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add references in simplex tree even for arithmetic filtration values
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@hschreiber
hschreiber committed Aug 26, 2024
1 parent 4d80e13 commit ddb7d20
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Showing 3 changed files with 36 additions and 43 deletions.
71 changes: 32 additions & 39 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 @@ -129,16 +129,6 @@ class Simplex_tree {
/** \brief Set of nodes sharing a same parent in the simplex tree. */
typedef Simplex_tree_siblings<Simplex_tree, Dictionary> Siblings;



/**
* @brief Equals @ref Filtration_value if @ref SimplexTreeOptions::store_filtration is false or the type
* corresponds to a native arithmetic type (int, double, etc.). Equals to a reference of @ref Filtration_value
* otherwise.
*/
using Filtration_value_rep = std::conditional_t<Options::store_filtration && !std::is_arithmetic_v<Filtration_value>,
Filtration_value&, Filtration_value>;

struct Key_simplex_base_real {
Key_simplex_base_real() : key_(-1) {}
void assign_key(Simplex_key k) { key_ = k; }
Expand All @@ -157,7 +147,7 @@ class Simplex_tree {
Filtration_value maxval;
Extended_filtration_data() {}

Extended_filtration_data(const Filtration_value_rep vmin, const Filtration_value_rep vmax)
Extended_filtration_data(const Filtration_value& vmin, const Filtration_value& vmax)
: minval(vmin), maxval(vmax)
{}
};
Expand All @@ -166,12 +156,12 @@ class Simplex_tree {

struct Filtration_simplex_base_real {
Filtration_simplex_base_real() : filt_(0) {}
void assign_filtration(const Filtration_value_rep f) { filt_ = f; }
const Filtration_value_rep filtration() const { return filt_; }
void assign_filtration(const Filtration_value& f) { filt_ = f; }
const Filtration_value& filtration() const { return filt_; }
Filtration_value& filtration_raw() { return filt_; }
const Filtration_value& filtration_raw() const { return filt_; }

static constexpr const Filtration_value_rep get_infinity() { return inf_; }
static constexpr const Filtration_value& get_infinity() { return inf_; }

private:
Filtration_value filt_;
Expand All @@ -183,11 +173,14 @@ class Simplex_tree {
struct Filtration_simplex_base_dummy {
Filtration_simplex_base_dummy() {}

void assign_filtration(const Filtration_value_rep GUDHI_CHECK_code(f))
void assign_filtration(const Filtration_value& GUDHI_CHECK_code(f))
{
GUDHI_CHECK(f == Filtration_value(), "filtration value specified for a complex that does not store them");
}
Filtration_value filtration() const { return 0; }
const Filtration_value& filtration() const { return null_; }

private:
static constexpr const Filtration_value null_ = Filtration_value();
};
typedef typename std::conditional<Options::store_filtration, Filtration_simplex_base_real,
Filtration_simplex_base_dummy>::type Filtration_simplex_base;
Expand Down Expand Up @@ -610,7 +603,7 @@ class Simplex_tree {
*
* Same as `filtration()`, but does not handle `null_simplex()`.
*/
static const Filtration_value_rep filtration_(Simplex_handle sh) {
static const Filtration_value& filtration_(Simplex_handle sh) {
GUDHI_CHECK (sh != null_simplex(), "null simplex");
return sh->second.filtration();
}
Expand Down Expand Up @@ -638,7 +631,7 @@ class Simplex_tree {
* Called on the null_simplex, it returns infinity.
* If SimplexTreeOptions::store_filtration is false, returns 0.
*/
static const Filtration_value_rep filtration(Simplex_handle sh) {
static const Filtration_value& filtration(Simplex_handle sh) {
if (sh != null_simplex()) {
return sh->second.filtration();
} else {
Expand All @@ -649,7 +642,7 @@ class Simplex_tree {
/** \brief Sets the filtration value of a simplex.
* \exception std::invalid_argument In debug mode, if sh is a null_simplex.
*/
void assign_filtration(Simplex_handle sh, const Filtration_value_rep fv) {
void assign_filtration(Simplex_handle sh, const Filtration_value& fv) {
GUDHI_CHECK(sh != null_simplex(),
std::invalid_argument("Simplex_tree::assign_filtration - cannot assign filtration on null_simplex"));
sh->second.assign_filtration(fv);
Expand Down Expand Up @@ -879,7 +872,7 @@ class Simplex_tree {
*/
template <class RandomVertexHandleRange = std::initializer_list<Vertex_handle>>
std::pair<Simplex_handle, bool> insert_simplex_raw(const RandomVertexHandleRange& simplex,
const Filtration_value_rep filtration) {
const Filtration_value& filtration) {
Siblings * curr_sib = &root_;
std::pair<Simplex_handle, bool> res_insert;
auto vi = simplex.begin();
Expand Down Expand Up @@ -950,7 +943,7 @@ class Simplex_tree {
* .end() return input iterators, with 'value_type' Vertex_handle. */
template<class InputVertexRange = std::initializer_list<Vertex_handle>>
std::pair<Simplex_handle, bool> insert_simplex(const InputVertexRange & simplex,
const Filtration_value_rep filtration = Filtration_value()) {
const Filtration_value& filtration = Filtration_value()) {
auto first = std::begin(simplex);
auto last = std::end(simplex);

Expand Down Expand Up @@ -980,7 +973,7 @@ class Simplex_tree {
template <class InputVertexRange = std::initializer_list<Vertex_handle>>
std::pair<Simplex_handle, bool> insert_simplex_and_subfaces(
const InputVertexRange& Nsimplex,
const Filtration_value_rep filtration = Filtration_value())
const Filtration_value& filtration = Filtration_value())
{
auto first = std::begin(Nsimplex);
auto last = std::end(Nsimplex);
Expand Down Expand Up @@ -1010,7 +1003,7 @@ class Simplex_tree {
std::pair<Simplex_handle, bool> rec_insert_simplex_and_subfaces_sorted(Siblings* sib,
ForwardVertexIterator first,
ForwardVertexIterator last,
const Filtration_value_rep filt)
const Filtration_value& filt)
{
// An alternative strategy would be:
// - try to find the complete simplex, if found (and low filtration) exit
Expand Down Expand Up @@ -1422,7 +1415,7 @@ class Simplex_tree {
* The complex does not need to be empty before calling this function. However, if a vertex is
* already present, its filtration value is not modified, unlike with other insertion functions. */
template <class VertexRange>
void insert_batch_vertices(VertexRange const& vertices, const Filtration_value_rep filt = Filtration_value()) {
void insert_batch_vertices(VertexRange const& vertices, const Filtration_value& filt = Filtration_value()) {
auto verts = vertices | boost::adaptors::transformed([&](auto v){
return Dit_value_t(v, Node(&root_, filt)); });
root_.members_.insert(boost::begin(verts), boost::end(verts));
Expand Down Expand Up @@ -1496,7 +1489,7 @@ class Simplex_tree {
*/
void insert_edge_as_flag( Vertex_handle u
, Vertex_handle v
, const Filtration_value_rep fil
, const Filtration_value& fil
, int dim_max
, std::vector<Simplex_handle>& added_simplices)
{
Expand Down Expand Up @@ -1610,7 +1603,7 @@ class Simplex_tree {
*/
void compute_punctual_expansion( Vertex_handle v
, Siblings * sib
, const Filtration_value_rep fil
, const Filtration_value& fil
, int k //k == dim_max - dimension simplices in sib
, std::vector<Simplex_handle>& added_simplices )
{ //insertion always succeeds because the edge {u,v} used to not be here.
Expand Down Expand Up @@ -1659,7 +1652,7 @@ class Simplex_tree {
void create_local_expansion(
Simplex_handle sh_v //Node with label v which has just been inserted
, Siblings *curr_sib //Siblings containing the node sh_v
, const Filtration_value_rep fil_uv //Fil value of the edge uv in the zz filtration
, const Filtration_value& fil_uv //Fil value of the edge uv in the zz filtration
, int k //Stopping condition for recursion based on max dim
, std::vector<Simplex_handle> &added_simplices) //range of all new simplices
{ //pick N^+(v)
Expand All @@ -1685,7 +1678,7 @@ class Simplex_tree {
*/
void siblings_expansion(
Siblings * siblings // must contain elements
, const Filtration_value_rep fil
, const Filtration_value& fil
, int k // == max_dim expansion - dimension curr siblings
, std::vector<Simplex_handle> & added_simplices )
{
Expand Down Expand Up @@ -1729,7 +1722,7 @@ class Simplex_tree {
void create_expansion(Siblings * siblings,
Dictionary_it& s_h,
Dictionary_it& next,
const Filtration_value_rep fil,
const Filtration_value& fil,
int k,
std::vector<Simplex_handle>* added_simplices = nullptr)
{
Expand Down Expand Up @@ -1776,7 +1769,7 @@ class Simplex_tree {
static void intersection(std::vector<std::pair<Vertex_handle, Node> >& intersection,
Dictionary_it begin1, Dictionary_it end1,
Dictionary_it begin2, Dictionary_it end2,
const Filtration_value_rep filtration_) {
const Filtration_value& filtration_) {
if (begin1 == end1 || begin2 == end2)
return; // ----->>
while (true) {
Expand Down Expand Up @@ -2024,7 +2017,7 @@ class Simplex_tree {
* than it was before. However, `upper_bound_dimension()` will return the old value, which remains a valid upper
* bound. If you care, you can call `dimension()` to recompute the exact dimension.
*/
bool prune_above_filtration(const Filtration_value_rep filtration) {
bool prune_above_filtration(const Filtration_value& filtration) {
if (filtration == Filtration_simplex_base_real::get_infinity())
return false; // ---->>
bool modified = rec_prune_above_filtration(root(), filtration);
Expand All @@ -2034,7 +2027,7 @@ class Simplex_tree {
}

private:
bool rec_prune_above_filtration(Siblings* sib, const Filtration_value_rep filt) {
bool rec_prune_above_filtration(Siblings* sib, const Filtration_value& filt) {
auto&& list = sib->members();
bool modified = false;
bool emptied = false;
Expand Down Expand Up @@ -2212,12 +2205,12 @@ class Simplex_tree {
* @param[in] efd Structure containing the minimum and maximum values of the original filtration. This the output of `extend_filtration()`.
* @return A pair containing the original filtration value of the simplex as well as the simplex type.
*/
std::pair<Filtration_value, Extended_simplex_type> decode_extended_filtration(const Filtration_value_rep f,
std::pair<Filtration_value, Extended_simplex_type> decode_extended_filtration(const Filtration_value& f,
const Extended_filtration_data& efd)
{
std::pair<Filtration_value, Extended_simplex_type> p;
const Filtration_value_rep minval = efd.minval;
const Filtration_value_rep maxval = efd.maxval;
const Filtration_value& minval = efd.minval;
const Filtration_value& maxval = efd.maxval;
if (f >= -2 && f <= -1) {
p.first = minval + (maxval-minval)*(f + 2); p.second = Extended_simplex_type::UP;
} else if (f >= 1 && f <= 2) {
Expand Down Expand Up @@ -2254,7 +2247,7 @@ class Simplex_tree {
Filtration_value minval = Filtration_simplex_base_real::get_infinity();
Filtration_value maxval = -Filtration_simplex_base_real::get_infinity();
for (auto sh = root_.members().begin(); sh != root_.members().end(); ++sh) {
const Filtration_value_rep f = this->filtration(sh);
const Filtration_value& f = this->filtration(sh);
minval = std::min(minval, f);
maxval = std::max(maxval, f);
maxvert = std::max(sh->first, maxvert);
Expand Down Expand Up @@ -2282,7 +2275,7 @@ class Simplex_tree {
// Create cone on simplex
vr.push_back(maxvert);
if (this->dimension(sh) == 0) {
const Filtration_value_rep v = this->filtration(sh);
const Filtration_value& v = this->filtration(sh);
Filtration_value scaled_v = (v - minval) * scale;
// Assign ascending value between -2 and -1 to vertex
this->assign_filtration(sh, -2 + scaled_v);
Expand Down Expand Up @@ -2476,7 +2469,7 @@ class Simplex_tree {
* @param[in] filt_value The new filtration value.
* @param[in] min_dim The minimal dimension. Default value is 0.
*/
void reset_filtration(const Filtration_value_rep filt_value, int min_dim = 0) {
void reset_filtration(const Filtration_value& filt_value, int min_dim = 0) {
rec_reset_filtration(&root_, filt_value, min_dim);
clear_filtration(); // Drop the cache.
}
Expand All @@ -2487,7 +2480,7 @@ class Simplex_tree {
* @param[in] filt_value The new filtration value.
* @param[in] min_depth The minimal depth.
*/
void rec_reset_filtration(Siblings * sib, const Filtration_value_rep filt_value, int min_depth) {
void rec_reset_filtration(Siblings * sib, const Filtration_value& filt_value, int min_depth) {
for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) {
if (min_depth <= 0) {
sh->second.assign_filtration(filt_value);
Expand Down
4 changes: 2 additions & 2 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 @@ -39,13 +39,13 @@ struct GUDHI_EMPTY_BASE_CLASS_OPTIMIZATION Simplex_tree_node_explicit_storage
SimplexTree::Hooks_simplex_base,
boost::empty_value<typename SimplexTree::Simplex_data> {
typedef typename SimplexTree::Siblings Siblings;
typedef typename SimplexTree::Filtration_value_rep Filtration_value_rep;
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() : children_(nullptr) {}

Simplex_tree_node_explicit_storage(Siblings* sib, const Filtration_value_rep filtration) : children_(sib)
Simplex_tree_node_explicit_storage(Siblings* sib, const Filtration_value& filtration) : children_(sib)
{
this->assign_filtration(filtration);
}
Expand Down
4 changes: 2 additions & 2 deletions src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ class Simplex_tree_siblings {
template<class T> friend class Simplex_tree_boundary_opposite_vertex_simplex_iterator;

typedef typename SimplexTree::Vertex_handle Vertex_handle;
typedef typename SimplexTree::Filtration_value_rep Filtration_value;
typedef typename SimplexTree::Filtration_value Filtration_value;
typedef typename SimplexTree::Node Node;
typedef MapContainer Dictionary;
typedef typename MapContainer::iterator Dictionary_it;
Expand Down Expand Up @@ -76,7 +76,7 @@ class Simplex_tree_siblings {
* between input filtration_value and the value already
* present in the node.
*/
void insert(Vertex_handle v, const Filtration_value filtration_value) {
void insert(Vertex_handle v, const Filtration_value& filtration_value) {
auto ins = members_.emplace(v, Node(this, filtration_value));
if (!ins.second){
unify_births(ins.first->second.filtration_raw(), filtration_value);
Expand Down

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