Fix problem with plot_semivariogram.py

This is a quick fix for the fact that plot_semivariogram.py would fail
when the inputed mapping file contains more categories than the ones in
the distance matrix.

Fixes #1378
DOC: Cleanup comments and some print statements
Merge pull request #1743 from ElDeveloper/semivariogram-updates

Fix problem with plot_semivariogram.py