Introduction
Software
Experiment
Data processing
Post-processing and results evaluation
Advanced discussions
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Once your processed your images, removed your background, etc, you are ready to extract peaks. Searching for diffraction spots in usually performed using peaksearch.
To do so, you should look at some random peaks from several images by zooming in (in Fabian) and check out their intensity. Try to estimate a threshold value above which you have a peak and no junk. The threshold should separates peaks from background (everything above the threshold value is a peak, everything below is background).
You can also define several threshold values and see the result.
You can then start the PeakSearch algorithm:
peaksearch.py -n 'stem' -f 'first image number' -l 'last image number' -d 'background' -t 'threshold value 1' -t 'threshold value 2' -t 'threshold value 3' etc
To check the outcome of the peak search, you can load the peaks which were found into Fabian and see if they match the actual peak positions.
To do this, you have to go click on CrystTools –> Peaks –> Read peaks and choose the .flt file which PeakSearch just created. They should appear as red circles on the diffraction image.
You can switch on/off the diffraction spots by clicking on CrystTools –> Peaks –> Show.
