Multiparameter simplextree

src/Simplex_tree/include/gudhi/Simplex_tree.h

@@ -1754,6 +1754,17 @@ class Simplex_tree {
   /** \brief Upper bound on the dimension of the simplicial complex.*/
   int dimension_;
   bool dimension_to_be_lowered_ = false;
+
+//MULTIPERS STUFF
+public: 
+  void set_number_of_parameters(unsigned int num){
+		number_of_parameters_ = num;
+	}
+	unsigned int get_number_of_parameters() const{
+		return number_of_parameters_;
+	}
+private:
+	unsigned int number_of_parameters_;
 };
 
 // Print a Simplex_tree in os.

src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h

@@ -31,11 +31,14 @@ struct Simplex_tree_node_explicit_storage : SimplexTree::Filtration_simplex_base
   typedef typename SimplexTree::Filtration_value Filtration_value;
   typedef typename SimplexTree::Simplex_key Simplex_key;
 
-  Simplex_tree_node_explicit_storage(Siblings * sib = nullptr,
-                                     Filtration_value filtration = 0)
+  Simplex_tree_node_explicit_storage(Siblings * sib,
+                                     Filtration_value filtration) //MULTIPERS : init to 0 not possible
       : children_(sib) {
     this->assign_filtration(filtration);
   }
+  Simplex_tree_node_explicit_storage() // Empty constructor necessary
+      : children_(nullptr) {
+  }
 
   /*
    * Assign children to the node

src/python/CMakeLists.txt

@@ -55,6 +55,7 @@ if(PYTHONINTERP_FOUND)
     # Cython modules
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_utils', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'simplex_tree', ")
+    set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'simplex_tree_multi', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'rips_complex', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'cubical_complex', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'periodic_cubical_complex', ")
@@ -154,6 +155,7 @@ if(PYTHONINTERP_FOUND)
 
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'off_utils', ")
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'simplex_tree', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'simplex_tree_multi', ")
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'rips_complex', ")
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'cubical_complex', ")
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'periodic_cubical_complex', ")

src/python/gudhi/simplex_tree_multi.pxd

@@ -0,0 +1,102 @@
+# This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+# See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+# Author(s):       Vincent Rouvreau
+#
+# Copyright (C) 2016 Inria
+#
+# Modification(s):
+#	- 2022 David Loiseaux, Hannah Schreiber: adapt for multipersistence. 
+#   - YYYY/MM Author: Description of the modification
+
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.utility cimport pair
+from libcpp cimport bool
+from libcpp.string cimport string
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 Inria"
+__license__ = "MIT"
+
+ctypedef int dimension_type
+ctypedef vector[double] point_type
+ctypedef double filtration_value_type
+ctypedef vector[double] filtration_type
+ctypedef vector[int] simplex_type
+ctypedef vector[simplex_type] simplex_list
+ctypedef vector[pair[pair[int,int], pair[double, double]]] edge_list 
+ctypedef vector[int] euler_char_list
+
+cdef extern from "Simplex_tree_interface_multi.h" namespace "Gudhi":
+	cdef cppclass Simplex_tree_options_multidimensional_filtration:
+		pass
+
+	cdef cppclass Simplex_tree_multi_simplex_handle "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_multidimensional_filtration>::Simplex_handle":
+		pass
+
+	cdef cppclass Simplex_tree_multi_simplices_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_multidimensional_filtration>::Complex_simplex_iterator":
+		Simplex_tree_multi_simplices_iterator() nogil
+		Simplex_tree_multi_simplex_handle& operator*() nogil
+		Simplex_tree_multi_simplices_iterator operator++() nogil
+		bint operator!=(Simplex_tree_multi_simplices_iterator) nogil
+
+	cdef cppclass Simplex_tree_multi_skeleton_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_multidimensional_filtration>::Skeleton_simplex_iterator":
+		Simplex_tree_multi_skeleton_iterator() nogil
+		Simplex_tree_multi_simplex_handle& operator*() nogil
+		Simplex_tree_multi_skeleton_iterator operator++() nogil
+		bint operator!=(Simplex_tree_multi_skeleton_iterator) nogil
+
+	cdef cppclass Simplex_tree_multi_boundary_iterator "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_multidimensional_filtration>::Boundary_simplex_iterator":
+		Simplex_tree_multi_boundary_iterator() nogil
+		Simplex_tree_multi_simplex_handle& operator*() nogil
+		Simplex_tree_multi_boundary_iterator operator++() nogil
+		bint operator!=(Simplex_tree_multi_boundary_iterator) nogil
+
+
+	cdef cppclass Simplex_tree_multi_interface "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_multidimensional_filtration>":
+		Simplex_tree_multi_interface() nogil
+		Simplex_tree_multi_interface(Simplex_tree_multi_interface&) nogil
+		filtration_type simplex_filtration(vector[int] simplex) nogil
+		void assign_simplex_filtration(vector[int] simplex, filtration_type filtration) nogil
+		void initialize_filtration() nogil
+		int num_vertices() nogil
+		int num_simplices() nogil
+		void set_dimension(int dimension) nogil
+		dimension_type dimension() nogil
+		dimension_type upper_bound_dimension() nogil
+		bool find_simplex(vector[int] simplex) nogil
+		bool insert(vector[int] simplex, filtration_type filtration) nogil
+		vector[pair[simplex_type, filtration_type]] get_star(vector[int] simplex) nogil
+		vector[pair[simplex_type, filtration_type]] get_cofaces(vector[int] simplex, int dimension) nogil
+		void expansion(int max_dim) nogil except +
+		void remove_maximal_simplex(simplex_type simplex) nogil
+		bool prune_above_filtration(filtration_type filtration) nogil
+		# bool make_filtration_non_decreasing() nogil
+		# void compute_extended_filtration() nogil
+		Simplex_tree_multi_interface* collapse_edges(int nb_collapse_iteration) nogil except +
+		void reset_filtration(filtration_type filtration, int dimension) nogil
+		bint operator==(Simplex_tree_multi_interface) nogil
+		# Iterators over Simplex tree
+		pair[simplex_type, filtration_type] get_simplex_and_filtration(Simplex_tree_multi_simplex_handle f_simplex) nogil
+		Simplex_tree_multi_simplices_iterator get_simplices_iterator_begin() nogil
+		Simplex_tree_multi_simplices_iterator get_simplices_iterator_end() nogil
+		vector[Simplex_tree_multi_simplex_handle].const_iterator get_filtration_iterator_begin() nogil
+		vector[Simplex_tree_multi_simplex_handle].const_iterator get_filtration_iterator_end() nogil
+		Simplex_tree_multi_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil
+		Simplex_tree_multi_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil
+		pair[Simplex_tree_multi_boundary_iterator, Simplex_tree_multi_boundary_iterator] get_boundary_iterators(vector[int] simplex) nogil except +
+		# Expansion with blockers
+		ctypedef bool (*blocker_func_t)(vector[int], void *user_data)
+		void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data)
+
+		## MULTIPERS STUFF
+		void reset_keys() nogil
+		int get_key(const simplex_type) nogil
+		void set_key(simplex_type, int) nogil
+		void fill_lowerstar(vector[double], int) nogil
+		simplex_list get_simplices_of_dimension(int) nogil
+		edge_list get_edge_list() nogil
+		euler_char_list euler_char(vector[filtration_type]) nogil
+		void resize_all_filtrations(int) nogil
+		void set_number_of_parameters(int) nogil
+		int get_number_of_parameters() nogil