Page History
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Citation for psocake (and other psana-based programs): @Article{Thayer2017, author="Thayer, J. and Damiani, D. and Ford, C. and Dubrovin, M. and Gaponenko, I. and O'Grady, C. P. and Kroeger, W. and Pines, J. and Lane, T. J. and Salnikov, A. and Schneider, D. and Tookey, T. and Weaver, M. and Yoon, C. H. and Perazzo, A.", title="Data systems for the Linac coherent light source", journal="Advanced Structural and Chemical Imaging", year="2017", month="Jan", day="14", volume="3", number="1", pages="3", issn="2198-0926", doi="10.1186/s40679-016-0037-7", url="https://doi.org/10.1186/s40679-016-0037-7"} @article{Damiani:zw5004, author = "Damiani, D. and Dubrovin, M. and Gaponenko, I. and Kroeger, W. and Lane, T. J. and Mitra, A. and O'Grady, C. P. and Salnikov, A. and Sanchez-Gonzalez, A. and Schneider, D. and Yoon, C. H.", title = "{Linac Coherent Light Source data analysis using {it psana}}", journal = "Journal of Applied Crystallography", year = "2016", volume = "49", number = "2", pages = "672--679", month = "Apr", doi = {10.1107/S1600576716004349}, url = {http://dx.doi.org/10.1107/S1600576716004349}, } |
Please connect to psana machines via NoMachine for less lag in graphics. Instructions here: Remote Visualization
Starting psocake in SFX mode
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# PSOCAKE2 (Run 17 or older) function psocake2 () { echo "Activating psocake py2" source /reg/g/psdm/etc/psconda.sh -py2 source /reg/g/cfel/crystfel/crystfel-0.8.0/setup-sh # CrystFEL compatible version for psocake2 } # PSOCAKE3 (Run 18 or newer) function psocake3 () { echo "Activating psocake py3" source /reg/g/psdm/etc/psconda.sh -py3 source /reg/g/cfel/crystfel/crystfel-0.9.1/setup-sh # Crystfel compatible version for psocake3 } # CCP4 (version may change) source /reg/common/package/ccp4-7.1/bin/ccp4.setup-sh # XDS export PATH=/reg/common/package/XDS-INTEL64_Linux_x86_64:$PATH |
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Mask making
In this section, let's you will learn how to mask out pixels that should not be used for analysis (such as dead pixels and shadows), mask out the jet streak at the centre of the detector, and mask out the water ring (just for fun!). Masked out regions are ignored during peak finding and during Bragg spot integration.
Note: the Image Panel must be in the default "greyscale" colormap for the mask colors to display properly.
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$ squeue -u <username> |
For more information on which queue you are allowed to use, see Batch Nodes And QueuesJobs
A logfile of the peak finding is also saved under the same directory, <jobID>.log.
If the status stays in PD or SUSP mode for awhile, then you may want to kill the jobs. To kill a batch job, type "scancel <jobID>".
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Overview
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