def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog='v.{} - {}\n{}'.format(
INFO['version'], INFO['author'], INFO['license']),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver', '--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v', '--verbose',
action='count', default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q', '--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
# nothing here yet!
# avoid mandatory arguments whenever possible
arg_parser.add_argument(
'-m', '--mode',
nargs=2, default=('t1', 'tr'),
help='set display/calculation mode [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q',
'--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('--t1',
metavar='X',
type=float,
default=1000,
help='set the T1 value in ms [%(default)s]')
arg_parser.add_argument('--tr',
metavar='X',
type=float,
default=100,
help='set the TR value in ms [%(default)s]')
arg_parser.add_argument('--fa',
metavar='X',
type=float,
default=None,
help='set the FA value in deg [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q',
'--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument('-d',
'--dir',
metavar='DIR',
default='.',
help='set working directory [%(default)s]')
arg_parser.add_argument('-e',
'--extradir',
metavar='FOLDER',
default='nifti',
help='set output subdirectory [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q',
'--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument(
'-n',
'--name',
metavar='NAME',
default=None,
choices=AVAILABLES,
help='playground selection (from: %(choices)s) [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog='v.{} - {}\n{}'.format(INFO['version'], INFO['author'],
INFO['license']),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q',
'--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument(
'-i',
'--indirect',
action='store_true',
help='use acquisition params instead of sequence params [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q',
'--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument('-d',
'--dirpath',
metavar='DIR',
default='.',
help='set working directory [%(default)s]')
arg_parser.add_argument('-n',
'--val_name',
metavar='NAME',
default=None,
help='set values name ( [%(default)s]')
arg_parser.add_argument('-a',
'--val_interval',
metavar=('MIN', 'MAX'),
type=float,
nargs=2,
default=None,
help='set interval of values [%(default)s]')
arg_parser.add_argument('-u',
'--val_units',
metavar='UNITS',
default=None,
help='set units for values [%(default)s]')
arg_parser.add_argument('-m',
'--mask_filepath',
metavar='FILE',
default=None,
help='set exact mask file [%(default)s]')
arg_parser.add_argument(
'--reg_ref_ext',
metavar='FILE_EXT',
default=pml.EXT['reg_ref'],
help='file extension of registration reference flag [%(default)s]')
arg_parser.add_argument(
'--corr_ref_ext',
metavar='FILE_EXT',
default=pml.EXT['corr_ref'],
help='file extension of correlation reference flag [%(default)s]')
arg_parser.add_argument(
'--tmp_dir',
metavar='SUBDIR',
default='tmp',
help='subdirectory where to store temporary files [%(default)s]')
arg_parser.add_argument(
'--reg_dir',
metavar='SUBDIR',
default='reg',
help='subdirectory where to store registration files [%(default)s]')
arg_parser.add_argument(
'--msk_dir',
metavar='SUBDIR',
default='msk',
help='subdirectory where to store masking files [%(default)s]')
arg_parser.add_argument(
'--cmp_dir',
metavar='SUBDIR',
default='cmp',
help='subdirectory where to store comparing files [%(default)s]')
arg_parser.add_argument(
'--fig_dir',
metavar='SUBDIR',
default='fig',
help='subdirectory where to store figures [%(default)s]')
return arg_parser
def plot(fig, params=None, title=TITLE.split(':')[1].strip()):
axs = fig.subplots(1, 1, squeeze=False, sharex='row', sharey='row')
te = params['te'] = np.linspace(params['te_start'], params['te_stop'],
params['te_num'])
params['rest_tissue_m0'] = _normalize_qty(params, 'rest_', '_m0')
params['actv_tissue_m0'] = _normalize_qty(params, 'actv_', '_m0')
rest = group_params('rest', params)
actv = group_params('actv', params)
both = group_params('both', params)
if params['mode'] == 'No MT':
both['mtr'] = dict(arterial=0.0, capillary=0.0, venous=0.0, tissue=0.0)
ss_rest = signals_perfusion(rest['m0'], rest['t1'], rest['t2s'],
params['fa'], params['tr'], params['te'],
rest['perfusion'], both['mtr'], both['wc'])
ss_actv = signals_perfusion(actv['m0'], actv['t1'], actv['t2s'],
params['fa'], params['tr'], params['te'],
actv['perfusion'], both['mtr'], both['wc'])
ds = ss_actv - ss_rest
if params['mode'] == 'Difference':
mtoff = dict(arterial=0.0, capillary=0.0, venous=0.0, tissue=0.0)
ss_rest_mtoff = signals_perfusion(rest['m0'], rest['t1'], rest['t2s'],
params['fa'], params['tr'],
params['te'], rest['perfusion'],
mtoff, both['wc'])
ss_actv_mtoff = signals_perfusion(actv['m0'], actv['t1'], actv['t2s'],
params['fa'], params['tr'],
params['te'], actv['perfusion'],
mtoff, both['wc'])
ds_mton = ds
ds_mtoff = ss_actv_mtoff - ss_rest_mtoff
ds = ds_mtoff - ds_mton
ds_tot = np.sum(ds, axis=0)
if params['mode'] == 'Difference':
te_i = np.argmin(np.abs(ds_tot))
te_name = 'Zero Crossing'
title = 'Difference Signal Variation upon Activation'
else:
te_i = np.argmax(ds_tot)
te_name = 'Optimal'
title = 'Signal Variation upon Activation'
colors = dict(
arterial='#cc3333',
capillary='#cc66cc',
venous='#3333cc',
tissue='#33cc33',
)
ax = axs[0, 0]
for j, name in enumerate(COMPARTMENTS):
if params['show_' + name]:
ax.plot(te, ds[j], label=name.title(), color=colors[name])
if params['show_total']:
ax.plot(te, ds_tot, label='Total', color='#000000')
if params['show_opt']:
ax.axvline(x=te[te_i], color='#999999', linestyle='dashed')
title += fmt(
'\n' + te_name + ' $T_{{E}} = {:.1f}\\pm{:.1f}\\;\\mathrm{{ms}}$',
te[te_i], te[1] - te[0])
params['tes_meas'] = [params[f'te{i}_meas'] for i in range(1, 4)]
for te_meas in params['tes_meas']:
ax.axvline(x=te_meas, color='#cccccc', linestyle='dotted')
ax.set_title(title)
ax.legend()
ax.set_ylabel('$\\Delta S$ / arb. units')
ax.set_xlabel('$T_E$ / ms')
if params['y_min'] != params['y_max']:
ax.set_ylim([params['y_min'], params['y_max']])
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q',
'--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument(
'-i',
'--in_filepaths',
metavar=('MAG_FILE', 'PHS_FILE'),
nargs=2,
default=('mag_coils.nii.gz', 'phs_coils.nii.gz'),
help='set input magnitude and phase filepaths [%(default)s]')
arg_parser.add_argument(
'-o',
'--out_filepaths',
metavar=('MAG_FILE', 'PHS_FILE'),
nargs=2,
default=('mag.nii.gz', 'phs.nii.gz'),
help='set output magnitude and phase filepaths [%(default)s]')
arg_parser.add_argument(
'-p',
'--q_filepath',
metavar='FILE',
default=None,
help='set output quality metric filepath [%(default)s]')
arg_parser.add_argument('-m',
'--method',
metavar='STR',
default='block_adaptive_iter',
help=' [%(default)s]')
arg_parser.add_argument(
'-mk',
'--method_kws',
metavar='STR',
default=None,
help='Additional keyword parameters for the method [%(default)s]')
arg_parser.add_argument('-c',
'--compression',
metavar='STR',
default='compress_svd',
help=' [%(default)s]')
arg_parser.add_argument(
'-ck',
'--compression_kws',
metavar='STR',
default=None,
help='Additional keyword parameters for the compression [%(default)s]')
arg_parser.add_argument(
'-a',
'--coil_axis',
metavar='N',
default=-1,
help='Axis along which the single coils are stored [%(default)s]')
arg_parser.add_argument(
'-s',
'--split_axis',
metavar='N',
default=None,
help='Axis along which input shall be split [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q',
'--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument('-i',
'--input',
metavar='DIR',
default='.',
help='set input directory [%(default)s]')
arg_parser.add_argument('-o',
'--output',
metavar='DIR',
default='.',
help='set output directory [%(default)s]')
arg_parser.add_argument(
'-r',
'--recursive',
action='store_true',
help='Force descending into subdirectories [%(default)s]')
arg_parser.add_argument('-e',
'--meta_subpath',
metavar='DIR',
default=pmc.META_EXT,
help='set extra input subdirectory [%(default)s]')
arg_parser.add_argument('-a',
'--data_subpath',
metavar='DIR',
default='nii',
help='set extra input subdirectory [%(default)s]')
arg_parser.add_argument(
'-m',
'--method',
metavar='METHOD',
default='generic',
help='set computation target and method [%(default)s]')
arg_parser.add_argument(
'-n',
'--options',
metavar='OPTS',
default='{}',
help='set JSON-formatted options dictionary [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q',
'--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument('-i',
'--input',
metavar='FILE',
default=None,
required=True,
help='set input filepath [%(default)s]')
arg_parser.add_argument('-o',
'--output',
metavar='FILE',
default=None,
help='set output filepath [%(default)s]')
arg_parser.add_argument(
'-s',
'--smoothing',
metavar='SIGMA',
type=float,
default=0.0,
help='value of Gaussian smoothing\'s sigma [%(default)s]')
arg_parser.add_argument('-a',
'--threshold',
metavar='METHOD|X',
default='otsu',
help='thresholding method or value [%(default)s]')
arg_parser.add_argument('-A',
'--threshold_opts',
metavar='JSON',
default='{"bins":"sqrt"}',
help='comparison directive [%(default)s]')
arg_parser.add_argument('-c',
'--comparison',
metavar='">"|">="|"<"|"<="|"="|"!="',
default='>',
help='comparison directive [%(default)s]')
arg_parser.add_argument(
'-e',
'--erosion_iter',
metavar='N',
type=int,
default=0,
help='number of postprocess binary erosion iterations [%(default)s]')
arg_parser.add_argument(
'-d',
'--dilation_iter',
metavar='N',
type=int,
default=0,
help='number of postprocess binary dilation iterations [%(default)s]')
arg_parser.add_argument('-t',
'--dtype',
metavar='TYPE',
default='int',
help='data type of the output [%(default)s]')
return arg_parser