Fix persistent_betti_numbers in Persistent_cohomology to make it work with cubical

Cython examples renaming and fixing



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1439 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ab84ba3acd6241257f1787e29ac2e3ac005bbd80

6 files changed, 22 insertions, 1 deletions

diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py
index 85b700a8..8d6483af 100755
--- a/src/cython/doc/conf.py
+++ b/src/cython/doc/conf.py
@@ -32,10 +32,10 @@ sys.path.insert(0, os.path.abspath('..'))
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'matplotlib.sphinxext.plot_directive',
     'sphinx.ext.autodoc',
     'sphinx.ext.doctest',
     'sphinx.ext.todo',
-    'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
@@ -43,6 +43,9 @@ extensions = [
 ]
 
 todo_include_todos = True
+# plot option : do not show hyperlinks (Source code, png, hires.png, pdf)
+plot_html_show_source_link = False
+plot_html_show_formats = False
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
diff --git a/src/cython/doc/img/graphical_tools_representation.png b/src/cython/doc/img/graphical_tools_representation.png
new file mode 100644
index 00000000..9759f7ba
--- /dev/null
+++ b/src/cython/doc/img/graphical_tools_representation.png
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index 5245d69d..89e09d70 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -61,3 +61,8 @@ Persistence cohomology
 ======================
 
 .. include:: persistent_cohomology_sum.rst
+
+Persistence graphical tools
+===========================
+
+.. include:: persistence_graphical_tools_sum.rst
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
new file mode 100755
index 00000000..95bbd343
--- /dev/null
+++ b/src/cython/doc/pyplots/barcode_persistence.py
@@ -0,0 +1,5 @@
+import gudhi
+
+periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt')
+diag = periodic_cc.persistence()
+gudhi.barcode_persistence(diag)
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
new file mode 100755
index 00000000..ceeeceb3
--- /dev/null
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -0,0 +1,6 @@
+import gudhi
+
+alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off')
+alpha_complex.initialize_filtration()
+diag = alpha_complex.persistence()
+gudhi.diagram_persistence(diag)
diff --git a/src/cython/doc/pyplots/show_palette_values.py b/src/cython/doc/pyplots/show_palette_values.py
new file mode 100755
index 00000000..e72a55fd
--- /dev/null
+++ b/src/cython/doc/pyplots/show_palette_values.py
@@ -0,0 +1,2 @@
+import gudhi
+gudhi.show_palette_values(alpha=1.0)