initial checkin

git-svn-id: https://phat.googlecode.com/svn/trunk@2 8e3bb3c2-eed4-f18f-5264-0b6c94e6926d

3 files changed, 178 insertions, 0 deletions

diff --git a/include/phat/helpers/dualize.h b/include/phat/helpers/dualize.h
new file mode 100644
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+++ b/include/phat/helpers/dualize.h
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+/*  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 {

+    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 );

+    

+        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_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();

+        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 );

+

+        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.init( dual_matrix, dual_dims );

+    }

+}

diff --git a/include/phat/helpers/misc.h b/include/phat/helpers/misc.h
new file mode 100644
index 0000000..93af132
--- /dev/null
+++ b/include/phat/helpers/misc.h
@@ -0,0 +1,75 @@
+/*  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 <map>

+#include <algorithm>

+#include <queue>

+#include <cassert>

+#include <sstream>

+#include <algorithm>

+#include <iomanip>

+#include <cmath>

+#include <cstdlib>

+     

+// 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;

+}

+

+// 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

+    #include <time.h>

+    #define omp_get_wtime() (float)clock() / (float)CLOCKS_PER_SEC

+#endif

+

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

+

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

+

+namespace phat { 

+    typedef phat::sparse_pivot_column default_representation;

+}

diff --git a/include/phat/helpers/thread_local_storage.h b/include/phat/helpers/thread_local_storage.h
new file mode 100644
index 0000000..ce3c1ed
--- /dev/null
+++ b/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; 

+};