def test_ica_additional():
"""Test additional ICA functionality
"""
stop2 = 500
raw = io.Raw(raw_fname, preload=True).crop(0, stop, False).crop(1.5)
picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
eog=False, exclude='bads')
test_cov = read_cov(test_cov_name)
events = read_events(event_name)
picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
eog=False, exclude='bads')
epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
baseline=(None, 0), preload=True)
# for testing eog functionality
picks2 = pick_types(raw.info, meg=True, stim=False, ecg=False,
eog=True, exclude='bads')
epochs_eog = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks2,
baseline=(None, 0), preload=True)
test_cov2 = deepcopy(test_cov)
ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4,
n_pca_components=4)
assert_true(ica.info is None)
ica.decompose_raw(raw, picks[:5])
assert_true(isinstance(ica.info, Info))
assert_true(ica.n_components_ < 5)
ica = ICA(n_components=3, max_pca_components=4,
n_pca_components=4)
assert_raises(RuntimeError, ica.save, '')
ica.decompose_raw(raw, picks=None, start=start, stop=stop2)
# test warnings on bad filenames
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
ica_badname = op.join(op.dirname(tempdir), 'test-bad-name.fif.gz')
ica.save(ica_badname)
read_ica(ica_badname)
assert_true(len(w) == 2)
# test decim
ica = ICA(n_components=3, max_pca_components=4,
n_pca_components=4)
raw_ = raw.copy()
for _ in range(3):
raw_.append(raw_)
n_samples = raw_._data.shape[1]
ica.decompose_raw(raw, picks=None, decim=3)
assert_true(raw_._data.shape[1], n_samples)
# test expl var
ica = ICA(n_components=1.0, max_pca_components=4,
n_pca_components=4)
ica.decompose_raw(raw, picks=None, decim=3)
assert_true(ica.n_components_ == 4)
# epochs extraction from raw fit
assert_raises(RuntimeError, ica.get_sources_epochs, epochs)
# test reading and writing
test_ica_fname = op.join(op.dirname(tempdir), 'test-ica.fif')
for cov in (None, test_cov):
ica = ICA(noise_cov=cov, n_components=2, max_pca_components=4,
n_pca_components=4)
with warnings.catch_warnings(record=True): # ICA does not converge
ica.decompose_raw(raw, picks=picks, start=start, stop=stop2)
sources = ica.get_sources_epochs(epochs)
assert_true(ica.mixing_matrix_.shape == (2, 2))
assert_true(ica.unmixing_matrix_.shape == (2, 2))
assert_true(ica.pca_components_.shape == (4, len(picks)))
assert_true(sources.shape[1] == ica.n_components_)
for exclude in [[], [0]]:
ica.exclude = [0]
ica.save(test_ica_fname)
ica_read = read_ica(test_ica_fname)
assert_true(ica.exclude == ica_read.exclude)
# test pick merge -- add components
ica.pick_sources_raw(raw, exclude=[1])
assert_true(ica.exclude == [0, 1])
# -- only as arg
ica.exclude = []
ica.pick_sources_raw(raw, exclude=[0, 1])
assert_true(ica.exclude == [0, 1])
# -- remove duplicates
ica.exclude += [1]
ica.pick_sources_raw(raw, exclude=[0, 1])
assert_true(ica.exclude == [0, 1])
# test basic include
ica.exclude = []
ica.pick_sources_raw(raw, include=[1])
ica_raw = ica.sources_as_raw(raw)
assert_true(ica.exclude == [ica_raw.ch_names.index(e) for e in
ica_raw.info['bads']])
# test filtering
d1 = ica_raw._data[0].copy()
with warnings.catch_warnings(record=True): # dB warning
ica_raw.filter(4, 20)
assert_true((d1 != ica_raw._data[0]).any())
d1 = ica_raw._data[0].copy()
with warnings.catch_warnings(record=True): # dB warning
ica_raw.notch_filter([10])
assert_true((d1 != ica_raw._data[0]).any())
ica.n_pca_components = 2
ica.save(test_ica_fname)
ica_read = read_ica(test_ica_fname)
assert_true(ica.n_pca_components == ica_read.n_pca_components)
# check type consistency
attrs = ('mixing_matrix_ unmixing_matrix_ pca_components_ '
'pca_explained_variance_ _pre_whitener')
f = lambda x, y: getattr(x, y).dtype
for attr in attrs.split():
assert_equal(f(ica_read, attr), f(ica, attr))
ica.n_pca_components = 4
ica_read.n_pca_components = 4
ica.exclude = []
ica.save(test_ica_fname)
ica_read = read_ica(test_ica_fname)
for attr in ['mixing_matrix_', 'unmixing_matrix_', 'pca_components_',
'pca_mean_', 'pca_explained_variance_',
'_pre_whitener']:
assert_array_almost_equal(getattr(ica, attr),
getattr(ica_read, attr))
assert_true(ica.ch_names == ica_read.ch_names)
assert_true(isinstance(ica_read.info, Info))
assert_raises(RuntimeError, ica_read.decompose_raw, raw)
sources = ica.get_sources_raw(raw)
sources2 = ica_read.get_sources_raw(raw)
assert_array_almost_equal(sources, sources2)
_raw1 = ica.pick_sources_raw(raw, exclude=[1])
_raw2 = ica_read.pick_sources_raw(raw, exclude=[1])
assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0])
os.remove(test_ica_fname)
# check scrore funcs
for name, func in score_funcs.items():
if name in score_funcs_unsuited:
continue
scores = ica.find_sources_raw(raw, target='EOG 061', score_func=func,
start=0, stop=10)
assert_true(ica.n_components_ == len(scores))
# check univariate stats
scores = ica.find_sources_raw(raw, score_func=stats.skew)
# check exception handling
assert_raises(ValueError, ica.find_sources_raw, raw,
target=np.arange(1))
params = []
params += [(None, -1, slice(2), [0, 1])] # varicance, kurtosis idx params
params += [(None, 'MEG 1531')] # ECG / EOG channel params
for idx, ch_name in product(*params):
ica.detect_artifacts(raw, start_find=0, stop_find=50, ecg_ch=ch_name,
eog_ch=ch_name, skew_criterion=idx,
var_criterion=idx, kurt_criterion=idx)
## score funcs epochs ##
# check score funcs
for name, func in score_funcs.items():
if name in score_funcs_unsuited:
continue
scores = ica.find_sources_epochs(epochs_eog, target='EOG 061',
score_func=func)
assert_true(ica.n_components_ == len(scores))
# check univariate stats
scores = ica.find_sources_epochs(epochs, score_func=stats.skew)
# check exception handling
assert_raises(ValueError, ica.find_sources_epochs, epochs,
target=np.arange(1))
# ecg functionality
ecg_scores = ica.find_sources_raw(raw, target='MEG 1531',
score_func='pearsonr')
with warnings.catch_warnings(record=True): # filter attenuation warning
ecg_events = ica_find_ecg_events(raw,
sources[np.abs(ecg_scores).argmax()])
assert_true(ecg_events.ndim == 2)
# eog functionality
eog_scores = ica.find_sources_raw(raw, target='EOG 061',
score_func='pearsonr')
with warnings.catch_warnings(record=True): # filter attenuation warning
eog_events = ica_find_eog_events(raw,
sources[np.abs(eog_scores).argmax()])
assert_true(eog_events.ndim == 2)
# Test ica fiff export
ica_raw = ica.sources_as_raw(raw, start=0, stop=100)
assert_true(ica_raw.last_samp - ica_raw.first_samp == 100)
assert_true(len(ica_raw._filenames) == 0) # API consistency
ica_chans = [ch for ch in ica_raw.ch_names if 'ICA' in ch]
assert_true(ica.n_components_ == len(ica_chans))
test_ica_fname = op.join(op.abspath(op.curdir), 'test-ica_raw.fif')
ica.n_components = np.int32(ica.n_components)
ica_raw.save(test_ica_fname, overwrite=True)
ica_raw2 = io.Raw(test_ica_fname, preload=True)
assert_allclose(ica_raw._data, ica_raw2._data, rtol=1e-5, atol=1e-4)
ica_raw2.close()
os.remove(test_ica_fname)
# Test ica epochs export
ica_epochs = ica.sources_as_epochs(epochs)
assert_true(ica_epochs.events.shape == epochs.events.shape)
sources_epochs = ica.get_sources_epochs(epochs)
assert_array_equal(ica_epochs.get_data(), sources_epochs)
ica_chans = [ch for ch in ica_epochs.ch_names if 'ICA' in ch]
assert_true(ica.n_components_ == len(ica_chans))
assert_true(ica.n_components_ == ica_epochs.get_data().shape[1])
assert_true(ica_epochs.raw is None)
assert_true(ica_epochs.preload is True)
# test float n pca components
ica.pca_explained_variance_ = np.array([0.2] * 5)
ica.n_components_ = 0
for ncomps, expected in [[0.3, 1], [0.9, 4], [1, 1]]:
ncomps_ = _check_n_pca_components(ica, ncomps)
assert_true(ncomps_ == expected)
def test_ica_additional():
"""Test additional ICA functionality"""
stop2 = 500
raw = io.Raw(raw_fname, preload=True).crop(0, stop, False).crop(1.5)
picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
eog=False, exclude='bads')
test_cov = read_cov(test_cov_name)
events = read_events(event_name)
picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
eog=False, exclude='bads')
epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
baseline=(None, 0), preload=True)
# for testing eog functionality
picks2 = pick_types(raw.info, meg=True, stim=False, ecg=False,
eog=True, exclude='bads')
epochs_eog = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks2,
baseline=(None, 0), preload=True)
test_cov2 = deepcopy(test_cov)
ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4,
n_pca_components=4)
assert_true(ica.info is None)
with warnings.catch_warnings(record=True):
ica.fit(raw, picks[:5])
assert_true(isinstance(ica.info, Info))
assert_true(ica.n_components_ < 5)
ica = ICA(n_components=3, max_pca_components=4,
n_pca_components=4)
assert_raises(RuntimeError, ica.save, '')
with warnings.catch_warnings(record=True):
ica.fit(raw, picks=None, start=start, stop=stop2)
# test warnings on bad filenames
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
ica_badname = op.join(op.dirname(tempdir), 'test-bad-name.fif.gz')
ica.save(ica_badname)
read_ica(ica_badname)
assert_true(len(w) == 2)
# test decim
ica = ICA(n_components=3, max_pca_components=4,
n_pca_components=4)
raw_ = raw.copy()
for _ in range(3):
raw_.append(raw_)
n_samples = raw_._data.shape[1]
with warnings.catch_warnings(record=True):
ica.fit(raw, picks=None, decim=3)
assert_true(raw_._data.shape[1], n_samples)
# test expl var
ica = ICA(n_components=1.0, max_pca_components=4,
n_pca_components=4)
with warnings.catch_warnings(record=True):
ica.fit(raw, picks=None, decim=3)
assert_true(ica.n_components_ == 4)
# epochs extraction from raw fit
assert_raises(RuntimeError, ica.get_sources, epochs)
# test reading and writing
test_ica_fname = op.join(op.dirname(tempdir), 'test-ica.fif')
for cov in (None, test_cov):
ica = ICA(noise_cov=cov, n_components=2, max_pca_components=4,
n_pca_components=4)
with warnings.catch_warnings(record=True): # ICA does not converge
ica.fit(raw, picks=picks, start=start, stop=stop2)
sources = ica.get_sources(epochs).get_data()
assert_true(ica.mixing_matrix_.shape == (2, 2))
assert_true(ica.unmixing_matrix_.shape == (2, 2))
assert_true(ica.pca_components_.shape == (4, len(picks)))
assert_true(sources.shape[1] == ica.n_components_)
for exclude in [[], [0]]:
ica.exclude = [0]
ica.save(test_ica_fname)
ica_read = read_ica(test_ica_fname)
assert_true(ica.exclude == ica_read.exclude)
ica.exclude = []
ica.apply(raw, exclude=[1])
assert_true(ica.exclude == [])
ica.exclude = [0, 1]
ica.apply(raw, exclude=[1])
assert_true(ica.exclude == [0, 1])
ica_raw = ica.get_sources(raw)
assert_true(ica.exclude == [ica_raw.ch_names.index(e) for e in
ica_raw.info['bads']])
# test filtering
d1 = ica_raw._data[0].copy()
with warnings.catch_warnings(record=True): # dB warning
ica_raw.filter(4, 20)
assert_true((d1 != ica_raw._data[0]).any())
d1 = ica_raw._data[0].copy()
with warnings.catch_warnings(record=True): # dB warning
ica_raw.notch_filter([10])
assert_true((d1 != ica_raw._data[0]).any())
ica.n_pca_components = 2
ica.save(test_ica_fname)
ica_read = read_ica(test_ica_fname)
assert_true(ica.n_pca_components == ica_read.n_pca_components)
# check type consistency
attrs = ('mixing_matrix_ unmixing_matrix_ pca_components_ '
'pca_explained_variance_ _pre_whitener')
f = lambda x, y: getattr(x, y).dtype
for attr in attrs.split():
assert_equal(f(ica_read, attr), f(ica, attr))
ica.n_pca_components = 4
ica_read.n_pca_components = 4
ica.exclude = []
ica.save(test_ica_fname)
ica_read = read_ica(test_ica_fname)
for attr in ['mixing_matrix_', 'unmixing_matrix_', 'pca_components_',
'pca_mean_', 'pca_explained_variance_',
'_pre_whitener']:
assert_array_almost_equal(getattr(ica, attr),
getattr(ica_read, attr))
assert_true(ica.ch_names == ica_read.ch_names)
assert_true(isinstance(ica_read.info, Info))
sources = ica.get_sources(raw)[:, :][0]
sources2 = ica_read.get_sources(raw)[:, :][0]
assert_array_almost_equal(sources, sources2)
_raw1 = ica.apply(raw, exclude=[1])
_raw2 = ica_read.apply(raw, exclude=[1])
assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0])
os.remove(test_ica_fname)
# check scrore funcs
for name, func in score_funcs.items():
if name in score_funcs_unsuited:
continue
scores = ica.score_sources(raw, target='EOG 061', score_func=func,
start=0, stop=10)
assert_true(ica.n_components_ == len(scores))
# check univariate stats
scores = ica.score_sources(raw, score_func=stats.skew)
# check exception handling
assert_raises(ValueError, ica.score_sources, raw,
target=np.arange(1))
params = []
params += [(None, -1, slice(2), [0, 1])] # varicance, kurtosis idx params
params += [(None, 'MEG 1531')] # ECG / EOG channel params
for idx, ch_name in product(*params):
ica.detect_artifacts(raw, start_find=0, stop_find=50, ecg_ch=ch_name,
eog_ch=ch_name, skew_criterion=idx,
var_criterion=idx, kurt_criterion=idx)
with warnings.catch_warnings(record=True):
idx, scores = ica.find_bads_ecg(raw, method='ctps')
assert_equal(len(scores), ica.n_components_)
idx, scores = ica.find_bads_ecg(raw, method='correlation')
assert_equal(len(scores), ica.n_components_)
idx, scores = ica.find_bads_ecg(epochs, method='ctps')
assert_equal(len(scores), ica.n_components_)
assert_raises(ValueError, ica.find_bads_ecg, epochs.average(),
method='ctps')
assert_raises(ValueError, ica.find_bads_ecg, raw,
method='crazy-coupling')
idx, scores = ica.find_bads_eog(raw)
assert_equal(len(scores), ica.n_components_)
raw.info['chs'][raw.ch_names.index('EOG 061') - 1]['kind'] = 202
idx, scores = ica.find_bads_eog(raw)
assert_true(isinstance(scores, list))
assert_equal(len(scores[0]), ica.n_components_)
# check score funcs
for name, func in score_funcs.items():
if name in score_funcs_unsuited:
continue
scores = ica.score_sources(epochs_eog, target='EOG 061',
score_func=func)
assert_true(ica.n_components_ == len(scores))
# check univariate stats
scores = ica.score_sources(epochs, score_func=stats.skew)
# check exception handling
assert_raises(ValueError, ica.score_sources, epochs,
target=np.arange(1))
# ecg functionality
ecg_scores = ica.score_sources(raw, target='MEG 1531',
score_func='pearsonr')
with warnings.catch_warnings(record=True): # filter attenuation warning
ecg_events = ica_find_ecg_events(raw,
sources[np.abs(ecg_scores).argmax()])
assert_true(ecg_events.ndim == 2)
# eog functionality
eog_scores = ica.score_sources(raw, target='EOG 061',
score_func='pearsonr')
with warnings.catch_warnings(record=True): # filter attenuation warning
eog_events = ica_find_eog_events(raw,
sources[np.abs(eog_scores).argmax()])
assert_true(eog_events.ndim == 2)
# Test ica fiff export
ica_raw = ica.get_sources(raw, start=0, stop=100)
assert_true(ica_raw.last_samp - ica_raw.first_samp == 100)
assert_true(len(ica_raw._filenames) == 0) # API consistency
ica_chans = [ch for ch in ica_raw.ch_names if 'ICA' in ch]
assert_true(ica.n_components_ == len(ica_chans))
test_ica_fname = op.join(op.abspath(op.curdir), 'test-ica_raw.fif')
ica.n_components = np.int32(ica.n_components)
ica_raw.save(test_ica_fname, overwrite=True)
ica_raw2 = io.Raw(test_ica_fname, preload=True)
assert_allclose(ica_raw._data, ica_raw2._data, rtol=1e-5, atol=1e-4)
ica_raw2.close()
os.remove(test_ica_fname)
# Test ica epochs export
ica_epochs = ica.get_sources(epochs)
assert_true(ica_epochs.events.shape == epochs.events.shape)
ica_chans = [ch for ch in ica_epochs.ch_names if 'ICA' in ch]
assert_true(ica.n_components_ == len(ica_chans))
assert_true(ica.n_components_ == ica_epochs.get_data().shape[1])
assert_true(ica_epochs.raw is None)
assert_true(ica_epochs.preload is True)
# test float n pca components
ica.pca_explained_variance_ = np.array([0.2] * 5)
ica.n_components_ = 0
for ncomps, expected in [[0.3, 1], [0.9, 4], [1, 1]]:
ncomps_ = _check_n_pca_components(ica, ncomps)
assert_true(ncomps_ == expected)