Update preprocesses and processes of ambient noise calculation

[frostforestcdjl]

1. Modify the processes in downsample.py to be nearly identical as in MSNoise.
2. Include mask retrieval in data.py and apply mask in model.py
3. Import and apply partial hanning taper, cosine taper, and doing demean in stft in model.py
4. Comment cloud data comparison in mseed1.py and mseed2.py for updating existing waveforms and CCFs.
5. Include passing arguments of token_file, protocol, and bucket in run_downsample.py and run_cctorch.py.
6. update utils.py to include functions used in other updated files.

[frostforestcdjl]

Overlap ratio can be modified in model.py. It may be good to arrange it as an argument of run.py