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Sections in this tutorial
- Starting psocake
- Mask making
- Peak finding
- Jumping to interesting images based on the number of peaks
Indexing crystals
Psocake is a graphical user interface (GUI) for looking at detector images at LCLS. By the end of this tutorial, you will be able to generate mask, find peaks in your images and index crystal diffraction patterns.
- Starting psocake
- Mask making
- Peak finding
- Jumping to interesting images based on the number of peaks
Indexing crystals
Starting psocake
Make sure you have the psana environment setup (psana python Setup) before starting this tutorial. Also, check out a kerberos ticket by typing “kinit” which is needed for communicating with the experiment e-Log.
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Examine the peaks found by zooming in/out with the middle mouse scroll (or a two finger slide on a Mac touchpad). Notice that the Bragg peaks are composed of 2 to 6 connected pixels. Setting the radius to 2 sets a 5x5 cyan boundary around the Bragg peaks (radius x 2+1 = 5). Change the following values in the Peak Finder panel.
- Set npix_min: 2
- Set npix_max: 5
- radius: 2
Hover the mouse pointer over the Bragg peaks to study the intensities. Notice that the weaker pixel intensities inside a Bragg peak is around 80 ADUs. The sum of the Bragg peak pixels are above 400 ADUs. Set the following values:
Set amax_thr:
80- Set atot_thr: 400
Move the green square over the water ring to study the level of background noise in the ROI Histogram panel. Notice that the water ring intensities can go up to 160 ADUs. Signal to noise ration seems to be around 4, so set the following values.
- thr_low: 160
- thr_high: 160
- son_min: 4
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