Instrumented code for counting:
* added counters to addition in cohomology and ChainWrapper
* rips-pairwise-cohomology counts the maximum elements stored in the cycles
* added alphashapes3d-cohomology
* moved progress_display from DynamicPersistence to StaticPersistence
#ifndef __WEIGHTED_RIPS_H__
#define __WEIGHTED_RIPS_H__
#include <vector>
#include <string>
#include "simplex.h"
#include "rips.h"
#include <boost/iterator/counting_iterator.hpp>
/**
* WeightedRipsSimplex class
*
* This class sits as an invisible layer between the Simplex datatype passed
* to WeightedRips and the class itself. The need for this layer is the need
* to store the ``value'' (max inter-vertex distance) of each simplex in the
* Weighted Rips complex--something that the user of the class does not need
* to be aware of.
*/
template<class Simplex_, class DistanceType_>
class WeightedRipsSimplex : public Simplex_
{
public:
typedef typename Simplex_::Vertex Vertex;
typedef typename Simplex_::VertexContainer VertexContainer;
typedef DistanceType_ DistanceType;
WeightedRipsSimplex(Simplex_ s) : Simplex_(s) { }
void setSimplexValue(const DistanceType &sv) { simplexValue = sv; }
DistanceType getSimplexValue() const { return simplexValue; }
protected:
DistanceType simplexValue;
};
/**
* WeightedRips class
*
* Class providing basic operations to work with Rips complexes. It implements Bron-Kerbosch algorithm,
* and provides simple wrappers for various functions.
*
* Distances_ is expected to define types IndexType and DistanceType as well as
* provide operator()(...) which given two IndexTypes should return
* the distance between them. There should be methods begin() and end()
* for iterating over IndexTypes as well as a method size().
*/
template<class Distances_, class Simplex_ = Simplex<typename Distances_::IndexType> >
class WeightedRips : public Rips<Distances_, Simplex_>
{
public:
/* redeclaring the typedefs because they cannot be inherited at compile-time */
typedef Distances_ Distances;
typedef typename Distances::IndexType IndexType;
typedef typename Distances::DistanceType DistanceType;
typedef WeightedRipsSimplex<Simplex_, DistanceType> Simplex;
typedef typename Simplex::Vertex Vertex; // should be the same as IndexType
typedef typename Simplex::VertexContainer VertexContainer;
class Evaluator;
class Comparison;
public:
WeightedRips(const Distances& distances):
Rips<Distances_, Simplex_>(distances) {}
template<class Functor>
void generate(Dimension k, DistanceType max, const Functor& f) const;
};
/**
* DistanceDataStackingFunctor class
*
* Class providing a functor that is to be called by WeightedRips::generate(). This functor
* takes as an argument (to its constructor) the original functor passed by the user to
* generate(), and a new ``double'' functor is created. Assuming that the functor acts on
* simplices, first the value of the simplex is computed (the radius at which the simplex
* appears in the weighted Rips complex), the data field of the simplex is populated with
* this value, and then the original functor is called (it has no idea that it was
* intercepted).
*/
template<class Rips_, class Functor_>
class DistanceDataStackingFunctor
{
public:
typedef typename Rips_::Simplex Simplex_;
DistanceDataStackingFunctor(const Rips_ &r, const Functor_ &f):
rips(r), original_functor(f) { }
void operator()(const Simplex_ &s) const
{
Simplex_ s_new(s);
s_new.setSimplexValue (rips.distance(s_new, s_new));
original_functor (s_new);
}
private:
const Rips_ &rips;
const Functor_ &original_functor;
};
template<class Distances_, class Simplex_>
template<class Functor>
void WeightedRips<Distances_, Simplex_>::generate(Dimension k, DistanceType max, const Functor &f) const
{
Rips<Distances_,Simplex_>::generate(k, max, DistanceDataStackingFunctor<WeightedRips<Distances_, Simplex_>,Functor>(*this, f));
}
template<class Distances_, class Simplex_>
class WeightedRips<Distances_, Simplex_>::Evaluator: public Rips<Distances_,Simplex_>::Evaluator
{
public:
Evaluator(const Distances& distances):
Rips<Distances_, Simplex_>::Evaluator(distances) {}
DistanceType operator()(const Simplex& s) const { return s.getSimplexValue(); }
};
template<class Distances_, class Simplex_>
class WeightedRips<Distances_, Simplex_>::Comparison: public Rips<Distances_,Simplex_>::Comparison
{
public:
Comparison(const Distances& distances):
Rips<Distances_, Simplex_>::Comparison(distances) {}
bool operator()(const Simplex& s1, const Simplex& s2) const
{
if (s1.dimension() != s2.dimension())
return s1.dimension() < s2.dimension();
return s1.getSimplexValue() < s2.getSimplexValue();
}
};
#endif // __WEIGHTED_RIPS_H__