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Calculate spike train auto-correlation time ('timescale') #266

Merged
merged 7 commits into from
Nov 8, 2019
Merged

Calculate spike train auto-correlation time ('timescale') #266

merged 7 commits into from
Nov 8, 2019

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AlexVanMeegen
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Hey!

This PR provides an implementation to calculate the auto-correlation time of a binned spike train. The definition of the auto-correlation time is ambiguous, here the definition used in [1, 2] is implemented because the square in the integral (see docstring) reduces the influence of noise due to finite observation times.

The implementation was joint work with @morales-gregorio.

Cheers,
Alex

[1] Wieland, S., Bernardi, D., Schwalger, T., & Lindner, B. (2015). Slow fluctuations in recurrent networks of spiking neurons. Physical Review E, 92(4), 040901.
[2] van Meegen, A., & van Albada, S. J. (2019). A Microscopic Theory of Intrinsic Timescales in Spiking Neural Networks. arXiv preprint arXiv:1909.01908.

@pep8speaks
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pep8speaks commented Oct 31, 2019 •
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Hello @AlexVanMeegen! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2019-11-07 16:37:36 UTC

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coveralls commented Oct 31, 2019 •
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Coverage Status

Coverage increased (+0.03%) to 83.024% when pulling bf76eff on AlexVanMeegen:feature_timescale into 5b5a023 on NeuralEnsemble:master.

@AlexVanMeegen
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Mmm, should I turn the docstrings into raw strings to satisfy PEP8?

dizcza
dizcza reviewed Nov 7, 2019
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Finally, I've found time to take a closer look.
Besides my comments, please fix pep issues. You can do this with autopep8 command line.
We can also meet and discuss the changes as well.

And don't forget to add yourself and Aitor to the authors list, if you're not there already!

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@dizcza
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dizcza commented Nov 7, 2019

Mmm, should I turn the docstrings into raw strings to satisfy PEP8?

Maybe, it requires two slashes: \\tau_\\mathrm{max}

@AlexVanMeegen
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AlexVanMeegen commented Nov 7, 2019 •
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Maybe, it requires two slashes: \tau_\mathrm{max}

The two slashes are causing PEP8 to complain. The only way to resolve this is to turn the strings into raw strings, that way I can get rid of the double slashes (it does not interpret them anymore as escape sequences).

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Here you go, @dizcza, new things to check ;)

dizcza
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Regarding the docstring, your solution works, I've checked. And since I don't know an alternative solution that does not put ugly r in the docs prefix and yet does not trigger pep8 complaints, let's use it.

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@dizcza dizcza merged commit 2967dac into NeuralEnsemble:master Nov 8, 2019
@AlexVanMeegen AlexVanMeegen deleted the feature_timescale branch November 8, 2019 16:45
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Thanks for the review!

@AlexVanMeegen AlexVanMeegen mentioned this pull request Nov 11, 2019
Merged
pbouss pushed a commit to INM-6/elephant that referenced this pull request Nov 25, 2019
Squashed commit of the following:
4e55c82 
commit 59e6412
Author: pbouss <[email protected]>
Date:   Wed Nov 20 09:46:54 2019 +0100

    Feature/spade duration (NeuralEnsemble#263)

    * Corrected error message

    * Doc. for Holm-Bonferroni

    * Changed calculation of duration for output of patterns

    * fixed calculation of duration for the signature

    * Pass spectrum to concepts_to_output function

    * Bug fixed in vairable assignment: concept

commit de077d6
Author: Danylo Ulianych <[email protected]>
Date:   Tue Nov 19 16:17:52 2019 +0100

    Use fftconvolve instead of np.correlate in cross_correlation_histogram (NeuralEnsemble#273)

    * cch np.correlate -> fftconvolve

    * moved internal functions in cross_correlation_histogram to a separate class

    * added BinnedSpikeTrain.get_num_of_spikes() function

    * added BinnedSpikeTrain.binarize() function

commit 059ccf5
Author: pbouss <[email protected]>
Date:   Fri Nov 15 16:24:58 2019 +0100

    Homogeneous Poisson Process with refr. period (NeuralEnsemble#261)

commit f378f07
Author: Alexander van Meegen <[email protected]>
Date:   Tue Nov 12 10:23:29 2019 +0100

    Feature timescale (NeuralEnsemble#271)

    * Implementation of timescale calculation

    * Use cross_corr_coef of CCH function

    * Check that tau_max is an integer multiple of binsize

commit 82f307f
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 11:09:44 2019 +0100

    fixed BinnedSpikeTrain.bin_edges property (NeuralEnsemble#257)

    * fixed BinnedSpikeTrain.bin_edges property

    * bin_edges: include t_stop if spiketrain duration is divisible by binsize

    * BinnedSpikeTrain: warn if binning discards the spikes in the last (excluded) bin

    * reuse is_binary func from utility.py

commit bd684f5
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 10:14:34 2019 +0100

    Refactored unitary event (NeuralEnsemble#251)

    * completely removed misleading N arg - num. of neurons, which is always extracted from the data

    * fixed inverse_hash_from_pattern for long N > int64; added test_hash_inverse_longpattern

    * UE: deprecation warning

commit 2967dac
Author: Alexander van Meegen <[email protected]>
Date:   Fri Nov 8 16:38:27 2019 +0100

    Calculate spike train auto-correlation time ('timescale') (NeuralEnsemble#266)

    * Implementation of timescale calculation

commit 092d2fb
Author: Michael Denker <[email protected]>
Date:   Fri Nov 8 12:33:32 2019 +0100

    Added a simplified to correctly handle division with Compound Units (NeuralEnsemble#270)

    .magnitude -> .simplified.magnitude

commit 5dfa042
Author: Danylo Ulianych <[email protected]>
Date:   Thu Oct 31 15:54:30 2019 +0100

    elephant v0.6.4 [workshop] (NeuralEnsemble#268)

commit 5b5a023
Author: Danylo Ulianych <[email protected]>
Date:   Tue Oct 22 16:10:16 2019 +0200

    neo v0.8.0 compatible (NeuralEnsemble#256)

    * fixes for neo v0.8.0

    * upd array_annotation comment

    * added todo for neo empty array_annotations

commit eac914c
Author: PaulinaDabrowska <[email protected]>
Date:   Tue Oct 22 16:09:41 2019 +0200

    Improved doc string of covariance() and corrcoef() (NeuralEnsemble#260)

    * corrected explanation of the formula used in corrcoef and covariance (in the doc string)

    * pep8

commit 434cacd
Author: Robin Gutzen <[email protected]>
Date:   Mon Oct 21 13:56:38 2019 +0200

    keep array_annotations in the output of signal_processing functions (NeuralEnsemble#258)

    * pass array_annotations on to output of signal_processing functions

    * test keep array_annotations for zscore, butter, hilbert

commit 15acc90
Author: Danylo Ulianych <[email protected]>
Date:   Thu Oct 17 12:19:51 2019 +0200

    removed unused debug code in spade/fast_fca (NeuralEnsemble#249)

    * removed dead code
    * small speedup

commit ce9e7ac
Author: Björn Müller <[email protected]>
Date:   Wed Oct 16 10:25:09 2019 +0200

    Performance and API enhancement for STTC (NeuralEnsemble#244)

    * Speedup for STTC
    * Implemented spike search in other sptr with numpy search

    Memory complexity: O(max(n1, n2)) (exactly max(n1, n2) is used
    additionally at peak)
    Runtime complexity: O(max(n1, n2)*log(max(n1, n2))), because search
    happens n1 times with log(n2) for binary search (or n2 times with
    log(n1))

commit a833a96
Author: Alessandra Stella <[email protected]>
Date:   Wed Oct 9 15:21:41 2019 +0200

    [spade] fixed the calculation of the duration of a pattern in the output (NeuralEnsemble#254)

    * fixed the calculation of the duration of a pattern, in the output of spade. Previously, the calculation of the pattern duration was not always correct, depending on the order of lags and neurons. We fixed the bug by accounting the duration independently from the order of neurons;
    * added raise ValueErrors in code when the output_format is not one of the two parameters allowed
    * fixed bug of undefined spectrum type when running spade without surrogates (only FIM)

commit c78af7e
Author: Alessandra Stella <[email protected]>
Date:   Thu Sep 12 16:15:43 2019 +0200

    Updated authors list - alessandra and peter
pbouss pushed a commit to INM-6/elephant that referenced this pull request Dec 3, 2019
Squashed commit of the following:
a3800b1 
commit b116804
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 25 12:31:36 2019 +0100

    Fast covariance() and Pearson corrcoef() (NeuralEnsemble#274)

    clarified the difference in the implementation of CrossCorrHist.cross_corr_coef() and the reference book "Analysis of parallel spike trains", 2010

commit 59e6412
Author: pbouss <[email protected]>
Date:   Wed Nov 20 09:46:54 2019 +0100

    Feature/spade duration (NeuralEnsemble#263)

    * Corrected error message

    * Doc. for Holm-Bonferroni

    * Changed calculation of duration for output of patterns

    * fixed calculation of duration for the signature

    * Pass spectrum to concepts_to_output function

    * Bug fixed in vairable assignment: concept

commit de077d6
Author: Danylo Ulianych <[email protected]>
Date:   Tue Nov 19 16:17:52 2019 +0100

    Use fftconvolve instead of np.correlate in cross_correlation_histogram (NeuralEnsemble#273)

    * cch np.correlate -> fftconvolve

    * moved internal functions in cross_correlation_histogram to a separate class

    * added BinnedSpikeTrain.get_num_of_spikes() function

    * added BinnedSpikeTrain.binarize() function

commit 059ccf5
Author: pbouss <[email protected]>
Date:   Fri Nov 15 16:24:58 2019 +0100

    Homogeneous Poisson Process with refr. period (NeuralEnsemble#261)

commit f378f07
Author: Alexander van Meegen <[email protected]>
Date:   Tue Nov 12 10:23:29 2019 +0100

    Feature timescale (NeuralEnsemble#271)

    * Implementation of timescale calculation

    * Use cross_corr_coef of CCH function

    * Check that tau_max is an integer multiple of binsize

commit 82f307f
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 11:09:44 2019 +0100

    fixed BinnedSpikeTrain.bin_edges property (NeuralEnsemble#257)

    * fixed BinnedSpikeTrain.bin_edges property

    * bin_edges: include t_stop if spiketrain duration is divisible by binsize

    * BinnedSpikeTrain: warn if binning discards the spikes in the last (excluded) bin

    * reuse is_binary func from utility.py

commit bd684f5
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 10:14:34 2019 +0100

    Refactored unitary event (NeuralEnsemble#251)

    * completely removed misleading N arg - num. of neurons, which is always extracted from the data

    * fixed inverse_hash_from_pattern for long N > int64; added test_hash_inverse_longpattern

    * UE: deprecation warning

commit 2967dac
Author: Alexander van Meegen <[email protected]>
Date:   Fri Nov 8 16:38:27 2019 +0100

    Calculate spike train auto-correlation time ('timescale') (NeuralEnsemble#266)

    * Implementation of timescale calculation

commit 092d2fb
Author: Michael Denker <[email protected]>
Date:   Fri Nov 8 12:33:32 2019 +0100

    Added a simplified to correctly handle division with Compound Units (NeuralEnsemble#270)

    .magnitude -> .simplified.magnitude

commit 5dfa042
Author: Danylo Ulianych <[email protected]>
Date:   Thu Oct 31 15:54:30 2019 +0100

    elephant v0.6.4 [workshop] (NeuralEnsemble#268)

commit 5b5a023
Author: Danylo Ulianych <[email protected]>
Date:   Tue Oct 22 16:10:16 2019 +0200

    neo v0.8.0 compatible (NeuralEnsemble#256)

    * fixes for neo v0.8.0

    * upd array_annotation comment

    * added todo for neo empty array_annotations

commit eac914c
Author: PaulinaDabrowska <[email protected]>
Date:   Tue Oct 22 16:09:41 2019 +0200

    Improved doc string of covariance() and corrcoef() (NeuralEnsemble#260)

    * corrected explanation of the formula used in corrcoef and covariance (in the doc string)

    * pep8

commit 434cacd
Author: Robin Gutzen <[email protected]>
Date:   Mon Oct 21 13:56:38 2019 +0200

    keep array_annotations in the output of signal_processing functions (NeuralEnsemble#258)

    * pass array_annotations on to output of signal_processing functions

    * test keep array_annotations for zscore, butter, hilbert

commit 15acc90
Author: Danylo Ulianych <[email protected]>
Date:   Thu Oct 17 12:19:51 2019 +0200

    removed unused debug code in spade/fast_fca (NeuralEnsemble#249)

    * removed dead code
    * small speedup

commit ce9e7ac
Author: Björn Müller <[email protected]>
Date:   Wed Oct 16 10:25:09 2019 +0200

    Performance and API enhancement for STTC (NeuralEnsemble#244)

    * Speedup for STTC
    * Implemented spike search in other sptr with numpy search

    Memory complexity: O(max(n1, n2)) (exactly max(n1, n2) is used
    additionally at peak)
    Runtime complexity: O(max(n1, n2)*log(max(n1, n2))), because search
    happens n1 times with log(n2) for binary search (or n2 times with
    log(n1))

commit a833a96
Author: Alessandra Stella <[email protected]>
Date:   Wed Oct 9 15:21:41 2019 +0200

    [spade] fixed the calculation of the duration of a pattern in the output (NeuralEnsemble#254)

    * fixed the calculation of the duration of a pattern, in the output of spade. Previously, the calculation of the pattern duration was not always correct, depending on the order of lags and neurons. We fixed the bug by accounting the duration independently from the order of neurons;
    * added raise ValueErrors in code when the output_format is not one of the two parameters allowed
    * fixed bug of undefined spectrum type when running spade without surrogates (only FIM)

commit c78af7e
Author: Alessandra Stella <[email protected]>
Date:   Thu Sep 12 16:15:43 2019 +0200

    Updated authors list - alessandra and peter
dizcza added a commit to INM-6/elephant that referenced this pull request Dec 10, 2019
@dizcza
Squashed commit of the following:
cd9d960 
commit 0d44cd7
Author: Danylo Ulianych <[email protected]>
Date:   Thu Dec 5 10:25:48 2019 +0100

    unitary event decorate_deprecated_N refactoring (NeuralEnsemble#278)

commit b116804
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 25 12:31:36 2019 +0100

    Fast covariance() and Pearson corrcoef() (NeuralEnsemble#274)

    clarified the difference in the implementation of CrossCorrHist.cross_corr_coef() and the reference book "Analysis of parallel spike trains", 2010

commit 59e6412
Author: pbouss <[email protected]>
Date:   Wed Nov 20 09:46:54 2019 +0100

    Feature/spade duration (NeuralEnsemble#263)

    * Corrected error message

    * Doc. for Holm-Bonferroni

    * Changed calculation of duration for output of patterns

    * fixed calculation of duration for the signature

    * Pass spectrum to concepts_to_output function

    * Bug fixed in vairable assignment: concept

commit de077d6
Author: Danylo Ulianych <[email protected]>
Date:   Tue Nov 19 16:17:52 2019 +0100

    Use fftconvolve instead of np.correlate in cross_correlation_histogram (NeuralEnsemble#273)

    * cch np.correlate -> fftconvolve

    * moved internal functions in cross_correlation_histogram to a separate class

    * added BinnedSpikeTrain.get_num_of_spikes() function

    * added BinnedSpikeTrain.binarize() function

commit 059ccf5
Author: pbouss <[email protected]>
Date:   Fri Nov 15 16:24:58 2019 +0100

    Homogeneous Poisson Process with refr. period (NeuralEnsemble#261)

commit f378f07
Author: Alexander van Meegen <[email protected]>
Date:   Tue Nov 12 10:23:29 2019 +0100

    Feature timescale (NeuralEnsemble#271)

    * Implementation of timescale calculation

    * Use cross_corr_coef of CCH function

    * Check that tau_max is an integer multiple of binsize

commit 82f307f
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 11:09:44 2019 +0100

    fixed BinnedSpikeTrain.bin_edges property (NeuralEnsemble#257)

    * fixed BinnedSpikeTrain.bin_edges property

    * bin_edges: include t_stop if spiketrain duration is divisible by binsize

    * BinnedSpikeTrain: warn if binning discards the spikes in the last (excluded) bin

    * reuse is_binary func from utility.py

commit bd684f5
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 10:14:34 2019 +0100

    Refactored unitary event (NeuralEnsemble#251)

    * completely removed misleading N arg - num. of neurons, which is always extracted from the data

    * fixed inverse_hash_from_pattern for long N > int64; added test_hash_inverse_longpattern

    * UE: deprecation warning

commit 2967dac
Author: Alexander van Meegen <[email protected]>
Date:   Fri Nov 8 16:38:27 2019 +0100

    Calculate spike train auto-correlation time ('timescale') (NeuralEnsemble#266)

    * Implementation of timescale calculation

commit 092d2fb
Author: Michael Denker <[email protected]>
Date:   Fri Nov 8 12:33:32 2019 +0100

    Added a simplified to correctly handle division with Compound Units (NeuralEnsemble#270)

    .magnitude -> .simplified.magnitude

commit 5dfa042
Author: Danylo Ulianych <[email protected]>
Date:   Thu Oct 31 15:54:30 2019 +0100

    elephant v0.6.4 [workshop] (NeuralEnsemble#268)

commit 5b5a023
Author: Danylo Ulianych <[email protected]>
Date:   Tue Oct 22 16:10:16 2019 +0200

    neo v0.8.0 compatible (NeuralEnsemble#256)

    * fixes for neo v0.8.0

    * upd array_annotation comment

    * added todo for neo empty array_annotations

commit eac914c
Author: PaulinaDabrowska <[email protected]>
Date:   Tue Oct 22 16:09:41 2019 +0200

    Improved doc string of covariance() and corrcoef() (NeuralEnsemble#260)

    * corrected explanation of the formula used in corrcoef and covariance (in the doc string)

    * pep8

commit 434cacd
Author: Robin Gutzen <[email protected]>
Date:   Mon Oct 21 13:56:38 2019 +0200

    keep array_annotations in the output of signal_processing functions (NeuralEnsemble#258)

    * pass array_annotations on to output of signal_processing functions

    * test keep array_annotations for zscore, butter, hilbert

commit 15acc90
Author: Danylo Ulianych <[email protected]>
Date:   Thu Oct 17 12:19:51 2019 +0200

    removed unused debug code in spade/fast_fca (NeuralEnsemble#249)

    * removed dead code
    * small speedup

commit ce9e7ac
Author: Björn Müller <[email protected]>
Date:   Wed Oct 16 10:25:09 2019 +0200

    Performance and API enhancement for STTC (NeuralEnsemble#244)

    * Speedup for STTC
    * Implemented spike search in other sptr with numpy search

    Memory complexity: O(max(n1, n2)) (exactly max(n1, n2) is used
    additionally at peak)
    Runtime complexity: O(max(n1, n2)*log(max(n1, n2))), because search
    happens n1 times with log(n2) for binary search (or n2 times with
    log(n1))

commit a833a96
Author: Alessandra Stella <[email protected]>
Date:   Wed Oct 9 15:21:41 2019 +0200

    [spade] fixed the calculation of the duration of a pattern in the output (NeuralEnsemble#254)

    * fixed the calculation of the duration of a pattern, in the output of spade. Previously, the calculation of the pattern duration was not always correct, depending on the order of lags and neurons. We fixed the bug by accounting the duration independently from the order of neurons;
    * added raise ValueErrors in code when the output_format is not one of the two parameters allowed
    * fixed bug of undefined spectrum type when running spade without surrogates (only FIM)

commit c78af7e
Author: Alessandra Stella <[email protected]>
Date:   Thu Sep 12 16:15:43 2019 +0200

    Updated authors list - alessandra and peter
dizcza added a commit to INM-6/elephant that referenced this pull request Jan 9, 2020
@dizcza
Squashed commit of the following:
ac19914 
commit 08e23a8
Author: pbouss <[email protected]>
Date:   Fri Dec 20 15:20:01 2019 +0100

    SPADE refactored if-else statements (NeuralEnsemble#285)

    Simplified code complexity by move if-else blocks here and there

commit fce24ad
Author: pbouss <[email protected]>
Date:   Tue Dec 17 12:23:00 2019 +0100

    Bug fixed while dealing with the units of the refr. period (NeuralEnsemble#283)

commit 8200eef
Author: pbouss <[email protected]>
Date:   Fri Dec 13 16:11:22 2019 +0100

    Feature/spade speed up (NeuralEnsemble#280)

    * Remove while loop, change mpi-use in pvalue spec

    * Use sparse representation of the BinnedSpikeTrain

    * refactored false discovery rate

    * reorganized errors for test_signature_significance

    * Implement filtering for pattern subsets

    when not performing pattern set reduction
    check for subset patterns trivially
    explained by longer patterns with the
    same n_occ due to the moving window

    * Adapt tests to new filtering proceidure

    * Always apply subset filtering

commit 160e8e2
Author: Danylo Ulianych <[email protected]>
Date:   Wed Dec 11 15:44:04 2019 +0100

    fixed bug in BinnedSpikeTrain.sparsity (NeuralEnsemble#281)

commit 0d44cd7
Author: Danylo Ulianych <[email protected]>
Date:   Thu Dec 5 10:25:48 2019 +0100

    unitary event decorate_deprecated_N refactoring (NeuralEnsemble#278)

commit b116804
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 25 12:31:36 2019 +0100

    Fast covariance() and Pearson corrcoef() (NeuralEnsemble#274)

    clarified the difference in the implementation of CrossCorrHist.cross_corr_coef() and the reference book "Analysis of parallel spike trains", 2010

commit 59e6412
Author: pbouss <[email protected]>
Date:   Wed Nov 20 09:46:54 2019 +0100

    Feature/spade duration (NeuralEnsemble#263)

    * Corrected error message

    * Doc. for Holm-Bonferroni

    * Changed calculation of duration for output of patterns

    * fixed calculation of duration for the signature

    * Pass spectrum to concepts_to_output function

    * Bug fixed in vairable assignment: concept

commit de077d6
Author: Danylo Ulianych <[email protected]>
Date:   Tue Nov 19 16:17:52 2019 +0100

    Use fftconvolve instead of np.correlate in cross_correlation_histogram (NeuralEnsemble#273)

    * cch np.correlate -> fftconvolve

    * moved internal functions in cross_correlation_histogram to a separate class

    * added BinnedSpikeTrain.get_num_of_spikes() function

    * added BinnedSpikeTrain.binarize() function

commit 059ccf5
Author: pbouss <[email protected]>
Date:   Fri Nov 15 16:24:58 2019 +0100

    Homogeneous Poisson Process with refr. period (NeuralEnsemble#261)

commit f378f07
Author: Alexander van Meegen <[email protected]>
Date:   Tue Nov 12 10:23:29 2019 +0100

    Feature timescale (NeuralEnsemble#271)

    * Implementation of timescale calculation

    * Use cross_corr_coef of CCH function

    * Check that tau_max is an integer multiple of binsize

commit 82f307f
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 11:09:44 2019 +0100

    fixed BinnedSpikeTrain.bin_edges property (NeuralEnsemble#257)

    * fixed BinnedSpikeTrain.bin_edges property

    * bin_edges: include t_stop if spiketrain duration is divisible by binsize

    * BinnedSpikeTrain: warn if binning discards the spikes in the last (excluded) bin

    * reuse is_binary func from utility.py

commit bd684f5
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 10:14:34 2019 +0100

    Refactored unitary event (NeuralEnsemble#251)

    * completely removed misleading N arg - num. of neurons, which is always extracted from the data

    * fixed inverse_hash_from_pattern for long N > int64; added test_hash_inverse_longpattern

    * UE: deprecation warning

commit 2967dac
Author: Alexander van Meegen <[email protected]>
Date:   Fri Nov 8 16:38:27 2019 +0100

    Calculate spike train auto-correlation time ('timescale') (NeuralEnsemble#266)

    * Implementation of timescale calculation

commit 092d2fb
Author: Michael Denker <[email protected]>
Date:   Fri Nov 8 12:33:32 2019 +0100

    Added a simplified to correctly handle division with Compound Units (NeuralEnsemble#270)

    .magnitude -> .simplified.magnitude

commit 5dfa042
Author: Danylo Ulianych <[email protected]>
Date:   Thu Oct 31 15:54:30 2019 +0100

    elephant v0.6.4 [workshop] (NeuralEnsemble#268)

commit 5b5a023
Author: Danylo Ulianych <[email protected]>
Date:   Tue Oct 22 16:10:16 2019 +0200

    neo v0.8.0 compatible (NeuralEnsemble#256)

    * fixes for neo v0.8.0

    * upd array_annotation comment

    * added todo for neo empty array_annotations

commit eac914c
Author: PaulinaDabrowska <[email protected]>
Date:   Tue Oct 22 16:09:41 2019 +0200

    Improved doc string of covariance() and corrcoef() (NeuralEnsemble#260)

    * corrected explanation of the formula used in corrcoef and covariance (in the doc string)

    * pep8

commit 434cacd
Author: Robin Gutzen <[email protected]>
Date:   Mon Oct 21 13:56:38 2019 +0200

    keep array_annotations in the output of signal_processing functions (NeuralEnsemble#258)

    * pass array_annotations on to output of signal_processing functions

    * test keep array_annotations for zscore, butter, hilbert
dizcza added a commit to INM-6/elephant that referenced this pull request Jan 10, 2020
@dizcza
Squashed commit of the following:
8aa9f49 
commit 731bbe4
Author: pbouss <[email protected]>
Date:   Fri Jan 10 12:15:45 2020 +0100

    Feature/joint isi dithering (NeuralEnsemble#275)

commit 08e23a8
Author: pbouss <[email protected]>
Date:   Fri Dec 20 15:20:01 2019 +0100

    SPADE refactored if-else statements (NeuralEnsemble#285)

    Simplified code complexity by move if-else blocks here and there

commit fce24ad
Author: pbouss <[email protected]>
Date:   Tue Dec 17 12:23:00 2019 +0100

    Bug fixed while dealing with the units of the refr. period (NeuralEnsemble#283)

commit 8200eef
Author: pbouss <[email protected]>
Date:   Fri Dec 13 16:11:22 2019 +0100

    Feature/spade speed up (NeuralEnsemble#280)

    * Remove while loop, change mpi-use in pvalue spec

    * Use sparse representation of the BinnedSpikeTrain

    * refactored false discovery rate

    * reorganized errors for test_signature_significance

    * Implement filtering for pattern subsets

    when not performing pattern set reduction
    check for subset patterns trivially
    explained by longer patterns with the
    same n_occ due to the moving window

    * Adapt tests to new filtering proceidure

    * Always apply subset filtering

commit 160e8e2
Author: Danylo Ulianych <[email protected]>
Date:   Wed Dec 11 15:44:04 2019 +0100

    fixed bug in BinnedSpikeTrain.sparsity (NeuralEnsemble#281)

commit 0d44cd7
Author: Danylo Ulianych <[email protected]>
Date:   Thu Dec 5 10:25:48 2019 +0100

    unitary event decorate_deprecated_N refactoring (NeuralEnsemble#278)

commit b116804
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 25 12:31:36 2019 +0100

    Fast covariance() and Pearson corrcoef() (NeuralEnsemble#274)

    clarified the difference in the implementation of CrossCorrHist.cross_corr_coef() and the reference book "Analysis of parallel spike trains", 2010

commit 59e6412
Author: pbouss <[email protected]>
Date:   Wed Nov 20 09:46:54 2019 +0100

    Feature/spade duration (NeuralEnsemble#263)

    * Corrected error message

    * Doc. for Holm-Bonferroni

    * Changed calculation of duration for output of patterns

    * fixed calculation of duration for the signature

    * Pass spectrum to concepts_to_output function

    * Bug fixed in vairable assignment: concept

commit de077d6
Author: Danylo Ulianych <[email protected]>
Date:   Tue Nov 19 16:17:52 2019 +0100

    Use fftconvolve instead of np.correlate in cross_correlation_histogram (NeuralEnsemble#273)

    * cch np.correlate -> fftconvolve

    * moved internal functions in cross_correlation_histogram to a separate class

    * added BinnedSpikeTrain.get_num_of_spikes() function

    * added BinnedSpikeTrain.binarize() function

commit 059ccf5
Author: pbouss <[email protected]>
Date:   Fri Nov 15 16:24:58 2019 +0100

    Homogeneous Poisson Process with refr. period (NeuralEnsemble#261)

commit f378f07
Author: Alexander van Meegen <[email protected]>
Date:   Tue Nov 12 10:23:29 2019 +0100

    Feature timescale (NeuralEnsemble#271)

    * Implementation of timescale calculation

    * Use cross_corr_coef of CCH function

    * Check that tau_max is an integer multiple of binsize

commit 82f307f
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 11:09:44 2019 +0100

    fixed BinnedSpikeTrain.bin_edges property (NeuralEnsemble#257)

    * fixed BinnedSpikeTrain.bin_edges property

    * bin_edges: include t_stop if spiketrain duration is divisible by binsize

    * BinnedSpikeTrain: warn if binning discards the spikes in the last (excluded) bin

    * reuse is_binary func from utility.py

commit bd684f5
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 10:14:34 2019 +0100

    Refactored unitary event (NeuralEnsemble#251)

    * completely removed misleading N arg - num. of neurons, which is always extracted from the data

    * fixed inverse_hash_from_pattern for long N > int64; added test_hash_inverse_longpattern

    * UE: deprecation warning

commit 2967dac
Author: Alexander van Meegen <[email protected]>
Date:   Fri Nov 8 16:38:27 2019 +0100

    Calculate spike train auto-correlation time ('timescale') (NeuralEnsemble#266)

    * Implementation of timescale calculation

commit 092d2fb
Author: Michael Denker <[email protected]>
Date:   Fri Nov 8 12:33:32 2019 +0100

    Added a simplified to correctly handle division with Compound Units (NeuralEnsemble#270)

    .magnitude -> .simplified.magnitude

commit 5dfa042
Author: Danylo Ulianych <[email protected]>
Date:   Thu Oct 31 15:54:30 2019 +0100

    elephant v0.6.4 [workshop] (NeuralEnsemble#268)

commit 5b5a023
Author: Danylo Ulianych <[email protected]>
Date:   Tue Oct 22 16:10:16 2019 +0200

    neo v0.8.0 compatible (NeuralEnsemble#256)

    * fixes for neo v0.8.0

    * upd array_annotation comment

    * added todo for neo empty array_annotations

commit eac914c
Author: PaulinaDabrowska <[email protected]>
Date:   Tue Oct 22 16:09:41 2019 +0200

    Improved doc string of covariance() and corrcoef() (NeuralEnsemble#260)

    * corrected explanation of the formula used in corrcoef and covariance (in the doc string)

    * pep8

commit 434cacd
Author: Robin Gutzen <[email protected]>
Date:   Mon Oct 21 13:56:38 2019 +0200

    keep array_annotations in the output of signal_processing functions (NeuralEnsemble#258)

    * pass array_annotations on to output of signal_processing functions

    * test keep array_annotations for zscore, butter, hilbert
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@AlexVanMeegen @pep8speaks @coveralls @dizcza