Rebuilt plot_sinogram_profiles.py for 4D tof data

[robbietuk]

Changes in this pull request

Built plot_projdata_profiles.py to replace plot_sinogram_profiles.py. This allows for TOF data to be handled. I added significant error handling and what I hope is a better user experience. It does break backwards compatabity.

I need to add a the ability to read v6.0 STIR projection data.

Testing performed

Include a pytest (commented out)

Related issues

#1363

Checklist before requesting a review

• [] I have performed a self-review of my code
• [] I have added docstrings/doxygen in line with the guidance in the developer guide
• [] I have implemented unit tests that cover any new or modified functionality (if applicable)
• [] The code builds and runs on my machine
• [] documentation/release_XXX.md has been updated with any functionality change (if applicable)

[robbietuk]

A few usage observations

[KrisThielemans]

I'm happy with this and would be ok to merge (after an update to release_6.1.htm)

[KrisThielemans]

pytest fails with

ModuleNotFoundError: No module named 'examples'

Could be solved by adding it to the pythonpath first (would need to be done both for GHA and AppVeyor). Alternatively, we do it better via #1392

[KrisThielemans]

@robbietuk want to finish this one? I think only needs

• setting python path for pytest
• updating release notes.

I'm hoping to release 6.3 soon, as it has a major bug fix. We could leave this for later if you have no time now.

[KrisThielemans]

@robbietuk hopefully the pytest work-around is fine. Can you please add something to release_6.3.htm?

[KrisThielemans]

This should be fine now. ok to squash merge?

[KrisThielemans]

GHA is fine but AppVeyor fails

=========================== test session starts =============================
platform win32 -- Python 3.8.20, pytest-8.3.4, pluggy-1.5.0
rootdir: C:\projects\stir\src
collected 25 items / 1 error
=================================== ERRORS ====================================
_________ ERROR collecting swig/test/python/test_projdata_profiles.py _________
swig\test\python\test_projdata_profiles.py:8: in <module>
_________ ERROR collecting swig/test/python/test_projdata_profiles.py _________
swig\test\python\test_projdata_profiles.py:8: in <module>
    from examples.python.plot_projdata_profiles import compress_and_extract_1d_from_nd_array
..\examples\python\plot_projdata_profiles.py:35: in <module>
    def get_projdata_from_file_as_numpy(filename: str) -> np.ndarray | None:
E   TypeError: unsupported operand type(s) for |: 'type' and 'NoneType'

I think this is because python 3.8 is too old for this type of hinting.

[KrisThielemans]

I'd prefer to support python 3.8 and 3.9 for a bit longer. https://typing.readthedocs.io/en/latest/guides/modernizing.html seems to say from __future__ import annotations could do the trick even for python 3.7. Alternatively, https://adamj.eu/tech/2022/01/15/python-type-hints-how-to-split-types-by-python-version/ could provide some hints on how to cope with this

[robbietuk]

Feel free to do anything to merge this. Thank you for getting the pytesting working. I hope my Union[] fix resolves the Appveyor issue

[KrisThielemans]

Union didn't work, but it looks like importing annotations does (at least in my test). let's see

[KrisThielemans]

success! (at least for 3.8)