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commit 36f88de Merge: 824dbcc 7b70d0b Author: Thomas Samuel Binns <[email protected]> Date: Tue Oct 24 17:35:30 2023 +0200 Merge branch 'hackathon_2023' of https://github.com/tsbinns/mne-connectivity into hackathon_2023 commit 824dbcc Author: Thomas Samuel Binns <[email protected]> Date: Mon Oct 23 18:58:14 2023 +0200 refactor epochs functions commit 7b70d0b Author: Thomas Samuel Binns <[email protected]> Date: Tue Oct 24 17:34:19 2023 +0200 bug fix refactoring commit dd46076 Author: Thomas Samuel Binns <[email protected]> Date: Tue Oct 24 17:21:07 2023 +0200 bug fix refactoring commit 71fa86c Author: Thomas Samuel Binns <[email protected]> Date: Tue Oct 24 16:59:30 2023 +0200 bug fix refactoring commit 2ce29eb Author: Thomas Samuel Binns <[email protected]> Date: Tue Oct 24 16:44:02 2023 +0200 bug fix refactoring commit ffdf82f Author: Thomas Samuel Binns <[email protected]> Date: Tue Oct 24 14:39:34 2023 +0200 refactor new funcs commit 0c4d5c6 Author: Thomas Samuel Binns <[email protected]> Date: Tue Oct 24 14:26:36 2023 +0200 bug fix refactoring commit 3e93cea Author: Thomas Samuel Binns <[email protected]> Date: Tue Oct 24 11:55:24 2023 +0200 refactor new funcs commit 174efc7 Author: Thomas Samuel Binns <[email protected]> Date: Mon Oct 23 22:24:32 2023 +0200 refactor new funcs commit 5d5d74d Author: Thomas Samuel Binns <[email protected]> Date: Mon Oct 23 19:04:04 2023 +0200 refactor new funcs commit 014c22e Author: Thomas Samuel Binns <[email protected]> Date: Mon Oct 23 19:03:18 2023 +0200 refactor new funcs commit 6282e67 Author: Thomas Samuel Binns <[email protected]> Date: Mon Oct 23 18:58:14 2023 +0200 refactor new funcs
mne-tools · Oct 24, 2023 · 5bad5fb · 5bad5fb
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diff --git a/doc/api.rst b/doc/api.rst
@@ -47,6 +47,7 @@ on numpy array inputs.
    phase_slope_index
    vector_auto_regression
    spectral_connectivity_epochs
+   spectral_connectivity_epochs_multivariate
    spectral_connectivity_time
 
 Reading functions

diff --git a/examples/granger_causality.py b/examples/granger_causality.py
@@ -20,7 +20,7 @@
 
 import mne
 from mne.datasets.fieldtrip_cmc import data_path
-from mne_connectivity import spectral_connectivity_epochs
+from mne_connectivity import spectral_connectivity_epochs_multivariate
 
 ###############################################################################
 # Background
@@ -161,10 +161,10 @@
 indices_ba = (np.array([signals_b]), np.array([signals_a]))  # B => A
 
 # compute Granger causality
-gc_ab = spectral_connectivity_epochs(
+gc_ab = spectral_connectivity_epochs_multivariate(
     epochs, method=['gc'], indices=indices_ab, fmin=5, fmax=30,
     rank=(np.array([5]), np.array([5])), gc_n_lags=20)  # A => B
-gc_ba = spectral_connectivity_epochs(
+gc_ba = spectral_connectivity_epochs_multivariate(
     epochs, method=['gc'], indices=indices_ba, fmin=5, fmax=30,
     rank=(np.array([5]), np.array([5])), gc_n_lags=20)  # B => A
 freqs = gc_ab.freqs
@@ -262,10 +262,10 @@
 # %%
 
 # compute GC on time-reversed signals
-gc_tr_ab = spectral_connectivity_epochs(
+gc_tr_ab = spectral_connectivity_epochs_multivariate(
     epochs, method=['gc_tr'], indices=indices_ab, fmin=5, fmax=30,
     rank=(np.array([5]), np.array([5])), gc_n_lags=20)  # TR[A => B]
-gc_tr_ba = spectral_connectivity_epochs(
+gc_tr_ba = spectral_connectivity_epochs_multivariate(
     epochs, method=['gc_tr'], indices=indices_ba, fmin=5, fmax=30,
     rank=(np.array([5]), np.array([5])), gc_n_lags=20)  # TR[B => A]
 
@@ -317,7 +317,7 @@
 
 # %%
 
-gc_ab_60 = spectral_connectivity_epochs(
+gc_ab_60 = spectral_connectivity_epochs_multivariate(
     epochs, method=['gc'], indices=indices_ab, fmin=5, fmax=30,
     rank=(np.array([5]), np.array([5])), gc_n_lags=60)  # A => B
 
@@ -375,7 +375,7 @@
 # %%
 
 try:
-    spectral_connectivity_epochs(
+    spectral_connectivity_epochs_multivariate(
         epochs, method=['gc'], indices=indices_ab, fmin=5, fmax=30, rank=None,
         gc_n_lags=20, verbose=False)  # A => B
     print('Success!')

diff --git a/examples/mic_mim.py b/examples/mic_mim.py
@@ -25,7 +25,9 @@
 import mne
 from mne import EvokedArray, make_fixed_length_epochs
 from mne.datasets.fieldtrip_cmc import data_path
-from mne_connectivity import seed_target_indices, spectral_connectivity_epochs
+from mne_connectivity import (seed_target_indices,
+                              spectral_connectivity_epochs,
+                              spectral_connectivity_epochs_multivariate)
 
 ###############################################################################
 # Background
@@ -87,7 +89,7 @@
 target_names = [epochs.info['ch_names'][idx] for idx in targets]
 
 # multivariate imaginary part of coherency
-(mic, mim) = spectral_connectivity_epochs(
+(mic, mim) = spectral_connectivity_epochs_multivariate(
     epochs, method=['mic', 'mim'], indices=multivar_indices, fmin=5, fmax=30,
     rank=None)
 
@@ -290,7 +292,7 @@
 # %%
 
 indices = (np.array([[*seeds, *targets]]), np.array([[*seeds, *targets]]))
-gim = spectral_connectivity_epochs(
+gim = spectral_connectivity_epochs_multivariate(
     epochs, method='mim', indices=indices, fmin=5, fmax=30, rank=None,
     verbose=False)
 
@@ -342,7 +344,7 @@
 
 # %%
 
-(mic_red, mim_red) = spectral_connectivity_epochs(
+(mic_red, mim_red) = spectral_connectivity_epochs_multivariate(
     epochs, method=['mic', 'mim'], indices=multivar_indices, fmin=5, fmax=30,
     rank=([25], [25]))
 

diff --git a/mne_connectivity/__init__.py b/mne_connectivity/__init__.py
@@ -15,7 +15,9 @@
 from .effective import phase_slope_index
 from .envelope import envelope_correlation, symmetric_orth
 from .io import read_connectivity
-from .spectral import spectral_connectivity_time, spectral_connectivity_epochs
+from .spectral import (spectral_connectivity_time,
+                       spectral_connectivity_epochs,
+                       spectral_connectivity_epochs_multivariate)
 from .vector_ar import vector_auto_regression, select_order
 from .utils import (check_indices, check_multivariate_indices, degree,
                     seed_target_indices, seed_target_multivariate_indices)
diff --git a/mne_connectivity/spectral/__init__.py b/mne_connectivity/spectral/__init__.py
@@ -1,2 +1,3 @@
-from .epochs import spectral_connectivity_epochs
+from .epochs_bivariate import spectral_connectivity_epochs
+from .epochs_multivariate import spectral_connectivity_epochs_multivariate
 from .time import spectral_connectivity_time