Python ICA.sources_as_raw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 sources_as_raw [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 sources_as_raw [as 别名]
n_pca_components=1.0
max_pca_components=None

subjects_dir = '/home/qdong/data/'
subject_path = subjects_dir + subject#Set the data path of the subject
#raw_fname = subject_path + '/MEG/ssp_cleaned_%s_audi_cued-raw_cle.fif' %subject
raw_fname = subject_path + '/MEG/%s_audi_cued-raw_cle.fif' %subject
raw_basename = os.path.splitext(os.path.basename(raw_fname))[0]
raw = Raw(raw_fname, preload=True)
picks = mne.fiff.pick_types(raw.info, meg=True, eeg=False, eog=False, 
                            stim=False, exclude='bads')
ica = ICA(n_components=n_components, n_pca_components=n_pca_components,  max_pca_components=max_pca_components, random_state=0)
ica.decompose_raw(raw, picks=picks, decim=3)
if trigger == 'resp':
    add_from_raw = mne.fiff.pick_types(raw.info, meg=False, resp=True, exclude='bads')
    sources_add = ica.sources_as_raw(raw, picks=add_from_raw)
    events = mne.find_events(sources_add, stim_channel=res_ch_name)
    raw_basename += '_resp'
elif trigger == 'stim':
    add_from_raw = mne.fiff.pick_types(raw.info, meg=False, stim=True, exclude='bads')
    sources_add = ica.sources_as_raw(raw, picks=add_from_raw)
    events = mne.find_events(sources_add, stim_channel=sti_ch_name)
    raw_basename += '_stim'
else:
    print "Incorrect trigger."
    sys.exit()
  # drop non-data channels (ICA sources are type misc)
  #ica.n_pca_components=None
picks = mne.fiff.pick_types(sources_add.info, meg=False, misc=True, exclude='bads')

  #Compare different bandwith of ICA components: 2-4, 4-8, 8-12, 12-16, 16-20Hz

# 需要导入模块: from mne.preprocessing import ICA [as 别名]
# 或者: from mne.preprocessing.ICA import sources_as_raw [as 别名]
n_pca_components=1.0
max_pca_components=None

subjects_dir = '/home/qdong/freesurfer/subjects/'
subject_path = subjects_dir + subject#Set the data path of the subject
#raw_fname = subject_path + '/MEG/ssp_cleaned_%s_audi_cued-raw_cle.fif' %subject
raw_fname = subject_path + '/MEG/%s_audi_cued-raw_cle.fif' %subject
raw_basename = os.path.splitext(os.path.basename(raw_fname))[0]
raw = Raw(raw_fname, preload=True)
picks = mne.fiff.pick_types(raw.info, meg=True, eeg=False, eog=False, 
                            stim=False, exclude='bads')
ica = ICA(n_components=n_components, n_pca_components=n_pca_components,  max_pca_components=max_pca_components, random_state=0)
ica.decompose_raw(raw, picks=picks, decim=3)

add_resp_raw = mne.fiff.pick_types(raw.info, meg=False, resp=True, exclude='bads')
sources_resp_add = ica.sources_as_raw(raw, picks=add_resp_raw)
resp_events = mne.find_events(sources_resp_add, stim_channel=res_ch_name)

add_stim_raw = mne.fiff.pick_types(raw.info, meg=False, stim=True, exclude='bads')
sources_stim_add = ica.sources_as_raw(raw, picks=add_stim_raw)
stim_events = mne.find_events(sources_stim_add, stim_channel=sti_ch_name)

stim_picks = mne.fiff.pick_types(sources_stim_add.info, meg=False, misc=True, exclude='bads')
resp_picks = mne.fiff.pick_types(sources_resp_add.info, meg=False, misc=True, exclude='bads')
  #Compare different bandwith of ICA components: 2-4, 4-8, 8-12, 12-16, 16-20Hz
l_f=2
Brain_idx=[]#The index of ICA related with trigger channels
for i in [4, 8, 12, 16]:
    h_f = i
    if l_f != 2:
      sources_stim_add = ica.sources_as_raw(raw, picks=add_stim_raw)

# 需要导入模块: from mne.preprocessing import ICA [as 别名]
# 或者: from mne.preprocessing.ICA import sources_as_raw [as 别名]
def test_ica_additional():
    """Test additional functionality
    """
    stop2 = 500

    test_cov2 = deepcopy(test_cov)
    ica = ICA(noise_cov=test_cov2, n_components=3, max_pca_components=4,
              n_pca_components=4)
    ica.decompose_raw(raw, picks[:5])
    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)

    # 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), 'ica_test.fif')
    for cov in (None, test_cov):
        ica = ICA(noise_cov=cov, n_components=3, max_pca_components=4,
                  n_pca_components=4)
        ica.decompose_raw(raw, picks=picks, start=start, stop=stop2)
        sources = ica.get_sources_epochs(epochs)
        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])

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

        ica.n_pca_components = 2
        ica.save(test_ica_fname)
        ica_read = read_ica(test_ica_fname)
        assert_true(ica.n_pca_components ==
                    ica_read.n_pca_components)
        ica.n_pca_components = 4
        ica_read.n_pca_components = 4

        ica.exclude = []
        ica.save(test_ica_fname)
        ica_read = read_ica(test_ica_fname)

        assert_true(ica.ch_names == ica_read.ch_names)

        assert_true(np.allclose(ica.mixing_matrix_, ica_read.mixing_matrix_,
                                rtol=1e-16, atol=1e-32))
        assert_array_equal(ica.pca_components_,
                           ica_read.pca_components_)
        assert_array_equal(ica.pca_mean_, ica_read.pca_mean_)
        assert_array_equal(ica.pca_explained_variance_,
                           ica_read.pca_explained_variance_)
        assert_array_equal(ica._pre_whitener, ica_read._pre_whitener)

        # assert_raises(RuntimeError, ica_read.decompose_raw, raw)
        sources = ica.get_sources_raw(raw)
        sources2 = ica_read.get_sources_raw(raw)
        assert_array_almost_equal(sources, sources2)

        _raw1 = ica.pick_sources_raw(raw, exclude=[1])
        _raw2 = ica_read.pick_sources_raw(raw, exclude=[1])
        assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0])

    os.remove(test_ica_fname)
    # score funcs raw, with catch since "ties preclude exact" warning
    # XXX this should be fixed by a future PR...
    with warnings.catch_warnings(True) as w:
        sfunc_test = [ica.find_sources_raw(raw, target='EOG 061',
                score_func=n, start=0, stop=10)
                for n, f in score_funcs.items()]
    # score funcs raw

    # check lenght of scores
    [assert_true(ica.n_components_ == len(scores)) for scores in sfunc_test]

    # check univariate stats
    scores = ica.find_sources_raw(raw, score_func=stats.skew)
    # check exception handling
    assert_raises(ValueError, ica.find_sources_raw, raw,
                  target=np.arange(1))

    ## score funcs epochs ##
#.........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 sources_as_raw [as 别名]
def test_ica_additional():
    """Test additional functionality
    """
    stop2 = 500

    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)

    # 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), 'ica_test.fif')
    for cov in (None, test_cov):
        ica = ICA(noise_cov=cov, n_components=3, max_pca_components=4,
                  n_pca_components=4)
        ica.decompose_raw(raw, picks=picks, start=start, stop=stop2)
        sources = ica.get_sources_epochs(epochs)
        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])

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

        ica.n_pca_components = 2
        ica.save(test_ica_fname)
        ica_read = read_ica(test_ica_fname)
        assert_true(ica.n_pca_components ==
                    ica_read.n_pca_components)
        ica.n_pca_components = 4
        ica_read.n_pca_components = 4

        ica.exclude = []
        ica.save(test_ica_fname)
        ica_read = read_ica(test_ica_fname)

        assert_true(ica.ch_names == ica_read.ch_names)
        assert_true(isinstance(ica_read.info, Info))  # XXX improve later
        assert_true(np.allclose(ica.mixing_matrix_, ica_read.mixing_matrix_,
                                rtol=1e-16, atol=1e-32))
        assert_array_equal(ica.pca_components_,
                           ica_read.pca_components_)
        assert_array_equal(ica.pca_mean_, ica_read.pca_mean_)
        assert_array_equal(ica.pca_explained_variance_,
                           ica_read.pca_explained_variance_)
        assert_array_equal(ica._pre_whitener, ica_read._pre_whitener)

        # assert_raises(RuntimeError, ica_read.decompose_raw, raw)
        sources = ica.get_sources_raw(raw)
        sources2 = ica_read.get_sources_raw(raw)
        assert_array_almost_equal(sources, sources2)

        _raw1 = ica.pick_sources_raw(raw, exclude=[1])
        _raw2 = ica_read.pick_sources_raw(raw, exclude=[1])
        assert_array_almost_equal(_raw1[:, :][0], _raw2[:, :][0])

    os.remove(test_ica_fname)
    # check scrore funcs
    for name, func in score_funcs.items():
        if name in score_funcs_unsuited:
            continue
        scores = ica.find_sources_raw(raw, target='EOG 061', score_func=func,
                                      start=0, stop=10)
        assert_true(ica.n_components_ == len(scores))

    # check univariate stats
    scores = ica.find_sources_raw(raw, score_func=stats.skew)
    # check exception handling
    assert_raises(ValueError, ica.find_sources_raw, raw,
                  target=np.arange(1))

    params = []
    params += [(None, -1, slice(2), [0, 1])]  # varicance, kurtosis idx params
#.........这里部分代码省略.........