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Diffstat (limited to 'include/gudhi/Bitmap_cubical_complex.h')
-rw-r--r--include/gudhi/Bitmap_cubical_complex.h130
1 files changed, 58 insertions, 72 deletions
diff --git a/include/gudhi/Bitmap_cubical_complex.h b/include/gudhi/Bitmap_cubical_complex.h
index f395de65..969daba6 100644
--- a/include/gudhi/Bitmap_cubical_complex.h
+++ b/include/gudhi/Bitmap_cubical_complex.h
@@ -31,10 +31,11 @@
#endif
#include <limits>
-#include <utility> // for pair<>
+#include <utility> // for pair<>
#include <algorithm> // for sort
#include <vector>
#include <numeric> // for iota
+#include <cstddef>
namespace Gudhi {
@@ -43,7 +44,8 @@ namespace cubical_complex {
// global variable, was used just for debugging.
const bool globalDbg = false;
-template <typename T> class is_before_in_filtration;
+template <typename T>
+class is_before_in_filtration;
/**
* @brief Cubical complex represented as a bitmap.
@@ -60,11 +62,10 @@ class Bitmap_cubical_complex : public T {
//*********************************************//
// Typedefs and typenames
//*********************************************//
- typedef size_t Simplex_key;
+ typedef std::size_t Simplex_key;
typedef typename T::filtration_type Filtration_value;
typedef Simplex_key Simplex_handle;
-
//*********************************************//
// Constructors
//*********************************************//
@@ -77,12 +78,12 @@ class Bitmap_cubical_complex : public T {
/**
* Constructor form a Perseus-style file.
**/
- Bitmap_cubical_complex(const char* perseus_style_file) :
- T(perseus_style_file), key_associated_to_simplex(this->total_number_of_cells + 1) {
+ Bitmap_cubical_complex(const char* perseus_style_file)
+ : T(perseus_style_file), key_associated_to_simplex(this->total_number_of_cells + 1) {
if (globalDbg) {
std::cerr << "Bitmap_cubical_complex( const char* perseus_style_file )\n";
}
- for (size_t i = 0; i != this->total_number_of_cells; ++i) {
+ for (std::size_t i = 0; i != this->total_number_of_cells; ++i) {
this->key_associated_to_simplex[i] = i;
}
// we initialize this only once, in each constructor, when the bitmap is constructed.
@@ -97,10 +98,9 @@ class Bitmap_cubical_complex : public T {
* with filtration on top dimensional cells.
**/
Bitmap_cubical_complex(const std::vector<unsigned>& dimensions,
- const std::vector<Filtration_value>& top_dimensional_cells) :
- T(dimensions, top_dimensional_cells),
- key_associated_to_simplex(this->total_number_of_cells + 1) {
- for (size_t i = 0; i != this->total_number_of_cells; ++i) {
+ const std::vector<Filtration_value>& top_dimensional_cells)
+ : T(dimensions, top_dimensional_cells), key_associated_to_simplex(this->total_number_of_cells + 1) {
+ for (std::size_t i = 0; i != this->total_number_of_cells; ++i) {
this->key_associated_to_simplex[i] = i;
}
// we initialize this only once, in each constructor, when the bitmap is constructed.
@@ -118,10 +118,10 @@ class Bitmap_cubical_complex : public T {
**/
Bitmap_cubical_complex(const std::vector<unsigned>& dimensions,
const std::vector<Filtration_value>& top_dimensional_cells,
- std::vector< bool > directions_in_which_periodic_b_cond_are_to_be_imposed) :
- T(dimensions, top_dimensional_cells, directions_in_which_periodic_b_cond_are_to_be_imposed),
- key_associated_to_simplex(this->total_number_of_cells + 1) {
- for (size_t i = 0; i != this->total_number_of_cells; ++i) {
+ std::vector<bool> directions_in_which_periodic_b_cond_are_to_be_imposed)
+ : T(dimensions, top_dimensional_cells, directions_in_which_periodic_b_cond_are_to_be_imposed),
+ key_associated_to_simplex(this->total_number_of_cells + 1) {
+ for (std::size_t i = 0; i != this->total_number_of_cells; ++i) {
this->key_associated_to_simplex[i] = i;
}
// we initialize this only once, in each constructor, when the bitmap is constructed.
@@ -142,9 +142,7 @@ class Bitmap_cubical_complex : public T {
/**
* Returns number of all cubes in the complex.
**/
- size_t num_simplices()const {
- return this->total_number_of_cells;
- }
+ std::size_t num_simplices() const { return this->total_number_of_cells; }
/**
* Returns a Simplex_handle to a cube that do not exist in this complex.
@@ -159,14 +157,12 @@ class Bitmap_cubical_complex : public T {
/**
* Returns dimension of the complex.
**/
- inline size_t dimension()const {
- return this->sizes.size();
- }
+ inline std::size_t dimension() const { return this->sizes.size(); }
/**
* Return dimension of a cell pointed by the Simplex_handle.
**/
- inline unsigned dimension(Simplex_handle sh)const {
+ inline unsigned dimension(Simplex_handle sh) const {
if (globalDbg) {
std::cerr << "unsigned dimension(const Simplex_handle& sh)\n";
}
@@ -199,7 +195,7 @@ class Bitmap_cubical_complex : public T {
/**
* Return the key of a cube pointed by the Simplex_handle.
**/
- Simplex_key key(Simplex_handle sh)const {
+ Simplex_key key(Simplex_handle sh) const {
if (globalDbg) {
std::cerr << "Simplex_key key(const Simplex_handle& sh)\n";
}
@@ -217,7 +213,7 @@ class Bitmap_cubical_complex : public T {
std::cerr << "Simplex_handle simplex(Simplex_key key)\n";
}
if (key != null_key()) {
- return this->simplex_associated_to_key[ key ];
+ return this->simplex_associated_to_key[key];
}
return null_simplex();
}
@@ -246,8 +242,8 @@ class Bitmap_cubical_complex : public T {
/**
* Boundary_simplex_range class provides ranges for boundary iterators.
**/
- typedef typename std::vector< Simplex_handle >::iterator Boundary_simplex_iterator;
- typedef typename std::vector< Simplex_handle > Boundary_simplex_range;
+ typedef typename std::vector<Simplex_handle>::iterator Boundary_simplex_iterator;
+ typedef typename std::vector<Simplex_handle> Boundary_simplex_range;
/**
* Filtration_simplex_iterator class provides an iterator though the whole structure in the order of filtration.
@@ -257,13 +253,13 @@ class Bitmap_cubical_complex : public T {
**/
class Filtration_simplex_range;
- class Filtration_simplex_iterator : std::iterator< std::input_iterator_tag, Simplex_handle > {
+ class Filtration_simplex_iterator : std::iterator<std::input_iterator_tag, Simplex_handle> {
// Iterator over all simplices of the complex in the order of the indexing scheme.
// 'value_type' must be 'Simplex_handle'.
public:
- Filtration_simplex_iterator(Bitmap_cubical_complex* b) : b(b), position(0) { }
+ Filtration_simplex_iterator(Bitmap_cubical_complex* b) : b(b), position(0) {}
- Filtration_simplex_iterator() : b(NULL), position(0) { }
+ Filtration_simplex_iterator() : b(NULL), position(0) {}
Filtration_simplex_iterator operator++() {
if (globalDbg) {
@@ -288,14 +284,14 @@ class Bitmap_cubical_complex : public T {
return (*this);
}
- bool operator==(const Filtration_simplex_iterator& rhs)const {
+ bool operator==(const Filtration_simplex_iterator& rhs) const {
if (globalDbg) {
std::cerr << "bool operator == ( const Filtration_simplex_iterator& rhs )\n";
}
- return ( this->position == rhs.position);
+ return (this->position == rhs.position);
}
- bool operator!=(const Filtration_simplex_iterator& rhs)const {
+ bool operator!=(const Filtration_simplex_iterator& rhs) const {
if (globalDbg) {
std::cerr << "bool operator != ( const Filtration_simplex_iterator& rhs )\n";
}
@@ -306,14 +302,14 @@ class Bitmap_cubical_complex : public T {
if (globalDbg) {
std::cerr << "Simplex_handle operator*()\n";
}
- return this->b->simplex_associated_to_key[ this->position ];
+ return this->b->simplex_associated_to_key[this->position];
}
friend class Filtration_simplex_range;
private:
Bitmap_cubical_complex<T>* b;
- size_t position;
+ std::size_t position;
};
/**
@@ -326,7 +322,7 @@ class Bitmap_cubical_complex : public T {
typedef Filtration_simplex_iterator const_iterator;
typedef Filtration_simplex_iterator iterator;
- Filtration_simplex_range(Bitmap_cubical_complex<T>* b) : b(b) { }
+ Filtration_simplex_range(Bitmap_cubical_complex<T>* b) : b(b) {}
Filtration_simplex_iterator begin() {
if (globalDbg) {
@@ -348,8 +344,6 @@ class Bitmap_cubical_complex : public T {
Bitmap_cubical_complex<T>* b;
};
-
-
//*********************************************//
// Methods to access iterators from the container:
@@ -357,9 +351,7 @@ class Bitmap_cubical_complex : public T {
* boundary_simplex_range creates an object of a Boundary_simplex_range class
* that provides ranges for the Boundary_simplex_iterator.
**/
- Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) {
- return this->get_boundary_of_a_cell(sh);
- }
+ Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) { return this->get_boundary_of_a_cell(sh); }
/**
* filtration_simplex_range creates an object of a Filtration_simplex_range class
@@ -374,8 +366,6 @@ class Bitmap_cubical_complex : public T {
}
//*********************************************//
-
-
//*********************************************//
// Elements which are in Gudhi now, but I (and in all the cases I asked also Marc) do not understand why they are
// there.
@@ -390,43 +380,41 @@ class Bitmap_cubical_complex : public T {
* Function needed for compatibility with Gudhi. Not useful for other purposes.
**/
std::pair<Simplex_handle, Simplex_handle> endpoints(Simplex_handle sh) {
- std::vector< size_t > bdry = this->get_boundary_of_a_cell(sh);
+ std::vector<std::size_t> bdry = this->get_boundary_of_a_cell(sh);
if (globalDbg) {
std::cerr << "std::pair<Simplex_handle, Simplex_handle> endpoints( Simplex_handle sh )\n";
std::cerr << "bdry.size() : " << bdry.size() << std::endl;
}
// this method returns two first elements from the boundary of sh.
if (bdry.size() < 2)
- throw("Error in endpoints in Bitmap_cubical_complex class. The cell have less than two elements in the "
- "boundary.");
+ throw(
+ "Error in endpoints in Bitmap_cubical_complex class. The cell have less than two elements in the "
+ "boundary.");
return std::make_pair(bdry[0], bdry[1]);
}
-
/**
* Class needed for compatibility with Gudhi. Not useful for other purposes.
**/
class Skeleton_simplex_range;
- class Skeleton_simplex_iterator : std::iterator< std::input_iterator_tag, Simplex_handle > {
+ class Skeleton_simplex_iterator : std::iterator<std::input_iterator_tag, Simplex_handle> {
// Iterator over all simplices of the complex in the order of the indexing scheme.
// 'value_type' must be 'Simplex_handle'.
public:
- Skeleton_simplex_iterator(Bitmap_cubical_complex* b, size_t d) : b(b), dimension(d) {
+ Skeleton_simplex_iterator(Bitmap_cubical_complex* b, std::size_t d) : b(b), dimension(d) {
if (globalDbg) {
- std::cerr << "Skeleton_simplex_iterator ( Bitmap_cubical_complex* b , size_t d )\n";
+ std::cerr << "Skeleton_simplex_iterator ( Bitmap_cubical_complex* b , std::size_t d )\n";
}
// find the position of the first simplex of a dimension d
this->position = 0;
- while (
- (this->position != b->data.size()) &&
- (this->b->get_dimension_of_a_cell(this->position) != this->dimension)
- ) {
+ while ((this->position != b->data.size()) &&
+ (this->b->get_dimension_of_a_cell(this->position) != this->dimension)) {
++this->position;
}
}
- Skeleton_simplex_iterator() : b(NULL), position(0), dimension(0) { }
+ Skeleton_simplex_iterator() : b(NULL), position(0), dimension(0) {}
Skeleton_simplex_iterator operator++() {
if (globalDbg) {
@@ -434,10 +422,8 @@ class Bitmap_cubical_complex : public T {
}
// increment the position as long as you did not get to the next element of the dimension dimension.
++this->position;
- while (
- (this->position != this->b->data.size()) &&
- (this->b->get_dimension_of_a_cell(this->position) != this->dimension)
- ) {
+ while ((this->position != this->b->data.size()) &&
+ (this->b->get_dimension_of_a_cell(this->position) != this->dimension)) {
++this->position;
}
return (*this);
@@ -459,14 +445,14 @@ class Bitmap_cubical_complex : public T {
return (*this);
}
- bool operator==(const Skeleton_simplex_iterator& rhs)const {
+ bool operator==(const Skeleton_simplex_iterator& rhs) const {
if (globalDbg) {
std::cerr << "bool operator ==\n";
}
- return ( this->position == rhs.position);
+ return (this->position == rhs.position);
}
- bool operator!=(const Skeleton_simplex_iterator& rhs)const {
+ bool operator!=(const Skeleton_simplex_iterator& rhs) const {
if (globalDbg) {
std::cerr << "bool operator != ( const Skeleton_simplex_iterator& rhs )\n";
}
@@ -481,9 +467,10 @@ class Bitmap_cubical_complex : public T {
}
friend class Skeleton_simplex_range;
+
private:
Bitmap_cubical_complex<T>* b;
- size_t position;
+ std::size_t position;
unsigned dimension;
};
@@ -497,7 +484,7 @@ class Bitmap_cubical_complex : public T {
typedef Skeleton_simplex_iterator const_iterator;
typedef Skeleton_simplex_iterator iterator;
- Skeleton_simplex_range(Bitmap_cubical_complex<T>* b, unsigned dimension) : b(b), dimension(dimension) { }
+ Skeleton_simplex_range(Bitmap_cubical_complex<T>* b, unsigned dimension) : b(b), dimension(dimension) {}
Skeleton_simplex_iterator begin() {
if (globalDbg) {
@@ -533,8 +520,8 @@ class Bitmap_cubical_complex : public T {
friend class is_before_in_filtration<T>;
protected:
- std::vector< size_t > key_associated_to_simplex;
- std::vector< size_t > simplex_associated_to_key;
+ std::vector<std::size_t> key_associated_to_simplex;
+ std::vector<std::size_t> simplex_associated_to_key;
}; // Bitmap_cubical_complex
template <typename T>
@@ -542,7 +529,7 @@ void Bitmap_cubical_complex<T>::initialize_simplex_associated_to_key() {
if (globalDbg) {
std::cerr << "void Bitmap_cubical_complex<T>::initialize_elements_ordered_according_to_filtration() \n";
}
- this->simplex_associated_to_key = std::vector<size_t>(this->data.size());
+ this->simplex_associated_to_key = std::vector<std::size_t>(this->data.size());
std::iota(std::begin(simplex_associated_to_key), std::end(simplex_associated_to_key), 0);
#ifdef GUDHI_USE_TBB
tbb::parallel_sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(),
@@ -552,16 +539,15 @@ void Bitmap_cubical_complex<T>::initialize_simplex_associated_to_key() {
#endif
// we still need to deal here with a key_associated_to_simplex:
- for ( size_t i = 0 ; i != simplex_associated_to_key.size() ; ++i ) {
- this->key_associated_to_simplex[ simplex_associated_to_key[i] ] = i;
+ for (std::size_t i = 0; i != simplex_associated_to_key.size(); ++i) {
+ this->key_associated_to_simplex[simplex_associated_to_key[i]] = i;
}
}
template <typename T>
class is_before_in_filtration {
public:
- explicit is_before_in_filtration(Bitmap_cubical_complex<T> * CC)
- : CC_(CC) { }
+ explicit is_before_in_filtration(Bitmap_cubical_complex<T>* CC) : CC_(CC) {}
bool operator()(const typename Bitmap_cubical_complex<T>::Simplex_handle& sh1,
const typename Bitmap_cubical_complex<T>::Simplex_handle& sh2) const {
@@ -573,8 +559,8 @@ class is_before_in_filtration {
return fil1 < fil2;
}
// in this case they are on the same filtration level, so the dimension decide.
- size_t dim1 = CC_->get_dimension_of_a_cell(sh1);
- size_t dim2 = CC_->get_dimension_of_a_cell(sh2);
+ std::size_t dim1 = CC_->get_dimension_of_a_cell(sh1);
+ std::size_t dim2 = CC_->get_dimension_of_a_cell(sh2);
if (dim1 != dim2) {
return dim1 < dim2;
}
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