[REF] Refactor and clean utils.input_files module

[NicolasGensollen]

Closes #1308

[NicolasGensollen]

@AliceJoubert I think this is ready for review.

To be honest, I'm not fully convinced by the factory pattern I ended up using. I feel that it is a bit too complex compared to directly importing the pattern getter functions.

One of the main issue I see with my proposal is that when you do

pattern = query_pattern_factory(QueryPatternName.T1W_LINEAR)(...)

The IDE is not able to tell you the expected arguments of the pattern getter that the factory is returning. So you basically have to find it and check its signature to know about it, which isn't great...

Also, considering our hackathon project, this code will be moved out of Clinica soonish and is likely to be refactored further. Having a dedicated library is one more reason to have the pattern getters as public functions of the API, since users might want to check their doc page.

Let me know what you think.

[AliceJoubert]

Thanks for the work @NicolasGensollen ! I agree with you, it's important to not be obligated to search in the code for the input types.

Maybe with the hackathon we will decide on a structure that will be easier to factorize and use in a factory instead of importing all the functions. Anyways, it will be redefined at that moment so it is fine if this PR is not optimal.

I would vote for importing the functions right away and not use the factory 🙏

[AliceJoubert]

The description for this function needs to be changed a bit since t1_volume_native_tpm was removed. I cannot ping you at the right lines with the diff but all the examples here use t1_volume_native_tpm.