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--- processing:clean-diamond-anvil-cell-data [2019/09/03 15:55] – smerkel
+++ processing:clean-diamond-anvil-cell-data [2019/09/03 18:13] (current) – smerkel
@@ Line 9: / Line 9: @@
 ===== Shadows =====
+Diamond anvil cells have a limited opening and create shadows due to the seat supporting the diamonds.
+We we started multigrain crystallography experiments, we though this was going to be a problem and created a script called [[software:remove-shadow|timelessDACShadow]] to do so.
+As a matter of fact, this is not very useful as there simply nothing in these regions. You can probably leave the shadows as they are.
 ===== Diamond spots removal =====
@@ Line 41: / Line 47: @@
 Final step: ''timelessDiamondSpotRemoval [options] save'', to save the clean images in new files.
-==== Example ====
+==== Detailed example ====
+[{{:processing:diamondremoval:orginal-image.jpg?direct&300 | Original diffraction image.}}]
+[{{ :processing:diamondremoval:diamond-removed-median.jpg?direct&300|Same image, after running the diamond removal script}}]
+In the above example, the ''timelessDiamondSpotRemoval'' script is used to
+  * remove the median
+  * erase the image region with diamond spots.
+The exact command with ran was
+   timelessDiamondSpotRemoval -P Images/ -n imagestem_ -f 0990 -l 1000 -d 5 -m image_median.edf --newpath=DiamRem/ --filtersize=11 --growXY=10 --growXYO=10 -t 0.75 save
+The parameters were chosen as follow
+  * ''Images/'' was the path to the images to process,
+  * We processed images ''imagestem_00990.edf'' to ''imagestem_01000.edf'',
+  * The file with the median image was ''image_median.edf''
+  * We saved the new images in ''DiamRem/''
+  * ''filtersize=11'' was a good setting to detect diamond spots, and only those. A smaller value was catching sample peaks as well,
+  * ''growXY=10'': grow the mask by 10 pixels in both x and y,
+  * ''growXYO'': grow the mask by 10 pixels in omega, but also x and y (in addition to the previous growth),
+  * a threshold of 0.75 (relative units) worked well.
+Note that the number of pixels used to grow the mask may be different from the final size of the mask. The final mask will be larger than your settings (there is a scaling applied somewhere).
+As a test, the image below shows the [[processing:search_for_peaks|sample peaks we extracted]] from the final image. This would not have been possible on the raw diffraction image.
+[{{ :processing:diamondremoval:diamond-removed-median-peaks.jpg?direct&300 | Peaks extracted from the diffraction image, after running the diamond removal script }}]
+==== Inpainting ====
+By default, the [[software:timelessDiamondSpotRemoval|timelessDiamondSpotRemoval script]] replaces the masked region with the median intensity of the image. Sometimes, this can lead to problems.
+In such case, you can use //inpainting// which will try to fill the gap as well as possible. This is done by adding ''--inpaint True'' to the command line arguments.
+The script will be significantly slower, but gaps will be filled with values matching the mask's surroundings. As a matter of fact, we have had little use of this option but, at least, it is available.
+[{{:processing:diamondremoval:diamond-removed-median.jpg?direct&300 | Diffraction image, after running the diamond removal script and replacing masked values with the image median}}]
+[{{ :processing:diamondremoval:diamond-removed-inpaint.jpg?direct&300|Same diffraction image, after running the diamond removal script and replacing masked values with inpainting}}]
-[{{:processing:diamondremoval:orginal-image.jpg?direct&300 | Original diffraction image. )}}][{{ :processing:diff-1345-peaks.jpg?300|Same image showing peaks after peak search }}]