Merge dev to geometric #7680
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Merge dev to geometric #7680
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Use uint8 instead of int8 in `LabelStats`. ### 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). - [ ] 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: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@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 <!--- 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). - [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>
### 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 <!--- 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). - [ ] 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>
…#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 /> [](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>
Fixes # . ### Description Add arm support ### 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). - [ ] 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>
Fixes Project-MONAI#7523 ### 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). - [ ] 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>
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 <!--- 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. - [ 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>
Fixes Project-MONAI#7533 ### Description A few sentences describing the changes proposed in this pull request. ### 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). - [ ] 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>
…NAI#7551) Fixes Project-MONAI#7550 ### 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). - [ ] 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>
### 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 <!--- 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. - [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>
…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 <!--- 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. - [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: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
…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 <!--- 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). - [ ] 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 <b.pai@maastrichtuniversity.nl> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.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 <!--- 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`. - [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>
workaround for Project-MONAI#7575 ### 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). - [ ] 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>
…s/patchembedding.py (Project-MONAI#7564) ### Description When you choose to put the argument `pos_embed_type='sincos'` in the `PatchEmbeddingBlock` class, it still return a learnable positional encoding To reproduce: ```python from monai.networks.blocks import PatchEmbeddingBlock patcher = PatchEmbeddingBlock( in_channels=1, img_size=(32, 32, 32), patch_size=(8, 8, 8), hidden_size=96, num_heads=8, pos_embed_type="sincos", dropout_rate=0.5, ) print(patcher.position_embeddings.requires_grad) >>> True ``` In the literature, we sometimes use either positional encoding in sincos which are fixed and non-trainable as in the original Attention Is All You Need [paper](https://arxiv.org/abs/1706.03762) or a learnable positional embedding as in the ViT [paper](https://arxiv.org/abs/2010.11929). If you choose to use a sincos, then it seems that is must be fixed which is not the case here. I'm not completely sure of the desired result in MONAI since there's already a learnable possibility, so if we choose sincos we'd like gradient-free parameters. However the documentation of `build_sincos_position_embedding`in the `pos_embed_utils.py`files stipulate: "The sin-cos position embedding as a learnable parameter" which seems a bit confusing. Especially as the encoding construction function seems to aim to set the require gradient to False (see below) ```python pos_embed = nn.Parameter(pos_emb) pos_embed.requires_grad = False return pos_embed ``` But these changes are not maintained by torch's `copy_` function, which does not copy gradient parameters (see the cpp code https://github.com/pytorch/pytorch/blob/148a8de6397be6e4b4ca1508b03b82d117bfb03c/torch/csrc/lazy/ts_backend/tensor_aten_ops.cpp#L51). This `copy_`is used in the `PatchEmbeddingBlock` class to instantiate the positional embedding. I propose a small fix to overcome this problem as well as test cases to ensure that positional embedding behaves correctly. ### 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. - [x] 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…sed (Project-MONAI#7584) Fixes inconsistent alpha parameter/docs for RandGibbsNoise/RandGibbsNoised ### 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: John Zielke <j.l.zielke@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes Project-MONAI#7585 . ### Description Because the NNI test takes too much time, the previous behavior did not get caught with the dry-run mode of HPO Gen ### 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). --------- Signed-off-by: Mingxin Zheng <mingxinz@nvidia.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
Workaround for Project-MONAI#7575 ### Description - Due to the impact of Project-MONAI#7575, the operation to set the device within nnUNetV2Runner will become ineffective. This PR is intended to resolve this issue. - Add a version check for Project-MONAI#7575, will revisit after the update from pytorch team. ### 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). - [ ] 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>
Fixes # 1. ### Description Fixed typo. ### Types of changes - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [x] In-line docstrings updated. Signed-off-by: Vladimir Chernyi <57420464+scalyvladimir@users.noreply.github.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
Fixes Project-MONAI#7540 . ### Description This PR: 1. add logging file and meta file into BundleWorkflow 2. add the sequence form of meta files check for ConfigWorkflow ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Yiheng Wang <vennw@nvidia.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>
Fixes Project-MONAI#7541 ### 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). - [ ] 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: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
…ng class is not set to 0 (Project-MONAI#7602) Fixes Project-MONAI#7594 ### Description Only warn users that the ratio of a missing class is set to 0, when it wasn't already set to 0 by the user, in `generate_label_classes_crop_centers`, function being used by `RandCropByLabelClasses` transform. ### 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. - [x] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`.⚠️ See notes - [x] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`.⚠️ See notes - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. ### Notes regarding tests Some tests were failing, see details: <details> ====================================================================== ERROR: test_cuda_0_2_batches_1_dimensions_1_channels_2_classes_2_mixtures (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 288, in test_cuda gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/networks/layers/gmm.py", line 44, in __init__ self.compiled_extension = load_module( File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_1_2_1_Linux_3_10_12_22_12_1' ====================================================================== ERROR: test_cuda_1_1_batches_1_dimensions_5_channels_2_classes_1_mixtures (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 288, in test_cuda gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/networks/layers/gmm.py", line 44, in __init__ self.compiled_extension = load_module( File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_5_2_1_Linux_3_10_12_22_12_1' ====================================================================== ERROR: test_cuda_2_1_batches_2_dimensions_2_channels_4_classes_4_mixtures (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 288, in test_cuda gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/networks/layers/gmm.py", line 44, in __init__ self.compiled_extension = load_module( File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_2_4_1_Linux_3_10_12_22_12_1' ====================================================================== ERROR: test_cuda_3_1_batches_3_dimensions_1_channels_2_classes_1_mixtures (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 288, in test_cuda gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/networks/layers/gmm.py", line 44, in __init__ self.compiled_extension = load_module( File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_1_2_1_Linux_3_10_12_22_12_1_v1' ====================================================================== ERROR: test_load (tests.test_gmm.GMMTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2096, in _run_ninja_build subprocess.run( File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/tests/test_gmm.py", line 311, in test_load load_module("gmm", {"CHANNEL_COUNT": 2, "MIXTURE_COUNT": 2, "MIXTURE_SIZE": 3}, verbose_build=True) File "/home/szabolcslorincz/MONAI/monai/_extensions/loader.py", line 89, in load_module module = load( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1306, in load return _jit_compile( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1710, in _jit_compile _write_ninja_file_and_build_library( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 1823, in _write_ninja_file_and_build_library _run_ninja_build( File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 2112, in _run_ninja_build raise RuntimeError(message) from e RuntimeError: Error building extension 'gmm_2_2_3_Linux_3_10_12_22_12_1' ====================================================================== ERROR: test_spacing_35 (tests.test_spacing.TestSpacingCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_spacing.py", line 289, in test_spacing res: MetaTensor = tr(**call_param) # type: ignore File "/home/szabolcslorincz/MONAI/monai/transforms/spatial/array.py", line 525, in __call__ data_array = self.sp_resample( File "/home/szabolcslorincz/MONAI/monai/transforms/spatial/array.py", line 223, in __call__ return spatial_resample( File "/home/szabolcslorincz/MONAI/monai/transforms/spatial/functional.py", line 178, in spatial_resample img = affine_xform(img.unsqueeze(0), theta=xform.to(img), spatial_size=spatial_size).squeeze(0) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1511, in _wrapped_call_impl return self._call_impl(*args, **kwargs) File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1520, in _call_impl return forward_call(*args, **kwargs) File "/home/szabolcslorincz/MONAI/monai/networks/layers/spatial_transforms.py", line 584, in forward grid = nn.functional.affine_grid(theta=theta[:, :sr], size=list(dst_size), align_corners=self.align_corners) File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/nn/functional.py", line 4418, in affine_grid return torch.affine_grid_generator(theta, size, align_corners) torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 840.00 MiB. GPU 0 has a total capacity of 8.00 GiB of which 0 bytes is free. Including non-PyTorch memory, this process has 17179869184.00 GiB memory in use. Of the allocated memory 6.47 GiB is allocated by PyTorch, and 156.63 MiB is reserved by PyTorch but unallocated. If reserved but unallocated memory is large try setting PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True to avoid fragmentation. See documentation for Memory Management (https://pytorch.org/docs/stable/notes/cuda.html#environment-variables) ====================================================================== FAIL: test_seg_res_net_1_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 108, in test_seg_res_net onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 233543 / 1451520 (16.1%) Greatest absolute difference: 0.0014852285385131836 at index (0, 19, 12, 13, 22) (up to 0.0001 allowed) Greatest relative difference: 589.0405883789062 at index (0, 32, 21, 16, 15) (up to 0.001 allowed) ====================================================================== FAIL: test_unet_4_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 57, in test_unet onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 6705 / 49152 (13.6%) Greatest absolute difference: 0.0015408992767333984 at index (11, 0, 21, 27) (up to 0.0001 allowed) Greatest relative difference: 51.80112838745117 at index (14, 0, 25, 19) (up to 0.001 allowed) ====================================================================== FAIL: test_unet_5_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 57, in test_unet onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 6218 / 49152 (12.7%) Greatest absolute difference: 0.0015670061111450195 at index (2, 0, 23, 14) (up to 0.0001 allowed) Greatest relative difference: 7.987473964691162 at index (8, 0, 27, 8) (up to 0.001 allowed) ====================================================================== FAIL: test_unet_6_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 57, in test_unet onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 6743 / 49152 (13.7%) Greatest absolute difference: 0.0015552043914794922 at index (1, 1, 9, 11) (up to 0.0001 allowed) Greatest relative difference: 2.0317020416259766 at index (11, 0, 19, 21) (up to 0.001 allowed) ====================================================================== FAIL: test_unet_7_cuda (tests.test_convert_to_onnx.TestConvertToOnnx) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_convert_to_onnx.py", line 57, in test_unet onnx_model = convert_to_onnx( File "/home/szabolcslorincz/MONAI/monai/networks/utils.py", line 709, in convert_to_onnx assert_fn(r1.cpu(), convert_to_tensor(r2, dtype=r1.dtype), rtol=rtol, atol=atol) # type: ignore File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1520, in assert_close raise error_metas[0].to_error(msg) AssertionError: Tensor-likes are not close! Mismatched elements: 6823 / 49152 (13.9%) Greatest absolute difference: 0.0018431544303894043 at index (10, 0, 9, 19) (up to 0.0001 allowed) Greatest relative difference: 4.297887325286865 at index (13, 0, 12, 13) (up to 0.001 allowed) ====================================================================== FAIL: test_shape_2 (tests.test_multi_scale.TestMultiScale) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/parameterized/parameterized.py", line 620, in standalone_func return func(*(a + p.args), **p.kwargs, **kw) File "/home/szabolcslorincz/MONAI/tests/test_multi_scale.py", line 59, in test_shape np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val, rtol=1e-5) File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/numpy/testing/_private/utils.py", line 1504, in assert_allclose assert_array_compare(compare, actual, desired, err_msg=str(err_msg), File "/usr/lib/python3.10/contextlib.py", line 79, in inner return func(*args, **kwds) File "/home/szabolcslorincz/MONAI/venv/lib/python3.10/site-packages/numpy/testing/_private/utils.py", line 797, in assert_array_compare raise AssertionError(msg) AssertionError: Not equal to tolerance rtol=1e-05, atol=0 Mismatched elements: 1 / 1 (100%) Max absolute difference: 0. Max relative difference: 0. x: array(0.715212, dtype=float32) y: array(0.715228) ---------------------------------------------------------------------- Ran 14392 tests in 2252.916s FAILED (failures=6, errors=6, skipped=450) --------- Signed-off-by: Szabolcs Botond Lorincz Molnar <szabolcs.lorincz@mvision.ai> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
### 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). - [ ] 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: Nic Ma <nma@nvidia.com>
…Project-MONAI#7605) Fixes Project-MONAI#7564 . ### Description As discussed, a small simplification for the creation of sincos positional encoding where we don't need to use the `torch.no_grad()` context or copy the tensor with `copy_` from torch which doesn't preserve the `requires_grad` attribute here. The changes are simple and are linked to the corresponding comment Project-MONAI#7564, the output is already in float32 so it doesn't seem particularly necessary to apply the conversion previously done. ### 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). - [ ] 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: Lucas Robinet <robinet.lucas@iuct-oncopole.fr> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
…ciated tests (Project-MONAI#7587) ### Description This PR aims to clarify and harmonise the code for the DiceLoss variants in the `monai/losses/dice.py` file. With the `to_onehot_y` `softmax` and `sigmoid` arguments, I didn't necessarily understand the ValueError that occurred when I passed a target of size NH[WD]. I had a bit of trouble reading the documentation and understanding it. I thought that they had to be the same shape as they are displayed, unlike the number of dimensions in the input, so I added that. Besides, in the documentation is written: ```python """ raises: ValueError: When number of channels for target is neither 1 nor the same as input. """ ``` Trying to reproduce this, we give an input with a number of channels $N$ and target a number of channels of $M$, with $M \neq N$ and $M > 1$. ```python loss = DiceCELoss() input = torch.rand(1, 4, 3, 3) target = torch.randn(1, 2, 3, 3) loss(input, target) >: AssertionError: ground truth has different shape (torch.Size([1, 2, 3, 3])) from input (torch.Size([1, 4, 3, 3])) ``` This error in the Dice is an `AssertionError` and not a `ValueError` as expected and the explanation can be confusing and doesn't give a clear idea of the error here. The classes concerned and harmonised are `DiceFocalLoss`, `DiceCELoss` and `GeneralizedDiceFocalLoss` with the addition of tests that behave correctly and handle this harmonisation. Also, feel free to modify or make suggestions regarding the changes made in the docstring to make them more understandable (in my opinion, but other readers and users will probably have a different view). ### 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. - [ ] 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 <luca.robinet@gmail.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>
Fixes Project-MONAI#7623 ### 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). - [ ] 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>
Fixes Project-MONAI#7601 . ### Description Support not save artifacts. ### 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). - [ ] 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: binliu <binliu@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes [tutorial Project-MONAI#1689](Project-MONAI/tutorials#1689) ### Description Uninstall opencv included in base image. ### 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). - [ ] 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>
Fixes Project-MONAI#7628 . ### Description A few sentences describing the changes proposed in this pull request. ### 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). - [ ] 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: Mingxin <mingxinz@nvidia.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
- Remove source code of numcodecs. - Add check for only build from source when arm architecture. - Removed the hardcoding of “python3.10”. ### 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). - [ ] 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>
Fixes Project-MONAI/model-zoo#568. ### Description Remove memory_pool_limit in trt config ### 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). - [ ] 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>
Fixes Project-MONAI#7658. ### Description set mlflow>=1.28.0,<=2.11.3 mlflow/mlflow#11740 ### 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). - [ ] 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: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
### Description This PR fixed the three issues within the test code that could cause problems during CICD. Three issues: tests/test_pad_collation.py line 120: supposed to be assertEqual, but not assertTure? or it will always be true. tests/test_to_numpy.py line 74: Same as above. tests/test_auto3dseg.py line 370: typo? two same asserts next to each other. tests/test_compose.py line 719, 725, 727: Should be assertEqual instead of assertTrue ### 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). - [ ] 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: Han Wang <freddie.wanah@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
### Description Some test cases use try/except command, instead of catch exceptions with assertRaise. This will cause extra execution time according to the experimental tests. ### 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). - [ ] 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: Han Wang <freddie.wanah@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Fixes Project-MONAI#7567 . ### Description MedicalNetPerceptualSimilarity: Add multi-channel support for 3Dvolumes. The current version of the code in the dev branch already largely supports that besides the following: medicalnet_* require inputs to have a single channel. This PR passes the multi-channel volume channel-wise to the networks and concatenates the resulting feature vectors. The existing code takes care of averaging over channels and spatially. ### 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Fabian Klopfer <fabian.klopfer@ieee.org> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Workaround for Project-MONAI#7690 ### Description Updated with flake8-bugbear, causing the B909 error. A workaround fix was made for the flake8-bugbear version because the 24.4.21 update contained some false positives. Fore more information, see PyCQA/flake8-bugbear#467 ### 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). - [ ] 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>
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This will get |
Fixes Project-MONAI#7692 ### Description Fix AttributeError in 'PerceptualLoss' ### 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). - [ ] 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>
…NAI#7675) Fixes Project-MONAI#7660 `indices_` may not always be a shallow copy for F-order input as it constantly converts to C-order https://github.com/Project-MONAI/MONAI/blob/ffd4454b576abd4eaae30b364f41c213e30dca4c/monai/transforms/utils.py#L2209 https://github.com/Project-MONAI/MONAI/blob/ffd4454b576abd4eaae30b364f41c213e30dca4c/monai/utils/type_conversion.py#L262 ### 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). - [ ] 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: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Hi @ericspod, I updated the fork. Also I create another PR directly merge origin/dev to origin/geomtric but there is a warning that "This branch is out-of-date with the base branch". Maybe let's merge this one first? |
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@KumoLiu I think we can close this, yes? |
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.