# HG changeset patch
# User Dmitriy Morozov <morozov@cs.duke.edu>
# Date 1189673013 14400
# Node ID b2cb83a28329e6c2eb37069585c84cebf13d1fbe
# Parent b0d6c9162de3c6cc220903e5b636b6918505bf52# Parent 04d667548959b03f9ff52b89635265c8147e9611
Merged in changes from master
diff -r b0d6c9162de3 -r b2cb83a28329 README
--- a/README Thu Sep 13 04:42:39 2007 -0400
+++ b/README Thu Sep 13 04:43:33 2007 -0400
@@ -5,11 +5,11 @@
boost - great set of C++ libraries
Doxygen - for building documentation
libcwd - for debugging only (is not needed by default)
- synaps - for solving polynomial (for kinetic kernel), which in turn requires GMP
+ synaps - for solving polynomials (for kinetic kernel), which in turn requires GMP
Configuration
The path to CGAL's Makefile is expected to be set in $CGAL_MAKEFILE, the rest
- is just usual CMake configuration
+ is just the usual CMake configuration
Building
To build examples, create a directory build (to keep everything in one place),
diff -r b0d6c9162de3 -r b2cb83a28329 examples/alphashapes/CMakeLists.txt
--- a/examples/alphashapes/CMakeLists.txt Thu Sep 13 04:42:39 2007 -0400
+++ b/examples/alphashapes/CMakeLists.txt Thu Sep 13 04:43:33 2007 -0400
@@ -4,5 +4,5 @@
foreach (t ${targets})
add_executable (${t} ${t}.cpp ${external_sources})
- target_link_libraries (${t} ${libraries} ${cgal_libraries})
+ target_link_libraries (${t} ${cgal_libraries})
endforeach (t ${targets})
diff -r b0d6c9162de3 -r b2cb83a28329 examples/alphashapes/alphashapes3d.cpp
--- a/examples/alphashapes/alphashapes3d.cpp Thu Sep 13 04:42:39 2007 -0400
+++ b/examples/alphashapes/alphashapes3d.cpp Thu Sep 13 04:43:33 2007 -0400
@@ -32,7 +32,16 @@
for (AlphaSimplex3DVector::const_iterator cur = alpha_ordering.begin(); cur != alpha_ordering.end(); ++cur)
af.append(*cur);
af.fill_simplex_index_map();
+ std::cout << "Filled simplex-index map" << std::endl;
af.pair_simplices(af.begin(), af.end());
std::cout << "Simplices paired" << std::endl;
+
+ for (AlphaFiltration::Index i = af.begin(); i != af.end(); ++i)
+ if (i->is_paired())
+ {
+ if (i->sign())
+ std::cout << i->dimension() << " " << i->value() << " " << i->pair()->value() << std::endl;
+ } //else std::cout << i->value() << std::endl;
+
}
diff -r b0d6c9162de3 -r b2cb83a28329 examples/grid/grid2Dvineyard.hpp
--- a/examples/grid/grid2Dvineyard.hpp Thu Sep 13 04:42:39 2007 -0400
+++ b/examples/grid/grid2Dvineyard.hpp Thu Sep 13 04:43:33 2007 -0400
@@ -108,25 +108,25 @@
VertexIndex vv(&vertices_[grid()->seq(x,y+1)]);
VertexIndex vd(&vertices_[grid()->seq(x+1,y+1)]);
- Simplex sh(v);
+ Simplex sh(2, v);
sh.add(vh); filtration_->append(sh); // Horizontal edge
sh.add(vd); filtration_->append(sh); // "Horizontal" triangle
- Simplex sv(v);
+ Simplex sv(2, v);
sv.add(vv); filtration_->append(sv); // Vertical edge
sv.add(vd); filtration_->append(sv); // "Vertical" triangle
- Simplex sd(v);
+ Simplex sd(2, v);
sd.add(vd); filtration_->append(sd); // Diagonal edge
if (y == grid()->ysize() - 2)
{
- Simplex s(vv);
+ Simplex s(1, vv);
s.add(vd); filtration_->append(s); // Top edge
}
if (x == grid()->xsize() - 2)
{
- Simplex s(vh);
+ Simplex s(1, vh);
s.add(vd); filtration_->append(s); // Right edge
}
}
diff -r b0d6c9162de3 -r b2cb83a28329 include/topology/filtration.hpp
--- a/include/topology/filtration.hpp Thu Sep 13 04:42:39 2007 -0400
+++ b/include/topology/filtration.hpp Thu Sep 13 04:43:33 2007 -0400
@@ -22,9 +22,13 @@
Filtration<S, FS, V>::
pair_simplices(Index bg, Index end)
{
+ int i = 0;
Dout(dc::filtration, "Entered: compute_pairing");
for (Index j = bg; j != end; ++j)
{
+ if (i++ % 10000 == 0)
+ std::cout << i << " simplices processed" << std::endl;
+
Dout(dc::filtration|flush_cf|continued_cf, *j << ": ");
init_cycle_trail(j);
Cycle& bdry = j->cycle();
diff -r b0d6c9162de3 -r b2cb83a28329 include/topology/lowerstarfiltration.hpp
--- a/include/topology/lowerstarfiltration.hpp Thu Sep 13 04:42:39 2007 -0400
+++ b/include/topology/lowerstarfiltration.hpp Thu Sep 13 04:43:33 2007 -0400
@@ -17,7 +17,7 @@
// Record vertex order
for(typename VertexIndexList::const_iterator cur = tmp_list.begin(); cur != tmp_list.end(); ++cur)
- (*cur)->set_order(vertex_order.push_back(VertexDescriptor(*cur, Parent::append(Simplex(*cur)))));
+ (*cur)->set_order(vertex_order.push_back(VertexDescriptor(*cur, Parent::append(Simplex(0, *cur)))));
}
template<class VI, class Smplx, class FltrSmplx, class Vnrd>
diff -r b0d6c9162de3 -r b2cb83a28329 include/topology/simplex.h
--- a/include/topology/simplex.h Thu Sep 13 04:42:39 2007 -0400
+++ b/include/topology/simplex.h Thu Sep 13 04:43:33 2007 -0400
@@ -1,6 +1,6 @@
/*
* Author: Dmitriy Morozov
- * Department of Computer Science, Duke University, 2005 -- 2006
+ * Department of Computer Science, Duke University, 2005 -- 2007
*/
#ifndef __SIMPLEX_H__
@@ -9,7 +9,8 @@
#include "utilities/sys.h"
#include "utilities/debug.h"
-#include <set>
+#include <vector>
+#include <algorithm>
#include <list>
#include <iostream>
@@ -30,7 +31,7 @@
typedef V Vertex;
typedef SimplexWithVertices<Vertex> Self;
- typedef std::set<Vertex> VertexContainer;
+ typedef std::vector<Vertex> VertexContainer;
typedef std::list<Self> Cycle;
/// \name Constructors
@@ -43,8 +44,10 @@
vertices_(bg, end) {}
SimplexWithVertices(const VertexContainer& v):
vertices_(v) {}
- SimplexWithVertices(Vertex v):
- vertices_() { vertices_.insert(v); }
+ SimplexWithVertices(Dimension d, Vertex v):
+ vertices_() { vertices_.reserve(d+1); add(v); }
+ SimplexWithVertices(Dimension d):
+ vertices_(d+1) {}
/// @}
/// \name Core
@@ -55,9 +58,9 @@
/// \name Vertex manipulation
/// @{
- bool contains(const Vertex& v) const { return (vertices_.find(v) != vertices_.end()); }
+ bool contains(const Vertex& v) const;
const VertexContainer& vertices() const { return vertices_; }
- void add(const Vertex& v) { vertices_.insert(v); }
+ void add(const Vertex& v);
/// @}
/// \name Assignment and comparison
@@ -147,8 +150,8 @@
Parent(bg, end) {}
SimplexWithAttachment(const Parent& s):
Parent(s) {}
- SimplexWithAttachment(VertexIndex vi):
- Parent(vi), attachment(vi) {}
+ SimplexWithAttachment(Dimension d, VertexIndex vi):
+ Parent(d, vi), attachment(vi) {}
/// @}
void set_attachment(VertexIndex v) { attachment = v; }
diff -r b0d6c9162de3 -r b2cb83a28329 include/topology/simplex.hpp
--- a/include/topology/simplex.hpp Thu Sep 13 04:42:39 2007 -0400
+++ b/include/topology/simplex.hpp Thu Sep 13 04:43:33 2007 -0400
@@ -16,15 +16,30 @@
for (typename VertexContainer::const_iterator cur = vertices_.begin(); cur != vertices_.end(); ++cur)
{
- bdry.push_back(*this);
+ bdry.push_back(Self(dimension() - 1));
Self& s = bdry.back();
- s.vertices_.erase(*cur);
+ std::remove_copy(vertices_.begin(), vertices_.end(), s.vertices_.begin(), *cur);
}
return bdry;
}
template<class V>
+bool
+SimplexWithVertices<V>::
+contains(const Vertex& v) const
+{
+ typename VertexContainer::const_iterator location = std::lower_bound(vertices_.begin(), vertices_.end(), v);
+ return ((location == vertices_.end()) || (*location == v));
+}
+
+template<class V>
+void
+SimplexWithVertices<V>::
+add(const Vertex& v)
+{ vertices_.push_back(v); std::sort(vertices_.begin(), vertices_.end()); }
+
+template<class V>
std::ostream&
SimplexWithVertices<V>::
operator<<(std::ostream& out) const
diff -r b0d6c9162de3 -r b2cb83a28329 include/utilities/types.h
--- a/include/utilities/types.h Thu Sep 13 04:42:39 2007 -0400
+++ b/include/utilities/types.h Thu Sep 13 04:43:33 2007 -0400
@@ -5,7 +5,7 @@
/* Types */
typedef bool Sign;
-typedef short int Dimension;
+typedef unsigned short int Dimension;
const Sign POS = true;
const Sign NEG = false;
typedef double RealType;