| e1bf529 | Nic Ma | 06 July 2020, 17:41:53 UTC | [DLMED] update DiceMetric (#700) | 06 July 2020, 17:41:53 UTC |
| 07e8a6f | Wenqi Li | 06 July 2020, 12:57:02 UTC | adds cron jobs (#694) * adds cron jobs * remove temp. action event * update based on comments * remove temp. action event | 06 July 2020, 12:57:02 UTC |
| 91d56cb | Wenqi Li | 05 July 2020, 15:46:54 UTC | pin research version (#698) | 05 July 2020, 15:46:54 UTC |
| 33dab6f | Nic Ma | 03 July 2020, 15:49:01 UTC | [DLMED] fix random zoom issue (#693) | 03 July 2020, 15:49:01 UTC |
| 7241a9e | Nic Ma | 03 July 2020, 14:40:12 UTC | Update typehints for all the transforms (#690) * [DLMED] update typehints for transforms * [MONAI] python code formatting * [DLMED] fix typo * [DLMED] fix flake8 issue * [DLMED] fix flake8 error * [DLMED] update post transforms * [DLMED] update according to comments * [MONAI] python code formatting * [DLMED] fix flake8 error * [DLMED] remove align_corners typehints * [DLMED] update according to comments * update to fix flake8 Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 03 July 2020, 14:40:12 UTC |
| 3a812df | Nic Ma | 03 July 2020, 10:50:30 UTC | Refine all import in source code (#692) * [DLMED] update import * [DLMED] update notebooks * [DLMED] update relative import * [DLMED] update relative import * [DLMED] restore research import Co-authored-by: root <root@apt-sh-ai.nvidia.com> | 03 July 2020, 10:50:30 UTC |
| c57efd3 | Nic Ma | 03 July 2020, 09:14:06 UTC | [DLMED] fix data contiguous issue (#691) | 03 July 2020, 09:14:06 UTC |
| d5e56ab | Wenqi Li | 03 July 2020, 01:27:41 UTC | fixes #688 (#689) | 03 July 2020, 01:27:41 UTC |
| 18c3398 | Wenqi Li | 02 July 2020, 17:52:14 UTC | update changelog (#685) | 02 July 2020, 17:52:14 UTC |
| eeaa958 | Wenqi Li | 02 July 2020, 17:09:49 UTC | adds tutorial links (#686) | 02 July 2020, 17:09:49 UTC |
| d65db40 | Nic Ma | 02 July 2020, 17:00:40 UTC | [DLMED] update examples (#687) | 02 July 2020, 17:00:40 UTC |
| 640852a | Nic Ma | 02 July 2020, 11:01:47 UTC | [DLMED] fix min windows test issue (#683) | 02 July 2020, 11:01:47 UTC |
| 7826c5e | Wenqi Li | 02 July 2020, 10:22:33 UTC | adds a colab tutorial (#675) | 02 July 2020, 10:22:33 UTC |
| 17cc205 | Nic Ma | 02 July 2020, 10:11:34 UTC | 681 Add Tensor support for DataStats transform (#682) * [DLMED] add Tensor support to DataStats transform * [DLMED] update doc-string to highlight * [DLMED] update according to comments | 02 July 2020, 10:11:34 UTC |
| 8f3160a | Nic Ma | 02 July 2020, 09:57:42 UTC | 679 Add missing links for Decathlon and tutorials (#680) * [DLMED] add missing links * [DLMED] update according to comments | 02 July 2020, 09:57:42 UTC |
| 2f89aa0 | Nic Ma | 02 July 2020, 09:48:59 UTC | 676 Update all the quick import in modules (#677) * [DLMED] update quick import * [DLMED] fix typo * [DLMED] fix flake8 error * [DLMED] update according to comments | 02 July 2020, 09:48:59 UTC |
| 12d3d45 | Nic Ma | 02 July 2020, 02:35:22 UTC | 671 add docs web page for apps folder (#673) * [DLMED] add docs for apps * [DLMED] fix flake8 error | 02 July 2020, 02:35:22 UTC |
| ef77a4b | Wenqi Li | 01 July 2020, 23:18:33 UTC | allows for adaptive size in "resize" (#674) * allows for adaptive resize * fixes typo | 01 July 2020, 23:18:33 UTC |
| a389586 | Wenqi Li | 01 July 2020, 15:55:34 UTC | update dataset links (#669) | 01 July 2020, 15:55:34 UTC |
| c0f4771 | Nic Ma | 01 July 2020, 15:39:33 UTC | 651 Tutorial for public datasets (#661) * [DLMED] add public dataset tutorial * [DLMED] add to README * [DLMED] update according to comments | 01 July 2020, 15:39:33 UTC |
| 1482301 | Nic Ma | 01 July 2020, 14:38:16 UTC | [DLMED] update datasets (#672) | 01 July 2020, 14:38:16 UTC |
| c503164 | Wenqi Li | 01 July 2020, 13:41:01 UTC | 663 - update default padding mode (#668) * update padding mode * update docstrings | 01 July 2020, 13:41:01 UTC |
| b3de1ae | Nic Ma | 01 July 2020, 12:17:29 UTC | 665 Update align_corner to support multiple values (#667) * [DLMED] update align_corner * [MONAI] python code formatting Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 01 July 2020, 12:17:29 UTC |
| 89bd681 | Wenqi Li | 01 July 2020, 11:51:04 UTC | update version requirement (#666) | 01 July 2020, 11:51:04 UTC |
| c655aed | Nic Ma | 01 July 2020, 11:05:42 UTC | 659 Fix doc-string issue of Randomizable (#660) * [DLMED] update doc-string of Randomizable * [MONAI] python code formatting * [DLMED] update according to comments Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 01 July 2020, 11:05:42 UTC |
| f78721d | Wenqi Li | 30 June 2020, 22:32:10 UTC | 552-fixes elastic2d spacing (#648) * fixes #552 * update * compatible with torch1.4/1.5 | 30 June 2020, 22:32:10 UTC |
| cd1e7f3 | Wenqi Li | 30 June 2020, 16:33:16 UTC | fixes docstrings for Transform and MapTransform (#658) * fixes docstrings * update based on comments Co-authored-by: Nic Ma <nma@nvidia.com> | 30 June 2020, 16:33:16 UTC |
| f42fbbf | Wenqi Li | 30 June 2020, 16:23:04 UTC | 517-allows for adaptive window sizes (#645) * allows for adaptive window sizes * update based on comments * update docstring * update to support adaptive window sizes | 30 June 2020, 16:23:04 UTC |
| b7e2e19 | Nic Ma | 30 June 2020, 13:33:24 UTC | 591 add DecathlonDataset (#650) * [DLMED] add DecathlonDataset * [DLMED] add unit test * [DLMED] update MD5 values * [MONAI] python code formatting * [DLMED] add optional import * [DLMED] add gdown for windows * [DLMED] update tests dependency * [DLMED] add more tests * [DLMED] add skip_if_quick * [DLMED] update according to comments Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 30 June 2020, 13:33:24 UTC |
| 217b56c | Nic Ma | 30 June 2020, 12:29:20 UTC | 655 Add/update ensure_tuple_rep for transforms (#656) * [DLMED] update doc-strings for ensure_tuple_rep * [MONAI] python code formatting Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 30 June 2020, 12:29:20 UTC |
| 11fc31d | Wenqi Li | 30 June 2020, 10:35:41 UTC | update transform docs (#649) * update transform docs * [MONAI] python code formatting Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com> | 30 June 2020, 10:35:41 UTC |
| 5d13ce9 | Nic Ma | 30 June 2020, 09:43:28 UTC | [DLMED] fix html format issue in highlights page (#654) | 30 June 2020, 09:43:28 UTC |
| 824a0a4 | Nic Ma | 30 June 2020, 08:42:42 UTC | [DLMED] update doc-string of shape (#652) | 30 June 2020, 08:42:42 UTC |
| a9a3c91 | Wenqi Li | 30 June 2020, 01:41:50 UTC | update maptransform docstring (#641) Co-authored-by: Nic Ma <nma@nvidia.com> | 30 June 2020, 01:41:50 UTC |
| 805c99a | Nic Ma | 29 June 2020, 16:19:05 UTC | 540 update highlight features document (#536) * [DLMED] add highlight v0.2 * [DLMED] update according to comments * [DLMED] update arch chart * [DLMED] update highlight features page * [DLMED] update highlights * [DLMED] refine Transforms and Datasets * [DLMED] add multiple transform chains * [DLMED] update chart * [DLMED] add items to transforms doc * [DLMED] add 3rd party transforms * [DLMED] update all old modules * [DLMED] add workflows and research * revise highlight.md * [DLMED] add GAN to doc * adds figures * adds figures * update figures * update * Update highlights.md * Update highlights.md * [DLMED] add chart for Datasets * Update highlights.md * Update highlights.md * [DLMED] update some format issues * update readme * update section header * [DLMED] update module chart * [DLMED] add post transforms chart * [DLMED] update post_transforms * [DLMED] update according to the comments * [DLMED] update readthedocs Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 29 June 2020, 16:19:05 UTC |
| bd15d22 | Mark Graham | 29 June 2020, 15:32:33 UTC | Updates metric tracking so checkpoints are saved correctly (#643) | 29 June 2020, 15:32:33 UTC |
| 0fa6461 | Nic Ma | 29 June 2020, 15:22:23 UTC | 642 add post transform tutorial (#647) * [DLMED] add post_transform notebook * [DLMED] update post transform notebook * [DLMED] update notebook chart | 29 June 2020, 15:22:23 UTC |
| 24dd411 | Wenqi Li | 29 June 2020, 15:07:48 UTC | fixes #644 (#646) | 29 June 2020, 15:07:48 UTC |
| db9dfda | Wenqi Li | 29 June 2020, 06:06:43 UTC | updates runtests.sh usage message (#638) * updates runtests usage message * update according to #595 * updates runtests usage message * update according to #595 * update based on comments Co-authored-by: Nic Ma <nma@nvidia.com> | 29 June 2020, 06:06:43 UTC |
| 0df82a7 | Nic Ma | 29 June 2020, 05:57:23 UTC | 634 dictionary level LabelToContourd (#640) * [DLMED] add dictionay version `LabelToContour` * [DLMED] add unit tests * [MONAI] python code formatting Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 29 June 2020, 05:57:23 UTC |
| 39f6df5 | Wenqi Li | 29 June 2020, 05:44:11 UTC | Fixes array transforms docstring (#635) * update monai/transforms/utility/array.py docstrings * update monai/transforms/spatial/array.py docstrings * update monai/transforms/intensity/array.py docstrings * update monai/transforms/croppad/array.py docstrings * fixes conf.py Co-authored-by: Nic Ma <nma@nvidia.com> | 29 June 2020, 05:44:11 UTC |
| 4a2a094 | Nic Ma | 29 June 2020, 05:33:58 UTC | 629 Update progress_bar and replace tqdm in notebook (#633) * [DLMED] update progress bar * [MONAI] python code formatting Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 29 June 2020, 05:33:58 UTC |
| c0b486e | Wenqi Li | 29 June 2020, 05:04:00 UTC | updates documentation link -- docs.monai.io (#637) * update documentation links * [MONAI] python code formatting Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 29 June 2020, 05:04:00 UTC |
| 30f860d | Alex Powers | 28 June 2020, 17:20:04 UTC | 630 Lambda Transform (#639) * Implementing lambda transform * Fixing flake errors | 28 June 2020, 17:20:04 UTC |
| e8c26a2 | wuyuanhang94 | 27 June 2020, 15:33:48 UTC | Add edge detection for mask image (#599) * Add edge detection for mask image * [MONAI] python code formatting Co-authored-by: Yi Wu <yiw@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com> | 27 June 2020, 15:33:48 UTC |
| 9d0396b | Nic Ma | 27 June 2020, 15:04:45 UTC | 583 Array level random crop by pos / neg label (#628) * [DLMED] add array version Random Pos/Neg crop transform * [DLMED] update doc-string according to the comments * [DLMED] fix flake8 issue * [DLMED] fix List flake8 * [DLMED] add List typing * fixes docstring: monai/data/utils.py:docstring of monai.data.utils.to_affine_nd:22: WARNING: Unknown target name: "affine". Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 27 June 2020, 15:04:45 UTC |
| c7289d7 | Wenqi Li | 27 June 2020, 14:47:14 UTC | fixes docstrings (#631) Co-authored-by: Nic Ma <nma@nvidia.com> | 27 June 2020, 14:47:14 UTC |
| 7efbeda | Benjamin Gorman | 26 June 2020, 21:37:16 UTC | Docstring additions (#632) * add exceptions to docstrings fixes DAR401 errors raised by darglint. DAR401: The docstring is missing an exception raised. * fix whitespace and indentation in docstrings fixes 000 errors raised by darglint. 000: Syntax, formatting, and style. remove singleline docstrings: they do not allow for easy additions. * fix docstring section capitalization * remove unnecessary type hints from docstrings fixes DAR103 errors raised by darglint. DAR103: The docstring parameter type doesn't match function. * add parameter descriptions to docstring fixes DAR101 errors raised by darglint. DAR101: The docstring is missing a parameter in the definition. | 26 June 2020, 21:37:16 UTC |
| 7a08b2a | Alex Powers | 26 June 2020, 20:51:10 UTC | 614 ScaleIntensityRangePercentiles transform (#615) * Adding ScaleIntensityRangePercentiles array transform * Adding ScaleIntensityRangePercentilesd dictionary transform * Adding percentile scaling transforms to docs * Adding basic unit tests * Doc and code formatting * Adding docstring example * Adding alternate percentile scaling * Accounting for divide by zero | 26 June 2020, 20:51:10 UTC |
| d25e4e5 | Benjamin Gorman | 26 June 2020, 18:13:36 UTC | 484 incorporate enumerations (#619) * add monai/utils/enums.py contains the str subsets * incorporate enumeration NumpyPadMode * incorporate enumeration GridSampleMode test case removed since __init__ now requires a valid mode and padding_mode even if __call__ overrides them * incorporate enumeration InterpolateMode * incorporate enumeration UpsampleMode * incorporate enumeration BlendMode * incorporate enumeration PytorchPadMode * incorporate enumeration GridSamplePadMode * incorporate enumeration Average * incorporate enumeration MetricReduction * incorporate enumeration LossReduction * incorporate enumeration Weight * incorporate enumeration Normalisation * incorporate enumeration Activation * incorporate enumeration ChannelMatching * incorporate enumeration Method * incorporate union GridSampleMode InterpolateMode "nearest" left as default since it is valid for both enums * include enumerations in tests/ any enum function which uses a default value uses an enum * update type hinting of enum sequences Sequence[object] was to allow a mixed sequence of enum and str to pass the type check. However this would be a rare occurrence and would have no reason for being. Of higher concern it allows any sequenced subclass of object to pass the type check. * add explicit enum type hint to instance variables | 26 June 2020, 18:13:36 UTC |
| 379c959 | Wenqi Li | 26 June 2020, 10:24:33 UTC | model parallel training research (#616) * adds network * adds basic training * update loading * working prototype * update validation set * [MONAI] Add author; paper info; PDDCA18 (#6) + Author + Early accept + PDDCA18 link * Update README.md * adds network * adds basic training * update loading * working prototype * update validation set * [MONAI] Update TRAIN_PATH, VAL_PATH (#8) + Update TRAIN_PATH, VAL_PATH * [MONAI] Add data link (#7) + Add data link https://drive.google.com/file/d/1A2zpVlR3CkvtkJPvtAF3-MH0nr1WZ2Mn/view?usp=sharing * fixes typos * tested new dataset * print more infor, checked new dataset * [MONAI] Add paper link (#9) Add paper link https://arxiv.org/abs/2006.12575 * [MONAI] Use dice loss + focal loss to train (#10) Use dice loss + focal loss to train * [MONAI] Support non-one-hot ground truth (#11) Support non-one-hot ground truth * fixes format and docstrings, adds argparser options * resume the focal_loss * adds tests * [MONAI] Support non-one-hot ground truth (#11) Support non-one-hot ground truth * adds tests * update docstring * [MONAI] Keep track of best validation scores (#12) Keep track of best validation scores * model saving * adds window sampling * update readme * update docs * fixes flake8 error * update window sampling * fixes model name * fixes channel size issue * [MONAI] Update --pretrain, --lr (#13) + lr from 5e-4 to 1e-3 because we use mean for class channel instead of sum for class channel. + pretrain path is consistent with current model_name. * [MONAI] Pad image; elastic; best class model (#14) * [MONAI] Pad image; elastic; best class model + Pad image bigger than crop_size, avoid potential issues in RandCropByPosNegLabeld + Use Rand3DElasticd + Save best model for each class * Update train.py Co-authored-by: Wenqi Li <wenqil@nvidia.com> * flake8 fixes * removes -1 cropsize deform * testing commands * fixes unit tests * update spatial padding * [MONAI] Add full image deform augmentation (#15) + Add full image deform augmentation by Rand3DElasticd + Please use latest MONAI in https://github.com/Project-MONAI/MONAI/pull/623 * Adding py.typed * updating setup.py to comply with black * update based on comments * excluding research from packaging * update tests * update setup.py Co-authored-by: Wentao Zhu <wentaozhu1991@gmail.com> Co-authored-by: Neil Tenenholtz <ntenenz@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> | 26 June 2020, 10:24:33 UTC |
| f262355 | Neil Tenenholtz | 26 June 2020, 09:14:48 UTC | Adding py.typed (#626) * Adding py.typed * updating setup.py to comply with black | 26 June 2020, 09:14:48 UTC |
| e2ca7e8 | Nic Ma | 26 June 2020, 08:36:53 UTC | [DLMED] fix notebook format issue (#627) | 26 June 2020, 08:36:53 UTC |
| 7524357 | Wenqi Li | 26 June 2020, 04:17:31 UTC | fixes macos test (#624) Co-authored-by: Nic Ma <nma@nvidia.com> | 26 June 2020, 04:17:31 UTC |
| 3479515 | Benjamin Gorman | 26 June 2020, 01:36:04 UTC | Make str subset parameters consistent (#618) * make str subset parameters consistent - make parameter names match underlying function - make parameter docstrings uniform - add set notation to communicate str subset - add 'Defaults to' for default values - add 'See also' for underlying function Co-authored-by: Cameron Trentz <cameron-trentz@uiowa.edu> * update notebooks with parameter name change interp_order -> mode fix spelling * update tests with parameter name change order -> mode interp_order -> mode mode -> padding_mode Co-authored-by: Cameron Trentz <cameron-trentz@uiowa.edu> | 26 June 2020, 01:36:04 UTC |
| 2516f80 | Wentao Zhu | 25 June 2020, 23:16:59 UTC | [MONAI] Add whole image deform support in Rand3DElasticd (#623) * [MONAI] Rand3DElasticd supports whole image deform + Rand3DElasticd supports whole image deform * [MONAI] add whole image deform example + add whole image deform example (-1, -1, -1) * [MONAI] Add whole image deform support Co-authored-by: Wentao Zhu <wentaoz@nvidia.com> | 25 June 2020, 23:16:59 UTC |
| 75fe852 | Nic Ma | 25 June 2020, 15:15:16 UTC | 606 support random patch without PosNeg ratio (#613) * [DLMED] add support to None pos/neg ratio * [DLMED] fix notebook format * [DLMED] update according to comments * [DLMED] update spatial shape * [MONAI] python code formatting * [DLMED] update flake8 issue Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 25 June 2020, 15:15:16 UTC |
| 4cf675f | Eric Kerfoot | 25 June 2020, 14:13:16 UTC | Adding GAN Networks and Example (#622) * Adding generator and discriminator networks plus example notebook * [MONAI] python code formatting Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 25 June 2020, 14:13:16 UTC |
| acb4e69 | Nic Ma | 25 June 2020, 08:41:49 UTC | [DLMED] fix pos / neg crop bug for One-Hot (#620) | 25 June 2020, 08:41:49 UTC |
| 5f59492 | Wenqi Li | 25 June 2020, 07:54:41 UTC | update importerror/system messages (#617) | 25 June 2020, 07:54:41 UTC |
| 72e1726 | Wenqi Li | 24 June 2020, 16:21:57 UTC | Focal loss one-hot target (#611) * [MONAI] Support non-one-hot ground truth (#11) Support non-one-hot ground truth * adds tests * update docstring * update based on comments Co-authored-by: Wentao Zhu <wentaozhu1991@gmail.com> | 24 June 2020, 16:21:57 UTC |
| 2d9c21a | Wenqi Li | 24 June 2020, 12:43:19 UTC | minor documentation fixes for v0.2.0rc1 (#610) * update documentation * update installation doc | 24 June 2020, 12:43:19 UTC |
| 30adc8e | Nic Ma | 24 June 2020, 07:22:27 UTC | 581 add BorderPad transform (#607) * [DLMED] add BorderPad transform * [DLMED] add unit tests and doc * [MONAI] python code formatting * [DLMED] remove typo Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 24 June 2020, 07:22:27 UTC |
| 801e216 | Nic Ma | 23 June 2020, 17:16:50 UTC | 577 update MeanDice handler (#600) * [DLMED] update MeanDice handler * [DLMED] update according to comments * [MONAI] python code formatting * [DLMED] update according to comments Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 23 June 2020, 17:16:50 UTC |
| cc431b2 | Hans Johnson | 23 June 2020, 16:57:06 UTC | Trivial none return type (#503) * Trivially determined type annotations added These types were injected by pyre with manual review. * ENH: Reformat to conform to the black formatting standard. * ENH: Adding trivial types. * Need type annotation for 'factories' (hint: "factories: Dict[<type>, <type>] = ...") monai/networks/layers/factories.py:77: error: * Assert value set to proper type after initialization. error: "None" not callable, error: Item "None" of "Optional[Logger]" has no attribute "info" * Returning Any from function declared to return "bool" * error: Signature of "randomize" incompatible with supertype "Randomizable" * Need type annotation for variables initialized to [] error: Need type annotation for '_predictions' (hint: "_predictions: List[<type>] = ...") error: Need type annotation for '_targets' (hint: "_targets: List[<type>] = ...") * Incompatible types in assignment error: (expression has type "Generator[Any, None, None]", variable has type "None") * Incompatible types in assignment: "List[Any]" error: Incompatible types in assignment (expression has type "List[Any]", variable has type "None") | 23 June 2020, 16:57:06 UTC |
| 4f9e0cd | Nic Ma | 23 June 2020, 16:16:17 UTC | [DLMED] add multi-gpu to inference (#605) | 23 June 2020, 16:16:17 UTC |
| bcfba89 | Wenqi Li | 22 June 2020, 15:45:04 UTC | adds divisible pad transform (#602) * adds divisible pad transform * fixes sphinx_autodoc_typehints * update based on comments * skip padding if padwidth are zeros | 22 June 2020, 15:45:04 UTC |
| d37f92d | Nic Ma | 20 June 2020, 14:40:32 UTC | [DLMED] add ITK transform to the notebook (#597) | 20 June 2020, 14:40:32 UTC |
| ea772a5 | Nic Ma | 19 June 2020, 11:40:30 UTC | Refine workflow iteration to add input data to output (#587) * [DLMED] refine workflows * [MONAI] python code formatting * [DLMED] update according to comments Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 19 June 2020, 11:40:30 UTC |
| 9b0fab3 | Wenqi Li | 19 June 2020, 11:25:28 UTC | Update CI script and optional import (#595) - adds new min-dep CI tests - adds an option to exclude namespace package in optional import | 19 June 2020, 11:25:28 UTC |
| 1aa3379 | Nic Ma | 18 June 2020, 22:47:33 UTC | 580 add ConcatItems transform (#582) * [DLMED] add ConcatItems transform * [MONAI] python code formatting * [DLMED] fix type hints * [DLMED] update according to comments * [DLMED] fix typo Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 18 June 2020, 22:47:33 UTC |
| c98da0d | Nic Ma | 17 June 2020, 16:47:16 UTC | [DLMED] add @skip_if_quick (#584) | 17 June 2020, 16:47:16 UTC |
| afedafd | Nic Ma | 17 June 2020, 16:27:39 UTC | 568 add MedNIST dataset with download (#571) * [DLMED] add MedNIST dataset * [MONAI] python code formatting * [DLMED] add unit tests * [MONAI] python code formatting * [DLMED] remove typo * [DLMED] update according to the comments * [MONAI] python code formatting * [DLMED] fix type hints error * [DLMED] update check_md5 * [DLMED] update according to comments * [DLMED] fix type hints Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 17 June 2020, 16:27:39 UTC |
| 8be13c2 | Wenqi Li | 17 June 2020, 13:48:48 UTC | 198 optional import (#551) * initial optional import * fixes CI * fixes packaging issue, lazy import handlers * additional args to version checker * revise setup.cfg * adds an installation guide * print sys info * fixes typo * update based on comments * fixes 'TypeError: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases' | 17 June 2020, 13:48:48 UTC |
| 8c25540 | Wenqi Li | 17 June 2020, 09:31:23 UTC | Adds infer example (#575) * adds cople net * update cuda tests * adds inference example | 17 June 2020, 09:31:23 UTC |
| e2e934a | Nic Ma | 16 June 2020, 19:31:32 UTC | 576 remove output_postfix in post transforms (#578) * [DLMED] remove output_postfix * [MONAI] python code formatting * [DLMED] fix flake8 error Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 16 June 2020, 19:31:32 UTC |
| 051ce89 | myron | 16 June 2020, 17:17:57 UTC | adding class DiceMetric based on compute_meandice func, and account for nans (#574) Co-authored-by: am <am> | 16 June 2020, 17:17:57 UTC |
| ad49a61 | Wenqi Li | 16 June 2020, 10:32:58 UTC | Adds Cople net (#572) * adds cople net * update cuda tests | 16 June 2020, 10:32:58 UTC |
| 22d975b | Benjamin Gorman | 15 June 2020, 21:28:59 UTC | reformat runtests.sh (#553) The reformat seeks to improve clarity in what tests have been ran, are currently being run, and if tests have passed or failed. The reformat also strives to improve consistency. - add blue, green, red, bold output - remove ``MYPYPATH`` from flake8 - fix bug ``"$(which mypy)"`` used for pytype - fix consistency in segmentation - fix consistency in separator length - fix consistency in camelCase usage - fix consistency in variable naming - fix consistency in indentation length - fix consistency in cmdPrefix usage - fix consistency in equality checks - fix consistency in whitespace usage Co-authored-by: Cameron Trentz <cameron-trentz@uiowa.edu> | 15 June 2020, 21:28:59 UTC |
| 2f3b1b7 | Wenqi Li | 15 June 2020, 16:52:45 UTC | adds up/down sampling blocks (#566) * adds up/down sampling blocks * update based on comments * update based on comments | 15 June 2020, 16:52:45 UTC |
| afd4c24 | Nic Ma | 15 June 2020, 13:39:54 UTC | 567 add CopyKeys transform (#570) * [DLMED] add CopyKeys transform * [MONAI] python code formatting * [DLMED] update according to comments Co-authored-by: monai-bot <monai.miccai2019@gmail.com> | 15 June 2020, 13:39:54 UTC |
| cd34d5d | Wenqi Li | 15 June 2020, 11:59:20 UTC | adds an aspp layer (#569) | 15 June 2020, 11:59:20 UTC |
| 84b0609 | Wenqi Li | 14 June 2020, 16:45:45 UTC | adds a se layer and tests (#563) * adds a se layer and tests * update based on comments | 14 June 2020, 16:45:45 UTC |
| 9956da3 | Nic Ma | 14 June 2020, 16:07:27 UTC | [DLMED] update meta name (#564) | 14 June 2020, 16:07:27 UTC |
| 49fb67b | Wenqi Li | 14 June 2020, 14:27:35 UTC | adds sphinx_autodoc_typehints to conf.py (#558) | 14 June 2020, 14:27:35 UTC |
| a408552 | Jan Sellner | 13 June 2020, 13:33:33 UTC | Change docstring parameter ordering (#560) Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 13 June 2020, 13:33:33 UTC |
| 960cb13 | Jan Sellner | 13 June 2020, 13:03:38 UTC | Adapt warning message to new parameter names (#559) | 13 June 2020, 13:03:38 UTC |
| ff8fa2b | Nic Ma | 13 June 2020, 12:12:12 UTC | [DLMED] update docs of Itentity transform (#557) | 13 June 2020, 12:12:12 UTC |
| 51d4306 | MarcosVillacanas | 13 June 2020, 00:33:15 UTC | Windows Format Paths added (commented) (#548) * marcosvillacanas-windowsPaths added (commented) * black format * code duplication solved * images order back to original Co-authored-by: Nic Ma <nma@nvidia.com> | 13 June 2020, 00:33:15 UTC |
| 23da148 | Wenqi Li | 12 June 2020, 23:49:38 UTC | fixes 549-arraydataset-len (#556) | 12 June 2020, 23:49:38 UTC |
| a62a0aa | Michal Brzus | 12 June 2020, 22:42:11 UTC | Identity transform (#555) * added Identity transform to transforms.spatial and transforms.intensity and unit tests for those functions * updating files * Add Identity transform tests * Add identity transform dictionary wrapper with unit test * Refactor with black * Update identity dict wrapper * Move and update Identity transform * Update files * Fix docstring * Fix typo in test_identityd.py | 12 June 2020, 22:42:11 UTC |
| f03373c | Nic Ma | 12 June 2020, 17:07:27 UTC | 542 use PIL Image for PNG writer (#543) * [DLMED] update PNG writer * [DLMED] update unit tests * [MONAI] python code formatting * [DLMED] fix interplate warning * [DLMED] fix interplate issue * [DLMED] update according to comments * [DLMED] update doc-string * [DLMED] update segmentation_saver and png_saver * [DLMED] update according to comments Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 12 June 2020, 17:07:27 UTC |
| d42f15d | Wenqi Li | 12 June 2020, 16:42:41 UTC | remove flake8-mypy tests (#550) | 12 June 2020, 16:42:41 UTC |
| bafd361 | Nic Ma | 12 June 2020, 12:34:03 UTC | [DLMED] set data type for labels (#547) | 12 June 2020, 12:34:03 UTC |
| 0859c95 | Wenqi Li | 12 June 2020, 06:55:44 UTC | fixes logger (#539) | 12 June 2020, 06:55:44 UTC |
| 46c2628 | Wenqi Li | 12 June 2020, 06:44:43 UTC | fixes windows ci (#545) | 12 June 2020, 06:44:43 UTC |
| 5859095 | Nic Ma | 12 June 2020, 05:56:31 UTC | [DLMED] fix integration test issue (#541) | 12 June 2020, 05:56:31 UTC |
| 03bba65 | Yuan-Ting Hsieh (謝沅廷) | 12 June 2020, 02:15:33 UTC | Add one-hot support in KeepLargestConnectedComponent and related tests (#524) * Add one-hot support in KeepLargestConnectedComponent and related tests * [MONAI] python code formatting * Use applied_labels instead of applied_values and applied_channel_indices * [MONAI] python code formatting * Fix merge error * Remove background and remove default for applied_labels * [MONAI] python code formatting Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com> | 12 June 2020, 02:15:33 UTC |
| a1a5d6d | Wenqi Li | 12 June 2020, 02:06:36 UTC | 232 remove scipy requirement from core (#538) * revises rotate/rand_rotate * fixes typing errors * fixes integration tests * remove unused import/variables * remove scipy dep from core Co-authored-by: Nic Ma <nma@nvidia.com> | 12 June 2020, 02:06:36 UTC |
| 34fbb5c | Wenqi Li | 12 June 2020, 01:52:09 UTC | 232 revise rotate (#532) * revises rotate/rand_rotate * fixes typing errors * fixes integration tests * remove unused import/variables | 12 June 2020, 01:52:09 UTC |
