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 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)