def setup(self):
self.orig_path = os.getcwd()
self.tmpdir = tempfile.mkdtemp()
setup_fname = os.path.abspath('setup_example.py')
self.perm_fname = os.path.abspath('cli/permute_isc_within.py')
os.chdir(self.tmpdir)
subprocess.call(['python', setup_fname, 'test'])
print os.listdir('.')
f = h5py.File('test.h5')
E = subject.Exp(f)
print self.config
E.setup(self.config, create_conds=True)
cond = E.get_cond('test_cond')
for run in E.iter_runs(cond):
run.threshold(cond.attrs['threshold'], save=True)
E.gen_composite('test_cond')
isc_within(E, cond)
E.gen_cond_thresh('test_cond')
E.f.file.flush()
self.E = E
def setup(self):
self.orig_path = os.getcwd()
self.tmpdir = tempfile.mkdtemp()
setup_fname = os.path.abspath("setup_example.py")
self.perm_fname = os.path.abspath("cli/permute_isc_within.py")
os.chdir(self.tmpdir)
subprocess.call(["python", setup_fname, "test"])
print os.listdir(".")
f = h5py.File("test.h5")
E = subject.Exp(f)
print self.config
E.setup(self.config, create_conds=True)
cond = E.get_cond("test_cond")
for run in E.iter_runs(cond):
run.threshold(cond.attrs["threshold"], save=True)
E.gen_composite("test_cond")
isc_within(E, cond)
E.gen_cond_thresh("test_cond")
E.f.file.flush()
self.E = E
for condname in config['conds']:
cond = E.get_cond(condname)
for run in E.iter_runs(condname):
run.threshold(cond.attrs['threshold'], save=True)
# Alignment -------------------------------------------
a1 = E.f['rois/audenv_3mm_gdboth_wordscram_mean_thr0.2'][
...] #TODO remove hardcoded roi?
aud_env = cond['audio_env']
# Calculate lags over range, then set offset
lags = xrange(-5, 5)
for run in E.iter_runs(condname):
data = run.load(roi=a1, standardized=True,
threshold=True) #slice(None,None,None))
corrs = [lagcor(data, aud_env, h=h) for h in lags]
print corrs
offset = lags[np.argmax(corrs)]
run.attrs['offset'] = offset
# With offsets down, can generate composite
if condname != "dummy": E.gen_composite(condname)
# ISC Calculations ----------------------------------------
cond1 = E.get_cond('wordscram') # conditions for calculations
cond2 = E.get_cond('wordscram2')
# Run calculations
isc_within(E, cond1)
isc_between(E, cond1, cond2, method='inter-subject')
# Iterate over conditions ---------------------------------
for condname in config['conds']:
cond = E.get_cond(condname)
for run in E.iter_runs(condname):
run.threshold(cond.attrs['threshold'], save=True)
# Alignment -------------------------------------------
a1 = E.f['rois/audenv_3mm_gdboth_wordscram_mean_thr0.2'][...] #TODO remove hardcoded roi?
aud_env = cond['audio_env']
# Calculate lags over range, then set offset
lags = xrange(-5,5)
for run in E.iter_runs(condname):
data = run.load(roi=a1, standardized=True, threshold=True)#slice(None,None,None))
corrs = [lagcor(data, aud_env, h=h) for h in lags]
print corrs
offset = lags[np.argmax(corrs)]
run.attrs['offset'] = offset
# With offsets down, can generate composite
if condname != "dummy":E.gen_composite(condname)
# ISC Calculations ----------------------------------------
cond1 = E.get_cond('wordscram') # conditions for calculations
cond2 = E.get_cond('wordscram2')
# Run calculations
isc_within(E, cond1)
isc_between(E, cond1, cond2, method='inter-subject')