Scripts#

`PIV`	Particle image velocimetry (PIV) analysis on an image sequence.
`apply_mask`	Apply mask on PIV data.
`batch_gen_preview`	Batch generate preview images from nd2 files.
`batch_mean_velocity`	Batch mean velocity computation from PIV data.
`batch_spatial_correlation`	Batch spatial correlation computation.
`batch_to_tif`	Batch convert *.nd2 files to .tif images by calling `to_tif.py`.
`batch_to_vid`	Batch convert .tif images to .avi by calling `to_vid.py` (more details can be found in to_vid.py doc string).
`batch_velocity_autocorr`	Batch velocity autocorrelation computation.
`bpass`	Convert *.nd2 file to image sequence and apply bandpass filter to each image.
`bpass_mh`	Convert *.nd2 file to image sequence and apply bandpass filter to each image.
`check_bif_piv`	A slider bar application for checking bifurcation PIV data.
`check_traj`	Check trajectory data by plotting on top of raw images.
`circulation_order_parameter`	Compute circulation order parameter according to Wioland 2013.
`cleanup_tif`	Delete all the .tif files generated by `to_tif.py` script, in a given directory.
`collect_preview`	Collect all the tif files under preview folder into the main folder.
`correction`	Subpixel correction of droplet trajectory data, based on cross-boundary fitting and circle fitting.
`crop_channel`	Crop channels from bifurcation AN images.
`de_piv_script`	A script to run PIV on all the nd2 files in a given folder.
`extract`	This program extracts light-weight information from data generated by bacteria.vi at Clement lab, PMMH, ESPCI.
`faster_cropping`	A GUI miniapp to quickly define crop region for bifurcation experiment images.
`flowrate`	This script compute "volumetric flow rate" in a channel from 2D PIV data.
`gen_preview`	Generete preview images of given folder.
`ij_piv`	Invoke ImageJ2 to run PIV macro `PIV_STACK_directory.ijm` based on `PIV_.jar` plugin, in headless mode.
`manual_entry_droplets`	A simple graphical interface to manually input droplet coords which are not found by the automatic algorithm.
`mean_velocity`	Compute mean velocity of PIV data.
`moving_mask_piv`	This script performs PIV on the flow field in a moving droplet.
`myautodoc`	Extract docstrings from .py files and write them in .rst files in docs/source folder.
`network_monitor`	Copy from Geekforgeeks https://www.geeksforgeeks.org/python-script-to-monitor-network-connection-and-saving-into-log-file/.
`piv_drop`	Perform PIV analysis on an image sequence of bacteria in a droplet.
`piv_overlay`	Generate PIV arrow overlayed images for PIV visual inspection and illustration.
`remove_background`	This script removes the stationary background of a tif sequence in a given folder.
`rename_ij_piv`	Rename the PIV data file generated by the ImageJ macro `_0.txt` to my format `{:05d}.csv`.
`small_imseq`	Concentration has always been derived from the bright field images.
`spatial_correlation`	Compute correlation length of velocity and velocity orientation.
`to_tif`	Convert .nd2 or .raw file to image sequence of raw and 8-bit grayscale images.
`to_vid`	Convert all the image sequence in a given folder to videos (avi).
`track_droplets`	This code is intended for tracking droplets using `cv2.HoughCircle()` algorithm.
`velocity_autocorr`	Apply autocorrelation analysis on sequential PIV data.
`wrap_piv`	Put PIV data from separated text files into a .mat file, in order to keep the number of files small and meantime save some storage space.