merge master#207

Nic-Ma · 2021-08-27T08:52:13Z

Fixes # .

Description

A few sentences describing the changes proposed in this pull request.

Status

Ready/Work in progress/Hold

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
Breaking change (fix or new feature that would cause existing functionality to change).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
Quick tests passed locally by running ./runtests.sh --quick --unittests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance TTA Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] enhance doc-string for spatial shape Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add ill test case Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update test error Signed-off-by: Nic Ma <nma@nvidia.com> * update docstring and add more test cases Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [DLMED] add link to doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance the sanity check Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add RandCoarseDropout Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add dict version transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] updated according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] init the transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] complete array transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add dict transform and inverse tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix mypy type Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change to enhance Resize transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix TTA Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix mypy error Signed-off-by: Nic Ma <nma@nvidia.com>

* added stain norm and tests Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * import changes Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * changed stain extraction tests Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * edited stain norm tests Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * convert floats to float32 Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * added uint8 assumption to docstring Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * add error case Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * formatting change Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * modify tests wrt cupy import Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * minor change to pass lint test Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * import changes Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * refactored classes Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * Restructure and rename transforms Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * added dict transform Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * Move stain_extractor to init Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Exclude pathology transform tests from mini tests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix type checking for cupy ndarray Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Include pathology transform tests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update to cupy 9.0.0 Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove exact version for cupy Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * add to docs Signed-off-by: Neha Srivathsa <nsrivathsa@nvidia.com> * Organize into stain dir Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add/update init files Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Transit all from cupy to numpy Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update imports Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update test cases for numpy Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Rename to NormalizeHEStains and NormalizeHEStainsD Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add dictionary variant names Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix typing and formatting Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update test cases Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix clip max Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix var typing Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix a typing issue Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update default values, and change D to d Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add image value check Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add test cases for negative and invalid values Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> Co-authored-by: Neha Srivathsa <nsrivathsa@nvidia.com> Co-authored-by: nsrivathsa <81264348+nsrivathsa@users.noreply.github.com>

* Add DatasetCalculator Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update docstring Signed-off-by: Yiheng Wang <vennw@nvidia.com> * use multiprocessing Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update to use dataset and other places Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update to support array return Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update with new testcases and change name Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update min test Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update unittest Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix vstack error Signed-off-by: Yiheng Wang <vennw@nvidia.com>

…m part of dataset (#2667) * [DLMED] add RandCompose Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change to enhance RandLambda Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove RandCompose Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix format Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add inverse operation Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix subprogress issue Signed-off-by: Nic Ma <nma@nvidia.com>

* Restructure transforms into a directory Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix a typo Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> Co-authored-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Moved fourier functions to their own class. Modified RandKSpaceSpikeNoised. 1. Allow RandKSpaceSpikeNoised to work with arbitrary keys. 2. Introduced Fourier transform to keep the forward/backward fourier mappings. Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com> * removed old code Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com> * Ignore torch.fft tests if not present Ignore tests with versions of Pytorch which lack the module fft. Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com> * update Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com> * typing update Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com> * added unit test for Fourier Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com> * added unit test for Fourier Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com> * fixing black Signed-off-by: Yaniel Cabrera <yaniel.cabrera@gmail.com>

This is to address an issue in the bibtex conversion. Signed-off-by: Tom Vercauteren <tom.vercauteren@kcl.ac.uk>

… meta data (#2685) * [DLMED] add IntensityStats transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add dict version transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance ShiftIntensity transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change to utility Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] adjust to look_up_option Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add multi-processing test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add mask option Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance error message Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add pickle test Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] enhance pickle test Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] update doc-strings of Affine transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix format issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove coord link Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Mohammad Adil <madil@nvidia.com>

* 2d/3d patchembedding Signed-off-by: Wenqi Li <wenqil@nvidia.com> * minor updates for selfattention Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 2d vit Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes type hint Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update unetr Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit test Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Add transform to fill holes and to filter (#2678) Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de> * Change name of label filter class (#2678) Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de> * Change fill holes to growing logic (#2678) Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de> * Fix missing entry in min_tests (#2678) Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de> * Fix review comments (#2678) Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de> * Remove batch dim and add one-hot handling (#2678) Signed-off-by: Sebastian Penhouet <sebastian.penhouet@airamed.de> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Sebastian Penhouet <sebastian.penhouet@airamed.de>

* Remove unnecessary use of comprehension * Remove unnecessary comprehension (#2718) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement (#2717) * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement * Unnecessary `else`/`elif` used after `raise` PYL-R1720 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> * Replace ternary syntax with if expression (#2716) * Replace ternary syntax with if expression * fixes Duplicate dictionary keys PYL-W0109 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove Unused variable data_ 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> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * fixes scaler type 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: monai-bot <monai.miccai2019@gmail.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> Co-authored-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Update Mish to default PyTorch 1.9 version

* [DLMED] add Histogram normalize Signed-off-by: Nic Ma <nma@nvidia.com>

* Added OneOf class Signed-off-by: Lyndon Boone <lyndonboone8@gmail.com> * Clean up OneOf constructor Signed-off-by: Lyndon Boone <lyndonboone8@gmail.com> * add flatten, len and unit test Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * Added unit tests and inverse method Signed-off-by: Lyndon Boone <lyndonboone8@gmail.com> * rename test Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * flatten tests Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * add inverse Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* no extension check for user specified reader; allow Path object

* [DLMED] add round_values Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix continuously run Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] remove out-date comment Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* RandGaussianNoise and SavitzkyGolaySmooth Torch/NumpyTransforms Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* enhance dynunet docstrings Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Signed-off-by: Everett Lacey <elacey@nvidia.com>

* Add NVTX handlers Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* [DLMED] add ToDevice transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix type-hints Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] inherit Transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add kwargs Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] enhance doc Signed-off-by: Nic Ma <nma@nvidia.com> * Update monai/data/dataset.py Co-authored-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Nic Ma <nma@nvidia.com> * Update monai/data/dataset.py Co-authored-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

* get number of data conversions Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * improve docs Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * move fn to utility Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * code format Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

print backends of all MONAI transforms

* print backends of all MONAI transforms Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * Pad base class Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Mohammad Adil <madil@nvidia.com>

…tensity (#2815) * torch transforms - RandRicianNoise, StdShiftIntensity, RandStdShiftIntensity Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * unused imports Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * NdarrayTensorUnion Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * code review Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * simplify backend Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * code format Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix test Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * in place transforms Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Implement NVTX Range decorator and context manager Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Implement unittests for nvtx range Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update utils init Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove Range transform in favor of Range decorator Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstrings Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update description Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove optional Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change torch testing to numpy testing Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Handle special methods Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change typing Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * REmove torch.nn Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update method resolution logic Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update tests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change _call_impl to __call__ Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove debugging outputs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

torch transforms - RandRicianNoise, StdShiftIntensity, RandStdShiftIntensity

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* all close Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * assert_allclose Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * NormalizeIntensity Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* Change default methods for nn.Module Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove DataLoader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* all close Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * assert_allclose Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * ScaleIntensity Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* backends -> backend Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * code format Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * code format2 Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* [DLMED] support random fill Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update for test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update dict transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix mypy Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] support auto computing min and max 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> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

backends -> backend

* enhance swish Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add inplace to swish Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add efn features Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add more pretrained weights url Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix flake8 errors Signed-off-by: Yiheng Wang <vennw@nvidia.com> * use look up option Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix deepsource issues Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix type issues Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* resume github premerge tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #2821 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update group names Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* add pre-commit Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* Local Patch Shuffle Transform Initial Version Added Signed-off-by: vnath <vnath@nvidia.com>

Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* [DLMED] add support to fill outside Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add paper link for cutout Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

wyli and others added 30 commits July 23, 2021 09:52

fixes randbiasfield (#2645)

a566dc6

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

1979 Enhance TTA to align with Invertd args and support no label (#2654)

325775b

* [DLMED] enhance TTA Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>

new theme (#2657)

8d4f45f

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

2635 enhance UNet doc for the typical use case (#2659)

aaeebd6

* [DLMED] enhance doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance the sanity check Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

add citation metadata (#2663)

35e45df

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Change MONAI author from a person to en entity (#2690)

9ecb0e1

This is to address an issue in the bibtex conversion. Signed-off-by: Tom Vercauteren <tom.vercauteren@kcl.ac.uk>

[DLMED] update int method (#2696)

03a8372

Signed-off-by: Nic Ma <nma@nvidia.com>

Increase timeout of tests (#2711)

4298b14

Signed-off-by: Mohammad Adil <madil@nvidia.com>

[DLMED] add select_fn for MaskIntensity (#2726)

2f1c7a5

Signed-off-by: Nic Ma <nma@nvidia.com>

Reorganize datasets and metrics in pathology (#2742)

ce4960d

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> Co-authored-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Update Mish to default PyTorch 1.9 version (#2733)

33184fa

* Update Mish to default PyTorch 1.9 version

2691 Add HistogramIntensity transform (#2738)

f9bc713

* [DLMED] add Histogram normalize Signed-off-by: Nic Ma <nma@nvidia.com>

Nvtx transform (#2713)

8726dd5

2743 - no extension check for user specified reader (#2751)

a7d4574

* no extension check for user specified reader; allow Path object

2746 Add round support to AsDiscrete transform (#2753)

2ca9710

* [DLMED] add round_values Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

rijobro and others added 29 commits August 17, 2021 17:15

RandGaussianNoise and SavitzkyGolaySmooth Torch/NumpyTransforms (#2740)

cf6edc7

* RandGaussianNoise and SavitzkyGolaySmooth Torch/NumpyTransforms Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

enhance dynunet docstrings (#2792)

0840dbb

* enhance dynunet docstrings Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Update license example (#2788)

cc31355

Signed-off-by: Everett Lacey <elacey@nvidia.com>

Add NVTX handlers (#2765)

46d5f2a

* Add NVTX handlers Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

[DLMED] enhance samples crop (#2804)

ce196e0

Signed-off-by: Nic Ma <nma@nvidia.com>

print backends of all MONAI transforms (#2801)

5fe5a0b

print backends of all MONAI transforms

Pad base class (#2802)

7659869

* print backends of all MONAI transforms Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * Pad base class Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

[DLMED] enhance CropForegroundd transform (#2808)

2c7ec57

Signed-off-by: Nic Ma <nma@nvidia.com>

sunset premerge self-hosted pipelines (#2803)

c39f6fa

Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Mohammad Adil <madil@nvidia.com>

sunset nightly tests (#2820)

aad8bb2

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Torch flip (#2822)

fab8467

torch transforms - RandRicianNoise, StdShiftIntensity, RandStdShiftIntensity

all close (#2829)

b4def1a

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Update Range decorator (#2834)

38ecaef

* Change default methods for nn.Module Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove DataLoader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

ShiftIntensityd, RandShiftIntensityd (#2839)

26f8446

backends -> backend

temp. resume github premerge tests (#2853)

1065dad

* resume github premerge tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #2821 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update group names Signed-off-by: Wenqi Li <wenqil@nvidia.com>

CI: pre-commit (#2843)

ce139f6

* add pre-commit Signed-off-by: Jirka <jirka.borovec@seznam.cz>

Local Patch Shuffle Transform Initial Version Added (#2757)

3eb71c7

* Local Patch Shuffle Transform Initial Version Added Signed-off-by: vnath <vnath@nvidia.com>

extend ResNet pretrained info (#2854)

dd56514

Signed-off-by: Jirka <jirka.borovec@seznam.cz>

2707 Fill the outside of holes (#2848)

f981ad0

* [DLMED] add support to fill outside Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add paper link for cutout Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Nic-Ma merged commit d860018 into Nic-Ma:2856-fix-coarse-dropout Aug 27, 2021

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Nic-Ma merged 70 commits intoNic-Ma:2856-fix-coarse-dropoutfrom
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