Add numpy ndarray to init a cubical and a periodic one

4 files changed, 84 insertions, 19 deletions

diff --git a/src/python/doc/cubical_complex_user.rst b/src/python/doc/cubical_complex_user.rst
index b13b500e..21806038 100644
--- a/src/python/doc/cubical_complex_user.rst
+++ b/src/python/doc/cubical_complex_user.rst
@@ -142,8 +142,8 @@ 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],
+    from numpy import array as np_array
+    periodic_cc = pcc(numpy_array = np_array([[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..2ec0146a 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=''):
+                 numpy_array=None, perseus_file=''):
         """CubicalComplex constructor from dimensions and
         top_dimensional_cells or from a Perseus-style file name.
 
@@ -58,16 +58,31 @@ cdef class CubicalComplex:
 
         Or
 
+        :param numpy_array: Filtration values in a d-array.
+        :type numpy_array: numpy ndarray
+
+        Or
+
         :param perseus_file: A Perseus-style file name.
         :type perseus_file: string
         """
 
     # 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 == ''):
+                  numpy_array=None, perseus_file=''):
+        if ((dimensions is not None) and (top_dimensional_cells is not None)
+            and (numpy_array is 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 None) and (perseus_file != ''):
+        elif ((dimensions is None) and (top_dimensional_cells is None)
+            and (numpy_array is not None) and (perseus_file == '')):
+            if isinstance(numpy_array, np.ndarray):
+                dimensions = list(numpy_array.shape)
+                top_dimensional_cells = numpy_array.flatten().tolist()
+                self.thisptr = new Bitmap_cubical_complex_base_interface(dimensions, top_dimensional_cells)
+            else:
+                print("numpy_array is not an instance of ndarray. It is a " + type(numpy_array))
+        elif ((dimensions is None) and (top_dimensional_cells is None)
+            and (numpy_array 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 +199,4 @@ 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..8318b7d3 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=''):
+                 numpy_array=None, periodic_dimensions=None, perseus_file=''):
         """PeriodicCubicalComplex constructor from dimensions and
         top_dimensional_cells or from a Perseus-style file name.
 
@@ -60,16 +60,41 @@ cdef class PeriodicCubicalComplex:
 
         Or
 
+        :param numpy_array: Filtration values in a d-array.
+        :type numpy_array: 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
         """
 
     # 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 != ''):
+                  numpy_array=None, periodic_dimensions=None,
+                  perseus_file=''):
+        if ((dimensions is not None) and (top_dimensional_cells is not None)
+            and (numpy_array is 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 (numpy_array is not None) and (periodic_dimensions is not None)
+            and (perseus_file == '')):
+            if isinstance(numpy_array, np.ndarray):
+                dimensions = list(numpy_array.shape)
+                top_dimensional_cells = numpy_array.flatten().tolist()
+                self.thisptr = new Periodic_cubical_complex_base_interface(dimensions,
+                                                                           top_dimensional_cells,
+                                                                           periodic_dimensions)
+            else:
+                print("numpy_array is not an instance of ndarray. It is a " + type(numpy_array))
+        elif ((dimensions is None) and (top_dimensional_cells is None)
+            and (numpy_array 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:
@@ -186,4 +211,4 @@ 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..a37d7821 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
+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(
+        numpy_array=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(
+        numpy_array=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