diff options
13 files changed, 67 insertions, 61 deletions
diff --git a/src/cython/data/2000_random_points_on_3D_Torus.csv b/data/pandas/2000_random_points_on_3D_Torus.csv index c1fefb9f..c1fefb9f 100644 --- a/src/cython/data/2000_random_points_on_3D_Torus.csv +++ b/data/pandas/2000_random_points_on_3D_Torus.csv diff --git a/src/cython/data/2500_random_points_on_5D_Sphere.csv b/data/pandas/2500_random_points_on_5D_Sphere.csv index f7cc8e84..f7cc8e84 100644 --- a/src/cython/data/2500_random_points_on_5D_Sphere.csv +++ b/data/pandas/2500_random_points_on_5D_Sphere.csv diff --git a/src/cython/data/500_random_points_on_3D_Torus.csv b/data/pandas/500_random_points_on_3D_Torus.csv index adb6e1da..adb6e1da 100644 --- a/src/cython/data/500_random_points_on_3D_Torus.csv +++ b/data/pandas/500_random_points_on_3D_Torus.csv diff --git a/src/cython/cython/cubical_complex.pyx b/src/cython/cython/cubical_complex.pyx index 3441b2e9..321fc22a 100644 --- a/src/cython/cython/cubical_complex.pyx +++ b/src/cython/cython/cubical_complex.pyx @@ -2,6 +2,7 @@ from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair from libcpp.string cimport string +from libcpp cimport bool import os """This file is part of the Gudhi Library. The Gudhi library @@ -39,7 +40,7 @@ cdef extern from "Cubical_complex_interface.h" namespace "Gudhi": 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) + Cubical_complex_persistence_interface(Bitmap_cubical_complex_base_interface * st, bool persistence_dim_max) vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence) vector[int] betti_numbers() vector[int] persistent_betti_numbers(double from_value, double to_value) @@ -75,20 +76,16 @@ cdef class CubicalComplex: # The real cython constructor def __cinit__(self, dimensions=None, top_dimensional_cells=None, perseus_file=''): - if ((dimensions is not None) or (top_dimensional_cells is not None) and - (perseus_file is not '')): - print("CubicalComplex can be constructed from dimensions and " - "top_dimensional_cells or from a perseus file style name.") - else: - if dimensions is not None: - if top_dimensional_cells is not None: - self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells) + if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file is ''): + self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells) + elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''): + if os.path.isfile(perseus_file): + self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file) else: - if perseus_file is not '': - if os.path.isfile(perseus_file): - self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file) - else: - print("file " + perseus_file + " not found.") + print("file " + perseus_file + " not found.") + else: + print("CubicalComplex can be constructed from dimensions and " + "top_dimensional_cells or from a perseus file style name.") def __dealloc__(self): if self.thisptr != NULL: @@ -138,7 +135,7 @@ cdef class CubicalComplex: if self.pcohptr != NULL: del self.pcohptr if self.thisptr != NULL: - self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr) + self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr, True) cdef vector[pair[int, pair[double, double]]] persistence_result if self.pcohptr != NULL: persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence) diff --git a/src/cython/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx index d56eb5b1..c1b25f31 100644 --- a/src/cython/cython/periodic_cubical_complex.pyx +++ b/src/cython/cython/periodic_cubical_complex.pyx @@ -2,6 +2,7 @@ from cython cimport numeric from libcpp.vector cimport vector from libcpp.utility cimport pair from libcpp.string cimport string +from libcpp cimport bool import os """This file is part of the Gudhi Library. The Gudhi library @@ -39,7 +40,7 @@ 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::Cubical_complex_interface<Gudhi::cubical_complex::Bitmap_cubical_complex_periodic_boundary_conditions_base<double>>>": - Periodic_cubical_complex_persistence_interface(Periodic_cubical_complex_base_interface * st) + Periodic_cubical_complex_persistence_interface(Periodic_cubical_complex_base_interface * st, bool persistence_dim_max) vector[pair[int, pair[double, double]]] get_persistence(int homology_coeff_field, double min_persistence) vector[int] betti_numbers() vector[int] persistent_betti_numbers(double from_value, double to_value) @@ -75,21 +76,16 @@ cdef class PeriodicCubicalComplex: # The real cython constructor def __cinit__(self, dimensions=None, top_dimensional_cells=None, perseus_file=''): - if ((dimensions is not None) or (top_dimensional_cells is not None) and - (perseus_file is not '')): - print("PeriodicCubicalComplex can be constructed from dimensions" - " and top_dimensional_cells or from a perseus file style " - "name.") - else: - if dimensions is not None: - if top_dimensional_cells is not None: - self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells) + if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file is ''): + self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells) + elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file is not ''): + if os.path.isfile(perseus_file): + self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file) else: - if perseus_file is not '': - if os.path.isfile(perseus_file): - self.thisptr = new Periodic_cubical_complex_base_interface(perseus_file) - else: - print("file " + perseus_file + " not found.") + print("file " + perseus_file + " not found.") + else: + print("CubicalComplex can be constructed from dimensions and " + "top_dimensional_cells or from a perseus file style name.") def __dealloc__(self): if self.thisptr != NULL: @@ -139,7 +135,7 @@ cdef class PeriodicCubicalComplex: if self.pcohptr != NULL: del self.pcohptr if self.thisptr != NULL: - self.pcohptr = new Periodic_cubical_complex_persistence_interface(self.thisptr) + self.pcohptr = new Periodic_cubical_complex_persistence_interface(self.thisptr, True) cdef vector[pair[int, pair[double, double]]] persistence_result if self.pcohptr != NULL: persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence) diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py index 8e534061..d74eba57 100755 --- a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -33,11 +33,12 @@ parser = argparse.ArgumentParser(description='AlphaComplex creation from ' 'points read in a OFF file.', epilog='Example: ' 'example/alpha_complex_diagram_persistence_from_off_file_example.py ' - '../data/points/tore3D_1307.off ' + '-f ../data/points/tore3D_300.off -a 0.6' '- Constructs a alpha complex with the ' 'points from the given file. File format ' 'is X1, X2, ..., Xn') parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5) parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') args = parser.parse_args() @@ -45,12 +46,18 @@ args = parser.parse_args() with open(args.file, 'r') as f: first_line = f.readline() if (first_line == 'OFF\n') or (first_line == 'nOFF\n'): - print("#####################################################################") print("AlphaComplex creation from points read in a OFF file") - alpha_complex = gudhi.AlphaComplex(off_file=args.file, max_alpha_square=0.5) + + message = "AlphaComplex with max_edge_length=" + repr(args.max_alpha_square) + print(message) + + alpha_complex = gudhi.AlphaComplex(off_file=args.file, max_alpha_square=args.max_alpha_square) - diag = alpha_complex.persistence(homology_coeff_field=2, min_persistence=0.1) + message = "Number of simplices=" + repr(alpha_complex.num_simplices()) + print(message) + + diag = alpha_complex.persistence() print("betti_numbers()=") print(alpha_complex.betti_numbers()) diff --git a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index e6ba94e1..a9545ee9 100755 --- a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -51,7 +51,7 @@ def is_file_perseus(file): parser = argparse.ArgumentParser(description='Periodic cubical complex from a ' 'perseus file style name.', epilog='Example: ' - './periodic_cubical_complex_from_perseus_file_example.py' + './periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py' ' -f ../data/bitmap/CubicalTwoSphere.txt') parser.add_argument("-f", "--file", type=str, required=True) diff --git a/src/cython/example/random_cubical_complex_example.py b/src/cython/example/random_cubical_complex_persistence_example.py index 147eaa49..1c55f777 100755 --- a/src/cython/example/random_cubical_complex_example.py +++ b/src/cython/example/random_cubical_complex_persistence_example.py @@ -34,10 +34,10 @@ __license__ = "GPL v3" parser = argparse.ArgumentParser(description='Random cubical complex.', epilog='Example: ' - './random_cubical_complex_example.py 10 10 10' - ' - Constructs a random cubical complex in a ' - 'dimension [10, 10, 10] (aka. 1000 random ' - 'top dimensional cells).') + './random_cubical_complex_persistence_example.py' + ' 10 10 10 - Constructs a random cubical ' + 'complex in a dimension [10, 10, 10] (aka. ' + '1000 random top dimensional cells).') parser.add_argument('dimension', type=int, nargs="*", help='Cubical complex dimensions') diff --git a/src/cython/example/rips_complex_from_file_example.py b/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py index fae72443..bcf2fbcb 100755 --- a/src/cython/example/rips_complex_from_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py @@ -36,27 +36,33 @@ print("RipsComplex creation from points read in a file") parser = argparse.ArgumentParser(description='RipsComplex creation from ' 'points read in a file.', epilog='Example: ' - 'example/rips_complex_from_file_example.py ' - 'data/2000_random_points_on_3D_Torus.csv ' + 'example/rips_complex_diagram_persistence_with_pandas_interface_example.py ' + '../data/2000_random_points_on_3D_Torus.csv ' '- Constructs a rips complex with the ' 'points from the given file. File format ' 'is X1, X2, ..., Xn') -parser.add_argument('file', type=argparse.FileType('r')) +parser.add_argument("-f", "--file", type=str, required=True) +parser.add_argument("-e", "--max-edge-length", type=float, default=0.5) +parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams') + args = parser.parse_args() points = pandas.read_csv(args.file, header=None) -print("RipsComplex with max_edge_length=0.7") +message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length) +print(message) rips_complex = gudhi.RipsComplex(points=points.values, - max_dimension=len(points.values[0]), max_edge_length=0.7) + max_dimension=len(points.values[0]), max_edge_length=args.max_edge_length) + +message = "Number of simplices=" + repr(rips_complex.num_simplices()) +print(message) rips_complex.initialize_filtration() -diag = rips_complex.persistence(homology_coeff_field=2, min_persistence=0.3) +diag = rips_complex.persistence() print("betti_numbers()=") print(rips_complex.betti_numbers()) -gudhi.diagram_persistence(diag) - -gudhi.barcode_persistence(diag) +if args.no_diagram == False: + gudhi.diagram_persistence(diag) diff --git a/src/cython/example/rips_complex_example.py b/src/cython/example/rips_complex_from_points_example.py index 65246c9c..1a22d8e3 100755 --- a/src/cython/example/rips_complex_example.py +++ b/src/cython/example/rips_complex_from_points_example.py @@ -36,6 +36,3 @@ rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]], print("filtered_tree=", rips.get_filtered_tree()) print("star([0])=", rips.get_star_tree([0])) print("coface([0], 1)=", rips.get_coface_tree([0], 1)) - -print("persistence(homology_coeff_field=2, min_persistence=0)=") -print(rips.persistence(homology_coeff_field=2, min_persistence=0)) diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py index cc33ed6e..bf5f17a2 100755 --- a/src/cython/example/simplex_tree_example.py +++ b/src/cython/example/simplex_tree_example.py @@ -64,6 +64,3 @@ print("num_vertices=", st.num_vertices()) print("skeleton_tree[2]=", st.get_skeleton_tree(2)) print("skeleton_tree[1]=", st.get_skeleton_tree(1)) print("skeleton_tree[0]=", st.get_skeleton_tree(0)) - -print("persistence(homology_coeff_field=2, min_persistence=0)=") -print(st.persistence(homology_coeff_field=2, min_persistence=0)) diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h index faabc497..1ff0e09b 100644 --- a/src/cython/include/Persistent_cohomology_interface.h +++ b/src/cython/include/Persistent_cohomology_interface.h @@ -34,6 +34,7 @@ template<class FilteredComplex> class Persistent_cohomology_interface : public persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp> { private: + /* * Compare two intervals by dimension, then by length. */ @@ -56,18 +57,23 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol public: Persistent_cohomology_interface(FilteredComplex* stptr) - : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr, true), + : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr), + stptr_(stptr) { } + + Persistent_cohomology_interface(FilteredComplex* stptr, bool persistence_dim_max) + : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr, + persistence_dim_max), stptr_(stptr) { } std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) { persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>::init_coefficients(homology_coeff_field); persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>::compute_persistent_cohomology(min_persistence); - + // Custom sort and output persistence cmp_intervals_by_dim_then_length cmp(stptr_); auto persistent_pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>::get_persistent_pairs(); std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp); - + std::vector<std::pair<int, std::pair<double, double>>> persistence; for (auto pair : persistent_pairs) { persistence.push_back(std::make_pair(stptr_->dimension(get<0>(pair)), @@ -77,7 +83,7 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol return persistence; } - + private: // A copy FilteredComplex* stptr_; diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py index af4c34ef..c8df8089 100755 --- a/src/cython/test/test_cubical_complex.py +++ b/src/cython/test/test_cubical_complex.py @@ -82,5 +82,5 @@ def test_dimension_constructor(): assert cub.__is_persistence_defined() == False assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))] assert cub.__is_persistence_defined() == True - assert cub.betti_numbers() == [1, 0] - assert cub.persistent_betti_numbers(0, 1000) == [1, 0] + assert cub.betti_numbers() == [1, 0, 0] + assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0] |