def main(argv):
import getopt
# every possible variable
con = None
roi = None
sub = None
try:
# figure out this line
opts, args = getopt.getopt(argv, "h:m:c:s:j:v:r",
["mask=", "contrast=", "sub="])
except getopt.GetoptError:
print(
'run_cd_match_searchlight.py -m <maskfile> -c <contrast> -s <sub>')
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print(
'run_cd_match_searchlight.py -m <maskfile> -c <contrast> -s <sub>'
)
sys.exit()
elif opt in ("-m", "--mask"):
roi = arg
elif opt in ("-s", "--sub"):
sub = arg
elif opt in ("-j", "--jobs"):
analysisSettings["searchlight"]["n_jobs"] = int(arg)
elif opt in ("-v", "--verbose"):
analysisSettings["searchlight"]["verbose"] = int(arg)
elif opt in ("-r", "--radius"):
analysisSettings["searchlight"]["radius"] = int(arg)
# if not con:
# print "not a valid contrast... exiting"
# sys.exit(1)
if None in [sub, roi]:
print("Argument missing")
sys.exit(2)
logger = pu.setup_logger(os.path.join(paths['root'], 'analysis', sub,
'multivariate', 'searchlight',
"lss"),
fname="{}_CDMatch-MainRel".format(roi))
run_subject(sub,
roi,
settings=projectSettings,
options=analysisSettings,
logger=logger)
pu.write_to_logger("Session ended at " + str(datetime.now()),
logger=logger)
def main(_):
import getopt
# every possible variable
roi = FLAGS.mask
sub = FLAGS.sub
phase = FLAGS.phase
debug = FLAGS.debug
analysis = FLAGS.analysis
if FLAGS.jobs:
analysisSettings["searchlight"]["n_jobs"] = int(FLAGS.jobs)
if FLAGS.verbosity:
analysisSettings["searchlight"]["verbose"] = int(FLAGS.verbose)
if FLAGS.radius:
analysisSettings["searchlight"]["radius"] = int(FLAGS.radius)
# if not con:
# print "not a valid contrast... exiting"
# sys.exit(1)
if None in [sub, roi]:
print("Argument missing")
sys.exit(2)
logger = pu.setup_logger(os.path.join(paths['root'], 'analysis', sub,
'multivariate', 'searchlight',
"lss"),
fname="{}_{}-Match.log".format(roi, FLAGS.phase))
mask_file = os.path.join(paths["root"], "derivatives", sub, "masks",
"{}.nii.gz".format(roi))
if analysis == "cvsl":
pu.write_to_logger("Running MVPA", logger)
sl = CVSearchlight(sub,
mask_file,
phase=phase,
settings=analysisSettings["searchlight"],
logger=logger,
permutations=FLAGS.permutations)
slargs = {}
elif analysis == "rsa":
pu.write_to_logger("Running RSA", logger)
raw_models_df = pu.load_labels(
os.path.join(paths["code"], "labels/raw_models.csv"))
sl = RSASearchlight(sub,
mask_file,
phase=phase,
settings=analysisSettings["searchlight"],
logger=logger)
if FLAGS.phase == "CD":
sl.fmri_data = pu.index_img(sl.fmri_data, sl.selector.Match == '1')
sl.labels = sl.labels[sl.selector.Match == '1']
sl.selector = sl.labels
modelrdms, modelnames = get_cd_models(raw_models_df, sl.labels)
else:
modelnames = [
"mainrel", "rel", "numchar", "humanratings", "typicality",
"w2vdiff", "concatword", "accuracy", "rstpostprob9",
"rstpostprob79", "bart79thresh", "rstpostprob270",
"bartregressacc", "accregressbart"
]
model_rdms = get_model_rdms(raw_models_df, modelnames)
# modelrdms = model_rdms[(model_rdms.type == "full")].dropna(axis=1).values[:, 2:].astype(np.float64)
# deal with NAs in bart thresh
rdms = model_rdms[model_rdms.type == "full"]
bart = rdms[rdms.name == "rstpostprob79"].iloc[:, 2:].fillna(0)
acc = rdms[rdms.name == "accuracy"].iloc[:, 2:].fillna(0)
bart_regress_acc = sm.OLS(bart.T, acc.T).fit().resid
acc_regress_bart = sm.OLS(acc.T, bart.T).fit().resid
modelrdms = model_rdms[(
model_rdms.type == "full")].iloc[:,
2:].fillna(0).values.astype(
np.float64)
modelrdms = np.concatenate(
[modelrdms,
np.vstack([bart_regress_acc, acc_regress_bart])],
axis=0)
slargs = {"modelrdms": modelrdms}
else:
pu.write_to_logger("wrong analysis specified, exiting...", logger)
sys.exit(2)
if not debug:
_ = sl.run(**slargs)
pu.write_to_logger("Session ended at " + str(datetime.now()),
logger=logger)