A framework for a rapid reproducible design, analysis and plotting of experiments in neuroscience and psychology.
Project description
Please refer to the online documentation for a more in depth explanation how to use the package.
What is it?
psychopy_ext is a framework for a rapid design, analysis and plotting of experiments in neuroscience and psychology.
Unlike PsychoPy, PyMVPA or matplotlib that are very flexible and support multiple options to suit everyone’s needs, the underlying philosophy of psychopy_ext is to act as the glue at a higher level of operation by choosing reasonable defaults for these packages and providing patterns for common tasks with a minimal user intervention.
Features
Easy to run and rerun everything
Neat project organization
Templates for building and analyzing experiments (behavioral & fMRI)
Simplified descriptive statistics
Pretty plotting
Automatic running (unit testing) of experiments
Automatic GUI and command-line interpreter
Custom needs? Inherit & customize: everything is a class!
Built-in simple models of vision (Pixel-wise difference, GaborJet, and HMAX’99)
Installation
pip install psychopy_ext
Quick start
First, find demo files in site-packages (where is it?). Copy them to your home folder or another location of your choice (but where you have write permission). Now check the demos:
For people who use a keyboard:
In a terminal, navigate to the demos folder
Type python run.py main exp run. Do the experiment!
Type python run.py main analysis run to see how well you did.
For people who use PsychoPy app:
In coder view, open run.py file from the demos folder
Click the green running man to run it.
Click on the run button. Do the experiment!
When done, choose the analysis tab and click on run to see how well you did.
For people who use a mouse on Windows:
In a file browser, navigate to the demos folder
Double-click click on run.bat
Click on the run button. Do the experiment!
When done, choose the analysis tab, and click on run to see how well you did.
When done with the demo, inspect main.py file to see how it works, and build your experiment using this template, or try more demos.
Current state of affairs
psychopy_ext is currently stable, meaning that I use it myself daily but there are some limitations:
fMRI analyses (fmri module) have not been thoroughly tested yet (no unit tests) but has been used extensively in my own research.
plots work well but might still require fine tuning and may be unable to handle missing values etc.
Future roadmap (a wishlist):
README generation with the most common commands
Automatic summary of typical commands for CLI
More robust command-line operation
Browser-based project management tool
info and rp should become classes with tips, lists etc
Full fMRI preprocessing support (maybe)
Generate full papers via Open Science Paper and PythonTeX
Force metadata by turning exp_plan into a class
Integrated Bayesian statistics
Dependencies
Required
Python 2.6+ (but tested only with 2.7)
docutils (technically it is not mandatory but it will allow rendering docstrings on screen by the exp class)
Optional
PyMVPA 2.0+ (required for the fmri class)
NiBabel (required for the fmri class)
(Note: if there isn’t a binary package for your Windows platform and your Python version, try Christoph Gohlke’s Unofficial Binaries)
License
Copyright 2010-2013 Jonas Kubilius (http://klab.lt)
Laboratories of Biological and Experimental Psychology, KU Leuven (Belgium)
GNU General Public License v3 or later
Included external packages and functions (covered by a compatible license): combinations, combinations_with_replacement, OrderedDict, HMAX, GaborJet
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