def get_protocol(self):
try:
bval_scale = float(self.bvalScale.text())
except:
bval_scale = 1
return load_bvec_bval(bvec=self.bvecFileInput.text(),
bval=self.bvalFileInput.text(),
bval_scale=bval_scale)
def run(self, args):
bvec = os.path.realpath(args.bvec)
bval = os.path.realpath(args.bval)
if args.output_file:
output_prtcl = os.path.realpath(args.output_file)
else:
output_prtcl = os.path.join(
os.path.dirname(bvec),
os.path.splitext(os.path.basename(bvec))[0] + '.prtcl')
if args.bval_scale_factor:
bval_scale_factor = float(args.bval_scale_factor)
else:
bval_scale_factor = 'auto'
protocol = load_bvec_bval(bvec=bvec,
bval=bval,
bval_scale=bval_scale_factor)
if args.G is None and args.maxG is not None:
if os.path.isfile(str(args.maxG)):
protocol.add_column_from_file('maxG',
os.path.realpath(str(args.maxG)),
1)
else:
protocol.add_column('maxG', float(args.maxG))
if args.Delta is not None:
add_sequence_timing_column_to_protocol(protocol, 'Delta',
args.Delta,
args.sequence_timing_units)
if args.delta is not None:
add_sequence_timing_column_to_protocol(protocol, 'delta',
args.delta,
args.sequence_timing_units)
if args.TE is not None:
add_sequence_timing_column_to_protocol(protocol, 'TE', args.TE,
args.sequence_timing_units)
if args.TR is not None:
add_sequence_timing_column_to_protocol(protocol, 'TR', args.TR,
args.sequence_timing_units)
if args.G is not None:
add_column_to_protocol(protocol, 'G', args.G, 1)
mdt.protocols.write_protocol(protocol, output_prtcl)
