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* add dummy filter Signed-off-by: Holger Roth <hroth@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * adds docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * rename filter example Signed-off-by: Holger Roth <hroth@nvidia.com> * add license header Signed-off-by: Holger Roth <hroth@nvidia.com> Signed-off-by: Holger Roth <hroth@nvidia.com>
* fixes 4907 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes test cases Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] enhance stats Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add tests Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] fix tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] correct code folder Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] keep backward compatible Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Update swin_unetr.py fixed potential issue with discrepant data types Signed-off-by: Bardia Khosravi <bardiakhosravi95@gmail.com> Signed-off-by: Bardia Khosravi <bardiakhosravi95@gmail.com>
* video dataset Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* Replace range(len(...)) with enumerate(...)
* add a mean iou handler and the unitest. Signed-off-by: binliu <binliu@nvidia.com> * add MeanIoUHandler to documentation Signed-off-by: binliu <binliu@nvidia.com> * add test_handler_mean_iou to min_tests.py Signed-off-by: binliu <binliu@nvidia.com> * change the metric name in unitest of iou from dice to iou. Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: binliu <binliu@nvidia.com>
* Improve FL ExchangeObject printing and summary Signed-off-by: Holger Roth <hroth@nvidia.com> * add type annotation Signed-off-by: Holger Roth <hroth@nvidia.com> * testing summary string Signed-off-by: Wenqi Li <wenqil@nvidia.com> * typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Holger Roth <hroth@nvidia.com>
* provide init channel dim Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * provide a default for get Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Improve data type conversion performance Signed-off-by: Gigon Bae <gbae@nvidia.com> * Update monai/utils/type_conversion.py Co-authored-by: Gregory Lee <grlee77@gmail.com> Signed-off-by: Gigon Bae <gbae@nvidia.com> Co-authored-by: Gregory Lee <grlee77@gmail.com> Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com>
enhance subprocess tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* optional grid for base class api consistency Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * docs update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * initial pytorch tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update min tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update dtype Signed-off-by: Wenqi Li <wenqil@nvidia.com> * tested compiled prefer numpy backend for integer interp mode Signed-off-by: Wenqi Li <wenqil@nvidia.com> * extend type annotations Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes a typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Adding __str__ to MetaTensor Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Adding docstrings Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Smooth field meshgrid fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
* fixes spatial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4938 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip if no scipy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip if no cupy Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Add num_worker for cucim read region Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittest for multithread cucim Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstring Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
* Minor fix for workflows Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Minor fix for workflows Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Minor fix for workflows Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
monai env vars
* adds new keyword Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4962 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4964 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Fix For RandSmoothDeform Component Order Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix For RandSmoothDeform Component Order Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
…4986) Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>
Two very minor changes to wording.
* enhance worker_init_fn Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Holger Roth <hroth@nvidia.com>
Fixes #4993 ### Status **Ready** ### 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`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com>
### Description This defines an abstract dense block class and a convolutional dense block using `Convolution` or `ResidualUnit` classes. A number of existing networks use dense blocks but have their own implementations that should be left as-is since these are reference implementations, but further definitions should use a common definition. I will have a network to submit as a bundle that uses this. ### Status **Ready** ### 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: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Fixes #5001. ### Description Raise error if no weights are converted. ### Status **Ready** ### 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: Holger Roth <hroth@nvidia.com>
Fixes #4996 . ### Description This PR enhanced the `ConfigParser` to support nested new ID. ### 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: Nic Ma <nma@nvidia.com>
### Description Post transform to remove small objects. Merge Project-MONAI/DocImages#13 when happy. ### Status **Ready** ### 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. Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Fixes #5553 ### Description Promote specified children of specified items to the level of item. ### 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. - [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: Behrooz <3968947+drbeh@users.noreply.github.com>
Fixes #5566 ### 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: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: PedroFerreiradaCosta <pedro.hpf.costa@gmail.com> Fixes #5417 . ### Description Makes SSIM loss depend on metric instead of the other way around (the loss was computing the metric). Returns contrastive sensitivity if the boolean `full` is True when calling `_compute_metric()` Adds unit test to `test_ssim_metric.py` to check if contrastive sensitivity output is working as expected. ### Types of changes - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [x] New tests added to cover the changes. - [x] 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: PedroFerreiradaCosta <pedro.hpf.costa@gmail.com>
Part of #5517. ### Description When we have a list of transforms, we may want these transforms to do in random order. Add `RandomOrder` which is a subclass of `Compose` to provide the ability to apply a list of transformations in random order. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [x] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: KumoLiu <yunl@nvidia.com>
Part of #5385 . ### Description This PR added support to override the predefined configs in the experiment tracking settings. ### 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: Nic Ma <nma@nvidia.com>
simpler integration 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`. - [ ] 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: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
Fixes # . ### Description - Make the current nuclick transform tensor enabled. - Add option to use Gaussian Filter over user clicks. - Option to choose initial seed point based on distance transform instead of random - Optimize patch/boundary box creation logic for nuclei cells - The same transform should be useful to create an interactive nuclick classification model ### 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>
Signed-off-by: Ben Murray <ben.murray@gmail.com> ### Description This is part of the work towards #4855. It adds: - a lazy `apply` method - A transform-like wrapper for `apply` called `Apply` ~- `MetaMatrix` and related functionality to represent abstracted grid and matrix transforms with metadata~ - A universal `resample` function that can be used to apply grid / matrix transforms ~- Functional spatial and croppad implementations that define but don't apply transforms~ ### 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. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Ben Murray <ben.murray@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>
…ls (#5598) Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Fixes # . Throw error with description when there are no valid user click/signals ### Description Instead of torch.stack error, provide readable description when the signal is not valid, and no valid bounding boxes could be created based on user click points. 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: Sachidanand Alle <sachidanand.alle@gmail.com>
Fixes #5333 . ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Dženan Zukić <dzenan.zukic@kitware.com> Co-authored-by: Mingxin Zheng <mingxinz@nvidia.com>
Making Algo base to have more generic inputs. Signed-off-by: myron <amyronenko@nvidia.com>
Fixes #5596 Fixes #5088 ### Description simplify the conda env ### 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: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #5611 ### Description skip the padding to make smaller memory footprint when the patch size is 0 or None for a particular dimension ### 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: Wenqi Li <wenqil@nvidia.com>
adds CheckLabelShaped transform under monai.apps.auto3dseg: - to check if image shape and label shape are the same. Currently, we usually don't check for it, which results in potentially a non-descriptive crash later, when computing loss or metric. - to correct label shape if it is very similar to image shape. Unfortunately some datasets, such as Hecktor22, has some labels (masks) with a slightly different shapes (difference in only 1 voxel). And because of that a user will have to either re-save the whole dataset, or account for it during the training loop (which is inconvenient). this utility auto corrects it. We also already have this auto-correction in DataAnalyzer, and with this transform, DataAnalyzer logic is simplified. Signed-off-by: myron <amyronenko@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
Fixes #5573 When using CacheDataset , and DataLoader num_workers==0, we convert ProxyList to List in disable_share_memory_cache() but if we're already inside DDP (DistributedDataParallel), we should not do such conversion, as it will crash. we should continue using ProxyList() ### 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: myron <amyronenko@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>
Signed-off-by: binliu <binliu@nvidia.com> Fixes #5385 . ### Description This PR is about to enhance the mlflow handler in monai to track more details in the experiment. Here are a few enhancements that needs to be added through this PR. - API for users to add experiment/run name in MLFlow - API for users to log customized params for each run - Methods to log result images - Methods to log optimizer params - (optional) additional metric_names as a user argument to override the default engine.state.metrics to instruct MLFlow about metrics to log After adding these enhancements, some tests listed below should be excuted. - Make sure this handler works in multi-gpu environment - Make sure this handler works in all existed bundles ### 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. - [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. - [x] API for users to add experiment/run name in MLFlow - [x] API for users to log customized params for each run - [x] Methods to log result images - [x] Methods to log optimizer params - [x] Make sure this handler works in multi-gpu environment - [ ] Make sure this handler works in all existed bundles Signed-off-by: binliu <binliu@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>
Fixes #5613 ### Description - `runtime_cache=False`: the default v1.0.1 behaviour - `runtime_cache=True` or `"thread"`: single process, for caching cuda tensors - `runtime_cache="process"`: single process workflow + multiprocess dataloader - `runtime_cache=` user-provided object, could be used to pass a container shared among processes I feel in this way the user can determine what to use instead of guessing and providing an automated solution... let me know what you think @myron @Nic-Ma, I'm fine if this is eventually merged or not merged ### 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`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: function2 <function2-llx@outlook.com> Fixes #5634. ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [ ] Non-breaking change (fix or new feature that would not break existing functionality). - [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`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: function2 <function2-llx@outlook.com>
Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com> part of #5637 ### 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: Wenqi Li <wenqil@nvidia.com>
Fixes #5605. ### Description Fix missing type annotations so `./runtests.sh --mypy` now finds 0 warnings. ### 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: Felix Schnabel <f.schnabel@tum.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
AutoRunner class improvements - adds auto-runner option **templates_path_or_url** to optionally accept a local templates folder location. The default (None) is the same: to download the release zip e.g. AutoRunner(templates_path_or_url='/my/local/algorithm_templates') - enhances **algos** input option to define a subset of algorithm names to run (e.g. AutoRunner(algos=['segresnet','dints']) ### 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`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: myron <amyronenko@nvidia.com>
Fixes #5616 Fixes #5617 ### 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] 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: Behrooz <3968947+drbeh@users.noreply.github.com>
### Description
We've had feedback that with MetaTensors, `x.__repr__` is overly
verbose. This is used frequently when debugging with an IDE for example.
The problem is accentuated with e.g., `x.max()`. Here, a single value is
hidden by over 50 lines of text.
Example:
```python
import monai.transforms as mt
loader = mt.LoadImage(image_only=True)
x = loader(x)
print(x.max().__repr__())
```
<details>
<summary>Output</summary>
```
tensor(2906.1714)
Metadata
sizeof_hdr: 348
extents: 0
session_error: 0
dim_info: 0
dim: [ 3 161 338 61 1 1 1 1]
intent_p1: 0.0
intent_p2: 0.0
intent_p3: 0.0
intent_code: 0
datatype: 16
bitpix: 32
slice_start: 0
pixdim: [1. 1. 1. 2.000296 0. 0. 0. 0. ]
vox_offset: 0.0
scl_slope: nan
scl_inter: nan
slice_end: 0
slice_code: 0
xyzt_units: 2
cal_max: 0.0
cal_min: 0.0
slice_duration: 0.0
toffset: 0.0
glmax: 0
glmin: 0
qform_code: 1
sform_code: 0
quatern_b: -0.4889228641986847
quatern_c: 0.5108369588851929
quatern_d: -0.4703003466129303
qoffset_x: -77.69402313232422
qoffset_y: 218.0015411376953
qoffset_z: -808.5780029296875
srow_x: [0. 0. 0. 0.]
srow_y: [0. 0. 0. 0.]
srow_z: [0. 0. 0. 0.]
affine: tensor([[ 3.5726e-02, -2.8526e-03, 1.9990e+00, -7.7694e+01],
[-9.9619e-01, 7.9544e-02, 7.1691e-02, 2.1800e+02],
[-7.9595e-02, -9.9683e-01, 1.3722e-07, -8.0858e+02],
[ 0.0000e+00, 0.0000e+00, 0.0000e+00, 1.0000e+00]],
dtype=torch.float64)
original_affine: [[ 3.57263708e-02 -2.85262855e-03 1.99901100e+00 -7.76940231e+01]
[-9.96186848e-01 7.95440337e-02 7.16907652e-02 2.18001541e+02]
[-7.95951681e-02 -9.96827272e-01 1.37223043e-07 -8.08578003e+02]
[ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]]
as_closest_canonical: False
spatial_shape: [161 338 61]
space: RAS
original_channel_dim: no_channel
filename_or_obj: /Users/rich/Downloads/sub-verse004_ct.nii.gz
Applied operations
[]
Is batch?: False
```
</details>
I'm proposing that the `__repr__` and `__str__` match that of
`torch.Tensor`. If users want meta data they can use `x.print_verbose()`
or `print(x.meta)`.
### 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] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Follow up of issue #5530 #5528 and (closed) PR #5547 ### Description Add test case for a binary classification task in `test_vis_gradcam` ### 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. - [x] In-line docstrings updated. Signed-off-by: Geevarghese George <thatgeeman@users.noreply.github.com>
Fixes #5649 . ### Description Add the `auto_close` parameter to mlflow_handler so that it can close the mlflow run according to given value. Update the default handler parameter, so that trainer and evaluator could have `True` value on `auto_close`. ### 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: binliu <binliu@nvidia.com>
The line `optional_import("cv2")` causes the security light of my macOS
to light up in green, even for the lowest level command e.g., `import
monai`. I was worried I had a virus until I realised what was causing
it! To avoid worrying other users, I suggest we only import when a user
is using the `VideoDataset`.
### 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: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
Status
Ready/Work in progress/Hold
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.