merge master by Nic-Ma · Pull Request #141 · Nic-Ma/MONAI

Nic-Ma · 2021-06-22T14:50:17Z

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.

* 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]>

* [DLMED] add EarlyStop handler Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] enhance validation handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] add set_trainer support Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more check Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments 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: Wenqi Li <[email protected]>

* [DLMED] change to save patch_index in meta_dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove error import Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* Enabled partial checkpoint loading Allowing partial loading of a model via strict=False. Signed-off-by: Petru-Daniel Tudosiu <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] simplify strict arg Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* less warning msg; remove PILImage types Signed-off-by: Wenqi Li <[email protected]> * remove engine type Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * add quick py36 37 tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit deaed40. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 3e8d8f4. Signed-off-by: Wenqi Li <[email protected]> * min test exclude senet test Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit 31f40a0. Signed-off-by: Wenqi Li <[email protected]> * update get gpu id Signed-off-by: Wenqi Li <[email protected]> * update docsstrings Signed-off-by: Wenqi Li <[email protected]>

* Add ProbNMS to transforts/post/array Signed-off-by: Behrooz <[email protected]> * Implement ProbNMSDict Signed-off-by: Behrooz <[email protected]> * Update the usage and add unittests Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Correct docs Signed-off-by: Behrooz <[email protected]> * Correct test case Signed-off-by: Behrooz <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

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

* Implement garbage collector handler Signed-off-by: Behrooz <[email protected]> * Make trigger_event lower case Signed-off-by: Behrooz <[email protected]> * Add unittest for garbage collector Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Exclude from min test Signed-off-by: Behrooz <[email protected]> * Fix a typo Signed-off-by: Behrooz <[email protected]> * Fix a bug Signed-off-by: Behrooz <[email protected]>

* [DLMED] add strict_shape option Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * update test case Signed-off-by: Wenqi Li <[email protected]> * fixes test config Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] enhance decathlon datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Behrooz <[email protected]>

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

* adds docker tag action Signed-off-by: Wenqi Li <[email protected]> * adds tag info Signed-off-by: Wenqi Li <[email protected]> * update versioneer Signed-off-by: Wenqi Li <[email protected]>

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]>

* [DLMED] add unit tests 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]>

…t_transform` (#2384) * [DLMED] enhance all doc-string of handlers Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

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

* refactoring decollate Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]> * more test cases and fixes Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes pytype error Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] enhance crop and pad doc-strings Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add `the` Signed-off-by: Nic Ma <[email protected]> * [DLMED] add examples Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

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

* update not nan docstring Signed-off-by: Yiheng Wang <[email protected]> * fix black error Signed-off-by: Yiheng Wang <[email protected]> * Fix indentation errors Signed-off-by: Yiheng Wang <[email protected]>

* initial gmm commit Signed-off-by: charliebudd <[email protected]>

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

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

* Add blossom pre-merge pipeline Signed-off-by: Mohammad Adil <[email protected]>

* [DLMED] add min tests command Signed-off-by: Nic Ma <[email protected]> * [DLMED] update CI script Signed-off-by: Nic Ma <[email protected]>

* [DKMED] add CSV datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] add group feature Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add optional install 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] add doc-strings Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add CSVDataset for non-iterable data Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add CSVIterableDataset base Signed-off-by: Nic Ma <[email protected]> * [DLMED] add CSVIterableDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] support multiple processes Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix docs-build Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI 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] change sys.platform Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip if windows Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add col_types arg Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

yiheng-wang-nv and others added 30 commits March 31, 2021 14:22

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]>

enhance min/exact version check (#1937)

23f98f3

fixes ThreadDataLoader (#1945)

baf1bec

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

fixes itk dep. version (#1944)

a6b8f2a

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

Add progress bar to LesionFROC (#1951)

fbce3c2

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

pipeline for releasing the docker images (#1953)

501026b

* adds docker tag action Signed-off-by: Wenqi Li <[email protected]> * adds tag info Signed-off-by: Wenqi Li <[email protected]> * update versioneer Signed-off-by: Wenqi Li <[email protected]>

remove unused RandomizableTransform (#1952)

81cfbf0

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

eddyleelin and others added 29 commits June 9, 2021 22:21

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]>

2380 fix inverse bug of CenterScaleCropd transform (#2383)

6e65fe6

* [DLMED] add unit tests 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 and enhance wrong doc-strings of all batch_transform and `outpu…

82fc4c1

…t_transform` (#2384) * [DLMED] enhance all doc-string of handlers Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

[DLMED] drop inheritance for future inverse feature (#2385)

4d9e8aa

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

temp. skip pytype on macos (#2392)

2f1afa8

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

[DLMED] add missing arg detach (#2393)

f3f9584

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

2390 Add docstring for not nans (#2395)

b829fe9

* update not nan docstring Signed-off-by: Yiheng Wang <[email protected]> * fix black error Signed-off-by: Yiheng Wang <[email protected]> * Fix indentation errors Signed-off-by: Yiheng Wang <[email protected]>

JIT compiled gaussian mixture model (GMM) (#1802)

67e68f6

* initial gmm commit Signed-off-by: charliebudd <[email protected]>

fixes loader (#2398)

162b54a

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

fixes jit concurrent build (#2405)

b653799

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

Add blossom pre-merge pipeline (21/June) (#2382)

fb7d9f1

* Add blossom pre-merge pipeline Signed-off-by: Mohammad Adil <[email protected]>

Add min tests cmd to runtests script (#2400)

8cda6c1

* [DLMED] add min tests command Signed-off-by: Nic Ma <[email protected]> * [DLMED] update CI script Signed-off-by: Nic Ma <[email protected]>

Nic-Ma merged commit c523d6b into Nic-Ma:2290-rerun-cachedataset Jun 22, 2021

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merge master#141

merge master#141
Nic-Ma merged 375 commits intoNic-Ma:2290-rerun-cachedatasetfrom
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Nic-Ma commented Jun 22, 2021

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Nic-Ma commented Jun 22, 2021

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