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video_behavior_tracking

This python package provides scripts and functions for extracting behavioral data (position, velocity, acceleration, head direction) from video for Loren Frank's datasets.

Animal behavior is tracked via an overhead video camera and red and green LEDs mounted on the head of the animal. Standard image processing techniques (color thresholding, gaussian blurring, dilation and erosion) are used to extract the position of the LEDS in the video.

Because the LEDs can be occluded due to recording equipment wires or the animal tilting its head down, Kalman filtering and smoothing is used to impute data missing from occlusions, extract variables not directly observed (velocity, acceleration) and take advantage of multiple sensors.

kalman filtering and smoothing example1 kalman filtering and smoothing example1
Kalman smoothing Whole dataset

Installation

pip install video_behavior_tracking

OR

conda install -c edeno video_behavior_tracking

Usage

Steps

  1. Create a config.json file
  2. Run track_behavior to extract the data
  3. Run adjust_time on the pos files to correct the epoch time.

track_behavior is a script that runs via the command line. It will output a <animal>pos<day>.mat file in the Loren Frank data format.

track_behavior VIDEO_FILENAME_PATH CONFIG_FILE_PATH

Two elements are needed to run track_behavior:

  • VIDEO_FILENAME_PATH -- path to the video file. The video file is expected to be in the following format: <date>_<animal>_<epoch>.<optional_flag_depending_on_preprocessing>.<file_format>

    where file_format can be .h264, .avi, .mp4

  • CONFIG_FILE_PATH -- a path to a simple .json configuration file. The function video_behavior_tracking.utils.write_config can be used to put the data in the proper format. An example of the format is below.

{
    "cm_to_pixels": 0.06545,
    "date_to_day": {
        "20161114": 1,
        "20161115": 2,
        "20161116": 3,
        "20161117": 4,
        "20161118": 5,
        "20161119": 6,
        "20161121": 7
    }
}

This file has two variables.

  • cm_to_pixels -- the ratio of centimeters to pixels.
  • date_to_day -- in order to convert date of the video recording to day of recording.

The function video_behavior_tracking.utils.adjust_time will have to be run after processing the files to make sure each epoch starts five minutes after the last.

Optional flags

  • --save_path SAVE_PATH can be added to save the
  • --save_video can be added to create a video file with the estimated head position and direction imposed on the original video.

Development Note

In order to release to conda, after conda skeleton command, need to change the package in meta.yml from opencv-python to opencv.