def four_mbm_parse(four_mbm_parser):
return parse(four_mbm_parser, ["--first-two-mbm1-lsq12-max-pairs=22",
"--first-two-mbm2-lsq12-max-pairs", "23",
"--last-two-mbm1-lsq12-max-pairs=24",
"--last-two-mbm2-lsq12-max-pairs=25",
"--first-two-mbm1-bootstrap", "--first-two-mbm2-bootstrap",
"--last-two-mbm1-bootstrap", "--last-two-mbm2-bootstrap"])
def main(args):
p = CompoundParser([
execution_parser, application_parser, registration_parser,
AnnotatedParser(parser=mk_mbm_parser(), namespace="mbm")
])
options = parse(p, args[1:])
stages = asymmetry_pipeline(options).stages
execute(stages, options)
def main(args):
p = CompoundParser(
[execution_parser,
application_parser,
registration_parser,
AnnotatedParser(parser=mbm_parser, namespace="mbm")])
options = parse(p, args[1:])
stages = asymmetry_pipeline(options).stages
execute(stages, options)
def main(args):
# TODO rewrite using `mk_application`
p = CompoundParser([
execution_parser, application_parser, registration_parser,
tamarack_parser,
AnnotatedParser(parser=mbm_parser, namespace="mbm")
])
options = parse(p, args[1:])
stages = tamarack_pipeline(options).stages
execute(stages, options)
def main(args):
# this is probably too much heavy machinery since the options aren't tree-shaped; could just use previous style
p = CompoundParser(
[execution_parser,
application_parser,
registration_parser, #cast=RegistrationConf),
lsq12_parser])
options = parse(p, args[1:])
stages = LSQ12_pipeline(options).stages
execute(stages, options)
def main(args):
# TODO rewrite using `mk_application`
p = CompoundParser(
[execution_parser,
application_parser,
registration_parser,
tamarack_parser,
AnnotatedParser(parser=mbm_parser, namespace="mbm")])
options = parse(p, args[1:])
stages = tamarack_pipeline(options).stages
execute(stages, options)
def main(args):
# this is probably too much heavy machinery since the options aren't tree-shaped; could just use previous style
p = CompoundParser([
execution_parser,
application_parser,
registration_parser, #cast=RegistrationConf),
lsq12_parser
])
options = parse(p, args[1:])
stages = LSQ12_pipeline(options).stages
execute(stages, options)
def main(args):
p = CompoundParser(
[execution_parser,
application_parser,
registration_parser,
#twolevel_parser,
AnnotatedParser(parser=mk_mbm_parser(with_common_space=False), namespace="mbm"), # TODO use this before 1st-/2nd-level args
# TODO to combine the information from all three MBM parsers,
# could use `ConfigArgParse`r `_source_to_settings` (others?) to check whether an option was defaulted
# or user-specified, allowing the first/second-level options to override the general mbm settings
#AnnotatedParser(parser=mbm_parser, namespace="first_level", prefix="first-level"),
#AnnotatedParser(parser=mbm_parser, namespace="second_level", prefix="second-level"),
#stats_parser
#segmentation_parser
]) # TODO add more stats parsers?
options = parse(p, args[1:])
execute(two_level_pipeline(options).stages, options)
def main(args):
p = CompoundParser([
execution_parser,
application_parser,
registration_parser,
#twolevel_parser,
AnnotatedParser(
parser=mk_mbm_parser(with_common_space=False),
namespace="mbm"), # TODO use this before 1st-/2nd-level args
# TODO to combine the information from all three MBM parsers,
# could use `ConfigArgParse`r `_source_to_settings` (others?) to check whether an option was defaulted
# or user-specified, allowing the first/second-level options to override the general mbm settings
#AnnotatedParser(parser=mbm_parser, namespace="first_level", prefix="first-level"),
#AnnotatedParser(parser=mbm_parser, namespace="second_level", prefix="second-level"),
#stats_parser
#segmentation_parser
]) # TODO add more stats parsers?
options = parse(p, args[1:])
execute(two_level_pipeline(options).stages, options)
def f():
options = parse(p, sys.argv[1:])
execute(pipeline(options).stages, options)
def f():
options = parse(p, sys.argv[1:])
execute(pipeline(options).stages, options)
def application_parse(two_mbm_parser):
return parse(CompoundParser([application_parser,
AnnotatedParser(parser=two_mbm_parser, prefix="two-mbms", namespace="two-mbms")]),
["--two-mbms-mbm1-bootstrap", "--two-mbms-mbm2-bootstrap",
"--two-mbms-mbm1-lsq12-max-pairs", "23", "--two-mbms-mbm2-lsq12-max-pairs=24", "img_1.mnc"])
def two_mbm_parse(two_mbm_parser):
return parse(two_mbm_parser, ["--mbm1-lsq12-max-pairs=22", "--mbm1-bootstrap", "--mbm2-bootstrap"])
p = CompoundParser(
[execution_parser,
application_parser,
registration_parser,
lsq6_parser,
# TODO: either switch back to automatically unpacking as part of `parse`
# or write a helper to do \ns: C(**vars(ns))
lsq12_parser, # should be MBM or build_model ...
nlin_parser,
#AnnotatedParser(parser=BaseParser(addLSQ12ArgumentGroup), namespace='lsq12-inter-subj'),
#addNLINArgumentGroup,
stats_parser,
chain_parser])
# TODO could abstract and then parametrize by prefix/ns ??
options = parse(p, sys.argv[1:])
# TODO: the registration resolution should be set somewhat outside
# of any actual function? Maybe the right time to set this, is here
# when options are gathered?
if not options.registration.resolution:
# if the target for the registration_chain comes from the pride_of_models
# we can not use the registration_targets() function. The pride_of_models
# works in a fairly different way, so we will separate out that option.
if options.lsq6.target_type == TargetType.pride_of_models:
pride_of_models_mapping = get_pride_of_models_mapping(options.lsq6.target_file,
options.application.output_directory,
options.application.pipeline_name)
# all initial models that are part of the pride of models must have
# the same resolution (it's currently a requirement). So we can get the
# resolution from any of the RegistrationTargets: