merge master#99
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Nic-Ma merged 236 commits intoNic-Ma:2150-enhance-metrics-reportfrom May 7, 2021
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* update openmp flag Signed-off-by: Wenqi Li <[email protected]> * improves boundtype docs Signed-off-by: Wenqi Li <[email protected]> * update setup.py Signed-off-by: Wenqi Li <[email protected]> * input validation 1d Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * merge upstream changes Signed-off-by: Wenqi Li <[email protected]> * tests enums Signed-off-by: Wenqi Li <[email protected]> * init. test grid pull Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * test grid_pull Signed-off-by: Wenqi Li <[email protected]> * fixes min test Signed-off-by: Wenqi Li <[email protected]> * adds device tests Signed-off-by: Wenqi Li <[email protected]> * bwd tests Signed-off-by: Wenqi Li <[email protected]>
move transforms out of compose file. this is backwards compatible.
* pad_collation Signed-off-by: Richard Brown <[email protected]> * increase number of test cases to ensure required testing errors Signed-off-by: Richard Brown <[email protected]> * determinism in setUp Signed-off-by: Richard Brown <[email protected]> * pad collate for list of lists Signed-off-by: Richard Brown <[email protected]> * code format Signed-off-by: Richard Brown <[email protected]> * allow padding options Signed-off-by: Richard Brown <[email protected]>
decollate batch
enhance random range parameters If element `i` is iterable, then `uniform[-rotate_range[i][0], rotate_range[i][1])` will be used to generate the rotation parameter for the ith dimension. If not, `uniform[-rotate_range[i], rotate_range[i])` will be used. This can be altered on a per-dimension basis. E.g., `((0,3), 1, ...)`: for dim0, rotation will be in range `[0, 3]`, and for dim1 `[-1, 1]` will be used. Setting a single value will use `[-x, x]` for dim0 and nothing for the remaining dimensions. Backwards compatibility is ensured because the old behaviour used to do `uniform[-rotate_range[i], rotate_range[i])`, and this PR just adds the possibility to do `uniform[-rotate_range[i][0], rotate_range[i][1])`.
* Fixing issues preventing loss functions from being compatible with Torchscript Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Adding conditional skip to Torchscript tests Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] fix length > 1024 issue in string list all gather 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] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more test Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Yiheng Wang <[email protected]>
* DeleteChannel array, dictionary, tests Signed-off-by: Leo Tam <[email protected]> * formatting Signed-off-by: Leo Tam <[email protected]> * DeleteChannel array, dictionary, tests Signed-off-by: Leo Tam <[email protected]> * Register in transform init Signed-off-by: Leo Tam <[email protected]> * clean comment Signed-off-by: Leo Tam <[email protected]> * Dict init Signed-off-by: Leo Tam <[email protected]> * Register D and Dict Signed-off-by: Leo Tam <[email protected]> * Style fix Signed-off-by: Leo Tam <[email protected]> * Safety cast Signed-off-by: Leo Tam <[email protected]> * Changinging names from DeleteChannel to RemoveRepeatedChannel Signed-off-by: Leo Tam <[email protected]> * Lint fixes Signed-off-by: Leo Tam <[email protected]> * Test import fix, autofix again Signed-off-by: Leo Tam <[email protected]>
Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
* update distcall Signed-off-by: Wenqi Li <[email protected]> * update final closing Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
* Add ToPIL transformation Signed-off-by: Behrooz <[email protected]> * Add ToPILd, ToPILD, ToPILDict Signed-off-by: Behrooz <[email protected]> * Remove has_pil Signed-off-by: Behrooz <[email protected]> * Include ToPIL, ToPILd, ToPILD, and ToPILDict Also include ToNumpyD, ToNumpyDict, TorchVisionD, and TorchVisionDict Signed-off-by: Behrooz <[email protected]> * Fix a typing issue Signed-off-by: Behrooz <[email protected]> * Fix PIL optional import Signed-off-by: Behrooz <[email protected]> * Add unittests for ToPIL and ToPILD Signed-off-by: Behrooz <[email protected]> * Fix formatting Signed-off-by: Behrooz <[email protected]> * Fix formatting Signed-off-by: Behrooz <[email protected]> * Add PILImage.Image as the input for ToNumpy and ToTensor Signed-off-by: Behrooz <[email protected]> * Fix type checking issue for PIL.Image.Image Signed-off-by: Behrooz <[email protected]> * Change PILImage_fromarray to lower case Signed-off-by: Behrooz <[email protected]>
add RandomizableTransform
* Add more tests to test_deepgrow_dataset Signed-off-by: YuanTingHsieh <[email protected]>
* Add inference transforms Signed-off-by: YuanTingHsieh <[email protected]> * Remove unused import Signed-off-by: YuanTingHsieh <[email protected]> * Fix review comments Signed-off-by: YuanTingHsieh <[email protected]> Co-authored-by: SACHIDANAND ALLE <[email protected]>
* [DLMED] add RandAxisFlip transforms Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
fix big endianness problem for dictionary reading. Also allow dictionary image_only
* [DLMED] add AutoAdjustChannel transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dict version transform Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix doc-build 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]> * [DLMED] update according to Wenqi's comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc-strings 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]>
Allow missing keys
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Update load pretrain for densenet Signed-off-by: Yiheng Wang <[email protected]> * Fix isort issue Signed-off-by: Yiheng Wang <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
* [DLMED] add suqeeze to handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* fixes #1285 Signed-off-by: Wenqi Li <[email protected]> * adds test Signed-off-by: Wenqi Li <[email protected]>
* fixes #1685 Signed-off-by: Wenqi Li <[email protected]> * add temp test Signed-off-by: Wenqi Li <[email protected]> * adds docstring Signed-off-by: Wenqi Li <[email protected]> * fixes dist sampler Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes type hint issue Signed-off-by: Wenqi Li <[email protected]>
* fixes data type in switching Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>
* Implement CuImageReader and OpenSlideReader Signed-off-by: Behrooz <[email protected]> * Add unittests for CuImageReader Signed-off-by: Behrooz <[email protected]> * Add unittests for OpenSlideReader Signed-off-by: Behrooz <[email protected]> * Sort imports Signed-off-by: Behrooz <[email protected]> * Add correct boundaries Signed-off-by: Behrooz <[email protected]> * Add test cases for reading patches on a grid for CuImage Signed-off-by: Behrooz <[email protected]> * Add patch whole slide imaging dataset for pathology Signed-off-by: Behrooz <[email protected]> * Add test case for read patches for OpenSlide Signed-off-by: Behrooz <[email protected]> * flake8 and few minor changes Signed-off-by: Behrooz <[email protected]> * black Signed-off-by: Behrooz <[email protected]> * flake8 Signed-off-by: Behrooz <[email protected]> * Add kwargs to CuImageReader and OpenSlideReader's read method Signed-off-by: Behrooz <[email protected]> * Change the type hint from np.dtype to DTypeLike Signed-off-by: Behrooz <[email protected]> * Fix a bug Signed-off-by: Behrooz <[email protected]> * Implement WSIReader and unittests Signed-off-by: Behrooz <[email protected]> * Minor updates Signed-off-by: Behrooz <[email protected]> * Fix few typing issues Signed-off-by: Behrooz <[email protected]> * Revert datasets Signed-off-by: Behrooz <[email protected]> * Add shape property to openslide image object Reverse size to be compatible with output size (hxw) Signed-off-by: Behrooz <[email protected]> * Add untittest for loading the whole image Reverse the size accroding to the WSIReader Signed-off-by: Behrooz <[email protected]> * Update the whole image size Signed-off-by: Behrooz <[email protected]> * Remove optional size Signed-off-by: Behrooz <[email protected]> * Remove optional dtype Signed-off-by: Behrooz <[email protected]> * Remove _get_spatial_shape return type Signed-off-by: Behrooz <[email protected]> * Reverse the orders of dimensions of `location` to be compatible with image shape Signed-off-by: Behrooz <[email protected]> * Change test cases to use smaller image and revese location's dimensions Signed-off-by: Behrooz <[email protected]> * Replace the test TIFF and some upgrades Signed-off-by: Behrooz <[email protected]> * Update dependencies for OpenSlide Signed-off-by: Behrooz <[email protected]> * Update unittests for OpenSlide and CuImage Signed-off-by: Behrooz <[email protected]> * Fix openslide dependency Signed-off-by: Behrooz <[email protected]> * Fix doc dependencies Signed-off-by: Behrooz <[email protected]> * Minor changes Signed-off-by: Behrooz <[email protected]> * Few variable name changes Signed-off-by: Behrooz <[email protected]> * Add EnsureChannelFirst Signed-off-by: Behrooz <[email protected]> * Add metadata to WSIReader Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* enhance persistent temp Signed-off-by: Wenqi Li <[email protected]> * fixes windows file rename issue Signed-off-by: Wenqi Li <[email protected]> * enhance multiprocess LMDB Signed-off-by: Wenqi Li <[email protected]> * remove usued vars Signed-off-by: Wenqi Li <[email protected]> * fixes LGTM errors Signed-off-by: Wenqi Li <[email protected]> * remove comparison-with-callable (W0143) Signed-off-by: Wenqi Li <[email protected]> * fixes pylint W0231 Signed-off-by: Wenqi Li <[email protected]> * fixes PYL-R1705 Signed-off-by: Wenqi Li <[email protected]> * fixes PYL-R1720 Signed-off-by: Wenqi Li <[email protected]> * fixes PTC-W0060 Signed-off-by: Wenqi Li <[email protected]> * fixes PYL-W0105 Signed-off-by: Wenqi Li <[email protected]> * fixes PTC-W0016 Signed-off-by: Wenqi Li <[email protected]>
* update box_start/end for deepgrow Signed-off-by: Richard Brown <[email protected]> * add test Signed-off-by: Richard Brown <[email protected]>
* [DLMED] add logging 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]>
* [DLMED] fix classification issue Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add detach for Tensor Signed-off-by: Nic Ma <[email protected]> * fixes test Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* adding error messaging for unsupported tensor shapes Signed-off-by: chaliebudd <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]>
* [DLMED] Enhance unit test and doc-string Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] enhance unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] fix shallow copy issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add patch_index to RandWeightedCrop Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* update readme Signed-off-by: Wenqi Li <[email protected]> * update index Signed-off-by: Wenqi Li <[email protected]> * relative links Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
* Added RicianNoise transform Signed-off-by: Lyndon Boone <[email protected]> * Use ensure_tuple_rep in channel-wise RandRicianNoise transform Signed-off-by: Lyndon Boone <[email protected]> * Added RandRicianNoised transform Signed-off-by: Lyndon Boone <[email protected]> * Autofixed coding style errors Signed-off-by: Lyndon Boone <[email protected]> * Added paper reference for RandRicianNoise in docstring Signed-off-by: Lyndon Boone <[email protected]> * Added unit test for RandRicianNoise transform Signed-off-by: Lyndon Boone <[email protected]> * Added unit test for RandRicianNoised transform Signed-off-by: Lyndon Boone <[email protected]> * Fixed mypy typing issues Signed-off-by: Lyndon Boone <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Jeff VanOss <[email protected]>
* update compose Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* adds tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * torch Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 6a2e7a2. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 9fc84df. Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
* create meta data key if necessary Signed-off-by: Richard Brown <[email protected]> * add orientationd too Signed-off-by: Richard Brown <[email protected]>
* update build option Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit f22cdeb. Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: masadcv <[email protected]>
* fixes subprocess transforms Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * add SelectItemsd alias Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Temporarily changing crf test to allow some errors Signed-off-by: chaliebudd <[email protected]> * changing to unittest assert Signed-off-by: chaliebudd <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Implement ToCupy Signed-off-by: Behrooz <[email protected]> * Add unittests for ToCupy and ToCupyd Signed-off-by: Behrooz <[email protected]> * Add docs Signed-off-by: Behrooz <[email protected]> * Reformat Signed-off-by: Behrooz <[email protected]> * Add CuPy to NumPy Signed-off-by: Behrooz <[email protected]> * Add unittests for ToNumpy and ToNumpyd for CuPy input Signed-off-by: Behrooz <[email protected]> * Add has_cp Signed-off-by: Behrooz <[email protected]>
* Transposed Signed-off-by: Richard Brown <[email protected]> * convert numpy array to list Signed-off-by: Richard Brown <[email protected]>
* skip most recent pytype Signed-off-by: Richard Brown <[email protected]> * avoid pytype 2021.05.04 Signed-off-by: Richard Brown <[email protected]> * pytype<2021 Signed-off-by: Richard Brown <[email protected]> * old attrs Signed-off-by: Richard Brown <[email protected]>
* skip RandAffine if possible Signed-off-by: Richard Brown <[email protected]> * add randaffined Signed-off-by: Richard Brown <[email protected]> * mypy fix Signed-off-by: Richard Brown <[email protected]> * check consistency Signed-off-by: Richard Brown <[email protected]>
* [DLMED] use shutil.move instead 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]> Co-authored-by: Wenqi Li <[email protected]>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
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Types of changes
./runtests.sh --codeformat --coverage../runtests.sh --quick.make htmlcommand in thedocs/folder.