No-data masking occurs, if a Band's no-data value is set:
  
   Band band = new Band("AOT", ...);
   band.setGeophysicalNoDataValue(-999.0);
   band.setNoDataValueUsed(true);

Internally, we create a so called valid-mask expression, which is the band-maths expression used to determine valid pixels. Depending on the no-data value,source code snippet above would produce the valid-mask expression "fneq(AOT,-999.0)", where AOT refers to the geophysical (image) sample.

If the raw data type of a band is different from the geophysical data type, e.g.

   Band band = new Band("AOT", ...);
   band.setNoDataValue(-999);
   band.setNoDataValueUsed(true);

the expression can be simplified to "AOT.raw != -999", where AOT.raw refers to the raw (image) sample. Accessing raw sample data and evaluating the raw (integer) expression is much faster and simpler.