axopy 0.2.3

Description:

axopy 0.2.3

Documentation: https://axopy.readthedocs.io
Axo-Pythonic synapses are those in which an axon synapses upon a Python
program. AxoPy aims to facilitate such connections between electrophysiolgical
signals and machines by making it easy for researchers to develop
human-computer interface experiments. If you’ve ever found yourself spending
more time thinking about how to implement your experiments than thinking about
what the experiment should be, AxoPy may be able to help.
AxoPy consists of:

Graphical interface
Central to AxoPy is the graphical user interface providing visual feedback
to the subject and controlling the flow of the experiment. The GUI is
backed by PyQt5, and you’re free to implement customized graphical elements
if those built in to AxoPy don’t suit your needs.

Data acquisition
AxoPy establishes a fairly simple API for communicating with input
hardware, so all that’s usually needed is a bit of middleware to get going.
Check out pytrigno or pymcc to see what this is like. A couple input
devices are built in (keyboard, noise generator), so examples run without
needing special hardware.

Data storage
Data is stored in a file structure with common file formats (CSV and HDF5)
so you can a) start working with data as soon as an experiment session is
over and b) you don’t need anything but standard tools (pandas, h5py) to do
so. A high-level interface to the storage structure is also provided to
make traversing a dataset simple.

Pipeline processing
Estimating intentions of the user from raw electrophysiological signals
often involves a large number of processing operations. AxoPy facilitates
flexible construction of pipelines that can be reused in different parts of
an experiment and re-used for offline post-processing, etc.



Quickstart

Installation

pip
AxoPy is available on PyPI, so the following should get it installed if
you’re using a standard Python installation with pip:
$ pip install axopy
Note: if you have Python < 3.5, pip will not be able to install the
pyqt5 package for you because wheels for pyqt5 are only provided for
Python >= 3.5. If you are stuck on an older version of Python, consider using
conda (described below, works for any Python version) or installing Qt5 and
PyQt5 yourself before running the command above.
See the development documentation for information on setting up
a development environment to work on AxoPy itself.


conda
AxoPy is also available on conda-forge, so if you’re using (Ana)conda with
any Python version, you can install it with:
$ conda install -c conda-forge axopy



Hello, AxoPy
Here’s a minimal example to display some randomly generated signals in an
“oscilloscope”:
import axopy

daq = axopy.daq.NoiseGenerator(rate=1000, num_channels=4, read_size=100)
exp = axopy.experiment.Experiment(daq=daq)
exp.run(axopy.task.Oscilloscope())


Next Steps
Check out the documentation for more information on creating experiments. Some
examples are also available.



Contributing
Please feel free to share any thoughts or opinions about the design and
implementation of this software by opening an issue on GitHub. Constructive feedback is
welcomed and appreciated.
GitHub issues also serve as the support channel, at least for now. Questions
about how to do something are usually great opportunities to improve
documentation, so you may be asked about your thoughts on where the answers
should go.
If you want to contribute code, open a pull request. Bug fix pull requests are
always welcome. For feature additions, breaking changes, etc. check if there is
an open issue discussing the change and reference it in the pull request. If
there isn’t one, it is recommended to open one with your rationale for the
change before spending significant time preparing the pull request.
Ideally, new/changed functionality should come with tests and documentation. If
you are new to contributing, it is perfectly fine to open a work-in-progress
pull request and have it iteratively reviewed. See the development
documentation for instructions on setting up a development environment,
running tests, and building the documentation.