def parse(args):
"""Parse the command-line arguments of the `view` command.
Parameters
----------
args : list of str
List of arguments, without the command name.
Returns
-------
View
Filled structure
"""
struct = View()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
"""
Parameters
----------
args : list of str
Command line arguments (without the command name)
Returns
-------
Convert
Filled structure
"""
struct = Convert()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-m', '--meta'):
struct.meta = {}
while cli.next_isvalue(args):
val, *args = args
if '=' not in val:
raise ValueError(f'Metadata should have format KEY=VAL '
f'without whitespaces. Found {val} '
f'alone.')
key, val = val.split('=')
struct.meta[key] = val
elif tag in ('-c', '--casting'):
cli.check_next_isvalue(args, tag)
struct.cast, *args = args
elif tag in ('-dt', '--dtype'):
cli.check_next_isvalue(args, tag)
struct.dtype, *args = args
elif tag in ('-f', '--format'):
cli.check_next_isvalue(args, tag)
struct.format, *args = args
elif tag in ('-o', '--output'):
struct.output = []
while cli.next_isvalue(args):
val, *args = args
struct.output.append(val)
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
"""
Parameters
----------
args
Returns
-------
"""
struct = Orient()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-l', '--layout'):
cli.check_next_isvalue(args, tag)
struct.layout, *args = args
elif tag in ('-v', '--voxel-size'):
struct.voxel_size = []
while cli.next_isvalue(args):
val, *args = args
if val.lower() in ('self', 'like'):
struct.voxel_size = val
break
struct.voxel_size.append(float(val))
elif tag in ('-c', '--center'):
struct.center = []
while cli.next_isvalue(args):
val, *args = args
if val.lower() in ('self', 'like'):
struct.center = val
break
struct.center.append(float(val))
elif tag in ('-k', '--like'):
struct.like, *args = args
elif tag in ('-o', '--output'):
struct.output = []
while cli.next_isvalue(args):
val, *args = args
struct.output.append(val)
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
struct = Vexp()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-t', '--type'):
cli.check_next_isvalue(args, tag)
struct.type, *args = args
elif tag in ('-u', '--unit'):
cli.check_next_isvalue(args, tag)
struct.unit, *args = args
elif tag in ('-b', '--bound'):
cli.check_next_isvalue(args, tag)
struct.bound, *args = args
elif tag in ('-n', '--nb-steps'):
cli.check_next_isvalue(args, tag)
struct.nb_steps, *args = args
struct.nb_steps = int(struct.nb_steps)
elif tag in ('-inv', '--inverse'):
val = False
if cli.next_isvalue(args):
val, *args = args
if val[0] == 'f':
val = False
elif val[0] == 't':
val = True
else:
val = bool(int(val))
struct.inv = val
elif tag in ('-o', '--output'):
struct.output = []
while cli.next_isvalue(args):
val, *args = args
struct.output.append(val)
elif tag in ('-cpu', '--cpu'):
struct.device = 'cpu'
elif tag in ('-gpu', '--gpu'):
struct.device = 'cuda'
if cli.next_isvalue(args):
gpu, *args = args
struct.device = 'cuda:{:d}'.format(int(gpu))
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
"""
Parameters
----------
args
Returns
-------
"""
struct = Chunk()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-d', '--dim', '--dimension'):
cli.check_next_isvalue(args, tag)
struct.dim, *args = args
struct.dim = int(struct.dim)
elif tag in ('-n', '--chunk'):
cli.check_next_isvalue(args, tag)
struct.chunk, *args = args
struct.chunk = int(struct.chunk)
elif tag in ('-o', '--output'):
struct.output = []
while cli.next_isvalue(args):
val, *args = args
struct.output.append(val)
elif tag in ('t', '--transform'):
if not cli.next_isvalue(args):
struct.transform = ['{dir}{sep}{base}_2_{i}.lta']
else:
struct.transform = []
while cli.next_isvalue(args):
val, *args = args
struct.transform.append(val)
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
"""
Parameters
----------
args : list of str
Command line arguments (without the command name)
Returns
-------
Info
Filled structure
"""
struct = Info()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-m', '--meta'):
struct.meta = []
while cli.next_isvalue(args):
val, *args = args
struct.meta.append(val)
elif tag in ('-s', '--stat'):
struct.stat = True
if cli.next_isvalue(args):
val, *args = args
if val.lower().startswith('f'):
val = False
elif val.lower().startswith('t'):
val = True
struct.stat = bool(int(val))
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
struct = Crop()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-s', '--size'):
struct.size = []
while cli.next_isvalue(args):
val, *args = args
if val.lower() in ('vox', 'ras'):
struct.size_space = val
else:
struct.size.append(float(val))
elif tag in ('-c', '--center'):
struct.center = []
while cli.next_isvalue(args):
val, *args = args
if val.lower() in ('vox', 'ras'):
struct.center_space = val
else:
struct.center.append(float(val))
elif tag in ('-b', '--bounding-box'):
struct.bbox = True
if cli.next_isvalue(args):
struct.bbox = float(args.pop(0))
elif tag in ('-k', '--like'):
cli.check_next_isvalue(args, tag)
struct.like = args.pop(0)
elif tag in ('-o', '--output'):
struct.output = []
while cli.next_isvalue(args):
val, *args = args
struct.output.append(val)
elif tag in ('-t', '--transform'):
if not cli.next_isvalue(args):
struct.transform = ['{dir}{sep}{base}.crop.lta']
else:
struct.transform = []
while cli.next_isvalue(args):
val, *args = args
struct.transform.append(val)
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
struct = Pad()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-s', '--size'):
struct.size = []
while cli.next_isvalue(args):
val, *args = args
if val.lower() in ('vox', 'ras'):
struct.size_space = val
elif '(' in val or '[' in val:
bracket = ')' if '(' in val else ']'
while cli.next_isvalue(args):
tmp, *args = args
val += tmp
if bracket in tmp:
val = ast.literal_eval(val)
struct.size.append(val)
break
else:
struct.size.append(float(val))
elif tag in ('-k', '--like'):
cli.check_next_isvalue(args, tag)
struct.like = args.pop(0)
elif tag in ('-b', '--bound'):
cli.check_next_isvalue(args, tag)
struct.bound = args.pop(0)
if struct.bound not in ('zero', 'dft', 'dct', 'dct2', 'replicate'):
struct.bound = float(struct.bound)
if struct.bound == 'zero':
struct.bound = 0.
elif tag in ('-o', '--output'):
struct.output = []
while cli.next_isvalue(args):
val, *args = args
struct.output.append(val)
elif tag in ('-t', '--transform'):
if not cli.next_isvalue(args):
struct.transform = ['{dir}{sep}{base}.crop.lta']
else:
struct.transform = []
while cli.next_isvalue(args):
val, *args = args
struct.transform.append(val)
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
"""Parse AutoGrad's command-line arguments"""
# This is the object that we will populate
options = Composer()
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
# Parse transforms
if tag in (*trf, *itrf):
args = parse_transform([tag, *args], options)
# Help -> return empty option
elif tag in ('-h', '--help'):
print(help)
return {}
# Parse remaining top-level tags
elif tag in ('-t', '--target'):
cli.check_next_isvalue(args, tag)
options.target, *args = args
elif tag in ('-o', '--output'):
cli.check_next_isvalue(args, tag)
options.output, *args = args
elif tag in ('-ou', '--output-unit'):
cli.check_next_isvalue(args, tag)
options.output_unit, *args = args
elif tag in ('-cpu', '--cpu'):
options.device = 'cpu'
elif tag in ('-gpu', '--gpu'):
options.device = 'cuda'
if cli.next_isvalue(args):
gpu, *args = args
options.device = 'cuda:{:d}'.format(int(gpu))
# Something went wrong
else:
raise ParseError(f'Unknown tag {tag}')
return options
def parse(args):
"""
Parameters
----------
args
Returns
-------
"""
struct = Patch()
cli.check_next_isvalue(args)
struct.file = args.pop(0)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-n', '--size'):
struct.size = []
while cli.next_isvalue(args):
struct.size.append(int(args.pop(0)))
elif tag in ('-s', '--stride'):
struct.stride = []
while cli.next_isvalue(args):
struct.stride.append(int(args.pop(0)))
elif tag in ('-o', '--output'):
struct.output = []
while cli.next_isvalue(args):
struct.output.append(args.pop(0))
elif tag in ('t', '--transform'):
if not cli.next_isvalue(args):
struct.transform = ['{dir}{sep}{base}_to_{i}_{j}_{k}.lta']
else:
struct.transform = []
while cli.next_isvalue(args):
struct.transform.append(args.pop(0))
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse_transform(args, options):
tag, *args = args
# is it an inversed transform?
inv = False
if tag in itrf:
inv = True
if tag.startswith('--'):
tag = tag.split('--inverse')[0]
else:
tag = '-' + tag[2:]
opt = (struct.Linear if tag in lin else struct.Displacement
if tag in disp else struct.Velocity if tag in vel else None)
opt = opt()
opt.inv = inv
cli.check_next_isvalue(args, tag)
opt.file, *args = args
if isinstance(opt, struct.Velocity) and cli.next_isvalue(args):
opt.json, *args = args
while cli.next_istag(args):
tag, *args = args
if isinstance(opt, struct.Displacement) and tag in ('-n', '--order'):
cli.check_next_isvalue(args, tag)
opt.order, *args = args
opt.order = int(opt.order)
if isinstance(opt, struct.Displacement) and tag in ('-u', '--unit'):
cli.check_next_isvalue(args, tag)
opt.unit, *args = args
else:
args = [tag, *args]
break
options.transformations.append(opt)
return args
def parse(args):
"""Parse the command-line arguments of the `nipool` command.
Parameters
----------
args : list of str
List of arguments, without the command name.
Returns
-------
Pool
Filled structure
"""
struct = Pool()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-w', '--window'):
struct.window = []
while cli.next_isvalue(args):
val, *args = args
struct.window.append(int(val))
elif tag in ('-s', '--stride'):
struct.stride = []
while cli.next_isvalue(args):
val, *args = args
struct.stride.append(int(val))
elif tag in ('-m', '--method'):
cli.check_next_isvalue(args, tag)
struct.method, *args = args
elif tag in ('-cpu', '--cpu'):
struct.device = 'cpu'
elif tag in ('-gpu', '--gpu'):
struct.device = 'cuda'
if cli.next_isvalue(args):
gpu, *args = args
struct.device = 'cuda:{:d}'.format(int(gpu))
elif tag in ('-d', '--dim', '--dimension'):
cli.check_next_isvalue(args, tag)
struct.dim, *args = args
elif tag in ('-o', '--output'):
struct.output = []
while cli.next_isvalue(args):
val, *args = args
struct.output.append(val)
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
"""Parse AutoGrad's command-line arguments"""
# This is the object that we will populate
options = struct.Reslicer()
# Get input files
while cli.next_isvalue(args):
val, *args = args
options.files.append(val)
while args:
if not cli.next_istag(args):
break
tag, *args = args
# Parse transforms
if tag in (*trf, *itrf):
args = parse_transform([tag, *args], options)
# Help -> return empty option
elif tag in ('-h', '--help'):
print(help)
return {}
# Parse remaining top-level tags
elif tag in ('-t', '--target'):
cli.check_next_isvalue(args, tag)
options.target, *args = args
elif tag in ('-o', '--output'):
options.output = []
while cli.next_isvalue(args):
val, *args = args
options.output.append(val)
elif tag in ('-i', '-inter', '--interpolation'):
cli.check_next_isvalue(args, tag)
options.interpolation, *args = args
options.interpolation = int(options.interpolation)
elif tag in ('-b', '-bnd', '--bound'):
cli.check_next_isvalue(args, tag)
options.bound, *args = args
elif tag in ('-p', '--prefilter'):
cli.check_next_isvalue(args, tag)
options.prefilter, *args = args
options.prefilter = (True if options.prefilter.lower()[0] in 'ty'
else False if options.prefilter.lower()[0]
in 'fn' else bool(int(options.prefilter)))
elif tag in ('-x', '-ex', '--extrapolate'):
options.extrapolate = False
elif tag in ('-v', '-vx', '--voxel-size'):
options.voxel_size = []
while cli.next_isvalue(args):
val, *args = args
options.voxel_size.append(float(val))
elif tag in ('-cpu', '--cpu'):
options.device = 'cpu'
elif tag in ('-gpu', '--gpu'):
options.device = 'cuda'
if cli.next_isvalue(args):
gpu, *args = args
options.device = 'cuda:{:d}'.format(int(gpu))
# Something went wrong
else:
print(help)
raise cli.ParseError(f'Argument {tag} does not seem to '
f'belong to a group')
return options
def parse(args):
"""Parse the command-line arguments of the `inpaint` command.
Parameters
----------
args : list of str
List of arguments, without the command name.
Returns
-------
InPaint
Filled structure
"""
struct = InPaint()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-m', '--missing'):
struct.missing = []
while cli.next_isvalue(args):
val, *args = args
struct.missing.append(float(val))
elif tag in ('-nrls', '--max-rls'):
cli.check_next_isvalue(args, tag)
struct.max_rls, *args = args
struct.max_rls = int(struct.max_rls)
elif tag in ('-trls', '--tol-rls'):
cli.check_next_isvalue(args, tag)
struct.tol_rls, *args = args
struct.tol_rls = float(struct.tol_rls)
elif tag in ('-ncg', '--max-cg'):
cli.check_next_isvalue(args, tag)
struct.max_cg, *args = args
struct.max_cg = int(struct.max_cg)
elif tag in ('-tcg', '--tol-cg'):
cli.check_next_isvalue(args, tag)
struct.tol_cg, *args = args
struct.tol_cg = float(struct.tol_cg)
elif tag in ('-cpu', '--cpu'):
struct.device = 'cpu'
elif tag in ('-gpu', '--gpu'):
struct.device = 'cuda'
if cli.next_isvalue(args):
gpu, *args = args
struct.device = 'cuda:{:d}'.format(int(gpu))
elif tag in ('-o', '--output'):
struct.output = []
while cli.next_isvalue(args):
val, *args = args
struct.output.append(val)
elif tag in ('-v', '--verbose'):
struct.verbose = 1
if cli.next_isvalue(args):
struct.verbose, *args = args
struct.verbose = int(struct.verbose)
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
def parse(args):
"""Parse the command-line arguments of the `denoise_mri` command.
Parameters
----------
args : list of str
List of arguments, without the command name.
Returns
-------
DenoiseMRI
Filled structure
"""
struct = DenoiseMRI()
struct.files = []
while cli.next_isvalue(args):
val, *args = args
struct.files.append(val)
while args:
if cli.next_isvalue(args):
raise ParseError(f'Value {args[0]} does not seem to belong '
f'to a tag.')
tag, *args = args
if tag in ('-s', '--lam_scl'):
cli.check_next_isvalue(args, tag)
struct.lam_scl, *args = args
struct.lam_scl = float(struct.lam_scl)
elif tag in ('-lr', '--learning_rate'):
cli.check_next_isvalue(args, tag)
struct.learning_rate, *args = args
struct.learning_rate = float(struct.learning_rate)
elif tag in ('-n', '--max_iter'):
cli.check_next_isvalue(args, tag)
struct.max_iter, *args = args
struct.max_iter = int(struct.max_iter)
elif tag in ('-t', '--tolerance'):
cli.check_next_isvalue(args, tag)
struct.tolerance, *args = args
struct.tolerance = float(struct.tolerance)
elif tag in ('-cpu', '--cpu'):
struct.device = 'cpu'
elif tag in ('-gpu', '--gpu'):
struct.device = 'cuda'
if cli.next_isvalue(args):
gpu, *args = args
struct.device = 'cuda:{:d}'.format(int(gpu))
elif tag in ('-o', '--dir_out'):
cli.check_next_isvalue(args, tag)
struct.dir_out, *args = args
struct.dir_out = str(struct.dir_out)
elif tag in ('-v', '--verbose'):
cli.check_next_isvalue(args, tag)
struct.verbose, *args = args
struct.verbose = bool(struct.verbose)
elif tag in ('-h', '--help'):
print(help)
return None
else:
raise ParseError(f'Unknown tag {tag}')
return struct
