Feature added: Get WSI at mpp #7574

NikolasSchmitz · 2024-03-25T01:25:09Z

Description

In this pull request, the feature to retrieve a whole slide image at a given mpp (microns per pixel) resolution was implemented for every WSIReader class in the function get_wsi_at_mpp.

While the implementations in the OpenslideWSIReader and CuCIMWSIReader classes were tested thoroughly, I could not find a suitable TIFF file for testing with the TiffFileWSIReader class.

For resizing, I have used PIL.Image.resize for Openslide and TiffFile, and cucim.sklearn.transform.resize for CuCIM. Originally, I used cv2.resize, but since the package isn't listed in requirements-dev.txt, I explored alternative solutions."

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.

Please let me know what you think and how I can improve this feature.

Best
Niko

(Last PR was closed, because I changed the branch name to include the ticket id)

…si_reader.py

…izing function to Image.resize, cucim.skimage.transform.resize

…roject-MONAI#7308) ### Description Based on the discussion topic [here](Project-MONAI#7161 (comment)), we implemented the Conjugate-Gradient algorithm for linear operator inversion, and Stein's Unbiased Risk Estimator (SURE) [1] loss for ground-truth-date free diffusion process guidance that is proposed in [2] and illustrated in the algorithm below: <img width="650" alt="Screenshot 2023-12-10 at 10 19 25 PM" src="https://github.com/Project-MONAI/MONAI/assets/8581162/97069466-cbaf-44e0-b7a7-ae9deb8fd7f2"> The Conjugate-Gradient (CG) algorithm is used to solve for the inversion of the linear operator in Line-4 in the algorithm above, where the linear operator is too large to store explicitly as a matrix (such as FFT/IFFT of an image) and invert directly. Instead, we can solve for the linear inversion iteratively as in CG. The SURE loss is applied for Line-6 above. This is a differentiable loss function that can be used to train/giude an operator (e.g. neural network), where the pseudo ground truth is available but the reference ground truth is not. For example, in the MRI reconstruction, the pseudo ground truth is the zero-filled reconstruction and the reference ground truth is the fully sampled reconstruction. The reference ground truth is not available due to the lack of fully sampled. **Reference** [1] Stein, C.M.: Estimation of the mean of a multivariate normal distribution. Annals of Statistics 1981 [[paper link](https://projecteuclid.org/journals/annals-of-statistics/volume-9/issue-6/Estimation-of-the-Mean-of-a-Multivariate-Normal-Distribution/10.1214/aos/1176345632.full)] [2] B. Ozturkler et al. SMRD: SURE-based Robust MRI Reconstruction with Diffusion Models. MICCAI 2023 [[paper link](https://arxiv.org/pdf/2310.01799.pdf)] ### Types of changes  - [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. - [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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: chaoliu <[email protected]> Signed-off-by: cxlcl <[email protected]> Signed-off-by: chaoliu <[email protected]> Signed-off-by: YunLiu <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> Signed-off-by: Nikolas Schmitz <[email protected]>

Signed-off-by: Nikolas Schmitz <[email protected]>

for more information, see https://pre-commit.ci Signed-off-by: Nikolas Schmitz <[email protected]>

Signed-off-by: Nikolas Schmitz <[email protected]>

Signed-off-by: monai-bot <[email protected]> Signed-off-by: monai-bot <[email protected]> Signed-off-by: Nikolas Schmitz <[email protected]>

Signed-off-by: Nikolas Schmitz <[email protected]>

…ject-MONAI#7569) Fixes Project-MONAI#7451 ### Description Reduces the length of error messages and error messages being propagated twice. This helps debug better when long `ConfigComponent`s are being instantiated. Refer to issue Project-MONAI#7451 for more details ### Types of changes  - [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). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [x] 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. Signed-off-by: Suraj Pai <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

Fixes Project-MONAI#2872 ### Description Implementation of mixup, cutmix and cutout as described in the original papers. Current implementation support both, the dictionary-based batches and tuples of tensors. ### Types of changes  - [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`. - [x] 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: Juan Pablo de la Cruz Gutiérrez <[email protected]> Signed-off-by: monai-bot <[email protected]> Signed-off-by: elitap <[email protected]> Signed-off-by: Felix Schnabel <[email protected]> Signed-off-by: YanxuanLiu <[email protected]> Signed-off-by: ytl0623 <[email protected]> Signed-off-by: Dženan Zukić <[email protected]> Signed-off-by: KumoLiu <[email protected]> Signed-off-by: YunLiu <[email protected]> Signed-off-by: Ishan Dutta <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: kaibo <[email protected]> Signed-off-by: heyufan1995 <[email protected]> Signed-off-by: binliu <[email protected]> Signed-off-by: axel.vlaminck <[email protected]> Signed-off-by: Ibrahim Hadzic <[email protected]> Signed-off-by: Behrooz <[email protected]> Signed-off-by: Timothy Baker <[email protected]> Signed-off-by: Mathijs de Boer <[email protected]> Signed-off-by: Fabian Klopfer <[email protected]> Signed-off-by: Lucas Robinet <[email protected]> Signed-off-by: Lucas Robinet <[email protected]> Signed-off-by: chaoliu <[email protected]> Signed-off-by: cxlcl <[email protected]> Signed-off-by: chaoliu <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]> Co-authored-by: elitap <[email protected]> Co-authored-by: Felix Schnabel <[email protected]> Co-authored-by: YanxuanLiu <[email protected]> Co-authored-by: ytl0623 <[email protected]> Co-authored-by: Dženan Zukić <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> Co-authored-by: YunLiu <[email protected]> Co-authored-by: Ishan Dutta <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Kaibo Tang <[email protected]> Co-authored-by: Yufan He <[email protected]> Co-authored-by: binliunls <[email protected]> Co-authored-by: Ben Murray <[email protected]> Co-authored-by: axel.vlaminck <[email protected]> Co-authored-by: Mingxin Zheng <[email protected]> Co-authored-by: Ibrahim Hadzic <[email protected]> Co-authored-by: Dr. Behrooz Hashemian <[email protected]> Co-authored-by: Timothy J. Baker <[email protected]> Co-authored-by: Mathijs de Boer <[email protected]> Co-authored-by: Mathijs de Boer <[email protected]> Co-authored-by: Fabian Klopfer <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Lucas Robinet <[email protected]> Co-authored-by: Lucas Robinet <[email protected]> Co-authored-by: cxlcl <[email protected]>

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

drbeh · 2024-04-09T15:47:58Z

@NikolasSchmitz, I resolved the conflicts and updated the PR. Let's focus on the functionality and make this PR ready for reviewing. We can take care of any other issue once the PR is ready and please feel free to reach out to me or the working group if you still have any questions. Thanks for taking on this feature.

NikolasSchmitz · 2024-04-09T22:56:30Z

Thank you @drbeh ! I now marked it as ready for review.

monai/data/wsi_reader.py

ericspod · 2024-04-22T14:57:35Z

@drbeh would you be able to review this? I think you're best qualified here. I made some minor comments about print and code duplication but otherwise it seems fine to me without having tested it. Thanks!

JHancox

Thanks for the effort @NikolasSchmitz. A welcome addition! I agree with @ericspod about the refactoring to remove duplication - that would be great.

monai/data/wsi_reader.py

NikolasSchmitz · 2024-05-16T17:16:27Z

Thank you for the feedback, @JHancox . Unfortunately, I couldn't join the meeting because I was on my way home from ICLR.
I will review the code and provide my updates as soon as possible.

… reduce redundancy; for get_mpp of TiffFileWSIReader: added check to prevent division by zero error.

NikolasSchmitz · 2024-07-31T18:25:13Z

I factored out the actual resizing of the image into _resize_to_mpp_res() and kept the tolerance checks in get_wsi_at_mpp(). I had some problems with specific tiff files and the TiffFile backend. Some files had zero as X/Y Resolution, which led to a division by zero error in the function get_mpp (added a check for that in the new commit).
One tiff file from a Philips scanner that I tested had unobtainable mpp values using get_mpp. In this case, the tags do exist (openslide can find them), but they must be read and parsed from the property philips_metadata as XML. I have not implemented a fix for this yet, but please let me know if this is needed. In this particular case, the best option would be to use Openslide as the backend, although there might be users who prefer Tifffile.

monai/data/wsi_reader.py

ericspod · 2024-08-01T11:55:31Z

There are lines added/removed to two other files that don't need to be changed in this PR, tests/test_regularization.py is causing a conflict for example. I would remove those and we can use black here through Github to resolve formatting issues if we need to.

NikolasSchmitz · 2024-08-01T21:47:03Z

There are lines added/removed to two other files that don't need to be changed in this PR, tests/test_regularization.py is causing a conflict for example. I would remove those and we can use black here through Github to resolve formatting issues if we need to.

Thanks for the info. Interesting though, haven't noticed that these files were changed. Perhaps through one of the coding style checks.

Signed-off-by: Nikolas Schmitz <[email protected]>

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ericspod · 2024-08-07T11:15:23Z

There's a few changes to do but it looks good in general. We do need tests for these new methods as well so please look at the existing WSI tests to see what needs to be added to cover new functionality. The flake8 and DCO fixes can be done at the end. Thanks!

…ces to BaseWSIReader; Edited docstrings

for more information, see https://pre-commit.ci

ericspod · 2024-09-25T17:31:42Z

monai/data/wsi_reader.py

+        mpp_list = [self.get_mpp(wsi, lvl) for lvl in range(wsi.resolutions["level_count"])]
+        closest_lvl = self._find_closest_level("mpp", mpp, mpp_list, 0, 5)
+
+        within_tolerance, closest_level_is_bigger = super()._compute_mpp_tolerances(closest_lvl, mpp_list, mpp, atol, rtol)


Suggested change

within_tolerance, closest_level_is_bigger = super()._compute_mpp_tolerances(closest_lvl, mpp_list, mpp, atol, rtol)

within_tolerance, closest_level_is_bigger = self._compute_mpp_tolerances(closest_lvl, mpp_list, mpp, atol, rtol)

If you're not overriding the method in this class you can refer to it through self as it will be inherited.

Same in other places below.

Nikolas Schmitz added 5 commits March 22, 2024 14:07

Added function get_img_at_mpp to class OpenSlideWSIReader of module w…

f3e7d03

…si_reader.py

Added get_img_at_mpp to class CuCIMWSIReader

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Added function get_img_at_mpp to class TifffileWSIReader; changed res…

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…izing function to Image.resize, cucim.skimage.transform.resize

Small changes

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Small changes

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NikolasSchmitz mentioned this pull request Mar 25, 2024

WSIReader support for reading by mpp or magnification #4980

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NikolasSchmitz force-pushed the 4980-get-wsi-at-mpp branch from 0b7322e to 1c10112 Compare March 27, 2024 00:38

cxlcl and others added 6 commits March 27, 2024 01:47

Renamed function to get_wsi_at_mpp

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Signed-off-by: Nikolas Schmitz <[email protected]>

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for more information, see https://pre-commit.ci Signed-off-by: Nikolas Schmitz <[email protected]>

Reformatted wsi_reader.py

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auto updates (Project-MONAI#7577)

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Signed-off-by: monai-bot <[email protected]> Signed-off-by: monai-bot <[email protected]> Signed-off-by: Nikolas Schmitz <[email protected]>

Fixed return type

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NikolasSchmitz force-pushed the 4980-get-wsi-at-mpp branch from 1c10112 to ae704f3 Compare March 27, 2024 00:49

NikolasSchmitz and others added 3 commits March 27, 2024 02:04

Small fixes

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Signed-off-by: Nikolas Schmitz <[email protected]>

NikolasSchmitz force-pushed the 4980-get-wsi-at-mpp branch from a65ef4a to 3264079 Compare March 27, 2024 01:08

Merge branch 'dev' into 4980-get-wsi-at-mpp

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

NikolasSchmitz marked this pull request as ready for review April 9, 2024 22:55

ericspod requested a review from drbeh April 22, 2024 14:53

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Updated function get_wsi_at_mpp; added function _resize_to_mpp_res to…

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… reduce redundancy; for get_mpp of TiffFileWSIReader: added check to prevent division by zero error.

Minor fixes: removed unnecessary comments

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NikolasSchmitz and others added 6 commits August 3, 2024 00:20

Merge branch 'dev' into 4980-get-wsi-at-mpp

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Signed-off-by: Nikolas Schmitz <[email protected]>

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Added function _compute_mpp_target_res to BaseWSIReader

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Added new feature and merged updates from main repository

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Added function _compute_mpp_target_res to BaseWSIReader

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ericspod and others added 8 commits August 7, 2024 12:15

Merge branch 'dev' into 4980-get-wsi-at-mpp

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Added a function _compute_mpp_tolerances which checks the mpp toleran…

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…ces to BaseWSIReader; Edited docstrings

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Merge branch 'Project-MONAI:dev' into 4980-get-wsi-at-mpp

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Feature added: Get WSI at mpp #7574

Feature added: Get WSI at mpp #7574

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	within_tolerance, closest_level_is_bigger = super()._compute_mpp_tolerances(closest_lvl, mpp_list, mpp, atol, rtol)
	within_tolerance, closest_level_is_bigger = self._compute_mpp_tolerances(closest_lvl, mpp_list, mpp, atol, rtol)

Feature added: Get WSI at mpp #7574

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