merge master by Nic-Ma · Pull Request #134 · Nic-Ma/MONAI

Nic-Ma · 2021-06-17T01:33:27Z

Fixes # .

Description

A few sentences describing the changes proposed in this pull request.

Status

Ready/Work in progress/Hold

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
Breaking change (fix or new feature that would cause existing functionality to change).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh --codeformat --coverage.
Quick tests passed locally by running ./runtests.sh --quick.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

Signed-off-by: Nic Ma <[email protected]>

Allowing the choice of epoch and iteration interval. Signed-off-by: Petru-Daniel Tudosiu <[email protected]>

* [DLMED] enhance list_collate Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update based on comments Co-authored-by: Wenqi Li <[email protected]> Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add slicing support in datasets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc-strings and typehints Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* download_if_not_exist Signed-off-by: Behrooz <[email protected]> * Update cuimage reader tests Signed-off-by: Behrooz <[email protected]> * Update openslide reader tests Signed-off-by: Behrooz <[email protected]> * Update the file path to be relative to the test file Signed-off-by: Behrooz <[email protected]> * Update patch wsi dataset tests Signed-off-by: Behrooz <[email protected]> * Update smartcache patch wsi dataset tests Signed-off-by: Behrooz <[email protected]> * Revert "download_if_not_exist" This reverts commit a4c65f3. Signed-off-by: Behrooz <[email protected]> * Update with download_url Signed-off-by: Behrooz <[email protected]> * [MONAI] python code formatting

* Implement random bias field transform Signed-off-by: Yiheng Wang <[email protected]>

* Fixing error in saving non-pytorch-variable parameters for backwards pass Signed-off-by: chaliebudd <[email protected]> * Adding unit tests to check bilateral filter backwards runs Signed-off-by: chaliebudd <[email protected]> * fixing typo introduced by merge Signed-off-by: chaliebudd <[email protected]> * code reformatting Signed-off-by: chaliebudd <[email protected]>

* fixes warping Signed-off-by: Wenqi Li <[email protected]> * fixes types Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes warnings in setup.cfg, config, deprecated assertexecption Signed-off-by: Wenqi Li <[email protected]>

* Remove assert statement from non-test files * Remove redundant `None` default * Use `is` to compare type of objects * Refactor unnecessary `else` / `elif` when `if` block has a `raise` statement * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement * runtests.sh --autofix Signed-off-by: Wenqi Li <[email protected]> * autofix/7d8e8b86-113e-4a5a-8d0d-c621aab7b5f2 Signed-off-by: Wenqi Li <[email protected]> * fixes assert types Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Behrooz <[email protected]>

* Implement MaskedInferenceWSIDataset for pathology inference Signed-off-by: Behrooz <[email protected]> * Update pathology init Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Remove last elemnt of cum_num_patches Signed-off-by: Behrooz <[email protected]> * Add unittest with multiple cases for MaskedInferenceWSIDataset Signed-off-by: Behrooz <[email protected]> * sort imports in init Signed-off-by: Behrooz <[email protected]> * Remove list dataset Signed-off-by: Behrooz <[email protected]> * Remove try/except and add type hint Signed-off-by: Behrooz <[email protected]> * Convert the sample output to a list Signed-off-by: Behrooz <[email protected]> * Remove some type hints Signed-off-by: Behrooz <[email protected]> * Remove prints Signed-off-by: Behrooz <[email protected]> * Update based on commnets Signed-off-by: Behrooz <[email protected]> * Update patch_size Signed-off-by: Behrooz <[email protected]> * Update unittests Signed-off-by: Behrooz <[email protected]> * Add more type hints Signed-off-by: Behrooz <[email protected]>

* remove unused in_channels in LNCC Signed-off-by: Wenqi Li <[email protected]> * update integration tests Signed-off-by: Wenqi Li <[email protected]> * extending warp options Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] enhance brats transform Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* Fix stdshift type error Signed-off-by: Yiheng Wang <[email protected]> * Add dtype testcases Signed-off-by: Yiheng Wang <[email protected]>

* Implement ProbMapGenerator handler Signed-off-by: Behrooz <[email protected]> * Update doc and init Signed-off-by: Behrooz <[email protected]> * Sort init imports Signed-off-by: Behrooz <[email protected]> * Add unittest for ProbMapGenerator Signed-off-by: Behrooz <[email protected]> * Ignore if ignite is not available Signed-off-by: Behrooz <[email protected]> * Update Engine import Signed-off-by: Behrooz <[email protected]> * Exclude from min-test Signed-off-by: Behrooz <[email protected]> * Address all the comments Signed-off-by: Behrooz <[email protected]> * Fix file path and dtype Signed-off-by: Behrooz <[email protected]>

* Implement MaskedInferenceWSIDataset for pathology inference Signed-off-by: Behrooz <[email protected]> * Update pathology init Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Remove last elemnt of cum_num_patches Signed-off-by: Behrooz <[email protected]> * Add unittest with multiple cases for MaskedInferenceWSIDataset Signed-off-by: Behrooz <[email protected]> * sort imports in init Signed-off-by: Behrooz <[email protected]> * Remove list dataset Signed-off-by: Behrooz <[email protected]> * Remove try/except and add type hint Signed-off-by: Behrooz <[email protected]> * Convert the sample output to a list Signed-off-by: Behrooz <[email protected]> * Remove some type hints Signed-off-by: Behrooz <[email protected]> * Implement FROC calcualtion for pathology Signed-off-by: Behrooz <[email protected]> * Update ProbNMS doctring Signed-off-by: Behrooz <[email protected]> * Update docs and change namings Signed-off-by: Behrooz <[email protected]> * Fix a bug and minor changes Signed-off-by: Behrooz <[email protected]> * Minor changes Signed-off-by: Behrooz <[email protected]> * Fix docstring formatting Signed-off-by: Behrooz <[email protected]> * Add a type hint Signed-off-by: Behrooz <[email protected]> * Implement unittests for EvaluateTumorFROC Signed-off-by: Behrooz <[email protected]> * Ignore type for np.amax Signed-off-by: Behrooz <[email protected]> * Remove space Signed-off-by: Behrooz <[email protected]> * Ignore type for range instead of np.amax Signed-off-by: Behrooz <[email protected]> * Skip test if PIL is not available Signed-off-by: Behrooz <[email protected]> * Update docstring Signed-off-by: Behrooz <[email protected]> * Skip ground truth generating if PIL is not available Signed-off-by: Behrooz <[email protected]> * Update unittest Signed-off-by: Behrooz <[email protected]> * Remove print Signed-off-by: Behrooz <[email protected]> * Rename TumorFROC and add few type hints Signed-off-by: Behrooz <[email protected]> * Rename evaluators to metrics Signed-off-by: Behrooz <[email protected]> * Remove non-relevant files Signed-off-by: Behrooz <[email protected]> * Rename to LesionFROC and minor changes Signed-off-by: Behrooz <[email protected]> * Update test Signed-off-by: Behrooz <[email protected]>

Signed-off-by: Behrooz <[email protected]>

* Rename the prob map producer unittest to match the module Signed-off-by: Behrooz <[email protected]> * Change probs_map to prob_map Signed-off-by: Behrooz <[email protected]> * Prepend image_inference_outputs with temp to be ignored Signed-off-by: Behrooz <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

* followup of #1878, fixes tests, remove json loading Signed-off-by: Wenqi Li <[email protected]> * Update test ordinal numbers Signed-off-by: Behrooz <[email protected]> Co-authored-by: Behrooz <[email protected]>

* clip variance to be >= 0 Signed-off-by: kate-sann5100 <[email protected]> * max for torch1.6 Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* update to use pytorch2103 Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] SaveImage supports patch data Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

This reverts commit 4bd26f9. Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* [DLMED] update affine data Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc-build issue Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

* [DLMED] fix endian issue of nibabel header Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

* fixes 2316 Signed-off-by: Wenqi Li <[email protected]>

* initial MMAR model download and extract Signed-off-by: Wenqi Li <[email protected]> * fixes zip file without base folder Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]> * unique ids test Signed-off-by: Wenqi Li <[email protected]> * revise based on comments Signed-off-by: Wenqi Li <[email protected]> * add model path support Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: masadcv <[email protected]>

* masked loss wrapper Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update 2 all_gather APIs Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove pytorch version limit Signed-off-by: Nic Ma <[email protected]> * [DLMED] optimize perf by joining strings Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] remove unnecessary import Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add deprecated warning Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] change concat default to True Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* fixes #2333 Signed-off-by: Wenqi Li <[email protected]> * remove the win. workaround Signed-off-by: Wenqi Li <[email protected]>

* fixes-mypy Signed-off-by: Wenqi Li <[email protected]>

* Add size option for UpSample Signed-off-by: Yiheng Wang <[email protected]> * adjust indentation Signed-off-by: Yiheng Wang <[email protected]>

* fixes #2345 Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]>

* Merge branch dev into 2320-preserve-transform-dict-order Signed-off-by: Wenqi Li <[email protected]> * Preserve ordering of input data dict to RandWeightedCropd and RandCropByPosNegLabeld Added shallow copies of data dict to the return list of dicts to preserve order of data (input dict). Signed-off-by: Eddy Lin <[email protected]> Signed-off-by: Edward Lin <[email protected]> Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* Adding deprecated decorators Signed-off-by: Eric Kerfoot <[email protected]> * Adding deprecated decorators Signed-off-by: Eric Kerfoot <[email protected]> * Updates from comments Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* adds an option to run distributed test cases Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* 561 497 Provide metrics base APIs (#2291) * [DLMED] add metric base class Signed-off-by: Nic Ma <[email protected]> * [DLMED] update meandice and auc Signed-off-by: Nic Ma <[email protected]> * [DLMED] extract reduce API Signed-off-by: Nic Ma <[email protected]> * [DLMED] update regression metrics Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the other metrics and enhance unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add doc-strings and update unit tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pytype issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix all the mypy issues Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix integration test Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pytype issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more sanity check Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to Yiheng's comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to Wenqi's comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] change to "_compute()" and "aggregate()" Signed-off-by: Nic Ma <[email protected]> * [DLMED] add compute_list() Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> * [DLMED] update according to comments 1. re-define base classes in 3 levels to make it more clear and flexible to extend 2. added self-contained variables in metrics to provide easier API 3. added reset() and sync() logic 4. added distributed data parallel logic for all the metrics Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] optimize base classes Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify integration tests to use new APIs Signed-off-by: Nic Ma <[email protected]> * [DLMED] update based on comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add synced=False in add() Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * full ci/cd for feature branches Signed-off-by: Wenqi Li <[email protected]> * [DLMED] update aggregate() Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* skip download if http 500 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] enhance GradCam return type Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* fixes #2374 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add from_dict utility Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* temp quick test Signed-off-by: Wenqi Li <[email protected]> * fixes basic unet tests Signed-off-by: Wenqi Li <[email protected]> * upgrade tests Signed-off-by: Wenqi Li <[email protected]> * upgrade cron Signed-off-by: Wenqi Li <[email protected]> * update base Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * update condition Signed-off-by: Wenqi Li <[email protected]> * update cuda Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 1e448f6. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp quick test" This reverts commit 6563e84. Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit e246bde. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit 794d517. Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]>

* adds partial weight util Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * update coverage config Signed-off-by: Wenqi Li <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]> * unit tests Signed-off-by: Wenqi Li <[email protected]> * tests, examples Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * compatible_mod_state -> copy_model_state Signed-off-by: Wenqi Li <[email protected]> * tests/test_set_mod_state.py -> tests/test_copy_model_state.py Signed-off-by: Wenqi Li <[email protected]> * inplace False checkpoint loader Signed-off-by: Wenqi Li <[email protected]>

Nic-Ma and others added 30 commits March 29, 2021 08:12

[DLMED] support single item (#1884)

a1f938a

Signed-off-by: Nic Ma <[email protected]>

Epoch/Iteration interval (#1870)

9f6ceeb

Allowing the choice of epoch and iteration interval. Signed-off-by: Petru-Daniel Tudosiu <[email protected]>

[DLMED] add data_root_dir arg (#1890)

f3ccbac

Signed-off-by: Nic Ma <[email protected]>

Implement random bias field transform (#1886)

f0c9c18

* Implement random bias field transform Signed-off-by: Yiheng Wang <[email protected]>

Update WSIReader for CuCIM (#1876)

1612ec3

Signed-off-by: Behrooz <[email protected]>

remove unused in_channels in LNCC (#1903)

ca8481f

* remove unused in_channels in LNCC Signed-off-by: Wenqi Li <[email protected]> * update integration tests Signed-off-by: Wenqi Li <[email protected]> * extending warp options Signed-off-by: Wenqi Li <[email protected]>

1905 Enhance the brats transform (#1906)

b1d45ee

* [DLMED] enhance brats transform Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

Fix stdshift type error (#1907)

2a7e1ce

* Fix stdshift type error Signed-off-by: Yiheng Wang <[email protected]> * Add dtype testcases Signed-off-by: Yiheng Wang <[email protected]>

Update CuCIM (#1909)

613f25e

Signed-off-by: Behrooz <[email protected]>

Update pathology unittests (#1910)

5fec791

Signed-off-by: Behrooz <[email protected]>

Implement dice_focal loss (#1914)

ba127a2

Signed-off-by: Yiheng Wang <[email protected]>

followup of #1878 (#1913)

debc561

* followup of #1878, fixes tests, remove json loading Signed-off-by: Wenqi Li <[email protected]> * Update test ordinal numbers Signed-off-by: Behrooz <[email protected]> Co-authored-by: Behrooz <[email protected]>

1868-fix-potential-inf-in-lncc-loss (#1915)

32e540f

* clip variance to be >= 0 Signed-off-by: kate-sann5100 <[email protected]> * max for torch1.6 Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

1919 - test pt 2103 (#1920)

4bd26f9

* update to use pytorch2103 Signed-off-by: Wenqi Li <[email protected]>

fixes typos (#1924)

d9e68c8

Signed-off-by: Wenqi Li <[email protected]>

Revert "1919 - test pt 2103 (#1920)" (#1925)

e7d3d66

This reverts commit 4bd26f9. Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

skip warp tests before torch 18 (#1927)

e871ee3

Signed-off-by: Wenqi Li <[email protected]>

update docstrings (#1931)

e80cc4a

Signed-off-by: Wenqi Li <[email protected]>

update get_package_version (#1930)

30523c0

Signed-off-by: Wenqi Li <[email protected]>

wyli and others added 29 commits June 6, 2021 08:40

fixes integration test (#2312)

316449b

Signed-off-by: Wenqi Li <[email protected]>

optional strict check (#2309)

509c2c1

Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

2316 Make saved affine match data content (#2322)

27e64e0

* [DLMED] update affine data Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc-build issue Signed-off-by: Nic Ma <[email protected]>

Modify initialize function (#2324)

a961918

Signed-off-by: Yiheng Wang <[email protected]>

2316 load image with big-endian header (#2325)

a5376df

* fixes 2316 Signed-off-by: Wenqi Li <[email protected]>

fix typo in crf args name (#2327)

e0f250c

Signed-off-by: masadcv <[email protected]>

573 masked loss wrapper (#2313)

1fa03c2

* masked loss wrapper Signed-off-by: Wenqi Li <[email protected]>

2333 conditionally install pytype (#2334)

a536462

* fixes #2333 Signed-off-by: Wenqi Li <[email protected]> * remove the win. workaround Signed-off-by: Wenqi Li <[email protected]>

Fixes mypy issue (#2340)

6476cee

* fixes-mypy Signed-off-by: Wenqi Li <[email protected]>

2342 Add size option for UpSample (#2344)

3de16a0

* Add size option for UpSample Signed-off-by: Yiheng Wang <[email protected]> * adjust indentation Signed-off-by: Yiheng Wang <[email protected]>

2345 no default mmar home for pytorch < 1.6 (#2346)

cbf2521

* fixes #2345 Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]>

update install cmd (#2352)

5aceade

Signed-off-by: Wenqi Li <[email protected]>

[DLMED] enhance docs (#2353)

7975275

Signed-off-by: Nic Ma <[email protected]>

fixes #2355 (#2356)

0b599ef

Signed-off-by: Wenqi Li <[email protected]>

[DLMED] enhance doc-string of Invertd (#2358)

2e5c11e

Signed-off-by: Nic Ma <[email protected]>

2239 adds a runtests.sh option to run distributed test cases (#2306)

f968f4a

* adds an option to run distributed test cases Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

[DLMED] fix jupyter util issue (#2361)

c1b5028

Signed-off-by: Nic Ma <[email protected]>

2362 skip MMAR downloading if the remote has http 500 (#2363)

fe3521f

* skip download if http 500 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

2374 multiprocess for non-exist persistent cache dir (#2375)

ddd0c75

* fixes #2374 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

Nic-Ma merged commit e7be49f into Nic-Ma:2380-fix-center-scale-crop Jun 17, 2021

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merge master#134

merge master#134
Nic-Ma merged 361 commits intoNic-Ma:2380-fix-center-scale-cropfrom
Project-MONAI:dev

Nic-Ma commented Jun 17, 2021

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Nic-Ma commented Jun 17, 2021

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