EXFEL data process repo (xfl_dp)
It's a package called xfl_dp written for post processing of XFEL AGIPD data preprocessed by cheetah. The package is written in Python 3.X.
Features
The package performs triming out black images, intensity normalization, applying AGIPD geometry to stitch frames and writing frames and their corresponding pulseIDs and trainIDs in the cxi file.
Required dependencies:
- NumPy
- h5py
- cfelpyutils
How to use
You can import the package or use it as a command line tool:
$ python3 -m xfl_dp --help
usage: __main__.py [-h] [-n] [-o] [-v] rnum cnum tag [limit] [outpath]
Run XFEL post processing of cheetah data
positional arguments:
rnum run number
cnum cheetah number
tag cheetah tag associated with the current run (written after
a hyphen in the cheetah folder name)
limit minimum ADU value to trim out black images
outpath output folder location to write processed data
optional arguments:
-h, --help show this help message and exit
-n, --normalize normalize frame intensities
-off, --offline offline - run not in Maxwell cluster for debug purposes
-v, --verbosity increase output verbosity
$ python -m xfl_dp -v 206 0 mll 500 -off
List of typed arguments:
normalize = False
cnum = 0
verbosity = True
tag = mll
limit = 20000
outpath =
offline = True
rnum = 206
cheetah data is located in /gpfs/exfel/u/scratch/MID/201802/p002200/cheetah/hdf5/r0206-mll/XFEL-r0206-c00.cxi
Writing data to folder: /Users/simply_nicky/OneDrive/programming/XFEL/hdf5/r0206-processed/XFEL-r0206-c01-processed.cxi
Done