Harmonize mrc density format extents with rest of code.

Harmonize mrc density format extents with rest of code.

To have x-dimension varying the fastest, density extents have to be
defined having z first. This patch ensures, that the mrc file format
is read in line with the data layout used in the for, e.g., the
Gauss transformation.

Change-Id: I3a1a9f215d95dfbc50ea5938bb1d724ac4263556