Smoothing

Based on work in my thesis the smoothing code has been updated. The normalized root mean squared error is used to set a minimum value the smoothing can't go under. This is set to 1e-4 by default and was found to be a good value after testing. Effectively this means values smaller than 1e-4 * the peak max will get smoothed out of the system. This prevents a lot of noise that was sometimes left in then the L-point indicated that values as low as 1e-7 * peak max could be kept

This release also has various other small fixes in it