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Refactor HoVerNet post-processing#5618

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bhashemian merged 41 commits intoProject-MONAI:devfrom
bhashemian:hovernet-post
Dec 5, 2022
Merged

Refactor HoVerNet post-processing#5618
bhashemian merged 41 commits intoProject-MONAI:devfrom
bhashemian:hovernet-post

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@bhashemian bhashemian commented Nov 30, 2022 •
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Fixes #5616
Fixes #5617

Description

A few sentences describing the changes proposed in this pull request.

Types of changes

  • 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.

@bhashemian bhashemian marked this pull request as draft November 30, 2022 22:48
@bhashemian
Make type_prediction optional
9ebd464 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Restructure
bd9f36b 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update unittests
3764ad1 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update dictionary wrapper
43ce643 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update docs
d015dc8 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update unittests
220dfe2 
Signed-off-by: Behrooz <[email protected]>
@bhashemian bhashemian marked this pull request as ready for review December 1, 2022 02:57
@bhashemian bhashemian requested review from JHancox and KumoLiu December 1, 2022 02:57
KumoLiu
KumoLiu reviewed Dec 1, 2022
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@bhashemian bhashemian marked this pull request as draft December 1, 2022 15:36
bhashemian and others added 12 commits December 1, 2022 10:37
@bhashemian
Refactor GenerateInstanceBorder
4144996 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update GenerateDistanceMap
a2a17f8 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update dict wrappers
f1e7047 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update GenerateWatershedMarkersd
e36e0a7 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
docs and formatting
8263514 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
docs and formatting
1998d7f 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
add unittests
eb1a6f5 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add HoVerNetTypeMapPostProcessingd and unittests
6fb1e5e 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Refactor HoVerNetTypeMapPostProcessing and HoVerNetTypeMapPostProcess…
18ea67b 
…ingd

Signed-off-by: Behrooz <[email protected]>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
027cb11 
for more information, see https://pre-commit.ci
@bhashemian
formatting
912f9e1 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'hovernet-post' of github.com:drbeh/MONAI into hovernet-…
9ded9d4 
…post
KumoLiu
KumoLiu reviewed Dec 2, 2022
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Thanks for refactoring the post-processing! Just leave few comments. And if you could test it in your inference pipeline to check it functionality, that would be great!

JHancox
JHancox reviewed Dec 2, 2022
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@bhashemian
address commnets
6890f70 
Signed-off-by: Behrooz <[email protected]>
JHancox
JHancox reviewed Dec 2, 2022
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JHancox
JHancox approved these changes Dec 2, 2022
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@bhashemian bhashemian requested a review from wyli December 2, 2022 17:53
KumoLiu
KumoLiu reviewed Dec 3, 2022
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@bhashemian bhashemian requested a review from KumoLiu December 5, 2022 02:22
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bhashemian commented Dec 5, 2022

@KumoLiu thanks for your comments. Please let me know if you have any other comments. Otherwise, let's merge this.

@bhashemian bhashemian enabled auto-merge (squash) December 5, 2022 02:23
@bhashemian bhashemian requested a review from Nic-Ma December 5, 2022 02:43
KumoLiu
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Have tested in my pipeline, works well, thanks!

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bhashemian commented Dec 5, 2022

Hi @wyli @Nic-Ma, could you please help merging this PR. Thanks

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Nic-Ma commented Dec 5, 2022

/build

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wyli commented Dec 5, 2022

/build

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wyli commented Dec 5, 2022

/build

@bhashemian bhashemian merged commit 16b13a4 into Project-MONAI:dev Dec 5, 2022
@bhashemian bhashemian deleted the hovernet-post branch December 5, 2022 20:54
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@JHancox JHancox JHancox approved these changes

@KumoLiu KumoLiu KumoLiu approved these changes

@wyli wyli Awaiting requested review from wyli

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma Nic-Ma is a code owner

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Successfully merging this pull request may close these issues.

HoVerNetPostProcessing to include all branches HoVerNetNuclearTypePostProcessing not working with default arguments

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@bhashemian @Nic-Ma @wyli @JHancox @KumoLiu