def field_conversion_method(field_image, image=None,
get_position_field=True):
data = np.zeros_like(field_image.data, dtype=np.float32)
# Matrix to go from voxel to world space
if image is not None:
voxel_2_xyz = image.voxel_2_mm
vol_ext = image.vol_ext
field = Image.from_data(data, image.get_header())
else:
voxel_2_xyz = field_image.voxel_2_mm
vol_ext = field_image.vol_ext
field = Image.from_data(data, field_image.get_header())
voxels = np.mgrid[[slice(i) for i in vol_ext]]
voxels = [d.reshape(vol_ext, order='F') for d in voxels]
mms = [voxel_2_xyz[i][3] + sum(voxel_2_xyz[i][k] * voxels[k]
for k in range(len(voxels)))
for i in range(len(voxel_2_xyz) - (4 - len(vol_ext)))]
input_data = np.squeeze(field_image.data)
field_data = np.squeeze(data)
mms = np.squeeze(mms)
if get_position_field:
for i in range(data.shape[-1]):
# Output is the deformation/position field
field_data[..., i] = input_data[..., i] + mms[i]
else:
for i in range(data.shape[-1]):
# Output is the displacement field
field_data[..., i] = input_data[..., i] - mms[i]
return field
def initialise_field(im, affine=None):
"""
Create a field image from the specified target image.
Sets the data to 0.
Parameters:
-----------
:param im: The target image. Mandatory.
:param affine: The initial affine transformation
:return: Return the created field object
"""
vol_ext = im.vol_ext
dims = list()
dims.extend(vol_ext)
while len(dims) < 4:
dims.extend([1])
dims.extend([len(vol_ext)])
# Inititalise with zero
data = np.zeros(dims, dtype=np.float32)
field = Image.from_data(data, im.get_header())
# We have supplied an affine transformation
if affine is not None:
if affine.shape != (4, 4):
raise RegError('Input affine transformation '
'should be a 4x4 matrix.')
# The updated transformation
transform = affine * im.voxel_2_mm
field.update_transformation(transform)
return field
def initialise_jacobian_field(im, affine=None):
"""
Create a jacobian field image from the specified target image/field.
Sets the data to 0.
Parameters:
-----------
:param im: The target image/field. Mandatory.
:param affine: The initial affine transformation
:return: Return the created jacobian field object. Each jacobian is stored in a vector of size 9 in row major order
"""
vol_ext = np.array(im.vol_ext)
dims = list()
dims.extend(vol_ext)
while len(dims) < 4:
dims.extend([1])
num_dims = len(vol_ext[vol_ext>1])
dims.extend([num_dims**2])
# Inititalise with zero
data = np.zeros(dims, dtype=np.float32)
jacfield = Image.from_data(data, im.get_header())
jacfield.set_matrix_data_attributes(num_dims, num_dims)
# We have supplied an affine transformation
if affine is not None:
if affine.shape != (4, 4):
raise RegError('Input affine transformation '
'should be a 4x4 matrix.')
# The updated transformation
transform = affine * im.voxel_2_mm
jacfield.update_transformation(transform)
return jacfield
def exponentiate(self):
"""
Compute the exponential of this velocity field using the
scaling and squaring approach.
The velocity field is in the tangent space of the manifold and the
displacement field is the actual manifold and the transformation
between the velocity field and the displacement field is given by
the exponential chart.
:param disp_image: Displacement field image that will be
updated with the exponentiated velocity field.
"""
self.__do_init_check()
data = self.field.data
result_data = np.zeros(self.field.data.shape)
result = Image.from_data(result_data, self.field.get_header())
# Important: Need to specify which axes to use
norm = np.linalg.norm(data, axis=data.ndim-1)
max_norm = np.max(norm[:])
if max_norm < 0:
raise ValueError('Maximum norm is invalid.')
if max_norm == 0:
return result
pix_dims = np.asarray(self.field.zooms)
# ignore NULL dimensions
min_size = np.min(pix_dims[pix_dims > 0])
num_steps = max(0,np.ceil(np.log2(max_norm / (min_size / 2))).astype('int'))
# Approximate the initial exponential
init = 1 << num_steps
result.data = data / init
dfc = DisplacementFieldComposer()
# Do the squaring step to perform the integration
# The exponential is num_steps times recursive composition of
# the field with itself, which is equivalant to integration over
# the unit interval.
for _ in range(0, num_steps):
result = dfc.compose(result, result)
return result