I have to work with numerous Landsat surface reflectance product that I downloaded from http://landsat.usgs.gov/CDR_LSR.php. The product comes with a QA data with information on clouds and shadows that can be used to mask the data. Has anyone here used python to apply these mask or know of any working libraries.

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you can embed Orfeo Toolbox in Python in order to process your remote sensing data, including applying masks. There is a Python interface for OTB and the Bandmath can be used to apply a mask.

You can also use gdal for the same purpose, it also has the tools necessary for masking an image (see gdal_calc.py) and there is also a python interface.

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