.h
@@ -0,0 +1,52 @@
+/*  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; 
+};