def get_align_angles(img, axes="zyx"):
"""
Returns the angles needed to rotate an image to align it with the specified axes
:param img: A CZYX image as a 4d numpy array. The image that will be measured to get the
alignment angles. The image will not be altered by this function
:param axes: string, that must be an arrangement of 'xyz'
The major axis will be aligned with the first one, the minor with the last one.
'zyx' by default
:return: A list of tuple pairs, containing the axis indices and angles to rotate along the paired
axis. Meant to be passed into align_major
"""
if getattr(img, 'ndim', 0) < 3:
raise ValueError('img must be at least a 3d numpy array')
axis_map = {'x': 0, 'y': 1, 'z': 2}
if not isinstance(axes, str) or len(axes) != 3 or not all(a in axis_map for a in axes):
raise ValueError("axes must be an arrangement of 'xyz'")
# axes parameter string turned into a list of indices
axis_list = [axis_map[a] for a in axes]
maj_axis_i = axis_list[0]
# unit vectors for x, y, and z axis
axis_vectors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# slices for selecting yz, xz, and xy components from vectors
slices = (slice(1, 3), slice(0, 3, 2), slice(0, 2))
# index of the major axis (0, 1, or 2)
maj_axis = axis_vectors[axis_list[0]]
min_axis = axis_vectors[axis_list[-1]]
img_maj_axis, img_min_axis = get_major_minor_axis(img)
angles = []
for a in range(3):
if a != maj_axis_i:
# rotate around other two axis (e.g if aligning major to Z axis, rotate around Y and X to get there)
angle = angle_between(maj_axis[slices[a]], img_maj_axis[slices[a]])
angles.append([a, -angle])
img_maj_axis = np.dot(_get_rotation_matrix(a, angle), img_maj_axis)
img_min_axis = np.dot(_get_rotation_matrix(a, angle), img_min_axis)
# final rotation goes around major axis to align the minor axis properly
# has to be done last
angles.append([maj_axis_i, angle_between(min_axis[slices[maj_axis_i]], img_min_axis[slices[maj_axis_i]])])
return angles
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