def BSpline_SyN_ANTs_transform_image(setting, IN=None, out=None):
fixedIm_address = su.address_generator(setting, 'Im', cn=IN, type_im=0)
movingIm_address = su.address_generator(setting, 'Im', cn=IN, type_im=1)
transform0 = su.address_generator(setting,
'DVF_nonRigid_composed',
cn=IN,
out=out)
nonRigid_MovedImage_address = su.address_generator(setting,
'nonRigid_MovedImage',
cn=IN,
out=out)
number_of_threads = setting['numberOfThreads']
script = su.address_generator(setting,
'nonRigidTransformMovedImageScript',
cn=IN,
out=out)
log = script + '_log'
setLogFile(log)
with open(script, "w") as textScr:
# please note that the last registration that you did, should be the first transform parameters
textScr.write(ANTsP.header_transform())
textScr.write(ANTsP.write_number_of_threads(number_of_threads))
textScr.write(ANTsP.write_input_image(movingIm_address))
textScr.write(ANTsP.write_reference_image(fixedIm_address))
textScr.write(ANTsP.write_transform_parameters(transform0))
textScr.write(ANTsP.write_dimension(setting['dimension']))
textScr.write(ANTsP.write_output(nonRigid_MovedImage_address))
textScr.write(
ANTsP.write_default_pixel_value(setting['defaultPixelValue']))
textScr.write(ANTsP.transform_image(number_of_transforms=1))
textScr.write(ANTsP.footer())
textScr.close()
os.chmod(script, 0o774)
os.system(script)
def affine_ANTs_transform_image(setting, cn=None):
fixedIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=0)
movingIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=1)
affineOutMat = su.address_generator(setting, 'affineOutMat', cn=cn)
affine_MovedImage_address = su.address_generator(setting,
'affine_MovedImage',
cn=cn)
number_of_threads = setting['numberOfThreads']
script = su.address_generator(setting,
'affineTransformMovedImageScript',
cn=cn)
with open(script, "w") as textScr:
# please note that the last registration that you did, should be the first transform parameters
textScr.write(ANTsP.header_transform())
textScr.write(ANTsP.write_number_of_threads(number_of_threads))
textScr.write(ANTsP.write_input_image(movingIm_address))
textScr.write(ANTsP.write_reference_image(fixedIm_address))
textScr.write(ANTsP.write_transform_parameters(affineOutMat))
textScr.write(ANTsP.write_dimension(setting['dimension']))
textScr.write(ANTsP.write_output(affine_MovedImage_address))
textScr.write(
ANTsP.write_default_pixel_value(setting['defaultPixelValue']))
textScr.write(ANTsP.transform_image(number_of_transforms=1))
textScr.write(ANTsP.footer())
textScr.close()
os.chmod(script, 0o774)
os.system(script)
def affine_ANTs(setting, cn=None):
fixedIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=0)
movingIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=1)
affineFolder = su.address_generator(setting, 'affineFolder', cn=cn)
if not os.path.exists(affineFolder):
os.makedirs(affineFolder)
output_name = su.address_generator(setting, 'affineOut', cn=cn)
number_of_threads = setting['numberOfThreads']
affine_script = su.address_generator(setting, 'affineScript', cn=cn)
with open(affine_script, "w") as textScr:
textScr.write(ANTsP.header_registration())
textScr.write(ANTsP.write_number_of_threads(number_of_threads))
textScr.write(ANTsP.write_fixed_image(fixedIm_address))
textScr.write(ANTsP.write_moving_image(movingIm_address))
textScr.write(ANTsP.write_dimension(setting['dimension']))
textScr.write(ANTsP.write_output(output_name))
if setting['useMask']:
textScr.write(
ANTsP.write_fixed_mask(
su.address_generator(setting,
setting['MaskName_Affine'][0],
cn=cn,
type_im=0)))
textScr.write(
ANTsP.write_moving_mask(
su.address_generator(setting,
setting['MaskName_Affine'][0],
cn=cn,
type_im=1)))
textScr.write(ANTsP.affine_EMPIRE10(use_mask=setting['useMask']))
textScr.write(ANTsP.footer())
textScr.close()
os.chmod(affine_script, 0o774)
os.system(affine_script)
def BSpline_SyN_ANTs_transform(setting,
cn=None,
out=None,
number_of_transforms=2):
if 'nonrigid_number_of_transform' in setting.keys():
number_of_transforms = setting[
'nonrigid_number_of_transform'] # remove later
fixedIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=0)
movingIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=1)
if number_of_transforms == 1:
transform0 = su.address_generator(setting,
'DVF_nonRigid0',
cn=cn,
out=out)
if number_of_transforms == 2:
transform0 = su.address_generator(setting,
'DVF_nonRigid1',
cn=cn,
out=out)
transform1 = su.address_generator(setting,
'DVF_nonRigid0',
cn=cn,
out=out)
DVF_nonRigid_composed = su.address_generator(setting,
'DVF_nonRigid_composed',
cn=cn,
out=out)
number_of_threads = setting['numberOfThreads']
nonrigid_transform_script = su.address_generator(setting,
'nonRigidTransformScript',
cn=cn,
out=out)
with open(nonrigid_transform_script, "w") as textScr:
# please note that the last registration that you did, should be the first transform parameters
textScr.write(ANTsP.header_transform())
textScr.write(ANTsP.write_number_of_threads(number_of_threads))
textScr.write(ANTsP.write_input_image(movingIm_address))
textScr.write(ANTsP.write_reference_image(fixedIm_address))
textScr.write(
ANTsP.write_transform_parameters(transform0, transform_number=0))
if number_of_transforms > 1:
textScr.write(
ANTsP.write_transform_parameters(transform1,
transform_number=1))
textScr.write(ANTsP.write_dimension(setting['dimension']))
textScr.write(ANTsP.write_output(DVF_nonRigid_composed))
textScr.write(
ANTsP.write_default_pixel_value(setting['defaultPixelValue']))
textScr.write(
ANTsP.transform(number_of_transforms=number_of_transforms))
textScr.write(ANTsP.footer())
textScr.close()
os.chmod(nonrigid_transform_script, 0o774)
os.system(nonrigid_transform_script)
def BSpline_SyN_ANTs_final_transform(setting, cn=None, outfinal=None):
fixedIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=0)
movingIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=1)
transform1 = su.address_generator(setting,
'DVF_nonRigid0_final',
cn=cn,
outfinal=outfinal)
transform0 = su.address_generator(setting,
'DVF_nonRigid1_final',
cn=cn,
outfinal=outfinal)
DVF_nonRigid_composed = su.address_generator(setting,
'DVF_nonRigid_composed_final',
cn=cn,
outfinal=outfinal)
number_of_threads = setting['numberOfThreads']
script = su.address_generator(setting,
'nonRigidTransformScript_final',
cn=cn,
outfinal=outfinal)
with open(script, "w") as textScr:
# please note that the last registration that you did, should be the first transform parameters
textScr.write(ANTsP.header_transform())
textScr.write(ANTsP.write_number_of_threads(number_of_threads))
textScr.write(ANTsP.write_input_image(movingIm_address))
textScr.write(ANTsP.write_reference_image(fixedIm_address))
textScr.write(
ANTsP.write_transform_parameters(transform0, transform_number=0))
textScr.write(
ANTsP.write_transform_parameters(transform1, transform_number=1))
textScr.write(ANTsP.write_dimension(setting['dimension']))
textScr.write(ANTsP.write_output(DVF_nonRigid_composed))
textScr.write(
ANTsP.write_default_pixel_value(setting['defaultPixelValue']))
textScr.write(ANTsP.transform(number_of_transforms=2))
textScr.write(ANTsP.footer())
textScr.close()
os.chmod(script, 0o774)
os.system(script)
def affine_ANTs_transform(setting, cn=None):
fixedIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=0)
movingIm_address = su.address_generator(setting, 'Im', cn=cn, type_im=1)
affineOutMat = su.address_generator(setting, 'affineOutMat', cn=cn)
affineDVF_address = su.address_generator(setting, 'affineDVF', cn=cn)
number_of_threads = setting['numberOfThreads']
affine_transform_script = su.address_generator(setting,
'affineTransformScript',
cn=cn)
with open(affine_transform_script, "w") as textScr:
textScr.write(ANTsP.header_transform())
textScr.write(ANTsP.write_number_of_threads(number_of_threads))
textScr.write(ANTsP.write_input_image(movingIm_address))
textScr.write(ANTsP.write_reference_image(fixedIm_address))
textScr.write(ANTsP.write_transform_parameters(affineOutMat))
textScr.write(ANTsP.write_dimension(setting['dimension']))
textScr.write(ANTsP.write_output(affineDVF_address))
textScr.write(
ANTsP.write_default_pixel_value(setting['defaultPixelValue']))
textScr.write(ANTsP.transform(number_of_transforms=1))
textScr.write(ANTsP.footer())
textScr.close()
os.chmod(affine_transform_script, 0o774)
os.system(affine_transform_script)
def BSpline_SyN_ANTs(setting, cn=None, out=None):
if 'ImageType_Registration' in setting.keys():
image_type_registration = setting['ImageType_Registration']
else:
image_type_registration = 'Im'
fixed_im_address = su.address_generator(setting,
image_type_registration,
cn=cn,
type_im=0)
moving_im_address = su.address_generator(setting,
image_type_registration,
cn=cn,
type_im=1)
output_name = su.address_generator(setting, 'DVF_nonRigid', cn=cn, out=out)
initial_transform = su.address_generator(setting,
'DVF_perturb',
cn=cn,
out=out)
number_of_threads = setting['numberOfThreads']
nonrigid_script = su.address_generator(setting,
'nonRigidScript',
cn=cn,
out=out)
folder_address = su.address_generator(setting,
'nonRigidFolder',
cn=cn,
out=out)
if not os.path.exists(folder_address):
os.makedirs(folder_address)
with open(nonrigid_script, "w") as textScr:
textScr.write(ANTsP.header_registration())
textScr.write(ANTsP.write_number_of_threads(number_of_threads))
textScr.write(ANTsP.write_fixed_image(fixed_im_address))
textScr.write(ANTsP.write_moving_image(moving_im_address))
textScr.write(ANTsP.write_initial_transform(initial_transform))
textScr.write(ANTsP.write_dimension(setting['dimension']))
textScr.write(ANTsP.write_output(output_name))
if setting['useMask']:
textScr.write(
ANTsP.write_fixed_mask(
su.address_generator(setting,
setting['MaskName_BSpline'],
cn=cn,
type_im=0)))
textScr.write(
ANTsP.write_moving_mask(
su.address_generator(setting,
setting['MaskName_BSpline'],
cn=cn,
type_im=1)))
if os.path.isfile(
su.address_generator(setting, 'ParameterFolder') +
setting['NonRigidParameter']):
with open(
su.address_generator(setting, 'ParameterFolder') +
setting['NonRigidParameter'], 'r') as f_parameter:
parameter_str = f_parameter.read()
textScr.write('command="antsRegistration ' + parameter_str + '"')
else:
textScr.write(ANTsP.BSpline_SyN_EMPIRE10(setting))
textScr.write(ANTsP.footer())
textScr.close()
os.chmod(nonrigid_script, 0o774)
os.system(nonrigid_script)
def bspline_syn_ants_final(setting, cn=None, outfinal=None):
if 'ImageType_Registration' in setting.keys():
image_type_registration = setting['ImageType_Registration']
else:
image_type_registration = 'Im'
fixed_im_address = su.address_generator(setting,
image_type_registration,
cn=cn,
type_im=0)
moving_im_address = su.address_generator(setting,
image_type_registration,
cn=cn,
type_im=1)
output_name = su.address_generator(setting,
'DVF_nonRigid_final',
cn=cn,
outfinal=outfinal)
initial_transform = su.address_generator(setting,
'DVF_perturb_final',
cn=cn,
outfinal=outfinal)
number_of_threads = setting['numberOfThreads']
nonrigid_script_final = su.address_generator(setting,
'nonRigidScript_final',
cn=cn,
outfinal=outfinal)
with open(nonrigid_script_final, "w") as textScr:
textScr.write(ANTsP.header_registration())
textScr.write(ANTsP.write_number_of_threads(number_of_threads))
textScr.write(ANTsP.write_fixed_image(fixed_im_address))
textScr.write(ANTsP.write_moving_image(moving_im_address))
textScr.write(ANTsP.write_initial_transform(initial_transform))
textScr.write(ANTsP.write_dimension(setting['dimension']))
textScr.write(ANTsP.write_output(output_name))
if setting['useMask']:
textScr.write(
ANTsP.write_fixed_mask(
su.address_generator(setting,
setting['MaskName_BSpline_Final'],
cn=cn,
type_im=0)))
textScr.write(
ANTsP.write_moving_mask(
su.address_generator(setting,
setting['MaskName_BSpline_Final'],
cn=cn,
type_im=1)))
if os.path.isfile(
su.address_generator(setting, 'ParameterFolder') +
setting['NonRigidParameter_final']):
with open(
su.address_generator(setting, 'ParameterFolder') +
setting['NonRigidParameter_final'], 'r') as f_parameter:
parameter_str = f_parameter.read()
textScr.write('command="antsRegistration ' + parameter_str + '"')
else:
textScr.write(ANTsP.bspline_syn_empire10_final(setting))
textScr.write(ANTsP.footer())
textScr.close()
os.chmod(nonrigid_script_final, 0o774)
os.system(nonrigid_script_final)