Why use psychopy_ext?

Successful accumulation of knowledge is critically dependent on the ability to verify and replicate every part of a scientific conduct. Python and its scientific packages have greatly fostered the ability to share and build upon experimental and analysis code. However, while open access to publications is immediately perceived as desired, open sourcing experiment and analysis code is often ignored or met with a grain of skepticism in the neuroscience community, and for a good reason: many publications would be difficult to reproduce from start to end given typically poor coding skills, lack of version control habits, and the prevalence of manual implementation of many tasks (such as statistical analyses or plotting), leading to a reproducible research in theory but not in practice.

I argue that the primary reason of such unreproducible research is the lack of tools that would seamlessly enact good coding and sharing standards. Here I propose a framework tailored to the needs of the neuroscience community that ties together project organization, creation of experiments, behavioral and functional magnetic resonance imaging (fMRI) data analyses, and publication quality (i.e., pretty) plotting using a unified and relatively rigid interface. 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.

For example, each experiment is expected to be a module with classes in it representing different parts of scientific conduct (e.g., stimulus presentation or data analysis), and methods representing an atomic task at hand (e.g., showing experimental instructions or running a support vector machine analysis). Such organization is not only natural and easy to follow in an object-oriented environment but also allows an automatic generation of a command line and graphic user interfaces for customizing and executing these tasks conveniently. Due to a rigid structure, psychopy_ext can more successfully than typical packages address realistic user cases. For instance, running a support vector machine on fMRI data involves multiple steps of preprocessing, aggregating over relevant axes, combining results over participants, and, ideally, unit testing. Since it is impossible to guess the particular configuration at hand, typically the user has to implement these steps manually. However, thanks to a common design pattern in analyses deriving from psychopy_ext, these operations can be performed seamlessly out of the box.

While these choices might be limiting in certain cases, the aim of psychopy_ext is to provide an intuitive basic framework for building transparent and shareable research projects.