"Data analysis == Piece of cake"
Sections in this tutorial
It is always a good idea for the people doing analysis to be able to look at 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 images, jump to images of interest, generate masks, change the x,y,z positions of your detector, find peaks in your images and index crystal diffraction patterns.
Starting psocake in SFX mode
If you are on a psana machine, set up your environment by adding these lines to .bashrc (or your start up script):
Type "psocake" on your terminal to open up the GUI. For crystallography, we will need to open it in sfx mode (-m):
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.
Or you can also use the -e and -r arguments for the experiment and the run number:
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:
CxiDs1.0:Cspad.0 is the full detector name. DscCsPad is the simpler DAQ alias. Psocake can understand both naming conventions.
To check psocake version:
Don’t worry if you don’t remember these arguments. You can view argument options using --help:
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 ('Cntrl+z' to suspend psocake that is running then 'bg' to run psocake in the background), type the following command:
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 efficient format for storing large data. XTCs 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 /res.
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.
In this section, let's learn how to mask out pixels that should not be used for analysis (such as dead pixels), mask out the jet streak at the centre of the detector, and mask out the water ring (just for fun!).
Note: the Image Panel must be in the default "greyscale" colormap for the mask colors to display properly.
1) In the mask panel, click on "Use psana mask". This will mask out the following pixels that should not be used for analysis; calib, status, edge, central, unbonded pixels, unbonded pixel neighbor pixels. These masked pixels are shown as green on the image panel.
2) On the mask panel, click on "Use streak mask". This will mask out strong intensities originating from the edges of the central asics. The streak mask varies shot-to-shot.
3) To make a donut mask over the water ring, click on "Use user-defined mask". This will bring up a cyan circle, cyan polygon and cyan square mask generators.
Select "Toggle" in Masking mode. Move the cyan circle to the centre of the detector by dragging the circle. Resize the cyan circle by dragging the diamond on the perimeter. Once you are happy with the position, click "mask circular ROI" button on the mask panel.
Increase the cyan circle again by dragging the diamond on the perimeter. Click "mask circular ROI" button on the mask panel. Because we are in the "toggle" mode, the previous mask gets toggled and disappears. The area that does not overlap with the previous mask get masked out.
To save the user-defined mask, click on "Save static mask" on the mask panel which will save the mask in the scratch folder. This will combine the green and blue masks into a single mask. For this example, your mask will be saved here:
/reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/mask.npy (unassembled 3D ndarray)
/reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/mask.txt (2D text)
You can load the user-defined mask using the "Load mask" button and selecting mask.npy.
mask.txt is compatible with the calibration manager application, calibman.
To delete the mask on the screen, select "Unmask" under Masking mode. Drag a blue circle mask generator over the detector and click "Stamp circular mask".
In this section, we will find peaks on the detector image. To find the peaks on the image, set the "Algorithm" to “Droplet” in the Peak Finder panel. Details of the peak finding algorithm is given here: Hit and Peak Finding Algorithms#Twothreshold"Dropletfinder". You should notice peaks being highlights in the Image panel.
- Set npix_min: 2
- Set npix_max: 8
- radius: 2
- thr_low: 120
- thr_high: 250
- son_min: 7
Hover the mouse pointer over the Bragg peaks to study the intensities. The sum of the Bragg peak pixels are above 500 ADUs. Set the following values:
- Set atot_thr: 500
- Run(s): 10
- Queue: psanaq
- CPUs: 2
- Number of events to process: 50
At the time of writing this documentation, psanaq is quite busy processing 7466 jobs. 6612 jobs are pending. 854 jobs are currently running. For more information on which queue you are allowed to use, see Batch System Analysis Jobs#BatchNodes
Jumping to interesting images based on the number of peaks
In the small data panel, you should see the CXIDB filename:
- filename: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/cxitut13_0010.cxi
- dataset: /entry_1/result_1/nPeaksAll
First things first, crystal indexing requires an accurate detector geometry. Latest CXI geometry files can be found here: Geometry history
Detector panels can manually adjusted using: calibman
- In the diffraction geometry panel, set "Detector distance" to 156mm.
- In the indexing panel, tick "Indexing on". If indexing succeeds, the integrated (predicted) peaks will be marked with magenta circles. These triple rings represent the integration radius. A magenta triangle means wait. If indexing fails, you will see a magenta X.
- If you see magenta circles and magenta unitcell appear, congratulations! You have indexed your first pattern using psocake.
- 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).
Indexing panel uses CrystFEL to index the diffraction patterns, so the input parameters in the indexing panel should be familiar to you if you've used indexamajig before.
CrystFEL geometry: This geometry file is automatically converted from our psana geometry to CrystFEL geometry for you. Feel free to look inside .temp.geom. If you have a CrystFEL geometry file that you know is good, you can simply type it in. Psocake will never modify this file even if you change the "detector distance" in the diffraction geometry panel. (Just don't name your geometry .temp.geom, it will get overridden). You can also deploy the CrystFEL geometry as a psana geometry by clicking "Deploy CrystFEL geometry" in the indexing panel.
Integration radii: These 3 numbers define the radius of two concentric rings about each Bragg spot. Inner ring is used to integrate the Bragg spot and the outer ring is used to estimate the background. Try adjusting these numbers and see what is being integrated on screen. It should be large enough to fit a Bragg spot inside the inner ring.
PDB: If you have a CrystFEL unitcell, you can constrain the indexing algorithms to look for this unit cell.
Indexing method: Default is mosflm-noretry, dirax. "retry" is used to speed up mosflm (it can take few seconds).
Tolerance: These 4 numbers define how much wriggle room you want for indexing. 5, 5, 5 are the tolerance level for unitcell axes a, b, c. 1.5 is the tolerance level for the angles alpha, beta, gamma.
Extra CrystFEL parameters: You can enter extra parameters for indexamajig in this field. It will be appended at the end of the command line, e.g. --profile will turn on the processing timing information.
Let's try to index another diffraction pattern at event 44.
- In the experiment parameters panel, set Event Number to 44.
- You should see the magenta triangle appear again. Wait few seconds and hopefully you will have indexed another pattern.
Hopefully, you have indexed this diffraction pattern. Notice that the unitcell parameters are a bit off compared to what is expected. Let's load a CrystFEL unitcell file to help the indexer along.
- In the Indexing panel, set the PDB field to: /reg/d/psdm/cxi/cxitut13/scratch/psocake/lys.cell
- Run(s): 10
- Sample name: lysozyme
- Queue: psanaq
- CPUs: 24
- Keep CXI images: On
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_0010.stream
You can check the status of your indexing job here: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/status_index.txt
Psocake saves the detector images of only the hits in the .cxi file. It is likely that you may want to reindex these files to optimize the indexing rate. If you anticipate that you have finalized the indexing parameters, set 'Keep CXI images' to Off. It will delete the detector images in your .cxi file which will free up your precious disk space for doing other things.
As with peak finding, you can launch indexing jobs on multiple runs by specifying runs in the Run(s) field.
Indexing multiple lattices
CrystFEL can index multiple lattices per image. Set "Extra CrystFEL parameters" to --multi,--no-check-peaks. This will enable "subtract and retry" method.
Indexing pump-probe experiments
In a pump probe experiment, it is sometimes desirable to index only certain events, e.g index only the pumped crystals. This information is recorded in the EVR which psocake saves in the .cxi file.
So if you want to index only the hits with laser on (say EVR1: 182), then type the following in the "Index condition" field:
182 in #evr1#
Psocake will also accept combinations using AND/OR:
182 in #evr1# and 173 in #evr1#
You can attach a tag to the stream filename by using the "Tag" field, e.g. evr182 would produce cxitut13_0010_evr182.stream.
Let's check whether your detector is well centered with respect to your beam. You want the centre to be as accurate as possible (at least to a pixel accuracy) for high indexing rates (>40%).
Load the powder rings generated by clicking the "Load image" button in the Image Control panel. Open "cxitut13_0010_maxHits.npy". Adjust the intensity as necessary.
Draw resolution rings by ticking "Resolution rings" in the Diffraction Geometry panel. You can change the ring resolution by typing number in "Resolution (pixels)". Type 165 and see whether your powder rings overlap with the resolution rings. If they do, then the detector is centered. If not, then you can click on the "Deploy automatically centred geometry" to recenter your detector. If you are unhappy with the results, you can use "Deploy manually centred geometry" which will shift the detector centre to the centre of the green ROI circle.
Since we are at run10, the newly deployed geometry file is named 10-end.data. If there already exists a geometry file with the same name, it will be renamed to 10-end.data-<timeModified>
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
For viewing the electron density, use coot contained inside phenix.
Beam Parameters for Publications
Please send bug reports/comments:
Tiny url for this tutorial: http://tinyurl.com/zj4m23n