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I already have the SNAP 7, and I can’t run sen2cor 2.08 directly from it. However, I can alternatively use the command prompt but it can only take the L1C images as input. My problem now is that I want to eliminate clouds from my Sentinel-2 L2A image. My advisor wants me to do it with sen2cor. I know that I can always find new images cloud-free from the scihub_copernicus website, but he wants me to figure it out based on the L2A image. Any suggestions?

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If your L2A images were processed using Sen2cor, you already have a cloud mask inside the .safe structure at 60m (S2X_MSIL2A_YEARMONBTHDAY.SAFE\GRANULE\IMGNAME\IMG_DATA\R60m). If you don't have this you can apply sen2cor on the same image (Level 1) to obtain it. Otherwise you should use a different method rather than Sen2cor.

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