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# Psocake (Run 18 or newer) source /reg/g/psdm/etc/psconda.sh -py3 # Psocake (Run 17 or older) source /reg/g/psdm/etc/psconda.sh # CrystFEL source /reg/g/cfel/crystfel/crystfel-dev0.9.1/setup-sh # 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:$PATH |
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For this tutorial
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, we will look at experiment cxic00318, run 124, detector jungfrau4M, event 33.
Type "psocake" on your terminal to open up the GUI. For crystallography, we will need to open it in sfx mode (-m):
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$ psocake -m sfx |
1) There are four parameters required to uniquely identify an image at LCLS. Type the (1) experiment name, (2) run number, (3) detector name, and (4) event number in the Experiment Parameters panel.For this tutorial, we will look at experiment cxitut13, run 10, detector DscCsPad, event 11.
2) You can specify the experiment parameters as command line arguments in psocake using the psana-style experiment run string. This is the recommended way of starting psocake:
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$ psocake$ psocake exp=cxitut13cxic00318:run=10124 -d DscCsPad -n 11jungfrau4M -m sfx |
Or you can also use the -e and -r arguments for the experiment and the run number:
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$ psocake -e cxitut13cxic00318 -r 10124 -d DscCsPadjungfrau4M -n 11 -m sfx |
Note: GUI widgets may not respond properly when the GUI is first displayed. Clicking on the terminal window or resizing the GUI will fix this.
During the experiment, you have access to Fast Feedback System which allows you to run psocake from Fast Feedback (FFB) nodes. To do this, append -a ffb. Note that only psffb has access to the data on FFB:
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$ psocake -e cxitut13cxic00318 -r 10124 -d DscCsPadjungfrau4M -n 11 -m sfx -a ffb |
Note that available detector names will be printed on the terminal once you have typed in the experiment name and the run number.
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#######################################
# Available area detectors:
# ('CxiDs1.0:CspadJungfrau.0', 'DscCsPadjungfrau4M', '')
####################################### |
CxiDs1.0:CspadJungfrau.0 is the full detector name. DscCsPad is jungfrau4M is the simpler DAQ alias. DAQ alias. In most cases, Psocake can understand both naming conventions.
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Psocake should have generated directories and files in the experiment directory. At LCLS, all experiments are stored here: /reg/d/psdm/<instrument>/<experiment>. Let's take a moment and check out our directory structure. Either open a new terminal (Remember to 'ssh psana') or use the current terminal ('CntrlCtrl+z' to suspend psocake that is running then 'bg' to run psocake in the background), type the following command:
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$ ls /reg/d/psdm/cxi/cxitut13cxic00318 calib ftc hdf5 results scratch stats usr usrdaq xtc |
calib: This is where all psana calibration is stored. Detector geometry, pedestals, gain, common mode constants, and bad pixelmap.
xtc: This is where all your raw data is stored. XTC is a simple and an efficient format for storing large data . XTCs which can be read using psana. Note you have 4 months to analyse your data before xtcs are moved off to tape.
scratch: This is where psocake saves all the files like .cxi and .stream. This directory is not backed up, so important files need to be move to /resbacked up in /results.
results (or res): This is the results directory which is backed up on tape. After completing your analysis, your results/data should be moved here.
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