4. Changelog¶
A list of new features, improvements, and bug-fixes in each release.
4.1. v0.6 (Active)¶
4.1.1. New features¶
- Adds the ability to extend temporal filters to be acausal (past the time of the spike)
- Adds an
RBF
class for estimating a nonlinearity using tiled radial basis functions.
4.1.2. API changes¶
- Removes outdated
stimulustools.rolling_window
method. - In fixing a bug in
linear_response
, then method now returns an array of the same shape as the stimulus input, rather than one shorter by the length of the filter whose response is computed.
4.1.3. Bug fixes¶
- Fixes a bug in the
Sigmoid
nonlinearity due do shuffled dictionary keys - Fixes bug in
linear_response
, which was supposed to take a filter, but actually took a reverse-correlation. - Fixes incorrect documentation for
stimulustools.slicestim
.
4.2. v0.5 (17 Nov 2016)¶
4.2.1. New features¶
- Better handling of low-rank STA component signs in
filtertools.lowranksta
. - Functionality for embedding STA animations into HTML, via
visualizations.anim_to_html()
. - New classes for estimating nonlinearities:
Binterp
,Sigmoid
andGaussianProcess
. These follow thescikit-learn
interface, meaning they havefit()
andpredict()
methods, which returnself
.
4.2.2. API changes¶
- Renamed
filtertools.getsta
->filtertools.sta
- Renamed
filtertools.getste
->filtertools.ste
- Renamed
filtertools.getstc
->filtertools.stc
- Renamed
visualizations.rasterandpsth
->visualizations.raster_and_psth
- Renamed
visualizations.plotcells
->visualizations.plot_cells
- Renamed
visualizations.plotsta
->visualizations.plot_sta
- Renamed
visualizations.playrates
->visualizations.play_rates
- Renamed
visualizations.playsta
->visualizations.play_sta
spiketools.binspikes
andspiketools.estfr
no longer return the time axis. Only the binned spikes and firing rate are returned, respectively.- Removed
containers
module. filtertools.rolling_window
has been moved to thestimulustools
module, and is renamedslicestim
.rolling_window
is an alias forslicestim
, for the time being, which raises a warning about future deprecation.- Renamed
stimulustools.stimcov
->stimulustools.cov
. - Renamed
stimulustools.upsample_stim
->stimulustools.upsample
. - Renamed
stimulustools.downsample_stim
->stimulustools.downsample
.
4.3. v0.4 (December 11 2015)¶
4.3.1. New features¶
- Adds a containers module that contains two classes, and Experiment and a Filter class, for managing stimuli and spikes (Experiment) and spike-triggered averages (Filter).
- New and improved ellipse and contour fitting code (filtertools.rfsize, filtertools.get_ellipse, visualizations.ellipse)
- New function filtertools.resample which is a thin wrapper around scipy.signal.resample
4.3.2. API changes¶
- Flipped the expected dimensions of stimuli and filters to have the temporal dimension first. E.g. functions now expect (time, space, space) or (time, space) instead of (space, space, time) or (space, time).
- Changes the default value of the argument in rolling_window to time_axis=0, to be consistent with the rest of pyret (after the flipped dimensions switch)
- Removes the prinangles function (does not really belong in the filtertools module, or even in pyret at all)
- Updated pyret.plotsta function
- Reworked filtertools.getste to be a generator, and modified getsta and getstc to consume that generator.
4.4. v0.3 (June 25 2015)¶
4.4.1. API changes¶
- Changed the filtertools module’s getste, getsta, and getstc to use generators. The getste function now returns a generator that yields samples from the spike-triggered ensemble, while getsta and getstc consume that generator in order to compute their results.
4.5. v0.2 (February 1 2015)¶
This is a major release with a number of API changes, enhancements, and bug fixes.
The main focus has been on adding thorough documentation of all the packages and functions available.
4.5.1. API changes¶
- Changed the
filterlength
,numSamples
andspatialSmoothing
optional arguments tofilter_length
,num_samples
andspatialSmoothing
infiltertools.py
- Changed the
numTrials
tonum_trials
inspiketools.py
- Changed the
triallength
,spatialFrame
,temporalFilter
andboxdims
optional arguments totrial_length
,spatial_filter
,temporal_filter
andbox_dims
invisualizations.py
- Changed the
stim
paramteer tostimulus
instimulustools.py
- Added a function
sample(rate)
tospiketools.py
which draws spikes from a Poisson distribution with the given rate. - Renamed the
spikingevent
class inspiketools.py
toSpikingEvent
- Renamed the attributes
startTime
,stopTime
and functionstrialCounts
,eventStats
ofSpikingEvent
tostart_time
,stop_time
andtrial_counts
,event_stats
- Moved the
peakdet
function from thepeakdetect.py
module tospiketools.py
. Removed thepeakdetect.py
module - Renamed the functions
getellipseparams
andgetellipse
toget_ellipse_params
andfit_ellipse
infiltertools.py
- Renamed the functions
upsamplestim
anddownsamplestim
toupsample_stim
anddownsample_stim
instimulustools.py
4.5.2. General package changes¶
- Removed the (Igor and Baccus lab specific) module
binary.py
- Documentation via
sphinx
is included in thedoc/
folder
4.5.3. Known issues¶
- Installing with
pip
has not been tested. - Installing with
python setup.py install
is known to not work on some machines.