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4822 remove deprecated class call in EnsureChannelFirst#4823

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wyli merged 23 commits intoProject-MONAI:devfrom
KumoLiu:update-ensurechannelfirst
Aug 4, 2022
Merged

4822 remove deprecated class call in EnsureChannelFirst#4823
wyli merged 23 commits intoProject-MONAI:devfrom
KumoLiu:update-ensurechannelfirst

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@KumoLiu KumoLiu commented Aug 3, 2022 •
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Fixes #4822 .
Fixed #4828 .

Description

Remove AddChannel and AsChannelFirst call in EnsureChannelFirst.
Update example in dataset's docstring.
Replace AsChannelFirst with EnsureChannelFirstd in deepgrow dataset
Replace AsChannelFirst with EnsureChannelFirstd in utils_create_transform_ims

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.

KumoLiu and others added 18 commits July 21, 2022 18:21
@KumoLiu
Merge remote-tracking branch 'origin/dev' into dev
5d6df61
@KumoLiu
Merge branch 'Project-MONAI:dev' into dev
26004e0
@KumoLiu
Merge remote-tracking branch 'origin/dev' into dev
b066bb0
@KumoLiu
Merge remote-tracking branch 'yliu/HEAD' into dev
8f9ae3d
@KumoLiu
add Metatenosr support in ConcatItemd
3ee8593 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
Merge remote-tracking branch 'origin/dev' into dev
c1b571e
@KumoLiu
Merge branch 'support-metatensor-in-concatitemd' into dev
5a29019
@KumoLiu
fix flake8 error
790a92b 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
fix flake8 error
9e8a9d3 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
Merge remote-tracking branch 'origin/dev' into dev
4fe9858
@KumoLiu
Merge remote-tracking branch 'origin/releasing/0.9.1' into dev
095e6d8
@KumoLiu
Merge remote-tracking branch 'origin/dev' into dev
821adc3
@KumoLiu
Merge remote-tracking branch 'origin/dev' into dev
96337ad
@KumoLiu
Merge remote-tracking branch 'origin/dev' into dev
94e5198
@KumoLiu
Merge remote-tracking branch 'origin/dev' into dev
8c991e1
@KumoLiu
remove deprecated class in EnsureChannelFirst
b251b31 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
Merge branch 'support-metatensor-in-concatitemd' into update-ensurech…
9ee01e5 
…annelfirst
@KumoLiu
fix flake8 error
62941b7 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu KumoLiu requested review from Nic-Ma, ericspod, rijobro and wyli August 3, 2022 11:24
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wyli commented Aug 3, 2022 •
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Should this be updated @Nic-Ma?

MONAI/monai/bundle/utils.py

Line 59 in 9317d14

{"_target_": "AddChanneld", "keys": "image"},

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Nic-Ma commented Aug 3, 2022

Definitely.

Hi @KumoLiu ,

Please also update this part.

Thanks.

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KumoLiu commented Aug 3, 2022

Should these also be updated? @Nic-Ma

MONAI/monai/transforms/utils_create_transform_ims.py

Lines 210 to 212 in d0b8bc0

transforms = Compose(
[LoadImaged(keys), AddChanneld(keys), ScaleIntensityd(CommonKeys.IMAGE), Rotate90d(keys, spatial_axes=[0, 2])]
)

MONAI/monai/apps/deepgrow/dataset.py

Lines 126 to 135 in d0b8bc0

return Compose(
[
LoadImaged(keys=keys),
AsChannelFirstd(keys=keys),
Orientationd(keys=keys, axcodes="RAS"),
Spacingd(keys=keys, pixdim=pixdim, mode=mode),
FromMetaTensord(keys=keys),
ToNumpyd(keys=keys + [PostFix.meta(k) for k in keys]),
]
)

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Nic-Ma commented Aug 3, 2022

Hi @KumoLiu ,

Please update the DeepGrow one, I think we should keep the utils_create_transform_ims.py to provide the transform images in doc-string.
@wyli Could you please help confirm it?

Thanks in advance.

@wyli
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wyli commented Aug 3, 2022

agreed, I think we should update the deepgrow one to use EnsureChannelFirstd instead of AsChannelFirstd (cc @SachidanandAlle @diazandr3s)

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KumoLiu commented Aug 4, 2022

Hi @wyli @Nic-Ma,

I confirmed that AddChanneld here won't change the transform images in doc-string. I will also update it.

MONAI/monai/transforms/utils_create_transform_ims.py

Lines 210 to 212 in f317aeb

transforms = Compose(
[LoadImaged(keys), AddChanneld(keys), ScaleIntensityd(CommonKeys.IMAGE), Rotate90d(keys, spatial_axes=[0, 2])]
)

Thanks!

KumoLiu added 2 commits August 4, 2022 10:24
@KumoLiu
update channel operation
dfd6ea4 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
fix flake8 error
671a928 
Signed-off-by: KumoLiu <[email protected]>
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wyli commented Aug 4, 2022

/build

@wyli wyli enabled auto-merge (squash) August 4, 2022 09:31
@wyli wyli merged commit 63d06b2 into Project-MONAI:dev Aug 4, 2022
@KumoLiu KumoLiu deleted the update-ensurechannelfirst branch May 8, 2023 06:02
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@wyli wyli wyli approved these changes

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

@rijobro rijobro Awaiting requested review from rijobro

@ericspod ericspod Awaiting requested review from ericspod ericspod is a code owner

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Bug in deepgrow dataset EnsureChannelFirst calls AddChannel which is deprecated

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@KumoLiu @wyli @Nic-Ma