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

1 files changed, 81 insertions, 0 deletions

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)]}