Tracks the movement of cells from a video source.
This is an example initial properties file:
cellType: bacilli
timestep: 1.0 # second
maxSpeed: 12.0 # microns per second
maxSpin: 1.57 # radians per second
minGrowth: -2.0 # microns
maxGrowth: 9.0 # microns
minWidth: 3.0 # microns
maxWidth: 9.0 # microns
minLength: 10.0 # microns
maxLength: 48.0 # microns
delimiter: " "
---
name x y width length rotation
A 160 105 6 18 1.61
B 156 125 6 17 2.00
C 165 130 6 16 2.00
D 170 113 6 16 1.61
You can start with one or more cell properties. The rotation is specified in radians.
Images must all be placed in a directory. The images are found using a pattern in the command line. For example, for the images "./input/frame001.png", "./input/frame002.png", ..., you would use "-i frame%03d.png" to find the images.
Command line help:
$ python main.py --help
usage: main.py [-h] [-v] [-q] [-l FILE] [-p N] [-s N] [-f N] -i PATTERN -o
DIRECTORY -c FILE
optional arguments:
-h, --help show this help message and exit
-v, --verbose give more output (additive)
-q, --quiet give less output (additive)
-l FILE, --log FILE path to a verbose appending log
-p N, --processes N number of extra processes allowed
-s N, --start N starting image number (default: 0)
-f N, --finish N final image number (default until last image
required arguments:
-i PATTERN, --input PATTERN
input filename pattern (example: "image%03d.png")
-o DIRECTORY, --output DIRECTORY
path to the output directory
-c FILE, --config FILE
filename of the configuration file
python main.py -s 0 -f 19 -i ./input/frame%03d.png -o ./output/ -c ./config.yml
python main.py -s 0 -f 53 -i ./data1_input/frame%03d.png -o ./output_data1/ -c ./config1.yml