def get_center(positions, cutoff):
""" This function returns the approximate position with the most neighbors within the specified cutoff. If multiple
positions have the most neighbors, the position with the lowest standard deviation of the distances to its
neighbors is returned. """
x_minimum, x_maximum, y_minimum, y_maximum, z_minimum, z_maximum = grid_characteristics(
positions)[:-1]
x_center, y_center, z_center = [
round((x_minimum + x_maximum) / 2, 1),
round((y_minimum + y_maximum) / 2, 1),
round((z_minimum + z_maximum) / 2, 1)
]
x_length, y_length, z_length = [
round(x_maximum - x_minimum, 1),
round(y_maximum - y_minimum, 1),
round(z_maximum - z_minimum, 1)
]
grid = generate_grid([x_center, y_center, z_center],
[x_length, y_length, z_length], 0.1)
tree = cKDTree(positions)
length_positions = len(positions)
less_positions = [
positions[x]
for x in set(tree.query(grid, distance_upper_bound=0.1)[1])
if x != length_positions
]
small_tree = cKDTree(less_positions)
indices_lists = small_tree.query_ball_tree(tree, cutoff)
indices_maximal_neighbors = []
maximal_neighbours = max([len(x) for x in indices_lists])
for index, x in enumerate(indices_lists):
if len(x) == maximal_neighbours:
indices_maximal_neighbors.append(index)
if len(indices_maximal_neighbors) > 1:
minimal_stddev = None
index_minimal_stddev = None
for index in indices_maximal_neighbors:
stddev = standard_deviation([
distance(x, less_positions[index])
for x in [positions[x] for x in indices_lists[index]]
])
if minimal_stddev is None:
minimal_stddev = stddev
index_minimal_stddev = index
elif stddev < minimal_stddev:
minimal_stddev = stddev
index_minimal_stddev = index
return [
less_positions[index_minimal_stddev],
indices_lists[index_minimal_stddev]
]
else:
return [
less_positions[indices_maximal_neighbors[0]],
indices_lists[indices_maximal_neighbors[0]]
]
directory = os.getcwd() + '/pyrod'
logger = setup_logger('main', directory, debugging)
update_user('\n'.join(logo), logger)
logger.debug('\n'.join(
[': '.join(list(_)) for _ in config.items('directory')]))
# defining grid
if config.has_section('test grid parameters'):
logger.debug('\n'.join([
': '.join(list(_)) for _ in config.items('test grid parameters')
]))
center, edge_lengths, name = test_grid_parameters(config)
# determine space resulting in less than 100000 grid points
space = 0.5
space_found = False
while not space_found:
grid = generate_grid(center, edge_lengths, space)
if len(grid) < 100000:
space_found = True
pdb_grid(grid, name, '{}/test'.format(directory))
update_user('Writing test grid to {}/test.'.format(directory),
logger)
else:
if space == 0.5:
space += 0.5
else:
space += 1
# point properties
if config.has_section('point properties parameters'):
logger.debug('\n'.join([
': '.join(list(_))
for _ in config.items('point properties parameters')