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Adding a median filter for 2/3D images#5307

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wyli merged 12 commits intoProject-MONAI:devfrom
dzenanz:medianFilter
Oct 12, 2022
Merged

Adding a median filter for 2/3D images#5307
wyli merged 12 commits intoProject-MONAI:devfrom
dzenanz:medianFilter

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@dzenanz dzenanz commented Oct 10, 2022

Co-authored-by: @ebrahimebrahim. Closes #5264.

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.

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dzenanz commented Oct 10, 2022

One test fails, I don't know why.

@dzenanz dzenanz marked this pull request as draft October 10, 2022 14:44
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dzenanz commented Oct 11, 2022

@wyli and @ebrahimebrahim can you provide some feedback? Or take over the PR?

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wyli commented Oct 11, 2022

sure, I'll try to finalize this one..

ericspod
ericspod reviewed Oct 11, 2022
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ebrahimebrahim commented Oct 11, 2022

I think it looks good; thanks for working on this!

Some useful features, which could potentially be put off to future work:

  • be generic to spatial dimensionality. there is no reason it has to focus on 3D images only
  • add padding_mode options similar to those supported by other monai filters. torch.nn.functional.conv3d only does zero or "same" padding I think, so torch.nn.functional.pad may need to get involved to provide other options such as padding by a nonzero constant

ebrahimebrahim
ebrahimebrahim reviewed Oct 11, 2022
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ericspod
ericspod reviewed Oct 11, 2022
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ericspod
ericspod reviewed Oct 11, 2022
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@dzenanz
Fix the last unit test regression failure
79abfd1
@dzenanz
Eric's review feedback
5ec512a
@dzenanz
Rely on same padding type instead of computing it
7b04b02
@dzenanz
WIP: 2D support
613f556 
ERROR: test_value_15 (__main__.TestMedianSmoothd)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/dzenan/MONAI/tests/test_median_smoothd.py", line 72, in test_value
    result = MedianSmoothd(**argments)(image)
  File "/home/dzenan/MONAI/monai/transforms/intensity/dictionary.py", line 1020, in __call__
    d[key] = self.converter(d[key])
  File "/home/dzenan/MONAI/monai/transforms/intensity/array.py", line 1165, in __call__
    out_t: torch.Tensor = median_filter_instance(img_t.unsqueeze(0)).squeeze(0)
  File "/usr/local/lib/python3.10/dist-packages/torch/nn/modules/module.py", line 1130, in _call_impl
    return forward_call(*input, **kwargs)
  File "/home/dzenan/MONAI/monai/networks/layers/simplelayers.py", line 519, in forward
    x = median_filter(x, self.window, self.kernel)
  File "/home/dzenan/MONAI/monai/networks/layers/simplelayers.py", line 475, in median_filter
    features: torch.Tensor = F.conv3d(in_tensor.reshape(c, 1, *sshape), kernel, padding="same", stride=1)
RuntimeError: Expected 4-dimensional input for 4-dimensional weight[3, 1, 1, 3], but got 5-dimensional input of size [1, 1, 1, 3, 3] instead

----------------------------------------------------------------------
Ran 20 tests in 0.828s
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dzenanz commented Oct 11, 2022

I am stuck again. Judging by debugger's inspection, we are passing both 4D tensor and 4D kernel for 2D test case to F.conv3d() on line 475.

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dzenanz commented Oct 11, 2022

What we really want is pad with 'replicate' mode. Otherwise zeroes creep in all around the edges. With the small test images that is super-obvious, but it might be hard to debug with realistic-sized images later on, especially for other people.

@wyli If you can take a crack at this modification, that would be great. Otherwise I could give it a shot later, perhaps in a new PR.

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fixes tests
e1ebaa1 
Signed-off-by: Wenqi Li <[email protected]>
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wyli commented Oct 11, 2022

What we really want is pad with 'replicate' mode. Otherwise zeroes creep in all around the edges. With the small test images that is super-obvious, but it might be hard to debug with realistic-sized images later on, especially for other people.

@wyli If you can take a crack at this modification, that would be great. Otherwise I could give it a shot later, perhaps in a new PR.

sure, I'll stop here with constant padding 0 for a basic implementation...

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make demo images
925f69a 
Signed-off-by: Wenqi Li <[email protected]>
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wyli commented Oct 11, 2022

added an example here Project-MONAI/DocImages#16

@wyli wyli marked this pull request as ready for review October 11, 2022 22:05
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wyli commented Oct 11, 2022

/build

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wyli commented Oct 12, 2022

/build

@wyli wyli enabled auto-merge (squash) October 12, 2022 11:16
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looks good to me, padding mode and separable approximations are left for future PRs.

@wyli wyli changed the title Adding a median filter for 3D images Adding a median filter for 2/3D images Oct 12, 2022
@wyli wyli merged commit 9731823 into Project-MONAI:dev Oct 12, 2022
@dzenanz dzenanz deleted the medianFilter branch October 13, 2022 19:03
@dzenanz dzenanz mentioned this pull request Oct 13, 2022
Merged
wyli added a commit that referenced this pull request Oct 14, 2022
@dzenanz @wyli
Use replication padding in Median filter (#5329)
e081510 
Ref #5264. Follow-up to #5307. This is a more normal, intuitive variant
of median filtering.

Signed-off-by: Dženan Zukić <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
bhashemian pushed a commit to JHancox/MONAI that referenced this pull request Oct 20, 2022
@dzenanz @wyli @bhashemian
Use replication padding in Median filter (Project-MONAI#5329)
6426ed0 
Ref Project-MONAI#5264. Follow-up to Project-MONAI#5307. This is a more normal, intuitive variant
of median filtering.

Signed-off-by: Dženan Zukić <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Behrooz <[email protected]>
wyli pushed a commit that referenced this pull request Oct 24, 2022
@dzenanz @wyli
Adding a median filter for 3D images (#5307)
c33b7ea 
Co-authored-by: @ebrahimebrahim. Closes #5264.

<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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).
- [x] 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`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.
wyli added a commit that referenced this pull request Oct 24, 2022
@dzenanz @wyli
Use replication padding in Median filter (#5329)
aed8fe5 
Ref #5264. Follow-up to #5307. This is a more normal, intuitive variant
of median filtering.

Signed-off-by: Dženan Zukić <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
wyli pushed a commit that referenced this pull request Oct 24, 2022
@dzenanz @wyli
Adding a median filter for 3D images (#5307)
bc23df4 
Co-authored-by: @ebrahimebrahim. Closes #5264.

<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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).
- [x] 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`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.
wyli added a commit that referenced this pull request Oct 24, 2022
@dzenanz @wyli
Use replication padding in Median filter (#5329)
e33b2ac 
Ref #5264. Follow-up to #5307. This is a more normal, intuitive variant
of median filtering.

Signed-off-by: Dženan Zukić <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
KumoLiu pushed a commit that referenced this pull request Nov 2, 2022
@dzenanz @KumoLiu
Adding a median filter for 3D images (#5307)
9ec6471 
Co-authored-by: @ebrahimebrahim. Closes #5264.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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).
- [x] 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`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: KumoLiu <[email protected]>
KumoLiu pushed a commit that referenced this pull request Nov 2, 2022
@dzenanz @wyli @KumoLiu
Use replication padding in Median filter (#5329)
615a43b 
Ref #5264. Follow-up to #5307. This is a more normal, intuitive variant
of median filtering.

Signed-off-by: Dženan Zukić <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: KumoLiu <[email protected]>
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@wyli wyli wyli approved these changes

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

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Add median image filter as a transform

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