Merge pull request GUDHI#846 from mglisse/cubical-misc

More cubical clean-ups

src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h

@@ -25,6 +25,7 @@
 #include <vector>
 #include <numeric>  // for iota
 #include <cstddef>
+#include <stdexcept>
 
 namespace Gudhi {
 
@@ -112,7 +113,7 @@ class Bitmap_cubical_complex : public T {
   /**
    * Returns number of all cubes in the complex.
    **/
-  std::size_t num_simplices() const { return this->total_number_of_cells; }
+  std::size_t num_simplices() const { return this->data.size(); }
 
   /**
    * Returns a Simplex_handle to a cube that do not exist in this complex.
@@ -136,12 +137,12 @@ class Bitmap_cubical_complex : public T {
 #ifdef DEBUG_TRACES
     std::clog << "unsigned dimension(const Simplex_handle& sh)\n";
 #endif
-    if (sh != null_simplex()) return this->get_dimension_of_a_cell(sh);
-    return -1;
+    GUDHI_CHECK(sh != null_simplex(), std::logic_error("Only real cells have a dimension"));
+    return this->get_dimension_of_a_cell(sh);
   }
 
   /**
-   * Return the filtration of a cell pointed by the Simplex_handle.
+   * Return the filtration of a cell pointed by the Simplex_handle, or +inf for `null_simplex()`.
    **/
   Filtration_value filtration(Simplex_handle sh) {
 #ifdef DEBUG_TRACES
@@ -271,9 +272,6 @@ class Bitmap_cubical_complex : public T {
     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 {
@@ -348,7 +346,7 @@ class Bitmap_cubical_complex : public T {
   };
 
   /**
-   * @brief Class needed for compatibility with Gudhi. Not useful for other purposes.
+   * @brief A range containing all the cells of dimension at most k.
    **/
   class Skeleton_simplex_range {
     // Range over the simplices of the complex in the order of the filtration.
@@ -381,7 +379,7 @@ class Bitmap_cubical_complex : public T {
   };
 
   /**
-   * Function needed for compatibility with Gudhi. Not useful for other purposes.
+   * Returns a range containing all the cells of dimension at most `dimension`.
    **/
   Skeleton_simplex_range skeleton_simplex_range(unsigned dimension) {
 #ifdef DEBUG_TRACES

src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h

@@ -61,7 +61,7 @@ class Bitmap_cubical_complex_base {
   /**
    *Default constructor
    **/
-  Bitmap_cubical_complex_base() : total_number_of_cells(0) {}
+  Bitmap_cubical_complex_base() {}
   /**
    * There are a few constructors of a Bitmap_cubical_complex_base class.
    * First one, that takes vector<unsigned>, creates an empty bitmap of a dimension equal
@@ -541,7 +541,7 @@ class Bitmap_cubical_complex_base {
   //****************************************************************************************************************//
   //****************************************************************************************************************//
 
-  inline std::size_t number_cells() const { return this->total_number_of_cells; }
+  inline std::size_t number_cells() const { return this->data.size(); }
 
   //****************************************************************************************************************//
   //****************************************************************************************************************//
@@ -557,7 +557,6 @@ class Bitmap_cubical_complex_base {
   std::vector<unsigned> sizes;
   std::vector<unsigned> multipliers;
   std::vector<T> data;
-  std::size_t total_number_of_cells;
 
   template <class F> void for_each_vertex_rec(F&&f, std::size_t base, int dim);
   void propagate_from_vertices_rec(int special_dim, int current_dim, std::size_t base);
@@ -574,7 +573,6 @@ class Bitmap_cubical_complex_base {
       this->data = std::vector<T>(multiplier, std::numeric_limits<T>::infinity());
     else
       this->data = std::vector<T>(multiplier, -std::numeric_limits<T>::infinity());
-    this->total_number_of_cells = multiplier;
   }
 
   std::size_t compute_position_in_bitmap(const std::vector<unsigned>& counter) {

src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h

@@ -289,7 +289,6 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c
       this->data = std::vector<T>(multiplier, std::numeric_limits<T>::infinity());
     else
       this->data = std::vector<T>(multiplier, -std::numeric_limits<T>::infinity());
-    this->total_number_of_cells = multiplier;
   }
   Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& sizes);
   Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& dimensions,

src/python/gudhi/cubical_complex.pyx

@@ -29,17 +29,17 @@ __license__ = "MIT"
 np.import_array()
 
 cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
-    cdef cppclass Bitmap_cubical_complex_base_interface "Gudhi::Cubical_complex::Cubical_complex_interface":
-        Bitmap_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] cells, bool input_top_cells) nogil except +
-        Bitmap_cubical_complex_base_interface(const char* perseus_file) nogil except +
+    cdef cppclass Bitmap_cubical_complex_interface "Gudhi::Cubical_complex::Cubical_complex_interface":
+        Bitmap_cubical_complex_interface(vector[unsigned] dimensions, vector[double] cells, bool input_top_cells) nogil except +
+        Bitmap_cubical_complex_interface(const char* perseus_file) nogil except +
         int num_simplices() nogil
         int dimension() nogil
         vector[unsigned] shape() nogil
         vector[double] data
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Cubical_complex_interface>":
-        Cubical_complex_persistence_interface(Bitmap_cubical_complex_base_interface * st, bool persistence_dim_max) nogil
+        Cubical_complex_persistence_interface(Bitmap_cubical_complex_interface * st, bool persistence_dim_max) nogil
         void compute_persistence(int homology_coeff_field, double min_persistence) nogil except +
         vector[pair[int, pair[double, double]]] get_persistence() nogil
         vector[vector[int]] cofaces_of_cubical_persistence_pairs() nogil
@@ -54,7 +54,7 @@ cdef class CubicalComplex:
     computational mathematics (specially rigorous numerics) and image
     analysis.
     """
-    cdef Bitmap_cubical_complex_base_interface * thisptr
+    cdef Bitmap_cubical_complex_interface * thisptr
     cdef Cubical_complex_persistence_interface * pcohptr
     cdef bool _built_from_vertices
 
@@ -127,11 +127,11 @@ cdef class CubicalComplex:
 
     def _construct_from_cells(self, vector[unsigned] dimensions, vector[double] cells, bool input_top_cells):
         with nogil:
-            self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, cells, input_top_cells)
+            self.thisptr = new Bitmap_cubical_complex_interface(dimensions, cells, input_top_cells)
 
     def _construct_from_file(self, const char* filename):
         with nogil:
-            self.thisptr = new Bitmap_cubical_complex_base_interface(filename)
+            self.thisptr = new Bitmap_cubical_complex_interface(filename)
 
     def __dealloc__(self):
         if self.thisptr != NULL:

src/python/gudhi/periodic_cubical_complex.pyx

@@ -27,9 +27,9 @@ __license__ = "MIT"
 np.import_array()
 
 cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
-    cdef cppclass Periodic_cubical_complex_base_interface "Gudhi::Cubical_complex::Periodic_cubical_complex_interface":
-        Periodic_cubical_complex_base_interface(vector[unsigned] dimensions, vector[double] cells, vector[bool] periodic_dimensions, bool input_top_cells) nogil except +
-        Periodic_cubical_complex_base_interface(const char* perseus_file) nogil except +
+    cdef cppclass Periodic_cubical_complex_interface "Gudhi::Cubical_complex::Periodic_cubical_complex_interface":
+        Periodic_cubical_complex_interface(vector[unsigned] dimensions, vector[double] cells, vector[bool] periodic_dimensions, bool input_top_cells) nogil except +
+        Periodic_cubical_complex_interface(const char* perseus_file) nogil except +
         int num_simplices() nogil
         int dimension() nogil
         vector[unsigned] shape() nogil
@@ -38,7 +38,7 @@ cdef extern from "Cubical_complex_interface.h" namespace "Gudhi":
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Periodic_cubical_complex_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Cubical_complex::Periodic_cubical_complex_interface>":
-        Periodic_cubical_complex_persistence_interface(Periodic_cubical_complex_base_interface * st, bool persistence_dim_max) nogil
+        Periodic_cubical_complex_persistence_interface(Periodic_cubical_complex_interface * st, bool persistence_dim_max) nogil
         void compute_persistence(int homology_coeff_field, double min_persistence) nogil except +
         vector[pair[int, pair[double, double]]] get_persistence() nogil
         vector[vector[int]] cofaces_of_cubical_persistence_pairs() nogil
@@ -53,7 +53,7 @@ cdef class PeriodicCubicalComplex:
     in computational mathematics (specially rigorous numerics) and image
     analysis.
     """
-    cdef Periodic_cubical_complex_base_interface * thisptr
+    cdef Periodic_cubical_complex_interface * thisptr
     cdef Periodic_cubical_complex_persistence_interface * pcohptr
     cdef bool _built_from_vertices
 
@@ -137,11 +137,11 @@ cdef class PeriodicCubicalComplex:
 
     def _construct_from_cells(self, vector[unsigned] dimensions, vector[double] cells, vector[bool] periodic_dimensions, bool input_top_cells):
         with nogil:
-            self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, cells, periodic_dimensions, input_top_cells)
+            self.thisptr = new Periodic_cubical_complex_interface(dimensions, cells, periodic_dimensions, input_top_cells)
 
     def _construct_from_file(self, const char* filename):
         with nogil:
-            self.thisptr = new Periodic_cubical_complex_base_interface(filename)
+            self.thisptr = new Periodic_cubical_complex_interface(filename)
 
     def __dealloc__(self):
         if self.thisptr != NULL: