Merge last trunk modifications

persistence file reader Python interface
persistence_graphical_tools improvement (max_plots and max_barcodes, and from a persistence file)



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2604 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: db80333d4f34151be0c32024af597d90d221a97f

4 files changed, 18 insertions, 12 deletions

diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index bc731f12..13198162 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -14,12 +14,14 @@ This function is useful to show the color palette values of dimension:
 .. testcode::
 
     import gudhi
-    gudhi.show_palette_values(alpha=1.0)
+    plt = gudhi.show_palette_values(alpha=1.0)
+    plt.show()
 
 .. plot::
 
     import gudhi
-    gudhi.show_palette_values(alpha=1.0)
+    plt = gudhi.show_palette_values(alpha=1.0)
+    plt.show()
 
 Show persistence as a barcode
 -----------------------------
@@ -32,7 +34,8 @@ This function can display the persistence result as a barcode:
     
     periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
     diag = periodic_cc.persistence()
-    gudhi.plot_persistence_barcode(diag)
+    plt = gudhi.plot_persistence_barcode(diag)
+    plt.show()
 
 .. plot::
 
@@ -40,7 +43,8 @@ This function can display the persistence result as a barcode:
 
     periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
     diag = periodic_cc.persistence()
-    gudhi.plot_persistence_barcode(diag)
+    plt = gudhi.plot_persistence_barcode(diag)
+    plt.show()
 
 Show persistence as a diagram
 -----------------------------
@@ -54,8 +58,8 @@ This function can display the persistence result as a diagram:
     rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
-    pplot.show()
+    plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    plt.show()
 
 .. plot::
 
@@ -64,5 +68,5 @@ This function can display the persistence result as a diagram:
     rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
-    pplot.show()
+    plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    plt.show()
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
index b021049f..9cd3149d 100755
--- a/src/cython/doc/pyplots/barcode_persistence.py
+++ b/src/cython/doc/pyplots/barcode_persistence.py
@@ -2,4 +2,5 @@ import gudhi
 
 periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
 diag = periodic_cc.persistence()
-gudhi.plot_persistence_barcode(diag)
+plt = gudhi.plot_persistence_barcode(diag)
+plt.show()
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
index 56d6c50f..30661965 100755
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -3,5 +3,5 @@ import gudhi
 rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
 simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
 diag = simplex_tree.persistence()
-pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
-pplot.show()
+plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+plt.show()
diff --git a/src/cython/doc/pyplots/show_palette_values.py b/src/cython/doc/pyplots/show_palette_values.py
index e72a55fd..fdf9645f 100755
--- a/src/cython/doc/pyplots/show_palette_values.py
+++ b/src/cython/doc/pyplots/show_palette_values.py
@@ -1,2 +1,3 @@
 import gudhi
-gudhi.show_palette_values(alpha=1.0)
+plt = gudhi.show_palette_values(alpha=1.0)
+plt.show()