Visualisation

Create per-condition videos with generate_circ_stim_ufmf

This function generates .mp4 videos for each individual condition within an experiment. Each video contains:

  • The behavioural video of the flies (recorded in IR)
  • The visual stimulus displayed as a ring around the outside of the circular arena image, reconstructed from the pattern file used during the experiment
  • 2-second trajectory traces of the flies superimposed on the image

The videos are played at 2x real time — only every other frame from the original 30 fps video is used.

Requirements

The function should be run from within each experiment’s directory. Inside this directory there must be:

  • The .ufmf video of the entire experiment
  • The .mat LOG file
  • A subdirectory containing trx.mat from FlyTracker

The function also depends on two external resources:

  • The JAABA repository (for video reading utilities)
  • The patterns folder (patterns/Patterns_optomotor/) — the function reads the LOG metadata to determine which pattern was used for each condition and opens the corresponding .mat pattern file to reconstruct the stimulus display

Usage

% Generate videos for all conditions in the current experiment directory
generate_circ_stim_ufmf()

% Generate videos for specific conditions only
generate_circ_stim_ufmf([1, 3, 5])

The function iterates through each condition logged in the LOG file, determines the repetition number (rep 1 if condition index ≤ n_conditions, rep 2 otherwise), and calls create_stim_video_loop to render each video.

ImportantComputer-specific paths

The following paths are hardcoded and must be updated if running on a different computer:

  • Path to the JAABA repository — currently set to /Users/burnettl/Documents/Non-GitHub-Repos/JAABA-master
  • Path to the patterns folder — must point to the patterns/Patterns_optomotor/ directory
  • Output directory — where the generated .mp4 files are saved
Note

The stimulus speed shown in the video is not currently linked to the actual speed used during the experiment — the pattern animation plays at a fixed rate.

Automated video generation

When the automated pipeline processes experiments via daily_processing.py, stimulus videos can be generated automatically as part of the processing step if the make_videos flag is set to true when calling process_freely_walking_data. The .mp4 files are then copied to the network 2_processed directory alongside the processed data. See the Pipeline page for details.