Cloud mask - SNAP sentinel 2

I haven’t done anything so far besides importing my raster image to SNAP

Where did you download it and how did you import it?

Make sure you import it via File > Import > Optical > Sentinel-2 > L2A

I downloaded it from the scihub.copernicus website.
If I try to go file>import>optical sensor>sentinel2>L2A when browsing for the image. I can’t find it.

File/Import/Optical Sensors/Sentinel-2/S2-MSI L2A
The file you should open is the *.xml


which snap tool would be more useful to apply a cloud mask to sentinel2 products, and eliminate the value of clouds of clouds and shadows

I appreciate any input

please have a look here:

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Can you tell me than how can i use cloud mask on NDSI image which i have calculated using S2A MSIL1C?

You can apply Idepix to your L1C products: Optical>Preprocessing>Masking>Idepix

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Hello!! appreciated StephP
After the fourth point I don’t understand you, you could be more specific. Thank you

Hello Abruescas
Thanks for your input, I would like to know what parameters I should use the idepix tool to remove the value of the pixels from the clouds in an S2A-Misilc image.

Thanks in advance.

How can i apply idepix to MODIS products

you first install it via the Plugins menu

Make sure you download MODIS L1B Calibrated Radiance products:

Then you apply IDEPIX

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I have the following problem, I already applied cloud mask with idepix to sentinel 2 and modis, remove the value of the pixels corresponding to the clouds using the Band-Math tool, save in the default Snap format (Beam-Dimap) but when opening them In the Sig Qgis tool the cloud masks do not appear, and the pixels of the clouds are still there, it is as if nothing had been done. I tried to save and use another format I tried with Geo-Tiff format but I only get one file with the information of all the bands, and I want the bands to be individual (one file for each band) also that the pixels of the clouds do not interfere with the other pixels and be able to visualize the results in another Sig tool to verify.

I appreciate any input.

QGIS cannot read the valid-pixel expressions or masks which belong to a BEAM DIMAP product, they are only used in SNAP. For QGIS the raster is simply a matrix with values. GeoTiff also doesn’t store such metadata.

If you want to permanently remove these values, you have to replace the raster values, for example in the band maths.

IF band_1 == mask THEN 0 ELSE band_1

This replaces any pixel within the mask by zero . If you then open the raster in QGIS you can set 0 as the NoData value (in the transparency tab): S1 tile in QGIS: Zero values

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Thank you very much Abraun, it has been very helpful

I have resampled the image to 20 m, but if I apply idepix tool to masking cloud. it gives me the following error:


do you have solution about that? thanks before!

Some time ago this has been reported for a different use case.
Please have a look at this issue ticket (SNAP-561). Especially at the comment below.

Good night Sir,

Is the similar procedure for Sentinel 2A Level-2A?
Atmospheric correction applied to Top-Of-Atmosphere (TOA) Level-1C. So, the Level-2A output is an orthoimage Bottom-Of-Atmosphere (BOA) corrected reflectance product( The IdePex Sentinel 2 MSI have an option for write ToA reflectance to the target product and other option for write feature values to the target product. What to do in this case?
Thank you for your valuable response.

IdePix doesn’t work on L2A data. You can run it on L1C and then merge the result with the L2A data.
Or you can use the cloud mask of the L2A product directly.

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Thank you Sir,
Do you have a link of a tutorial for cloud mask the L2A using the second option? Grateful for your advise.