diff --git a/README.md b/README.md index daca5270726c844fe6bb3f20c9eaa72b0394dcb7..11e17e0fd700b7433d26f809a1c13f5fc330e6a6 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,45 @@ To run Chore.jar in the command line, you must have [Java 8](https://docs.oracle ``` export JAVA_HOME=`/usr/libexec/java_home -v 1.8.0` -java -Xincgc -Xms4000m -Xmx4000m -jar /Volumes/TOSHIBA/Chore.jar -t 20 -p 0.105 --plugin Reoutline::exp --plugin Respine::0.23::tapered=0.28,1,2 --plugin SpinesForward::rebias --minimum-biased 3 -S --plugin LarvaCast::angle -N all -o nNpsSlLwWaAmkbcdxyuvorP /path/to/folder/of/each/experiment +java -Xincgc -Xms4000m -Xmx4000m -jar /Volumes/TOSHIBA/Chore.jar -t 20 -p 0.105 --plugin Reoutline::exp --plugin Respine::0.23::tapered=0.28,1,2 --plugin SpinesForward::rebias --minimum-biased 3 -S --plugin LarvaCast::angle -N all -o nNpsSlLwWaAmkbcdxyuvorPM /path/to/folder/of/each/experiment ``` -The path to each folder follows: /genotype/protocol/date. The command above produces one `.dat` file for each larva tracked within the folder. To batch process `.dat` files for each genotype, check out the Jupyter notebook in directory [Choreograph](https://gitlab.pasteur.fr/anzhou/dgrp-behavior/-/blob/main/Choreograph) \ No newline at end of file +The path to each folder follows: /genotype/protocol/date. The command above produces one `.dat` file for each larva tracked within the folder. To batch process `.dat` files for each genotype, check out the Jupyter notebook in directory [Choreograph](https://gitlab.pasteur.fr/anzhou/dgrp-behavior/-/blob/main/Choreograph) + +Below are the full definitions of Choreograph metrics + +``` +t time -- always the first column unless included again +f frame -- the frame number +D id -- the object ID +n number -- the number of objects tracked +N goodnumber -- the number of objects passing the criteria given +p persistence -- length of time object is tracked +e area +s speed +S angular -- angular speed +l length -- measured along major axis, not curve of object +L rellength -- instantaneous length/average length +w width +W relwidth -- instantaneous width/average width +a aspect -- length/width +A relaspect -- instantaneous aspect/average aspect +m midline -- length measured along the curve of object +M morphwidth -- mean width of body about midline +k kink -- head/tail angle difference from body (in degrees) +b bias -- fractional excess of time spent moving one way +P pathlen -- distance traveled forwards (backwards=negative) +c curve -- average angle (in degrees) between body split into 5 segments +d dir -- consistency of direction of motion +x loc_x -- x coordinate of object (mm) +y loc_y -- y coordinate of object (mm) +u vel_x -- x velocity (mm/sec) +v vel_y -- y velocity (mm/sec) +o orient -- orientation of body (degrees, only guaranteed modulo pi) +r crab -- speed perpendicular to body orientation +C custom -- calls plugin +1 tap -- whether a tap (stimulus 1) has occurred +2 puff -- whether a puff (stimulus 2) has occurred +3 stim3 -- whether the first custom stimulus has occurred +4 stim4 -- whether the second custom stimulus has occurred + +``` \ No newline at end of file