The first step is the measurement of the grown of root angles based on a set of still images taken over time from a digital camera. There are 161 sets of these images, located in the directory on the web
http://phytomorph.wisc.edu/osgschool/datasets/
in files 1.tar through 161.tar (inclusive)
The first step is to find the set of base and axial root angles for each set of images as they grow. Fortunately, that's been done for you. Unfortunately, it has been implemented in matlab. We've already compiled this matlab for you, and written a wrapper script to take care of most of the details.
on the user school submit machine, in the directory ~gthain, there is a file findAngles, which is the compiled matlab program. The matlab program takes as an argument the index of the tar file to analyze (i.e. 151). Given that, it will open 151.tar and create two files, 151_angle_1.csv and 151_angle_2.csv
However, this compiled matlab program can't be run on it's own. It can only be run from the runMatlab.pl wrapper (also provided in that directory), which takes as its argument the name of the compiled matlab program, followed by that program's arguments (if any). Because runMatlab.pl is the "real" executable, note that findAngles must be transfered along with the rest of the input files. runMatlab.pl requires three tarballs as inputs: r2001b.tar.gz SLIBS1.tar.gz and SLIBS.tar.gz (again, in the same directory).
Once all 161 instances have finished, there is some smoothing that needs to happen. This is done with the averagePhenotypes2 compiled matlab program, which sould be run just as above. This matlab program takes no arguments, but assumes that the file genotypes.csv exists in it's current directory (provided), and that angles.tar exists there also. angles.tar is a tar file, containing all the angle output files generated by findAngles.