SBAUtil 0.0.4

Semi-automatic Pipeline for Markerless Pose Estimation and Behavior classification of mouse.

SBA

Untility functions for interaction classifcation.

Installation

pip install SBAUtil

Tutorial

import SBA

Initalize the configuration file:

SBA.initConfig('./',projectName = "newProject", experimenter = "Yiyang")

dynamic cut

SIMBA gives error if the h5file input from DLC contains a portion where there is only one mouse. SBA.batch_dynamic_cropVideo will dynamically crop out this portion based on the given h5file from DLC.

SBA.batch_dynamic_cropVideo(config_path,videos,h5files,fps,videoType="avi")

Post SIMBA processing

SBA.finalizeSimBaOutput(config, simbaFiles, classifier ,destDir = None)

TODO: a more detailed tutorial; better interface;