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software:timelessdiamondspotremoval

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software:timelessdiamondspotremoval [2019/02/12 14:53] – created smerkelsoftware:timelessdiamondspotremoval [2019/09/03 15:43] (current) – smerkel
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 Usage: Usage:
- - diamondSpotRemoval.py [options] spots: test spot detection parameters + - timelessDiamondSpotRemoval [options] spots: test spot detection parameters 
- - diamondSpotRemoval.py [options] plotMask: try to create a mask a plot an overlay of images and corresponding mask + - timelessDiamondSpotRemoval [options] plotMask: try to create a mask a plot an overlay of images and corresponding mask 
- - diamondSpotRemoval.py  [options] clearMask: create a mask and display images with median and mask removed + - timelessDiamondSpotRemoval  [options] clearMask: create a mask and display images with median and mask removed 
- - diamondSpotRemoval.py  [options] save: save new images with median and mask removed in EDF+ - timelessDiamondSpotRemoval  [options] save: save new images with median and mask removed in EDF
  
 Basic examples: Basic examples:
- - diamondSpotRemoval.py -P Edf-P02-Ti-Close -n P02-Ti-02_ -m P02-Ti-02_m20100.edf -f 50 -l 65 spots + - timelessDiamondSpotRemoval -P Edf-P02-Ti-Close -n P02-Ti-02_ -m P02-Ti-02_m20100.edf -f 50 -l 65 spots 
- - diamondSpotRemoval.py -P Edf-P02-Ti-Close -n P02-Ti-02_ -m P02-Ti-02_m20100.edf -f 50 -l 65 -s Edf-P02-Ti-Close-Filtered save+ - timelessDiamondSpotRemoval -P Edf-P02-Ti-Close -n P02-Ti-02_ -m P02-Ti-02_m20100.edf -f 50 -l 65 -s Edf-P02-Ti-Close-Filtered save
  
 Complex example: Complex example:
- - diamondSpotRemoval.py -P Edf-P02-Ti-Close -n P02-Ti-02_ -m P02-Ti-02_m20100.edf -f 50 -l 65 --growXY=25 --growXYO=2 --c_rawy=1097 --c_rawz=922 --radius=300 --filtersize=3 -t 1.5 -s Edf-P02-Ti-Close-Filtered/ save+ - timelessDiamondSpotRemoval -P Edf-P02-Ti-Close -n P02-Ti-02_ -m P02-Ti-02_m20100.edf -f 50 -l 65 --growXY=25 --growXYO=2 --c_rawy=1097 --c_rawz=922 --radius=300 --filtersize=3 -t 1.5 -s Edf-P02-Ti-Close-Filtered/ save
  
 Typically, you start by testing the spot parameters and improve you match by playing with the threshold and filtersize parameter, and you then try creating a mask. Typically, you start by testing the spot parameters and improve you match by playing with the threshold and filtersize parameter, and you then try creating a mask.
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   --c_rawz C_RAWZ       Raw Z position of beam center (can be read directly in Fabian, plot your image with orientation 1 0 0 1, it is the first number displayed to locate the cursor). Used to ignore a disk at the center of the image. If you have large intensity spots which are not diamond in there.   --c_rawz C_RAWZ       Raw Z position of beam center (can be read directly in Fabian, plot your image with orientation 1 0 0 1, it is the first number displayed to locate the cursor). Used to ignore a disk at the center of the image. If you have large intensity spots which are not diamond in there.
   --radius RADIUS       Radius of disk to ignore around the beam center (in pixels, optional). c_rawy and c_rawz are mendatory if you want to use this option. . Used to ignore a disk at the center of the image. If you have large intensity spots which are not diamond in there.   --radius RADIUS       Radius of disk to ignore around the beam center (in pixels, optional). c_rawy and c_rawz are mendatory if you want to use this option. . Used to ignore a disk at the center of the image. If you have large intensity spots which are not diamond in there.
 +  --inpaint INPAINT     If set to True, fill diamond mask with inpainting. If not set, diamond mask is filled with median value.
 </code> </code>
software/timelessdiamondspotremoval.1549979607.txt.gz · Last modified: (external edit)