def test_pickle():
ds = datasets.get_uts()
ds_2 = load.unpickle(file_path('uts-py2.pickle'))
assert_dataobj_equal(ds_2, ds)
ds_3 = load.unpickle(file_path('uts-py3.pickle'))
assert_dataobj_equal(ds_3, ds)
def test_melt_ndvar():
"Test table.melt_ndvar()"
ds = datasets.get_uts(True)
ds = ds.sub("A == 'a1'")
lds = table.melt_ndvar('uts', ds=ds)
ok_('time' in lds)
assert_is_instance(lds['time'], Var)
assert_array_equal(np.unique(lds['time'].x), ds['uts'].time)
# no ds
lds2 = table.melt_ndvar(ds['uts'])
assert_dataobj_equal(lds2['uts'], lds['uts'])
# sensor
lds = table.melt_ndvar("utsnd.summary(time=(0.1, 0.2))",
ds=ds,
varname='summary')
eq_(set(lds['sensor'].cells), set(ds['utsnd'].sensor.names))
# NDVar out
lds = table.melt_ndvar("utsnd", 'sensor', ds=ds)
ok_('utsnd' in lds)
assert_is_instance(lds['utsnd'], NDVar)
assert_dataobj_equal(lds[:ds.n_cases, 'utsnd'],
ds.eval("utsnd.sub(sensor='0')"))
# more than one dimensions
assert_raises(ValueError, table.melt_ndvar, 'utsnd', ds=ds)
def test_melt_ndvar():
"Test table.melt_ndvar()"
ds = datasets.get_uts(True)
ds = ds.sub("A == 'a1'")
lds = table.melt_ndvar("uts", ds=ds)
ok_("time" in lds)
ok_(isvar(lds["time"]))
eq_(set(lds["time"].x), set(ds["uts"].time.x))
# no ds
lds2 = table.melt_ndvar(ds["uts"])
assert_dataobj_equal(lds2["uts"], lds["uts"])
# sensor
lds = table.melt_ndvar("utsnd.summary(time=(0.1, 0.2))", ds=ds, varname="summary")
eq_(set(lds["sensor"].cells), set(ds["utsnd"].sensor.names))
# NDVar out
lds = table.melt_ndvar("utsnd", "sensor", ds=ds)
ok_("utsnd" in lds)
ok_(isndvar(lds["utsnd"]))
assert_dataobj_equal(lds[: ds.n_cases, "utsnd"], ds.eval("utsnd.sub(sensor='0')"))
# more than one dimensions
assert_raises(ValueError, table.melt_ndvar, "utsnd", ds=ds)
def test_ttest_ind():
"Test testnd.ttest_ind()"
ds = datasets.get_uts(True)
# basic
res = testnd.ttest_ind('uts', 'A', 'a1', 'a0', ds=ds)
eq_(repr(res), "<ttest_ind 'uts', 'A', 'a1' (n=30), 'a0' (n=30)>")
assert_less(res.p_uncorrected.min(), 0.05)
# persistence
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
eq_(repr(res_), "<ttest_ind 'uts', 'A', 'a1' (n=30), 'a0' (n=30)>")
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
# cluster
res = testnd.ttest_ind('uts', 'A', 'a1', 'a0', ds=ds, tail=1, samples=1)
# persistence
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
# nd
res = testnd.ttest_ind('utsnd',
'A',
'a1',
'a0',
ds=ds,
pmin=0.05,
samples=2)
eq_(res._cdist.n_clusters, 10)
# zero variance
ds['utsnd'].x[:, 1, 10] = 0.
assert_raises(ZeroVariance, testnd.ttest_ind, 'utsnd', 'A', ds=ds)
def test_corr():
"Test testnd.corr()"
ds = datasets.get_uts(True)
# add correlation
Y = ds['Y']
utsnd = ds['utsnd']
utsnd.x[:, 3:5, 50:65] += Y.x[:, None, None]
res = testnd.corr('utsnd', 'Y', ds=ds)
repr(res)
for s, t in product('01234', (0.1, 0.2, 0.35)):
target = test.Correlation(utsnd.sub(sensor=s, time=t), Y).r
assert_almost_equal(res.r.sub(sensor=s, time=t), target, 10)
res = testnd.corr('utsnd', 'Y', 'rm', ds=ds)
repr(res)
res = testnd.corr('utsnd', 'Y', ds=ds, samples=10, pmin=0.05)
repr(res)
res = testnd.corr('utsnd', 'Y', ds=ds, samples=10, tfce=True)
repr(res)
# persistence
string = pickle.dumps(res, protocol=pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
assert_dataobj_equal(res.p, res_.p)
def test_t_contrast():
ds = datasets.get_uts()
# simple contrast
res = testnd.t_contrast_rel('uts', 'A', 'a1>a0', 'rm', ds=ds, samples=10,
pmin=0.05)
repr(res)
res_ = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=ds)
assert_array_equal(res.t.x, res_.t.x)
assert_in('samples', repr(res))
# complex contrast
res = testnd.t_contrast_rel('uts', 'A%B', 'min(a0|b0>a1|b0, a0|b1>a1|b1)',
'rm', ds=ds, samples=10, pmin=0.05)
res_b0 = testnd.ttest_rel('uts', 'A%B', ('a0', 'b0'), ('a1', 'b0'), 'rm',
ds=ds)
res_b1 = testnd.ttest_rel('uts', 'A%B', ('a0', 'b1'), ('a1', 'b1'), 'rm',
ds=ds)
assert_array_equal(res.t.x, np.min([res_b0.t.x, res_b1.t.x], axis=0))
# persistence
string = pickle.dumps(res, protocol=pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p, res_.p)
# contrast with "*"
res = testnd.t_contrast_rel('uts', 'A%B', 'min(a1|b0>a0|b0, a1|b1>a0|b1)',
'rm', ds=ds, tail=1)
def test_t_contrast():
ds = datasets.get_uts()
# simple contrast
res = testnd.t_contrast_rel('uts', 'A', 'a1>a0', 'rm', ds=ds, samples=10,
pmin=0.05)
repr(res)
res_ = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=ds)
assert_array_equal(res.t.x, res_.t.x)
assert_in('samples', repr(res))
# complex contrast
res = testnd.t_contrast_rel('uts', 'A%B', 'min(a0|b0>a1|b0, a0|b1>a1|b1)',
'rm', ds=ds, samples=10, pmin=0.05)
res_b0 = testnd.ttest_rel('uts', 'A%B', ('a0', 'b0'), ('a1', 'b0'), 'rm',
ds=ds)
res_b1 = testnd.ttest_rel('uts', 'A%B', ('a0', 'b1'), ('a1', 'b1'), 'rm',
ds=ds)
assert_array_equal(res.t.x, np.min([res_b0.t.x, res_b1.t.x], axis=0))
# persistence
string = pickle.dumps(res, protocol=pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p, res_.p)
# contrast with "*"
res = testnd.t_contrast_rel('uts', 'A%B', 'min(a1|b0>a0|b0, a1|b1>a0|b1)',
'rm', ds=ds, tail=1)
def test_ttest_ind():
"Test testnd.ttest_ind()"
ds = datasets.get_uts(True)
# basic
res = testnd.ttest_ind('uts', 'A', 'a1', 'a0', ds=ds)
repr(res)
assert_less(res.p_uncorrected.min(), 0.05)
# persistence
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
repr(res_)
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
# cluster
res = testnd.ttest_ind('uts', 'A', 'a1', 'a0', ds=ds, tail=1, samples=1)
# persistence
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
# nd
res = testnd.ttest_ind('utsnd', 'A', 'a1', 'a0', ds=ds, pmin=0.05, samples=2)
eq_(res._cdist.n_clusters, 10)
def test_samples_sesssions():
set_log_level('warning', 'mne')
SampleExperiment = import_attr(sample_path / 'sample_experiment_sessions.py', 'SampleExperiment')
tempdir = TempDir()
datasets.setup_samples_experiment(tempdir, 2, 1, 2)
root = join(tempdir, 'SampleExperiment')
e = SampleExperiment(root)
# bad channels
e.make_bad_channels('0111')
eq_(e.load_bad_channels(), ['MEG 0111'])
eq_(e.load_bad_channels(session='sample2'), [])
e.show_bad_channels()
e.merge_bad_channels()
eq_(e.load_bad_channels(session='sample2'), ['MEG 0111'])
e.show_bad_channels()
# rejection
for _ in e:
for epoch in ('target1', 'target2'):
e.set(epoch=epoch)
e.make_rej(auto=2e-12)
ds = e.load_evoked('R0000', epoch='target2')
e.set(session='sample1')
ds2 = e.load_evoked('R0000')
assert_dataobj_equal(ds2, ds)
# super-epoch
ds1 = e.load_epochs(epoch='target1')
ds2 = e.load_epochs(epoch='target2')
ds_super = e.load_epochs(epoch='super')
assert_dataobj_equal(ds_super['meg'], combine((ds1['meg'], ds2['meg'])))
def test_result():
"Test boosting results"
ds = datasets._get_continuous()
# convolve function
y = convolve([ds['h1'], ds['h2']], [ds['x1'], ds['x2']])
y.name = 'y'
assert_dataobj_equal(y, ds['y'])
# test prediction with res.h and res.h_scaled
res = boosting(ds['y'], ds['x1'], 0, 1)
y1 = convolve(res.h_scaled, ds['x1'])
x_scaled = ds['x1'] / res.x_scale
y2 = convolve(res.h, x_scaled)
y2 *= res.y_scale
y2 += y1.mean() - y2.mean() # mean can't be reconstructed
assert_dataobj_equal(y1, y2, decimal=12)
# test NaN checks (modifies data)
ds['x2'].x[1, 50] = np.nan
assert_raises(ValueError, boosting, ds['y'], ds['x2'], 0, .5)
assert_raises(ValueError, boosting, ds['y'], ds['x2'], 0, .5, False)
ds['x2'].x[1, :] = 1
assert_raises(ValueError, boosting, ds['y'], ds['x2'], 0, .5)
ds['y'].x[50] = np.nan
assert_raises(ValueError, boosting, ds['y'], ds['x1'], 0, .5)
assert_raises(ValueError, boosting, ds['y'], ds['x1'], 0, .5, False)
def test_melt_ndvar():
"Test table.melt_ndvar()"
ds = datasets.get_uts(True)
ds = ds.sub("A == 'a1'")
lds = table.melt_ndvar('uts', ds=ds)
ok_('time' in lds)
ok_(isvar(lds['time']))
eq_(set(lds['time'].x), set(ds['uts'].time.x))
# no ds
lds2 = table.melt_ndvar(ds['uts'])
assert_dataobj_equal(lds2['uts'], lds['uts'])
# sensor
lds = table.melt_ndvar("utsnd.summary(time=(0.1, 0.2))", ds=ds, varname='summary')
eq_(set(lds['sensor'].cells), set(ds['utsnd'].sensor.names))
# NDVar out
lds = table.melt_ndvar("utsnd", 'sensor', ds=ds)
ok_('utsnd' in lds)
ok_(isndvar(lds['utsnd']))
assert_dataobj_equal(lds[:ds.n_cases, 'utsnd'], ds.eval("utsnd.sub(sensor='0')"))
# more than one dimensions
assert_raises(ValueError, table.melt_ndvar, 'utsnd', ds=ds)
def test_ttest_rel():
"Test testnd.ttest_rel()"
ds = datasets.get_uts(True)
# basic
res = testnd.ttest_rel('uts', 'A%B', ('a1', 'b1'), ('a0', 'b0'), 'rm',
ds=ds, samples=100)
eq_(repr(res), "<ttest_rel 'uts', 'A x B', ('a1', 'b1'), ('a0', 'b0'), "
"'rm' (n=15), samples=100, p >= 0.000>")
# persistence
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
repr(res_)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
# collapsing cells
res2 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=ds)
assert_less(res2.p_uncorrected.min(), 0.05)
assert_equal(res2.n, res.n)
# reproducibility
res3 = testnd.ttest_rel('uts', 'A%B', ('a1', 'b1'), ('a0', 'b0'), 'rm',
ds=ds, samples=100)
assert_dataset_equal(res3.find_clusters(maps=True), res.clusters)
testnd.configure(0)
res4 = testnd.ttest_rel('uts', 'A%B', ('a1', 'b1'), ('a0', 'b0'), 'rm',
ds=ds, samples=100)
assert_dataset_equal(res4.find_clusters(maps=True), res.clusters)
testnd.configure(-1)
sds = ds.sub("B=='b0'")
# thresholded, UTS
testnd.configure(0)
res0 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=sds, pmin=0.1,
samples=100)
tgt = res0.find_clusters()
testnd.configure(-1)
res1 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=sds, pmin=0.1,
samples=100)
assert_dataset_equal(res1.find_clusters(), tgt)
# thresholded, UTSND
testnd.configure(0)
res0 = testnd.ttest_rel('utsnd', 'A', 'a1', 'a0', 'rm', ds=sds, pmin=0.1,
samples=100)
tgt = res0.find_clusters()
testnd.configure(-1)
res1 = testnd.ttest_rel('utsnd', 'A', 'a1', 'a0', 'rm', ds=sds, pmin=0.1,
samples=100)
assert_dataset_equal(res1.find_clusters(), tgt)
# TFCE, UTS
testnd.configure(0)
res0 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=sds, tfce=True,
samples=10)
tgt = res0.compute_probability_map()
testnd.configure(-1)
res1 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=sds, tfce=True,
samples=10)
assert_dataobj_equal(res1.compute_probability_map(), tgt)
def test_ttest_rel():
"Test testnd.ttest_rel()"
ds = datasets.get_uts(True)
# basic
res = testnd.ttest_rel('uts', 'A%B', ('a1', 'b1'), ('a0', 'b0'), 'rm',
ds=ds, samples=100)
repr(res)
# persistence
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
repr(res_)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
# collapsing cells
res2 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=ds)
assert_less(res2.p_uncorrected.min(), 0.05)
assert_equal(res2.n, res.n)
# reproducibility
res3 = testnd.ttest_rel('uts', 'A%B', ('a1', 'b1'), ('a0', 'b0'), 'rm',
ds=ds, samples=100)
assert_dataset_equal(res3.find_clusters(maps=True), res.clusters)
testnd.configure(0)
res4 = testnd.ttest_rel('uts', 'A%B', ('a1', 'b1'), ('a0', 'b0'), 'rm',
ds=ds, samples=100)
assert_dataset_equal(res4.find_clusters(maps=True), res.clusters)
testnd.configure(-1)
sds = ds.sub("B=='b0'")
# thresholded, UTS
testnd.configure(0)
res0 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=sds, pmin=0.1,
samples=100)
tgt = res0.find_clusters()
testnd.configure(-1)
res1 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=sds, pmin=0.1,
samples=100)
assert_dataset_equal(res1.find_clusters(), tgt)
# thresholded, UTSND
testnd.configure(0)
res0 = testnd.ttest_rel('utsnd', 'A', 'a1', 'a0', 'rm', ds=sds, pmin=0.1,
samples=100)
tgt = res0.find_clusters()
testnd.configure(-1)
res1 = testnd.ttest_rel('utsnd', 'A', 'a1', 'a0', 'rm', ds=sds, pmin=0.1,
samples=100)
assert_dataset_equal(res1.find_clusters(), tgt)
# TFCE, UTS
testnd.configure(0)
res0 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=sds, tfce=True,
samples=10)
tgt = res0.compute_probability_map()
testnd.configure(-1)
res1 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=sds, tfce=True,
samples=10)
assert_dataobj_equal(res1.compute_probability_map(), tgt)
def test_ndvar_index(x, dimname, index, a_index, index_repr=True):
"Helper function for test_ndvar_indexing"
ax = x.get_axis(dimname)
index_prefix = (full_slice,) * ax
if dimname != 'case':
dim = x.get_dim(dimname)
assert_equal(dim.dimindex(index), a_index)
if index_repr is not False:
if index_repr is True:
index_repr = index
eq_(dim._index_repr(a_index), index_repr)
x_array = x.x[index_prefix + (a_index,)]
x1 = x.sub(**{dimname: index})
x2 = x[index_prefix + (index,)]
assert_array_equal(x1.x, x_array)
assert_dataobj_equal(x2, x1)
def test_dataset_indexing():
"""Test Dataset indexing"""
ds = datasets.get_uv()
# indexing values
eq_(ds['A', 1], ds['A'][1])
eq_(ds[1, 'A'], ds['A'][1])
# indexing variables
assert_dataobj_equal(ds[:, 'A'], ds['A'])
assert_dataobj_equal(ds['A', :], ds['A'])
assert_dataobj_equal(ds[:10, 'A'], ds['A'][:10])
assert_dataobj_equal(ds['A', :10], ds['A'][:10])
# new Dataset through indexing
ds2 = Dataset()
ds2['A'] = ds['A']
assert_dataset_equal(ds[('A',)], ds2)
ds2['B'] = ds['B']
assert_dataset_equal(ds['A', 'B'], ds2)
assert_dataset_equal(ds[('A', 'B'), :10], ds2[:10])
assert_dataset_equal(ds[:10, ('A', 'B')], ds2[:10])
# assigning value
ds[2, 'A'] = 'hello'
eq_(ds[2, 'A'], 'hello')
ds['A', 2] = 'not_hello'
eq_(ds[2, 'A'], 'not_hello')
# assigning new factor
ds['C', :] = 'c'
ok_(np.all(ds.eval("C == 'c'")))
# assigning new Var
ds['D1', :] = 5.
ds[:, 'D2'] = 5.
assert_array_equal(ds['D1'], 5)
assert_array_equal(ds['D2'], 5)
# test illegal names
f = Factor('aaabbb')
assert_raises(ValueError, ds.__setitem__, '%dsa', f)
assert_raises(ValueError, ds.__setitem__, '432', f)
assert_raises(ValueError, ds.__setitem__, ('%dsa', slice(None)), 'value')
assert_raises(ValueError, ds.__setitem__, (slice(None), '%dsa'), 'value')
assert_raises(ValueError, ds.__setitem__, ('432', slice(None)), 4.)
assert_raises(ValueError, ds.__setitem__, (slice(None), '432'), 4.)
# deleting items
del ds['A']
ok_('A' not in ds)
assert_raises(KeyError, ds.__getitem__, 'A')
del ds['B', 'rm']
ok_('B' not in ds and 'rm' not in ds)
def test_dataset_indexing():
"""Test Dataset indexing"""
ds = datasets.get_uv()
# indexing values
eq_(ds['A', 1], ds['A'][1])
eq_(ds[1, 'A'], ds['A'][1])
# indexing variables
assert_dataobj_equal(ds[:, 'A'], ds['A'])
assert_dataobj_equal(ds['A', :], ds['A'])
assert_dataobj_equal(ds[:10, 'A'], ds['A'][:10])
assert_dataobj_equal(ds['A', :10], ds['A'][:10])
# new Dataset through indexing
ds2 = Dataset()
ds2['A'] = ds['A']
assert_dataset_equal(ds[('A',)], ds2)
ds2['B'] = ds['B']
assert_dataset_equal(ds['A', 'B'], ds2)
assert_dataset_equal(ds[('A', 'B'), :10], ds2[:10])
assert_dataset_equal(ds[:10, ('A', 'B')], ds2[:10])
# assigning value
ds[2, 'A'] = 'hello'
eq_(ds[2, 'A'], 'hello')
ds['A', 2] = 'not_hello'
eq_(ds[2, 'A'], 'not_hello')
# assigning new factor
ds['C', :] = 'c'
ok_(np.all(ds.eval("C == 'c'")))
# assigning new Var
ds['D1', :] = 5.
ds[:, 'D2'] = 5.
assert_array_equal(ds['D1'], 5)
assert_array_equal(ds['D2'], 5)
# test illegal names
f = Factor('aaabbb')
assert_raises(ValueError, ds.__setitem__, '%dsa', f)
assert_raises(ValueError, ds.__setitem__, '432', f)
assert_raises(ValueError, ds.__setitem__, ('%dsa', slice(None)), 'value')
assert_raises(ValueError, ds.__setitem__, (slice(None), '%dsa'), 'value')
assert_raises(ValueError, ds.__setitem__, ('432', slice(None)), 4.)
assert_raises(ValueError, ds.__setitem__, (slice(None), '432'), 4.)
# deleting items
del ds['A']
ok_('A' not in ds)
assert_raises(KeyError, ds.__getitem__, 'A')
del ds['B', 'rm']
ok_('B' not in ds and 'rm' not in ds)
def test_corr():
"Test testnd.corr()"
ds = datasets.get_uts(True)
# add correlation
Y = ds['Y']
utsnd = ds['utsnd']
utsnd.x[:, 3:5, 50:65] += Y.x[:, None, None]
res = testnd.corr('utsnd', 'Y', 'rm', ds=ds)
repr(res)
res = testnd.corr('utsnd', 'Y', 'rm', ds=ds, samples=10, pmin=0.05)
repr(res)
# persistence
string = pickle.dumps(res, protocol=pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
assert_dataobj_equal(res.p, res_.p)
def test_corr():
"Test testnd.corr()"
ds = datasets.get_uts(True)
# add correlation
Y = ds['Y']
utsnd = ds['utsnd']
utsnd.x[:, 3:5, 50:65] += Y.x[:, None, None]
res = testnd.corr('utsnd', 'Y', 'rm', ds=ds)
repr(res)
res = testnd.corr('utsnd', 'Y', 'rm', ds=ds, samples=10, pmin=0.05)
repr(res)
# persistence
string = pickle.dumps(res, protocol=pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
assert_dataobj_equal(res.p, res_.p)
def test_interaction():
"Test Interaction"
ds = datasets.get_uv()
A = ds['A']
B = ds['B']
i = A % B
# eq for sequence
assert_array_equal(i == A % B, True)
assert_array_equal(i == B % A, False)
assert_array_equal(i == A, False)
assert_array_equal(i == ds['fltvar'], False)
assert_array_equal(ds.eval("A%B") == Factor(ds['A']) % B, True)
# eq for element
for a, b in product(A.cells, B.cells):
assert_array_equal(i == (a, b), np.logical_and(A == a, B == b))
# Interaction.as_factor()
a = Factor('aabb')
i = a % Factor('cdcd')
assert_dataobj_equal(i.as_factor(), Factor(['a c', 'a d', 'b c', 'b d']))
i = a % Factor(['c', '', 'c', ''])
assert_dataobj_equal(i.as_factor(), Factor(['a c', 'a', 'b c', 'b']))
# pickling
ip = pickle.loads(pickle.dumps(i))
assert_dataobj_equal(ip, i)
def test_test_experiment():
"Test event labeling with the EventExperiment subclass of MneExperiment"
e = EventExperiment()
# test defaults
eq_(e.get('session'), 'cheese')
eq_(e.get('model'), 'name')
# test event labeling
ds = e.label_events(gen_triggers())
name = Factor([e.variables['name'][t] for t in TRIGGERS], name='name')
assert_dataobj_equal(ds['name'], name)
tgt = ds['trigger'].as_factor(e.variables['backorder'], 'backorder')
assert_dataobj_equal(ds['backorder'], tgt)
tgt = ds['trigger'].as_factor(e.variables['taste'], 'taste')
assert_dataobj_equal(ds['taste'], tgt)
assert_array_equal(ds['i_start'], I_START)
assert_array_equal(ds['subject'] == SUBJECT, True)
# tests disabled (trigger-shift applied in load_events):
# ---
# assert_equal(ds['i_start'], I_START + round(0.03 * SAMPLINGRATE))
# # test without trigger shift
# e.trigger_shift = 0
# ds = e.label_events(gen_triggers())
# assert_equal(ds['i_start'], I_START)
# # trigger shift dict
# e2 = EventExperimentTriggerShiftDict('', False)
# ds = e2.label_events(gen_triggers())
# assert_equal(ds['i_start'], I_START + round(0.04 * SAMPLINGRATE))
# epochs
eq_(e._epochs['cheese'].tmin, -0.2)
eq_(e._epochs['cheese-leicester'].tmin, -0.1)
eq_(e._epochs['cheese-tilsit'].tmin, -0.2)
def test_interaction():
"Test Interaction"
ds = datasets.get_uv()
A = ds['A']
B = ds['B']
i = A % B
# eq for sequence
assert_array_equal(i == A % B, True)
assert_array_equal(i == B % A, False)
assert_array_equal(i == A, False)
assert_array_equal(i == ds['fltvar'], False)
assert_array_equal(ds.eval("A%B") == Factor(ds['A']) % B, True)
# eq for element
for a, b in product(A.cells, B.cells):
assert_array_equal(i == (a, b), np.logical_and(A == a, B == b))
# Interaction.as_factor()
a = Factor('aabb')
i = a % Factor('cdcd')
assert_dataobj_equal(i.as_factor(), Factor(['a c', 'a d', 'b c', 'b d']))
i = a % Factor(['c', '', 'c', ''])
assert_dataobj_equal(i.as_factor(), Factor(['a c', 'a', 'b c', 'b']))
# pickling
ip = pickle.loads(pickle.dumps(i))
assert_dataobj_equal(ip, i)
def test_ttest_1samp():
"Test testnd.ttest_1samp()"
ds = datasets.get_uts(True)
# no clusters
res0 = testnd.ttest_1samp('uts', sub="A == 'a0'", ds=ds)
assert_less(res0.p_uncorrected.min(), 0.05)
repr0 = repr(res0)
assert_in("'uts'", repr0)
assert_not_in('clusters', repr0)
assert_not_in('mintime', repr0)
# sub as array
res1 = testnd.ttest_1samp('uts', sub=ds.eval("A == 'a0'"), ds=ds)
repr1 = repr(res1)
assert_not_equal(repr1, repr0)
# clusters without resampling
res1 = testnd.ttest_1samp('uts', sub="A == 'a0'", ds=ds, samples=0,
pmin=0.05, tstart=0, tstop=0.6, mintime=0.05)
assert_equal(res1.clusters.n_cases, 1)
assert_not_in('p', res1.clusters)
repr1 = repr(res1)
assert_in('clusters', repr1)
assert_in('samples', repr1)
assert_in('mintime', repr1)
# persistence
string = pickle.dumps(res1, pickle.HIGHEST_PROTOCOL)
res1_ = pickle.loads(string)
assert_equal(repr(res1_), repr1)
assert_dataobj_equal(res1.p_uncorrected, res1_.p_uncorrected)
# clusters with resampling
res2 = testnd.ttest_1samp('uts', sub="A == 'a0'", ds=ds, samples=10,
pmin=0.05, tstart=0, tstop=0.6, mintime=0.05)
assert_equal(res2.clusters.n_cases, 1)
assert_equal(res2.samples, 10)
assert_in('p', res2.clusters)
repr2 = repr(res2)
assert_in('samples', repr2)
# clusters with permutations
dss = ds.sub("logical_and(A=='a0', B=='b0')")[:8]
res3 = testnd.ttest_1samp('uts', sub="A == 'a0'", ds=dss, samples=10000,
pmin=0.05, tstart=0, tstop=0.6, mintime=0.05)
assert_equal(res3.clusters.n_cases, 2)
assert_equal(res3.samples, -1)
assert_less(res3.clusters['p'].x.min(), 0.05)
repr3 = repr(res3)
assert_in('samples', repr3)
# nd
dss = ds.sub("A == 'a0'")
res = testnd.ttest_1samp('utsnd', ds=dss, samples=1)
res = testnd.ttest_1samp('utsnd', ds=dss, pmin=0.05, samples=1)
res = testnd.ttest_1samp('utsnd', ds=dss, tfce=True, samples=1)
# TFCE properties
res = testnd.ttest_1samp('utsnd', sub="A == 'a0'", ds=ds, samples=1)
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res = pickle.loads(string)
tfce_clusters = res.find_clusters(pmin=0.05)
peaks = res.find_peaks()
assert_equal(tfce_clusters.eval("p.min()"), peaks.eval("p.min()"))
masked = res.masked_parameter_map(pmin=0.05)
assert_array_equal(masked.abs().x <= res.t.abs().x, True)
def test_var():
"Test Var objects"
base = Factor('aabbcde')
# initialization
x = np.arange(4)
y = Var(x)
assert_array_equal(y, x)
y = Var(x, repeat=2)
assert_array_equal(y, x.repeat(2))
y = Var(x, repeat=x)
assert_array_equal(y, x.repeat(x))
y = Var.from_dict(base, {'a': 5, 'e': 8}, default=0)
assert_array_equal(y.x, [5, 5, 0, 0, 0, 0, 8])
assert_raises(TypeError, Var, x, info=1)
# basic operations
info = {'a': 1}
v = Var([1., 2., 3., -4.], 'v', info=info)
c = 2
v2 = Var([2., 2., 3., 3.], 'w', info=info)
eq_(v.info, info)
for op, iop, desc in OPERATORS:
target = op(v.x, c)
vtarget = op(v.x, v2.x)
# op
if desc == '+':
w = v.copy()
w.x = iop(w.x, c)
else:
w = op(v, c)
eq_(w.info, {'a': 1, 'longname': 'v %s %s' % (desc, c)})
assert_array_equal(w, target)
# with Var
w = op(v, v2)
eq_(w.info, {'a': 1, 'longname': 'v %s w' % desc})
assert_array_equal(w, vtarget)
# i-op
w = v.copy()
w = iop(w, c)
assert_array_equal(w, target)
# i-op with Var
w = v.copy()
w = iop(w, v2)
assert_array_equal(w, vtarget)
# methods
w = v.abs()
eq_(w.info, {'a': 1, 'longname': 'abs(v)'})
assert_array_equal(w, np.abs(v.x))
x = w.log()
eq_(x.info, {'a': 1, 'longname': 'log(abs(v))'})
assert_array_equal(x, np.log(w.x))
# assignment
tgt1 = np.arange(10)
tgt2 = np.tile(np.arange(5), 2)
v = Var(np.arange(10))
v[v > 4] = np.arange(5)
assert_array_equal(v, tgt2)
v[5:] = np.arange(5, 10)
assert_array_equal(v, tgt1)
v = Var(np.arange(10))
v[v > 4] = Var(np.arange(5))
assert_array_equal(v, tgt2)
v[5:] = Var(np.arange(5, 10))
assert_array_equal(v, tgt1)
# .count()
v = Var([1., 2., 1.11, 2., 1.11, 4.])
assert_array_equal(v.count(), [0, 0, 0, 1, 1, 0])
# .split()
y = Var(np.arange(16))
for i in xrange(1, 9):
split = y.split(i)
eq_(len(split.cells), i)
# .as_factor()
v = Var(np.arange(4))
assert_dataobj_equal(v.as_factor(), Factor('0123'))
assert_dataobj_equal(v.as_factor({0: 'a'}), Factor(['a', '', '', '']))
assert_dataobj_equal(v.as_factor({(0, 1): 'a', (2, 3): 'b'}), Factor('aabb'))
assert_dataobj_equal(v.as_factor({(0, 1): 'a', 2: 'b', 'default': 'c'}),
Factor('aabc'))
assert_dataobj_equal(v.as_factor({(0, 1): 'a', (2, 'default'): 'b'}),
Factor('aabb'))
def test_ttest_rel():
"Test testnd.ttest_rel()"
ds = datasets.get_uts(True)
# basic
res = testnd.ttest_rel('uts',
'A%B', ('a1', 'b1'), ('a0', 'b0'),
'rm',
ds=ds,
samples=100)
eq_(
repr(res), "<ttest_rel 'uts', 'A x B', ('a1', 'b1'), ('a0', 'b0'), "
"'rm' (n=15), samples=100, p=.000>")
# alternate argspec
ds1 = Dataset()
ds1['a1b1'] = ds.eval("uts[A%B == ('a1', 'b1')]")
ds1['a0b0'] = ds.eval("uts[A%B == ('a0', 'b0')]")
res1 = testnd.ttest_rel('a1b1', 'a0b0', ds=ds1, samples=100)
assert_dataobj_equal(res1.t, res.t)
eq_(repr(res1), "<ttest_rel 'a1b1', 'a0b0' (n=15), samples=100, p=.000>")
# persistence
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
repr(res_)
assert_equal(repr(res_), repr(res))
assert_dataobj_equal(res.p_uncorrected, res_.p_uncorrected)
# collapsing cells
res2 = testnd.ttest_rel('uts', 'A', 'a1', 'a0', 'rm', ds=ds)
assert_less(res2.p_uncorrected.min(), 0.05)
assert_equal(res2.n, res.n)
# reproducibility
res3 = testnd.ttest_rel('uts',
'A%B', ('a1', 'b1'), ('a0', 'b0'),
'rm',
ds=ds,
samples=100)
assert_dataset_equal(res3.find_clusters(maps=True), res.clusters)
configure(n_workers=0)
res4 = testnd.ttest_rel('uts',
'A%B', ('a1', 'b1'), ('a0', 'b0'),
'rm',
ds=ds,
samples=100)
assert_dataset_equal(res4.find_clusters(maps=True), res.clusters)
configure(n_workers=True)
sds = ds.sub("B=='b0'")
# thresholded, UTS
configure(n_workers=0)
res0 = testnd.ttest_rel('uts',
'A',
'a1',
'a0',
'rm',
ds=sds,
pmin=0.1,
samples=100)
tgt = res0.find_clusters()
configure(n_workers=True)
res1 = testnd.ttest_rel('uts',
'A',
'a1',
'a0',
'rm',
ds=sds,
pmin=0.1,
samples=100)
assert_dataset_equal(res1.find_clusters(), tgt)
# thresholded, UTSND
configure(n_workers=0)
res0 = testnd.ttest_rel('utsnd',
'A',
'a1',
'a0',
'rm',
ds=sds,
pmin=0.1,
samples=100)
tgt = res0.find_clusters()
configure(n_workers=True)
res1 = testnd.ttest_rel('utsnd',
'A',
'a1',
'a0',
'rm',
ds=sds,
pmin=0.1,
samples=100)
assert_dataset_equal(res1.find_clusters(), tgt)
# TFCE, UTS
configure(n_workers=0)
res0 = testnd.ttest_rel('uts',
'A',
'a1',
'a0',
'rm',
ds=sds,
tfce=True,
samples=10)
tgt = res0.compute_probability_map()
configure(n_workers=True)
res1 = testnd.ttest_rel('uts',
'A',
'a1',
'a0',
'rm',
ds=sds,
tfce=True,
samples=10)
assert_dataobj_equal(res1.compute_probability_map(), tgt)
# zero variance
ds['utsnd'].x[:, 1, 10] = 0.
res = testnd.ttest_rel('utsnd', 'A', match='rm', ds=ds)
eq_(res.t.x[1, 10], 0)
def test_anova():
"Test testnd.anova()"
ds = datasets.get_uts(True)
testnd.anova('utsnd', 'A*B', ds=ds)
for samples in (0, 2):
logging.info("TEST: samples=%r" % samples)
testnd.anova('utsnd', 'A*B', ds=ds, samples=samples)
testnd.anova('utsnd', 'A*B', ds=ds, samples=samples, pmin=0.05)
testnd.anova('utsnd', 'A*B', ds=ds, samples=samples, tfce=True)
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, samples=0, pmin=0.05)
repr(res)
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, samples=2, pmin=0.05)
repr(res)
# persistence
string = pickle.dumps(res, protocol=pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_equal(repr(res_), repr(res))
# threshold-free
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, samples=10)
repr(res)
assert_in('A clusters', res.clusters.info)
assert_in('B clusters', res.clusters.info)
assert_in('A x B clusters', res.clusters.info)
# no clusters
res = testnd.anova('uts', 'B', sub="A=='a1'", ds=ds, samples=5, pmin=0.05,
mintime=0.02)
repr(res)
assert_in('v', res.clusters)
assert_in('p', res.clusters)
# all effects with clusters
res = testnd.anova('uts', 'A*B*rm', ds=ds, samples=5, pmin=0.05,
tstart=0.1, mintime=0.02)
assert_equal(set(res.clusters['effect'].cells), set(res.effects))
# some effects with clusters, some without
res = testnd.anova('uts', 'A*B*rm', ds=ds, samples=5, pmin=0.05,
tstart=0.37, mintime=0.02)
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_dataobj_equal(res.clusters, res_.clusters)
# test multi-effect results (with persistence)
# UTS
res = testnd.anova('uts', 'A*B*rm', ds=ds, samples=5)
repr(res)
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
resr = pickle.loads(string)
tf_clusters = resr.find_clusters(pmin=0.05)
peaks = resr.find_peaks()
assert_dataobj_equal(tf_clusters, res.find_clusters(pmin=0.05))
assert_dataobj_equal(peaks, res.find_peaks())
assert_equal(tf_clusters.eval("p.min()"), peaks.eval("p.min()"))
unmasked = resr.f[0]
masked = resr.masked_parameter_map(effect=0, pmin=0.05)
assert_array_equal(masked.x <= unmasked.x, True)
# reproducibility
res0 = testnd.anova('utsnd', 'A*B*rm', ds=ds, pmin=0.05, samples=5)
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, pmin=0.05, samples=5)
assert_dataset_equal(res.clusters, res0.clusters)
testnd.configure(0)
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, pmin=0.05, samples=5)
assert_dataset_equal(res.clusters, res0.clusters)
testnd.configure(-1)
# permutation
eelbrain._stats.permutation._YIELD_ORIGINAL = 1
samples = 4
# raw
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, samples=samples)
for dist in res._cdist:
eq_(len(dist.dist), samples)
assert_array_equal(dist.dist, dist.parameter_map.abs().max())
# TFCE
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, tfce=True, samples=samples)
for dist in res._cdist:
eq_(len(dist.dist), samples)
assert_array_equal(dist.dist, dist.tfce_map.abs().max())
# thresholded
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, pmin=0.05, samples=samples)
clusters = res.find_clusters()
for dist, effect in izip(res._cdist, res.effects):
effect_idx = clusters.eval("effect == %r" % effect)
vmax = clusters[effect_idx, 'v'].abs().max()
eq_(len(dist.dist), samples)
assert_array_equal(dist.dist, vmax)
eelbrain._stats.permutation._YIELD_ORIGINAL = 0
# 1d TFCE
testnd.configure(0)
res = testnd.anova('utsnd.rms(time=(0.1, 0.3))', 'A*B*rm', ds=ds, tfce=True, samples=samples)
testnd.configure(-1)
def test_clusterdist():
"Test _ClusterDist class"
shape = (10, 6, 6, 4)
locs = [[0, 0, 0],
[1, 0, 0],
[1, 1, 0],
[0, 1, 0]]
x = np.random.normal(0, 1, shape)
sensor = Sensor(locs, ['0', '1', '2', '3'])
sensor.set_connectivity(connect_dist=1.1)
dims = ('case', UTS(-0.1, 0.1, 6), Ordered('dim2', range(6), 'unit'),
sensor)
y = NDVar(x, dims)
# test connecting sensors
logging.info("TEST: connecting sensors")
bin_map = np.zeros(shape[1:], dtype=np.bool8)
bin_map[:3, :3, :2] = True
pmap = np.random.normal(0, 1, shape[1:])
np.clip(pmap, -1, 1, pmap)
pmap[bin_map] = 2
cdist = _ClusterDist(y, 0, 1.5)
print(repr(cdist))
cdist.add_original(pmap)
print(repr(cdist))
assert_equal(cdist.n_clusters, 1)
assert_array_equal(cdist._original_cluster_map == cdist._cids[0],
cdist._crop(bin_map).swapaxes(0, cdist._nad_ax))
assert_equal(cdist.parameter_map.dims, y.dims[1:])
# test connecting many sensors
logging.info("TEST: connecting sensors")
bin_map = np.zeros(shape[1:], dtype=np.bool8)
bin_map[:3, :3] = True
pmap = np.random.normal(0, 1, shape[1:])
np.clip(pmap, -1, 1, pmap)
pmap[bin_map] = 2
cdist = _ClusterDist(y, 0, 1.5)
cdist.add_original(pmap)
assert_equal(cdist.n_clusters, 1)
assert_array_equal(cdist._original_cluster_map == cdist._cids[0],
cdist._crop(bin_map).swapaxes(0, cdist._nad_ax))
# test keeping sensors separate
logging.info("TEST: keeping sensors separate")
bin_map = np.zeros(shape[1:], dtype=np.bool8)
bin_map[:3, :3, 0] = True
bin_map[:3, :3, 2] = True
pmap = np.random.normal(0, 1, shape[1:])
np.clip(pmap, -1, 1, pmap)
pmap[bin_map] = 2
cdist = _ClusterDist(y, 1, 1.5)
cdist.add_original(pmap)
assert_equal(cdist.n_clusters, 2)
# criteria
ds = datasets.get_uts(True)
res = testnd.ttest_rel('utsnd', 'A', match='rm', ds=ds, samples=0, pmin=0.05)
assert_less(res.clusters['duration'].min(), 0.01)
eq_(res.clusters['n_sensors'].min(), 1)
res = testnd.ttest_rel('utsnd', 'A', match='rm', ds=ds, samples=0, pmin=0.05,
mintime=0.02, minsensor=2)
assert_greater_equal(res.clusters['duration'].min(), 0.02)
eq_(res.clusters['n_sensors'].min(), 2)
# 1d
res1d = testnd.ttest_rel('utsnd.sub(time=0.1)', 'A', match='rm', ds=ds,
samples=0, pmin=0.05)
assert_dataobj_equal(res1d.p_uncorrected, res.p_uncorrected.sub(time=0.1))
# TFCE
logging.info("TEST: TFCE")
sensor = Sensor(locs, ['0', '1', '2', '3'])
sensor.set_connectivity(connect_dist=1.1)
dims = ('case', UTS(-0.1, 0.1, 4), sensor,
Ordered('dim2', range(10), 'unit'))
y = NDVar(np.random.normal(0, 1, (10, 4, 4, 10)), dims)
cdist = _ClusterDist(y, 3, None)
cdist.add_original(y.x[0])
cdist.finalize()
assert_equal(cdist.dist.shape, (3,))
# I/O
string = pickle.dumps(cdist, pickle.HIGHEST_PROTOCOL)
cdist_ = pickle.loads(string)
assert_equal(repr(cdist_), repr(cdist))
# find peaks
x = np.array([[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[7, 7, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 7, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[5, 7, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 6, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 7, 5, 5, 0, 0],
[0, 0, 0, 0, 5, 4, 4, 4, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 4, 0, 0],
[0, 0, 0, 0, 7, 0, 0, 3, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]])
tgt = np.equal(x, 7)
peaks = cdist._find_peaks(x)
logging.debug(' detected: \n%s' % (peaks.astype(int)))
logging.debug(' target: \n%s' % (tgt.astype(int)))
assert_array_equal(peaks, tgt)
def test_clusterdist():
"Test _ClusterDist class"
shape = (10, 6, 6, 4)
locs = [[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0]]
x = np.random.normal(0, 1, shape)
sensor = Sensor(locs, ['0', '1', '2', '3'])
sensor.set_connectivity(connect_dist=1.1)
dims = ('case', UTS(-0.1, 0.1, 6), Scalar('dim2', range(6),
'unit'), sensor)
y = NDVar(x, dims)
# test connecting sensors
logging.info("TEST: connecting sensors")
bin_map = np.zeros(shape[1:], dtype=np.bool8)
bin_map[:3, :3, :2] = True
pmap = np.random.normal(0, 1, shape[1:])
np.clip(pmap, -1, 1, pmap)
pmap[bin_map] = 2
cdist = _ClusterDist(y, 0, 1.5)
print(repr(cdist))
cdist.add_original(pmap)
print(repr(cdist))
assert_equal(cdist.n_clusters, 1)
assert_array_equal(cdist._original_cluster_map == cdist._cids[0],
cdist._crop(bin_map).swapaxes(0, cdist._nad_ax))
assert_equal(cdist.parameter_map.dims, y.dims[1:])
# test connecting many sensors
logging.info("TEST: connecting sensors")
bin_map = np.zeros(shape[1:], dtype=np.bool8)
bin_map[:3, :3] = True
pmap = np.random.normal(0, 1, shape[1:])
np.clip(pmap, -1, 1, pmap)
pmap[bin_map] = 2
cdist = _ClusterDist(y, 0, 1.5)
cdist.add_original(pmap)
assert_equal(cdist.n_clusters, 1)
assert_array_equal(cdist._original_cluster_map == cdist._cids[0],
cdist._crop(bin_map).swapaxes(0, cdist._nad_ax))
# test keeping sensors separate
logging.info("TEST: keeping sensors separate")
bin_map = np.zeros(shape[1:], dtype=np.bool8)
bin_map[:3, :3, 0] = True
bin_map[:3, :3, 2] = True
pmap = np.random.normal(0, 1, shape[1:])
np.clip(pmap, -1, 1, pmap)
pmap[bin_map] = 2
cdist = _ClusterDist(y, 1, 1.5)
cdist.add_original(pmap)
assert_equal(cdist.n_clusters, 2)
# criteria
ds = datasets.get_uts(True)
res = testnd.ttest_rel('utsnd',
'A',
match='rm',
ds=ds,
samples=0,
pmin=0.05)
assert_less(res.clusters['duration'].min(), 0.01)
eq_(res.clusters['n_sensors'].min(), 1)
res = testnd.ttest_rel('utsnd',
'A',
match='rm',
ds=ds,
samples=0,
pmin=0.05,
mintime=0.02,
minsensor=2)
assert_greater_equal(res.clusters['duration'].min(), 0.02)
eq_(res.clusters['n_sensors'].min(), 2)
# 1d
res1d = testnd.ttest_rel('utsnd.sub(time=0.1)',
'A',
match='rm',
ds=ds,
samples=0,
pmin=0.05)
assert_dataobj_equal(res1d.p_uncorrected, res.p_uncorrected.sub(time=0.1))
# TFCE
logging.info("TEST: TFCE")
sensor = Sensor(locs, ['0', '1', '2', '3'])
sensor.set_connectivity(connect_dist=1.1)
time = UTS(-0.1, 0.1, 4)
scalar = Scalar('scalar', range(10), 'unit')
dims = ('case', time, sensor, scalar)
np.random.seed(0)
y = NDVar(np.random.normal(0, 1, (10, 4, 4, 10)), dims)
cdist = _ClusterDist(y, 3, None)
cdist.add_original(y.x[0])
cdist.finalize()
assert_equal(cdist.dist.shape, (3, ))
# I/O
string = pickle.dumps(cdist, pickle.HIGHEST_PROTOCOL)
cdist_ = pickle.loads(string)
assert_equal(repr(cdist_), repr(cdist))
# find peaks
x = np.array([[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[7, 7, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 7, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[5, 7, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 6, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 7, 5, 5, 0, 0],
[0, 0, 0, 0, 5, 4, 4, 4, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 4, 0, 0],
[0, 0, 0, 0, 7, 0, 0, 3, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]])
tgt = np.equal(x, 7)
peaks = find_peaks(x, cdist._connectivity)
logging.debug(' detected: \n%s' % (peaks.astype(int)))
logging.debug(' target: \n%s' % (tgt.astype(int)))
assert_array_equal(peaks, tgt)
# testnd permutation result
res = testnd.ttest_1samp(y, tfce=True, samples=3)
assert_allclose(np.sort(res._cdist.dist),
[77.5852307, 119.1976153, 217.6270428])
# parc with TFCE on unconnected dimension
configure(False)
x = np.random.normal(0, 1, (10, 5, 2, 4))
time = UTS(-0.1, 0.1, 5)
categorial = Categorial('categorial', ('a', 'b'))
y = NDVar(x, ('case', time, categorial, sensor))
y0 = NDVar(x[:, :, 0], ('case', time, sensor))
y1 = NDVar(x[:, :, 1], ('case', time, sensor))
res = testnd.ttest_1samp(y, tfce=True, samples=3)
res_parc = testnd.ttest_1samp(y, tfce=True, samples=3, parc='categorial')
res0 = testnd.ttest_1samp(y0, tfce=True, samples=3)
res1 = testnd.ttest_1samp(y1, tfce=True, samples=3)
# cdist
eq_(res._cdist.shape, (4, 2, 5))
# T-maps don't depend on connectivity
assert_array_equal(res.t.x[:, 0], res0.t.x)
assert_array_equal(res.t.x[:, 1], res1.t.x)
assert_array_equal(res_parc.t.x[:, 0], res0.t.x)
assert_array_equal(res_parc.t.x[:, 1], res1.t.x)
# TFCE-maps should always be the same because they're unconnected
assert_array_equal(res.tfce_map.x[:, 0], res0.tfce_map.x)
assert_array_equal(res.tfce_map.x[:, 1], res1.tfce_map.x)
assert_array_equal(res_parc.tfce_map.x[:, 0], res0.tfce_map.x)
assert_array_equal(res_parc.tfce_map.x[:, 1], res1.tfce_map.x)
# Probability-maps should depend on what is taken into account
p_a = res0.compute_probability_map().x
p_b = res1.compute_probability_map().x
assert_array_equal(res_parc.compute_probability_map(categorial='a').x, p_a)
assert_array_equal(res_parc.compute_probability_map(categorial='b').x, p_b)
p_parc = res_parc.compute_probability_map()
assert_array_equal(p_parc.x, res.compute_probability_map().x)
ok_(np.all(p_parc.sub(categorial='a').x >= p_a))
ok_(np.all(p_parc.sub(categorial='b').x >= p_b))
configure(True)
def test_ndvar():
"Test the NDVar class"
ds = datasets.get_uts(utsnd=True)
x = ds['utsnd']
# meaningful slicing
assert_raises(KeyError, x.sub, sensor='5')
assert_equal(x.sub(sensor='4'), x.x[:, 4])
assert_equal(x.sub(sensor=['4', '3', '2']), x.x[:, [4, 3, 2]])
assert_equal(x.sub(sensor=['4']), x.x[:, [4]])
assert_equal(x.sub(case=1, sensor='4'), x.x[1, 4])
# setup indices
s_case = slice(10, 13)
s_sensor = slice('2', '4')
s_time = slice(0.1, 0.2)
b_case = np.bincount([10, 11, 12], minlength=len(x)).astype(bool)
b_sensor = np.array([False, False, True, True, False])
b_time = np.bincount(range(30, 40), minlength=len(x.time)).astype(bool)
a_case = np.arange(10, 13)
a_sensor = ['2', '3']
a_time = np.arange(0.1, 0.2, 0.01)
# slicing with different index kinds
tgt = x.x[s_case, 2:4, 30:40]
eq_(tgt.shape, (3, 2, 10))
# single
assert_equal(x.sub(case=s_case, sensor=s_sensor, time=s_time), tgt)
assert_equal(x.sub(case=a_case, sensor=a_sensor, time=a_time), tgt)
assert_equal(x.sub(case=b_case, sensor=b_sensor, time=b_time), tgt)
# bool & slice
assert_equal(x.sub(case=b_case, sensor=s_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=b_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=s_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=b_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=b_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=s_sensor, time=b_time), tgt)
# bool & array
assert_equal(x.sub(case=b_case, sensor=a_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=b_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=a_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=b_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=b_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=a_sensor, time=b_time), tgt)
# slice & array
assert_equal(x.sub(case=s_case, sensor=a_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=s_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=a_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=s_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=s_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=a_sensor, time=s_time), tgt)
# all three
assert_equal(x.sub(case=a_case, sensor=b_sensor, time=s_time), tgt)
assert_equal(x.sub(case=a_case, sensor=s_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=a_sensor, time=s_time), tgt)
assert_equal(x.sub(case=b_case, sensor=s_sensor, time=a_time), tgt)
assert_equal(x.sub(case=s_case, sensor=a_sensor, time=b_time), tgt)
assert_equal(x.sub(case=s_case, sensor=b_sensor, time=a_time), tgt)
# norm
y = x / x.norm('sensor')
assert_allclose(y.norm('sensor'), 1.)
y = ds['uts'].mean('case').norm('time')
assert_is_instance(y, float)
# Var
v_case = Var(b_case)
assert_equal(x.sub(case=v_case, sensor=b_sensor, time=a_time), tgt)
# univariate result
assert_dataobj_equal(x.sub(sensor='2', time=0.1),
Var(x.x[:, 2, 30], x.name))
eq_(x.sub(case=0, sensor='2', time=0.1), x.x[0, 2, 30])
# baseline correction
x_bl = x - x.summary(time=(None, 0))
# assert that the baseline is 0
bl = x_bl.summary('case', 'sensor', time=(None, 0))
ok_(abs(bl) < 1e-10, "Baseline correction")
# NDVar as index
sens_mean = x.mean(('case', 'time'))
idx = sens_mean > 0
pos = sens_mean[idx]
assert_array_equal(pos.x > 0, True)
# NDVar as index along one dimension
x_tc = x.sub(sensor='1')
x_time = NDVar(x_tc.time.times >= 0.3, dims=(x_tc.time,))
assert_dataobj_equal(x_tc[x_time], x_tc.sub(time=(0.3, None)))
# out of range index
assert_raises(ValueError, x.sub, time=(0.1, 0.81))
assert_raises(IndexError, x.sub, time=(-0.25, 0.1))
# iteration
for i, xi in enumerate(x):
assert_dataobj_equal(xi, x[i])
if i > 4:
break
def test_sample():
set_log_level('warning', 'mne')
# import from file: http://stackoverflow.com/a/67692/166700
SampleExperiment = import_attr(sample_path / 'sample_experiment.py', 'SampleExperiment')
tempdir = TempDir()
datasets.setup_samples_experiment(tempdir, 3, 2)
root = join(tempdir, 'SampleExperiment')
e = SampleExperiment(root)
eq_(e.get('subject'), 'R0000')
eq_(e.get('subject', subject='R0002'), 'R0002')
# events
e.set('R0001', rej='')
ds = e.load_selected_events(epoch='target')
assert ds.n_cases == 39
ds = e.load_selected_events(epoch='auditory')
assert ds.n_cases == 20
ds = e.load_selected_events(epoch='av')
assert ds.n_cases == 39
# evoked cache invalidated by change in bads
e.set('R0001', rej='', epoch='target')
ds = e.load_evoked()
eq_(ds[0, 'evoked'].info['bads'], [])
e.make_bad_channels(['MEG 0331'])
ds = e.load_evoked()
eq_(ds[0, 'evoked'].info['bads'], ['MEG 0331'])
e.set(rej='man', model='modality')
sds = []
for _ in e:
e.make_rej(auto=2.5e-12)
sds.append(e.load_evoked())
ds = e.load_evoked('all')
assert_dataobj_equal(combine(sds), ds)
# test with data parameter
megs = [e.load_evoked(cat='auditory')['meg'] for _ in e]
res = e.load_test('a>v', 0.05, 0.2, 0.05, samples=100, data='sensor.rms',
sns_baseline=False, make=True)
meg_rms = combine(meg.rms('sensor') for meg in megs).mean('case', name='auditory')
assert_dataobj_equal(res.c1_mean, meg_rms, decimal=21)
res = e.load_test('a>v', 0.05, 0.2, 0.05, samples=100, data='sensor.mean',
sns_baseline=False, make=True)
meg_mean = combine(meg.mean('sensor') for meg in megs).mean('case', name='auditory')
assert_dataobj_equal(res.c1_mean, meg_mean, decimal=21)
# e._report_subject_info() broke with non-alphabetic subject order
subjects = e.get_field_values('subject')
ds = Dataset()
ds['subject'] = Factor(reversed(subjects))
ds['n'] = Var(range(3))
s_table = e._report_subject_info(ds, '')
# test multiple epochs with same time stamp
class Experiment(SampleExperiment):
epochs = SampleExperiment.epochs.copy()
Experiment.epochs['v1'] = {'base': 'visual', 'vars': {'shift': 'Var([0.0], repeat=len(side))'}}
Experiment.epochs['v2'] = {'base': 'visual', 'vars': {'shift': 'Var([0.1], repeat=len(side))'}}
Experiment.epochs['vc'] = {'sub_epochs': ('v1', 'v2'), 'post_baseline_trigger_shift': 'shift', 'post_baseline_trigger_shift_max': 0.1, 'post_baseline_trigger_shift_min': 0.0}
e = Experiment(root)
ds = e.load_epochs(baseline=True, epoch='vc')
v1 = ds.sub("epoch=='v1'", 'meg').sub(time=(0, 0.199))
v2 = ds.sub("epoch=='v2'", 'meg').sub(time=(-0.1, 0.099))
assert_dataobj_equal(v1, v2, decimal=20)
# duplicate subject
class BadExperiment(SampleExperiment):
groups = {'group': ('R0001', 'R0002', 'R0002')}
assert_raises(DefinitionError, BadExperiment, root)
# non-existing subject
class BadExperiment(SampleExperiment):
groups = {'group': ('R0001', 'R0003', 'R0002')}
assert_raises(DefinitionError, BadExperiment, root)
# unsorted subjects
class Experiment(SampleExperiment):
groups = {'group': ('R0002', 'R0000', 'R0001')}
e = Experiment(root)
eq_([s for s in e], ['R0000', 'R0001', 'R0002'])
# changes
class Changed(SampleExperiment):
variables = {
'event': {(1, 2, 3, 4): 'target', 5: 'smiley', 32: 'button'},
'side': {(1, 3): 'left', (2, 4): 'right_changed'},
'modality': {(1, 2): 'auditory', (3, 4): 'visual'}
}
tests = {
'twostage': {
'kind': 'two-stage',
'stage 1': 'side_left + modality_a',
'vars': {
'side_left': "side == 'left'",
'modality_a': "modality == 'auditory'",
}
},
'novars': {
'kind': 'two-stage',
'stage 1': 'side + modality'
},
}
e = Changed(root)
# changed variable, while a test with model=None is not changed
class Changed(Changed):
variables = {
'side': {(1, 3): 'left', (2, 4): 'right_changed'},
'modality': {(1, 2): 'auditory', (3, 4): 'visual_changed'}
}
e = Changed(root)
# changed variable, unchanged test with vardef=None
class Changed(Changed):
variables = {
'side': {(1, 3): 'left', (2, 4): 'right_changed'},
'modality': {(1, 2): 'auditory', (3, 4): 'visual_changed'}
}
e = Changed(root)
# ICA
# ---
e = SampleExperiment(root)
ica_path = e.make_ica(raw='ica')
e.set(raw='ica1-40', model='')
e.make_rej(auto=2e-12, overwrite=True)
ds1 = e.load_evoked(raw='ica1-40')
ica = e.load_ica(raw='ica')
ica.exclude = [0, 1, 2]
ica.save(ica_path)
ds2 = e.load_evoked(raw='ica1-40')
assert not np.allclose(ds1['meg'].x, ds2['meg'].x, atol=1e-20), "ICA change ignored"
def test_factor():
"Test basic Factor functionality"
# initializing
assert_array_equal(Factor('ab'), ['a', 'b'])
assert_array_equal(Factor('ab', repeat=2), ['a', 'a', 'b', 'b'])
assert_array_equal(Factor('ab', repeat=np.array([2, 1])), ['a', 'a', 'b'])
empty_factor = Factor([])
eq_(len(empty_factor), 0)
assert_dataobj_equal(Factor(np.empty(0)), empty_factor)
# from Factor
f = Factor('aabbcc')
assert_array_equal(Factor(f), f)
assert_array_equal(Factor(f, labels={'a': 'b'}), Factor('bbbbcc'))
# removing a cell
f = Factor('aabbcc')
eq_(f.cells, ('a', 'b', 'c'))
eq_(f.n_cells, 3)
f[f == 'c'] = 'a'
eq_(f.cells, ('a', 'b'))
eq_(f.n_cells, 2)
# cell order
a = np.tile(np.arange(3), 3)
# alphabetical
f = Factor(a, labels={0: 'c', 1: 'b', 2: 'a'})
eq_(f.cells, ('a', 'b', 'c'))
# ordered
f = Factor(a, labels=((0, 'c'), (1, 'b'), (2, 'a')))
eq_(f.cells, ('c', 'b', 'a'))
eq_(f[:2].cells, ('c', 'b'))
f[f == 'b'] = 'c'
eq_(f.cells, ('c', 'a'))
# label length
lens = [2, 5, 32, 2, 32, 524]
f = Factor(['a' * l for l in lens], 'f')
fl = f.label_length()
assert_array_equal(fl, lens)
eq_(fl.info['longname'], 'f.label_length()')
lens2 = [3, 5, 32, 2, 32, 523]
f2 = Factor(['b' * l for l in lens2], 'f2')
assert_array_equal(fl - f2.label_length(), [a - b for a, b in zip(lens, lens2)])
# equality
f = Factor('aabbcc')
assert_equal(f == Factor('aabbcc'), True)
assert_equal(f == Factor('bbccaa'), False)
assert_equal(f == Factor('aabxxx'), (True, True, True, False, False, False))
assert_equal(f == Var(np.ones(6)), False)
# Factor.as_var()
assert_array_equal(f.as_var(dict(list(zip('abc', list(range(3)))))), [0, 0, 1, 1, 2, 2])
assert_array_equal(f.as_var({'a': 1}, 2), [1, 1, 2, 2, 2, 2])
assert_raises(KeyError, f.as_var, {'a': 1})
# Factor.floodfill()
f = Factor([' ', ' ', '1', '2', ' ', ' ', '3', ' ', ' ', '2', ' ', ' ', '1'])
regions = [ 1, 1, 1, 2, 2, 2, 3, 3, 3, 2, 2, 1, 1]
regions2 = [ 1, 1, 1, 2, 2, 3, 3, 2, 2, 2, 2, 1, 1]
regions3 = [ 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2]
target3 = ['1', '1', '1', '2', '2', '2', '3', '3', '2', '2', '2', '2', '1']
target_p = [' ', ' ', '1', '2', '2', '2', '3', '3', '3', '2', '2', '2', '1']
assert_array_equal(f.floodfill(regions, ' '), Var(regions).as_factor())
assert_array_equal(f.floodfill(regions2, ' '), Var(regions2).as_factor())
assert_array_equal(f.floodfill(regions3, ' '), target3)
assert_array_equal(f.floodfill('previous', ' '), target_p)
f = Factor(['', '', 'a', '', 'e', 'r', ''])
assert_array_equal(f.floodfill([1, 1, 1, 11, 11, 11, 11]), Factor('aaaeerr'))
def test_factor():
"Test basic Factor functionality"
# initializing
assert_array_equal(Factor('ab'), ['a', 'b'])
assert_array_equal(Factor('ab', repeat=2), ['a', 'a', 'b', 'b'])
assert_array_equal(Factor('ab', repeat=np.array([2, 1])), ['a', 'a', 'b'])
empty_factor = Factor([])
eq_(len(empty_factor), 0)
assert_dataobj_equal(Factor(np.empty(0)), empty_factor)
# from Factor
f = Factor('aabbcc')
assert_array_equal(Factor(f), f)
assert_array_equal(Factor(f, labels={'a': 'b'}), Factor('bbbbcc'))
# removing a cell
f = Factor('aabbcc')
eq_(f.cells, ('a', 'b', 'c'))
eq_(f.n_cells, 3)
f[f == 'c'] = 'a'
eq_(f.cells, ('a', 'b'))
eq_(f.n_cells, 2)
# cell order
a = np.tile(np.arange(3), 3)
# alphabetical
f = Factor(a, labels={0: 'c', 1: 'b', 2: 'a'})
eq_(f.cells, ('a', 'b', 'c'))
# ordered
f = Factor(a, labels=((0, 'c'), (1, 'b'), (2, 'a')))
eq_(f.cells, ('c', 'b', 'a'))
eq_(f[:2].cells, ('c', 'b'))
f[f == 'b'] = 'c'
eq_(f.cells, ('c', 'a'))
# label length
lens = [2, 5, 32, 2, 32, 524]
f = Factor(['a' * l for l in lens], 'f')
fl = f.label_length()
assert_array_equal(fl, lens)
eq_(fl.info['longname'], 'f.label_length()')
lens2 = [3, 5, 32, 2, 32, 523]
f2 = Factor(['b' * l for l in lens2], 'f2')
assert_array_equal(fl - f2.label_length(), [a - b for a, b in zip(lens, lens2)])
# equality
f = Factor('aabbcc')
assert_equal(f == Factor('aabbcc'), True)
assert_equal(f == Factor('bbccaa'), False)
assert_equal(f == Factor('aabxxx'), (True, True, True, False, False, False))
assert_equal(f == Var(np.ones(6)), False)
# Factor.as_var()
assert_array_equal(f.as_var(dict(zip('abc', range(3)))), [0, 0, 1, 1, 2, 2])
assert_array_equal(f.as_var({'a': 1}, 2), [1, 1, 2, 2, 2, 2])
assert_raises(KeyError, f.as_var, {'a': 1})
# Factor.floodfill()
f = Factor([' ', ' ', '1', '2', ' ', ' ', '3', ' ', ' ', '2', ' ', ' ', '1'])
regions = [ 1, 1, 1, 2, 2, 2, 3, 3, 3, 2, 2, 1, 1]
regions2 = [ 1, 1, 1, 2, 2, 3, 3, 2, 2, 2, 2, 1, 1]
regions3 = [ 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2]
target3 = ['1', '1', '1', '2', '2', '2', '3', '3', '2', '2', '2', '2', '1']
target_p = [' ', ' ', '1', '2', '2', '2', '3', '3', '3', '2', '2', '2', '1']
assert_array_equal(f.floodfill(regions, ' '), Var(regions).as_factor())
assert_array_equal(f.floodfill(regions2, ' '), Var(regions2).as_factor())
assert_array_equal(f.floodfill(regions3, ' '), target3)
assert_array_equal(f.floodfill('previous', ' '), target_p)
f = Factor(['', '', 'a', '', 'e', 'r', ''])
assert_array_equal(f.floodfill([1, 1, 1, 11, 11, 11, 11]), Factor('aaaeerr'))
def test_model():
"Test Model class"
a = Factor('ab', repeat=3, name='a')
b = Factor('ab', tile=3, name='b')
u = Var([1, 1, 1, -1, -1, -1], 'u')
v = Var([1., 2., 3., 4., 5., 6.], 'v')
w = Var([1., 0., 0., 1., 1., 0.], 'w')
# model repr
m = a * b + v
eq_(repr(m), "a + b + a % b + v")
lines = ("intercept a b a x b v",
"-----------------------------",
"1 1 1 1 1",
"1 1 0 0 2",
"1 1 1 1 3",
"1 0 0 0 4",
"1 0 1 0 5",
"1 0 0 0 6")
eq_(str(m), '\n'.join(lines))
eq_(str(m.head(2)), '\n'.join(lines[:4]))
eq_(str(m.tail(2)), '\n'.join(lines[:2] + lines[-2:]))
# model without explicit names
x1 = Factor('ab', repeat=2)
x2 = Factor('ab', tile=2)
m = x1 * x2
eq_(repr(m), "<?> + <?> + <?> % <?>")
# catch explicit intercept
intercept = Factor('i', repeat=4, name='intercept')
assert_raises(ValueError, a.__mul__, intercept)
# different var/factor combinations
eq_(a * b, a + b + a % b)
eq_(a * v, a + v + a % v)
eq_(a * (v + w), a + v + w + a % v + a % w)
# parametrization
m = v + w + v * w
p = m._parametrize('dummy')
eq_(p.column_names, ['intercept', 'v', 'w', 'v * w'])
assert_array_equal(p.x[:, p.terms['intercept']], 1)
assert_array_equal(p.x[:, p.terms['v']], v.x[:, None])
assert_array_equal(p.x[:, p.terms['w']], w.x[:, None])
assert_array_equal(p.x[:, p.terms['v * w']], (v * w).x[:, None])
# persistence
mp = pickle.loads(pickle.dumps(m, pickle.HIGHEST_PROTOCOL))
assert_array_equal(m.full, mp.full)
# nested Vars
m = (v + w) * u
assert_dataobj_equal(m.effects[2], u)
assert_dataobj_equal(m.effects[3], v * u)
assert_dataobj_equal(m.effects[4], w * u)
m = u * (v + w)
assert_dataobj_equal(m.effects[0], u)
assert_dataobj_equal(m.effects[3], u * v)
assert_dataobj_equal(m.effects[4], u * w)
m = (v + w) % u
assert_dataobj_equal(m.effects[0], v * u)
assert_dataobj_equal(m.effects[1], w * u)
m = u % (v + w)
assert_dataobj_equal(m.effects[0], u * v)
assert_dataobj_equal(m.effects[1], u * w)
def test_ndvar():
"Test the NDVar class"
ds = datasets.get_uts(utsnd=True)
x = ds['utsnd']
# meaningful slicing
assert_raises(KeyError, x.sub, sensor='5')
assert_equal(x.sub(sensor='4'), x.x[:, 4])
assert_equal(x.sub(sensor=['4', '3', '2']), x.x[:, [4, 3, 2]])
assert_equal(x.sub(sensor=['4']), x.x[:, [4]])
assert_equal(x.sub(case=1, sensor='4'), x.x[1, 4])
# setup indices
s_case = slice(10, 13)
s_sensor = slice(2, 4)
s_time = x.time._slice(0.1, 0.2)
b_case = np.zeros(ds.n_cases, dtype=bool)
b_case[s_case] = True
b_sensor = np.array([False, False, True, True, False])
b_time = np.arange(s_time.start, s_time.stop)
a_case = np.arange(10, 13)
a_sensor = np.arange(2, 4)
a_time = np.arange(x.time.dimindex(0.1), x.time.dimindex(0.2))
# slicing with different index kinds
tgt = x.x[s_case, s_sensor, s_time]
eq_(tgt.shape, (3, 2, 10))
# single
assert_equal(x.sub(case=s_case, sensor=s_sensor, time=s_time), tgt)
assert_equal(x.sub(case=a_case, sensor=a_sensor, time=a_time), tgt)
assert_equal(x.sub(case=b_case, sensor=b_sensor, time=b_time), tgt)
# bool & slice
assert_equal(x.sub(case=b_case, sensor=s_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=b_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=s_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=b_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=b_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=s_sensor, time=b_time), tgt)
# bool & array
assert_equal(x.sub(case=b_case, sensor=a_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=b_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=a_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=b_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=b_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=a_sensor, time=b_time), tgt)
# slice & array
assert_equal(x.sub(case=s_case, sensor=a_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=s_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=a_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=s_sensor, time=a_time), tgt)
assert_equal(x.sub(case=a_case, sensor=s_sensor, time=s_time), tgt)
assert_equal(x.sub(case=s_case, sensor=a_sensor, time=s_time), tgt)
# all three
assert_equal(x.sub(case=a_case, sensor=b_sensor, time=s_time), tgt)
assert_equal(x.sub(case=a_case, sensor=s_sensor, time=b_time), tgt)
assert_equal(x.sub(case=b_case, sensor=a_sensor, time=s_time), tgt)
assert_equal(x.sub(case=b_case, sensor=s_sensor, time=a_time), tgt)
assert_equal(x.sub(case=s_case, sensor=a_sensor, time=b_time), tgt)
assert_equal(x.sub(case=s_case, sensor=b_sensor, time=a_time), tgt)
# Var
v_case = Var(b_case)
assert_equal(x.sub(case=v_case, sensor=b_sensor, time=a_time), tgt)
# univariate result
assert_dataobj_equal(x.sub(sensor=2, time=0.1),
Var(x.x[:, 2, a_time[0]], x.name))
eq_(x.sub(case=0, sensor=2, time=0.1), x.x[0, 2, a_time[0]])
# baseline correction
x_bl = x - x.summary(time=(None, 0))
# assert that the baseline is 0
bl = x_bl.summary('case', 'sensor', time=(None, 0))
ok_(abs(bl) < 1e-10, "Baseline correction")
# NDVar as index
sens_mean = x.mean(('case', 'time'))
idx = sens_mean > 0
pos = sens_mean[idx]
assert_array_equal(pos.x > 0, True)
# NDVar as index along one dimension
x_tc = x.sub(sensor='1')
x_time = NDVar(x_tc.time.times >= 0.3, dims=(x_tc.time,))
assert_dataobj_equal(x_tc[x_time], x_tc.sub(time=(0.3, None)))
# out of range index
assert_raises(ValueError, x.sub, time=(0.1, 0.81))
assert_raises(ValueError, x.sub, time=(-0.25, 0.1))
def test_anova():
"Test testnd.anova()"
ds = datasets.get_uts(True)
testnd.anova('utsnd', 'A*B', ds=ds)
for samples in (0, 2):
logging.info("TEST: samples=%r" % samples)
testnd.anova('utsnd', 'A*B', ds=ds, samples=samples)
testnd.anova('utsnd', 'A*B', ds=ds, samples=samples, pmin=0.05)
testnd.anova('utsnd', 'A*B', ds=ds, samples=samples, tfce=True)
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, samples=0, pmin=0.05)
eq_(
repr(res), "<anova 'utsnd', 'A*B*rm', samples=0, pmin=0.05, "
"'A': 17 clusters, 'B': 20 clusters, 'A x B': 22 clusters>")
res = testnd.anova('utsnd',
'A*B*rm',
match='rm',
ds=ds,
samples=2,
pmin=0.05)
eq_(
repr(res),
"<anova 'utsnd', 'A*B*rm', match='rm', samples=2, pmin=0.05, "
"'A': 17 clusters, p >= 0.000, 'B': 20 clusters, p >= 0.000, "
"'A x B': 22 clusters, p >= 0.000>")
# persistence
string = pickle.dumps(res, protocol=pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_equal(repr(res_), repr(res))
# threshold-free
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, samples=10)
repr(res)
assert_in('A clusters', res.clusters.info)
assert_in('B clusters', res.clusters.info)
assert_in('A x B clusters', res.clusters.info)
# no clusters
res = testnd.anova('uts',
'B',
sub="A=='a1'",
ds=ds,
samples=5,
pmin=0.05,
mintime=0.02)
repr(res)
assert_in('v', res.clusters)
assert_in('p', res.clusters)
# all effects with clusters
res = testnd.anova('uts',
'A*B*rm',
ds=ds,
samples=5,
pmin=0.05,
tstart=0.1,
mintime=0.02)
assert_equal(set(res.clusters['effect'].cells), set(res.effects))
# some effects with clusters, some without
res = testnd.anova('uts',
'A*B*rm',
ds=ds,
samples=5,
pmin=0.05,
tstart=0.37,
mintime=0.02)
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res_ = pickle.loads(string)
assert_dataobj_equal(res.clusters, res_.clusters)
# test multi-effect results (with persistence)
# UTS
res = testnd.anova('uts', 'A*B*rm', ds=ds, samples=5)
repr(res)
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
resr = pickle.loads(string)
tf_clusters = resr.find_clusters(pmin=0.05)
peaks = resr.find_peaks()
assert_dataobj_equal(tf_clusters, res.find_clusters(pmin=0.05))
assert_dataobj_equal(peaks, res.find_peaks())
assert_equal(tf_clusters.eval("p.min()"), peaks.eval("p.min()"))
unmasked = resr.f[0]
masked = resr.masked_parameter_map(effect=0, pmin=0.05)
assert_array_equal(masked.x <= unmasked.x, True)
# reproducibility
res0 = testnd.anova('utsnd', 'A*B*rm', ds=ds, pmin=0.05, samples=5)
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, pmin=0.05, samples=5)
assert_dataset_equal(res.clusters, res0.clusters)
configure(n_workers=0)
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, pmin=0.05, samples=5)
assert_dataset_equal(res.clusters, res0.clusters)
configure(n_workers=True)
# permutation
eelbrain._stats.permutation._YIELD_ORIGINAL = 1
samples = 4
# raw
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, samples=samples)
for dist in res._cdist:
eq_(len(dist.dist), samples)
assert_array_equal(dist.dist, dist.parameter_map.abs().max())
# TFCE
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, tfce=True, samples=samples)
for dist in res._cdist:
eq_(len(dist.dist), samples)
assert_array_equal(dist.dist, dist.tfce_map.abs().max())
# thresholded
res = testnd.anova('utsnd', 'A*B*rm', ds=ds, pmin=0.05, samples=samples)
clusters = res.find_clusters()
for dist, effect in izip(res._cdist, res.effects):
effect_idx = clusters.eval("effect == %r" % effect)
vmax = clusters[effect_idx, 'v'].abs().max()
eq_(len(dist.dist), samples)
assert_array_equal(dist.dist, vmax)
eelbrain._stats.permutation._YIELD_ORIGINAL = 0
# 1d TFCE
configure(n_workers=0)
res = testnd.anova('utsnd.rms(time=(0.1, 0.3))',
'A*B*rm',
ds=ds,
tfce=True,
samples=samples)
configure(n_workers=True)
# zero variance
ds['utsnd'].x[:, 1, 10] = 0.
assert_raises(ZeroVariance, testnd.anova, 'utsnd', 'A', ds=ds)
assert_raises(ZeroVariance, testnd.anova, 'utsnd', 'A*B*rm', ds=ds)
def test_celltable():
"Test the Celltable class."
ds = datasets.get_uts()
ds['cat'] = Factor('abcd', repeat=15)
ct = Celltable('Y', 'A', ds=ds)
eq_(ct.n_cases, 60)
eq_(ct.n_cells, 2)
ct = Celltable('Y', 'A', match='rm', ds=ds)
eq_(ct.n_cases, 30)
eq_(ct.n_cells, 2)
# cat argument
ct = Celltable('Y', 'cat', cat=('c', 'b'), ds=ds)
eq_(ct.n_cases, 30)
eq_(ct.X[0], 'c')
eq_(ct.X[-1], 'b')
assert_raises(ValueError, Celltable, 'Y', 'cat', cat=('c', 'e'), ds=ds)
ct = Celltable('Y', 'A', match='rm', ds=ds)
eq_(ct.n_cases, 30)
assert np.all(ct.groups['a0'] == ct.groups['a1'])
ct = Celltable('Y', 'cat', match='rm', cat=('c', 'b'), ds=ds)
eq_(ct.n_cases, 30)
eq_(ct.X[0], 'c')
eq_(ct.X[-1], 'b')
# catch unequal length
assert_raises(ValueError, Celltable, ds['Y', :-1], 'cat', ds=ds)
assert_raises(ValueError, Celltable, ds['Y', :-1], 'cat', match='rm', ds=ds)
# coercion of numerical X
X = ds.eval("A == 'a0'")
ct = Celltable('Y', X, cat=(None, None), ds=ds)
eq_(('False', 'True'), ct.cat)
assert_array_equal(ct.data['True'], ds['Y', X])
ct = Celltable('Y', X, cat=(True, False), ds=ds)
eq_(('True', 'False'), ct.cat)
assert_array_equal(ct.data['True'], ds['Y', X])
# test coercion of Y
ct = Celltable(ds['Y'].x, 'A', ds=ds)
assert_is_instance(ct.Y, np.ndarray)
ct = Celltable(ds['Y'].x, 'A', ds=ds, coercion=asvar)
assert_is_instance(ct.Y, Var)
# test sub
ds_sub = ds.sub("A == 'a0'")
ct_sub = Celltable('Y', 'B', ds=ds_sub)
ct = Celltable('Y', 'B', sub="A == 'a0'", ds=ds)
assert_dataobj_equal(ct_sub.Y, ct.Y)
# test sub with rm
ct_sub = Celltable('Y', 'B', match='rm', ds=ds_sub)
ct = Celltable('Y', 'B', match='rm', sub="A == 'a0'", ds=ds)
assert_dataobj_equal(ct_sub.Y, ct.Y)
# Interaction match
ct = Celltable('Y', 'A', match='B % rm', ds=ds)
ok_(ct.all_within)
assert_dataobj_equal(combine((ct.data['a0'], ct.data['a1'])), ds['Y'])
# test rm sorting
ds = Dataset()
ds['rm'] = Factor('abc', repeat=4)
ds['Y'] = Var(np.arange(3.).repeat(4))
ds['X'] = Factor('ab', repeat=2, tile=3)
idx = np.arange(12)
np.random.shuffle(idx)
ds = ds[idx]
ct = Celltable('Y', 'X', 'rm', ds=ds)
assert_array_equal(ct.match, Factor('abc', tile=2))
assert_array_equal(ct.Y, np.tile(np.arange(3.), 2))
assert_array_equal(ct.X, Factor('ab', repeat=3))
def test_ttest_1samp():
"Test testnd.ttest_1samp()"
ds = datasets.get_uts(True)
# no clusters
res0 = testnd.ttest_1samp('uts', sub="A == 'a0'", ds=ds)
assert_less(res0.p_uncorrected.min(), 0.05)
repr0 = repr(res0)
assert_in("'uts'", repr0)
assert_not_in('clusters', repr0)
assert_not_in('mintime', repr0)
# sub as array
res1 = testnd.ttest_1samp('uts', sub=ds.eval("A == 'a0'"), ds=ds)
repr1 = repr(res1)
assert_not_equal(repr1, repr0)
# clusters without resampling
res1 = testnd.ttest_1samp('uts',
sub="A == 'a0'",
ds=ds,
samples=0,
pmin=0.05,
tstart=0,
tstop=0.6,
mintime=0.05)
assert_equal(res1.clusters.n_cases, 1)
assert_not_in('p', res1.clusters)
repr1 = repr(res1)
assert_in('clusters', repr1)
assert_in('samples', repr1)
assert_in('mintime', repr1)
# persistence
string = pickle.dumps(res1, pickle.HIGHEST_PROTOCOL)
res1_ = pickle.loads(string)
assert_equal(repr(res1_), repr1)
assert_dataobj_equal(res1.p_uncorrected, res1_.p_uncorrected)
# clusters with resampling
res2 = testnd.ttest_1samp('uts',
sub="A == 'a0'",
ds=ds,
samples=10,
pmin=0.05,
tstart=0,
tstop=0.6,
mintime=0.05)
assert_equal(res2.clusters.n_cases, 1)
assert_equal(res2.samples, 10)
assert_in('p', res2.clusters)
repr2 = repr(res2)
assert_in('samples', repr2)
# clusters with permutations
dss = ds.sub("logical_and(A=='a0', B=='b0')")[:8]
res3 = testnd.ttest_1samp('uts',
sub="A == 'a0'",
ds=dss,
samples=10000,
pmin=0.05,
tstart=0,
tstop=0.6,
mintime=0.05)
assert_equal(res3.clusters.n_cases, 2)
assert_equal(res3.samples, -1)
assert_less(res3.clusters['p'].x.min(), 0.05)
repr3 = repr(res3)
assert_in('samples', repr3)
# nd
dss = ds.sub("A == 'a0'")
res = testnd.ttest_1samp('utsnd', ds=dss, samples=1)
res = testnd.ttest_1samp('utsnd', ds=dss, pmin=0.05, samples=1)
res = testnd.ttest_1samp('utsnd', ds=dss, tfce=True, samples=1)
# TFCE properties
res = testnd.ttest_1samp('utsnd', sub="A == 'a0'", ds=ds, samples=1)
string = pickle.dumps(res, pickle.HIGHEST_PROTOCOL)
res = pickle.loads(string)
tfce_clusters = res.find_clusters(pmin=0.05)
peaks = res.find_peaks()
assert_equal(tfce_clusters.eval("p.min()"), peaks.eval("p.min()"))
masked = res.masked_parameter_map(pmin=0.05)
assert_array_equal(masked.abs().x <= res.t.abs().x, True)
# zero variance
ds['utsnd'].x[:, 1, 10] = 0.
ds['utsnd'].x[:, 2, 10] = 0.1
res = testnd.ttest_1samp('utsnd', ds=ds)
eq_(res.t.x[1, 10], 0.)
assert_greater(res.t.x[2, 10], 1e10)
def test_celltable():
"Test the Celltable class."
ds = datasets.get_uts()
ds['cat'] = Factor('abcd', repeat=15)
ct = Celltable('Y', 'A', ds=ds)
eq_(ct.n_cases, 60)
eq_(ct.n_cells, 2)
eq_(repr(ct), "Celltable(Y, A)")
eq_(repr(Celltable(ds['Y'].x, 'A', ds=ds)), "Celltable(<ndarray>, A)")
eq_(repr(Celltable(ds['Y'].x, ds['A'].x, ds=ds)),
"Celltable(<ndarray>, <Factor>)")
ct = Celltable('Y', 'A', match='rm', ds=ds)
eq_(ct.n_cases, 30)
eq_(ct.n_cells, 2)
# cat argument
ct = Celltable('Y', 'cat', cat=('c', 'b'), ds=ds)
eq_(ct.n_cases, 30)
eq_(ct.X[0], 'c')
eq_(ct.X[-1], 'b')
assert_raises(ValueError, Celltable, 'Y', 'cat', cat=('c', 'e'), ds=ds)
ct = Celltable('Y', 'A', match='rm', ds=ds)
eq_(ct.n_cases, 30)
assert np.all(ct.groups['a0'] == ct.groups['a1'])
ct = Celltable('Y', 'cat', match='rm', cat=('c', 'b'), ds=ds)
eq_(ct.n_cases, 30)
eq_(ct.X[0], 'c')
eq_(ct.X[-1], 'b')
# catch unequal length
assert_raises(ValueError, Celltable, ds['Y', :-1], 'cat', ds=ds)
assert_raises(ValueError, Celltable, ds['Y', :-1], 'cat', match='rm', ds=ds)
# coercion of numerical X
X = ds.eval("A == 'a0'")
ct = Celltable('Y', X, cat=(None, None), ds=ds)
eq_(('False', 'True'), ct.cat)
assert_array_equal(ct.data['True'], ds['Y', X])
ct = Celltable('Y', X, cat=('True', 'False'), ds=ds)
eq_(('True', 'False'), ct.cat)
assert_array_equal(ct.data['True'], ds['Y', X])
# test coercion of Y
ct = Celltable(ds['Y'].x, 'A', ds=ds)
assert_is_instance(ct.Y, np.ndarray)
ct = Celltable(ds['Y'].x, 'A', ds=ds, coercion=asvar)
assert_is_instance(ct.Y, Var)
# test sub
ds_sub = ds.sub("A == 'a0'")
ct_sub = Celltable('Y', 'B', ds=ds_sub)
ct = Celltable('Y', 'B', sub="A == 'a0'", ds=ds)
assert_dataobj_equal(ct_sub.Y, ct.Y)
# test sub with rm
ct_sub = Celltable('Y', 'B', match='rm', ds=ds_sub)
ct = Celltable('Y', 'B', match='rm', sub="A == 'a0'", ds=ds)
assert_dataobj_equal(ct_sub.Y, ct.Y)
# Interaction match
ct = Celltable('Y', 'A', match='B % rm', ds=ds)
ok_(ct.all_within)
assert_dataobj_equal(combine((ct.data['a0'], ct.data['a1'])), ds['Y'])
# test rm sorting
ds = Dataset()
ds['rm'] = Factor('abc', repeat=4)
ds['Y'] = Var(np.arange(3.).repeat(4))
ds['X'] = Factor('ab', repeat=2, tile=3)
idx = np.arange(12)
np.random.shuffle(idx)
ds = ds[idx]
ct = Celltable('Y', 'X', 'rm', ds=ds)
assert_array_equal(ct.match, Factor('abc', tile=2))
assert_array_equal(ct.Y, np.tile(np.arange(3.), 2))
assert_array_equal(ct.X, Factor('ab', repeat=3))
def test_var():
"Test Var objects"
base = Factor('aabbcde')
# initialization
x = np.arange(4)
y = Var(x)
assert_array_equal(y, x)
y = Var(x, repeat=2)
assert_array_equal(y, x.repeat(2))
y = Var(x, repeat=x)
assert_array_equal(y, x.repeat(x))
y = Var.from_dict(base, {'a': 5, 'e': 8}, default=0)
assert_array_equal(y.x, [5, 5, 0, 0, 0, 0, 8])
assert_raises(TypeError, Var, x, info=1)
# basic operations
info = {'a': 1}
v = Var([1., 2., 3., -4.], 'v', info=info)
c = 2
v2 = Var([2., 2., 3., 3.], 'w', info=info)
eq_(v.info, info)
for op, iop, desc in OPERATORS:
target = op(v.x, c)
vtarget = op(v.x, v2.x)
# op
if desc == '+':
w = v.copy()
w.x = iop(w.x, c)
else:
w = op(v, c)
eq_(w.info, {'a': 1, 'longname': 'v %s %s' % (desc, c)})
assert_array_equal(w, target)
# with Var
w = op(v, v2)
eq_(w.info, {'a': 1, 'longname': 'v %s w' % desc})
assert_array_equal(w, vtarget)
# i-op
w = v.copy()
w = iop(w, c)
assert_array_equal(w, target)
# i-op with Var
w = v.copy()
w = iop(w, v2)
assert_array_equal(w, vtarget)
# methods
w = v.abs()
eq_(w.info, {'a': 1, 'longname': 'abs(v)'})
assert_array_equal(w, np.abs(v.x))
x = w.log()
eq_(x.info, {'a': 1, 'longname': 'log(abs(v))'})
assert_array_equal(x, np.log(w.x))
# assignment
tgt1 = np.arange(10)
tgt2 = np.tile(np.arange(5), 2)
v = Var(np.arange(10))
v[v > 4] = np.arange(5)
assert_array_equal(v, tgt2)
v[5:] = np.arange(5, 10)
assert_array_equal(v, tgt1)
v = Var(np.arange(10))
v[v > 4] = Var(np.arange(5))
assert_array_equal(v, tgt2)
v[5:] = Var(np.arange(5, 10))
assert_array_equal(v, tgt1)
# .count()
v = Var([1., 2., 1.11, 2., 1.11, 4.])
assert_array_equal(v.count(), [0, 0, 0, 1, 1, 0])
# .split()
y = Var(np.arange(16))
for i in range(1, 9):
split = y.split(i)
eq_(len(split.cells), i)
# .as_factor()
v = Var(np.arange(4))
assert_dataobj_equal(v.as_factor(), Factor('0123'))
assert_dataobj_equal(v.as_factor({0: 'a'}), Factor(['a', '', '', '']))
assert_dataobj_equal(v.as_factor({(0, 1): 'a', (2, 3): 'b'}), Factor('aabb'))
assert_dataobj_equal(v.as_factor({(0, 1): 'a', 2: 'b', 'default': 'c'}),
Factor('aabc'))
assert_dataobj_equal(v.as_factor({(0, 1): 'a', (2, 'default'): 'b'}),
Factor('aabb'))
def test_clusterdist():
"Test _ClusterDist class"
shape = (10, 6, 6, 4)
locs = [[0, 0, 0],
[1, 0, 0],
[1, 1, 0],
[0, 1, 0]]
x = np.random.normal(0, 1, shape)
sensor = Sensor(locs, ['0', '1', '2', '3'])
sensor.set_connectivity(connect_dist=1.1)
dims = ('case', UTS(-0.1, 0.1, 6), Ordered('dim2', list(range(6)), 'unit'),
sensor)
y = NDVar(x, dims)
# test connecting sensors
logging.info("TEST: connecting sensors")
bin_map = np.zeros(shape[1:], dtype=np.bool8)
bin_map[:3, :3, :2] = True
pmap = np.random.normal(0, 1, shape[1:])
np.clip(pmap, -1, 1, pmap)
pmap[bin_map] = 2
cdist = _ClusterDist(y, 0, 1.5)
print(repr(cdist))
cdist.add_original(pmap)
print(repr(cdist))
assert_equal(cdist.n_clusters, 1)
assert_array_equal(cdist._original_cluster_map == cdist._cids[0],
cdist._crop(bin_map).swapaxes(0, cdist._nad_ax))
assert_equal(cdist.parameter_map.dims, y.dims[1:])
# test connecting many sensors
logging.info("TEST: connecting sensors")
bin_map = np.zeros(shape[1:], dtype=np.bool8)
bin_map[:3, :3] = True
pmap = np.random.normal(0, 1, shape[1:])
np.clip(pmap, -1, 1, pmap)
pmap[bin_map] = 2
cdist = _ClusterDist(y, 0, 1.5)
cdist.add_original(pmap)
assert_equal(cdist.n_clusters, 1)
assert_array_equal(cdist._original_cluster_map == cdist._cids[0],
cdist._crop(bin_map).swapaxes(0, cdist._nad_ax))
# test keeping sensors separate
logging.info("TEST: keeping sensors separate")
bin_map = np.zeros(shape[1:], dtype=np.bool8)
bin_map[:3, :3, 0] = True
bin_map[:3, :3, 2] = True
pmap = np.random.normal(0, 1, shape[1:])
np.clip(pmap, -1, 1, pmap)
pmap[bin_map] = 2
cdist = _ClusterDist(y, 1, 1.5)
cdist.add_original(pmap)
assert_equal(cdist.n_clusters, 2)
# criteria
ds = datasets.get_uts(True)
res = testnd.ttest_rel('utsnd', 'A', match='rm', ds=ds, samples=0, pmin=0.05)
assert_less(res.clusters['duration'].min(), 0.01)
eq_(res.clusters['n_sensors'].min(), 1)
res = testnd.ttest_rel('utsnd', 'A', match='rm', ds=ds, samples=0, pmin=0.05,
mintime=0.02, minsensor=2)
assert_greater_equal(res.clusters['duration'].min(), 0.02)
eq_(res.clusters['n_sensors'].min(), 2)
# 1d
res1d = testnd.ttest_rel('utsnd.sub(time=0.1)', 'A', match='rm', ds=ds,
samples=0, pmin=0.05)
assert_dataobj_equal(res1d.p_uncorrected, res.p_uncorrected.sub(time=0.1))
# TFCE
logging.info("TEST: TFCE")
sensor = Sensor(locs, ['0', '1', '2', '3'])
sensor.set_connectivity(connect_dist=1.1)
dims = ('case', UTS(-0.1, 0.1, 4), sensor,
Ordered('dim2', list(range(10)), 'unit'))
y = NDVar(np.random.normal(0, 1, (10, 4, 4, 10)), dims)
cdist = _ClusterDist(y, 3, None)
cdist.add_original(y.x[0])
cdist.finalize()
assert_equal(cdist.dist.shape, (3,))
# I/O
string = pickle.dumps(cdist, pickle.HIGHEST_PROTOCOL)
cdist_ = pickle.loads(string)
assert_equal(repr(cdist_), repr(cdist))
# find peaks
x = np.array([[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[7, 7, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 7, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[5, 7, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 6, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 7, 5, 5, 0, 0],
[0, 0, 0, 0, 5, 4, 4, 4, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 4, 0, 0],
[0, 0, 0, 0, 7, 0, 0, 3, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]])
tgt = np.equal(x, 7)
peaks = cdist._find_peaks(x)
logging.debug(' detected: \n%s' % (peaks.astype(int)))
logging.debug(' target: \n%s' % (tgt.astype(int)))
assert_array_equal(peaks, tgt)