Tracks the movement of cells from a video source.
This is an example initial properties file:
# Initial property file (line commented out)
0.33 #dt, or the number of hours per frame
26 #init_length of bacteria
6 #init_width of bacteria
3 #max speed
0.3141592653589793 #max spin
20 #number of ideal universes
3 #max x motion
3 #max y motion
7 #max x resolution
7 #max y resolution
0.3141592653589793 #max rotation
21 #max rotation resolution
0 #minimum height increase
3 #maximum height increase
4 #height increase resolution
31 #maximum length of single bacteria before splitting
13 #minimum length of any bacteria
0.25 #beginning of split ratio
0.75 #end of split ratio
20 #split ratio resolution
#NOTE: The program will ignore comments
pos:x pos:y length rotation
160 105 20 1.605
156 125 17 1.997
165 130 14 1.997
170 113 15 1.605
You can start with one or more cell properties. The rotation is specified in radians.
Also, you may specify the names manually:
# Initial property file
0.33
26
6
3
0.3141592653589793
20
3
3
7
7
0.3141592653589793
21
0
3
4
31
13
0.25
0.75
20
name pos:x pos:y length rotation
"00" 160 105 20 1.605
"01" 156 125 17 1.997
"10" 165 130 14 1.997
"11" 170 113 15 1.605
Images must all be placed in a directory. The default is ./frames/ directory, but you can change the name as long as you input the directory in the command line. The names of the images must match 0.png, 1.png, 2.png, and so on.
Command line help:
usage: main.py [-h] [-d DIRECTORY] [-s N] [-f N] [--dist] [-w WORKERS] [-j JOBS] [--keep KEEP] [--strategy STRATEGY] [--cluster CLUSTER] -i
PATTERN -o DIRECTORY -c FILE -x FILE -t TEMP -e TEMP
optional arguments:
-h, --help show this help message and exit
-d DIRECTORY, --debug DIRECTORY
path to the debug directory (enables debug mode)
-s N, --start N starting image (default: 0)
-f N, --finish N final image (defaults to until last image)
--dist use distance-based objective function
-w WORKERS, --workers WORKERS
number of parallel workers (defaults to number of processors)
-j JOBS, --jobs JOBS number of jobs per frame (defaults to --workers/-w)
--keep KEEP number of top solutions kept (must be equal or less than --jobs/-j)
--strategy STRATEGY one of "best-wins", "worst-wins", "extreme-wins"
--cluster CLUSTER dask cluster address (defaults to local cluster)
required arguments:
-i PATTERN, --input PATTERN
input filename pattern (e.g. "image%03d.png")
-o DIRECTORY, --output DIRECTORY
path to the output directory
-c FILE, --config FILE
path to the configuration file
-x FILE, --initial FILE
path to the initial cell configuration
-t TEMP, --temp TEMP starting temperature for the simulated annealing
-e TEMP, --endtemp TEMP
ending temperature for the simulated annealing
python "./main.py" --start 0 --finish 13 --debug "./debug" --input "./input/frame%03d.png" --output "$TEST_DIR/output" --config "./config.json" --initial "./cells.0.csv" --temp 10 --endtemp 0.01