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"Data analysis == Piece of cake"
Sections in this tutorial
It is important always a good idea for the people doing analysis to be able to look at the their detector images and probe intensity values. Given that a typical LCLS experiment has millions of snapshots to choose from, it is also critical that you can quickly select images of interest and set regions of interest using masks. By the end of this tutorial, you will be able to browse imageimages, jump to images of interest, generate maskmasks, find peaks in your images and index crystal diffraction patterns.
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Citation for psocake (and other psana-based programs): @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}, } |
Starting psocake in SFX mode
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$ psocake --help |
Mask making
In this example, let's mask out pixels that should not be used for analysis, mask out the jet streak at the centre of the detector, and mask out the water ring.
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You can load the user-defined mask using the "Load user-defined mask" button and selecting mask.npy.
Peak finding
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Jumping to interesting images based on the number of peaks
In the small data panel, type the CXIDB filename:
- filename: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/cxitut13_0010.cxi
- dataset: /entry_1/result_1/nPeaksAll
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- dataset: /entry_1/result_1/index
Indexing crystals
First things first, crystal indexing requires an accurate detector geometry. Latest CXI geometry files can be found here: Geometry history
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- In the diffraction geometry panel, set "Detector distance" to 156mm. Try incrementing this distance in 1mm step till the unit cell parameters are as close as possible to lys.cell. The optimum detector distance is around 158mm.
Everytime the "Detector distance" value is changed by the user, psocake converts the psana geometry (in /reg/d/psdm/cxi/cxitut13/calib/CsPad\:\:CalibV1/CxiDs1.0\:Cspad.0/geometry/10-11.data) to a CrystFEL geom file (in /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/<runNumber>/.temp.geom). - Try drawing a resolution ring on top of the water ring by using “Resolution (pixels)” field. If your detector distance is correct, the crystallographic resolution ring should display 3.2A.
- Run(s): 10
- Sample name: lysozyme
- Queue: psanaq
- CPUs: 24
- Keep CXI images: Off
If you would like to save the detector images in the .cxi file, turn on "Keep CXI images". Only set this to true, if you anticipate that you will want to reindex this run. Otherwise, it's just a total waste of your precious disk space.
As with peak finding, you can launch indexing jobs on multiple runs by specifying runs in the Run(s) field.
Indexing will take some time to complete. If successful, you should see a stream file in: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/cxitut13_10.stream
Jumping to indexed images
In the small data panel, type the CXIDB filename:
- filename: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/cxitut13_0010.cxi
- dataset: /entry_1/result_1/index
Bug/Comments:
Please send bug reports/comments to Chuck:
yoon82@slac.stanford.edu