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To run a precompiled version of cctbx:
source ~monarin/cida
To install psana-conda and cctbx,
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A sample of job submission command can be found here: /reg/d/psdm/xpp/xpptut15/res/exafel_demo/
Old instructions (no need if above works):
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For cctbx, see http://viper.lbl.gov/cctbx.xfel/index.php/Installation#Standard_installation_using_PSDM
Calibration
| Averaging dark images | cxi.mpi_average -x expname -r runno -a detector_address -d dez_offset -v -g gain_scale_factor -R * -R tell CDL to get the raw images. Option: Using bsub for i in `seq min max`; do bsub -n 12 -q psana_queue -o avg_r$i.log mpirun cxi.mpi_average -x expname -r $i -a detector_address -d dez_offset -v -g gain_scale_factor; done |
| Create mask | cxi.make_dials_mask --maxproj-min=Light_ADU -o mask.pickle Dark_avg.cbf Dark_std.cbf Light_max.cbf |
| Calibration using composite powder image | cspad.quadrants_cbf Light_max.cbf -p Option: to combine all light-max images cxi.cspad_average *_max*.cbf -m all_max.cbf |
| Deploy new calibration | cxi.cbfheader2slaccalib cbf_header=experiment_calibration_cc.cbf Option: organize calibration file mv /exp/calib/0-end.data/address/geometry0-end.data 0-end.data.v0 cp /new/geometry/0-end.data 0-end.data.v1 ln -s 0-end.data.v1 0-end.data |
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