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Merged
merged 1 commit into from
Mar 22, 2018
Merged

Code formatter script also in submodules #140

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2 changes: 1 addition & 1 deletion code_formatter.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ done
# Find all python files in code directories
python_files=""
for dir in $code_directories; do
python_files="$python_files `ls $dir/*.py`"
python_files="$python_files $(find $dir -name '*.py')"
done
[[ $# != 0 ]] && python_files=$@

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17 changes: 9 additions & 8 deletions pygem/params/ffdparams.py
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Expand Up @@ -126,7 +126,7 @@ def position_vertices(self):
:rtype: numpy.ndarray
"""
return self.origin_box + np.vstack([
np.zeros((1, 3)),
np.zeros((1, 3)),
self.rotation_matrix.dot(np.diag(self.lenght_box)).T
])

Expand Down Expand Up @@ -330,16 +330,17 @@ def save(self, filename, write_deformed=True):

if write_deformed:
box_points = np.array([
lattice_x_coords.ravel() + self.array_mu_x.ravel() *
self.lenght_box[0],
lattice_y_coords.ravel() + self.array_mu_y.ravel() *
self.lenght_box[1],
lattice_z_coords.ravel() + self.array_mu_z.ravel() *
self.lenght_box[2]
lattice_x_coords.ravel() +
self.array_mu_x.ravel() * self.lenght_box[0],
lattice_y_coords.ravel() +
self.array_mu_y.ravel() * self.lenght_box[1],
lattice_z_coords.ravel() +
self.array_mu_z.ravel() * self.lenght_box[2]
])
else:
box_points = np.array([
lattice_x_coords.ravel(), lattice_y_coords.ravel(),
lattice_x_coords.ravel(),
lattice_y_coords.ravel(),
lattice_z_coords.ravel()
])

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32 changes: 10 additions & 22 deletions pygem/params/rbfparams.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@

import numpy as np


class RBFParameters(object):
"""
Class that handles the Radial Basis Functions parameters in terms of RBF
Expand Down Expand Up @@ -41,24 +42,12 @@ def __init__(self):
self.basis = 'gaussian_spline'
self.radius = 0.5
self.power = 2
self.original_control_points = np.array([
[0., 0., 0.],
[0., 0., 1.],
[0., 1., 0.],
[1., 0., 0.],
[0., 1., 1.],
[1., 0., 1.],
[1., 1., 0.],
[1., 1., 1.]])
self.deformed_control_points = np.array([
[0., 0., 0.],
[0., 0., 1.],
[0., 1., 0.],
[1., 0., 0.],
[0., 1., 1.],
[1., 0., 1.],
[1., 1., 0.],
[1., 1., 1.]])
self.original_control_points = np.array(
[[0., 0., 0.], [0., 0., 1.], [0., 1., 0.], [1., 0., 0.],
[0., 1., 1.], [1., 0., 1.], [1., 1., 0.], [1., 1., 1.]])
self.deformed_control_points = np.array(
[[0., 0., 0.], [0., 0., 1.], [0., 1., 0.], [1., 0., 0.],
[0., 1., 1.], [1., 0., 1.], [1., 1., 0.], [1., 1., 1.]])

@property
def n_control_points(self):
Expand Down Expand Up @@ -108,9 +97,9 @@ def read_parameters(self, filename='parameters_rbf.prm'):

if len(lines) != self.n_control_points:
raise TypeError("The number of control points must be equal both in"
"the 'original control points' and in the 'deformed"
"control points' section of the parameters file"
"({0!s})".format(filename))
"the 'original control points' and in the 'deformed"
"control points' section of the parameters file"
"({0!s})".format(filename))

self.deformed_control_points = np.zeros((self.n_control_points, 3))
for line, i in zip(lines, list(range(0, self.n_control_points))):
Expand Down Expand Up @@ -233,4 +222,3 @@ def save(self, filename, write_deformed=True):
else:
writer.SetInputData(data)
writer.Write()

34 changes: 10 additions & 24 deletions tests/test_ffdparams.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,12 +62,8 @@ def test_class_members_default_rotation_matrix(self):

def test_class_members_default_position_vertices(self):
params = FFDParameters()
expected_matrix = np.array([
[0., 0., 0.],
[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.]
])
expected_matrix = np.array([[0., 0., 0.], [1., 0., 0.], [0., 1., 0.],
[0., 0., 1.]])
np.testing.assert_array_almost_equal(params.position_vertices,
expected_matrix)

Expand Down Expand Up @@ -177,12 +173,10 @@ def test_read_parameters_position_vertex_0_origin(self):
def test_read_parameters_position_vertex_0(self):
params = FFDParameters(n_control_points=[3, 2, 2])
params.read_parameters('tests/test_datasets/parameters_sphere.prm')
position_vertices = np.array([
[-20.0, -55.0, -45.0],
[24.17322326, -52.02107006, -53.05309404],
[-20., 29.41000412, -13.77579136],
[-2.82719042, -85.65053198, 37.85915459]
])
position_vertices = np.array(
[[-20.0, -55.0, -45.0], [24.17322326, -52.02107006, -53.05309404],
[-20., 29.41000412,
-13.77579136], [-2.82719042, -85.65053198, 37.85915459]])

np.testing.assert_array_almost_equal(params.position_vertices,
position_vertices)
Expand Down Expand Up @@ -260,22 +254,14 @@ def test_build_bounding_box_2(self):
params = FFDParameters()
params.build_bounding_box(cube)

expected_matrix = np.array([
[0., 0., 0.],
[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.]
])
expected_matrix = np.array([[0., 0., 0.], [1., 0., 0.], [0., 1., 0.],
[0., 0., 1.]])
np.testing.assert_almost_equal(
params.position_vertices, expected_matrix, decimal=5)

def test_set_position_of_vertices(self):
expected_matrix = np.array([
[0., 0., 0.],
[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.]
])
expected_matrix = np.array([[0., 0., 0.], [1., 0., 0.], [0., 1., 0.],
[0., 0., 1.]])
tops = np.array([1., 1., 1.])
params = FFDParameters()
params.origin_box = expected_matrix[0]
Expand Down
12 changes: 3 additions & 9 deletions tests/test_rbfparams.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,15 +6,9 @@

from pygem import RBFParameters

unit_cube = np.array([
[0., 0., 0.],
[0., 0., 1.],
[0., 1., 0.],
[1., 0., 0.],
[0., 1., 1.],
[1., 0., 1.],
[1., 1., 0.],
[1., 1., 1.]])
unit_cube = np.array([[0., 0., 0.], [0., 0., 1.], [0., 1., 0.], [1., 0., 0.],
[0., 1., 1.], [1., 0., 1.], [1., 1., 0.], [1., 1., 1.]])


class TestRBFParameters(TestCase):
def test_class_members_default_basis(self):
Expand Down