def _compose_transforms(transformDirectory, invert=False):
"""Strings together transofrm files in the correct order to apply a transform.
"""
transforms = []
if not invert:
if '1Warp.nii.gz' in os.listdir(transformDirectory):
SyN_file = os.path.join(transformDirectory, '1Warp.nii.gz')
field = ants.image_read(SyN_file)
transform = ants.transform_from_displacement_field(field)
if transform is None: # Adds compatibility with ANTsPy 2.0+
transform = _transform_from_displacement_field(field)
transforms.append(transform)
if '0GenericAffine.mat' in os.listdir(transformDirectory):
affine_file = os.path.join(transformDirectory,
'0GenericAffine.mat')
transforms.append(ants.read_transform(affine_file))
else:
if '0GenericAffine.mat' in os.listdir(transformDirectory):
affine_file = os.path.join(transformDirectory,
'0GenericAffine.mat')
transforms.append(ants.read_transform(affine_file).invert())
if '1InverseWarp.nii.gz' in os.listdir(transformDirectory):
inv_file = os.path.join(transformDirectory, '1InverseWarp.nii.gz')
field = ants.image_read(inv_file)
transform = ants.transform_from_displacement_field(field)
if transform is None: # Adds compatibility with ANTsPy 2.0+
transform = _transform_from_displacement_field(field)
transforms.append(transform)
return ants.compose_ants_transforms(transforms)
def test_read_write_transform(self):
for tx in self.txs:
filename = mktemp(suffix='.mat')
ants.write_transform(tx, filename)
tx2 = ants.read_transform(filename)
# file doesnt exist
with self.assertRaises(Exception):
ants.read_transform('blah-blah.mat')
def planewise_affine(fixed, moving, return_transforms=False):
zshift = get_zshift(fixed, moving)
fixed = to_numpy(fixed)
moving = to_numpy(moving)
size_z = fixed.shape[0]
warped = np.zeros_like(fixed)
transforms = [None]*size_z
for z in prog_percent(list(range(max((0, -zshift)), min((size_z, -zshift + size_z))))):
mov = ants.from_numpy(moving[z + zshift].swapaxes(0, 1))
fix = ants.from_numpy(fixed[z].swapaxes(0, 1))
res = ants.registration(mov, fix,
type_of_transform='Affine',
reg_iterations=[500, 500, 500],
grad_step=.1,
verbose=True)
t = ants.read_transform(res['fwdtransforms'][0])
transforms[z] = t
trans = ants.apply_ants_transform_to_image(t, mov, fix)
warped[z] = trans.numpy().swapaxes(0, 1)
if return_transforms:
return warped, (transforms, zshift)
return warped
def motion_correction(brain_master,
brain_slave,
motcorr_directory,
printlog,
meanbrain,
suffix=''):
motCorr_brain_master = []
motCorr_brain_slave = []
durations = []
transform_matrix = []
for i in range(np.shape(brain_master)[-1]):
#printlog('Aligning brain volume {}'.format(i))
t0 = time()
#First, align given master volume to master meanbrain
with stderr_redirected(): # to prevent dumb itk gaussian error bullshit infinite printing
# note meanbrain is already an ants object
motCorr_vol = ants.registration(meanbrain, ants.from_numpy(brain_master[:,:,:,i]), type_of_transform='SyN')
motCorr_brain_master.append(motCorr_vol['warpedmovout'].numpy())
transformlist = motCorr_vol['fwdtransforms']
#Use warp parameters on slave volume if provided
if brain_slave:
motCorr_brain_slave.append(ants.apply_transforms(meanbrain,ants.from_numpy(brain_slave[:,:,:,i]),transformlist).numpy())
#Lets immediately grab the transform file because otherwise I think it is auto deleted due to "tmp" status...?
#Indeed I think CentOS possibly perges /tmp pretty frequently
#printlog('fwd_files: {}'.format(transformlist))
for x in transformlist:
if '.mat' in x:
temp = ants.read_transform(x)
transform_matrix.append(temp.parameters)
os.remove(x)
#printlog('Deleted fwd: {}'.format(x))
# Delete invtransforms for /tmp directory size issue. note that .mat are shared, so only need to delete .nii.gz
transformlist = motCorr_vol['invtransforms']
#printlog('inv_files: {}'.format(transformlist))
for x in transformlist:
if '.mat' not in x:
os.remove(x)
#printlog('Deleted inv: {}'.format(x))
print(F"[{i+1}]") #IMPORTANT FOR COMMUNICATION WITH DATAFLOW MAIN
sys.stdout.flush()
# Save motcorr brains
save_motCorr_brain(motCorr_brain_master, motcorr_directory, suffix='red'+suffix)
if brain_slave:
save_motCorr_brain(motCorr_brain_slave, motcorr_directory, suffix='green'+suffix)
# Save transforms
transform_matrix = np.array(transform_matrix)
save_file = os.path.join(motcorr_directory, 'motcorr_params{}'.format(suffix))
np.save(save_file,transform_matrix)
def get_zshift(fixed, moving):
fixed_ants = to_ants(fixed)
moving_ants = to_ants(moving)
res = ants.registration(fixed_ants, moving_ants,
type_of_transform='Translation',
grad_step=.2)
t = ants.read_transform(res['fwdtransforms'][0])
zshift_float = t.parameters[-1]
zshift = int(round(zshift_float))
return zshift
def transform_coordinates(coordinates, from_imaging, to_imaging,
file_invMatrix):
"""coordinate transformation from one imaging modality to other; coordinates must be included as integers"""
transformed = {'points': [], 'indices': []}
physical_points = ants.transform_index_to_physical_point(
from_imaging, coordinates)
transformed['points'] = ants.apply_ants_transform(
ants.read_transform(file_invMatrix), physical_points)
transformed['indices'] = ants.transform_physical_point_to_index(
image=to_imaging, point=transformed['points'])
return transformed
def transform_rois(fixed, moving, rois, **kwargs):
def set_ifn(key, val):
if not key in kwargs:
kwargs[key] = val
set_ifn('type_of_transform', 'Affine')
set_ifn('reg_iterations', [500, 500, 500])
set_ifn('grad_step', .1)
res = ants.registration(fixed, moving, **kwargs)
t = ants.read_transform(res['fwdtransforms'][0])
xyzs = rois[:, :3]
rs = rois[:, 3:]
xyzs_transformed = np.array(list(map(lambda xyz: transform_xyz(t.invert(), xyz, moving, fixed), xyzs)))
return np.concatenate([xyzs_transformed, rs], axis=1)
def main(input_path, transform_path, resampled_image_path):
if resampled_image_path is None and transform_path is None:
raise ValueError('You must provide the path to at least one output')
try:
import ants
except ImportError as e:
message = 'Install ANTS for registration: pip install antspyx'
raise ModuleNotFoundError(message) from e
import numpy as np
import torchio as tio
reference = ants.image_read(str(tio.datasets.Colin27().t1.path))
floating = ants.image_read(input_path)
results = ants.registration(reference, floating, type_of_transform='Affine')
if transform_path is not None:
transform = ants.read_transform(results['fwdtransforms'][0])
affine = np.eye(4)
affine[:3] = transform.parameters.reshape(4, 3).T
affine = tio.io._from_itk_convention(affine)
tio.io.write_matrix(affine, transform_path)
if resampled_image_path is not None:
ants.image_write(results['warpedmovout'], resampled_image_path)
return 0
def ANTsCoregisterMultiprocessing(self,
file_fixed,
file_moving,
subj,
input_folder,
flag,
step,
status,
run=1):
"""Performs Co-Registration taking advantage of multicores, i.e. multiple subjects processed in parallel"""
status.put(tuple([file_fixed, file_moving, subj]))
prev_reg = glob.glob(
os.path.join(input_folder + "/" +
self.cfg['preprocess'][flag]['prefix'] + 'run*' +
os.path.basename(file_moving)))
if not prev_reg:
print('\tNo previous registration found, starting with first run')
filename_save = os.path.join(
input_folder, self.cfg['preprocess'][flag]['prefix'] + 'run' +
str(run) + '_' + os.path.basename(file_moving))
elif re.search(r'\w+{}.'.format('CT_'), file_moving,
re.IGNORECASE) and file_moving.endswith('.nii'):
print('\tNo second run for CT-MRI registrations possible.')
return
else:
allruns = [
re.search(r'\w+(run)([\d.]+)', x).group(2) for x in prev_reg
]
lastrun = int(sorted(allruns)[-1])
file_moving = os.path.join(
input_folder,
self.cfg["preprocess"]["registration"]["prefix"] + 'run' +
str(lastrun) + '_' +
os.path.basename(file_moving)) # update for second run
run = lastrun + 1
n4prefix = self.cfg['preprocess']['ANTsN4']['prefix']
basename = '{}{}'.format(n4prefix, file_moving.split(n4prefix)[1])
filename_save = os.path.join(
input_folder, self.cfg['preprocess'][flag]['prefix'] + 'run' +
str(run) + '_' + basename)
print(filename_save)
log_filename = os.path.join(
ROOTDIR, 'logs',
"log_Registration_using_ANTs_{}_run_{}_".format(subj, str(run)) +
time.strftime("%Y%m%d-%H%M%S") + '.txt')
imaging = dict()
for idx, file_id in enumerate([file_fixed, file_moving]):
sequence = ants.image_read(
file_id) # load data and resample images if necessary
imaging[idx] = Imaging.resampleANTs(
mm_spacing=self.cfg['preprocess']['registration']
['resample_spacing'],
ANTsImageObject=sequence,
file_id=file_id,
method=int(
self.cfg['preprocess']['registration']['resample_method']))
if run == 1:
metric = self.cfg['preprocess']['registration']['metric'][0]
else:
self.cfg['preprocess']['registration'][
'default_registration'] = 'yes' # TODO: must be changed if non-default works
metric = self.cfg['preprocess']['registration']['metric'][0]
if self.cfg['preprocess']['registration'][
'default_registration'] == 'yes':
registered_images = self.default_registration(imaging,
file_fixed,
file_moving,
log_filename,
metric=metric,
step=step)
else:
registered_images = self.custom_registration(
imaging, file_fixed, file_moving, input_folder + '/',
log_filename, run)
key2rename = {
'fwdtransforms':
['{}_0GenericAffineRegistration.mat'.format(step), 1],
'invtransforms': ['{}_1InvWarpMatrix.mat'.format(step), 0]
}
for key, value in key2rename.items():
Transform = ants.read_transform(registered_images[key][value[1]])
ants.write_transform(Transform,
os.path.join(input_folder, value[0]))
ants.image_write(registered_images['warpedmovout'],
filename=filename_save)
FileOperations.create_folder(os.path.join(input_folder, "debug"))
if run > 1: # Previous registrations are moved to debug-folder
prev_reg = ''.join(prev_reg) if type(
prev_reg) == list else prev_reg
filename_dest = re.sub(
r'({}run[0-9]_)+({})'.format(
self.cfg['preprocess']['registration']['prefix'],
self.cfg['preprocess']['ANTsN4']['prefix']),
'{}RUNPREV{}_{}'.format(
self.cfg['preprocess']['registration']['prefix'], lastrun,
self.cfg['preprocess']['ANTsN4']['prefix']),
os.path.basename(prev_reg))
shutil.move(prev_reg,
os.path.join(input_folder, 'debug', filename_dest))
create_mask = True
if create_mask and 't1' in file_moving and not os.path.isfile(
os.path.join(input_folder, 'brainmask_T1.nii')):
Imaging.create_brainmask(
input_folder,
subj=subj,
registered_images=registered_images['warpedmovout'])
mi = ants.image_read(ants.get_data("r64"))
tx = "Affine"
pnum = 0
tx = "SyN"
pnum = 1
metrics = ["MeanSquares", "GC", "Mattes"]
asr = 1
for m in range(0, len(metrics)):
mytx1 = ants.registration(
fixed=fi,
moving=mi,
type_of_transform=tx,
aff_metric=metrics[m],
aff_random_sampling_rate=asr,
)
p1 = ants.read_transform(mytx1["fwdtransforms"][pnum])
p1 = ants.get_ants_transform_parameters(p1)
for k in range(0, 2):
mytx2 = ants.registration(
fixed=fi,
moving=mi,
type_of_transform=tx,
aff_metric=metrics[m],
aff_random_sampling_rate=asr,
)
p2 = ants.read_transform(mytx2["fwdtransforms"][pnum])
p2 = ants.get_ants_transform_parameters(p2)
metval = ants.image_mutual_information(fi, mytx2["warpedmovout"])
chg = abs(p2 - p1).sum()
print(metrics[m] + " Change: try " + str(k) + " Is " + str(chg) +
" Similarity= " + str(metval))
def test_example(self):
# test ANTsPy/ANTsR example
fi = ants.image_read(ants.get_ants_data("r16"))
mi = ants.image_read(ants.get_ants_data("r27"))
txfile = ants.affine_initializer(fi, mi)
tx = ants.read_transform(txfile, dimension=2)
def __init__(self, filename='path', **options):
import ants
self.tx = ants.read_transform(filename, **options)
