Code and doc review with IFPEN :

plot_*: c'est quoi ce paramètre alpha ?

band_boot: Renommer en 'band', sans référence au bootstrap. Ne pas
l'utiliser dans la majorité des exemples / tutos.

max_plots: mettre une valeur par défaut, pour éviter qu'on se retrouve
trop facilement coincé à attendre 1h qu'il affiche des points.
Éventuellement afficher un message indiquant que certains points n'ont pas
été affichés et comment changer ça.

barcode: trier les barres par date de naissance (le faire
tout le temps ou avoir une option et le faire par défaut).



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3404 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cfa775e425fbf12da1758d601ccbd80a2c7d3bc9

8 files changed, 15 insertions, 15 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 b4487be4..10d4867a 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
@@ -38,7 +38,7 @@ parser = argparse.ArgumentParser(description='AlphaComplex creation from '
                                  'points from the given OFF file.')
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -64,7 +64,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
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 e3f362dc..28a8599c 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
@@ -40,7 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
 parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
 parser.add_argument("-d", "--limit_dimension", type=int, required=True)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -71,7 +71,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     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 c236d992..b19d7d8c 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
@@ -40,7 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
 parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
 parser.add_argument("-d", "--limit_dimension", type=int, required=True)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -71,7 +71,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     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 ed87806b..97983262 100755
--- a/src/cython/example/gudhi_graphical_tools_example.py
+++ b/src/cython/example/gudhi_graphical_tools_example.py
@@ -50,5 +50,5 @@ pplot.show()
 print("#####################################################################")
 print("Show diagram persistence example with a confidence band")
 
-pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2)
+pplot = gudhi.plot_persistence_diagram(persistence, band=0.2)
 pplot.show()
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
index aa82ef71..0af4397a 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -40,7 +40,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -80,5 +80,5 @@ print(simplex_tree.betti_numbers())
 invert_diag = [(diag[pers][0],(1.-diag[pers][1][0], 1.-diag[pers][1][1])) for pers in range(len(diag))]
 
 if args.no_diagram == False:
-    pplot = gudhi.plot_persistence_diagram(invert_diag, band_boot=args.band_boot)
+    pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band)
     pplot.show()
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 c8aac240..266c09ca 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
@@ -39,7 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -63,5 +63,5 @@ print("betti_numbers()=")
 print(simplex_tree.betti_numbers())
 
 if args.no_diagram == False:
-    pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+    pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
     pplot.show()
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 544b68c9..fede920c 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
@@ -39,7 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -66,7 +66,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
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 08ae5d07..1f562b5c 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
@@ -38,7 +38,7 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from '
                                  'points from the given OFF file')
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-i", "--intrisic_dim", type=int, required=True)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -61,7 +61,7 @@ with open(args.file, 'r') as f:
         print(st.betti_numbers())
     
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")