def testSortCoordinatesDistance(self):
""" Test the coordinate sorting wrt distances function. """
# Lets, use these coordinates.
coords = numpy.array([[2.0, 3.0, 0.0], [1.0, 2.0, 0.0],
[0.0, 0.0, 0.0], [-8.9, 12.0, 4.0]])
types1 = ["B", "A", "C", "A"]
types2 = ["D", "G", "C", "V"]
# -----------------------------------------------------------------------------
# Let the 3rd coordinates be the center.
center = 2
# Sort wrt distance, type, x, y, z
sorted_coords, sorted_distances, sorted_types1, sorted_types2 = \
sortCoordinatesDistance(coords, center, types1, types2)
# Setup reference.
ref_coords = numpy.array([[0.0, 0.0, 0.0],
[1.0, 2.0, 0.0],
[2.0, 3.0, 0.0],
[-8.9, 12.0, 4.0]])
ref_types1 = ["C", "A", "B", "A"]
ref_types2 = ["C", "G", "D", "V"]
ref_distances = [0.0, 2.2360679774997898, 3.6055512754639891, 15.46641522784126]
# Check.
self.assertTrue(numpy.allclose(sorted_coords, ref_coords))
self.assertTrue(numpy.allclose(sorted_distances, ref_distances))
self.assertListEqual(sorted_types1, ref_types1)
self.assertListEqual(sorted_types2, ref_types2)
# -----------------------------------------------------------------------------
# Let the 1st coordinates be the center.
center = 0
# Sort wrt distance, type, x, y, z
sorted_coords, sorted_distances, sorted_types1, sorted_types2 = \
sortCoordinatesDistance(coords, center, types1, types2)
# Setup reference.
ref_coords = numpy.array([[2.0, 3.0, 0.0],
[1.0, 2.0, 0.0],
[0.0, 0.0, 0.0],
[-8.9, 12.0, 4.0]])
ref_types1 = ["B", "A", "C", "A"]
ref_types2 = ["D", "G", "C", "V"]
ref_distances = [0.0, 1.4142135623730951, 3.6055512754639891, 14.690473103341498]
# Check.
self.assertTrue(numpy.allclose(sorted_coords, ref_coords))
self.assertTrue(numpy.allclose(sorted_distances, ref_distances))
self.assertListEqual(sorted_types1, ref_types1)
self.assertListEqual(sorted_types2, ref_types2)
def testSortCoordinatesDistance(self):
""" Test the coordinate sorting wrt distances function. """
# Lets, use these coordinates.
coords = numpy.array([[2.0, 3.0, 0.0], [1.0, 2.0, 0.0],
[0.0, 0.0, 0.0], [-8.9, 12.0, 4.0]])
types1 = ["B", "A", "C", "A"]
types2 = ["D", "G", "C", "V"]
# -----------------------------------------------------------------------------
# Let the 3rd coordinates be the center.
center = 2
# Sort wrt distance, type, x, y, z
sorted_coords, sorted_distances, sorted_types1, sorted_types2 = \
sortCoordinatesDistance(coords, center, types1, types2)
# Setup reference.
ref_coords = numpy.array([[0.0, 0.0, 0.0], [1.0, 2.0, 0.0],
[2.0, 3.0, 0.0], [-8.9, 12.0, 4.0]])
ref_types1 = ["C", "A", "B", "A"]
ref_types2 = ["C", "G", "D", "V"]
ref_distances = [
0.0, 2.2360679774997898, 3.6055512754639891, 15.46641522784126
]
# Check.
self.assertTrue(numpy.allclose(sorted_coords, ref_coords))
self.assertTrue(numpy.allclose(sorted_distances, ref_distances))
self.assertListEqual(sorted_types1, ref_types1)
self.assertListEqual(sorted_types2, ref_types2)
# -----------------------------------------------------------------------------
# Let the 1st coordinates be the center.
center = 0
# Sort wrt distance, type, x, y, z
sorted_coords, sorted_distances, sorted_types1, sorted_types2 = \
sortCoordinatesDistance(coords, center, types1, types2)
# Setup reference.
ref_coords = numpy.array([[2.0, 3.0, 0.0], [1.0, 2.0, 0.0],
[0.0, 0.0, 0.0], [-8.9, 12.0, 4.0]])
ref_types1 = ["B", "A", "C", "A"]
ref_types2 = ["D", "G", "C", "V"]
ref_distances = [
0.0, 1.4142135623730951, 3.6055512754639891, 14.690473103341498
]
# Check.
self.assertTrue(numpy.allclose(sorted_coords, ref_coords))
self.assertTrue(numpy.allclose(sorted_distances, ref_distances))
self.assertListEqual(sorted_types1, ref_types1)
self.assertListEqual(sorted_types2, ref_types2)
def __sortCoordinatesElementsAndMoveVectors(self):
"""
Private helper to sort the validated coordinate input,
and update the element order and move_vector indexing accordingly.
"""
# Set up the original indexing.
original_indexing = range(len(self._coordinates))
# Sort, and co-sort coordinates and indices.
(sorted_coords, dummy_distances, sorted_types_before, sorted_types_after, new_to_old_index) = \
sortCoordinatesDistance(coordinates = self._coordinates,
center = 0,
types1 = self._elements_before,
types2 = self._elements_after,
co_sort = original_indexing)
# Fix the move vectors.
if len(self._move_vectors) > 0:
old_to_new_index = []
for i in range(len(new_to_old_index)):
old_to_new_index.append(new_to_old_index.index(i))
# Fixt the move vector indexing.
move_vector_index = []
for v in self._move_vectors:
move_vector_index.append(old_to_new_index[v[0]])
# Setup and sort the backmapping.
help_index = range(len(move_vector_index))
to_sort = numpy.array(zip(help_index, move_vector_index))
sorted_indices = to_sort[numpy.argsort(to_sort[:, 1])]
# Construct the new move vectors.
new_move_vectors = []
for idx in sorted_indices:
new_move_vectors.append(
(idx[1], self._move_vectors[idx[0]][1]))
# Set the move vectors.
self._move_vectors = new_move_vectors
# Set the new data on the class.
self._coordinates = sorted_coords
self._elements_before = sorted_types_before
self._elements_after = sorted_types_after
def __sortCoordinatesElementsAndMoveVectors(self):
"""
Private helper to sort the validated coordinate input,
and update the element order and move_vector indexing accordingly.
"""
# Set up the original indexing.
original_indexing = range(len(self.__coordinates))
# Sort, and co-sort coordinates and indices.
(sorted_coords, dummy_distances, sorted_types_before, sorted_types_after, new_to_old_index) = \
sortCoordinatesDistance(coordinates = self.__coordinates,
center = 0,
types1 = self.__elements_before,
types2 = self.__elements_after,
co_sort = original_indexing)
# Fix the move vectors.
if len(self.__move_vectors) > 0:
old_to_new_index = []
for i in range(len(new_to_old_index)):
old_to_new_index.append(new_to_old_index.index(i))
# Fixt the move vector indexing.
move_vector_index = []
for v in self.__move_vectors:
move_vector_index.append( old_to_new_index[v[0]] )
# Setup and sort the backmapping.
help_index = range(len(move_vector_index))
to_sort = numpy.array(zip(help_index, move_vector_index))
sorted_indices = to_sort[numpy.argsort(to_sort[:,1])]
# Construct the new move vectors.
new_move_vectors = []
for idx in sorted_indices:
new_move_vectors.append( (idx[1], self.__move_vectors[idx[0]][1]) )
# Set the move vectors.
self.__move_vectors = new_move_vectors
# Set the new data on the class.
self.__coordinates = sorted_coords
self.__elements_before = sorted_types_before
self.__elements_after = sorted_types_after
def testSortCoordinatesDistance(self):
""" Test the coordinate sorting wrt distances function. """
# Lets, use these coordinates.
coords = numpy.array([[2.0,1.0,0.0],[1.0,2.0,0.0],[0.0,0.0,0.0],[-8.9,12.0,4.0]])
types = ["B","A","C","A"]
center = 2
# Sort - wrt distance,type,x,y,z
(sorted_coords, sorted_distances, sorted_types, co_sorted_types) = sortCoordinatesDistance(coords, center, types)
# Setup references.
ref_coords = numpy.array([[0.0,0.0,0.0],[1.0,2.0,0.0],[2.0,1.0,0.0],[-8.9,12.0,4.0]])
ref_types = ["C","A","B","A"]
ref_distances=numpy.array([numpy.linalg.norm(c) for c in ref_coords])
# Check.
self.assertAlmostEqual(numpy.linalg.norm(sorted_distances-ref_distances), 0.0, 10)
self.assertAlmostEqual(numpy.linalg.norm(sorted_coords-ref_coords), 0.0, 10)
self.assertEqual(sorted_types, ref_types)
def testSortCoordinatesDistance(self):
""" Test the coordinate sorting wrt distances function. """
# Lets, use these coordinates.
coords = numpy.array([[2.0, 1.0, 0.0], [1.0, 2.0, 0.0],
[0.0, 0.0, 0.0], [-8.9, 12.0, 4.0]])
types = ["B", "A", "C", "A"]
center = 2
# Sort - wrt distance,type,x,y,z
(sorted_coords, sorted_distances, sorted_types,
co_sorted_types) = sortCoordinatesDistance(coords, center, types)
# Setup references.
ref_coords = numpy.array([[0.0, 0.0, 0.0], [1.0, 2.0, 0.0],
[2.0, 1.0, 0.0], [-8.9, 12.0, 4.0]])
ref_types = ["C", "A", "B", "A"]
ref_distances = numpy.array([numpy.linalg.norm(c) for c in ref_coords])
# Check.
self.assertAlmostEqual(
numpy.linalg.norm(sorted_distances - ref_distances), 0.0, 10)
self.assertAlmostEqual(numpy.linalg.norm(sorted_coords - ref_coords),
0.0, 10)
self.assertEqual(sorted_types, ref_types)