2872 implementation of mixup, cutmix and cutout #7198

juampatronics · 2023-11-03T21:24:28Z

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

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.

juampatronics · 2023-11-03T21:43:18Z

I do not fully understand the reason for the error:

def call(self, data: torch.Tensor, labels: torch.Tensor | None = None):
TypeError: unsupported operand type(s) for |: 'torch._C._TensorMeta' and 'NoneType'

Is it because of Python versions < 3.10?. What confuses me is that that construct it is actually used in MONAIs code a lot already.

wyli

Thanks for the PR! These are useful data preprocessing/augmentation tools, how about moving these into the monai.transforms module? Please also use the randomizable API to introduce random factor into the transforms

MONAI/monai/transforms/transform.py

Line 174 in fbbb64b

class Randomizable(ThreadUnsafe, RandomizableTrait):

juampatronics · 2023-11-06T19:02:11Z

Happy to contribute again @wyli. I have been enjoying MONAI for quite some time already.

Sure, I will move it to the transforms modules. Should I keep it as a submodule called "regularization"?
My motivation was twofold: on the one side they expect a batch, as opposed to all other sort of transforms and therefore not "composable" with them, and their use is purely for regularization during training.

wyli · 2023-11-06T19:09:01Z

/black

Happy to contribute again @wyli. I have been enjoying MONAI for quite some time already.

Sure, I will move it to the transforms modules. Should I keep it as a submodule called "regularization"? My motivation was twofold: on the one side they expect a batch, as opposed to all other sort of transforms and therefore not "composable" with them, and their use is purely for regularization during training.

Cool, thanks @juampatronics, the plan looks good to me.

juampatronics · 2023-11-07T18:59:58Z

Done

wyli

thanks, it looks good to me, please fix the format errors, and update the docstring about the input shapes.

KumoLiu

Thanks for the pr.
LGTM, It would be great if you could include a little usage example in the docstring.

monai/transforms/regularization/dictionary.py

juampatronics · 2023-11-08T21:14:39Z

thanks, it looks good to me, please fix the format errors, and update the docstring about the input shapes.

Regretfully I did not manage to run ./runtests.sh --autofix under WSL. Running isort under Windows gives no error.

ericspod · 2023-11-09T13:53:47Z

Regretfully I did not manage to run ./runtests.sh --autofix under WSL. Running isort under Windows gives no error.

This might be related to versions of isort, please double check you have the most recent version. I wouldn't think WSL would be the issue here, which is a full Linux system really, but more likely what libraries you're using.

monai/transforms/regularization/array.py

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

for more information, see https://pre-commit.ci Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

for more information, see https://pre-commit.ci Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

for more information, see https://pre-commit.ci Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes # fix useless error msg in nnunetv2runner ### Description ### Types of changes - [x] Non-breaking change (fix or new feature that would not break existing functionality). Signed-off-by: elitap <elias.tappeiner@gmx.at> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7230. ### Description Fix the typing issues and the deprecation. Also always run type checking with Linux environment, since ForkServerContext is not available on Windows. ### Types of changes - [x] Non-breaking change (fix or new feature that would not break existing functionality). --------- Signed-off-by: Felix Schnabel <f.schnabel@tum.de> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…AI#7239) Fixes # . ### Description A few sentences describing the changes proposed in this pull request. ### 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`. - [ ] 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. Add new developer to blossom-ci trigger list Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Project-MONAI#7234) … MONAI with all dependencies on Windows Fixes Project-MONAI#6118 ### Description The Windows shell doesn't recognize single quotes to delimit a string at all, so on Windows you'll need to use double quotes. It's the same command no matter which type of quotes you use; after the shell does its processing, the argument is passed to pip with the quotation marks already removed. ### 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`. - [ ] 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: ytl0623 <david89062388@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7458 ### Description https://github.com/python/cpython/blob/a21c0c7def9a8495f1166d9b434dfc301cb92bff/Lib/importlib/abc.py#L68 ### 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`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7013 Project-MONAI#7478 ### Description replace `predict_from_raw_data` with `nnUNetPredictor` in test_nnunetv2runner ### 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`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7449 ### 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`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Use uint8 instead of int8 in `LabelStats`. ### 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`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes issue Project-MONAI#7425 ### Description Add a `sample_std` parameter to `RandGaussianNoise` and `RandGaussianNoised`. When True, the Gaussian's standard deviation is sampled uniformly from 0 to std (i.e., what is currently done). When False, the noise's standard deviation is non-random and set to std. The default for sample_std would be True for backwards compatibility. Changes were based on RandRicianNoise which already has a `sample_std` parameter and is similar to RandGaussianNoise in concept and implementation. ### 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. - [ ] 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: Timothy Baker <bakertim@umich.edu> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

### Description When training a model using MONAI metrics for experiment tracking, I tend to log which metrics I am using. Unfortunately, just sending the metrics objects to Tensorboard will result in a list like [CustomMetric1, CustomMetric2, <monai.metrics.Metric ...>, etc.] Adding `__repr__` and `__str__` methods to the base class will solve this small annoyance. The current implementation will only return the class name, but if a certain metric would wish to report more data for its `__repr__` string, this can be easily overridden in any subclass. ### 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`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…#7510) Bumps [al-cheb/configure-pagefile-action](https://github.com/al-cheb/configure-pagefile-action) from 1.3 to 1.4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/al-cheb/configure-pagefile-action/releases">al-cheb/configure-pagefile-action's releases</a>.</em></p> <blockquote> <h2>v1.4: Update task node version to 20</h2> <h1>configure-pagefile-action</h1> <p>This action is intended to configure Pagefile size and location for Windows images in GitHub Actions.</p> <h1>Available parameters</h1> <table> <thead> <tr> <th>Argument</th> <th>Description</th> <th>Format</th> <th>Default value</th> </tr> </thead> <tbody> <tr> <td><code>minimum-size</code></td> <td>Set minimum size of Pagefile</td> <td><code>2048MB</code>, <code>4GB</code>, <code>8GB</code> and etc</td> <td><code>8GB</code></td> </tr> <tr> <td><code>maximum-size</code></td> <td>Set maximum size of Pagefile</td> <td>The same like <code>minimum-size</code></td> <td><code>minimum-size</code></td> </tr> <tr> <td><code>disk-root</code></td> <td>Set disk root where Pagefile will be located</td> <td><code>C:</code> or <code>D:</code></td> <td><code>D:</code></td> </tr> </tbody> </table> <h1>Usage</h1> <pre><code>name: CI on: [push] jobs: build: runs-on: windows-latest steps: - name: configure Pagefile uses: al-cheb/configure-pagefile-action@v1.4 with: minimum-size: 8 <pre><code>- name: configure Pagefile uses: al-cheb/configure-pagefile-action@v1.4 with: minimum-size: 8 maximum-size: 16 disk-root: &quot;D:&quot; </code></pre> <p></code></pre></p> <h1>License</h1> <p>The scripts and documentation in this project are released under the <a href="https://github.com/al-cheb/configure-pagefile-action/blob/HEAD/LICENSE">MIT License</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/a3b6ebd6b634da88790d9c58d4b37a7f4a7b8708"><code>a3b6ebd</code></a> Merge pull request <a href="https://redirect.github.com/al-cheb/configure-pagefile-action/issues/20">#20</a> from mikehardy/mikehardy-patch-1</li> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/850626ff7d6f5665848a60cdc3b0ace19fa0b094"><code>850626f</code></a> build(deps): bump javascript dependencies / forward-port as needed</li> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/e7aac1b891d29f440ea916231d51d085206f9106"><code>e7aac1b</code></a> fix: use node 20</li> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/d940d2434c38e1a228580edc8f9421aafca9800d"><code>d940d24</code></a> build(deps): use v4 of setup-node action, use node 20</li> <li><a href="https://github.com/al-cheb/configure-pagefile-action/commit/dfdc038768fdb21f91ed75a5fa40890fb92f5919"><code>dfdc038</code></a> build(deps): bump actions/checkout from 3 to 4</li> <li>See full diff in <a href="https://github.com/al-cheb/configure-pagefile-action/compare/v1.3...v1.4">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=al-cheb/configure-pagefile-action&package-manager=github_actions&previous-version=1.3&new-version=1.4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes # . ### Description Add arm support ### 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`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7523 ### 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`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7547 ### Description Previously it was 'medical_resnet50_23datasets' for both identifier and string, which doesn't correspond to the name in the hubconf.py of Warvito's repo. Now it is the correct version (according to Warvitos repo) 'medicalnet_resnet50_23datasets'. The docs state it correctly already. ### 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Fabian Klopfer <fabian.klopfer@ieee.org> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Fixes Project-MONAI#7533 ### Description A few sentences describing the changes proposed in this pull request. ### 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`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…NAI#7551) Fixes Project-MONAI#7550 ### 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`. - [ ] 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: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

### Description Addition of the BarlowTwinsLoss class. This cost function is introduced in the http://proceedings.mlr.press/v139/zbontar21a/zbontar21a.pdf paper with the aim of disentangling the representations learned on two views of the same sample, making it a powerful tool for multimodal and unsupervised learning. This cost function is similar to the InfoNCE Loss function already implemented in MONAI (https://docs.monai.io/en/latest/_modules/monai/losses/contrastive.html#ContrastiveLoss). However, it differs in several respects: there is no l2-normalisation, but rather a z-normalisation. In addition, rather than working between pairs of embeddings, Barlow Twins seeks to decorrelate the components of the representations. ```math \mathcal{L}_{BT} := \sum_i (1 - \mathcal{C}_{ii})^2 + \lambda \sum_i \sum_{i\neq j} \mathcal{C}_{ij}^2 ``` with $\lambda$ a positive hyperparameters and $\mathcal{C}$ the cross-correlation matrix ### 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: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Signed-off-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Co-authored-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…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 <chaoliu@nvidia.com> Signed-off-by: cxlcl <chaoliucxl@gmail.com> Signed-off-by: chaoliu <chaoliucxl@gmail.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

…nics@gmail.com> I, Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>, hereby add my Signed-off-by to this commit: b899421 I, Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>, hereby add my Signed-off-by to this commit: aaa640f I, Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>, hereby add my Signed-off-by to this commit: c85976f I, Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>, hereby add my Signed-off-by to this commit: f2fe14e Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

KumoLiu · 2024-03-26T02:05:33Z

/build

KumoLiu · 2024-03-26T02:18:04Z

/build

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 <juampatronics@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: elitap <elias.tappeiner@gmx.at> Signed-off-by: Felix Schnabel <f.schnabel@tum.de> Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Signed-off-by: ytl0623 <david89062388@gmail.com> Signed-off-by: Dženan Zukić <dzenan.zukic@kitware.com> Signed-off-by: KumoLiu <yunl@nvidia.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Ishan Dutta <ishandutta0098@gmail.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: kaibo <ktang@unc.edu> Signed-off-by: heyufan1995 <heyufan1995@gmail.com> Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com> Signed-off-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Signed-off-by: Timothy Baker <bakertim@umich.edu> Signed-off-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Signed-off-by: Fabian Klopfer <fabian.klopfer@ieee.org> Signed-off-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Signed-off-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Signed-off-by: chaoliu <chaoliu@nvidia.com> Signed-off-by: cxlcl <chaoliucxl@gmail.com> Signed-off-by: chaoliu <chaoliucxl@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <64792179+monai-bot@users.noreply.github.com> Co-authored-by: elitap <elitap@users.noreply.github.com> Co-authored-by: Felix Schnabel <f.schnabel@tum.de> Co-authored-by: YanxuanLiu <104543031+YanxuanLiu@users.noreply.github.com> Co-authored-by: ytl0623 <david89062388@gmail.com> Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Ishan Dutta <ishandutta0098@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Kaibo Tang <ktang@unc.edu> Co-authored-by: Yufan He <59374597+heyufan1995@users.noreply.github.com> Co-authored-by: binliunls <107988372+binliunls@users.noreply.github.com> Co-authored-by: Ben Murray <ben.murray@gmail.com> Co-authored-by: axel.vlaminck <axel.vlaminck@gmail.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Co-authored-by: Dr. Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Co-authored-by: Timothy J. Baker <62781117+tim-the-baker@users.noreply.github.com> Co-authored-by: Mathijs de Boer <8137653+MathijsdeBoer@users.noreply.github.com> Co-authored-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Co-authored-by: Fabian Klopfer <fabian.klopfer@ieee.org> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Co-authored-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Co-authored-by: cxlcl <chaoliucxl@gmail.com>

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 <juampatronics@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: elitap <elias.tappeiner@gmx.at> Signed-off-by: Felix Schnabel <f.schnabel@tum.de> Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Signed-off-by: ytl0623 <david89062388@gmail.com> Signed-off-by: Dženan Zukić <dzenan.zukic@kitware.com> Signed-off-by: KumoLiu <yunl@nvidia.com> Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Signed-off-by: Ishan Dutta <ishandutta0098@gmail.com> Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: kaibo <ktang@unc.edu> Signed-off-by: heyufan1995 <heyufan1995@gmail.com> Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com> Signed-off-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Signed-off-by: Timothy Baker <bakertim@umich.edu> Signed-off-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Signed-off-by: Fabian Klopfer <fabian.klopfer@ieee.org> Signed-off-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Signed-off-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Signed-off-by: chaoliu <chaoliu@nvidia.com> Signed-off-by: cxlcl <chaoliucxl@gmail.com> Signed-off-by: chaoliu <chaoliucxl@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <64792179+monai-bot@users.noreply.github.com> Co-authored-by: elitap <elitap@users.noreply.github.com> Co-authored-by: Felix Schnabel <f.schnabel@tum.de> Co-authored-by: YanxuanLiu <104543031+YanxuanLiu@users.noreply.github.com> Co-authored-by: ytl0623 <david89062388@gmail.com> Co-authored-by: Dženan Zukić <dzenan.zukic@kitware.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com> Co-authored-by: Ishan Dutta <ishandutta0098@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Kaibo Tang <ktang@unc.edu> Co-authored-by: Yufan He <59374597+heyufan1995@users.noreply.github.com> Co-authored-by: binliunls <107988372+binliunls@users.noreply.github.com> Co-authored-by: Ben Murray <ben.murray@gmail.com> Co-authored-by: axel.vlaminck <axel.vlaminck@gmail.com> Co-authored-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: Ibrahim Hadzic <ibrahimhadzic45@gmail.com> Co-authored-by: Dr. Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Co-authored-by: Timothy J. Baker <62781117+tim-the-baker@users.noreply.github.com> Co-authored-by: Mathijs de Boer <8137653+MathijsdeBoer@users.noreply.github.com> Co-authored-by: Mathijs de Boer <m.deboer-41@umcutrecht.nl> Co-authored-by: Fabian Klopfer <fabian.klopfer@ieee.org> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Lucas Robinet <67736918+Lucas-rbnt@users.noreply.github.com> Co-authored-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Co-authored-by: cxlcl <chaoliucxl@gmail.com> Signed-off-by: Yu0610 <612410030@alum.ccu.edu.tw>

wyli reviewed Nov 4, 2023

View reviewed changes

wyli requested review from ericspod, Nic-Ma and KumoLiu November 7, 2023 20:36

wyli approved these changes Nov 7, 2023

View reviewed changes

KumoLiu approved these changes Nov 8, 2023

View reviewed changes

monai/transforms/regularization/dictionary.py Outdated Show resolved Hide resolved

KumoLiu reviewed Nov 16, 2023

View reviewed changes

monai/transforms/regularization/array.py Outdated Show resolved Hide resolved

juampatronics and others added 17 commits March 25, 2024 21:17

mixup, cutmix and cutout

79719fa

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

added rst file

1528cdf

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

[pre-commit.ci] auto fixes from pre-commit.com hooks

ff45686

for more information, see https://pre-commit.ci Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

added missing module

ea89145

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

refactor code as submodule of transforms module

d35c1b3

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

[pre-commit.ci] auto fixes from pre-commit.com hooks

1c54f1c

for more information, see https://pre-commit.ci Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

use the randomizable API

9b05593

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

used types compatible with python <3.10

83b2c98

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

used types compatible with python <3.10

efd5e99

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

fixed isort errors

f6af5cf

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

[pre-commit.ci] auto fixes from pre-commit.com hooks

8e7ec73

for more information, see https://pre-commit.ci Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

auto updates (Project-MONAI#7203)

5eb8c7f

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

changes from command ./runtests.sh --autofix

674812f

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

KumoLiu and others added 21 commits March 25, 2024 21:18

auto updates (Project-MONAI#7495)

01a8a24

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

fixed code format checks

7d48f9e

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

added feedback suggestions

292e84d

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

auto updates (Project-MONAI#7577)

2606758

Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

flake8 warnings

c9a6521

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

finally got sphinx format right

859852e

Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>

juampatronics force-pushed the 2872-mixup branch from d229c7a to 859852e Compare March 25, 2024 20:18

Merge branch 'dev' into 2872-mixup

070d963

KumoLiu enabled auto-merge (squash) March 26, 2024 02:05

Merge branch 'dev' into 2872-mixup

a59f41f

KumoLiu merged commit e5bebfc into Project-MONAI:dev Mar 26, 2024
28 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

2872 implementation of mixup, cutmix and cutout #7198

2872 implementation of mixup, cutmix and cutout #7198

juampatronics commented Nov 3, 2023 •

edited

Loading

juampatronics commented Nov 3, 2023

wyli left a comment

juampatronics commented Nov 6, 2023

wyli commented Nov 6, 2023 •

edited

Loading

juampatronics commented Nov 7, 2023

wyli left a comment

KumoLiu left a comment

juampatronics commented Nov 8, 2023

ericspod commented Nov 9, 2023

KumoLiu commented Mar 26, 2024

KumoLiu commented Mar 26, 2024

2872 implementation of mixup, cutmix and cutout #7198

2872 implementation of mixup, cutmix and cutout #7198

Conversation

juampatronics commented Nov 3, 2023 • edited Loading

Description

Types of changes

juampatronics commented Nov 3, 2023

wyli left a comment

Choose a reason for hiding this comment

juampatronics commented Nov 6, 2023

wyli commented Nov 6, 2023 • edited Loading

juampatronics commented Nov 7, 2023

wyli left a comment

Choose a reason for hiding this comment

KumoLiu left a comment

Choose a reason for hiding this comment

juampatronics commented Nov 8, 2023

ericspod commented Nov 9, 2023

KumoLiu commented Mar 26, 2024

KumoLiu commented Mar 26, 2024

juampatronics commented Nov 3, 2023 •

edited

Loading

wyli commented Nov 6, 2023 •

edited

Loading