Calibration of cspad using cxi02416, cctbx.xfel and DIALS
This page is not intended as a manual for processing XFEL data using cctbx.xfel and DIALS. Rather, this is a documentation of steps taken to calibrate the CSPAD using data collected at CXI in February 2016, on detector Ds2.
The initial metrology deployed by the beamline operator is sufficient to get initial indexing results. Important parameters given by the beamline operators:
- Data is contained in runs 2-16
- Detector address: CxiDs2.0:Cspad.0
- detz_offset (IE the distance from the sample position to the back of the detector rail): 568 mm
Indexing in cctbx.xfel typically is done in a series of trials. By this point, I had done two trials of indexing (trials 0 and 1), working out some spotfinding parameters and accounting for a beam center shift in the metrology. We join this walkthrough at trial 2.
With this information, and this phil file, we can index the data:
for i in `seq 2 16`; do cxi.mpi_submit input.experiment=cxi02416 output.output_dir=/reg/d/psdm/cxi/cxi02416/ftc/brewster/dials \ mp.nproc=36 mp.queue=psanaq output.split_logs=True input.dispatcher=cctbx.xfel.xtc_process \ input.target=cxi02416-lyso-t002.phil input.trial=2 input.run_num=$i; done
This command submits jobs for runs 2 through 16, using the DIALS backend of cctbx.xfel. After indexing is completed, we got 4920 indexed images, as can be shown by this command:
cd /reg/d/psdm/cxi/cxi02416/ftc/brewster/dials ls r0*/002/out/*.json | wc -l
Refine metrology (v1)
Let's call the metrology deployed by the beamline operator version 0 (v0). The following command will do an iterative joint hierarchical refinement of the components of the CSPAD detector. The new tile positions we call version 1 (v1).
bsub -q psanaq -o t002_1k.out cspad.cbf_metrology tag=t002_1k cxi02416-refine.phil reflections=indexed ../r0*/002/out n_subset=1000 split_dataset=True
The program first aggregates the requested number of images into a single dataset. Then, it refines the detector as a whole (including Z position and tilt). Using the new detector position, it refines the quadrants independently from each other, and then the 2x1 sensors, and then the individual panels. Finally, it converts the DIALS format metrology into the SLAC file format (0-end.data).
Here, I've asked it to pick 1000 images at random to refine using this phil file. split_dataset=True means the refinement is done twice independently, using odd numbered or even numbered images, each time using 1000 images. This will be useful later for evaluating the accuracy of the metrology. The output files will be named t002_1k*, set by the tag parameter. Finally, indexing produces two sets of reflection files, bright indexed reflections, and final integrated reflections (can include weak intensities). Here, I've chosen to refine only against the bright reflections by using reflections=indexed.
In order to get a sense of the magnitude of the shifts in panel position after refinement, use the program cxi.display_metrology. For example, the original detector geometry can be displayed thusly:
Compare it to the refined geometry:
You will see a small change in the origin (center arrow) and obvious changes in the quadrant positions. The relative positions of the sensors to each other will not change a large amount, though if you inspect the files themselves you will see changes.
Index using v1 metrology
In order to improve our metrology we will re-index using the new tile positions. We assume we don't have write access to the geometry file for this detector, namely /reg/d/psdm/cxi/cxi02416/calib/CsPad::CalibV1/CxiDs2.0:Cspad.0/geometry/0-end.data. To that end, we need a copy of the calibration directory for the experiment so we can modify it:
cd <a subfolder in your home directory> mkdir -p cxi02416/calib cd cxi02416/calib cp -r /reg/d/psdm/cxi/cxi02416/calib/* . cd CsPad::CalibV1/CxiDs2.0:Cspad.0/geometry mv 0-end.data 0-end.data.v0 ln -fns <path to 0-end.data.t002_1k_1> 0-end.data
We optionally use softlinks here to avoid duplicating data. We can now reprocess the data as trial 3:
for i in `seq 2 16`; do cxi.mpi_submit input.experiment=cxi02416 output.output_dir=/reg/d/psdm/cxi/cxi02416/ftc/brewster/dials \ mp.nproc=36 mp.queue=psanaq output.split_logs=True input.dispatcher=cctbx.xfel.xtc_process \ input.target=cxi02416/lyso-t003.phil input.trial=3 input.run_num=$i input.cfg=cxi02416-calibdir.cfg; done
The input phil file is the same as before. However, to instruct psana to use the modified calibration directory, we add a psana config file named cxi02416-calibdir.cfg with these lines:
[psana] calib-dir = <a subfolder in your home directory>/cxi02416/calib
If you have write permissions to your geometry folder, you don't need to use this config file or make a copy of your calibration directory. We recommend saving the original metrology like we did in the above example, by renaming it to 0-end.data.v0, so you can return to it as needed.
Indexing with the new metrology yielded 5484 indexed images.