Python preprocessing.ICA类代码示例

def test_ica_rank_reduction(method):
    """Test recovery ICA rank reduction."""
    _skip_check_picard(method)
    # Most basic recovery
    raw = read_raw_fif(raw_fname).crop(0.5, stop).load_data()
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')[:10]
    n_components = 5
    max_pca_components = len(picks)
    for n_pca_components in [6, 10]:
        with pytest.warns(UserWarning, match='did not converge'):
            ica = ICA(n_components=n_components,
                      max_pca_components=max_pca_components,
                      n_pca_components=n_pca_components,
                      method=method, max_iter=1).fit(raw, picks=picks)

        rank_before = _compute_rank_int(raw.copy().pick(picks), proj=False)
        assert_equal(rank_before, len(picks))
        raw_clean = ica.apply(raw.copy())
        rank_after = _compute_rank_int(raw_clean.copy().pick(picks),
                                       proj=False)
        # interaction between ICA rejection and PCA components difficult
        # to preduct. Rank_after often seems to be 1 higher then
        # n_pca_components
        assert (n_components < n_pca_components <= rank_after <=
                rank_before)

def test_ica_rank_reduction():
    """Test recovery of full data when no source is rejected"""
    # Most basic recovery
    raw = Raw(raw_fname).crop(0.5, stop, False)
    raw.load_data()
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')[:10]
    n_components = 5
    max_pca_components = len(picks)
    for n_pca_components in [6, 10]:
        with warnings.catch_warnings(record=True):  # non-convergence
            warnings.simplefilter('always')
            ica = ICA(n_components=n_components,
                      max_pca_components=max_pca_components,
                      n_pca_components=n_pca_components,
                      method='fastica', max_iter=1).fit(raw, picks=picks)

        rank_before = raw.estimate_rank(picks=picks)
        assert_equal(rank_before, len(picks))
        raw_clean = ica.apply(raw, copy=True)
        rank_after = raw_clean.estimate_rank(picks=picks)
        # interaction between ICA rejection and PCA components difficult
        # to preduct. Rank_after often seems to be 1 higher then
        # n_pca_components
        assert_true(n_components < n_pca_components <= rank_after <=
                    rank_before)

def test_ica_reset(method):
    """Test ICA resetting."""
    _skip_check_picard(method)
    raw = read_raw_fif(raw_fname).crop(0.5, stop).load_data()
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')[:10]

    run_time_attrs = (
        'pre_whitener_',
        'unmixing_matrix_',
        'mixing_matrix_',
        'n_components_',
        'n_samples_',
        'pca_components_',
        'pca_explained_variance_',
        'pca_mean_'
    )
    with pytest.warns(UserWarning, match='did not converge'):
        ica = ICA(
            n_components=3, max_pca_components=3, n_pca_components=3,
            method=method, max_iter=1).fit(raw, picks=picks)

    assert (all(hasattr(ica, attr) for attr in run_time_attrs))
    assert ica.labels_ is not None
    ica._reset()
    assert (not any(hasattr(ica, attr) for attr in run_time_attrs))
    assert ica.labels_ is not None

def test_plot_ica_panel():
    """Test plotting of ICA panel
    """
    ica = ICA(noise_cov=read_cov(cov_fname), n_components=2,
              max_pca_components=3, n_pca_components=3)
    ica.decompose_raw(raw, picks=ica_picks)
    ica.plot_sources_raw(raw)

def test_n_components_and_max_pca_components_none(method):
    """Test n_components and max_pca_components=None."""
    _skip_check_picard(method)
    raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data()
    events = read_events(event_name)
    picks = pick_types(raw.info, eeg=True, meg=False)
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)

    max_pca_components = None
    n_components = None
    random_state = 12345

    tempdir = _TempDir()
    output_fname = op.join(tempdir, 'test_ica-ica.fif')
    ica = ICA(max_pca_components=max_pca_components, method=method,
              n_components=n_components, random_state=random_state)
    with pytest.warns(None):  # convergence
        ica.fit(epochs)
    ica.save(output_fname)

    ica = read_ica(output_fname)

    # ICA.fit() replaced max_pca_components, which was previously None,
    # with the appropriate integer value.
    assert_equal(ica.max_pca_components, epochs.info['nchan'])
    assert ica.n_components is None

def test_eog_channel(method):
    """Test that EOG channel is included when performing ICA."""
    _skip_check_picard(method)
    raw = read_raw_fif(raw_fname, preload=True)
    events = read_events(event_name)
    picks = pick_types(raw.info, meg=True, stim=True, ecg=False,
                       eog=True, exclude='bads')
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)
    n_components = 0.9
    ica = ICA(n_components=n_components, method=method)
    # Test case for MEG and EOG data. Should have EOG channel
    for inst in [raw, epochs]:
        picks1a = pick_types(inst.info, meg=True, stim=False, ecg=False,
                             eog=False, exclude='bads')[:4]
        picks1b = pick_types(inst.info, meg=False, stim=False, ecg=False,
                             eog=True, exclude='bads')
        picks1 = np.append(picks1a, picks1b)
        ica.fit(inst, picks=picks1)
        assert (any('EOG' in ch for ch in ica.ch_names))
    # Test case for MEG data. Should have no EOG channel
    for inst in [raw, epochs]:
        picks1 = pick_types(inst.info, meg=True, stim=False, ecg=False,
                            eog=False, exclude='bads')[:5]
        ica.fit(inst, picks=picks1)
        assert not any('EOG' in ch for ch in ica.ch_names)

def test_ica_reset(method):
    """Test ICA resetting."""
    _skip_check_picard(method)
    raw = read_raw_fif(raw_fname).crop(0.5, stop).load_data()
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')[:10]

    run_time_attrs = (
        '_pre_whitener',
        'unmixing_matrix_',
        'mixing_matrix_',
        'n_components_',
        'n_samples_',
        'pca_components_',
        'pca_explained_variance_',
        'pca_mean_'
    )
    with warnings.catch_warnings(record=True):  # convergence
        ica = ICA(
            n_components=3, max_pca_components=3, n_pca_components=3,
            method=method, max_iter=1).fit(raw, picks=picks)

    assert_true(all(hasattr(ica, attr) for attr in run_time_attrs))
    assert_not_equal(ica.labels_, None)
    ica._reset()
    assert_true(not any(hasattr(ica, attr) for attr in run_time_attrs))
    assert_not_equal(ica.labels_, None)

def apply_ica(fname_filtered, n_components=0.99, decim=None):

    ''' Applies ICA to a list of (filtered) raw files. '''

    import mne
    from mne.preprocessing import ICA
    import os


    if isinstance(fname_filtered, list):
        fnfilt = fname_filtered
    else:
        if isinstance(fname_filtered, str):
            fnfilt = list([fname_filtered]) 
        else:
            fnfilt = list(fname_filtered)

    # loop across all filenames
    for fname in fnfilt:                    
        name  = os.path.split(fname)[1]
        print ">>>> perform ICA signal decomposition on :  "+name
        # load filtered data
        raw = mne.io.Raw(fname,preload=True)
        picks = mne.pick_types(raw.info, meg=True, exclude='bads')
        # ICA decomposition
        ica = ICA(n_components=n_components, max_pca_components=None)

        ica.fit(raw, picks=picks, decim=decim, reject={'mag': 5e-12})

        # save ICA object 
        fnica_out = fname.strip('-raw.fif') + '-ica.fif'
        # fnica_out = fname[0:len(fname)-4]+'-ica.fif'
        ica.save(fnica_out)

def run_ica(method):
    ica = ICA(n_components=20, method=method, random_state=0)
    t0 = time()
    ica.fit(raw, picks=picks, reject=reject)
    fit_time = time() - t0
    title = ('ICA decomposition using %s (took %.1fs)' % (method, fit_time))
    ica.plot_components(title=title)

def test_plot_instance_components():
    """Test plotting of components as instances of raw and epochs."""
    import matplotlib.pyplot as plt
    raw = _get_raw()
    picks = _get_picks(raw)
    ica = ICA(noise_cov=read_cov(cov_fname), n_components=2,
              max_pca_components=3, n_pca_components=3)
    with pytest.warns(RuntimeWarning, match='projection'):
        ica.fit(raw, picks=picks)
    fig = ica.plot_sources(raw, exclude=[0], title='Components')
    for key in ['down', 'up', 'right', 'left', 'o', '-', '+', '=', 'pageup',
                'pagedown', 'home', 'end', 'f11', 'b']:
        fig.canvas.key_press_event(key)
    ax = fig.get_axes()[0]
    line = ax.lines[0]
    _fake_click(fig, ax, [line.get_xdata()[0], line.get_ydata()[0]],
                'data')
    _fake_click(fig, ax, [-0.1, 0.9])  # click on y-label
    fig.canvas.key_press_event('escape')
    plt.close('all')
    epochs = _get_epochs()
    fig = ica.plot_sources(epochs, exclude=[0], title='Components')
    for key in ['down', 'up', 'right', 'left', 'o', '-', '+', '=', 'pageup',
                'pagedown', 'home', 'end', 'f11', 'b']:
        fig.canvas.key_press_event(key)
    # Test a click
    ax = fig.get_axes()[0]
    line = ax.lines[0]
    _fake_click(fig, ax, [line.get_xdata()[0], line.get_ydata()[0]], 'data')
    _fake_click(fig, ax, [-0.1, 0.9])  # click on y-label
    fig.canvas.key_press_event('escape')
    plt.close('all')

def test_n_components_none():
    """Test n_components=None."""
    raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data()
    events = read_events(event_name)
    picks = pick_types(raw.info, eeg=True, meg=False)
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)

    max_pca_components = 10
    n_components = None
    random_state = 12345

    tempdir = _TempDir()
    output_fname = op.join(tempdir, 'test_ica-ica.fif')

    ica = ICA(max_pca_components=max_pca_components,
              n_components=n_components, random_state=random_state)
    with warnings.catch_warnings(record=True):  # convergence
        ica.fit(epochs)
    ica.save(output_fname)

    ica = read_ica(output_fname)

    # ICA.fit() replaced max_pca_components, which was previously None,
    # with the appropriate integer value.
    assert_equal(ica.max_pca_components, 10)
    assert_is_none(ica.n_components)

def test_ica_reset():
    """Test ICA resetting"""
    raw = Raw(raw_fname).crop(0.5, stop, False)
    raw.load_data()
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')[:10]

    run_time_attrs = (
        '_pre_whitener',
        'unmixing_matrix_',
        'mixing_matrix_',
        'n_components_',
        'n_samples_',
        'pca_components_',
        'pca_explained_variance_',
        'pca_mean_'
    )
    with warnings.catch_warnings(record=True):
        ica = ICA(
            n_components=3, max_pca_components=3, n_pca_components=3,
            method='fastica', max_iter=1).fit(raw, picks=picks)

    assert_true(all(hasattr(ica, attr) for attr in run_time_attrs))
    ica._reset()
    assert_true(not any(hasattr(ica, attr) for attr in run_time_attrs))

 def decompose(self, X, y=None):
     raw_inst = RawArray(X.T, create_info(self.channel_names, self.fs, 'eeg', None))
     ica = ICA(method='extended-infomax')
     ica.fit(raw_inst)
     filters = np.dot(ica.unmixing_matrix_, ica.pca_components_[:ica.n_components_]).T
     topographies = np.linalg.inv(filters).T
     scores = self.get_scores(X, filters)
     return scores, filters, topographies

def test_plot_ica_panel():
    """Test plotting of ICA panel
    """
    ica_picks = fiff.pick_types(raw.info, meg=True, eeg=False, stim=False, ecg=False, eog=False, exclude="bads")
    cov = read_cov(cov_fname)
    ica = ICA(noise_cov=cov, n_components=2, max_pca_components=3, n_pca_components=3)
    ica.decompose_raw(raw, picks=ica_picks)
    ica.plot_sources_raw(raw)

def test_plot_ica_scores():
    """Test plotting of ICA scores
    """
    raw = _get_raw()
    ica_picks = pick_types(raw.info, meg=True, eeg=False, stim=False, ecg=False, eog=False, exclude="bads")
    ica = ICA(noise_cov=read_cov(cov_fname), n_components=2, max_pca_components=3, n_pca_components=3)
    ica.fit(raw, picks=ica_picks)
    ica.plot_scores([0.3, 0.2], axhline=[0.1, -0.1])
    assert_raises(ValueError, ica.plot_scores, [0.2])
    plt.close("all")