def ni_affine_pixdim_from_affine(affine_transform, strict=False):
"""
Given a square affine_transform,
return a new 3-dimensional AffineTransform
and the pixel dimensions in dimensions
greater than 3.
If strict is True, then an exception is raised if
the affine matrix is not diagonal with
positive entries in dimensions
greater than 3.
If strict is True, then the names of the range coordinates
must be LPS:('x+LR','y+PA','z+SI') or RAS:('x+RL','y+AP','z+SI'). If strict is False, and the names
are not either of these, LPS:('x+LR','y+PA','z+SI') are used.
If the names are RAS:('x+RL','y+AA','z+SI'), then the affine is flipped
so the result is in LPS:('x+LR','y+PA','z+SI').
NIFTI images have the first 3 dimensions as spatial, and the
remaining as non-spatial, with the 4th typically being time.
Parameters
----------
affine_transform : `AffineTransform`
Returns
-------
nifti_transform: `AffineTransform`
A 3-dimensional or less AffineTransform
pixdim : ndarray(np.float)
The pixel dimensions greater than 3.
>>> outnames = CS(('x+LR','y+PA','z+SI') + ('t',))
>>> innames = CS(['phase', 'j', 'frequency', 't'])
>>> af_tr = AT(outnames, innames, np.diag([2,-2,3,3.5,1]))
>>> print af_tr
AffineTransform(
function_domain=CoordinateSystem(coord_names=('x+LR', 'y+PA', 'z+SI', 't'), name='', coord_dtype=float64),
function_range=CoordinateSystem(coord_names=('phase', 'j', 'frequency', 't'), name='', coord_dtype=float64),
affine=array([[ 2. , 0. , 0. , 0. , 0. ],
[ 0. , -2. , 0. , 0. , 0. ],
[ 0. , 0. , 3. , 0. , 0. ],
[ 0. , 0. , 0. , 3.5, 0. ],
[ 0. , 0. , 0. , 0. , 1. ]])
)
>>> af_tr3dorless, p = ni_affine_pixdim_from_affine(af_tr)
>>> print af_tr3dorless
AffineTransform(
function_domain=CoordinateSystem(coord_names=('x+LR', 'y+PA', 'z+SI'), name='', coord_dtype=float64),
function_range=CoordinateSystem(coord_names=('x+LR', 'y+PA', 'z+SI'), name='', coord_dtype=float64),
affine=array([[ 2., 0., 0., 0.],
[ 0., -2., 0., 0.],
[ 0., 0., 3., 0.],
[ 0., 0., 0., 1.]])
)
>>> print p
[ 3.5]
"""
if ((not isinstance(affine_transform, AT)) or
(affine_transform.ndims[0] != affine_transform.ndims[1])):
raise ValueError('affine_transform must be a square AffineTransform' +
' to save as a NIFTI file')
ndim = affine_transform.ndims[0]
ndim3 = min(ndim, 3)
range_names = affine_transform.function_range.coord_names
if range_names[:ndim3] not in [lps_output_coordnames[:ndim3],
ras_output_coordnames[:ndim3]]:
if strict:
raise ValueError('strict is true and the range is not LPS or RAS, assuming LPS')
warnings.warn('range is not LPS or RAS, assuming LPS')
range_names = list(range_names)
range_names[:ndim3] = lps_output_coordnames[:ndim3]
range_names = tuple(range_names)
ndim = affine_transform.ndims[0]
nifti_indim = 'ijk'[:ndim] + 'tuvw'[ndim3:ndim]
nifti_outdim = range_names[:ndim3] + \
('t', 'u', 'v', 'w' )[ndim3:ndim]
nifti_transform = AT(CS(nifti_indim),
CS(nifti_outdim),
affine_transform.affine)
domain_names = affine_transform.function_domain.coord_names[:ndim3]
nifti_transform = nifti_transform.renamed_domain(dict(zip('ijk'[:ndim3],
domain_names)))
# now find the pixdims
A = nifti_transform.affine[3:,3:]
if (not np.allclose(np.diag(np.diag(A)), A)
or not np.all(np.diag(A) > 0)):
msg = "affine transformation matrix is not diagonal " + \
" with positive entries on diagonal, some information lost"
if strict:
raise ValueError('strict is true and %s' % msg)
warnings.warn(msg)
pixdim = np.fabs(np.diag(A)[:-1])
# find the 4x4 (or smaller)
A3d = np.identity(ndim3+1)
A3d[:ndim3,:ndim3] = nifti_transform.affine[:ndim3, :ndim3]
A3d[:ndim3,-1] = nifti_transform.affine[:ndim3, -1]
range_names = nifti_transform.function_range.coord_names[:ndim3]
nifti_3dorless_transform = AT(CS(domain_names),
CS(range_names),
A3d)
# if RAS, we flip, with a warning
if range_names[:ndim3] == ras_output_coordnames[:ndim3]:
signs = [-1,-1,1,1][:(ndim3+1)]
# silly, but 1d case is handled for consistency
if signs == [-1,-1]:
signs = [-1,1]
ras_to_lps = AT(CS(ras_output_coordnames[:ndim3]),
CS(lps_output_coordnames[:ndim3]),
np.diag(signs))
warnings.warn('affine_transform has RAS output_range, flipping to LPS')
nifti_3dorless_transform = compose(ras_to_lps, nifti_3dorless_transform)
return nifti_3dorless_transform, pixdim
