WIP: Restore thresholding for zeta, introduce adjustable lower limits for sigma and tau

Now there are different thresholds for the dens, zeta (not used at the moment), sigma, and tau. I left the old values that were in the code, but I think they should be updated. Maybe sigma > 1e-24 and tau > 1e-12 is better. This chage will however impact the tests, that will have to be changed.