Fixed errors introduced by upgrading the Eigen dependency to version 3.4.0
Recently eigen 3.4.0 was release and the codebase didn't compile with it. Most issues were simply indices of type double and there were also a lot of ambigious types caused, as far as I saw it, by namespace issues. The later was solved by removing using namespace Eigen;
and explicitly using Eigen::
prefix where nessecary.