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6007 reverse_indexing for PILReader #6008

Merged
merged 3 commits into from
Feb 16, 2023
Merged

6007 reverse_indexing for PILReader #6008

merged 3 commits into from
Feb 16, 2023

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wyli
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@wyli wyli commented Feb 15, 2023 •
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Fixes #6007

Description

  • reverse_indexing = False:
    to support consistency with PIL/torchvision
img = LoadImage(image_only=True, ensure_channel_first=True, reverse_indexing=False)("MONAI-logo_color.png")  # PILReader
torchvision.utils.save_image(img, "MONAI-logo_color_torchvision.png", normalize=True)
  • reverse_indexing = True:
    to support consistency with other backends in monai
img = LoadImage(image_only=True, ensure_channel_first=True, reader="PILReader", reverse_indexing=True)(filename)  # PIL backend
img_1 = LoadImage(image_only=True, ensure_channel_first=True, reader="ITKReader")(filename)  # itk backend
np.testing.assert_allclose(img, img_1)  # true

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

@wyli
fixes Project-MONAI#6007
e9acacf 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
holgerroth
holgerroth approved these changes Feb 15, 2023
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That's useful. Thanks!

@wyli
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wyli commented Feb 15, 2023

/build

@wyli
update docstrings
fc4e98e 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
Merge remote-tracking branch 'upstream/dev' into 6007-pil-reader
02da21b 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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wyli commented Feb 16, 2023

/build

@wyli wyli enabled auto-merge (squash) February 16, 2023 07:45
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wyli commented Feb 16, 2023

/build

@wyli wyli merged commit 94e9e17 into Project-MONAI:dev Feb 16, 2023
@wyli wyli deleted the 6007-pil-reader branch February 16, 2023 08:45
@wyli wyli mentioned this pull request Feb 16, 2023
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wyli added a commit to Project-MONAI/tutorials that referenced this pull request Feb 16, 2023
@wyli @pre-commit-ci
update load image tutorial (#1219)
4d4c565 
follow-up of Project-MONAI/MONAI#6008, adding
more examples

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [x] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [x] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
@wyli @pre-commit-ci
update load image tutorial (Project-MONAI#1219)
a3a5ea0 
follow-up of Project-MONAI/MONAI#6008, adding
more examples

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [x] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [x] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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@holgerroth holgerroth holgerroth approved these changes

@KumoLiu KumoLiu KumoLiu approved these changes

@ericspod ericspod Awaiting requested review from ericspod

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma

@yiheng-wang-nv yiheng-wang-nv Awaiting requested review from yiheng-wang-nv

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option for LoadImage to be compatible with torchvision save_image
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@wyli @holgerroth @KumoLiu