Difference between revisions of "Cxi02416 calibration"

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(Created page with "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 docume...")
 
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Calibration of cspad using cxi02416, cctbx.xfel and DIALS
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== 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.
 
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.
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== Initial indexing ==
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The initial metrology deployed by the beamline operator is sufficient to get initial indexing results.  Important parameters given by the beamline operators:
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* Data is contained in runs 2-16
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* Detector address: CxiDs2.0:Cspad.0
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* detz_offset (IE the distance from the sample position to the back of the detector rail): 568 mm
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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.
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With this information, and [[cxi02416-lyso-t002.phil | this phil file]], we can index the data:
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  for i in `seq 2 16`; do cxi.mpi_submit input.experiment=cxi02416 output.output_dir=/reg/d/psdm/cxi/cxi02416/ftc/brewster/dials \
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    mp.nproc=36 mp.queue=psanaq output.split_logs=True input.dispatcher=cctbx.xfel.xtc_process \
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    input.target=cxi02416-lyso-t002.phil input.trial=2 input.run_num=$i; done
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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:
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  cd /reg/d/psdm/cxi/cxi02416/ftc/brewster/dials
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  ls r0*/002/out/*.json | wc -l
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== Refine metrology (v1) ==
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== Index using v1 metrology ==
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== Refine metrology (v2) ==
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== Evaluate metrology ==
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== Deploy metrology ==

Revision as of 14:47, 21 March 2016

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.

Initial indexing

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)

Index using v1 metrology

Refine metrology (v2)

Evaluate metrology

Deploy metrology