merge master by Nic-Ma · Pull Request #419 · Nic-Ma/MONAI

Nic-Ma · 2022-06-02T05:29:20Z

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 --disttests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

* Adding discussion on format to bundle specification 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 Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

updates: - [github.com/asottile/pyupgrade: v2.31.0 → v2.31.1](asottile/pyupgrade@v2.31.0...v2.31.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [DLMED] change PatchIter to be a transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dict transform Signed-off-by: Nic Ma <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] store coords in dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] restore the doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] store more info Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Fix a logical error in level verification Signed-off-by: Behrooz <[email protected]>

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

* Refactor `if` expression * update clang format Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]>

* SplitDim Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * fix update meta Signed-off-by: Richard Brown <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* update mmar tests Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes pylint error Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* extend mlp Signed-off-by: Wenqi Li <[email protected]> * 0 mlp_dim Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* added 2D (normalized) surface dice metric Signed-off-by: Silvia Seidlitz <[email protected]> * exclude from min tests Signed-off-by: Wenqi Li <[email protected]> * more detailled docstring Signed-off-by: Silvia Seidlitz <[email protected]>

* Fix doc strings error Signed-off-by: Yiheng Wang <[email protected]> * remove duplicate places Signed-off-by: Yiheng Wang <[email protected]>

* update sys req Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * update code for torch>=1.7 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * autofix Signed-off-by: Wenqi Li <[email protected]> * fixes import Signed-off-by: Wenqi Li <[email protected]> * clear cache Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * remove temp cmd Signed-off-by: Wenqi Li <[email protected]>

* Update the existing functionality to comply with the `torchscript.jit.script` function. Signed-off-by: Ramon Emiliani <[email protected]>

* meta tensor Signed-off-by: Richard Brown <[email protected]>

* [DLMED] add kwargs for to() API Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

* update meta tensor api Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

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

to and from meta

* no skip if before pytorch 1.7 Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]>

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

* [DLMED] fix typo in bundle scripts Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support for AMP args Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

… and iterating across batches (#4137) `MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (#4137)

* [DLMED] update Workflow.py Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the engines Signed-off-by: Nic Ma <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Implement WSIReader with OpenSlide backend . Signed-off-by: Behrooz <[email protected]> * Add unittest for openslide Signed-off-by: Behrooz <[email protected]> * Add docs Signed-off-by: Behrooz <[email protected]> * formatting Signed-off-by: Behrooz <[email protected]> * Update imports and few fixes Signed-off-by: Behrooz <[email protected]> * Fix x,y in docstrings Signed-off-by: Behrooz <[email protected]> * Address comments Signed-off-by: Behrooz <[email protected]> * Remove x and y Signed-off-by: Behrooz <[email protected]>

* Implement PatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Add unittests Signed-off-by: Behrooz <[email protected]> * Add docs Signed-off-by: Behrooz <[email protected]> * Reorder imports Signed-off-by: Behrooz <[email protected]> * formatting: Signed-off-by: Behrooz <[email protected]> * Address comments Signed-off-by: Behrooz <[email protected]> * Update to be compatible with Dataset Signed-off-by: Behrooz <[email protected]> * Update reader to accept str, class, object Signed-off-by: Behrooz <[email protected]> * Add test cases for various reader and level arguments Signed-off-by: Behrooz <[email protected]> * Update comment about OpenSlide cache Signed-off-by: Behrooz <[email protected]> * Rename reader_name to backend Signed-off-by: Behrooz <[email protected]> * Add new test cases Signed-off-by: Behrooz <[email protected]> * Add unittests for openslide Signed-off-by: Behrooz <[email protected]> * Add new test cases Signed-off-by: Behrooz <[email protected]> * sorts Signed-off-by: Behrooz <[email protected]> * Add docstring for kwargs Signed-off-by: Behrooz <[email protected]>

* draft download Signed-off-by: Yiheng Wang <[email protected]> * update bundle download Signed-off-by: Yiheng Wang <[email protected]> * add url and load Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename args and remove a few places Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix flake8 issue Signed-off-by: Yiheng Wang <[email protected]> * enhance with reviews Signed-off-by: Yiheng Wang <[email protected]> * add instantiate for load Signed-off-by: Yiheng Wang <[email protected]> * fix black error Signed-off-by: Yiheng Wang <[email protected]> * add unittest Signed-off-by: Yiheng Wang <[email protected]> * add load to docs Signed-off-by: Yiheng Wang <[email protected]> * add skip Signed-off-by: Yiheng Wang <[email protected]> * add schemaerror Signed-off-by: Yiheng Wang <[email protected]> * fix partial places Signed-off-by: Yiheng Wang <[email protected]> * download zip bundle Signed-off-by: Yiheng Wang <[email protected]> * [DLMED] restore Exception for test Signed-off-by: Nic Ma <[email protected]> * update ts features Signed-off-by: Yiheng Wang <[email protected]> * add config_files test case Signed-off-by: Yiheng Wang <[email protected]> * enhance docstring example for args_file Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <[email protected]>

* workaround Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tifffile issue Signed-off-by: Nic Ma <[email protected]>

* fix the cases of multiple labels Signed-off-by: Can Zhao <[email protected]> * add examples Signed-off-by: Can Zhao <[email protected]> * docstring Signed-off-by: Can Zhao <[email protected]> * docstring and remove inverse Signed-off-by: Can Zhao <[email protected]> * docstring Signed-off-by: Can Zhao <[email protected]> * docstring Signed-off-by: Can Zhao <[email protected]>

* Adding tests 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 Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Trying to read output from failed process 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]> * Marking bundle_init as excluded Signed-off-by: Eric Kerfoot <[email protected]> * Marking bundle_init as excluded Signed-off-by: Eric Kerfoot <[email protected]> * Forgot a file Signed-off-by: Eric Kerfoot <[email protected]> * Marking bundle_utils as excluded Signed-off-by: Eric Kerfoot <[email protected]> * Marking bundle_init as excluded Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * 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>

* deprecate SegmentationSaver, TorchVisionFullyConvModel Signed-off-by: Wenqi Li <[email protected]> * fixes mintests Signed-off-by: Wenqi Li <[email protected]> * remove typing Signed-off-by: Wenqi Li <[email protected]>

improve dtype conversion

…ms (#4362) [DLMED] improve doc and tests Signed-off-by: Nic Ma <[email protected]>

skip resizing if spatial shape matches Signed-off-by: Wenqi Li <[email protected]>

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

* add box coder Signed-off-by: Can Zhao <[email protected]> * doc Signed-off-by: Can Zhao <[email protected]> * add security check Signed-off-by: Can Zhao <[email protected]> * docstring Signed-off-by: Can Zhao <[email protected]> * docstring Signed-off-by: Can Zhao <[email protected]> * Update test_box_coder.py * docstring Signed-off-by: Can Zhao <[email protected]> docstring Signed-off-by: Can Zhao <[email protected]> docstring Signed-off-by: Can Zhao <[email protected]> Update test_box_coder.py Signed-off-by: Can Zhao <[email protected]> * docstring Signed-off-by: Can Zhao <[email protected]> docstring Signed-off-by: Can Zhao <[email protected]> docstring Signed-off-by: Can Zhao <[email protected]> Update test_box_coder.py Signed-off-by: Can Zhao <[email protected]> docstring Signed-off-by: Can Zhao <[email protected]> Update test_box_coder.py Signed-off-by: Can Zhao <[email protected]> * update docstring Signed-off-by: Can Zhao <[email protected]>

workaround for 4375 Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add to doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] add min tests Signed-off-by: Nic Ma <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* add box -- mask converter Signed-off-by: Can Zhao <[email protected]> * add box mask transform Signed-off-by: Can Zhao <[email protected]> * add examples Signed-off-by: Can Zhao <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add examples Signed-off-by: Can Zhao <[email protected]> * add import Signed-off-by: Can Zhao <[email protected]> * add import Signed-off-by: Can Zhao <[email protected]> * add docstring Signed-off-by: Can Zhao <[email protected]> * update test Signed-off-by: Can Zhao <[email protected]> * update import Signed-off-by: Can Zhao <[email protected]> * update test Signed-off-by: Can Zhao <[email protected]> * change func name Signed-off-by: Can Zhao <[email protected]> * change func name Signed-off-by: Can Zhao <[email protected]> * change func name Signed-off-by: Can Zhao <[email protected]> * change func name Signed-off-by: Can Zhao <[email protected]> * [MONAI] code formatting Signed-off-by: monai-bot <[email protected]> * corrent a corner case in NMS Signed-off-by: Can Zhao <[email protected]> * update docstring, simplify convert_box_to_mask, add test cases Signed-off-by: Wenqi Li <[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: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

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

* [DLMED] support globals in eval(lambda) Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more test Signed-off-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…4.0.0` is used (#4397)

* Implement GridPatch and RandGridPatch Signed-off-by: Behrooz <[email protected]>

* Implement foreground mask Signed-off-by: Behrooz <[email protected]>

* Try 1 Signed-off-by: vnath <[email protected]> * dataset prep addition Signed-off-by: vnath <[email protected]> * Refactoring of transforms as there were loose hanging functions Signed-off-by: vnath <[email protected]> * Minor changes to transforms Signed-off-by: vnath <[email protected]> * Added test cases for all transforms Signed-off-by: vnath <[email protected]> * Removed dataset prep, it will be a part of tutorial, added opencv to dev requirements Signed-off-by: vnath <[email protected]> * Added Init for NuClick Signed-off-by: vnath <[email protected]> * Code formatting changes Signed-off-by: vnath <[email protected]> * Linting & Formatting Signed-off-by: vnath <[email protected]> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <[email protected]> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <[email protected]> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <[email protected]> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <[email protected]> * Minor in line docs need to be updated Signed-off-by: vnath <[email protected]> * Minor in line docs need to be updated Signed-off-by: vnath <[email protected]> * Adding Two Transforms & Test Cases Signed-off-by: vnath <[email protected]> * Formatted the PR Signed-off-by: vnath <[email protected]> * opencv changes Signed-off-by: vnath <[email protected]> * opencv changes Signed-off-by: vnath <[email protected]> * More optional import based changes Signed-off-by: vnath <[email protected]> * Removed opencv-python-headles as that does not workout Signed-off-by: vnath <[email protected]> * adding sk image back to requirement.txt till we figure out an alternative Signed-off-by: vnath <[email protected]> * Replaced MapTransform instead of Transform for SplitLabeld Signed-off-by: vnath <[email protected]> * Added skimage and cv2 requirements.txt as tests fail otherwise Signed-off-by: vnath <[email protected]> * Added MapTransform Inheritance to AddClickSignalsd Signed-off-by: vnath <[email protected]> * Spatial Pad Incorporated to ExtractPatchd Signed-off-by: vnath <[email protected]> * Remvoed comments and added doc-strings Signed-off-by: vnath <[email protected]> * codeformat Signed-off-by: vnath <[email protected]> * Adding NuClick Test to Min tests and removing opencv & scikit from requirements.txt Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed cv2 dependency after modification of FlattenLabeld Transform to use skimage functionality instead Signed-off-by: vnath <[email protected]> * Minor addition to doc string Signed-off-by: vnath <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * adds unit test case Signed-off-by: Wenqi Li <[email protected]> * remove unused import Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]> * Adding changes as docs and init arguments, 2 additional test cases Signed-off-by: vnath <[email protected]> * Minor changes Signed-off-by: vnath <[email protected]> * kwargs added to ExtractPatchd Signed-off-by: vnath <[email protected]> * Added a unit test for kwargs of SpatialPad in ExtractPatchd and a doc-string Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Behrooz Hashemian <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* Update wsi metadata names Signed-off-by: Behrooz <[email protected]> * Implement prob map handler Signed-off-by: Behrooz <[email protected]>

* enhance download Signed-off-by: Yiheng Wang <[email protected]> * [MONAI] code formatting Signed-off-by: monai-bot <[email protected]> * fixes #4432 Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

ericspod and others added 30 commits April 4, 2022 19:38

[pre-commit.ci] pre-commit suggestions (#4072)

c5bf120

updates: - [github.com/asottile/pyupgrade: v2.31.0 → v2.31.1](asottile/pyupgrade@v2.31.0...v2.31.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Fix a logical error in level verification (#4075)

b229e9c

* Fix a logical error in level verification Signed-off-by: Behrooz <[email protected]>

[DLMED] add allow_missing_reference (#4079)

b5e7fe1

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

extending the mlp module (#4089)

17529e7

* extend mlp Signed-off-by: Wenqi Li <[email protected]> * 0 mlp_dim Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

4073 Enhance DynUNet doc-strings (#4102)

af6560a

* Fix doc strings error Signed-off-by: Yiheng Wang <[email protected]> * remove duplicate places Signed-off-by: Yiheng Wang <[email protected]>

Make pixelshuffle scriptable (#4109)

4e7ca44

* Update the existing functionality to comply with the `torchscript.jit.script` function. Signed-off-by: Ramon Emiliani <[email protected]>

meta tensor (#4077)

1880d38

* meta tensor Signed-off-by: Richard Brown <[email protected]>

fixes pytorch version tests (#4127)

ccac5ff

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

update meta tensor api (#4131)

137164d

* update meta tensor api Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

runtests.sh isort (#4134)

5e180c6

Signed-off-by: Richard Brown <[email protected]>

update citation (#4133)

8544d9e

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

ToMetaTensor and FromMetaTensor transforms (#4115)

443fc0c

to and from meta

no skip if before pytorch 1.7 (#4139)

cc9c066

* no skip if before pytorch 1.7 Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]>

[DLMED] fix file name in meta (#4145)

e1a62f2

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

New wsireader (#4147)

cb9040e

MetaTensor: collate; decollate; dataset; dataloader; out=; indexing…

6dfb6a8

… and iterating across batches (#4137) `MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (#4137)

Disable pylint error and fix CI tests of new tifffile (#4162)

710781b

* workaround Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tifffile issue Signed-off-by: Nic Ma <[email protected]>

Can-Zhao and others added 29 commits May 26, 2022 20:12

improve dtype conversion (#4357)

b6302d7

improve dtype conversion

4348 Improve doc and unit tests for "correct center" of crop transfor…

1cfec68

…ms (#4362) [DLMED] improve doc and tests Signed-off-by: Nic Ma <[email protected]>

resize skip interpolation if spatial shapes match (#4369)

b96f8bd

skip resizing if spatial shape matches Signed-off-by: Wenqi Li <[email protected]>

fixes integration test (#4373)

d46904b

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

4375 workaround mlflow integration (#4376)

14f74cb

workaround for 4375 Signed-off-by: Wenqi Li <[email protected]>

Sliding window inference that supports multiple zoomed outputs (#4363)

ba2309c

add ATSS matcher for detection (#4350)

61a0dc3

4323 - review readme (#4390)

2c78bb0

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

add RetinaNet network (#4378)

9133e35

add anchor generators used for detection (#4336)

d635339

Define PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION only when `protobuf>=…

4dbbd86

…4.0.0` is used (#4397)

add hard_negative_sampler.py for detection (#4301)

a75dd05

GridPatch to Extract Tiles/Patches (#4321)

2f589c6

* Implement GridPatch and RandGridPatch Signed-off-by: Behrooz <[email protected]>

Foreground Tissue Mask (#4379)

27c37f2

* Implement foreground mask Signed-off-by: Behrooz <[email protected]>

4401 improve parser error message (#4402)

f540e34

Minor enhancement for several places (#4409)

a737d58

Move append items to list definition (#4417)

38b7943

Refactor Probability Map Producer Handler (#4382)

40373b2

* Update wsi metadata names Signed-off-by: Behrooz <[email protected]> * Implement prob map handler Signed-off-by: Behrooz <[email protected]>

Add detector utils (#4434)

4434a3f

add box selector (#4437)

bbc628d

Nic-Ma merged commit 5a16ec6 into Nic-Ma:enhance-ensure-tuple Jun 2, 2022

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merge master#419

merge master#419
Nic-Ma merged 123 commits intoNic-Ma:enhance-ensure-tuplefrom
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Nic-Ma commented Jun 2, 2022

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