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Merged
rijobro merged 8 commits into from
Apr 14, 2022
Merged

ToMetaTensor and FromMetaTensor transforms #4115

rijobro merged 8 commits into from
Apr 14, 2022

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@rijobro rijobro commented Apr 12, 2022

Requires this PR.

Description

Convert between dictionary data and MetaTensor. Will be useful for maintaining backwards compatibility. Not a breaking change, so can go into dev.

Status

Ready/Work in progress/Hold

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • New tests added to cover the changes.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

@rijobro rijobro requested review from Nic-Ma and wyli April 12, 2022 15:13
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rijobro commented Apr 12, 2022

The diff will decrease once the meta tensor PR has been merged. The only new functionality here should be in monai/transforms/meta_utility/dictionary.py.

@rijobro rijobro force-pushed the MetaTensor_transforms branch from f5491b8 to deb7951 Compare April 12, 2022 20:37
@rijobro rijobro closed this Apr 12, 2022
@rijobro rijobro force-pushed the MetaTensor_transforms branch from deb7951 to 1880d38 Compare April 12, 2022 20:42
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to and from meta
cc1188e 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro rijobro reopened this Apr 12, 2022
rijobro added 2 commits April 13, 2022 14:23
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Merge remote-tracking branch 'MONAI/dev' into MetaTensor_transforms
1290153
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add doc
8c237aa 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
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rijobro commented Apr 13, 2022

@wyli @Nic-Ma do you think you could have a look at this one. The tests seem to be good, so would like to merge. Going into dev as it's a non-breaking change.

wyli
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thanks, I think these transforms are useful during the migration of meta_dict -> metatensor, but eventually we don't need these, so I'm fine with or without this PR in dev, any ideas @Nic-Ma @ericspod ?

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rijobro commented Apr 13, 2022

In our codebase you're right that these would be temporary, but if a user has custom transforms, this would be useful.

Compose([
    LoadImaged(),  # will use MetaTensor
    CustomTransformd(),  # expects dict
    OtherMonaiTransformd(),  # will use MetaTensor
])

would become:

Compose([
    LoadImaged(),  # will use MetaTensor
    FromMetaTensord(),
    CustomTransformd(),  # expects dict
    ToMetaTensord(),
    OtherMonaiTransformd(),  # will use MetaTensor
])

@rijobro rijobro mentioned this pull request Apr 13, 2022
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ericspod commented Apr 13, 2022

These will be needed in the long run like @rijobro suggests.

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Thanks, it looks good to me.

@rijobro rijobro enabled auto-merge (squash) April 13, 2022 19:47
Nic-Ma
Nic-Ma approved these changes Apr 14, 2022
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@Nic-Ma Nic-Ma disabled auto-merge April 14, 2022 04:15
rijobro added 2 commits April 14, 2022 09:58
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Merge remote-tracking branch 'MONAI/dev' into MetaTensor_transforms
ee13b8f 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
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code format
3eaed0d 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
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rijobro commented Apr 14, 2022

/build

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rijobro commented Apr 14, 2022

@wyli , can you run blossom on this please?

@rijobro rijobro enabled auto-merge (squash) April 14, 2022 10:57
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wyli commented Apr 14, 2022

@wyli , can you run blossom on this please?

looks good, I'll merge this one soon.

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wyli commented Apr 14, 2022

/build

@rijobro rijobro merged commit 443fc0c into Project-MONAI:dev Apr 14, 2022
wyli added a commit that referenced this pull request Apr 14, 2022
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sync feature branch with dev (#4138)
3d98c8e 
* update citation (#4133)

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* `ToMetaTensor` and `FromMetaTensor` transforms (#4115)

to and from meta

Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro rijobro deleted the MetaTensor_transforms branch April 14, 2022 15:27
Can-Zhao added a commit to Can-Zhao/MONAI that referenced this pull request May 10, 2022
@Can-Zhao
Add comments
4379e90 
Add padding to filter to ensure same size after anti-aliasing

Use replicate padding insteadof zero padding to avoid artifacts for non-zero boundary

Reuse GaussianSmooth

4073 Enhance DynUNet doc-strings (Project-MONAI#4102)

* Fix doc strings error

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* remove duplicate places

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

4105 drops pt16 support (Project-MONAI#4106)

* update sys req

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp test

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update code for torch>=1.7

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* autofix

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes import

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* clear cache

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* remove temp cmd

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Make `pixelshuffle` scriptable (Project-MONAI#4109)

* Update the existing functionality to comply with the `torchscript.jit.script` function.

Signed-off-by: Ramon Emiliani <ramon@afxmedical.com>

meta tensor (Project-MONAI#4077)

* meta tensor

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

4084 Add kwargs for `Tensor.to()` in engines (Project-MONAI#4112)

* [DLMED] add kwargs for to() API

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

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] fix typo

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

* [DLMED] fix flake8

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

* [DLMED] update according to comments

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

fixes pytorch version tests (Project-MONAI#4127)

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update meta tensor api (Project-MONAI#4131)

* update meta tensor api

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

runtests.sh isort (Project-MONAI#4134)

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

update citation (Project-MONAI#4133)

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

`ToMetaTensor` and `FromMetaTensor` transforms (Project-MONAI#4115)

to and from meta

no skip if before pytorch 1.7 (Project-MONAI#4139)

* no skip if before pytorch 1.7

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

[DLMED] fix file name in meta (Project-MONAI#4145)

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

4116 Add support for advanced args of AMP (Project-MONAI#4132)

* [DLMED] fix typo in bundle scripts

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

* [DLMED] add support for AMP args

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

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] fix flake8

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

New wsireader (Project-MONAI#4147)

`MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (Project-MONAI#4137)

`MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (Project-MONAI#4137)
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@rijobro @ericspod @wyli @Nic-Ma