Generalize `SobelGradients` to 3D and Any Axis by bhashemian · Pull Request #5189 · Project-MONAI/MONAI

bhashemian · 2022-09-21T15:06:56Z

Description

This PR reimplement SobelGradients and SobelGradientsd using separable kernels and generalize it to images with any spatial dimension (2D, 3D, etc.) and option to calculate the gradient along any given axis.

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
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.

Signed-off-by: Behrooz <[email protected]>

monai/transforms/post/array.py

Signed-off-by: Behrooz <[email protected]>

KumoLiu

Thanks for your update, it looks good to me now!

monai/transforms/post/array.py

wyli

perhaps this need some refactoring for 3d as well

Signed-off-by: Behrooz <[email protected]>

…update-sobel-direction

KumoLiu · 2022-09-24T09:11:08Z

Hi @drbeh,
I have just added unittest in CalcualteInstanceSegmentationMap which used SobelGradients and found some different effects between cv2 and SobelGradients.
The difference between cv2 and SobelGradients also cause CalcualteInstanceSegmentationMap can't get correct instance segmentation results. So I just used cv2 now. I will withdraw my approval of this PR and please check it.
Here is my test code.

import cv2
from monai.transforms.post.array import SobelGradients

image = np.zeros([20,20])
image[5:15, 5:15] = 1

filter = SobelGradients(kernel_size=5)
mo_ret = filter(image[None]).squeeze()
cv_ret_0 = cv2.Sobel(image, cv2.CV_64F, 0, 1, ksize=5)
cv_ret_1 = cv2.Sobel(image, cv2.CV_64F, 1, 0, ksize=5)
mo_ret = 1 - (mo_ret - np.min(mo_ret)) / (np.max(mo_ret) - np.min(mo_ret))
cv_ret_0 = 1 - (cv_ret_0 - np.min(cv_ret_0)) / (np.max(cv_ret_0) - np.min(cv_ret_0))
cv_ret_1 = 1 - (cv_ret_1 - np.min(cv_ret_1)) / (np.max(cv_ret_1) - np.min(cv_ret_1))

fig, ax = plt.subplots(1,5,figsize = (50,10))
ax[0].imshow(mo_ret[0], cmap='gray')
ax[1].imshow(mo_ret[1], cmap='gray')
ax[2].imshow(cv_ret_0, cmap='gray')
ax[3].imshow(cv_ret_1, cmap='gray')
ax[4].imshow(mo_ret[0] - cv_ret_0, cmap='gray')

Thanks!

as comment

wyli · 2022-09-24T16:46:55Z

I have just added unittest in CalcualteInstanceSegmentationMap which used SobelGradients and found some different effects between cv2 and SobelGradients

@drbeh and I were discussing this in another thread, opencv uses the separable implementation cv2.getDerivKernels(1, 0, 5), that's slightly different from what we have here. but we haven't looked into the actual segmentation outcome differences.

KumoLiu · 2022-09-26T02:22:04Z

Just FYI, I showed the instance segmentation result from CalcualteInstanceSegmentationMap. The results are calculated with all the same components except for Sobel gradient.
cv2 - result

MONAI - result

Thanks!

JHancox · 2022-09-26T10:29:09Z

Sorry - inadvertantly closed the PR

tests/test_hovernet_loss.py

Signed-off-by: Behrooz <[email protected]>

bhashemian · 2022-10-28T12:40:28Z

@wyli @Nic-Ma @KumoLiu any other comments here? Thanks

wyli

The api looks good to me

monai/transforms/post/array.py

Signed-off-by: Behrooz <[email protected]>

Nic-Ma · 2022-10-31T11:13:57Z

/black

Nic-Ma · 2022-10-31T11:14:05Z

/build

wyli · 2022-10-31T12:44:57Z

/build

Fixes #5188 ### Description This PR reimplement `SobelGradients` and `SobelGradientsd` using separable kernels and generalize it to images with any spatial dimension (2D, 3D, etc.) and option to calculate the gradient along any given axis. ### Types of changes  - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [x] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. Signed-off-by: Behrooz <[email protected]> Signed-off-by: KumoLiu <[email protected]>

Fixes Project-MONAI#5188 ### Description This PR reimplement `SobelGradients` and `SobelGradientsd` using separable kernels and generalize it to images with any spatial dimension (2D, 3D, etc.) and option to calculate the gradient along any given axis. ### Types of changes  - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [x] New tests added to cover the changes. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. Signed-off-by: Behrooz <[email protected]> Signed-off-by: Yiheng Wang <[email protected]>

bhashemian added 5 commits September 21, 2022 14:15

Update SobelGradients to include gradient direction

3503cc2

Signed-off-by: Behrooz <[email protected]>

Add more checking to raise errors

c3dcb0d

Signed-off-by: Behrooz <[email protected]>

Add test cases

7b26dd5

Signed-off-by: Behrooz <[email protected]>

Update SobelGradientsd

852eba8

Signed-off-by: Behrooz <[email protected]>

Add test cases for SobelGradientsD

a1483dc

Signed-off-by: Behrooz <[email protected]>

bhashemian requested review from KumoLiu, Nic-Ma and wyli September 21, 2022 15:07

KumoLiu reviewed Sep 21, 2022

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bhashemian added 2 commits September 21, 2022 12:24

Merge branch 'dev' into update-sobel-direction

f3335c8

Update docstring

2b2b28e

Signed-off-by: Behrooz <[email protected]>

bhashemian requested a review from KumoLiu September 22, 2022 02:20

bhashemian enabled auto-merge (squash) September 22, 2022 02:20

KumoLiu previously approved these changes Sep 22, 2022

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Nic-Ma reviewed Sep 22, 2022

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wyli reviewed Sep 22, 2022

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bhashemian added 4 commits September 22, 2022 13:48

Address comments

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Signed-off-by: Behrooz <[email protected]>

Merge branch 'dev' into update-sobel-direction

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Type checking

54694b4

Signed-off-by: Behrooz <[email protected]>

Merge branch 'update-sobel-direction' of github.com:drbeh/MONAI into …

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…update-sobel-direction

KumoLiu mentioned this pull request Sep 26, 2022

Add CalculateInstanceSegmentationMap Transform #5173

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JHancox closed this Sep 26, 2022

auto-merge was automatically disabled September 26, 2022 10:27
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JHancox reopened this Sep 26, 2022

JHancox reviewed Oct 27, 2022

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Update sobel unittests

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Signed-off-by: Behrooz <[email protected]>

bhashemian force-pushed the update-sobel-direction branch from b126b91 to 7eb6ae5 Compare October 27, 2022 14:56

bhashemian added 3 commits October 27, 2022 14:33

Add normalize kernels and normalize gradients

a09c2ac

Signed-off-by: Behrooz <[email protected]>

Update unitests and add new test cases

6848a38

Signed-off-by: Behrooz <[email protected]>

Update hovernet unittests

3977784

Signed-off-by: Behrooz <[email protected]>

bhashemian changed the title ~~Update SobelGradients to include direction~~ Generalize SobelGradients to 3D and Any Axis Oct 27, 2022

bhashemian added 2 commits October 28, 2022 08:38

Merge branch 'dev' into update-sobel-direction

9146714

formatting

45c0cea

Signed-off-by: Behrooz <[email protected]>

bhashemian enabled auto-merge (squash) October 28, 2022 12:40

bhashemian requested review from JHancox, KumoLiu and Nic-Ma October 28, 2022 14:47

wyli approved these changes Oct 28, 2022

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bhashemian and others added 3 commits October 28, 2022 15:04

Make less call to min and max

8f23120

Signed-off-by: Behrooz <[email protected]>

Merge branch 'dev' into update-sobel-direction

8a9c4da

Merge branch 'dev' into update-sobel-direction

e399fb4

Merge branch 'dev' into update-sobel-direction

d4d8f4a

wyli disabled auto-merge October 31, 2022 12:44

wyli enabled auto-merge (squash) October 31, 2022 12:44

wyli merged commit e44f3b9 into Project-MONAI:dev Oct 31, 2022

bhashemian mentioned this pull request Oct 31, 2022

HoVerNet training pipeline Project-MONAI/tutorials#999

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bhashemian deleted the update-sobel-direction branch October 31, 2022 14:37

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