-- 
cgit v1.2.3

From d52036da23f887d56d13dd4f93c1049eb44301b1 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 3 Aug 2018 09:41:38 +0000
Subject: plot persistence density functionnality with its documentation Fix
 some documentation issue in other graphiacl tools Add scipy as a dependency

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3736 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6481f1d6aa176bcf587f8875298a91cd22ac0319
---
 src/cython/cython/persistence_graphical_tools.py   | 74 +++++++++++++++++++++-
 src/cython/doc/persistence_graphical_tools_ref.rst |  1 +
 .../doc/persistence_graphical_tools_user.rst       |  9 ++-
 src/cython/setup.py.in                             |  1 +
 4 files changed, 80 insertions(+), 5 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 216ab8d6..7f604368 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -1,7 +1,9 @@
 import matplotlib.pyplot as plt
 import matplotlib.patches as mpatches
 import numpy as np
+from scipy.stats import kde
 import os
+import math
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -79,6 +81,8 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
     :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
         A reasonable value is between 0.05 and 0.5 - default is 0.1.
     :type inf_delta: float.
+    :param legend: Display the dimension color legend (default is False).
+    :type legend: boolean.
     :returns: A matplotlib object containing horizontal bar plot of persistence
         (launch `show()` method on it to display it).
     """
@@ -154,6 +158,8 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
     :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
         A reasonable value is between 0.05 and 0.5 - default is 0.1.
     :type inf_delta: float.
+    :param legend: Display the dimension color legend (default is False).
+    :type legend: boolean.
     :returns: A matplotlib object containing diagram plot of persistence
         (launch `show()` method on it to display it).
     """
@@ -174,7 +180,6 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
         persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots]
 
     (min_birth, max_death) = __min_birth_max_death(persistence, band)
-    ind = 0
     delta = ((max_death - min_birth) * inf_delta)
     # Replace infinity values with max_death + delta for diagram to be more
     # readable
@@ -201,7 +206,6 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
             # Infinite death case for diagram to be nicer
             plt.scatter(interval[1][0], infinity, alpha=alpha,
                         color = palette[interval[0]])
-        ind = ind + 1
 
     if legend:
         dimensions = list(set(item[0] for item in persistence))
@@ -213,3 +217,69 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
     # Ends plot on infinity value and starts a little bit before min_birth
     plt.axis([axis_start, infinity, axis_start, infinity + delta])
     return plt
+
+def plot_persistence_density(persistence=[], persistence_file='', nbins=300,
+                             max_plots=1000, cmap=plt.cm.hot_r, legend=False):
+    """This function plots the persistence density from persistence values list
+    or from a :doc:`persistence file <fileformats>`. Be aware that this
+    function does not distinguish the dimension, it is up to you to select the
+    required one.
+
+    :param persistence: Persistence values list.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence_file: A :doc:`persistence file <fileformats>` style name
+        (reset persistence if both are set).
+    :type persistence_file: string
+    :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins
+        over data extents (default is 300)
+    :type nbins: int.
+    :param max_plots: number of maximal plots to be displayed
+        Set it to 0 to see all, Default value is 1000.
+        (persistence will be sorted by life time if max_plots is set)
+    :type max_plots: int.
+    :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r).
+    :type cmap: cf. matplotlib colormap.
+    :param legend: Display the color bar values (default is False).
+    :type legend: boolean.
+    :returns: A matplotlib object containing diagram plot of persistence
+        (launch `show()` method on it to display it).
+    """
+    if persistence_file is not '':
+        if os.path.isfile(persistence_file):
+            # Reset persistence
+            persistence = []
+            diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
+            for key in diag.keys():
+                for persistence_interval in diag[key]:
+                    persistence.append((key, persistence_interval))
+        else:
+            print("file " + persistence_file + " not found.")
+            return None
+
+    if max_plots > 0 and max_plots < len(persistence):
+        # Sort by life time, then takes only the max_plots elements
+        persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots]
+
+    # Set as numpy array birth and death (remove undefined values - inf and NaN)
+    birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+    death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+
+    # line display of equation : birth = death
+    x = np.linspace(death.min(), birth.max(), 1000)
+    plt.plot(x, x, color='k', linewidth=1.0)
+
+    # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
+    k = kde.gaussian_kde([birth,death])
+    xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j]
+    zi = k(np.vstack([xi.flatten(), yi.flatten()]))
+
+    # Make the plot
+    plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
+
+    if legend:
+        plt.colorbar()
+
+    plt.title('Persistence density')
+    plt.xlabel('Birth')
+    plt.ylabel('Death')
+    return plt
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_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index 292915eb..b21de06a 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -43,6 +43,9 @@ This function can display the persistence result as a diagram:
         legend=True)
     plt.show()
 
+Persistence density
+-------------------
+
 If you want more information on a specific dimension, for instance:
 
 .. plot::
@@ -56,7 +59,7 @@ If you want more information on a specific dimension, for instance:
         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)
+    # Display persistence density
+    plt = gudhi.plot_persistence_density([(dim,interval) for interval in diag[dim]],
+        max_plots=0, legend=True)
     plt.show()
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
index ee381a1b..22b2954e 100644
--- a/src/cython/setup.py.in
+++ b/src/cython/setup.py.in
@@ -49,6 +49,7 @@ setup(
     install_requires = [
         "matplotlib",
         "numpy",
+        "scipy",
         "cython",
         ],
 )
-- 
cgit v1.2.3


From feb6244de8f602e36fe101eb553ad5a6265665ee Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 3 Aug 2018 09:55:26 +0000
Subject: Add SciPy as a dependency in the installation process documentation

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3737 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2d9d2c3f32ba3af5e9565f89e986ac437370b68e
---
 src/cython/doc/installation.rst                    | 9 ++++++++-
 src/cython/doc/persistence_graphical_tools_sum.inc | 4 ++--
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index 43ff85c5..ff6c7273 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -143,7 +143,7 @@ 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>`
@@ -164,6 +164,13 @@ 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_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc
index d602daa7..c793a352 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`                                |
-- 
cgit v1.2.3


From 2f10f837b791a1b002a18f1ba2b22de918eb54fe Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 16 Aug 2018 13:40:06 +0000
Subject: Code review : Try to import module. Functions are unavailable if not
 available.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3785 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 53c89a30f7992aa8d20e8330628c03291cea6473
---
 .../modules/GUDHI_third_party_libraries.cmake      |   1 +
 src/cython/CMakeLists.txt                          |   8 +-
 src/cython/cython/persistence_graphical_tools.py   | 202 +++++++++++----------
 3 files changed, 108 insertions(+), 103 deletions(-)

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index f03c2177..1ad0c1fd 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -143,6 +143,7 @@ if( PYTHONINTERP_FOUND )
   find_python_module("pytest")
   find_python_module("matplotlib")
   find_python_module("numpy")
+  find_python_module("scipy")
 endif()
 
 if(NOT GUDHI_CYTHON_PATH)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 1849a6ec..542be9b0 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -54,10 +54,8 @@ if(CYTHON_FOUND)
   if(NUMPY_FOUND)
     add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}")
   endif()
-  if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
-  else()
-      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+  if(SCIPY_FOUND)
+    add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}")
   endif()
 
   message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - Sphinx is ${SPHINX_PATH}")
@@ -368,7 +366,7 @@ if(CYTHON_FOUND)
   add_gudhi_py_test(test_reader_utils)
 
   # Documentation generation is available through sphinx - requires all modules
-  if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_FOUND AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_FOUND AND SCIPY_FOUND AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
     # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
     # Images and biblio warnings because not found on developper version
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index e172c65b..e154c0b2 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -24,44 +24,42 @@ __author__ = "Vincent Rouvreau, Bertrand Michel"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
+def __min_birth_max_death(persistence, band=0.):
+    """This function returns (min_birth, max_death) from the persistence.
+
+    :param persistence: The persistence to plot.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param band: band
+    :type band: float.
+    :returns: (float, float) -- (min_birth, max_death).
+    """
+    # Look for minimum birth date and maximum death date for plot optimisation
+    max_death = 0
+    min_birth = persistence[0][1][0]
+    for interval in reversed(persistence):
+        if float(interval[1][1]) != float('inf'):
+            if float(interval[1][1]) > max_death:
+                max_death = float(interval[1][1])
+        if float(interval[1][0]) > max_death:
+            max_death = float(interval[1][0])
+        if float(interval[1][0]) < min_birth:
+            min_birth = float(interval[1][0])
+    if band > 0.:
+        max_death += band
+    return (min_birth, max_death)
+
+"""
+Only 13 colors for the palette
+"""
+palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
+           '#000000', '#880000', '#008800', '#000088', '#888800', '#880088',
+           '#008888']
+
 try:
     import matplotlib.pyplot as plt
     import matplotlib.patches as mpatches
     import numpy as np
-    from scipy.stats import kde
     import os
-    import math
-
-    def __min_birth_max_death(persistence, band=0.):
-        """This function returns (min_birth, max_death) from the persistence.
-
-        :param persistence: The persistence to plot.
-        :type persistence: list of tuples(dimension, tuple(birth, death)).
-        :param band: band
-        :type band: float.
-        :returns: (float, float) -- (min_birth, max_death).
-        """
-        # Look for minimum birth date and maximum death date for plot optimisation
-        max_death = 0
-        min_birth = persistence[0][1][0]
-        for interval in reversed(persistence):
-            if float(interval[1][1]) != float('inf'):
-                if float(interval[1][1]) > max_death:
-                    max_death = float(interval[1][1])
-            if float(interval[1][0]) > max_death:
-                max_death = float(interval[1][0])
-            if float(interval[1][0]) < min_birth:
-                min_birth = float(interval[1][0])
-        if band > 0.:
-            max_death += band
-        return (min_birth, max_death)
-
-    """
-    Only 13 colors for the palette
-    """
-    palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
-               '#000000', '#880000', '#008800', '#000088', '#888800', '#880088',
-               '#008888']
 
     def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
             max_barcodes=1000, inf_delta=0.1, legend=False):
@@ -220,71 +218,79 @@ try:
         plt.axis([axis_start, infinity, axis_start, infinity + delta])
         return plt
 
-    def plot_persistence_density(persistence=[], persistence_file='', nbins=300,
-                                 max_plots=1000, cmap=plt.cm.hot_r, legend=False):
-        """This function plots the persistence density from persistence values list
-        or from a :doc:`persistence file <fileformats>`. Be aware that this
-        function does not distinguish the dimension, it is up to you to select the
-        required one.
-
-        :param persistence: Persistence values list.
-        :type persistence: list of tuples(dimension, tuple(birth, death)).
-        :param persistence_file: A :doc:`persistence file <fileformats>` style name
-            (reset persistence if both are set).
-        :type persistence_file: string
-        :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins
-            over data extents (default is 300)
-        :type nbins: int.
-        :param max_plots: number of maximal plots to be displayed
-            Set it to 0 to see all, Default value is 1000.
-            (persistence will be sorted by life time if max_plots is set)
-        :type max_plots: int.
-        :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r).
-        :type cmap: cf. matplotlib colormap.
-        :param legend: Display the color bar values (default is False).
-        :type legend: boolean.
-        :returns: A matplotlib object containing diagram plot of persistence
-            (launch `show()` method on it to display it).
-        """
-        if persistence_file is not '':
-            if os.path.isfile(persistence_file):
-                # Reset persistence
-                persistence = []
-                diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
-                for key in diag.keys():
-                    for persistence_interval in diag[key]:
-                        persistence.append((key, persistence_interval))
-            else:
-                print("file " + persistence_file + " not found.")
-                return None
-
-        if max_plots > 0 and max_plots < len(persistence):
-            # Sort by life time, then takes only the max_plots elements
-            persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots]
-
-        # Set as numpy array birth and death (remove undefined values - inf and NaN)
-        birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
-        death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
-
-        # line display of equation : birth = death
-        x = np.linspace(death.min(), birth.max(), 1000)
-        plt.plot(x, x, color='k', linewidth=1.0)
-
-        # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
-        k = kde.gaussian_kde([birth,death])
-        xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j]
-        zi = k(np.vstack([xi.flatten(), yi.flatten()]))
-
-        # Make the plot
-        plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
-
-        if legend:
-            plt.colorbar()
-
-        plt.title('Persistence density')
-        plt.xlabel('Birth')
-        plt.ylabel('Death')
-        return plt
+    try:
+        from scipy.stats import kde
+        import math
+
+        def plot_persistence_density(persistence=[], persistence_file='', nbins=300,
+                                     max_plots=1000, cmap=plt.cm.hot_r, legend=False):
+            """This function plots the persistence density from persistence values list
+            or from a :doc:`persistence file <fileformats>`. Be aware that this
+            function does not distinguish the dimension, it is up to you to select the
+            required one.
+
+            :param persistence: Persistence values list.
+            :type persistence: list of tuples(dimension, tuple(birth, death)).
+            :param persistence_file: A :doc:`persistence file <fileformats>` style name
+                (reset persistence if both are set).
+            :type persistence_file: string
+            :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins
+                over data extents (default is 300)
+            :type nbins: int.
+            :param max_plots: number of maximal plots to be displayed
+                Set it to 0 to see all, Default value is 1000.
+                (persistence will be sorted by life time if max_plots is set)
+            :type max_plots: int.
+            :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r).
+            :type cmap: cf. matplotlib colormap.
+            :param legend: Display the color bar values (default is False).
+            :type legend: boolean.
+            :returns: A matplotlib object containing diagram plot of persistence
+                (launch `show()` method on it to display it).
+            """
+            if persistence_file is not '':
+                if os.path.isfile(persistence_file):
+                    # Reset persistence
+                    persistence = []
+                    diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
+                    for key in diag.keys():
+                        for persistence_interval in diag[key]:
+                            persistence.append((key, persistence_interval))
+                else:
+                    print("file " + persistence_file + " not found.")
+                    return None
+
+            if max_plots > 0 and max_plots < len(persistence):
+                # Sort by life time, then takes only the max_plots elements
+                persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots]
+
+            # Set as numpy array birth and death (remove undefined values - inf and NaN)
+            birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+            death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+
+            # line display of equation : birth = death
+            x = np.linspace(death.min(), birth.max(), 1000)
+            plt.plot(x, x, color='k', linewidth=1.0)
+
+            # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
+            k = kde.gaussian_kde([birth,death])
+            xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j]
+            zi = k(np.vstack([xi.flatten(), yi.flatten()]))
+
+            # Make the plot
+            plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
+
+            if legend:
+                plt.colorbar()
+
+            plt.title('Persistence density')
+            plt.xlabel('Birth')
+            plt.ylabel('Death')
+            return plt
+
+    except ImportError:
+        # Continue in case of import error, functions won't be available
+        pass
 
 except ImportError:
     # Continue in case of import error, functions won't be available
-- 
cgit v1.2.3


From efab7ccf5850ccc58018b7f856d209c4094e67c5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 16 Aug 2018 14:35:08 +0000
Subject: Bug fix

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3788 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: d8b898ca963d8d956307bb1dfd8abea1acbe6c96
---
 src/cython/cython/persistence_graphical_tools.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index e154c0b2..14c4cf3f 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -205,7 +205,6 @@ try:
                 # Infinite death case for diagram to be nicer
                 plt.scatter(interval[1][0], infinity, alpha=alpha,
                             color = palette[interval[0]])
-            ind = ind + 1
 
         if legend:
             dimensions = list(set(item[0] for item in persistence))
-- 
cgit v1.2.3


From b7354cd2ab0b265787348866da5d08cce15aee66 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 17 Aug 2018 09:38:55 +0000
Subject: Code review : add a parameter to select dimension for
 plot_persistence_density. Default is None and mix all dimensions

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3794 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 493f5ecfad2bcf0ee4a40ec7b315863c471d088f
---
 src/cython/cython/persistence_graphical_tools.py | 43 +++++++++++++++---------
 1 file changed, 28 insertions(+), 15 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 14c4cf3f..949f5c37 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -221,26 +221,31 @@ try:
         from scipy.stats import kde
         import math
 
-        def plot_persistence_density(persistence=[], persistence_file='', nbins=300,
-                                     max_plots=1000, cmap=plt.cm.hot_r, legend=False):
-            """This function plots the persistence density from persistence values list
-            or from a :doc:`persistence file <fileformats>`. Be aware that this
-            function does not distinguish the dimension, it is up to you to select the
-            required one.
+        def plot_persistence_density(persistence=[], persistence_file='',
+                                     nbins=300, max_plots=1000, dimension=None,
+                                     cmap=plt.cm.hot_r, legend=False):
+            """This function plots the persistence density from persistence
+            values list or from a :doc:`persistence file <fileformats>`. Be
+            aware that this function does not distinguish the dimension, it is
+            up to you to select the required one.
 
             :param persistence: Persistence values list.
             :type persistence: list of tuples(dimension, tuple(birth, death)).
-            :param persistence_file: A :doc:`persistence file <fileformats>` style name
-                (reset persistence if both are set).
+            :param persistence_file: A :doc:`persistence file <fileformats>`
+                style name (reset persistence if both are set).
             :type persistence_file: string
-            :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins
-                over data extents (default is 300)
+            :param nbins: Evaluate a gaussian kde on a regular grid of nbins x
+                nbins over data extents (default is 300)
             :type nbins: int.
             :param max_plots: number of maximal plots to be displayed
                 Set it to 0 to see all, Default value is 1000.
                 (persistence will be sorted by life time if max_plots is set)
             :type max_plots: int.
-            :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r).
+            :param dimension: the dimension to be selected in the intervals
+                (default is None to mix all dimensions).
+            :type dimension: int.
+            :param cmap: A matplotlib colormap (default is
+                matplotlib.pyplot.cm.hot_r).
             :type cmap: cf. matplotlib colormap.
             :param legend: Display the color bar values (default is False).
             :type legend: boolean.
@@ -259,13 +264,21 @@ try:
                     print("file " + persistence_file + " not found.")
                     return None
 
-            if max_plots > 0 and max_plots < len(persistence):
+            persistence_dim = []
+            if dimension is not None:
+                persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)]
+            else:
+                persistence_dim = persistence
+
+            if max_plots > 0 and max_plots < len(persistence_dim):
                 # Sort by life time, then takes only the max_plots elements
-                persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots]
+                persistence_dim = sorted(persistence_dim,
+                                     key=lambda life_time: life_time[1][1]-life_time[1][0],
+                                     reverse=True)[:max_plots]
 
             # Set as numpy array birth and death (remove undefined values - inf and NaN)
-            birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
-            death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+            birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+            death = np.asarray([(interval[1][1]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
 
             # line display of equation : birth = death
             x = np.linspace(death.min(), birth.max(), 1000)
-- 
cgit v1.2.3


From 1865751c055ad01ba159a13d22e42204195c2ccb Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 17 Aug 2018 09:50:15 +0000
Subject: Doc review : rephrase max_plots explanation

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3795 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f6059d3a242eed53dfdddb76ffed33f99892f4bc
---
 src/cython/cython/persistence_graphical_tools.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 949f5c37..0b3357f8 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -138,21 +138,22 @@ try:
 
     def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
             band=0., max_plots=1000, inf_delta=0.1, legend=False):
-        """This function plots the persistence diagram from persistence values list
-        or from a :doc:`persistence file <fileformats>`.
+        """This function plots the persistence diagram from persistence values
+        list or from a :doc:`persistence file <fileformats>`.
 
         :param persistence: Persistence values list.
         :type persistence: list of tuples(dimension, tuple(birth, death)).
         :param persistence_file: A :doc:`persistence file <fileformats>` style name
             (reset persistence if both are set).
         :type persistence_file: string
-        :param alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
+        :param alpha: plot transparency value (0.0 transparent through 1.0
+            opaque - default is 0.6).
         :type alpha: float.
         :param band: band (not displayed if :math:`\leq` 0. - default is 0.)
         :type band: float.
-        :param max_plots: number of maximal plots to be displayed
-            Set it to 0 to see all, Default value is 1000.
-            (persistence will be sorted by life time if max_plots is set)
+        :param max_plots: maximal number of points to display. Selected points
+            are those with the longest life time. Set it to 0 to see all,
+            default value is 1000.
         :type max_plots: int.
         :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
             A reasonable value is between 0.05 and 0.5 - default is 0.1.
@@ -237,9 +238,9 @@ try:
             :param nbins: Evaluate a gaussian kde on a regular grid of nbins x
                 nbins over data extents (default is 300)
             :type nbins: int.
-            :param max_plots: number of maximal plots to be displayed
-                Set it to 0 to see all, Default value is 1000.
-                (persistence will be sorted by life time if max_plots is set)
+            :param max_plots: maximal number of points to display. Selected points
+                are those with the longest life time. Set it to 0 to see all,
+                default value is 1000.
             :type max_plots: int.
             :param dimension: the dimension to be selected in the intervals
                 (default is None to mix all dimensions).
-- 
cgit v1.2.3


From 67ae5aa70e70097f72f868ebba1fa8e7ff96297d Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 17 Aug 2018 12:41:10 +0000
Subject: doc review : modification of persistence barcode example to make it
 more relevant

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3796 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 17acc09cdf7d09b13c177334efb1e309c4fd8d9c
---
 .../doc/persistence_graphical_tools_user.rst       | 25 +++++++++++-----------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index b21de06a..0047f9c8 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -19,12 +19,15 @@ 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
 -----------------------------
@@ -53,13 +56,9 @@ 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 persistence density
-    plt = gudhi.plot_persistence_density([(dim,interval) for interval in diag[dim]],
-        max_plots=0, legend=True)
+    plt = gudhi.plot_persistence_density(persistence_file=persistence_file,
+        max_plots=0, dimension=1, legend=True)
     plt.show()
-- 
cgit v1.2.3


From a5464d68d2848d21fc777809ab686b1bbf4e0139 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 17 Aug 2018 13:32:41 +0000
Subject: Code review : Add a bw_method parameter to plot_persistence_density
 for the standard deviation of the Gaussian

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3799 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3bbc988434951bb429acd44b1f31f8310bb9ba9c
---
 src/cython/cython/persistence_graphical_tools.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 0b3357f8..026e365d 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -223,7 +223,8 @@ try:
         import math
 
         def plot_persistence_density(persistence=[], persistence_file='',
-                                     nbins=300, max_plots=1000, dimension=None,
+                                     nbins=300, bw_method=None,
+                                     max_plots=1000, dimension=None,
                                      cmap=plt.cm.hot_r, legend=False):
             """This function plots the persistence density from persistence
             values list or from a :doc:`persistence file <fileformats>`. Be
@@ -238,6 +239,14 @@ try:
             :param nbins: Evaluate a gaussian kde on a regular grid of nbins x
                 nbins over data extents (default is 300)
             :type nbins: int.
+            :param bw_method: The method used to calculate the estimator
+                bandwidth. This can be 'scott', 'silverman', a scalar constant
+                or a callable. If a scalar, this will be used directly as
+                kde.factor. If a callable, it should take a gaussian_kde
+                instance as only parameter and return a scalar. If None
+                (default), 'scott' is used. See scipy.stats.gaussian_kde
+                documentation for more details.
+            :type bw_method: str, scalar or callable, optional.
             :param max_plots: maximal number of points to display. Selected points
                 are those with the longest life time. Set it to 0 to see all,
                 default value is 1000.
@@ -286,7 +295,7 @@ try:
             plt.plot(x, x, color='k', linewidth=1.0)
 
             # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
-            k = kde.gaussian_kde([birth,death])
+            k = kde.gaussian_kde([birth,death], bw_method=bw_method)
             xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j]
             zi = k(np.vstack([xi.flatten(), yi.flatten()]))
 
-- 
cgit v1.2.3


From 24c661e98b8f8e0f2c492fcf63e68615dbd9ae84 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 17 Aug 2018 13:45:08 +0000
Subject: Doc review : inf_delta explanation improvement

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3800 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 01fff74d79228431d77a46b713ac656ab7e84dc0
---
 src/cython/cython/persistence_graphical_tools.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 026e365d..4c8467bd 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -71,14 +71,16 @@ try:
         :param persistence_file: A :doc:`persistence file <fileformats>` style name
             (reset persistence if both are set).
         :type persistence_file: string
-        :param alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
+        :param alpha: barcode transparency value (0.0 transparent through 1.0
+            opaque - default is 0.6).
         :type alpha: float.
         :param max_barcodes: number of maximal barcodes to be displayed.
             Set it to 0 to see all, Default value is 1000.
             (persistence will be sorted by life time if max_barcodes is set)
         :type max_barcodes: int.
-        :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
-            A reasonable value is between 0.05 and 0.5 - default is 0.1.
+        :param inf_delta: Infinity is placed at ((max_death - min_birth) x
+            inf_delta) above the highest point. A reasonable value is between
+            0.05 and 0.5 - default is 0.1.
         :type inf_delta: float.
         :param legend: Display the dimension color legend (default is False).
         :type legend: boolean.
@@ -155,8 +157,9 @@ try:
             are those with the longest life time. Set it to 0 to see all,
             default value is 1000.
         :type max_plots: int.
-        :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
-            A reasonable value is between 0.05 and 0.5 - default is 0.1.
+        :param inf_delta: Infinity is placed at ((max_death - min_birth) x
+            inf_delta) above the highest point. A reasonable value is between
+            0.05 and 0.5 - default is 0.1.
         :type inf_delta: float.
         :param legend: Display the dimension color legend (default is False).
         :type legend: boolean.
-- 
cgit v1.2.3


From 7e1d78ec22e0e53bbf4a36aaea1b77fa48f5d40d Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 17 Aug 2018 13:58:46 +0000
Subject: Code review : Rename max_plots with max_intervals for persistence
 density

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3801 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8d20ee2f721b856bba69bc5bc10db26032649129
---
 src/cython/cython/persistence_graphical_tools.py    | 14 +++++++-------
 src/cython/doc/persistence_graphical_tools_user.rst |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 4c8467bd..96b579bd 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -250,10 +250,10 @@ try:
                 (default), 'scott' is used. See scipy.stats.gaussian_kde
                 documentation for more details.
             :type bw_method: str, scalar or callable, optional.
-            :param max_plots: maximal number of points to display. Selected points
-                are those with the longest life time. Set it to 0 to see all,
-                default value is 1000.
-            :type max_plots: int.
+            :param max_intervals: maximal number of intervals to display.
+                Selected points are those with the longest life time. Set it
+                to 0 to see all. Default value is 1000.
+            :type max_intervals: int.
             :param dimension: the dimension to be selected in the intervals
                 (default is None to mix all dimensions).
             :type dimension: int.
@@ -283,11 +283,11 @@ try:
             else:
                 persistence_dim = persistence
 
-            if max_plots > 0 and max_plots < len(persistence_dim):
-                # Sort by life time, then takes only the max_plots elements
+            if max_intervals > 0 and max_intervals < len(persistence_dim):
+                # Sort by life time, then takes only the max_intervals elements
                 persistence_dim = sorted(persistence_dim,
                                      key=lambda life_time: life_time[1][1]-life_time[1][0],
-                                     reverse=True)[:max_plots]
+                                     reverse=True)[:max_intervals]
 
             # Set as numpy array birth and death (remove undefined values - inf and NaN)
             birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index 0047f9c8..fda086c3 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -60,5 +60,5 @@ If you want more information on a specific dimension, for instance:
     persistence_file=gudhi.__root_source_dir__ + \
         '/data/persistence_diagram/rips_on_tore3D_1307.pers'
     plt = gudhi.plot_persistence_density(persistence_file=persistence_file,
-        max_plots=0, dimension=1, legend=True)
+        max_intervals=0, dimension=1, legend=True)
     plt.show()
-- 
cgit v1.2.3


From 6ebc098c9bbf233b5a4325faec04236feedab191 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 17 Aug 2018 14:48:08 +0000
Subject: Code review : rename max_plots and max_barcodes as max_intervals for
 peristence_graphical_tools

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3803 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ad73f7e6cc6d72c3ba24b5ac947265c78a29f387
---
 src/cython/cython/persistence_graphical_tools.py | 43 ++++++++++++++----------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 96b579bd..85d2a5ad 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -62,7 +62,8 @@ try:
     import os
 
     def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
-            max_barcodes=1000, inf_delta=0.1, legend=False):
+                                 max_intervals=1000, max_barcodes=1000,
+                                 inf_delta=0.1, legend=False):
         """This function plots the persistence bar code from persistence values list
         or from a :doc:`persistence file <fileformats>`.
 
@@ -74,10 +75,10 @@ try:
         :param alpha: barcode transparency value (0.0 transparent through 1.0
             opaque - default is 0.6).
         :type alpha: float.
-        :param max_barcodes: number of maximal barcodes to be displayed.
-            Set it to 0 to see all, Default value is 1000.
-            (persistence will be sorted by life time if max_barcodes is set)
-        :type max_barcodes: int.
+        :param max_intervals: maximal number of intervals to display.
+            Selected points are those with the longest life time. Set it
+            to 0 to see all. Default value is 1000.
+        :type max_intervals: int.
         :param inf_delta: Infinity is placed at ((max_death - min_birth) x
             inf_delta) above the highest point. A reasonable value is between
             0.05 and 0.5 - default is 0.1.
@@ -99,9 +100,13 @@ try:
                 print("file " + persistence_file + " not found.")
                 return None
 
-        if max_barcodes > 0 and max_barcodes < len(persistence):
-            # Sort by life time, then takes only the max_plots elements
-            persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_barcodes]
+        if max_barcodes is not 1000:
+            print('Deprecated parameter. It has been replaced by max_intervals')
+            max_intervals = max_barcodes
+
+        if max_intervals > 0 and max_intervals < len(persistence):
+            # Sort by life time, then takes only the max_intervals elements
+            persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_intervals]
 
         persistence = sorted(persistence, key=lambda birth: birth[1][0])
 
@@ -139,7 +144,7 @@ try:
         return plt
 
     def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
-            band=0., max_plots=1000, inf_delta=0.1, legend=False):
+            band=0., max_intervals=1000, max_plots=1000, inf_delta=0.1, legend=False):
         """This function plots the persistence diagram from persistence values
         list or from a :doc:`persistence file <fileformats>`.
 
@@ -153,10 +158,10 @@ try:
         :type alpha: float.
         :param band: band (not displayed if :math:`\leq` 0. - default is 0.)
         :type band: float.
-        :param max_plots: maximal number of points to display. Selected points
-            are those with the longest life time. Set it to 0 to see all,
-            default value is 1000.
-        :type max_plots: int.
+        :param max_intervals: maximal number of intervals to display.
+            Selected points are those with the longest life time. Set it
+            to 0 to see all. Default value is 1000.
+        :type max_intervals: int.
         :param inf_delta: Infinity is placed at ((max_death - min_birth) x
             inf_delta) above the highest point. A reasonable value is between
             0.05 and 0.5 - default is 0.1.
@@ -178,9 +183,13 @@ try:
                 print("file " + persistence_file + " not found.")
                 return None
 
-        if max_plots > 0 and max_plots < len(persistence):
-            # Sort by life time, then takes only the max_plots elements
-            persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots]
+        if max_plots is not 1000:
+            print('Deprecated parameter. It has been replaced by max_intervals')
+            max_intervals = max_plots
+
+        if max_intervals > 0 and max_intervals < len(persistence):
+            # Sort by life time, then takes only the max_intervals elements
+            persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_intervals]
 
         (min_birth, max_death) = __min_birth_max_death(persistence, band)
         delta = ((max_death - min_birth) * inf_delta)
@@ -227,7 +236,7 @@ try:
 
         def plot_persistence_density(persistence=[], persistence_file='',
                                      nbins=300, bw_method=None,
-                                     max_plots=1000, dimension=None,
+                                     max_intervals=1000, dimension=None,
                                      cmap=plt.cm.hot_r, legend=False):
             """This function plots the persistence density from persistence
             values list or from a :doc:`persistence file <fileformats>`. Be
-- 
cgit v1.2.3


From b301bf80daaac521f16d43120a8a30a2af9eb515 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 17 Aug 2018 15:29:19 +0000
Subject: Makes clearer dependencies for each function of persistence graphical
 tools

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3804 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7572f54368ff235f5e78df74121bf6b1ee107177
---
 src/cython/doc/persistence_graphical_tools_sum.inc  | 2 +-
 src/cython/doc/persistence_graphical_tools_user.rst | 9 +++++++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc
index c793a352..5577cf99 100644
--- a/src/cython/doc/persistence_graphical_tools_sum.inc
+++ b/src/cython/doc/persistence_graphical_tools_sum.inc
@@ -1,6 +1,6 @@
 =================================================================  ===================================  ===================================
 :Author: Vincent Rouvreau                                          :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
-:Requires: Matplotlib                                              Numpy                                Scipy
+:Requires: matplotlib                                              numpy                                scipy
 =================================================================  ===================================  ===================================
 
 +-----------------------------------------------------------------+-----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index fda086c3..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::
@@ -32,6 +35,9 @@ This function can display the persistence result as a barcode:
 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::
@@ -49,6 +55,9 @@ This function can display the persistence result as a diagram:
 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::
-- 
cgit v1.2.3


From 44aaa06e1da4a2e4557886c9c7096edbe9d00f53 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 10 Sep 2018 08:37:45 +0000
Subject: Doc review : Add a link to scipy.stats.gaussian_kde official
 documentation

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3878 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: dd6e1a4131be1ed0306a48f9b095e0d09ddee848
---
 src/cython/cython/persistence_graphical_tools.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 85d2a5ad..f5550e3a 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -256,8 +256,10 @@ try:
                 or a callable. If a scalar, this will be used directly as
                 kde.factor. If a callable, it should take a gaussian_kde
                 instance as only parameter and return a scalar. If None
-                (default), 'scott' is used. See scipy.stats.gaussian_kde
-                documentation for more details.
+                (default), 'scott' is used. See
+                `scipy.stats.gaussian_kde documentation
+                <http://scipy.github.io/devdocs/generated/scipy.stats.gaussian_kde.html>`_
+                for more details.
             :type bw_method: str, scalar or callable, optional.
             :param max_intervals: maximal number of intervals to display.
                 Selected points are those with the longest life time. Set it
-- 
cgit v1.2.3


From bdbbbc71e7d82526b24f76cc3b9916ad53919d41 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 10 Sep 2018 09:32:00 +0000
Subject: Code review : More explicit message when import fails in plot
 persistence graphical tools

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3881 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 96f9e3da3bd68d6cba65242b9890c4beb463c863
---
 src/cython/cython/persistence_graphical_tools.py | 309 ++++++++++++-----------
 1 file changed, 161 insertions(+), 148 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index f5550e3a..e66643d2 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -55,39 +55,39 @@ palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
            '#000000', '#880000', '#008800', '#000088', '#888800', '#880088',
            '#008888']
 
-try:
-    import matplotlib.pyplot as plt
-    import matplotlib.patches as mpatches
-    import numpy as np
-    import os
-
-    def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
-                                 max_intervals=1000, max_barcodes=1000,
-                                 inf_delta=0.1, legend=False):
-        """This function plots the persistence bar code from persistence values list
-        or from a :doc:`persistence file <fileformats>`.
-
-        :param persistence: Persistence values list.
-        :type persistence: list of tuples(dimension, tuple(birth, death)).
-        :param persistence_file: A :doc:`persistence file <fileformats>` style name
-            (reset persistence if both are set).
-        :type persistence_file: string
-        :param alpha: barcode transparency value (0.0 transparent through 1.0
-            opaque - default is 0.6).
-        :type alpha: float.
-        :param max_intervals: maximal number of intervals to display.
-            Selected points are those with the longest life time. Set it
-            to 0 to see all. Default value is 1000.
-        :type max_intervals: int.
-        :param inf_delta: Infinity is placed at ((max_death - min_birth) x
-            inf_delta) above the highest point. A reasonable value is between
-            0.05 and 0.5 - default is 0.1.
-        :type inf_delta: float.
-        :param legend: Display the dimension color legend (default is False).
-        :type legend: boolean.
-        :returns: A matplotlib object containing horizontal bar plot of persistence
-            (launch `show()` method on it to display it).
-        """
+def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
+                             max_intervals=1000, max_barcodes=1000,
+                             inf_delta=0.1, legend=False):
+    """This function plots the persistence bar code from persistence values list
+    or from a :doc:`persistence file <fileformats>`.
+
+    :param persistence: Persistence values list.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence_file: A :doc:`persistence file <fileformats>` style name
+        (reset persistence if both are set).
+    :type persistence_file: string
+    :param alpha: barcode transparency value (0.0 transparent through 1.0
+        opaque - default is 0.6).
+    :type alpha: float.
+    :param max_intervals: maximal number of intervals to display.
+        Selected points are those with the longest life time. Set it
+        to 0 to see all. Default value is 1000.
+    :type max_intervals: int.
+    :param inf_delta: Infinity is placed at ((max_death - min_birth) x
+        inf_delta) above the highest point. A reasonable value is between
+        0.05 and 0.5 - default is 0.1.
+    :type inf_delta: float.
+    :param legend: Display the dimension color legend (default is False).
+    :type legend: boolean.
+    :returns: A matplotlib object containing horizontal bar plot of persistence
+        (launch `show()` method on it to display it).
+    """
+    try:
+        import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
+        import numpy as np
+        import os
+
         if persistence_file is not '':
             if os.path.isfile(persistence_file):
                 # Reset persistence
@@ -143,34 +143,43 @@ try:
         plt.axis([axis_start, infinity, 0, ind])
         return plt
 
-    def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
-            band=0., max_intervals=1000, max_plots=1000, inf_delta=0.1, legend=False):
-        """This function plots the persistence diagram from persistence values
-        list or from a :doc:`persistence file <fileformats>`.
-
-        :param persistence: Persistence values list.
-        :type persistence: list of tuples(dimension, tuple(birth, death)).
-        :param persistence_file: A :doc:`persistence file <fileformats>` style name
-            (reset persistence if both are set).
-        :type persistence_file: string
-        :param alpha: plot transparency value (0.0 transparent through 1.0
-            opaque - default is 0.6).
-        :type alpha: float.
-        :param band: band (not displayed if :math:`\leq` 0. - default is 0.)
-        :type band: float.
-        :param max_intervals: maximal number of intervals to display.
-            Selected points are those with the longest life time. Set it
-            to 0 to see all. Default value is 1000.
-        :type max_intervals: int.
-        :param inf_delta: Infinity is placed at ((max_death - min_birth) x
-            inf_delta) above the highest point. A reasonable value is between
-            0.05 and 0.5 - default is 0.1.
-        :type inf_delta: float.
-        :param legend: Display the dimension color legend (default is False).
-        :type legend: boolean.
-        :returns: A matplotlib object containing diagram plot of persistence
-            (launch `show()` method on it to display it).
-        """
+    except ImportError:
+        print("This function is not available, you may be missing numpy and/or matplotlib.")
+
+def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
+        band=0., max_intervals=1000, max_plots=1000, inf_delta=0.1, legend=False):
+    """This function plots the persistence diagram from persistence values
+    list or from a :doc:`persistence file <fileformats>`.
+
+    :param persistence: Persistence values list.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence_file: A :doc:`persistence file <fileformats>` style name
+        (reset persistence if both are set).
+    :type persistence_file: string
+    :param alpha: plot transparency value (0.0 transparent through 1.0
+        opaque - default is 0.6).
+    :type alpha: float.
+    :param band: band (not displayed if :math:`\leq` 0. - default is 0.)
+    :type band: float.
+    :param max_intervals: maximal number of intervals to display.
+        Selected points are those with the longest life time. Set it
+        to 0 to see all. Default value is 1000.
+    :type max_intervals: int.
+    :param inf_delta: Infinity is placed at ((max_death - min_birth) x
+        inf_delta) above the highest point. A reasonable value is between
+        0.05 and 0.5 - default is 0.1.
+    :type inf_delta: float.
+    :param legend: Display the dimension color legend (default is False).
+    :type legend: boolean.
+    :returns: A matplotlib object containing diagram plot of persistence
+        (launch `show()` method on it to display it).
+    """
+    try:
+        import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
+        import numpy as np
+        import os
+
         if persistence_file is not '':
             if os.path.isfile(persistence_file):
                 # Reset persistence
@@ -230,104 +239,108 @@ try:
         plt.axis([axis_start, infinity, axis_start, infinity + delta])
         return plt
 
+    except ImportError:
+        print("This function is not available, you may be missing numpy and/or matplotlib.")
+
+def plot_persistence_density(persistence=[], persistence_file='',
+                             nbins=300, bw_method=None,
+                             max_intervals=1000, dimension=None,
+                             cmap=None, legend=False):
+    """This function plots the persistence density from persistence
+    values list or from a :doc:`persistence file <fileformats>`. Be
+    aware that this function does not distinguish the dimension, it is
+    up to you to select the required one.
+
+    :param persistence: Persistence values list.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence_file: A :doc:`persistence file <fileformats>`
+        style name (reset persistence if both are set).
+    :type persistence_file: string
+    :param nbins: Evaluate a gaussian kde on a regular grid of nbins x
+        nbins over data extents (default is 300)
+    :type nbins: int.
+    :param bw_method: The method used to calculate the estimator
+        bandwidth. This can be 'scott', 'silverman', a scalar constant
+        or a callable. If a scalar, this will be used directly as
+        kde.factor. If a callable, it should take a gaussian_kde
+        instance as only parameter and return a scalar. If None
+        (default), 'scott' is used. See
+        `scipy.stats.gaussian_kde documentation
+        <http://scipy.github.io/devdocs/generated/scipy.stats.gaussian_kde.html>`_
+        for more details.
+    :type bw_method: str, scalar or callable, optional.
+    :param max_intervals: maximal number of intervals to display.
+        Selected points are those with the longest life time. Set it
+        to 0 to see all. Default value is 1000.
+    :type max_intervals: int.
+    :param dimension: the dimension to be selected in the intervals
+        (default is None to mix all dimensions).
+    :type dimension: int.
+    :param cmap: A matplotlib colormap (default is
+        matplotlib.pyplot.cm.hot_r).
+    :type cmap: cf. matplotlib colormap.
+    :param legend: Display the color bar values (default is False).
+    :type legend: boolean.
+    :returns: A matplotlib object containing diagram plot of persistence
+        (launch `show()` method on it to display it).
+    """
     try:
+        import matplotlib.pyplot as plt
+        import numpy as np
         from scipy.stats import kde
+        import os
         import math
 
-        def plot_persistence_density(persistence=[], persistence_file='',
-                                     nbins=300, bw_method=None,
-                                     max_intervals=1000, dimension=None,
-                                     cmap=plt.cm.hot_r, legend=False):
-            """This function plots the persistence density from persistence
-            values list or from a :doc:`persistence file <fileformats>`. Be
-            aware that this function does not distinguish the dimension, it is
-            up to you to select the required one.
-
-            :param persistence: Persistence values list.
-            :type persistence: list of tuples(dimension, tuple(birth, death)).
-            :param persistence_file: A :doc:`persistence file <fileformats>`
-                style name (reset persistence if both are set).
-            :type persistence_file: string
-            :param nbins: Evaluate a gaussian kde on a regular grid of nbins x
-                nbins over data extents (default is 300)
-            :type nbins: int.
-            :param bw_method: The method used to calculate the estimator
-                bandwidth. This can be 'scott', 'silverman', a scalar constant
-                or a callable. If a scalar, this will be used directly as
-                kde.factor. If a callable, it should take a gaussian_kde
-                instance as only parameter and return a scalar. If None
-                (default), 'scott' is used. See
-                `scipy.stats.gaussian_kde documentation
-                <http://scipy.github.io/devdocs/generated/scipy.stats.gaussian_kde.html>`_
-                for more details.
-            :type bw_method: str, scalar or callable, optional.
-            :param max_intervals: maximal number of intervals to display.
-                Selected points are those with the longest life time. Set it
-                to 0 to see all. Default value is 1000.
-            :type max_intervals: int.
-            :param dimension: the dimension to be selected in the intervals
-                (default is None to mix all dimensions).
-            :type dimension: int.
-            :param cmap: A matplotlib colormap (default is
-                matplotlib.pyplot.cm.hot_r).
-            :type cmap: cf. matplotlib colormap.
-            :param legend: Display the color bar values (default is False).
-            :type legend: boolean.
-            :returns: A matplotlib object containing diagram plot of persistence
-                (launch `show()` method on it to display it).
-            """
-            if persistence_file is not '':
-                if os.path.isfile(persistence_file):
-                    # Reset persistence
-                    persistence = []
-                    diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
-                    for key in diag.keys():
-                        for persistence_interval in diag[key]:
-                            persistence.append((key, persistence_interval))
-                else:
-                    print("file " + persistence_file + " not found.")
-                    return None
-
-            persistence_dim = []
-            if dimension is not None:
-                persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)]
+        if persistence_file is not '':
+            if os.path.isfile(persistence_file):
+                # Reset persistence
+                persistence = []
+                diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
+                for key in diag.keys():
+                    for persistence_interval in diag[key]:
+                        persistence.append((key, persistence_interval))
             else:
-                persistence_dim = persistence
+                print("file " + persistence_file + " not found.")
+                return None
 
-            if max_intervals > 0 and max_intervals < len(persistence_dim):
-                # Sort by life time, then takes only the max_intervals elements
-                persistence_dim = sorted(persistence_dim,
-                                     key=lambda life_time: life_time[1][1]-life_time[1][0],
-                                     reverse=True)[:max_intervals]
+        persistence_dim = []
+        if dimension is not None:
+            persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)]
+        else:
+            persistence_dim = persistence
 
-            # Set as numpy array birth and death (remove undefined values - inf and NaN)
-            birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
-            death = np.asarray([(interval[1][1]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+        if max_intervals > 0 and max_intervals < len(persistence_dim):
+            # Sort by life time, then takes only the max_intervals elements
+            persistence_dim = sorted(persistence_dim,
+                                 key=lambda life_time: life_time[1][1]-life_time[1][0],
+                                 reverse=True)[:max_intervals]
 
-            # line display of equation : birth = death
-            x = np.linspace(death.min(), birth.max(), 1000)
-            plt.plot(x, x, color='k', linewidth=1.0)
+        # Set as numpy array birth and death (remove undefined values - inf and NaN)
+        birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+        death = np.asarray([(interval[1][1]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
 
-            # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
-            k = kde.gaussian_kde([birth,death], bw_method=bw_method)
-            xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j]
-            zi = k(np.vstack([xi.flatten(), yi.flatten()]))
+        # line display of equation : birth = death
+        x = np.linspace(death.min(), birth.max(), 1000)
+        plt.plot(x, x, color='k', linewidth=1.0)
 
-            # Make the plot
-            plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
+        # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
+        k = kde.gaussian_kde([birth,death], bw_method=bw_method)
+        xi, yi = np.mgrid[birth.min():birth.max():nbins*1j, death.min():death.max():nbins*1j]
+        zi = k(np.vstack([xi.flatten(), yi.flatten()]))
 
-            if legend:
-                plt.colorbar()
+        # default cmap value cannot be done at argument definition level as matplotlib is not yet defined.
+        if cmap is None:
+            cmap = plt.cm.hot_r
+        # Make the plot
+        plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
 
-            plt.title('Persistence density')
-            plt.xlabel('Birth')
-            plt.ylabel('Death')
-            return plt
+        if legend:
+            plt.colorbar()
 
-    except ImportError:
-        # Continue in case of import error, functions won't be available
-        pass
+        plt.title('Persistence density')
+        plt.xlabel('Birth')
+        plt.ylabel('Death')
+        return plt
 
-except ImportError:
-    # Continue in case of import error, functions won't be available
-    pass
+    except ImportError:
+        print("This function is not available, you may be missing numpy, matplotlib and/or scipy.")
-- 
cgit v1.2.3


From 338b2f41bd14f04193a0b2f6fb0a2321443be45b Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 2 Oct 2018 07:45:51 +0000
Subject: Doc review: max_intervals documentation in plot_persistence_density

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3917 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 90cfd77ad4aad4cdb0937f43dd4f802688f98295
---
 src/cython/cython/persistence_graphical_tools.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index e66643d2..139a2332 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -269,7 +269,8 @@ def plot_persistence_density(persistence=[], persistence_file='',
         <http://scipy.github.io/devdocs/generated/scipy.stats.gaussian_kde.html>`_
         for more details.
     :type bw_method: str, scalar or callable, optional.
-    :param max_intervals: maximal number of intervals to display.
+    :param max_intervals: maximal number of points used in the density
+        estimation.
         Selected points are those with the longest life time. Set it
         to 0 to see all. Default value is 1000.
     :type max_intervals: int.
-- 
cgit v1.2.3


From 5469c3637df2efd1a70a165484b992727782d15c Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 2 Oct 2018 07:51:22 +0000
Subject: Doc review :  "Selected points are" ->  "Selected intervals are"

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3918 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 79857a4609428fc623f8f4656762261ea664cf12
---
 src/cython/cython/persistence_graphical_tools.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 139a2332..abc205bb 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -70,7 +70,7 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
         opaque - default is 0.6).
     :type alpha: float.
     :param max_intervals: maximal number of intervals to display.
-        Selected points are those with the longest life time. Set it
+        Selected intervals are those with the longest life time. Set it
         to 0 to see all. Default value is 1000.
     :type max_intervals: int.
     :param inf_delta: Infinity is placed at ((max_death - min_birth) x
@@ -162,7 +162,7 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
     :param band: band (not displayed if :math:`\leq` 0. - default is 0.)
     :type band: float.
     :param max_intervals: maximal number of intervals to display.
-        Selected points are those with the longest life time. Set it
+        Selected intervals are those with the longest life time. Set it
         to 0 to see all. Default value is 1000.
     :type max_intervals: int.
     :param inf_delta: Infinity is placed at ((max_death - min_birth) x
@@ -271,7 +271,7 @@ def plot_persistence_density(persistence=[], persistence_file='',
     :type bw_method: str, scalar or callable, optional.
     :param max_intervals: maximal number of points used in the density
         estimation.
-        Selected points are those with the longest life time. Set it
+        Selected intervals are those with the longest life time. Set it
         to 0 to see all. Default value is 1000.
     :type max_intervals: int.
     :param dimension: the dimension to be selected in the intervals
-- 
cgit v1.2.3


From b4c51b3d92564e2e93e8fa4fe55f98cd06bba57a Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 2 Oct 2018 08:13:28 +0000
Subject: Code review : remove executable property Doc review : Rephrase
 inf_delta explanation

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3919 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b45697b675a20cdca7bb42fa7a555df6c35fe0fd
---
 src/cython/cython/persistence_graphical_tools.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)
 mode change 100755 => 100644 src/cython/cython/persistence_graphical_tools.py

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
old mode 100755
new mode 100644
index abc205bb..e63b350b
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -61,7 +61,7 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
     """This function plots the persistence bar code from persistence values list
     or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: Persistence values list.
+    :param persistence: Persistence intervals values list grouped by dimension.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
     :param persistence_file: A :doc:`persistence file <fileformats>` style name
         (reset persistence if both are set).
@@ -73,9 +73,9 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
         Selected intervals are those with the longest life time. Set it
         to 0 to see all. Default value is 1000.
     :type max_intervals: int.
-    :param inf_delta: Infinity is placed at ((max_death - min_birth) x
-        inf_delta) above the highest point. A reasonable value is between
-        0.05 and 0.5 - default is 0.1.
+    :param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x
+        inf_delta)` above :code:`max_death` value. A reasonable value is
+        between 0.05 and 0.5 - default is 0.1.
     :type inf_delta: float.
     :param legend: Display the dimension color legend (default is False).
     :type legend: boolean.
@@ -151,7 +151,7 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
     """This function plots the persistence diagram from persistence values
     list or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: Persistence values list.
+    :param persistence: Persistence intervals values list grouped by dimension.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
     :param persistence_file: A :doc:`persistence file <fileformats>` style name
         (reset persistence if both are set).
@@ -165,9 +165,9 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
         Selected intervals are those with the longest life time. Set it
         to 0 to see all. Default value is 1000.
     :type max_intervals: int.
-    :param inf_delta: Infinity is placed at ((max_death - min_birth) x
-        inf_delta) above the highest point. A reasonable value is between
-        0.05 and 0.5 - default is 0.1.
+    :param inf_delta: Infinity is placed at :code:`((max_death - min_birth) x
+        inf_delta)` above :code:`max_death` value. A reasonable value is
+        between 0.05 and 0.5 - default is 0.1.
     :type inf_delta: float.
     :param legend: Display the dimension color legend (default is False).
     :type legend: boolean.
@@ -251,7 +251,7 @@ def plot_persistence_density(persistence=[], persistence_file='',
     aware that this function does not distinguish the dimension, it is
     up to you to select the required one.
 
-    :param persistence: Persistence values list.
+    :param persistence: Persistence intervals values list grouped by dimension.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
     :param persistence_file: A :doc:`persistence file <fileformats>`
         style name (reset persistence if both are set).
-- 
cgit v1.2.3


From 2dde0fc4ea8f24173789a1ce9a9442cb02b96e86 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 2 Oct 2018 08:23:51 +0000
Subject: Doc review : Explain that plot persistence density function doesn't
 handle degenerate data

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3920 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7794f7959b98b0245e26077d2f2639f33655d5c9
---
 src/cython/cython/persistence_graphical_tools.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index e63b350b..d7be936f 100644
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -249,7 +249,8 @@ def plot_persistence_density(persistence=[], persistence_file='',
     """This function plots the persistence density from persistence
     values list or from a :doc:`persistence file <fileformats>`. Be
     aware that this function does not distinguish the dimension, it is
-    up to you to select the required one.
+    up to you to select the required one. This function also does not handle
+    degenerate data set (scipy correlation matrix inversion can fail).
 
     :param persistence: Persistence intervals values list grouped by dimension.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
-- 
cgit v1.2.3