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software:timelessdiamondspotremoval
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software:timelessdiamondspotremoval [2019/02/12 13:53] smerkel created |
software:timelessdiamondspotremoval [2019/09/03 13:43] (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: 2019/02/18 10:11 (external edit)
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