def update_hm(m2m_dir):
eeg_positions = os.path.join(m2m_dir, "eeg_positions")
print("Transforming EEG positions")
if not os.path.exists(eeg_positions):
os.mkdir(eeg_positions)
cap_file = os.path.abspath(
os.path.realpath(
os.path.join(SIMNIBSDIR, 'resources', 'ElectrodeCaps_MNI',
'EEG10-10_UI_Jurak_2007.csv')))
cap_out = os.path.join(eeg_positions, 'EEG10-10_UI_Jurak_2007.csv')
geo_out = os.path.join(eeg_positions, 'EEG10-10_UI_Jurak_2007.geo')
warp_coordinates(cap_file,
m2m_dir,
out_name=cap_out,
transformation_direction='mni2subject',
out_geo=geo_out)
def main():
args = parse_arguments(sys.argv[1:])
m2m_dir = os.path.abspath(
os.path.realpath(os.path.expanduser(args.m2mpath)))
if not os.path.isdir(m2m_dir):
raise IOError('Could not find directory: {0}'.format(args.m2mpath))
if args.out is not None:
fn_out = os.path.abspath(os.path.realpath(os.path.expanduser(
args.out)))
fn_geo = os.path.splitext(fn_out)[0] + '.geo'
else:
fn_out = None
fn_geo = None
if args.coords is not None:
coords = [float(d) for d in args.coords]
elif args.csv is not None:
coords = os.path.abspath(os.path.realpath(os.path.expanduser(
args.csv)))
if not os.path.isfile(coords):
raise IOError('Could not find CSV file: {0}'.format(args.csv))
else:
raise argparse.ArgumentTypeError('Plase use either -c or -s')
if args.coords is not None and args.csv is not None:
raise argparse.ArgumentError('Please use only -c or -s')
coords = transformations.warp_coordinates(
coords,
m2m_dir,
out_name=fn_out,
transformation_direction='mni2subject',
transformation_type=args.t,
out_geo=fn_geo)[1]
if fn_out is None:
np.set_printoptions(precision=2,
formatter={'float': lambda x: '{0:.2f}'.format(x)})
print('Transformed coodinates:\n{0}'.format(coords.squeeze()))
fn_geo = os.path.splitext(fn_out)[0] + '.geo'
else:
fn_out = None
fn_geo = None
if args.coords is not None:
coords = np.array([float(d) for d in args.coords])
elif args.csv is not None:
coords = os.path.abspath(os.path.realpath(os.path.expanduser(
args.csv)))
if not os.path.isfile(coords):
raise IOError('Could not find CSV file: {0}'.format(args.csv))
else:
raise argparse.ArgumentTypeError('Plase use either -c or -s')
if args.coords is not None and args.csv is not None:
raise argparse.ArgumentError('Please use only -c or -s')
coords = transformations.warp_coordinates(
coords,
m2m_dir,
out_name=fn_out,
transformation_direction='subject2mni',
transformation_type=args.t,
out_geo=fn_geo)[1]
if fn_out is None:
np.set_printoptions(precision=2,
formatter={'float': lambda x: '{0:.2f}'.format(x)})
print('Transformed coodinates:\n{0}'.format(coords.squeeze()))