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merge master#429

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Nic-Ma merged 183 commits intoNic-Ma:mainNic-Ma/MONAI:mainfrom Project-MONAI:devProject-MONAI/MONAI:devCopy head branch name to clipboardJul 8, 2022

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Commits on Apr 4, 2022

• Adding discussion on format to bundle specification (#4047)

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

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Commits on Apr 5, 2022

• 4060 Add PatchIter and PatchIterd transform (#4061)

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• Fix a logical error in level verification (#4075)

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Commits on Apr 6, 2022

• [DLMED] add allow_missing_reference (#4079)

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• autofixes: Refactor if expression and clangformat (#4081)

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Commits on Apr 7, 2022

• SplitDim (#3884)

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Commits on Apr 8, 2022

• update mmar tests (#4091)

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Commits on Apr 10, 2022

• extending the mlp module (#4089)

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• added 2D (normalized) surface dice metric (#4050)

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Commits on Apr 11, 2022

• 4073 Enhance DynUNet doc-strings (#4102)

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Commits on Apr 12, 2022

• 4105 drops pt16 support (#4106)

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• Make pixelshuffle scriptable (#4109)

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• meta tensor (#4077)

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Commits on Apr 13, 2022

• 4084 Add kwargs for Tensor.to() in engines (#4112)

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• fixes pytorch version tests (#4127)

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Commits on Apr 14, 2022

• update meta tensor api (#4131)

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• runtests.sh isort (#4134)

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• update citation (#4133)

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• ToMetaTensor and FromMetaTensor transforms (#4115)

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• no skip if before pytorch 1.7 (#4139)

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Commits on Apr 19, 2022

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

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• 4116 Add support for advanced args of AMP (#4132)

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Commits on Apr 20, 2022

• New wsireader (#4147)

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

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• 4148 Enhance engine iteration logic and the typehints (#4150)

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Commits on Apr 22, 2022

• Add OpenSlide support for new WSIReader (#4155)

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• Redesign PatchWSIDataset (#4152)

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• 4095 Add bundle download (#4114)

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Commits on Apr 23, 2022

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

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• Fixed an error in DiNTS model implementation and enabled act and norm layer options (#4157)

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• Split transform (#4153)

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Commits on Apr 25, 2022

• fix bundle download test issue (#4169)

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Commits on Apr 26, 2022

• 4094 Enhance ckpt_export to save config files (#4159)

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• Move RGB/RGBA checks to base class (#4171)

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• [CICD] To support temp dgx runner (#4175)

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• Test fix for AMP kwargs (#4178)

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Commits on Apr 27, 2022

• 4167 enhance bundle run logic (#4168)

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• 4172 aggregate with buffer copy (#4174)

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• 4173 Enhance decathlon datalist for test section format (#4186)

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• Add DeepEdit transforms and interaction (#4164)

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• Remove commented out code (#4187)

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• Remove unused global variable (#4189)

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• add adn unet (#4185)

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Commits on Apr 28, 2022

• [DLMED] enhance load_files (#4192)

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Commits on Apr 29, 2022

• enhance mean dice (#4163)

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• Make transforms optional (#4190)

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• 4200 workaround for ci apt (#4202)

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Commits on Apr 30, 2022

• Update the default value of lazy arg in the ConfigParser to True (#4203)

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Commits on May 2, 2022

• udpate md5 (#4213)

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Commits on May 3, 2022

• add swin_unetr model (#4074)

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Commits on May 5, 2022

• 4217 Update PyTorch docker to 22.04 (#4218)

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• Add InstanceNorm3dNVFuser support (#4194)

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Commits on May 6, 2022

• Update dice.py (#4234)

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• Bug fix and improvement in WSI (#4216)

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Commits on May 9, 2022

• Replace module (#4245)

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Commits on May 10, 2022

• Add GaussianSmooth as antialiasing filter in Resize (#4249)

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Commits on May 11, 2022

• 4235 fix 2204 nvfuser issue (#4241)

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• Update to Bundle Specifiation (#4250)

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• gradient based saliency (#4236)

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Commits on May 12, 2022

• 4256 Fix wrong spatial shape in SampleCrop transforms (#4263)

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Commits on May 13, 2022

• Split patch functionality for PatchWSIReader (#4251)

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• Implement NrrdReader (#4259)

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• 4269 - fixes resample mode typos (#4272)

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Commits on May 14, 2022

• unify spelling of metdata in docstrings (#4273)

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Commits on May 16, 2022

• optional nrrd (#4279)

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Commits on May 18, 2022

• 4281 - adds zero_centered option to AffineTransform (#4282)

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• Recursive NVTX Range (#4270)

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• add box mode convert in box_utils (#4254)

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Commits on May 19, 2022

• cron tutorial master to main (#4291)

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• track transforms (#4284)

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• add box center related funcs to box_utils (#4290)

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• Make the order of slices row-major (#4297)

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• 4293 local pre-commit check support (#4292)

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• merge certain files from feature/MetaTensor to dev (#4298)

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Commits on May 20, 2022

• add box iou into box utils (#4289)

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• fix RandAffine with randomize==False (#4304)

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• add box mode convert transform (#4302)

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Commits on May 22, 2022

• add box ops for affine and zoom (#4307)

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• update swin_unetr block parameter names (#4311)

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• 4312 Fix squeeze issue of get_mask_edges (#4313)

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Commits on May 23, 2022

• 4314 Enhance UnetResBlock (#4317)

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• multiprocessing test metatensor (#4308)

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Commits on May 24, 2022

• add box transforms for affine and zoom (#4309)

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• revise dice metric docstring, fixes testing data (#4329)

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• Add spatial crop and clip box to Box utils (#4316)

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• 4330 Fix GPU out of memory issue in tests (#4333)

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• add box flip transforms (#4334)

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Commits on May 25, 2022

• 4255 Update bundle download (#4331)

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• add box non_max_suppression (#4337)

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Commits on May 26, 2022

• 4343 adds interp mode (#4344)

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• 4354 workaround protobuf issue (#4355)

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• Sliding Patch WSI Dataset (#4239)

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• add feature pyramid network (FPN) for detection (#4342)

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• add box clip transforms (#4338)

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• Adding Bundle Utility Functions (#4324)

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• 4323 deprecate SegmentationSaver, TorchVisionFullyConvModel (#4347)

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• improve dtype conversion (#4357)

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Commits on May 27, 2022

• 4348 Improve doc and unit tests for "correct center" of crop transforms (#4362)

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• resize skip interpolation if spatial shapes match (#4369)

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• fixes integration test (#4373)

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• add box coder for detection (#4365)

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Commits on May 28, 2022

• 4375 workaround mlflow integration (#4376)

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• 4346 Enhance contribution guide for optional package (#4367)

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• Add transform between box and mask (#4366)

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

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• add ATSS matcher for detection (#4350)

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Commits on May 30, 2022

• 4323 - review readme (#4390)

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• add RetinaNet network (#4378)

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• Enhance expression logic of bundle config (#4377)

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• add anchor generators used for detection (#4336)

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• Define PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION only when protobuf>=4.0.0 is used (#4397)

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Commits on May 31, 2022

• add hard_negative_sampler.py for detection (#4301)

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• GridPatch to Extract Tiles/Patches (#4321)

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• Foreground Tissue Mask (#4379)

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• PR: NuClick Transforms Addition (#4266)

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• 4401 improve parser error message (#4402)

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• Minor enhancement for several places (#4409)

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• Move append items to list definition (#4417)

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Commits on Jun 1, 2022

• Refactor Probability Map Producer Handler (#4382)

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• 4426 Enhance download_url and fixes error msg (#4427)

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• Add detector utils (#4434)

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Commits on Jun 2, 2022

• add box selector (#4437)

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• test update checkout (#4440)

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• Enhance ensure_tuple for corner cases (#4439)

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• add random foreground crop for boxes (#4388)

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• Add prediction utils that enable inferer (#4438)

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• Add RetinaNet detector (#4400)

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Commits on Jun 3, 2022

• Masked Patch WSI Dataset (#4410)

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• add RetinaNet detector loss computation (#4446)

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• New segmentation loss functions and metrics (#4444)

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Commits on Jun 4, 2022

• 4451 adds testing file downloading (#4452)

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Commits on Jun 6, 2022

• matshow3d: supports subplot axes input (#4459)

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• Adding Thread Worker Option to ThreadDataLoader (#4252)

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Commits on Jun 7, 2022

• Add RotateBox90 transforms (#4460)

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• 4463 Enhance doc-string of Normalize and other places (#4464)

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• Add coco detection metrics (#4447)

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• add GIoU loss for box detection (#4454)

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Commits on Jun 8, 2022

• 4386 Update highlights for 0.9 release (#4419)

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Commits on Jun 9, 2022

• 4323 update changelog for 0.9.0 (#4470)

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Commits on Jun 10, 2022

• add box convert to world coordinate transform (#4476)

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• 4480 skip unused resampling (#4481)

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• 4477 4478 iterables enhancements (#4479)

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• Fixing SliceInferer Issue (#4482)

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Commits on Jun 12, 2022

• enhance swin_unetr relative position (#4486)

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Commits on Jun 13, 2022

• More Efficient GridPatch and RandGridPatch V2 (#4473)

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• 4489 Enhance hyperlinks of config syntax doc (#4490)

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Commits on Jun 15, 2022

• 4323 update docs release versions (#4494)

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• changed ngc download url (#4508)

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• Fixed generalized dice score (#4511)

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Commits on Jun 16, 2022

• Update bundle specification doc (#4512)

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• add ngc to PATH (#4517)

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• corner case in coco metric test (#4519)

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Commits on Jun 20, 2022

• Add youden_index and youden as aliases for bm (#4534)

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• MetaTensor non-breaking changes (#4539)

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Commits on Jun 21, 2022

• 4530 optional SummaryWriter (#4546)

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• Enhance type conversion of MetaTensor (#4549)

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Commits on Jun 22, 2022

• 4351 - adds StrEnum (#4556)

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• Move metatensor support into dev (update inverse, runtests.sh) (#4557)

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Commits on Jun 23, 2022

• Wrap Type to the typing of writer parameter of SaveImage (#4561)

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• add TORCH backend for RandHistogramShift (#4567)

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• correct code examples in box_utils docstring (#4572)

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Commits on Jun 24, 2022

• Fix incorrect documentation for ResampleToMatch (#4576)

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• correct a bug in convert_mask_to_box (#4583)

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• Fix error in the bundle script (#4584)

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Commits on Jun 26, 2022

• Add Unified Focal Loss (#4488)

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• 4502-implement-pydicomreader (#4550)

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Commits on Jun 27, 2022

• 4589 enable dropout in dynunet (#4590)

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• Move dictionary inserts to its definition (#4594)

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Commits on Jun 28, 2022

• 4578 add default return for ConfigParser (#4601)

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Commits on Jun 29, 2022

• mri utils added (#4552)

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• Hovernet and associated test script added (#4602)

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• Fix the location type returned in GridPatch when padding (#4598)

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Commits on Jun 30, 2022

• debug device conflict (#4614)

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• 4531 test/update deps versions (#4605)

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Commits on Jul 2, 2022

• fix: avoid duplicate log when multiple DataStats are used (#4623)

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Commits on Jul 5, 2022

• [pre-commit.ci] pre-commit suggestions (#4631)

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• Move metatensor support into dev branch (crop/pad) (#4548)

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• Move metatensor support into dev branch (#4562)

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• compat. torch 1.7/1.8 sw integration

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Commits on Jul 6, 2022

• 4641 PadListDataCollate for metatensor (#4642)

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• Fix casting of location dtype in GridPatch (#4635)

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Commits on Jul 7, 2022

• 4636 4637 backward compatible types (#4638)

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