Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Expose ITK Image to MONAI MetaTensor conversion #5897

Merged
merged 40 commits into from
Feb 20, 2023
Merged

Expose ITK Image to MONAI MetaTensor conversion #5897

merged 40 commits into from
Feb 20, 2023
+861 −2

Commits on Feb 7, 2023

  1. Copy file from other PR as is 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    b63742a View commit details
    Browse the repository at this point in the history

  2. Add testcases 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    1e64270 View commit details
    Browse the repository at this point in the history

  3. Add download of test data (not done) 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    7be26bb View commit details
    Browse the repository at this point in the history

  4. Formatting 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    daa8b57 View commit details
    Browse the repository at this point in the history

  5. Add a bit of type checking and todos for documentation; also make int… 

    …ernal functions private

Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    12bee7b View commit details
    Browse the repository at this point in the history

  6. Add __all__ 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    6bd53de View commit details
    Browse the repository at this point in the history

  7. Remove print test description 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    84c2ec1 View commit details
    Browse the repository at this point in the history

  8. Add missing licensing header 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    82bc671 View commit details
    Browse the repository at this point in the history

  9. Remove remove_border and update testcases to use ITKReader 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    5cb1be3 View commit details
    Browse the repository at this point in the history

  10. Upload CT_2D images and adjust tests 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    8307474 View commit details
    Browse the repository at this point in the history

  11. Formatting 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    f9e0545 View commit details
    Browse the repository at this point in the history

  12. Fit flake8 issues 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    a991f2b View commit details
    Browse the repository at this point in the history

  13. Inline metatensor_to_array, rename image_to_metatensor to itk_image_t… 

    …o_metatensor and partly fix dtype warning

Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    b080bc3 View commit details
    Browse the repository at this point in the history

  14. Add code from InsightSoftwareConsortium/itk-torch-transform-bridge#8 … 

    …and automatically download test data

Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    5af9094 View commit details
    Browse the repository at this point in the history

  15. Formatting 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    7f57cae View commit details
    Browse the repository at this point in the history

  16. Add itk_torch_affine_matrix_bridge functions to __init__.py 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    8cfc9f1 View commit details
    Browse the repository at this point in the history

  17. Fix a typo and move remove_border from testcode to sourcecode 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    9aca538 View commit details
    Browse the repository at this point in the history

  18. Rename file to itk_torch_bridge 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    a3f12af View commit details
    Browse the repository at this point in the history

  19. Fix __init__ file 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    9c6fe24 View commit details
    Browse the repository at this point in the history

  20. Move code into testcode since it should only be exposed to tests and … 

    …not users

Signed-off-by: Felix Schnabel <fschnabel007@gmail.com>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    822ea87 View commit details
    Browse the repository at this point in the history

  21. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci @Shadow-Devil
    pre-commit-ci[bot] authored and Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    9a05de5 View commit details
    Browse the repository at this point in the history

  22. Reformatting 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    60c9e0c View commit details
    Browse the repository at this point in the history

  23. Fix testcases 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    86a9b04 View commit details
    Browse the repository at this point in the history

  24. Fix typechecking 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    928c176 View commit details
    Browse the repository at this point in the history

  25. Download 2D images from MONAI-extra-test-data 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    e2657f1 View commit details
    Browse the repository at this point in the history

  26. Add reference image as parameter to itk_to_monai_affine and add test … 

    …case (also download second 3d image automatically)

Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    72c8f3a View commit details
    Browse the repository at this point in the history

  27. Fix typechecking 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    6af154a View commit details
    Browse the repository at this point in the history

  28. Increase tolerance on random testing 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    5582177 View commit details
    Browse the repository at this point in the history

  29. Set random seed for reproducibility 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    3513fd1 View commit details
    Browse the repository at this point in the history

  30. Formatting 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    1268357 View commit details
    Browse the repository at this point in the history

Commits on Feb 8, 2023

  1. Skip test_random_array if quick since it requires too much memory 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 8, 2023
    Configuration menu
    Copy the full SHA
    e1fc7c1 View commit details
    Browse the repository at this point in the history

  2. Code rearrangement, fix random state and skip right test 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 8, 2023
    Configuration menu
    Copy the full SHA
    fd1dcf1 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'dev' into feature/ITK_bridge

    @Shadow-Devil
    Shadow-Devil committed Feb 8, 2023
    Configuration menu
    Copy the full SHA
    7201955 View commit details
    Browse the repository at this point in the history

Commits on Feb 12, 2023

  1. Add metatensor_to_itk_image 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 12, 2023
    Configuration menu
    Copy the full SHA
    fa17d6c View commit details
    Browse the repository at this point in the history

  2. Remove prints in tests 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 12, 2023
    Configuration menu
    Copy the full SHA
    2cc437b View commit details
    Browse the repository at this point in the history

Commits on Feb 20, 2023

  1. Fix metatensor_to_itk_image 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 20, 2023
    Configuration menu
    Copy the full SHA
    11ae802 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'dev' into feature/ITK_bridge

    @Shadow-Devil
    Shadow-Devil committed Feb 20, 2023
    Configuration menu
    Copy the full SHA
    2c00d5d View commit details
    Browse the repository at this point in the history

  3. Add documentation 

    Signed-off-by: Felix Schnabel <f.schnabel@tum.de>
    @Shadow-Devil
    Shadow-Devil committed Feb 20, 2023
    Configuration menu
    Copy the full SHA
    681193a View commit details
    Browse the repository at this point in the history

  4. update gitignore 

    Signed-off-by: Wenqi Li <wenqil@nvidia.com>
    @wyli
    wyli committed Feb 20, 2023
    Configuration menu
    Copy the full SHA
    e0125ce View commit details
    Browse the repository at this point in the history

  5. skip slow tests, flexible dtype/channel_dim 

    Signed-off-by: Wenqi Li <wenqil@nvidia.com>
    @wyli
    wyli committed Feb 20, 2023
    Configuration menu
    Copy the full SHA
    8cc36bc View commit details
    Browse the repository at this point in the history