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3610 Add ascontiguous utility and check in CacheDataset#3614

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Nic-Ma:3610-add-ascontiguous
Jan 9, 2022
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3610 Add ascontiguous utility and check in CacheDataset#3614
wyli merged 13 commits into
Project-MONAI:devfrom
Nic-Ma:3610-add-ascontiguous

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@Nic-Ma Nic-Ma commented Jan 8, 2022 •
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Fixes #3610 .

Description

This PR added the ascontiguous utility and apply in CacheDataset.

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 and others added 11 commits February 1, 2021 19:15
@Nic-Ma
Merge pull request #19 from Project-MONAI/master
42a45e0 
merge master
@Nic-Ma
Merge pull request #32 from Project-MONAI/master
cd16a13 
merge master
@Nic-Ma
Merge pull request #180 from Project-MONAI/dev
6f87afd 
merge master
@Nic-Ma
Merge pull request #214 from Project-MONAI/dev
f398298 
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@Nic-Ma
Merge pull request #341 from Project-MONAI/dev
624fd0d 
merge master
@Nic-Ma
[DLMED] add ascontiguous
c04679b 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] add doc
23a6492 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] enhance CacheDataset
99a1eba 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] add unit test
7ec4802 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] export to utility
a016a3d 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] add to subclasses
da429e1 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma Nic-Ma marked this pull request as ready for review January 8, 2022 16:55
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Nic-Ma commented Jan 8, 2022

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/black

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Nic-Ma commented Jan 8, 2022

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/build

@Nic-Ma

Nic-Ma commented Jan 8, 2022

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I verified the PR with spleen segmentation pipeline.

Thanks.

@Nic-Ma Nic-Ma requested review from ericspod, rijobro and wyli January 8, 2022 16:56
@Nic-Ma Nic-Ma changed the title [WIP] 3610 Add ascontiguous utility and check in CacheDataset 3610 Add ascontiguous utility and check in CacheDataset Jan 8, 2022
Nic-Ma
Nic-Ma commented Jan 8, 2022
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Thanks, it looks good to me. (Torch contiguous can take additional parameters but I'm not sure if we need it at the moment. https://pytorch.org/docs/stable/generated/torch.Tensor.contiguous.html#torch.Tensor.contiguous)

@Nic-Ma
[DLMED] update according to comments
d5d6b7d 
Signed-off-by: Nic Ma <nma@nvidia.com>
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Nic-Ma commented Jan 9, 2022

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Thanks, it looks good to me. (Torch contiguous can take additional parameters but I'm not sure if we need it at the moment. https://pytorch.org/docs/stable/generated/torch.Tensor.contiguous.html#torch.Tensor.contiguous)

Thanks for your review, sure, I added kwargs for Tensor in the latest commit but didn't provide the arg for CacheDataset and explicitly set the memory_format in CacheDataset.

Thanks.

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Nic-Ma commented Jan 9, 2022

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/black

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Nic-Ma commented Jan 9, 2022

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/build

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wyli commented Jan 9, 2022

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Forgot to mention that 2 minor antipatterns were introduced: https://deepsource.io/gh/Project-MONAI/MONAI/run/a37b8f84-4ba2-4db2-b025-0ee5ee9ecc97/python/

@Nic-Ma
[DLMED] fix antipatterns
93cca40 
Signed-off-by: Nic Ma <nma@nvidia.com>
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Nic-Ma commented Jan 9, 2022

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Hi @wyli ,

Thanks for your reminder, I updated to fix the antipatterns and changed the utility function name to align with:
https://github.com/Project-MONAI/MONAI/blob/dev/monai/utils/type_conversion.py#L102

Thanks.

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Nic-Ma commented Jan 9, 2022

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/black

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/build

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Nic-Ma commented Jan 9, 2022

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/build

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/build

@wyli wyli enabled auto-merge (squash) January 9, 2022 14:33
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/build

@wyli wyli merged commit 3269851 into Project-MONAI:dev Jan 9, 2022
Can-Zhao pushed a commit to Can-Zhao/MONAI that referenced this pull request Jan 10, 2022
@Nic-Ma @Can-Zhao
3610 Add ascontiguous utility and check in CacheDataset (Project-MONA…
d739ff6 
…I#3614)

* [DLMED] add ascontiguous

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

* [DLMED] add doc

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

* [DLMED] enhance CacheDataset

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

* [DLMED] add unit test

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

* [DLMED] export to utility

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

* [DLMED] add to subclasses

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

* [DLMED] update according to comments

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

* [DLMED] fix antipatterns

Signed-off-by: Nic Ma <nma@nvidia.com>
wyli pushed a commit that referenced this pull request Jan 10, 2022
@Nic-Ma @wyli
3610 Add ascontiguous utility and check in CacheDataset (#3614)
941f7d3 
* [DLMED] add ascontiguous

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

* [DLMED] add doc

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

* [DLMED] enhance CacheDataset

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

* [DLMED] add unit test

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

* [DLMED] export to utility

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

* [DLMED] add to subclasses

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

* [DLMED] update according to comments

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

* [DLMED] fix antipatterns

Signed-off-by: Nic Ma <nma@nvidia.com>
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@wyli wyli wyli approved these changes
@rijobro rijobro Awaiting requested review from rijobro
@ericspod ericspod Awaiting requested review from ericspod ericspod is a code owner

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Add AsContiguous utility transform

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