Plot functions now returns a plot that can be modified before to be shown

Add confidence band in plot_persistence_diagram
Cythonization of read_lower_triangular_matrix_from_csv_file and read_persistence_intervals functions
Add Python tests of read functions


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2590 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 522ec31e9ad3a9a688875612d246114704b8c74e

17 files changed, 267 insertions, 18 deletions

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 8e99acfc..f16ae61d 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -359,7 +359,7 @@ If `only_this_dim` = -1, dimension is ignored and all lines are returned.
 If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
 (or where dimension is not specified) are returned.
 The return value is an `std::vector<std::pair<birth, death>>`
-where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+where `birth` a `double`, and `death` a `double`.
 Note: the function does not check that birth <= death.
 **/
 inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 99badffb..f427b3c5 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -100,7 +100,7 @@ if(CYTHON_FOUND)
   file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION "${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/")
+  file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
 
   if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     # If CGAL_VERSION >= 4.8.1, include subsampling
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 70ff6001..da709b8a 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -113,13 +113,13 @@ def plot_persistence_barcode(persistence, alpha=0.6):
     plt.show()
 
 def plot_persistence_diagram(persistence, alpha=0.6, band_boot=0.):
-    """This function plots the persistence diagram with confidence band.
+    """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 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
+    :param band_boot: bootstrap band (not displayed if :math:`\leq` 0.)
     :type band_boot: float.
     :returns: plot -- A diagram plot of persistence.
     """
diff --git a/src/cython/cython/reader_utils.pyx b/src/cython/cython/reader_utils.pyx
new file mode 100644
index 00000000..14976167
--- /dev/null
+++ b/src/cython/cython/reader_utils.pyx
@@ -0,0 +1,95 @@
+from cython cimport numeric
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+from libcpp.map cimport map
+from libcpp.pair cimport pair
+import os
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2017 INRIA
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2017 INRIA"
+__license__ = "GPL v3"
+
+cdef extern from "Reader_utils_interface.h" namespace "Gudhi":
+    vector[vector[double]] read_matrix_from_csv_file(string off_file, char separator)
+    map[int, vector[pair[double, double]]] read_pers_intervals_grouped_by_dimension(string filename)
+    vector[pair[double, double]] read_pers_intervals_in_dimension(string filename, int only_this_dim)
+
+def read_lower_triangular_matrix_from_csv_file(csv_file='', separator=';'):
+    """Read lower triangular matrix from a CSV style file.
+
+    :param csv_file: A CSV file style name.
+    :type csv_file: string
+    :param separator: The value separator in the CSV file. Default value is ';'
+    :type separator: char
+
+    :returns:  The lower triangular matrix.
+    :rtype: vector[vector[double]]
+    """
+    if csv_file is not '':
+        if os.path.isfile(csv_file):
+            return read_matrix_from_csv_file(str.encode(csv_file), str.encode(separator)[0])
+    print("file " + csv_file + " not set or not found.")
+    return []
+
+def read_persistence_intervals_grouped_by_dimension(persistence_file=''):
+    """Reads a file containing persistence intervals.
+    Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
+    The return value is an `map[dim, vector[pair[birth, death]]]`
+    where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+    Note: the function does not check that birth <= death.
+
+    :param persistence_file: A persistence file style name.
+    :type persistence_file: string
+
+    :returns:  The persistence pairs grouped by dimension.
+    :rtype: map[int, vector[pair[double, double]]]
+    """
+    if persistence_file is not '':
+        if os.path.isfile(persistence_file):
+            return read_pers_intervals_grouped_by_dimension(str.encode(persistence_file))
+    print("file " + persistence_file + " not set or not found.")
+    return []
+
+def read_persistence_intervals_in_dimension(persistence_file='', only_this_dim=-1):
+    """Reads a file containing persistence intervals.
+    Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
+    If `only_this_dim` = -1, dimension is ignored and all lines are returned.
+    If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim`
+    (or where dimension is not specified) are returned.
+    The return value is an `vector[pair[birth, death]]`
+    where `birth` a `double`, and `death` a `double`.
+    Note: the function does not check that birth <= death.
+
+    :param persistence_file: A persistence file style name.
+    :type persistence_file: string
+
+    :returns:  The persistence pairs grouped by dimension.
+    :rtype: map[int, vector[pair[double, double]]]
+    """
+    if persistence_file is not '':
+        if os.path.isfile(persistence_file):
+            return read_pers_intervals_in_dimension(str.encode(persistence_file), only_this_dim)
+    print("file " + persistence_file + " not set or not found.")
+    return []
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
index c06ac5a7..b021049f 100755
--- a/src/cython/doc/pyplots/barcode_persistence.py
+++ b/src/cython/doc/pyplots/barcode_persistence.py
@@ -1,5 +1,5 @@
 import gudhi
 
-periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='../3d_torus.txt')
+periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='3d_torus.txt')
 diag = periodic_cc.persistence()
 gudhi.plot_persistence_barcode(diag)
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
index b4714fe3..56d6c50f 100755
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ b/src/cython/doc/pyplots/diagram_persistence.py
@@ -1,5 +1,7 @@
 import gudhi
 
-alpha_complex = gudhi.AlphaComplex(off_file='../tore3D_300.off')
-diag = alpha_complex.persistence()
-gudhi.plot_persistence_diagram(diag)
+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()
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 adedc7d2..b4487be4 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
@@ -38,6 +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -63,7 +64,8 @@ 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")
 
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 2371c36c..e3f362dc 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
@@ -40,6 +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -70,8 +71,8 @@ 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")
 
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 5748aa8a..c236d992 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
@@ -40,6 +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('--no-diagram', default=False, action='store_true' , help='Flag for not to display the diagrams')
 
 args = parser.parse_args()
@@ -70,8 +71,8 @@ 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")
 
diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py
index bc3b16ec..ed87806b 100755
--- a/src/cython/example/gudhi_graphical_tools_example.py
+++ b/src/cython/example/gudhi_graphical_tools_example.py
@@ -44,4 +44,11 @@ gudhi.plot_persistence_barcode(persistence)
 print("#####################################################################")
 print("Show diagram persistence example")
 
-gudhi.plot_persistence_diagram(persistence)
+pplot = gudhi.plot_persistence_diagram(persistence)
+pplot.show()
+
+print("#####################################################################")
+print("Show diagram persistence example with a confidence band")
+
+pplot = gudhi.plot_persistence_diagram(persistence, band_boot=0.2)
+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 984dbf1b..3baebd17 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
@@ -39,6 +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()
@@ -61,4 +62,5 @@ print("betti_numbers()=")
 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()
diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py
index 4e5cd2c8..9bfea41c 100755
--- a/src/cython/example/rips_persistence_diagram.py
+++ b/src/cython/example/rips_persistence_diagram.py
@@ -39,4 +39,5 @@ simplex_tree = rips.create_simplex_tree(max_dimension=1)
 diag = simplex_tree.persistence(homology_coeff_field=2, min_persistence=0)
 print("diag=", diag)
 
-gudhi.plot_persistence_diagram(diag)
+pplot = gudhi.plot_persistence_diagram(diag)
+pplot.show()
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 4845eb47..6145e7f2 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
@@ -37,6 +37,7 @@ parser = argparse.ArgumentParser(description='TangentialComplex creation from '
                                  '- Constructs a tangential complex with the '
                                  'points from the given OFF file')
 parser.add_argument("-f", "--file", type=str, 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')
 
 args = parser.parse_args()
@@ -59,7 +60,8 @@ with open(args.file, 'r') as f:
         print(st.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")
 
diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in
index 34d7c3b5..ed2d28cc 100644
--- a/src/cython/gudhi.pyx.in
+++ b/src/cython/gudhi.pyx.in
@@ -30,6 +30,7 @@ include "cython/rips_complex.pyx"
 include "cython/cubical_complex.pyx"
 include "cython/periodic_cubical_complex.pyx"
 include "cython/persistence_graphical_tools.py"
+include "cython/reader_utils.pyx"
 include "cython/witness_complex.pyx"
 include "cython/strong_witness_complex.pyx"
 @GUDHI_CYTHON_ALPHA_COMPLEX@
diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h
new file mode 100644
index 00000000..b87b6cca
--- /dev/null
+++ b/src/cython/include/Reader_utils_interface.h
@@ -0,0 +1,54 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2017 INRIA
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef INCLUDE_READER_UTILS_INTERFACE_H_
+#define INCLUDE_READER_UTILS_INTERFACE_H_
+
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+namespace Gudhi {
+
+// Redefine functions with a different name in order the original name can be used in the Python version.
+std::vector<std::vector<double>> read_matrix_from_csv_file(const std::string& filename,
+                                                                const char separator = ';') {
+  return read_lower_triangular_matrix_from_csv_file<double>(filename, separator);
+}
+
+inline std::map<int, std::vector<std::pair<double, double>>>
+    read_pers_intervals_grouped_by_dimension(std::string const& filename) {
+  return read_persistence_intervals_grouped_by_dimension(filename);
+}
+
+inline std::vector<std::pair<double, double>>
+    read_pers_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
+  return read_persistence_intervals_in_dimension(filename, only_this_dim);
+}
+
+
+}  // namespace Gudhi
+
+
+#endif  // INCLUDE_READER_UTILS_INTERFACE_H_
diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h
index 6d813f4a..d06ee4bd 100644
--- a/src/cython/include/Rips_complex_interface.h
+++ b/src/cython/include/Rips_complex_interface.h
@@ -66,7 +66,7 @@ class Rips_complex_interface {
     } else {
       // Rips construction where values is a distance matrix
       Distance_matrix distances =
-          read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
+          Gudhi::read_lower_triangular_matrix_from_csv_file<Simplex_tree_interface<>::Filtration_value>(file_name);
       rips_complex_ = new Rips_complex<Simplex_tree_interface<>::Filtration_value>(distances, threshold);
     }
   }
diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py
new file mode 100755
index 00000000..517bf109
--- /dev/null
+++ b/src/cython/test/test_reader_utils.py
@@ -0,0 +1,81 @@
+import gudhi
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2017 INRIA
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2017 INRIA"
+__license__ = "GPL v3"
+
+
+def test_non_existing_csv_file():
+    # Try to open a non existing file
+    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file='pouetpouettralala.toubiloubabdou')
+    assert matrix == []
+
+def test_full_square_distance_matrix_csv_file():
+    # Create test file
+    test_file = open('full_square_distance_matrix.csv', 'w')
+    test_file.write('0;1;2;3;\n1;0;4;5;\n2;4;0;6;\n3;5;6;0;')
+    test_file.close()
+    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="full_square_distance_matrix.csv")
+    assert matrix == [[], [1.0], [2.0, 4.0], [3.0, 5.0, 6.0]]
+
+def test_lower_triangular_distance_matrix_csv_file():
+    # Create test file
+    test_file = open('lower_triangular_distance_matrix.csv', 'w')
+    test_file.write('\n1,\n2,3,\n4,5,6,\n7,8,9,10,')
+    test_file.close()
+    matrix = gudhi.read_lower_triangular_matrix_from_csv_file(csv_file="lower_triangular_distance_matrix.csv", separator=",")
+    assert matrix == [[], [1.0], [2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0, 10.0]]
+
+def test_non_existing_persistence_file():
+    # Try to open a non existing file
+    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='pouetpouettralala.toubiloubabdou')
+    assert persistence == []
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='pouetpouettralala.toubiloubabdou', only_this_dim=1)
+    assert persistence == []
+
+def test_read_persistence_intervals_without_dimension():
+    # Create test file
+    test_file = open('persistence_intervals_without_dimension.pers', 'w')
+    test_file.write('# Simple persistence diagram without dimension\n2.7 3.7\n9.6 14.\n34.2 34.974\n3. inf')
+    test_file.close()
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers')
+    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_without_dimension.pers', only_this_dim=15)
+    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_without_dimension.pers')
+    assert persistence == {-1: [(2.7, 3.7), (9.6, 14.0), (34.2, 34.974), (3.0, float('Inf'))]}
+
+def test_read_persistence_intervals_with_dimension():
+    # Create test file
+    test_file = open('persistence_intervals_with_dimension.pers', 'w')
+    test_file.write('# Simple persistence diagram with dimension\n0 2.7 3.7\n1 9.6 14.\n3 34.2 34.974\n1 3. inf')
+    test_file.close()
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers')
+    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    persistence = gudhi.read_persistence_intervals_in_dimension(persistence_file='persistence_intervals_with_dimension.pers', only_this_dim=1)
+    # BUG !!!
+    assert persistence == [[2.7, 3.7], [9.6, 14.], [34.2, 34.974], [3., float('Inf')]]
+    persistence = gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file='persistence_intervals_with_dimension.pers')
+    assert persistence == {0: [(2.7, 3.7)], 1: [(9.6, 14.0), (3.0, float('Inf'))], 3: [(34.2, 34.974)]}