| 4042356 | Nic Ma | 07 April 2020, 23:15:05 UTC | 238 add IO and transforms cache (#239) * [DLMED] add CacheDataset and CacheCompose * [DLMED] add speed test notebook and highlight doc * [DLMED] add notebook to README * [DLMED] fix typo in highlights * [DLMED] update cache API and integration test * [DLMED] move cache logic to CacheDataset directly * [DLMED] update spleen notebook and documentations * [DLMED] fixed typos in highlights * fixes docstring typos * revise cachedataset and compose * [DLMED] fix typo of '\r\n' Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 07 April 2020, 23:15:05 UTC |
| 12bde10 | Nic Ma | 07 April 2020, 14:55:43 UTC | [DLMED] add AdjustContrast transforms (#255) | 07 April 2020, 14:55:43 UTC |
| 2b2bd48 | Eric Kerfoot | 06 April 2020, 23:09:07 UTC | 240 export alias revisited (#241) * Added alias export code * Documentation update * Fix to unet.py * setattr fix Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 06 April 2020, 23:09:07 UTC |
| ca1dde4 | Nic Ma | 06 April 2020, 16:00:56 UTC | 251 AsChannelLast and ThresholdIntensity transforms (#254) * [DLMED] add AsChannelLast and ThresholdIntensity transforms * [DLMED] update alias * [DLMED] add to rst document | 06 April 2020, 16:00:56 UTC |
| a88f07a | Wenqi Li | 06 April 2020, 11:57:20 UTC | update nifti writer (#253) * update loader and writer - update nifti_write with resampling - adds original_affine to load_nifti - removes original_affine from spacing/orientation - fixes various typos in examples and docstrings | 06 April 2020, 11:57:20 UTC |
| c02a64a | Wenqi Li | 06 April 2020, 09:28:36 UTC | Readthedocs versioning (#252) * update doc website to use monai versioning * revise docs related contributing * revise docs building commands | 06 April 2020, 09:28:36 UTC |
| e3e79fc | Wenqi Li | 01 April 2020, 12:04:02 UTC | update aliases (#231) * update method/class aliases * fixes circular imports * compact imports for examples * update tests with compact imports * compact imports for monai/ * update docs * imports for notebooks * Changes to migrate CI to new DGX1 (#236) * To verify new DGX1 gh actions runner working. * Fix docker options in CI Co-authored-by: Isaac Yang <isaacy@nvidia.com> | 01 April 2020, 12:04:02 UTC |
| dbb3bc9 | Nic Ma | 01 April 2020, 10:32:17 UTC | 151 add classification tutorial based on MedNIST dataset (#235) * [DLMED] add MedNIST tutorial * [DLMED] develop all new tutorial based on MedNIST dataset | 01 April 2020, 10:32:17 UTC |
| ef2f1e9 | Isaac Yang | 31 March 2020, 20:10:01 UTC | Changes to migrate CI to new DGX1 (#236) * To verify new DGX1 gh actions runner working. * Fix docker options in CI | 31 March 2020, 20:10:01 UTC |
| 52716bf | Wenqi Li | 31 March 2020, 12:41:48 UTC | adds a utils section to contributing.md (#227) | 31 March 2020, 12:41:48 UTC |
| 1a2423f | Nic Ma | 31 March 2020, 09:13:23 UTC | 219 update ToTensor and SlidingWindow inference (#226) * [DLMED] update ToTensor and SlidingWindow inference * [DLMED] update as_tensor in transforms * [DLMED] update notebooks | 31 March 2020, 09:13:23 UTC |
| 3e5aa65 | Wenqi Li | 31 March 2020, 08:58:40 UTC | 228 automatic pip packaging and uploading (#230) * adding release workflow * upload artefacts * update release procedure * documentation in case of errors during releasing | 31 March 2020, 08:58:40 UTC |
| ec1d73d | Wenqi Li | 30 March 2020, 00:25:45 UTC | 197 set up versioneer and test releasing (#225) * set up versioning with versioneer 0.18 * revise setup cfg * update contributing.md * ci to display version numbers * ignore autogenerated files * Adds packaging tests - tests for python 3.x - adds license for setup.py - adds python3.x required in setup.cfg | 30 March 2020, 00:25:45 UTC |
| 32f8adb | Wenqi Li | 28 March 2020, 00:43:42 UTC | fixes integration test (missing original affine) (#223) | 28 March 2020, 00:43:42 UTC |
| 8072028 | Wenqi Li | 27 March 2020, 15:55:14 UTC | 86 tutorial updates (#183) * update nifti read notebook * revise notebook unet_segmentation_3d.ipynb * revise transformations - revise Spacing transforms to rely on the affines only - rectified a few typos * unit testing spacing transformations * update docs * update demo with spacing transform * fixes padding mode spacing * fixes load nifti * 3d transform tutorial * update notebooks * revised spacing, load nifti for readability * update example readme to include 3d transforms * fixes tensor contiguous in spatial transforms, fixes docs * update codecov xml for all branches * [DLMED] update spleen notebook Co-authored-by: Nic Ma <nma@nvidia.com> | 27 March 2020, 15:55:14 UTC |
| e657db0 | Eric Kerfoot | 27 March 2020, 15:03:54 UTC | 81 layer factory (#127) * Adding new factory concept. * Update to networks * [DLMED] add introduction of layer factory to highlights (#217) * adds factories doc to docs/ (#218) Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 27 March 2020, 15:03:54 UTC |
| 5ae87f8 | Nic Ma | 26 March 2020, 15:38:57 UTC | 209 loadnifti support multi-files (#213) * [DLMED] add multi-files support for LoadNifti * minor fixes load_nifti * update docstrings loadnifti Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 26 March 2020, 15:38:57 UTC |
| 434feb7 | Nic Ma | 26 March 2020, 12:52:24 UTC | 212 update README of examples (#214) * [DLMED] update README of examples * [DLMED] add dataset links to README * revise readme * remove duplicated yml Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 26 March 2020, 12:52:24 UTC |
| 8eb486d | Wenqi Li | 26 March 2020, 12:20:30 UTC | Fixes ci tests (#215) * fixes ci tests * fixes ci tests * [DLMED] fix several typos Co-authored-by: Nic Ma <nma@nvidia.com> | 26 March 2020, 12:20:30 UTC |
| 65b8e56 | Wenqi Li | 26 March 2020, 02:30:46 UTC | 210 integration tests for workflows (#211) * initial integration tests * update * separate the slow test, update rtol * fixes styles * resume unet 2d test * fixes flake8 error * config coverage xml | 26 March 2020, 02:30:46 UTC |
| 4256a14 | Nic Ma | 25 March 2020, 17:56:13 UTC | 203 develop pure pytorch examples (#204) * [DLMED] implement examples in PyTorch * [DLMED] add TensorBoard, NIftiSaver, CSVSaver to PyTorch examples | 25 March 2020, 17:56:13 UTC |
| 39fd982 | Nic Ma | 25 March 2020, 12:39:43 UTC | 201 refactor event handlers for flexibility (#202) * [DLMED] refactor handlers for flexibility * [DLMED] update according to comments * [DLMED] fix typo in NormalizeIntensity transform * [DLMED] update eval writer folder | 25 March 2020, 12:39:43 UTC |
| 1cbdcc3 | Wenqi Li | 25 March 2020, 09:45:39 UTC | revise github ci config (#208) * revise config * revise contrib guide | 25 March 2020, 09:45:39 UTC |
| c881c2d | Wenqi Li | 24 March 2020, 21:53:50 UTC | 196 config CI on github workflow (#207) * init. github workflow config * update to have checkoutv2 * coverage test * github ci * adding coverage report | 24 March 2020, 21:53:50 UTC |
| a54ccb2 | Nic Ma | 24 March 2020, 17:45:23 UTC | 186 dice loss support multi-labels task (#205) * [DLMED] add multi-labels support to DiceLoss * [DLMED] adjust according to comments * fixes generalized Dice w_func Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 24 March 2020, 17:45:23 UTC |
| 62cd378 | Wenqi Li | 24 March 2020, 15:23:55 UTC | 199 simplify instructions for pip install (#206) * fixes #199 * test docker image | 24 March 2020, 15:23:55 UTC |
| d191b09 | Nic Ma | 20 March 2020, 18:04:23 UTC | 191 develop determinism integration test (#195) * [DLMED] add determinism integration test and fix bugs * [DLMED] add determinism support to highlights * [DLMED] add transforms to the test * [DLMED] update to RandUniformPatch * fixes typos * fixes empty indicies issue in balanced sampling Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 20 March 2020, 18:04:23 UTC |
| e7b6564 | Wenqi Li | 20 March 2020, 09:16:33 UTC | 188 setup docker image (#192) * init. docker * fixes urls * update readme | 20 March 2020, 09:16:33 UTC |
| 9f10654 | Martin Huber | 19 March 2020, 21:35:40 UTC | 188 setuptools (#193) * added setuptools support updated README * removed relative paths * changed form exchanged raw install by pip install with folder flag | 19 March 2020, 21:35:40 UTC |
| 40a06b0 | Wenqi Li | 19 March 2020, 18:25:06 UTC | fixes pull request config (#194) | 19 March 2020, 18:25:06 UTC |
| 3568c2b | Nic Ma | 19 March 2020, 13:09:45 UTC | 181 use MONAI in pytorch medical segmentation program (#182) * [DLMED] add ScaleIntensityRanged and NormalizeIntensityd transforms * [DLMED] add pytorch example based on MSD spleen dataset * update docs for new transforms, revise typos/styles * [DLMED] add train notebook * [DLMED] update notebook with determinism * [DLMED] add image_threshold Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 19 March 2020, 13:09:45 UTC |
| c2b12d3 | Nic Ma | 18 March 2020, 02:46:57 UTC | [DLMED] fix typos in documentations (#185) | 18 March 2020, 02:46:57 UTC |
| 216298c | Wenqi Li | 16 March 2020, 14:48:33 UTC | 176 revise docs (#177) * [DLMED] add highlight features to README * [DLMED] add temp images path to highlight features * documentation updates - update readmet - update docs/ structure - merged highlights.md - update docs/Makefile commands * [DLMED] update end-to-end process chart * revise docstring for transforms/losses * update docs * update readthedocs * 179 add DeleteKeys transform (#180) * [DLMED] add DeleteKeys transform * [DLMED] remove unnecessary copy * update docs * fixes github urls * fixes sys.getsizeof test on mac Co-authored-by: Nic Ma <nma@nvidia.com> | 16 March 2020, 14:48:33 UTC |
| c40f739 | Nic Ma | 16 March 2020, 10:29:36 UTC | 179 add DeleteKeys transform (#180) * [DLMED] add DeleteKeys transform * [DLMED] remove unnecessary copy | 16 March 2020, 10:29:36 UTC |
| 895e0f2 | Nic Ma | 13 March 2020, 02:23:28 UTC | 165 update check all examples (#171) * [DLMED] add 3D classification inference examples * [DLMED] change UNet to 1 output * [DLMED] add 3D classification inference examples * [DLMED] update and clear all the examples also added unit tests for ClassificationSaver and Resized * [DLMED] fix transforms spatial axis issue and update unit tests * update demos: - unet: num_classes -> out_channels (signature consistency) - segmentation demo changed to binary ground truth - changed segmentation training dict to have validation every n iterations - segmentation demo image sizes to 128, window size to 96, lr 1e-3 (good results) - attach classification saver finalize() to Events.COMPLETE * [DLMED] fix tag_name bug, fix DenseNet3D bug, add comments Co-authored-by: root <root@apt-sh-ai.nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 13 March 2020, 02:23:28 UTC |
| 204e42d | Wenqi Li | 12 March 2020, 19:08:15 UTC | two stages ci (#172) | 12 March 2020, 19:08:15 UTC |
| e40917f | Mohammad Adil | 12 March 2020, 01:49:14 UTC | Adding dict-based and random spatial transforms. (#163) Co-authored-by: Nic Ma <nma@nvidia.com> | 12 March 2020, 01:49:14 UTC |
| 3a8f99c | Nic Ma | 12 March 2020, 01:26:24 UTC | 160 develop TensorBoard event handler (#161) Co-authored-by: Kevin Lu <kevlu@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 12 March 2020, 01:26:24 UTC |
| 5b1f258 | Wenqi Li | 11 March 2020, 10:07:50 UTC | add dictionary-based wrapper random spatial transforms (#166) | 11 March 2020, 10:07:50 UTC |
| d166f6a | Mohammad Adil | 10 March 2020, 12:24:42 UTC | 152-random-rotate (#155) * Add RandomRotate. | 10 March 2020, 12:24:42 UTC |
| 5c49f8f | Nic Ma | 10 March 2020, 12:05:38 UTC | 156 event handlers support arbitrary format (#159) | 10 March 2020, 12:05:38 UTC |
| 35da65c | Wenqi Li | 10 March 2020, 11:28:00 UTC | spacing and orientation; revise transforms cropping and zooming (#162) | 10 March 2020, 11:28:00 UTC |
| 39b2cb2 | Nic Ma | 09 March 2020, 21:10:52 UTC | 144 loadnifti transform common dataset (#145) * [DLMED] add LoadNifti transform and common Dataset * [DLMED] update according to comments * [DLMED] fix typo * [DLMED] update example to use latest API * [DLMED] update code to add more features * [DLMED] update to AsChannelFirst * [DLMED] update to use np.moveaxis API instead * [DLMED] update according to comments * update generalized dice to be consistent with the changes in dice loss Co-authored-by: Wenqi Li <wenqil@nvidia.com> | 09 March 2020, 21:10:52 UTC |
| 7304182 | Wenqi Li | 09 March 2020, 17:17:39 UTC | 112 combining spatial transforms (#131) * affine transforms * randomised affine and elastic deformation * add unit tests * add a 2D notebook demo * add speed demo | 09 March 2020, 17:17:39 UTC |
| 1e230ed | Mohammad Adil | 09 March 2020, 10:55:26 UTC | Adding RandomFlip. (#154) | 09 March 2020, 10:55:26 UTC |
| 03bebf5 | Mohammad Adil | 09 March 2020, 10:20:27 UTC | 152-random-zoom (#153) | 09 March 2020, 10:20:27 UTC |
| b850167 | Wenqi Li | 08 March 2020, 16:39:17 UTC | update doc api deps (#158) | 08 March 2020, 16:39:17 UTC |
| 2bda586 | Ben Murray | 06 March 2020, 01:57:04 UTC | 58-implement-transform-adaptor-2: Re-adding work via new branch as th… (#143) | 06 March 2020, 01:57:04 UTC |
| db05942 | Mohammad Adil | 06 March 2020, 01:41:23 UTC | Fix gpu zoom errors. (#149) | 06 March 2020, 01:41:23 UTC |
| 445a568 | Mohammad Adil | 05 March 2020, 19:54:38 UTC | 107-zoom (#138) * Adding zoom transform and tests. * Fix import error. | 05 March 2020, 19:54:38 UTC |
| 7f29477 | Wenqi Li | 05 March 2020, 13:36:44 UTC | 133 dataset and example with dict transforms (#134) * [DLMED] add UNet example with dict based transforms * [DLMED] temporarily remove constants, will discuss after GTC * [DLMED] adjust default behavior according to comments | 05 March 2020, 13:36:44 UTC |
| 28ad305 | Wenqi Li | 05 March 2020, 12:13:06 UTC | 113-gaussian-noise (#139) | 05 March 2020, 12:13:06 UTC |
| f39e8c1 | Wenqi Li | 05 March 2020, 12:03:54 UTC | 108-resize (#125) * Add Resize transform (spatial scaling). * Adding tests. | 05 March 2020, 12:03:54 UTC |
| f5ccf2a | Mohammad Adil | 05 March 2020, 04:07:40 UTC | Adding rotation transform. (#126) | 05 March 2020, 04:07:40 UTC |
| cd4cc54 | Nic Ma | 05 March 2020, 02:51:05 UTC | [DLMED] add 3D medical image classification example (#142) | 05 March 2020, 02:51:05 UTC |
| fbc4b5c | Wenqi Li | 04 March 2020, 19:07:33 UTC | fixes #100 Transform synchronization (#128) * fixes #100 Transform synchronization * set random state returns self | 04 March 2020, 19:07:33 UTC |
| 3fed596 | Wenqi Li | 04 March 2020, 18:03:59 UTC | 130 generate batch data from transform (#132) * [DLMED] add RandomPosNegLabelCrop 1. generate batch data in crop transform. 2. general crop transform at venilla level. 3. crop out batch data based on positive/negative ratio. | 04 March 2020, 18:03:59 UTC |
| ec57b73 | Mohammad Adil | 04 March 2020, 00:07:58 UTC | 109-spatial-flip (#124) * Add spatial flip to transforms. * Add tests and fix errors. * Fix unit tests. | 04 March 2020, 00:07:58 UTC |
| a65b182 | Wenqi Li | 01 March 2020, 10:17:21 UTC | update densenet (#129) | 01 March 2020, 10:17:21 UTC |
| 86e9e54 | Wenqi Li | 28 February 2020, 17:58:12 UTC | add rand rot90 transforms and dictionary-based counterparts (#106) * add (rand) rot90 transforms * add randomize interface | 28 February 2020, 17:58:12 UTC |
| a79e2cb | Nic Ma | 28 February 2020, 10:22:58 UTC | 120 fix MeanDice Nan issue for all zero data (#121) * [DLMED] fix MeanDice Nan issue for all zero data * [DLMED] update unit tests for ComputeMeanDice * update dice metric * [DLMED] remove smooth and skip all labels=0 * [DLMED] update docstring and unit test error Co-authored-by: Wenqi Li <wenqi.li@ucl.ac.uk> | 28 February 2020, 10:22:58 UTC |
| 1539813 | Wenqi Li | 26 February 2020, 19:16:39 UTC | add generalised dice loss and test, updated dice loss (#122) * add generalised dice loss and test, updated dice loss | 26 February 2020, 19:16:39 UTC |
| 822d568 | Wenqi Li | 26 February 2020, 12:04:03 UTC | add highresnet and shape tests (#119) | 26 February 2020, 12:04:03 UTC |
| deb4b4e | Wenqi Li | 25 February 2020, 16:45:53 UTC | fixes linting false negatives, fixes examples/unet_segmentation_3d.py py35 (#118) | 25 February 2020, 16:45:53 UTC |
| 45f1f16 | Nic Ma | 21 February 2020, 12:45:46 UTC | 92-port-resnext3d (#105) * [DLMED] implement ResNeXt3D and unit test | 21 February 2020, 12:45:46 UTC |
| 7beaa51 | Mohammad Adil | 21 February 2020, 08:45:39 UTC | Fixes notebook (#103) * fixes notebook imports * Fixes all notebooks and unet example (#97). * Update notebook with tensorboard display. | 21 February 2020, 08:45:39 UTC |
| fd6539f | Nic Ma | 20 February 2020, 15:08:38 UTC | [DLMED] add support to DenseNet3D (#104) fixes #104 Densely Connected Convolutional Networks | 20 February 2020, 15:08:38 UTC |
| 7768864 | Mohammad Adil | 20 February 2020, 12:05:43 UTC | Temp fix nifti_reader (#100) | 20 February 2020, 12:05:43 UTC |
| 448b61a | Wenqi Li | 19 February 2020, 14:35:15 UTC | 17 unit tests for each mvp component and workflow (#83) * unit test -- mean_dice handler * unit test -- stats handler * integration test -- sliding window | 19 February 2020, 14:35:15 UTC |
| 5e12c5d | Mohammad Adil | 13 February 2020, 20:09:59 UTC | 40-validation-early-stop (#73) * Adding MVP example for Validation every epoch with Early Stopping. * Add every_n_epochs and update python example. * Fix flake8 errors. * Update example to work with StatsHandler. Co-authored-by: Wenqi Li <wenqi.li@ucl.ac.uk> | 13 February 2020, 20:09:59 UTC |
| d5e610f | Wenqi Li | 13 February 2020, 19:34:28 UTC | 39 sliding window workflow (#56) * [DLMED] add support to SlidingWindow inference and image padding * [DLMED] add Nifti writer for model output data * [DLMED] add checkpoint loader as ignite event-handler Co-authored-by: Wenqi Li <wenqi.li@ucl.ac.uk> Co-authored-by: Nic Ma <mpcmvp@163.com> Co-authored-by: Mohammad Adil <madil@nvidia.com> | 13 February 2020, 19:34:28 UTC |
| 01c3f0b | Wenqi Li | 13 February 2020, 17:49:21 UTC | rearrange the modules (#69) * update folders * rearrange files * add missing copyrights * update folder structure readme * mv utils to each module * merge utils/readme to monai/readme * resolves code import * resolves style issues * resolves examples import * create layer factories | 13 February 2020, 17:49:21 UTC |
| eea97b5 | Wenqi Li | 13 February 2020, 17:28:32 UTC | remove unused deps (#75) | 13 February 2020, 17:28:32 UTC |
| f3ce2da | Ben Murray | 12 February 2020, 16:53:07 UTC | 59 preprocessor compose functionality (#60) * 59-compose-functionality: adding Compose class and unit test class * 59-compose-functionality: adding documentation to compose * 59-compose-functionality: adding essential compose unit tests * 59-compose-functionality: updated tests to fix flake failures * update examples (dependencies) Co-authored-by: Wenqi Li <wenqi.li@ucl.ac.uk> | 12 February 2020, 16:53:07 UTC |
| 38ef7a8 | Nic Ma | 12 February 2020, 15:11:00 UTC | 7 training stats event handler (#71) * [DLMED] add bunch handler structure and stats_handler example * [DLMED] update StatsHandler referring to ignite metric style * revise StatsHandler, update the training example to test the StatsHandler Co-authored-by: Wenqi Li <wenqi.li@ucl.ac.uk> | 12 February 2020, 15:11:00 UTC |
| 3e0fdc4 | Wenqi Li | 12 February 2020, 12:13:29 UTC | fixes dice loss (#70) * fixes typos in dice loss * fixes examples | 12 February 2020, 12:13:29 UTC |
| 99c16f4 | Isaac Yang | 10 February 2020, 21:39:27 UTC | Automatically publish document to ReadTheDocs (#68) * Automatically publish document to ReadTheDocs 1. Installing PyTorch CPU to reduce memory 2. Connect apidocs building process with build-inited event 3. Webhook will be added * Fix flake8 issue * Fix over-indentation | 10 February 2020, 21:39:27 UTC |
| b90d5f1 | Wenqi Li | 10 February 2020, 19:13:06 UTC | using cuda:0 and cuda:1 for the ci tests, fixes integration test (#67) | 10 February 2020, 19:13:06 UTC |
| f430475 | Nic Ma | 10 February 2020, 17:56:07 UTC | 40 mean_dice metric (#66) * [DLMED] add mean_dice metric and to_one_hot tool * [DLMED] add support to multi-classes output * [DLMED] add unit tests and support to add sigmoid and softmax * merge utils/to_onehot.py and networks/utils/one_hot into networks/utils/one_hot * additional dice loss test cases Co-authored-by: Wenqi Li <wenqi.li@ucl.ac.uk> | 10 February 2020, 17:56:07 UTC |
| 26bc651 | nvkevlu | 07 February 2020, 11:02:12 UTC | 41 tensorboard logging (#48) fixes #41 * add tensorboard logging with animated gif image logging * Update img2tensorboardutils.py * Update unet_segmentation_3d.py Co-authored-by: Nic Ma <mpcmvp@163.com> | 07 February 2020, 11:02:12 UTC |
| 962cb11 | Eric Kerfoot | 07 February 2020, 09:02:26 UTC | 42 multi gpu (#49) fixes #49 * Adding adaptation to use the default Ignite supervised training function with multiple GPUs using data parallelism * Update test_parallel_execution.py * Add decorator to expect failure if no GPUs. (#51) Co-authored-by: Mohammad Adil <madil@nvidia.com> | 07 February 2020, 09:02:26 UTC |
| 294f6e1 | Wenqi Li | 06 February 2020, 18:56:23 UTC | separate linting and runtests (#54) | 06 February 2020, 18:56:23 UTC |
| 9f95f0a | Wenqi Li | 06 February 2020, 18:04:47 UTC | adding contributing.md (#55) | 06 February 2020, 18:04:47 UTC |
| c1c9602 | Wenqi Li | 06 February 2020, 16:04:48 UTC | 38 update issue and PR templates (#50) * Update issue templates * Update PR template | 06 February 2020, 16:04:48 UTC |
| 7b2d73f | Wenqi Li | 04 February 2020, 15:53:00 UTC | 11 integration test resolves conflicts (#36) * Adding integration test for segmentation with UNet * update integration test for MVP * enable CI commands * update README.md, pytorch-ignite dep 0.3.0 * rm torchvision dep Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: Isaac Yang <isaacy@nvidia.com> | 04 February 2020, 15:53:00 UTC |
| f01ff46 | Wenqi Li | 25 January 2020, 02:40:25 UTC | extracting notebook example as python file (#45) | 25 January 2020, 02:40:25 UTC |
| 8db6400 | Isaac Yang | 24 January 2020, 17:10:18 UTC | Add script to run unit tests in GPU runner (nvcr.io/nvidia/pytorch:19.10-py3) (#34) | 24 January 2020, 17:10:18 UTC |
| 5550925 | Nic Ma | 23 January 2020, 10:50:47 UTC | [DLMED] add event-handler to save checkpoint (#35) | 23 January 2020, 10:50:47 UTC |
| 1390701 | Nic Ma | 22 January 2020, 14:48:40 UTC | 9 intensity normalisation transform (#25) * [DLMED] implement intensity normalization transform design according to our latest discussion: 1. input data is dict format with keys for fields. 2. only based on PyTorch and data shape is channel_last. * 9 part a adding test intensity normalisation transform (#33) * Adding script to run unit tests and example test cases (#29) Adding script to run unit tests and example test cases * initial unit tests for dice loss (#27) * initial unit tests for 2d/3d unet * unit tests update - triggering unit tests via github workflow - renamed testconvolutions.py to test_convolutions.py - test unet test cases as variables for readability * initial unit tests for 2d/3d unet (#26) * initial unit tests for 2d/3d unet * unit tests update - triggering unit tests via github workflow - renamed testconvolutions.py to test_convolutions.py - test unet test cases as variables for readability * 14 code examples of monai input data pipeline (#24) * fixes cardiac example * update example cardiac segmentation * Create .gitlab-ci.yml (#30) an initial step towards #19 * tests intensity normalizer - revised to support both `[key]` and `key` as an input for apply_keys - added `NumpyImageTestCase2D` and `TorchImageTestCase2D` * style updates and new test cases: - adding copyright notice - validate user input before setting class member - one line space after copyright - testing multiple keys input data Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: Isaac Yang <isaacy@nvidia.com> * [DLMED] simplify intensity normalization transform for MVP Co-authored-by: Wenqi Li <wenqi.li@ucl.ac.uk> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com> Co-authored-by: Isaac Yang <isaacy@nvidia.com> | 22 January 2020, 14:48:40 UTC |
| 2fd7d6d | Eric Kerfoot | 22 January 2020, 14:10:43 UTC | 2 nifti stream and patch transforms (#28) * initial unit tests for 2d/3d unet * adding license info * Adding definitions for reading Nifti files in streams and stream transforms for selecting patches (windowing) * Remove tests * Renaming fix * Update arrayutils.py * Removed blank lines in comments * Added Dataset based Nifti reader, grid patch sampler, and transforms * Added example segmentation notebook * Cleanup deletion * Update cardiac_segmentation.ipynb Co-authored-by: Wenqi Li <wenqi.li@ucl.ac.uk> | 22 January 2020, 14:10:43 UTC |
| eef2941 | Isaac Yang | 17 January 2020, 17:01:10 UTC | Create .gitlab-ci.yml (#30) an initial step towards #19 | 17 January 2020, 17:01:10 UTC |
| de1fbe0 | Wenqi Li | 17 January 2020, 16:48:15 UTC | 14 code examples of monai input data pipeline (#24) * fixes cardiac example * update example cardiac segmentation | 17 January 2020, 16:48:15 UTC |
| 4bd517a | Wenqi Li | 17 January 2020, 13:37:34 UTC | initial unit tests for 2d/3d unet (#26) * initial unit tests for 2d/3d unet * unit tests update - triggering unit tests via github workflow - renamed testconvolutions.py to test_convolutions.py - test unet test cases as variables for readability | 17 January 2020, 13:37:34 UTC |
| a2fc227 | Wenqi Li | 17 January 2020, 13:35:23 UTC | initial unit tests for dice loss (#27) * initial unit tests for 2d/3d unet * unit tests update - triggering unit tests via github workflow - renamed testconvolutions.py to test_convolutions.py - test unet test cases as variables for readability | 17 January 2020, 13:35:23 UTC |
| 9d90ba0 | Eric Kerfoot | 17 January 2020, 12:11:57 UTC | Adding script to run unit tests and example test cases (#29) Adding script to run unit tests and example test cases | 17 January 2020, 12:11:57 UTC |
| eb9189d | Wenqi Li | 13 January 2020, 16:58:21 UTC | Merge pull request #23 from Project-MONAI/21-coding-style fixes https://github.com/Project-MONAI/MONAI/issues/21 | 13 January 2020, 16:58:21 UTC |
| 05b248c | Wenqi Li | 13 January 2020, 16:49:50 UTC | aliasLock -> alias_lock | 13 January 2020, 16:49:50 UTC |
| d60b9a2 | Wenqi Li | 13 January 2020, 16:46:05 UTC | Merge branch 'master' into 21-coding-style resolving license info conflicts. | 13 January 2020, 16:46:05 UTC |
| c49febd | Eric Kerfoot | 13 January 2020, 15:01:29 UTC | License Addition to Every Source File (#22) * Added license to every .py file * Cleanup * Update license | 13 January 2020, 15:01:29 UTC |
| 1f521a1 | Wenqi Li | 13 January 2020, 14:35:09 UTC | update the function signatures | 13 January 2020, 14:35:09 UTC |
