merge master#128
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Nic-Ma merged 351 commits intoNic-Ma:2348-enhance-doc-invertdfrom Jun 11, 2021
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Signed-off-by: Nic Ma <[email protected]>
* fixes #1857, SpatialCrop is compatible with tensors Signed-off-by: Wenqi Li <[email protected]> * update val comparisons Signed-off-by: Wenqi Li <[email protected]>
* Optimize speed and support any dimensions Signed-off-by: Yiheng Wang <[email protected]> * Fix black issue Signed-off-by: Yiheng Wang <[email protected]> * Add unittest and docstrings Signed-off-by: Yiheng Wang <[email protected]> * Modify box size and others Signed-off-by: Yiheng Wang <[email protected]> * Add pathology nms Signed-off-by: Yiheng Wang <[email protected]> * Update docs Signed-off-by: Yiheng Wang <[email protected]> * Update pathology nms Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] fix read permission issue Signed-off-by: Nic Ma <[email protected]>
* fix lr finder
* [DLMED] add MapLabelValue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add missing doc-string 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]>
* Add unittests for SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Turn off shuffle for SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* fixes #1848 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 563e7ea. Signed-off-by: Wenqi Li <[email protected]>
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]>
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]>
* [DLMED] add more type to decollate 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 CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue 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]>
Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Isaac Yang <[email protected]>
* update ci/cd to remove duplicated jobs Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Isaac Yang <[email protected]> Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* additional deepgrow workflow events Signed-off-by: Wenqi Li <[email protected]> * remove the attach method Signed-off-by: Wenqi Li <[email protected]>
* 2304 enhance image dataset to handle meta Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[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]>
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Fixes # .
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A few sentences describing the changes proposed in this pull request.
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./runtests.sh --codeformat --coverage../runtests.sh --quick.make htmlcommand in thedocs/folder.