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Merge pull request #1121 from hschreiber/simplex_tree_custom_copy_con…
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[Simplex tree] Additional copy constructor for Simplex_tree
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@VincentRouvreau
VincentRouvreau authored Sep 13, 2024
2 parents 4b327a9 + d813c89 commit 903f210
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Showing 4 changed files with 275 additions and 61 deletions.
102 changes: 85 additions & 17 deletions src/Simplex_tree/include/gudhi/Simplex_tree.h
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
* - 2023/05 Clément Maria: Edge insertion method for flag complexes
* - 2023/05 Hannah Schreiber: Factorization of expansion methods
* - 2023/08 Hannah Schreiber (& Clément Maria): Add possibility of stable simplex handles.
* - 2024/08 Hannah Schreiber: Addition of customizable copy constructor.
* - YYYY/MM Author: Description of the modification
*/

Expand Down Expand Up @@ -132,6 +133,7 @@ class Simplex_tree {

struct Key_simplex_base_real {
Key_simplex_base_real() : key_(-1) {}
Key_simplex_base_real(Simplex_key k) : key_(k) {}
void assign_key(Simplex_key k) { key_ = k; }
Simplex_key key() const { return key_; }
private:
Expand All @@ -143,6 +145,7 @@ class Simplex_tree {
void assign_key(Simplex_key);
Simplex_key key() const;
};

struct Extended_filtration_data {
Filtration_value minval;
Filtration_value maxval;
Expand All @@ -154,14 +157,20 @@ class Simplex_tree {

struct Filtration_simplex_base_real {
Filtration_simplex_base_real() : filt_(0) {}
Filtration_simplex_base_real(Filtration_value f) : filt_(f) {}
void assign_filtration(Filtration_value f) { filt_ = f; }
Filtration_value filtration() const { return filt_; }
private:
Filtration_value filt_;
};
struct Filtration_simplex_base_dummy {
Filtration_simplex_base_dummy() {}
void assign_filtration(Filtration_value GUDHI_CHECK_code(f)) { GUDHI_CHECK(f == 0, "filtration value specified for a complex that does not store them"); }
Filtration_simplex_base_dummy(Filtration_value GUDHI_CHECK_code(f)) {
GUDHI_CHECK(f == 0, "filtration value specified for a complex that does not store them");
}
void assign_filtration(Filtration_value GUDHI_CHECK_code(f)) {
GUDHI_CHECK(f == 0, "filtration value specified for a complex that does not store them");
}
Filtration_value filtration() const { return 0; }
};
typedef typename std::conditional<Options::store_filtration, Filtration_simplex_base_real,
Expand Down Expand Up @@ -245,7 +254,7 @@ class Simplex_tree {
typedef boost::iterator_range<Simplex_vertex_iterator> Simplex_vertex_range;
/** \brief Range over the cofaces of a simplex. */
typedef typename std::conditional<Options::link_nodes_by_label,
Optimized_cofaces_simplex_filtered_range, // faster implem
Optimized_cofaces_simplex_filtered_range, // faster implementation
std::vector<Simplex_handle>>::type Cofaces_simplex_range;

/** \private
Expand Down Expand Up @@ -345,7 +354,7 @@ class Simplex_tree {
/** \brief Returns a range over the vertices of a simplex.
*
* The order in which the vertices are visited is the decreasing order for < on Vertex_handles,
* which is consequenlty
* which is consequently
* equal to \f$(-1)^{\text{dim} \sigma}\f$ the canonical orientation on the simplex.
*/
Simplex_vertex_range simplex_vertex_range(Simplex_handle sh) const {
Expand Down Expand Up @@ -402,6 +411,29 @@ class Simplex_tree {
filtration_vect_(),
dimension_(-1) { }

/**
* @brief Construct the simplex tree as the copy of a given simplex tree with eventually different template
* parameters.
* Therefore, should provide a method converting the filtration values of one tree to the another. All other values
* are already implicitly convertible if the concept of @ref SimplexTreeOptions is respected (note that there is
* an eventual loss of precision or an undefined behaviour if a value is converted into a new type too small to
* contain it). Any extra data (@ref Simplex_data) stored in the simplices are ignored in the copy for now.
*
* @tparam OtherSimplexTreeOptions Options of the given simplex tree.
* @tparam F Method taking an OtherSimplexTreeOptions::Filtration_value as input and returning an
* Options::Filtration_value.
* @param complex_source Simplex tree to copy.
* @param translate_filtration_value Method taking an OtherSimplexTreeOptions::Filtration_value from the source tree
* as input and returning the corresponding Options::Filtration_value in the new tree.
*/
template<typename OtherSimplexTreeOptions, typename F>
Simplex_tree(const Simplex_tree<OtherSimplexTreeOptions>& complex_source, F&& translate_filtration_value) {
#ifdef DEBUG_TRACES
std::clog << "Simplex_tree custom copy constructor" << std::endl;
#endif // DEBUG_TRACES
copy_from(complex_source, translate_filtration_value);
}

/** \brief User-defined copy constructor reproduces the whole tree structure. */
Simplex_tree(const Simplex_tree& complex_source) {
#ifdef DEBUG_TRACES
Expand Down Expand Up @@ -471,27 +503,63 @@ class Simplex_tree {
auto root_source = complex_source.root_;

// root members copy
root_.members() = Dictionary(boost::container::ordered_unique_range, root_source.members().begin(), root_source.members().end());
root_.members() =
Dictionary(boost::container::ordered_unique_range, root_source.members().begin(), root_source.members().end());
// Needs to reassign children
for (auto& map_el : root_.members()) {
map_el.second.assign_children(&root_);
}
rec_copy(&root_, &root_source);
rec_copy<Options::store_key>(
&root_, &root_source, [](const Filtration_value& fil) -> const Filtration_value& { return fil; });
}

// Copy from complex_source to "this"
template<typename OtherSimplexTreeOptions, typename F>
void copy_from(const Simplex_tree<OtherSimplexTreeOptions>& complex_source, F&& translate_filtration_value) {
null_vertex_ = complex_source.null_vertex_;
filtration_vect_.clear();
dimension_ = complex_source.dimension_;
auto root_source = complex_source.root_;

// root members copy
if constexpr (!Options::stable_simplex_handles) root_.members().reserve(root_source.size());
for (auto& p : root_source.members()){
if constexpr (Options::store_key && OtherSimplexTreeOptions::store_key) {
auto it = root_.members().try_emplace(
root_.members().end(), p.first, &root_, translate_filtration_value(p.second.filtration()), p.second.key());
} else {
auto it = root_.members().try_emplace(
root_.members().end(), p.first, &root_, translate_filtration_value(p.second.filtration()));
}
}

rec_copy<OtherSimplexTreeOptions::store_key>(&root_, &root_source, translate_filtration_value);
}

/** \brief depth first search, inserts simplices when reaching a leaf. */
void rec_copy(Siblings *sib, Siblings *sib_source) {
for (auto sh = sib->members().begin(), sh_source = sib_source->members().begin();
sh != sib->members().end(); ++sh, ++sh_source) {
template<bool store_key, typename OtherSiblings, typename F>
void rec_copy(Siblings *sib, OtherSiblings *sib_source, F&& translate_filtration_value) {
auto sh_source = sib_source->members().begin();
for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh, ++sh_source) {
update_simplex_tree_after_node_insertion(sh);
if (has_children(sh_source)) {
Siblings * newsib = new Siblings(sib, sh_source->first);
if constexpr (!Options::stable_simplex_handles) {
newsib->members_.reserve(sh_source->second.children()->members().size());
}
for (auto & child : sh_source->second.children()->members())
newsib->members_.emplace_hint(newsib->members_.end(), child.first, Node(newsib, child.second.filtration()));
rec_copy(newsib, sh_source->second.children());
for (auto & child : sh_source->second.children()->members()){
if constexpr (store_key && Options::store_key) {
newsib->members_.emplace_hint(
newsib->members_.end(),
child.first,
Node(newsib, translate_filtration_value(child.second.filtration()), child.second.key()));
} else {
newsib->members_.emplace_hint(newsib->members_.end(),
child.first,
Node(newsib, translate_filtration_value(child.second.filtration())));
}
}
rec_copy<store_key>(newsib, sh_source->second.children(), translate_filtration_value);
sh->second.assign_children(newsib);
}
}
Expand Down Expand Up @@ -1432,9 +1500,9 @@ class Simplex_tree {
*
* Nodes with label @p u get affected only if a Node with label @p v is in their same
* siblings set.
* We then try to insert "ponctually" @p v all over the subtree rooted
* We then try to insert "punctually" @p v all over the subtree rooted
* at `Node(u)`. Each insertion of a Node with @p v label induces a local
* expansion at this Node (as explained above) and a sequence of "ponctual"
* expansion at this Node (as explained above) and a sequence of "punctual"
* insertion of `Node(v)` in the subtree rooted at sibling nodes of the new node,
* on its left.
*/
Expand Down Expand Up @@ -1479,7 +1547,7 @@ class Simplex_tree {

//for all siblings containing a Node labeled with u (including the root), run
//compute_punctual_expansion
//todo parallelise
//todo parallelize
List_max_vertex* nodes_with_label_u = nodes_by_label(u);//all Nodes with u label

GUDHI_CHECK(nodes_with_label_u != nullptr,
Expand Down Expand Up @@ -1798,7 +1866,7 @@ class Simplex_tree {
if (blocker_result) {
blocked_new_sib_vertex_list.push_back(new_sib_member->first);
// update data structures for all deleted simplices
// can be done in the loop as part of another datastructure
// can be done in the loop as part of another data structure
update_simplex_tree_before_node_removal(new_sib_member);
}
}
Expand Down Expand Up @@ -1972,7 +2040,7 @@ class Simplex_tree {
return true;
};

//TODO: `if constexpr` replacable by `std::erase_if` in C++20? Has a risk of additional runtime,
//TODO: `if constexpr` replaceable by `std::erase_if` in C++20? Has a risk of additional runtime,
//so to benchmark first.
if constexpr (Options::stable_simplex_handles) {
modified = false;
Expand Down Expand Up @@ -2312,7 +2380,7 @@ class Simplex_tree {
static Simplex_handle simplex_handle_from_node(Node& node) {
if constexpr (Options::stable_simplex_handles){
//Relies on the Dictionary type to be boost::container::map<Vertex_handle, Node>.
//If the type changes or boost fondamentally changes something on the structure of their map,
//If the type changes or boost fundamentally changes something on the structure of their map,
//a safer/more general but much slower version is:
// if (node.children()->parent() == label) { // verifies if node is a leaf
// return children->oncles()->find(label);
Expand Down
25 changes: 14 additions & 11 deletions src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@
#define GUDHI_EMPTY_BASE_CLASS_OPTIMIZATION
#endif

#include <vector>
#include <boost/core/empty_value.hpp>

namespace Gudhi {
Expand All @@ -33,21 +32,25 @@ namespace Gudhi {
*
* It stores explicitly its own filtration value and its own Simplex_key.
*/
template<class SimplexTree>
struct GUDHI_EMPTY_BASE_CLASS_OPTIMIZATION Simplex_tree_node_explicit_storage : SimplexTree::Filtration_simplex_base,
SimplexTree::Key_simplex_base,
SimplexTree::Hooks_simplex_base,
boost::empty_value<typename SimplexTree::Simplex_data> {
template <class SimplexTree>
struct GUDHI_EMPTY_BASE_CLASS_OPTIMIZATION Simplex_tree_node_explicit_storage
: SimplexTree::Filtration_simplex_base,
SimplexTree::Key_simplex_base,
SimplexTree::Hooks_simplex_base,
boost::empty_value<typename SimplexTree::Simplex_data> {
typedef typename SimplexTree::Siblings Siblings;
typedef typename SimplexTree::Filtration_value Filtration_value;
typedef typename SimplexTree::Simplex_key Simplex_key;
typedef typename SimplexTree::Simplex_data Simplex_data;

Simplex_tree_node_explicit_storage(Siblings * sib = nullptr,
Filtration_value filtration = 0)
: children_(sib) {
this->assign_filtration(filtration);
}
Simplex_tree_node_explicit_storage(Siblings* sib = nullptr, Filtration_value filtration = 0)
: SimplexTree::Filtration_simplex_base(filtration), children_(sib)
{}

//will fail to compile when called with SimplexTree::Options::store_key is false.
Simplex_tree_node_explicit_storage(Siblings* sib, Filtration_value filtration, Simplex_key key)
: SimplexTree::Filtration_simplex_base(filtration), SimplexTree::Key_simplex_base(key), children_(sib)
{}

/*
* Assign children to the node
Expand Down
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