MIL example by myron · Pull Request #431 · Project-MONAI/tutorials

myron · 2021-11-01T06:10:43Z

This adds an example of MIL classification from WSI images.

Let's discuss, which components we can move to MONAI core.
I think we can move MILmodel and ImageExtractPatches transform.
There are more components we can move too (or just keep them here as part of the tutorial)

2d_classification/MIL/mil_classify_monai.py

bhashemian

It's better to move this file to pathology/multi_instance_learning/ folder. Thanks

myron · 2021-11-04T06:16:08Z

I've moved it to pathology/multiple_instance_learning folder and updated the code to import existing components from monai (newly added and fixed components/transforms)

myron · 2021-11-04T06:19:58Z

There are some utility functions left here, I intend to keep them in the tutorial without adding to monai core:

AverageMeter
distributed_all_gather
LabelEncodeIntegerGraded
SimpleTileFlip

@drbeh sounds good?

bhashemian · 2021-11-04T14:04:22Z

There are some utility functions left here, I intend to keep them in the tutorial without adding to monai core:

AverageMeter

distributed_all_gather

LabelEncodeIntegerGraded

SimpleTileFlip

@drbeh sounds good?

Thanks @myron!
At the end, we have to move all this components to MONA but it is about what the most we can add into MONAI for this release, so let's see what else we can implement till Nov 18.
LabelEncodeIntegerGraded seems to be an important piece, isn't it?

myron · 2021-11-04T20:17:05Z

LabelEncodeIntegerGraded - a way to embed class (when a class is a relative tumor grade). I've not run into it much previously, so it's probably not very common. We could consider it adding it

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myron · 2021-11-08T07:17:10Z

I've updated the tutorial

using collate function to reassemble data (from list of dicts)
adjustments for the changes in transforms

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bhashemian

@myron could you please remove datalist_panda_0.json, upload it here, and add download instruction in the notebook:

dataset_url = "https://drive.google.com/uc?id=........."
dataset_path = "datalist_panda_0.json"
gdown.download(dataset_url, dataset_path, quiet=False)

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Signed-off-by: Behrooz <[email protected]>

Nic-Ma

Thanks for the quick update, I feel it overall looks good to me now, just several minor comments inline.
@drbeh , I saw you set request change, do you have any more comments?

Thanks in advance.

pathology/multiple_instance_learning/README.md

pathology/multiple_instance_learning/panda_mil_train_evaluate_pytorch_gpu.py

myron · 2021-11-19T22:16:59Z

I've made the changes

bhashemian · 2021-11-22T13:07:59Z

@myron can you address the unresolved comments so that we can merge this example?

bhashemian

Just waiting for #431 (comment) to be addressed.

bhashemian · 2021-11-23T00:52:40Z

@Nic-Ma, the PR looks good to me. Have your comments been addressed? Do you have any other comment? Thanks

Nic-Ma · 2021-11-23T01:41:55Z

Paste the comments from Daguang:

Do we need “pip install "git+https://github.com/Project-MONAI/MONAI#egg=monai[tifffile,imagecodecs]"”? This is a MONAI tutorial and people should have MONAI installed already.
Can you add some figures for the curves? Training loss and validation curve.

Thanks.

bhashemian · 2021-11-23T15:54:28Z

@myron

For the dependencies, you can follow the “Install dependencies" section of other pathology notebook: https://github.com/Project-MONAI/tutorials/blob/master/pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb

First, you can check if MONAI is install or not, and then install it only if the user doesn’t have MONAI installed. Also you can do the same for the individual dependencies, so if the user has MONAI installed but not the dependencies, you can install them only if they are not already installed:

!python -c "import monai" || pip install -q git+https://github.com/Project-MONAI/MONAI#egg=MONAI[tifffile,imagecodecs]
!python -c "import tifffile " || pip install -q tifffile
!python -c "import imagecodecs " || pip install -q imagecodecs

Signed-off-by: myron <[email protected]>

myron · 2021-11-23T18:55:25Z

I've added the curves

myron · 2021-11-23T18:56:44Z

@myron

For the dependencies, you can follow the “Install dependencies" section of other pathology notebook: https://github.com/Project-MONAI/tutorials/blob/master/pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb

First, you can check if MONAI is install or not, and then install it only if the user doesn’t have MONAI installed. Also you can do the same for the individual dependencies, so if the user has MONAI installed but not the dependencies, you can install them only if they are not already installed:
!python -c "import monai" || pip install -q git+https://github.com/Project-MONAI/MONAI#egg=MONAI[tifffile,imagecodecs]
!python -c "import tifffile " || pip install -q tifffile
!python -c "import imagecodecs " || pip install -q imagecodecs

I mean, I know how to do it. But what do you suggest to put in README for users? do you want to add all these instructions (seems pretty verbose and complicated). I think we can keep it as is. Thanks
Especially since other tutorials (most), don't specify anything e.g. https://github.com/myron/tutorials/tree/master/pathology/tumor_detection

Signed-off-by: myron <[email protected]>

bhashemian

@myron there are few formatting issues that I mentioned. Apart from that it looks good to me.
@Nic-Ma do you have any other comment?

pathology/multiple_instance_learning/README.md

Signed-off-by: myron <[email protected]>

myron · 2021-11-24T23:01:17Z

done

Nic-Ma · 2021-11-25T01:54:18Z

Hi @drbeh ,

I see you marked request change which blocks merging this PR, do you have any more comments?

Thanks.

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Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]> Co-authored-by: Dong Yang <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: nvahmadi <[email protected]> Co-authored-by: Vishwesh <[email protected]> Co-authored-by: vnath <[email protected]> Co-authored-by: myron <[email protected]> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

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Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes 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Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see 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* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change arch code keys * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]>

* MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (Project-MONAI#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (Project-MONAI#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (Project-MONAI#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (Project-MONAI#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]> Co-authored-by: Dong Yang <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: nvahmadi <[email protected]> Co-authored-by: Vishwesh <[email protected]> Co-authored-by: vnath <[email protected]> Co-authored-by: myron <[email protected]> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (Project-MONAI#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (Project-MONAI#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (Project-MONAI#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (Project-MONAI#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]>

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (Project-MONAI#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (Project-MONAI#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (Project-MONAI#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (Project-MONAI#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change arch code keys * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]>

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am and others added 2 commits November 7, 2021 23:12

MIL example

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myron mentioned this pull request Nov 8, 2021

Add tutorial for multiple instance learning (MIL) code for 2D pathology WSI classification (ETA 11/12/2021) Project-MONAI/MONAI#2781

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myron and others added 5 commits November 13, 2021 17:20

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myron marked this pull request as ready for review November 19, 2021 00:19

bhashemian added 2 commits November 19, 2021 01:36

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bhashemian and others added 2 commits November 24, 2021 18:51

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Nic-Ma merged commit 0e19962 into Project-MONAI:master Nov 25, 2021

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