def angle_axis2euler(theta, vector, is_normalized=False):
"""
Convert angle, axis pair to Euler angles
Parameters
----------
theta : scalar
angle of rotation
vector : 3 element sequence
vector specifying axis for rotation.
is_normalized : bool, optional
True if vector is already normalized (has norm of 1). Default
False
Returns
-------
z : scalar
y : scalar
x : scalar
Rotations in radians around z, y, x axes, respectively
Examples
--------
>>> z, y, x = angle_axis2euler(0, [1, 0, 0])
>>> np.allclose((z, y, x), 0)
True
Notes
-----
It's possible to reduce the amount of calculation a little, by
combining parts of the ``angle_axis2mat`` and ``mat2euler``
functions, but the reduction in computation is small, and the code
repetition is large.
"""
# Delayed import to avoid cyclic dependencies
import nibabel.quaternions as nq
M = nq.angle_axis2mat(theta, vector, is_normalized)
return mat2euler(M)
def transformEuler(eul1,rot_type,rot):
mat1 = euler2mat(*eul1)
if rot_type == "angle_axis":
ang1,ax1 = rot
tmat1 = angle_axis2mat(ax1,ang1)
elif rot_type == "mat":
tmat1 = rot
elif rot_type == "euler":
eul1 = rot
tmat1 = euler2mat(*eul1)
elif rot_type == "towards":
targ_vec1,ang1 = rot
cur_vec1 = euler2mat(*eul1)[:,0]
ax_rot1 = cross(cur_vec1,targ_vec1)
tmat1 = angle_axis2mat(ang1,ax_rot1)
else: raise Exception("rotation type %s not understood"%rot_type)
mat1new = dot(tmat1,mat1)
return mat2euler(mat1new)
def minRot(ax1, ax2):
"find the rotation matrix that takes ax1 to ax2"
if almostEq(ax1, ax2):
L.debug("minRot: same vector")
return eye(3)
elif almostEq(ax1, -ax2):
L.debug("minRot: opp vector")
return -diag([-1, -1, 0])
else:
ax_rot = cross(ax2, ax1)
return angle_axis2mat(angBetween(ax1, ax2), ax_rot)
def transformEuler(eul1, rot_type, rot):
mat1 = euler2mat(*eul1)
if rot_type == "angle_axis":
ang1, ax1 = rot
tmat1 = angle_axis2mat(ax1, ang1)
elif rot_type == "mat":
tmat1 = rot
elif rot_type == "euler":
eul1 = rot
tmat1 = euler2mat(*eul1)
elif rot_type == "towards":
targ_vec1, ang1 = rot
cur_vec1 = euler2mat(*eul1)[:, 0]
ax_rot1 = cross(cur_vec1, targ_vec1)
tmat1 = angle_axis2mat(ang1, ax_rot1)
else:
raise Exception("rotation type %s not understood" % rot_type)
mat1new = dot(tmat1, mat1)
return mat2euler(mat1new)
def minRot(ax1,ax2):
"find the rotation matrix that takes ax1 to ax2"
if almostEq(ax1,ax2):
L.debug("minRot: same vector")
return eye(3)
elif almostEq(ax1,-ax2):
L.debug("minRot: opp vector")
return -diag([-1,-1,0])
else:
ax_rot = cross(ax2,ax1)
return angle_axis2mat(angBetween(ax1,ax2),ax_rot)
def create_transform(table, slice, row):
""" Iterates through the motion data table and generates transformation matrices
Args:
param1: motion_trajectory_data (numpy array)
param2: slice number
param3: row number (k-space line)
Returns:
transformation object corresponding to a 4x4 transformation matrix
"""
shift = table[slice, row, 0]
angle = (table[slice, row, 1])
axis = table[slice, row, 2]
rot_matrix = quaternions.angle_axis2mat(angle, axis)
affine_transform = affine_translate(sitk.AffineTransform(3), shift[0],
shift[1], shift[2])
combined_transform = affine_rotate(affine_transform, rot_matrix)
return combined_transform
def angle_axis2euler(theta, vector, is_normalized=False):
""" Convert angle, axis pair to Euler angles
Parameters
----------
theta : scalar
angle of rotation
vector : 3 element sequence
vector specifying axis for rotation.
is_normalized : bool, optional
True if vector is already normalized (has norm of 1). Default
False
Returns
-------
z : scalar
y : scalar
x : scalar
Rotations in radians around z, y, x axes, respectively
Examples
--------
>>> z, y, x = angle_axis2euler(0, [1, 0, 0])
>>> np.allclose((z, y, x), 0)
True
Notes
-----
It's possible to reduce the amount of calculation a little, by
combining parts of the ``angle_axis2mat`` and ``mat2euler``
functions, but the reduction in computation is small, and the code
repetition is large.
"""
# delayed import to avoid cyclic dependencies
import nibabel.quaternions as nq
M = nq.angle_axis2mat(theta, vector, is_normalized)
return mat2euler(M)
def applyRotEul(eul, ang, ax):
return mat2euler(dot(angle_axis2mat(-ang, ax), euler2mat(*eul)))
def applyRotVec(x, ang, ax, origin):
return dot(angle_axis2mat(ang, ax), x - origin[:, None]) + origin[:, None]
def applyTwist(thread, twist1, twist2):
"twist the ends"
_, or1, _, or2 = getState(thread)
thread.applyMotion(zeros(3), angle_axis2mat(twist1, or1), zeros(3),
angle_axis2mat(twist2, or2))
def applyRotEul(eul,ang,ax):
return mat2euler(dot(angle_axis2mat(-ang,ax),euler2mat(*eul)))
def applyRotVec(x,ang,ax,origin):
"rotate a vector x by ang around axis defined by ray origin+ax"
return dot(angle_axis2mat(ang,ax),x-origin[:,None])+origin[:,None]
def applyRotEul(eul,ang,ax):
"compose a rotation of ang around ax with rotation given by euler angles eul"
return mat2euler(dot(angle_axis2mat(ang,ax),euler2mat(*eul)))
import mayavi.mlab as mlab
import numpy as np
from nibabel.quaternions import angle_axis2mat
x, y, z = xyz = np.load("xyz.npy")
# orig line
mlab.clf()
mlab.plot3d(x, y, z, color=(1, 0, 0), tube_radius=.1)
# fit quads to both ends
tri_inds = [0, 1, 2]
theta = .5
p0, p1, p2 = (xyz[:, i] for i in tri_inds)
ax_normal = np.cross(p1 - p0, p2 - p0)
ax_tan = p1 - p0
ax_rot = np.dot(angle_axis2mat(theta, ax_normal), ax_tan)
t = np.linspace(-2, 2, 30)
for ax in ax_normal, ax_tan, ax_rot:
x, y, z = p0[:, None] + ax[:, None] * t[None, :]
mlab.plot3d(x, y, z, color=(0, 1, 0), tube_radius=.1)
def applyTwist(thread,twist1,twist2):
"twist the ends"
_,or1,_,or2 = getState(thread)
thread.applyMotion(zeros(3),angle_axis2mat(twist1,or1),zeros(3),angle_axis2mat(twist2,or2))
import mayavi.mlab as mlab
import numpy as np
from nibabel.quaternions import angle_axis2mat
x,y,z = xyz = np.load("xyz.npy")
# orig line
mlab.clf()
mlab.plot3d(x,y,z,color=(1,0,0),tube_radius=.1)
# fit quads to both ends
tri_inds = [0,1,2]
theta = .5
p0,p1,p2 = (xyz[:,i] for i in tri_inds)
ax_normal = np.cross(p1-p0,p2-p0)
ax_tan = p1 - p0
ax_rot = np.dot(angle_axis2mat(theta,ax_normal),ax_tan)
t = np.linspace(-2,2,30)
for ax in ax_normal,ax_tan,ax_rot:
x,y,z = p0[:,None] + ax[:,None]*t[None,:]
mlab.plot3d(x,y,z,color=(0,1,0),tube_radius=.1)
def applyRotVec(x,ang,ax,origin):
return dot(angle_axis2mat(ang,ax),x-origin[:,None])+origin[:,None]