Integrate more python tools

[zhucaoxiang]

I have made some changes to some python tools. Personally, I would like to integrate all functions into one class, such that it is convenient to use and portable.

In spec.py from the pythontools branch, I have implemented/moved some plotting functions for SPEC and put them into the SPEC class （Each function is documented).

Here is a way to use it.

from spec import SPEC
# you can also do something like '%run spec.py

test = SPEC('spec_output.sp.h5')
# plot pressure profile
plt.figure()
test.plot_pressure(normalize=False)
# plot KAM surfaces (using FourSurf)
plt.figure()
test.plot_kam_surface()
# poincare plot
test.plot_poincare()

This is just to motivate some discussions on working together with more SPEC python functions.