def rotate(data,
axis=(1., 0, 0),
angle=0.,
center=None,
mode="constant",
interpolation="linear"):
"""
rotates data around axis by a given angle
Parameters
----------
data: ndarray
3d array
axis: tuple
axis to rotate by angle about
axis = (x,y,z)
angle: float
center: tuple or None
origin of rotation (cz,cy,cx) in pixels
if None, center is the middle of data
mode: string
boundary mode, one of the following:
'constant'
pads with zeros
'edge'
pads with edge values
'wrap'
pads with the repeated version of the input
interpolation, string
interpolation mode, one of the following
'linear'
'nearest'
Returns
-------
res: ndarray
rotated array (same shape as input)
"""
if center is None:
center = tuple([s // 2 for s in data.shape])
cx, cy, cz = center
m = np.dot(
mat4_translate(cx, cy, cz),
np.dot(mat4_rotate(angle, *axis), mat4_translate(-cx, -cy, -cz)))
m = np.linalg.inv(m)
return affine(data, m, mode=mode, interpolation=interpolation)
def shift(data, shift=(0, 0, 0), mode="constant", interpolation="linear"):
"""
translates 3d data by given amount
Parameters
----------
data: ndarray
3d array
shift : float or sequence
The shift along the axes. If a float, `shift` is the same for each axis.
If a sequence, `shift` should contain one value for each axis.
mode: string
boundary mode, one of the following:
'constant'
pads with zeros
'edge'
pads with edge values
'wrap'
pads with the repeated version of the input
interpolation, string
interpolation mode, one of the following
'linear'
'nearest'
Returns
-------
res: ndarray
shifted array (same shape as input)
"""
if np.isscalar(shift):
shift = (shift, ) * 3
if len(shift) != 3:
raise ValueError("shift (%s) should be of length 3!")
shift = -np.array(shift)
return affine(data,
mat4_translate(*shift),
mode=mode,
interpolation=interpolation)
def translate(data, shift=(0, 0, 0), mode="constant", interpolation="linear"):
"""
translates 3d data by given amount
Parameters
----------
data: ndarray
3d array
shift: tuple, ndarray
the shift in pixels (dx,dy,dz)
mode: string
boundary mode, one of the following:
'constant'
pads with zeros
'edge'
pads with edge values
'wrap'
pads with the repeated version of the input
interpolation, string
interpolation mode, one of the following
'linear'
'nearest'
Returns
-------
res: ndarray
shifted array (same shape as input)
"""
if len(shift) != 3:
raise ValueError("shift (%s) should be of length 3!")
return affine(data,
mat4_translate(*shift),
mode=mode,
interpolation=interpolation)