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thanks, the code change looks good, could you please sign your commit: https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md#signing-your-work |
reduce redundant operations in DiceFocalLoss, initially caused oom Signed-off-by: Ryan Clanton <[email protected]>
for more information, see https://pre-commit.ci Signed-off-by: Ryan Clanton <[email protected]>
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Thanks Wyli, should be signed now, best |
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/black |
Signed-off-by: monai-bot <[email protected]>
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/build |
Can-Zhao
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May 10, 2022
* Update dice.py reduce redundant operations in DiceFocalLoss, initially caused oom Signed-off-by: Ryan Clanton <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Ryan Clanton <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[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]>
wyli
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May 13, 2022
* add swin_unetr model (#4074) * add swin_unetr model Signed-off-by: kbressem <[email protected]> * 4217 Update PyTorch docker to 22.04 (#4218) * [DLMED] update to 22.04 Signed-off-by: Nic Ma <[email protected]> * fixes unit test tests.test_lr_finder Signed-off-by: Wenqi Li <[email protected]> * test new_empty Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Signed-off-by: kbressem <[email protected]> * Add InstanceNorm3dNVFuser support (#4194) * implement the base class 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 * add unittest 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 * autofix Signed-off-by: Yiheng Wang <[email protected]> * switch to call apex directly Signed-off-by: Yiheng Wang <[email protected]> * uncomment unittest Signed-off-by: Yiheng Wang <[email protected]> * add apex install link in docstring Signed-off-by: Yiheng Wang <[email protected]> * add channels_last_3d test case Signed-off-by: Yiheng Wang <[email protected]> * rewrite types Signed-off-by: Yiheng Wang <[email protected]> * change types Signed-off-by: Yiheng Wang <[email protected]> * add docstrings 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: Wenqi Li <[email protected]> Signed-off-by: kbressem <[email protected]> * Update dice.py (#4234) * Update dice.py reduce redundant operations in DiceFocalLoss, initially caused oom Signed-off-by: Ryan Clanton <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Ryan Clanton <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[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]> Signed-off-by: kbressem <[email protected]> * Bug fix and improvement in WSI (#4216) * Make all transforms optional Signed-off-by: Behrooz <[email protected]> * Update wsireader tests Signed-off-by: Behrooz <[email protected]> * Remove optional from PersistentDataset and its derivatives Signed-off-by: Behrooz <[email protected]> * Add unittests for cache without transform Signed-off-by: Behrooz <[email protected]> * Add default replace_rate Signed-off-by: Behrooz <[email protected]> * Add default value Signed-off-by: Behrooz <[email protected]> * Set default replace_rate to 0.1 Signed-off-by: Behrooz <[email protected]> * Update metadata to include path Signed-off-by: Behrooz <[email protected]> * Adds SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Add unittests for SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Update references Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Remove smart cache Signed-off-by: Behrooz <[email protected]> * Remove unused imports Signed-off-by: Behrooz <[email protected]> * Add path metadata for OpenSlide Signed-off-by: Behrooz <[email protected]> * Update metadata to be unified across different backends Signed-off-by: Behrooz <[email protected]> * Update wsi metadata for multi wsi objects Signed-off-by: Behrooz <[email protected]> * Add unittests for wsi metadata Signed-off-by: Behrooz <[email protected]> Signed-off-by: kbressem <[email protected]> * Replace module (#4245) * replace modules Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * replace_module -> replace_modules Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> Signed-off-by: kbressem <[email protected]> * Add GaussianSmooth as antialiasing filter in Resize (#4249) Signed-off-by: Can Zhao <[email protected]> Signed-off-by: kbressem <[email protected]> * 4235 fix 2204 nvfuser issue (#4241) * reproduce issue Signed-off-by: Yiheng Wang <[email protected]> * remove 22.01 02 Signed-off-by: Yiheng Wang <[email protected]> * remove other workflows Signed-off-by: Yiheng Wang <[email protected]> * run on pull request Signed-off-by: Yiheng Wang <[email protected]> * remove sleep Signed-off-by: Yiheng Wang <[email protected]> * test single layer forward Signed-off-by: Yiheng Wang <[email protected]> * add has_nvfuser Signed-off-by: Yiheng Wang <[email protected]> * add check within factory Signed-off-by: Yiheng Wang <[email protected]> * revert to original cron.yml 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 old pt issue Signed-off-by: Yiheng Wang <[email protected]> * change to return directly if no cuda Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: kbressem <[email protected]> * Update to Bundle Specifiation (#4250) * Update to bundle specifiation 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 * Adding description in spec discussing the saved Torchscript object's file storage behaviour, and tweaking ckpt_export to add .json extension Signed-off-by: Eric Kerfoot <[email protected]> * Annotating optional bundle files Signed-off-by: Eric Kerfoot <[email protected]> * Adjusted ckpt_export test Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: kbressem <[email protected]> * Implement NrrdReader and NrrdImage classes Signed-off-by: kbressem <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: kbressem <[email protected]> * run auto style fixes on image_reader.py Signed-off-by: kbressem <[email protected]> * add NrrdReader to monai/data/__init__.py Signed-off-by: kbressem <[email protected]> * Change the way spatial information is handled in NrrdReader Signed-off-by: kbressem <[email protected]> * add tests for NrrdReader Signed-off-by: kbressem <[email protected]> * Add NrrdReader to list of possible readers for LoadImage Signed-off-by: kbressem <[email protected]> * autofix formating Signed-off-by: kbressem <[email protected]> * autofix formating Signed-off-by: kbressem <[email protected]> * change NrrdImage class to namedtuple and make flake8 happy Signed-off-by: kbressem <[email protected]> * Add pynrrd to requirements Signed-off-by: kbressem <[email protected]> * correct typing for namedtumple make flake8 happy Signed-off-by: kbressem <[email protected]> * Add pynrrd info to `get_optional_config_values` Changed NrrdImage to dataclass Signed-off-by: kbressem <[email protected]> * exclude test_nrrd_reader.py from min tests Signed-off-by: kbressem <[email protected]> * add pynrrd to config files Signed-off-by: kbressem <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change the way space is handled in the header. Now, if space is not in header, it is assumed to be LPS and converted to RAS. If space is defined and not LPS, nothing is done to prevent wrong conversions. Signed-off-by: kbressem <[email protected]> * add `TestLoadSaveNrrd` where it is tested if a nrrd file, created by ITKWriter can be loaded again. 2D and 3D files with no channels are tested Signed-off-by: kbressem <[email protected]> * autofix format Co-authored-by: kbressem <[email protected]>
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reduce redundant operations in DiceFocalLoss, initially caused oom
Fixes # None
Description
A few sentences describing the changes proposed in this pull request.
I was reaching out of memory error on DiceFocalLoss, I notice redundant operations within such as including background and to_onehot_y and replaced with one operation. In my situation there is 95 labels and appears to not be completely deleted before trying to onehot in focal loss as well.
Status
Ready/Work in progress/Hold
The function is working for me, Ready
Types of changes