Running this code

Download sample data file (see next section for information on how this file was created)

wget http://mag.gmu.edu/git-data/GaryQ-Physics/magnetosphere/SCARR5_GM_IO2/IO2/3d__var_3_e20031120-070000-000.out.cdf
# or
curl -O http://mag.gmu.edu/git-data/GaryQ-Physics/magnetosphere/SCARR5_GM_IO2/IO2/3d__var_3_e20031120-070000-000.out.cdf

Install Kameleon

https://ccmc.gsfc.nasa.gov/Kameleon/Quick_start.html#kameleon-installers

Install SciPy compatable with Python 2.7 (Kameleon is not Python 3 compatable)

~/kameleon/bin/pip install scipy==0.16

Run Kameleon using Python 2.7

~/kameleon/bin/python2 cut_plane.py

Converting .out to .cdf

Download kameleon-converter-5.2.0.tgz located at

http://mag.gmu.edu/git-data/GaryQ-Physics/magnetosphere/kameleon-converter/

into /tmp. Follow the compilation instructions in the package. This process is complicated and requires first compiling libcdf. Libargtable2 packages may be needed and packages for Ubuntu are at the above URL.

Download the .out files

wget -m -nH -R index*,*.gif --cut-dirs=2 http://mag.gmu.edu/git-data/sblake/SCARR5_GM_IO2/

Convert the files

cd SCARR5_GM_IO2/IO2
ls -1 3d_*.out | xargs -i /tmp/kameleon-converter/kameleon-converter-v5.2.0/kameleon -v -f cdf -m batsrus -o . {}