3531 Add args to subclass of CacheDataset #3532

Nic-Ma · 2021-12-22T00:31:13Z

Fixes #3531 .

Description

This PR added new args of CacheDataset to subclasses.

Status

Ready

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.

merge master

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

Nic-Ma · 2021-12-22T00:31:44Z

/black

Nic-Ma · 2021-12-22T00:31:49Z

/build

monai/apps/datasets.py

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

wyli

Looks good, note that the download utility also accepts a progress bar flag

Nic-Ma · 2021-12-22T07:05:38Z

Looks good, note that the download utility also accepts a progress bar flag

Hi @wyli ,

Do you think it's better to apply this progress bar arg for both CacheDataset and download?

Thanks.

wyli · 2021-12-22T07:17:09Z

Looks good, note that the download utility also accepts a progress bar flag

Hi @wyli ,

Do you think it's better to apply this progress bar arg for both CacheDataset and download?

Thanks.

Im fine with either option, as long as the docstring is consistent with it...

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

Nic-Ma · 2021-12-22T08:26:15Z

Hi @wyli ,

I updated the logic to apply progress arg for both.

Thanks.

wyli · 2021-12-22T11:33:17Z

/build

wyli · 2021-12-22T12:18:42Z

/build

Nic-Ma · 2021-12-22T13:33:07Z

/build

Nic-Ma · 2021-12-22T14:10:31Z

/build

Nic-Ma · 2021-12-22T14:51:27Z

Mark the Blossom error for future reference:

2021-12-22T14:40:04.5597947Z Traceback (most recent call last):
2021-12-22T14:40:04.5599020Z   File "/opt/conda/lib/python3.8/site-packages/parameterized/parameterized.py", line 533, in standalone_func
2021-12-22T14:40:04.5599815Z     return func(*(a + p.args), **p.kwargs)
2021-12-22T14:40:04.5600883Z   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_cucim_transform.py", line 79, in test_tramsforms_numpy_single
2021-12-22T14:40:04.5601701Z     output = CuCIM(**params)(input)
2021-12-22T14:40:04.5602662Z   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/transforms/utility/array.py", line 1216, in __call__
2021-12-22T14:40:04.5603525Z     return self.transform(data, *self.args, **self.kwargs)
2021-12-22T14:40:04.5604556Z   File "/opt/conda/lib/python3.8/site-packages/cucim/core/operations/intensity/zoom.py", line 153, in zoom
2021-12-22T14:40:04.5605353Z     kernel = CUDA_KERNELS.get_function("zoom_out_kernel")
2021-12-22T14:40:04.5606092Z   File "cupy/_core/raw.pyx", line 485, in cupy._core.raw.RawModule.get_function
2021-12-22T14:40:04.5606984Z   File "cupy/_core/raw.pyx", line 96, in cupy._core.raw.RawKernel.kernel.__get__
2021-12-22T14:40:04.5607845Z   File "cupy/_core/raw.pyx", line 113, in cupy._core.raw.RawKernel._kernel
2021-12-22T14:40:04.5608663Z   File "cupy/_util.pyx", line 59, in cupy._util.memoize.decorator.ret
2021-12-22T14:40:04.5609428Z   File "cupy/_core/raw.pyx", line 547, in cupy._core.raw._get_raw_module
2021-12-22T14:40:04.5610153Z   File "cupy/_core/core.pyx", line 1961, in cupy._core.core.compile_with_cache
2021-12-22T14:40:04.5610923Z   File "cupy/_core/core.pyx", line 2030, in cupy._core.core.compile_with_cache
2021-12-22T14:40:04.5612189Z   File "/opt/conda/lib/python3.8/site-packages/cupy/cuda/compiler.py", line 434, in compile_with_cache
2021-12-22T14:40:04.5612955Z     return _compile_with_cache_cuda(
2021-12-22T14:40:04.5613953Z   File "/opt/conda/lib/python3.8/site-packages/cupy/cuda/compiler.py", line 502, in _compile_with_cache_cuda
2021-12-22T14:40:04.5614666Z     mod.load(cubin)
2021-12-22T14:40:04.5615438Z   File "cupy/cuda/function.pyx", line 241, in cupy.cuda.function.Module.load
2021-12-22T14:40:04.5616490Z   File "cupy/cuda/function.pyx", line 243, in cupy.cuda.function.Module.load
2021-12-22T14:40:04.5617757Z   File "cupy_backends/cuda/api/driver.pyx", line 253, in cupy_backends.cuda.api.driver.moduleLoadData
2021-12-22T14:40:04.5619107Z   File "cupy_backends/cuda/api/driver.pyx", line 125, in cupy_backends.cuda.api.driver.check_status
2021-12-22T14:40:04.5620761Z cupy_backends.cuda.api.driver.CUDADriverError: CUDA_ERROR_UNSUPPORTED_PTX_VERSION: the provided PTX was compiled with an unsupported toolchain.

Thanks.

Nic-Ma · 2021-12-22T14:51:40Z

/build

wyli · 2021-12-22T15:46:41Z

/build

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

* 3415 Update WSIReader (#3417) * Update WSIReader level/location/size calculation Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update location downsampling Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update tests and add a new test case Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update few names and logics Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix the dependency issue Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Check for imagecodecs + tifffile Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove new test case that uses too much memory Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add new case and ignore level=0 for TiffFile Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Address comments Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> * update create_file_basename (#3436) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Update TiffFile backend in WSIReader (#3438) * Update TiffFile backend to read only the entire image Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * 3429 Enhance the scalar write logic of TensorBoardStatsHandler (#3431) * [DLMED] extract write logic 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] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * 3430 support dataframes and streams in CSVDataset (#3440) * [DLMED] add dataframe Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance CSV iterable dataset Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typehints Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add comment 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] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix file close issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix doc 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> * Add base class for workflows (#3445) * [DLMED] add BaseWorkflow Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] add *args, **kwargs Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> * Enhance deprecated arg for kwargs in CSV datasets (#3446) * [DLMED] fix deprecated arg 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> * 3293 Remove extra deep supervision modules of DynUNet (#3427) * enhance dynunet Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix black issue Signed-off-by: Yiheng Wang <vennw@nvidia.com> * use strict=False Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix black 21.12 error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * enhance code and update docstring Signed-off-by: Yiheng Wang <vennw@nvidia.com> * 471- fixes deprecated args (#3447) * fixes deprecated args Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * improve error message if reader nott available (#3457) improve error message if reader nott available * adds the missing imports (#3462) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise MILModel docstring (#3459) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * deprecate reduction (#3464) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3444 Add DatasetFunc (#3456) * [DLMED] add dataset generator Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add DatasetGenerator Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix wrong test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove return Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update rtol for CI Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> * Add missing components to API doc (#3468) * [DLMED] add missing docs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add missing components Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix test Signed-off-by: Nic Ma <nma@nvidia.com> * 3466 3467 Add `channel_wise` and correct doc-string (#3469) * [DLMED] add channel-wise Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] skip test if before 1.7 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> * [DLMED] remove cls (#3475) Signed-off-by: Nic Ma <nma@nvidia.com> * Add Iteration base class (#3472) * [DLMED] add Iteration base class 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> * fix link error (#3488) Signed-off-by: Yiheng Wang <vennw@nvidia.com> * 3465 Support string as dtype (#3478) * [DLMED] support string dtype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to 0.4.7 (#3483) Signed-off-by: Nic Ma <nma@nvidia.com> * Improve NVTX Range Naming (#3484) * Update to not include number for the name of the first range Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update CuCIM and TorchVision wrappers to include name Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update nvtx range to append undelying class for wrapper tranforms Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add new test cases to cover changes Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update cucim and torchvision check Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * 3471 3491 Add example images for intensity transforms (#3494) * [DLMED] add missing images Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix 3471 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <nma@nvidia.com> * Make bending energy loss invariant to resolution (#3493) * make bending energy loss invariant to resolution fixes #3485 Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com> * set BendingEnergyLoss default normalize to False Maybe it's more important that the default behavior match usage of the term "bending energy" elsewhere, rather than that it be the most convenient behavior. Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com> * Removes redundant casting -- ensure tuple (#3495) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3498 Correct `kwargs` arg for `convert_to_torchscript` (#3499) * [DLMED] correct kwargs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix grammar Signed-off-by: Nic Ma <nma@nvidia.com> * update tests with 1.10.1 (#3500) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3501 Add dict version SavitzkyGolaySmoothd (#3502) * [DLMED] add SavitzkyGolaySmoothd Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * remove file (#3507) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * avoid 60.0.0 (#3514) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] add 6 new transform images (#3512) Signed-off-by: Nic Ma <nma@nvidia.com> * support of reversed indexing (#3508) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Adding Torchscript utility functions (#3138) * Adding Torchscript utility functions Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [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 <monai.miccai2019@gmail.com> * Adding Torchscript utility functions Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Added test for extra files Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updates Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com> * 3517 Refine AddCoordinateChannels transform (#3524) * [DLMED] change to utility transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance args Signed-off-by: Nic Ma <nma@nvidia.com> * 3521 Copyright header update (#3522) * adds missing item Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update the contributing guide Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update copyright headers Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3521 - adds a util to check the licence info (#3523) * util to check the licence info Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update flags Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3350 Remove PyTorch 1.5.x related logic and mark versions for all new APIs (#3526) * [DLMED] clarify old APIs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * 3533 Update PyTorch docker to 21.12 (#3534) * [DLMED] update to 21.12 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add PyTorch 1.9 test Signed-off-by: Nic Ma <nma@nvidia.com> * 3531 Add args to subclass of CacheDataset (#3532) * [DLMED] add missing args Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update progress arg Signed-off-by: Nic Ma <nma@nvidia.com> * 3525 Fix invertible issue in OneOf compose (#3530) * [DLMED] fix oneof Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update index Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * Revert "[DLMED] update according to comments" This reverts commit c6c3a35. Signed-off-by: Nic Ma <nma@nvidia.com> * Revert "[DLMED] update index" This reverts commit 649a7c5. Signed-off-by: Nic Ma <nma@nvidia.com> * 3535 - drop python 36 support (#3536) * drop py36 support Signed-off-by: Wenqi Li <wenqil@nvidia.com> * drop 20.09 test because of python min version 3.6 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * error->warning, revise copyright Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3541 has cupy check (#3544) * has cupy check Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3053 release *_dist.py tests memory to avoid OOM (#3537) * adds min. memory testing utils Signed-off-by: Wenqi Li <wenqil@nvidia.com> * include valueerror for robust outcome Signed-off-by: Wenqi Li <wenqil@nvidia.com> * ensure float Signed-off-by: Wenqi Li <wenqil@nvidia.com> * msg improvements Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update threshold Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove ref Signed-off-by: Wenqi Li <wenqil@nvidia.com> * separate disttests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3539 Remove decollate warning (#3545) * [DLMED] remove warning Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance set_determinism (#3547) Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> * Smooth Deform (#3551) * Adding smooth deform transform Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Docs update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Type fixing Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [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 <monai.miccai2019@gmail.com> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [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 <eric.kerfoot@kcl.ac.uk> * Fix for moveaxis Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding example images, random field sized reduced to (10,10,10) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Changed backend Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * Tweak Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> * 3552 - runtest.sh defaults to no build/install (#3555) * runtest.sh defaults to no build/install Signed-off-by: Wenqi Li <wenqil@nvidia.com> * following test case conventions for multiprocessing - adding `_dist` to multiprocessing test cases - decouple multiprocessing LMDB tests from `test_lmdbdataset` Signed-off-by: Wenqi Li <wenqil@nvidia.com> * exclude lmdbdataset tests in min_tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> * Remove apply_same_field (#3556) Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * skipping pretraining network loading when downloading is unsuccessful (#3558) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] fix mypy errors (#3562) Signed-off-by: Nic Ma <nma@nvidia.com> * 3559 Enhance `DatasetSummary` for several points (#3560) * [DLMED] update dataset summary Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance data type Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> * add box util in monai/data * add box util in monai/data * [pre-commit.ci] pre-commit suggestions (#3568) 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> * 3565 - adds metadata when loading dicom series (#3566) * adds metadata when loading dicom series Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes timed tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 3580 - create codeql-analysis.yml (#3579) * Create codeql-analysis.yml Signed-off-by: Wenqi Li <wenqil@nvidia.com> * build cpp Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes Multiplication result converted to larger type Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes url parsing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 498 Add logger_handler to LrScheduleHandler (#3570) * [DLMED] add log handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] test CI Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix logging Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] temp test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix wrong unit test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix wrong test cases Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Ebrahim Ebrahim <ebrahim.mt@gmail.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Nic-Ma and others added 7 commits February 1, 2021 19:15

Merge pull request #19 from Project-MONAI/master

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Merge pull request #32 from Project-MONAI/master

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Merge pull request #180 from Project-MONAI/dev

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Merge pull request #214 from Project-MONAI/dev

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Merge pull request #328 from Project-MONAI/dev

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merge master

[DLMED] add missing args

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

Merge branch 'dev' into enhance-decathlon-dataset

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Nic-Ma requested review from rijobro, wyli and ericspod December 22, 2021 00:31

wyli reviewed Dec 22, 2021

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[DLMED] update according to comments

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

wyli approved these changes Dec 22, 2021

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[DLMED] update progress arg

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

Nic-Ma force-pushed the enhance-decathlon-dataset branch from c1a7494 to c2bc9a3 Compare December 22, 2021 08:24

Merge branch 'dev' into enhance-decathlon-dataset

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wyli enabled auto-merge (squash) December 22, 2021 09:01

wyli disabled auto-merge December 22, 2021 15:05

wyli enabled auto-merge (squash) December 22, 2021 15:46

wyli merged commit 9caa1d0 into Project-MONAI:dev Dec 22, 2021

wyli mentioned this pull request Dec 23, 2021

cupy_backends.cuda.api.driver.CUDADriverError #3541

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3531 Add args to subclass of CacheDataset #3532

3531 Add args to subclass of CacheDataset #3532

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3531 Add args to subclass of CacheDataset #3532

3531 Add args to subclass of CacheDataset #3532

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