Added code to expose the persistence_diagram class, the bottleneck_distance function and the point class to python.
Most of the commonly used methods for each class have been exported.
The constructor for point now requires that a data argument be provided along with x and y coord. This needs to be made optional.
The constructor for persistence_diagram could possibly be rewritten as well.
#include <utilities/log.h>
#if LOGGING
static rlog::RLogChannel* rlARSimplex3D = DEF_CHANNEL("ar/simplex3d", rlog::Log_Debug);
#endif
ARSimplex3D::
ARSimplex3D(const ARSimplex3D& s): Parent(s)
{
attached_ = s.attached_;
alpha_ = s.alpha_;
rho_ = s.rho_;
s_ = s.s_;
v_ = s.v_;
phi_const_ = s.phi_const_;
}
ARSimplex3D::
ARSimplex3D(const Parent::Vertex& v)
{
Parent::add(v);
}
ARSimplex3D::
ARSimplex3D(const ::Vertex& v, const Point& z): alpha_(0), rho_(0), v_(0), attached_(false)
{
for (int i = 0; i < 4; ++i)
if (v.cell()->vertex(i)->point() == v.point())
Parent::add(v.cell()->vertex(i));
s_ = CGAL::squared_distance((*Parent::vertices().begin())->point(), z);
// phi_const_ will be set by an edge
}
ARSimplex3D::
ARSimplex3D(const Edge& e)
{
Cell_handle c = e.first;
Parent::add(c->vertex(e.second));
Parent::add(c->vertex(e.third));
}
ARSimplex3D::
ARSimplex3D(const Edge& e, const Point& z, SimplexPhiMap& simplices, const Delaunay& Dt, Facet_circulator facet_bg)
{
Cell_handle c = e.first;
Parent::add(c->vertex(e.second));
Parent::add(c->vertex(e.third));
Facet_circulator cur = facet_bg;
while (Dt.is_infinite(*cur)) ++cur;
SimplexPhiMap::const_iterator cur_iter = simplices.find(ARSimplex3D(*cur));
RealValue min = cur_iter->first.alpha();
RealValue phi_const_min = cur_iter->first.phi_const();
VertexSet::const_iterator v2 = Parent::vertices().begin();
VertexSet::const_iterator v1 = v2++;
const Point& p1 = (*v1)->point();
const Point& p2 = (*v2)->point();
attached_ = false;
rho_ = CGAL::squared_radius(p1, p2);
if (facet_bg != 0) do
{
int i0 = (*cur).first->index(*v1);
int i1 = (*cur).first->index(*v2);
int i = 6 - i0 - i1 - (*cur).second;
if (Dt.is_infinite(cur->first->vertex(i)))
{
++cur; continue;
// FIXME: what do we do with infinite cofaces (i.e., what
// phi_const does a simplex get if its dual Voronoi cell is
// infinite?
}
Point p3 = (*cur).first->vertex(i)->point();
if (CGAL::side_of_bounded_sphere(p1, p2, p3) == CGAL::ON_BOUNDED_SIDE)
attached_ = true;
SimplexPhiMap::const_iterator cur_iter = simplices.find(ARSimplex3D(*cur));
RealValue val = cur_iter->first.alpha();
if (val < min) min = val;
RealValue phi_const_val = cur_iter->first.phi_const();
if (phi_const_val < phi_const_min) phi_const_min = phi_const_val;
++cur;
} while (cur != facet_bg);
if (attached_)
alpha_ = min;
else
alpha_ = rho_;
phi_const_ = phi_const_min;
// update phi_const_ for v1 and v2 if necessary
SimplexPhiMap::iterator v1_iter = simplices.find(ARSimplex3D(*v1));
SimplexPhiMap::iterator v2_iter = simplices.find(ARSimplex3D(*v2));
if (phi_const_ < v1_iter->second) v1_iter->second = phi_const_;
if (phi_const_ < v2_iter->second) v2_iter->second = phi_const_;
s_ = CGAL::squared_distance(z, K::Segment_3(p1,p2).supporting_line());
Point origin(0,0,0);
Point cc = origin + ((p1 - origin) + (p2 - origin))/2; // CGAL is funny
v_ = CGAL::squared_distance(z, cc) - s_;
}
ARSimplex3D::
ARSimplex3D(const Facet& f)
{
Cell_handle c = f.first;
for (int i = 0; i < 4; ++i)
if (i != f.second)
Parent::add(c->vertex(i));
}
ARSimplex3D::
ARSimplex3D(const Facet& f, const Point& z, const SimplexPhiMap& simplices, const Delaunay& Dt)
{
Cell_handle c = f.first;
for (int i = 0; i < 4; ++i)
if (i != f.second)
Parent::add(c->vertex(i));
Cell_handle o = c->neighbor(f.second);
int oi = o->index(c);
VertexSet::const_iterator v3 = Parent::vertices().begin();
VertexSet::const_iterator v1 = v3++;
VertexSet::const_iterator v2 = v3++;
const Point& p1 = (*v1)->point();
const Point& p2 = (*v2)->point();
const Point& p3 = (*v3)->point();
rho_ = squared_radius(p1, p2, p3);
attached_ = false;
if (!Dt.is_infinite(c->vertex(f.second)) &&
CGAL::side_of_bounded_sphere(p1, p2, p3,
c->vertex(f.second)->point()) == CGAL::ON_BOUNDED_SIDE)
attached_ = true;
else if (!Dt.is_infinite(o->vertex(oi)) &&
CGAL::side_of_bounded_sphere(p1, p2, p3,
o->vertex(oi)->point()) == CGAL::ON_BOUNDED_SIDE)
attached_ = true;
else
alpha_ = rho_;
if (Dt.is_infinite(c))
{
SimplexPhiMap::const_iterator o_iter = simplices.find(ARSimplex3D(*o,z));
if (attached_) alpha_ = o_iter->first.alpha();
phi_const_ = o_iter->first.phi_const(); // FIXME: it's probably the other way around
}
else if (Dt.is_infinite(o))
{
SimplexPhiMap::const_iterator c_iter = simplices.find(ARSimplex3D(*c,z));
if (attached_) alpha_ = c_iter->first.alpha();
phi_const_ = c_iter->first.phi_const(); // FIXME: it's probably the other way around
}
else
{
SimplexPhiMap::const_iterator o_iter = simplices.find(ARSimplex3D(*o,z));
SimplexPhiMap::const_iterator c_iter = simplices.find(ARSimplex3D(*c,z));
if (attached_) alpha_ = std::min(c_iter->first.alpha(), o_iter->first.alpha());
phi_const_ = std::min(c_iter->first.phi_const(), o_iter->first.phi_const());
}
Point cc = CGAL::circumcenter(p1, p2, p3);
v_ = CGAL::squared_distance(z, K::Plane_3(p1,p2,p3));
s_ = CGAL::squared_distance(z, cc) - v_;
}
ARSimplex3D::
ARSimplex3D(const Cell& c, const Point& z): attached_(false)
{
for (int i = 0; i < 4; ++i)
Parent::add(c.vertex(i));
VertexSet::const_iterator v = Parent::vertices().begin();
Point p1 = (*v++)->point();
Point p2 = (*v++)->point();
Point p3 = (*v++)->point();
Point p4 = (*v)->point();
rho_ = alpha_ = CGAL::squared_radius(p1, p2, p3, p4);
s_ = 0;
v_ = CGAL::squared_distance(z, CGAL::circumcenter(p1, p2, p3, p4));
phi_const_ = rho_ - v_;
}
ARSimplex3D::Cycle
ARSimplex3D::boundary() const
{
Cycle bdry;
Parent::Cycle pbdry = Parent::boundary();
for (Parent::Cycle::const_iterator cur = pbdry.begin(); cur != pbdry.end(); ++cur)
bdry.push_back(*cur);
return bdry;
}
bool
ARSimplex3D::AlphaOrder::
operator()(const ARSimplex3D& first, const ARSimplex3D& second) const
{
if (first.alpha() == second.alpha())
return (first.dimension() < second.dimension());
else
return (first.alpha() < second.alpha());
}
std::ostream&
ARSimplex3D::
operator<<(std::ostream& out) const
{
out << this << ": ";
for (VertexSet::const_iterator cur = Parent::vertices().begin(); cur != Parent::vertices().end(); ++cur)
out << &(**cur) << ", ";
out << "value = " << value();
return out;
}
void update_simplex_phi_map(const ARSimplex3D& s, ARSimplex3D::SimplexPhiMap& simplices)
{
simplices[s] = s.phi_const();
}
void fill_alpha_order(const Delaunay& Dt, const Point& z, ARSimplex3DVector& alpha_order)
{
ARSimplex3D::SimplexPhiMap simplices;
for(Cell_iterator cur = Dt.finite_cells_begin(); cur != Dt.finite_cells_end(); ++cur)
update_simplex_phi_map(ARSimplex3D(*cur, z), simplices);
rLog(rlARSimplex3D, "Cells inserted");
for(Vertex_iterator cur = Dt.finite_vertices_begin(); cur != Dt.finite_vertices_end(); ++cur)
simplices[ARSimplex3D(*cur, z)] = 0; // only one tetrahedron can have non-negative phi_const value
// (namely the one containing z); all other simplices will have a
// negative phi_const value, so 0 is safe
rLog(rlARSimplex3D, "Vertices inserted");
for(Facet_iterator cur = Dt.finite_facets_begin(); cur != Dt.finite_facets_end(); ++cur)
update_simplex_phi_map(ARSimplex3D(*cur, z, simplices, Dt), simplices);
rLog(rlARSimplex3D, "Facets inserted");
for(Edge_iterator cur = Dt.finite_edges_begin(); cur != Dt.finite_edges_end(); ++cur)
update_simplex_phi_map(ARSimplex3D(*cur, z, simplices, Dt, Dt.incident_facets(*cur)), simplices);
rLog(rlARSimplex3D, "Edges inserted");
// Sort simplices by their alpha values
alpha_order.resize(simplices.size()); ARSimplex3DVector::iterator out = alpha_order.begin();
for (ARSimplex3D::SimplexPhiMap::const_iterator in = simplices.begin(); in != simplices.end(); ++in, ++out)
*out = in->first;
std::sort(alpha_order.begin(), alpha_order.end(), ARSimplex3D::AlphaOrder());
// Update phi_const for vertices
for (ARSimplex3DVector::iterator cur = alpha_order.begin(); cur != alpha_order.end(); ++cur)
if (cur->dimension() == 0) cur->set_phi_const(simplices[*cur]);
}