def run(self):
''' run the unwarp resample
'''
# get the spherical harmonics coefficients from parsing
# the given .coeff file xor .grad file
if hasattr(self.args, 'gradfile') and self.args.gradfile:
self.coeffs = coeffs.get_coefficients(self.args.vendor,
self.args.gradfile)
else:
self.coeffs = coeffs.get_coefficients(self.args.vendor,
self.args.coeffile)
self.vol, self.m_rcs2ras = utils.get_vol_affine(self.args.infile)
self.unwarper = Unwarper(self.vol, self.m_rcs2ras, self.args.vendor,
self.coeffs, self.args.infile)
if hasattr(self.args, 'fovmin') and self.args.fovmin:
self.unwarper.fovmin = float(self.args.fovmin)
if hasattr(self.args, 'fovmax') and self.args.fovmax:
self.unwarper.fovmax = float(self.args.fovmax)
if hasattr(self.args, 'numpoints') and self.args.numpoints:
self.unwarper.numpoints = int(self.args.numpoints)
if hasattr(self.args, 'warp') and self.args.warp:
self.unwarper.warp = True
if hasattr(self.args, 'nojac') and self.args.nojac:
self.unwarper.nojac = True
if hasattr(self.args, 'order') and self.args.order:
self.unwarper.order = int(self.args.order)
self.unwarper.run()
class GradientUnwarpRunner(object):
''' Takes the option datastructure after parsing the commandline.
run() method performs the actual unwarping
write() method performs the writing of the unwarped volume
'''
def __init__(self, args):
''' constructor takes the option datastructure which is the
result of (options, args) = parser.parse_args()
'''
self.args = args
self.unwarper = None
log.setLevel(logging.INFO)
if hasattr(self.args, 'verbose'):
log.setLevel(logging.DEBUG)
def run(self):
''' run the unwarp resample
'''
# get the spherical harmonics coefficients from parsing
# the given .coeff file xor .grad file
if hasattr(self.args, 'gradfile') and self.args.gradfile:
self.coeffs = coeffs.get_coefficients(self.args.vendor,
self.args.gradfile)
else:
self.coeffs = coeffs.get_coefficients(self.args.vendor,
self.args.coeffile)
self.vol, self.m_rcs2ras = utils.get_vol_affine(self.args.infile)
self.unwarper = Unwarper(self.vol, self.m_rcs2ras, self.args.vendor, self.coeffs, self.args.infile )
if hasattr(self.args, 'fovmin') and self.args.fovmin:
self.unwarper.fovmin = float(self.args.fovmin)
if hasattr(self.args, 'fovmax') and self.args.fovmax:
self.unwarper.fovmax = float(self.args.fovmax)
if hasattr(self.args, 'numpoints') and self.args.numpoints:
self.unwarper.numpoints = int(self.args.numpoints)
if hasattr(self.args, 'warp') and self.args.warp:
self.unwarper.warp = True
if hasattr(self.args, 'nojac') and self.args.nojac:
self.unwarper.nojac = True
if hasattr(self.args, 'order') and self.args.order:
self.unwarper.order = int(self.args.order)
if hasattr(self.args, 'outfilewarp') and self.args.outfilewarp:
self.unwarper.outfilewarp = self.args.outfilewarp
self.unwarper.run()
def write(self):
self.unwarper.write(self.args.outfile)
class GradientUnwarpRunner(object):
''' Takes the option datastructure after parsing the commandline.
run() method performs the actual unwarping
write() method performs the writing of the unwarped volume
'''
def __init__(self, args):
''' constructor takes the option datastructure which is the
result of (options, args) = parser.parse_args()
'''
self.args = args
self.unwarper = None
log.setLevel(logging.INFO)
if hasattr(self.args, 'verbose'):
log.setLevel(logging.DEBUG)
def run(self):
''' run the unwarp resample
'''
# get the spherical harmonics coefficients from parsing
# the given .coeff file xor .grad file
if hasattr(self.args, 'gradfile') and self.args.gradfile:
self.coeffs = coeffs.get_coefficients(self.args.vendor,
self.args.gradfile)
else:
self.coeffs = coeffs.get_coefficients(self.args.vendor,
self.args.coeffile)
self.vol, self.m_rcs2ras = utils.get_vol_affine(self.args.infile)
self.unwarper = Unwarper(self.vol, self.m_rcs2ras, self.args.vendor,
self.coeffs, self.args.infile, self.args.hcp)
if hasattr(self.args, 'fovmin') and self.args.fovmin:
self.unwarper.fovmin = float(self.args.fovmin)
if hasattr(self.args, 'fovmax') and self.args.fovmax:
self.unwarper.fovmax = float(self.args.fovmax)
if hasattr(self.args, 'numpoints') and self.args.numpoints:
self.unwarper.numpoints = int(self.args.numpoints)
if hasattr(self.args, 'warp') and self.args.warp:
self.unwarper.warp = True
if hasattr(self.args, 'nojac') and self.args.nojac:
self.unwarper.nojac = True
if hasattr(self.args, 'order') and self.args.order:
self.unwarper.order = int(self.args.order)
self.unwarper.run()
def write(self):
self.unwarper.write(self.args.outfile)
def run(self):
''' run the unwarp resample
'''
# get the spherical harmonics coefficients from parsing
# the given .coeff file xor .grad file
if hasattr(self.args, 'gradfile') and self.args.gradfile:
self.coeffs = coeffs.get_coefficients(self.args.vendor,
self.args.gradfile)
else:
self.coeffs = coeffs.get_coefficients(self.args.vendor,
self.args.coeffile)
self.vol, self.m_rcs2ras = utils.get_vol_affine(self.args.infile)
self.unwarper = Unwarper(self.vol, self.m_rcs2ras, self.args.vendor,
self.coeffs, self.args.infile, self.args.hcp)
if hasattr(self.args, 'fovmin') and self.args.fovmin:
self.unwarper.fovmin = float(self.args.fovmin)
if hasattr(self.args, 'fovmax') and self.args.fovmax:
self.unwarper.fovmax = float(self.args.fovmax)
if hasattr(self.args, 'numpoints') and self.args.numpoints:
self.unwarper.numpoints = int(self.args.numpoints)
if hasattr(self.args, 'warp') and self.args.warp:
self.unwarper.warp = True
if hasattr(self.args, 'nojac') and self.args.nojac:
self.unwarper.nojac = True
if hasattr(self.args, 'order') and self.args.order:
self.unwarper.order = int(self.args.order)
self.unwarper.run()
