Currently, the only way for NoiseChisel to ignore some pixels in an image is to set them to NaN before calling NoiseChisel. While this is an easy operation with something like Gnuastro's Arithmetic program, in a large pipeline, it is slow (a whole new 32-bit floating-point image has to be created), and will just add to its complexity.

For pipeline scenarios, it is better to simply have their masks as an unsigned 8-bit integer (with value 1 for pixels to ignore and 0 for pixels to use) and feed that along with the original image to NoiseChisel (such mask images can also be wonderfully compressed, so their size will also be very insignificant). 

Upon reading the input data, NoiseChisel can simply read the mask image also and set all the masked pixels to NaN internally (before any operation). In this way no later part of the programs above need to be changed.

So NoiseChisel (and other data analysis programs like Statistics, Segment, MakeCatalog) should have a '--mask' option to allow the

This task was defined after a discussion with Sylvain Mottet.