Add CalculateInstanceSegmentationMap Transform
#5173
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Signed-off-by: KumoLiu <yunl@nvidia.com>
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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Signed-off-by: KumoLiu <yunl@nvidia.com>
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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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@KumoLiu Could you please review items in the PR descriptions, check everything that you have already done, and remove any one that is not relevant (e.g. Breaking change...)? |
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Signed-off-by: KumoLiu <yunl@nvidia.com>
to `GenerateInstanceBorder` Signed-off-by: KumoLiu <yunl@nvidia.com>
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@KumoLiu has tested it with the actual pipeline and it is working as expected.
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The mean dice on three-fold cross-validation for Lizard dataset is 0.8256. |
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/black |
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/build |
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/build |
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Fixes #5310 . ### Description Add a post transform to process NP branch output(an output branch in HoVerNet) which turns the probability map from the network into the instance segmentation result. ### 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). - [x] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: KumoLiu <yunl@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> Signed-off-by: KumoLiu <yunl@nvidia.com>
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Fixes Project-MONAI#5310 . ### Description Add a post transform to process NP branch output(an output branch in HoVerNet) which turns the probability map from the network into the instance segmentation result. ### 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). - [x] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: KumoLiu <yunl@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> Signed-off-by: Yiheng Wang <vennw@nvidia.com>
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Fixes Project-MONAI#5310 . ### Description Add a post transform to process NP branch output(an output branch in HoVerNet) which turns the probability map from the network into the instance segmentation result. ### 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). - [x] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: KumoLiu <yunl@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> Signed-off-by: Yiheng Wang <vennw@nvidia.com>
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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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Fixes #5310 .
Description
Add a post transform to process NP branch output(an output branch in HoVerNet) which turns the probability map from the network into the instance segmentation result.
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.