def load_spatial_image(filename):
img = load_image(filename)
in_coords = list(img.coordmap.function_domain.coord_names)
other_coords = filter(lambda x: x not in 'ijk', in_coords)
if other_coords:
idata = np.asanyarray(img)
cm_3d = copy(img.coordmap)
while other_coords:
c = other_coords.pop()
slicing = [slice(None)] * idata.ndim
slicing[in_coords.index(c)] = 0
idata = idata[slicing]
cm_3d = ni_api.drop_io_dim(cm_3d, c)
img = ni_api.Image(idata.copy(), cm_3d)
del idata
return img
def slice_timewise(img, t):
"""Utility function to slice a 4D image timewise. Naturally, the
image is assumed to be 4 dimensional, with a 5x5 affine.
Parameters
----------
img : NIPY Image
t : int
time index
Returns
-------
a 3D image, whose affine has only spatial coordinates in its range
"""
if len(img.shape) != 4 or img.affine.shape != (5,5):
raise ValueError('This is not a 4D image')
t_ax = timedim(img)
slicing = [ slice(None) ] * 4
slicing[t_ax] = t
cm_3d = ni_api.drop_io_dim(img.coordmap, 't')
return ni_api.Image(np.asarray(img)[slicing], cm_3d)
