Made storing negative simplices in StaticPersistence parameter-based, so that DynamicPersistence works again
#include <utilities/log.h>
/* Implementation */
Grid2DVineyard::
Grid2DVineyard(Grid2D* g): vertices_(g->size())
{
grid_stack_.push_back(g);
for (CoordinateIndex i = 0; i < g->size(); ++i)
vertices_[i].set_index(i);
evaluator_ = new StaticEvaluator(grid(), 0);
vineyard_ = new Vineyard(evaluator_);
filtration_ = new LSFiltration(vertices_.begin(), vertices_.end(), VertexComparison(grid()), vineyard_);
add_simplices();
}
Grid2DVineyard::
~Grid2DVineyard()
{
delete filtration_;
delete vineyard_;
delete evaluator_;
}
void
Grid2DVineyard::
compute_pairing()
{
filtration_->fill_simplex_index_map();
filtration_->pair_simplices(filtration_->begin(), filtration_->end());
vineyard_->start_vines(filtration_->begin(), filtration_->end());
}
void
Grid2DVineyard::
compute_vineyard(Grid2D* g, bool explicit_events)
{
AssertMsg(filtration_->is_paired(), "Simplices must be paired for a vineyard to be computed");
typedef Traits::Kinetic_kernel::Point_1 Point;
typedef Traits::Kinetic_kernel::Function_kernel::Construct_function CF;
typedef Traits::Kinetic_kernel::Motion_function F;
Traits tr(0,1);
Simulator::Handle sp = tr.simulator_handle();
ActivePointsTable::Handle apt = tr.active_points_1_table_handle();
Sort sort(tr, SortVisitor(this));
// Setup the (linear) trajectories
std::cout << "Setting up trajectories" << std::endl;
CF cf;
kinetic_map_.clear();
for (VertexIndex cur = vertices_.begin(); cur != vertices_.end(); ++cur)
{
ValueType val0 = (*grid())(cur->index());
ValueType val1 = (*g)(cur->index());
F x = cf(F::NT(val0), F::NT(val1 - val0)); // x = val0 + (val1 - val0)*t
Point p(x);
cur->set_kinetic_key(apt->insert(p));
kinetic_map_[cur->kinetic_key()] = cur->get_order();
if (cur->index() % 10000 == 0)
std::cout << "Added trajectory: " << cur->index() << " " << val0 << " " << val1 << std::endl;
}
// Process all the events (compute the vineyard in the process)
change_evaluator(new KineticEvaluator(sp, apt, num_grids() - 1));
if (explicit_events)
{
while (sp->next_event_time() < 1)
{
std::cout << "Next event time: " << sp->next_event_time() << std::endl;
sp->set_current_event_number(sp->current_event_number() + 1);
std::cout << "Processed event" << std::endl;
}
} else
sp->set_current_time(1.0);
std::cout << "Processed " << sp->current_event_number() << " events" << std::endl;
// Add the grid to the stack
grid_stack_.push_back(g);
change_evaluator(new StaticEvaluator(grid(), num_grids() - 1));
vineyard_->record_diagram(filtration_->begin(), filtration_->end());
}
void
Grid2DVineyard::
swap(Key a, Key b)
{
VertexOrderIndex ao = kinetic_map_[a], bo = kinetic_map_[b];
AssertMsg(filtration_->get_vertex_cmp()(ao, bo), "In swap(a,b), a must precede b");
filtration_->transpose_vertices(ao);
AssertMsg(filtration_->get_vertex_cmp()(bo, ao), "In swap(a,b), b must precede a after the transposition");
}
void
Grid2DVineyard::
add_simplices()
{
// Takes advantage of LowerStarFiltration's smart append (which allows faces
// to be inserted after cofaces, since everything is rearranged in the
// proper lower star order anyway). Also note that vertices were added by
// LowerStarFiltration's constructor
for (CoordinateIndex x = 0; x < grid()->xsize() - 1; ++x)
for (CoordinateIndex y = 0; y < grid()->ysize() - 1; ++y)
{
VertexIndex v(&vertices_[grid()->seq(x,y)]);
VertexIndex vh(&vertices_[grid()->seq(x+1,y)]);
VertexIndex vv(&vertices_[grid()->seq(x,y+1)]);
VertexIndex vd(&vertices_[grid()->seq(x+1,y+1)]);
Simplex sh(2, v);
sh.add(vh); filtration_->append(sh); // Horizontal edge
sh.add(vd); filtration_->append(sh); // "Horizontal" triangle
Simplex sv(2, v);
sv.add(vv); filtration_->append(sv); // Vertical edge
sv.add(vd); filtration_->append(sv); // "Vertical" triangle
Simplex sd(2, v);
sd.add(vd); filtration_->append(sd); // Diagonal edge
if (y == grid()->ysize() - 2)
{
Simplex s(1, vv);
s.add(vd); filtration_->append(s); // Top edge
}
if (x == grid()->xsize() - 2)
{
Simplex s(1, vh);
s.add(vd); filtration_->append(s); // Right edge
}
}
}
void
Grid2DVineyard::
change_evaluator(Evaluator* eval)
{
AssertMsg(evaluator_ != 0, "change_evaluator() assumes that existing evaluator is not null");
delete evaluator_;
evaluator_ = eval;
vineyard_->set_evaluator(evaluator_);
}