Table of Contents
Search for peaks
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.
Peak search script
You can then start the PeakSearch algorithm:
peaksearch.py -n stem -f first_image_number -l last_image_number -t threshold1 -t threshold2 -t threshold3 etc
You are working with a dataset in which the background has not been removed in a previous operation, you can add the option -d background where background is the name of you background file. Typically, this could be the median that you calculated at some point.
If you already removed the background (in the diamond spot removal step, for instance), you should not remove any background anymore. This would remove the background twice!
Full example
peaksearch.py -n ../Data/data -f 0 -l 111 -d ../Data/median.edf -t 20
in which
- ../Data/: path to the folder with the .edf files,
- data: the stem (common part) of the .edf files;
- 0: number of the first .edf file,
- 111: number of the last .edf file,
- ../Data/median.edf: name and path of the median image,
- 20: a threshold over which to identify peaks (you can request multiple thresholds with multiple -t options).
There are other parameters you can apply. To get a full list:
peaksearch.py -h
Merging peaks
There is a command to merge peaks extracted with different thresholds into a single peak file, I believe, but I can not remember how to do so.
Evaluating results
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.
Below is an example of Fabian showing a diffraction image in Fabian after background processing and artifact removing as well as the same image with peaks overlay after a peak search.
