Fix persistent_betti_numbers in Persistent_cohomology to make it work with cubical

Cython examples renaming and fixing



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1439 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ab84ba3acd6241257f1787e29ac2e3ac005bbd80

2 files changed, 56 insertions, 37 deletions

diff --git a/src/cython/example/alpha_complex_from_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
index 81c4c0b7..8e534061 100755
--- a/src/cython/example/alpha_complex_from_file_example.py
+++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import gudhi
-import pandas
 import argparse
 
 """This file is part of the Gudhi Library. The Gudhi library
@@ -30,35 +29,35 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-print("#####################################################################")
-print("AlphaComplex creation from points read in a file")
-
 parser = argparse.ArgumentParser(description='AlphaComplex creation from '
-                                 'points read in a file.',
+                                 'points read in a OFF file.',
                                  epilog='Example: '
-                                 'example/alpha_complex_from_file_example.py '
-                                 'data/500_random_points_on_3D_Torus.csv '
+                                 'example/alpha_complex_diagram_persistence_from_off_file_example.py '
+                                 '../data/points/tore3D_1307.off '
                                  '- Constructs a alpha 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('--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("AlphaComplex with max_alpha_square=0.5")
-
-alpha_complex = gudhi.AlphaComplex(points=points.values,
-                                   max_alpha_square=0.5)
-
-alpha_complex.initialize_filtration()
-diag = alpha_complex.persistence(homology_coeff_field=2, min_persistence=0.1)
-
-print("betti_numbers()=")
-print(alpha_complex.betti_numbers())
-
-if args.no_diagram == False:
-    gudhi.diagram_persistence(diag)
-    gudhi.barcode_persistence(diag)
+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)
+    
+        diag = alpha_complex.persistence(homology_coeff_field=2, min_persistence=0.1)
+    
+        print("betti_numbers()=")
+        print(alpha_complex.betti_numbers())
+    
+        if args.no_diagram == False:
+            gudhi.diagram_persistence(diag)
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/cubical_complex_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
index 23f7ece6..e6ba94e1 100755
--- a/src/cython/example/cubical_complex_from_perseus_file_example.py
+++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -1,10 +1,7 @@
 #!/usr/bin/env python
 
 import gudhi
-import numpy
 import argparse
-import operator
-import os
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -32,25 +29,48 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-parser = argparse.ArgumentParser(description='Cubical complex from a perseus'
-                                 'file style name.',
+def is_file_perseus(file):
+    num_lines = open(file).read().count('\n')
+    try:
+        f = open(file)
+        num_dim = int(f.readline())
+        coeff = 1
+        for dim in range(0, num_dim):
+            try:
+                line = int(f.readline())
+                coeff *= abs(line)
+            except ValueError:
+                return False
+        if num_lines == (1 + num_dim + coeff):
+            return True
+        else:
+            return False
+    except ValueError:
+        return False
+
+parser = argparse.ArgumentParser(description='Periodic cubical complex from a '
+                                 'perseus file style name.',
                                  epilog='Example: '
-                                 './cubical_complex_from_perseus_file_example.py'
+                                 './periodic_cubical_complex_from_perseus_file_example.py'
                                  ' -f ../data/bitmap/CubicalTwoSphere.txt')
 
 parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument('--no-barcode', default=False, action='store_true' , help='Flag for not to display the barcodes')
 
 args = parser.parse_args()
 
-if os.access(args.file, os.R_OK):
+if is_file_perseus(args.file):
     print("#####################################################################")
-    print("CubicalComplex creation")
-    cubical_complex = gudhi.CubicalComplex(perseus_file=args.file)
+    print("PeriodicCubicalComplex creation")
+    periodic_cubical_complex = gudhi.PeriodicCubicalComplex(perseus_file=args.file)
 
-    print("persistence(homology_coeff_field=2, min_persistence=0)=")
-    print(cubical_complex.persistence(homology_coeff_field=2, min_persistence=0))
+    print("persistence(homology_coeff_field=3, min_persistence=0)=")
+    diag = periodic_cubical_complex.persistence(homology_coeff_field=3, min_persistence=0)
+    print(diag)
 
     print("betti_numbers()=")
-    print(cubical_complex.betti_numbers())
+    print(periodic_cubical_complex.betti_numbers())
+    if args.no_barcode == False:
+        gudhi.barcode_persistence(diag)
 else:
-    print(args.file, "is unreachable")
+    print(args.file, "is not a valid perseus style file")