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3581 Enhance slice_channels utility function#3585

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Nic-Ma merged 11 commits into
Project-MONAI:devfrom
Nic-Ma:3581-enhance-onehot
Jan 7, 2022
Merged

3581 Enhance slice_channels utility function#3585
Nic-Ma merged 11 commits into
Project-MONAI:devfrom
Nic-Ma:3581-enhance-onehot

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@Nic-Ma

@Nic-Ma Nic-Ma commented Jan 5, 2022

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Fixes #3581 .

Description

This PR enhanced the slice_channels utility function to select channels on specified dim.

Status

Ready

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.

@Nic-Ma

Nic-Ma commented Jan 5, 2022

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/black

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Nic-Ma commented Jan 5, 2022

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/build

@Nic-Ma
[DLMED] enhance slice_channels
a274e48 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma Nic-Ma force-pushed the 3581-enhance-onehot branch from ec468ce to a274e48 Compare January 5, 2022 16:18
@Nic-Ma

Nic-Ma commented Jan 5, 2022

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/build

@Nic-Ma

Nic-Ma commented Jan 5, 2022

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Hi @wyli @holgerroth ,

Do you think I also need to enhance the DiceLoss and AsDiscrete transform to support slice_channels in them?
Or just leave this logic to users to call slice_channels directly (current status of this PR)?
I prefer to not change loss and post transform so far.

Thanks in advance.

@Nic-Ma Nic-Ma requested review from ericspod, rijobro and wyli January 5, 2022 16:21
wyli
wyli reviewed Jan 5, 2022
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Comment thread monai/networks/utils.py Outdated
@Nic-Ma
[DLMED] update according to comments
43dbc2a 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma Nic-Ma requested a review from wyli January 5, 2022 23:19
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/black

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Nic-Ma commented Jan 5, 2022

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/build

wyli
wyli reviewed Jan 6, 2022
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Comment thread tests/test_sample_slices.py Outdated
wyli
wyli reviewed Jan 6, 2022
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Comment thread monai/networks/utils.py
@Nic-Ma
[DLMED] update according to comments
41a158c 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma

Nic-Ma commented Jan 6, 2022 •
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Hi @wyli ,

BTW, I think maybe something wrong updated in the CI configs?

Error while finding module specification for 'pip' (AttributeError: module '__main__' has no attribute '__file__')

Thanks.

wyli
wyli approved these changes Jan 6, 2022
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looks good to me, I put some minor comments

Comment thread monai/networks/utils.py
Comment thread tests/test_sample_slices.py Outdated
@wyli

wyli commented Jan 6, 2022

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Hi @wyli ,

BTW, I think maybe something wrong updated in the CI configs?

Error while finding module specification for 'pip' (AttributeError: module '__main__' has no attribute '__file__')

Thanks.

looks like it's from setuptools and the new version is yanked https://pypi.org/project/setuptools/60.3.0/

@Nic-Ma

Nic-Ma commented Jan 6, 2022

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Hi @wyli ,
BTW, I think maybe something wrong updated in the CI configs?

Error while finding module specification for 'pip' (AttributeError: module '__main__' has no attribute '__file__')

Thanks.

looks like it's from setuptools and the new version is yanked https://pypi.org/project/setuptools/60.3.0/

Hi @wyli ,

I see your PR #3597 passed the CI tests, so you have updated something to fix the CI software issue?

Thanks.

@wyli

wyli commented Jan 6, 2022

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Hi @wyli ,
BTW, I think maybe something wrong updated in the CI configs?

Error while finding module specification for 'pip' (AttributeError: module '__main__' has no attribute '__file__')

Thanks.

looks like it's from setuptools and the new version is yanked https://pypi.org/project/setuptools/60.3.0/

Hi @wyli ,

I see your PR #3597 passed the CI tests, so you have updated something to fix the CI software issue?

Thanks.

I rerun the tests and it should work fine, I think the error version has been removed by the maintainers.

Nic-Ma added 3 commits January 6, 2022 22:13
@Nic-Ma
[DLMED] remove test
1fce201 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] add flag
63d4dbd 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
Merge branch 'dev' into 3581-enhance-onehot
b3268d8
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Nic-Ma commented Jan 6, 2022

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/black

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Nic-Ma commented Jan 6, 2022

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/build

wyli
wyli approved these changes Jan 6, 2022
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Thanks, it looks good to me.

@Nic-Ma Nic-Ma enabled auto-merge (squash) January 6, 2022 23:54
@Nic-Ma Nic-Ma merged commit 91777d0 into Project-MONAI:dev Jan 7, 2022
Can-Zhao pushed a commit to Can-Zhao/MONAI that referenced this pull request Jan 10, 2022
@Nic-Ma @Can-Zhao
3581 Enhance slice_channels utility function (Project-MONAI#3585)
7d8bad4 
* [DLMED] enhance slice_channels

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] remove test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add flag

Signed-off-by: Nic Ma <nma@nvidia.com>
wyli pushed a commit that referenced this pull request Jan 10, 2022
@Nic-Ma @wyli
3581 Enhance slice_channels utility function (#3585)
fe1a259 
* [DLMED] enhance slice_channels

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] remove test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add flag

Signed-off-by: Nic Ma <nma@nvidia.com>
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Reviewers

@wyli wyli wyli approved these changes
@ericspod ericspod Awaiting requested review from ericspod ericspod is a code owner
@rijobro rijobro Awaiting requested review from rijobro

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Add support to only keep selected classes in one_hot

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@Nic-Ma @wyli