def returnWedgeVolume(self, size, rotation=None):
"""Return the wedge volume in full size and zero in the center
@param size: size of wedge
@type size: C{list}
@param rotation: rotation (3-dim vector if Euler angles)
@type rotation: C{list}
@return: wedge volume
@rtype: Numpy array
"""
assert len(size) == 3, "returnWedgeVolume: size must be 3-dim list"
if self._volume is not None and np.array_equal(self._volume_shape,
size):
pass
else:
self._create_wedge_volume(size)
from pytom.tompy.transform import rotate3d, fourier_reduced2full, fftshift
isodd = self._volume_shape[2] % 2
wedge_vol = fftshift(fourier_reduced2full(self._volume, isodd))
if rotation is not None: # rotate the wedge first
assert len(rotation) == 3
wedge_vol = rotate3d(wedge_vol,
rotation[0],
rotation[1],
rotation[2],
order=1)
return wedge_vol
def apply(self, data, rotation=None):
"""
@param rotation: apply rotation to the wedge first
"""
# if no missing wedge
if self.start_ang == -90 and self.end_ang == 90:
return data
if self._volume is not None and np.array_equal(self._volume_shape,
data.shape):
pass
else:
self._create_wedge_volume(data.shape)
if rotation is not None: # rotate the wedge first
assert len(rotation) == 3
from pytom.tompy.transform import rotate3d, fourier_reduced2full, fourier_full2reduced, fftshift, ifftshift
isodd = self._volume_shape[2] % 2
filter_vol = fftshift(fourier_reduced2full(self._volume, isodd))
filter_vol = rotate3d(filter_vol,
rotation[0],
rotation[1],
rotation[2],
order=1) # linear interp!
filter_vol = fourier_full2reduced(ifftshift(filter_vol))
else:
filter_vol = self._volume
from pytom.tompy.transform import fourier_filter
res = fourier_filter(data, filter_vol, False)
return res
def applyTransforms(cls, volume, shifts, angles, axis=None):
import transform
npVol = transform.translate3d(volume, shifts[0], shifts[1], shifts[2])
volume = transform.rotate3d(npVol,
angles[0],
angles[1],
angles[2],
center=axis)
return volume
def apply(self, data, rotation=None):
if rotation is not None: # rotate the wedge first
assert len(rotation) == 3
from transform import rotate3d, fourier_full2reduced, ifftshift
filter_vol = rotate3d(self._whole_volume, rotation[0], rotation[1],
rotation[2])
filter_vol = fourier_full2reduced(ifftshift(filter_vol))
else:
filter_vol = self._volume
from transform import fourier_filter
res = fourier_filter(data, filter_vol, False)
return res