piv_drop#

Perform PIV analysis on an image sequence of bacteria in a droplet.

Syntax

python piv_drop.py image_folder save_folder winsize overlap dt mask_dir

  • image_folder – folder containing .tif image sequence

  • save_folder – folder to save PIV data

  • winsize, overlap, dt – regular params

  • mask_dir – mask image dir

Test

python piv_drop.py test_images\piv_drop test_images\piv_drop 40 20 0.02 test_images\piv_drop\mask.tif

Edit

  • Dec 09, 2021 – Initial commit.

  • Dec 16, 2021 – i) use PIV_masked() as the core algorithm, ii) implement multiprocessing with Pool

  • Jan 16, 2022 – add info print, can be used with “>>” to write log.

  • Feb 15, 2022 – remove printing steps to avoid log file spamming.

  • Mar 03, 2022 – i) Reverse the multi-thread code to linear, ii) use droplet_image class for the script, iii) no longer print PIV settings to screen, save a piv_params json instead

  • Jan 05, 2023 – Adapt myimagelib import style.

  • Feb 08, 2023 – Rewrite in function wrapper form, to make autodoc work properly. (autodoc import the script and execute it, so anything outside if __name__=="__main__" will be executed, causing problems)