Is it possible to extract only the valid data area in bcf to hdf5？

Hi,
When I use a bruker SEM to collect EBSD data, if my actual collection area is a small area in the current display area (by mask), the area inside the mask is the valid area, and the area outside the mask is the invalid area. In fact, it will cause a lot of black invalid areas in the ipf map from ctf. At the same time, although the bcf file is very small, it will become huge after converting to hdf5, and the "pattern" of the invalid area is all 0. I would like to ask, since the bcf2hdf5 program can report the coordinates of the valid area, is it possible to convert only the valid area into hdf5 file?
Thanks!