Ejemplo n.º 1
0
def read_cmd_args(argv):
    import argparse
    parser = argparse.ArgumentParser(description='MMVT freeview preprocessing')
    parser.add_argument('-b',
                        '--bipolar',
                        help='bipolar',
                        required=False,
                        default=0,
                        type=au.is_true)
    parser.add_argument('--overwrite_aseg_file',
                        help='overwrite_aseg_file',
                        required=False,
                        default=0,
                        type=au.is_true)
    parser.add_argument('--create_volume_file',
                        help='create_volume_file',
                        required=False,
                        default=1,
                        type=au.is_true)
    parser.add_argument('--electrodes_pos_fname',
                        help='electrodes_pos_fname',
                        required=False,
                        default='')
    parser.add_argument('--way_points',
                        help='way_points',
                        required=False,
                        default=0,
                        type=au.is_true)
    pu.add_common_args(parser)
    args = utils.Bag(au.parse_parser(parser, argv))
    args.necessary_files = {'mri': ['T1.mgz', 'orig.mgz']}
    # print(args)
    return args
Ejemplo n.º 2
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def read_cmd_args(argv=None):
    import argparse
    parser = argparse.ArgumentParser(description='MMVT template preprocessing')
    parser.add_argument('--flag', help='', required=False, default='')
    pu.add_common_args(parser)
    args = utils.Bag(au.parse_parser(parser, argv))
    return args
Ejemplo n.º 3
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def read_cmd_args(argv=None):
    import argparse
    from src.utils import args_utils as au
    parser = argparse.ArgumentParser(description='MMVT stim preprocessing')
    parser.add_argument('-c', '--conditions', help='conditions names', required=False, default='contrast', type=au.str_arr_type)
    parser.add_argument('--mat_fname', help='matlab connection file name', required=False, default='')
    parser.add_argument('--mat_field', help='matlab connection field name', required=False, default='')
    parser.add_argument('--labels_exclude', help='rois to exclude', required=False, default='unknown,corpuscallosum',
                        type=au.str_arr_type)
    parser.add_argument('--bipolar', help='', required=False, default=0, type=au.is_true)
    parser.add_argument('--norm_by_percentile', help='', required=False, default=1, type=au.is_true)
    parser.add_argument('--norm_percs', help='', required=False, default='1,99', type=au.int_arr_type)
    parser.add_argument('--stat', help='', required=False, default=STAT_DIFF, type=int)
    parser.add_argument('--windows', help='', required=False, default=0, type=int)
    parser.add_argument('--t_max', help='', required=False, default=0, type=int)
    parser.add_argument('--threshold_percentile', help='', required=False, default=0, type=int)
    parser.add_argument('--threshold', help='', required=False, default=0, type=float)
    parser.add_argument('--color_map', help='', required=False, default='jet')
    parser.add_argument('--symetric_colors', help='', required=False, default=1, type=au.is_true)
    parser.add_argument('--data_max', help='', required=False, default=0, type=float)
    parser.add_argument('--data_min', help='', required=False, default=0, type=float)
    pu.add_common_args(parser)

    args = utils.Bag(au.parse_parser(parser, argv))
    if len(args.conditions) == 1:
        args.stat = STAT_AVG
    print(args)
    return args
Ejemplo n.º 4
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def read_cmd_args(argv=None):
    import argparse
    parser = argparse.ArgumentParser(description='MMVT anatomy preprocessing')
    parser.add_argument('--template_subject', help='template subject', required=False, default='fsaverage')
    parser.add_argument('--surf_name', help='surf_name', required=False, default='pial')
    parser.add_argument('--cerebellum_segmentation_loose', help='', required=False, default=1, type=au.is_true)
    parser.add_argument('--overwrite', help='overwrite', required=False, default=0, type=au.is_true)
    parser.add_argument('--overwrite_subcorticals', help='overwrite', required=False, default=0, type=au.is_true)
    parser.add_argument('--overwrite_annotation', help='overwrite_annotation', required=False, default=0, type=au.is_true)
    parser.add_argument('--overwrite_morphing_labels', help='overwrite_morphing_labels', required=False, default=0, type=au.is_true)
    parser.add_argument('--overwrite_hemis_srf', help='overwrite_hemis_srf', required=False, default=0, type=au.is_true)
    parser.add_argument('--overwrite_labels_ply_files', help='overwrite_labels_ply_files', required=False, default=0, type=au.is_true)
    parser.add_argument('--overwrite_faces_verts', help='overwrite_faces_verts', required=False, default=0, type=au.is_true)
    parser.add_argument('--overwrite_ply_files', help='overwrite_ply_files', required=False, default=0, type=au.is_true)
    parser.add_argument('--solve_labels_collisions', help='solve_labels_collisions', required=False, default=0, type=au.is_true)
    parser.add_argument('--morph_labels_from_fsaverage', help='morph_labels_from_fsaverage', required=False, default=1, type=au.is_true)
    parser.add_argument('--fs_labels_fol', help='fs_labels_fol', required=False, default='')
    pu.add_common_args(parser)
    args = utils.Bag(au.parse_parser(parser, argv))
    args.necessary_files = {'mri': ['aseg.mgz', 'norm.mgz', 'ribbon.mgz', 'T1.mgz', 'orig.mgz'],
        'surf': ['rh.pial', 'lh.pial', 'rh.inflated', 'lh.inflated', 'lh.curv', 'rh.curv', 'rh.sphere.reg',
                 'lh.sphere.reg', 'lh.white', 'rh.white', 'rh.smoothwm','lh.smoothwm'],
        'mri:transforms' : ['talairach.xfm']}
    if args.overwrite:
        args.overwrite_annotation = True
        args.overwrite_morphing_labels = True
        args.overwrite_hemis_srf = True
        args.overwrite_labels_ply_files = True
        args.overwrite_faces_verts = True
        args.overwrite_fs_files = True
    print(args)
    return args
Ejemplo n.º 5
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def read_cmd_args(argv=None):
    import argparse
    from src.utils import args_utils as au
    parser = argparse.ArgumentParser(description='MMVT template preprocessing')
    pu.add_common_args(parser)
    args = utils.Bag(au.parse_parser(parser))
    print(args)
    return args
Ejemplo n.º 6
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def read_cmd_args(argv=None):
    import argparse
    from src.utils import args_utils as au
    parser = argparse.ArgumentParser(description='MMVT template preprocessing')
    pu.add_common_args(parser)
    args = utils.Bag(au.parse_parser(parser))
    # print(args)
    return args
Ejemplo n.º 7
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def read_cmd_args(argv):
    import argparse
    from src.utils import args_utils as au
    parser = argparse.ArgumentParser(description='MMVT freeview preprocessing')
    parser.add_argument('-b', '--bipolar', help='bipolar', required=False, default=0, type=au.is_true)
    parser.add_argument('--overwrite_aseg_file', help='overwrite_aseg_file', required=False, default=0, type=au.is_true)
    parser.add_argument('--create_volume_file', help='create_volume_file', required=False, default=1, type=au.is_true)
    parser.add_argument('--electrodes_pos_fname', help='electrodes_pos_fname', required=False, default='')
    parser.add_argument('--way_points', help='way_points', required=False, default=0, type=au.is_true)
    pu.add_common_args(parser)
    args = utils.Bag(au.parse_parser(parser, argv))
    args.necessary_files = {'mri': ['T1.mgz', 'orig.mgz']}
    print(args)
    return args
Ejemplo n.º 8
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def read_cmd_args(argv=None):
    import argparse
    from src.utils import args_utils as au
    parser = argparse.ArgumentParser(description='MMVT stim preprocessing')
    parser.add_argument('--stim_channel', help='stim channel', required=True)
    parser.add_argument('--colors_map', help='activity colors map', required=False, default='OrRd')
    parser.add_argument('--norm_percs', help='normalization percerntiles', required=False, type=au.int_arr_type, default='1,95')
    parser.add_argument('--downsample', help='downsample', required=False, type=int, default=1)
    parser.add_argument('--file_frefix', help='file_frefix', required=False, default='psd_')
    parser.add_argument('--error_radius', help='error_radius', required=False, default=3, type=int)
    parser.add_argument('--elec_length', help='elec_length', required=False, default=4, type=int)
    pu.add_common_args(parser)
    args = utils.Bag(au.parse_parser(parser))
    print(args)
    return args
Ejemplo n.º 9
0
def read_cmd_args(argv=None):
    from src.utils import args_utils as au
    import argparse
    parser = argparse.ArgumentParser(description='MMVT electrodes preprocessing')
    parser.add_argument('-b', '--bipolar', help='bipolar', required=False, default=0, type=au.is_true)
    parser.add_argument('--good_channels', help='good channels', required=False, default='', type=au.str_arr_type)
    parser.add_argument('--bad_channels', help='bad channels', required=False, default='', type=au.str_arr_type)
    parser.add_argument('--from_t', help='from_t', required=False, default='0', type=au.float_arr_type)# float) # was -500
    parser.add_argument('--to_t', help='to_t', required=False, default='0', type=au.float_arr_type) # was 2000
    parser.add_argument('--from_t_ind', help='from_t_ind', required=False, default=0, type=int) # was -500
    parser.add_argument('--to_t_ind', help='to_t_ind', required=False, default=-1, type=int) # was 2000
    parser.add_argument('--indices_shift', help='indices_shift', required=False, default=0, type=int) # was 1000
    parser.add_argument('--conditions', help='conditions', required=False, default='')
    parser.add_argument('--raw_fname', help='raw fname', required=False, default='no_raw_fname_given')
    parser.add_argument('--ref_elec', help='referece electrode', required=False, default='')
    parser.add_argument('--stat', help='stat', required=False, default=STAT_DIFF, type=int)
    parser.add_argument('--electrodes_names_field', help='electrodes_names_field', required=False, default='names')
    parser.add_argument('--moving_average_window_size', help='', required=False, default=0, type=int)
    parser.add_argument('--field_cond_template', help='', required=False, default='{}')
    parser.add_argument('--input_type', help='', required=False, default='ERP')
    parser.add_argument('--input_matlab_fname', help='', required=False, default='')

    parser.add_argument('--start_time', help='', required=False, default='')
    parser.add_argument('--seizure_time', help='', required=False, default='')
    parser.add_argument('--window_length', help='', required=False, default=0, type=float)
    parser.add_argument('--seizure_onset_time', help='', required=False, default=0, type=float)
    parser.add_argument('--baseline_delta', help='', required=False, default=0, type=float)
    parser.add_argument('--time_format', help='', required=False, default='%H:%M:%S')

    parser.add_argument('--electrodes_groups_coloring_fname', help='', required=False, default='electrodes_groups_coloring.csv')
    parser.add_argument('--ras_xls_sheet_name', help='ras_xls_sheet_name', required=False, default='')
    parser.add_argument('--do_plot', help='do plot', required=False, default=0, type=au.is_true)
    pu.add_common_args(parser)
    args = utils.Bag(au.parse_parser(parser, argv))
    args.ignore_missing = True
    for field in ['from_t', 'to_t']:
        if len(args[field]) == 1:
            args[field] = args[field][0]
    args.necessary_files = {'electrodes': ['{subject}_RAS.csv']}
    print(args)
    return args
Ejemplo n.º 10
0
Archivo: ct.py Proyecto: keshava/mmvt
def read_cmd_args(argv=None):
    import argparse
    parser = argparse.ArgumentParser(description='MMVT CT preprocessing')
    parser.add_argument('--ct_raw_input_fol',
                        help='',
                        required=False,
                        default='')
    parser.add_argument('--ct_fol', help='', required=False, default='')
    parser.add_argument('--ct_org_name',
                        help='',
                        required=False,
                        default='ct_org.mgz')
    parser.add_argument('--nnv_ct_name',
                        help='',
                        required=False,
                        default='ct_no_large_negative_values.mgz')
    parser.add_argument('--register_ct_name',
                        help='',
                        required=False,
                        default='ct_reg_to_mr.mgz')
    parser.add_argument('--negative_threshold',
                        help='',
                        required=False,
                        default=-200,
                        type=int)
    parser.add_argument('--no_negatives',
                        help='',
                        required=False,
                        default=True,
                        type=au.is_true)
    parser.add_argument('--register_cost_function',
                        help='',
                        required=False,
                        default='nmi')
    parser.add_argument('--ct_threshold',
                        help='',
                        required=False,
                        type=float,
                        default=2000)
    parser.add_argument('--overwrite',
                        help='',
                        required=False,
                        default=0,
                        type=au.is_true)
    parser.add_argument('--print_only',
                        help='',
                        required=False,
                        default=False,
                        type=au.is_true)
    parser.add_argument('--ask_before',
                        help='',
                        required=False,
                        default=False,
                        type=au.is_true)
    parser.add_argument('--debug',
                        help='',
                        required=False,
                        default=False,
                        type=au.is_true)

    # find_electrodes:
    parser.add_argument('--n_components',
                        help='',
                        required=False,
                        default=0,
                        type=int)
    parser.add_argument('--n_groups',
                        help='',
                        required=False,
                        default=0,
                        type=int)
    parser.add_argument('--brain_mask_fname',
                        help='',
                        required=False,
                        default='')
    parser.add_argument('--output_fol',
                        help='',
                        required=False,
                        default=None,
                        type=au.str_or_none)
    parser.add_argument('--clustering_method',
                        help='',
                        required=False,
                        default='knn')
    parser.add_argument('--max_iters',
                        help='',
                        required=False,
                        default=5,
                        type=int)
    parser.add_argument('--cylinder_error_radius',
                        help='',
                        required=False,
                        default=3,
                        type=float)
    parser.add_argument('--min_elcs_for_lead',
                        help='',
                        required=False,
                        default=4,
                        type=int)
    parser.add_argument('--max_dist_between_electrodes',
                        help='',
                        required=False,
                        default=20,
                        type=float)
    parser.add_argument('--min_cylinders_ang',
                        help='',
                        required=False,
                        default=0.1,
                        type=float)
    parser.add_argument('--ct_thresholds',
                        help='',
                        required=False,
                        default='99,99.9,99.95,99.99,99.995,99.999',
                        type=au.float_arr_type)
    parser.add_argument('--min_joined_items_num',
                        help='',
                        required=False,
                        default=1,
                        type=int)
    parser.add_argument('--min_distance_beteen_electrodes',
                        help='',
                        required=False,
                        default=2,
                        type=float)

    # Dell
    parser.add_argument('--voxels',
                        help='',
                        required=False,
                        default='',
                        type=au.list_of_int_lists_type)
    parser.add_argument('--voxel',
                        help='',
                        required=False,
                        default='',
                        type=au.int_arr_type)  # 102,99,131
    parser.add_argument('--pixels_around_voxel',
                        help='',
                        required=False,
                        default=30,
                        type=int)
    parser.add_argument('--interactive',
                        help='',
                        required=False,
                        default=0,
                        type=au.is_true)
    parser.add_argument('--electrodes_names',
                        help='',
                        required=False,
                        default='',
                        type=au.str_arr_type)
    parser.add_argument('--group_name', help='', required=False, default='')
    parser.add_argument('--elc_name', help='', required=False, default='')
    parser.add_argument('--fig_name', help='', required=False, default='')
    parser.add_argument('--isotropization_type',
                        help='',
                        required=False,
                        default=1,
                        type=int)

    pu.add_common_args(parser)
    args = utils.Bag(au.parse_parser(parser, argv))
    pu.set_default_folders(args)
    args.necessary_files = {'mri': ['brain.mgz']}

    global SUBJECTS_DIR, MMVT_DIR
    SUBJECTS_DIR = args.mri_dir
    MMVT_DIR = args.mmvt_dir
    print('Subjects dir: {}'.format(SUBJECTS_DIR))
    print('MMVT dir: {}'.format(MMVT_DIR))
    return args