merge master#333
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Nic-Ma merged 273 commits intoNic-Ma:3539-remove-decollate-warningfrom Dec 23, 2021
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Signed-off-by: Nic Ma <[email protected]>
* add multimodal transformers Signed-off-by: ahatamizadeh <[email protected]>
…op_centers`, `generate_pos_neg_label_crop_centers`, `generate_label_classes_crop_centers` (#2958) torch map_binary_to_indices, map_classes_to_indices, correct_crop_centers, generate_pos_neg_label_crop_centers, generate_label_classes_crop_centers
* Implement CuCIM wrapper transfrom Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
* Update with cupy.ndarray Signed-off-by: Behrooz <[email protected]> * Change to use has_cp Signed-off-by: Behrooz <[email protected]> * Change the format Signed-off-by: Behrooz <[email protected]> * Fix a bug Signed-off-by: Behrooz <[email protected]>
* Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]>
* fixes tutorial issue 352 Signed-off-by: Wenqi Li <[email protected]> * simplified Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance tensor transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix mypy Signed-off-by: Nic Ma <[email protected]>
…abelClasses`, `RandCropByLabelClassesd` (#2967) Signed-off-by: Richard Brown <[email protected]>
* enhance affinegrid to use torch backend Signed-off-by: Wenqi Li <[email protected]> * style fixes Signed-off-by: Wenqi Li <[email protected]> * codeformat fixes Signed-off-by: Wenqi Li <[email protected]> * backend affien grid Signed-off-by: Wenqi Li <[email protected]> * device support Signed-off-by: Wenqi Li <[email protected]> * less lookup Signed-off-by: Wenqi Li <[email protected]> * create grid with torch backend Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * default to torch create grid Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]> * randaffine with create grid Signed-off-by: Wenqi Li <[email protected]> * create_grid backend change for spatial transforms Signed-off-by: Wenqi Li <[email protected]> * create control grid tensor Signed-off-by: Wenqi Li <[email protected]> * enhance spatial, and crop xforms - Update test_rand_deform_grid.py - center_scale_crop - center_spatial_crop - rand_scale_crop - rand_spatial_crop - rand_spatial_crop_samples Signed-off-by: Wenqi Li <[email protected]> * fixes invert Signed-off-by: Wenqi Li <[email protected]> * tensor resize, unit test fixes Signed-off-by: Wenqi Li <[email protected]>
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]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add dataset generator Signed-off-by: Nic Ma <[email protected]> * [DLMED] add DatasetGenerator Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix wrong test Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove return Signed-off-by: Nic Ma <[email protected]> * [DLMED] update rtol for CI Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] add missing docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] add missing components Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add channel-wise Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip test if before 1.7 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: Nic Ma <[email protected]>
* [DLMED] add Iteration base class 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]>
Signed-off-by: Yiheng Wang <[email protected]>
* [DLMED] support string dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* Update to not include number for the name of the first range Signed-off-by: Behrooz <[email protected]> * Update CuCIM and TorchVision wrappers to include name Signed-off-by: Behrooz <[email protected]> * Update nvtx range to append undelying class for wrapper tranforms Signed-off-by: Behrooz <[email protected]> * Add new test cases to cover changes Signed-off-by: Behrooz <[email protected]> * Update cucim and torchvision check Signed-off-by: Behrooz <[email protected]>
* [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]>
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Fixes # .
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./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.