Release Notes

Elephant 0.8.0 release notes

New features

• The parallel module is a new experimental module (https://github.com/NeuralEnsemble/elephant/pull/307) to run python functions concurrently. Supports native (pythonic) ProcessPollExecutor and MPI. Not limited to Elephant functional.
• Added an optional refractory_period argument, set to None by default, to dither_spikes function (https://github.com/NeuralEnsemble/elephant/pull/297).
• Added cdf and icdf functions in Kernel class to correctly estimate the median index, needed for instantaneous_rate function in statistics.py (https://github.com/NeuralEnsemble/elephant/pull/313).
• Added an optional center_kernel argument, set to True by default (to behave as in Elephant <0.8.0 versions) to instantaneous_rate function in statistics.py (https://github.com/NeuralEnsemble/elephant/pull/313).

New tutorials

• Analysis of Sequences of Synchronous EvenTs (ASSET) tutorial: https://elephant.readthedocs.io/en/latest/tutorials/asset.html
• Parallel module tutorial: https://elephant.readthedocs.io/en/latest/tutorials/parallel.html

Optimization

• Optimized ASSET runtime by a factor of 10 and more (https://github.com/NeuralEnsemble/elephant/pull/259, https://github.com/NeuralEnsemble/elephant/pull/333).

Python 2.7 and 3.5 deprecation

Python 2.7 and 3.5 are deprecated and will not be maintained by the end of 2020. Switch to Python 3.6+.

Breaking changes

• Naming convention changes (binsize -> bin_size, etc.) in almost all Elephant functions (https://github.com/NeuralEnsemble/elephant/pull/316).

Elephant 0.7.0 release notes

Breaking changes

• [gpfa] GPFA dimensionality reduction method is rewritten in easy-to-use scikit-learn class style format (https://github.com/NeuralEnsemble/elephant/pull/287):

gpfa = GPFA(bin_size=20*pq.ms, x_dim=8)
results = gpfa.fit_transform(spiketrains, returned_data=['xorth', 'xsm'])

New tutorials

• GPFA dimensionality reduction method: https://elephant.readthedocs.io/en/latest/tutorials/gpfa.html
• Unitary Event Analysis of coordinated spiking activity: https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html
• (Introductory) statistics module: https://elephant.readthedocs.io/en/latest/tutorials/statistics.html

Deprecations

• Python 2.7 support will be dropped on Dec 31, 2020. Please switch to Python 3.6, 3.7, or 3.8.
• [spike train generation] homogeneous_poisson_process_with_refr_period(), introduced in v0.6.4, is deprecated and will be deleted in v0.8.0. Use homogeneous_poisson_process(refractory_period=…) instead.
• [pandas bridge] pandas_bridge module is deprecated and will be deleted in v0.8.0.

New features

• New documentation style, guidelines, tutorials, and more (https://github.com/NeuralEnsemble/elephant/pull/294).
• Python 3.8 support (https://github.com/NeuralEnsemble/elephant/pull/282).
• [spike train generation] Added refractory_period flag in homogeneous_poisson_process() (https://github.com/NeuralEnsemble/elephant/pull/292) and inhomogeneous_poisson_process() (https://github.com/NeuralEnsemble/elephant/pull/295) functions. The default is refractory_period=None, meaning no refractoriness.
• [spike train correlation] cross_correlation_histogram() supports different t_start and t_stop of input spiketrains.
• [waveform features] waveform_width() function extracts the width (trough-to-peak TTP) of a waveform (https://github.com/NeuralEnsemble/elephant/pull/279).
• [signal processing] Added scaleopt flag in pairwise_cross_correlation() to mimic the behavior of Matlab’s xcorr() function (https://github.com/NeuralEnsemble/elephant/pull/277). The default is scaleopt=unbiased to be consistent with the previous versions of Elephant.
• [spike train surrogates] Joint-ISI dithering method via JointISI class (https://github.com/NeuralEnsemble/elephant/pull/275).

Bug fixes

• [spike train correlation] Fix CCH Border Correction (https://github.com/NeuralEnsemble/elephant/pull/298). Now, the border correction in cross_correlation_histogram() correctly reflects the number of bins used for the calculation at each lag. The correction factor is now unity at full overlap.
• [phase analysis] spike_triggered_phase() incorrect behavior when the spike train and the analog signal had different time units (https://github.com/NeuralEnsemble/elephant/pull/270).

Performance

• [spade] SPADE x7 speedup (https://github.com/NeuralEnsemble/elephant/pull/280, https://github.com/NeuralEnsemble/elephant/pull/285, https://github.com/NeuralEnsemble/elephant/pull/286). Moreover, SPADE is now able to handle all surrogate types that are available in Elephant, as well as more types of statistical corrections.
• [conversion] Fast & memory-efficient covariance() and Pearson corrcoef() (https://github.com/NeuralEnsemble/elephant/pull/274). Added flag fast=True by default in both functions.
• [conversion] Use fast fftconvolve instead of np.correlate in cross_correlation_histogram() (https://github.com/NeuralEnsemble/elephant/pull/273).

Elephant 0.6.4 release notes

This release has been made for the “1st Elephant User Workshop” (https://www.humanbrainproject.eu/en/education/participatecollaborate/infrastructure-events-trainings/1st-elephant-user-workshop-accelerate-structured-and-reproducibl).

Main features

• neo v0.8.0 compatible

New modules

• GPFA - Gaussian-process factor analysis - dimensionality reduction method for neural trajectory visualization (https://github.com/NeuralEnsemble/elephant/pull/233). _Note: the API could change in the future._

Bug fixes

• [signal processing] Keep array_annotations in the output of signal processing functions (https://github.com/NeuralEnsemble/elephant/pull/258).
• [SPADE] Fixed the calculation of the duration of a pattern in the output (https://github.com/NeuralEnsemble/elephant/pull/254).
• [statistics] Fixed automatic kernel selection yields incorrect values (https://github.com/NeuralEnsemble/elephant/pull/246).

Improvements

• Vectorized spike_time_tiling_coefficient() function - got rid of a double for-loop (https://github.com/NeuralEnsemble/elephant/pull/244)
• Reduced the number of warnings during the tests (https://github.com/NeuralEnsemble/elephant/pull/238).
• Removed unused debug code in spade/fast_fca.py (https://github.com/NeuralEnsemble/elephant/pull/249).
• Improved doc string of covariance() and corrcoef() (https://github.com/NeuralEnsemble/elephant/pull/260).

Elephant 0.6.3 release notes

July 22nd 2019

The release v0.6.3 is mostly about improving maintenance.

New functions

• waveform_features module

  • Waveform signal-to-noise ratio (https://github.com/NeuralEnsemble/elephant/pull/219).

• Added support for Butterworth sosfiltfilt - numerically stable (in particular, higher order) filtering (https://github.com/NeuralEnsemble/elephant/pull/234).

Bug fixes

• Fixed neo version typo in requirements file (https://github.com/NeuralEnsemble/elephant/pull/218)
• Fixed broken docs (https://github.com/NeuralEnsemble/elephant/pull/230, https://github.com/NeuralEnsemble/elephant/pull/232)
• Fixed issue with 32-bit arch (https://github.com/NeuralEnsemble/elephant/pull/229)

Other changes

• Added issue templates (https://github.com/NeuralEnsemble/elephant/pull/226)
• Single VERSION file (https://github.com/NeuralEnsemble/elephant/pull/231)

Elephant 0.6.2 release notes

April 23rd 2019

New functions

• signal_processing module

  • New functions to calculate the area under a time series and the derivative of a time series.

Other changes

• Added support to initialize binned spike train representations with a matrix
• Multiple bug fixes

Elephant 0.6.1 release notes

April 1st 2019

New functions

• signal_processing module

  • New function to calculate the cross-correlation function for analog signals.

• spade module

  • Spatio-temporal spike pattern detection now includes the option to assess significance also based on time-lags of patterns, in addition to patterns size and frequency (referred to as 3D pattern spectrum).

Other changes

• This release fixes a number of compatibility issues in relation to API breaking changes in the Neo library.
• Fixed error in STTC calculation (spike time tiling coefficient)
• Minor bug fixes

Elephant 0.6.0 release notes

October 12th 2018

New functions

• cell_assembly_detection module

  • New function to detect higher-order correlation structures such as patterns in parallel spike trains based on Russo et al, 2017.

• wavelet_transform() function in signal_prosessing.py module

  • Function for computing wavelet transform of a given time series based on Le van Quyen et al. (2001)

Other changes

• Switched to multiple requirements.txt files which are directly read into the setup.py
• instantaneous_rate() accepts now list of spiketrains
• Minor bug fixes

Elephant 0.5.0 release notes

April 4nd 2018

New functions

• change_point_detection module:

  • New function to detect changes in the firing rate

• spike_train_correlation module:

  • New function to calculate the spike time tiling coefficient

• phase_analysis module:

  • New function to extract spike-triggered phases of an AnalogSignal

• unitary_event_analysis module:

  • Added new unit test to the UE function to verify the method based on data of a recent [Re]Science publication

Other changes

• Minor bug fixes

Elephant 0.4.3 release notes

March 2nd 2018

Other changes

• Bug fixes in spade module:

  • Fixed an incompatibility with the latest version of an external library

Elephant 0.4.2 release notes

March 1st 2018

New functions

• spike_train_generation module:

  • inhomogeneous_poisson() function

• Modules for Spatio Temporal Pattern Detection (SPADE) spade_src:

  • Module SPADE: spade.py

• Module statistics.py:

  • Added CV2 (coefficient of variation for non-stationary time series)

• Module spike_train_correlation.py:

  • Added normalization in cross-correlation histogram() (CCH)

Other changes

• Adapted the setup.py to automatically install the spade modules including the compiled C files fim.so
• Included testing environment for MPI in travis.yml
• Changed function arguments in current_source_density.py to neo.AnalogSignal instead list of neo.AnalogSignal objects
• Fixes to travis and setup configuration files
• Fixed bug in ISI function isi(), statistics.py module
• Fixed bug in dither_spikes(), spike_train_surrogates.py
• Minor bug fixes

Elephant 0.4.1 release notes

March 23rd 2017

Other changes

• Fix in setup.py to correctly import the current source density module

Elephant 0.4.0 release notes

March 22nd 2017

New functions

• spike_train_generation module:

  • peak detection: peak_detection()

• Modules for Current Source Density: current_source_density_src

  • Module Current Source Density: KCSD.py
  • Module for Inverse Current Source Density: icsd.py

API changes

• Interoperability between Neo 0.5.0 and Elephant

  • Elephant has adapted its functions to the changes in Neo 0.5.0, most of the functionality behaves as before
  • See Neo documentation for recent changes: http://neo.readthedocs.io/en/latest/whatisnew.html

Other changes

• Fixes to travis and setup configuration files.
• Minor bug fixes.
• Added module six for Python 2.7 backwards compatibility

Elephant 0.3.0 release notes

April 12st 2016

New functions

• spike_train_correlation module:

  • cross correlation histogram: cross_correlation_histogram()

• spike_train_generation module:

  • single interaction process (SIP): single_interaction_process()
  • compound Poisson process (CPP): compound_poisson_process()

• signal_processing module:

  • analytic signal: hilbert()

• sta module:

  • spike field coherence: spike_field_coherence()

• Module to represent kernels: kernels module
• Spike train metrics / dissimilarity / synchrony measures: spike_train_dissimilarity module
• Unitary Event (UE) analysis: unitary_event_analysis module
• Analysis of Sequences of Synchronous EvenTs (ASSET): asset module

API changes

• Function instantaneous_rate() now uses kernels as objects defined in the kernels module. The previous implementation of the function using the make_kernel() function is deprecated, but still temporarily available as oldfct_instantaneous_rate().

Other changes

• Fixes to travis and readthedocs configuration files.

Elephant 0.2.1 release notes

February 18th 2016

Other changes

Minor bug fixes.

Elephant 0.2.0 release notes

September 22nd 2015

New functions

• Added covariance function covariance() in the spike_train_correlation module
• Added complexity pdf complexity_pdf() in the statistics module
• Added spike train extraction from analog signals via threshold detection the in spike_train_generation module
• Added coherence() function for analog signals in the spectral module
• Added Cumulant Based Inference for higher-order of Correlation (CuBIC) in the cubic module for correlation analysis of parallel recorded spike trains

API changes

• Optimized kernel bandwidth in rate_estimation function: Calculates the optimized kernel width when the paramter kernel width is specified as auto

Other changes

• Optimized creation of sparse matrices: The creation speed of the sparse matrix inside the BinnedSpikeTrain class is optimized
• Added Izhikevich neuron simulator in the make_spike_extraction_test_data module
• Minor improvements to the test and continous integration infrastructure