====== Masking diamond anvil cell shadows ======

This script is part of the [[software:timelesstools|TIMEleSS tools]]. It is meant to be used when [[processing:clean-diamond-anvil-cell-data|cleaning up diamond anvil cell data]]

<code>
timelessDACShadow -h

Dealing with shadows in 3D-XRD in the DAC
This is part of the TIMEleSS project
http://timeless.texture.rocks

usage: timelessDACShadow [OPTIONS]

Usage:
 - timelessDACShadow [options]

Basic example:
- timelessDACShadow  -s New_Data_Path -n P02-Ti-02_ -f 60 -l 70

Complex example:
- timelessDACShadow -P Edf-P02-Ti-Close -s Edf-P02-Ti-Close-Filtered -n P02-Ti-02_ -f 50 -l 65 --filtersize=1 -t 1.5 --c_rawy=1041 --c_rawz=1000 --radius=350

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 (required)
  -l LAST, --last LAST  First image number (required)
  -s NEWPATH, --newpath NEWPATH
                        Path to save the new EDF image. Be careful not to overwrite yuor current files! (required)
  -P PATH, --path PATH  Path to EDF images. 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 pixels). Default is 4
  -t THRESHOLD, --threshold THRESHOLD
                        Threshold for shadow, in multiples of image mean intensity. Default is 1.0
  --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 low intensity in the center, the script might end up masking real data.
  --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 low intensity in the center, the script might end up masking real data.
  --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 low intensity in the center, the script might end up masking real data.
</code>