Rename barcode_persistence and diagram_persistence functions

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2204 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f91e283fa6b6b02198ae28a44f41bd761c1c1f48

15 files changed, 22 insertions, 24 deletions

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 2a3d9f63..d7287a66 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -73,7 +73,7 @@ def show_palette_values(alpha=0.6):
 
     plt.show()
 
-def barcode_persistence(persistence, alpha=0.6):
+def plot_barcode_persistence(persistence, alpha=0.6):
     """This function plots the persistence bar code.
 
     :param persistence: The persistence to plot.
@@ -108,7 +108,7 @@ def barcode_persistence(persistence, alpha=0.6):
     plt.axis([axis_start, infinity, 0, ind])
     plt.show()
 
-def diagram_persistence(persistence, alpha=0.6):
+def plot_diagram_persistence(persistence, alpha=0.6):
     """This function plots the persistence diagram.
 
     :param persistence: The persistence to plot.
diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst
index a12021c4..3d7e4fc7 100644
--- a/src/cython/doc/persistence_graphical_tools_ref.rst
+++ b/src/cython/doc/persistence_graphical_tools_ref.rst
@@ -4,5 +4,5 @@ Persistence graphical tools reference manual
 
 .. autofunction:: gudhi.__min_birth_max_death
 .. autofunction:: gudhi.show_palette_values
-.. autofunction:: gudhi.barcode_persistence
-.. autofunction:: gudhi.diagram_persistence
+.. autofunction:: gudhi.plot_barcode_persistence
+.. autofunction:: gudhi.plot_diagram_persistence
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index 1a5195c5..2644aa11 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -33,7 +33,7 @@ This function can display the persistence result as a barcode:
     
     periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
     diag = periodic_cc.persistence()
-    gudhi.barcode_persistence(diag)
+    gudhi.plot_barcode_persistence(diag)
 
 .. plot::
 
@@ -41,7 +41,7 @@ This function can display the persistence result as a barcode:
 
     periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
     diag = periodic_cc.persistence()
-    gudhi.barcode_persistence(diag)
+    gudhi.plot_barcode_persistence(diag)
 
 Show persistence as a diagram
 -----------------------------
@@ -55,7 +55,7 @@ This function can display the persistence result as a diagram:
     rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    gudhi.diagram_persistence(diag)
+    gudhi.plot_diagram_persistence(diag)
 
 .. plot::
 
@@ -64,4 +64,4 @@ This function can display the persistence result as a diagram:
     rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    gudhi.diagram_persistence(diag)
+    gudhi.plot_diagram_persistence(diag)
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
index 95bbd343..9fcb33d0 100755
--- a/src/cython/doc/pyplots/barcode_persistence.py
+++ b/src/cython/doc/pyplots/barcode_persistence.py
@@ -2,4 +2,4 @@ import gudhi
 
 periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt')
 diag = periodic_cc.persistence()
-gudhi.barcode_persistence(diag)
+gudhi.plot_barcode_persistence(diag)
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
index b006b0bf..fbb6e60b 100755
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -2,4 +2,4 @@ import gudhi
 
 alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off')
 diag = alpha_complex.persistence()
-gudhi.diagram_persistence(diag)
+gudhi.plot_diagram_persistence(diag)
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 ae03aa67..9714b382 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
@@ -63,7 +63,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.diagram_persistence(diag)
+            gudhi.plot_diagram_persistence(diag)
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py
index 04a59b44..cd64704b 100755
--- a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py
+++ b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py
@@ -42,8 +42,6 @@ parser.add_argument("-t", "--threshold", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
 
 args = parser.parse_args()
-print(repr(float('inf')))
-print(repr(math.sqrt(float('inf'))))
 with open(args.file, 'r') as f:
     first_line = f.readline()
     if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index 6c3e3a8a..3addf708 100755
--- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -34,7 +34,7 @@ parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex crea
                                  epilog='Example: '
                                  'example/witness_complex_diagram_persistence_from_off_file_example.py '
                                  '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
-                                 '- Constructs a alpha complex with the '
+                                 '- Constructs a strong witness complex with the '
                                  'points from the given OFF file.')
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
@@ -70,7 +70,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            gudhi.diagram_persistence(diag)
+            gudhi.plot_diagram_persistence(diag)
 
     else:
         print(args.file, "is not a valid OFF file")
diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 7f04a98e..1e7d788a 100755
--- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -34,7 +34,7 @@ parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation f
                                  epilog='Example: '
                                  'example/witness_complex_diagram_persistence_from_off_file_example.py '
                                  '-f ../data/points/tore3D_300.off -a 1.0 -n 20 -d 2'
-                                 '- Constructs a alpha complex with the '
+                                 '- Constructs a weak witness complex with the '
                                  'points from the given OFF file.')
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
@@ -70,7 +70,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            gudhi.diagram_persistence(diag)
+            gudhi.plot_diagram_persistence(diag)
 
     else:
         print(args.file, "is not a valid OFF file")
diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py
index 40558bee..f1aa5d73 100755
--- a/src/cython/example/gudhi_graphical_tools_example.py
+++ b/src/cython/example/gudhi_graphical_tools_example.py
@@ -39,9 +39,9 @@ print("Show barcode persistence example")
 persistence = [(2, (1.0, float('inf'))), (1, (1.4142135623730951, float('inf'))),
                (1, (1.4142135623730951, float('inf'))), (0, (0.0, float('inf'))),
                (0, (0.0, 1.0)), (0, (0.0, 1.0)), (0, (0.0, 1.0))]
-gudhi.barcode_persistence(persistence)
+gudhi.plot_barcode_persistence(persistence)
 
 print("#####################################################################")
 print("Show diagram persistence example")
 
-gudhi.diagram_persistence(persistence)
+gudhi.plot_diagram_persistence(persistence)
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 a9545ee9..128706b2 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
@@ -71,6 +71,6 @@ if is_file_perseus(args.file):
     print("betti_numbers()=")
     print(periodic_cubical_complex.betti_numbers())
     if args.no_barcode == False:
-        gudhi.barcode_persistence(diag)
+        gudhi.plot_barcode_persistence(diag)
 else:
     print(args.file, "is not a valid perseus style file")
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index 2b726f90..5f1416be 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -64,7 +64,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.diagram_persistence(diag)
+            gudhi.plot_diagram_persistence(diag)
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
index eb1c4ed5..4f888e77 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -64,7 +64,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.diagram_persistence(diag)
+            gudhi.plot_diagram_persistence(diag)
     else:
         print(args.file, "is not a valid OFF file")
 
diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py
index e485b2f5..3d51f379 100755
--- a/src/cython/example/rips_persistence_diagram.py
+++ b/src/cython/example/rips_persistence_diagram.py
@@ -39,4 +39,4 @@ simplex_tree = rips.create_simplex_tree(max_dimension=1)
 diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0)
 print("diag=", diag)
 
-gudhi.diagram_persistence(diag)
+gudhi.plot_diagram_persistence(diag)
diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
index be4c40be..a3fc9911 100755
--- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -59,7 +59,7 @@ with open(args.file, 'r') as f:
         print(st.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.diagram_persistence(diag)
+            gudhi.plot_diagram_persistence(diag)
     else:
         print(args.file, "is not a valid OFF file")