merge master#352
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Nic-Ma merged 315 commits intoNic-Ma:3665-add-label-transformfrom Jan 14, 2022
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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]>
Signed-off-by: Nic Ma <[email protected]>
* relax atol for a100 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes #3071 Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * add tf32 tests Signed-off-by: Wenqi Li <[email protected]> * fixes rtol wit tf32 Signed-off-by: Wenqi Li <[email protected]> * detect tf32 Signed-off-by: Wenqi Li <[email protected]> * update flag Signed-off-by: Wenqi Li <[email protected]> * fixes testing util Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance random computation Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
…3079) * Torch `CropForeground`, `HistogramNormalize`, `RandHistogramShift` Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add MLFlowHandler Signed-off-by: Nic Ma <[email protected]> * [DLMED] add optional import Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc format Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
…rop` (#3078) Torch `AddCoordinateChannels`, `ExtremePointsChannel`, `RandWeightedCrop`
* [DLMED] fix wrong doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* fixes 33097 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]>
* [DLMED] update intensity transforms Signed-off-by: Nic Ma <[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]>
Signed-off-by: Nic Ma <[email protected]>
* update get_rank calls Signed-off-by: Wenqi Li <[email protected]> * relaxing atol/rtol in tests.test_savitzky_golay_filter Signed-off-by: Wenqi Li <[email protected]> * skip timing for cpu only tests Signed-off-by: Wenqi Li <[email protected]> * fixes import ContentTooShortError Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* avoid re-creation of AddChannel in EnsureChannelFirst
…dComponents (#3647) * [DLMED] support single channel One-Hot 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: Wenqi Li <[email protected]>
* [DLMED] add missing doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance correct centers Signed-off-by: Nic Ma <[email protected]>
* option to occlude all channels simultaneously
* removed duplicated Signed-off-by: Wenqi Li <[email protected]> * update gitignore to ignore readthedocs autobuild Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* ignore some flake8 errors Signed-off-by: Wenqi Li <[email protected]> * fixes #3660 2003->2106 Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add default values Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo 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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Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.