Intermediate commit while converting to the new architecture
* Converted Filtration into StaticPersistence and DynamicPersistenceTrails
(both right now work with the underlying std::vector rather than std::list order)
* Filtration is now just an auxilliary glue (a map between Complex and Persistence)
* Whether chains are vectors or lists can be interchanged
* Added PersistenceDiagram with a simple bottleneck_distance() function
* Converted triangle, alphashapes3d, and cech-complex examples
* Lots of organizational changes
(factoring utilities out into containers.h, indirect.h, property-maps.h)
* Trying to document along the way with NaturalDocs-type comments
/* Implementations */
#ifdef LOGGING
static rlog::RLogChannel* rlOrderList = DEF_CHANNEL("utilities/orderlist", rlog::Log_Debug);
#endif // LOGGING
template<class T>
void
OrderList<T>::
swap(iterator i, iterator j)
{
typename Parent::iterator i_base = i.get_base();
typename Parent::iterator j_base = j.get_base();
std::swap(i_base->tag, j_base->tag);
// Exchange the actual elements in the list --- so that iterators behave as expected
typename Parent::iterator after_j = boost::next(j_base);
Parent::splice(i_base, *this, j_base);
Parent::splice(after_j, *this, i_base);
}
template<class T>
template<class BinaryPredicate>
void
OrderList<T>::
sort(BinaryPredicate cmp)
{
Parent::sort(OrderListNodeComparison<T, BinaryPredicate>(cmp));
OrderType cur_order = 0;
for (typename Parent::iterator cur = Parent::begin(); cur != Parent::end(); ++cur)
cur->tag = cur_order++;
}
template<class T>
typename OrderList<T>::iterator
OrderList<T>::
push_back(const_reference x)
{
if (empty())
Parent::push_back(NodeType(x, 0));
else
Parent::push_back(NodeType(x, last().get_base()->tag + 1));
return last();
}
template<class T>
typename OrderList<T>::iterator
OrderList<T>::
insert(iterator p, const_reference x)
{
typename Parent::iterator p_base = p.get_base();
OrderType tag = (p_base++)->tag + 1;
typename Parent::iterator new_base = Parent::insert(p_base, NodeType(x, tag));
if (p_base->tag != tag)
return iterator(new_base);
// Find non-overflowing region
unsigned int num_elements = 1, maximum = 1, lower = tag, upper = tag, level = 0;
float inv_density = 1;
typename Parent::iterator prev = p_base, next = p_base;
--(--prev); ++next; // move prev back twice to skip over the newly inserted element
do
{
lower &= ~(1 << level);
upper |= (1 << level);
maximum <<= 1; inv_density *= density_threshold;
++level;
while (prev != Parent::end() && prev->tag >= lower) { --prev; ++num_elements; }
while (next != Parent::end() && next->tag <= upper) { ++next; ++num_elements; }
} while (inv_density * num_elements >= maximum);
++num_elements; // for the extra element inserted
rLog(rlOrderList, "%i, %i, %i", num_elements, lower, upper);
rLog(rlOrderList, "prev is at the end: %i", (prev == Parent::end()));
rLog(rlOrderList, "next is at the end: %i", (next == Parent::end()));
// Reorder
AssertMsg((upper - lower + 1)/num_elements > 0, "Spacing between new tags must be non-zero");
for (unsigned int i = 0; i < num_elements; ++i)
{
(++prev)->tag = lower + i*((upper - lower + 1)/num_elements);
rLog(rlOrderList, "%i", prev->tag);
AssertMsg(prev->tag != 0 || prev == Parent::begin(), "Cannot assign 0 tag except at the beginning of OrderList");
}
AssertMsg(++prev == next, "prev + num_elements != next in OrderList::insert()");
return iterator(new_base);
}
template<class T>
void
OrderList<T>::
show_elements() const
{
for (const_iterator cur = begin(); cur != end(); ++cur)
std::cout << *(cur.get_base()) << std::endl;
std::cout << std::endl;
}
/* OrderComparison */
template<class T>
int
OrderList<T>::OrderComparison::
compare(ComparableType a, ComparableType b) const
{
if (a.get_base()->tag == b.get_base()->tag) return 0;
if (a.get_base()->tag < b.get_base()->tag) return -1;
return 1;
}
template<class T>
bool
OrderList<T>::OrderComparison::
operator()(ComparableType a, ComparableType b) const
{
return (compare(a,b) < 0);
}