merge master#360
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Nic-Ma merged 335 commits intoNic-Ma:3482-add-configcomponentfrom Jan 26, 2022
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Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance random computation Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
…3079) * Torch `CropForeground`, `HistogramNormalize`, `RandHistogramShift` Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add MLFlowHandler Signed-off-by: Nic Ma <[email protected]> * [DLMED] add optional import Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc format Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
…rop` (#3078) Torch `AddCoordinateChannels`, `ExtremePointsChannel`, `RandWeightedCrop`
* [DLMED] fix wrong doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* fixes 33097 Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] update intensity transforms Signed-off-by: Nic Ma <[email protected]>
* [DLMED] update all the other transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CPU test Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* adds new tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes the tests Signed-off-by: Wenqi Li <[email protected]> * split yml Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>
* feat: refactor seg-net for easier use Signed-off-by: BenTenmann <[email protected]>
* ignores E402 Module level import not at top of file Signed-off-by: Wenqi Li <[email protected]> * exlcude Signed-off-by: Wenqi Li <[email protected]> * ignore Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] add state attr Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix integration test Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add integration test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more random test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
…gLabel (#3129) Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* add alias tests Signed-off-by: Wenqi Li <[email protected]> * monai.losses.dice Signed-off-by: Wenqi Li <[email protected]> * monai.utils.deprecated Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.senet Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.dynunet Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.unet Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.densenet Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.ahnet Signed-off-by: Wenqi Li <[email protected]> * only check for the existing modules Signed-off-by: Wenqi Li <[email protected]> * fixes docs Signed-off-by: Wenqi Li <[email protected]>
* upgrade torch image to 2109 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * more time for fast training Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit a5b4447. Signed-off-by: Wenqi Li <[email protected]>
* add griddistortion Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix pre-commit ci black error Signed-off-by: Yiheng Wang <[email protected]> * add unittest Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* [DLMED] add metric example Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* update rand grid distortion Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes formatting and errors Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add Tensor to CropForegroundd transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance data conversion Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests and fix convert tensor issue Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
…tatement (#3147) * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement * black --skip-magic-trailing-comma Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]>
* update versioning Signed-off-by: Wenqi Li <[email protected]> * build docker Signed-off-by: Wenqi Li <[email protected]> * install docker Signed-off-by: Wenqi Li <[email protected]> * remove selfhosted Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * ubuntu cpu tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * test docker options Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * exclude open slide tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * temp checkout Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 error Signed-off-by: Wenqi Li <[email protected]> * skip weights downloading when http error out Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add missing doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance correct centers Signed-off-by: Nic Ma <[email protected]>
* option to occlude all channels simultaneously
* removed duplicated Signed-off-by: Wenqi Li <[email protected]> * update gitignore to ignore readthedocs autobuild Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* ignore some flake8 errors Signed-off-by: Wenqi Li <[email protected]> * fixes #3660 2003->2106 Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add default values Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
install fresh from conda or install dependencies using environment-dev.yml Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* DictPostFixes Signed-off-by: Richard Brown <[email protected]> * use fn Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* update folder layout Signed-off-by: Wenqi Li <[email protected]> * revise create_file_basename util Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update based on comments Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* [DLMED] change to warning Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more error message Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify the messages Signed-off-by: Nic Ma <[email protected]>
* [DLMED] fix channel_dim issue in ITKReader, add it in NibabelReader Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] restore LoadImaged test Signed-off-by: Nic Ma <[email protected]>
allow test image creation to save to different folders and with different file names
* support stack of images with channels Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
… is 0 (#3690) * [DLMED] check 0 length Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dist tests Signed-off-by: Nic Ma <[email protected]>
* remove tensor-array convertions Signed-off-by: Wenqi Li <[email protected]> * update backend Signed-off-by: Wenqi Li <[email protected]> * update tests, remove meshgrid warnings Signed-off-by: Wenqi Li <[email protected]> * fixes typing issue Signed-off-by: Wenqi Li <[email protected]> * fixes import Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] update ignite to 0.4.8 Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix format issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* add dev mode collate Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* add benchmarking warp against python itk Signed-off-by: kate-sann5100 <[email protected]>
* fix differentiability of generalized Dice loss Signed-off-by: Josafat-Mattias Burmeister <[email protected]> * fix weight clamping for the case that is True Signed-off-by: Josafat-Mattias Burmeister <[email protected]> * add test case for batch mode Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
… comma (#3711) * [DLMED] add support to config delimiter Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo 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]>
* fixes grid_sample, interpolate URLs Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
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Fixes # .
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A few sentences describing the changes proposed in this pull request.
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./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.