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padding and cropping classes use MetaTensor #4371

Merged
merged 48 commits into from
Jun 6, 2022
Merged

padding and cropping classes use MetaTensor #4371

merged 48 commits into from
Jun 6, 2022

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rijobro
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@rijobro rijobro commented May 27, 2022 •
edited by wyli
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Description

Pad transforms use MetaTensor to allow inverse.

also fixes #4435

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.

TODO

Name Array implementation Dict implementation Array test Dict test
SpatialPad ✔️ ✔️ ✔️ ✔️
BorderPad ✔️ ✔️ ✔️ ✔️
DivisiblePad ✔️ ✔️ ✔️ ✔️
SpatialCrop ✔️ ✔️ ✔️ ✔️
CenterSpatialCrop ✔️ ✔️ ✔️ ✔️
CenterScaleCrop ✔️ ✔️ ✔️ ✔️
RandSpatialCrop ✔️ ✔️ ✔️ ✔️
RandScaleCrop ✔️ ✔️ ✔️ ✔️
RandSpatialCropSamples ✔️ ✔️ ✔️ ✔️
CropForeground ✔️ ✔️ ✔️ ✔️
RandWeightedCrop ✔️ ✔️ ✔️ ✔️
RandCropByPosNegLabel ✔️ ✔️ ✔️ ✔️
RandCropByLabelClasses ✔️ ✔️ ✔️ ✔️
ResizeWithPadOrCop ✔️ ✔️ ✔️ ✔️

@rijobro rijobro requested review from wyli, ericspod and Nic-Ma May 27, 2022 14:24
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wyli commented May 31, 2022

/black

monai-bot and others added 3 commits May 31, 2022 12:41
@wyli wyli force-pushed the MetaTensor_pad branch from 034869f to 7fd4836 Compare May 31, 2022 13:39
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rijobro commented May 31, 2022

@wyli PR is getting very big as I'm doing all padding and cropping. Apologies for that, it's a hard one to split.

@rijobro rijobro marked this pull request as draft May 31, 2022 16:43
@rijobro
fixes
6cbe948 
Signed-off-by: Richard Brown <[email protected]>
@rijobro rijobro changed the title padding classes use MetaTensor for inverse padding and cropping classes use MetaTensor Jun 1, 2022
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rijobro commented Jun 1, 2022 •
edited
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@wyli Could you create unit tests for the _forward_meta methods? I added test_meta_update to test_pad.py (link). I wanted to check that for out = padder(im), the input metadata was unchanged, and out had been updated. I see that the output affine is only 2x2. Could you check this? Putting the same check for cropping would be good too.

Equally we would want to check that the affine isn't modified when we don't crop/pad from the origin.

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wyli commented Jun 1, 2022

@wyli Could you create unit tests for the _forward_meta methods?

sure let me add some basic tests to this PR now...

rijobro and others added 2 commits June 1, 2022 11:52
@rijobro
crop foreground
a16040b 
Signed-off-by: Richard Brown <[email protected]>
@wyli
update pad test meta
89ed8c1 
adds meta tests pad/crop

Signed-off-by: Wenqi Li <[email protected]>
@wyli wyli force-pushed the MetaTensor_pad branch from 432573b to 89ed8c1 Compare June 1, 2022 11:14
wyli
wyli reviewed Jun 1, 2022
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tests/test_pad.py Outdated Show resolved Hide resolved
@rijobro
RandWeightedCrop
83bae7f 
Signed-off-by: Richard Brown <[email protected]>
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rijobro commented Jun 1, 2022

@wyli thanks for the help here. I'm off for a week, feel free to continue this without me if you want to. All transforms have been updated, just need to get all the linting happy. I suspect #4435 will need to be addressed first.

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wyli commented Jun 1, 2022

@wyli thanks for the help here. I'm off for a week, feel free to continue this without me if you want to. All transforms have been updated, just need to get all the linting happy. I suspect #4435 will need to be addressed first.

thanks! I'll try to merge this one soon.

wyli and others added 15 commits June 1, 2022 21:26
@wyli
fixes test_hausdorff_distance
3966e94 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes sphinx
aa26a26 
Signed-off-by: Wenqi Li <[email protected]>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
6685b7f 
for more information, see https://pre-commit.ci
@wyli
Merge branch 'feature/MetaTensor' into MetaTensor_pad
56e17f0
@wyli
fixes Project-MONAI#4435
38decb7 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes typing
c1b918d 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes typing
a89d3e6 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes test_pad_collation
ea6a480 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
temp disable zoom tests
fb05435 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
flake8 fixes
83393e1 
Signed-off-by: Wenqi Li <[email protected]>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
b5e5176 
for more information, see https://pre-commit.ci
@wyli
fixes test_resize_with_pad_or_cropd
2e1d1ce 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
temp disable test_box_transform
e0dd4e6 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
checkout unnecessary changes
56998ea 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
compatibility
42f85bb 
Signed-off-by: Wenqi Li <[email protected]>
@wyli wyli force-pushed the MetaTensor_pad branch from 46c1a15 to 180fefd Compare June 6, 2022 12:54
@wyli wyli force-pushed the MetaTensor_pad branch from 180fefd to 9a92b26 Compare June 6, 2022 13:01
@wyli
gpu test
6c56810 
Signed-off-by: Wenqi Li <[email protected]>
@wyli wyli marked this pull request as ready for review June 6, 2022 15:09
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wyli commented Jun 6, 2022

cropping with multiple random samples (basic applied_operations collating/decollating work fine)

from monai.transforms import EnsureChannelFirst, LoadImage, RandSpatialCropSamples, SaveImage

filename = "~/Downloads/avg152T1_LR_nifti.nii.gz"
img = LoadImage()(filename)
img = EnsureChannelFirst()(img)
img = RandSpatialCropSamples(roi_size=(40, 50, 60), random_size=False, num_samples=3)(img)
for i in img:
    SaveImage(resample=False)(i)

Screenshot 2022-06-06 at 16 23 58

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wyli approved these changes Jun 6, 2022
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merging this for now as the basic functionality works nicely, but it will need another discussion/refactoring for the design of modules such as the PadBase class

MONAI/monai/transforms/croppad/array.py

Line 80 in 6c56810

class PadBase(InvertibleTransform):
cc @Nic-Ma @ericspod

@wyli wyli merged commit 04e5a14 into Project-MONAI:feature/MetaTensor Jun 6, 2022
@wyli wyli mentioned this pull request Jun 6, 2022
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@wyli wyli wyli approved these changes

@ericspod ericspod Awaiting requested review from ericspod

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma

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@rijobro @wyli @monai-bot