diff --git a/navipy/trajectories/test_markers.py b/navipy/trajectories/test_markers.py
index 811bd6850a11a6ab82031dfb68f2843fb53ba1a7..abe4e1bef9e2fd928635ddc702b1cacdff852c0e 100644
--- a/navipy/trajectories/test_markers.py
+++ b/navipy/trajectories/test_markers.py
@@ -38,16 +38,16 @@ class TestMarkersTransform(unittest.TestCase):
mode=cmode)
np.testing.assert_allclose(origin, [0, 0, 0],
atol=1e-07,
- err_msg='origin&mode '+cmode)
+ err_msg='origin&mode ' + cmode)
np.testing.assert_allclose(x_axis, [1, 0, 0],
atol=1e-07,
- err_msg='x-axis&mode '+cmode)
+ err_msg='x-axis&mode ' + cmode)
np.testing.assert_allclose(y_axis, [0, 1, 0],
atol=1e-07,
- err_msg='y-axis&mode '+cmode)
+ err_msg='y-axis&mode ' + cmode)
np.testing.assert_allclose(z_axis, [0, 0, 1],
atol=1e-07,
- err_msg='z-axis&mode '+cmode)
+ err_msg='z-axis&mode ' + cmode)
def test_triangle2bodyaxis_wrongmode(self):
"""Certain mode are not supported"""
@@ -98,16 +98,15 @@ class TestMarkersTransform(unittest.TestCase):
np.testing.assert_almost_equal(perspective, [0, 0, 0, 1])
def test_twomarker2euler(self):
- angles = np.pi*(np.random.rand(3) - 0.5)
+ angles = np.pi * (np.random.rand(3) - 0.5)
angles[0] *= 2
# angle[1] is not multipliy because in range [-pi/2,pi/2]
angles[2] *= 2
mark0 = pd.Series(data=0, index=['x', 'y', 'z'])
for axis_alignement, euler_axes, known_angle in zip(
['x-axis', 'z-axis', 'y-axis'],
- ['rzyx', 'ryxz', 'rzxy'],
+ ['szyx', 'syxz', 'szxy'],
[angles[2], angles[2], angles[2]]):
-
triangle_mode = 'x-axis=median-from-0'
transform = compose_matrix(angles=angles,
axes=euler_axes)
diff --git a/navipy/trajectories/transformations.py b/navipy/trajectories/transformations.py
index bd594235036b9a995a234f7b548142608e1dabaf..9fcb6946ed4a6becaf340016d1c70bb5716492cb 100644
--- a/navipy/trajectories/transformations.py
+++ b/navipy/trajectories/transformations.py
@@ -8,14 +8,14 @@ from scipy.optimize import minimize
_modes = []
for axel in ['x-axis', 'y-axis', 'z-axis']:
for marker in range(3):
- _modes.append(axel+'=median-from-{}'.format(marker))
+ _modes.append(axel + '=median-from-{}'.format(marker))
for axel in ['x-axis', 'y-axis', 'z-axis']:
for marki in range(3):
for markj in range(3):
if marki == markj:
continue
- _modes.append(axel+'={}-{}'.format(marki, markj))
+ _modes.append(axel + '={}-{}'.format(marki, markj))
def determine_mode(mode):
@@ -34,7 +34,7 @@ def determine_mode(mode):
method = 'aligned-with'
elif len(cmode) == 3:
apexes = int(cmode[-1])
- method = cmode[0]+'-'+cmode[1]
+ method = cmode[0] + '-' + cmode[1]
return axel, apexes, method
@@ -44,7 +44,7 @@ def normalise_vec(vec):
if np.linalg.norm(vec) > 0:
vec = vec / np.linalg.norm(vec)
else:
- vec = vec*np.nan
+ vec = vec * np.nan
return vec
@@ -231,36 +231,36 @@ rotation convention.
The temporary rotation convention used two determine the euler angles are:
- * rzyx, for axis alignment x-axis
- * rzxy, for axis alignment y-axis
- * ryxz, for axis alignment z-axis
+ * szyx, for axis alignment x-axis
+ * szxy, for axis alignment y-axis
+ * syxz, for axis alignment z-axis
Note: If you know the angle in your rotation convention, then you \
can run this function through a minimisation procedure with free parameter \
known angle until you get the desired orientation (see twomarkers2euler)
"""
- vector = mark1-mark0
+ vector = mark1 - mark0
vector = normalise_vec(vector)
if axis_alignement == 'x-axis':
- axes_convention = 'rzyx'
- beta = np.arcsin(-vector.z)
- alpha = np.arctan2(vector.y/np.cos(beta),
- vector.x/np.cos(beta))
+ axes_convention = 'szyx'
+ beta = np.arcsin(vector.z)
+ alpha = np.arctan2(-vector.y / np.cos(beta),
+ vector.x / np.cos(beta))
gamma = known_angle
angles = [alpha, beta, gamma]
elif axis_alignement == 'y-axis':
- axes_convention = 'rzxy'
- gamma = np.arcsin(vector.z)
- alpha = np.arctan2(-vector.x/np.cos(gamma),
- vector.y/np.cos(gamma))
+ axes_convention = 'szxy'
+ gamma = np.arcsin(-vector.z)
+ alpha = np.arctan2(vector.x / np.cos(gamma),
+ vector.y / np.cos(gamma))
beta = known_angle
angles = [alpha, gamma, beta]
elif axis_alignement == 'z-axis':
- axes_convention = 'ryxz'
- gamma = np.arcsin(-vector.y)
- beta = np.arctan2(vector.x/np.cos(gamma),
- vector.z/np.cos(gamma))
+ axes_convention = 'syxz'
+ gamma = np.arcsin(vector.y)
+ beta = np.arctan2(-vector.x / np.cos(gamma),
+ vector.z / np.cos(gamma))
alpha = known_angle
angles = [beta, gamma, alpha]
else:
@@ -278,7 +278,7 @@ def twomarkers2euler_score(x, mark0, mark1,
This function is used by twomarkers2euler within the minimisation of scipy
"""
angles, axes_convention = twomarkers2euler_easy_euleraxes(
- mark0, mark1, axis_alignement, x)
+ mark0, mark1, axis_alignement, x[0])
matrix = ht.compose_matrix(
angles=angles, axes=axes_convention)
_, _, angles, _, _ = ht.decompose_matrix(matrix, axes=euler_axes)
@@ -299,19 +299,19 @@ def twomarkers2euler(mark0, mark1, axis_alignement,
raise KeyError(
'Axis aligment {} is not supported'.format(
axis_alignement))
- known_angles = np.nan*np.zeros(3)
+ known_angles = np.nan * np.zeros(3)
# Find the first rotation axis
index = euler_axes.find(axis_alignement[0])
if index < 1:
raise KeyError(
'Axis aligment {} can not work with euler_axes {}'.format(
axis_alignement, euler_axes))
- known_angles[index-1] = known_angle
+ known_angles[index - 1] = known_angle
args = (mark0, mark1, axis_alignement, known_angles, euler_axes)
res = minimize(twomarkers2euler_score, x0=known_angle, args=args,
method=method, tol=tol)
angles, axes_convention = twomarkers2euler_easy_euleraxes(
- mark0, mark1, axis_alignement, res.x)
+ mark0, mark1, axis_alignement, res.x[0])
# Build rotation matrix and decompse
matrix = ht.compose_matrix(
angles=angles, axes=axes_convention)