add monai-based scripts for dataset conversion, training, and inference

[naga-karthik]

This PR adds all the required scripts for bids-msd dataset conversion, training and running inference with MONAI models.

[jcohenadad]

@naga-karthik is this PR ready for use/review? We have a collaborator in Berlin who has challenging 7T images and I'd like to give this contrast-agnostic model a try

[naga-karthik]

Hey @jcohenadad, yes the PR is ready. We will be merging it this week. Meanwhile, the inference script is also ready to use. For --chkp-path please use

/home/GRAMES.POLYMTL.CA/u114716/duke/projects/ivadomed/contrast-agnostic-seg/models/monai

as the model is currently stored there

[jcohenadad]

I'm having issues installing the deps:

Terminal output

```console (/Users/julien/code/contrast-agnostic-softseg-spinalcord/venv) julien-macbook:~/code/contrast-agnostic-softseg-spinalcord/monai $ pip install -r requirements_inference.txt Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu Collecting dynamic_network_architectures==0.2 (from -r requirements_inference.txt (line 1)) Using cached dynamic_network_architectures-0.2.tar.gz (20 kB) Preparing metadata (setup.py) ... done Collecting joblib==1.3.0 (from -r requirements_inference.txt (line 2)) Obtaining dependency information for joblib==1.3.0 from https://files.pythonhosted.org/packages/1e/f2/6ec7eb9e48c88c750da04050a5ba8250ca9949dfcf6e624ccee12d2fc653/joblib-1.3.0-py3-none-any.whl.metadata Using cached joblib-1.3.0-py3-none-any.whl.metadata (5.4 kB) Collecting loguru==0.7.0 (from -r requirements_inference.txt (line 3)) Using cached loguru-0.7.0-py3-none-any.whl (59 kB) Collecting monai[nibabel]==1.2.0 (from -r requirements_inference.txt (line 4)) Obtaining dependency information for monai[nibabel]==1.2.0 from https://files.pythonhosted.org/packages/2e/39/444fc5b2fb0e9d9d432a2e1efaf75d68b0aee94d7559c8b9969e2f62c5a4/monai-1.2.0-202306081546-py3-none-any.whl.metadata Using cached monai-1.2.0-202306081546-py3-none-any.whl.metadata (10 kB) Collecting scipy==1.11.2 (from -r requirements_inference.txt (line 5)) Obtaining dependency information for scipy==1.11.2 from https://files.pythonhosted.org/packages/03/c3/5162f7d23a12c62cf0630f6cce20932f166fca7cb5513ed9af56b5618ba6/scipy-1.11.2-cp39-cp39-macosx_10_9_x86_64.whl.metadata Downloading scipy-1.11.2-cp39-cp39-macosx_10_9_x86_64.whl.metadata (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.1/54.1 kB 1.0 MB/s eta 0:00:00 Collecting numpy==1.24.4 (from -r requirements_inference.txt (line 6)) Obtaining dependency information for numpy==1.24.4 from https://files.pythonhosted.org/packages/9a/cd/d5b0402b801c8a8b56b04c1e85c6165efab298d2f0ab741c2406516ede3a/numpy-1.24.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata Downloading numpy-1.24.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (5.6 kB) ERROR: Could not find a version that satisfies the requirement torch==2.0.0+cpu (from versions: 1.7.1, 1.8.0, 1.8.1, 1.9.0, 1.9.1, 1.10.0, 1.10.1, 1.10.2, 1.11.0, 1.12.0, 1.12.1, 1.13.0, 1.13.1, 2.0.0, 2.0.1, 2.1.0) ERROR: No matching distribution found for torch==2.0.0+cpu (/Users/julien/code/contrast-agnostic-softseg-spinalcord/venv) julien-macbook:~/code/contrast-agnostic-softseg-spinalcord/monai $ python Python 3.9.18 (main, Sep 11 2023, 08:38:23) [Clang 14.0.6 ] :: Anaconda, Inc. on darwin Type "help", "copyright", "credits" or "license" for more information. >>> (/Users/julien/code/contrast-agnostic-softseg-spinalcord/venv) julien-macbook:~/code/contrast-agnostic-softseg-spinalcord/monai $ git log commit 4694169352fb962f607e7684fe778677adc123dc (HEAD -> nk/monai, origin/nk/monai) Author: Naga Karthik Date: Sun Oct 8 15:49:00 2023 -0400 fix bug with torch.clamp setting bg values to 0.5 ```

[valosekj]

I'm having issues installing the deps:

I had the same issue on my local macboook, I had to remove packages versions; see updated requirements from canproco repo.

Then I ran:

 conda create -n monai python=3.8
 conda activate monai
 pip install -r requirements.txt

[jcohenadad]

I'm having issues installing the deps:

I had the same issue on my local macboook, I had to remove packages versions; see updated requirements from canproco repo.

Then I ran:

 conda create -n monai python=3.8
 conda activate monai
 pip install -r requirements.txt

Thank you @valosekj -- there see to be some confusion about Python's version: https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/pull/60/files#diff-45765be45b87970b013c24cdb66c4f4ad139e802f0f013e0bbf56ecf249478eeR12

[jcohenadad]

I have another error with python 3.8:

Terminal output

```console julien-macbook:~ $ conda create -n monai python=3.8 Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /Users/julien/miniconda3/envs/monai added / updated specs: - python=3.8 The following packages will be downloaded: package | build ---------------------------|----------------- pip-23.2.1 | py38hecd8cb5_0 2.6 MB python-3.8.18 | h5ee71fb_0 14.4 MB setuptools-68.0.0 | py38hecd8cb5_0 946 KB wheel-0.41.2 | py38hecd8cb5_0 109 KB ------------------------------------------------------------ Total: 18.0 MB The following NEW packages will be INSTALLED: ca-certificates pkgs/main/osx-64::ca-certificates-2023.08.22-hecd8cb5_0 libcxx pkgs/main/osx-64::libcxx-14.0.6-h9765a3e_0 libffi pkgs/main/osx-64::libffi-3.4.4-hecd8cb5_0 ncurses pkgs/main/osx-64::ncurses-6.4-hcec6c5f_0 openssl pkgs/main/osx-64::openssl-3.0.11-hca72f7f_2 pip pkgs/main/osx-64::pip-23.2.1-py38hecd8cb5_0 python pkgs/main/osx-64::python-3.8.18-h5ee71fb_0 readline pkgs/main/osx-64::readline-8.2-hca72f7f_0 setuptools pkgs/main/osx-64::setuptools-68.0.0-py38hecd8cb5_0 sqlite pkgs/main/osx-64::sqlite-3.41.2-h6c40b1e_0 tk pkgs/main/osx-64::tk-8.6.12-h5d9f67b_0 wheel pkgs/main/osx-64::wheel-0.41.2-py38hecd8cb5_0 xz pkgs/main/osx-64::xz-5.4.2-h6c40b1e_0 zlib pkgs/main/osx-64::zlib-1.2.13-h4dc903c_0 Proceed ([y]/n)? y Downloading and Extracting Packages Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate monai # # To deactivate an active environment, use # # $ conda deactivate julien-macbook:~ $ conda activate monai (monai) julien-macbook:~ $ cd code/contrast-agnostic-softseg-spinalcord/ (monai) julien-macbook:~/code/contrast-agnostic-softseg-spinalcord $ cd monai/ (monai) julien-macbook:~/code/contrast-agnostic-softseg-spinalcord/monai $ pip install -r requirements_inference.txt Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu Collecting dynamic_network_architectures==0.2 (from -r requirements_inference.txt (line 1)) Using cached dynamic_network_architectures-0.2.tar.gz (20 kB) Preparing metadata (setup.py) ... done Collecting joblib==1.3.0 (from -r requirements_inference.txt (line 2)) Obtaining dependency information for joblib==1.3.0 from https://files.pythonhosted.org/packages/1e/f2/6ec7eb9e48c88c750da04050a5ba8250ca9949dfcf6e624ccee12d2fc653/joblib-1.3.0-py3-none-any.whl.metadata Using cached joblib-1.3.0-py3-none-any.whl.metadata (5.4 kB) Collecting loguru==0.7.0 (from -r requirements_inference.txt (line 3)) Using cached loguru-0.7.0-py3-none-any.whl (59 kB) Collecting monai[nibabel]==1.2.0 (from -r requirements_inference.txt (line 4)) Obtaining dependency information for monai[nibabel]==1.2.0 from https://files.pythonhosted.org/packages/2e/39/444fc5b2fb0e9d9d432a2e1efaf75d68b0aee94d7559c8b9969e2f62c5a4/monai-1.2.0-202306081546-py3-none-any.whl.metadata Using cached monai-1.2.0-202306081546-py3-none-any.whl.metadata (10 kB) ERROR: Ignored the following versions that require a different python version: 1.11.0 Requires-Python <3.13,>=3.9; 1.11.0rc1 Requires-Python <3.13,>=3.9; 1.11.0rc2 Requires-Python <3.13,>=3.9; 1.11.1 Requires-Python <3.13,>=3.9; 1.11.2 Requires-Python <3.13,>=3.9; 1.11.3 Requires-Python <3.13,>=3.9 ERROR: Could not find a version that satisfies the requirement scipy==1.11.2 (from versions: 0.8.0, 0.9.0, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.12.1, 0.13.0, 0.13.1, 0.13.2, 0.13.3, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 1.5.4, 1.6.0, 1.6.1, 1.6.2, 1.6.3, 1.7.0, 1.7.1, 1.7.2, 1.7.3, 1.8.0rc1, 1.8.0rc2, 1.8.0rc3, 1.8.0rc4, 1.8.0, 1.8.1, 1.9.0rc1, 1.9.0rc2, 1.9.0rc3, 1.9.0, 1.9.1, 1.9.2, 1.9.3, 1.10.0rc1, 1.10.0rc2, 1.10.0, 1.10.1) ERROR: No matching distribution found for scipy==1.11.2 ```

[jcohenadad]

same issue when targetting requirements.txt instead of requirements_inference.txt

Terminal output

```console (monai) julien-macbook:~/code/contrast-agnostic-softseg-spinalcord/monai $ pip install -r requirements.txt Collecting dynamic_network_architectures==0.2 (from -r requirements.txt (line 1)) Using cached dynamic_network_architectures-0.2.tar.gz (20 kB) Preparing metadata (setup.py) ... done Collecting joblib==1.3.0 (from -r requirements.txt (line 2)) Obtaining dependency information for joblib==1.3.0 from https://files.pythonhosted.org/packages/1e/f2/6ec7eb9e48c88c750da04050a5ba8250ca9949dfcf6e624ccee12d2fc653/joblib-1.3.0-py3-none-any.whl.metadata Using cached joblib-1.3.0-py3-none-any.whl.metadata (5.4 kB) Collecting loguru==0.7.0 (from -r requirements.txt (line 3)) Using cached loguru-0.7.0-py3-none-any.whl (59 kB) Collecting matplotlib==3.7.2 (from -r requirements.txt (line 4)) Obtaining dependency information for matplotlib==3.7.2 from https://files.pythonhosted.org/packages/b2/b6/c6596fbc30899e6da31450053054d7da61a21a3f510544fb7cb7658a3de3/matplotlib-3.7.2-cp38-cp38-macosx_10_12_x86_64.whl.metadata Downloading matplotlib-3.7.2-cp38-cp38-macosx_10_12_x86_64.whl.metadata (5.6 kB) Collecting monai[all]==1.2.0 (from -r requirements.txt (line 5)) Obtaining dependency information for monai[all]==1.2.0 from https://files.pythonhosted.org/packages/2e/39/444fc5b2fb0e9d9d432a2e1efaf75d68b0aee94d7559c8b9969e2f62c5a4/monai-1.2.0-202306081546-py3-none-any.whl.metadata Using cached monai-1.2.0-202306081546-py3-none-any.whl.metadata (10 kB) Collecting numpy==1.24.4 (from -r requirements.txt (line 6)) Obtaining dependency information for numpy==1.24.4 from https://files.pythonhosted.org/packages/11/10/943cfb579f1a02909ff96464c69893b1d25be3731b5d3652c2e0cf1281ea/numpy-1.24.4-cp38-cp38-macosx_10_9_x86_64.whl.metadata Downloading numpy-1.24.4-cp38-cp38-macosx_10_9_x86_64.whl.metadata (5.6 kB) Collecting pytorch_lightning==2.0.4 (from -r requirements.txt (line 7)) Obtaining dependency information for pytorch_lightning==2.0.4 from https://files.pythonhosted.org/packages/e9/70/9c2587d7a566c1e656b5fcdbc1d01afd34675d8418b8fc4da3eb4d9bc808/pytorch_lightning-2.0.4-py3-none-any.whl.metadata Downloading pytorch_lightning-2.0.4-py3-none-any.whl.metadata (23 kB) Collecting scikit_learn==1.3.0 (from -r requirements.txt (line 8)) Obtaining dependency information for scikit_learn==1.3.0 from https://files.pythonhosted.org/packages/33/cb/0e41fad5b30fd66925e47952ddc720d078bdfd8397584a4873ec1cf590ca/scikit_learn-1.3.0-cp38-cp38-macosx_10_9_x86_64.whl.metadata Downloading scikit_learn-1.3.0-cp38-cp38-macosx_10_9_x86_64.whl.metadata (11 kB) ERROR: Ignored the following versions that require a different python version: 1.11.0 Requires-Python <3.13,>=3.9; 1.11.0rc1 Requires-Python <3.13,>=3.9; 1.11.0rc2 Requires-Python <3.13,>=3.9; 1.11.1 Requires-Python <3.13,>=3.9; 1.11.2 Requires-Python <3.13,>=3.9; 1.11.3 Requires-Python <3.13,>=3.9; 1.25.0 Requires-Python >=3.9; 1.25.0rc1 Requires-Python >=3.9; 1.25.1 Requires-Python >=3.9; 1.25.2 Requires-Python >=3.9; 1.26.0 Requires-Python <3.13,>=3.9; 1.26.0b1 Requires-Python <3.13,>=3.9; 1.26.0rc1 Requires-Python <3.13,>=3.9; 3.8.0 Requires-Python >=3.9; 3.8.0rc1 Requires-Python >=3.9 ERROR: Could not find a version that satisfies the requirement scipy==1.11.2 (from versions: 0.8.0, 0.9.0, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.12.1, 0.13.0, 0.13.1, 0.13.2, 0.13.3, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 1.5.4, 1.6.0, 1.6.1, 1.6.2, 1.6.3, 1.7.0, 1.7.1, 1.7.2, 1.7.3, 1.8.0rc1, 1.8.0rc2, 1.8.0rc3, 1.8.0rc4, 1.8.0, 1.8.1, 1.9.0rc1, 1.9.0rc2, 1.9.0rc3, 1.9.0, 1.9.1, 1.9.2, 1.9.3, 1.10.0rc1, 1.10.0rc2, 1.10.0, 1.10.1) ERROR: No matching distribution found for scipy==1.11.2 ```

[naga-karthik]

@jcohenadad can you try installing the dependencies now? I think the +cpu in torch package was causing the issue. I removed it in latest commit.

Please stick to python=3.9 as my code is based on 3.9. (however, for simply running the inference script, the python versions shouldn't matter much, as we're using basic python commands. But using 3.9 will keep it consistent with the rest of the monai code)

[jcohenadad]

2e3528269754b30986e636b45e57bfe51df1b1fb fixed it 🎉

Terminal output

```console (py39) julien-macbook:~/code/contrast-agnostic-softseg-spinalcord/monai $ pip install -r requirements_inference.txt Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu Collecting dynamic_network_architectures==0.2 (from -r requirements_inference.txt (line 1)) Using cached dynamic_network_architectures-0.2.tar.gz (20 kB) Preparing metadata (setup.py) ... done Collecting joblib==1.3.0 (from -r requirements_inference.txt (line 2)) Obtaining dependency information for joblib==1.3.0 from https://files.pythonhosted.org/packages/1e/f2/6ec7eb9e48c88c750da04050a5ba8250ca9949dfcf6e624ccee12d2fc653/joblib-1.3.0-py3-none-any.whl.metadata Using cached joblib-1.3.0-py3-none-any.whl.metadata (5.4 kB) Collecting loguru==0.7.0 (from -r requirements_inference.txt (line 3)) Using cached loguru-0.7.0-py3-none-any.whl (59 kB) Collecting monai[nibabel]==1.2.0 (from -r requirements_inference.txt (line 4)) Obtaining dependency information for monai[nibabel]==1.2.0 from https://files.pythonhosted.org/packages/2e/39/444fc5b2fb0e9d9d432a2e1efaf75d68b0aee94d7559c8b9969e2f62c5a4/monai-1.2.0-202306081546-py3-none-any.whl.metadata Using cached monai-1.2.0-202306081546-py3-none-any.whl.metadata (10 kB) Collecting scipy==1.11.2 (from -r requirements_inference.txt (line 5)) Obtaining dependency information for scipy==1.11.2 from https://files.pythonhosted.org/packages/03/c3/5162f7d23a12c62cf0630f6cce20932f166fca7cb5513ed9af56b5618ba6/scipy-1.11.2-cp39-cp39-macosx_10_9_x86_64.whl.metadata Using cached scipy-1.11.2-cp39-cp39-macosx_10_9_x86_64.whl.metadata (54 kB) Collecting numpy==1.24.4 (from -r requirements_inference.txt (line 6)) Obtaining dependency information for numpy==1.24.4 from https://files.pythonhosted.org/packages/9a/cd/d5b0402b801c8a8b56b04c1e85c6165efab298d2f0ab741c2406516ede3a/numpy-1.24.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata Using cached numpy-1.24.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (5.6 kB) Collecting torch==2.0.0 (from -r requirements_inference.txt (line 8)) Downloading https://download.pytorch.org/whl/cpu/torch-2.0.0-cp39-none-macosx_10_9_x86_64.whl (139.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.8/139.8 MB 6.1 MB/s eta 0:00:00 Collecting nibabel (from monai[nibabel]==1.2.0->-r requirements_inference.txt (line 4)) Using cached nibabel-5.1.0-py3-none-any.whl (3.3 MB) Collecting filelock (from torch==2.0.0->-r requirements_inference.txt (line 8)) Obtaining dependency information for filelock from https://files.pythonhosted.org/packages/5e/5d/97afbafd9d584ff1b45fcb354a479a3609bd97f912f8f1f6c563cb1fae21/filelock-3.12.4-py3-none-any.whl.metadata Downloading filelock-3.12.4-py3-none-any.whl.metadata (2.8 kB) Collecting typing-extensions (from torch==2.0.0->-r requirements_inference.txt (line 8)) Obtaining dependency information for typing-extensions from https://files.pythonhosted.org/packages/24/21/7d397a4b7934ff4028987914ac1044d3b7d52712f30e2ac7a2ae5bc86dd0/typing_extensions-4.8.0-py3-none-any.whl.metadata Downloading typing_extensions-4.8.0-py3-none-any.whl.metadata (3.0 kB) Collecting sympy (from torch==2.0.0->-r requirements_inference.txt (line 8)) Downloading https://download.pytorch.org/whl/sympy-1.12-py3-none-any.whl (5.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.7/5.7 MB 12.9 MB/s eta 0:00:00 Collecting networkx (from torch==2.0.0->-r requirements_inference.txt (line 8)) Using cached networkx-3.1-py3-none-any.whl (2.1 MB) Collecting jinja2 (from torch==2.0.0->-r requirements_inference.txt (line 8)) Downloading https://download.pytorch.org/whl/Jinja2-3.1.2-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 4.6 MB/s eta 0:00:00 Collecting MarkupSafe>=2.0 (from jinja2->torch==2.0.0->-r requirements_inference.txt (line 8)) Obtaining dependency information for MarkupSafe>=2.0 from https://files.pythonhosted.org/packages/62/9b/4908a57acf39d8811836bc6776b309c2e07d63791485589acf0b6d7bc0c6/MarkupSafe-2.1.3-cp39-cp39-macosx_10_9_x86_64.whl.metadata Downloading MarkupSafe-2.1.3-cp39-cp39-macosx_10_9_x86_64.whl.metadata (3.0 kB) Collecting packaging>=17 (from nibabel->monai[nibabel]==1.2.0->-r requirements_inference.txt (line 4)) Obtaining dependency information for packaging>=17 from https://files.pythonhosted.org/packages/ec/1a/610693ac4ee14fcdf2d9bf3c493370e4f2ef7ae2e19217d7a237ff42367d/packaging-23.2-py3-none-any.whl.metadata Downloading packaging-23.2-py3-none-any.whl.metadata (3.2 kB) Collecting mpmath>=0.19 (from sympy->torch==2.0.0->-r requirements_inference.txt (line 8)) Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 9.1 MB/s eta 0:00:00 Downloading joblib-1.3.0-py3-none-any.whl (301 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 301.9/301.9 kB 3.0 MB/s eta 0:00:00 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[jcohenadad]

I understand the benefits in duplicating code to isolate other projects (eg https://github.com/ivadomed/canproco/pull/44/files), but it comes at a cost of a lack of testing/feedback from the team. I strongly suggest to keep only one codebase/documentation, and iterate on that codebase/documentation.

[valosekj]

@jcohenadad can you try installing the dependencies now? I think the +cpu in torch package was causing the issue. I removed it in latest commit.

Please stick to python=3.9 as my code is based on 3.9. (however, for simply running the inference script, the python versions shouldn't matter much, as we're using basic python commands. But using 3.9 will keep it consistent with the rest of the monai code)

Working for me as well! Thanks! I updated the canproco files in https://github.com/ivadomed/canproco/pull/44/commits/688d1a0f99f98171825644da4bf5d5c972be38c6 to be in line with this PR.

[naga-karthik]

merging to Sandrine's branch -- discussed in the internal meeting