Merge of branch plot_persistence_density_vincent

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3927 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a996b8e1ddcdb53f9ea6dff341ae5f1bad26639c

4 files changed, 35 insertions, 16 deletions

diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index 43576ec9..ef2f7af2 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -195,7 +195,7 @@ The following examples require the `Matplotlib <http://matplotlib.org>`_:
     * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
 
-Numpy
+NumPy
 =====
 
 The :doc:`persistence graphical tools </persistence_graphical_tools_user>`
@@ -216,6 +216,13 @@ The following examples require the `NumPy <http://numpy.org>`_:
     * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
 
+SciPy
+=====
+
+The :doc:`persistence graphical tools </persistence_graphical_tools_user>`
+module requires `SciPy <http://scipy.org>`_, a Python-based ecosystem of
+open-source software for mathematics, science, and engineering.
+
 Threading Building Blocks
 =========================
 
diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst
index a2c6bcef..54aff4bc 100644
--- a/src/cython/doc/persistence_graphical_tools_ref.rst
+++ b/src/cython/doc/persistence_graphical_tools_ref.rst
@@ -9,3 +9,4 @@ Persistence graphical tools reference manual
 .. autofunction:: gudhi.__min_birth_max_death
 .. autofunction:: gudhi.plot_persistence_barcode
 .. autofunction:: gudhi.plot_persistence_diagram
+.. autofunction:: gudhi.plot_persistence_density
diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc
index d602daa7..5577cf99 100644
--- a/src/cython/doc/persistence_graphical_tools_sum.inc
+++ b/src/cython/doc/persistence_graphical_tools_sum.inc
@@ -1,11 +1,11 @@
 =================================================================  ===================================  ===================================
 :Author: Vincent Rouvreau                                          :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
-:Requires: Matplotlib                                              Numpy
+:Requires: matplotlib                                              numpy                                scipy
 =================================================================  ===================================  ===================================
 
 +-----------------------------------------------------------------+-----------------------------------------------------------------------+
 | .. figure::                                                     | These graphical tools comes on top of persistence results and allows  |
-|      img/graphical_tools_representation.png                     | the user to build easily barcode and persistence diagram.             |
+|      img/graphical_tools_representation.png                     | the user to build easily persistence barcode, diagram or density.     |
 |                                                                 |                                                                       |
 +-----------------------------------------------------------------+-----------------------------------------------------------------------+
 |  :doc:`persistence_graphical_tools_user`                        | :doc:`persistence_graphical_tools_ref`                                |
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index 292915eb..b2124fdd 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -12,6 +12,9 @@ Definition
 Show persistence as a barcode
 -----------------------------
 
+.. note::
+    this function requires matplotlib and numpy to be available
+
 This function can display the persistence result as a barcode:
 
 .. plot::
@@ -19,16 +22,22 @@ This function can display the persistence result as a barcode:
 
     import gudhi
 
-    perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt'
-    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file)
-    diag = periodic_cc.persistence()
-    print("diag = ", diag)
-    plt = gudhi.plot_persistence_barcode(diag)
-    plt.show()
+    off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off'
+    point_cloud = gudhi.read_off(off_file=off_file)
+
+    rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.7)
+    simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
+    diag = simplex_tree.persistence(min_persistence=0.4)
+
+    plot = gudhi.plot_persistence_barcode(diag)
+    plot.show()
 
 Show persistence as a diagram
 -----------------------------
 
+.. note::
+    this function requires matplotlib and numpy to be available
+
 This function can display the persistence result as a diagram:
 
 .. plot::
@@ -43,6 +52,12 @@ This function can display the persistence result as a diagram:
         legend=True)
     plt.show()
 
+Persistence density
+-------------------
+
+.. note::
+    this function requires matplotlib, numpy and scipy to be available
+
 If you want more information on a specific dimension, for instance:
 
 .. plot::
@@ -50,13 +65,9 @@ If you want more information on a specific dimension, for instance:
 
     import gudhi
 
+    # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
     persistence_file=gudhi.__root_source_dir__ + \
         '/data/persistence_diagram/rips_on_tore3D_1307.pers'
-    diag = \
-        gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\
-            persistence_file)
-    dim = 1
-    # Display all points with some transparency
-    plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]],
-        max_plots=0, alpha=0.1)
+    plt = gudhi.plot_persistence_density(persistence_file=persistence_file,
+        max_intervals=0, dimension=1, legend=True)
     plt.show()