Modified cohomology code (unweighted and weighted) so that it doesn't use std::map for boundary computations, which should optimize memory usage.
/*
* Author: Dmitriy Morozov
* Department of Computer Science, Duke University, 2007
*/
#ifndef __AR_VINEYARD_H__
#define __AR_VINEYARD_H__
#include <boost/signals.hpp>
#include <boost/bind.hpp>
#include <list>
#include <vector>
#include "topology/conesimplex.h"
#include "topology/filtration.h"
#include "geometry/kinetic-sort.h"
#include "geometry/simulator.h"
#include "ar-simplex3d.h"
#include "ar-function-kernel.h"
template <class Simulator_>
class ARConeSimplex3D: public ConeSimplex<ARSimplex3D>
{
public:
typedef ConeSimplex<ARSimplex3D> Parent;
typedef ARSimplex3D ARSimplex3D;
/// \name Simulator types
/// @{
typedef Simulator_ Simulator;
typedef typename Simulator::FunctionKernel FunctionKernel;
typedef typename FunctionKernel::Function Function;
/// @}
/// \name ThresholdSort types
/// @{
typedef std::list<Function> ThresholdList;
typedef typename ThresholdList::iterator ThresholdListIterator;
struct ThresholdTrajectoryExtractor
{ Function operator()(ThresholdListIterator i) const { return *i; } };
typedef KineticSort<ThresholdListIterator,
ThresholdTrajectoryExtractor, Simulator> ThresholdSort;
/// @}
typedef boost::signal<void (Simulator*)> NewMaxSignal;
public:
ARConeSimplex3D(const ARSimplex3D& s, bool coned = false);
ARConeSimplex3D(const Parent& p): Parent(p) {} // crucial for boundary() to work correctly
ARConeSimplex3D(const ARConeSimplex3D& other): // need explicit copy-constructor because of the signal
Parent(other, other.coned()),
thresholds_(other.thresholds_) {}
const ThresholdList& thresholds() const { return thresholds_; }
NewMaxSignal& new_max_signal() { return new_max_signal_; }
const Function& max_threshold() const { return thresholds_.back(); }
void schedule_thresholds(Simulator* simulator);
// need explicit operator= because of the signal
ARConeSimplex3D& operator=(const ARConeSimplex3D& other) { Parent::operator=(other); thresholds_ = other.thresholds_; return *this; }
private:
ThresholdList thresholds_;
ThresholdSort thresholds_sort_;
NewMaxSignal new_max_signal_;
void swap_thresholds(ThresholdListIterator i, Simulator* simulator);
};
/**
* Encapsulated filtration, and provides compute_vineyard() functionality.
*/
class ARVineyard
{
public:
typedef ARVineyard Self;
/// \name FunctionKernel and Simulator types
/// @{
typedef ARFunctionKernel FunctionKernel;
typedef FunctionKernel::Function Function;
typedef Simulator<FunctionKernel> SimulatorAR;
/// @}
/// \name Filtration types
/// @{
typedef ARConeSimplex3D<SimulatorAR> ConeSimplex3D;
typedef Filtration<ConeSimplex3D> FiltrationAR;
typedef FiltrationAR::Simplex Simplex;
typedef FiltrationAR::Index Index;
typedef FiltrationAR::Vineyard Vineyard;
typedef Vineyard::Evaluator Evaluator;
/// @}
/// \name SimplexSort types
/// @{
struct SimplexTrajectoryExtractor
{ Function operator()(Index i) const { return i->max_threshold(); } };
typedef KineticSort<Index, SimplexTrajectoryExtractor, SimulatorAR> SimplexSort;
typedef SimplexSort::iterator SimplexSortIterator;
class ThresholdChangeSlot; // used to notify of change in max threshold
/// @}
typedef std::list<Point> PointList;
class StaticEvaluator;
class KineticEvaluator;
public:
ARVineyard(const PointList& points, const Point& z);
~ARVineyard();
void compute_pairing();
void compute_vineyard(double max_radius);
const FiltrationAR* filtration() const { return filtration_; }
const Vineyard* vineyard() const { return vineyard_; }
public:
void swap(Index i, SimulatorAR* simulator); ///< For kinetic sort
private:
void add_simplices();
void change_evaluator(Evaluator* eval);
private:
FiltrationAR* filtration_;
Vineyard* vineyard_;
Evaluator* evaluator_;
Point z_;
Delaunay dt_;
#if 0
private:
// Serialization
friend class boost::serialization::access;
ARVineyard() {}
template<class Archive>
void serialize(Archive& ar, version_type )
{
// FIXME
};
#endif
};
//BOOST_CLASS_EXPORT(ARVineyard)
#ifdef COUNTERS
static Counter* cARVineyardTrajectoryKnee = GetCounter("ar/vineyard/trajectoryknee");
#endif
class ARVineyard::ThresholdChangeSlot
{
public:
ThresholdChangeSlot(SimplexSortIterator iter, SimplexSort* sort,
Vineyard* vineyard, SimulatorAR* sort_simulator):
iter_(iter), sort_(sort), vineyard_(vineyard), sort_simulator_(sort_simulator) { iter_->element->new_max_signal().connect(*this); }
void operator()(SimulatorAR* simulator)
{
Count(cARVineyardTrajectoryKnee);
sort_->update_trajectory(iter_, sort_simulator_);
if (iter_->element->sign())
vineyard_->record_knee(iter_->element);
else
vineyard_->record_knee(iter_->element->pair());
}
private:
SimplexSortIterator iter_;
SimplexSort* sort_; // could make both of these static
Vineyard* vineyard_; // currently inefficient since there is
// only one SimplexSort and one Vineyard,
// but each is stored in every slot
SimulatorAR* sort_simulator_;
};
class ARVineyard::StaticEvaluator: public Evaluator
{
public:
StaticEvaluator() {}
virtual RealType time() const { return 0; }
virtual RealType value(const Simplex& s) const { return s.value(); }
};
class ARVineyard::KineticEvaluator: public Evaluator
{
public:
KineticEvaluator(SimulatorAR* simplex_sort_simulator,
SimulatorAR* trajectory_sort_simulator):
simplex_sort_simulator_(simplex_sort_simulator),
trajectory_sort_simulator_(trajectory_sort_simulator) {}
virtual RealType time() const { return std::max(simplex_sort_simulator_->current_time(), trajectory_sort_simulator_->current_time()); }
virtual RealType value(const Simplex& s) const { return FunctionKernel::value_at(s.max_threshold(), time()); }
private:
SimulatorAR* simplex_sort_simulator_;
SimulatorAR* trajectory_sort_simulator_;
};
#include "ar-vineyard.hpp"
#endif // __AR_VINEYARD_H__