# HG changeset patch
# User Dmitriy Morozov <morozov@cs.duke.edu>
# Date 1190289769 14400
# Node ID aee8f549d3249b95d581c2dc441bd3032b4e572d
# Parent  addeb7563cb2209f83318943ac85fa85f5960c52
Added ability to not store trails in pair_simplices() computation

diff -r addeb7563cb2 -r aee8f549d324 examples/alphashapes/alphashapes3d.cpp
--- a/examples/alphashapes/alphashapes3d.cpp	Thu Sep 20 07:31:40 2007 -0400
+++ b/examples/alphashapes/alphashapes3d.cpp	Thu Sep 20 08:02:49 2007 -0400
@@ -43,7 +43,7 @@
 		af.append(*cur);
 	af.fill_simplex_index_map();
 	std::cout << "Filled simplex-index map" << std::endl;
-	af.pair_simplices(af.begin(), af.end());
+	af.pair_simplices(af.begin(), af.end(), false);
 	std::cout << "Simplices paired" << std::endl;
 
 	for (AlphaFiltration::Index i = af.begin(); i != af.end(); ++i)
diff -r addeb7563cb2 -r aee8f549d324 examples/cech-complex/cech-complex.cpp
--- a/examples/cech-complex/cech-complex.cpp	Thu Sep 20 07:31:40 2007 -0400
+++ b/examples/cech-complex/cech-complex.cpp	Thu Sep 20 08:02:49 2007 -0400
@@ -73,6 +73,9 @@
 
 int main(int argc, char** argv) 
 {
+	SetFrequency(GetCounter("filtration/pair"), 10000);
+	SetTrigger(GetCounter("filtration/pair"), GetCounter(""));
+
 	// Read in the point set and compute its Delaunay triangulation
 	std::istream& in = std::cin;
 	int ambient_d, homology_d;	
@@ -114,7 +117,7 @@
 
 	// Compute persistence
 	cf.fill_simplex_index_map();
-	cf.pair_simplices(cf.begin(), cf.end());
+	cf.pair_simplices(cf.begin(), cf.end(), false);
 	std::cout << "Simplices paired" << std::endl;
 
 	for (CechFiltration::Index i = cf.begin(); i != cf.end(); ++i)
diff -r addeb7563cb2 -r aee8f549d324 include/topology/filtration.h
--- a/include/topology/filtration.h	Thu Sep 20 07:31:40 2007 -0400
+++ b/include/topology/filtration.h	Thu Sep 20 08:02:49 2007 -0400
@@ -59,8 +59,8 @@
 		/// \name Core Functionality
 		/// @{
 		/// Computes RU decomposition of the simplices in [bg, end) range, assuming that everything before bg has been paired 
-		void 							pair_simplices(Index bg, Index end);
-		void 							pair_simplices()							{ pair_simplices(begin(), end()); }
+		void 							pair_simplices(Index bg, Index end, bool store_trails = true);
+		void 							pair_simplices(bool store_trails = true)	{ pair_simplices(begin(), end(), store_trails); }
 		bool							transpose(Index i, bool maintain_lazy = true);
 		bool							is_paired() const;
 		Index							append(const Simplex& s);					///< Appends s to the filtration
@@ -107,6 +107,7 @@
 		void							pairing_switch(Index i, Index j);
 		
 		bool 							paired;
+		bool							trails_stored;
 		SimplexMap						inverse_simplices;
 
 		Vineyard*						vineyard_;
diff -r addeb7563cb2 -r aee8f549d324 include/topology/filtration.hpp
--- a/include/topology/filtration.hpp	Thu Sep 20 07:31:40 2007 -0400
+++ b/include/topology/filtration.hpp	Thu Sep 20 08:02:49 2007 -0400
@@ -44,8 +44,13 @@
 template<class S, class FS, class V>
 void 
 Filtration<S, FS, V>::
-pair_simplices(Index bg, Index end)
+pair_simplices(Index bg, Index end, bool store_trails)
 {
+	if (!is_paired())
+		trails_stored = store_trails;
+	else
+		trails_stored &= store_trails;
+
 	rLog(rlFiltration, "Entered: compute_pairing");
 	for (Index j = bg; j != end; ++j)
 	{
@@ -81,7 +86,7 @@
 			rLog(rlFiltration, "  Adding: [%s] + [%s]", 
 							   tostring(bdry).c_str(), tostring(i->pair()->cycle()).c_str());
 			bdry.add(i->pair()->cycle(), get_consistency_cmp());
-			i->pair()->trail().append(j, get_consistency_cmp());
+			if (store_trails)	i->pair()->trail().append(j, get_consistency_cmp());
 			Count(cFiltrationPairTrailLength);
 			rLog(rlFiltration, "After addition: %s", tostring(bdry).c_str());
 		}
@@ -107,6 +112,7 @@
 transpose(Index i, bool maintain_lazy)
 {
 	AssertMsg(vineyard() != 0, "We must have a vineyard for transpositions");
+	AssertMsg(trails_stored, "We must have trails (matrix U) to perform transpositions");
 	
 	Index i_orig = i++;