Add Classification Result Post Process for HoVerNet #5186
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Signed-off-by: KumoLiu <yunl@nvidia.com>
Signed-off-by: KumoLiu <yunl@nvidia.com>
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Signed-off-by: KumoLiu <yunl@nvidia.com>
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Hi @KumoLiu, thanks for submitting this PR. it seems that this PR is still not ready for reviewing yet. Can you remove redundant files, review and address the checklist in the PR description, resolve the failed tests, and update docs before moving forward with review? Thanks
Signed-off-by: KumoLiu <yunl@nvidia.com>
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Hi @drbeh, I have reviewed items in this PR description, check everything that I have already done, and removed irrelevant lines. Some tests will continue to be unsuccessful since #5173 hasn't been merged. But could you please help review this PR first and let me know if you have any advice? Thanks in advance! |
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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Signed-off-by: KumoLiu <yunl@nvidia.com>
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Are you using the testing data? tests/testing_data/hovernet_test_data_raw.npz
If not, please remove it. Thanks
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Yes, thanks for pointing it out, I removed it in the latest commit! |
for more information, see https://pre-commit.ci Signed-off-by: KumoLiu <yunl@nvidia.com>
Signed-off-by: KumoLiu <yunl@nvidia.com>
Signed-off-by: KumoLiu <yunl@nvidia.com>
Signed-off-by: monai-bot <monai.miccai2019@gmail.com> - auto style fixing - bump versioneer to 0.23 from 0.19 Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: KumoLiu <yunl@nvidia.com>
Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Signed-off-by: KumoLiu <yunl@nvidia.com>
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@JHancox do you have any comments on this PR? |
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Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes #5180. ### Description For the post-process in HoVerNet, now we have PR #5173 to process the segmentation output(which has been merged) and PR #5186 to process the classification output(which is under review now). We want a whole transform containing these two components which can be easily used in the MONAI model zoo bundle. Here has a draft version of how to combine these components, if anyone has any suggestions, please feel free to take it out. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] 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`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: KumoLiu <yunl@nvidia.com> Signed-off-by: yunliu <yunl@nvidia.com> Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com>
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Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes Project-MONAI#5180. ### Description For the post-process in HoVerNet, now we have PR Project-MONAI#5173 to process the segmentation output(which has been merged) and PR Project-MONAI#5186 to process the classification output(which is under review now). We want a whole transform containing these two components which can be easily used in the MONAI model zoo bundle. Here has a draft version of how to combine these components, if anyone has any suggestions, please feel free to take it out. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] 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`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: KumoLiu <yunl@nvidia.com> Signed-off-by: yunliu <yunl@nvidia.com> Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
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Signed-off-by: KumoLiu yunl@nvidia.com
Fixes #5180.
Description
Add classification post-process script for HoVerNet.
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.