def _run_interface(self, runtime):
transforms = []
invert_transform_flags = []
if isdefined(self.inputs.transform_1):
transforms.append(self.inputs.transform_1)
invert_transform_flags.append(self.inputs.invert_1)
if isdefined(self.inputs.transform_2):
transforms.append(self.inputs.transform_2)
invert_transform_flags.append(self.inputs.invert_2)
if isdefined(self.inputs.transform_3):
transforms.append(self.inputs.transform_3)
invert_transform_flags.append(self.inputs.invert_3)
#output file
split = splitext(os.path.basename(self.inputs.input_image))
self.inputs.output_image = os.getcwd() + os.sep + split[0] + split[1]
if '_space-' in self.inputs.output_image:
self.inputs.output_image = re.sub(
'_space-[A-z]*_', "_space-" + self.inputs.target_space + "_",
self.inputs.output_image)
#combine transformation files and output flags
transforms_zip = zip(transforms, invert_transform_flags)
transform_string = ' '.join([
'-t [ ' + str(t) + ' , ' + str(int(f)) + ' ]'
for t, f in transforms_zip if t != None
])
cmdline = "antsApplyTransforms --float -v 1 -e 3 -d 3 -n " + self.inputs.interpolation + " -i " + self.inputs.input_image + " " + transform_string + " -r " + self.inputs.reference_image + " -o " + self.inputs.output_image
cmd(cmdline)
return runtime
def _run_interface(self, runtime):
normalization_type = self.inputs.normalization_type
#Setup ANTs command line arguments
if isdefined(self.inputs.user_ants_command):
cmdline, self.inputs.normalization_type = self.read_user_command_line(
)
self._set_outputs()
cmdline = self.replace_user_command_line(cmdline)
else:
self._set_outputs()
cmdline = self.default_command_line()
print(self.inputs)
#Run antsRegistration on command line
print("Ants command line:\n", cmdline)
p = cmd(cmdline)
if self.inputs.normalization_type in ['rigid', 'affine']:
#Convert linear transforms from .mat to .txt. antsRegistration produces .mat file based on output
#prefix, but this format seems to be harder to work with / lead to downstream errors
#If linear transform, then have to apply transformations to input image
self.apply_linear_transforms()
if isdefined(self.inputs.rotation_error) or isdefined(
self.inputs.translation_error):
if self.inputs.rotation_error != [
0, 0, 0
] and self.inputs.translation_error != [0, 0, 0]:
print('Warning: Applying misalignment')
print("\tRotation:", self.inputs.rotation_error)
print("\tTranslation:", self.inputs.translation_error)
exit(1)
self.apply_misalignment()
return runtime
def _run_interface(self, runtime):
#Get extension for input transformation files
ext_1 = splitext(self.inputs.transform_1)[1]
ext_2 = splitext(self.inputs.transform_2)[1]
if ext_1 in ['.mat', '.txt'] and ext_2 in ['.mat', '.txt']:
self.inputs.out_file = os.getcwd(
) + os.sep + 'composite_affine.mat'
elif ext_1 == '.h5' or ext_2 == '.h5':
self.inputs.out_file = os.getcwd() + os.sep + 'composite_warp.h5'
cmd("CompositeTransformUtil --assemble " + ' '.join([
self.inputs.out_file, self.inputs.transform_1,
self.inputs.transform_2
]))
return runtime
def apply_linear_transforms(self):
#Command line to
if not os.path.exists(self.inputs.warped_image):
cmdline = "antsApplyTransforms -e 3 -d 3 -n Linear -i " + self.inputs.moving_image + " -t " + self.inputs.out_matrix + " -r " + self.inputs.fixed_image + " -o " + self.inputs.warped_image
print(cmdline)
cmd(cmdline)
if not os.path.exists(self.inputs.out_matrix_inverse):
cmdline = "antsApplyTransforms -e 3 -d 3 -n Linear -i " + self.inputs.moving_image + " -t " + self.inputs.out_matrix + " -r " + self.inputs.fixed_image + " -o Linear[" + self.inputs.out_matrix_inverse + ",1]"
print(cmdline)
cmd(cmdline)
def mat2txt(self, ii_fn, oo_fn):
print(ii_fn, oo_fn)
tfm = sitk.ReadTransform(ii_fn)
sitk.WriteTransform(tfm, oo_fn)
return 0
def _run_interface(self, runtime):
quantNode = self._quantCommand()
quantNode.inputs = self.inputs
init_command = quantNode.cmdline
modified_command = []
self.inputs.out_file = quantNode.inputs.out_file
for f in init_command.split(' '):
if os.path.exists(f):
f = check_gz(f)
elif f == quantNode.inputs.out_file and splitext(
f)[1] == '.nii.gz':
f = splitext(f)[0] + '.nii'
self.inputs.out_file = f
modified_command.append(f)
print(modified_command)
command = ' '.join(modified_command)
print(command)
cmd(command)
print("Out file", self.inputs.out_file)
return runtime
def apply_misalignment(self):
com = center_of_mass(nib.load(self.inputs.fixed_image).get_data())
img = nib.load(self.inputs.fixed_image)
com_world = [
img.affine[0, 3] + com[0] * img.affine[0, 2],
img.affine[1, 3] + com[1] * img.affine[1, 1],
img.affine[2, 3] + com[2] * img.affine[2, 0]
]
tfm = sitk.VersorRigid3DTransform()
rotations_radians = list(np.pi * np.array(self.inputs.rotation_error) /
180.)
tfm.SetParameters(rotations_radians + self.inputs.translation_error)
tfm.SetFixedParameters(com_world)
print('Center of Mass :', com_world)
print(tfm.GetParameters())
print(tfm.GetFixedParameters())
misalign_matrix = os.getcwd(
) + os.sep + 'misalignment_rot_x-{}_y-{}_z-{}_trans_x-{}_y-{}_z-{}.tfm'.format(
*self.inputs.rotation_error, *self.inputs.translation_error)
sitk.WriteTransform(tfm, misalign_matrix)
print('Warning: misaligning PET to MRI alignment using file',
misalign_matrix)
cmdline = "antsApplyTransforms -e 3 -d 3 -n Linear -i " + self.inputs.moving_image + " -t " + misalign_matrix + " " + self.inputs.out_matrix + " -r " + self.inputs.fixed_image + " -o Linear[" + self.inputs.out_matrix + ",0]"
print(cmdline)
cmd(cmdline)
cmdline = "antsApplyTransforms -e 3 -d 3 -n Linear -i " + self.inputs.moving_image + " -t " + misalign_matrix + " " + self.inputs.out_matrix + " -r " + self.inputs.fixed_image + " -o Linear[" + self.inputs.out_matrix_inverse + ",1]"
print(cmdline)
cmd(cmdline)
cmdline = "antsApplyTransforms -e 3 -d 3 -n Linear -i " + self.inputs.moving_image + " -t " + self.inputs.out_matrix + " -r " + self.inputs.fixed_image + " -o " + self.inputs.warped_image
print(cmdline)
cmd(cmdline)
cmdline = "antsApplyTransforms -e 3 -d 3 -n Linear -i " + self.inputs.fixed_image + " -t " + self.inputs.out_matrix_inverse + " -r " + self.inputs.moving_image + " -o " + self.inputs.inverse_warped_image
print(cmdline)
cmd(cmdline)