Python mne.concatenate_raws函数代码示例

def test_edf_data():
    """Test reading raw edf files"""
    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)

    # Make sure concatenation works
    raw_concat = concatenate_raws([raw_py.copy(), raw_py])
    assert_equal(raw_concat.n_times, 2 * raw_py.n_times)

    # 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)

def test_data():
    """Test reading raw nicolet files."""
    tempdir = _TempDir()
    raw = read_raw_nicolet(fname, preload=False)
    raw_preload = read_raw_nicolet(fname, preload=True)
    picks = [2, 3, 12, 13]
    assert_array_equal(raw[picks, 20:30][0], raw_preload[picks, 20:30][0])

    # Make sure concatenation works
    raw2 = concatenate_raws([raw_preload.copy(), raw_preload])

    # Test saving and reading
    out_fname = op.join(tempdir, 'test_nicolet_raw.fif')
    raw2.save(out_fname, tmax=raw.times[-1])
    raw2 = Raw(out_fname)

    full_data = raw_preload._data
    data1, times1 = raw[:10:3, 10:12]
    data2, times2 = raw2[:10:3, 10:12]
    data3, times3 = raw2[[0, 3, 6, 9], 10:12]
    assert_array_almost_equal(data1, full_data[:10:3, 10:12], 9)
    assert_array_almost_equal(data1, data2, 9)
    assert_array_almost_equal(data1, data3, 9)
    assert_array_almost_equal(times1, times2)
    assert_array_almost_equal(times1, times3)

def test_data():
    """Test reading raw kit files
    """
    raw_py = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path,
                          stim=list(range(167, 159, -1)), slope='+',
                          stimthresh=1, preload=True)
    print(repr(raw_py))

    # Binary file only stores the sensor channels
    py_picks = pick_types(raw_py.info, exclude='bads')
    raw_bin = op.join(data_dir, 'test_bin_raw.fif')
    raw_bin = Raw(raw_bin, preload=True)
    bin_picks = pick_types(raw_bin.info, stim=True, exclude='bads')
    data_bin, _ = raw_bin[bin_picks]
    data_py, _ = raw_py[py_picks]

    # this .mat was generated using the Yokogawa MEG Reader
    data_Ykgw = op.join(data_dir, 'test_Ykgw.mat')
    data_Ykgw = scipy.io.loadmat(data_Ykgw)['data']
    data_Ykgw = data_Ykgw[py_picks]

    assert_array_almost_equal(data_py, data_Ykgw)

    py_picks = pick_types(raw_py.info, stim=True, ref_meg=False,
                          exclude='bads')
    data_py, _ = raw_py[py_picks]
    assert_array_almost_equal(data_py, data_bin)

    # Make sure concatenation works
    raw_concat = concatenate_raws([raw_py.copy(), raw_py])
    assert_equal(raw_concat.n_times, 2 * raw_py.n_times)

def test_bdf_data():
    """Test reading raw bdf files
    """
    raw_py = read_raw_edf(bdf_path, montage=montage_path, eog=eog,
                          misc=misc, preload=True)
    picks = pick_types(raw_py.info, meg=False, eeg=True, exclude='bads')
    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(bdf_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)

    # Manually checking that float coordinates are imported
    assert_true((raw_py.info['chs'][0]['eeg_loc']).any())
    assert_true((raw_py.info['chs'][25]['eeg_loc']).any())
    assert_true((raw_py.info['chs'][63]['eeg_loc']).any())

    # Make sure concatenation works
    raw_concat = concatenate_raws([raw_py.copy(), raw_py])
    assert_equal(raw_concat.n_times, 2 * raw_py.n_times)

def test_io_egi():
    """Test importing EGI simple binary files"""
    # test default
    tempdir = _TempDir()
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always', category=RuntimeWarning)
        raw = read_raw_egi(egi_fname, include=None)
        assert_true('RawEGI' in repr(raw))
        raw.load_data()  # currently does nothing
        assert_equal(len(w), 1)
        assert_true(w[0].category == RuntimeWarning)
        msg = 'Did not find any event code with more than one event.'
        assert_true(msg in '%s' % w[0].message)

    include = ['TRSP', 'XXX1']
    raw = read_raw_egi(egi_fname, include=include)
    repr(raw)
    repr(raw.info)

    assert_equal('eeg' in raw, True)
    out_fname = op.join(tempdir, 'test_egi_raw.fif')
    raw.save(out_fname)

    raw2 = Raw(out_fname, preload=True)
    data1, times1 = raw[:10, :]
    data2, times2 = raw2[:10, :]
    assert_array_almost_equal(data1, data2, 9)
    assert_array_almost_equal(times1, times2)

    eeg_chan = [c for c in raw.ch_names if 'EEG' in c]
    assert_equal(len(eeg_chan), 256)
    picks = pick_types(raw.info, eeg=True)
    assert_equal(len(picks), 256)
    assert_equal('STI 014' in raw.ch_names, True)

    events = find_events(raw, stim_channel='STI 014')
    assert_equal(len(events), 2)  # ground truth
    assert_equal(np.unique(events[:, 1])[0], 0)
    assert_true(np.unique(events[:, 0])[0] != 0)
    assert_true(np.unique(events[:, 2])[0] != 0)
    triggers = np.array([[0, 1, 1, 0], [0, 0, 1, 0]])

    # test trigger functionality
    assert_raises(RuntimeError, _combine_triggers, triggers, None)
    triggers = np.array([[0, 1, 0, 0], [0, 0, 1, 0]])
    events_ids = [12, 24]
    new_trigger = _combine_triggers(triggers, events_ids)
    assert_array_equal(np.unique(new_trigger), np.unique([0, 12, 24]))

    assert_raises(ValueError, read_raw_egi, egi_fname,
                  include=['Foo'])
    assert_raises(ValueError, read_raw_egi, egi_fname,
                  exclude=['Bar'])
    for ii, k in enumerate(include, 1):
        assert_true(k in raw.event_id)
        assert_true(raw.event_id[k] == ii)

    # Make sure concatenation works
    raw_concat = concatenate_raws([raw.copy(), raw])
    assert_equal(raw_concat.n_times, 2 * raw.n_times)

def test_crop_more():
    """Test more cropping."""
    raw = mne.io.read_raw_fif(fif_fname).crop(0, 11).load_data()
    raw._data[:] = np.random.RandomState(0).randn(*raw._data.shape)
    onset = np.array([0.47058824, 2.49773765, 6.67873287, 9.15837097])
    duration = np.array([0.89592767, 1.13574672, 1.09954739, 0.48868752])
    annotations = mne.Annotations(onset, duration, 'BAD')
    raw.set_annotations(annotations)
    assert len(raw.annotations) == 4
    delta = 1. / raw.info['sfreq']
    offset = raw.first_samp * delta
    raw_concat = mne.concatenate_raws(
        [raw.copy().crop(0, 4 - delta),
         raw.copy().crop(4, 8 - delta),
         raw.copy().crop(8, None)])
    assert_allclose(raw_concat.times, raw.times)
    assert_allclose(raw_concat[:][0], raw[:][0])
    assert raw_concat.first_samp == raw.first_samp
    boundary_idx = np.where(
        raw_concat.annotations.description == 'BAD boundary')[0]
    assert len(boundary_idx) == 2
    raw_concat.annotations.delete(boundary_idx)
    boundary_idx = np.where(
        raw_concat.annotations.description == 'EDGE boundary')[0]
    assert len(boundary_idx) == 2
    raw_concat.annotations.delete(boundary_idx)
    assert len(raw_concat.annotations) == 4
    assert_array_equal(raw_concat.annotations.description,
                       raw.annotations.description)
    assert_allclose(raw.annotations.duration, duration)
    assert_allclose(raw_concat.annotations.duration, duration)
    assert_allclose(raw.annotations.onset, onset + offset)
    assert_allclose(raw_concat.annotations.onset, onset + offset,
                    atol=1. / raw.info['sfreq'])

def test_events_long():
    """Test events."""
    data_path = testing.data_path()
    raw_fname = data_path + '/MEG/sample/sample_audvis_trunc_raw.fif'
    raw = read_raw_fif(raw_fname, preload=True)
    raw_tmin, raw_tmax = 0, 90

    tmin, tmax = -0.2, 0.5
    event_id = dict(aud_l=1, vis_l=3)

    # select gradiometers
    picks = pick_types(raw.info, meg='grad', eeg=False, eog=True,
                       stim=True, exclude=raw.info['bads'])

    # load data with usual Epochs for later verification
    raw = concatenate_raws([raw, raw.copy(), raw.copy(), raw.copy(),
                            raw.copy(), raw.copy()])
    assert 110 < raw.times[-1] < 130
    raw_cropped = raw.copy().crop(raw_tmin, raw_tmax)
    events_offline = find_events(raw_cropped)
    epochs_offline = Epochs(raw_cropped, events_offline, event_id=event_id,
                            tmin=tmin, tmax=tmax, picks=picks, decim=1,
                            reject=dict(grad=4000e-13, eog=150e-6),
                            baseline=None)
    epochs_offline.drop_bad()

    # create the mock-client object
    rt_client = MockRtClient(raw)
    rt_epochs = RtEpochs(rt_client, event_id, tmin, tmax, picks=picks, decim=1,
                         reject=dict(grad=4000e-13, eog=150e-6), baseline=None,
                         isi_max=1.)

    rt_epochs.start()
    rt_client.send_data(rt_epochs, picks, tmin=raw_tmin, tmax=raw_tmax,
                        buffer_size=1000)

    expected_events = epochs_offline.events.copy()
    expected_events[:, 0] = expected_events[:, 0] - raw_cropped.first_samp
    assert np.all(expected_events[:, 0] <=
                  (raw_tmax - tmax) * raw.info['sfreq'])
    assert_array_equal(rt_epochs.events, expected_events)
    assert len(rt_epochs) == len(epochs_offline)

    data_picks = pick_types(epochs_offline.info, meg='grad', eeg=False,
                            eog=True,
                            stim=False, exclude=raw.info['bads'])

    for ev_num, ev in enumerate(rt_epochs.iter_evoked()):
        if ev_num == 0:
            X_rt = ev.data[None, data_picks, :]
            y_rt = int(ev.comment)  # comment attribute contains the event_id
        else:
            X_rt = np.concatenate((X_rt, ev.data[None, data_picks, :]), axis=0)
            y_rt = np.append(y_rt, int(ev.comment))

    X_offline = epochs_offline.get_data()[:, data_picks, :]
    y_offline = epochs_offline.events[:, 2]
    assert_array_equal(X_rt, X_offline)
    assert_array_equal(y_rt, y_offline)

def test_read_vhdr_annotations_and_events():
    """Test load brainvision annotations and parse them to events."""
    sfreq = 1000.0
    expected_orig_time = 1384359243.794231
    expected_onset_latency = np.array(
        [0, 486., 496., 1769., 1779., 3252., 3262., 4935., 4945., 5999., 6619.,
         6629., 7629., 7699.]
    )
    expected_annot_description = [
        'New Segment/', 'Stimulus/S253', 'Stimulus/S255', 'Stimulus/S254',
        'Stimulus/S255', 'Stimulus/S254', 'Stimulus/S255', 'Stimulus/S253',
        'Stimulus/S255', 'Response/R255', 'Stimulus/S254', 'Stimulus/S255',
        'SyncStatus/Sync On', 'Optic/O  1'
    ]
    expected_events = np.stack([
        expected_onset_latency,
        np.zeros_like(expected_onset_latency),
        [99999, 253, 255, 254, 255, 254, 255, 253, 255, 1255, 254, 255, 99998,
         2001],
    ]).astype('int64').T
    expected_event_id = {'New Segment/': 99999, 'Stimulus/S253': 253,
                         'Stimulus/S255': 255, 'Stimulus/S254': 254,
                         'Response/R255': 1255, 'SyncStatus/Sync On': 99998,
                         'Optic/O  1': 2001}

    raw = read_raw_brainvision(vhdr_path, eog=eog)

    # validate annotations
    assert raw.annotations.orig_time == expected_orig_time
    assert_allclose(raw.annotations.onset, expected_onset_latency / sfreq)
    assert_array_equal(raw.annotations.description, expected_annot_description)

    # validate event extraction
    events, event_id = events_from_annotations(raw)
    assert_array_equal(events, expected_events)
    assert event_id == expected_event_id

    # validate that None gives us a sorted list
    expected_none_event_id = {desc: idx + 1 for idx, desc in enumerate(sorted(
        event_id.keys()))}
    events, event_id = events_from_annotations(raw, event_id=None)
    assert event_id == expected_none_event_id

    # Add some custom ones, plus a 2-digit one
    s_10 = 'Stimulus/S 10'
    raw.annotations.append([1, 2, 3], 10, ['ZZZ', s_10, 'YYY'])
    expected_event_id.update(YYY=10001, ZZZ=10002)  # others starting at 10001
    expected_event_id[s_10] = 10
    _, event_id = events_from_annotations(raw)
    assert event_id == expected_event_id

    # Concatenating two shouldn't change the resulting event_id
    # (BAD and EDGE should be ignored)
    with pytest.warns(RuntimeWarning, match='expanding outside'):
        raw_concat = concatenate_raws([raw.copy(), raw.copy()])
    _, event_id = events_from_annotations(raw_concat)
    assert event_id == expected_event_id

def test_mf_skips():
    """Test processing of data with skips."""
    raw = read_raw_fif(skip_fname, preload=True)
    raw.fix_mag_coil_types()
    raw.pick_channels(raw.ch_names[:50])  # fast and inaccurate
    kwargs = dict(st_only=True, coord_frame='meg', int_order=4, ext_order=3)
    # smoke test that this runs
    maxwell_filter(raw, st_duration=17., skip_by_annotation=(), **kwargs)
    # and this one, too, which will process some all-zero data
    maxwell_filter(raw, st_duration=2., skip_by_annotation=(), **kwargs)
    with pytest.raises(ValueError, match='duration'):
        # skips decrease acceptable duration
        maxwell_filter(raw, st_duration=17., **kwargs)
    onsets, ends = _annotations_starts_stops(
        raw, ('edge', 'bad_acq_skip'), 'skip_by_annotation', invert=True)
    assert (ends - onsets).min() / raw.info['sfreq'] == 2.
    assert (ends - onsets).max() / raw.info['sfreq'] == 3.
    for st_duration in (2., 3.):
        raw_sss = maxwell_filter(raw, st_duration=st_duration, **kwargs)
        for start, stop in zip(onsets, ends):
            orig_data = raw[:, start:stop][0]
            new_data = raw_sss[:, start:stop][0]
            if (stop - start) / raw.info['sfreq'] >= st_duration:
                # Should be modified
                assert not np.allclose(new_data, orig_data, atol=1e-20)
            else:
                # Should not be modified
                assert_allclose(new_data, orig_data, atol=1e-20)
    # Processing an individual file and concat should be equivalent to
    # concat then process
    raw.crop(0, 1)
    raw_sss = maxwell_filter(raw, st_duration=1., **kwargs)
    raw_sss_concat = concatenate_raws([raw_sss, raw_sss.copy()])
    raw_concat = concatenate_raws([raw.copy(), raw.copy()])
    raw_concat_sss = maxwell_filter(raw_concat, st_duration=1., **kwargs)
    raw_concat_sss_bad = maxwell_filter(raw_concat, st_duration=1.,
                                        skip_by_annotation=(), **kwargs)
    data_c = raw_concat[:][0]
    data_sc = raw_sss_concat[:][0]
    data_cs = raw_concat_sss[:][0]
    data_csb = raw_concat_sss_bad[:][0]
    assert not np.allclose(data_cs, data_c, atol=1e-20)
    assert not np.allclose(data_cs, data_csb, atol=1e-20)
    assert_allclose(data_sc, data_cs, atol=1e-20)

def prepare(datafiles, read_events = True):
    """Given list of files, return MNE RawArray with the data in them. If 
    read_events is True (as by default), also return a numpy array with events."""
    rawdata = mne.concatenate_raws([file_to_raw(f) for f in datafiles]) 
    if read_events:
        eventfiles = [file.replace("_data", "_events") for file in datafiles]
        events = np.concatenate([pd.read_csv(f).values[:,1:] for f in eventfiles])
        return rawdata, events
    else:
        return rawdata, None        

def test_raw():
    """ Test bti conversion to Raw object """
    for pdf, config, hs, exported in zip(pdf_fnames, config_fnames, hs_fnames,
                                         exported_fnames):
        # rx = 2 if 'linux' in pdf else 0
        assert_raises(ValueError, read_raw_bti, pdf, 'eggs')
        assert_raises(ValueError, read_raw_bti, pdf, config, 'spam')
        if op.exists(tmp_raw_fname):
            os.remove(tmp_raw_fname)
        ex = Raw(exported, preload=True)
        ra = read_raw_bti(pdf, config, hs)
        assert_true('RawBTi' in repr(ra))
        assert_equal(ex.ch_names[:NCH], ra.ch_names[:NCH])
        assert_array_almost_equal(ex.info['dev_head_t']['trans'],
                                  ra.info['dev_head_t']['trans'], 7)
        dig1, dig2 = [np.array([d['r'] for d in r_.info['dig']])
                      for r_ in (ra, ex)]
        assert_array_almost_equal(dig1, dig2, 18)
        coil1, coil2 = [np.concatenate([d['loc'].flatten()
                        for d in r_.info['chs'][:NCH]])
                        for r_ in (ra, ex)]
        assert_array_almost_equal(coil1, coil2, 7)

        loc1, loc2 = [np.concatenate([d['loc'].flatten()
                      for d in r_.info['chs'][:NCH]])
                      for r_ in (ra, ex)]
        assert_allclose(loc1, loc2)

        assert_array_equal(ra._data[:NCH], ex._data[:NCH])
        assert_array_equal(ra._cals[:NCH], ex._cals[:NCH])

        # check our transforms
        for key in ('dev_head_t', 'dev_ctf_t', 'ctf_head_t'):
            if ex.info[key] is None:
                pass
            else:
                assert_true(ra.info[key] is not None)
                for ent in ('to', 'from', 'trans'):
                    assert_allclose(ex.info[key][ent],
                                    ra.info[key][ent])

        # Make sure concatenation works
        raw_concat = concatenate_raws([ra.copy(), ra])
        assert_equal(raw_concat.n_times, 2 * ra.n_times)

        ra.save(tmp_raw_fname)
        re = Raw(tmp_raw_fname)
        print(re)
        for key in ('dev_head_t', 'dev_ctf_t', 'ctf_head_t'):
            assert_true(isinstance(re.info[key], dict))
            this_t = re.info[key]['trans']
            assert_equal(this_t.shape, (4, 4))
            # cehck that matrix by is not identity
            assert_true(not np.allclose(this_t, np.eye(4)))
        os.remove(tmp_raw_fname)

def load_raw_data(subject, test=False):
    """Load Raw data from files.

    For a given subject, csv files are loaded, converted to MNE raw instance
    and concatenated.
    If test is True, training data are composed of series 1 to 8 and test data
    of series 9 and test. Otherwise, training data are series 1 to 6 and test
    data series 7 and 8.
    """
    fnames_train = glob('../data/train/subj%d_series*_data.csv' % (subject))
    fnames_train.sort()
    if test:
        fnames_test = glob('../data/test/subj%d_series*_data.csv' % (subject))
        fnames_test.sort()
    else:
        fnames_test = fnames_train[-2:]
        fnames_train = fnames_train[:-2]

    # read and concatenate all the files
    raw_train = [creat_mne_raw_object(fname) for fname in fnames_train]
    raw_train = concatenate_raws(raw_train)
    # pick eeg signal
    picks = pick_types(raw_train.info, eeg=True)

    # get training data
    data_train = raw_train._data[picks].T
    labels_train = raw_train._data[32:].T

    raw_test = [creat_mne_raw_object(fname, read_events=not test) for fname in
                fnames_test]
    raw_test = concatenate_raws(raw_test)
    data_test = raw_test._data[picks].T

    # extract labels if validating on series 7&8
    labels_test = None
    if not test:
        labels_test = raw_test._data[32:].T

    return data_train, labels_train, data_test, labels_test

def test_clean_eog_ecg():
    """Test mne clean_eog_ecg"""
    check_usage(mne_clean_eog_ecg)
    tempdir = _TempDir()
    raw = concatenate_raws([Raw(f) for f in [raw_fname, raw_fname, raw_fname]])
    raw.info['bads'] = ['MEG 2443']
    use_fname = op.join(tempdir, op.basename(raw_fname))
    raw.save(use_fname)
    with ArgvSetter(('-i', use_fname, '--quiet')):
        mne_clean_eog_ecg.run()
    fnames = glob.glob(op.join(tempdir, '*proj.fif'))
    assert_true(len(fnames) == 2)  # two projs
    fnames = glob.glob(op.join(tempdir, '*-eve.fif'))
    assert_true(len(fnames) == 3)  # raw plus two projs

def test_clean_eog_ecg(tmpdir):
    """Test mne clean_eog_ecg."""
    check_usage(mne_clean_eog_ecg)
    tempdir = str(tmpdir)
    raw = concatenate_raws([read_raw_fif(f)
                            for f in [raw_fname, raw_fname, raw_fname]])
    raw.info['bads'] = ['MEG 2443']
    use_fname = op.join(tempdir, op.basename(raw_fname))
    raw.save(use_fname)
    with ArgvSetter(('-i', use_fname, '--quiet')):
        mne_clean_eog_ecg.run()
    for key, count in (('proj', 2), ('-eve', 3)):
        fnames = glob.glob(op.join(tempdir, '*%s.fif' % key))
        assert len(fnames) == count

def test_clean_eog_ecg():
    """Test mne clean_eog_ecg."""
    check_usage(mne_clean_eog_ecg)
    tempdir = _TempDir()
    raw = concatenate_raws([read_raw_fif(f) for f in [raw_fname, raw_fname, raw_fname]])
    raw.info["bads"] = ["MEG 2443"]
    use_fname = op.join(tempdir, op.basename(raw_fname))
    raw.save(use_fname)
    with ArgvSetter(("-i", use_fname, "--quiet")):
        mne_clean_eog_ecg.run()
    fnames = glob.glob(op.join(tempdir, "*proj.fif"))
    assert_true(len(fnames) == 2)  # two projs
    fnames = glob.glob(op.join(tempdir, "*-eve.fif"))
    assert_true(len(fnames) == 3)  # raw plus two projs