def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-t', '--type', help='connection type', required=False, default='')
parser.add_argument('--threshold', help='connection threshold', required=False, default=0, type=int)
args = su.parse_args(parser, argv)
rois_file_exist = op.isfile(op.join(su.get_mmvt_dir(), args.subject, 'rois_con.npz'))
electrodes_file_exist = op.isfile(op.join(su.get_mmvt_dir(), args.subject, 'electrodes_con.npz'))
if args.type == '':
if rois_file_exist and electrodes_file_exist:
raise Exception('More than one connection file exist, please select one using the -t flag')
elif rois_file_exist:
args.type = 'rois'
elif electrodes_file_exist:
args.type = 'electrodes'
else:
raise Exception('No connection file was found!\n'+
'ROIs connection file: rois_con.npz\n' +
'Electrodes connection file: electrodes_con.npz')
elif args.type == 'rois':
if not rois_file_exist:
raise Exception('You chose ROIs connection, but the file rois_con.npz does not exist!')
elif args.type == 'electrodes':
if not electrodes_file_exist:
raise Exception('You chose electrodes connection, but the file electrodes_con.npz does not exist!')
return args
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('--python_cmd',
help='python cmd',
required=False,
default=sys.executable)
return su.Bag(au.parse_parser(parser, argv))
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('--stat',
help='conds stat',
required=False,
default=STAT_DIFF)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-r', '--radius', help='radius', required=False, default=0.15, type=float)
parser.add_argument('-p', '--pos_file', help='position file', required=False, default='', type=su.str_arr_type)
args = su.parse_args(parser, argv)
if len(args.subjects) == 0:
args.subjects = [args.subject]
if len(args.pos_file) == 0:
args.pos_file = [''] * len(args.subjects)
pos_files = []
for subject, pos_file in zip(args.subjects, args.pos_file):
args.subject = subject
pos_files_fol = op.join(su.get_mmvt_dir(), args.subject, 'electrodes')
if pos_file == '':
pos_file_options = glob.glob(op.join(pos_files_fol, 'electrodes*positions*.npz'))
if args.bipolar:
pos_file_options = [fname for fname in pos_file_options if 'bipolar' in fname]
else:
pos_file_options = [fname for fname in pos_file_options if 'bipolar' not in fname]
if len(pos_file_options) == 0:
raise Exception('No electrodes position files in {}!'.format(pos_files_fol))
elif len(pos_file_options) == 1:
pos_file = pos_file_options[0]
print('electrodes file: {}'.format(pos_file))
else:
raise Exception('More than one electrodes positions files in {}'.format(pos_files_fol) +
'please indicate which one using the -p flag')
pos_files.append(pos_file)
args.pos_file = pos_files
if len(args.pos_file) == 1:
args.pos_file = args.pos_file[0]
return args
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-o',
'--output_path',
help='output path',
required=False,
default='')
parser.add_argument('-i',
'--image_name',
help='image name',
required=False,
default='')
parser.add_argument('-q',
'--quality',
help='render quality',
required=False,
default=60,
type=int)
parser.add_argument('--smooth_figure',
help='smooth figure',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--hide_lh',
help='hide left hemi',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--hide_rh',
help='hide right hemi',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--hide_subs',
help='hide sub corticals',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--show_elecs',
help='show electrodes',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--show_only_lead',
help='show only current lead',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--curr_elec',
help='current electrode',
required=False,
default='')
parser.add_argument('--show_connections',
help='show connections',
required=False,
default=None,
type=su.is_true_or_none)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-r',
'--radius',
help='radius',
required=False,
default=0.15,
type=float)
parser.add_argument('-p',
'--pos_file',
help='position file',
required=False,
default='',
type=su.str_arr_type)
args = su.parse_args(parser, argv)
if len(args.subjects) == 0:
args.subjects = [args.subject]
if len(args.pos_file) == 0:
args.pos_file = [''] * len(args.subjects)
pos_files = []
for subject, pos_file in zip(args.subjects, args.pos_file):
args.subject = subject
pos_files_fol = op.join(su.get_mmvt_dir(), args.subject, 'electrodes')
if pos_file == '':
pos_file_template = op.join(pos_files_fol,
'electrodes*positions*.npz')
pos_file_options = glob.glob(pos_file_template)
if args.bipolar:
pos_file_options = [
fname for fname in pos_file_options if 'bipolar' in fname
]
else:
pos_file_options = [
fname for fname in pos_file_options
if 'bipolar' not in fname
]
if len(pos_file_options) == 0:
raise Exception(
'No electrodes position files ({}) in {}!'.format(
op.join(pos_files_fol, 'electrodes*positions*.npz'),
pos_files_fol))
elif len(pos_file_options) == 1:
pos_file = pos_file_options[0]
print('electrodes file: {}'.format(pos_file))
else:
pos_file = su.select_one_file(pos_file_options,
pos_file_template,
'electrodes positions files')
else:
pos_file = op.join(pos_files_fol,
'{}.npz'.format(su.namebase(pos_file)))
if not op.isfile(pos_file):
raise ("Can't find pos file! {}".format(pos_file))
pos_files.append(pos_file)
args.pos_file = pos_files
if len(args.pos_file) == 1:
args.pos_file = args.pos_file[0]
return args
def read_args(argv=None):
parser = su.add_default_args()
# Add more args here
parser.add_argument('--script_name', required=True)
parser.add_argument('--script_params',
required=False,
default='',
type=su.str_arr_type)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-b', '--bipolar', help='bipolar', required=True, type=su.is_true)
parser.add_argument('-q', '--quality', help='render quality', required=False, default=60, type=int)
parser.add_argument('--labeling', help="electrodes' labeling file name", required=False)
parser.add_argument('--output_path', help='output path', required=False, default='electrodes_labeling')
parser.add_argument('--rel_output_path', help='relative output path', required=False, default=True, type=su.is_true)
parser.add_argument('--smooth_figure', help='smooth figure', required=False, default=False, type=su.is_true)
parser.add_argument('--hide_lh', help='hide left hemi', required=False, default=False, type=su.is_true)
parser.add_argument('--hide_rh', help='hide right hemi', required=False, default=False, type=su.is_true)
parser.add_argument('--hide_subs', help='hide sub corticals', required=False, default=False, type=su.is_true)
return su.parse_args(parser, argv)
def read_args(argv=None, raise_exp=True):
parser = su.add_default_args()
# Add more args here
# print('argv: {}'.format(sys.argv))
if raise_exp:
return su.parse_args(parser, argv, raise_exception_if_subject_is_empty=False)
else:
try:
args = su.parse_args(parser, argv, raise_exception_if_subject_is_empty=False)
except:
args = None
return args
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-o', '--output_path', help='output path', required=False, default='')
parser.add_argument('-i', '--image_name', help='image name', required=False, default='')
parser.add_argument('-q', '--quality', help='render quality', required=False, default=60, type=int)
parser.add_argument('--smooth_figure', help='smooth figure', required=False, default=False, type=su.is_true)
parser.add_argument('--hide_lh', help='hide left hemi', required=False, default=None, type=su.is_true_or_none)
parser.add_argument('--hide_rh', help='hide right hemi', required=False, default=None, type=su.is_true_or_none)
parser.add_argument('--hide_subs', help='hide sub corticals', required=False, default=None, type=su.is_true_or_none)
parser.add_argument('--show_elecs', help='show electrodes', required=False, default=None, type=su.is_true_or_none)
parser.add_argument('--show_only_lead', help='show only current lead', required=False, default=None, type=su.is_true_or_none)
parser.add_argument('--curr_elec', help='current electrode', required=False, default='')
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('--overwrite_blend',
help='',
required=False,
default=0,
type=su.is_true)
parser.add_argument('--import_in_blender',
help='',
required=False,
default=0,
type=su.is_true)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-r',
'--radius',
help='radius',
required=False,
default=0.15,
type=float)
parser.add_argument('-p',
'--pos_file',
help='position file',
required=False,
default='',
type=su.str_arr_type)
args = su.parse_args(parser, argv)
if len(args.subjects) == 0:
args.subjects = [args.subject]
if len(args.pos_file) == 0:
args.pos_file = [''] * len(args.subjects)
pos_files = []
for subject, pos_file in zip(args.subjects, args.pos_file):
args.subject = subject
pos_files_fol = op.join(su.get_mmvt_dir(), args.subject, 'electrodes')
if pos_file == '':
pos_file_options = glob.glob(
op.join(pos_files_fol, 'electrodes*positions*.npz'))
if args.bipolar:
pos_file_options = [
fname for fname in pos_file_options if 'bipolar' in fname
]
else:
pos_file_options = [
fname for fname in pos_file_options
if 'bipolar' not in fname
]
if len(pos_file_options) == 0:
raise Exception('No electrodes position files in {}!'.format(
pos_files_fol))
elif len(pos_file_options) == 1:
pos_file = pos_file_options[0]
print('electrodes file: {}'.format(pos_file))
else:
raise Exception(
'More than one electrodes positions files in {}'.format(
pos_files_fol) +
'please indicate which one using the -p flag')
pos_files.append(pos_file)
args.pos_file = pos_files
if len(args.pos_file) == 1:
args.pos_file = args.pos_file[0]
return args
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-t', '--threshold', help='threshold', required=True, type=float)
parser.add_argument('--play_type', help='what to play', required=True)
parser.add_argument('--play_from', help='from when to play', required=False, default=0, type=int)
parser.add_argument('--play_to', help='until when to play', required=True, type=int)
parser.add_argument('--play_dt', help='play dt', required=False, default=1, type=int)
parser.add_argument('--output_path', help='output path', required=True)
parser.add_argument('--rel_output_path', help='relative output path', required=False, default=True, type=su.is_true)
parser.add_argument('--quality', help='render quality', required=False, default=60, type=int)
parser.add_argument('--smooth_figure', help='smooth figure', required=False, default=False, type=su.is_true)
parser.add_argument('--selection_type', help='selection type (diff, conds, spec_cond)', required=False, default='diff')
parser.add_argument('--hide_lh', help='hide left hemi', required=False, default=False, type=su.is_true)
parser.add_argument('--hide_rh', help='hide right hemi', required=False, default=False, type=su.is_true)
parser.add_argument('--hide_subs', help='hide sub corticals', required=False, default=False, type=su.is_true)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-b',
'--bipolar',
help='bipolar',
required=True,
type=su.is_true)
parser.add_argument('-q',
'--quality',
help='render quality',
required=False,
default=60,
type=int)
parser.add_argument('--labeling',
help="electrodes' labeling file name",
required=False)
parser.add_argument('--output_path',
help='output path',
required=False,
default='electrodes_labeling')
parser.add_argument('--rel_output_path',
help='relative output path',
required=False,
default=True,
type=su.is_true)
parser.add_argument('--smooth_figure',
help='smooth figure',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--hide_lh',
help='hide left hemi',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--hide_rh',
help='hide right hemi',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--hide_subs',
help='hide sub corticals',
required=False,
default=False,
type=su.is_true)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('--stat',
help='conds stat',
required=False,
default=STAT_DIFF)
parser.add_argument('--modality',
help='modality',
required=False,
default='meg')
parser.add_argument('--load_data',
help='load_data',
required=False,
default=1,
type=su.is_true)
parser.add_argument('--overwrite_sensors',
required=False,
default=0,
type=su.is_true)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-t',
'--type',
help='connection type',
required=False,
default='')
parser.add_argument('--threshold',
help='connection threshold',
required=False,
default=0,
type=int)
args = su.parse_args(parser, argv)
rois_file_exist = op.isfile(
op.join(su.get_mmvt_dir(), args.subject, 'rois_con.npz'))
electrodes_file_exist = op.isfile(
op.join(su.get_mmvt_dir(), args.subject, 'electrodes_con.npz'))
if args.type == '':
if rois_file_exist and electrodes_file_exist:
raise Exception(
'More than one connection file exist, please select one using the -t flag'
)
elif rois_file_exist:
args.type = 'rois'
elif electrodes_file_exist:
args.type = 'electrodes'
else:
raise Exception('No connection file was found!\n' +
'ROIs connection file: rois_con.npz\n' +
'Electrodes connection file: electrodes_con.npz')
elif args.type == 'rois':
if not rois_file_exist:
raise Exception(
'You chose ROIs connection, but the file rois_con.npz does not exist!'
)
elif args.type == 'electrodes':
if not electrodes_file_exist:
raise Exception(
'You chose electrodes connection, but the file electrodes_con.npz does not exist!'
)
return args
def read_args(argv=None):
parser = su.add_default_args()
# Add more args here
parser.add_argument('-q', '--quality', help='render quality', required=False, default=60, type=int)
parser.add_argument('--inflated', required=False, default='0,1', type=su.bool_arr_type)
parser.add_argument('--inflated_ratio', required=False, default=0.5, type=float)
parser.add_argument('--background_color', required=False, default='black,white', type=su.str_arr_type)
parser.add_argument('--lighting', required=False, default='1.0,0.7', type=su.float_arr_type)
parser.add_argument('--transparency', required=False, default=0.0, type=float)
parser.add_argument('--light_layers_depth', required=False, default=0, type=int)
parser.add_argument('--rendering_in_the_background', required=False, default=0, type=su.is_true)
parser.add_argument('--clusters_type', required=False, default='')
parser.add_argument('--dpi', required=False, default=100, type=int)
parser.add_argument('--overwrite', required=False, default=1, type=su.is_true)
parser.add_argument('--colors_map', required=False, default='')
parser.add_argument('--x_left_crop', required=False, default=400, type=float)
parser.add_argument('--x_right_crop', required=False, default=400, type=float)
parser.add_argument('--y_top_crop', required=False, default=0, type=float)
parser.add_argument('--y_buttom_crop', required=False, default=0, type=float)
parser.add_argument('--w_fac', required=False, default=2, type=float)
parser.add_argument('--h_fac', required=False, default=3/2, type=float)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('--stat', help='conds stat', required=False, default=STAT_DIFF)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
# Add more args here
parser.add_argument('-q',
'--quality',
help='render quality',
required=False,
default=60,
type=int)
parser.add_argument('--inflated',
required=False,
default='0,1',
type=su.bool_arr_type)
parser.add_argument('--inflated_ratio',
required=False,
default=0.5,
type=float)
parser.add_argument('--background_color',
required=False,
default='black,white',
type=su.str_arr_type)
parser.add_argument('--lighting',
required=False,
default='1.0,0.7',
type=su.float_arr_type)
parser.add_argument('--transparency',
required=False,
default=0.0,
type=float)
parser.add_argument('--light_layers_depth',
required=False,
default=0,
type=int)
parser.add_argument('--rendering_in_the_background',
required=False,
default=0,
type=su.is_true)
parser.add_argument('--clusters_type', required=False, default='')
parser.add_argument('--dpi', required=False, default=100, type=int)
parser.add_argument('--overwrite',
required=False,
default=1,
type=su.is_true)
parser.add_argument('--colors_map', required=False, default='')
parser.add_argument('--x_left_crop',
required=False,
default=400,
type=float)
parser.add_argument('--x_right_crop',
required=False,
default=400,
type=float)
parser.add_argument('--y_top_crop', required=False, default=0, type=float)
parser.add_argument('--y_buttom_crop',
required=False,
default=0,
type=float)
parser.add_argument('--w_fac', required=False, default=2, type=float)
parser.add_argument('--h_fac', required=False, default=3 / 2, type=float)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('-o',
'--output_path',
help='output path',
required=False,
default='')
parser.add_argument('-i',
'--image_name',
help='image name',
required=False,
default='',
type=su.str_arr_type)
parser.add_argument('-q',
'--quality',
help='render quality',
required=False,
default=60,
type=int)
parser.add_argument('-c',
'--camera',
help='camera fname',
required=False,
default='',
type=su.str_arr_type)
parser.add_argument('--inflated',
required=False,
default=0,
type=su.is_true)
parser.add_argument('--inflated_ratio',
required=False,
default=1.0,
type=float)
parser.add_argument('--background_color', required=False, default='black')
parser.add_argument('--lighting', required=False, default=1.0, type=float)
parser.add_argument('--smooth_figure',
help='smooth figure',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--hide_lh',
help='hide left hemi',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--hide_rh',
help='hide right hemi',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--hide_subs',
help='hide sub corticals',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--show_elecs',
help='show electrodes',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--show_only_lead',
help='show only current lead',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--curr_elec',
help='current electrode',
required=False,
default='')
parser.add_argument('--show_connections',
help='show connections',
required=False,
default=None,
type=su.is_true_or_none)
parser.add_argument('--filter_nodes',
help='filter nodes',
required=False,
default=True,
type=su.is_true)
parser.add_argument('--interactive',
required=False,
default=1,
type=su.is_true)
parser.add_argument('--overwrite',
required=False,
default=1,
type=su.is_true)
args = su.parse_args(parser, argv)
return args
def read_args(argv=None):
parser = su.add_default_args()
# Add more args here
return su.parse_args(parser, argv)
def add_args():
parser = su.add_default_args()
parser.add_argument('-t',
'--threshold',
help='threshold',
required=False,
default=2.0,
type=float)
parser.add_argument('-q',
'--quality',
help='render quality',
required=False,
default=60,
type=int)
parser.add_argument('-p',
'--play_type',
help='what to play',
required=True)
parser.add_argument('--play_from',
help='from when to play',
required=False,
default=0,
type=int)
parser.add_argument('--play_to',
help='until when to play',
required=True,
type=int)
parser.add_argument('--play_dt',
help='play dt',
required=False,
default=1,
type=int)
parser.add_argument('--light_layers',
help='light_layers',
required=False,
default=0,
type=int)
parser.add_argument('--brain_trans',
help='brain_transparency',
required=False,
default=1,
type=float)
parser.add_argument('--output_path',
help='output path',
required=False,
default='')
parser.add_argument('--rel_output_path',
help='relative output path',
required=False,
default=True,
type=su.is_true)
parser.add_argument('--smooth_figure',
help='smooth figure',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--selection_type',
help='selection type (diff, conds, spec_cond)',
required=False,
default='diff')
parser.add_argument('--hide_lh',
help='hide left hemi',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--hide_rh',
help='hide right hemi',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--hide_subs',
help='hide sub corticals',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--filter_nodes',
help='filter nodes',
required=False,
default=True,
type=su.is_true)
parser.add_argument('--camera',
help='camera file',
required=False,
default='')
parser.add_argument('--set_to_camera_mode',
help='',
required=False,
default=False,
type=su.is_true)
parser.add_argument('--mark_electrodes',
help='mark_electrodes',
required=False,
default='',
type=su.str_arr_type)
parser.add_argument('--mark_electrodes_value',
help='mark_electrodes_value',
required=False,
default=0.1,
type=float)
parser.add_argument('--mark_other_electrodes',
help='mark_other_electrodes',
required=False,
default=False,
type=su.is_true)
return parser
def read_args(argv=None):
parser = su.add_default_args()
parser = add_args(parser)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
parser.add_argument('--python_cmd', help='python cmd', required=False, default=sys.executable)
return su.Bag(au.parse_parser(parser, argv))
def read_args(argv=None):
print('play_electrodes argv: {}'.format(argv))
parser = su.add_default_args()
parser = add_args(parser)
return su.parse_args(parser, argv)
def read_args(argv=None):
parser = su.add_default_args()
# Add more args here
return su.parse_args(parser, argv)