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)
"log_det_relative_first_level", file=analysis_csv)
for subj_id, subject in chain_output.determinants_from_common_avg_to_subject.items():
for timept, img in subject.time_pt_dict.items():
# these rows contain full_det, fwhm, inv_xfm, log_full_det, log_nlin_det,... (some more)
for i, row in img.iterrows():
#import pdb; pdb.set_trace()
if timept != subject.intersubject_registration_time_pt:
# TODO: this is not really the proper way of dealing with things. If
# the code above changes (i.e., if the filenames change) this won't work anymore...
from_subject_common_absolute = os.path.realpath(re.sub(".mnc", "_resampled_to_common.mnc", chain_output.determinants_from_subject_common_to_subject[subj_id].time_pt_dict[timept].ix[i].log_full_det.path))
from_subject_common_relative = os.path.realpath(re.sub(".mnc", "_resampled_to_common.mnc", chain_output.determinants_from_subject_common_to_subject[subj_id].time_pt_dict[timept].ix[i].log_nlin_det.path))
else:
from_subject_common_absolute = "NA"
from_subject_common_relative = "NA"
print(",".join([str(subj_id), str(timept), str(row.fwhm), os.path.realpath(row.log_full_det.path),
os.path.realpath(row.log_nlin_det.path), from_subject_common_absolute, from_subject_common_relative]),file=analysis_csv)
#, ",",
#chain_output.determinants_from_subject_common_to_subject[subj_id].time_pt_dict[timept].ix[i].log_full_det.path, ",",
#chain_output.determinants_from_subject_common_to_subject[subj_id].time_pt_dict[timept].ix[i].log_nlin_det.path
#)
analysis_csv.close()
#import pdb; pdb.set_trace()
#Namespace(non_rigid_xfms_to_common=non_rigid_xfms_to_common_avg,
# determinants_from_common_avg_to_subject=determinants_from_common_avg_to_subject,
# determinants_from_subject_common_to_subject
#chain_stages = chain(options).stages
execute(chain_result.stages, options)
