Move pandas files points into data/pandas

Fix example and tests
New persistence constructor for cubical to increase max_persistence_dim (and only for cubical, periodic or not)


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1442 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 243a843a65a82b9d3d8d564aa906c0a17eda176a

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))