This script is part of the TIMEleSS tools. It is meant to be used when cleaning up diamond anvil cell data
timelessDiamondSpotRemoval -h
Diamond spot removal for 3D-XRD in the DAC
This is part of the TIMEleSS project
http://timeless.texture.rocks
usage: usage: timelessDiamondSpotRemoval [options] todo
Usage:
- timelessDiamondSpotRemoval [options] spots: test spot detection parameters
- timelessDiamondSpotRemoval [options] plotMask: try to create a mask a plot an overlay of images and corresponding mask
- timelessDiamondSpotRemoval [options] clearMask: create a mask and display images with median and mask removed
- timelessDiamondSpotRemoval [options] save: save new images with median and mask removed in EDF
Basic examples:
- timelessDiamondSpotRemoval -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 -s Edf-P02-Ti-Close-Filtered save
Complex example:
- 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.
This is part of the TIMEleSS project
http://timeless.texture.rocks
positional arguments:
todo What shall we do? Options are spots, plotMask, clearMask, save
optional arguments:
-h, --help show this help message and exit
-n STEM, --stem STEM Stem for EDF image files (required)
-f FIRST, --first FIRST
First image number (mendatory)
-l LAST, --last LAST First image number (mendatory)
-m MEDIAN, --median MEDIAN
Name of median image (mendatory)
-P PATH, --path PATH Path to EDF images. Default is ./
--newpath NEWPATH Path to save the new EDF image. Default is ./
-d DIGITS, --digits DIGITS
Number of digits for file number. Default is 4
-e EXT, --ext EXT Extension for EDF images. Default is edf
--scale SCALE X dimension to which the image will be reduced (in pixels, the image is assumed to be square, used to blur the image). Default is 400
--filtersize FILTERSIZE
Width of median filter to ignore small spots in diamond detection (in pixels). Default is 4
-t THRESHOLD, --threshold THRESHOLD
Threshold for diamond spot detection, in multiples of image mean intensity. Default is 2.0
--growXY GROWXY Number of pixels to grow the mask in X and Y (useless in spot detection). Default is 15
--growXYO GROWXYO Number of pixels to grow the mask in X, Y, and omega (useless in spot detection). Default is 2
--c_rawy C_RAWY Raw Y 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.
--inpaint INPAINT If set to True, fill diamond mask with inpainting. If not set, diamond mask is filled with median value.