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I'm using the fmask algorithm to produce cloud masks for Sentinel2-L1C .safe directories. The output is always a single .img file. Afterwards I'd like to compute easy indices like the ndvi on the area where there are no clouds according to the fmask algorithm. As the L1C-data is still top of atmosphere data, I thought it'd be a good idea to first convert it to BOA with e.g. sen2cor.

So the workflow would look something like this:

L1C-Data --> Make cloudmask with fmask --> mask entire .safe-directory by outputted <cloudmask>.img-file from fmask --> convert to to boa with sen2cor --> compute ndvi

Now I don't know if it's possible and even a good idea to assign a NoData-value to certain areas of all bands within a L1C .safe dataset. Maybe someone has an idea on how to this in a little smarter way...

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