Plot functions now returns a plot that can be modified before to be shown

Add confidence band in plot_persistence_diagram
Cythonization of read_lower_triangular_matrix_from_csv_file and read_persistence_intervals functions
Add Python tests of read functions


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2590 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 522ec31e9ad3a9a688875612d246114704b8c74e

7 files changed, 25 insertions, 9 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 adedc7d2..b4487be4 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
@@ -38,6 +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -63,7 +64,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            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 2371c36c..e3f362dc 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
@@ -40,6 +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -70,8 +71,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
-
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            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 5748aa8a..c236d992 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
@@ -40,6 +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -70,8 +71,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
-
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            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 bc3b16ec..ed87806b 100755
--- a/src/cython/example/gudhi_graphical_tools_example.py
+++ b/src/cython/example/gudhi_graphical_tools_example.py
@@ -44,4 +44,11 @@ gudhi.plot_persistence_barcode(persistence)
 print("#####################################################################")
 print("Show diagram persistence example")
 
-gudhi.plot_persistence_diagram(persistence)
+pplot = gudhi.plot_persistence_diagram(persistence)
+pplot.show()
+
+print("#####################################################################")
+print("Show diagram persistence example with a confidence band")
+
+pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2)
+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 984dbf1b..3baebd17 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
@@ -39,6 +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -61,4 +62,5 @@ print("betti_numbers()=")
 print(simplex_tree.betti_numbers())
 
 if args.no_diagram == False:
-    gudhi.plot_persistence_diagram(diag)
+    pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+    pplot.show()
diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py
index 4e5cd2c8..9bfea41c 100755
--- a/src/cython/example/rips_persistence_diagram.py
+++ b/src/cython/example/rips_persistence_diagram.py
@@ -39,4 +39,5 @@ simplex_tree = rips.create_simplex_tree(max_dimension=1)
 diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0)
 print("diag=", diag)
 
-gudhi.plot_persistence_diagram(diag)
+pplot = gudhi.plot_persistence_diagram(diag)
+pplot.show()
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 4845eb47..6145e7f2 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
@@ -37,6 +37,7 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from '
                                  '- Constructs a tangential complex with the '
                                  'points from the given OFF file')
 parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-b", "--band_boot", 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()
@@ -59,7 +60,8 @@ with open(args.file, 'r') as f:
         print(st.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")