initial checkin

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

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diff --git a/include/phat/compute_persistence_pairs.h b/include/phat/compute_persistence_pairs.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/persistence_pairs.h>
+#include <phat/boundary_matrix.h>
+#include <phat/helpers/dualize.h>
+#include <phat/algorithms/twist_reduction.h>
+
+namespace phat {
+
+    template< typename ReductionAlgorithm, typename Representation >
+    void compute_persistence_pairs( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) {
+        ReductionAlgorithm reduce;
+        reduce( boundary_matrix );
+        pairs.clear();
+        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 );
+                index death = idx;
+                pairs.append_pair( birth, death );
+            }
+        }
+    }
+    
+    template< typename ReductionAlgorithm, typename Representation >
+    void compute_persistence_pairs_dualized( persistence_pairs& pairs, boundary_matrix< Representation >& boundary_matrix ) {
+        ReductionAlgorithm reduce;
+        const index nr_columns = boundary_matrix.get_num_cols();
+        dualize( boundary_matrix );
+        reduce( boundary_matrix );
+        pairs.clear();
+        for( index idx = 0; idx < nr_columns; idx++ ) {
+            if( !boundary_matrix.is_empty( idx ) ) {
+                index death = nr_columns - 1 - boundary_matrix.get_max_index( idx );
+                index birth = nr_columns - 1 - idx;
+                pairs.append_pair( birth, death );
+            }
+        }
+    }
+    
+    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 );
+    }
+
+}
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