id-manual-tools 0.0.7

Tools for using idtracker.ai

id manual tools

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Table of Contents

• Install
• Steps to track a video with idTracker.ai
  • 1 Download the episodes from Google Drive
  • 2 Prepare the videos
  • 3 Input parameters
    • 3.1 local_settings.py
    • 3.2 segmentation parameters
  • 4 Running idTracker.ai from terminal
  • 5 id_manual_tools
    • 5.1 id_manual_tools_get_nans
    • 5.2 id_manual_tools_set_corners
    • 5.3 id_manual_tools_correct_traj
    • 5.4 id_manual_tools_concatenate_traj
    • 5.5 id_manual_tools_plot_traj
• Contact

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Install

In the idTracker.ai environment: pip install id-manual-tools

Steps to track a video with idTracker.ai

1 Download the episodes from Google Drive

When downloading more than one file (or folder) of some GB each from Google Drive, Google tries to compres it but it can't, a bunch of files are then downloaded separately in the folder and you need to organize them.

These files should be saved at the external drive. Each one is around 4GB and you don't want to run out of space in the OS drive.

Once done, the files contain some extra numbers in their names (the video GX010128.MP4 is downloaded as GX010128-012.MP4, for example). You can rename each file individually or use the bash command rename -v 's/-[0-9]{3}././' *.MP4 to rename all of them at once

2 Prepare the videos

You don't want to track every 5 minuts episode individually and join them afterwards. The episodes (from the same experiment) must be concatenated using ffmpeg.

The larger the number of fishes in the experiment, the sorter the videos have to be so that idtracker.ai can track them. For up to 8 fishes, 30 minutes of 50fps videos (~90k frames) are ok for our computer. But try to track 30 minutes of 39 fish and your RAM will die (at least with our RAM with 64GB).

To concatenate all videos ended with 0154 in the current directory and write the output in the home directory you can run

ffmpeg -safe 0 -f concat -i <(find . -type f -name '*0154.MP4' -printf "file '$PWD/%p'\n" | sort) -c copy /home/jordi/0154.MP4

If you don't want to concatenate all of the videos and you want to specify the files you have to write an ordered file like (for example)

file './GX010154.MP4'
file './GX020154.MP4'
file './GX030154.MP4'

and then run ffmpeg -safe 0 -f concat -i file -c copy /home/jordi/0102030154.MP4

I use this name encoding, the lasts 4 digits are the video name and the firsts pairs are the episodes. So

• 010203040187.MP4 are episodes 01 02 03 and 04 of video 0187
• 0187.MP4 are all episodes of the video 0187

3 Input parameters

idTracker.ai has 3 levels of parameters with increasing priority.

1. constants.py file in the idtrackerai internal directory (you don't want to modify those parameters)
2. local_settings.py file in the current working directory that idtracker reads at startup
3. Segmentation parameters from the idtrackerai GUI or the .json file that you pass explicitly to idtrackerai

3.1 local_settings.py

Find complete info the official idtracker website.

You want to define the next parameters here:

• NUMBER_OF_JOBS_FOR_BACKGROUND_SUBTRACTION = -2
  • Currently, idtrackerai does not paralelize properly the background subtraction so this paramenter will have some effect in the future
• NUMBER_OF_JOBS_FOR_SEGMENTATION = 20
  • Currently, idtrackerai consume so much RAM in the segmentation process so you want to set the number of jobs somewhere arround 20 (although our computer has 36 cores)
• IDENTIFICATION_IMAGE_SIZE = 55
  • If you want to match identities after the tracking process, you have to fix the image size. In out videos 55 is a good value
• DATA_POLICY = 'idmatcher.ai'
  • This will remove useless data in the session directory whenm the tracking ends (this will free you from GBs of trash data)

3.2 segmentation parameters

The segmentation parameters will be unique for every video. To get them you have to run the command idtrackerai to enter the idtrackerai GUI. Here you will find extended info of that.

As a side note, a minimum area of ~400 px is perfect for our trackings.

I recommend using the GUI to set the segmentation parameters and save them in a .json file. Then you will use this file in to run idtrackerai from terminal

4 Running idTracker.ai from terminal

The command to run idtrackerai in the terminal is

idtrackerai terminal_mode --load file.json --exec track_video

This will print output in the terminal and will be shut down when you exit the terminal.

If you want to run idtracker.ai not worrying about accidental shut downs, then

nohup idtrackerai terminal_mode --load file.json --exec track_video > file.log 2>&1 &

will print the output to a file and will keep running when you exit the terminal

A mini bash script for various videos to track could be

#!/bin/bash
declare -a files=("0102030405060146" "0708091011120146" "0147" "0148" "0149")

for file in "${files[@]}"
do
    idtrackerai terminal_mode --load $file.json --exec track_video > $file.log 2>&1
done

And run it like nohup ./script.sh &

Keep track of the output file to check the status of the program

5 id_manual_tools

When tracked, you may use the id_manual_tools project

For now, id_manual_tools has 5 tools:

• 5.1 id_manual_tools_get_nans
• 5.2 id_manual_tools_set_corners
• 5.3 id_manual_tools_correct_traj
• 5.4 id_manual_tools_concatenate_traj
• 5.5 id_manual_tools_plot_traj

All of them are wrapped with Python's ArgParser and can be runned with -h flag to print some basic information about input/output.

5.1 id_manual_tools_get_nans

The first tool checks for nans in the trajectory file. The raw trajectories from idTracker.ai use to have some NaNs (less than 1% of the total data). It reads the file and print a .csv list of NaNs

5.2 id_manual_tools_set_corners

This tool opens the video to set the setting_points. A list of coordinates that we use to indicate the position of the tanck corners.

5.3 id_manual_tools_correct_traj

That's the main tool here. The trajectory corrector will use id_manual_tools_get_nans to look fort NaNs and will display a full matplotlib GUI to correct them using cubic interpolations. Aditionally, the user will be asked to write the corners of the tank using id_manual_tools_set_corners to crop the video and speed up the GUI.

This tool can also be used to correct suspicious high velicities (jumps) using a gaussian threshold.

id_manual_tools_correct_trajectories -s session_0146/ -video 0146.MP4 -fps 50 -n 10 -jumps_check_sigma 6

5.4 id_manual_tools_concatenate_traj

If your video has been tracked in chunks. You can concatenate them with this tool. It is a wrapper of idmatcher

5.5 id_manual_tools_plot_traj

This is used to make composed videos (the original video with the trajectories overlapped)

Contact

GitHub actions are recommended (issues, PR,...). Also, author's email is [e-mail]