Maisi morphological funcs #7893

Can-Zhao · 2024-07-01T15:58:37Z

Fixes # .

Description

Maisi morphological funcs

Types of changes

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.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

Signed-off-by: Can-Zhao <canz@nvidia.com>

…si_mor_canz

Signed-off-by: Can-Zhao <canz@nvidia.com>

mingxin-zheng · 2024-07-01T16:06:32Z

Hi @Can-Zhao , do you think it would be too much work to make this a general transform?

I think erode/dilate is general medical image operations, which may be used elsewhere. So making this a general utility function or transform may be helpful.

Signed-off-by: Can-Zhao <canz@nvidia.com>

Can-Zhao · 2024-07-01T16:27:30Z

Hi @Can-Zhao , do you think it would be too much work to make this a general transform?

I think erode/dilate is general medical image operations, which may be used elsewhere. So making this a general utility function or transform may be helpful.

It's a good idea, but maybe not in this PR...

Signed-off-by: Can-Zhao <canz@nvidia.com>

mingxin-zheng · 2024-07-02T02:29:07Z

It's a good idea, but maybe not in this PR...

Okay, we can make these functions in generation today, and in the future, move the implementation to transforms and use the transform in these functions.

monai/apps/generation/maisi/utils/morphological_ops.py

KumoLiu

Thanks for the PR, overall looks good to me. Several comments inline.

monai/apps/generation/maisi/utils/morphological_ops.py

tests/test_morphological_ops.py

KumoLiu · 2024-07-02T03:25:12Z

Hi @Can-Zhao, please help take a look at the format issue: https://github.com/Project-MONAI/MONAI/actions/runs/9754160317/job/26920608008?pr=7893#step:7:387. Thanks!

Signed-off-by: Can-Zhao <canz@nvidia.com>

Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Can Zhao <69829124+Can-Zhao@users.noreply.github.com>

Signed-off-by: Can-Zhao <canz@nvidia.com>

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Signed-off-by: Can-Zhao <canz@nvidia.com>

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Signed-off-by: Can-Zhao <canz@nvidia.com>

docs/source/apps.rst

Signed-off-by: Can-Zhao <canz@nvidia.com>

Can-Zhao · 2024-07-02T05:51:15Z

@KumoLiu Have you met this error? File "/workspace/MONAI/monai/utils/misc.py", line 27, in
from distutils.util import strtobool
ModuleNotFoundError: No module named 'distutils'

Can-Zhao · 2024-07-02T05:56:38Z

@KumoLiu Have you met this error? File "/workspace/MONAI/monai/utils/misc.py", line 27, in from distutils.util import strtobool ModuleNotFoundError: No module named 'distutils'

Nevermind, forgot I should do "pip install --upgrade --force-reinstall setuptools"

KumoLiu · 2024-07-02T06:04:24Z

Hi @Can-Zhao, please take a look at the ci error: https://github.com/Project-MONAI/MONAI/actions/runs/9755561869/job/26924281793?pr=7893#step:13:19908
Thanks.

Signed-off-by: Can-Zhao <canz@nvidia.com>

Can-Zhao · 2024-07-02T06:26:28Z

Hi @Can-Zhao, please take a look at the ci error: https://github.com/Project-MONAI/MONAI/actions/runs/9755561869/job/26924281793?pr=7893#step:13:19908 Thanks.

I'm confused why it cannot import the func. As python -m tests.test_morphological_ops is runnable on my machine. Nevertheless, I changed the way to import. If not working, I will need your help.

Signed-off-by: Can-Zhao <canz@nvidia.com>

Can-Zhao · 2024-07-02T07:05:23Z

@Nic-Ma @KumoLiu These erode and dilate functions are used in both Vista and MAISI. I was wondering if we should move it to somewhere else. If so, which folder would be a good choice? Or we may leave it here for now?

KumoLiu · 2024-07-02T07:17:55Z

@Nic-Ma @KumoLiu These erode and dilate functions are used in both Vista and MAISI. I was wondering if we should move it to somewhere else. If so, which folder would be a good choice? Or we may leave it here for now?

We can leave it here for now. And as @mingxin-zheng said, when we refactored it to inherit Transform next time, we can move it under transforms folder.
cc @Nic-Ma @ericspod @mingxin-zheng

Can-Zhao · 2024-07-02T10:01:30Z

@Nic-Ma @KumoLiu These erode and dilate functions are used in both Vista and MAISI. I was wondering if we should move it to somewhere else. If so, which folder would be a good choice? Or we may leave it here for now?

We can leave it here for now. And as @mingxin-zheng said, when we refactored it to inherit Transform next time, we can move it under transforms folder. cc @Nic-Ma @ericspod @mingxin-zheng

Cool! Then it seems this PR can be merged after passing the tests. Thanks!

KumoLiu · 2024-07-02T13:02:11Z

/build

Can-Zhao added 4 commits July 1, 2024 15:50

add mor funcs

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Merge branch 'dev' of https://github.com/Project-MONAI/MONAI into mai…

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black

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reformat

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Can-Zhao marked this pull request as ready for review July 1, 2024 16:26

Can-Zhao requested a review from KumoLiu July 1, 2024 16:26

Can-Zhao added 2 commits July 1, 2024 18:23

typo

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update docstring

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Can-Zhao requested a review from Nic-Ma July 1, 2024 18:53

This was referenced Jul 2, 2024

The monai-generative in requirements-dev.txt points to a deleted branch. Project-MONAI/tutorials#1747

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The monai-generative in requirements-dev.txt points to a deleted branch #7894

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Merge branch 'dev' into maisi_mor_canz

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add eps

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Update monai/apps/generation/maisi/utils/morphological_ops.py

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update docstring

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add 2d unit test

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KumoLiu merged commit 410109a into Project-MONAI:dev Jul 2, 2024
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Can-Zhao deleted the maisi_mor_canz branch July 2, 2024 16:49

mingxin-zheng mentioned this pull request Aug 8, 2024

Refactor morphological functions as transform (or transform utils) #8003

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Maisi morphological funcs #7893

Maisi morphological funcs #7893

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Maisi morphological funcs #7893

Maisi morphological funcs #7893

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