Merge master and resolve conflicts

10 files changed, 97 insertions, 41 deletions

diff --git a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
index 4079a469..727af4fa 100755
--- a/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
-    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
+    which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full
+    license details.
     Author(s):       Vincent Rouvreau
 
     Copyright (C) 2016 Inria
@@ -41,7 +45,7 @@ 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("##############################################################")
         print("AlphaComplex creation from points read in a OFF file")
 
         message = "AlphaComplex with max_edge_length=" + repr(args.max_alpha_square)
@@ -64,6 +68,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()
diff --git a/src/python/example/alpha_complex_from_points_example.py b/src/python/example/alpha_complex_from_points_example.py
index 844d7a82..73faf17c 100755
--- a/src/python/example/alpha_complex_from_points_example.py
+++ b/src/python/example/alpha_complex_from_points_example.py
@@ -46,8 +46,14 @@ if simplex_tree.find([4]):
 else:
     print("[4] Not found...")
 
+# Some insertions, simplex_tree needs to initialize filtrations
+simplex_tree.initialize_filtration()
+
 print("dimension=", simplex_tree.dimension())
-print("filtrations=", simplex_tree.get_filtration())
+print("filtrations=")
+for simplex_with_filtration in simplex_tree.get_filtration():
+    print("(%s, %.2f)" % tuple(simplex_with_filtration))
+
 print("star([0])=", simplex_tree.get_star([0]))
 print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1))
 
diff --git a/src/python/example/alpha_rips_persistence_bottleneck_distance.py b/src/python/example/alpha_rips_persistence_bottleneck_distance.py
index d5c33ec8..f156826d 100755
--- a/src/python/example/alpha_rips_persistence_bottleneck_distance.py
+++ b/src/python/example/alpha_rips_persistence_bottleneck_distance.py
@@ -3,9 +3,13 @@
 import gudhi
 import argparse
 import math
+import errno
+import os
 
-""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
-    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
+    which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full
+    license details.
     Author(s):       Vincent Rouvreau
 
     Copyright (C) 2016 Inria
@@ -36,7 +40,7 @@ with open(args.file, "r") as f:
     first_line = f.readline()
     if (first_line == "OFF\n") or (first_line == "nOFF\n"):
         point_cloud = gudhi.read_points_from_off_file(off_file=args.file)
-        print("#####################################################################")
+        print("##############################################################")
         print("RipsComplex creation from points read in a OFF file")
 
         message = "RipsComplex with max_edge_length=" + repr(args.threshold)
@@ -46,14 +50,15 @@ with open(args.file, "r") as f:
             points=point_cloud, max_edge_length=args.threshold
         )
 
-        rips_stree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+        rips_stree = rips_complex.create_simplex_tree(
+            max_dimension=args.max_dimension)
 
         message = "Number of simplices=" + repr(rips_stree.num_simplices())
         print(message)
 
         rips_diag = rips_stree.persistence()
 
-        print("#####################################################################")
+        print("##############################################################")
         print("AlphaComplex creation from points read in a OFF file")
 
         message = "AlphaComplex with max_edge_length=" + repr(args.threshold)
@@ -93,13 +98,13 @@ with open(args.file, "r") as f:
             print(message)
             max_b_distance = max(bottleneck_distance, max_b_distance)
 
-        print(
-            "================================================================================"
-        )
+        print("==============================================================")
         message = "Bottleneck distance is " + repr(max_b_distance)
         print(message)
 
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
+
 
     f.close()
diff --git a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index 4903667e..e1e572df 100755
--- a/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
-    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
+    which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full
+    license details.
     Author(s):       Vincent Rouvreau
 
     Copyright (C) 2016 Inria
@@ -44,8 +48,9 @@ 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("EuclideanStrongWitnessComplex creation from points read in a OFF file")
+        print("##############################################################")
+        print("EuclideanStrongWitnessComplex creation from points read "\
+            "in a OFF file")
 
         witnesses = gudhi.read_points_from_off_file(off_file=args.file)
         landmarks = gudhi.pick_n_random_points(
@@ -64,7 +69,8 @@ with open(args.file, "r") as f:
             witnesses=witnesses, landmarks=landmarks
         )
         simplex_tree = witness_complex.create_simplex_tree(
-            max_alpha_square=args.max_alpha_square, limit_dimension=args.limit_dimension
+            max_alpha_square=args.max_alpha_square,
+            limit_dimension=args.limit_dimension
         )
 
         message = "Number of simplices=" + repr(simplex_tree.num_simplices())
@@ -79,6 +85,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()
diff --git a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index 339a8577..58cb2bb5 100755
--- a/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
-    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
+    which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full
+    license details.
     Author(s):       Vincent Rouvreau
 
     Copyright (C) 2016 Inria
@@ -78,6 +82,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()
diff --git a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
index c692e66f..499171df 100755
--- a/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
+++ b/src/python/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -2,10 +2,14 @@
 
 import argparse
 import matplotlib.pyplot as plot
+import errno
+import os
 import gudhi
 
-""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
-    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
+    which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full
+    license details.
     Author(s):       Vincent Rouvreau
 
     Copyright (C) 2016 Inria
@@ -57,9 +61,10 @@ parser.add_argument(
 args = parser.parse_args()
 
 if is_file_perseus(args.file):
-    print("#####################################################################")
+    print("##################################################################")
     print("PeriodicCubicalComplex creation")
-    periodic_cubical_complex = gudhi.PeriodicCubicalComplex(perseus_file=args.file)
+    periodic_cubical_complex = gudhi.PeriodicCubicalComplex(
+        perseus_file=args.file)
 
     print("persistence(homology_coeff_field=3, min_persistence=0)=")
     diag = periodic_cubical_complex.persistence(
@@ -73,4 +78,5 @@ if is_file_perseus(args.file):
         gudhi.plot_persistence_barcode(diag)
         plot.show()
 else:
-    print(args.file, "is not a valid perseus style file")
+    raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                            args.file)
diff --git a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
index c757aca7..6f992508 100755
--- a/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/src/python/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
-    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
+    which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full
+    license details.
     Author(s):       Vincent Rouvreau
 
     Copyright (C) 2016 Inria
@@ -42,10 +46,11 @@ 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("##############################################################")
         print("RipsComplex creation from points read in a OFF file")
 
-        message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+        message = "RipsComplex with max_edge_length=" + \
+            repr(args.max_edge_length)
         print(message)
 
         point_cloud = gudhi.read_points_from_off_file(off_file=args.file)
@@ -68,6 +73,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()
diff --git a/src/python/example/rips_complex_from_points_example.py b/src/python/example/rips_complex_from_points_example.py
index 59d8a261..c05703c6 100755
--- a/src/python/example/rips_complex_from_points_example.py
+++ b/src/python/example/rips_complex_from_points_example.py
@@ -22,6 +22,9 @@ rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]], max_edge_lengt
 
 simplex_tree = rips.create_simplex_tree(max_dimension=1)
 
-print("filtrations=", simplex_tree.get_filtration())
+print("filtrations=")
+for simplex_with_filtration in simplex_tree.get_filtration():
+    print("(%s, %.2f)" % tuple(simplex_with_filtration))
+
 print("star([0])=", simplex_tree.get_star([0]))
 print("coface([0], 1)=", simplex_tree.get_cofaces([0], 1))
diff --git a/src/python/example/simplex_tree_example.py b/src/python/example/simplex_tree_example.py
index 30de00da..34833899 100755
--- a/src/python/example/simplex_tree_example.py
+++ b/src/python/example/simplex_tree_example.py
@@ -38,8 +38,15 @@ else:
 
 print("dimension=", st.dimension())
 
+print("simplices=")
+for simplex_with_filtration in st.get_simplices():
+    print("(%s, %.2f)" % tuple(simplex_with_filtration))
+
 st.initialize_filtration()
-print("filtration=", st.get_filtration())
+print("filtration=")
+for simplex_with_filtration in st.get_filtration():
+    print("(%s, %.2f)" % tuple(simplex_with_filtration))
+
 print("filtration[1, 2]=", st.filtration([1, 2]))
 print("filtration[4, 2]=", st.filtration([4, 2]))
 
diff --git a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
index f0df2189..85bade4a 100755
--- a/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/python/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -1,11 +1,15 @@
 #!/usr/bin/env python
 
 import argparse
+import errno
+import os
 import matplotlib.pyplot as plot
 import gudhi
 
-""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
-    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ -
+    which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full
+    license details.
     Author(s):       Vincent Rouvreau
 
     Copyright (C) 2016 Inria
@@ -19,7 +23,7 @@ __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
 
 parser = argparse.ArgumentParser(
-    description="TangentialComplex creation from " "points read in a OFF file.",
+    description="TangentialComplex creation from points read in a OFF file.",
     epilog="Example: "
     "example/tangential_complex_plain_homology_from_off_file_example.py "
     "-f ../data/points/tore3D_300.off -i 3"
@@ -41,10 +45,11 @@ 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("##############################################################")
         print("TangentialComplex creation from points read in a OFF file")
 
-        tc = gudhi.TangentialComplex(intrisic_dim=args.intrisic_dim, off_file=args.file)
+        tc = gudhi.TangentialComplex(intrisic_dim=args.intrisic_dim,
+            off_file=args.file)
         tc.compute_tangential_complex()
         st = tc.create_simplex_tree()
 
@@ -60,6 +65,7 @@ with open(args.file, "r") as f:
             gudhi.plot_persistence_diagram(diag, band=args.band)
             plot.show()
     else:
-        print(args.file, "is not a valid OFF file")
+        raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT),
+                                args.file)
 
     f.close()