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skip RandAffine if possible#2151

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wyli merged 5 commits into
Project-MONAI:devfrom
rijobro:2124-RandAffine_skip
May 6, 2021
Merged

skip RandAffine if possible#2151
wyli merged 5 commits into
Project-MONAI:devfrom
rijobro:2124-RandAffine_skip

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@rijobro

@rijobro rijobro commented May 6, 2021

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Fixes #2124.

Description

Skip RandAffine if possible.

Status

Ready

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

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

rijobro commented May 6, 2021

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When debugging, I put a print statement to verify that the first unit test skips the resampling, as expected.

@wyli

wyli commented May 6, 2021

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thanks, need something like

        if not self.rand_affine.do_transform and self.rand_affine.spatial_size is None:
            for idx, key in enumerate(self.keys):
                if self.rand_affine.resampler.as_tensor_output:
                    d[key] = torch.tensor(key)
                elif torch.is_tensor(d[key]):                    
                    d[key] = d[key].cpu().numpy()
            return d

for RandAffined

need to double-check the output data type, make sure that the PR doesn't change the dtype for integer image

@rijobro

rijobro commented May 6, 2021

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also need to think about the inverse for RandAffined...

@rijobro

rijobro commented May 6, 2021

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@wyli why would the dtype change if the image isn't modified? Because of the torch/numpy conversion?

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

wyli commented May 6, 2021

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the root cause is that the current resampling requires floats...

out = torch.nn.functional.grid_sample(
img.unsqueeze(0).float(),
grid.unsqueeze(0).float(),

if we bypass the resample step, I feel the datatype might be different, but I haven't checked all the details...

rijobro added 3 commits May 6, 2021 16:52
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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thanks!

@wyli wyli merged commit e816d18 into Project-MONAI:dev May 6, 2021
@rijobro rijobro deleted the 2124-RandAffine_skip branch May 7, 2021 08:24
@wyli

wyli commented May 7, 2021

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the dev branch had its 1024th merged pull request 🎉

@rijobro

rijobro commented May 7, 2021

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that was quick, it's only a few weeks old! 😅

yanielc pushed a commit to yanielc/MONAI that referenced this pull request May 10, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>
yanielc pushed a commit to yanielc/MONAI that referenced this pull request May 13, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>
yanielc pushed a commit to yanielc/MONAI that referenced this pull request May 13, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>
wyli pushed a commit that referenced this pull request May 26, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
wyli pushed a commit that referenced this pull request May 26, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
wyli pushed a commit that referenced this pull request May 26, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
wyli pushed a commit that referenced this pull request May 26, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
wyli pushed a commit that referenced this pull request May 26, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
wyli pushed a commit that referenced this pull request May 27, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
wyli pushed a commit that referenced this pull request May 27, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
wyli pushed a commit that referenced this pull request May 27, 2021
* skip RandAffine if possible

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

* add randaffined

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

* mypy fix

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

* check consistency

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
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RandAffine/RandAffined skipping the resampling if do_transform is False

2 participants