def setup_class(self):
basedir = os.path.split(os.path.abspath(__file__))[0]
fname_anscombe = os.path.join(basedir, 'data/anscombe.csv')
#a, b, solution, decimal
self.ts = {}
anscomb = np.genfromtxt(
fname_anscombe, delimiter=',',
names=True) #columns are x1, .., x4, y1, .., y4
for ii in range(1, 5):
anscombe_xy = [anscomb['x%s' % ii], anscomb['y%s' % ii]]
stand_xy = map(lambda s: standardize(s), anscombe_xy)
sol = [.8165, 3]
self.ts['anscombe%s' % ii] = anscombe_xy + sol
self.ts['anscombe_stand%s' % ii] = stand_xy + sol
a = np.arange(11)
self.ts['linear'] = [a, a * 2 + 10, 1]
#make 3 dim array
test = ['anscombe%s' % ii for ii in range(1, 5)] + ['linear']
#fix for order issues with dict
self.a_3dim = np.array(
[v[0] for k, v in self.ts.iteritems() if k in test])
self.b_3dim = np.array(
[v[1] for k, v in self.ts.iteritems() if k in test])
self.corrs_3dim = np.array(
[v[2] for k, v in self.ts.iteritems() if k in test])
def crosscor_full(A, B=None, nan_thresh=None):
"""From data (dims sub x seg x vox) calculate sub against others pattern cor
Parameters:
A: sub x seg x vox matrix
B: (optional) seg x vox matrix
Returns:
seg x seg correlation matrix
"""
# standardize all along last dim, so don't need to in correlation
A = standardize(A)
all_cors = []
# Within group correlations
if B is None:
others = sum_tc(A)
for sub in A:
# check for nan
to_remove = np.any(np.isnan(sub), axis=0)
if np.any(to_remove):
tmp_sub = sub[..., to_remove]
tmp_others = others[..., to_remove]
else:
tmp_sub, tmp_others = sub, others
# cross correlate (1 x seg x seg)
if nan_thresh is not None and to_remove.mean() > nan_thresh:
cormat = np.empty(sub.shape[0:1] * 2) * np.nan
else:
cormat = crosscor(tmp_sub,
standardize(tmp_others - tmp_sub),
standardized=True)
all_cors.append(cormat)
return np.array(all_cors)
# Between group correlations
else:
B = standardize(B)
for sub in A:
cormat = crosscor(sub, B, standardized=True)
all_cors.append(cormat)
return np.array(all_cors)
def load_mvpa(all_fnames, TRs, bad_vox, offset_TR, collapse=True):
"""Return matrix of shape (sub x seg x vox)
Parameters:
all_fnames: names of nifti files to load for sub dimension
TRs: dataframe with cond column and order column
bad_vox: mask with true for voxels to be discarded
offset_TR: TRs to shift timecourses before subsetting (to take into account lag, etc..)
collapse: whether to take mean along last axis
Notes:
If collapse is False, then sub and seg dims are lists.
"""
subs_list = []
for fname in all_fnames:
# Load Array
if type(fname) is str:
subname, ext = os.path.splitext(os.path.split(fname)[-1])
#subkey = "_".join(subname.split('_')[:2])
arr = np.load(fname)
else:
arr = fname
# Standardize, make sure no NaNs
arr = standardize(arr)[~bad_vox if bad_vox is not None else
Ellipsis] #TODO write more clearly
#arr = arr[ np.isnan(arr).sum(axis=-1) == 0] #remove any nans (from no var?)
# Get individual segments
# since it sorts in order of columns, will be sorted by cond first, then order
segs_list = []
cond_list = []
# TODO remove hard coded conditions
for ii, g in TRs.query("cond in ['Slumlord', 'Overview']").groupby(
['cond', 'order']):
#print ii
cond_list.append(ii)
segarr = subset_from_TRs(arr, g, offset=offset_TR)
segs_list.append(segarr)
# optionally collapse time dimension
if collapse:
mat = np.vstack([seg.mean(axis=1) for seg in segs_list])
subs_list.append(mat)
else:
subs_list.append(segs_list)
#print cond_list
M = np.array(
subs_list
) if collapse else subs_list # Make field array, with sub names?
return M
def crosscor_full(A, B=None, nan_thresh=None):
"""From data (dims sub x seg x vox) calculate sub against others pattern cor
Parameters:
A: sub x seg x vox matrix
B: (optional) seg x vox matrix
Returns:
seg x seg correlation matrix
"""
# standardize all along last dim, so don't need to in correlation
A = standardize(A)
all_cors = []
# Within group correlations
if B is None:
others = sum_tc(A)
for sub in A:
# check for nan
to_remove = np.any(np.isnan(sub), axis=0)
if np.any(to_remove):
tmp_sub = sub[...,to_remove]
tmp_others = others[..., to_remove]
else:
tmp_sub, tmp_others = sub, others
# cross correlate (1 x seg x seg)
if nan_thresh is not None and to_remove.mean() > nan_thresh:
cormat = np.empty(sub.shape[0:1]*2) * np.nan
else:
cormat = crosscor(tmp_sub, standardize(tmp_others - tmp_sub), standardized=True)
all_cors.append(cormat)
return np.array(all_cors)
# Between group correlations
else:
B = standardize(B)
for sub in A:
cormat = crosscor(sub, B, standardized=True)
all_cors.append(cormat)
return np.array(all_cors)
def load_mvpa(all_fnames, TRs, bad_vox, offset_TR, collapse=True):
"""Return matrix of shape (sub x seg x vox)
Parameters:
all_fnames: names of nifti files to load for sub dimension
TRs: dataframe with cond column and order column
bad_vox: mask with true for voxels to be discarded
offset_TR: TRs to shift timecourses before subsetting (to take into account lag, etc..)
collapse: whether to take mean along last axis
Notes:
If collapse is False, then sub and seg dims are lists.
"""
subs_list = []
for fname in all_fnames:
# Load Array
if type(fname) is str:
subname, ext = os.path.splitext(os.path.split(fname)[-1])
#subkey = "_".join(subname.split('_')[:2])
arr = np.load(fname)
else: arr = fname
# Standardize, make sure no NaNs
arr = standardize(arr)[~bad_vox if bad_vox is not None else Ellipsis] #TODO write more clearly
#arr = arr[ np.isnan(arr).sum(axis=-1) == 0] #remove any nans (from no var?)
# Get individual segments
# since it sorts in order of columns, will be sorted by cond first, then order
segs_list = []
cond_list = []
# TODO remove hard coded conditions
for ii, g in TRs.query("cond in ['Slumlord', 'Overview']").groupby(['cond', 'order']):
#print ii
cond_list.append(ii)
segarr = subset_from_TRs(arr, g, offset=offset_TR)
segs_list.append(segarr)
# optionally collapse time dimension
if collapse:
mat = np.vstack([seg.mean(axis=1) for seg in segs_list])
subs_list.append(mat)
else:
subs_list.append(segs_list)
#print cond_list
M = np.array(subs_list) if collapse else subs_list # Make field array, with sub names?
return M
def setup_class(self):
basedir = os.path.split(os.path.abspath(__file__))[0]
fname_anscombe = os.path.join(basedir, 'data/anscombe.csv')
#a, b, solution, decimal
self.ts = {}
anscomb = np.genfromtxt(fname_anscombe, delimiter=',', names=True) #columns are x1, .., x4, y1, .., y4
for ii in range(1,5):
anscombe_xy = [anscomb['x%s'%ii], anscomb['y%s'%ii]]
stand_xy = map(lambda s: standardize(s), anscombe_xy)
sol = [.8165, 3]
self.ts['anscombe%s'%ii] = anscombe_xy + sol
self.ts['anscombe_stand%s'%ii] = stand_xy + sol
a = np.arange(11)
self.ts['linear'] = [a, a*2 + 10, 1]
#make 3 dim array
test = ['anscombe%s'%ii for ii in range(1,5)] + ['linear']
#fix for order issues with dict
self.a_3dim = np.array([v[0] for k, v in self.ts.iteritems() if k in test])
self.b_3dim = np.array([v[1] for k, v in self.ts.iteritems() if k in test])
self.corrs_3dim = np.array([v[2] for k, v in self.ts.iteritems() if k in test])
def test_python_list(self): #can take python array
el = list(self.S1)
a = [el, el]
M = np.array([self.S1, self.S1])
assert_almost_equal(standardize(a), standardize(M))
def test_python_list(self): #can take python array
el = list(self.S1)
a = [el, el]
M = np.array([self.S1, self.S1])
assert_almost_equal(standardize(a), standardize(M))
def test_axis_arg(self): #axis arg returns arr with expected shape
tmp_M = np.array([np.ones(3), np.zeros(3)])
tmp_stand = standardize(tmp_M, axis=0)
assert_almost_equal(tmp_stand.shape, tmp_M.shape)
def test_inplace_equals_copy(self): #equal results for copy and inplace
S1_inplace = standardize(self.S1, inplace=True)
assert_almost_equal(standardize(self.S1), S1_inplace)
def test_standardize_out_equal_standardize_func(self):
summed = sum_tc(self.a, standardize_out=True)
assert_almost_equal(summed, standardize(summed))
def test_standardize_out_equal_standardize_func(self):
summed = sum_tc(self.a, standardize_out=True)
assert_almost_equal(summed, standardize(summed))
def test_returns_inplace_arg(self): #can work inplace
tmp_S1 = self.S1.copy()
assert tmp_S1 is standardize(tmp_S1, inplace=True)
def test_returns_copy_by_default(self): #returns copy by default
assert self.S1 is not standardize(self.S1)
# 1) operating on correlation matrix
# 2) subtract each sub from summed tc and take correlation
# 3) correlate with summed tc, use correction given by Wherry
from nose import with_setup
import numpy as np
from numpy.testing import assert_almost_equal
from pycorr.funcs_correlate import standardize, corsubs, crosscor, intersubcorr
np.random.seed(10)
dims = (2,2, 10)
nsubs = 3
subs = [np.random.random(dims) for ii in range(nsubs)]
for M in subs: M[0,0] = range(dims[-1]) #0,0 is 1:N
for M in subs: standardize(M, inplace=True)
subs[0][1,1] = np.NAN #1,1 sub 0 has a NaN timecourse
C_all = crosscor(subs, standardized=True)
C_all[1,1,0] = np.NAN
isc1 = intersubcorr(C_all)
M_ttl = np.nansum(subs, axis=0)
isc2 = np.array([corsubs(M, M_ttl-M) for M in subs]).transpose([1,2,0])
isc3_list = []
for M in subs:
r_all = corsubs(M, M_ttl)
s_all = np.std(M_ttl, axis=-1, ddof=1)
s_i = np.std(M, axis=-1, ddof=1)
M_cors = (r_all*s_all - s_i) / \
def test_returns_copy_by_default(self): #returns copy by default
assert self.S1 is not standardize(self.S1)
def test_returns_inplace_arg(self): #can work inplace
tmp_S1 = self.S1.copy()
assert tmp_S1 is standardize(tmp_S1, inplace=True)
def test_standardize_in_equal_standardize_func(self):
stand_a = standardize(self.a)
assert_almost_equal(sum_tc(self.a, standardize_subs=True),
sum_tc(stand_a, standardize_subs=False))
def test_standardize_in_equal_standardize_func(self):
stand_a = standardize(self.a)
assert_almost_equal(sum_tc(self.a, standardize_subs=True),
sum_tc(stand_a, standardize_subs=False))
def test_inplace_equals_copy(self): #equal results for copy and inplace
S1_inplace = standardize(self.S1, inplace=True)
assert_almost_equal(standardize(self.S1), S1_inplace)
def test_inplace_int(self): #int arrays never operate inplace
tmp_S1 = self.S1.astype(int)
assert tmp_S1 is not standardize(tmp_S1, inplace=True)
assert_almost_equal(standardize(tmp_S1),
standardize(tmp_S1, inplace=True))
def test_inplace_int(self): #int arrays never operate inplace
tmp_S1 = self.S1.astype(int)
assert tmp_S1 is not standardize(tmp_S1, inplace=True)
assert_almost_equal(standardize(tmp_S1), standardize(tmp_S1, inplace=True))
def test_no_demean(self):
print self.S1
print standardize(self.S1, demean=False)
assert not np.allclose(standardize(self.S1, demean=False).mean(), 0)
def test_axis_arg(self): #axis arg returns arr with expected shape
tmp_M = np.array([np.ones(3), np.zeros(3)])
tmp_stand = standardize(tmp_M, axis=0)
assert_almost_equal(tmp_stand.shape, tmp_M.shape)
def test_no_demean(self):
print self.S1
print standardize(self.S1, demean=False)
assert not np.allclose(standardize(self.S1, demean=False).mean(), 0)
# 3) correlate with summed tc, use correction given by Wherry
from nose import with_setup
import numpy as np
from numpy.testing import assert_almost_equal
from pycorr.funcs_correlate import standardize, corsubs, crosscor, intersubcorr
np.random.seed(10)
dims = (2, 2, 10)
nsubs = 3
subs = [np.random.random(dims) for ii in range(nsubs)]
for M in subs:
M[0, 0] = range(dims[-1]) #0,0 is 1:N
for M in subs:
standardize(M, inplace=True)
subs[0][1, 1] = np.NAN #1,1 sub 0 has a NaN timecourse
C_all = crosscor(subs, standardized=True)
C_all[1, 1, 0] = np.NAN
isc1 = intersubcorr(C_all)
M_ttl = np.nansum(subs, axis=0)
isc2 = np.array([corsubs(M, M_ttl - M) for M in subs]).transpose([1, 2, 0])
isc3_list = []
for M in subs:
r_all = corsubs(M, M_ttl)
s_all = np.std(M_ttl, axis=-1, ddof=1)
s_i = np.std(M, axis=-1, ddof=1)
M_cors = (r_all*s_all - s_i) / \