merge master#339
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Nic-Ma merged 284 commits intoNic-Ma:enhance-LrScheduleHandlerfrom Jan 4, 2022
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Signed-off-by: Behrooz <[email protected]>
* update multimodal doc and model names (Transchex) Signed-off-by: ahatamizadeh <[email protected]>
* remove deprecated Signed-off-by: Wenqi Li <[email protected]> * min-test list Signed-off-by: Wenqi Li <[email protected]> * preserves tests from tests/test_handler_transform_inverter.py Signed-off-by: Wenqi Li <[email protected]>
* enhance nightly test Signed-off-by: Wenqi Li <[email protected]> * print after the test for information Signed-off-by: Wenqi Li <[email protected]>
* dimension check for pretrained model weights This PR implements a dimension check, before trying to load pre-trained model weights. Signed-off-by: neuronflow <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Signed-off-by: neuronflow <[email protected]> * multi line split error Signed-off-by: neuronflow <[email protected]> Co-authored-by: monai-bot <[email protected]>
…tatement (#2996) * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement * Remove unnecessary lambda expression (#2997) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * type fixes Signed-off-by: Wenqi Li <[email protected]> * remove repeated init Signed-off-by: Wenqi Li <[email protected]> * fixes import, unused vars Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] add copy option Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance 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]>
* test 1.9.1 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 1f27a63. Signed-off-by: Wenqi Li <[email protected]>
* fixes cucim compatibility Signed-off-by: Wenqi Li <[email protected]> * simplified import Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] update highlights Signed-off-by: Nic Ma <[email protected]>
* release note v0.7 Signed-off-by: Wenqi Li <[email protected]> * adds whatsnew 07 Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] update README Signed-off-by: Nic Ma <[email protected]> * [DLMED] update what's new Signed-off-by: Nic Ma <[email protected]> * [DLMED] use whatsnew link Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add more doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] edit change log Signed-off-by: Nic Ma <[email protected]> * [DLMED] add command to get transform backend Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance the doc Signed-off-by: Nic Ma <[email protected]>
…dGaussianSharpen` (#2971) Torch `GaussianSmooth`, `RandGaussianSmooth`, `GaussianSharpen`, `RandGaussianSharpen`
* apply pyupgrade Signed-off-by: Jirka <[email protected]> * exclude monai/_version.py Signed-off-by: Jirka <[email protected]>
* enhance the release version string check Signed-off-by: GitHub <[email protected]> * update the releasing steps Signed-off-by: GitHub <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* [DLMED] update ignite 0.4.6 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <[email protected]>
* print dtype along with type Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
…SpikeNoise (#2974) GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpaceSpikeNoise
…std (#3044) Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* torch fgbgtoindices Signed-off-by: Wenqi Li <[email protected]> * unravel indices Signed-off-by: Wenqi Li <[email protected]> * simplified Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* [DLMED] fix spacing dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix dtype Signed-off-by: Nic Ma <[email protected]>
create example transform images
* [DLMED] add missing images Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix 3471 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <[email protected]>
* make bending energy loss invariant to resolution fixes #3485 Signed-off-by: Ebrahim Ebrahim <[email protected]> * set BendingEnergyLoss default normalize to False Maybe it's more important that the default behavior match usage of the term "bending energy" elsewhere, rather than that it be the most convenient behavior. Signed-off-by: Ebrahim Ebrahim <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] correct kwargs Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix grammar Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add SavitzkyGolaySmoothd 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: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Adding Torchscript utility functions Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Adding Torchscript utility functions Signed-off-by: Eric Kerfoot <[email protected]> * Added test for extra files Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* [DLMED] change to utility transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance args Signed-off-by: Nic Ma <[email protected]>
* adds missing item Signed-off-by: Wenqi Li <[email protected]> * update the contributing guide Signed-off-by: Wenqi Li <[email protected]> * update copyright headers Signed-off-by: Wenqi Li <[email protected]>
* util to check the licence info Signed-off-by: Wenqi Li <[email protected]> * update flags Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
… APIs (#3526) * [DLMED] clarify old APIs Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* [DLMED] update to 21.12 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add PyTorch 1.9 test Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add missing args Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update progress arg Signed-off-by: Nic Ma <[email protected]>
* [DLMED] fix oneof Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update index Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * Revert "[DLMED] update according to comments" This reverts commit c6c3a35. Signed-off-by: Nic Ma <[email protected]> * Revert "[DLMED] update index" This reverts commit 649a7c5. Signed-off-by: Nic Ma <[email protected]>
* drop py36 support Signed-off-by: Wenqi Li <[email protected]> * drop 20.09 test because of python min version 3.6 Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * error->warning, revise copyright Signed-off-by: Wenqi Li <[email protected]>
* has cupy check Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* adds min. memory testing utils Signed-off-by: Wenqi Li <[email protected]> * include valueerror for robust outcome Signed-off-by: Wenqi Li <[email protected]> * ensure float Signed-off-by: Wenqi Li <[email protected]> * msg improvements Signed-off-by: Wenqi Li <[email protected]> * update threshold Signed-off-by: Wenqi Li <[email protected]> * remove ref Signed-off-by: Wenqi Li <[email protected]> * separate disttests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] remove warning Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* Adding smooth deform transform Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Docs update Signed-off-by: Eric Kerfoot <[email protected]> * Type fixing Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Fix for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Adding example images, random field sized reduced to (10,10,10) Signed-off-by: Eric Kerfoot <[email protected]> * Changed backend Signed-off-by: Eric Kerfoot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Tweak Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]>
* runtest.sh defaults to no build/install Signed-off-by: Wenqi Li <[email protected]> * following test case conventions for multiprocessing - adding `_dist` to multiprocessing test cases - decouple multiprocessing LMDB tests from `test_lmdbdataset` Signed-off-by: Wenqi Li <[email protected]> * exclude lmdbdataset tests in min_tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
…#3558) Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] update dataset summary Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance data type Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
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Fixes # .
Description
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.