Hi @CirenSangzhu,
These are great questions! I think your figure 6 is reasonably close to the left half of figure 7 (this is the actual power spectrum, not the fitted CTF). I would try first cropping the power spectrum in figure 6 around just the low frequencies (i.e. +/- 0.35 [1/A], like in figure 7) before passing it to the contrast_normalization function, this might improve the scale a bit more by removing the high freq noise.
To your question, generally particle images don’t show any Thon rings because there is much less signal in a particle image relative to the whole micrograph. I.e. the particle images are swamped with noise, whereas the entire micrograph has enough signal from the diffraction pattern to show Thon rings at the low frequencies.
Best,
Michael