Python Scripted Calibration

First: do not run this on the Maxell gateway. Rather, salloc a node for yourself first:

salloc -p exfel/upex -t 01:00:00

where -p gives the partition to use: exfel or upex and -t the duration the node should be allocated. Then ssh onto that node.

(optionally) Set up the environment:

source setup_env.sh

On Maxwell execution rights might be stripped. If you get an error for the above command, first run:

chmod +x setup_env.sh

If running headless, be sure to set MPLBACKEND=Agg, via:

export MPLBACKEND=Agg

This is automatically done if you source the environment script.

Run the script:

python calibrate.py --input /gpfs/exfel/exp/SPB/201701/p002012/raw/r0100 \
   --output ../../test_out --mem-cells 30 --detector AGIPD --sequences 0,1

Here --input should point to a directory of RAW files for the detector you are calibrating. They will be output into the folder specified by --output, which will have the run number or the last folder in the hiearchy of the input appended. Additionally, you need to specify the number of --mem-cells used for the run, as well as the --detector. Finally, you can optionally specify to only process certain --sequences of files, matching the sequence numbers of the RAW input. These should be given as a comma-separated list.

You'll get a series of plots in the output directory as well.