Merge pull request #178 from VincentRouvreau/numpy_array_input_for_cubical

Fix #158 - Add numpy ndarray to init a cubical and a periodic one

4 files changed, 110 insertions, 20 deletions

diff --git a/src/python/doc/cubical_complex_user.rst b/src/python/doc/cubical_complex_user.rst
index b13b500e..56cf0170 100644
--- a/src/python/doc/cubical_complex_user.rst
+++ b/src/python/doc/cubical_complex_user.rst
@@ -142,8 +142,7 @@ Or it can be defined as follows:
 .. testcode::
 
     from gudhi import PeriodicCubicalComplex as pcc
-    periodic_cc = pcc(dimensions=[3,3],
-         top_dimensional_cells= [0, 0, 0, 0, 1, 0, 0, 0, 0],
+    periodic_cc = pcc(top_dimensional_cells = [[0, 0, 0], [0, 1, 0], [0, 0, 0]],
          periodic_dimensions=[True, False])
     result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \
         repr(periodic_cc.num_simplices()) + ' simplices.'
diff --git a/src/python/gudhi/cubical_complex.pyx b/src/python/gudhi/cubical_complex.pyx
index 011c407c..b7047d4f 100644
--- a/src/python/gudhi/cubical_complex.pyx
+++ b/src/python/gudhi/cubical_complex.pyx
@@ -5,7 +5,7 @@ from libcpp.string cimport string
 from libcpp cimport bool
 import os
 
-from numpy import array as np_array
+import numpy as np
 
 # This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
 # See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
@@ -47,7 +47,7 @@ cdef class CubicalComplex:
 
     # Fake constructor that does nothing but documenting the constructor
     def __init__(self, dimensions=None, top_dimensional_cells=None,
-                  perseus_file=''):
+                 perseus_file=''):
         """CubicalComplex constructor from dimensions and
         top_dimensional_cells or from a Perseus-style file name.
 
@@ -58,6 +58,12 @@ cdef class CubicalComplex:
 
         Or
 
+        :param top_dimensional_cells: A multidimensional array of cells
+            filtration values.
+        :type top_dimensional_cells: anything convertible to a numpy ndarray
+
+        Or
+
         :param perseus_file: A Perseus-style file name.
         :type perseus_file: string
         """
@@ -65,9 +71,19 @@ cdef class CubicalComplex:
     # The real cython constructor
     def __cinit__(self, dimensions=None, top_dimensional_cells=None,
                   perseus_file=''):
-        if (dimensions is not None) and (top_dimensional_cells is not None) and (perseus_file == ''):
+        if ((dimensions is not None) and (top_dimensional_cells is not None)
+            and (perseus_file == '')):
+            self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
+        elif ((dimensions is None) and (top_dimensional_cells is not None)
+            and (perseus_file == '')):
+            top_dimensional_cells = np.array(top_dimensional_cells,
+                                             copy = False,
+                                             order = 'F')
+            dimensions = top_dimensional_cells.shape
+            top_dimensional_cells = top_dimensional_cells.ravel(order='F')
             self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
-        elif (dimensions is None) and (top_dimensional_cells is None) and (perseus_file != ''):
+        elif ((dimensions is None) and (top_dimensional_cells is None)
+            and (perseus_file != '')):
             if os.path.isfile(perseus_file):
                 self.thisptr = new Bitmap_cubical_complex_base_interface(str.encode(perseus_file))
             else:
@@ -184,4 +200,4 @@ cdef class CubicalComplex:
         else:
             print("intervals_in_dim function requires persistence function"
                   " to be launched first.")
-        return np_array(intervals_result)
+        return np.array(intervals_result)
diff --git a/src/python/gudhi/periodic_cubical_complex.pyx b/src/python/gudhi/periodic_cubical_complex.pyx
index c89055db..eb96ab5f 100644
--- a/src/python/gudhi/periodic_cubical_complex.pyx
+++ b/src/python/gudhi/periodic_cubical_complex.pyx
@@ -5,7 +5,7 @@ from libcpp.string cimport string
 from libcpp cimport bool
 import os
 
-from numpy import array as np_array
+import numpy as np
 
 # This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
 # See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
@@ -47,7 +47,7 @@ cdef class PeriodicCubicalComplex:
 
     # Fake constructor that does nothing but documenting the constructor
     def __init__(self, dimensions=None, top_dimensional_cells=None,
-                  periodic_dimensions=None, perseus_file=''):
+                 periodic_dimensions=None, perseus_file=''):
         """PeriodicCubicalComplex constructor from dimensions and
         top_dimensional_cells or from a Perseus-style file name.
 
@@ -60,6 +60,14 @@ cdef class PeriodicCubicalComplex:
 
         Or
 
+        :param top_dimensional_cells: A multidimensional array of cells
+            filtration values.
+        :type top_dimensional_cells: anything convertible to a numpy ndarray
+        :param periodic_dimensions: A list of top dimensional cells periodicity value.
+        :type periodic_dimensions: list of boolean
+
+        Or
+
         :param perseus_file: A Perseus-style file name.
         :type perseus_file: string
         """
@@ -67,16 +75,32 @@ cdef class PeriodicCubicalComplex:
     # The real cython constructor
     def __cinit__(self, dimensions=None, top_dimensional_cells=None,
                   periodic_dimensions=None, perseus_file=''):
-        if (dimensions is not None) and (top_dimensional_cells is not None) and (periodic_dimensions is not None) and (perseus_file == ''):
-            self.thisptr = new Periodic_cubical_complex_base_interface(dimensions, top_dimensional_cells, periodic_dimensions)
-        elif (dimensions is None) and (top_dimensional_cells is None) and (periodic_dimensions is None) and (perseus_file != ''):
+        if ((dimensions is not None) and (top_dimensional_cells is not None)
+            and (periodic_dimensions is not None) and (perseus_file == '')):
+            self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
+                                                                       top_dimensional_cells,
+                                                                       periodic_dimensions)
+        elif ((dimensions is None) and (top_dimensional_cells is not None)
+            and (periodic_dimensions is not None) and (perseus_file == '')):
+            top_dimensional_cells = np.array(top_dimensional_cells,
+                                             copy = False,
+                                             order = 'F')
+            dimensions = top_dimensional_cells.shape
+            top_dimensional_cells = top_dimensional_cells.ravel(order='F')
+            self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
+                                                                       top_dimensional_cells,
+                                                                       periodic_dimensions)
+        elif ((dimensions is None) and (top_dimensional_cells is None)
+            and (periodic_dimensions is None) and (perseus_file != '')):
             if os.path.isfile(perseus_file):
                 self.thisptr = new Periodic_cubical_complex_base_interface(str.encode(perseus_file))
             else:
                 print("file " + perseus_file + " not found.")
         else:
-            print("CubicalComplex can be constructed from dimensions and "
-              "top_dimensional_cells or from a Perseus-style file name.")
+            print("CubicalComplex can be constructed from dimensions, "
+              "top_dimensional_cells and periodic_dimensions, or from "
+              "top_dimensional_cells and periodic_dimensions or from "
+              "a Perseus-style file name.")
 
     def __dealloc__(self):
         if self.thisptr != NULL:
@@ -186,4 +210,4 @@ cdef class PeriodicCubicalComplex:
         else:
             print("intervals_in_dim function requires persistence function"
                   " to be launched first.")
-        return np_array(intervals_result)
+        return np.array(intervals_result)
diff --git a/src/python/test/test_cubical_complex.py b/src/python/test/test_cubical_complex.py
index 68f54fbe..121da12a 100755
--- a/src/python/test/test_cubical_complex.py
+++ b/src/python/test/test_cubical_complex.py
@@ -1,4 +1,5 @@
-from gudhi import CubicalComplex
+from gudhi import CubicalComplex, PeriodicCubicalComplex
+import numpy as np
 
 """ This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
     See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
@@ -56,7 +57,7 @@ def test_dimension_or_perseus_file_constructor():
     assert cub.__is_persistence_defined() == False
 
 
-def test_dimension_simple_constructor():
+def simple_constructor(cub):
     cub = CubicalComplex(
         dimensions=[3, 3], top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9]
     )
@@ -67,12 +68,22 @@ def test_dimension_simple_constructor():
     assert cub.betti_numbers() == [1, 0, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0]
 
-
-def test_user_case_simple_constructor():
+def test_simple_constructor_from_top_cells():
     cub = CubicalComplex(
         dimensions=[3, 3],
-        top_dimensional_cells=[float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+        top_dimensional_cells=[1, 2, 3, 4, 5, 6, 7, 8, 9],
+    )
+    simple_constructor(cub)
+
+def test_simple_constructor_from_numpy_array():
+    cub = CubicalComplex(
+        top_dimensional_cells=np.array([[1, 2, 3],
+                                        [4, 5, 6],
+                                        [7, 8, 9]])
     )
+    simple_constructor(cub)
+
+def user_case_simple_constructor(cub):
     assert cub.__is_defined() == True
     assert cub.__is_persistence_defined() == False
     assert cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
@@ -83,6 +94,20 @@ def test_user_case_simple_constructor():
     )
     assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float("inf")))]
 
+def test_user_case_simple_constructor_from_top_cells():
+    cub = CubicalComplex(
+        dimensions=[3, 3],
+        top_dimensional_cells=[float("inf"), 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+    )
+    user_case_simple_constructor(cub)
+
+def test_user_case_simple_constructor_from_numpy_array():
+    cub = CubicalComplex(
+        top_dimensional_cells=np.array([[float("inf"), 0.0, 0.0],
+                                        [0.0, 1.0, 0.0],
+                                        [0.0, 0.0, 0.0]])
+    )
+    user_case_simple_constructor(cub)
 
 def test_dimension_file_constructor():
     # Create test file
@@ -96,3 +121,29 @@ def test_dimension_file_constructor():
     assert cub.__is_persistence_defined() == True
     assert cub.betti_numbers() == [1, 0, 0]
     assert cub.persistent_betti_numbers(0, 1000) == [1, 0, 0]
+
+def test_connected_sublevel_sets():
+    array_cells = np.array([[3, 3], [2, 2], [4, 4]])
+    linear_cells = [3, 3, 2, 2, 4, 4]
+    dimensions = [2, 3]
+    periodic_dimensions = [False, False]
+    # with a numpy array version
+    cub = CubicalComplex(top_dimensional_cells = array_cells)
+    assert cub.persistence() == [(0, (2.0, float("inf")))]
+    assert cub.betti_numbers() == [1, 0, 0]
+    # with vector of dimensions
+    cub = CubicalComplex(dimensions = dimensions,
+                         top_dimensional_cells = linear_cells)
+    assert cub.persistence() == [(0, (2.0, float("inf")))]
+    assert cub.betti_numbers() == [1, 0, 0]
+    # periodic with a numpy array version
+    cub = PeriodicCubicalComplex(top_dimensional_cells = array_cells,
+                                periodic_dimensions = periodic_dimensions)
+    assert cub.persistence() == [(0, (2.0, float("inf")))]
+    assert cub.betti_numbers() == [1, 0, 0]
+    # periodic with vector of dimensions
+    cub = PeriodicCubicalComplex(dimensions = dimensions,
+                                 top_dimensional_cells = linear_cells,
+                                 periodic_dimensions = periodic_dimensions)
+    assert cub.persistence() == [(0, (2.0, float("inf")))]
+    assert cub.betti_numbers() == [1, 0, 0]