I am posting here what I wrote in this other thread since it seems related to what is being discussed here.
http://forum.step.esa.int/t/isolated-nan-pixels-in-coherence-image/4920
The problem I have is that SNAP seems to be converting pixels with a zero value in the I or Q component of S1 SLC images into NaN. These NaNs are then propagated through a graph run on gpt. In that particular graph, the problem results in a coherence image with NaN values. SNAP converts those NaN values back to 0, but you would expect coherence values close to 1 for those pixels.
Complex numbers with zero-valued I or Q compenents should be treated as such, not as NaN. Is there a way to force gpt to do this?