Fix persistent_betti_numbers in Persistent_cohomology to make it work with cubical

Cython examples renaming and fixing



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

Former-commit-id: ab84ba3acd6241257f1787e29ac2e3ac005bbd80

12 files changed, 87 insertions, 48 deletions

diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index a7d1e463..5b371f2b 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -598,7 +598,7 @@ class Persistent_cohomology {
    */
   std::vector<int> betti_numbers() const {
     // Init Betti numbers vector with zeros until Simplicial complex dimension
-    std::vector<int> betti_numbers(cpx_->dimension(), 0);
+    std::vector<int> betti_numbers(dim_max_, 0);
 
     for (auto pair : persistent_pairs_) {
       // Count never ended persistence intervals
@@ -637,8 +637,7 @@ class Persistent_cohomology {
    */
   std::vector<int> persistent_betti_numbers(Filtration_value from, Filtration_value to) const {
     // Init Betti numbers vector with zeros until Simplicial complex dimension
-    std::vector<int> betti_numbers(cpx_->dimension(), 0);
-
+    std::vector<int> betti_numbers(dim_max_, 0);
     for (auto pair : persistent_pairs_) {
       // Count persistence intervals that covers the given interval
       // null_simplex test : if the function is called with to=+infinity, we still get something useful. And it will
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 823d5bb6..383dd08a 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -103,6 +103,9 @@ if(PYTHON_PATH AND CYTHON_PATH)
     file(GLOB GUDHI_CUBICAL_PERSEUS_FILES "${CMAKE_SOURCE_DIR}/data/bitmap/*cubicalcomplexdoc.txt")
     file(COPY ${GUDHI_CUBICAL_PERSEUS_FILES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
     file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+    # Persistence graphical tools examples
+    file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
+    file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
     if (UNIX)
       add_custom_target(html 
           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 247e119e..2a3d9f63 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -57,8 +57,7 @@ palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
 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).
+    :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.
     """
@@ -79,8 +78,7 @@ def barcode_persistence(persistence, alpha=0.6):
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
-    :param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is
-    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 persistence.
     """
@@ -115,8 +113,7 @@ def diagram_persistence(persistence, alpha=0.6):
 
     :param persistence: The persistence to plot.
     :type persistence: list of tuples(dimension, tuple(birth, death)).
-    :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity
-    line (default is 0.6).
+    :param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6).
     :type alpha: float.
     :returns: plot -- An diagram plot of persistence.
     """
diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py
index 85b700a8..8d6483af 100755
--- a/src/cython/doc/conf.py
+++ b/src/cython/doc/conf.py
@@ -32,10 +32,10 @@ sys.path.insert(0, os.path.abspath('..'))
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'matplotlib.sphinxext.plot_directive',
     'sphinx.ext.autodoc',
     'sphinx.ext.doctest',
     'sphinx.ext.todo',
-    'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
@@ -43,6 +43,9 @@ extensions = [
 ]
 
 todo_include_todos = True
+# plot option : do not show hyperlinks (Source code, png, hires.png, pdf)
+plot_html_show_source_link = False
+plot_html_show_formats = False
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
diff --git a/src/cython/doc/img/graphical_tools_representation.png b/src/cython/doc/img/graphical_tools_representation.png
new file mode 100644
index 00000000..9759f7ba
--- /dev/null
+++ b/src/cython/doc/img/graphical_tools_representation.png
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index 5245d69d..89e09d70 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -61,3 +61,8 @@ Persistence cohomology
 ======================
 
 .. include:: persistent_cohomology_sum.rst
+
+Persistence graphical tools
+===========================
+
+.. include:: persistence_graphical_tools_sum.rst
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
new file mode 100755
index 00000000..95bbd343
--- /dev/null
+++ b/src/cython/doc/pyplots/barcode_persistence.py
@@ -0,0 +1,5 @@
+import gudhi
+
+periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt')
+diag = periodic_cc.persistence()
+gudhi.barcode_persistence(diag)
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
new file mode 100755
index 00000000..ceeeceb3
--- /dev/null
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -0,0 +1,6 @@
+import gudhi
+
+alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off')
+alpha_complex.initialize_filtration()
+diag = alpha_complex.persistence()
+gudhi.diagram_persistence(diag)
diff --git a/src/cython/doc/pyplots/show_palette_values.py b/src/cython/doc/pyplots/show_palette_values.py
new file mode 100755
index 00000000..e72a55fd
--- /dev/null
+++ b/src/cython/doc/pyplots/show_palette_values.py
@@ -0,0 +1,2 @@
+import gudhi
+gudhi.show_palette_values(alpha=1.0)
diff --git a/src/cython/example/alpha_complex_from_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
index 81c4c0b7..8e534061 100755
--- a/src/cython/example/alpha_complex_from_file_example.py
+++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
 import gudhi
-import pandas
 import argparse
 
 """This file is part of the Gudhi Library. The Gudhi library
@@ -30,35 +29,35 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-print("#####################################################################")
-print("AlphaComplex creation from points read in a file")
-
 parser = argparse.ArgumentParser(description='AlphaComplex creation from '
-                                 'points read in a file.',
+                                 'points read in a OFF file.',
                                  epilog='Example: '
-                                 'example/alpha_complex_from_file_example.py '
-                                 'data/500_random_points_on_3D_Torus.csv '
+                                 'example/alpha_complex_diagram_persistence_from_off_file_example.py '
+                                 '../data/points/tore3D_1307.off '
                                  '- Constructs a alpha complex with the '
                                  'points from the given file. File format '
                                  'is X1, X2, ..., Xn')
-parser.add_argument('file', type=argparse.FileType('r'))
+parser.add_argument("-f", "--file", type=str, required=True)
 parser.add_argument('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
 
-points = pandas.read_csv(args.file, header=None)
-
-print("AlphaComplex with max_alpha_square=0.5")
-
-alpha_complex = gudhi.AlphaComplex(points=points.values,
-                                   max_alpha_square=0.5)
-
-alpha_complex.initialize_filtration()
-diag = alpha_complex.persistence(homology_coeff_field=2, min_persistence=0.1)
-
-print("betti_numbers()=")
-print(alpha_complex.betti_numbers())
-
-if args.no_diagram == False:
-    gudhi.diagram_persistence(diag)
-    gudhi.barcode_persistence(diag)
+with open(args.file, 'r') as f:
+    first_line = f.readline()
+    if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
+
+        print("#####################################################################")
+        print("AlphaComplex creation from points read in a OFF file")
+        alpha_complex = gudhi.AlphaComplex(off_file=args.file, max_alpha_square=0.5)
+    
+        diag = alpha_complex.persistence(homology_coeff_field=2, min_persistence=0.1)
+    
+        print("betti_numbers()=")
+        print(alpha_complex.betti_numbers())
+    
+        if args.no_diagram == False:
+            gudhi.diagram_persistence(diag)
+    else:
+        print(args.file, "is not a valid OFF file")
+
+    f.close()
diff --git a/src/cython/example/cubical_complex_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
index 23f7ece6..e6ba94e1 100755
--- a/src/cython/example/cubical_complex_from_perseus_file_example.py
+++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
@@ -1,10 +1,7 @@
 #!/usr/bin/env python
 
 import gudhi
-import numpy
 import argparse
-import operator
-import os
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -32,25 +29,48 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-parser = argparse.ArgumentParser(description='Cubical complex from a perseus'
-                                 'file style name.',
+def is_file_perseus(file):
+    num_lines = open(file).read().count('\n')
+    try:
+        f = open(file)
+        num_dim = int(f.readline())
+        coeff = 1
+        for dim in range(0, num_dim):
+            try:
+                line = int(f.readline())
+                coeff *= abs(line)
+            except ValueError:
+                return False
+        if num_lines == (1 + num_dim + coeff):
+            return True
+        else:
+            return False
+    except ValueError:
+        return False
+
+parser = argparse.ArgumentParser(description='Periodic cubical complex from a '
+                                 'perseus file style name.',
                                  epilog='Example: '
-                                 './cubical_complex_from_perseus_file_example.py'
+                                 './periodic_cubical_complex_from_perseus_file_example.py'
                                  ' -f ../data/bitmap/CubicalTwoSphere.txt')
 
 parser.add_argument("-f", "--file", type=str, required=True)
+parser.add_argument('--no-barcode', default=False, action='store_true' , help='Flag for not to display the barcodes')
 
 args = parser.parse_args()
 
-if os.access(args.file, os.R_OK):
+if is_file_perseus(args.file):
     print("#####################################################################")
-    print("CubicalComplex creation")
-    cubical_complex = gudhi.CubicalComplex(perseus_file=args.file)
+    print("PeriodicCubicalComplex creation")
+    periodic_cubical_complex = gudhi.PeriodicCubicalComplex(perseus_file=args.file)
 
-    print("persistence(homology_coeff_field=2, min_persistence=0)=")
-    print(cubical_complex.persistence(homology_coeff_field=2, min_persistence=0))
+    print("persistence(homology_coeff_field=3, min_persistence=0)=")
+    diag = periodic_cubical_complex.persistence(homology_coeff_field=3, min_persistence=0)
+    print(diag)
 
     print("betti_numbers()=")
-    print(cubical_complex.betti_numbers())
+    print(periodic_cubical_complex.betti_numbers())
+    if args.no_barcode == False:
+        gudhi.barcode_persistence(diag)
 else:
-    print(args.file, "is unreachable")
+    print(args.file, "is not a valid perseus style file")
diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h
index 58421799..faabc497 100644
--- a/src/cython/include/Persistent_cohomology_interface.h
+++ b/src/cython/include/Persistent_cohomology_interface.h
@@ -56,7 +56,7 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol
  public:
 
   Persistent_cohomology_interface(FilteredComplex* stptr)
-      : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr), 
+      : persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomology::Field_Zp>(*stptr, true), 
       stptr_(stptr) { }
 
   std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) {