Merge last trunk modifications

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



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

Former-commit-id: db80333d4f34151be0c32024af597d90d221a97f

8 files changed, 96 insertions, 49 deletions

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index da709b8a..fb837e29 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -1,5 +1,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
+import os
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -23,7 +24,7 @@ import numpy as np
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 """
 
-__author__ = "Vincent Rouvreau"
+__author__ = "Vincent Rouvreau, Bertrand Michel"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
@@ -63,7 +64,7 @@ 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 -- An horizontal bar plot of dimensions color.
+    :returns: plot the dimension palette values.
     """
     colors = []
     for color in palette:
@@ -74,18 +75,38 @@ def show_palette_values(alpha=0.6):
     plt.barh(y_pos, y_pos + 1, align='center', alpha=alpha, color=colors)
     plt.ylabel('Dimension')
     plt.title('Dimension palette values')
+    return plt
 
-    plt.show()
-
-def plot_persistence_barcode(persistence, alpha=0.6):
+def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=0):
     """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).
     :type alpha: float.
+    :param max_barcodes: number of maximal barcodes to be displayed
+        (persistence will be sorted by life time if max_barcodes is set)
+    :type max_barcodes: int.
     :returns: plot -- An horizontal bar plot of persistence.
     """
+    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_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]
+
     (min_birth, max_death) = __min_birth_max_death(persistence)
     ind = 0
     delta = ((max_death - min_birth) / 10.0)
@@ -110,19 +131,39 @@ def plot_persistence_barcode(persistence, alpha=0.6):
     plt.title('Persistence barcode')
     # Ends plot on infinity value and starts a little bit before min_birth
     plt.axis([axis_start, infinity, 0, ind])
-    plt.show()
+    return plt
 
-def plot_persistence_diagram(persistence, alpha=0.6, band_boot=0.):
+def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band_boot=0., max_plots=0):
     """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).
     :type alpha: float.
     :param band_boot: bootstrap band (not displayed if :math:`\leq` 0.)
     :type band_boot: float.
+    :param max_plots: number of maximal plots to be displayed
+    :type max_plots: int.
     :returns: plot -- A diagram plot of persistence.
     """
+    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]
+
     (min_birth, max_death) = __min_birth_max_death(persistence, band_boot)
     ind = 0
     delta = ((max_death - min_birth) / 10.0)
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 9d40a8b5..2acdac3c 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -183,10 +183,10 @@ cdef class SimplexTree:
         :returns:  true if the simplex was found, false otherwise.
         :rtype:  bool
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
-        return self.thisptr.find_simplex(complex)
+            csimplex.push_back(i)
+        return self.thisptr.find_simplex(csimplex)
 
     def insert(self, simplex, filtration=0.0):
         """This function inserts the given N-simplex and its subfaces with the
@@ -200,10 +200,10 @@ cdef class SimplexTree:
         :returns:  true if the simplex was found, false otherwise.
         :rtype:  bool
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
-        return self.thisptr.insert_simplex_and_subfaces(complex,
+            csimplex.push_back(i)
+        return self.thisptr.insert_simplex_and_subfaces(csimplex,
                                                         <double>filtration)
 
     def get_filtration(self):
@@ -232,35 +232,35 @@ cdef class SimplexTree:
         :returns:  The (simplices of the) skeleton of a maximum dimension.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[pair[vector[int], double]] skeletons \
+        cdef vector[pair[vector[int], double]] skeleton \
             = self.thisptr.get_skeleton(<int>dimension)
         ct = []
-        for filtered_complex in skeletons:
+        for filtered_simplex in skeleton:
             v = []
-            for vertex in filtered_complex.first:
+            for vertex in filtered_simplex.first:
                 v.append(vertex)
-            ct.append((v, filtered_complex.second))
+            ct.append((v, filtered_simplex.second))
         return ct
 
     def get_star(self, simplex):
-        """This function returns the stars of a given N-simplex.
+        """This function returns the star of a given N-simplex.
 
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :returns:  The (simplices of the) star of a simplex.
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
-        cdef vector[pair[vector[int], double]] stars \
-            = self.thisptr.get_star(complex)
+            csimplex.push_back(i)
+        cdef vector[pair[vector[int], double]] star \
+            = self.thisptr.get_star(csimplex)
         ct = []
-        for filtered_complex in stars:
+        for filtered_simplex in star:
             v = []
-            for vertex in filtered_complex.first:
+            for vertex in filtered_simplex.first:
                 v.append(vertex)
-            ct.append((v, filtered_complex.second))
+            ct.append((v, filtered_simplex.second))
         return ct
 
     def get_cofaces(self, simplex, codimension):
@@ -275,17 +275,17 @@ cdef class SimplexTree:
         :returns:  The (simplices of the) cofaces of a simplex
         :rtype:  list of tuples(simplex, filtration)
         """
-        cdef vector[int] complex
+        cdef vector[int] csimplex
         for i in simplex:
-            complex.push_back(i)
+            csimplex.push_back(i)
         cdef vector[pair[vector[int], double]] cofaces \
-            = self.thisptr.get_cofaces(complex, <int>codimension)
+            = self.thisptr.get_cofaces(csimplex, <int>codimension)
         ct = []
-        for filtered_complex in cofaces:
+        for filtered_simplex in cofaces:
             v = []
-            for vertex in filtered_complex.first:
+            for vertex in filtered_simplex.first:
                 v.append(vertex)
-            ct.append((v, filtered_complex.second))
+            ct.append((v, filtered_simplex.second))
         return ct
 
     def remove_maximal_simplex(self, simplex):
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index bc731f12..13198162 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -14,12 +14,14 @@ This function is useful to show the color palette values of dimension:
 .. testcode::
 
     import gudhi
-    gudhi.show_palette_values(alpha=1.0)
+    plt = gudhi.show_palette_values(alpha=1.0)
+    plt.show()
 
 .. plot::
 
     import gudhi
-    gudhi.show_palette_values(alpha=1.0)
+    plt = gudhi.show_palette_values(alpha=1.0)
+    plt.show()
 
 Show persistence as a barcode
 -----------------------------
@@ -32,7 +34,8 @@ This function can display the persistence result as a barcode:
     
     periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
     diag = periodic_cc.persistence()
-    gudhi.plot_persistence_barcode(diag)
+    plt = gudhi.plot_persistence_barcode(diag)
+    plt.show()
 
 .. plot::
 
@@ -40,7 +43,8 @@ This function can display the persistence result as a barcode:
 
     periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
     diag = periodic_cc.persistence()
-    gudhi.plot_persistence_barcode(diag)
+    plt = gudhi.plot_persistence_barcode(diag)
+    plt.show()
 
 Show persistence as a diagram
 -----------------------------
@@ -54,8 +58,8 @@ This function can display the persistence result as a diagram:
     rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
-    pplot.show()
+    plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    plt.show()
 
 .. plot::
 
@@ -64,5 +68,5 @@ This function can display the persistence result as a diagram:
     rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
     simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
     diag = simplex_tree.persistence()
-    pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
-    pplot.show()
+    plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    plt.show()
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
index b021049f..9cd3149d 100755
--- a/src/cython/doc/pyplots/barcode_persistence.py
+++ b/src/cython/doc/pyplots/barcode_persistence.py
@@ -2,4 +2,5 @@ import gudhi
 
 periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
 diag = periodic_cc.persistence()
-gudhi.plot_persistence_barcode(diag)
+plt = gudhi.plot_persistence_barcode(diag)
+plt.show()
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
index 56d6c50f..30661965 100755
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -3,5 +3,5 @@ import gudhi
 rips_complex = gudhi.RipsComplex(off_file='tore3D_1307.off', max_edge_length=0.2)
 simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
 diag = simplex_tree.persistence()
-pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
-pplot.show()
+plt = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+plt.show()
diff --git a/src/cython/doc/pyplots/show_palette_values.py b/src/cython/doc/pyplots/show_palette_values.py
index e72a55fd..fdf9645f 100755
--- a/src/cython/doc/pyplots/show_palette_values.py
+++ b/src/cython/doc/pyplots/show_palette_values.py
@@ -1,2 +1,3 @@
 import gudhi
-gudhi.show_palette_values(alpha=1.0)
+plt = gudhi.show_palette_values(alpha=1.0)
+plt.show()
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 45ce1916..09e7e992 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -70,14 +70,14 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
   }
 
   // Do not interface this function, only used in strong witness interface for complex creation
-  bool insert_simplex(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
-    Insertion_result result = Base::insert_simplex(complex, filtration);
+  bool insert_simplex(const std::vector<std::size_t>& simplex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex(simplex, filtration);
     return (result.second);
   }
 
   // Do not interface this function, only used in strong witness interface for complex creation
-  bool insert_simplex_and_subfaces(const std::vector<std::size_t>& complex, Filtration_value filtration = 0) {
-    Insertion_result result = Base::insert_simplex_and_subfaces(complex, filtration);
+  bool insert_simplex_and_subfaces(const std::vector<std::size_t>& simplex, Filtration_value filtration = 0) {
+    Insertion_result result = Base::insert_simplex_and_subfaces(simplex, filtration);
     return (result.second);
   }
 
diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py
index 2e281ee4..9a365823 100755
--- a/src/cython/test/test_cubical_complex.py
+++ b/src/cython/test/test_cubical_complex.py
@@ -67,7 +67,7 @@ def test_dimension_constructor():
                          top_dimensional_cells = [1,2,3,4,5,6,7,8,9])
     assert cub.__is_defined() == True
     assert cub.__is_persistence_defined() == False
-    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))]
+    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))]
     assert cub.__is_persistence_defined() == True
     assert cub.betti_numbers() == [1, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [0, 0]
@@ -80,7 +80,7 @@ def test_dimension_constructor():
     cub = CubicalComplex(perseus_file='CubicalOneSphere.txt')
     assert cub.__is_defined() == True
     assert cub.__is_persistence_defined() == False
-    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, 1.8446744073709552e+19))]
+    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))]
     assert cub.__is_persistence_defined() == True
     assert cub.betti_numbers() == [1, 0, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0]