…, then average

FIX: add working support for computation of multiple connectivity metrics at once, as indicated by existing docstring

FIX: correct calculation of PLV and coherence connectivity metrics

FIX: block_size parameter now actually corresponds to the size of blocks instead of number of blocks

ENH: add PLI and wPLI connectivity metrics

ENH: improve docstring and typechecks in code

ENH: streamline the public API with mne_connectivity.spectral_connectivity_epochs

ENH: enable averaging connectivity results over frequencies and epochs

…requency.tfr_array_multitaper

Co-authored-by: Adam Li <[email protected]>

Co-authored-by: Adam Li <[email protected]>

Co-authored-by: Adam Li <[email protected]>

…putation may be None

Co-authored-by: Britta Westner <[email protected]>

Co-authored-by: Britta Westner <[email protected]>

…nto spectral_time_hypyp

…specified indices when set

This change will minimize memory usage by default.

Add a short description for the block_size parameter to allow users to
better understand the memory usage of the spectral_connectivity_time
function.

Improve the readability of code by shortening variable names in
pairwise_pli.

Remove the regression test which tests against the spectral connectivity
 implementation in frites. The implementation in frites is erroneous,
 and therefore we should not test against it.

The block_size parameter is not useful, as testing shows that running
the computation in blocks of epochs does not have a meaningful effect on
 the speed of computation, but significantly increases memory usage.

Added a note on memory mapping in the docstring of
spectral_connectivity_time. Corrected some typos and inconsistent
backticks.

Removed redundant comments, clarified and fixed typos.

…nto spectral_connectivity_time_pairwise

Co-authored-by: Adam Li <[email protected]>

Co-authored-by: Adam Li <[email protected]>

Co-authored-by: Adam Li <[email protected]>

Add clear reference to MNE-Python functions.

Co-authored-by: Adam Li <[email protected]>

Add some comments to clarify the new test case for time-resolved
spectral connectivity.

…nto spectral_connectivity_time_pairwise

Add the corrected imaginary Phase-Locking-Value into the list of
available connectivity metrics.

All connectivity measures are now computed with only a single
computation of pairwise cross spectrum.

In some scenarios, users might want to specify the frequencies for
time-frequency decomposition also when using multitapering. These
changes allow users to specify the 'freqs' parameter to override the
automatically determined frequencies.

Add a new function spectral_connectivity_time_hilbert, which computes
connectivity on frequency bands using Hilbert transform on FIR-filtered
data.

Co-authored-by: Adam Li <[email protected]>

Co-authored-by: Adam Li <[email protected]>

Co-authored-by: Adam Li <[email protected]>

Revised documentation of spectral_connectivity_time.

Spectral connectivity computation failed if cwt_freqs was only a single
number or an array with a single entry due to invalid array slicing.

Fixed by incrementing the upper bound of the slice by one when
computing the average in a frequency band.

Compute a weighted average of the tapered cross spectra when using
the multitaper mode. Weighting is
derived from the concentration ratios between the DPSS windows.

This adds the option to use the edges of the signal at each epoch as
padding. The purpose of this is to avoid edge effects generated by the
time-frequency transformation methods.

Made the docstring more stylish, removed unnecessary things and
added better compliance with MNE-Python style guidelines.

The _spectral_connectivity function doesn't need defaults as these are
already spelled out in the main spectral_connectivity_time function
signature.

This reverts commit 42db712.

Sym is not a parameter of dpss_windows. (But is one of the underlying
scipy.signal.dpss)

This change will skip the rendering of the connectivity computation
progress bar if the logging level is not DEBUG. This is in line with
MNE-Python, where progress bars are not shown at INFO or higher logging
levels. Rendering the progress bar regardless of logging levels has the
potential to cause unnecessary clutter in users' log files.

Add a better description of the method + style nitpicks.