diff options
Diffstat (limited to 'src/cython/example')
-rwxr-xr-x | src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py | 15 | ||||
-rwxr-xr-x | src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py | 2 | ||||
-rwxr-xr-x | src/cython/example/random_cubical_complex_persistence_example.py (renamed from src/cython/example/random_cubical_complex_example.py) | 8 | ||||
-rwxr-xr-x | src/cython/example/rips_complex_diagram_persistence_with_pandas_interface_example.py (renamed from src/cython/example/rips_complex_from_file_example.py) | 24 | ||||
-rwxr-xr-x | src/cython/example/rips_complex_from_points_example.py (renamed from src/cython/example/rips_complex_example.py) | 3 | ||||
-rwxr-xr-x | src/cython/example/simplex_tree_example.py | 3 |
6 files changed, 31 insertions, 24 deletions
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)) |