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* [DLMED] add EarlyStop handler Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] enhance validation handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] add set_trainer support Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more check Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] change to save patch_index in meta_dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove error import Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* Enabled partial checkpoint loading Allowing partial loading of a model via strict=False. Signed-off-by: Petru-Daniel Tudosiu <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] simplify strict arg Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* less warning msg; remove PILImage types Signed-off-by: Wenqi Li <[email protected]> * remove engine type Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * add quick py36 37 tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit deaed40. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 3e8d8f4. Signed-off-by: Wenqi Li <[email protected]> * min test exclude senet test Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit 31f40a0. Signed-off-by: Wenqi Li <[email protected]> * update get gpu id Signed-off-by: Wenqi Li <[email protected]> * update docsstrings Signed-off-by: Wenqi Li <[email protected]>
* Add ProbNMS to transforts/post/array Signed-off-by: Behrooz <[email protected]> * Implement ProbNMSDict Signed-off-by: Behrooz <[email protected]> * Update the usage and add unittests Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Correct docs Signed-off-by: Behrooz <[email protected]> * Correct test case Signed-off-by: Behrooz <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Implement garbage collector handler Signed-off-by: Behrooz <[email protected]> * Make trigger_event lower case Signed-off-by: Behrooz <[email protected]> * Add unittest for garbage collector Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Exclude from min test Signed-off-by: Behrooz <[email protected]> * Fix a typo Signed-off-by: Behrooz <[email protected]> * Fix a bug Signed-off-by: Behrooz <[email protected]>
* [DLMED] add strict_shape option Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * update test case Signed-off-by: Wenqi Li <[email protected]> * fixes test config Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] enhance decathlon datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
* adds docker tag action Signed-off-by: Wenqi Li <[email protected]> * adds tag info Signed-off-by: Wenqi Li <[email protected]> * update versioneer Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* refactor docker building Signed-off-by: Wenqi Li <[email protected]>
* update docs deps. Signed-off-by: Wenqi Li <[email protected]> * fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972 Signed-off-by: Wenqi Li <[email protected]> * Revert "fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972" This reverts commit 1407400. Signed-off-by: Wenqi Li <[email protected]>
* Update garbage collection assertion to a more reliable one Signed-off-by: Behrooz <[email protected]> * Remove print Signed-off-by: Behrooz <[email protected]>
* Working ParameterScheduler Added a new ParameterScheduler handler and the required tests. Signed-off-by: Petru-Daniel Tudosiu <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add support for addtional events Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typehints Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* fixes #1965 Signed-off-by: Wenqi Li <[email protected]> * adds docstring Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance doc-strings Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>
* adding init efficientnet support Signed-off-by: masadcv <[email protected]> * fixing flake8 and further refactoring Signed-off-by: masadcv <[email protected]> * adding unittests for efficiennet Signed-off-by: masadcv <[email protected]> * making unittests backwards compatible python<3.8 Signed-off-by: masadcv <[email protected]> * fixed kitty unittests file path Signed-off-by: masadcv <[email protected]> * adding docstrings and minor refactoring Signed-off-by: masadcv <[email protected]> * fix flake8-py3 failing test Signed-off-by: masadcv <[email protected]> * generalize drop_connect for n-dim, fix/add unittests, remove assert Signed-off-by: masadcv <[email protected]> * fix failing unittest, CC0-license image for test Signed-off-by: masadcv <[email protected]> * refactoring code for review Signed-off-by: masadcv <[email protected]> * WIP fix mypy type hint errors Signed-off-by: masadcv <[email protected]> * fix cuda test error Signed-off-by: masadcv <[email protected]> * WIP fix test errors Signed-off-by: masadcv <[email protected]> * adding non-default shape tests Signed-off-by: masadcv <[email protected]> * remove 3d case from non-default shape test Signed-off-by: masadcv <[email protected]> * refactoring and updating docs Signed-off-by: masadcv <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] add TransformInverter handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support in SegmentationSaver handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>
* changelog for 0.5.0 Signed-off-by: Wenqi Li <[email protected]> * update changelog Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add TransformInverter handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support in SegmentationSaver handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] save mode into inverse dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix ToTensor inverse issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] change the replacement logic into util function Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] update highlights for 0.5 Signed-off-by: Nic Ma <[email protected]> * [DLMED] add invert transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more highlights Signed-off-by: Nic Ma <[email protected]> * [DLMED] add checkpointloader Signed-off-by: Nic Ma <[email protected]> * downscale image Signed-off-by: Wenqi Li <[email protected]> * downscale image Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * update desc Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* update convs docstrings Signed-off-by: Wenqi Li <[email protected]> * increase tol for cuda crf Signed-off-by: Wenqi Li <[email protected]> * update requirements according to docs/requirements Signed-off-by: Wenqi Li <[email protected]> * prune image Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] metrics support a list of tensor Signed-off-by: Nic Ma <[email protected]> * update workflow test Signed-off-by: Wenqi Li <[email protected]> * [DLMED] fix engine.state.output dict copy issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add num_workers Signed-off-by: Nic Ma <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * update docstrings Signed-off-by: Wenqi Li <[email protected]> * tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
…t_transform` (#2384) * [DLMED] enhance all doc-string of handlers Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* refactoring decollate Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]> * more test cases and fixes Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes pytype error Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance crop and pad doc-strings Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add `the` Signed-off-by: Nic Ma <[email protected]> * [DLMED] add examples Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* update not nan docstring Signed-off-by: Yiheng Wang <[email protected]> * fix black error Signed-off-by: Yiheng Wang <[email protected]> * Fix indentation errors Signed-off-by: Yiheng Wang <[email protected]>
* initial gmm commit Signed-off-by: charliebudd <[email protected]>
jit Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Add blossom pre-merge pipeline Signed-off-by: Mohammad Adil <[email protected]>
* [DLMED] add min tests command Signed-off-by: Nic Ma <[email protected]> * [DLMED] update CI script Signed-off-by: Nic Ma <[email protected]>
* [DKMED] add CSV datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] add group feature Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add optional install Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add doc-strings Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add CSVDataset for non-iterable data Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add CSVIterableDataset base Signed-off-by: Nic Ma <[email protected]> * [DLMED] add CSVIterableDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] support multiple processes Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix docs-build Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] change sys.platform Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip if windows Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add col_types arg Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] test mypy fix Signed-off-by: Nic Ma <[email protected]> * [DLMED] test commit Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix np.random Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix other numpy data type errors Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* added spikes transform Signed-off-by: Yaniel Cabrera <[email protected]>
* [DLMED] add image_only and unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]>
* add json config model support Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add -1 support for pixdim Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add scale_np = scale_np[:d] Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update accortding to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove image_only in Spacing and Orientation Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: am <am>
Signed-off-by: Dong Yang <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add TorchVisionClassificationModel Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* Add parameter unpacking for transforms Signed-off-by: Sebastian Penhouet <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add copy logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>
* Add query to NGC to get matched model URL and version. Allow mmar download with latest version or a specific version. Signed-off-by: Isaac Yang <[email protected]>
no need for default orig_size stored for invertible transforms
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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 --codeformat --coverage../runtests.sh --quick.make htmlcommand in thedocs/folder.