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To save the user-defined mask, click on "Save user-defined static mask" on the mask panel which will save the mask in the scratch folder. For this example, the mask will be saved here:
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You can load the user-defined mask using the "Load user-defined mask" button and selecting mask.npy.
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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: 6
- radius: 2
- 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 160 120 ADUs. A Bragg spot is at least 250 ADUs. Signal to noise ration seems to be high 7, so set the following values.
- thr_low: 160120
- 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 400 ADUs. Set the following values:
- Set atot_thr: 400
You can jump to other events to see if your peak parameters are well tuned. Once you are happy, let's launch the peak finder on the cluster.
The output directory on the peak finder panel should already be automatically set to: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake
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