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| Revision | Author | Date | Message | Commit Date |
|---|---|---|---|---|
| 4105299 | Mingxin Zheng | 06 September 2022, 14:57:58 UTC | [Ready for review] Auto3D functional fixes in the BundleGen module (#5087) ### Description Part of the requested improvements #5085 Planned fixes - [x] fold number is not being updated in generate() - [x] put absolute paths in the bundle configs - [x] break the auto-generated auto_config into multiple files. ### Status WIP ### 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: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> | 06 September 2022, 14:57:58 UTC |
| 8c4127b | Eric Kerfoot | 06 September 2022, 13:49:21 UTC | Slight Fix For Type Conversion (#5091) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> ### Description Using `view` to avoid copying doesn't actually work as intended in the type conversion to use `astype`. ### 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: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 06 September 2022, 13:49:21 UTC |
| 7fc5cf8 | Eric Kerfoot | 06 September 2022, 11:58:45 UTC | Fix for Numpy Unsigned Array Conversion (#5082) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> ### Description Numpy arrays with type uint16, uint32, and uint64 need to be converted to signed versions before conversion to Pytorch tensors. This is relevant because MR data is often stored in uint16 format. ### 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`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> | 06 September 2022, 11:58:45 UTC |
| b6016a9 | Holger Roth | 06 September 2022, 09:58:33 UTC | Use Ignite's interrupt api in MonaiAlgo (#5071) Fixes #4554. Requires latest Ignite RC. Also improves ClientAlgo docstrings formatting. ### Description A few sentences describing the changes proposed in this pull request. ### 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> Signed-off-by: Nic Ma <nma@nvidia.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@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> | 06 September 2022, 09:58:33 UTC |
| 05856ef | Wenqi Li | 05 September 2022, 23:22:26 UTC | 4909 remove deprecated args since v0.6 and v0.7 (#5055) Fixes #4909 ### 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: Wenqi Li <wenqil@nvidia.com> | 05 September 2022, 23:22:26 UTC |
| 2ed44aa | Eric Kerfoot | 05 September 2022, 15:01:10 UTC | Default prepare batch update (#5079) ### Description This allows `default_prepare_batch` to handle batches containing a single tensor or a pair of tensors. Normally if one uses array transforms you'll get an error saying the default batch function needs dictionaries so this will allow such transform sequences to be used without modification. ### Status **Work in progress** ### 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: Wenqi Li <831580+wyli@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 05 September 2022, 15:01:10 UTC |
| b1aa40d | Eric Kerfoot | 05 September 2022, 07:17:57 UTC | LogfileHandler (#5064) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> ### Description Adds a handler for directing logging information to a file once an `Engine` object starts and then doing the cleanup when it completes. ### 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. - [x] 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> | 05 September 2022, 07:17:57 UTC |
| 66df2b2 | Mingxin Zheng | 02 September 2022, 20:29:02 UTC | Ensemble 5008 (#5012) Initial draft for #5008 . ### Description Ensemble models for Auto3Dseg and external algorithm ### 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: Mingxin Zheng <mingxinz@nvidia.com> | 02 September 2022, 20:29:02 UTC |
| 52aed2b | Wenqi Li | 02 September 2022, 09:52:54 UTC | 4569 consistent rng for data loader (#5067) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #4569 ### Description with different `num_workers` the batch sampler's rng should be consistent, this PR keeps the initial random seed to achieve it. ### 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). # the previous results for num_wokers==0 might 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: Wenqi Li <wenqil@nvidia.com> | 02 September 2022, 09:52:54 UTC |
| f9e8e10 | Vishwesh | 02 September 2022, 08:02:05 UTC | Variance as a Metric for Active Learning (#4915) Signed-off-by: Vishwesh Nath <vnath@nvidia.com> ### Description Add a metric function which will return either 2D/3D spatial map depending upon input's dimensions or a single scalar value of mean/sum of variance given user's choice ### Status **Ready/Work in progress/Hold** ### 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: Vishwesh Nath <vnath@nvidia.com> Co-authored-by: Vishwesh Nath <vnath@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 02 September 2022, 08:02:05 UTC |
| 4780efe | Wenqi Li | 01 September 2022, 22:32:57 UTC | Revert "4966 fix deepedit get clicks" (#5066) Reverts Project-MONAI/MONAI#4969 cc @SachidanandAlle | 01 September 2022, 22:32:57 UTC |
| 8087dc5 | Behrooz Hashemian | 01 September 2022, 18:10:27 UTC | Sobel Gradients Operator (#5015) Fixes #4997 ### Description Implements Sobel gradients operators for a given size of kernel. ### 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> | 01 September 2022, 18:10:27 UTC |
| fdb16ac | Wenqi Li | 01 September 2022, 13:01:09 UTC | 4731 squeeze dim update meta (#5041) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes #4731 (additionally fixes https://github.com/Project-MONAI/tutorials/issues/569) ### Description squeeze dim drops a spatial axis should also update the affine ### 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: Wenqi Li <wenqil@nvidia.com> | 01 September 2022, 13:01:09 UTC |
| 63a198a | wojiazaiyugang | 01 September 2022, 12:15:29 UTC | 4966 fix deepedit get clicks (#4969) Fixes https://github.com/Project-MONAI/MONAI/issues/4966 ### 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: wojiazaiyugang <wojiazaiyugang@outlook.com> | 01 September 2022, 12:15:29 UTC |
| d3aeec3 | Nic Ma | 01 September 2022, 10:06:40 UTC | 5052 Fix bundle.load API (#5053) Fixes #5052 . ### Description This PR updated the `bundle.load` API to fix the wrong path issue. ### 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: Nic Ma <nma@nvidia.com> | 01 September 2022, 10:06:40 UTC |
| 857e92b | YunLiu | 01 September 2022, 07:00:49 UTC | update `cat_chns` arg's docstring (#5051) Signed-off-by: KumoLiu <yunl@nvidia.com> Fixes #5046 . ### Description update `cat_chns` arg's docstring in basic_unet. ### 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: KumoLiu <yunl@nvidia.com> | 01 September 2022, 07:00:49 UTC |
| a109d3a | Wenqi Li | 01 September 2022, 03:32:06 UTC | 4891 base class algo generator (#5042) ### Description part of #4891 with some misc fixes and tests. adds: - Algo class - AlgoGen class ### Status **Readyd** ### 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> Co-authored-by: Nic Ma <nma@nvidia.com> | 01 September 2022, 03:32:06 UTC |
| 3e79851 | Behrooz Hashemian | 31 August 2022, 22:18:42 UTC | Update HoVerNet model with enum keys (#5030) Fixes #5029 ### Description Add enums to define different branches of HoVerNet 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). Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 31 August 2022, 22:18:42 UTC |
| aa12381 | Behrooz Hashemian | 31 August 2022, 21:18:11 UTC | Implement TiffFile backend for WSIReader (#4972) * Implement TiffFileWSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 31 August 2022, 21:18:11 UTC |
| f49cc96 | Wenqi Li | 31 August 2022, 14:40:31 UTC | Fixes various typos and static analysis issues (#5039) ### Description mostly minor typo fixes ### Status **Ready** Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 31 August 2022, 14:40:31 UTC |
| d4f17d3 | Nic Ma | 31 August 2022, 07:58:10 UTC | 5027 Update PyTorch base docker to 22.08 (#5032) Fixes #5027 . ### Description This PR updated the PyTorch base docker to 22.08: https://catalog.ngc.nvidia.com/orgs/nvidia/containers/pytorch ### 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: Nic Ma <nma@nvidia.com> | 31 August 2022, 07:58:10 UTC |
| 6690cbe | deepsource-autofix[bot] | 30 August 2022, 22:18:15 UTC | Remove commented out code (#5035) closes https://github.com/Project-MONAI/MONAI/issues/5036 Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 30 August 2022, 22:18:15 UTC |
| 32fcd48 | wojiazaiyugang | 30 August 2022, 21:19:40 UTC | 4967 fix deepedit AddRandomGuidanceDeepEditd transform (#4970) Fixes https://github.com/Project-MONAI/MONAI/issues/4967 ### 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: wojiazaiyugang <wojiazaiyugang@outlook.com> | 30 August 2022, 21:19:40 UTC |
| 43cedc7 | André Dourson | 30 August 2022, 17:24:29 UTC | Adding transforms for signal (ECG, EEG for instance) (#4544) This change introduces the following transforms for 1d signal (example ECG , EEC, etc) "SignalRandDrop", "SignalRandScale", "SignalRandShift", "SignalResample", "SignalRandAddSine", "SignalRandAddSquarePulse", "SignalRandAddGaussianNoise", "SignalRandAddSinePartial", "SignalRandAddSquarePulsePartial", "SignalNormalize", "SignalStandardize", "SignalZeroPad", "SignalFillEmpty", "SignalRemoveFrequency", "SignalShortTimeFourier", "SignalContinousWavelet", ### 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: Andre Dourson <andre.dourson@gmail.com> | 30 August 2022, 17:24:29 UTC |
| b7974c3 | Behrooz Hashemian | 29 August 2022, 20:12:33 UTC | Compute HoVer Maps (#4945) Fixes #4932 ### Description Implements a transform to compute horizontal and vertical maps, which is used in HoVerNet pipeline. ### 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. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 29 August 2022, 20:12:33 UTC |
| d295e9e | Wenqi Li | 29 August 2022, 19:25:18 UTC | Update enums.py /typo (#5019) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Fixes a minor typo ### 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: Wenqi Li <wenqil@nvidia.com> | 29 August 2022, 19:25:18 UTC |
| da2d2d9 | Holger Roth | 27 August 2022, 07:08:43 UTC | add option to select state dict (#5017) Signed-off-by: Holger Roth <hroth@nvidia.com> Fixes #5016. ### Description If a model checkpoint contains several state dicts, the one defined by `save_dict_key` will be returned by `get_weights`; defaults to "model". If all state dicts should be returned, set `save_dict_key` to None. ### 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> | 27 August 2022, 07:08:43 UTC |
| 15ac45d | Mingxin Zheng | 26 August 2022, 20:07:55 UTC | Auto3D Task Module 1 (DataAnalyzer) for #4743 (#4765) ### Description Implemented a DataAnalyzer class to encapsulate data analysis module. As the beginning part of the auto3d/automl pipeline, the module shall find data and label from user inputs and generate a summary (dictionary) of data stats. The summary includes - file names, list, number of files; - dataset summary (basic information, image dimensions, number of classes, etc.); - individual data information (spacing, image size, number and size of the regions, etc.). The summary can be exported as a YAML file and a dictionary variable for use in Python Example Usage: ```python from monai.apps.auto3d.data_analyzer import DataAnalyzer datalist = { "testing": [{"image": "image_003.nii.gz"}], "training": [ {"fold": 0, "image": "image_001.nii.gz", "label": "label_001.nii.gz"}, {"fold": 0, "image": "image_002.nii.gz", "label": "label_002.nii.gz"}, {"fold": 1, "image": "image_001.nii.gz", "label": "label_001.nii.gz"}, {"fold": 1, "image": "image_004.nii.gz", "label": "label_004.nii.gz"}, ], } dataroot = '/datasets' # the directory where you have the image files (in this example we're using nii.gz) analyser = DataAnalyzer(datalist, dataroot) datastat = analyser.get_all_case_stats() # it will also generate a data_stats.yaml that saves the stats ``` ### Status Ready for Review Reference issue https://github.com/Project-MONAI/MONAI/issues/4743. ### 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] 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: Mingxin Zheng <mingxinz@nvidia.com> | 26 August 2022, 20:07:55 UTC |
| 8320a59 | Richard Brown | 26 August 2022, 18:50:21 UTC | remove small objects (#4998) ### Description Post transform to remove small objects. Merge https://github.com/Project-MONAI/DocImages/pull/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> | 26 August 2022, 18:50:21 UTC |
| 8278972 | Nic Ma | 26 August 2022, 17:15:06 UTC | 4996 Enhance `ConfigParser` to support nested new ID (#5003) 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> | 26 August 2022, 17:15:06 UTC |
| 1aabcbc | Holger Roth | 26 August 2022, 15:33:31 UTC | 5001 fix convert global weights (#5002) 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> | 26 August 2022, 15:33:31 UTC |
| 09993fa | Eric Kerfoot | 25 August 2022, 20:54:13 UTC | Denseblock Class (#4999) ### 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> | 25 August 2022, 20:54:13 UTC |
| d3b8072 | Wenqi Li | 25 August 2022, 12:10:09 UTC | 4993 clarify the installation issues monai/monai-weekly (#4995) 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> | 25 August 2022, 12:10:09 UTC |
| aa93129 | Holger Roth | 24 August 2022, 19:37:06 UTC | Improve MonaiAlgo (#4985) Signed-off-by: Holger Roth <hroth@nvidia.com> | 24 August 2022, 19:37:06 UTC |
| e343575 | Wenqi Li | 24 August 2022, 16:58:35 UTC | 4990 enhance worker_init_fn (#4991) * enhance worker_init_fn Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 24 August 2022, 16:58:35 UTC |
| 6c5cfd2 | Dave Mackey | 24 August 2022, 14:58:42 UTC | Update index.rst (#4989) Two very minor changes to wording. | 24 August 2022, 14:58:42 UTC |
| d9c80b9 | SACHIDANAND ALLE | 24 August 2022, 10:43:23 UTC | Support multiple click interactions per batch for DeepEdit training (#4986) Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> | 24 August 2022, 10:43:23 UTC |
| d5fc746 | Wenqi Li | 24 August 2022, 04:40:04 UTC | 4971 support of missing indexing in config parser (including minor patches for 4975, 4979) (#4977) * fixes #4975 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4971 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4979 Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 24 August 2022, 04:40:04 UTC |
| 32af32c | Eric Kerfoot | 23 August 2022, 15:41:08 UTC | Fix For RandSmoothDeform Component Order (#4973) * 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> | 23 August 2022, 15:41:08 UTC |
| f5520f3 | Wenqi Li | 23 August 2022, 08:04:00 UTC | 4958 adds description using `_desc_` in bundle config (#4963) * 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> | 23 August 2022, 08:04:00 UTC |
| eb18504 | Richard Brown | 22 August 2022, 16:49:04 UTC | monai env vars (#4952) monai env vars | 22 August 2022, 16:49:04 UTC |
| 1941283 | Eric Kerfoot | 20 August 2022, 12:08:02 UTC | Workflow Fix (#4944) * 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> | 20 August 2022, 12:08:02 UTC |
| f2bd04b | Behrooz Hashemian | 20 August 2022, 07:21:13 UTC | Multithread WSIReader for cucim backend (#4943) * 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> | 20 August 2022, 07:21:13 UTC |
| 8c15ead | Wenqi Li | 19 August 2022, 16:12:25 UTC | 4938 improve SpatialResample default values and fixes bugs (#4940) * 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> | 19 August 2022, 16:12:25 UTC |
| 4270cdf | Eric Kerfoot | 19 August 2022, 14:21:47 UTC | Meshgrid Fix For RandSmoothDeform (#4941) * 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> | 19 August 2022, 14:21:47 UTC |
| 009af55 | Wenqi Li | 19 August 2022, 10:03:13 UTC | 4856 resampling cupy backend for cuda-based spline interpolation (#4919) * 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> | 19 August 2022, 10:03:13 UTC |
| 2e2cae0 | Wenqi Li | 19 August 2022, 08:59:56 UTC | 4929 - enhance the subprocess tests to have detailed outputs (#4937) enhance subprocess tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 19 August 2022, 08:59:56 UTC |
| 99a0d91 | Gigon Bae | 19 August 2022, 06:10:49 UTC | Improve data type conversion performance in convert_to_numpy (#4934) * 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> | 19 August 2022, 06:10:49 UTC |
| abdb591 | Wenqi Li | 18 August 2022, 20:18:05 UTC | 4931- provide an initial channel dim (#4933) * 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> | 18 August 2022, 20:18:05 UTC |
| a541663 | Holger Roth | 18 August 2022, 10:27:13 UTC | Improve FL ExchangeObject printing and summary (#4925) * 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> | 18 August 2022, 10:27:13 UTC |
| 55caf94 | Wenqi Li | 18 August 2022, 07:17:17 UTC | 4920 integration test fixes (#4921) * fixes #4920 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * workaround #4917 Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 18 August 2022, 07:17:17 UTC |
| fb976d7 | binliunls | 16 August 2022, 19:15:17 UTC | 4910 Add the mean iou handler (#4916) * 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> | 16 August 2022, 19:15:17 UTC |
| 695507d | deepsource-autofix[bot] | 16 August 2022, 12:09:14 UTC | Replace range(len(...)) with enumerate(...) (#4918) * Replace range(len(...)) with enumerate(...) | 16 August 2022, 12:09:14 UTC |
| 7be203d | Richard Brown | 16 August 2022, 10:19:38 UTC | Video dataset (#4767) * video dataset Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> | 16 August 2022, 10:19:38 UTC |
| 342f4aa | Bardia Khosravi | 16 August 2022, 06:32:47 UTC | Issue with half precision training (#4913) 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> | 16 August 2022, 06:32:47 UTC |
| 4deb765 | Nic Ma | 15 August 2022, 15:27:27 UTC | 4563 Enhance the stats information of workflows (#4888) * [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> | 15 August 2022, 15:27:27 UTC |
| 535c6f1 | Wenqi Li | 14 August 2022, 23:21:04 UTC | 4907 invertd for resizing same spatial shapes (#4908) * 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> | 14 August 2022, 23:21:04 UTC |
| e0a7eff | Holger Roth | 12 August 2022, 18:13:53 UTC | Add dummy filter and base class for FL (#4899) * 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> | 12 August 2022, 18:13:53 UTC |
| d77b327 | Mohammad Zalbagi Darestani | 12 August 2022, 11:10:24 UTC | e2e-varnet (#4853) * initial commit of e2e-varnet Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial commit of e2e-varnet Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docstrings updated; model attributes changed and polished according to monai style Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added docs Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * reformatted varnet Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed varnet forward Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * major update to utils and modules to make them jit script compatible Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reformat fft_utils_t Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * made fft_utils_t compatible with pytorch==1.7.1 jit rules Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * removed redundancy between _t and normal funcs Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 12 August 2022, 11:10:24 UTC |
| e462467 | binliunls | 12 August 2022, 09:20:35 UTC | Add flexible unet for encoder-decoder structure (#4801) * Add flexible unet. A flexible U-Net implements an encoder-decoder network. This network uses U-Net as decoder and efficientnet-V1 family as encoder. The encoder type can be set by passing parameters 'efficientnet-b0, ..., efficientnet-b7, efficientnet-l2' to the initialize function. Signed-off-by: binliu <binliu@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix feature_channel name issue and input parameters issue. add a unit test file for flexible unet. Signed-off-by: binliunls <binliu@nvidia.com> * Add flexible unet to monai's documentation and modify the docstring of flexible unet Signed-off-by: binliunls <binliu@nvidia.com> * change the input size in unit test of flexible unet for CI/CD Signed-off-by: binliunls <binliu@nvidia.com> * modify the unit test file of flexible unet to make it works on CI/CD Signed-off-by: binliunls <binliu@nvidia.com> * add pretrain weight check in flexible unet unitest. Signed-off-by: binliunls <binliu@nvidia.com> * fix bias, dim, flexible_unet doc string problem, add @skip_if_quick to unitest since the download may cost a lot of time. Signed-off-by: binliunls <binliu@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix the if branch of adv_prop model to a simple equation. Signed-off-by: binliu <binliu@nvidia.com> * delete the useless legacy pool in init functin of FlexibleUNet, change the dim parameter of segmentation head to spatial_dims. Signed-off-by: binliu <binliu@nvidia.com> * modify the hints of features in unet_decoder forward function Signed-off-by: binliu <binliu@nvidia.com> * add a is_pad parameter to decided whether pad the upsampling features to fit encoder features Signed-off-by: binliu <binliu@nvidia.com> * delete the useless pool input Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: binliunls <binliu@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 12 August 2022, 09:20:35 UTC |
| 159b15f | Holger Roth | 11 August 2022, 18:20:38 UTC | 4846 send weight differences (#4876) * Add client_algo.py, monai_algo.py and exchange_object.py Signed-off-by: Warvito <ianonimato@hotmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add train test * test predict and get_weights * add test for exchange object * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix formatting * fixes style issues Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes style and doc Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes style issue Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * combine config files using one parser; use evaluate instead of predict to be closer with moani terminology * fix default return ids * allow standardized usage of bundle * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove comments * remove local path from configs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * support bundle root and use app root provided by FL system support weight differences formatting formatting test for trainer, change epoch separate train and eval parsers use monai network utils make config parsing more flexible; update tests rename variable and use network utils add docstrings [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci formatting Signed-off-by: Holger Roth <hroth@nvidia.com> | 11 August 2022, 18:20:38 UTC |
| aeebfd6 | Abhijeet Parida | 11 August 2022, 16:45:22 UTC | fix(VnetInputTransition): added custom out channels (#4895) * fix(VnetInputTransition): added custom out channels previously `out_channels` function argument was ignored in favoure of the fixed 16 * fix(vnetInputTransition): updated a error msg Signed-off-by: a-parida12 <abhijeet.parida@tum.de> * [MONAI] code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: a-parida12 <abhijeet.parida@tum.de> Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 11 August 2022, 16:45:22 UTC |
| 91cd926 | Wenqi Li | 11 August 2022, 14:16:24 UTC | 4754 default ToTensor.track_meta to None (#4874) * default totensor.track_meta to None Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments 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> | 11 August 2022, 14:16:24 UTC |
| 77a45b8 | Nic Ma | 11 August 2022, 13:06:14 UTC | 4862 Enhance docstring for the regular 2D image dims (#4892) * [DLMED] enhance docstring 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> | 11 August 2022, 13:06:14 UTC |
| b1ccd02 | Wenqi Li | 11 August 2022, 11:26:32 UTC | 233 - set up a backward compatibility policy (#4857) * set up a backward compatibility policy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments 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> | 11 August 2022, 11:26:32 UTC |
| 9858293 | Wenqi Li | 10 August 2022, 22:09:34 UTC | 4867 flexible torchvision fc models (#4873) * fixes torchvision fc models Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * flexible fc layer search Signed-off-by: Wenqi Li <wenqil@nvidia.com> * support identity layer Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update to use torchivision utils Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings 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> | 10 August 2022, 22:09:34 UTC |
| b087b11 | Eric Kerfoot | 10 August 2022, 16:05:46 UTC | Adding __str__ to MetaTensor (#4843) * 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> * [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> | 10 August 2022, 16:05:46 UTC |
| 38bc8fa | Wenqi Li | 10 August 2022, 10:12:48 UTC | 4854 fixes percentile (#4877) * fixes percentile Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 10 August 2022, 10:12:48 UTC |
| 6da25ae | Andres Diaz-Pinto | 09 August 2022, 14:55:27 UTC | Update DeepEdit transform (#4868) * Update DeepEdit transform Signed-off-by: Andres <diazandr3s@gmail.com> * Update transform arg type Signed-off-by: Andres <diazandr3s@gmail.com> * Update metatensor attribute Signed-off-by: Andres <diazandr3s@gmail.com> * Add check for compatibility Signed-off-by: Andres <diazandr3s@gmail.com> * Change to numpy array Signed-off-by: Andres <diazandr3s@gmail.com> | 09 August 2022, 14:55:27 UTC |
| 456caed | Behrooz Hashemian | 08 August 2022, 15:11:43 UTC | Deprecate Old Pathology Components (#4415) * Deprecate pathology datasets Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update min test exclusion Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update test file names for deprecated component and update prob map deprecation Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 08 August 2022, 15:11:43 UTC |
| 5d50618 | Wenqi Li | 08 August 2022, 12:16:01 UTC | 4848 849 4718 misc updates - adds device tests, docstrings (#4838) * test cuda Signed-off-by: Wenqi Li <wenqil@nvidia.com> * testing devices Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update test cases Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4848 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4718 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip tests for previous pt Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 08 August 2022, 12:16:01 UTC |
| e8d7c96 | Wenqi Li | 08 August 2022, 09:16:55 UTC | 4841 shuffle buffer for multiple epochs (#4847) fixes shuffle buffer Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 08 August 2022, 09:16:55 UTC |
| ac3d4f9 | Mohammad Zalbagi Darestani | 05 August 2022, 22:49:13 UTC | VarNetBlock (#4818) * initial varnetblock commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial varnetblock commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * still an initial commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added block utils and updated varnetblock Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed flake errors Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added docstrings; added block utils unittests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * corrected some namings in utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * did a minor fix to coil sensitivity model Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * did a minor fix to coil sensitivity model Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * did a minor fix to coil sensitivity model Signed-off-by: mersad95zd <m.zalbagi@gmail.com> | 05 August 2022, 22:49:13 UTC |
| df6979d | Walter Hugo Lopez Pinaya | 05 August 2022, 21:36:45 UTC | Add client_algo.py, monai_algo.py and exchange_object.py (#4612) (#4675) * Add client_algo.py, monai_algo.py and exchange_object.py (#4612) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add client_algo.py, monai_algo.py and exchange_object.py Signed-off-by: Warvito <ianonimato@hotmail.com> * add train test * test predict and get_weights * add test for exchange object * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix formatting * fixes style issues Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes style and doc Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes style issue Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * combine config files using one parser; use evaluate instead of predict to be closer with moani terminology * fix default return ids * allow standardized usage of bundle * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove comments * remove local path from configs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Holger Roth <hroth@nvidia.com> Co-authored-by: Holger Roth <6304754+holgerroth@users.noreply.github.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 05 August 2022, 21:36:45 UTC |
| 9901824 | Eric Kerfoot | 05 August 2022, 17:27:11 UTC | Change to EnsureChannelFirst to include behaviour from deprecated transforms (#4842) * Change to EnsureChannelFirst to include behaviour from deprecated transforms Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> | 05 August 2022, 17:27:11 UTC |
| a9095d0 | deepsource-autofix[bot] | 04 August 2022, 22:29:29 UTC | Refactor the comparison involving `not` (#4833) * Refactor the comparison involving `not` * Refactor `if` expression (#4835) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove methods with unnecessary super delegation. (#4834) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove assert statement from non-test files (#4836) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> | 04 August 2022, 22:29:29 UTC |
| 374fd25 | Eric Kerfoot | 04 August 2022, 19:56:24 UTC | Add Time Profiler Class (#4825) * Adding profiling manager Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding profiling manager Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Update tests Signed-off-by: eric <eric@bioeng471-lap.isd.kcl.ac.uk> * Fixes 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 * Fix 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 * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Darwin fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Remove multiprocessing test and update documentation 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 Co-authored-by: eric <eric@bioeng471-lap.isd.kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 04 August 2022, 19:56:24 UTC |
| 63d06b2 | YunLiu | 04 August 2022, 12:48:15 UTC | 4822 remove deprecated class call in `EnsureChannelFirst` (#4823) * add Metatenosr support in ConcatItemd Signed-off-by: KumoLiu <yunl@nvidia.com> * fix flake8 error Signed-off-by: KumoLiu <yunl@nvidia.com> * fix flake8 error Signed-off-by: KumoLiu <yunl@nvidia.com> * remove deprecated class in EnsureChannelFirst Signed-off-by: KumoLiu <yunl@nvidia.com> * fix flake8 error Signed-off-by: KumoLiu <yunl@nvidia.com> * update channel operation Signed-off-by: KumoLiu <yunl@nvidia.com> * fix flake8 error Signed-off-by: KumoLiu <yunl@nvidia.com> * fix deepgrow channel bug Signed-off-by: KumoLiu <yunl@nvidia.com> * remove unuse line Signed-off-by: KumoLiu <yunl@nvidia.com> | 04 August 2022, 12:48:15 UTC |
| f317aeb | Wenqi Li | 03 August 2022, 18:28:04 UTC | 4206 4621 4811 update c++/cuda extension installation instructions (#4826) update installation instructions Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 03 August 2022, 18:28:04 UTC |
| 63a5bac | Mohammad Zalbagi Darestani | 03 August 2022, 16:56:56 UTC | VarNet CoilSensitivityModel (#4817) * inital commit, it's a draft Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * dummy commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * add model functionality to sens model and complex_unet; polished sens model Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added docstring and unit tests; added inline comments to sens model forward Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed minor formatting issues; ready to review Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added a feature to check input and output channels of user-defined networks Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * checking input channels, leaving output channels for future Signed-off-by: mersad95zd <m.zalbagi@gmail.com> | 03 August 2022, 16:56:56 UTC |
| ef05b24 | Nic Ma | 03 August 2022, 15:58:26 UTC | 4814 Update PyTorch base docker to 22.07 (#4815) * [DLMED] update to 22.07 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix test error Signed-off-by: Nic Ma <nma@nvidia.com> * Update box_utils.py Co-authored-by: Can Zhao <69829124+Can-Zhao@users.noreply.github.com> | 03 August 2022, 15:58:26 UTC |
| d0b8bc0 | Wenqi Li | 03 August 2022, 14:24:40 UTC | 2948 - regex pruning metadata keys (#4819) * prune metadata keys Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 03 August 2022, 14:24:40 UTC |
| 9317d14 | YanxuanLiu | 03 August 2022, 07:29:58 UTC | correct blossom trigger list format (#4821) Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Co-authored-by: YanxuanLiu <yanxuanl@nvidia.com> | 03 August 2022, 07:29:58 UTC |
| 81fb7e4 | Mohammad Zalbagi Darestani | 02 August 2022, 09:36:40 UTC | 4643 varnet (#4706) * mri utils added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils with its unit test added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils updated with monai data converter Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * updated fft_util's docstring Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * apps.rst updated with fft_utils docstrings under the reconstruction module Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by adding dimension hins Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by removing redundant output type Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * test_fft_utils.py moved to the tests folder Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * created fft_utils_t, the torch-only version of fft_utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fft_utils_t updated with type ignore for mypy Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docs/source/networks.rst updated with fft_utils_t Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * manual fix for fft_utils_t output data types Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial mri_transforms added under apps/reconstruction Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * with PR1 files to avoid error Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 included Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 files finally removed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * putting test_mri_transforms under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * isort fixed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * ignore this commit, still in progress Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * created utils, array, and dictionary; still a very early-stage commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * completing transform arrays and dicts plus mri_utils and the unit tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move tests under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docs and tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fast-mri-reader initial commit; todo is the unittest Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * unittest added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * remove unncessary packages from the reader Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * manual installation of h5py added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * enum keys added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * h5py added to requirements-dev.txt Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * optional import of h5py Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed h5py dependency Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed h5py dependency again Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docstring; fixed import issue Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added h5py to relevant requirement files; updated fastmri_reader Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docs updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed os.path.basename Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial e2e-varnet commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed sensitivitymodel docstring Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * removed varnet from this PR; improved complex_unet, coil_sensitivity_model, varnetblock Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * changed BasicUnet to BasicUNet in complex_unet.py Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * removed assert; changed basic_unet import Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * complex_unet and utils updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * major update to utils and complex_unet; unittest added; minor fix in ssim_loss docstring Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor fix to unittest Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor typing fix in utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * removed inverse_complex_normalize Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed padding Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mri_utils formatted Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * add more inline comments to complex_unet Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Co-authored-by: Can Zhao <69829124+Can-Zhao@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 02 August 2022, 09:36:40 UTC |
| 3a8c421 | Wenqi Li | 01 August 2022, 14:46:13 UTC | 4769 adds a util to reset applied operations id (#4778) * set no ops id Signed-off-by: Wenqi Li <wenqil@nvidia.com> * make reset optional in datasets Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 01 August 2022, 14:46:13 UTC |
| 30d592c | Nic Ma | 01 August 2022, 13:25:34 UTC | 4791 Adapt affine arg to the Spacing transform (#4792) * [DLMED] adapt to affine Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> | 01 August 2022, 13:25:34 UTC |
| 4ae41e8 | Wenqi Li | 01 August 2022, 12:12:40 UTC | 4799 change deprecation warning category to provide more info at runtime (#4800) * fixes #4799 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * removes flake8-pyi Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update warning message Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 01 August 2022, 12:12:40 UTC |
| 288edee | 罗崚骁(LUO Lingxiao) | 29 July 2022, 15:37:02 UTC | Update patch merging with a for loop (#4793) * Update patch merging with a for loop Signed-off-by: function2 <luolx21@mails.tsinghua.edu.cn> * Make patch merging order backward compatible for 2D Signed-off-by: function2 <luolx21@mails.tsinghua.edu.cn> | 29 July 2022, 15:37:02 UTC |
| 2c89142 | Behrooz Hashemian | 29 July 2022, 14:51:12 UTC | Fix ProbMap locations (#4796) * Change from round to floor Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Explicit conversion to tuple for locs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 29 July 2022, 14:51:12 UTC |
| c1eaf42 | Wenqi Li | 29 July 2022, 06:10:55 UTC | 4789 adds a space type metadata field to metatensor (#4790) * adds meta[space] Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit test Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 29 July 2022, 06:10:55 UTC |
| 46d9026 | Wenqi Li | 28 July 2022, 12:24:36 UTC | 4779 fixes docstring (#4785) fixes docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 28 July 2022, 12:24:36 UTC |
| 5f019d7 | Wenqi Li | 28 July 2022, 11:10:17 UTC | 4772 adds test cases (#4773) * update test cases Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 28 July 2022, 11:10:17 UTC |
| a400cda | Wenqi Li | 28 July 2022, 06:51:04 UTC | 4774 dtype-percentile (#4775) fixes #4774 Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 28 July 2022, 06:51:04 UTC |
| 83ec156 | YanxuanLiu | 28 July 2022, 04:54:19 UTC | [CICD] Add YanxuanLiu as blossom trigger user (#4780) added YanxuanLiu as blossom trigger user Signed-off-by: YanxuanLiu <yanxuanl@nvidia.com> Co-authored-by: YanxuanLiu <yanxuanl@nvidia.com> | 28 July 2022, 04:54:19 UTC |
| 4831909 | Behrooz Hashemian | 27 July 2022, 15:45:13 UTC | Implement GridSplit using torch.as_strided (#4768) * Implement GridSplit using torch.as_strided Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 27 July 2022, 15:45:13 UTC |
| 31c4209 | Mohammad Zalbagi Darestani | 26 July 2022, 08:40:06 UTC | 4599 01 MRI SSIMLoss (#4713) * mri utils added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils with its unit test added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils updated with monai data converter Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * updated fft_util's docstring Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * apps.rst updated with fft_utils docstrings under the reconstruction module Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by adding dimension hins Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by removing redundant output type Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * test_fft_utils.py moved to the tests folder Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * created fft_utils_t, the torch-only version of fft_utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fft_utils_t updated with type ignore for mypy Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docs/source/networks.rst updated with fft_utils_t Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * manual fix for fft_utils_t output data types Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial mri_transforms added under apps/reconstruction Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * with PR1 files to avoid error Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 included Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 files finally removed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * putting test_mri_transforms under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * isort fixed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * ignore this commit, still in progress Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * created utils, array, and dictionary; still a very early-stage commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * completing transform arrays and dicts plus mri_utils and the unit tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move tests under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docs and tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fast-mri-reader initial commit; todo is the unittest Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * unittest added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * remove unncessary packages from the reader Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * manual installation of h5py added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * enum keys added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * h5py added to requirements-dev.txt Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * optional import of h5py Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed h5py dependency Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed h5py dependency again Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docstring; fixed import issue Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added h5py to relevant requirement files; updated fastmri_reader Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docs updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed os.path.basename Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * support for multi-channel inputs Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docstring fixed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor argument fix Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Co-authored-by: Can Zhao <69829124+Can-Zhao@users.noreply.github.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> | 26 July 2022, 08:40:06 UTC |
| 5d194ad | Wenqi Li | 26 July 2022, 06:03:53 UTC | 4632 - releasing v0.9.1 (#4762) * fixes #4761 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update v0.9.1 Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 26 July 2022, 06:03:53 UTC |
| 356d2d2 | Wenqi Li | 25 July 2022, 16:06:58 UTC | 4757 update patch merging (#4758) * update patch merging Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 25 July 2022, 16:06:58 UTC |
| 178e973 | Wenqi Li | 25 July 2022, 07:52:56 UTC | update changelog for v0.9.1 (#4744) * update changelog Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove warning msg Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update n workers for smaller testing memory usage Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 25 July 2022, 07:52:56 UTC |
| 6338ea4 | Richard Brown | 23 July 2022, 11:33:41 UTC | Permanent dataset hashes transforms (#4633) * permanent dataset hashes transforms Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * documentation Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * default to no hash Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 23 July 2022, 11:33:41 UTC |
