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You can convert your clouds and shadows to null / no data and then interpolate those "null areas" based on the surrounding values using the Fill nodata tool, see the documentation here: https://docs.qgis.org/2.8/en/docs/user_manual/processing_algs/gdalogr/gdal_analysis/fillnodata.html Additionally, there is a "fill gaps" tool. https://grass.osgeo.org/...

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