Add Gudhi namespace for reader_utils

Add confidence band in persistence_graphical_tools.py
Persistence_diagram returns a plot that is no more showed.


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2582 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4125f4f525057e89c8b0d5d164ea0b9d1df1bd72

9 files changed, 39 insertions, 22 deletions

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 238d99ad..1408681a 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -36,8 +36,8 @@ int main(int argc, char** argv) {
         " distance (set by default to zero). The program will now terminate \n";
     return -1;
   }
-  std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]);
-  std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]);
+  std::vector<std::pair<double, double>> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]);
+  std::vector<std::pair<double, double>> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]);
 
   double tolerance = 0.;
   if (argc == 4) {
diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
index 8517e7f6..d38808c7 100644
--- a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
@@ -57,7 +57,7 @@ int main(int argc, char * argv[]) {
 
   program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
 
-  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
+  Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
   Rips_complex rips_complex_from_file(distances, threshold);
 
   // Construct the Rips complex in a Simplex Tree
diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
index 7ae8126f..9e182f1e 100644
--- a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
+++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
@@ -32,7 +32,7 @@ int main(int argc, char **argv) {
   // Init of a Rips complex from a distance matrix in a csv file
   // Default separator is ';'
   // ----------------------------------------------------------------------------
-  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
+  Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
   Rips_complex rips_complex_from_file(distances, threshold);
 
   std::streambuf* streambufffer;
diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp
index fc2179f2..fc83f5f7 100644
--- a/src/Rips_complex/test/test_rips_complex.cpp
+++ b/src/Rips_complex/test/test_rips_complex.cpp
@@ -244,7 +244,7 @@ BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) {
   std::cout << "========== CSV FILE NAME = " << csv_file_name << " - Rips threshold=" <<
       rips_threshold << "==========" << std::endl;
 
-  Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
+  Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
   Rips_complex rips_complex_from_file(distances, rips_threshold);
 
   const int DIMENSION_1 = 1;
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index f1684d78..8e99acfc 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -37,6 +37,8 @@
 #include <vector>
 #include <utility>  // for pair
 
+namespace Gudhi {
+
 // Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented.
 // It is required for global functions and variables.
 
@@ -331,7 +333,7 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu
       }
     }
   }
-} // read_persistence_diagram_from_file
+}  // read_persistence_diagram_from_file
 
 /**
 Reads a file containing persistence intervals.
@@ -347,7 +349,7 @@ inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_in
     filename,
     boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
   return ret;
-} // read_persistence_diagram_from_file
+}  // read_persistence_diagram_from_file
 
 
 /**
@@ -367,6 +369,8 @@ inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dime
     filename, 
     boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
   return ret;
-} // read_persistence_diagram_from_file
+}  // read_persistence_diagram_from_file
+
+}  // namespace Gudhi
 
 #endif  // READER_UTILS_H_
diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp
index 95a73bd9..656e6f2e 100644
--- a/src/common/test/test_distance_matrix_reader.cpp
+++ b/src/common/test/test_distance_matrix_reader.cpp
@@ -36,7 +36,7 @@ BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix )
 {
   Distance_matrix from_lower_triangular;
   // Read lower_triangular_distance_matrix.csv file where the separator is a ','
-  from_lower_triangular = read_lower_triangular_matrix_from_csv_file<double>("lower_triangular_distance_matrix.csv",
+  from_lower_triangular = Gudhi::read_lower_triangular_matrix_from_csv_file<double>("lower_triangular_distance_matrix.csv",
                                                                              ',');
   for (auto& i : from_lower_triangular) {
     for (auto j : i) {
@@ -69,7 +69,7 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix )
 {
   Distance_matrix from_full_square;
   // Read full_square_distance_matrix.csv file where the separator is the default one ';'
-  from_full_square = read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv");
+  from_full_square = Gudhi::read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv");
   for (auto& i : from_full_square) {
     for (auto j : i) {
       std::cout << j << " ";
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index a984633e..70ff6001 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -5,7 +5,7 @@ import numpy as np
    (Geometric Understanding in Higher Dimensions) is a generic C++
    library for computational topology.
 
-   Author(s):       Vincent Rouvreau
+   Author(s):       Vincent Rouvreau, Bertrand Michel
 
    Copyright (C) 2016 INRIA
 
@@ -27,11 +27,13 @@ __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 INRIA"
 __license__ = "GPL v3"
 
-def __min_birth_max_death(persistence):
+def __min_birth_max_death(persistence, band_boot=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.
     :returns: (float, float) -- (min_birth, max_death).
     """
     # Look for minimum birth date and maximum death date for plot optimisation
@@ -45,6 +47,8 @@ def __min_birth_max_death(persistence):
             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
     return (min_birth, max_death)
 
 """
@@ -108,16 +112,18 @@ def plot_persistence_barcode(persistence, alpha=0.6):
     plt.axis([axis_start, infinity, 0, ind])
     plt.show()
 
-def plot_persistence_diagram(persistence, alpha=0.6):
-    """This function plots the persistence diagram.
+def plot_persistence_diagram(persistence, alpha=0.6, band_boot=0.):
+    """This function plots the persistence diagram with confidence band.
 
     :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).
     :type alpha: float.
-    :returns: plot -- An diagram plot of persistence.
+    :param band_boot: bootstrap band
+    :type band_boot: float.
+    :returns: plot -- A diagram plot of persistence.
     """
-    (min_birth, max_death) = __min_birth_max_death(persistence)
+    (min_birth, max_death) = __min_birth_max_death(persistence, band_boot)
     ind = 0
     delta = ((max_death - min_birth) / 10.0)
     # Replace infinity values with max_death + delta for diagram to be more
@@ -131,6 +137,9 @@ def plot_persistence_diagram(persistence, alpha=0.6):
     plt.plot(x, x, color='k', linewidth=1.0)
     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')
 
     # Draw points in loop
     for interval in reversed(persistence):
@@ -149,4 +158,4 @@ def plot_persistence_diagram(persistence, alpha=0.6):
     plt.ylabel('Death')
     # Ends plot on infinity value and starts a little bit before min_birth
     plt.axis([axis_start, infinity, axis_start, infinity + delta])
-    plt.show()
+    return plt
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index cae18323..bc731f12 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -51,16 +51,18 @@ This function can display the persistence result as a diagram:
 
     import gudhi
     
-    rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
+    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()
-    gudhi.plot_persistence_diagram(diag)
+    pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    pplot.show()
 
 .. plot::
 
     import gudhi
 
-    rips_complex = gudhi.RipsComplex(off_file='tore3D_300.off', max_edge_length=2.0)
+    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()
-    gudhi.plot_persistence_diagram(diag)
+    pplot = gudhi.plot_persistence_diagram(diag, band_boot=0.13)
+    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 4c21b98e..5951eedf 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
@@ -39,6 +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -64,7 +65,8 @@ with open(args.file, 'r') as f:
         print(simplex_tree.betti_numbers())
     
         if args.no_diagram == False:
-            gudhi.plot_persistence_diagram(diag)
+            pplot = gudhi.plot_persistence_diagram(diag, band_boot=args.band_boot)
+            pplot.show()
     else:
         print(args.file, "is not a valid OFF file")