Python ICA.n_components方法代码示例

# 需要导入模块: from mne.preprocessing import ICA [as 别名]
# 或者: from mne.preprocessing.ICA import n_components [as 别名]
def test_ica_additional():
    """Test additional ICA functionality"""
    tempdir = _TempDir()
    stop2 = 500
    raw = Raw(raw_fname).crop(1.5, stop, False)
    raw.load_data()
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')
    test_cov = read_cov(test_cov_name)
    events = read_events(event_name)
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)
    # test if n_components=None works
    with warnings.catch_warnings(record=True):
        ica = ICA(n_components=None,
                  max_pca_components=None,
                  n_pca_components=None, random_state=0)
        ica.fit(epochs, picks=picks, decim=3)
    # for testing eog functionality
    picks2 = pick_types(raw.info, meg=True, stim=False, ecg=False,
                        eog=True, exclude='bads')
    epochs_eog = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks2,
                        baseline=(None, 0), preload=True)

    test_cov2 = test_cov.copy()
    ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4,
              n_pca_components=4)
    assert_true(ica.info is None)
    with warnings.catch_warnings(record=True):
        ica.fit(raw, picks[:5])
    assert_true(isinstance(ica.info, Info))
    assert_true(ica.n_components_ < 5)

    ica = ICA(n_components=3, max_pca_components=4,
              n_pca_components=4)
    assert_raises(RuntimeError, ica.save, '')
    with warnings.catch_warnings(record=True):
        ica.fit(raw, picks=[1, 2, 3, 4, 5], start=start, stop=stop2)

    # test corrmap
    ica2 = ica.copy()
    corrmap([ica, ica2], (0, 0), threshold='auto', label='blinks', plot=True,
            ch_type="mag")
    corrmap([ica, ica2], (0, 0), threshold=2, plot=False, show=False)
    assert_true(ica.labels_["blinks"] == ica2.labels_["blinks"])
    assert_true(0 in ica.labels_["blinks"])
    plt.close('all')

    # test warnings on bad filenames
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        ica_badname = op.join(op.dirname(tempdir), 'test-bad-name.fif.gz')
        ica.save(ica_badname)
        read_ica(ica_badname)
    assert_naming(w, 'test_ica.py', 2)

    # test decim
    ica = ICA(n_components=3, max_pca_components=4,
              n_pca_components=4)
    raw_ = raw.copy()
    for _ in range(3):
        raw_.append(raw_)
    n_samples = raw_._data.shape[1]
    with warnings.catch_warnings(record=True):
        ica.fit(raw, picks=None, decim=3)
    assert_true(raw_._data.shape[1], n_samples)

    # test expl var
    ica = ICA(n_components=1.0, max_pca_components=4,
              n_pca_components=4)
    with warnings.catch_warnings(record=True):
        ica.fit(raw, picks=None, decim=3)
    assert_true(ica.n_components_ == 4)

    # epochs extraction from raw fit
    assert_raises(RuntimeError, ica.get_sources, epochs)
    # test reading and writing
    test_ica_fname = op.join(op.dirname(tempdir), 'test-ica.fif')
    for cov in (None, test_cov):
        ica = ICA(noise_cov=cov, n_components=2, max_pca_components=4,
                  n_pca_components=4)
        with warnings.catch_warnings(record=True):  # ICA does not converge
            ica.fit(raw, picks=picks, start=start, stop=stop2)
        sources = ica.get_sources(epochs).get_data()
        assert_true(ica.mixing_matrix_.shape == (2, 2))
        assert_true(ica.unmixing_matrix_.shape == (2, 2))
        assert_true(ica.pca_components_.shape == (4, len(picks)))
        assert_true(sources.shape[1] == ica.n_components_)

        for exclude in [[], [0]]:
            ica.exclude = [0]
            ica.labels_ = {'foo': [0]}
            ica.save(test_ica_fname)
            ica_read = read_ica(test_ica_fname)
            assert_true(ica.exclude == ica_read.exclude)
            assert_equal(ica.labels_, ica_read.labels_)
            ica.exclude = []
            ica.apply(raw, exclude=[1])
#.........这里部分代码省略.........

# 需要导入模块: from mne.preprocessing import ICA [as 别名]
# 或者: from mne.preprocessing.ICA import n_components [as 别名]
def test_ica_core():
    """Test ICA on raw and epochs"""
    raw = Raw(raw_fname).crop(1.5, stop, False)
    raw.load_data()
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')
    # XXX. The None cases helped revealing bugs but are time consuming.
    test_cov = read_cov(test_cov_name)
    events = read_events(event_name)
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)
    noise_cov = [None, test_cov]
    # removed None cases to speed up...
    n_components = [2, 1.0]  # for future dbg add cases
    max_pca_components = [3]
    picks_ = [picks]
    methods = ['fastica']
    iter_ica_params = product(noise_cov, n_components, max_pca_components,
                              picks_, methods)

    # # test init catchers
    assert_raises(ValueError, ICA, n_components=3, max_pca_components=2)
    assert_raises(ValueError, ICA, n_components=2.3, max_pca_components=2)

    # test essential core functionality
    for n_cov, n_comp, max_n, pcks, method in iter_ica_params:
        # Test ICA raw
        ica = ICA(noise_cov=n_cov, n_components=n_comp,
                  max_pca_components=max_n, n_pca_components=max_n,
                  random_state=0, method=method, max_iter=1)
        assert_raises(ValueError, ica.__contains__, 'mag')

        print(ica)  # to test repr

        # test fit checker
        assert_raises(RuntimeError, ica.get_sources, raw)
        assert_raises(RuntimeError, ica.get_sources, epochs)

        # test decomposition
        with warnings.catch_warnings(record=True):
            ica.fit(raw, picks=pcks, start=start, stop=stop)
            repr(ica)  # to test repr
        assert_true('mag' in ica)  # should now work without error

        # test re-fit
        unmixing1 = ica.unmixing_matrix_
        with warnings.catch_warnings(record=True):
            ica.fit(raw, picks=pcks, start=start, stop=stop)
        assert_array_almost_equal(unmixing1, ica.unmixing_matrix_)

        sources = ica.get_sources(raw)[:, :][0]
        assert_true(sources.shape[0] == ica.n_components_)

        # test preload filter
        raw3 = raw.copy()
        raw3.preload = False
        assert_raises(ValueError, ica.apply, raw3,
                      include=[1, 2])

        #######################################################################
        # test epochs decomposition
        ica = ICA(noise_cov=n_cov, n_components=n_comp,
                  max_pca_components=max_n, n_pca_components=max_n,
                  random_state=0)
        with warnings.catch_warnings(record=True):
            ica.fit(epochs, picks=picks)
        data = epochs.get_data()[:, 0, :]
        n_samples = np.prod(data.shape)
        assert_equal(ica.n_samples_, n_samples)
        print(ica)  # to test repr

        sources = ica.get_sources(epochs).get_data()
        assert_true(sources.shape[1] == ica.n_components_)

        assert_raises(ValueError, ica.score_sources, epochs,
                      target=np.arange(1))

        # test preload filter
        epochs3 = epochs.copy()
        epochs3.preload = False
        assert_raises(ValueError, ica.apply, epochs3,
                      include=[1, 2])

    # test for bug with whitener updating
    _pre_whitener = ica._pre_whitener.copy()
    epochs._data[:, 0, 10:15] *= 1e12
    ica.apply(epochs, copy=True)
    assert_array_equal(_pre_whitener, ica._pre_whitener)

    # test expl. var threshold leading to empty sel
    ica.n_components = 0.1
    assert_raises(RuntimeError, ica.fit, epochs)

    offender = 1, 2, 3,
    assert_raises(ValueError, ica.get_sources, offender)
    assert_raises(ValueError, ica.fit, offender)
    assert_raises(ValueError, ica.apply, offender)

# 需要导入模块: from mne.preprocessing import ICA [as 别名]
# 或者: from mne.preprocessing.ICA import n_components [as 别名]
def test_ica_additional(method):
    """Test additional ICA functionality."""
    _skip_check_picard(method)

    tempdir = _TempDir()
    stop2 = 500
    raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data()
    raw.del_proj()  # avoid warnings
    raw.set_annotations(Annotations([0.5], [0.5], ['BAD']))
    # XXX This breaks the tests :(
    # raw.info['bads'] = [raw.ch_names[1]]
    test_cov = read_cov(test_cov_name)
    events = read_events(event_name)
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')[1::2]
    epochs = Epochs(raw, events, None, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True, proj=False)
    epochs.decimate(3, verbose='error')
    assert len(epochs) == 4

    # test if n_components=None works
    ica = ICA(n_components=None, max_pca_components=None,
              n_pca_components=None, random_state=0, method=method, max_iter=1)
    with pytest.warns(UserWarning, match='did not converge'):
        ica.fit(epochs)
    # for testing eog functionality
    picks2 = np.concatenate([picks, pick_types(raw.info, False, eog=True)])
    epochs_eog = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks2,
                        baseline=(None, 0), preload=True)
    del picks2

    test_cov2 = test_cov.copy()
    ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4,
              n_pca_components=4, method=method)
    assert (ica.info is None)
    with pytest.warns(RuntimeWarning, match='normalize_proj'):
        ica.fit(raw, picks[:5])
    assert (isinstance(ica.info, Info))
    assert (ica.n_components_ < 5)

    ica = ICA(n_components=3, max_pca_components=4, method=method,
              n_pca_components=4, random_state=0)
    pytest.raises(RuntimeError, ica.save, '')

    ica.fit(raw, picks=[1, 2, 3, 4, 5], start=start, stop=stop2)

    # check passing a ch_name to find_bads_ecg
    with pytest.warns(RuntimeWarning, match='longer'):
        _, scores_1 = ica.find_bads_ecg(raw)
        _, scores_2 = ica.find_bads_ecg(raw, raw.ch_names[1])
    assert scores_1[0] != scores_2[0]

    # test corrmap
    ica2 = ica.copy()
    ica3 = ica.copy()
    corrmap([ica, ica2], (0, 0), threshold='auto', label='blinks', plot=True,
            ch_type="mag")
    corrmap([ica, ica2], (0, 0), threshold=2, plot=False, show=False)
    assert (ica.labels_["blinks"] == ica2.labels_["blinks"])
    assert (0 in ica.labels_["blinks"])
    # test retrieval of component maps as arrays
    components = ica.get_components()
    template = components[:, 0]
    EvokedArray(components, ica.info, tmin=0.).plot_topomap([0], time_unit='s')

    corrmap([ica, ica3], template, threshold='auto', label='blinks', plot=True,
            ch_type="mag")
    assert (ica2.labels_["blinks"] == ica3.labels_["blinks"])

    plt.close('all')

    ica_different_channels = ICA(n_components=2, random_state=0).fit(
        raw, picks=[2, 3, 4, 5])
    pytest.raises(ValueError, corrmap, [ica_different_channels, ica], (0, 0))

    # test warnings on bad filenames
    ica_badname = op.join(op.dirname(tempdir), 'test-bad-name.fif.gz')
    with pytest.warns(RuntimeWarning, match='-ica.fif'):
        ica.save(ica_badname)
    with pytest.warns(RuntimeWarning, match='-ica.fif'):
        read_ica(ica_badname)

    # test decim
    ica = ICA(n_components=3, max_pca_components=4,
              n_pca_components=4, method=method, max_iter=1)
    raw_ = raw.copy()
    for _ in range(3):
        raw_.append(raw_)
    n_samples = raw_._data.shape[1]
    with pytest.warns(UserWarning, match='did not converge'):
        ica.fit(raw, picks=picks[:5], decim=3)
    assert raw_._data.shape[1] == n_samples

    # test expl var
    ica = ICA(n_components=1.0, max_pca_components=4,
              n_pca_components=4, method=method, max_iter=1)
    with pytest.warns(UserWarning, match='did not converge'):
        ica.fit(raw, picks=None, decim=3)
    assert (ica.n_components_ == 4)
    ica_var = _ica_explained_variance(ica, raw, normalize=True)
#.........这里部分代码省略.........

# 需要导入模块: from mne.preprocessing import ICA [as 别名]
# 或者: from mne.preprocessing.ICA import n_components [as 别名]
def test_ica_additional():
    """Test additional ICA functionality
    """
    stop2 = 500
    raw = io.Raw(raw_fname, preload=True).crop(0, stop, False).crop(1.5)
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')
    test_cov = read_cov(test_cov_name)
    events = read_events(event_name)
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)
    # for testing eog functionality
    picks2 = pick_types(raw.info, meg=True, stim=False, ecg=False,
                        eog=True, exclude='bads')
    epochs_eog = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks2,
                        baseline=(None, 0), preload=True)

    test_cov2 = deepcopy(test_cov)
    ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4,
              n_pca_components=4)
    assert_true(ica.info is None)
    ica.decompose_raw(raw, picks[:5])
    assert_true(isinstance(ica.info, Info))
    assert_true(ica.n_components_ < 5)

    ica = ICA(n_components=3, max_pca_components=4,
              n_pca_components=4)
    assert_raises(RuntimeError, ica.save, '')
    ica.decompose_raw(raw, picks=None, start=start, stop=stop2)

    # test warnings on bad filenames
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        ica_badname = op.join(op.dirname(tempdir), 'test-bad-name.fif.gz')
        ica.save(ica_badname)
        read_ica(ica_badname)
    assert_true(len(w) == 2)

    # test decim
    ica = ICA(n_components=3, max_pca_components=4,
              n_pca_components=4)
    raw_ = raw.copy()
    for _ in range(3):
        raw_.append(raw_)
    n_samples = raw_._data.shape[1]
    ica.decompose_raw(raw, picks=None, decim=3)
    assert_true(raw_._data.shape[1], n_samples)

    # test expl var
    ica = ICA(n_components=1.0, max_pca_components=4,
              n_pca_components=4)
    ica.decompose_raw(raw, picks=None, decim=3)
    assert_true(ica.n_components_ == 4)

    # epochs extraction from raw fit
    assert_raises(RuntimeError, ica.get_sources_epochs, epochs)
    # test reading and writing
    test_ica_fname = op.join(op.dirname(tempdir), 'test-ica.fif')
    for cov in (None, test_cov):
        ica = ICA(noise_cov=cov, n_components=2, max_pca_components=4,
                  n_pca_components=4)
        with warnings.catch_warnings(record=True):  # ICA does not converge
            ica.decompose_raw(raw, picks=picks, start=start, stop=stop2)
        sources = ica.get_sources_epochs(epochs)
        assert_true(ica.mixing_matrix_.shape == (2, 2))
        assert_true(ica.unmixing_matrix_.shape == (2, 2))
        assert_true(ica.pca_components_.shape == (4, len(picks)))
        assert_true(sources.shape[1] == ica.n_components_)

        for exclude in [[], [0]]:
            ica.exclude = [0]
            ica.save(test_ica_fname)
            ica_read = read_ica(test_ica_fname)
            assert_true(ica.exclude == ica_read.exclude)
            # test pick merge -- add components
            ica.pick_sources_raw(raw, exclude=[1])
            assert_true(ica.exclude == [0, 1])
            #                 -- only as arg
            ica.exclude = []
            ica.pick_sources_raw(raw, exclude=[0, 1])
            assert_true(ica.exclude == [0, 1])
            #                 -- remove duplicates
            ica.exclude += [1]
            ica.pick_sources_raw(raw, exclude=[0, 1])
            assert_true(ica.exclude == [0, 1])

            # test basic include
            ica.exclude = []
            ica.pick_sources_raw(raw, include=[1])

            ica_raw = ica.sources_as_raw(raw)
            assert_true(ica.exclude == [ica_raw.ch_names.index(e) for e in
                                        ica_raw.info['bads']])

        # test filtering
        d1 = ica_raw._data[0].copy()
        with warnings.catch_warnings(record=True):  # dB warning
            ica_raw.filter(4, 20)
#.........这里部分代码省略.........

# 需要导入模块: from mne.preprocessing import ICA [as 别名]
# 或者: from mne.preprocessing.ICA import n_components [as 别名]
def test_ica_core(method):
    """Test ICA on raw and epochs."""
    _skip_check_picard(method)
    raw = read_raw_fif(raw_fname).crop(1.5, stop).load_data()

    # XXX. The None cases helped revealing bugs but are time consuming.
    test_cov = read_cov(test_cov_name)
    events = read_events(event_name)
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)
    noise_cov = [None, test_cov]
    # removed None cases to speed up...
    n_components = [2, 1.0]  # for future dbg add cases
    max_pca_components = [3]
    picks_ = [picks]
    methods = [method]
    iter_ica_params = product(noise_cov, n_components, max_pca_components,
                              picks_, methods)

    # # test init catchers
    pytest.raises(ValueError, ICA, n_components=3, max_pca_components=2)
    pytest.raises(ValueError, ICA, n_components=2.3, max_pca_components=2)

    # test essential core functionality
    for n_cov, n_comp, max_n, pcks, method in iter_ica_params:
        # Test ICA raw
        ica = ICA(noise_cov=n_cov, n_components=n_comp,
                  max_pca_components=max_n, n_pca_components=max_n,
                  random_state=0, method=method, max_iter=1)
        pytest.raises(ValueError, ica.__contains__, 'mag')

        print(ica)  # to test repr

        # test fit checker
        pytest.raises(RuntimeError, ica.get_sources, raw)
        pytest.raises(RuntimeError, ica.get_sources, epochs)

        # test decomposition
        with pytest.warns(UserWarning, match='did not converge'):
            ica.fit(raw, picks=pcks, start=start, stop=stop)
        repr(ica)  # to test repr
        assert ('mag' in ica)  # should now work without error

        # test re-fit
        unmixing1 = ica.unmixing_matrix_
        with pytest.warns(UserWarning, match='did not converge'):
            ica.fit(raw, picks=pcks, start=start, stop=stop)
        assert_array_almost_equal(unmixing1, ica.unmixing_matrix_)

        raw_sources = ica.get_sources(raw)
        # test for #3804
        assert_equal(raw_sources._filenames, [None])
        print(raw_sources)

        # test for gh-6271 (scaling of ICA traces)
        fig = raw_sources.plot()
        assert len(fig.axes[0].lines) in (4, 5)
        for line in fig.axes[0].lines[1:-1]:  # first and last are markers
            y = line.get_ydata()
            assert np.ptp(y) < 10
        plt.close('all')

        sources = raw_sources[:, :][0]
        assert (sources.shape[0] == ica.n_components_)

        # test preload filter
        raw3 = raw.copy()
        raw3.preload = False
        pytest.raises(RuntimeError, ica.apply, raw3,
                      include=[1, 2])

        #######################################################################
        # test epochs decomposition
        ica = ICA(noise_cov=n_cov, n_components=n_comp,
                  max_pca_components=max_n, n_pca_components=max_n,
                  random_state=0, method=method)
        with pytest.warns(None):  # sometimes warns
            ica.fit(epochs, picks=picks)
        data = epochs.get_data()[:, 0, :]
        n_samples = np.prod(data.shape)
        assert_equal(ica.n_samples_, n_samples)
        print(ica)  # to test repr

        sources = ica.get_sources(epochs).get_data()
        assert (sources.shape[1] == ica.n_components_)

        pytest.raises(ValueError, ica.score_sources, epochs,
                      target=np.arange(1))

        # test preload filter
        epochs3 = epochs.copy()
        epochs3.preload = False
        pytest.raises(RuntimeError, ica.apply, epochs3,
                      include=[1, 2])

    # test for bug with whitener updating
    _pre_whitener = ica.pre_whitener_.copy()
    epochs._data[:, 0, 10:15] *= 1e12
#.........这里部分代码省略.........