merge master by Nic-Ma · Pull Request #137 · Nic-Ma/MONAI

Nic-Ma · 2021-06-18T04:08:51Z

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.

* [DLMED] add slicing support in datasets Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update doc-strings and typehints Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* download_if_not_exist Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update cuimage reader tests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update openslide reader tests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update the file path to be relative to the test file Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update patch wsi dataset tests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update smartcache patch wsi dataset tests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Revert "download_if_not_exist" This reverts commit a4c65f3. Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update with download_url Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * [MONAI] python code formatting

* Implement random bias field transform Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* Fixing error in saving non-pytorch-variable parameters for backwards pass Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * Adding unit tests to check bilateral filter backwards runs Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * fixing typo introduced by merge Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * code reformatting Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk>

* fixes warping Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes types Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes warnings in setup.cfg, config, deprecated assertexecption Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 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 <wenqil@nvidia.com> * autofix/7d8e8b86-113e-4a5a-8d0d-c621aab7b5f2 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes assert types Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Implement MaskedInferenceWSIDataset for pathology inference Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update pathology init Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove last elemnt of cum_num_patches Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittest with multiple cases for MaskedInferenceWSIDataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * sort imports in init Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove list dataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove try/except and add type hint Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Convert the sample output to a list Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove some type hints Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove prints Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update based on commnets Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update patch_size Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update unittests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add more type hints Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* remove unused in_channels in LNCC Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update integration tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * extending warp options Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance brats transform Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Fix stdshift type error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Add dtype testcases Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* Implement ProbMapGenerator handler Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update doc and init Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Sort init imports Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittest for ProbMapGenerator Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Ignore if ignite is not available Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update Engine import Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Exclude from min-test Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Address all the comments Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix file path and dtype Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Implement MaskedInferenceWSIDataset for pathology inference Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update pathology init Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove last elemnt of cum_num_patches Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittest with multiple cases for MaskedInferenceWSIDataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * sort imports in init Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove list dataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove try/except and add type hint Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Convert the sample output to a list Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove some type hints Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Implement FROC calcualtion for pathology Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update ProbNMS doctring Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs and change namings Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix a bug and minor changes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Minor changes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix docstring formatting Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add a type hint Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Implement unittests for EvaluateTumorFROC Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Ignore type for np.amax Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove space Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Ignore type for range instead of np.amax Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Skip test if PIL is not available Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docstring Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Skip ground truth generating if PIL is not available Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update unittest Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove print Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Rename TumorFROC and add few type hints Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Rename evaluators to metrics Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove non-relevant files Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Rename to LesionFROC and minor changes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update test Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Rename the prob map producer unittest to match the module Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Change probs_map to prob_map Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Prepend image_inference_outputs with temp to be ignored Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* followup of #1878, fixes tests, remove json loading Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Update test ordinal numbers Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> Co-authored-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* clip variance to be >= 0 Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * max for torch1.6 Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* update to use pytorch2103 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] SaveImage supports patch data Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

This reverts commit 4bd26f9. Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add EarlyStop handler Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] enhance validation handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add set_trainer support Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more check Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] change to save patch_index in meta_dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove error import Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Enabled partial checkpoint loading Allowing partial loading of a model via strict=False. Signed-off-by: Petru-Daniel Tudosiu <petru.daniel@tudosiu.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] simplify strict arg Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix endian issue of nibabel header Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* fixes 2316 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* initial MMAR model download and extract Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes zip file without base folder Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * unique ids test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * add model path support Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk>

* masked loss wrapper Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] update 2 all_gather APIs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove pytorch version limit Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] optimize perf by joining strings Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] remove unnecessary import Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add deprecated warning Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] change concat default to True Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* fixes #2333 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove the win. workaround Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes-mypy Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Add size option for UpSample Signed-off-by: Yiheng Wang <vennw@nvidia.com> * adjust indentation Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* fixes #2345 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Merge branch dev into 2320-preserve-transform-dict-order Signed-off-by: Wenqi Li <wenqil@nvidia.com> * 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 <elindy26@gmail.com> Signed-off-by: Edward Lin <ell22@duke.edu> Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

* Adding deprecated decorators Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding deprecated decorators Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates from comments Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: Nic Ma <nma@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

* adds an option to run distributed test cases Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 561 497 Provide metrics base APIs (#2291) * [DLMED] add metric base class Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update meandice and auc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] extract reduce API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update regression metrics Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update all the other metrics and enhance unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add doc-strings and update unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix pytype issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix all the mypy issues Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix integration test Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix pytype issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more sanity check Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to Yiheng's comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to Wenqi's comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change to "_compute()" and "aggregate()" Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add compute_list() Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> * [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 <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] optimize base classes Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify integration tests to use new APIs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update based on comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add synced=False in add() Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * full ci/cd for feature branches Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] update aggregate() Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com>

* skip download if http 500 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance GradCam return type Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* fixes #2374 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add from_dict utility Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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

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

* [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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

Signed-off-by: Nic Ma <nma@nvidia.com>

* refactoring decollate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more test cases and fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes pytype error Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Nic-Ma and others added 30 commits March 29, 2021 21:40

Implement random bias field transform (#1886)

f0c9c18

* Implement random bias field transform Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Update WSIReader for CuCIM (#1876)

1612ec3

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

remove unused in_channels in LNCC (#1903)

ca8481f

* remove unused in_channels in LNCC Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update integration tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * extending warp options Signed-off-by: Wenqi Li <wenqil@nvidia.com>

1905 Enhance the brats transform (#1906)

b1d45ee

* [DLMED] enhance brats transform Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

Fix stdshift type error (#1907)

2a7e1ce

* Fix stdshift type error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Add dtype testcases Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Update CuCIM (#1909)

613f25e

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Update pathology unittests (#1910)

5fec791

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Implement dice_focal loss (#1914)

ba127a2

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

followup of #1878 (#1913)

debc561

* followup of #1878, fixes tests, remove json loading Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Update test ordinal numbers Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> Co-authored-by: Behrooz <3968947+behxyz@users.noreply.github.com>

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

32e540f

* clip variance to be >= 0 Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * max for torch1.6 Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

1919 - test pt 2103 (#1920)

4bd26f9

* update to use pytorch2103 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fixes typos (#1924)

d9e68c8

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

e7d3d66

This reverts commit 4bd26f9. Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

skip warp tests before torch 18 (#1927)

e871ee3

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update docstrings (#1931)

e80cc4a

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update get_package_version (#1930)

30523c0

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

enhance min/exact version check (#1937)

23f98f3

Nic-Ma and others added 29 commits June 7, 2021 14:45

2316 Fix endian order issue of Nibabel reader (#2326)

89ee6af

* [DLMED] fix endian issue of nibabel header Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

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

a5376df

* fixes 2316 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fix typo in crf args name (#2327)

e0f250c

Signed-off-by: masadcv <muhammad.asad@kcl.ac.uk>

573 masked loss wrapper (#2313)

1fa03c2

* masked loss wrapper Signed-off-by: Wenqi Li <wenqil@nvidia.com>

2333 conditionally install pytype (#2334)

a536462

* fixes #2333 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove the win. workaround Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Fixes mypy issue (#2340)

6476cee

* fixes-mypy Signed-off-by: Wenqi Li <wenqil@nvidia.com>

2342 Add size option for UpSample (#2344)

3de16a0

* Add size option for UpSample Signed-off-by: Yiheng Wang <vennw@nvidia.com> * adjust indentation Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

cbf2521

* fixes #2345 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update install cmd (#2352)

5aceade

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] enhance docs (#2353)

7975275

Signed-off-by: Nic Ma <nma@nvidia.com>

fixes #2355 (#2356)

0b599ef

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

2e5c11e

Signed-off-by: Nic Ma <nma@nvidia.com>

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 <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] fix jupyter util issue (#2361)

c1b5028

Signed-off-by: Nic Ma <nma@nvidia.com>

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

fe3521f

* skip download if http 500 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

ddd0c75

* fixes #2374 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

2380 fix inverse bug of CenterScaleCropd transform (#2383)

6e65fe6

* [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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 <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

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

4d9e8aa

Signed-off-by: Nic Ma <nma@nvidia.com>

Nic-Ma merged commit 65da722 into Nic-Ma:update-crop-doc-string Jun 18, 2021

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merge master#137

merge master#137
Nic-Ma merged 365 commits into
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Nic-Ma commented Jun 18, 2021

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