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For parsing and reformatting behavioral event logs.

Project description


Varys is a python package for anyone who has to work with behavioral data logs.

Chances are, you need that data in another format before you can work with it. If you’re like most of us, you have some collection of scripts around somewhere that can parse format A, other scripts that write format B, and somewhere in the middle you’ll sandwich some logic that actually has something to do with your experiment.

Our goal is to reduce the load down to this last bit.

Varys breaks its work into three segments: LogParser, EventBuilder, and FileWriter. Of these, only EventBuilder needs to be customized per experiment.

LogParser is meant to grow with time to be able to parse an increasingly diverse list of input types. At the moment we support simple TDF and CSV formats, as well as the FIDL format used by the eponymous software package from Washington University in St Louis. But we’re willing and interested to work with users to expand that list.

EventBuilder takes input from a LogParser, and turns it into a list of “event” dictionaries. These can contain arbitrary values, but at a minumum must contain “name,” “onset” and “duration.”

FileWriter takes these ordered dictionaries, then writes files consumable by analysis packages. At the time of this writing, we support SPM, FIDL, tab delimited .txt, and python’s Pickle, but here again we’re willing and eager to expand the list of supported formats.

We’ve thrown in some special options for working with neuroimaging data, for concatenating runs, and other fun stuff too.

So please, take a look at the examples list, see if any of them sound like your situation, and feel free to use them as a starting point for your own work.



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