New functionality and features

New method "Total spiking probability edges" (TPSE) for inferring functional connectivity (https://github.com/NeuralEnsemble/elephant/pull/560).

Bug fixes

Fixed expired SciPy deprecations and breaking changes related to sp.sqrt, ensuring continued compatibility with the latest version of SciPy (https://github.com/NeuralEnsemble/elephant/pull/616).
Addressed failing unit tests for neo_tools with Neo 0.13.0, ensuring compatibility with the latest Neo release (https://github.com/NeuralEnsemble/elephant/pull/617).

Documentation

Fixed a bug in the CI docs runner to resolve formatting issues, ensuring documentation build is tested (https://github.com/NeuralEnsemble/elephant/pull/615).

Other changes

added Python 3.12 CI runner to ensure compatibility with the latest Python language features (https://github.com/NeuralEnsemble/elephant/pull/611).
Integrated Trials object with GPFA, allowing for a more formal way of specifying trials (https://github.com/NeuralEnsemble/elephant/pull/610).

Selected dependency changes

scipy>=1.10.0
Support for Python 3.12

- Python
Published by Moritz-Alexander-Kern almost 2 years ago

Elephant's first major release is focused on providing a stable and consistent API consistency that will be maintained over the 1.x series of releases. In order to provide future support, this release will remove all features and API specifications that have been deprecated over the course of the last releases of the 0.x line. While work on the next generation of Elephant will commence, all new analysis capabilities will be consistently back-ported to become available in the 1.x release line.

Breaking changes

Removed deprecated features and naming introduced in #316 with Elephant release v0.8.0 (#488).
Removed the pandas_bridge module from Elephant in line with the deprecation plan introduced with Elephant v0.7.0 (#530).

Selected dependency changes

removed pandas from the dependencies (#530).

- Python
Published by Moritz-Alexander-Kern over 2 years ago

elephant - Release 0.14.0

New Functionality and Features

Added ASSET class initialization parameter to define the binning rounding error tolerance, allowing users to control the behavior of spike time binning (#585).
Enhanced ASSET function output messages and status information by replacing print statements with logging calls, introducing tqdm progress bars for looped steps, and providing control over INFO and DEBUG logging via parameters (#570).
Implemented logging instead of warnings in the roundbinningerrors() function in elephant/utils.py (#571).
Implemented trial handling, providing a unified framework for representing and accessing trial data, supporting diverse trial structures and a common API (#579).
Improved instantaneous_rate function to support trial data (#579). ## Bug Fixes
Added example to doc-string, handled one-dimensional arrays as input for xpositions, and added regression unit-tests in CSD.generatelfp (#594).
Modified the check for signal type in z_score when using inplace option to ensure it works correctly with np.float32 and np.float64 (#592). ## Documentation
Fixed documentation build on readthedocs by updating deprecated configuration key build.image to build.os (#596). ## Validations
Fixed spike time tiling coefficient calculation for unsorted spiketrains. The fix includes sorting the input spiketrains, additional input checks, and a validation test. (#564). ## Other Changes
Fixed several typos and grammatical errors in GPFA tutorial notebook (#587).
Updated the build_wheels action to use cibuildwheel version 2.13.1, enabling the building of wheels for Python 3.11 (#582).

- Python
Published by mdenker over 2 years ago

elephant - Release 0.13.0

New functionality and features

Implemented non-parametric spectral Granger causality analysis, extending the investigation of signal influence in the spectral domain. (#545)
Added functions to extract time bin and neuron information from Spike Sequence Events (SSEs) obtained using ASSET. (#549)

Bug fixes

Resolved issue with old references to the gin repository INM-6/elephant-data, ensuring accurate repository information. (#547)
Fixed the usage of deprecated numpy functions, which were removed with numpy 1.25.0. (#568)
Rectified a bug in spade, addressing a missing call of min_neu to specify the minimum number of neurons in a pattern. Also, added a regression test to verify the fix. (#575)
Corrected a bug in the complexity class that resulted in unexpected behavior when binary=False and spread=0. (#554)
Resolved a bug in cell assembly detection (CAD) that produced different results compared to the original MATLAB implementation. (#576)

Documentation

Addressed various formatting issues in docstrings that were causing warnings during documentation builds. (#553)
Updated the contributors guide: The guide now includes a step to install Elephant itself by adding a "pip install -e ." command to the instructions for setting up a development environment. (#566)

Validations

No changes

Other changes

Added codemeta.json for automated publication of Elephant release to ebrains knowledge graph. (#561, #562)
Added "howfairis" badge to README.md, indicating Elephant's compliance with fair-software.eu recommendations. (#551)
CI: Enhance security of github actions by specifying a particular commit for third party actions, to improve security against re-tagging attacks. (#565)
Separation of the multitaper_psd() function into segmented_multitaper_psd() and multitaper_psd() without segmentation. This restructuring was done to achieve consistency in the spectral module. (#556)
Improved reporting in testmultitapercohereperfectcohere: Updated the unittest to utilize the numpy assert array equal function. This enhancement aims to provide more detailed and informative traceback in case of failures. (#573)
Increased tolerance for Weigthed Phase-Lag Index (WPLI) ground truth test to avoid unitest to fail due minor differences in floating point operations (#572)
Added shields for twitter and fosstodon to README.md linking to Elephants accounts. (#532)

Selected dependency changes

no changes

- Python
Published by Moritz-Alexander-Kern over 2 years ago

elephant - Release 0.12.0

New functionality and features

ASSET: map pairwise distances matrix to disk while computing the cluster matrix to reduce memory usage. #498
multitaper cross spectrum: calculate the cross spectrum and the coherence as well as phase lag with the multitaper method. #525
weightedphaselag_index (WLPI), a measure of phase-synchronization based on the imaginary part of the complex-valued cross-spectrum of two signals. #411

Bug fixes

fixed and included additional unit tests for the multitaper_psd. #529
replaced deprecated numpy types with builtins to ensure compatibility with numpy >=1.24.0. #535

Documentation

fixed math rendering with sphinx 5.3.0. #527
added documentation for multitaper_psd. #531
updated the elephant logo to the current version. #534
removed version cap for sphinx extension sphinxcontrib-bibtex (previously set to ==1.0.0): citation style changed to name - year. #523
fixed various formatting issues in docstrings, e.g. indentations, missing quotation marks or missing citation references. #478
fixed documentation code examples and test code by introducing a doctest runner to CI. #503
changed heading "Spike-triggered LFP phase" to "Phase Analysis", remove wrong reference to tutorial from function reference. #540
add launch on ebrains button for elephant tutorials. #538

Validations

WPLI ‘ground-truth’-testing with: MATLABs package FieldTrip and its function ftconnectivitywpli() and its wrapper ftconnectivity(); as well as with python package MNE and its function spectralconnectivity(). #411

Other changes

Fix/CI: update deprecated actions and commands for github actions workflow. #522
added codemeta.json file for automatic registration of elephant releases to ebrains knowledge graph. #541

Selected dependency changes

Python >= 3.8. #536
numpy > 1.20. #536
quantities > 0.14.0. #542

- Python
Published by Moritz-Alexander-Kern about 3 years ago

elephant - Release 0.11.2

New functionality and features

new installation option to not compile c-extensions, e.g. pip install elephant --install-option='--no-compile' (#494)

Bug fixes

added CUDA/OpenCL sources for ASSET GPU acceleration to manifest.in, they are now included in the distribution package (#483)
fixed bug in elephant.kernels when passing a multi-dimensional kernel sigma, handling was added for 1-dimensional case (#499)
fixed bug in unitary_event_analysis that broke elephants build on arm based systems (#500)
fixed bug in elephant/spade_src/include/FPGrowth.h when using current versions of GCC for compilation (#508)
fixed bug in welch_psd, welch_cohere, replace 'hanning' with 'hann', to ensure compatibility with scipy=>1.9.0 (#511)

Documentation

fixed bug in CI documentation build (#492)
reformatted code examples to be used as doctests in the future (#502)
added specification and example for entries in the bibtex file to the "Contributing to Elephant" section (#504)
updated documentation on running unit tests from nosetest to pytest (#505)
fixed broken citation in change_point_detection, updated entry in bibtex file, added DOI (#513)

Optimizations

Include spike_train_synchrony in the init of elephant, now spike_train_synchrony module is imported automatically (#518)

Validations

added two validation tests for Victor-Purpura-distance to validate against original Matlab implementation in spike train dissimilarity (#482)

Other changes

re-added report to coveralls.io to github action CI (#480)
added OpenSSF (Open Source Security Foundations) best practices badge (#495)
improved documentation by adding links to documentation, bug tracker and source code on pypi (#496) (see: https://pypi.org/project/elephant/)
CI workflows for macOS updated from version 10 to macOS 11 and 12 (#509)

Selected dependency changes

removed scipy version cap on GitHub actions runners "docs" and "test-conda", by updating to libstdcxx-ng 12.1.0 from conda-forge (#490)
nixio added to test requirements, now nix files can be used in unit tests (#515)

- Python
Published by Moritz-Alexander-Kern over 3 years ago

elephant - Release 0.11.1

Bug fixes

Fix installation on macOS (#472)

Documentation

Added example to asset.discretise_spiketimes docstring (#468)

Optimizations

Performance improvement of Spike Time Tiling Coefficient (STTC) (#438)

Other changes

Continuous Integration (CI): added two workflows for macOS (#474)
Fixed failing unit test asset on macOS (#474)

Selected dependency changes

scipy >=1.5.4 (#473)

- Python
Published by Moritz-Alexander-Kern almost 4 years ago

elephant - Release 0.11.0

Breaking changes

For current source density measures electrode coordinates can no longer be supplied via a RecordingChannelGroup object as it is no longer supported in Neo v0.10.0 (#447)

New functionality and features

Redesigned elephant.spike_train_generation module using classes (old API is retained for compatibility) (#416)
Added function to calculate the multitaper power spectral density estimate in elephant.spectral (#417)
Added a boundary correction for the firing rate estimator elephant.statistics.instantaneous_rate with Gaussian kernels (#414)
Function to discretise spiketimes for a given spiketrain in elephant.conversion (#454)
Support for the new SpikeTrainList object of Neo (#447)

Bug fixes

Issue with unit scaling in BinnedSpikeTrain (#425)
Changed BinnedSpikeTrain to support quantities<0.12.4 (#418)
Fix FloatingPointError in ICSD (#421)
t_start information was lost while transposing LFP for current_source_density module (#432)
Fix neo_tools unit tests to work with Neo 0.10.0+ (#446)
Fixed various issues with consistency of bin boundaries of instantaneous rates (#453)

Documentation

Update tutorials ASSET and UE tutorial and datasets to use nixio >=1.5.0 (#441)
Updated spade tutorial to work with viziphant 0.2.0 (#444)
Fixed figures in the Granger causality tutorial (#434)
Add DOIs to documentation (#456)
Fixed random seed selection in some tutorials (#430)

Optimizations

Highly optimized run-time of the SPADE analysis (#419)
More efficient storage of spike complexities by the elephant.statistics.Complexity class (#412)
Updated elephant.signal_processing.zscore function for in-place operations (#440)

Other changes

Continuous Integration (CI) was moved to github actions (#451)
Change test framework from Nose to pytest (#413)
Added DOI with zenodo (#445)
Versioning for associated elephant-data repository for example datasets introduced (#463)

Selected dependency changes

nixio >= 1.5.0
neo >= 0.10.0
python >= 3.7

- Python
Published by mdenker almost 4 years ago

elephant - Release 0.10.0

Documentation

The documentation is revised and restructured by categories (https://github.com/NeuralEnsemble/elephant/pull/386) to simplify navigation on readthedocs and improve user experience. All citations used in Elephant are stored in a single BibTex file.

Optimizations

CUDA and OpenCL support

Analysis of Sequences of Synchronous EvenTs has become the first module in Elephant that supports CUDA and OpenCL (https://github.com/NeuralEnsemble/elephant/pull/351, https://github.com/NeuralEnsemble/elephant/pull/404, https://github.com/NeuralEnsemble/elephant/pull/399). Whether you have an Nvidia GPU or just run the analysis on a laptop with a built-in Intel graphics card, the speed-up is X100 and X1000 compared to a single CPU core. The computations are optimized to a degree that you can analyse and look for spike patterns in real data in several minutes of compute time on a laptop. The installation instructions are described in the install section.

Other optimizations

Surrogates: sped up bin shuffling (https://github.com/NeuralEnsemble/elephant/pull/400) and reimplemented the continuous time version (https://github.com/NeuralEnsemble/elephant/pull/397)
Improved memory efficiency of creating a BinnedSpikeTrain (https://github.com/NeuralEnsemble/elephant/pull/395)

New functionality and features

Synchrofact detection (https://github.com/NeuralEnsemble/elephant/pull/322) is a method to detect highly synchronous spikes (at the level of sampling rate precision with an option to extend this to jittered synchrony) and annotate or optionally remove them.
Added phase_locking_value, mean_phase_vector, and phase_difference functions (https://github.com/NeuralEnsemble/elephant/pull/385/files)
BinnedSpikeTrain:
- added to_spike_trains and time_slice functions (https://github.com/NeuralEnsemble/elephant/pull/390). Now you can slice a binned spike train as bst[:, i:j] or bst.time_slice(t_start, t_stop). Also, with to_spike_trains function, you can generate a realization of spike trains that maps to the same BinnedSpikeTrain object when binned.
- optional CSC format (https://github.com/NeuralEnsemble/elephant/pull/402)
- the copy parameter (False by default) in the binarize function makes a shallow copy, if set to True, of the output BinnedSpikeTrain object (https://github.com/NeuralEnsemble/elephant/pull/402)
Granger causality tutorial notebook (https://github.com/NeuralEnsemble/elephant/pull/393)
Unitary Event Analysis support multiple pattern hashes (https://github.com/NeuralEnsemble/elephant/pull/387)

Bug fixes

Account for unidirectional spiketrain->segment links in synchrofact deletion (https://github.com/NeuralEnsemble/elephant/pull/398)
Joint-ISI dithering: fixed a bug regarding first ISI bin (https://github.com/NeuralEnsemble/elephant/pull/396)
Fix LvR values from being off when units are in seconds (https://github.com/NeuralEnsemble/elephant/pull/389)

- Python
Published by dizcza almost 5 years ago

elephant - Release 0.9.0

This release is titled to accompany the 2nd Elephant User Workshop

Viziphant

Meet Viziphant, the visualization of Elephant analysis methods, at https://viziphant.readthedocs.io/en/latest/. This package provides support to easily plot and visualize the output of Elephant functions in a few lines of code.

Provenance tracking

Provenance is becoming a separate direction in Elephant. Many things are still to come, and we started with annotating time_histogram, instantaneous_rate and cross_correlation_histogram outputs to carry the information about the parameters these functions used. This allowed Viziphant, the visualization of Elephant analyses, to look for the .annotations dictionary of the output of these function to "understand" how the object has been generated and label the plot axes accordingly.

New functionality and features

Time-domain pairwise and conditional pairwise Granger causality measures (https://github.com/NeuralEnsemble/elephant/pull/332, https://github.com/NeuralEnsemble/elephant/pull/359)
Spike contrast function that measures the synchrony of spike trains (https://github.com/NeuralEnsemble/elephant/pull/354; thanks to @Broxy7 for bringing this in Elephant).
Revised local variability LvR (https://github.com/NeuralEnsemble/elephant/pull/346) as an alternative to the LV measure.
Three surrogate methods: Trial-shifting, Bin Shuffling, ISI dithering (https://github.com/NeuralEnsemble/elephant/pull/343).
Added a new function to generate spike trains: inhomogeneous_gamma_process (https://github.com/NeuralEnsemble/elephant/pull/339).
The output of instantaneous_rate function is now a 2D matrix of shape (time, len(spiketrains)) (https://github.com/NeuralEnsemble/elephant/issues/363). Not only can the users assess the averaged instantaneous rate (rates.mean(axis=1)) but also explore how much the instantaneous rate deviates from trial to trial (rates.std(axis=1)) (originally asked in https://github.com/NeuralEnsemble/elephant/issues/363).

Python 3 only

Python 2.7 and 3.5 support is dropped. You can still however enjoy the features of Elephant v0.9.0 with Python 2.7 or 3.5 by installing Elephant from this commit pip install git+https://github.com/NeuralEnsemble/elephant@295c6bd7fea196cf9665a78649fafedab5840cfa#egg=elephant[extras]
Added Python 3.9 support.

Optimization

You have been asking for direct numpy support for years. Added _t_start, _t_stop, and _bin_size attributes of BinnedSpikeTrain are guaranteed to be of the same units and hence are unitless (https://github.com/NeuralEnsemble/elephant/pull/378). It doesn't mean though that you need to care about units on your own: t_start, t_stop, and bin_size properties are still quantities with units. The .rescale() method of a BinnedSpikeTrain rescales the internal units to new ones in-place. The following Elephant functions are optimized with unitless BinnedSpikeTrain:
- crosscorrelationhistogram
- bin_shuffling (one of the surrogate methods)
- spiketraintimescale
X4 faster binning and overall BinnedSpikeTrain object creation (https://github.com/NeuralEnsemble/elephant/pull/368).
instantaneous_rate function is vectorized to work with a list of spike train trials rather than computing them in a loop (previously, for spiketrain in spiketrains; do compute instantaneous_rate(spiketrain); done), which brought X25 speedup (https://github.com/NeuralEnsemble/elephant/pull/362; thanks to @gyyang for the idea and original implementation).
Memory-efficient zscore function (https://github.com/NeuralEnsemble/elephant/pull/372).
Don't sort the input array in ISI function (https://github.com/NeuralEnsemble/elephant/pull/371), which reduces function algorithmic time complexity from O(N logN) to linear O(N). Now, when the input time array is not sorted, a warning is shown.
Vectorized Current Source Density generate_lfp function (https://github.com/NeuralEnsemble/elephant/pull/358).

Breaking changes

mpi4py package is removed from the extra requirements to allow pip install elephant[extras] on machines without MPI installed system-wide. Refer to MPI support installation page in elephant.
BinnedSpikeTrain (https://github.com/NeuralEnsemble/elephant/pull/368, https://github.com/NeuralEnsemble/elephant/pull/377):
- previously, when tstart/stop, if set manually, was outside of the shared time interval, only the shared [tstartshared=max(tstart), tstopshared=min(t_stop)] interval was implicitly considered without any warnings. Now an error is thrown with a description on how to fix it.
- removed lst_input, input_spiketrains, matrix_columns, matrix_rows (in favor of the new attribute - shape), tolerance, is_spiketrain, is_binned attributes from BinnedSpikeTrain class. Part of them are confusing (e.g., is_binned was just the opposite of is_spiketrain, but one can erroneously think that it's data is clipped to 0 and 1), and part of them - lst_input, input_spiketrains input data - should not have been saved as attributes of an object in the first place because the input spike trains are not used after the sparse matrix is created.
- now the users can directly access .sparse_matrix attribute of BinnedSpikeTrain to do efficient (yet unsafe in general) operations. For this reason, to_sparse_array() function, which does not make a copy, as one could think of, is deprecated.
instantaneous_rate function (https://github.com/NeuralEnsemble/elephant/pull/362):
- in case of multiple input spike trains, the output of the instantaneous rate function is (always) a 2D matrix of shape (time, len(spiketrains)) instead of a pseudo 1D array (previous behavior) of shape (time, 1) that contained the instantaneous rate summed across input spike trains;
- in case of multiple input spike trains, the user needs to manually provide the input kernel instead of auto, which is set by default, for the reason that it's currently not clear how to estimate the common kernel for a set of spike trains. If you have an idea how to do this, we`d appreciate if you let us know by getting in touch with us.

Other changes

waveform_snr function now directly takes a 2D or 3D waveforms matrix rather than a spike train (deprecated behavior).
Added a warning in fanofactor function when the input spiketrains vary in their durations (https://github.com/NeuralEnsemble/elephant/pull/341).
SPADE: New way to count patterns for multiple testing (https://github.com/NeuralEnsemble/elephant/pull/347)
GPFA renamed 'xsm' -> 'latentvariable' and 'xorth' -> 'latentvariable_orth'

Bug fixes

Instantaneous rate arrays were not centered at the origin for spike trains that are symmetric at t=0 with center_kernel=True option (https://github.com/NeuralEnsemble/elephant/pull/362).
The number of discarded spikes that fall into the last bin of a BinnedSpikeTrain object was incorrectly calculated (https://github.com/NeuralEnsemble/elephant/pull/368).
Fixed index selection in spike_triggered_phase (https://github.com/NeuralEnsemble/elephant/pull/382)
Fixed surrogates bugs:
- joint-ISI and shuffle ISI output spike trains were not sorted in time (https://github.com/NeuralEnsemble/elephant/pull/364);
- surrogates get arbitrary sampling_rate (https://github.com/NeuralEnsemble/elephant/pull/353), which relates to the provenance tracking issue;

- Python
Published by dizcza over 5 years ago

elephant - Release 0.8.0

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).
Added an optional tolerance argument, set to 1e-8 by default, to BinnedSpikeTrain class that accounts for rounding errors in the binning process of the input data (https://github.com/NeuralEnsemble/elephant/pull/305).

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).
Deprecated pandas_bridge module has been removed from a list of auto imports in elephant/__init__.py but can be still easily accessed by from elephant import pandas_bridge.

- Python
Published by dizcza over 5 years ago

elephant - Release 0.7.0

Breaking changes

GPFA dimensionality reduction method is rewritten in easy-to-use scikit-learn class style format (https://github.com/NeuralEnsemble/elephant/pull/287): python gpfa = GPFA(bin_size=20*pq.ms, x_dim=8) results = gpfa.fit_transform(spiketrains, returned_data=['xorth', 'xsm'])

New tutorials

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 tstart and tstop of input spiketrains (https://github.com/NeuralEnsemble/elephant/pull/291).
[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).

- Python
Published by dizcza almost 6 years ago

elephant - Release 0.6.4

This release has been made for the 1st Elephant User Workshop.

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.

Buf 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).

- Python
Published by dizcza over 6 years ago

elephant - Release 0.6.3

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).

Buf 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)

- Python
Published by dizcza over 6 years ago

elephant - Release 0.6.2

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

- Python
Published by mdenker almost 7 years ago

elephant - Release 0.6.1

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

- Python
Published by mdenker almost 7 years ago

elephant - Release 0.6.0

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

- Python
Published by alperyeg over 7 years ago

elephant - Release 0.5.0

Elephant 0.5.0 release notes

April 10th 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

- Python
Published by mdenker almost 8 years ago

elephant - Release 0.4.3

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

- Python
Published by mdenker almost 8 years ago

elephant - Release 0.4.2

Elephant 0.4.2 release notes

1st March 2018

New functions

spiketraingeneration 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 spiketraincorrelation.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 enviroment 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

- Python
Published by alperyeg almost 8 years ago

elephant - Release 0.4.1

Elephant 0.4.1 release notes

March 23rd 2017

Other changes

Fix in setup.py to correctly import the current source density module
For an overview of latest changes introduced in version 0.4.0 see here

- Python
Published by alperyeg almost 9 years ago

elephant - Release 0.4.0

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.

Other changes

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

- Python
Published by alperyeg almost 9 years ago

Recent Releases of elephant

elephant - Release 1.1.0

New functionality and features

Bug fixes

Documentation

Other changes

Selected dependency changes

elephant - Release 1.0.0

Breaking changes

Selected dependency changes

elephant - Release 0.14.0

New Functionality and Features

elephant - Release 0.13.0

New functionality and features

Bug fixes

Documentation

Validations

Other changes

Selected dependency changes

elephant - Release 0.12.0

New functionality and features

Bug fixes

Documentation

Validations

Other changes

Selected dependency changes

elephant - Release 0.11.2

New functionality and features

Bug fixes

Documentation

Optimizations

Validations

Other changes

Selected dependency changes

elephant - Release 0.11.1

Bug fixes

Documentation

Optimizations

Other changes

Selected dependency changes

elephant - Release 0.11.0

Breaking changes

New functionality and features

Bug fixes

Documentation

Optimizations

Other changes

Selected dependency changes

elephant - Release 0.10.0

Documentation

Optimizations

CUDA and OpenCL support

Other optimizations

New functionality and features

Bug fixes

elephant - Release 0.9.0

Viziphant

Provenance tracking

New functionality and features

Python 3 only

Optimization

Breaking changes

Other changes

Bug fixes

elephant - Release 0.8.0

New features

New tutorials

Optimization

Python 2.7 and 3.5 deprecation

Breaking changes

elephant - Release 0.7.0

Breaking changes

New tutorials

Deprecations

New features

Bug fixes

Performance

elephant - Release 0.6.4

Main features

New modules