diff options
Diffstat (limited to 'src/python/gudhi')
-rw-r--r-- | src/python/gudhi/alpha_complex.pyx | 13 | ||||
-rw-r--r-- | src/python/gudhi/cubical_complex.pyx | 2 | ||||
-rw-r--r-- | src/python/gudhi/euclidean_strong_witness_complex.pyx | 4 | ||||
-rw-r--r-- | src/python/gudhi/euclidean_witness_complex.pyx | 4 | ||||
-rw-r--r-- | src/python/gudhi/nerve_gic.pyx | 12 | ||||
-rw-r--r-- | src/python/gudhi/off_reader.pyx | 4 | ||||
-rw-r--r-- | src/python/gudhi/periodic_cubical_complex.pyx | 2 | ||||
-rw-r--r-- | src/python/gudhi/reader_utils.pyx | 16 | ||||
-rw-r--r-- | src/python/gudhi/rips_complex.pyx | 2 | ||||
-rw-r--r-- | src/python/gudhi/simplex_tree.pxd | 2 | ||||
-rw-r--r-- | src/python/gudhi/simplex_tree.pyx | 2 | ||||
-rw-r--r-- | src/python/gudhi/strong_witness_complex.pyx | 4 | ||||
-rw-r--r-- | src/python/gudhi/subsampling.pyx | 26 | ||||
-rw-r--r-- | src/python/gudhi/tangential_complex.pyx | 2 | ||||
-rw-r--r-- | src/python/gudhi/witness_complex.pyx | 4 |
15 files changed, 52 insertions, 47 deletions
diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx index 4ff37437..dab4b56f 100644 --- a/src/python/gudhi/alpha_complex.pyx +++ b/src/python/gudhi/alpha_complex.pyx @@ -26,11 +26,11 @@ __license__ = "GPL v3" cdef extern from "Alpha_complex_interface.h" namespace "Gudhi": cdef cppclass Alpha_complex_interface "Gudhi::alpha_complex::Alpha_complex_interface": - Alpha_complex_interface(vector[vector[double]] points) + Alpha_complex_interface(vector[vector[double]] points) except + # bool from_file is a workaround for cython to find the correct signature - Alpha_complex_interface(string off_file, bool from_file) - vector[double] get_point(int vertex) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + Alpha_complex_interface(string off_file, bool from_file) except + + vector[double] get_point(int vertex) except + + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + # AlphaComplex python interface cdef class AlphaComplex: @@ -71,7 +71,7 @@ cdef class AlphaComplex: def __cinit__(self, points = None, off_file = ''): if off_file: if os.path.isfile(off_file): - self.thisptr = new Alpha_complex_interface(str.encode(off_file), True) + self.thisptr = new Alpha_complex_interface(off_file.encode('utf-8'), True) else: print("file " + off_file + " not found.") else: @@ -98,8 +98,7 @@ cdef class AlphaComplex: :rtype: list of float :returns: the point. """ - cdef vector[double] point = self.thisptr.get_point(vertex) - return point + return self.thisptr.get_point(vertex) def create_simplex_tree(self, max_alpha_square = float('inf')): """ diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx index 28913a32..1dd30b4e 100644 --- a/src/python/gudhi/cubical_complex.pyx +++ b/src/python/gudhi/cubical_complex.pyx @@ -87,7 +87,7 @@ cdef class CubicalComplex: elif ((dimensions is None) and (top_dimensional_cells is None) and (perseus_file != '')): if os.path.isfile(perseus_file): - self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file)) + self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file.encode('utf-8')) else: print("file " + perseus_file + " not found.", file=sys.stderr) else: diff --git a/src/python/gudhi/euclidean_strong_witness_complex.pyx b/src/python/gudhi/euclidean_strong_witness_complex.pyx index 9889f92c..aca6084e 100644 --- a/src/python/gudhi/euclidean_strong_witness_complex.pyx +++ b/src/python/gudhi/euclidean_strong_witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "GPL v3" cdef extern from "Euclidean_strong_witness_complex_interface.h" namespace "Gudhi": cdef cppclass Euclidean_strong_witness_complex_interface "Gudhi::witness_complex::Euclidean_strong_witness_complex_interface": Euclidean_strong_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + vector[double] get_point(unsigned vertex) # EuclideanStrongWitnessComplex python interface diff --git a/src/python/gudhi/euclidean_witness_complex.pyx b/src/python/gudhi/euclidean_witness_complex.pyx index e3ce0e82..fb0c2201 100644 --- a/src/python/gudhi/euclidean_witness_complex.pyx +++ b/src/python/gudhi/euclidean_witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "GPL v3" cdef extern from "Euclidean_witness_complex_interface.h" namespace "Gudhi": cdef cppclass Euclidean_witness_complex_interface "Gudhi::witness_complex::Euclidean_witness_complex_interface": Euclidean_witness_complex_interface(vector[vector[double]] landmarks, vector[vector[double]] witnesses) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + vector[double] get_point(unsigned vertex) # EuclideanWitnessComplex python interface diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx index 5eb9be0d..022466c5 100644 --- a/src/python/gudhi/nerve_gic.pyx +++ b/src/python/gudhi/nerve_gic.pyx @@ -182,7 +182,7 @@ cdef class CoverComplex: :returns: Read file status. """ if os.path.isfile(off_file): - return self.thisptr.read_point_cloud(str.encode(off_file)) + return self.thisptr.read_point_cloud(off_file.encode('utf-8')) else: print("file " + off_file + " not found.", file=sys.stderr) return False @@ -214,7 +214,7 @@ cdef class CoverComplex: :type color_file_name: string """ if os.path.isfile(color_file_name): - self.thisptr.set_color_from_file(str.encode(color_file_name)) + self.thisptr.set_color_from_file(color_file_name.encode('utf-8')) else: print("file " + color_file_name + " not found.", file=sys.stderr) @@ -235,7 +235,7 @@ cdef class CoverComplex: :type cover_file_name: string """ if os.path.isfile(cover_file_name): - self.thisptr.set_cover_from_file(str.encode(cover_file_name)) + self.thisptr.set_cover_from_file(cover_file_name.encode('utf-8')) else: print("file " + cover_file_name + " not found.", file=sys.stderr) @@ -268,7 +268,7 @@ cdef class CoverComplex: :type func_file_name: string """ if os.path.isfile(func_file_name): - self.thisptr.set_function_from_file(str.encode(func_file_name)) + self.thisptr.set_function_from_file(func_file_name.encode('utf-8')) else: print("file " + func_file_name + " not found.", file=sys.stderr) @@ -309,7 +309,7 @@ cdef class CoverComplex: :type graph_file_name: string """ if os.path.isfile(graph_file_name): - self.thisptr.set_graph_from_file(str.encode(graph_file_name)) + self.thisptr.set_graph_from_file(graph_file_name.encode('utf-8')) else: print("file " + graph_file_name + " not found.", file=sys.stderr) @@ -370,7 +370,7 @@ cdef class CoverComplex: :param type: either "GIC" or "Nerve". :type type: string """ - self.thisptr.set_type(str.encode(type)) + self.thisptr.set_type(type.encode('utf-8')) def set_verbose(self, verbose): """Specifies whether the program should display information or not. diff --git a/src/python/gudhi/off_reader.pyx b/src/python/gudhi/off_reader.pyx index ef8f420a..0a828b83 100644 --- a/src/python/gudhi/off_reader.pyx +++ b/src/python/gudhi/off_reader.pyx @@ -28,11 +28,11 @@ def read_points_from_off_file(off_file=''): :type off_file: string :returns: The point set. - :rtype: vector[vector[double]] + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): - return read_points_from_OFF_file(str.encode(off_file)) + return read_points_from_OFF_file(off_file.encode('utf-8')) else: print("file " + off_file + " not found.", file=sys.stderr) return [] diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx index 4ec06524..fd08b976 100644 --- a/src/python/gudhi/periodic_cubical_complex.pyx +++ b/src/python/gudhi/periodic_cubical_complex.pyx @@ -95,7 +95,7 @@ cdef class PeriodicCubicalComplex: elif ((dimensions is None) and (top_dimensional_cells is None) and (periodic_dimensions is None) and (perseus_file != '')): if os.path.isfile(perseus_file): - self.thisptr = new Periodic_cubical_complex_base_interface(str.encode(perseus_file)) + self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file.encode('utf-8')) else: print("file " + perseus_file + " not found.", file=sys.stderr) else: diff --git a/src/python/gudhi/reader_utils.pyx b/src/python/gudhi/reader_utils.pyx index 345c92f8..fe1c3a2e 100644 --- a/src/python/gudhi/reader_utils.pyx +++ b/src/python/gudhi/reader_utils.pyx @@ -34,30 +34,30 @@ def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'): :type separator: char :returns: The lower triangular matrix. - :rtype: vector[vector[double]] + :rtype: List[List[float]] """ if csv_file: if path.isfile(csv_file): - return read_matrix_from_csv_file(str.encode(csv_file), ord(separator[0])) + return read_matrix_from_csv_file(csv_file.encode('utf-8'), ord(separator[0])) print("file " + csv_file + " not set or not found.") return [] def read_persistence_intervals_grouped_by_dimension(persistence_file=''): """Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death - The return value is an `map[dim, vector[pair[birth, death]]]` - where `dim` is an `int`, `birth` a `double`, and `death` a `double`. + The return value is a `dict(dim, list(tuple(birth, death)))` + where `dim` is an `int`, `birth` a `float`, and `death` a `float`. Note: the function does not check that birth <= death. :param persistence_file: A persistence file style name. :type persistence_file: string :returns: The persistence pairs grouped by dimension. - :rtype: map[int, vector[pair[double, double]]] + :rtype: Dict[int, List[Tuple[float, float]]] """ if persistence_file: if path.isfile(persistence_file): - return read_pers_intervals_grouped_by_dimension(str.encode(persistence_file)) + return read_pers_intervals_grouped_by_dimension(persistence_file.encode('utf-8')) print("file " + persistence_file + " not set or not found.") return [] @@ -80,7 +80,7 @@ def read_persistence_intervals_in_dimension(persistence_file='', only_this_dim=- """ if persistence_file: if path.isfile(persistence_file): - return np_array(read_pers_intervals_in_dimension(str.encode( - persistence_file), only_this_dim)) + return np_array(read_pers_intervals_in_dimension(persistence_file.encode( + 'utf-8'), only_this_dim)) print("file " + persistence_file + " not set or not found.") return [] diff --git a/src/python/gudhi/rips_complex.pyx b/src/python/gudhi/rips_complex.pyx index 722cdcdc..deb8057a 100644 --- a/src/python/gudhi/rips_complex.pyx +++ b/src/python/gudhi/rips_complex.pyx @@ -28,7 +28,7 @@ cdef extern from "Rips_complex_interface.h" namespace "Gudhi": void init_matrix(vector[vector[double]] values, double threshold) void init_points_sparse(vector[vector[double]] values, double threshold, double sparse) void init_matrix_sparse(vector[vector[double]] values, double threshold, double sparse) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, int dim_max) except + # RipsComplex python interface cdef class RipsComplex: diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 1066d44b..96d14079 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -39,7 +39,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": vector[pair[vector[int], double]] get_star(vector[int] simplex) vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, int dimension) - void expansion(int max_dim) + void expansion(int max_dim) except + void remove_maximal_simplex(vector[int] simplex) bool prune_above_filtration(double filtration) bool make_filtration_non_decreasing() diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 85d25492..b18627c4 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -508,7 +508,7 @@ cdef class SimplexTree: """ if self.pcohptr != NULL: if persistence_file != '': - self.pcohptr.write_output_diagram(str.encode(persistence_file)) + self.pcohptr.write_output_diagram(persistence_file.encode('utf-8')) else: print("persistence_file must be specified") else: diff --git a/src/python/gudhi/strong_witness_complex.pyx b/src/python/gudhi/strong_witness_complex.pyx index 2c33c3f2..9f89d3ae 100644 --- a/src/python/gudhi/strong_witness_complex.pyx +++ b/src/python/gudhi/strong_witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "MIT" cdef extern from "Strong_witness_complex_interface.h" namespace "Gudhi": cdef cppclass Strong_witness_complex_interface "Gudhi::witness_complex::Strong_witness_complex_interface": Strong_witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + # StrongWitnessComplex python interface cdef class StrongWitnessComplex: diff --git a/src/python/gudhi/subsampling.pyx b/src/python/gudhi/subsampling.pyx index b1812087..f77c6f75 100644 --- a/src/python/gudhi/subsampling.pyx +++ b/src/python/gudhi/subsampling.pyx @@ -33,13 +33,15 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi The iteration starts with the landmark `starting point`. :param points: The input point set. - :type points: vector[vector[double]]. + :type points: Iterable[Iterable[float]]. Or :param off_file: An OFF file style name. :type off_file: string + And in both cases + :param nb_points: Number of points of the subsample. :type nb_points: unsigned. :param starting_point: The iteration starts with the landmark `starting \ @@ -47,15 +49,15 @@ def choose_n_farthest_points(points=None, off_file='', nb_points=0, starting_poi index is chosen randomly. :type starting_point: unsigned. :returns: The subsample point set. - :rtype: vector[vector[double]] + :rtype: List[List[float]]. """ if off_file: if os.path.isfile(off_file): if starting_point == '': - return subsampling_n_farthest_points_from_file(str.encode(off_file), + return subsampling_n_farthest_points_from_file(off_file.encode('utf-8'), nb_points) else: - return subsampling_n_farthest_points_from_file(str.encode(off_file), + return subsampling_n_farthest_points_from_file(off_file.encode('utf-8'), nb_points, starting_point) else: @@ -74,21 +76,23 @@ def pick_n_random_points(points=None, off_file='', nb_points=0): """Subsample a point set by picking random vertices. :param points: The input point set. - :type points: vector[vector[double]]. + :type points: Iterable[Iterable[float]]. Or :param off_file: An OFF file style name. :type off_file: string + And in both cases + :param nb_points: Number of points of the subsample. :type nb_points: unsigned. :returns: The subsample point set. - :rtype: vector[vector[double]] + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): - return subsampling_n_random_points_from_file(str.encode(off_file), + return subsampling_n_random_points_from_file(off_file.encode('utf-8'), nb_points) else: print("file " + off_file + " not found.") @@ -103,22 +107,24 @@ def sparsify_point_set(points=None, off_file='', min_squared_dist=0.0): between any two points is greater than or equal to min_squared_dist. :param points: The input point set. - :type points: vector[vector[double]]. + :type points: Iterable[Iterable[float]]. Or :param off_file: An OFF file style name. :type off_file: string + And in both cases + :param min_squared_dist: Minimum squared distance separating the output \ points. :type min_squared_dist: float. :returns: The subsample point set. - :rtype: vector[vector[double]] + :rtype: List[List[float]] """ if off_file: if os.path.isfile(off_file): - return subsampling_sparsify_points_from_file(str.encode(off_file), + return subsampling_sparsify_points_from_file(off_file.encode('utf-8'), min_squared_dist) else: print("file " + off_file + " not found.") diff --git a/src/python/gudhi/tangential_complex.pyx b/src/python/gudhi/tangential_complex.pyx index 0083033c..6391488c 100644 --- a/src/python/gudhi/tangential_complex.pyx +++ b/src/python/gudhi/tangential_complex.pyx @@ -66,7 +66,7 @@ cdef class TangentialComplex: def __cinit__(self, intrisic_dim, points=None, off_file=''): if off_file: if os.path.isfile(off_file): - self.thisptr = new Tangential_complex_interface(intrisic_dim, str.encode(off_file), True) + self.thisptr = new Tangential_complex_interface(intrisic_dim, off_file.encode('utf-8'), True) else: print("file " + off_file + " not found.") else: diff --git a/src/python/gudhi/witness_complex.pyx b/src/python/gudhi/witness_complex.pyx index b032a5a1..e589d006 100644 --- a/src/python/gudhi/witness_complex.pyx +++ b/src/python/gudhi/witness_complex.pyx @@ -22,9 +22,9 @@ __license__ = "MIT" cdef extern from "Witness_complex_interface.h" namespace "Gudhi": cdef cppclass Witness_complex_interface "Gudhi::witness_complex::Witness_complex_interface": Witness_complex_interface(vector[vector[pair[size_t, double]]] nearest_landmark_table) - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square) except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, - unsigned limit_dimension) + unsigned limit_dimension) except + # WitnessComplex python interface cdef class WitnessComplex: |