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--- processing:search_for_peaks [2019/02/14 22:11] – smerkel
+++ processing:search_for_peaks [2019/02/20 22:51] (current) – smerkel
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-===== Search for peaks =====
+====== Search for peaks ======
 Once your processed your images, removed your background, etc, you are ready to extract peaks.
@@ 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 ====
@@ Line 20: / Line 41: @@
 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.
+[{{: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 }}]