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--- processing:search_for_peaks [2019/02/14 22:12] – smerkel
+++ processing:search_for_peaks [2026/08/10 10:55] (current) – smerkel
@@ Line 1: / Line 1: @@
-===== Search for peaks =====
+====== 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 [[software:peaksearch|peaksearch]].
-To do so, you should look at some random peaks from several images by zooming in (in [[software:fabian|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).
+To do so, you should look at some random peaks from several images by zooming in (in the [[software:timeless_viewer|TIMEleSS Viewer]]) 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.
@@ Line 11: / Line 11: @@
 You can then start the [[software:peaksearch|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
+  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 [[software:fabian|Fabian]] and see if they match the actual peak positions.
+To check the outcome of the peak search, you can load the peaks which were found into the [[software:timeless_viewer|TIMEleSS Viewer]] and see if they match the actual peak positions.
+To do this, you have to go click on //3D-XRD extra// --> //Read peaks from..// and choose the //.flt// file which PeakSearch just created. Then select //3D-XRD extra// --> //Show peaks//
+They should appear as red circles on the diffraction image.
+You can switch on/off the diffraction spots by clicking on //3D-XRD extra// --> //Show peaks//.
-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.
+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. We now use the [[software:timeless_viewer|TIMEleSS Viewer]] and it should look quite similar.
-You can switch on/off the diffraction spots by clicking on //CrystTools// --> //Peaks// --> //Show//.
+[{{:processing:diff-1345-diamond-removed.jpg?300 |Diffraction image in Fabian after background processing and artifact removing)}}][{{ :processing:diff-1345-peaks.jpg?300|Same image showing peaks after peak search }}]