Python fiff.read_evoked函数代码示例

def test_evoked_standard_error():
    """Test calculation and read/write of standard error
    """
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0))
    evoked = [epochs.average(), epochs.standard_error()]
    fiff.write_evoked(op.join(tempdir, 'evoked.fif'), evoked)
    evoked2 = read_evoked(op.join(tempdir, 'evoked.fif'), [0, 1])
    evoked3 = [read_evoked(op.join(tempdir, 'evoked.fif'), 'Unknown'),
               read_evoked(op.join(tempdir, 'evoked.fif'), 'Unknown',
                           kind='standard_error')]
    for evoked_new in [evoked2, evoked3]:
        assert_true(evoked_new[0]._aspect_kind ==
                    fiff.FIFF.FIFFV_ASPECT_AVERAGE)
        assert_true(evoked_new[0].kind == 'average')
        assert_true(evoked_new[1]._aspect_kind ==
                    fiff.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_evoked_proj():
    """Test SSP proj operations
    """
    for proj in [True, False]:
        ave = read_evoked(fname, setno=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_evoked(fname, setno=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
    """
    # upsample, write it out, read it in
    ave = read_evoked(fname, 0)
    sfreq_normal = ave.info['sfreq']
    ave.resample(2 * sfreq_normal)
    write_evoked(op.join(tempdir, 'evoked.fif'), ave)
    ave_up = read_evoked(op.join(tempdir, 'evoked.fif'), 0)

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

    # and compare the original to the downsampled upsampled version
    ave_new = read_evoked(op.join(tempdir, 'evoked.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_io_evoked():
    """Test IO for evoked data (fif + gz) with integer and str args
    """
    ave = read_evoked(fname, 0)

    write_evoked(op.join(tempdir, 'evoked.fif'), ave)
    ave2 = read_evoked(op.join(tempdir, 'evoked.fif'))

    # 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)

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

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

def test_evoked_to_nitime():
    """ Test to_nitime """
    aves = read_evoked(fname, [0, 1, 2, 3])
    evoked_ts = aves[0].to_nitime()
    assert_equal(evoked_ts.data, aves[0].data)

    picks2 = [1, 2]
    aves = read_evoked(fname, [0, 1, 2, 3])
    evoked_ts = aves[0].to_nitime(picks=picks2)
    assert_equal(evoked_ts.data, aves[0].data[picks2])

def test_evoked_detrend():
    """Test for detrending evoked data
    """
    ave = read_evoked(fname, 0)
    ave_normal = read_evoked(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_io_multi_evoked():
    """Test IO for multiple evoked datasets
    """
    aves = read_evoked(fname, [0, 1, 2, 3])
    write_evoked('evoked.fif', aves)
    aves2 = read_evoked('evoked.fif', [0, 1, 2, 3])
    for [ave, ave2] in zip(aves, aves2):
        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.last, ave2.last)
        assert_equal(ave.first, ave2.first)

def test_meg_field_interpolation_helmet():
    """Test interpolation of MEG field onto helmet
    """
    evoked = read_evoked(evoked_fname, setno='Left Auditory')
    info = evoked.info
    surf = get_meg_helmet_surf(info)
    # let's reduce the number of channels by a bunch to speed it up
    info['bads'] = info['ch_names'][:200]
    # bad ch_type
    assert_raises(ValueError, make_surface_mapping, info, surf, 'foo')
    # bad mode
    assert_raises(ValueError, make_surface_mapping, info, surf, 'meg',
                  mode='foo')
    # no picks
    evoked_eeg = pick_types_evoked(evoked, meg=False, eeg=True)
    assert_raises(RuntimeError, make_surface_mapping, evoked_eeg.info,
                  surf, 'meg')
    # bad surface def
    nn = surf['nn']
    del surf['nn']
    assert_raises(KeyError, make_surface_mapping, info, surf, 'meg')
    surf['nn'] = nn
    cf = surf['coord_frame']
    del surf['coord_frame']
    assert_raises(KeyError, make_surface_mapping, info, surf, 'meg')
    surf['coord_frame'] = cf
    # now do it
    data = make_surface_mapping(info, surf, 'meg', mode='fast')
    assert_array_equal(data.shape, (304, 106))  # data onto surf

def test_io_evoked():
    """Test IO for evoked data
    """
    ave = read_evoked(fname)

    ave.crop(tmin=0)

    write_evoked('evoked.fif', ave)
    ave2 = read_evoked('evoked.fif')

    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.last, ave2.last)
    assert_equal(ave.first, ave2.first)

def test_plot_topomap():
    """Testing topomap plotting
    """
    # evoked
    evoked = fiff.read_evoked(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')
    with warnings.catch_warnings(True):  # delaunay triangulation warning
        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
    evoked.proj = False  # let's fake it like they haven't been applied
    plot_evoked_topomap(evoked, 0.1, 'mag', proj='interactive')
    assert_raises(RuntimeError, plot_evoked_topomap, evoked, np.repeat(.1, 50))
    assert_raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6])

    # projs
    projs = read_proj(ecg_fname)[:7]
    plot_projs_topomap(projs)
    plt.close('all')

def test_plot_topomap():
    """Test topomap plotting
    """
    # evoked
    warnings.simplefilter('always', UserWarning)
    with warnings.catch_warnings(record=True):
        evoked = fiff.read_evoked(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
        evoked.proj = False  # let's fake it like they haven't been applied
        plot_evoked_topomap(evoked, 0.1, 'mag', proj='interactive')
        assert_raises(RuntimeError, plot_evoked_topomap, evoked,
                      np.repeat(.1, 50))
        assert_raises(ValueError, plot_evoked_topomap, evoked, [-3e12, 15e6])

        projs = read_proj(ecg_fname)
        projs = [p for p in projs if p['desc'].lower().find('eeg') < 0]
        plot_projs_topomap(projs)
        plt.close('all')
        for ch in evoked.info['chs']:
            if ch['coil_type'] == fiff.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_drop_channels_mixin():
    """Test channels-dropping functionality
    """
    evoked = read_evoked(fname, setno=0, proj=True)
    drop_ch = evoked.ch_names[:3]
    ch_names = evoked.ch_names[3:]
    evoked.drop_channels(drop_ch)
    assert_equal(ch_names, evoked.ch_names)
    assert_equal(len(ch_names), len(evoked.data))

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

    write_evokeds(op.join(tempdir, 'evoked.fif'), ave)
    ave2 = read_evokeds(op.join(tempdir, 'evoked.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)

    # 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 deprecation warning for read_evoked and write_evoked
    # XXX should be deleted for 0.9 release
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        ave = read_evoked(fname, setno=0)
        assert_true(w[0].category == DeprecationWarning)
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        write_evoked(op.join(tempdir, 'evoked.fif'), ave)
        assert_true(w[0].category == DeprecationWarning)

    # test read_evokeds and write_evokeds
    types = ['Left Auditory', 'Right Auditory', 'Left visual', 'Right visual']
    aves1 = read_evokeds(fname)
    aves2 = read_evokeds(fname, [0, 1, 2, 3])
    aves3 = read_evokeds(fname, types)
    write_evokeds(op.join(tempdir, 'evoked.fif'), aves1)
    aves4 = read_evokeds(op.join(tempdir, 'evoked.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)

def test_as_data_frame():
    """Test Pandas exporter"""
    ave = read_evoked(fname, [0])[0]
    assert_raises(ValueError, ave.as_data_frame, picks=np.arange(400))
    df = ave.as_data_frame()
    assert_true((df.columns == ave.ch_names).all())
    df = ave.as_data_frame(use_time_index=False)
    assert_true('time' in df.columns)
    assert_array_equal(df.values[:, 1], ave.data[0] * 1e13)
    assert_array_equal(df.values[:, 3], ave.data[2] * 1e15)

def test_io_multi_evoked():
    """Test IO for multiple evoked datasets
    """
    aves = read_evoked(fname, [0, 1, 2, 3])
    write_evoked(op.join(tempdir, 'evoked.fif'), aves)
    aves2 = read_evoked(op.join(tempdir, 'evoked.fif'), [0, 1, 2, 3])
    types = ['Left Auditory', 'Right Auditory', 'Left visual', 'Right visual']
    aves3 = read_evoked(op.join(tempdir, 'evoked.fif'), types)
    for aves_new in [aves2, aves3]:
        for [ave, ave_new] in zip(aves, aves_new):
            assert_array_almost_equal(ave.data, ave_new.data)
            assert_array_almost_equal(ave.times, ave_new.times)
            assert_equal(ave.nave, ave_new.nave)
            assert_equal(ave.kind, ave_new.kind)
            assert_equal(ave._aspect_kind, ave_new._aspect_kind)
            assert_equal(ave.last, ave_new.last)
            assert_equal(ave.first, ave_new.first)
    # this should throw an error since there are mulitple datasets
    assert_raises(ValueError, read_evoked, fname)