[MRG] [BUG] [ENH] [WIP] Bug fixes and enhancements for time-resolved …

…spectral connectivity estimation (#104)

doc/authors.inc

@@ -7,3 +7,4 @@
 .. _Szonja Weigl: https://github.com/weiglszonja
 .. _Kenji Marshall: https://github.com/kenjimarshall
 .. _Sezan Mert: https://github.com/SezanMert
+.. _Santeri Ruuskanen: https://github.com/ruuskas

doc/conf.py

@@ -197,7 +197,8 @@
     'use_edit_page_button': False,
     'navigation_with_keys': False,
     'show_toc_level': 1,
-    'navbar_end': ['version-switcher', 'navbar-icon-links'],
+    'navbar_end': ['theme-switcher', 'version-switcher', 'navbar-icon-links'],
+    'secondary_sidebar_items': ['page-toc'],
 }
 # Custom sidebar templates, maps document names to template names.
 html_sidebars = {

doc/whats_new.rst

@@ -19,27 +19,35 @@ Here we list a changelog of MNE-connectivity.
 Version 0.5 (Unreleased)
 ------------------------
 
-...
+This version has major changes in :func:`mne_connectivity.spectral_connectivity_time`. Several bugs are fixed, and the
+function now computes static connectivity over time, as opposed to static connectivity over trials computed by  :func:`mne_connectivity.spectral_connectivity_epochs`.
 
 Enhancements
 ~~~~~~~~~~~~
 
-- 
+- Add the ``PLI`` and ``wPLI`` methods in :func:`mne_connectivity.spectral_connectivity_time` by `Santeri Ruuskanen`_ (:gh:`104`).
+- Improve the documentation of :func:`mne_connectivity.spectral_connectivity_time` by `Santeri Ruuskanen`_ (:gh:`104`).
+- Add the option to average connectivity across epochs and frequencies in :func:`mne_connectivity.spectral_connectivity_time` by `Santeri Ruuskanen`_ (:gh:`104`).
+- Select multitaper frequencies automatically in :func:`mne_connectivity.spectral_connectivity_time` similarly to :func:`mne_connectivity.spectral_connectivity_epochs` by `Santeri Ruuskanen`_ (:gh:`104`).
 
 Bug
 ~~~
 
-- 
+- When using the ``multitaper`` mode in :func:`mne_connectivity.spectral_connectivity_time`, average CSD over tapers instead of the complex signal by `Santeri Ruuskanen`_ (:gh:`104`).
+- Average over time when computing connectivity measures in :func:`mne_connectivity.spectral_connectivity_time` by `Santeri Ruuskanen`_ (:gh:`104`).
+- Fix support for multiple connectivity methods in calls to :func:`mne_connectivity.spectral_connectivity_time` by `Santeri Ruuskanen`_ (:gh:`104`).
+- Fix bug with the ``indices`` parameter in :func:`mne_connectivity.spectral_connectivity_time`, the behavior is now as expected by `Santeri Ruuskanen`_ (:gh:`104`).
+- Fix bug with parallel computation in :func:`mne_connectivity.spectral_connectivity_time`, add instructions for memory mapping in doc by `Santeri Ruuskanen`_ (:gh:`104`).
 
 API
 ~~~
 
-- 
+- Streamline the API of :func:`mne_connectivity.spectral_connectivity_time` with :func:`mne_connectivity.spectral_connectivity_epochs` by `Santeri Ruuskanen`_ (:gh:`104`).
 
 Authors
 ~~~~~~~
 
-* 
+* `Santeri Ruuskanen`_
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

environment.yml

@@ -1,4 +1,4 @@
-name: mne
+name: mne-connectivity
 channels:
 - conda-forge
 dependencies:
@@ -20,5 +20,5 @@ dependencies:
 - pyvista>=0.32
 - pyvistaqt>=0.4
 - pyqt!=5.15.3
-- mne
+- mne>=1.0
 - h5netcdf

mne_connectivity/conftest.py

@@ -151,6 +151,6 @@ def _check_skip_backend(name):
         if not has_imageio_ffmpeg():
             pytest.skip("Test skipped, requires imageio-ffmpeg")
     if name == 'pyvistaqt' and not _check_qt_version():
-        pytest.skip("Test skipped, requires PyQt5.")
+        pytest.skip("Test skipped, requires Python Qt bindings.")
     if name == 'pyvistaqt' and not has_pyvistaqt():
         pytest.skip("Test skipped, requires pyvistaqt")

mne_connectivity/spectral/epochs.py

@@ -859,6 +859,7 @@ def spectral_connectivity_epochs(data, names=None, method='coh', indices=None,
 
     See Also
     --------
+    mne_connectivity.spectral_connectivity_time
     mne_connectivity.SpectralConnectivity
     mne_connectivity.SpectroTemporalConnectivity
 
@@ -873,7 +874,9 @@ def spectral_connectivity_epochs(data, names=None, method='coh', indices=None,
     connectivity structure. Within each Epoch, it is assumed that the spectral
     measure is stationary. The spectral measures implemented in this function
     are computed across Epochs. **Thus, spectral measures computed with only
-    one Epoch will result in errorful values.**
+    one Epoch will result in errorful values and spectral measures computed
+    with few Epochs will be unreliable.** Please see
+    ``spectral_connectivity_time`` for time-resolved connectivity estimation.
 
     The spectral densities can be estimated using a multitaper method with
     digital prolate spheroidal sequence (DPSS) windows, a discrete Fourier
@@ -891,11 +894,11 @@ def spectral_connectivity_epochs(data, names=None, method='coh', indices=None,
         indices = (np.array([0, 0, 0]),    # row indices
                    np.array([2, 3, 4]))    # col indices
 
-        con_flat = spectral_connectivity(data, method='coh',
-                                         indices=indices, ...)
+        con = spectral_connectivity_epochs(data, method='coh',
+                                           indices=indices, ...)
 
-    In this case con_flat.shape = (3, n_freqs). The connectivity scores are
-    in the same order as defined indices.
+    In this case con.get_data().shape = (3, n_freqs). The connectivity scores
+    are in the same order as defined indices.
 
     **Supported Connectivity Measures**
 

mne_connectivity/spectral/tests/test_spectral.py

@@ -2,14 +2,8 @@
 from numpy.testing import (assert_allclose, assert_array_almost_equal,
                            assert_array_less)
 import pytest
-import warnings
-
-import mne
-from mne import (EpochsArray, SourceEstimate, create_info,
-                 make_fixed_length_epochs)
+from mne import (EpochsArray, SourceEstimate, create_info)
 from mne.filter import filter_data
-from mne.utils import _resource_path
-from mne_bids import BIDSPath, read_raw_bids
 
 from mne_connectivity import (
     SpectralConnectivity, spectral_connectivity_epochs,
@@ -478,15 +472,109 @@ def test_epochs_tmin_tmax(kind):
     assert len(w) == 1  # just one even though there were multiple epochs
 
 
-@pytest.mark.parametrize('method', ['coh', 'plv'])
+@pytest.mark.parametrize('method', ['coh', 'plv', 'pli', 'wpli'])
+@pytest.mark.parametrize(
+    'mode', ['cwt_morlet', 'multitaper'])
+@pytest.mark.parametrize('data_option', ['sync', 'random'])
+def test_spectral_connectivity_time_phaselocked(method, mode, data_option):
+    """Test time-resolved spectral connectivity with simulated phase-locked
+    data."""
+    rng = np.random.default_rng(0)
+    n_epochs = 5
+    n_channels = 3
+    n_times = 1000
+    sfreq = 250
+    data = np.zeros((n_epochs, n_channels, n_times))
+    if data_option == 'random':
+        # Data is random, there should be no consistent phase differences.
+        data = rng.random((n_epochs, n_channels, n_times))
+    if data_option == 'sync':
+        # Data consists of phase-locked 10Hz sine waves with constant phase
+        # difference within each epoch.
+        wave_freq = 10
+        epoch_length = n_times / sfreq
+        for i in range(n_epochs):
+            for c in range(n_channels):
+                phase = rng.random() * 10
+                x = np.linspace(-wave_freq * epoch_length * np.pi + phase,
+                                wave_freq * epoch_length * np.pi + phase,
+                                n_times)
+                data[i, c] = np.squeeze(np.sin(x))
+    # the frequency band should contain the frequency at which there is a
+    # hypothesized "connection"
+    freq_band_low_limit = (8.)
+    freq_band_high_limit = (13.)
+    cwt_freqs = np.arange(freq_band_low_limit, freq_band_high_limit + 1)
+    con = spectral_connectivity_time(data, method=method, mode=mode,
+                                     sfreq=sfreq, fmin=freq_band_low_limit,
+                                     fmax=freq_band_high_limit,
+                                     cwt_freqs=cwt_freqs, n_jobs=1,
+                                     faverage=True, average=True, sm_times=0)
+    assert con.shape == (n_channels ** 2, len(con.freqs))
+    con_matrix = con.get_data('dense')[..., 0]
+    if data_option == 'sync':
+        # signals are perfectly phase-locked, connectivity matrix should be
+        # a lower triangular matrix of ones
+        assert np.allclose(con_matrix,
+                           np.tril(np.ones(con_matrix.shape),
+                                   k=-1),
+                           atol=0.01)
+    if data_option == 'random':
+        # signals are random, all connectivity values should be small
+        # 0.5 is picked rather arbitrarily such that the obsolete wrong
+        # implementation fails
+        assert np.all(con_matrix) <= 0.5
+
+
+@pytest.mark.parametrize('method', ['coh', 'plv', 'pli', 'wpli'])
+@pytest.mark.parametrize(
+    'cwt_freqs', [[8., 10.], [8, 10], 10., 10])
+def test_spectral_connectivity_time_cwt_freqs(method, cwt_freqs):
+    """Test time-resolved spectral connectivity with int and float values for
+    cwt_freqs."""
+    rng = np.random.default_rng(0)
+    n_epochs = 5
+    n_channels = 3
+    n_times = 1000
+    sfreq = 250
+    data = np.zeros((n_epochs, n_channels, n_times))
+
+    # Data consists of phase-locked 10Hz sine waves with constant phase
+    # difference within each epoch.
+    wave_freq = 10
+    epoch_length = n_times / sfreq
+    for i in range(n_epochs):
+        for c in range(n_channels):
+            phase = rng.random() * 10
+            x = np.linspace(-wave_freq * epoch_length * np.pi + phase,
+                            wave_freq * epoch_length * np.pi + phase,
+                            n_times)
+            data[i, c] = np.squeeze(np.sin(x))
+    # the frequency band should contain the frequency at which there is a
+    # hypothesized "connection"
+    con = spectral_connectivity_time(data, method=method, mode='cwt_morlet',
+                                     sfreq=sfreq, fmin=np.min(cwt_freqs),
+                                     fmax=np.max(cwt_freqs),
+                                     cwt_freqs=cwt_freqs, n_jobs=1,
+                                     faverage=True, average=True, sm_times=0)
+    assert con.shape == (n_channels ** 2, len(con.freqs))
+    con_matrix = con.get_data('dense')[..., 0]
+
+    # signals are perfectly phase-locked, connectivity matrix should be
+    # a lower triangular matrix of ones
+    assert np.allclose(con_matrix, np.tril(np.ones(con_matrix.shape), k=-1),
+                       atol=0.01)
+
+
+@pytest.mark.parametrize('method', ['coh', 'plv', 'pli', 'wpli'])
 @pytest.mark.parametrize(
     'mode', ['cwt_morlet', 'multitaper'])
 def test_spectral_connectivity_time_resolved(method, mode):
     """Test time-resolved spectral connectivity."""
     sfreq = 50.
     n_signals = 3
     n_epochs = 2
-    n_times = 256
+    n_times = 1000
     trans_bandwidth = 2.
     tmin = 0.
     tmax = (n_times - 1) / sfreq
@@ -502,22 +590,21 @@ def test_spectral_connectivity_time_resolved(method, mode):
 
     # define some frequencies for cwt
     freqs = np.arange(3, 20.5, 1)
-    n_freqs = len(freqs)
 
     # run connectivity estimation
     con = spectral_connectivity_time(
-        data, freqs=freqs, method=method, mode=mode)
-    assert con.shape == (n_epochs, n_signals * 2, n_freqs, n_times)
+        data, sfreq=sfreq, cwt_freqs=freqs, method=method, mode=mode,
+        n_cycles=5)
+    assert con.shape == (n_epochs, n_signals ** 2, len(con.freqs))
     assert con.get_data(output='dense').shape == \
-        (n_epochs, n_signals, n_signals, n_freqs, n_times)
-
-    # average over time
-    conn_data = con.get_data(output='dense').mean(axis=-1)
-    conn_data = conn_data.mean(axis=-1)
+        (n_epochs, n_signals, n_signals, len(con.freqs))
 
     # test the simulated signal
     triu_inds = np.vstack(np.triu_indices(n_signals, k=1)).T
 
+    # average over frequencies
+    conn_data = con.get_data(output='dense').mean(axis=-1)
+
     # the indices at which there is a correlation should be greater
     # then the rest of the components
     for epoch_idx in range(n_epochs):
@@ -526,95 +613,6 @@ def test_spectral_connectivity_time_resolved(method, mode):
                    for idx, jdx in triu_inds)
 
 
-@pytest.mark.parametrize('method', ['coh', 'plv'])
-@pytest.mark.parametrize(
-    'mode', ['morlet', 'multitaper'])
-def test_time_resolved_spectral_conn_regression(method, mode):
-    """Regression test against original implementation in Frites.
-
-    To see how the test dataset was generated, see
-    ``benchmarks/single_epoch_conn.py``.
-    """
-    test_file_path_str = str(_resource_path(
-        'mne_connectivity.tests',
-        f'data/test_frite_dataset_{mode}_{method}.npy'))
-    test_conn = np.load(test_file_path_str)
-
-    # paths to mne datasets - sample ECoG
-    bids_root = mne.datasets.epilepsy_ecog.data_path()
-
-    # first define the BIDS path and load in the dataset
-    bids_path = BIDSPath(root=bids_root, subject='pt1', session='presurgery',
-                         task='ictal', datatype='ieeg', extension='.vhdr')
-    with warnings.catch_warnings():
-        warnings.simplefilter("ignore")
-        raw = read_raw_bids(bids_path=bids_path, verbose=False)
-    line_freq = raw.info['line_freq']
-
-    # Pick only the ECoG channels, removing the ECG channels
-    raw.pick_types(ecog=True)
-
-    # drop bad channels
-    raw.drop_channels(raw.info['bads'])
-
-    # only pick the first three channels to lower RAM usage
-    raw = raw.pick_channels(raw.ch_names[:3])
-
-    # Load the data
-    raw.load_data()
-
-    # Then we remove line frequency interference
-    raw.notch_filter(line_freq)
-
-    # crop data and then Epoch
-    raw_copy = raw.copy()
-    raw = raw.crop(tmin=0, tmax=4, include_tmax=False)
-    epochs = make_fixed_length_epochs(raw=raw, duration=2., overlap=1.)
-
-    ######################################################################
-    # Perform basic test to match simulation data using time-resolved spec
-    ######################################################################
-    # compare data to original run using Frites
-    freqs = [30, 90]
-
-    # mode was renamed in mne-connectivity
-    if mode == 'morlet':
-        mode = 'cwt_morlet'
-    conn = spectral_connectivity_time(
-        epochs, freqs=freqs, n_jobs=1, method=method, mode=mode)
-
-    # frites only stores the upper triangular parts of the raveled array
-    row_triu_inds, col_triu_inds = np.triu_indices(len(raw.ch_names), k=1)
-    conn_data = conn.get_data(output='dense')[
-        :, row_triu_inds, col_triu_inds, ...]
-    assert_array_almost_equal(conn_data, test_conn)
-
-    ######################################################################
-    # Give varying set of frequency bands and frequencies to perform cWT
-    ######################################################################
-    raw = raw_copy.crop(tmin=0, tmax=10, include_tmax=False)
-    ch_names = epochs.ch_names
-    epochs = make_fixed_length_epochs(raw=raw, duration=5, overlap=0.)
-
-    # sampling rate of my data
-    sfreq = raw.info['sfreq']
-
-    # frequency bands of interest
-    fois = np.array([[4, 8], [8, 12], [12, 16], [16, 32]])
-
-    # frequencies of Continuous Morlet Wavelet Transform
-    freqs = np.arange(4., 32., 1)
-
-    # compute coherence
-    cohs = spectral_connectivity_time(
-        epochs, names=None, method=method, indices=None,
-        sfreq=sfreq, foi=fois, sm_times=0.5, sm_freqs=1, sm_kernel='hanning',
-        mode=mode, mt_bandwidth=None, freqs=freqs, n_cycles=5)
-    assert cohs.get_data(output='dense').shape == (
-        len(epochs), len(ch_names), len(ch_names), len(fois), len(epochs.times)
-    )
-
-
 def test_save(tmp_path):
     """Test saving results of spectral connectivity."""
     rng = np.random.RandomState(0)