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To run the script, use the executable file run.sh in the folder scripts. It works on a cluster where a SLURM manager is installed, typing the command:

sbatch scripts/run.sh

To run it in parallel mpi4py and the h5py Python modules are needed. h5py must be built with MPI support (instructions can be found here http://docs.h5py.org/en/latest/mpi.html).

WARNING! The main script hitfinding.py is now set to work on the specific CXIDB file cxidb-78.cxi (downloadable at the linked page). To change the files to work on, change cfgfile/XXX.ini and the run.sh file accordingly. Moreover, to change the directories where the data are taken from or/and saved, change the following variables in the code in the main script:

dir_darkrun = '/absolut_path_to_folder'

dir_raw_data = '/XXX/'

wdir = '/XXX/'

Statistical Hit-finder

The script performs a series of preprocessing steps on diffraction data collected at the CXI Instrument @LCLS X-ray Free Electron Laser facility ([1,2]):

• pedestals (dark subtraction)
• per-column correction [3]
• pixels' gain calculation
• poisson mask determination
• mean photon count per pixel calculation
• loglikelihood score calculation

The ipython notebooks file (included in the folder ipynb -- FOLDER TO BE INCLUDED) perform:

• normalization of the scores
• definition of a suitable threshold
• data plotting