merge master #214

Nic-Ma · 2021-09-08T02:59:54Z

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 <[email protected]>

* [DLMED] enhance TTA Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

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

Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance the sanity check Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add RandCoarseDropout Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dict version transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] updated according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

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

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

* Add DatasetCalculator Signed-off-by: Yiheng Wang <[email protected]> * update docstring Signed-off-by: Yiheng Wang <[email protected]> * use multiprocessing Signed-off-by: Yiheng Wang <[email protected]> * update to use dataset and other places Signed-off-by: Yiheng Wang <[email protected]> * update to support array return Signed-off-by: Yiheng Wang <[email protected]> * update with new testcases and change name Signed-off-by: Yiheng Wang <[email protected]> * update min test Signed-off-by: Yiheng Wang <[email protected]> * update unittest Signed-off-by: Yiheng Wang <[email protected]> * fix vstack error Signed-off-by: Yiheng Wang <[email protected]>

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

* Restructure transforms into a directory Signed-off-by: Behrooz <[email protected]> * Fix a typo Signed-off-by: Behrooz <[email protected]> Co-authored-by: Behrooz <[email protected]>

* 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 <[email protected]> * removed old code Signed-off-by: Yaniel Cabrera <[email protected]> * Ignore torch.fft tests if not present Ignore tests with versions of Pytorch which lack the module fft. Signed-off-by: Yaniel Cabrera <[email protected]> * update Signed-off-by: Yaniel Cabrera <[email protected]> * typing update Signed-off-by: Yaniel Cabrera <[email protected]> * added unit test for Fourier Signed-off-by: Yaniel Cabrera <[email protected]> * added unit test for Fourier Signed-off-by: Yaniel Cabrera <[email protected]> * fixing black Signed-off-by: Yaniel Cabrera <[email protected]>

This is to address an issue in the bibtex conversion. Signed-off-by: Tom Vercauteren <[email protected]>

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

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

Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Mohammad Adil <[email protected]>

* 2d/3d patchembedding Signed-off-by: Wenqi Li <[email protected]> * minor updates for selfattention Signed-off-by: Wenqi Li <[email protected]> * 2d vit Signed-off-by: Wenqi Li <[email protected]> * fixes type hint Signed-off-by: Wenqi Li <[email protected]> * update unetr Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]>

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

* 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 <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]> * Replace ternary syntax with if expression (#2716) * Replace ternary syntax with if expression * fixes Duplicate dictionary keys PYL-W0109 Signed-off-by: Wenqi Li <[email protected]> * remove Unused variable data_ 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]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * fixes scaler type Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Behrooz <[email protected]> Co-authored-by: Behrooz <[email protected]>

* Update Mish to default PyTorch 1.9 version

* [DLMED] add Histogram normalize Signed-off-by: Nic Ma <[email protected]>

* Added OneOf class Signed-off-by: Lyndon Boone <[email protected]> * Clean up OneOf constructor Signed-off-by: Lyndon Boone <[email protected]> * add flatten, len and unit test Signed-off-by: Richard Brown <[email protected]> * Added unit tests and inverse method Signed-off-by: Lyndon Boone <[email protected]> * rename test Signed-off-by: Richard Brown <[email protected]> * flatten tests Signed-off-by: Richard Brown <[email protected]> * add inverse Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Richard Brown <[email protected]>

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

* [DLMED] add round_values 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]>

* [DLMED] fix continuously run Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] remove out-date comment Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* all close Signed-off-by: Richard Brown <[email protected]> * assert_allclose Signed-off-by: Richard Brown <[email protected]> * ScaleIntensity Signed-off-by: Richard Brown <[email protected]>

* backends -> backend Signed-off-by: Richard Brown <[email protected]> * code format Signed-off-by: Richard Brown <[email protected]> * code format2 Signed-off-by: Richard Brown <[email protected]>

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

backends -> backend

* enhance swish Signed-off-by: Yiheng Wang <[email protected]> * add inplace to swish Signed-off-by: Yiheng Wang <[email protected]> * add efn features Signed-off-by: Yiheng Wang <[email protected]> * add more pretrained weights url Signed-off-by: Yiheng Wang <[email protected]> * fix flake8 errors Signed-off-by: Yiheng Wang <[email protected]> * use look up option Signed-off-by: Yiheng Wang <[email protected]> * fix deepsource issues Signed-off-by: Yiheng Wang <[email protected]> * fix type issues Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* resume github premerge tests Signed-off-by: Wenqi Li <[email protected]> * fixes #2821 Signed-off-by: Wenqi Li <[email protected]> * update group names Signed-off-by: Wenqi Li <[email protected]>

* add pre-commit Signed-off-by: Jirka <[email protected]>

* Local Patch Shuffle Transform Initial Version Added Signed-off-by: vnath <[email protected]>

Signed-off-by: Jirka <[email protected]>

* [DLMED] add support to fill outside Signed-off-by: Nic Ma <[email protected]> * [DLMED] add paper link for cutout Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* Add deepedit transforms Signed-off-by: Andres <[email protected]> * Run unittests - autofix Signed-off-by: Andres <[email protected]> * Update transform Signed-off-by: Andres <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

…ty, RepeatChannel (#2840)

…il, ToTensor, Transpose (#2850) * backends -> backend Signed-off-by: Richard Brown <[email protected]> * code format Signed-off-by: Richard Brown <[email protected]> * code format2 Signed-off-by: Richard Brown <[email protected]> * AddChannel, AsChannelFirst, AsChannelLast, EnsureChannelFirst, Identity, RepeatChannel Signed-off-by: Richard Brown <[email protected]> * moveaxis backwards compatible Signed-off-by: Richard Brown <[email protected]> * code format Signed-off-by: Richard Brown <[email protected]> * EnsureType, RemoveRepeatedChannel, SplitChannel, ToCupy, ToNumpy, ToPil, ToTensor, Transpose Signed-off-by: Richard Brown <[email protected]> * trigger ci/cd Signed-off-by: Richard Brown <[email protected]> * permute requires positive indices Signed-off-by: Richard Brown <[email protected]> * correct permute Signed-off-by: Richard Brown <[email protected]> * correct permute Signed-off-by: Richard Brown <[email protected]> * has_pil Signed-off-by: Richard Brown <[email protected]>

* add classification support for ViT Model Signed-off-by: ahatamizadeh <[email protected]> * add classification support for ViT Model Signed-off-by: ahatamizadeh <[email protected]> * add classification support for ViT Model Signed-off-by: ahatamizadeh <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] add args to ThreadDataLoader Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>

…_at_least (#2859) * DataStats, LabelToMask, Lambda, RandLambda, SqueezeDim, is_module_ver_at_least Signed-off-by: Richard Brown <[email protected]>

* update cron tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * update gpu info Signed-off-by: Wenqi Li <[email protected]> * tmp tests Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit 3a5b8f8. Signed-off-by: Wenqi Li <[email protected]> * Revert "tmp tests" This reverts commit e960dac. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 911c332. Signed-off-by: Wenqi Li <[email protected]>

* fixes #2639 Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* split CI package Signed-off-by: Jirka <[email protected]> * tmpdir Signed-off-by: Jirka <[email protected]> * tmpdir Signed-off-by: Jirka <[email protected]>

* Implement SplitOnGrid Signed-off-by: Behrooz <[email protected]> * Implement dictionary-based SplitOnGrid Signed-off-by: Behrooz <[email protected]> * Update inits Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Change imports Signed-off-by: Behrooz <[email protected]> * Update input logic in SplitOnGrid) Signed-off-by: Behrooz <[email protected]> * Add unittests for SplitOnGrid and SplitOnGridDict Signed-off-by: Behrooz <[email protected]> * Sort import Signed-off-by: Behrooz <[email protected]> * Remove imports Signed-off-by: Behrooz <[email protected]> * Address comments Signed-off-by: Behrooz <[email protected]> * Remove optional Signed-off-by: Behrooz <[email protected]> * Address thread safety issues Signed-off-by: Behrooz <[email protected]>

…2900) * [DLMED] fix type issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify the change Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>

* rename n_classes Signed-off-by: Jirka <[email protected]> * back compatibility Signed-off-by: Jirka <[email protected]>

Signed-off-by: Behrooz <[email protected]> * Update special method replacement

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

fixes randbiasfield (#2645)

a566dc6

Signed-off-by: Wenqi Li <[email protected]>

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

325775b

* [DLMED] enhance TTA Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

new theme (#2657)

8d4f45f

Signed-off-by: Wenqi Li <[email protected]>

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

aaeebd6

* [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance the sanity check Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

add citation metadata (#2663)

35e45df

Signed-off-by: Wenqi Li <[email protected]>

Restructure pathology transforms (#2671)

7f42efe

* Restructure transforms into a directory Signed-off-by: Behrooz <[email protected]> * Fix a typo Signed-off-by: Behrooz <[email protected]> Co-authored-by: Behrooz <[email protected]>

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 <[email protected]>

[DLMED] update int method (#2696)

03a8372

Signed-off-by: Nic Ma <[email protected]>

Increase timeout of tests (#2711)

4298b14

Signed-off-by: Mohammad Adil <[email protected]>

[DLMED] add select_fn for MaskIntensity (#2726)

2f1c7a5

Signed-off-by: Nic Ma <[email protected]>

Reorganize datasets and metrics in pathology (#2742)

ce4960d

Signed-off-by: Behrooz <[email protected]> Co-authored-by: Behrooz <[email protected]>

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 <[email protected]>

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 <[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]>

rijobro and others added 29 commits August 25, 2021 00:22

Scale intensity (#2832)

fa5bc15

* all close Signed-off-by: Richard Brown <[email protected]> * assert_allclose Signed-off-by: Richard Brown <[email protected]> * ScaleIntensity Signed-off-by: Richard Brown <[email protected]>

backends -> backend (#2838)

acf4a9f

* backends -> backend Signed-off-by: Richard Brown <[email protected]> * code format Signed-off-by: Richard Brown <[email protected]> * code format2 Signed-off-by: Richard Brown <[email protected]>

ShiftIntensityd, RandShiftIntensityd (#2839)

26f8446

backends -> backend

temp. resume github premerge tests (#2853)

1065dad

* resume github premerge tests Signed-off-by: Wenqi Li <[email protected]> * fixes #2821 Signed-off-by: Wenqi Li <[email protected]> * update group names Signed-off-by: Wenqi Li <[email protected]>

CI: pre-commit (#2843)

ce139f6

* add pre-commit Signed-off-by: Jirka <[email protected]>

Local Patch Shuffle Transform Initial Version Added (#2757)

3eb71c7

* Local Patch Shuffle Transform Initial Version Added Signed-off-by: vnath <[email protected]>

extend ResNet pretrained info (#2854)

dd56514

Signed-off-by: Jirka <[email protected]>

2707 Fill the outside of holes (#2848)

f981ad0

* [DLMED] add support to fill outside Signed-off-by: Nic Ma <[email protected]> * [DLMED] add paper link for cutout Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Add deepedit transforms (#2810)

f99ebda

* Add deepedit transforms Signed-off-by: Andres <[email protected]> * Run unittests - autofix Signed-off-by: Andres <[email protected]> * Update transform Signed-off-by: Andres <[email protected]>

[DLMED] add missing return (#2857)

321454c

Signed-off-by: Nic Ma <[email protected]>

add cupy tests (#2858)

aa5fa1d

Signed-off-by: Wenqi Li <[email protected]>

AddChannel, AsChannelFirst, AsChannelLast, EnsureChannelFirst, Identi…

fe6ac0a

…ty, RepeatChannel (#2840)

Add thread args to ThreadBuffer (#2862)

895592e

* [DLMED] add args to ThreadDataLoader Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>

DataStats, LabelToMask, Lambda, RandLambda, SqueezeDim, is_module_ver…

a25b733

…_at_least (#2859) * DataStats, LabelToMask, Lambda, RandLambda, SqueezeDim, is_module_ver_at_least Signed-off-by: Richard Brown <[email protected]>

2639 documentation for the deprecated API (#2865)

e9f6e51

* fixes #2639 Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]>

[DLMED] enhance doc-string of ToDevice (#2874)

b0c83db

Signed-off-by: Nic Ma <[email protected]>

[DLMED] simplify random seed (#2875)

9990179

Signed-off-by: Nic Ma <[email protected]>

[DLMED] enhance image reader doc-string for multi-files (#2876)

7bfa428

Signed-off-by: Nic Ma <[email protected]>

split CI package (#2863)

50dcf8d

* split CI package Signed-off-by: Jirka <[email protected]> * tmpdir Signed-off-by: Jirka <[email protected]> * tmpdir Signed-off-by: Jirka <[email protected]>

rename n_classes to num_classes (#2842)

1ecf5b6

* rename n_classes Signed-off-by: Jirka <[email protected]> * back compatibility Signed-off-by: Jirka <[email protected]>

Update NVTX Range (#2890)

b770793

Signed-off-by: Behrooz <[email protected]> * Update special method replacement

List Comprehension for ITC (#2906)

e24f1b1

Nic-Ma merged commit f398298 into Nic-Ma:main Sep 8, 2021

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merge master #214

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Nic-Ma commented Sep 8, 2021

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merge master #214

merge master #214

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Nic-Ma commented Sep 8, 2021

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