merge master #339
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merge master #339
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Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
* update multimodal doc and model names (Transchex) Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>
* remove deprecated Signed-off-by: Wenqi Li <wenqil@nvidia.com> * min-test list Signed-off-by: Wenqi Li <wenqil@nvidia.com> * preserves tests from tests/test_handler_transform_inverter.py Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* enhance nightly test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * print after the test for information Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* dimension check for pretrained model weights This PR implements a dimension check, before trying to load pre-trained model weights. Signed-off-by: neuronflow <zournyque@gmail.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: neuronflow <zournyque@gmail.com> * multi line split error Signed-off-by: neuronflow <zournyque@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
…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 <wenqil@nvidia.com> * remove repeated init Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes import, unused vars 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>
* [DLMED] add copy option Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance test Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
* test 1.9.1 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 1f27a63. Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* fixes cucim compatibility Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified import Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] update highlights Signed-off-by: Nic Ma <nma@nvidia.com>
* release note v0.7 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds whatsnew 07 Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] update README Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update what's new Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] use whatsnew link Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] add more doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] edit change log Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add command to get transform backend Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance the doc Signed-off-by: Nic Ma <nma@nvidia.com>
…dGaussianSharpen` (#2971) Torch `GaussianSmooth`, `RandGaussianSmooth`, `GaussianSharpen`, `RandGaussianSharpen`
* apply pyupgrade Signed-off-by: Jirka <jirka.borovec@seznam.cz> * exclude monai/_version.py Signed-off-by: Jirka <jirka.borovec@seznam.cz>
* enhance the release version string check Signed-off-by: GitHub <noreply@github.com> * update the releasing steps Signed-off-by: GitHub <noreply@github.com> Co-authored-by: Nic Ma <nma@nvidia.com>
* [DLMED] update ignite 0.4.6 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <nma@nvidia.com>
* print dtype along with type Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
…SpikeNoise (#2974) GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpaceSpikeNoise
…std (#3044) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* torch fgbgtoindices Signed-off-by: Wenqi Li <wenqil@nvidia.com> * unravel indices Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>
* [DLMED] fix spacing dtype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix dtype Signed-off-by: Nic Ma <nma@nvidia.com>
create example transform images
* [DLMED] add missing images Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix 3471 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <nma@nvidia.com>
* make bending energy loss invariant to resolution fixes #3485 Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com> * 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 <ebrahim.ebrahim@kitware.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] correct kwargs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix grammar Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] add SavitzkyGolaySmoothd Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Adding Torchscript utility functions 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 * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * Adding Torchscript utility functions Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Added test for extra files 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 * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Update 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 * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates 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 * Updates Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates 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> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com>
* [DLMED] change to utility transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance args Signed-off-by: Nic Ma <nma@nvidia.com>
* adds missing item Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update the contributing guide Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update copyright headers Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* util to check the licence info Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update flags Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>
… APIs (#3526) * [DLMED] clarify old APIs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] update to 21.12 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add PyTorch 1.9 test Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] add missing args Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update progress arg Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] fix oneof Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update index Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * Revert "[DLMED] update according to comments" This reverts commit c6c3a35. Signed-off-by: Nic Ma <nma@nvidia.com> * Revert "[DLMED] update index" This reverts commit 649a7c5. Signed-off-by: Nic Ma <nma@nvidia.com>
* drop py36 support Signed-off-by: Wenqi Li <wenqil@nvidia.com> * drop 20.09 test because of python min version 3.6 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * error->warning, revise copyright Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* has cupy check Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* adds min. memory testing utils Signed-off-by: Wenqi Li <wenqil@nvidia.com> * include valueerror for robust outcome Signed-off-by: Wenqi Li <wenqil@nvidia.com> * ensure float Signed-off-by: Wenqi Li <wenqil@nvidia.com> * msg improvements Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update threshold Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove ref Signed-off-by: Wenqi Li <wenqil@nvidia.com> * separate disttests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] remove warning Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
* Adding smooth deform transform Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Docs update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Type fixing 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 * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * 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 for moveaxis Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix for moveaxis Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding example images, random field sized reduced to (10,10,10) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Changed backend Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * Tweak 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> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
* runtest.sh defaults to no build/install Signed-off-by: Wenqi Li <wenqil@nvidia.com> * following test case conventions for multiprocessing - adding `_dist` to multiprocessing test cases - decouple multiprocessing LMDB tests from `test_lmdbdataset` Signed-off-by: Wenqi Li <wenqil@nvidia.com> * exclude lmdbdataset tests in min_tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
…#3558) Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] update dataset summary Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance data type Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
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Fixes # .
Description
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./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.