Support installing SCT natively on Windows

[joshuacwnewton]

Context

Currently, it is not possible to install SCT natively on Windows. Because of this, some sort of virtualization software (e.g. WSL, Docker, a VM) that mimics a UNIX-based environment is needed to run SCT on Windows.

Setting up this virtualization software is often challenging and confusing for our users. So, there is a pressing need to improve this experience -- for example, by streamlining the documentation (#3610).

This issue, however, is for the more radical approach: ditching WSL/Docker/VMs entirely by installing SCT natively on Windows. It's possible that this would require more work than is feasible, so I'm opening this issue as a place to record an initial investigation.

Remaining work

After the initial investigation from (1, 2, 3, 4), there are a number of outstanding tasks required to ensure Windows compatibility:

• Turn spinalcordtoolbox into a pip-installable PyPI package #1526
  • Note: This may be optional if we can cobble together a similar sort of install_sct script for Windows that takes care of the same steps that our UNIX script handles.
  • EDIT: I was indeed able to create an install_sct.bat file that takes care of the install steps.
• Uploading the built binaries_win.zip to OSF (and patching sct_download_data).
  • Note: This contains 7/8 binaries, but currently excludes isct_propseg. See this issue.
  • EDIT: I uploaded the binaries to GitHub instead.
• Adding a native Windows CI runner for our test suite.
• Fixing windows-specific issues and test failures:
  • isct_propseg builds with errors on Windows 10 #3694
    • NB: This issue will stay open as a WONTFIX for now, but will still be used for future updates.
  • On Windows, saving an Image to a file with an open file pointer causes OSError: [Errno 22] Invalid argument #3695
  • sct_run_batch shell script usage is incompatible with native Windows installations #3696
  • Windows-built isct_AntsSliceReg binary causes minor failures in registration/moco test results  #3697
  • Replace hardcoded / in path strings with the use of os.path.join #3707
  • Avoid the use of /tmp when outputting temporary files #3708
  • Include win32 in OS-specific checks that involve sys.platform #3709
  • isct_dice_coefficient requires an updated CMakeLists.txt file to build correctly #3710
  • Replace existing run_proc calls with sct_script.main() calls #3711
    • NB: This issue did not actually need to be fixed in order for all of the tests to pass on Windows.
  • Stop trying to catch IsADirectoryError, and instead check isdir first #3712
  • Fix extra \r by using newline='' in calls to open() when working with csv.writer #3713
  • reorient_data() repeatedly overwrites the same temporary file, causing FileExistsError #3714
• Add documentation to demonstrate this new installation method.
  • I've temporarily put instructions in this GitHub gist
  • But, these instructions will need to be folded into our RTD (once we feel comfortable displaying a native Windows installation, of course.)
• Expanding our test suite to (attempt to) compensate for the lack of a history of user testing on Windows.

[joshuacwnewton]

1. Bare-minimum pip install (no PyPI, binaries, PATH modifications, etc.)

The first thing I wanted to try was simply installing SCT and its dependencies on Windows as-is to see what sort of snags we run into:

1. Download and install Python 3.7.9 x64 executable via this page
2. Clone spinalcordtoolbox repo
3. Setup a virtualenv in the SCT directory by running:

   cd <sct-repo-clone-location>
   python -m venv venv_sct
   cd venv_sct/Scripts
   activate
   # upgrade because default p3.7 pip won't resolve dependency conflicts correctly
   python -m pip install --upgrade pip setuptools wheel

4. Install SCT's dependencies by running:

   cd ../..
   pip install -r requirements.txt

5. Install SCT by running:

   pip install -e .
   

6. Verify installation with

   sct_check_dependencies
   

Log of the above steps

(venv_sct) C:\Users\Joshua\repos\spinalcordtoolbox\venv_sct\Scripts>    python -m pip install --upgrade pip setuptools wheel
Collecting pip
  Using cached pip-22.0.3-py3-none-any.whl (2.1 MB)
Collecting setuptools
  Using cached setuptools-60.8.2-py3-none-any.whl (1.1 MB)
Collecting wheel
  Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB)
Installing collected packages: pip, setuptools, wheel
  Attempting uninstall: pip
    Found existing installation: pip 20.1.1
    Uninstalling pip-20.1.1:
      Successfully uninstalled pip-20.1.1
  Attempting uninstall: setuptools
    Found existing installation: setuptools 47.1.0
    Uninstalling setuptools-47.1.0:
      Successfully uninstalled setuptools-47.1.0
Successfully installed pip-22.0.3 setuptools-60.8.2 wheel-0.37.1

(venv_sct) C:\Users\Joshua\repos\spinalcordtoolbox\venv_sct\Scripts>    cd ../..

(venv_sct) C:\Users\Joshua\repos\spinalcordtoolbox>    pip install -r requirements.txt
Looking in links: https://download.pytorch.org/whl/cpu/torch_stable.html
Ignoring torch: markers 'sys_platform == "darwin"' don't match your environment
Ignoring torchvision: markers 'sys_platform == "darwin"' don't match your environment
warning: missing-index-doctype

× The package index page being used does not have a proper HTML doctype declaration.
╰─> Problematic URL: https://download.pytorch.org/whl/cpu/torch_stable.html

note: This is an issue with the page at the URL mentioned above.
hint: You might need to reach out to the owner of that package index, to get this fixed. See https://github.com/pypa/pip/issues/10825 for context.
Collecting colored
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Collecting pillow>=4.1.1
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Collecting kiwisolver>=1.0.1
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Collecting fonttools>=4.22.0
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Collecting packaging>=20.0
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Collecting cycler>=0.10
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Collecting python-dateutil>=2.7
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Requirement already satisfied: setuptools in c:\users\joshua\repos\spinalcordtoolbox\venv_sct\lib\site-packages (from nibabel->-r requirements.txt (line 9)) (60.8.2)
Collecting pytz>=2017.3
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Collecting pluggy<2.0,>=0.12
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Collecting tomli>=1.0.0
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Collecting iniconfig
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Collecting colorama
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Collecting py>=1.8.2
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Collecting attrs>=19.2.0
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Collecting importlib-metadata>=0.12
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Collecting atomicwrites>=1.0
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Collecting coverage[toml]>=5.2.1
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Collecting certifi>=2017.4.17
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Collecting charset-normalizer~=2.0.0
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Collecting types-setuptools>=57.0.0
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Collecting PyWavelets>=1.1.1
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Collecting imageio>=2.4.1
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Collecting tifffile>=2019.7.26
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Collecting networkx>=2.2
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Collecting threadpoolctl>=2.0.0
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Collecting google-pasta>=0.1.6
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Collecting termcolor>=1.1.0
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  Preparing metadata (setup.py) ... done
Requirement already satisfied: wheel>=0.26 in c:\users\joshua\repos\spinalcordtoolbox\venv_sct\lib\site-packages (from tensorflow~=1.15.0->-r requirements.txt (line 25)) (0.37.1)
Collecting tensorflow-estimator==1.15.1
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Collecting wrapt>=1.11.1
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Collecting absl-py>=0.7.0
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Collecting numpy
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Collecting astor>=0.6.0
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Collecting tensorboard>=1.15.0
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Collecting cryptography>=1.3.4
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Collecting pyOpenSSL>=0.14
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Collecting mock>=2.0.0
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Collecting cffi>=1.12
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Collecting click
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Collecting dictdiffer
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Collecting typing-extensions>=3.6.4
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Collecting zipp>=0.5
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  Preparing metadata (setup.py) ... done
Building wheels for collected packages: colored, gast, transforms3d, termcolor, future, docopt
  Building wheel for colored (setup.py) ... done
  Created wheel for colored: filename=colored-1.4.3-py3-none-any.whl size=14342 sha256=1ba886a043458c95b9102075f40273a610a418c37e486a987c4645fcfe7c05ec
  Stored in directory: c:\users\joshua\appdata\local\pip\cache\wheels\4a\f6\00\835e81851bc345428a253721c8bdad0062721dfb861bc6e752
  Building wheel for gast (setup.py) ... done
  Created wheel for gast: filename=gast-0.2.2-py3-none-any.whl size=7554 sha256=a43f20d442c07dc841dc3e5640a33a0a33fd16142556abf42bf90794835dcf18
  Stored in directory: c:\users\joshua\appdata\local\pip\cache\wheels\21\7f\02\420f32a803f7d0967b48dd823da3f558c5166991bfd204eef3
  Building wheel for transforms3d (setup.py) ... done
  Created wheel for transforms3d: filename=transforms3d-0.3.1-py3-none-any.whl size=59385 sha256=ece1aaabe73a44b9b1f2549b5fe84914b5370fd5e1d0d648263ac8573f1ef8a5
  Stored in directory: c:\users\joshua\appdata\local\pip\cache\wheels\b5\b7\93\8985551f83720ce37548a5b543c75380bb707955a9c2c5d28c
  Building wheel for termcolor (setup.py) ... done
  Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4848 sha256=f29384b12c459940698cf311137fa746fdd75b9c9e2a4a0b2bb768ac4b57e974
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  Building wheel for future (setup.py) ... done
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=60fd11850e7794e12229d7f902c95fdc98585e8527e874ac378de00f57860f15
  Stored in directory: c:\users\joshua\appdata\local\pip\cache\wheels\56\b0\fe\4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
  Building wheel for docopt (setup.py) ... done
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13723 sha256=f6923aed3a35b79396d5b79e4fa8338ed26406d53c079e30d4d34d3936f7ea36
  Stored in directory: c:\users\joshua\appdata\local\pip\cache\wheels\72\b0\3f\1d95f96ff986c7dfffe46ce2be4062f38ebd04b506c77c81b9
Successfully built colored gast transforms3d termcolor future docopt
Installing collected packages: xlwt, types-setuptools, transforms3d, termcolor, tensorflow-estimator, SimpleITK, raven, pytz, PyQt5_sip, iniconfig, docopt, dictdiffer, colored, certifi, bids-validator, zipp, wrapt, win32-setctime, werkzeug, urllib3, typing-extensions, tomli, threadpoolctl, sqlalchemy, six, requirements-parser, pyyaml, pyqt5, pyparsing, pycparser, py, psutil, protobuf, pillow, numpy, num2words, networkx, mock, kiwisolver, joblib, interface-meta, idna, gast, future, fonttools, cycler, coverage, colorama, charset-normalizer, attrs, atomicwrites, astor, wquantiles, tqdm, torch, tifffile, scipy, requests, PyWavelets, python-dateutil, packaging, opt-einsum, onnxruntime, loguru, keras-preprocessing, importlib-metadata, imageio, h5py, grpcio, google-pasta, Deprecated, cffi, absl-py, torchvision, scikit-learn, scikit-image, pluggy, pandas, nibabel, matplotlib, markdown, keras-applications, humanize, cryptography, click, torchio, tensorboard, seaborn, pytest, pyOpenSSL, Keras, formulaic, dipy, csv-diff, tensorflow, pytest-cov, pytest_console_scripts, pybids, ivadomed
Successfully installed Deprecated-1.2.13 Keras-2.3.1 PyQt5_sip-4.19.19 PyWavelets-1.2.0 SimpleITK-2.1.1 absl-py-1.0.0 astor-0.8.1 atomicwrites-1.4.0 attrs-21.4.0 bids-validator-1.8.9 certifi-2021.10.8 cffi-1.15.0 charset-normalizer-2.0.11 click-8.0.3 colorama-0.4.4 colored-1.4.3 coverage-6.3.1 cryptography-36.0.1 csv-diff-1.1 cycler-0.11.0 dictdiffer-0.9.0 dipy-1.4.1 docopt-0.6.2 fonttools-4.29.1 formulaic-0.2.4 future-0.18.2 gast-0.2.2 google-pasta-0.2.0 grpcio-1.43.0 h5py-2.10.0 humanize-3.14.0 idna-3.3 imageio-2.15.0 importlib-metadata-4.10.1 iniconfig-1.1.1 interface-meta-1.2.4 ivadomed-2.9.3 joblib-1.1.0 keras-applications-1.0.8 keras-preprocessing-1.1.2 kiwisolver-1.3.2 loguru-0.6.0 markdown-3.3.6 matplotlib-3.5.1 mock-4.0.3 networkx-2.6.3 nibabel-3.2.2 num2words-0.5.10 numpy-1.18.5 onnxruntime-1.7.0 opt-einsum-3.3.0 packaging-21.3 pandas-1.3.5 pillow-9.0.1 pluggy-1.0.0 protobuf-3.19.4 psutil-5.9.0 py-1.11.0 pyOpenSSL-22.0.0 pybids-0.14.0 pycparser-2.21 pyparsing-2.4.7 pyqt5-5.11.3 pytest-7.0.0 pytest-cov-3.0.0 pytest_console_scripts-1.2.2 python-dateutil-2.8.2 pytz-2021.3 pyyaml-6.0 raven-6.10.0 requests-2.27.1 requirements-parser-0.5.0 scikit-image-0.19.1 scikit-learn-1.0.2 scipy-1.7.3 seaborn-0.11.2 six-1.16.0 sqlalchemy-1.3.24 tensorboard-1.15.0 tensorflow-1.15.5 tensorflow-estimator-1.15.1 termcolor-1.1.0 threadpoolctl-3.1.0 tifffile-2021.11.2 tomli-2.0.1 torch-1.5.0+cpu torchio-0.18.73 torchvision-0.6.0+cpu tqdm-4.62.3 transforms3d-0.3.1 types-setuptools-57.4.9 typing-extensions-4.0.1 urllib3-1.26.8 werkzeug-2.0.3 win32-setctime-1.1.0 wquantiles-0.6 wrapt-1.13.3 xlwt-1.3.0 zipp-3.7.0

(venv_sct) C:\Users\Joshua\repos\spinalcordtoolbox>pip install -e .
Obtaining file:///C:/Users/Joshua/repos/spinalcordtoolbox
  Preparing metadata (setup.py) ... done
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-dev

(venv_sct) C:\Users\Joshua\repos\spinalcordtoolbox>sct_check_dependencies

(venv_sct) C:\Users\Joshua\repos\spinalcordtoolbox>
--
Spinal Cord Toolbox (dev)

sct_check_dependencies
--

SCT info:
- version: dev
- path: c:\users\joshua\repos\spinalcordtoolbox
OS: not identified (Windows-10-10.0.19041-SP0)
CPU cores: Available: 8, Used by ITK functions: 8
RAM: Total: 16232MB, Used: 6877MB, Available: 9355MB
Check Python executable.............................[OK]
  Using bundled python 3.7.9 (tags/v3.7.9:13c94747c7, Aug 17 2020, 18:58:18) [MSC v.1900 64 bit (AMD64)] at c:\users\joshua\repos\spinalcordtoolbox\venv_sct\scripts\python.exe
Check if data are installed.........................[FAIL]
Check if colored is installed.......................[OK] (1.4.3)
Check if dipy is installed..........................[OK] (1.4.1)
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras (2.3.1) is installed.................[OK] (2.3.1)
Check if ivadomed is installed......................[OK] (2.9.3)
Check if matplotlib is installed....................[OK] (3.5.1)
Check if nibabel is installed.......................[OK] (3.2.2)
Check if numpy is installed.........................[OK] (1.18.5)
Check if onnxruntime is installed...................[OK] (1.7.0)
Check if pandas is installed........................[OK] (1.3.5)
Check if psutil is installed........................[OK] (5.9.0)
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3)
Check if pytest is installed........................[OK] (7.0.0)
Check if pytest-cov is installed....................[OK] (3.0.0)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.27.1)
Check if requirements-parser is installed...........[OK]
Check if scipy is installed.........................[OK] (1.7.3)
Check if scikit-image is installed..................[OK] (0.19.1)
Check if scikit-learn is installed..................[OK] (1.0.2)
Check if tensorflow is installed....................[OK] (1.15.5)
Check if torch (1.5.0+cpu) is installed.............[OK] (1.5.0+cpu)
Check if torchvision (0.6.0+cpu) is installed.......[OK] (0.6.0+cpu)
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.62.3)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3 is installed.......................[OK] (1.26.8)
Check if pytest_console_scripts is installed........[OK]
Check if wquantiles is installed....................[OK] (0.4)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if figure can be opened with matplotlib.......[OK] (Using GUI backend: 'QtAgg')
Check if figure can be opened with PyQt.............[OK]
Check FSLeyes version...............................Exit code 1 occurred. Please report this issue on SCT GitHub: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues

The whole process went (more or less) without a snag? All of our dependecies have Windows versions, and they all installed OK into a native Windows Python 3.7 venv. The only real issue was with the sct_check_dependencies call, which stalled out, and is likely a platform-specific bug that I'd need to look into.

The next step, I think, will be to try running sct_testing to see what kind of errors pop up. I assume there will be many, given the lack of ANTs binaries!

[joshuacwnewton]

2. Running sct_testing as-is

First and foremost, trying to run sct_testing triggers an ImportError due to fcntl being unavailable on Windows. Once I temporarily disabled it for testing purposes using a simple try, except, the testing suite could run.

Next, I manually ran sct_download_data to install the various missing dependencies (as without install_sct, they do not get installed automatically). After that, I re-ran the tests, and here's the short summary:

======================================================================================================= short test summary info =======================================================================================================
FAILED testing/api/test_aggregate_slicewise.py::test_save_as_csv - AssertionError: assert [] == ['dev', 'Fake..., '45.5', ...]
FAILED testing/api/test_aggregate_slicewise.py::test_save_as_csv_extract_metric - AssertionError: assert [] == ['dev', '', '...label_0', ...]
FAILED testing/api/test_centerline.py::test_get_centerline_optic[params0] - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/api/test_centerline.py::test_get_centerline_optic[params1] - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/api/test_centerline.py::test_get_centerline_optic[params2] - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/api/test_image.py::test_add_suffix - AssertionError: assert 'var/lib/usr\\t2sfx.nii.gz' == 'var/lib/usr/t2sfx.nii.gz'
FAILED testing/api/test_image.py::test_splitext - AssertionError: assert ('folder\\image', '.nii.gz') == ('folder/image', '.nii.gz')
FAILED testing/api/test_qc_parallel.py::test_many_qc - PermissionError: [Errno 13] Permission denied: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\sct-qc-iptt881n\\_json'
FAILED testing/api/test_register.py::test_register_step_ants_slice_regularized_registration - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/api/test_reports.py::test_label_vertebrae - PermissionError: [Errno 13] Permission denied: '/tmp\\_json'
FAILED testing/api/test_reports.py::test_propseg - PermissionError: [Errno 13] Permission denied: '/tmp\\_json'
FAILED testing/api/test_sct_run_batch.py::test_config_with_args_warning - PermissionError: [Errno 13] Permission denied: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\tmpd8clh7an.json'
FAILED testing/api/test_sct_run_batch.py::test_config_extra_value_warning - PermissionError: [Errno 13] Permission denied: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\tmprhxdkwdg.yml'
FAILED testing/api/test_sct_run_batch.py::test_only_one_include - PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\tmpg__2qbg...
FAILED testing/api/test_sct_run_batch.py::test_non_executable_task - AssertionError: Script already executable
FAILED testing/api/test_sct_run_batch.py::test_no_sessions - PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\tmpbybl688j\\lo...
FAILED testing/api/test_sct_run_batch.py::test_separate_sessions - PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\tmp5o_zw4...
FAILED testing/api/test_straightening.py::test_straighten - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/api/test_transfo.py::test_transfo_null - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/api/test_transfo.py::test_transfo_figure_out_ants_frame_exhaustive - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/api/test_transfo.py::test_transfo_exhaustive_wrt_orientations - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/api/test_transfo.py::test_transfo_skip_pix2phys - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli.py::test_scripts_with_no_args_as_subprocess[subprocess-isct_convert_binary_to_trilinear] - assert 0 is 2
FAILED testing/cli/test_cli.py::test_scripts_with_no_args_as_subprocess[subprocess-isct_minc2volume-viewer] - assert 0 is 2
FAILED testing/cli/test_cli_sct_analyze_texture.py::test_sct_analyze_texture_image_data_within_threshold - FileExistsError: [WinError 183] Cannot create a file when that file already exists: 't2_contrast_1_45.nii.gz' -> 't2_2reor...
FAILED testing/cli/test_cli_sct_apply_transfo.py::test_sct_apply_transfo_output_image_attributes[template/template/PAM50_small_t2.nii.gz-t2/t2.nii.gz-t2/warp_template2anat.nii.gz-PAM50_small_t2_reg.nii-remaining_args0] - OSError:...
FAILED testing/cli/test_cli_sct_apply_transfo.py::test_sct_apply_transfo_output_image_attributes[template/template/PAM50_small_t2.nii.gz-t2/t2.nii.gz-t2/warp_template2anat.nii.gz-PAM50_small_t2_reg-crop1.nii-remaining_args1] - OS...
FAILED testing/cli/test_cli_sct_apply_transfo.py::test_sct_apply_transfo_output_image_attributes[template/template/PAM50_small_t2.nii.gz-t2/t2.nii.gz-t2/warp_template2anat.nii.gz-PAM50_small_t2_reg-crop2.nii-remaining_args2] - OS...
FAILED testing/cli/test_cli_sct_apply_transfo.py::test_sct_apply_transfo_output_image_attributes[template/template/PAM50_small_t2.nii.gz-t2/t2.nii.gz-t2/warp_template2anat.nii.gz-PAM50_small_t2_reg-concatWarp.nii-remaining_args3]
FAILED testing/cli/test_cli_sct_apply_transfo.py::test_sct_apply_transfo_output_image_attributes[template/template/PAM50_small_t2.nii.gz-dmri/dmri.nii.gz-t2/warp_template2anat.nii.gz-PAM50_small_t2_reg-4Dref.nii-remaining_args4]
FAILED testing/cli/test_cli_sct_apply_transfo.py::test_sct_apply_transfo_output_image_attributes[dmri/dmri.nii.gz-t2/t2.nii.gz-mt/warp_t22mt1.nii.gz-PAM50_small_t2_reg-4Din.nii-remaining_args5] - OSError: [WinError 193] %1 is not...
FAILED testing/cli/test_cli_sct_compute_hausdorff_distance.py::test_sct_compute_hausdorff_distance_null_values - RuntimeError
FAILED testing/cli/test_cli_sct_concat_transfo.py::test_sct_concat_transfo_no_checks - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_create_mask.py::test_sct_create_mask_no_checks[mt/mt1.nii.gz-coord,15x17-10] - OSError: [Errno 22] Invalid argument: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\sct-20220209144718.515788-create_mask-...
FAILED testing/cli/test_cli_sct_create_mask.py::test_sct_create_mask_no_checks[mt/mt1.nii.gz-point,mt/mt1_point.nii.gz-10] - OSError: [Errno 22] Invalid argument: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\sct-20220209144718.60871...
FAILED testing/cli/test_cli_sct_create_mask.py::test_sct_create_mask_no_checks[mt/mt1.nii.gz-center-10] - OSError: [Errno 22] Invalid argument: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\sct-20220209144718.725965-create_mask-s12xt...
FAILED testing/cli/test_cli_sct_create_mask.py::test_sct_create_mask_no_checks[dmri/dmri.nii.gz-center-10] - OSError: [Errno 22] Invalid argument: 'data_RPI.nii'
FAILED testing/cli/test_cli_sct_deepseg_gm.py::test_sct_deepseg_gm_check_dice_coefficient_against_groundtruth - PermissionError: [Errno 13] Permission denied: 'c:\\users\\joshua\\repos\\spinalcordtoolbox\\data\\sct_testing_data\\...
FAILED testing/cli/test_cli_sct_deepseg_lesion.py::test_sct_deepseg_lesion_no_checks - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_deepseg_sc.py::test_sct_deepseg_sc_check_output_exists - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_deepseg_sc.py::test_sct_deepseg_sc_qc_report_exists - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_detect_pmj.py::test_sct_detect_pmj_check_euclidean_distance_against_groundtruth - RuntimeError
FAILED testing/cli/test_cli_sct_dice_coefficient.py::test_sct_dice_coefficient_check_output_against_groundtruth - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_dmri_moco.py::test_sct_dmri_moco_check_params - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_dmri_moco.py::test_sct_dmri_moco_sagittal_no_checks - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_fmri_moco.py::test_sct_fmri_moco_no_checks - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_get_centerline.py::test_sct_get_centerline_no_checks - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_image.py::test_sct_image_display_warp_check_output_exists - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_label_vertebrae.py::test_sct_label_vertebrae_consistent_disc - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_label_vertebrae.py::test_sct_label_vertebrae_initfile_qc_no_checks - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_label_vertebrae.py::test_sct_label_vertebrae_high_value_warning - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_label_vertebrae.py::test_sct_label_vertebrae_clean_labels - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_label_vertebrae.py::test_sct_label_vertebrae_disc_discontinuity_center_of_mass_error - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_propseg.py::test_sct_propseg_check_dice_coefficient_against_groundtruth - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_propseg.py::test_isct_propseg_compatibility - AssertionError: isct_propseg does not seem to be compatible with your system or is no up-to-date... Please contact SCT administrators.
FAILED testing/cli/test_cli_sct_propseg.py::test_sct_propseg_o_flag - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_qc.py::test_sct_qc_no_checks - PermissionError: [Errno 13] Permission denied: './qc\\_json'
FAILED testing/cli/test_cli_sct_register_multimodal.py::test_sct_register_multimodal_mask_files_exist - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_register_multimodal.py::test_sct_register_multimodal_mt0_image_data_within_threshold[False-step=1,algo=syn,type=im,iter=1,smooth=1,shrink=2,metric=MI-mt/mt0_reg_syn_goldstandard.nii.gz] - OSError: ...
FAILED testing/cli/test_cli_sct_register_multimodal.py::test_sct_register_multimodal_mt0_image_data_within_threshold[False-step=1,algo=slicereg,type=im,iter=5,smooth=0,metric=MeanSquares-mt/mt0_reg_slicereg_goldstandard.nii.gz]
FAILED testing/cli/test_cli_sct_register_multimodal.py::test_sct_register_multimodal_mt0_image_data_within_threshold[True-step=1,algo=centermassrot,type=seg,rot_method=pca-None] - OSError: [WinError 193] %1 is not a valid Win32 a...
FAILED testing/cli/test_cli_sct_register_multimodal.py::test_sct_register_multimodal_mt0_image_data_within_threshold[True-step=1,algo=centermassrot,type=imseg,rot_method=hog-None] - OSError: [WinError 193] %1 is not a valid Win32...
FAILED testing/cli/test_cli_sct_register_multimodal.py::test_sct_register_multimodal_mt0_image_data_within_threshold[True-step=1,algo=centermassrot,type=imseg,rot_method=pcahog-None] - OSError: [WinError 193] %1 is not a valid Wi...
FAILED testing/cli/test_cli_sct_register_multimodal.py::test_sct_register_multimodal_mt0_image_data_within_threshold[True-step=1,algo=columnwise,type=seg,smooth=1-None] - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_register_multimodal.py::test_sct_register_multimodal_with_softmask - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_register_to_template.py::test_sct_register_to_template_non_rpi_template - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_register_to_template.py::test_sct_register_to_template_non_rpi_data - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_register_to_template.py::test_sct_register_to_template_dice_coefficient_against_groundtruth[template/template/PAM50_small_cord.nii.gz-remaining_args0] - OSError: [WinError 193] %1 is not a valid Wi...
FAILED testing/cli/test_cli_sct_register_to_template.py::test_sct_register_to_template_dice_coefficient_against_groundtruth[c:\\users\\joshua\\repos\\spinalcordtoolbox\\data/PAM50/template/PAM50_cord.nii.gz-remaining_args1] - OSE...
FAILED testing/cli/test_cli_sct_smooth_spinalcord.py::test_sct_smooth_spinalcord_check_output_files - RuntimeError
FAILED testing/cli/test_cli_sct_straighten_spinalcord.py::test_sct_straighten_spinalcord_no_checks - OSError: [WinError 193] %1 is not a valid Win32 application
FAILED testing/cli/test_cli_sct_warp_template.py::test_sct_warp_template_no_checks - OSError: [WinError 193] %1 is not a valid Win32 application
ERROR testing/cli/test_cli_sct_dmri_moco.py::test_sct_dmri_moco_with_mask_check_params - OSError: [Errno 22] Invalid argument: 'C:\\Users\\Joshua\\AppData\\Local\\Temp\\sct-20220209144818.636103-create_mask-gg3abl69\\line.nii'
=========================================================================== 72 failed, 294 passed, 18 skipped, 26996 warnings, 1 error in 385.55s (0:06:25) ===========================================================================

Alrighty! There are 73 issues (72 failures + 1 error) to unpack here:

• 49/72: Compiled binary compatibility errors
  • 46/72: OSError: [WinError 193] %1 is not a valid Win32 application
  • 3/72 isct_ binary compatibility errors
• 7/72: PermissionError: [Errno 13] Permission denied (--> filepath)
• 5/72: OSError: [Errno 22] Invalid argument
• 3/72: PermissionError: [WinError 32] The process cannot access the file because it is being used by another process
• 3/72: RuntimeError
• 2/72: Line-separator errors (e.g. assert 'var/lib/usr\\t2sfx.nii.gz' == 'var/lib/usr/t2sfx.nii.gz')
• 2/72: AssertionError: assert [] == ['dev', 'Fake..., '45.5', ...]
• 1/72: AssertionError: Script already executable
• 1/72: FileExistsError: [WinError 183] Cannot create a file when that file already exists

So... a cursory look suggests that while the majority of errors are due to not having compiled binaries for Windows, there will be quite a bit of extra work on top of that to pin down pesky Windows-specific filesystem errors.

[joshuacwnewton]

3. Compiling binaries (ANTs, isct_) on Windows

Given the test failures in #3682 (comment), the elephant in the room here is compiling our C++ binaries on Windows.

Important links

• We have a rough outline of how to do this for Linux and macOS on this dev Wiki page, however some of the instructions are a little imprecise, and there aren't currently any Windows instructions.
• ANTs' current documentation has instructions for compiling ANTs on Windows 10, but they... suggest to use WSL then compile within an Ubuntu environment, which I presume is not what we want given that we want to try to support Windows natively.
• Thankfully, however, there's an old thread on ANTs' source-forge page that suggests native Windows compilation is possible!
• Tangentially related: @kousu has spent some time on compiling our binaries via CI workflows in Use binaries that are packaged by the spinalcordtoolbox-binaries repo #2668, which could help to demystify and standardize this procedure even more.

Compiling ANTs

1. Download and install CMake (specifically, cmake-3.23.0-rc1-windows-x86_64.msi).
2. Download and install Visual Studio 2015 (to use as a CMake generator)
   • Download the "DVD" (.iso) version of "Visual Studio Community 2015 with Update 3"
   • Mount the .iso file then run the vs_community.exe executable.
   • Unselect everything except the "Visual C++"-related packages
   • Open Visual Studio 2015 to complete the first-time setup, then close it.
3. Download and compile zlib
   • Download and extract zlib source code
   • Open cmake, and select the zlib source code directory for "Where is the source code"
   • Create a build/ directory inside the zlib source code directory, then select it for "Where to build the binaries"
   • Click "Configure", then select "Visual Studio 14 2015" and "x64"
   • Once that's finished running, click "Generate".
   • Click "Open Project".
   • In one of the top dropdowns, select "Release" instead of "Debug"
   • Click "Build > Build Solution"
4. Download and compile ANTs
   • Download the Source Code (.zip) for the latest stable release
     • NB: Make sure you download the source code to location with a very short path! Otherwise, you may run into this ITK issue while compiling ANTs. I sure did!
   • Open CMake, and select the ANTs source code directory for "Where is the source code"
   • Create a build/ directory outside of the ANTs source code directory, then select it for "Where to build the binaries"
   • Click "Configure", then select "Visual Studio 14 2015" and "x64"
   • This will fail with an error "Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR)".
   • Click "Add Entry" and add ZLIB_LIBRARY (Example).
   • Click "Advanced" checkbox, then change the existing ZLIB_INCLUDE_DIR to wherever you built zlib. (Example)
   • Find the existing entry for "BUILD_TESTING" with and uncheck the box to turn the bool value to "OFF"
     • This is a fix for Build fails at ANTSFetchData target due to Kitware API removing MD5 checksums ANTsX/ANTs#1236
   • Click "Configure" again, then "Generate".
   • Click "Open Project".
   • In one of the top dropdowns, select "Release" instead of "Debug"
   • Click "Build > Build Solution"
   • (Optional) Copy the necessary binaries to the ${SCT_DIR}/bin directory, renaming them to append isct_ and remove .exe accordingly.

Compiling isct_spine_detect and isct_train_svm

The ctrDetect binaries have already been compiled for Windows. :)

Compiling isct_dice_coefficient

These steps assume you've compiled ANTs ahead of time (see above), as the steps here rely on having a compiled copy of ITK to refer to.

1. Compile isct_dice_coefficient
   • Bugfixes needed prior to compilation:
     • In CMakeLists.txt, change the entire TARGET_LINK_LIBRARIES command to `target_link_libraries(isct_dice_coefficient ${ITK_LIBRARIES})
   • Create a folder build/ inside ${SCT_DIR}/dev/isct_dice_coefficient
   • Open CMake, and target ${SCT_DIR}/dev/isct_dice_coefficient and ${SCT_DIR}/dev/isct_dice_coefficient/build for the source code and build directories respectively.
   • Run Configure, which should fail, because the ITK_DIR variable isn't set.
   • Set the ITK_DIR variable to the directory where ITK was built for the ANTs compilation step (for me, this was C:/Users/Joshua/Documents/ANTs/build/ITKv5-build), then re-run Configure.
   • Click Generate.
   • Click Open Project.
   • Change "Debug" to "Release" in the top dropdown.
   • Click Build Project.

Compiling isct_propseg

However, I'm having some difficulty compiling isct_propseg: I'm running into many C++ errors and warnings, and I believe this would require a bit of cleanup of the isct_propseg code. This isn't a new problem, as @zougloub already had to go through this process once before in #1685.

Given that there have been suggestions to promote sct_deepseg_sc/sct_deepseg over sct_propseg, it's possible that not being able to compile isct_propseg isn't the end of the world; theoretically, SCT would still be very usable on windows without putting in the effort to clean up the C++ code.

That's 7/8 binaries taken care of! It's just isct_propseg that's the problematic one.

[joshuacwnewton]

4. Bugfixes for Windows-specific test failures

Since I was able to get a (mostly) complete set of Windows binaries, our test failures have fallen from 73 to ~50. I'm going to continue to try to get that number down even further.

EDIT: I've gotten the test failures from 50 to 9: #3699

For the remaining test failures (see #3699 (comment)), I believe they will require some discussion and further digging. So, I'll make a write-up of the trickier test failures in individual issues, so that we can discuss the remaining work required for this task as a team.

[joshuacwnewton]

After the above comments, I've summarized the remaining work to be done in the description of this issue: #3682 (comment)

I'll also continue to update the description as new developments occur in other issues.

[joshuacwnewton]

I'm going to mark this issue as solved by #3719.

The bulk of the work has been completed, and when new issues arise, they get discussed in subsequent issues with the "Windows Compatibility" tag (as has been done for #3740).

So, I think the need for a singular issue documenting the core progress is no longer needed. :)