merge master#349
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Nic-Ma merged 300 commits intoNic-Ma:3578-enhance-keep-largestfrom Jan 12, 2022
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* [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]>
* enhance the release version string check Signed-off-by: GitHub <[email protected]> * update the releasing steps Signed-off-by: GitHub <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* [DLMED] update ignite 0.4.6 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <[email protected]>
* print dtype along with type Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
…SpikeNoise (#2974) GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpaceSpikeNoise
…std (#3044) Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* torch fgbgtoindices Signed-off-by: Wenqi Li <[email protected]> * unravel indices Signed-off-by: Wenqi Li <[email protected]> * simplified Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* [DLMED] fix spacing dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix dtype Signed-off-by: Nic Ma <[email protected]>
create example transform images
* [DLMED] fix crop performance issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] use default to avoid overflow Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI error Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* apply yesqa Signed-off-by: Jirka <[email protected]> * rev Signed-off-by: Jirka <[email protected]> * expand Signed-off-by: Jirka <[email protected]> * plugins Signed-off-by: Jirka <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* create images Signed-off-by: Richard Brown <[email protected]> * use brats Signed-off-by: Richard Brown <[email protected]> * update Signed-off-by: Richard Brown <[email protected]> * working Signed-off-by: Richard Brown <[email protected]> * rename file Signed-off-by: Richard Brown <[email protected]> * optional import matplotlib Signed-off-by: Richard Brown <[email protected]> * docstrings Signed-off-by: Richard Brown <[email protected]> * store images in https://github.com/Project-MONAI/DocImages Signed-off-by: Richard Brown <[email protected]> * extra transform example images Signed-off-by: Richard Brown <[email protected]> * most transforms Signed-off-by: Richard Brown <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] fix complex array issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test issue Signed-off-by: Nic Ma <[email protected]>
* Adding documentation for AutoEncoder and VarAutoEncoder Signed-off-by: Eric Kerfoot <[email protected]>
* [pre-commit.ci] pre-commit suggestions updates: - [github.com/asottile/pyupgrade: v2.27.0 → v2.29.0](asottile/pyupgrade@v2.27.0...v2.29.0) * fixes #3071 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: Wenqi Li <[email protected]>
* update workflow Signed-off-by: Wenqi Li <[email protected]> * fixes gpu tests Signed-off-by: Wenqi Li <[email protected]>
* correct panelled example images Signed-off-by: Richard Brown <[email protected]>
* 2755 Add b-spline kernel option Signed-off-by: kate-sann5100 <[email protected]>
* adds integration tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * cache pip Signed-off-by: Wenqi Li <[email protected]> * fixes conc Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 5a931c6. Signed-off-by: Wenqi Li <[email protected]> * print outcome Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* fixes RandGaussianSmooth Signed-off-by: Wenqi Li <[email protected]> * minor fixes Signed-off-by: Wenqi Li <[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]>
* drop py36 support Signed-off-by: Wenqi Li <[email protected]> * drop 20.09 test because of python min version 3.6 Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * error->warning, revise copyright Signed-off-by: Wenqi Li <[email protected]>
* has cupy check Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* adds min. memory testing utils Signed-off-by: Wenqi Li <[email protected]> * include valueerror for robust outcome Signed-off-by: Wenqi Li <[email protected]> * ensure float Signed-off-by: Wenqi Li <[email protected]> * msg improvements Signed-off-by: Wenqi Li <[email protected]> * update threshold Signed-off-by: Wenqi Li <[email protected]> * remove ref Signed-off-by: Wenqi Li <[email protected]> * separate disttests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] remove warning Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* Adding smooth deform transform Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Docs update Signed-off-by: Eric Kerfoot <[email protected]> * Type fixing 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]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix 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 for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Fix for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Adding example images, random field sized reduced to (10,10,10) Signed-off-by: Eric Kerfoot <[email protected]> * Changed backend Signed-off-by: Eric Kerfoot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Tweak 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]>
* runtest.sh defaults to no build/install Signed-off-by: Wenqi Li <[email protected]> * following test case conventions for multiprocessing - adding `_dist` to multiprocessing test cases - decouple multiprocessing LMDB tests from `test_lmdbdataset` Signed-off-by: Wenqi Li <[email protected]> * exclude lmdbdataset tests in min_tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
…#3558) Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] update dataset summary Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance data type Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
updates: - [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0](pre-commit/pre-commit-hooks@v4.0.1...v4.1.0) - [github.com/asottile/pyupgrade: v2.29.0 → v2.31.0](asottile/pyupgrade@v2.29.0...v2.31.0) - [github.com/asottile/yesqa: v1.2.3 → v1.3.0](asottile/yesqa@v1.2.3...v1.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* adds metadata when loading dicom series Signed-off-by: Wenqi Li <[email protected]> * fixes timed tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* Create codeql-analysis.yml Signed-off-by: Wenqi Li <[email protected]> * build cpp Signed-off-by: Wenqi Li <[email protected]> * fixes Multiplication result converted to larger type Signed-off-by: Wenqi Li <[email protected]> * fixes url parsing Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add log handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] test CI Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix logging Signed-off-by: Nic Ma <[email protected]> * [DLMED] temp test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong test cases Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance slice_channels 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] remove test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add flag Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add kwargs Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
* [DLMED] add ascontiguous Signed-off-by: Nic Ma <[email protected]> * [DLMED] add doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance CacheDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] export to utility Signed-off-by: Nic Ma <[email protected]> * [DLMED] add to subclasses Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix antipatterns Signed-off-by: Nic Ma <[email protected]>
* adds a conda test Signed-off-by: Wenqi Li <[email protected]> * openslide windows Signed-off-by: Wenqi Li <[email protected]> * conda create Signed-off-by: Wenqi Li <[email protected]> * fixes lmdb Signed-off-by: Wenqi Li <[email protected]> * fixes windows paging Signed-off-by: Wenqi Li <[email protected]> * fixes matplotlib version Signed-off-by: Wenqi Li <[email protected]> * fixes openslide conda Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]> * try to fix windows paging Signed-off-by: Wenqi Li <[email protected]> * update cpuonly tests Signed-off-by: Wenqi Li <[email protected]> * fixes windows install Signed-off-by: Wenqi Li <[email protected]> * update comments Signed-off-by: Wenqi Li <[email protected]>
* 3616 test downloading issues Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* 0-d array Signed-off-by: Wenqi Li <[email protected]> * handling string types Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add kwargs for torch APIs 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]>
* [DLMED] update GridPatchDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update for windows Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix windows test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update test Signed-off-by: Nic Ma <[email protected]>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
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./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.