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--- processing:clean-diamond-anvil-cell-data [2019/09/03 17:08] – smerkel
+++ processing:clean-diamond-anvil-cell-data [2026/08/10 10:51] (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 30: / Line 36: @@
 In addition, you can define a disk, at the center of the image, in which nothing should be removed. This option is for samples with very intense diffraction spots on the inner rings which could be confused with diamond spots based on intensity criteria.
+==== Is it necessary ? ====
+If your sample peaks not overlapp with those of diamonds, this is not necessary. You will have extra peaks from the diamonds, which you will not index, and that is all. In many cases, it works just fine.
+If diamond spots are a problem, instructions are below.
 ==== Step by step instructions ====
@@ Line 41: / Line 53: @@
 Final step: ''timelessDiamondSpotRemoval [options] save'', to save the clean images in new files.
-==== Detailed xample ====
+==== Detailed example ====
 [{{:processing:diamondremoval:orginal-image.jpg?direct&300 | Original diffraction image.}}]
@@ Line 61: / Line 73: @@
   * ''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).
+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}}]