Python mne.read_evokeds函数代码示例

def test_render_report():
    """Test rendering -*.fif files for mne report.
    """

    report = Report(info_fname=raw_fname)
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        report.parse_folder(data_path=base_dir)
    assert_true(len(w) == 1)

    # Check correct paths and filenames
    assert_true(raw_fname in report.fnames)
    assert_true(event_name in report.fnames)
    assert_true(report.data_path == base_dir)

    # Check if all files were rendered in the report
    fnames = glob.glob(op.join(base_dir, '*.fif'))
    bad_name = 'test_ctf_comp_raw-eve.fif'
    decrement = any(fname.endswith(bad_name) for fname in fnames)
    fnames = [fname for fname in fnames if
              fname.endswith(('-eve.fif', '-ave.fif', '-cov.fif',
                              '-sol.fif', '-fwd.fif', '-inv.fif',
                              '-src.fif', '-trans.fif', 'raw.fif',
                              'sss.fif', '-epo.fif')) and
              not fname.endswith(bad_name)]
    # last file above gets created by another test, and it shouldn't be there

    for fname in fnames:
        assert_true(''.join(report.html).find(op.basename(fname)) != -1)

    assert_equal(len(report.fnames), len(fnames))
    assert_equal(len(report.html), len(report.fnames))

    evoked1 = read_evokeds(evoked1_fname)
    evoked2 = read_evokeds(evoked2_fname)
    assert_equal(len(report.fnames) + len(evoked1) + len(evoked2) - 2,
                 report.initial_id - decrement)

    # Check saving functionality
    report.data_path = tempdir
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

    # Check add_section functionality
    fig = evoked1[0].plot(show=False)
    report.add_section(figs=fig,  # test non-list input
                       captions=['evoked response'])
    assert_equal(len(report.html), len(fnames) + 1)
    assert_equal(len(report.html), len(report.fnames))
    assert_raises(ValueError, report.add_section, figs=[fig, fig],
                  captions='H')

    # Check saving same report to new filename
    report.save(fname=op.join(tempdir, 'report2.html'), open_browser=False)
    assert_true(op.isfile(op.join(tempdir, 'report2.html')))

    # Check overwriting file
    report.save(fname=op.join(tempdir, 'report.html'), open_browser=False,
                overwrite=True)
    assert_true(op.isfile(op.join(tempdir, 'report.html')))

def test_evoked_arithmetic():
    """Test evoked arithmetic
    """
    ev = read_evokeds(fname, condition=0)
    ev1 = EvokedArray(np.ones_like(ev.data), ev.info, ev.times[0], nave=20)
    ev2 = EvokedArray(-np.ones_like(ev.data), ev.info, ev.times[0], nave=10)

    # combine_evoked([ev1, ev2]) should be the same as ev1 + ev2:
    # data should be added according to their `nave` weights
    # nave = ev1.nave + ev2.nave
    ev = ev1 + ev2
    assert_equal(ev.nave, ev1.nave + ev2.nave)
    assert_allclose(ev.data, 1. / 3. * np.ones_like(ev.data))
    ev = ev1 - ev2
    assert_equal(ev.nave, ev1.nave + ev2.nave)
    assert_equal(ev.comment, ev1.comment + ' - ' + ev2.comment)
    assert_allclose(ev.data, np.ones_like(ev1.data))
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        ev = merge_evoked([ev1, ev2])
    assert_true(len(w) >= 1)
    assert_allclose(ev.data, 1. / 3. * np.ones_like(ev.data))

    # default comment behavior if evoked.comment is None
    old_comment1 = ev1.comment
    old_comment2 = ev2.comment
    ev1.comment = None
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        ev = ev1 - ev2
        assert_equal(ev.comment, 'unknown')
    ev1.comment = old_comment1
    ev2.comment = old_comment2

    # equal weighting
    ev = combine_evoked([ev1, ev2], weights='equal')
    assert_allclose(ev.data, np.zeros_like(ev1.data))

    # combine_evoked([ev1, ev2], weights=[1, 0]) should yield the same as ev1
    ev = combine_evoked([ev1, ev2], weights=[1, 0])
    assert_equal(ev.nave, ev1.nave)
    assert_allclose(ev.data, ev1.data)

    # simple subtraction (like in oddball)
    ev = combine_evoked([ev1, ev2], weights=[1, -1])
    assert_allclose(ev.data, 2 * np.ones_like(ev1.data))

    assert_raises(ValueError, combine_evoked, [ev1, ev2], weights='foo')
    assert_raises(ValueError, combine_evoked, [ev1, ev2], weights=[1])

    # grand average
    evoked1, evoked2 = read_evokeds(fname, condition=[0, 1], proj=True)
    ch_names = evoked1.ch_names[2:]
    evoked1.info['bads'] = ['EEG 008']  # test interpolation
    evoked1.drop_channels(evoked1.ch_names[:1])
    evoked2.drop_channels(evoked2.ch_names[1:2])
    gave = grand_average([evoked1, evoked2])
    assert_equal(gave.data.shape, [len(ch_names), evoked1.data.shape[1]])
    assert_equal(ch_names, gave.ch_names)
    assert_equal(gave.nave, 2)

def test_evoked_proj():
    """Test SSP proj operations
    """
    for proj in [True, False]:
        ave = read_evokeds(fname, condition=0, proj=proj)
        assert_true(all(p['active'] == proj for p in ave.info['projs']))

        # test adding / deleting proj
        if proj:
            assert_raises(ValueError, ave.add_proj, [],
                          {'remove_existing': True})
            assert_raises(ValueError, ave.del_proj, 0)
        else:
            projs = deepcopy(ave.info['projs'])
            n_proj = len(ave.info['projs'])
            ave.del_proj(0)
            assert_true(len(ave.info['projs']) == n_proj - 1)
            ave.add_proj(projs, remove_existing=False)
            assert_true(len(ave.info['projs']) == 2 * n_proj - 1)
            ave.add_proj(projs, remove_existing=True)
            assert_true(len(ave.info['projs']) == n_proj)

    ave = read_evokeds(fname, condition=0, proj=False)
    data = ave.data.copy()
    ave.apply_proj()
    assert_allclose(np.dot(ave._projector, data), ave.data)

def test_evoked_resample():
    """Test for resampling of evoked data
    """
    tempdir = _TempDir()
    # upsample, write it out, read it in
    ave = read_evokeds(fname, 0)
    sfreq_normal = ave.info['sfreq']
    ave.resample(2 * sfreq_normal)
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
    ave_up = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)

    # compare it to the original
    ave_normal = read_evokeds(fname, 0)

    # and compare the original to the downsampled upsampled version
    ave_new = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 0)
    ave_new.resample(sfreq_normal)

    assert_array_almost_equal(ave_normal.data, ave_new.data, 2)
    assert_array_almost_equal(ave_normal.times, ave_new.times)
    assert_equal(ave_normal.nave, ave_new.nave)
    assert_equal(ave_normal._aspect_kind, ave_new._aspect_kind)
    assert_equal(ave_normal.kind, ave_new.kind)
    assert_equal(ave_normal.last, ave_new.last)
    assert_equal(ave_normal.first, ave_new.first)

    # for the above to work, the upsampling just about had to, but
    # we'll add a couple extra checks anyway
    assert_true(len(ave_up.times) == 2 * len(ave_normal.times))
    assert_true(ave_up.data.shape[1] == 2 * ave_normal.data.shape[1])

def test_evoked_io_from_epochs():
    """Test IO of evoked data made from epochs
    """
    # offset our tmin so we don't get exactly a zero value when decimating
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter("always")
        epochs = Epochs(raw, events[:4], event_id, tmin + 0.011, tmax, picks=picks, baseline=(None, 0), decim=5)
    assert_true(len(w) == 1)
    evoked = epochs.average()
    evoked.save(op.join(tempdir, "evoked-ave.fif"))
    evoked2 = read_evokeds(op.join(tempdir, "evoked-ave.fif"))[0]
    assert_allclose(evoked.data, evoked2.data, rtol=1e-4, atol=1e-20)
    assert_allclose(evoked.times, evoked2.times, rtol=1e-4, atol=1 / evoked.info["sfreq"])

    # now let's do one with negative time
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter("always")
        epochs = Epochs(raw, events[:4], event_id, 0.1, tmax, picks=picks, baseline=(0.1, 0.2), decim=5)
    evoked = epochs.average()
    evoked.save(op.join(tempdir, "evoked-ave.fif"))
    evoked2 = read_evokeds(op.join(tempdir, "evoked-ave.fif"))[0]
    assert_allclose(evoked.data, evoked2.data, rtol=1e-4, atol=1e-20)
    assert_allclose(evoked.times, evoked2.times, rtol=1e-4, atol=1e-20)

    # should be equivalent to a cropped original
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter("always")
        epochs = Epochs(raw, events[:4], event_id, -0.2, tmax, picks=picks, baseline=(0.1, 0.2), decim=5)
    evoked = epochs.average()
    evoked.crop(0.099, None)
    assert_allclose(evoked.data, evoked2.data, rtol=1e-4, atol=1e-20)
    assert_allclose(evoked.times, evoked2.times, rtol=1e-4, atol=1e-20)

def test_evoked_standard_error():
    """Test calculation and read/write of standard error
    """
    raw, events, picks = _get_data()
    tempdir = _TempDir()
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0))
    evoked = [epochs.average(), epochs.standard_error()]
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), evoked)
    evoked2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'), [0, 1])
    evoked3 = [read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 'Unknown'),
               read_evokeds(op.join(tempdir, 'evoked-ave.fif'), 'Unknown',
                            kind='standard_error')]
    for evoked_new in [evoked2, evoked3]:
        assert_true(evoked_new[0]._aspect_kind ==
                    FIFF.FIFFV_ASPECT_AVERAGE)
        assert_true(evoked_new[0].kind == 'average')
        assert_true(evoked_new[1]._aspect_kind ==
                    FIFF.FIFFV_ASPECT_STD_ERR)
        assert_true(evoked_new[1].kind == 'standard_error')
        for ave, ave2 in zip(evoked, evoked_new):
            assert_array_almost_equal(ave.data, ave2.data)
            assert_array_almost_equal(ave.times, ave2.times)
            assert_equal(ave.nave, ave2.nave)
            assert_equal(ave._aspect_kind, ave2._aspect_kind)
            assert_equal(ave.kind, ave2.kind)
            assert_equal(ave.last, ave2.last)
            assert_equal(ave.first, ave2.first)

def test_io_evoked():
    """Test IO for evoked data (fif + gz) with integer and str args
    """
    tempdir = _TempDir()
    ave = read_evokeds(fname, 0)

    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), ave)
    ave2 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))[0]

    # This not being assert_array_equal due to windows rounding
    assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-3))
    assert_array_almost_equal(ave.times, ave2.times)
    assert_equal(ave.nave, ave2.nave)
    assert_equal(ave._aspect_kind, ave2._aspect_kind)
    assert_equal(ave.kind, ave2.kind)
    assert_equal(ave.last, ave2.last)
    assert_equal(ave.first, ave2.first)
    assert_true(repr(ave))

    # test compressed i/o
    ave2 = read_evokeds(fname_gz, 0)
    assert_true(np.allclose(ave.data, ave2.data, atol=1e-16, rtol=1e-8))

    # test str access
    condition = 'Left Auditory'
    assert_raises(ValueError, read_evokeds, fname, condition, kind='stderr')
    assert_raises(ValueError, read_evokeds, fname, condition,
                  kind='standard_error')
    ave3 = read_evokeds(fname, condition)
    assert_array_almost_equal(ave.data, ave3.data, 19)

    # test read_evokeds and write_evokeds
    aves1 = read_evokeds(fname)[1::2]
    aves2 = read_evokeds(fname, [1, 3])
    aves3 = read_evokeds(fname, ['Right Auditory', 'Right visual'])
    write_evokeds(op.join(tempdir, 'evoked-ave.fif'), aves1)
    aves4 = read_evokeds(op.join(tempdir, 'evoked-ave.fif'))
    for aves in [aves2, aves3, aves4]:
        for [av1, av2] in zip(aves1, aves):
            assert_array_almost_equal(av1.data, av2.data)
            assert_array_almost_equal(av1.times, av2.times)
            assert_equal(av1.nave, av2.nave)
            assert_equal(av1.kind, av2.kind)
            assert_equal(av1._aspect_kind, av2._aspect_kind)
            assert_equal(av1.last, av2.last)
            assert_equal(av1.first, av2.first)
            assert_equal(av1.comment, av2.comment)

    # test warnings on bad filenames
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        fname2 = op.join(tempdir, 'test-bad-name.fif')
        write_evokeds(fname2, ave)
        read_evokeds(fname2)
    assert_naming(w, 'test_evoked.py', 2)

    # constructor
    assert_raises(TypeError, Evoked, fname)

def test_evoked_detrend():
    """Test for detrending evoked data."""
    ave = read_evokeds(fname, 0)
    ave_normal = read_evokeds(fname, 0)
    ave.detrend(0)
    ave_normal.data -= np.mean(ave_normal.data, axis=1)[:, np.newaxis]
    picks = pick_types(ave.info, meg=True, eeg=True, exclude='bads')
    assert_true(np.allclose(ave.data[picks], ave_normal.data[picks],
                            rtol=1e-8, atol=1e-16))

def test_plot_topomap():
    """Test topomap plotting
    """
    # evoked
    warnings.simplefilter("always", UserWarning)
    with warnings.catch_warnings(record=True):
        evoked = read_evokeds(evoked_fname, "Left Auditory", baseline=(None, 0))
        evoked.plot_topomap(0.1, "mag", layout=layout)
        plot_evoked_topomap(evoked, None, ch_type="mag")
        times = [0.1, 0.2]
        plot_evoked_topomap(evoked, times, ch_type="eeg")
        plot_evoked_topomap(evoked, times, ch_type="grad")
        plot_evoked_topomap(evoked, times, ch_type="planar1")
        plot_evoked_topomap(evoked, times, ch_type="planar2")
        plot_evoked_topomap(evoked, times, ch_type="grad", show_names=True)

        p = plot_evoked_topomap(evoked, times, ch_type="grad", show_names=lambda x: x.replace("MEG", ""))
        subplot = [x for x in p.get_children() if isinstance(x, matplotlib.axes.Subplot)][0]
        assert_true(
            all("MEG" not in x.get_text() for x in subplot.get_children() if isinstance(x, matplotlib.text.Text))
        )

        # Test title
        def get_texts(p):
            return [x.get_text() for x in p.get_children() if isinstance(x, matplotlib.text.Text)]

        p = plot_evoked_topomap(evoked, times, ch_type="eeg")
        assert_equal(len(get_texts(p)), 0)
        p = plot_evoked_topomap(evoked, times, ch_type="eeg", title="Custom")
        texts = get_texts(p)
        assert_equal(len(texts), 1)
        assert_equal(texts[0], "Custom")

        # delaunay triangulation warning
        with warnings.catch_warnings(record=True):
            plot_evoked_topomap(evoked, times, ch_type="mag", layout="auto")
        assert_raises(
            RuntimeError, plot_evoked_topomap, evoked, 0.1, "mag", proj="interactive"
        )  # projs have already been applied

        # change to no-proj mode
        evoked = read_evokeds(evoked_fname, "Left Auditory", baseline=(None, 0), proj=False)
        plot_evoked_topomap(evoked, 0.1, "mag", proj="interactive")
        assert_raises(RuntimeError, plot_evoked_topomap, evoked, np.repeat(0.1, 50))
        assert_raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6])

        projs = read_proj(ecg_fname)
        projs = [pp for pp in projs if pp["desc"].lower().find("eeg") < 0]
        plot_projs_topomap(projs)
        plt.close("all")
        for ch in evoked.info["chs"]:
            if ch["coil_type"] == FIFF.FIFFV_COIL_EEG:
                if ch["eeg_loc"] is not None:
                    ch["eeg_loc"].fill(0)
                ch["loc"].fill(0)
        assert_raises(RuntimeError, plot_evoked_topomap, evoked, times, ch_type="eeg")

def test_hash_evoked():
    """Test evoked hashing."""
    ave = read_evokeds(fname, 0)
    ave_2 = read_evokeds(fname, 0)
    assert_equal(hash(ave), hash(ave_2))
    # do NOT use assert_equal here, failing output is terrible
    assert_true(pickle.dumps(ave) == pickle.dumps(ave_2))

    ave_2.data[0, 0] -= 1
    assert_not_equal(hash(ave), hash(ave_2))

def test_evoked_to_nitime():
    """ Test to_nitime """
    ave = read_evokeds(fname, 0)
    evoked_ts = ave.to_nitime()
    assert_equal(evoked_ts.data, ave.data)

    picks2 = [1, 2]
    ave = read_evokeds(fname, 0)
    evoked_ts = ave.to_nitime(picks=picks2)
    assert_equal(evoked_ts.data, ave.data[picks2])

def test_hash_evoked():
    """Test evoked hashing."""
    ave = read_evokeds(fname, 0)
    ave_2 = read_evokeds(fname, 0)
    assert hash(ave) == hash(ave_2)
    assert ave == ave_2
    # do NOT use assert_equal here, failing output is terrible
    assert pickle.dumps(ave) == pickle.dumps(ave_2)

    ave_2.data[0, 0] -= 1
    assert hash(ave) != hash(ave_2)

def test_evoked_aspects(aspect_kind, tmpdir):
    """Test handling of evoked aspects."""
    # gh-6359
    ave = read_evokeds(fname, 0)
    ave._aspect_kind = aspect_kind
    assert 'Evoked' in repr(ave)
    # for completeness let's try a round-trip
    temp_fname = op.join(str(tmpdir), 'test-ave.fif')
    ave.save(temp_fname)
    ave_2 = read_evokeds(temp_fname, condition=0)
    assert_allclose(ave.data, ave_2.data)
    assert ave.kind == ave_2.kind

def test_plot_trans():
    """Test plotting of -trans.fif files and MEG sensor layouts
    """
    evoked = read_evokeds(evoked_fname)[0]
    with warnings.catch_warnings(record=True):  # 4D weight tables
        bti = read_raw_bti(pdf_fname, config_fname, hs_fname, convert=True,
                           preload=False).info
    infos = dict(
        Neuromag=evoked.info,
        CTF=read_raw_ctf(ctf_fname).info,
        BTi=bti,
        KIT=read_raw_kit(sqd_fname).info,
    )
    for system, info in infos.items():
        ref_meg = False if system == 'KIT' else True
        plot_trans(info, trans_fname, subject='sample', meg_sensors=True,
                   subjects_dir=subjects_dir, ref_meg=ref_meg)
    # KIT ref sensor coil def not defined
    assert_raises(RuntimeError, plot_trans, infos['KIT'], None,
                  meg_sensors=True, ref_meg=True)
    info = infos['Neuromag']
    assert_raises(ValueError, plot_trans, info, trans_fname,
                  subject='sample', subjects_dir=subjects_dir,
                  ch_type='bad-chtype')
    assert_raises(TypeError, plot_trans, 'foo', trans_fname,
                  subject='sample', subjects_dir=subjects_dir)
    # no-head version
    plot_trans(info, None, meg_sensors=True, dig=True, coord_frame='head')
    # EEG only with strange options
    with warnings.catch_warnings(record=True) as w:
        plot_trans(evoked.copy().pick_types(meg=False, eeg=True).info,
                   trans=trans_fname, meg_sensors=True)
    assert_true(['Cannot plot MEG' in str(ww.message) for ww in w])

def test_plot_topomap_neuromag122():
    """Test topomap plotting."""
    res = 8
    fast_test = dict(res=res, contours=0, sensors=False)
    evoked = read_evokeds(evoked_fname, 'Left Auditory',
                          baseline=(None, 0))
    evoked.pick_types(meg='grad')
    evoked.pick_channels(evoked.ch_names[:122])
    ch_names = ['MEG %03d' % k for k in range(1, 123)]
    for c in evoked.info['chs']:
        c['coil_type'] = FIFF.FIFFV_COIL_NM_122
    evoked.rename_channels({c_old: c_new for (c_old, c_new) in
                            zip(evoked.ch_names, ch_names)})
    layout = find_layout(evoked.info)
    assert layout.kind.startswith('Neuromag_122')
    evoked.plot_topomap(times=[0.1], **fast_test)

    proj = Projection(active=False,
                      desc="test", kind=1,
                      data=dict(nrow=1, ncol=122,
                                row_names=None,
                                col_names=evoked.ch_names, data=np.ones(122)),
                      explained_var=0.5)

    plot_projs_topomap([proj], info=evoked.info, **fast_test)
    plot_projs_topomap([proj], layout=layout, **fast_test)
    pytest.raises(RuntimeError, plot_projs_topomap, [proj], **fast_test)