| a20ff4e | Nic Ma | 08 June 2022, 16:23:01 UTC | 4386 Update highlights for 0.9 release (#4419) * [DLMED] enhance doc according to user's feedback Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update fast training tutorial Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add bundle description Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add swin unetr Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add ImageWriter Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add DeepEdit Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add Nuclick for Nuclei segmentation Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update pathology Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] clear files Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add detection Signed-off-by: Nic Ma <nma@nvidia.com> * docs update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] fix wrong links Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update detection chart Signed-off-by: Nic Ma <nma@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 08 June 2022, 16:23:01 UTC |
| df4a7d7 | Can Zhao | 07 June 2022, 18:55:25 UTC | add GIoU loss for box detection (#4454) | 07 June 2022, 18:55:25 UTC |
| 7d77322 | Can Zhao | 07 June 2022, 16:09:06 UTC | Add coco detection metrics (#4447) | 07 June 2022, 16:09:06 UTC |
| f00e9be | Nic Ma | 07 June 2022, 15:24:39 UTC | 4463 Enhance doc-string of Normalize and other places (#4464) [DLMED] enhance docs Signed-off-by: Nic Ma <nma@nvidia.com> | 07 June 2022, 15:24:39 UTC |
| f3cbba2 | Can Zhao | 07 June 2022, 06:30:54 UTC | Add RotateBox90 transforms (#4460) * add box rot90 Signed-off-by: Can Zhao <canz@nvidia.com> * docstring Signed-off-by: Can Zhao <canz@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docstring typos Signed-off-by: Can Zhao <canz@nvidia.com> * add case k=0 Signed-off-by: Can Zhao <canz@nvidia.com> * typo Signed-off-by: Can Zhao <canz@nvidia.com> * fix bug Signed-off-by: Can Zhao <canz@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 07 June 2022, 06:30:54 UTC |
| 22924f5 | Eric Kerfoot | 06 June 2022, 20:25:18 UTC | Adding Thread Worker Option to ThreadDataLoader (#4252) * Adding thread worker option to ThreadDataLoader 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 * Fixes Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fixes Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Reworking of implementation with global data 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 Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Tweak to cleanup Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Try to disable thread test to see if global data is causing failure Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Undoing 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 * Fix 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> | 06 June 2022, 20:25:18 UTC |
| f025193 | Wenqi Li | 06 June 2022, 07:10:58 UTC | matshow3d: supports subplot axes input (#4459) * support of subplots axes input Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 06 June 2022, 07:10:58 UTC |
| db02f07 | Wenqi Li | 04 June 2022, 06:25:08 UTC | 4451 adds testing file downloading (#4452) adds download link Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 04 June 2022, 06:25:08 UTC |
| c2347fb | João Lourenço Silva | 03 June 2022, 21:07:51 UTC | New segmentation loss functions and metrics (#4444) * Added GeneralizedDiceFocalLoss to losses. Added GeneralizedDiceScore to metrics. Added function to check whether tensors are binarized to metrics.util and refactored metrics to use it. Signed-off-by: João Lourenço Silva <joao.lourenco.silva@tecnico.ulisboa.pt> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Refactored monai.metrics.utils.is_binary_tensor function to receive name of the tensor as argument and issue warnings directly * Refactored metric classes to use is_binary_tensor function | 03 June 2022, 21:07:51 UTC |
| 4cddaa8 | Can Zhao | 03 June 2022, 15:30:08 UTC | add RetinaNet detector loss computation (#4446) | 03 June 2022, 15:30:08 UTC |
| 07306c0 | Behrooz Hashemian | 03 June 2022, 02:44:41 UTC | Masked Patch WSI Dataset (#4410) * Implement MaskedPatchWSIDataset Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update the min verison for skimage to 0.19.0 Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add channel last for wsireader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Replace all wsi patch key related with WSIPatchKeys Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update ProbMapKeys.NAME Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update GridPatch and iter_patch to support no padding Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add threshold for filtering to grid patch Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 03 June 2022, 02:44:41 UTC |
| e2f160d | Can Zhao | 02 June 2022, 21:30:58 UTC | Add RetinaNet detector (#4400) | 02 June 2022, 21:30:58 UTC |
| 5d7eb10 | Can Zhao | 02 June 2022, 17:53:18 UTC | Add prediction utils that enable inferer (#4438) | 02 June 2022, 17:53:18 UTC |
| bbb35e2 | Can Zhao | 02 June 2022, 15:11:30 UTC | add random foreground crop for boxes (#4388) | 02 June 2022, 15:11:30 UTC |
| cfd1562 | Nic Ma | 02 June 2022, 10:20:54 UTC | Enhance ensure_tuple for corner cases (#4439) | 02 June 2022, 10:20:54 UTC |
| 187fec8 | Wenqi Li | 02 June 2022, 08:31:23 UTC | test update checkout (#4440) | 02 June 2022, 08:31:23 UTC |
| bbc628d | Can Zhao | 02 June 2022, 02:49:53 UTC | add box selector (#4437) | 02 June 2022, 02:49:53 UTC |
| 4434a3f | Can Zhao | 01 June 2022, 19:34:13 UTC | Add detector utils (#4434) | 01 June 2022, 19:34:13 UTC |
| d8d24ee | Yiheng Wang | 01 June 2022, 18:58:27 UTC | 4426 Enhance download_url and fixes error msg (#4427) * enhance download Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [MONAI] code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * fixes https://github.com/Project-MONAI/MONAI/issues/4432 Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 01 June 2022, 18:58:27 UTC |
| 40373b2 | Behrooz Hashemian | 01 June 2022, 13:13:18 UTC | Refactor Probability Map Producer Handler (#4382) * Update wsi metadata names Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Implement prob map handler Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 01 June 2022, 13:13:18 UTC |
| 38b7943 | deepsource-autofix[bot] | 31 May 2022, 22:57:29 UTC | Move append items to list definition (#4417) | 31 May 2022, 22:57:29 UTC |
| a737d58 | Nic Ma | 31 May 2022, 19:35:51 UTC | Minor enhancement for several places (#4409) | 31 May 2022, 19:35:51 UTC |
| f540e34 | Wenqi Li | 31 May 2022, 18:40:51 UTC | 4401 improve parser error message (#4402) | 31 May 2022, 18:40:51 UTC |
| 554de62 | Vishwesh | 31 May 2022, 17:36:01 UTC | PR: NuClick Transforms Addition (#4266) * Try 1 Signed-off-by: vnath <vnath@nvidia.com> * dataset prep addition Signed-off-by: vnath <vnath@nvidia.com> * Refactoring of transforms as there were loose hanging functions Signed-off-by: vnath <vnath@nvidia.com> * Minor changes to transforms Signed-off-by: vnath <vnath@nvidia.com> * Added test cases for all transforms Signed-off-by: vnath <vnath@nvidia.com> * Removed dataset prep, it will be a part of tutorial, added opencv to dev requirements Signed-off-by: vnath <vnath@nvidia.com> * Added Init for NuClick Signed-off-by: vnath <vnath@nvidia.com> * Code formatting changes Signed-off-by: vnath <vnath@nvidia.com> * Linting & Formatting Signed-off-by: vnath <vnath@nvidia.com> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <vnath@nvidia.com> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <vnath@nvidia.com> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <vnath@nvidia.com> * Fixed Flake 8 & opencv addition to requirement & env files Signed-off-by: vnath <vnath@nvidia.com> * Minor in line docs need to be updated Signed-off-by: vnath <vnath@nvidia.com> * Minor in line docs need to be updated Signed-off-by: vnath <vnath@nvidia.com> * Adding Two Transforms & Test Cases Signed-off-by: vnath <vnath@nvidia.com> * Formatted the PR Signed-off-by: vnath <vnath@nvidia.com> * opencv changes Signed-off-by: vnath <vnath@nvidia.com> * opencv changes Signed-off-by: vnath <vnath@nvidia.com> * More optional import based changes Signed-off-by: vnath <vnath@nvidia.com> * Removed opencv-python-headles as that does not workout Signed-off-by: vnath <vnath@nvidia.com> * adding sk image back to requirement.txt till we figure out an alternative Signed-off-by: vnath <vnath@nvidia.com> * Replaced MapTransform instead of Transform for SplitLabeld Signed-off-by: vnath <vnath@nvidia.com> * Added skimage and cv2 requirements.txt as tests fail otherwise Signed-off-by: vnath <vnath@nvidia.com> * Added MapTransform Inheritance to AddClickSignalsd Signed-off-by: vnath <vnath@nvidia.com> * Spatial Pad Incorporated to ExtractPatchd Signed-off-by: vnath <vnath@nvidia.com> * Remvoed comments and added doc-strings Signed-off-by: vnath <vnath@nvidia.com> * codeformat Signed-off-by: vnath <vnath@nvidia.com> * Adding NuClick Test to Min tests and removing opencv & scikit from requirements.txt Signed-off-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed cv2 dependency after modification of FlattenLabeld Transform to use skimage functionality instead Signed-off-by: vnath <vnath@nvidia.com> * Minor addition to doc string Signed-off-by: vnath <vnath@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds unit test case Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove unused import Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Adding changes as docs and init arguments, 2 additional test cases Signed-off-by: vnath <vnath@nvidia.com> * Minor changes Signed-off-by: vnath <vnath@nvidia.com> * kwargs added to ExtractPatchd Signed-off-by: vnath <vnath@nvidia.com> * Added a unit test for kwargs of SpatialPad in ExtractPatchd and a doc-string Signed-off-by: vnath <vnath@nvidia.com> Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 31 May 2022, 17:36:01 UTC |
| 27c37f2 | Behrooz Hashemian | 31 May 2022, 16:18:36 UTC | Foreground Tissue Mask (#4379) * Implement foreground mask Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 31 May 2022, 16:18:36 UTC |
| 2f589c6 | Behrooz Hashemian | 31 May 2022, 14:37:27 UTC | `GridPatch` to Extract Tiles/Patches (#4321) * Implement GridPatch and RandGridPatch Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 31 May 2022, 14:37:27 UTC |
| a75dd05 | Can Zhao | 31 May 2022, 08:39:48 UTC | add hard_negative_sampler.py for detection (#4301) | 31 May 2022, 08:39:48 UTC |
| 4dbbd86 | Harutaka Kawamura | 30 May 2022, 20:59:29 UTC | Define `PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION` only when `protobuf>=4.0.0` is used (#4397) | 30 May 2022, 20:59:29 UTC |
| d635339 | Can Zhao | 30 May 2022, 20:03:49 UTC | add anchor generators used for detection (#4336) | 30 May 2022, 20:03:49 UTC |
| 8cdd692 | Nic Ma | 30 May 2022, 18:58:12 UTC | Enhance expression logic of bundle config (#4377) * [DLMED] support globals in eval(lambda) Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more test Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 30 May 2022, 18:58:12 UTC |
| 9133e35 | Can Zhao | 30 May 2022, 16:22:14 UTC | add RetinaNet network (#4378) | 30 May 2022, 16:22:14 UTC |
| 2c78bb0 | Wenqi Li | 30 May 2022, 15:19:39 UTC | 4323 - review readme (#4390) review readme Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 30 May 2022, 15:19:39 UTC |
| 61a0dc3 | Can Zhao | 28 May 2022, 19:10:58 UTC | add ATSS matcher for detection (#4350) | 28 May 2022, 19:10:58 UTC |
| ba2309c | Can Zhao | 28 May 2022, 17:42:56 UTC | Sliding window inference that supports multiple zoomed outputs (#4363) | 28 May 2022, 17:42:56 UTC |
| 95c1e80 | Can Zhao | 28 May 2022, 16:36:37 UTC | Add transform between box and mask (#4366) * add box -- mask converter Signed-off-by: Can Zhao <canz@nvidia.com> * add box mask transform Signed-off-by: Can Zhao <canz@nvidia.com> * add examples Signed-off-by: Can Zhao <canz@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add examples Signed-off-by: Can Zhao <canz@nvidia.com> * add import Signed-off-by: Can Zhao <canz@nvidia.com> * add import Signed-off-by: Can Zhao <canz@nvidia.com> * add docstring Signed-off-by: Can Zhao <canz@nvidia.com> * update test Signed-off-by: Can Zhao <canz@nvidia.com> * update import Signed-off-by: Can Zhao <canz@nvidia.com> * update test Signed-off-by: Can Zhao <canz@nvidia.com> * change func name Signed-off-by: Can Zhao <canz@nvidia.com> * change func name Signed-off-by: Can Zhao <canz@nvidia.com> * change func name Signed-off-by: Can Zhao <canz@nvidia.com> * change func name Signed-off-by: Can Zhao <canz@nvidia.com> * [MONAI] code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * corrent a corner case in NMS Signed-off-by: Can Zhao <canz@nvidia.com> * update docstring, simplify convert_box_to_mask, add test cases Signed-off-by: Wenqi Li <wenqil@nvidia.com> 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: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 28 May 2022, 16:36:37 UTC |
| 827e1e5 | Nic Ma | 28 May 2022, 15:46:47 UTC | 4346 Enhance contribution guide for optional package (#4367) * [DLMED] add to doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add min tests Signed-off-by: Nic Ma <nma@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 28 May 2022, 15:46:47 UTC |
| 14f74cb | Wenqi Li | 28 May 2022, 14:49:25 UTC | 4375 workaround mlflow integration (#4376) workaround for 4375 Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 28 May 2022, 14:49:25 UTC |
| f76dd1c | Can Zhao | 27 May 2022, 20:54:44 UTC | add box coder for detection (#4365) * add box coder Signed-off-by: Can Zhao <canz@nvidia.com> * doc Signed-off-by: Can Zhao <canz@nvidia.com> * add security check Signed-off-by: Can Zhao <canz@nvidia.com> * docstring Signed-off-by: Can Zhao <canz@nvidia.com> * docstring Signed-off-by: Can Zhao <canz@nvidia.com> * Update test_box_coder.py * docstring Signed-off-by: Can Zhao <canz@nvidia.com> docstring Signed-off-by: Can Zhao <canz@nvidia.com> docstring Signed-off-by: Can Zhao <canz@nvidia.com> Update test_box_coder.py Signed-off-by: Can Zhao <canz@nvidia.com> * docstring Signed-off-by: Can Zhao <canz@nvidia.com> docstring Signed-off-by: Can Zhao <canz@nvidia.com> docstring Signed-off-by: Can Zhao <canz@nvidia.com> Update test_box_coder.py Signed-off-by: Can Zhao <canz@nvidia.com> docstring Signed-off-by: Can Zhao <canz@nvidia.com> Update test_box_coder.py Signed-off-by: Can Zhao <canz@nvidia.com> * update docstring Signed-off-by: Can Zhao <canz@nvidia.com> | 27 May 2022, 20:54:44 UTC |
| d46904b | Wenqi Li | 27 May 2022, 18:50:38 UTC | fixes integration test (#4373) Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 27 May 2022, 18:50:38 UTC |
| b96f8bd | Wenqi Li | 27 May 2022, 14:49:55 UTC | resize skip interpolation if spatial shapes match (#4369) skip resizing if spatial shape matches Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 27 May 2022, 14:49:55 UTC |
| 1cfec68 | Nic Ma | 27 May 2022, 02:53:21 UTC | 4348 Improve doc and unit tests for "correct center" of crop transforms (#4362) [DLMED] improve doc and tests Signed-off-by: Nic Ma <nma@nvidia.com> | 27 May 2022, 02:53:21 UTC |
| b6302d7 | Richard Brown | 26 May 2022, 23:45:51 UTC | improve dtype conversion (#4357) improve dtype conversion | 26 May 2022, 23:45:51 UTC |
| 6b4d9eb | Wenqi Li | 26 May 2022, 22:15:36 UTC | 4323 deprecate SegmentationSaver, TorchVisionFullyConvModel (#4347) * deprecate SegmentationSaver, TorchVisionFullyConvModel Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes mintests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 26 May 2022, 22:15:36 UTC |
| b892aa5 | Eric Kerfoot | 26 May 2022, 21:13:31 UTC | Adding Bundle Utility Functions (#4324) * Adding tests 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 Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Trying to read output from failed process 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> * Marking bundle_init as excluded Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Marking bundle_init as excluded Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Forgot a file Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Marking bundle_utils as excluded Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Marking bundle_init as excluded 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> * 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> | 26 May 2022, 21:13:31 UTC |
| 0dac288 | Can Zhao | 26 May 2022, 20:12:33 UTC | add box clip transforms (#4338) * fix the cases of multiple labels Signed-off-by: Can Zhao <canz@nvidia.com> * add examples Signed-off-by: Can Zhao <canz@nvidia.com> * docstring Signed-off-by: Can Zhao <canz@nvidia.com> * docstring and remove inverse Signed-off-by: Can Zhao <canz@nvidia.com> * docstring Signed-off-by: Can Zhao <canz@nvidia.com> * docstring Signed-off-by: Can Zhao <canz@nvidia.com> | 26 May 2022, 20:12:33 UTC |
| a5ca749 | Can Zhao | 26 May 2022, 18:06:23 UTC | add feature pyramid network (FPN) for detection (#4342) * add FPN Signed-off-by: Can Zhao <canz@nvidia.com> | 26 May 2022, 18:06:23 UTC |
| 95b7c4f | Behrooz Hashemian | 26 May 2022, 14:50:05 UTC | Sliding Patch WSI Dataset (#4239) Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 26 May 2022, 14:50:05 UTC |
| 29c6219 | Wenqi Li | 26 May 2022, 12:37:13 UTC | 4354 workaround protobuf issue (#4355) * workaround protobuf issue Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update env var Signed-off-by: Wenqi Li <wenqil@nvidia.com> * config env Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] update for test Signed-off-by: Nic Ma <nma@nvidia.com> * revert init workaround Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] update visualize Signed-off-by: Nic Ma <nma@nvidia.com> * revert init change Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com> | 26 May 2022, 12:37:13 UTC |
| 15eda2a | Wenqi Li | 26 May 2022, 07:21:44 UTC | 4343 adds interp mode (#4344) * adds interp mode Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 26 May 2022, 07:21:44 UTC |
| eb60b9c | Can Zhao | 25 May 2022, 12:20:08 UTC | add box non_max_suppression (#4337) * add nms Signed-off-by: Can Zhao <canz@nvidia.com> * add COMPUTE_DTYPE Signed-off-by: Can Zhao <canz@nvidia.com> | 25 May 2022, 12:20:08 UTC |
| f8d862e | Yiheng Wang | 25 May 2022, 11:00:51 UTC | 4255 Update bundle download (#4331) * update bundle download Signed-off-by: Yiheng Wang <vennw@nvidia.com> * modify a few doc strings Signed-off-by: Yiheng Wang <vennw@nvidia.com> * ignore mypy error of net object Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update docstrings Signed-off-by: Yiheng Wang <vennw@nvidia.com> * rewrite source and repo descriptions Signed-off-by: Yiheng Wang <vennw@nvidia.com> * refine docstrings Signed-off-by: Yiheng Wang <vennw@nvidia.com> * change progress pop arg format Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add more descriptions about load fun Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add get_state_dict according to comments Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [MONAI] code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * revert mis-modified space Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 25 May 2022, 11:00:51 UTC |
| 9e8fbaf | Can Zhao | 24 May 2022, 21:05:17 UTC | add box flip transforms (#4334) * add box flip transforms Signed-off-by: Can Zhao <canz@nvidia.com> | 24 May 2022, 21:05:17 UTC |
| 4a0a336 | Nic Ma | 24 May 2022, 19:57:11 UTC | 4330 Fix GPU out of memory issue in tests (#4333) * [DLMED] enhance test cases Signed-off-by: Nic Ma <nma@nvidia.com> | 24 May 2022, 19:57:11 UTC |
| 6c8e4ab | Can Zhao | 24 May 2022, 18:10:31 UTC | Add spatial crop and clip box to Box utils (#4316) * add clip box to image into box_utils Signed-off-by: Can Zhao <canz@nvidia.com> | 24 May 2022, 18:10:31 UTC |
| 2bd56dc | Wenqi Li | 24 May 2022, 10:47:53 UTC | revise dice metric docstring, fixes testing data (#4329) * improve test cases Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 24 May 2022, 10:47:53 UTC |
| a1dc54a | Can Zhao | 24 May 2022, 08:52:13 UTC | add box transforms for affine and zoom (#4309) * add box transforms for affine and zoom Signed-off-by: Can Zhao <canz@nvidia.com> * add missed alias Signed-off-by: Can Zhao <canz@nvidia.com> * add in all Signed-off-by: Can Zhao <canz@nvidia.com> * add comment Signed-off-by: Can Zhao <canz@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move inver affine from array to dict Signed-off-by: Can Zhao <canz@nvidia.com> * only for debugging Signed-off-by: Can Zhao <canz@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * debugged for inverse transform, add unit test Signed-off-by: Can Zhao <canz@nvidia.com> * debugged Signed-off-by: Can Zhao <canz@nvidia.com> * debugged inverse transform Signed-off-by: Can Zhao <canz@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reformat Signed-off-by: Can Zhao <canz@nvidia.com> * typo Signed-off-by: Can Zhao <canz@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 24 May 2022, 08:52:13 UTC |
| 07de215 | Wenqi Li | 23 May 2022, 17:41:30 UTC | multiprocessing test metatensor (#4308) * fixes multiprocessing fixes unit test update reduce fixes mypy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove unused Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 23 May 2022, 17:41:30 UTC |
| 46f3074 | Yiheng Wang | 23 May 2022, 08:08:07 UTC | 4314 Enhance UnetResBlock (#4317) modify unetresblock Signed-off-by: Yiheng Wang <vennw@nvidia.com> | 23 May 2022, 08:08:07 UTC |
| 65f1f54 | Yiheng Wang | 22 May 2022, 12:13:07 UTC | 4312 Fix squeeze issue of `get_mask_edges` (#4313) * fix squeeze issue Signed-off-by: Yiheng Wang <vennw@nvidia.com> | 22 May 2022, 12:13:07 UTC |
| 655c8e7 | Ali Hatamizadeh | 22 May 2022, 11:16:34 UTC | update swin_unetr block parameter names (#4311) * update swin_unetr block name Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com> | 22 May 2022, 11:16:34 UTC |
| 98adb50 | Can Zhao | 22 May 2022, 10:27:49 UTC | add box ops for affine and zoom (#4307) * add box_ops for zoom box transforms Signed-off-by: Can Zhao <canz@nvidia.com> | 22 May 2022, 10:27:49 UTC |
| e58086d | Can Zhao | 20 May 2022, 17:09:29 UTC | add box mode convert transform (#4302) * add box transform Signed-off-by: Can Zhao <canz@nvidia.com> | 20 May 2022, 17:09:29 UTC |
| 1d5e85a | Richard Brown | 20 May 2022, 11:07:34 UTC | fix RandAffine with randomize==False (#4304) * fix RandAffine with randomize==False Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> | 20 May 2022, 11:07:34 UTC |
| a129499 | Can Zhao | 20 May 2022, 10:16:27 UTC | add box iou into box utils (#4289) * add box iou funcs Signed-off-by: Can Zhao <canz@nvidia.com> * add box iou funcs to init Signed-off-by: Can Zhao <canz@nvidia.com> | 20 May 2022, 10:16:27 UTC |
| 068b507 | Richard Brown | 19 May 2022, 21:42:37 UTC | merge certain files from feature/MetaTensor to dev (#4298) * merge certain files from feature/MetaTensor to dev Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * remove_extra_metadata Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> | 19 May 2022, 21:42:37 UTC |
| 5a5d47f | Wenqi Li | 19 May 2022, 19:58:19 UTC | 4293 local pre-commit check support (#4292) * local pre-commit Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * indent 4 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 19 May 2022, 19:58:19 UTC |
| 1ff12b9 | Behrooz Hashemian | 19 May 2022, 18:45:40 UTC | Make the order of slices row-major (#4297) * Make the order of slices row-major Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove a comment Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 19 May 2022, 18:45:40 UTC |
| fdec959 | Can Zhao | 19 May 2022, 17:58:12 UTC | add box center related funcs to box_utils (#4290) * add box center related funcs to box_utils Signed-off-by: Can Zhao <canz@nvidia.com> | 19 May 2022, 17:58:12 UTC |
| d7767cd | Richard Brown | 19 May 2022, 12:24:57 UTC | track transforms (#4284) * track transforms Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * transforms -> applied operations Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> | 19 May 2022, 12:24:57 UTC |
| 2dfee17 | Richard Brown | 19 May 2022, 11:30:56 UTC | cron tutorial master to main (#4291) cron master to main Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> | 19 May 2022, 11:30:56 UTC |
| 6eaa3ab | Can Zhao | 18 May 2022, 19:03:25 UTC | add box mode convert in box_utils (#4254) * add box_utils and unit tests Signed-off-by: Can Zhao <canz@nvidia.com> | 18 May 2022, 19:03:25 UTC |
| db32095 | Behrooz Hashemian | 18 May 2022, 16:50:47 UTC | Recursive NVTX Range (#4270) * Make Range to be recuresivley applied Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Deferred import Compose Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstring Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * address comment Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 18 May 2022, 16:50:47 UTC |
| cd77e91 | Wenqi Li | 18 May 2022, 13:01:47 UTC | 4281 - adds zero_centered option to `AffineTransform` (#4282) * update norm xform Signed-off-by: Wenqi Li <wenqil@nvidia.com> * consistent API Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comment Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 18 May 2022, 13:01:47 UTC |
| f4ff8e2 | Richard Brown | 16 May 2022, 12:32:02 UTC | optional nrrd (#4279) * optional nrrd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> | 16 May 2022, 12:32:02 UTC |
| e8d2d4f | Keno | 14 May 2022, 10:41:56 UTC | unify spelling of metdata in docstrings (#4273) Changed `meta data` -> `metadata`, `meta-data` -> `metadata`, `Meta data` -> `Metadata`, `Meta-data` -> `Metadata` in docstrings of .py files Signed-off-by: kbressem <kenobressem@gmail.com> | 14 May 2022, 10:41:56 UTC |
| db34747 | Wenqi Li | 13 May 2022, 23:13:07 UTC | 4269 - fixes resample mode typos (#4272) fixes resample mode typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 13 May 2022, 23:13:07 UTC |
| 0c243b9 | Keno | 13 May 2022, 17:47:51 UTC | Implement NrrdReader (#4259) * add swin_unetr model (#4074) * add swin_unetr model Signed-off-by: kbressem <kenobressem@gmail.com> * 4217 Update PyTorch docker to 22.04 (#4218) * [DLMED] update to 22.04 Signed-off-by: Nic Ma <nma@nvidia.com> * fixes unit test tests.test_lr_finder Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test new_empty Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Signed-off-by: kbressem <kenobressem@gmail.com> * Add InstanceNorm3dNVFuser support (#4194) * implement the base class Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [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 <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * autofix Signed-off-by: Yiheng Wang <vennw@nvidia.com> * switch to call apex directly Signed-off-by: Yiheng Wang <vennw@nvidia.com> * uncomment unittest Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add apex install link in docstring Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add channels_last_3d test case Signed-off-by: Yiheng Wang <vennw@nvidia.com> * rewrite types Signed-off-by: Yiheng Wang <vennw@nvidia.com> * change types Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add docstrings Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Signed-off-by: kbressem <kenobressem@gmail.com> * Update dice.py (#4234) * Update dice.py reduce redundant operations in DiceFocalLoss, initially caused oom Signed-off-by: Ryan Clanton <55164720+ryancinsight@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Ryan Clanton <55164720+ryancinsight@users.noreply.github.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> 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> Signed-off-by: kbressem <kenobressem@gmail.com> * Bug fix and improvement in WSI (#4216) * Make all transforms optional Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update wsireader tests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove optional from PersistentDataset and its derivatives Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for cache without transform Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add default replace_rate Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add default value Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Set default replace_rate to 0.1 Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update metadata to include path Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Adds SmartCachePatchWSIDataset Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for SmartCachePatchWSIDataset Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update references Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove smart cache Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove unused imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add path metadata for OpenSlide Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update metadata to be unified across different backends Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update wsi metadata for multi wsi objects Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for wsi metadata Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Signed-off-by: kbressem <kenobressem@gmail.com> * Replace module (#4245) * replace modules Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * replace_module -> replace_modules Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Signed-off-by: kbressem <kenobressem@gmail.com> * Add GaussianSmooth as antialiasing filter in Resize (#4249) Signed-off-by: Can Zhao <canz@nvidia.com> Signed-off-by: kbressem <kenobressem@gmail.com> * 4235 fix 2204 nvfuser issue (#4241) * reproduce issue Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove 22.01 02 Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove other workflows Signed-off-by: Yiheng Wang <vennw@nvidia.com> * run on pull request Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove sleep Signed-off-by: Yiheng Wang <vennw@nvidia.com> * test single layer forward Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add has_nvfuser Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add check within factory Signed-off-by: Yiheng Wang <vennw@nvidia.com> * revert to original cron.yml Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [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 <vennw@nvidia.com> * change to return directly if no cuda Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Signed-off-by: kbressem <kenobressem@gmail.com> * Update to Bundle Specifiation (#4250) * Update to bundle specifiation 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 * 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 <eric.kerfoot@kcl.ac.uk> * Annotating optional bundle files Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adjusted ckpt_export test Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix 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> Signed-off-by: kbressem <kenobressem@gmail.com> * Implement NrrdReader and NrrdImage classes Signed-off-by: kbressem <kenobressem@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: kbressem <kenobressem@gmail.com> * run auto style fixes on image_reader.py Signed-off-by: kbressem <kenobressem@gmail.com> * add NrrdReader to monai/data/__init__.py Signed-off-by: kbressem <kenobressem@gmail.com> * Change the way spatial information is handled in NrrdReader Signed-off-by: kbressem <kenobressem@gmail.com> * add tests for NrrdReader Signed-off-by: kbressem <kenobressem@gmail.com> * Add NrrdReader to list of possible readers for LoadImage Signed-off-by: kbressem <kenobressem@gmail.com> * autofix formating Signed-off-by: kbressem <kenobressem@gmail.com> * autofix formating Signed-off-by: kbressem <kenobressem@gmail.com> * change NrrdImage class to namedtuple and make flake8 happy Signed-off-by: kbressem <kenobressem@gmail.com> * Add pynrrd to requirements Signed-off-by: kbressem <kenobressem@gmail.com> * correct typing for namedtumple make flake8 happy Signed-off-by: kbressem <kenobressem@gmail.com> * Add pynrrd info to `get_optional_config_values` Changed NrrdImage to dataclass Signed-off-by: kbressem <kenobressem@gmail.com> * exclude test_nrrd_reader.py from min tests Signed-off-by: kbressem <kenobressem@gmail.com> * add pynrrd to config files Signed-off-by: kbressem <kenobressem@gmail.com> * [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 <kenobressem@gmail.com> * 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 <kenobressem@gmail.com> * autofix format Co-authored-by: kbressem <kenobressem@charite.de> | 13 May 2022, 17:47:51 UTC |
| 1dfeb74 | Behrooz Hashemian | 13 May 2022, 12:05:48 UTC | Split patch functionality for `PatchWSIReader` (#4251) * Add split patch support to patch wsi dataset Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Rename the split test Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update GridSplit and revert PatchWSIDataset Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add support for various sizes to split different keys Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Few fixes Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * formatting Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * simplify return for grid (1, 1) Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docsting for size in gridsplitd Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 13 May 2022, 12:05:48 UTC |
| 812275a | Nic Ma | 12 May 2022, 10:37:08 UTC | 4256 Fix wrong spatial shape in SampleCrop transforms (#4263) * [DLMED] fix spatial shape issue Signed-off-by: Nic Ma <nma@nvidia.com> * fixes codeql analysis Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 12 May 2022, 10:37:08 UTC |
| 0bbeb1e | Richard Brown | 11 May 2022, 17:08:20 UTC | gradient based saliency (#4236) * gradient based saliency Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * replace modules Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * reuse modelwithhooks Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * support of empty target Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove module.backward, add docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 11 May 2022, 17:08:20 UTC |
| 56190dd | Eric Kerfoot | 11 May 2022, 13:28:52 UTC | Update to Bundle Specifiation (#4250) * Update to bundle specifiation 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 * 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 <eric.kerfoot@kcl.ac.uk> * Annotating optional bundle files Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adjusted ckpt_export test Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix 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> | 11 May 2022, 13:28:52 UTC |
| 557c129 | Yiheng Wang | 11 May 2022, 09:10:47 UTC | 4235 fix 2204 nvfuser issue (#4241) * reproduce issue Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove 22.01 02 Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove other workflows Signed-off-by: Yiheng Wang <vennw@nvidia.com> * run on pull request Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove sleep Signed-off-by: Yiheng Wang <vennw@nvidia.com> * test single layer forward Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add has_nvfuser Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add check within factory Signed-off-by: Yiheng Wang <vennw@nvidia.com> * revert to original cron.yml Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [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 <vennw@nvidia.com> * change to return directly if no cuda Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> | 11 May 2022, 09:10:47 UTC |
| 7fbf3c4 | Can Zhao | 10 May 2022, 16:22:22 UTC | Add GaussianSmooth as antialiasing filter in Resize (#4249) Signed-off-by: Can Zhao <canz@nvidia.com> | 10 May 2022, 16:22:22 UTC |
| 5536cc3 | Richard Brown | 09 May 2022, 14:57:21 UTC | Replace module (#4245) * replace modules Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * replace_module -> replace_modules Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> | 09 May 2022, 14:57:21 UTC |
| 209db9e | Behrooz Hashemian | 06 May 2022, 19:28:08 UTC | Bug fix and improvement in WSI (#4216) * Make all transforms optional Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update wsireader tests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove optional from PersistentDataset and its derivatives Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for cache without transform Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add default replace_rate Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add default value Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Set default replace_rate to 0.1 Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update metadata to include path Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Adds SmartCachePatchWSIDataset Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for SmartCachePatchWSIDataset Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update references Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove smart cache Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove unused imports Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add path metadata for OpenSlide Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update metadata to be unified across different backends Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update wsi metadata for multi wsi objects Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests for wsi metadata Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 06 May 2022, 19:28:08 UTC |
| 5f00bf1 | Ryan Clanton | 06 May 2022, 11:10:59 UTC | Update dice.py (#4234) * Update dice.py reduce redundant operations in DiceFocalLoss, initially caused oom Signed-off-by: Ryan Clanton <55164720+ryancinsight@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Ryan Clanton <55164720+ryancinsight@users.noreply.github.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> 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> | 06 May 2022, 11:10:59 UTC |
| 66f3280 | Yiheng Wang | 05 May 2022, 05:26:52 UTC | Add InstanceNorm3dNVFuser support (#4194) * implement the base class Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [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 <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * autofix Signed-off-by: Yiheng Wang <vennw@nvidia.com> * switch to call apex directly Signed-off-by: Yiheng Wang <vennw@nvidia.com> * uncomment unittest Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add apex install link in docstring Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add channels_last_3d test case Signed-off-by: Yiheng Wang <vennw@nvidia.com> * rewrite types Signed-off-by: Yiheng Wang <vennw@nvidia.com> * change types Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add docstrings Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 05 May 2022, 05:26:52 UTC |
| b10364c | Nic Ma | 05 May 2022, 04:37:41 UTC | 4217 Update PyTorch docker to 22.04 (#4218) * [DLMED] update to 22.04 Signed-off-by: Nic Ma <nma@nvidia.com> * fixes unit test tests.test_lr_finder Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test new_empty Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com> | 05 May 2022, 04:37:41 UTC |
| e093d0b | Ali Hatamizadeh | 03 May 2022, 23:27:38 UTC | add swin_unetr model (#4074) * add swin_unetr model | 03 May 2022, 23:27:38 UTC |
| 30ad90d | Wenqi Li | 02 May 2022, 10:26:12 UTC | udpate md5 (#4213) Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 02 May 2022, 10:26:12 UTC |
| d4a924c | Nic Ma | 30 April 2022, 10:20:01 UTC | Update the default value of `lazy` arg in the ConfigParser to `True` (#4203) | 30 April 2022, 10:20:01 UTC |
| 0db84a0 | Wenqi Li | 29 April 2022, 21:35:15 UTC | 4200 workaround for ci apt (#4202) * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * workaround Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> | 29 April 2022, 21:35:15 UTC |
| 1331432 | Behrooz | 29 April 2022, 20:29:31 UTC | Make transforms optional (#4190) * Make all transforms optional Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> | 29 April 2022, 20:29:31 UTC |
| 9af6332 | Yiheng Wang | 29 April 2022, 18:52:33 UTC | enhance mean dice (#4163) Signed-off-by: Yiheng Wang <vennw@nvidia.com> | 29 April 2022, 18:52:33 UTC |
| 05b9d31 | Nic Ma | 28 April 2022, 11:17:39 UTC | [DLMED] enhance load_files (#4192) Signed-off-by: Nic Ma <nma@nvidia.com> | 28 April 2022, 11:17:39 UTC |
| df177fd | Wenqi Li | 27 April 2022, 22:33:09 UTC | add adn unet (#4185) Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> | 27 April 2022, 22:33:09 UTC |
| be3d22f | deepsource-autofix[bot] | 27 April 2022, 18:51:01 UTC | Remove unused global variable (#4189) * Remove unused global variable | 27 April 2022, 18:51:01 UTC |
| c9b2d06 | deepsource-autofix[bot] | 27 April 2022, 16:28:33 UTC | Remove commented out code (#4187) * Remove commented out code * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 27 April 2022, 16:28:33 UTC |
| 5777041 | Andres Diaz-Pinto | 27 April 2022, 14:51:55 UTC | Add DeepEdit transforms and interaction (#4164) * Add DeepEdit transforms and interaction Signed-off-by: Andres Diaz-Pinto <diazandr3s@gmail.com> | 27 April 2022, 14:51:55 UTC |
| 641a079 | Nic Ma | 27 April 2022, 12:31:11 UTC | 4173 Enhance decathlon datalist for `test` section format (#4186) * [DLMED] enhance test datalist Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 27 April 2022, 12:31:11 UTC |
