Refactoring, adding tests and installing instructions

[garciadias]

Hello Ibrahim,

I am an ML engineer at King's College London. I am working on building Visual Language models on MRI, and your work is very similar to the type of architecture I am trying to create.
Congratulations on your article, and thank you for sharing the code.

Since I will use your code as a baseline comparison and inspiration for my development, I decided to clean and refactor the code. I am sharing here a PR to include tests, python environment settings and docker instructions to easily build and run the code.

For this PR, I tried not to change the code in any significant way. There were some undefined variables and errors that I had to fix in order to run the tests, but they are very minimal.

Here you can see the output of running the tests:

======================================================================================= test session starts ========================================================================================
platform linux -- Python 3.11.11, pytest-8.3.5, pluggy-1.5.0
rootdir: /data/rgd/CT2Rep
configfile: pyproject.toml
plugins: cov-6.1.1, torchtyping-0.1.5, typeguard-2.13.3
collected 126 items                                                                                                                                                                                

tests/CT2Rep/ctvit/ctvit/test_attention.py .........................                                                                                                                         [ 19%]
tests/CT2Rep/ctvit/ctvit/test_ctvit.py ...........s.......ss...ssss.ss                                                                                                                       [ 44%]
tests/CT2Rep/ctvit/ctvit/test_t5.py ..........s..                                                                                                                                            [ 54%]
tests/CT2Rep/modules/test_metrics.py .......                                                                                                                                                 [ 60%]
tests/CT2Rep/modules/test_tokenizers.py ...........ss..                                                                                                                                      [ 72%]
tests/CT2Rep/modules/test_training.py ....s.....                                                                                                                                             [ 80%]
tests/CT2Rep/modules/test_utils.py .....................                                                                                                                                     [ 96%]
tests/CT2Rep/test_main.py ....                                                                                                                                                               [100%]

========================================================================================= warnings summary =========================================================================================
tests/CT2Rep/modules/test_training.py::test_train_epoch
  /data/rgd/CT2Rep/.venv/lib/python3.11/site-packages/torch/optim/lr_scheduler.py:136: UserWarning: Detected call of `lr_scheduler.step()` before `optimizer.step()`. In PyTorch 1.1.0 and later, you should call them in the opposite order: `optimizer.step()` before `lr_scheduler.step()`.  Failure to do this will result in PyTorch skipping the first value of the learning rate schedule. See more details at https://pytorch.org/docs/stable/optim.html#how-to-adjust-learning-rate
    warnings.warn("Detected call of `lr_scheduler.step()` before `optimizer.step()`. "

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================================================ 113 passed, 13 skipped, 1 warning in 3.73s ============================================================================

============================= Coverage Report =======================================
Name                                            Stmts   Miss  Cover
-------------------------------------------------------------------
src/ct2rep/CT2Rep/main.py                          77     13    83%
src/ct2rep/CT2Rep/models/ct2rep.py                 26     17    35%
src/ct2rep/CT2Rep/modules/att_model.py            215    197     8%
src/ct2rep/CT2Rep/modules/caption_model.py        222    211     5%
src/ct2rep/CT2Rep/modules/data_ct.py               90     73    19%
src/ct2rep/CT2Rep/modules/dataloaders.py           26     19    27%
src/ct2rep/CT2Rep/modules/encoder_decoder.py      277    212    23%
src/ct2rep/CT2Rep/modules/loss.py                  15      9    40%
src/ct2rep/CT2Rep/modules/metrics.py               14      3    79%
src/ct2rep/CT2Rep/modules/optimizers.py             9      6    33%
src/ct2rep/CT2Rep/modules/tokenizers.py            75      3    96%
src/ct2rep/CT2Rep/modules/trainer.py              150     13    91%
src/ct2rep/CT2Rep/modules/utils.py                 32      0   100%
src/ct2rep/CT2Rep/modules/visual_extractor.py      16     11    31%
src/ct2rep/ctvit/ctvit/attention.py               181      1    99%
src/ct2rep/ctvit/ctvit/ctvit.py                   323    175    46%
src/ct2rep/ctvit/ctvit/t5.py                       54      1    98%
-------------------------------------------------------------------
TOTAL                                            1802    964    47%

If you are happy to collaborate, I would keep sending PRs to improve the code, eliminate duplications and improve test coverage.

I am also a MONAI collaborator, so I would happily help you get your model listed on MONAI bundles.

Many thanks,

Rafael