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)