def beams(self):
if self._loaded:
bl = self._blist
del self._blist
return bl
bl = [tfb.tfbeam_from_file(f, **self._b_kwargs) for f in self._blist]
self.__beam_sanity_check(bl)
del self._blist
return bl
def perform_activation_ttest(dir=None, ptr=None):
if dir is not None:
glob_str = os.path.join(dir, "s_beam*spatnorm*mat")
mat_files = glob.glob(glob_str)
# get all beams in dir, with subject and condition labels for each beam
beam_list = [tfbeam_from_file(mfile, fixed_comparison="F dB") for mfile in mat_files]
subj_labels = range(1, len(beam_list) + 1)
cond_labels = [1] * len(subj_labels)
a_comp = bstat.BeamActivationAverager(beam_list, subj_labels, cond_labels)
elif ptr is not None:
a_comp = bstat.BeamActivationAverager.from_matlab_ptr_file(ptr, ratio_type="F dB")
# do an activation test on condition 1
one_samp_t = bstat.SnPMOneSampT(a_comp, 1, 0, force_half_perms=True)
s_res = one_samp_t.test()
return s_res, one_samp_t.avg_beams[0]
def _main(mode='real'):
condition_1_spec = [
('subj1', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub1/s_beamtf_listenfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj2', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub2/s_beamtf_listenfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj3', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub3/s_beamtf_listenfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj4', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub4/s_beamtf_listenfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj5', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub5/s_beamtf_listenfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj6', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub6/s_beamtf_listenfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
]
condition_2_spec = [
('subj1', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub1/s_beamtf_speakfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj2', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub2/s_beamtf_speakfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj3', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub3/s_beamtf_speakfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj4', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub4/s_beamtf_speakfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj5', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub5/s_beamtf_speakfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
('subj6', '/Users/mike/workywork/nutmeg-py/data/meg_6subj2cond/sub6/s_beamtf_speakfirst75Lhemi_firlsbp200_bf_SAM_all_spatnorm.mat'),
]
if mode=='real':
c1 = Condition(subjs=[Subject(name=nm, fpath=fp)
for nm, fp in condition_1_spec],
cname='listen_first')
c2 = Condition(subjs=[Subject(name=nm, fpath=fp)
for nm, fp in condition_2_spec],
cname='speak_first')
demo = ListOfConditions(conditions=[c1, c2])
return demo
elif mode=='synth_contrast':
from nutmeg.stats.tests import synth_activations
n_subjs = 6
def save_beams(bl, sl, cl):
pl = []
for b, s, c in zip(bl, sl, cl):
p = 'synth_beam_s%d_c%d'%(s, c)
pl.append(os.path.abspath(p)+'.npy')
b.save(p)
return pl
beam = tfbeam.tfbeam_from_file(condition_1_spec[0][1],
fixed_comparison='F dB')
c1b = synth_activations.synthetic_gaussian_activity_like(
beam, n_beams=n_subjs,
tf_pts=[ (t,1) for t in xrange(4,13) ],
locs = ( (-20,-30,-30), (-15,3,15), (-18,15,0) ),
size=14.,
mode='activation'
)
c1_subjs = range(1,n_subjs+1)
c1_labels = [1] * n_subjs
c1_paths = save_beams(c1b, c1_subjs, c1_labels)
c2b = synth_activations.synthetic_gaussian_activity_like(
beam, n_beams=n_subjs,
tf_pts=[ (t,1) for t in xrange(4,13) ],
locs = ( (-20,-30,-30), (-15,3,15), (-18,15,0) ),
size=14.,
mode='activation', pval=.1
)
c2_subjs = range(1,n_subjs+1)
c2_labels = [2] * n_subjs
c2_paths = save_beams(c2b, c2_subjs, c2_labels)
c3b = synth_activations.synthetic_gaussian_activity_like(
beam, n_beams=n_subjs, mode='activation',
tf_pts=[ (t,1) for t in xrange(4,13) ],
locs = ( (-20,-30,-30), (-15,3,15), (-18,15,0) ),
size=14.
)
c3_subjs = range(1,n_subjs+1)
c3_labels = [3] * n_subjs
c3_paths = save_beams(c3b, c3_subjs, c3_labels)
c4b = synth_activations.synthetic_gaussian_activity_like(
beam, n_beams=n_subjs, mode='activation', pval=.6,
tf_pts=[ (t,1) for t in xrange(4,13) ],
locs = ( (-20,-30,-30), (-15,3,15), (-18,15,0) ),
size=14.
)
c4_subjs = range(1,n_subjs+1)
c4_labels = [4] * n_subjs
c4_paths = save_beams(c4b, c4_subjs, c4_labels)
conds = [ Condition(subjs=[Subject(name=str(nm), fpath=fp)
for nm, fp in zip(subjs, paths)],
name=cname)
for subjs, paths, cname in zip( [c1_subjs, c2_subjs,
c3_subjs, c4_subjs],
[c1_paths, c2_paths,
c3_paths, c4_paths],
['1', '2', '3', '4'] ) ]
demo = ListOfConditions(conditions=conds)
return demo