Python event.find_events函数代码示例

def test_bdf_stim_channel():
    """Test BDF stim channel."""
    # test if last channel is detected as STIM by default
    raw_py = _test_raw_reader(read_raw_edf, input_fname=bdf_path,
                              stim_channel='auto')
    assert channel_type(raw_py.info, raw_py.info["nchan"] - 1) == 'stim'

    # test BDF file with wrong scaling info in header - this should be ignored
    # for BDF stim channels
    events = [[242, 0, 4],
              [310, 0, 2],
              [952, 0, 1],
              [1606, 0, 1],
              [2249, 0, 1],
              [2900, 0, 1],
              [3537, 0, 1],
              [4162, 0, 1],
              [4790, 0, 1]]
    with pytest.deprecated_call(match='stim_channel'):
        raw = read_raw_edf(bdf_stim_channel_path, preload=True)
    bdf_events = find_events(raw)
    assert_array_equal(events, bdf_events)
    raw = read_raw_edf(bdf_stim_channel_path, preload=False,
                       stim_channel='auto')
    bdf_events = find_events(raw)
    assert_array_equal(events, bdf_events)

def test_edf_data():
    """Test edf files"""
    _test_raw_reader(read_raw_edf, input_fname=edf_path, stim_channel=None)
    raw_py = read_raw_edf(edf_path, preload=True)
    # Test saving and loading when annotations were parsed.
    tempdir = _TempDir()
    raw_file = op.join(tempdir, 'test-raw.fif')
    raw_py.save(raw_file, overwrite=True, buffer_size_sec=1)
    Raw(raw_file, preload=True)

    edf_events = find_events(raw_py, output='step', shortest_event=0,
                             stim_channel='STI 014')

    # onset, duration, id
    events = [[0.1344, 0.2560, 2],
              [0.3904, 1.0000, 2],
              [2.0000, 0.0000, 3],
              [2.5000, 2.5000, 2]]
    events = np.array(events)
    events[:, :2] *= 512  # convert time to samples
    events = np.array(events, dtype=int)
    events[:, 1] -= 1
    events[events[:, 1] <= 0, 1] = 1
    events[:, 1] += events[:, 0]

    onsets = events[:, [0, 2]]
    offsets = events[:, [1, 2]]

    events = np.zeros((2 * events.shape[0], 3), dtype=int)
    events[0::2, [0, 2]] = onsets
    events[1::2, [0, 1]] = offsets

    assert_array_equal(edf_events, events)

def test_edf_annotations():
    """Test if events are detected correctly in a typical MNE workflow."""

    # test an actual file
    raw = read_raw_edf(edf_path, preload=True)
    edf_events = find_events(raw, output='step', shortest_event=0,
                             stim_channel='STI 014')

    # onset, duration, id
    events = [[0.1344, 0.2560, 2],
              [0.3904, 1.0000, 2],
              [2.0000, 0.0000, 3],
              [2.5000, 2.5000, 2]]
    events = np.array(events)
    events[:, :2] *= 512  # convert time to samples
    events = np.array(events, dtype=int)
    events[:, 1] -= 1
    events[events[:, 1] <= 0, 1] = 1
    events[:, 1] += events[:, 0]

    onsets = events[:, [0, 2]]
    offsets = events[:, [1, 2]]

    events = np.zeros((2 * events.shape[0], 3), dtype=int)
    events[0::2, [0, 2]] = onsets
    events[1::2, [0, 1]] = offsets

    assert_array_equal(edf_events, events)

def test_edf_data():
    """Test edf files."""
    raw = _test_raw_reader(read_raw_edf, input_fname=edf_path,
                           stim_channel=None, exclude=['Ergo-Left', 'H10'])
    raw_py = read_raw_edf(edf_path, preload=True)
    assert_equal(len(raw.ch_names) + 2, len(raw_py.ch_names))
    # Test saving and loading when annotations were parsed.
    edf_events = find_events(raw_py, output='step', shortest_event=0,
                             stim_channel='STI 014')

    # onset, duration, id
    events = [[0.1344, 0.2560, 2],
              [0.3904, 1.0000, 2],
              [2.0000, 0.0000, 3],
              [2.5000, 2.5000, 2]]
    events = np.array(events)
    events[:, :2] *= 512  # convert time to samples
    events = np.array(events, dtype=int)
    events[:, 1] -= 1
    events[events[:, 1] <= 0, 1] = 1
    events[:, 1] += events[:, 0]

    onsets = events[:, [0, 2]]
    offsets = events[:, [1, 2]]

    events = np.zeros((2 * events.shape[0], 3), dtype=int)
    events[0::2, [0, 2]] = onsets
    events[1::2, [0, 1]] = offsets

    assert_array_equal(edf_events, events)

def test_stim_channel():
    """Test reading raw edf files with stim channel."""
    raw_py = read_raw_edf(edf_path, misc=range(-4, 0), stim_channel=139,
                          preload=True)

    picks = pick_types(raw_py.info, meg=False, eeg=True,
                       exclude=['EDF Annotations'])
    data_py, _ = raw_py[picks]

    print(raw_py)  # to test repr
    print(raw_py.info)  # to test Info repr

    # this .mat was generated using the EEG Lab Biosemi Reader
    raw_eeglab = io.loadmat(edf_eeglab_path)
    raw_eeglab = raw_eeglab['data'] * 1e-6  # data are stored in microvolts
    data_eeglab = raw_eeglab[picks]

    assert_array_almost_equal(data_py, data_eeglab, 10)
    events = find_edf_events(raw_py)
    assert_true(len(events) - 1 == len(find_events(raw_py)))  # start not found

    # Test uneven sampling
    raw_py = read_raw_edf(edf_uneven_path, stim_channel=None)
    data_py, _ = raw_py[0]
    # this .mat was generated using the EEG Lab Biosemi Reader
    raw_eeglab = io.loadmat(edf_uneven_eeglab_path)
    raw_eeglab = raw_eeglab['data']
    data_eeglab = raw_eeglab[0]

    # match upsampling
    upsample = len(data_eeglab) / len(raw_py)
    data_py = np.repeat(data_py, repeats=upsample)
    assert_array_equal(data_py, data_eeglab)

    assert_raises(RuntimeError, read_raw_edf, edf_path, preload=False,
                  stim_channel=-1)

    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        raw = read_raw_edf(edf_stim_resamp_path, verbose=True, stim_channel=-1)
    assert_equal(len(w), 2)
    assert_true(any('Events may jitter' in str(ww.message) for ww in w))
    assert_true(any('truncated' in str(ww.message) for ww in w))
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        raw[:]
    assert_equal(len(w), 0)

    events = raw_py.find_edf_events()
    assert_true(len(events) == 0)

def test_edf_data():
    """Test edf files."""
    raw = _test_raw_reader(read_raw_edf, input_fname=edf_path,
                           stim_channel=None, exclude=['Ergo-Left', 'H10'],
                           verbose='error')
    raw_py = read_raw_edf(edf_path, stim_channel='auto', preload=True)

    assert_equal(len(raw.ch_names) + 2, len(raw_py.ch_names))
    # Test saving and loading when annotations were parsed.
    edf_events = find_events(raw_py, output='step', shortest_event=0,
                             stim_channel='STI 014')

    # onset, duration, id
    events = [[0.1344, 0.2560, 2],
              [0.3904, 1.0000, 2],
              [2.0000, 0.0000, 3],
              [2.5000, 2.5000, 2]]
    events = np.array(events)
    events[:, :2] *= 512  # convert time to samples
    events = np.array(events, dtype=int)
    events[:, 1] -= 1
    events[events[:, 1] <= 0, 1] = 1
    events[:, 1] += events[:, 0]

    onsets = events[:, [0, 2]]
    offsets = events[:, [1, 2]]

    events = np.zeros((2 * events.shape[0], 3), dtype=int)
    events[0::2, [0, 2]] = onsets
    events[1::2, [0, 1]] = offsets

    assert_array_equal(edf_events, events)

    # Test with number of records not in header (-1).
    tempdir = _TempDir()
    broken_fname = op.join(tempdir, 'broken.edf')
    with open(edf_path, 'rb') as fid_in:
        fid_in.seek(0, 2)
        n_bytes = fid_in.tell()
        fid_in.seek(0, 0)
        rbytes = fid_in.read(int(n_bytes * 0.4))
    with open(broken_fname, 'wb') as fid_out:
        fid_out.write(rbytes[:236])
        fid_out.write(b'-1      ')
        fid_out.write(rbytes[244:])
    with pytest.warns(RuntimeWarning,
                      match='records .* not match the file size'):
        raw = read_raw_edf(broken_fname, preload=True, stim_channel='auto')
        read_raw_edf(broken_fname, exclude=raw.ch_names[:132], preload=True,
                     stim_channel='auto')

def test_stim_channel():
    """Test reading raw edf files with stim channel."""
    raw_py = read_raw_edf(edf_path, misc=range(-4, 0), stim_channel=139,
                          preload=True)

    picks = pick_types(raw_py.info, meg=False, eeg=True,
                       exclude=['EDF Annotations'])
    data_py, _ = raw_py[picks]

    print(raw_py)  # to test repr
    print(raw_py.info)  # to test Info repr

    # this .mat was generated using the EEG Lab Biosemi Reader
    raw_eeglab = io.loadmat(edf_eeglab_path)
    raw_eeglab = raw_eeglab['data'] * 1e-6  # data are stored in microvolts
    data_eeglab = raw_eeglab[picks]

    assert_array_almost_equal(data_py, data_eeglab, 10)
    events = find_edf_events(raw_py)
    assert (len(events) - 1 == len(find_events(raw_py)))  # start not found

    # Test uneven sampling
    raw_py = read_raw_edf(edf_uneven_path, stim_channel=None)
    data_py, _ = raw_py[0]
    # this .mat was generated using the EEG Lab Biosemi Reader
    raw_eeglab = io.loadmat(edf_uneven_eeglab_path)
    raw_eeglab = raw_eeglab['data']
    data_eeglab = raw_eeglab[0]

    # match upsampling
    upsample = len(data_eeglab) / len(raw_py)
    data_py = np.repeat(data_py, repeats=upsample)
    assert_array_equal(data_py, data_eeglab)

    pytest.raises(RuntimeError, read_raw_edf, edf_path, preload=False,
                  stim_channel=-1)

    with pytest.warns(RuntimeWarning,
                      match='Interpolating stim .* Events may jitter'):
        raw = read_raw_edf(edf_stim_resamp_path, verbose=True, stim_channel=-1)
    with pytest.warns(None) as w:
        raw[:]
    assert len(w) == 0

    events = raw_py.find_edf_events()
    assert (len(events) == 0)

def test_find_events_and_events_from_annot_are_the_same():
    """Test that old behaviour and new produce the same events."""
    EXPECTED_EVENTS = [[68, 0, 2],
                       [199, 0, 2],
                       [1024, 0, 3],
                       [1280, 0, 2]]
    raw = read_raw_edf(edf_path, preload=True, stim_channel='auto')
    raw_shell = _get_empty_raw_with_valid_annot(edf_path)
    assert raw_shell.info['meas_date'] == raw.info['meas_date']
    assert raw_shell.info['sfreq'] == raw.info['sfreq']
    assert raw_shell.first_samp == raw.first_samp

    events_from_find_events = find_events(raw)
    assert_array_equal(events_from_find_events, EXPECTED_EVENTS)

    annot = read_annotations(edf_path)
    raw_shell.set_annotations(annot)
    event_id = _get_edf_default_event_id(annot.description)
    event_id.pop('start')
    events_from_EFA, _ = events_from_annotations(raw_shell, event_id=event_id,
                                                 use_rounding=False)

    assert_array_equal(events_from_EFA, events_from_find_events)

# cue onset.
tmin, tmax = 1., 3.
event_id = dict(hands=2, feet=3)
subject = 1
runs = [6, 10, 14]  # motor imagery: hands vs feet

raw_files = [read_raw_edf(f, preload=True,verbose=False) for f in eegbci.load_data(subject, runs) ]
raw = concatenate_raws(raw_files)

# strip channel names
raw.info['ch_names'] = [chn.strip('.') for chn in raw.info['ch_names']]

# Apply band-pass filter
raw.filter(7., 35., method='iir')

events = find_events(raw, shortest_event=0, stim_channel='STI 014')
picks = pick_types(raw.info, meg=False, eeg=True, stim=False, eog=False,
                   exclude='bads')

# Read epochs (train will be done only between 1 and 2s)
# Testing will be done with a running classifier
epochs = Epochs(raw, events, event_id, tmin, tmax, proj=True, picks=picks,
                baseline=None, preload=True, add_eeg_ref=False,verbose=False)
labels = epochs.events[:, -1] - 2

# get epochs
epochs_data = epochs.get_data()

# compute covariance matrices
covmats = Covariances().fit_transform(epochs_data) 

for s,subject in enumerate(subjects):
    
    print('Processing Subject %s' %(subject))
    raw_files = [read_raw_edf(f, preload=True,verbose=False) for f in eegbci.load_data(subject, runs)]
    raw = concatenate_raws(raw_files)

    picks = pick_types(raw.info, meg=False, eeg=True, stim=False, eog=False,
                       exclude='bads')
    # subsample elecs
    picks = picks[::2]
    
    # Apply band-pass filter
    raw.filter(7., 35., method='iir',picks=picks)
    
    events = find_events(raw, shortest_event=0, stim_channel='STI 014',verbose=False)



    # Read epochs (train will be done only between 1 and 2s)
    # Testing will be done with a running classifier
    epochs = Epochs(raw, events, event_id, tmin, tmax, proj=True, picks=picks,
                    baseline=None, preload=True, add_eeg_ref=False,verbose = False)
                    
    labels = epochs.events[:, -1] - 2
    X = epochs.get_data()
    
    for i,c in enumerate(classifiers):
        
        r = cross_val_score(classifiers[c],X,labels,cv=10,n_jobs=-1)
        results[s,i] = np.mean(r)