Improve, clean up, and comment more the FIR code

The FIR code (FIR.py and FIRtools.py) need to be further cleaned up and have additional comments added to them. Some ideas for clean up:

• Improve the input and output data variables to more simplify what data is carried around
• Where possible, move functions into class methods
• Expand and add comments to explain the steps in each method
• Fix the FIXMEs
• I don't know if it is a problem, but minimizing repeated code by making new methods/functions is helpful
• ...