-- 
cgit v1.2.3

From 3ce013afc21df5d05d663dd17a6640cec9af4aed Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 24 Apr 2018 12:31:44 +0000
Subject: Fix Python tangential complex version

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3392 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f0d9e008229a6cd7868f4afd11eaf3c566e81adf
---
 src/cython/CMakeLists.txt                                 |  2 +-
 src/cython/cython/tangential_complex.pyx                  | 15 +++++++++------
 src/cython/doc/tangential_complex_user.rst                |  7 ++++---
 ...ential_complex_plain_homology_from_off_file_example.py |  5 +++--
 src/cython/include/Tangential_complex_interface.h         | 13 ++++---------
 src/cython/test/test_tangential_complex.py                |  2 +-
 6 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index b19cc550..f9721b46 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -183,7 +183,7 @@ if(CYTHON_FOUND)
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+             --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
     add_gudhi_py_test(test_tangential_complex)
 
diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx
index d55bb050..44a3a96a 100644
--- a/src/cython/cython/tangential_complex.pyx
+++ b/src/cython/cython/tangential_complex.pyx
@@ -33,9 +33,9 @@ __license__ = "GPL v3"
 
 cdef extern from "Tangential_complex_interface.h" namespace "Gudhi":
     cdef cppclass Tangential_complex_interface "Gudhi::tangential_complex::Tangential_complex_interface":
-        Tangential_complex_interface(vector[vector[double]] points)
+        Tangential_complex_interface(int intrisic_dim, vector[vector[double]] points)
         # bool from_file is a workaround for cython to find the correct signature
-        Tangential_complex_interface(string off_file, bool from_file)
+        Tangential_complex_interface(int intrisic_dim, string off_file, bool from_file)
         vector[double] get_point(unsigned vertex)
         unsigned number_of_vertices()
         unsigned number_of_simplices()
@@ -54,9 +54,12 @@ cdef class TangentialComplex:
     cdef Tangential_complex_interface * thisptr
 
     # Fake constructor that does nothing but documenting the constructor
-    def __init__(self, points=None, off_file=''):
+    def __init__(self, intrisic_dim, points=None, off_file=''):
         """TangentialComplex constructor.
 
+        :param intrisic_dim: Intrinsic dimension of the manifold.
+        :type intrisic_dim: integer
+
         :param points: A list of points in d-Dimension.
         :type points: list of list of double
 
@@ -67,17 +70,17 @@ cdef class TangentialComplex:
         """
 
     # The real cython constructor
-    def __cinit__(self, points=None, off_file=''):
+    def __cinit__(self, intrisic_dim, points=None, off_file=''):
         if off_file is not '':
             if os.path.isfile(off_file):
-                self.thisptr = new Tangential_complex_interface(str.encode(off_file), True)
+                self.thisptr = new Tangential_complex_interface(intrisic_dim, str.encode(off_file), True)
             else:
                 print("file " + off_file + " not found.")
         else:
             if points is None:
                 # Empty tangential construction
                 points=[]
-            self.thisptr = new Tangential_complex_interface(points)
+            self.thisptr = new Tangential_complex_interface(intrisic_dim, points)
                 
 
     def __dealloc__(self):
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index efa6d7ce..fafb3193 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -122,8 +122,8 @@ This example builds the Tangential complex of point set read in an OFF file.
 .. testcode::
 
     import gudhi
-    tc = gudhi.TangentialComplex(off_file=gudhi.__root_source_dir__ + \
-        '/data/points/alphacomplexdoc.off')
+    tc = gudhi.TangentialComplex(intrisic_dim = 1,
+        off_file=gudhi.__root_source_dir__ + '/data/points/alphacomplexdoc.off')
     result_str = 'Tangential contains ' + repr(tc.num_simplices()) + \
         ' simplices - ' + repr(tc.num_vertices()) + ' vertices.'
     print(result_str)
@@ -169,7 +169,8 @@ simplices.
 .. testcode::
 
    import gudhi
-   tc = gudhi.TangentialComplex(points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]])
+   tc = gudhi.TangentialComplex(intrisic_dim = 1,
+       points=[[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]])
    result_str = 'Tangential contains ' + repr(tc.num_vertices()) + ' vertices.'
    print(result_str)
 
diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
index 6145e7f2..08ae5d07 100755
--- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -33,10 +33,11 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from '
                                  'points read in a OFF file.',
                                  epilog='Example: '
                                  'example/tangential_complex_plain_homology_from_off_file_example.py '
-                                 '-f ../data/points/tore3D_300.off'
+                                 '-f ../data/points/tore3D_300.off -i 3'
                                  '- Constructs a tangential complex with the '
                                  'points from the given OFF file')
 parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument("-i", "--intrisic_dim", type=int, required=True)
 parser.add_argument("-b", "--band_boot", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
@@ -48,7 +49,7 @@ with open(args.file, 'r') as f:
         print("#####################################################################")
         print("TangentialComplex creation from points read in a OFF file")
         
-        tc = gudhi.TangentialComplex(off_file=args.file)
+        tc = gudhi.TangentialComplex(intrisic_dim = args.intrisic_dim, off_file=args.file)
         st = tc.create_simplex_tree()
     
         message = "Number of simplices=" + repr(st.num_simplices())
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 0c3a510e..aef50424 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -45,24 +45,19 @@ class Tangential_complex_interface {
   using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>;
 
  public:
-  Tangential_complex_interface(const std::vector<std::vector<double>>& points) {
+  Tangential_complex_interface(int intrisic_dim, const std::vector<std::vector<double>>& points) {
     Dynamic_kernel k;
-    unsigned intrisic_dim = 0;
-    if (points.size() > 0)
-      intrisic_dim = points[0].size() - 1;
 
     tangential_complex_ = new TC(points, intrisic_dim, k);
     tangential_complex_->compute_tangential_complex();
     num_inconsistencies_ = tangential_complex_->number_of_inconsistent_simplices();
   }
 
-  Tangential_complex_interface(const std::string& off_file_name, bool from_file = true) {
-    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
+  Tangential_complex_interface(int intrisic_dim, const std::string& off_file_name, bool from_file = true) {
     Dynamic_kernel k;
-    unsigned intrisic_dim = 0;
+
+    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
     std::vector<Point_d> points = off_reader.get_point_cloud();
-    if (points.size() > 0)
-      intrisic_dim = points[0].size() - 1;
 
     tangential_complex_ = new TC(points, intrisic_dim, k);
     tangential_complex_->compute_tangential_complex();
diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py
index 8aa4023c..ca9d936d 100755
--- a/src/cython/test/test_tangential_complex.py
+++ b/src/cython/test/test_tangential_complex.py
@@ -29,7 +29,7 @@ __license__ = "GPL v3"
 
 def test_tangential():
     point_list = [[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]]
-    tc = TangentialComplex(points=point_list)
+    tc = TangentialComplex(intrisic_dim = 1, points=point_list)
     assert tc.__is_defined() == True
     assert tc.num_vertices() == 4
 
-- 
cgit v1.2.3


From 62861adfd2de672d3d90e2fbade499fe76e5bca7 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 25 Apr 2018 06:50:12 +0000
Subject: persistence_pairs Python version

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3393 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5ee633545ca5754b605cdd789ca9720f5936998a
---
 src/cython/cython/simplex_tree.pyx                 | 20 +++++++++++++++++
 .../include/Persistent_cohomology_interface.h      | 26 ++++++++++++++++++++++
 2 files changed, 46 insertions(+)

diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 0cb575d2..755cdc02 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -64,6 +64,7 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
         vector[int] persistent_betti_numbers(double from_value, double to_value)
         vector[pair[double,double]] intervals_in_dimension(int dimension)
         void write_output_diagram(string diagram_file_name)
+        vector[pair[vector[int], vector[int]]] persistence_pairs()
 
 # SimplexTree python interface
 cdef class SimplexTree:
@@ -486,6 +487,25 @@ cdef class SimplexTree:
                   " to be launched first.")
         return intervals_result
 
+    def persistence_pairs(self):
+        """This function returns the persistence pairs of the simplicial
+        complex.
+
+        :returns: The persistence intervals.
+        :rtype:  list of pair of list of int
+
+        :note: intervals_in_dim function requires
+            :func:`persistence()<gudhi.SimplexTree.persistence>`
+            function to be launched first.
+        """
+        cdef vector[pair[vector[int],vector[int]]] persistence_pairs_result
+        if self.pcohptr != NULL:
+            persistence_pairs_result = self.pcohptr.persistence_pairs()
+        else:
+            print("persistence_pairs function requires persistence function"
+                  " to be launched first.")
+        return persistence_pairs_result
+
     def write_persistence_diagram(self, persistence_file=''):
         """This function writes the persistence intervals of the simplicial
         complex in a user given file name.
diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h
index 55028fd0..e8889444 100644
--- a/src/cython/include/Persistent_cohomology_interface.h
+++ b/src/cython/include/Persistent_cohomology_interface.h
@@ -85,6 +85,32 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
     return persistence;
   }
 
+  std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs() {
+    auto pairs = persistent_cohomology::Persistent_cohomology<FilteredComplex,
+      persistent_cohomology::Field_Zp>::get_persistent_pairs();
+
+    std::vector<std::pair<std::vector<int>, std::vector<int>>> persistence_pairs;
+    persistence_pairs.reserve(pairs.size());
+    for (auto pair : pairs) {
+      std::vector<int> birth;
+      if (get<0>(pair) != stptr_->null_simplex()) {
+        for (auto vertex : stptr_->simplex_vertex_range(get<0>(pair))) {
+          birth.push_back(vertex);
+        }
+      }
+
+      std::vector<int> death;
+      if (get<1>(pair) != stptr_->null_simplex()) {
+        for (auto vertex : stptr_->simplex_vertex_range(get<1>(pair))) {
+          death.push_back(vertex);
+        }
+      }
+
+      persistence_pairs.push_back(std::make_pair(birth,death));
+    }
+    return persistence_pairs;
+  }
+
  private:
   // A copy
   FilteredComplex* stptr_;
-- 
cgit v1.2.3


From 7ac3c086c6c794ac8c493a2c3abbd59624e81c06 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 27 Apr 2018 13:00:38 +0000
Subject: Code and doc review with IFPEN : plot_*: c'est quoi ce paramètre
 alpha ?
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

band_boot: Renommer en 'band', sans référence au bootstrap. Ne pas
l'utiliser dans la majorité des exemples / tutos.

max_plots: mettre une valeur par défaut, pour éviter qu'on se retrouve
trop facilement coincé à attendre 1h qu'il affiche des points.
Éventuellement afficher un message indiquant que certains points n'ont pas
été affichés et comment changer ça.

barcode: trier les barres par date de naissance (le faire
tout le temps ou avoir une option et le faire par défaut).



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3404 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cfa775e425fbf12da1758d601ccbd80a2c7d3bc9
---
 src/cython/cython/persistence_graphical_tools.py   | 41 +++++++++++++---------
 .../doc/persistence_graphical_tools_user.rst       |  4 +--
 src/cython/doc/pyplots/diagram_persistence.py      |  2 +-
 ...ex_diagram_persistence_from_off_file_example.py |  4 +--
 ...ex_diagram_persistence_from_off_file_example.py |  4 +--
 ...ex_diagram_persistence_from_off_file_example.py |  4 +--
 .../example/gudhi_graphical_tools_example.py       |  2 +-
 ...istence_from_correlation_matrix_file_example.py |  4 +--
 ...ersistence_from_distance_matrix_file_example.py |  4 +--
 ...ex_diagram_persistence_from_off_file_example.py |  4 +--
 ...complex_plain_homology_from_off_file_example.py |  4 +--
 11 files changed, 42 insertions(+), 35 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index fb837e29..f7dadb53 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -28,13 +28,13 @@ __author__ = "Vincent Rouvreau, Bertrand Michel"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-def __min_birth_max_death(persistence, band_boot=0.):
+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_boot: bootstrap band
-    :type band_boot: float.
+    :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
@@ -48,8 +48,8 @@ def __min_birth_max_death(persistence, band_boot=0.):
             max_death = float(interval[1][0])
         if float(interval[1][0]) < min_birth:
             min_birth = float(interval[1][0])
-    if band_boot > 0.:
-        max_death += band_boot
+    if band > 0.:
+        max_death += band
     return (min_birth, max_death)
 
 """
@@ -77,16 +77,17 @@ def show_palette_values(alpha=0.6):
     plt.title('Dimension palette values')
     return plt
 
-def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=0):
+def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=1000):
     """This function plots the persistence bar code.
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
     :param persistence_file: A persistence file style name (reset persistence if both are set).
     :type persistence_file: string
-    :param alpha: alpha value in [0.0, 1.0] for horizontal bars (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
+    :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.
     :returns: plot -- An horizontal bar plot of persistence.
@@ -107,6 +108,8 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
         # 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]
 
+    persistence = sorted(persistence, key=lambda birth: birth[1][0])
+
     (min_birth, max_death) = __min_birth_max_death(persistence)
     ind = 0
     delta = ((max_death - min_birth) / 10.0)
@@ -120,12 +123,14 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
             # Finite death case
             plt.barh(ind, (interval[1][1] - interval[1][0]), height=0.8,
                      left = interval[1][0], alpha=alpha,
-                     color = palette[interval[0]])
+                     color = palette[interval[0]],
+                     linewidth=0)
         else:
             # Infinite death case for diagram to be nicer
             plt.barh(ind, (infinity - interval[1][0]), height=0.8,
                      left = interval[1][0], alpha=alpha,
-                     color = palette[interval[0]])
+                     color = palette[interval[0]],
+                     linewidth=0)
         ind = ind + 1
 
     plt.title('Persistence barcode')
@@ -133,18 +138,20 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
     plt.axis([axis_start, infinity, 0, ind])
     return plt
 
-def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band_boot=0., max_plots=0):
+def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band=0., max_plots=1000):
     """This function plots the persistence diagram with an optional confidence band.
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
     :param persistence_file: A persistence file style name (reset persistence if both are set).
     :type persistence_file: string
-    :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (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_boot: bootstrap band (not displayed if :math:`\leq` 0.)
-    :type band_boot: 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)
     :type max_plots: int.
     :returns: plot -- A diagram plot of persistence.
     """
@@ -164,7 +171,7 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban
         # 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]
 
-    (min_birth, max_death) = __min_birth_max_death(persistence, band_boot)
+    (min_birth, max_death) = __min_birth_max_death(persistence, band)
     ind = 0
     delta = ((max_death - min_birth) / 10.0)
     # Replace infinity values with max_death + delta for diagram to be more
@@ -179,8 +186,8 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban
     plt.plot(x, [infinity] * len(x), linewidth=1.0, color='k', alpha=alpha)
     plt.text(axis_start, infinity, r'$\infty$', color='k', alpha=alpha)
     # bootstrap band
-    if band_boot > 0.:
-        plt.fill_between(x, x, x+band_boot, alpha=alpha, facecolor='red')
+    if band > 0.:
+        plt.fill_between(x, x, x+band, alpha=alpha, facecolor='red')
 
     # Draw points in loop
     for interval in reversed(persistence):
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index a5523d23..290b13c3 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -62,7 +62,7 @@ This function can display the persistence result as a diagram:
     rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    plt = gudhi.plot_persistence_diagram(diag)
     plt.show()
 
 .. plot::
@@ -73,5 +73,5 @@ This function can display the persistence result as a diagram:
     rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    plt = gudhi.plot_persistence_diagram(diag)
     plt.show()
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
index ac20bf47..5abf52b9 100755
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -5,5 +5,5 @@ point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + \
 rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2)
 simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
 diag = simplex_tree.persistence()
-plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+plt = gudhi.plot_persistence_diagram(diag)
 plt.show()
diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
index b4487be4..10d4867a 100755
--- a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -38,7 +38,7 @@ parser = argparse.ArgumentParser(description='AlphaComplex creation from '
                                  'points from the given OFF file.')
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, default=0.5)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -64,7 +64,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
index e3f362dc..28a8599c 100755
--- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py
@@ -40,7 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
 parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
 parser.add_argument("-d", "--limit_dimension", type=int, required=True)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -71,7 +71,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
index c236d992..b19d7d8c 100755
--- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py
@@ -40,7 +40,7 @@ parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-a", "--max_alpha_square", type=float, required=True)
 parser.add_argument("-n", "--number_of_landmarks", type=int, required=True)
 parser.add_argument("-d", "--limit_dimension", type=int, required=True)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -71,7 +71,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
 
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py
index ed87806b..97983262 100755
--- a/src/cython/example/gudhi_graphical_tools_example.py
+++ b/src/cython/example/gudhi_graphical_tools_example.py
@@ -50,5 +50,5 @@ pplot.show()
 print("#####################################################################")
 print("Show diagram persistence example with a confidence band")
 
-pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2)
+pplot = gudhi.plot_persistence_diagram(persistence, band=0.2)
 pplot.show()
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
index aa82ef71..0af4397a 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py
@@ -40,7 +40,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-c", "--min_edge_correlation", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -80,5 +80,5 @@ print(simplex_tree.betti_numbers())
 invert_diag = [(diag[pers][0],(1.-diag[pers][1][0], 1.-diag[pers][1][1])) for pers in range(len(diag))]
 
 if args.no_diagram == False:
-    pplot = gudhi.plot_persistence_diagram(invert_diag, band_boot=args.band_boot)
+    pplot = gudhi.plot_persistence_diagram(invert_diag, band=args.band)
     pplot.show()
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index c8aac240..266c09ca 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -39,7 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -63,5 +63,5 @@ print("betti_numbers()=")
 print(simplex_tree.betti_numbers())
 
 if args.no_diagram == False:
-    pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+    pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
     pplot.show()
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
index 544b68c9..fede920c 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py
@@ -39,7 +39,7 @@ parser = argparse.ArgumentParser(description='RipsComplex creation from '
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-e", "--max_edge_length", type=float, default=0.5)
 parser.add_argument("-d", "--max_dimension", type=int, default=1)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -66,7 +66,7 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
index 08ae5d07..1f562b5c 100755
--- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
+++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py
@@ -38,7 +38,7 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from '
                                  'points from the given OFF file')
 parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument("-i", "--intrisic_dim", type=int, required=True)
-parser.add_argument("-b", "--band_boot", type=float, default=0.)
+parser.add_argument("-b", "--band", type=float, default=0.)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -61,7 +61,7 @@ with open(args.file, 'r') as f:
         print(st.betti_numbers())
     
         if args.no_diagram == False:
-            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot = gudhi.plot_persistence_diagram(diag, band=args.band)
             pplot.show()
     else:
         print(args.file, "is not a valid OFF file")
-- 
cgit v1.2.3


From 50bff0fced63e298ae9952a192f8e1b70d9abfb8 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 27 Apr 2018 14:46:06 +0000
Subject: persistence_graphical_tools documentation clarification

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3405 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5b38ba745e20585c35263e2880b8511299e11129
---
 src/cython/cython/persistence_graphical_tools.py | 25 +++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index f7dadb53..98e875b0 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -64,7 +64,8 @@ def show_palette_values(alpha=0.6):
 
     :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6).
     :type alpha: float.
-    :returns: plot the dimension palette values.
+    :returns: A matplotlib object containing dimension palette values (launch
+        `show()` method on it to display it).
     """
     colors = []
     for color in palette:
@@ -78,11 +79,13 @@ def show_palette_values(alpha=0.6):
     return plt
 
 def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=1000):
-    """This function plots the persistence bar code.
+    """This function plots the persistence bar code from persistence values list
+    or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: The persistence to plot.
+    :param persistence: Persistence values list.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
-    :param persistence_file: A persistence file 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 alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
     :type alpha: float.
@@ -90,7 +93,8 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
         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.
-    :returns: plot -- An horizontal bar plot of persistence.
+    :returns: A matplotlib object containing horizontal bar plot of persistence
+        (launch `show()` method on it to display it).
     """
     if persistence_file is not '':
         if os.path.isfile(persistence_file):
@@ -139,11 +143,13 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
     return plt
 
 def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band=0., max_plots=1000):
-    """This function plots the persistence diagram with an optional confidence band.
+    """This function plots the persistence diagram from persistence values list
+    or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: The persistence to plot.
+    :param persistence: Persistence values list.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
-    :param persistence_file: A persistence file 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 alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
     :type alpha: float.
@@ -153,7 +159,8 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban
         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.
-    :returns: plot -- A diagram plot of persistence.
+    :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):
-- 
cgit v1.2.3


From 0902c35ad4701d78a91b30e2d055a529f4de01d5 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 27 Apr 2018 16:03:43 +0000
Subject: Remove show_palette_values Add legend flag to display the legend Set
 rips threshold to 0.3 for users not to be surprised when playing with
 threshold

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3406 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 03999711eafb81748a82b5725482a9f0d4307861
---
 src/cython/cython/persistence_graphical_tools.py   | 43 ++++++++++------------
 src/cython/doc/persistence_graphical_tools_ref.rst |  1 -
 .../doc/persistence_graphical_tools_user.rst       | 22 +----------
 src/cython/doc/pyplots/diagram_persistence.py      |  2 +-
 src/cython/doc/pyplots/show_palette_values.py      |  3 --
 .../example/gudhi_graphical_tools_example.py       |  5 ---
 6 files changed, 23 insertions(+), 53 deletions(-)
 delete mode 100755 src/cython/doc/pyplots/show_palette_values.py

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 98e875b0..118fdd1a 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -1,4 +1,5 @@
 import matplotlib.pyplot as plt
+import matplotlib.patches as mpatches
 import numpy as np
 import os
 
@@ -59,26 +60,8 @@ palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
            '#000000', '#880000', '#008800', '#000088', '#888800', '#880088',
            '#008888']
  
-def show_palette_values(alpha=0.6):
-    """This function shows palette color values in function of the dimension.
-
-    :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6).
-    :type alpha: float.
-    :returns: A matplotlib object containing dimension palette values (launch
-        `show()` method on it to display it).
-    """
-    colors = []
-    for color in palette:
-        colors.append(color)
-
-    y_pos = np.arange(len(palette))
-
-    plt.barh(y_pos, y_pos + 1, align='center', alpha=alpha, color=colors)
-    plt.ylabel('Dimension')
-    plt.title('Dimension palette values')
-    return plt
-
-def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=1000):
+def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
+        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>`.
 
@@ -93,6 +76,9 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
         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.
+    :type inf_delta: float.
     :returns: A matplotlib object containing horizontal bar plot of persistence
         (launch `show()` method on it to display it).
     """
@@ -116,7 +102,7 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
 
     (min_birth, max_death) = __min_birth_max_death(persistence)
     ind = 0
-    delta = ((max_death - min_birth) / 10.0)
+    delta = ((max_death - min_birth) * inf_delta)
     # Replace infinity values with max_death + delta for bar code to be more
     # readable
     infinity = max_death + delta
@@ -137,12 +123,16 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max
                      linewidth=0)
         ind = ind + 1
 
+    if legend:
+        dimensions = list(set(item[0] for item in persistence))
+        plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions])
     plt.title('Persistence barcode')
     # Ends plot on infinity value and starts a little bit before min_birth
     plt.axis([axis_start, infinity, 0, ind])
     return plt
 
-def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band=0., max_plots=1000):
+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>`.
 
@@ -159,6 +149,9 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban
         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 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.
     :returns: A matplotlib object containing diagram plot of persistence
         (launch `show()` method on it to display it).
     """
@@ -180,7 +173,7 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban
 
     (min_birth, max_death) = __min_birth_max_death(persistence, band)
     ind = 0
-    delta = ((max_death - min_birth) / 10.0)
+    delta = ((max_death - min_birth) * inf_delta)
     # Replace infinity values with max_death + delta for diagram to be more
     # readable
     infinity = max_death + delta
@@ -208,6 +201,10 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban
                         color = palette[interval[0]])
         ind = ind + 1
 
+    if legend:
+        dimensions = list(set(item[0] for item in persistence))
+        plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions])
+
     plt.title('Persistence diagram')
     plt.xlabel('Birth')
     plt.ylabel('Death')
diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst
index 27c2f68a..a69c8ba2 100644
--- a/src/cython/doc/persistence_graphical_tools_ref.rst
+++ b/src/cython/doc/persistence_graphical_tools_ref.rst
@@ -3,6 +3,5 @@ Persistence graphical tools reference manual
 ============================================
 
 .. autofunction:: gudhi.__min_birth_max_death
-.. autofunction:: gudhi.show_palette_values
 .. autofunction:: gudhi.plot_persistence_barcode
 .. autofunction:: gudhi.plot_persistence_diagram
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index 290b13c3..46f871c7 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -5,24 +5,6 @@ Definition
 .. include:: persistence_graphical_tools_sum.rst
 
 
-Show palette values
--------------------
-
-This function is useful to show the color palette values of dimension:
-
-
-.. testcode::
-
-    import gudhi
-    plt = gudhi.show_palette_values(alpha=1.0)
-    plt.show()
-
-.. plot::
-
-    import gudhi
-    plt = gudhi.show_palette_values(alpha=1.0)
-    plt.show()
-
 Show persistence as a barcode
 -----------------------------
 
@@ -59,7 +41,7 @@ This function can display the persistence result as a diagram:
     import gudhi
     
     point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off')
-    rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2)
+    rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
     plt = gudhi.plot_persistence_diagram(diag)
@@ -70,7 +52,7 @@ This function can display the persistence result as a diagram:
     import gudhi
 
     point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off')
-    rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2)
+    rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
     plt = gudhi.plot_persistence_diagram(diag)
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
index 5abf52b9..3bab0ca1 100755
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -2,7 +2,7 @@ import gudhi
 
 point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + \
     '/data/points/tore3D_1307.off')
-rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.2)
+rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3)
 simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
 diag = simplex_tree.persistence()
 plt = gudhi.plot_persistence_diagram(diag)
diff --git a/src/cython/doc/pyplots/show_palette_values.py b/src/cython/doc/pyplots/show_palette_values.py
deleted file mode 100755
index fdf9645f..00000000
--- a/src/cython/doc/pyplots/show_palette_values.py
+++ /dev/null
@@ -1,3 +0,0 @@
-import gudhi
-plt = gudhi.show_palette_values(alpha=1.0)
-plt.show()
diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py
index 97983262..d21d44c2 100755
--- a/src/cython/example/gudhi_graphical_tools_example.py
+++ b/src/cython/example/gudhi_graphical_tools_example.py
@@ -28,11 +28,6 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-print("#####################################################################")
-print("Show palette colors values for dimension")
-
-gudhi.show_palette_values()
-
 print("#####################################################################")
 print("Show barcode persistence example")
 
-- 
cgit v1.2.3


From 71840751fcd4771d126c0ebe2f63a02c14e67186 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 2 May 2018 08:00:44 +0000
Subject: Add Python Simplex_tree make_filtration_non_decreasing interface and
 its tests

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3409 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6a3af66b3d90c6114886e54c5c34287a13f4b863
---
 src/cython/cython/simplex_tree.pyx   | 23 +++++++++++++++++++
 src/cython/test/test_simplex_tree.py | 44 ++++++++++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+)

diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 755cdc02..38740f4f 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -55,6 +55,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         void expansion(int max_dim)
         void remove_maximal_simplex(vector[int] simplex)
         bool prune_above_filtration(double filtration)
+        bool make_filtration_non_decreasing()
 
 cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi":
     cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>":
@@ -400,6 +401,28 @@ cdef class SimplexTree:
         """
         self.thisptr.expansion(max_dim)
 
+    def make_filtration_non_decreasing(self):
+        """Browse the simplex tree to ensure the filtration is not decreasing.
+        The simplex tree is browsed starting from the root until the leaf, and
+        the filtration values are set with their parent value (increased), in
+        case the values are decreasing.
+
+        :returns: The filtration modification information.
+        :rtype: bint
+
+
+        .. note::
+
+            Some simplex tree functions require the filtration to be valid.
+            make_filtration_non_decreasing function is not launching
+            :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>`
+            but returns the filtration modification
+            information. If the complex has changed , please call
+            :func:`initialize_filtration()<gudhi.SimplexTree.initialize_filtration>`
+            to recompute it.
+        """
+        return self.thisptr.make_filtration_non_decreasing()
+
     def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False):
         """This function returns the persistence of the simplicial complex.
 
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index 6dec5d94..bc16183a 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -161,3 +161,47 @@ def test_automatic_dimension():
     assert st.upper_bound_dimension() == 2
     assert st.dimension() == 1
     assert st.upper_bound_dimension() == 1
+
+def test_make_filtration_non_decreasing():
+    st = SimplexTree()
+    assert st.__is_defined() == True
+    assert st.__is_persistence_defined() == False
+
+    # Inserted simplex:
+    #    1
+    #    o
+    #   /X\
+    #  o---o---o---o
+    #  2   0   3\X/4
+    #            o
+    #            5
+    assert st.insert([2, 1, 0], filtration=2.0) == True
+    assert st.insert([3, 0], filtration=2.0) == True
+    assert st.insert([3, 4, 5], filtration=2.0) == True
+
+    assert st.make_filtration_non_decreasing() == False
+
+    # Because of non decreasing property of simplex tree, { 0 } , { 1 } and
+    # { 0, 1 } are going to be set from value 2.0 to 1.0
+    st.insert([0, 1, 6, 7], filtration=1.0);
+
+    assert st.make_filtration_non_decreasing() == False
+
+    # Modify specific values to test make_filtration_non_decreasing
+    st.assign_filtration([0,1,6,7], 0.8);
+    st.assign_filtration([0,1,6], 0.9);
+    st.assign_filtration([0,6], 0.6);
+    st.assign_filtration([3,4,5], 1.2);
+    st.assign_filtration([3,4], 1.1);
+    st.assign_filtration([4,5], 1.99);
+
+    assert st.make_filtration_non_decreasing() == True
+
+    assert st.filtration([0,1,6,7]) == 1.
+    assert st.filtration([0,1,6]) == 1.
+    assert st.filtration([0,1]) == 1.
+    assert st.filtration([0]) == 1.
+    assert st.filtration([1]) == 1.
+    assert st.filtration([3,4,5]) == 2.
+    assert st.filtration([3,4]) == 2.
+    assert st.filtration([4,5]) == 2.
-- 
cgit v1.2.3


From 90bb34c0e81b57ed85131ccaa638f457338c9219 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 23 May 2018 08:22:35 +0000
Subject: Modify documentation for Simplex_tree make_filtration_non_decreasing

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3452 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 304779c7952985d651750aded78cb32c6e583555
---
 src/Simplex_tree/include/gudhi/Simplex_tree.h | 5 ++---
 src/cython/cython/simplex_tree.pyx            | 6 ++----
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 7456cb1f..d9e2d73e 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1238,9 +1238,8 @@ class Simplex_tree {
   }
 
  public:
-  /** \brief Browse the simplex tree to ensure the filtration is not decreasing.
-   * The simplex tree is browsed starting from the root until the leaf, and the filtration values are set with their
-   * parent value (increased), in case the values are decreasing.
+  /** \brief This function ensures that each simplex has a higher filtration value than its faces by increasing the
+   * filtration values.
    * @return The filtration modification information.
    * \post Some simplex tree functions require the filtration to be valid. `make_filtration_non_decreasing()`
    * function is not launching `initialize_filtration()` but returns the filtration modification information. If the
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 38740f4f..667fd40b 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -402,10 +402,8 @@ cdef class SimplexTree:
         self.thisptr.expansion(max_dim)
 
     def make_filtration_non_decreasing(self):
-        """Browse the simplex tree to ensure the filtration is not decreasing.
-        The simplex tree is browsed starting from the root until the leaf, and
-        the filtration values are set with their parent value (increased), in
-        case the values are decreasing.
+        """This function ensures that each simplex has a higher filtration
+        value than its faces by increasing the filtration values.
 
         :returns: The filtration modification information.
         :rtype: bint
-- 
cgit v1.2.3


From 4b6d52d1a1b16f4026b9eb98495ac6fe1aa95281 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 23 May 2018 08:45:19 +0000
Subject: Legend in the right bottom corner

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3453 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 221e39777dd55397a0260a2c83f590db610fdb76
---
 src/cython/cython/persistence_graphical_tools.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 118fdd1a..4629018c 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -125,7 +125,9 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
 
     if legend:
         dimensions = list(set(item[0] for item in persistence))
-        plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions])
+        plt.legend(handles=[mpatches.Patch(color=palette[dim],
+                                           label=str(dim)) for dim in dimensions],
+                   loc='lower right')
     plt.title('Persistence barcode')
     # Ends plot on infinity value and starts a little bit before min_birth
     plt.axis([axis_start, infinity, 0, ind])
-- 
cgit v1.2.3


From d0aa6ea5b543c4692f6e42d12252b03d5e43a255 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 30 May 2018 20:53:45 +0000
Subject: Add install requires matplotlib and numpy in setup.py Add Python test
 fail explanation

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3494 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1bac18228a22ea718bb8c77d38efdf84f9b228eb
---
 src/cython/doc/installation.rst | 3 +++
 src/cython/setup.py.in          | 7 +++++++
 2 files changed, 10 insertions(+)

diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index c182f176..28d9dba2 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -43,6 +43,9 @@ following command in a terminal:
     export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
     ctest -R py_test
 
+If tests fail, please try to :code:`import gudhi` and check the errors.
+The problem can come from a third-party library bad link or installation.
+
 Documentation
 =============
 
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
index c767e93d..eda1ee04 100644
--- a/src/cython/setup.py.in
+++ b/src/cython/setup.py.in
@@ -46,4 +46,11 @@ setup(
     version='@GUDHI_VERSION@',
     url='http://gudhi.gforge.inria.fr/',
     ext_modules = cythonize(gudhi),
+
+    #install_requires = required,
+    install_requires = [
+        "matplotlib",
+        "numpy",
+        "cython",
+        ],
 )
-- 
cgit v1.2.3