[ENH, WIP] Multivariate connectivity methods (imaginary coherence and Granger causality)

mne_connectivity/__init__.py

@@ -11,10 +11,13 @@
 from .base import (Connectivity, EpochConnectivity, EpochSpectralConnectivity,
                    EpochSpectroTemporalConnectivity, EpochTemporalConnectivity,
                    SpectralConnectivity, SpectroTemporalConnectivity,
-                   TemporalConnectivity)
+                   TemporalConnectivity, MultivariateSpectralConnectivity,
+                   MultivariateSpectroTemporalConnectivity)
 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,
+                       multivariate_spectral_connectivity_epochs)
 from .vector_ar import vector_auto_regression, select_order
-from .utils import check_indices, degree, seed_target_indices
+from .utils import (check_indices, degree, seed_target_indices,
+                    multivariate_seed_target_indices)

mne_connectivity/io.py

@@ -6,10 +6,12 @@
 from .base import (Connectivity, EpochConnectivity, EpochSpectralConnectivity,
                    EpochSpectroTemporalConnectivity, EpochTemporalConnectivity,
                    SpectralConnectivity, SpectroTemporalConnectivity,
-                   TemporalConnectivity)
+                   TemporalConnectivity, BaseMultivariateConnectivity,
+                   MultivariateSpectralConnectivity,
+                   MultivariateSpectroTemporalConnectivity)
 
 
-def _xarray_to_conn(array, cls_func):
+def _xarray_to_conn(array, cls_func, restore_attrs):
     """Create connectivity class from xarray.
 
     Parameters
@@ -18,6 +20,10 @@ def _xarray_to_conn(array, cls_func):
         Xarray containing the connectivity data.
     cls_func : Connectivity class
         The function of the connectivity class to use.
+    restore_attrs : bool
+        Whether or not to restore the nature of attributes of the class that
+        were modified to enable saving with HDF5 (only relevant for multivariate
+        connectivity classes).
 
     Returns
     -------
@@ -57,6 +63,11 @@ def _xarray_to_conn(array, cls_func):
     conn = cls_func(
         data=data, names=names, metadata=metadata, **array.attrs
     )
+
+    # restore attrs modified for saving (for multivariate connectivity only)
+    if restore_attrs:
+        conn._restore_attrs()
+
     return conn
 
 
@@ -97,10 +108,20 @@ def read_connectivity(fname):
         'EpochConnectivity': EpochConnectivity,
         'EpochTemporalConnectivity': EpochTemporalConnectivity,
         'EpochSpectralConnectivity': EpochSpectralConnectivity,
-        'EpochSpectroTemporalConnectivity': EpochSpectroTemporalConnectivity
+        'EpochSpectroTemporalConnectivity': EpochSpectroTemporalConnectivity,
+        'MultivariateSpectralConnectivity': MultivariateSpectralConnectivity,
+        'MultivariateSpectroTemporalConnectivity': \
+            MultivariateSpectroTemporalConnectivity
     }
     cls_func = conn_cls[data_structure_name]
 
+    # checks whether ragged attrs of the class padded for saving need to be
+    # restored (so far only the case for multivariate connectivity)
+    if issubclass(cls_func, BaseMultivariateConnectivity):
+        restore_attrs = True
+    else:
+        restore_attrs = False
+
     # get the data as a new connectivity container
-    conn = _xarray_to_conn(conn_da, cls_func)
+    conn = _xarray_to_conn(conn_da, cls_func, restore_attrs)
     return conn

mne_connectivity/spectral/__init__.py

@@ -1,2 +1,3 @@
 from .epochs import spectral_connectivity_epochs
+from .epochs_multivariate import multivariate_spectral_connectivity_epochs
 from .time import spectral_connectivity_time