multipers 2.2.3__cp310-cp310-win_amd64.whl → 2.3.0__cp310-cp310-win_amd64.whl

multipers/simplex_tree_multi.pxd

@@ -1,133 +1,133 @@
-# 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
-from libcpp.map cimport map
-
-from libc.stdint cimport intptr_t, int32_t
-
-__author__ = "Vincent Rouvreau"
-__copyright__ = "Copyright (C) 2016 Inria"
-__license__ = "MIT"
-
-
-from multipers.filtrations cimport *
-
-
-ctypedef int dimension_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
-
-ctypedef vector[unsigned int] boundary_type
-ctypedef vector[boundary_type] boundary_matrix
-
-cdef extern from "Simplex_tree_multi_interface.h" namespace "Gudhi::multiparameter::python_interface":
-
-  cdef cppclass Simplex_tree_multi_simplex_handle[F=*]:
-    pass
-
-  cdef cppclass Simplex_tree_multi_simplices_iterator[F=*]:
-    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[F=*]:
-    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[F=*]:
-    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[F=*, value_type=*]:
-    ctypedef pair[simplex_type, F*] simplex_filtration_type
-    Simplex_tree_multi_interface() nogil
-    Simplex_tree_multi_interface(Simplex_tree_multi_interface&) nogil
-    F* simplex_filtration(const vector[int]& simplex) nogil
-    void assign_simplex_filtration(vector[int]& simplex, const F& filtration) noexcept 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, F& filtration) noexcept nogil
-    # vector[simplex_filtration_type] get_star(const vector[int]& simplex) nogil
-    # vector[simplex_filtration_type] get_cofaces(const vector[int]& simplex, int dimension) nogil
-    void expansion(int max_dim)  except + nogil
-    void remove_maximal_simplex(simplex_type simplex) nogil
-    # bool prune_above_filtration(filtration_type filtration) nogil
-    bool prune_above_dimension(int dimension) nogil
-    bool make_filtration_non_decreasing()  except + nogil
-    # void compute_extended_filtration() nogil
-    # Simplex_tree_multi_interface* collapse_edges(int nb_collapse_iteration)  except + nogil
-    void reset_filtration(const F& filtration, int dimension) nogil
-    bint operator==(Simplex_tree_multi_interface) nogil
-    # Iterators over Simplex tree
-    pair[simplex_type,F*] get_simplex_and_filtration(Simplex_tree_multi_simplex_handle f_simplex) nogil
-    Simplex_tree_multi_simplices_iterator[F] get_simplices_iterator_begin() nogil
-    Simplex_tree_multi_simplices_iterator[F] get_simplices_iterator_end() nogil
-    vector[Simplex_tree_multi_simplex_handle[F]].const_iterator get_filtration_iterator_begin() nogil
-    vector[Simplex_tree_multi_simplex_handle[F]].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)  except + nogil
-    # 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 set_keys_to_enumerate() nogil const
-    int get_key(const simplex_type) nogil
-    void set_key(simplex_type, int) nogil
-    void fill_lowerstar(const F&, int) except+ nogil
-    simplex_list get_simplices_of_dimension(int) nogil
-    edge_list get_edge_list() nogil
-    # euler_char_list euler_char(const vector[filtration_type]&) nogil
-    void resize_all_filtrations(int) nogil
-    void set_number_of_parameters(int) nogil
-    int get_number_of_parameters() nogil
-    void serialize(char* buffer, const size_t buffer_size)  except + nogil
-    void deserialize(const char* buffer, const size_t buffer_size)  except + nogil
-    size_t get_serialization_size() nogil
-    void clear() nogil
-  
-    
-    void from_std(char*, size_t, int, F&) nogil
-    void to_std(intptr_t, Line[double],int ) nogil 
-    void to_std_linear_projection(intptr_t, vector[double]) nogil
-    void squeeze_filtration_inplace(vector[vector[double]] &, bool) nogil
-    void squeeze_filtration(intptr_t, vector[vector[double]] &) nogil
-    vector[vector[vector[value_type]]] get_filtration_values(const vector[int]&) nogil
-
-
-    pair[boundary_matrix, vector[One_critical_filtration[value_type]]] simplextree_to_boundary_filtration()
-    vector[pair[ vector[vector[value_type]],boundary_matrix]] simplextree_to_scc()
-    vector[pair[ vector[vector[vector[value_type]]],boundary_matrix]] kcritical_simplextree_to_scc()
-
-    vector[pair[ vector[vector[vector[value_type]]],boundary_matrix]] function_simplextree_to_scc()
-    pair[vector[vector[value_type]],boundary_matrix ] simplextree_to_ordered_bf()
-    # vector[map[value_type,int32_t]] build_idx_map(const vector[int]&) nogil
-    # pair[vector[vector[int32_t]],vector[vector[int32_t]]] get_pts_indices(const vector[map[value_type,int32_t]]&, const vector[vector[value_type]]&) nogil
-    pair[vector[vector[int32_t]],vector[vector[int32_t]]] pts_to_indices(vector[vector[value_type]]&, vector[int]&) nogil
-
+# 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
+from libcpp.map cimport map
+
+from libc.stdint cimport intptr_t, int32_t
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016 Inria"
+__license__ = "MIT"
+
+
+from multipers.filtrations cimport *
+
+
+ctypedef int dimension_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
+
+ctypedef vector[unsigned int] boundary_type
+ctypedef vector[boundary_type] boundary_matrix
+
+cdef extern from "Simplex_tree_multi_interface.h" namespace "Gudhi::multiparameter::python_interface":
+
+  cdef cppclass Simplex_tree_multi_simplex_handle[F=*]:
+    pass
+
+  cdef cppclass Simplex_tree_multi_simplices_iterator[F=*]:
+    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[F=*]:
+    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[F=*]:
+    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[F=*, value_type=*]:
+    ctypedef pair[simplex_type, F*] simplex_filtration_type
+    Simplex_tree_multi_interface() nogil
+    Simplex_tree_multi_interface(Simplex_tree_multi_interface&) nogil
+    F* simplex_filtration(const vector[int]& simplex) nogil
+    void assign_simplex_filtration(vector[int]& simplex, const F& filtration) noexcept 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, F& filtration) noexcept nogil
+    # vector[simplex_filtration_type] get_star(const vector[int]& simplex) nogil
+    # vector[simplex_filtration_type] get_cofaces(const vector[int]& simplex, int dimension) nogil
+    void expansion(int max_dim)  except + nogil
+    void remove_maximal_simplex(simplex_type simplex) nogil
+    # bool prune_above_filtration(filtration_type filtration) nogil
+    bool prune_above_dimension(int dimension) nogil
+    bool make_filtration_non_decreasing()  except + nogil
+    # void compute_extended_filtration() nogil
+    # Simplex_tree_multi_interface* collapse_edges(int nb_collapse_iteration)  except + nogil
+    void reset_filtration(const F& filtration, int dimension) nogil
+    bint operator==(Simplex_tree_multi_interface) nogil
+    # Iterators over Simplex tree
+    pair[simplex_type,F*] get_simplex_and_filtration(Simplex_tree_multi_simplex_handle f_simplex) nogil
+    Simplex_tree_multi_simplices_iterator[F] get_simplices_iterator_begin() nogil
+    Simplex_tree_multi_simplices_iterator[F] get_simplices_iterator_end() nogil
+    vector[Simplex_tree_multi_simplex_handle[F]].const_iterator get_filtration_iterator_begin() nogil
+    vector[Simplex_tree_multi_simplex_handle[F]].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)  except + nogil
+    # 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 set_keys_to_enumerate() nogil const
+    int get_key(const simplex_type) nogil
+    void set_key(simplex_type, int) nogil
+    void fill_lowerstar(const F&, int) except+ nogil
+    simplex_list get_simplices_of_dimension(int) nogil
+    edge_list get_edge_list() nogil
+    # euler_char_list euler_char(const vector[filtration_type]&) nogil
+    void resize_all_filtrations(int) nogil
+    void set_number_of_parameters(int) nogil
+    int get_number_of_parameters() nogil
+    void serialize(char* buffer, const size_t buffer_size)  except + nogil
+    void deserialize(const char* buffer, const size_t buffer_size)  except + nogil
+    size_t get_serialization_size() nogil
+    void clear() nogil
+  
+    
+    void from_std(char*, size_t, int, F&) nogil
+    void to_std(intptr_t, Line[double],int ) nogil 
+    void to_std_linear_projection(intptr_t, vector[double]) nogil
+    void squeeze_filtration_inplace(vector[vector[double]] &, bool) nogil
+    void squeeze_filtration(intptr_t, vector[vector[double]] &) nogil
+    vector[vector[vector[value_type]]] get_filtration_values(const vector[int]&) nogil
+
+
+    pair[boundary_matrix, vector[One_critical_filtration[value_type]]] simplextree_to_boundary_filtration()
+    vector[pair[ vector[vector[value_type]],boundary_matrix]] simplextree_to_scc()
+    vector[pair[ vector[vector[vector[value_type]]],boundary_matrix]] kcritical_simplextree_to_scc()
+
+    vector[pair[ vector[vector[vector[value_type]]],boundary_matrix]] function_simplextree_to_scc()
+    pair[vector[vector[value_type]],boundary_matrix ] simplextree_to_ordered_bf()
+    # vector[map[value_type,int32_t]] build_idx_map(const vector[int]&) nogil
+    # pair[vector[vector[int32_t]],vector[vector[int32_t]]] get_pts_indices(const vector[map[value_type,int32_t]]&, const vector[vector[value_type]]&) nogil
+    pair[vector[vector[int32_t]],vector[vector[int32_t]]] pts_to_indices(vector[vector[value_type]]&, vector[int]&) nogil
+

multipers/simplex_tree_multi.pyx

@@ -51,15 +51,14 @@ cimport cython
 from gudhi.simplex_tree import SimplexTree ## Small hack for typing
 from typing import Iterable,Literal,Optional
 from tqdm import tqdm
-import multipers.grids as mpg
-
+from multipers.grids import Lstrategies, compute_grid
 from multipers.point_measure import signed_betti, rank_decomposition_by_rectangles, sparsify
 
 from warnings import warn
 
 SAFE_CONVERSION=False #Slower but at least it works everywhere
 
-_available_strategies =mpg.Lstrategies
+_available_strategies =Lstrategies
 
 
 
@@ -796,7 +795,8 @@ cdef class SimplexTreeMulti_KFi32:
                         file.write(str(i) + " ")
                     file.write("; ")
                     for f in F:
-                        file.write(str(f) + " ")
+                        for fi in f:
+                            file.write(str(fi) + " ")
                     file.write("\n")
                     bar.update(1)
         file.close()
@@ -850,7 +850,7 @@ cdef class SimplexTreeMulti_KFi32:
         # removes nan
         filtrations_values = [filtration[:-1] if np.isnan(filtration[-1]) else filtration for filtration in filtrations_values]
 
-        return mpg.compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
+        return compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
 
 
 
@@ -2223,7 +2223,7 @@ cdef class SimplexTreeMulti_Fi32:
         # removes nan
         filtrations_values = [filtration[:-1] if np.isnan(filtration[-1]) else filtration for filtration in filtrations_values]
 
-        return mpg.compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
+        return compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
 
 
 
@@ -3262,7 +3262,8 @@ cdef class SimplexTreeMulti_KFi64:
                         file.write(str(i) + " ")
                     file.write("; ")
                     for f in F:
-                        file.write(str(f) + " ")
+                        for fi in f:
+                            file.write(str(fi) + " ")
                     file.write("\n")
                     bar.update(1)
         file.close()
@@ -3316,7 +3317,7 @@ cdef class SimplexTreeMulti_KFi64:
         # removes nan
         filtrations_values = [filtration[:-1] if np.isnan(filtration[-1]) else filtration for filtration in filtrations_values]
 
-        return mpg.compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
+        return compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
 
 
 
@@ -4689,7 +4690,7 @@ cdef class SimplexTreeMulti_Fi64:
         # removes nan
         filtrations_values = [filtration[:-1] if np.isnan(filtration[-1]) else filtration for filtration in filtrations_values]
 
-        return mpg.compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
+        return compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
 
 
 
@@ -5728,7 +5729,8 @@ cdef class SimplexTreeMulti_KFf32:
                         file.write(str(i) + " ")
                     file.write("; ")
                     for f in F:
-                        file.write(str(f) + " ")
+                        for fi in f:
+                            file.write(str(fi) + " ")
                     file.write("\n")
                     bar.update(1)
         file.close()
@@ -5782,7 +5784,7 @@ cdef class SimplexTreeMulti_KFf32:
         # removes nan
         filtrations_values = [filtration[:-1] if np.isnan(filtration[-1]) else filtration for filtration in filtrations_values]
 
-        return mpg.compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
+        return compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
 
 
 
@@ -7155,7 +7157,7 @@ cdef class SimplexTreeMulti_Ff32:
         # removes nan
         filtrations_values = [filtration[:-1] if np.isnan(filtration[-1]) else filtration for filtration in filtrations_values]
 
-        return mpg.compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
+        return compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
 
 
 
@@ -8194,7 +8196,8 @@ cdef class SimplexTreeMulti_KFf64:
                         file.write(str(i) + " ")
                     file.write("; ")
                     for f in F:
-                        file.write(str(f) + " ")
+                        for fi in f:
+                            file.write(str(fi) + " ")
                     file.write("\n")
                     bar.update(1)
         file.close()
@@ -8248,7 +8251,7 @@ cdef class SimplexTreeMulti_KFf64:
         # removes nan
         filtrations_values = [filtration[:-1] if np.isnan(filtration[-1]) else filtration for filtration in filtrations_values]
 
-        return mpg.compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
+        return compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
 
 
 
@@ -9621,7 +9624,7 @@ cdef class SimplexTreeMulti_Ff64:
         # removes nan
         filtrations_values = [filtration[:-1] if np.isnan(filtration[-1]) else filtration for filtration in filtrations_values]
 
-        return mpg.compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)
+        return compute_grid(filtrations_values, resolution=resolution,strategy=grid_strategy,drop_quantiles=drop_quantiles)