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* 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]>
Signed-off-by: Wenqi Li <[email protected]>
* handling error Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit 60661ae. Signed-off-by: Wenqi Li <[email protected]>
* update dev version Signed-off-by: Wenqi Li <[email protected]> * typo fix Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
TTA progress bar, use torch for mode, add label meta_data
* follow up of #1992 Signed-off-by: Wenqi Li <[email protected]> * update spacing inverse Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] update TransformInverter Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix deepcopy 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]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add nearest test cases Signed-off-by: Nic Ma <[email protected]>
* adds a what's new page Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add SaliencyInferer Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance CAM logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Co-authored-by: Richard Brown <[email protected]> Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Richard Brown <[email protected]>
* [DLMED] enhance unit tests 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] add warning 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]>
* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]>
* allow slicing with SpatialCrop(d) Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: chaliebudd <[email protected]>
* fixes docstring Signed-off-by: Wenqi Li <[email protected]> * update example Signed-off-by: Wenqi Li <[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
Signed-off-by: Can Zhao <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
* [DLMED] enhance ToTensor Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
#2455) * add clara_train_covid19_3d_ct_classification and clara_train_covid19_annotation_ct_lung_1 point to pt version of covid19 lung annotation model Signed-off-by: Holger Roth <[email protected]>
* [DLMED] add pad options Signed-off-by: Nic Ma <[email protected]> * [DLMED] add to dict transforms Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
Signed-off-by: ahatamizadeh <[email protected]>
* [DLMED] update ignite to 0.4.5 Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add dynamic data list in CacheDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support to PersistentDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update_data -> set_data Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Holger Roth <[email protected]>
…grow (#2442) Signed-off-by: vnath <[email protected]>
…2315) * [WIP] 2220 Decollate batch into list of tensors after model forward (#2244) * [DLMED] add support for Activation transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] change all the array level post transforms to channel-first Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the IO, utility, post transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] update engines for list of dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the event handlers Signed-off-by: Nic Ma <[email protected]> * [DLMED] support non-batch data Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update based on the latest APIs Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix all the unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove unused import Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix integration test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix integration tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix integration tests 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 support to copy scalar Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix broken tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix unit tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] simplify CSV saver Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add copy_scalar_to_batch util Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] change to preprocessing and postprocessing Signed-off-by: Nic Ma <[email protected]> * [DLMED] change file name to postprocessing Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo in doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] add Decollated back Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to use ignite v0.4.5 metrics API Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix conflicts Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * fixes #2452 Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]>
* deprecation fixes Signed-off-by: Eric Kerfoot <[email protected]> * deprecation fixes Signed-off-by: Eric Kerfoot <[email protected]> * deprecation fixes Signed-off-by: Eric Kerfoot <[email protected]> * deprecation fixes Signed-off-by: Eric Kerfoot <[email protected]> * deprecation fixes Signed-off-by: Eric Kerfoot <[email protected]> * deprecation fixes Signed-off-by: Eric Kerfoot <[email protected]> * deprecation fixes Signed-off-by: Eric Kerfoot <[email protected]>
* enhance version compare Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * remove unused Signed-off-by: Wenqi Li <[email protected]> * remove unused vars Signed-off-by: Wenqi Li <[email protected]> * update debug info Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * non integer comparison Signed-off-by: Wenqi Li <[email protected]> * adds tests Signed-off-by: Wenqi Li <[email protected]> * no temp tests Signed-off-by: Wenqi Li <[email protected]> * update test Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* [DLMED] add deprecated decorator Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Jeff VanOss <[email protected]>
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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.