Data Processing at SACLA

Obtaining metadata like detector position

1) AgBeh (silver behenate). Determine detector distance and beam center --> update SACLA-provided *.geom file (CrystFEL format) --> run sacla geom to json on *.geom to get equivalent for DIALS processing

2) h5_mpi_submit --> launches dials.stills_process with process.phil, and queueing options Specify what runs (integers)

DIALS workflow

dials.import file.h5 (the h5 will have 1000's of images in it) --> datablock.json. Has experimental models as abstracted from image header

dials.find_spots datablock.json --> strong.pickle

dials.index strong.pickle datablock.json --> indexed.pickle experiments.json

dials.refine --> refined_experiments.json refined_reflections.pickle

dials.integrate

Aggregate processing at XFELS

Need to submit a single job for each *.h5 file (manually, or write a script) Instead of running the individual steps: dials.stills_process *.h5 process.phil

Phil file must have good parameters for data processing. Take one from previous users.