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Add CalculateInstanceSegmentationMap Transform#5173

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Nic-Ma merged 102 commits intoProject-MONAI:devfrom
KumoLiu:postprocess
Nov 1, 2022
Merged

Add CalculateInstanceSegmentationMap Transform#5173
Nic-Ma merged 102 commits intoProject-MONAI:devfrom
KumoLiu:postprocess

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@KumoLiu KumoLiu commented Sep 19, 2022

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

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • 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.

@KumoLiu KumoLiu marked this pull request as ready for review September 21, 2022 02:34
@KumoLiu KumoLiu changed the title [WIP] Add post transform for HoVerNet Add post transform for HoVerNet Sep 21, 2022
@KumoLiu KumoLiu requested review from Nic-Ma, bhashemian and wyli and removed request for bhashemian September 21, 2022 02:34
@KumoLiu KumoLiu changed the title Add post transform for HoVerNet Add a post transform to process nucleus prediction branch output Sep 21, 2022
@KumoLiu KumoLiu changed the title Add a post transform to process nucleus prediction branch output Add a post transform to process nucleus prediction branch's output Sep 21, 2022
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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...)?

@bhashemian bhashemian changed the title Add a post transform to process nucleus prediction branch's output HoVerNet Nucleus Prediction Postprocessing Sep 21, 2022
@KumoLiu KumoLiu requested a review from bhashemian October 17, 2022 02:20
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@KumoLiu has tested it with the actual pipeline and it is working as expected.

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KumoLiu commented Oct 31, 2022

The mean dice on three-fold cross-validation for Lizard dataset is 0.8256.

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Nic-Ma commented Oct 31, 2022

/black

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Nic-Ma commented Oct 31, 2022

/build

@Nic-Ma Nic-Ma enabled auto-merge (squash) October 31, 2022 14:18
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Nic-Ma commented Nov 1, 2022

/build

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Nic-Ma commented Nov 1, 2022

/build

@Nic-Ma Nic-Ma merged commit 5bdef46 into Project-MONAI:dev Nov 1, 2022
@KumoLiu KumoLiu deleted the postprocess branch November 1, 2022 07:01
KumoLiu added a commit that referenced this pull request Nov 2, 2022
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 <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Behrooz Hashemian <[email protected]>
Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: KumoLiu <[email protected]>
yiheng-wang-nv pushed a commit to yiheng-wang-nv/MONAI that referenced this pull request Nov 2, 2022
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 <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Behrooz Hashemian <[email protected]>
Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
yiheng-wang-nv pushed a commit to yiheng-wang-nv/MONAI that referenced this pull request Nov 2, 2022
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 <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Behrooz Hashemian <[email protected]>
Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
bhashemian added a commit that referenced this pull request Nov 16, 2022
Signed-off-by: KumoLiu <[email protected]>

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 <[email protected]>
Signed-off-by: yunliu <[email protected]>
Co-authored-by: Behrooz Hashemian <[email protected]>
bhashemian added a commit to bhashemian/MONAI that referenced this pull request Nov 23, 2022
Signed-off-by: KumoLiu <[email protected]>

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 <[email protected]>
Signed-off-by: yunliu <[email protected]>
Co-authored-by: Behrooz Hashemian <[email protected]>
Signed-off-by: Behrooz <[email protected]>
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Process NP branch output(an output branch in HoVerNet) which turns the probability map from the network into the instance segmentation result

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