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processing:search_for_peaks
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processing:search_for_peaks [2019/02/14 21:11] smerkel |
processing:search_for_peaks [2019/02/20 21:51] (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. | 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: | 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 ==== | ==== Evaluating results ==== | ||
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| You can switch on/off the diffraction spots by clicking on //CrystTools// --> //Peaks// --> //Show//. | 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 }}] | ||
processing/search_for_peaks.1550178678.txt.gz · Last modified: 2019/02/18 10:11 (external edit)
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