def test_compute_proj_raw():
"""Test SSP computation on raw"""
# Test that the raw projectors work
raw_time = 2.5 # Do shorter amount for speed
raw = Raw(raw_fname, preload=True).crop(0, raw_time, False)
for ii in (0.25, 0.5, 1, 2):
with warnings.catch_warnings(True) as w:
projs = compute_proj_raw(raw, duration=ii - 0.1, stop=raw_time,
n_grad=1, n_mag=1, n_eeg=0)
assert_true(len(w) == 1)
# test that you can compute the projection matrix
projs = activate_proj(projs)
proj, nproj, U = make_projector(projs, raw.ch_names, bads=[])
assert_true(nproj == 2)
assert_true(U.shape[1] == 2)
# test that you can save them
raw.info['projs'] += projs
raw.save(op.join(tempdir, 'foo_%d_raw.fif' % ii), overwrite=True)
# Test that purely continuous (no duration) raw projection works
with warnings.catch_warnings(True) as w:
projs = compute_proj_raw(raw, duration=None, stop=raw_time,
n_grad=1, n_mag=1, n_eeg=0)
assert_true(len(w) == 1)
# test that you can compute the projection matrix
projs = activate_proj(projs)
proj, nproj, U = make_projector(projs, raw.ch_names, bads=[])
assert_true(nproj == 2)
assert_true(U.shape[1] == 2)
# test that you can save them
raw.info['projs'] += projs
raw.save(op.join(tempdir, 'foo_rawproj_continuous_raw.fif'))
# test resampled-data projector, upsampling instead of downsampling
# here to save an extra filtering (raw would have to be LP'ed to be equiv)
raw_resamp = cp.deepcopy(raw)
raw_resamp.resample(raw.info['sfreq'] * 2, n_jobs=2)
with warnings.catch_warnings(True) as w:
projs = compute_proj_raw(raw_resamp, duration=None, stop=raw_time,
n_grad=1, n_mag=1, n_eeg=0)
projs = activate_proj(projs)
proj_new, _, _ = make_projector(projs, raw.ch_names, bads=[])
assert_array_almost_equal(proj_new, proj, 4)
# test with bads
raw.load_bad_channels(bads_fname) # adds 2 bad mag channels
with warnings.catch_warnings(True) as w:
projs = compute_proj_raw(raw, n_grad=0, n_mag=0, n_eeg=1)
# test that bad channels can be excluded
proj, nproj, U = make_projector(projs, raw.ch_names,
bads=raw.ch_names)
assert_array_almost_equal(proj, np.eye(len(raw.ch_names)))
def test_load_bad_channels():
"""Test reading/writing of bad channels
"""
# Load correctly marked file (manually done in mne_process_raw)
raw_marked = Raw(fif_bad_marked_fname)
correct_bads = raw_marked.info['bads']
raw = Raw(fif_fname)
# Make sure it starts clean
assert_array_equal(raw.info['bads'], [])
# Test normal case
raw.load_bad_channels(bad_file_works)
# Write it out, read it in, and check
raw.save(op.join(tempdir, 'foo_raw.fif'))
raw_new = Raw(op.join(tempdir, 'foo_raw.fif'))
assert_equal(correct_bads, raw_new.info['bads'])
# Reset it
raw.info['bads'] = []
# Test bad case
assert_raises(ValueError, raw.load_bad_channels, bad_file_wrong)
# Test forcing the bad case
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
raw.load_bad_channels(bad_file_wrong, force=True)
n_found = sum(['1 bad channel' in str(ww.message) for ww in w])
assert_equal(n_found, 1) # there could be other irrelevant errors
# write it out, read it in, and check
raw.save(op.join(tempdir, 'foo_raw.fif'), overwrite=True)
raw_new = Raw(op.join(tempdir, 'foo_raw.fif'))
assert_equal(correct_bads, raw_new.info['bads'])
# Check that bad channels are cleared
raw.load_bad_channels(None)
raw.save(op.join(tempdir, 'foo_raw.fif'), overwrite=True)
raw_new = Raw(op.join(tempdir, 'foo_raw.fif'))
assert_equal([], raw_new.info['bads'])
def test_load_bad_channels():
"""Test reading/writing of bad channels
"""
# Load correctly marked file (manually done in mne_process_raw)
raw_marked = Raw(fif_bad_marked_fname)
correct_bads = raw_marked.info['bads']
raw = Raw(fif_fname)
# Make sure it starts clean
assert_array_equal(raw.info['bads'], [])
# Test normal case
raw.load_bad_channels(bad_file_works)
# Write it out, read it in, and check
raw.save(op.join(tempdir, 'foo_raw.fif'))
raw_new = Raw(op.join(tempdir, 'foo_raw.fif'))
assert_equal(correct_bads, raw_new.info['bads'])
# Reset it
raw.info['bads'] = []
# Test bad case
assert_raises(ValueError, raw.load_bad_channels, bad_file_wrong)
# Test forcing the bad case
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
raw.load_bad_channels(bad_file_wrong, force=True)
n_found = sum(['1 bad channel' in str(ww.message) for ww in w])
assert_equal(n_found, 1) # there could be other irrelevant errors
# write it out, read it in, and check
raw.save(op.join(tempdir, 'foo_raw.fif'), overwrite=True)
raw_new = Raw(op.join(tempdir, 'foo_raw.fif'))
assert_equal(correct_bads, raw_new.info['bads'])
# Check that bad channels are cleared
raw.load_bad_channels(None)
raw.save(op.join(tempdir, 'foo_raw.fif'), overwrite=True)
raw_new = Raw(op.join(tempdir, 'foo_raw.fif'))
assert_equal([], raw_new.info['bads'])
def test_load_bad_channels():
"""Test reading/writing of bad channels
"""
# Load correctly marked file (manually done in mne_process_raw)
raw_marked = Raw(fif_bad_marked_fname)
correct_bads = raw_marked.info['bads']
raw = Raw(fif_fname)
# Make sure it starts clean
assert_array_equal(raw.info['bads'], [])
# Test normal case
raw.load_bad_channels(bad_file_works)
# Write it out, read it in, and check
raw.save(op.join(tempdir, 'foo_raw.fif'))
raw_new = Raw(op.join(tempdir, 'foo_raw.fif'))
assert_equal(correct_bads, raw_new.info['bads'])
# Reset it
raw.info['bads'] = []
# Test bad case
assert_raises(ValueError, raw.load_bad_channels, bad_file_wrong)
# Test forcing the bad case
with warnings.catch_warnings(record=True) as w:
raw.load_bad_channels(bad_file_wrong, force=True)
assert_equal(len(w), 1)
# write it out, read it in, and check
raw.save(op.join(tempdir, 'foo_raw.fif'))
raw_new = Raw(op.join(tempdir, 'foo_raw.fif'))
assert_equal(correct_bads, raw_new.info['bads'])
# Check that bad channels are cleared
raw.load_bad_channels(None)
raw.save(op.join(tempdir, 'foo_raw.fif'))
raw_new = Raw(op.join(tempdir, 'foo_raw.fif'))
assert_equal([], raw_new.info['bads'])
def test_load_bad_channels():
"""Test reading/writing of bad channels
"""
# Load correctly marked file (manually done in mne_process_raw)
raw_marked = Raw(fif_bad_marked_fname)
correct_bads = raw_marked.info['bads']
raw = Raw(fif_fname)
# Make sure it starts clean
assert_array_equal(raw.info['bads'], [])
# Test normal case
raw.load_bad_channels(bad_file_works)
# Write it out, read it in, and check
raw.save('foo_raw.fif')
raw_new = Raw('foo_raw.fif')
assert_equal(correct_bads, raw_new.info['bads'])
# Reset it
raw.info['bads'] = []
# Test bad case
assert_raises(ValueError, raw.load_bad_channels, bad_file_wrong)
# Test forcing the bad case
with warnings.catch_warnings(record=True) as w:
raw.load_bad_channels(bad_file_wrong, force=True)
assert_equal(len(w), 1)
# write it out, read it in, and check
raw.save('foo_raw.fif')
raw_new = Raw('foo_raw.fif')
assert_equal(correct_bads, raw_new.info['bads'])
# Check that bad channels are cleared
raw.load_bad_channels(None)
raw.save('foo_raw.fif')
raw_new = Raw('foo_raw.fif')
assert_equal([], raw_new.info['bads'])
