Code

Multitaper psd segmentation#556

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Moritz-Alexander-Kern merged 154 commits intoNeuralEnsemble:masterNeuralEnsemble/elephant:masterfrom INM-6:hotfix/multitaper_psd_segmentationINM-6/elephant:hotfix/multitaper_psd_segmentationCopy head branch name to clipboardJun 6, 2023

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Commits

Commits on Jan 11, 2021

• Initial commit multitaper psd estimate

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• Fix wrong variable

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• Fix minor bug

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• Fix variable name

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• Fix typos

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Commits on Jan 17, 2021

• Add functionality to generate test data

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• Use rfftfreq to generate frequencies instead of fftfreq

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• Add example for comparison for multitaper and welch

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Commits on Jan 25, 2021

• Refactor NW -> nw

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• Refactor NW -> nw in the test section

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Commits on Feb 12, 2021

• Add functionality to multitaper to handle frequency resolution

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• Remove subsampling

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• Initial commit for multitaper_psd tests

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Commits on Feb 15, 2021

• Merge branch 'master' into feature/multitaper_psd_estimate

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• Run all tests in test_spectral.py

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• Tests for multitaper_psd (copied/adapted from welch_psd)

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Commits on Feb 22, 2021

• Added quantities and their handling to multitaper psd

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• Remove code doubling for one/multi dim case, minor edits

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• Clean up examples

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• Correct test, remove wrong test

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• Fixed PEP8 issues

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• Removed if __name__ == '__main__'

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• multitaper_psd -> psd refactor

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Commits on Apr 16, 2021

• Refactor frequency_resolution -> peak_resolution

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• Refactor frequency_resolution -> peak_resolution in test_spectral.py

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• Added a test comparing multitaper_psd against nitime multitaper implementation

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Commits on May 28, 2021

• WIP multitaper cross spectrum

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Commits on Jun 18, 2021

• Added multitaper_coherence draft function

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• Removed the line regarding None for peak_resolution

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• Added a note regarding parameter hierarchy and a line of code to ensure that peak_resolution is the primary parameter.

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• Refactor slepain_fcts -> slepian_fcts

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• Added a comment that sym=False in dpss is used for spectral analysis

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• Changed elif to if for the second num_tapers check

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• Added a comment regarding broadcasting if data has more than 1 dim

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• Adjusted comparison to nitime to use both rtol and atol

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• Changed num_tapers to be of type int (not int64)

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• Added tests for peak_resolution, num_tapers and nw parameter hierarchy

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Commits on Jul 2, 2021

• [WIP] multitaper_cross_spectrum and multitaper_coherence clean up

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Commits on Oct 1, 2021

• Fix multiapter coherence, add return_onsided parameter

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• Initial commit multitaper psd estimate

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  e0bb3a7

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• Fix wrong variable

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  9b6ec18

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• Fix minor bug

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• Fix variable name

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• Fix typos

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• Improve memory efficiency of _create_sparse_matrix in BinnedSpikeTrain class (NeuralEnsemble#395)

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• Add functionality to generate test data

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• Use rfftfreq to generate frequencies instead of fftfreq

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• Add example for comparison for multitaper and welch

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• Joint-ISI dithering: fixed a bug regarding first ISI bin (NeuralEnsemble#396)

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• Refactor NW -> nw

  

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• Refactor NW -> nw in the test section

  

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• CUDA accelerated ASSET (NeuralEnsemble#351)

  

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• Bin-Shuffling: reimplemented the continuos time version (NeuralEnsemble#397)

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• Account for unidirectional spiketrain->segment links in synchrofact deletion (NeuralEnsemble#398)

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• Speed up bin shuffling (NeuralEnsemble#400)

  

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• Memory efficient and faster implementation of ASSET pmat analytical (NeuralEnsemble#399)

  

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• missing comma in BibTeX entry (NeuralEnsemble#401)

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• Add functionality to multitaper to handle frequency resolution

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• Remove subsampling

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• Initial commit for multitaper_psd tests

  

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• Run all tests in test_spectral.py

  

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  6dc83e9

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• Tests for multitaper_psd (copied/adapted from welch_psd)

  

  rjurkus

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• Added quantities and their handling to multitaper psd

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• Remove code doubling for one/multi dim case, minor edits

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• Clean up examples

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• Correct test, remove wrong test

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• Fixed PEP8 issues

  

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• Removed if __name__ == '__main__'

  

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• multitaper_psd -> psd refactor

  

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• Refactor frequency_resolution -> peak_resolution

  

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• Refactor frequency_resolution -> peak_resolution in test_spectral.py

  

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• Added a test comparing multitaper_psd against nitime multitaper implementation

  

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• Removed the line regarding None for peak_resolution

  

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• Added a note regarding parameter hierarchy and a line of code to ensure that peak_resolution is the primary parameter.

  

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• Refactor slepain_fcts -> slepian_fcts

  

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• Added a comment that sym=False in dpss is used for spectral analysis

  

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• Changed elif to if for the second num_tapers check

  

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• Added a comment regarding broadcasting if data has more than 1 dim

  

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• Adjusted comparison to nitime to use both rtol and atol

  

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• Changed num_tapers to be of type int (not int64)

  

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  a7d7078

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• Added tests for peak_resolution, num_tapers and nw parameter hierarchy

  

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  85e4868

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• Merge branch 'feature/multitaper_psd_estimate' of github.com:INM-6/elephant into feature/multitaper_psd_estimate

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• Implementation of multitaper cross spectrum

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• Merge branch 'feature/multitaper_cross_spectrum' of github.com:INM-6/elephant into feature/multitaper_cross_spectrum

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Commits on Oct 4, 2021

• Take real part to avoid warning

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Commits on Oct 7, 2021

• Add segmentation of signal to multitaper_psd

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• Merge branch 'feature/multitaper_psd_estimate_segments' into feature/multitaper_cross_spectrum_segments

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• Add segmentation to multitaper_cross_spectrum, adapt multiatper_coherence

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• Correct adding new axis

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• Merge branch 'feature/multitaper_psd_estimate_segments' into feature/multitaper_cross_spectrum_segments

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• Remove printing number of tapers

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• Merge branch 'feature/multitaper_psd_estimate_segments' into feature/multitaper_cross_spectrum_segments

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• Remove printing functions

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Commits on Oct 8, 2021

• Add frequency resolution to multiatper_psd

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Commits on Nov 3, 2021

• Code factor issue fix (else is not necessary)

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• Fixed a typo in multitaper_psd docstring

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• Consistent language and formatting in Raises section of multitaper_psd docstring

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• Fixed a typo in a comment of multitaper_psd, also:

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Commits on Nov 5, 2021

• Update docstring peak_resolution

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• Removed basic Raises section entries

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Commits on Nov 16, 2021

• Merge branch 'feature/multitaper_psd_estimate' into feature/multitaper_cross_spectrum

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• Merge branch 'feature/multitaper_cross_spectrum_segments' into feature/multitaper_cross_spectrum

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• Add proper segementation to cross spectrum estimate

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• Correct checks

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Commits on Dec 9, 2021

• Updated test_spectral.py test_multitaper_psd_against_nitime to download data from the elephant-data repo (using test_spike_train_synchrony.py and test_unitary_event_analysis.py approach)

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Commits on Dec 10, 2021

• Restore test_spectral.py to the version before git-annex commit

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Commits on Nov 3, 2022

• Merge current master

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• Update docstrings of spectral.py

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Commits on Nov 4, 2022

• Add unittests for cross-spectrum, start unit tests for coherence

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Commits on Nov 8, 2022

• Add unit tests, clean up

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• Fixed the intermittently failing test_multitaper_cohere_no_cohere

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Commits on Nov 10, 2022

• Applied the frequency_resolution parameter in multitaper_coherence()

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Commits on Nov 16, 2022

• Fixed the intermittently failing test_multitaper_cross_spectrum_behavior

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Commits on Nov 18, 2022

• Added missing exception tests in test_multitaper_cross_spectrum_errors

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• Added three unit tests

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• Removed an unnecessary conditional statement

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Commits on Nov 23, 2022

• Fixed tests

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• Rearranged tests

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Commits on Nov 24, 2022

• Added new functions to the documentation

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• Fixed docstring

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Commits on Nov 28, 2022

• Replaced the intermittently failing test fix with a frequency domain approach

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• Merge branch 'master' into feature/multitaper_cross_spectrum

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Commits on Jan 17, 2023

• Addressed part of Junji's comments and included his suggestions

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• Replace with

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Commits on Jan 20, 2023

• Addressed yet another part of Junji's comments

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• Merge branch 'feature/multitaper_cross_spectrum' of https://github.com/INM-6/elephant into feature/multitaper_cross_spectrum

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Commits on Jan 24, 2023

• Start separation of multitaper functions and segmentation functions

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Commits on Jan 27, 2023

• First version outsourced segmentation

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• Continued implementation of separated segmentation function

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• Included overlap parameter in _segmented_apply_func call;

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Commits on Jan 31, 2023

• Attach units in mutlitaper_cross_spectrum and the segmented version; tapered_signals should not use signals, but the underlying and modified numpy array

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• Add check for units clause attaching units, add documentation

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• signal -> signals

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• Updated tests for multitaper_cross_spectrum; Added segmented_multitaper_cross_spectrum test case

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• Update documnetation

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• Merge branch 'feature/multitaper_cross_spectrum' of github.com:INM-6/elephant into feature/multitaper_cross_spectrum

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• Correct bug regarding zero-padding signal with overlap in segmentation

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• Added one-sided vs two-sided spectrum test to the segmented_multitaper_cross_spectrum test case (copied from multitaper_cross_spectrum test case)

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• Removed if __name__ = '__main__' from the spectral.py

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• Added a parameter hierarchy test to the segmented_multitaper_cross_spectrum test case

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• Added a basic overlap test

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Commits on Feb 1, 2023

• Edited parameter hierarchy note

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Commits on Feb 3, 2023

• Fixed the signal stacking in case of AnalogSignal in multitaper_coherence

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• Moved numpy array extraction from AnalogSignal to the segmented_multitaper_cross_spectrum

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• Added an input type test (AnalogSignal vs np.ndarray) to the Multitaper Coherence test case

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Commits on Feb 10, 2023

• Addressed the majority of the comments

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• Fixed default value lines in docstrings

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Commits on Feb 13, 2023

• Added segmented_multitaper_cross_spectrum to autosummary and __all__;

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Commits on Feb 14, 2023

• Fixed documentation and added missing bits to the docstrings

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Commits on Feb 17, 2023

• Merge remote-tracking branch 'origin/feature/multitaper_cross_spectrum' into hotfix/multitaper_psd_segmentation

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• Initial commit for separating segmentation from multitaper_psd [WIP]

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Commits on Feb 27, 2023

• Merge remote-tracking branch 'origin/master' into hotfix/multitaper_psd_segmentation

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Commits on Apr 5, 2023

• Extended the segmented multitaper psd test case with a parameter hierarchy test

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• Removed duplicated code in multitaper_psd

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