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[ENH] Multiple improvements to spectral_connectivity_time #113
Commits on Aug 31, 2022
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FIX: compute connectivity over multiple tapers when mode='multitaper'…
…, 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
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require MNE-Python 1.0 or newer due to breaking changes in mne.time_f…
…requency.tfr_array_multitaper
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Commits on Sep 1, 2022
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update docstring: connectivity is not averaged over Epochs by default
Co-authored-by: Adam Li <[email protected]>
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Co-authored-by: Adam Li <[email protected]>
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update docstring: faverage is False by default
Co-authored-by: Adam Li <[email protected]>
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update docstring: lower bound of frequency range for connectivity com…
…putation may be None Co-authored-by: Britta Westner <[email protected]>
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update docstring: fmax may be None
Co-authored-by: Britta Westner <[email protected]>
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Commits on Sep 2, 2022
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Merge branch 'spectral_time' of github.com:ruuskas/mne-connectivity i…
…nto spectral_time_hypyp
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Commits on Sep 5, 2022
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fix bug with indices: connectivity is now computed correctly between …
…specified indices when set
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Commits on Sep 7, 2022
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Commits on Sep 12, 2022
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Commits on Sep 22, 2022
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Change block_size default to 1
This change will minimize memory usage by default.
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Add documentation for block_size
Add a short description for the block_size parameter to allow users to better understand the memory usage of the spectral_connectivity_time function.
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Change for more useful variable names
Improve the readability of code by shortening variable names in pairwise_pli.
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Commits on Oct 5, 2022
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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.
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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.
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Added a note on memory mapping in the docstring of spectral_connectivity_time. Corrected some typos and inconsistent backticks.
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Removed redundant comments, clarified and fixed typos.
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Commits on Oct 16, 2022
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Commits on Oct 17, 2022
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Merge branch 'spectral_time' of github.com:ruuskas/mne-connectivity i…
…nto spectral_connectivity_time_pairwise
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Commits on Oct 19, 2022
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Co-authored-by: Adam Li <[email protected]>
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Co-authored-by: Adam Li <[email protected]>
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Add clear reference to MNE-Python functions. Co-authored-by: Adam Li <[email protected]>
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Add some comments to clarify the new test case for time-resolved spectral connectivity.
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Merge branch 'spectral_time' of github.com:ruuskas/mne-connectivity i…
…nto spectral_connectivity_time_pairwise
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Commits on Oct 28, 2022
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Add the corrected imaginary Phase-Locking-Value into the list of available connectivity metrics.
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Commits on Oct 31, 2022
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All connectivity measures are now computed with only a single computation of pairwise cross spectrum.
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Commits on Nov 1, 2022
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Add the option to specify freqs in all modes
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.
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Commits on Nov 2, 2022
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Add connectivity with Hilbert transform
Add a new function spectral_connectivity_time_hilbert, which computes connectivity on frequency bands using Hilbert transform on FIR-filtered data.
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Commits on Nov 9, 2022
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Co-authored-by: Adam Li <[email protected]>
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Co-authored-by: Adam Li <[email protected]>
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DOC: Add note on memory mapping
Co-authored-by: Adam Li <[email protected]>
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Revised documentation of spectral_connectivity_time.
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BUG: Fix 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.
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Commits on Nov 10, 2022
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Commits on Nov 14, 2022
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Compute weighted average over CSD
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.
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Add option to use part of signal as padding
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.
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Commits on Nov 15, 2022
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Update the docstring of spectral_connectivity_time
Made the docstring more stylish, removed unnecessary things and added better compliance with MNE-Python style guidelines.
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The _spectral_connectivity function doesn't need defaults as these are already spelled out in the main spectral_connectivity_time function signature.
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Commits on Nov 17, 2022
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Commits on Nov 18, 2022
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Revert "Add connectivity with Hilbert transform"
This reverts commit 42db712.
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Commits on Nov 24, 2022
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Sym is not a parameter of dpss_windows. (But is one of the underlying scipy.signal.dpss)
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Only show progress bar if verbosity level is DEBUG
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.
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