Cubical complex unitary tests

Using pytest because of unittest bug on __function in cython


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1332 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bbb829104ddb14173cdb066c40e73273fac0c720

4 files changed, 119 insertions, 15 deletions

diff --git a/src/cython/Makefile b/src/cython/Makefile
index 75adbf3a..fdf4956c 100644
--- a/src/cython/Makefile
+++ b/src/cython/Makefile
@@ -6,6 +6,8 @@ test:
 	python test/test_mini_simplex_tree.py
 	python test/test_rips_complex.py
 	python test/test_alpha_complex.py
+	python test/test_witness_complex.py
+	python -m pytest test/test_cubical_complex.py
 
 example:
 	python example/simplex_tree_example.py
diff --git a/src/cython/src/cython/cubical_complex.pyx b/src/cython/src/cython/cubical_complex.pyx
index 98f0526a..375d2e0c 100644
--- a/src/cython/src/cython/cubical_complex.pyx
+++ b/src/cython/src/cython/cubical_complex.pyx
@@ -2,6 +2,7 @@ from cython cimport numeric
 from libcpp.vector cimport vector
 from libcpp.utility cimport pair
 from libcpp.string cimport string
+import os
 
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
@@ -52,7 +53,8 @@ cdef class CubicalComplex:
 
     cdef Cubical_complex_persistence_interface * pcohptr
 
-    def __cinit__(self, dimensions=None, top_dimensional_cells=None, perseus_file=''):
+    def __cinit__(self, dimensions=None, top_dimensional_cells=None,
+                  perseus_file=''):
         """CubicalComplex constructor from dimensions and
         top_dimensional_cells or from a perseus file style name.
 
@@ -61,11 +63,20 @@ cdef class CubicalComplex:
            top_dimensional_cells (list): A list of top dimensional cells.
            perseus_file (string): A perseus file style name.
          """
-        if dimensions is not None:
-            if top_dimensional_cells is not None:
-                self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
+        if (((dimensions is not None) or (top_dimensional_cells is not None)) and
+             (perseus_file is not '')):
+            print("CubicalComplex can be constructed from dimensions and "
+                  "top_dimensional_cells or from a perseus file style name.")
         else:
-            self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file)
+            if dimensions is not None:
+                if top_dimensional_cells is not None:
+                    self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
+            else:
+                if perseus_file is not '':
+                    if os.path.isfile(perseus_file):
+                        self.thisptr = new Bitmap_cubical_complex_base_interface(perseus_file)
+                    else:
+                        print("file " + perseus_file + " not found.")
 
     def __dealloc__(self):
         if self.thisptr != NULL:
@@ -73,6 +84,12 @@ cdef class CubicalComplex:
         if self.pcohptr != NULL:
             del self.pcohptr
 
+    def __is_defined(self):
+        return self.thisptr != NULL
+
+    def __is_persistence_defined(self):
+        return self.pcohptr != NULL
+
     def persistence(self, homology_coeff_field=11, min_persistence=0):
         """This function returns the persistence of the simplicial complex.
 
@@ -88,7 +105,8 @@ cdef class CubicalComplex:
         """
         if self.pcohptr != NULL:
             del self.pcohptr
-        self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr)
+        if self.thisptr != NULL:
+            self.pcohptr = new Cubical_complex_persistence_interface(self.thisptr)
         cdef vector[pair[int, pair[double, double]]] persistence_result
         if self.pcohptr != NULL:
             persistence_result = self.pcohptr.get_persistence(homology_coeff_field, min_persistence)
@@ -98,13 +116,13 @@ cdef class CubicalComplex:
         """This function returns the Betti numbers of the simplicial complex.
 
         :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
+
+        :warning: betti_numbers function requires persistence function to be
+        launched first.
         """
         cdef vector[int] bn_result
         if self.pcohptr != NULL:
             bn_result = self.pcohptr.betti_numbers()
-        else:
-            print("betti_numbers function requires persistence function"
-                  " to be launched first.")
         return bn_result
 
     def persistent_betti_numbers(self, from_value, to_value):
@@ -120,11 +138,11 @@ cdef class CubicalComplex:
 
         :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
         Bn]).
+
+        :warning: betti_numbers function requires persistence function to be
+        launched first.
         """
         cdef vector[int] pbn_result
         if self.pcohptr != NULL:
             pbn_result = self.pcohptr.persistent_betti_numbers(<double>from_value, <double>to_value)
-        else:
-            print("persistent_betti_numbers function requires persistence function"
-                  " to be launched first.")
         return pbn_result
diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py
new file mode 100755
index 00000000..9f5847f9
--- /dev/null
+++ b/src/cython/test/test_cubical_complex.py
@@ -0,0 +1,78 @@
+from gudhi import CubicalComplex
+
+"""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) 2016 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) 2016 INRIA"
+__license__ = "GPL v3"
+
+
+def test_empty_constructor():
+    # Try to create an empty CubicalComplex
+    cub = CubicalComplex()
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+def test_non_existing_perseus_file_constructor():
+    # Try to open a non existing file
+    cub = CubicalComplex(perseus_file='pouetpouettralala.toubiloubabdou')
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+def test_dimension_or_perseus_file_constructor():
+    # CubicalComplex can be constructed from dimensions and
+    # top_dimensional_cells OR from a perseus file style name.
+    cub = CubicalComplex(dimensions=[3, 3],
+                         top_dimensional_cells = [1,2,3,4,5,6,7,8,9],
+                         perseus_file='../data/bitmap/CubicalOneSphere.txt')
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+    cub = CubicalComplex(top_dimensional_cells = [1,2,3,4,5,6,7,8,9],
+                         perseus_file='../data/bitmap/CubicalOneSphere.txt')
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+    cub = CubicalComplex(dimensions=[3, 3],
+                         perseus_file='../data/bitmap/CubicalOneSphere.txt')
+    assert cub.__is_defined() == False
+    assert cub.__is_persistence_defined() == False
+
+def test_dimension_constructor():
+    cub = CubicalComplex(dimensions=[3, 3],
+                         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.__is_persistence_defined() == True
+    assert cub.betti_numbers() == [1, 0]
+    assert cub.persistent_betti_numbers(0, 1000) == [0, 0]
+
+def test_dimension_constructor():
+    cub = CubicalComplex(perseus_file='../data/bitmap/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.__is_persistence_defined() == True
+    assert cub.betti_numbers() == [1, 0]
+    assert cub.persistent_betti_numbers(0, 1000) == [1, 0]
diff --git a/src/cython/test/test_witness_complex.py b/src/cython/test/test_witness_complex.py
index f9bbe077..2891935d 100755
--- a/src/cython/test/test_witness_complex.py
+++ b/src/cython/test/test_witness_complex.py
@@ -31,11 +31,13 @@ __license__ = "GPL v3"
 
 class TestWitnessComplex(unittest.TestCase):
 
-    def test_infinite_alpha(self):
+    def test_witness_complex(self):
         point_list = [[0, 0], [1, 0], [0, 1], [1, 1]]
         witness = gudhi.WitnessComplex(points=point_list,
                                        number_of_landmarks=10)
 
+        # FIXME: Remove this line
+        witness.set_dimension(2)
 
         self.assertEqual(witness.num_simplices(), 13)
         self.assertEqual(witness.num_vertices(), 10)
@@ -46,8 +48,12 @@ class TestWitnessComplex(unittest.TestCase):
                          ([1, 2], 0.0), ([3], 0.0), ([4], 0.0), ([3, 4], 0.0),
                          ([5], 0.0), ([6], 0.0), ([7], 0.0), ([8], 0.0),
                          ([9], 0.0)])
-        self.assertEqual(witness.get_star_tree([0]), [])
-        self.assertEqual(witness.get_coface_tree([0], 1), [])
+
+        self.assertEqual(witness.get_coface_tree([2], 1),
+                         [([0, 2], 0.0), ([1, 2], 0.0)])
+        self.assertEqual(witness.get_star_tree([2]),
+                         [([0, 2], 0.0), ([1, 2], 0.0), ([2], 0.0)])
+
 
 if __name__ == '__main__':
     unittest.main()