Add proton CT runnable example

[acoussat]

Proton CT runnable example. The goal is to use it in connection with PCT in order to have a complete proton CT pipeline (from MC simulation to tomographic reconstruction) easily runnable.

The example is taken from PCT, from which it will probably be removed. This example was already somewhat available in GATE in the form of a GATE 9 to GATE 10 migration guide.

[acoussat]

Before merging, I'd like to finish PCT's "sibling" PR, just to make sure that everything works alright between the two software.

[SimonRit]

Before merging, I'd like to finish PCT's "sibling" PR, just to make sure that everything works alright between the two software.

We should reflect on what we will do in the future with PCT. There was a (dysfunctional) test using protonct.py which I suggest to remove
RTKConsortium/PCT@6659355

Could you discuss with @axel-grc what you want to do with PCT tests in the future? If you want to use protonct.py, it's not clear to me that it should be in the Gate repository, a link in the documentation to PCT is sufficient.

[acoussat]

I discussed yesterday with @tbaudier and @axel-grc about how to reorganize the code, here are my plans:

• create a proper proton CT example on the GATE side, as GATE already had an example but only in the form of a GATE 9 to GATE 10 conversion guide (https://opengate-python.readthedocs.io/en/10.0.3/user_guide/user_guide_how_to_convert_example_1.html) (done in this PR)
• still on the GATE side, make this proton CT example callable, which makes it easy for users to quickly generate proton CT data (done in this PR)
• create a Python example on PCT side which calls this new GATE script to generate data, then reconstruct it
• have this "end-to-end" example automatically called during PCT CI, which allows to check if PCT is compatible with the current GATE version
• include this example in PCT documentation, as in RTK

The PCT side is almost ready. Additionally, I finished updating AddTrackerUncertainty.py, for which @nkrah thinks it would make sense to have directly in GATE, but I leave that for a second round of PRs.

Of course let me know if you disagree with this plan, nothing is set in stone!

[SimonRit]

Sounds good. The callable proton CT will be part of the wheel I suppose.
I don't think AddTrackerUncertainty.py should be part of GATE but we can rediscuss it with @nkrah.

[nkrah]

I agree that AddTrackerUncertainty.py should be part of PCT. It is conceptually closer to the reconstruction than to the simulation.

@acoussat : Otherwise, what is the status of this and the sibling PR?