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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]>
* Implement FROC metric Signed-off-by: yiheng-wang-nv <[email protected]> * Fix doc error Signed-off-by: yiheng-wang-nv <[email protected]> * Change param lowercase Signed-off-by: yiheng-wang-nv <[email protected]> * Update calculate functions Signed-off-by: yiheng-wang-nv <[email protected]> * fix mypy error Signed-off-by: yiheng-wang-nv <[email protected]> * Update parameter names Signed-off-by: Yiheng Wang <[email protected]>
* fix RandZoomd collation Signed-off-by: Richard Brown <[email protected]> * dont check class ID on windows Signed-off-by: Richard Brown <[email protected]> * if elif change Signed-off-by: Richard Brown <[email protected]> * code review Signed-off-by: Richard Brown <[email protected]> * remove extra import Signed-off-by: Richard Brown <[email protected]> * win32 change Signed-off-by: Richard Brown <[email protected]> * changes Signed-off-by: Richard Brown <[email protected]> * update RandAxisFlipd Signed-off-by: Richard Brown <[email protected]> * help message more general Signed-off-by: Richard Brown <[email protected]> * more changes Signed-off-by: Richard Brown <[email protected]> * use torch Signed-off-by: Richard Brown <[email protected]> * wyli changes Signed-off-by: Richard Brown <[email protected]> * more changes Signed-off-by: Richard Brown <[email protected]> * skip test if win32 Signed-off-by: Richard Brown <[email protected]> * get default mp Signed-off-by: Wenqi Li <[email protected]> * dedicated fail test Signed-off-by: Richard Brown <[email protected]> * requires reason Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* Remove WSIReader from LoadImage Signed-off-by: Behrooz <[email protected]> * Remove WSIReader from LoadImaged Signed-off-by: Behrooz <[email protected]>
* add pretrain options Signed-off-by: Yiheng Wang <[email protected]>
* add pretrain options Signed-off-by: Yiheng Wang <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: Richard Brown <[email protected]>
batch inverse
* add pretrain options Signed-off-by: Yiheng Wang <[email protected]> * rewrite error message add test cases Signed-off-by: Yiheng Wang <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
* cron tutorial notebooks Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
* allow None for switch endianness Signed-off-by: Richard Brown <[email protected]> * add PIL testing Signed-off-by: Richard Brown <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>
* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]> * Jupyter utilities update Signed-off-by: Eric Kerfoot <[email protected]>
* [DLMED] update ROCAUC 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]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
test time augmentations
* fixes tutorial issue 150 Signed-off-by: Wenqi Li <[email protected]> * revise based on comments Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Richard Brown <[email protected]>
* [DLMED] enhance transform logging 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] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] ignore type warning Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] add eval mode in Evaluators 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]> Co-authored-by: Eric Kerfoot <[email protected]>
* [DLMED] enhance SmartCache Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: kate-sann5100 <[email protected]>
* 1837--collating Signed-off-by: Wenqi Li <[email protected]> * fixes transform device Signed-off-by: Wenqi Li <[email protected]> * reverting self.affine Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Richard Brown <[email protected]>
* conditional random field implementation Signed-off-by: charliebudd <[email protected]>
* [DLMED] fix affine error and thread-safe issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] update CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update typehints Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] make cachedataset to be thread-safe Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove inverse ID check Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] restore CacheDataset and inverse transform Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* Implement PatchWSIDataset and SmartCachePathWSIDataset Signed-off-by: Behrooz <[email protected]> * Remove label preprocessing and adopt new type of inputs Signed-off-by: Behrooz <[email protected]> * Update type hints Signed-off-by: Behrooz <[email protected]> * Add init file Signed-off-by: Behrooz <[email protected]> * Change grid_size to grid_shape Signed-off-by: Behrooz <[email protected]> * Add a unittest for PatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Add more unittests Signed-off-by: Behrooz <[email protected]> * Update docstrings and make minor changes Signed-off-by: Behrooz <[email protected]> * Convert labels to numpy to match the change in dataset Signed-off-by: Behrooz <[email protected]> * Update location from center to corner Signed-off-by: Behrooz <[email protected]> * Update unittests locations from center to corner Signed-off-by: Behrooz <[email protected]> * Update docs for pathology datasets Signed-off-by: Behrooz <[email protected]> * Update type hint and doc Signed-off-by: Behrooz <[email protected]> * Update docstrings Signed-off-by: Behrooz <[email protected]> * Format docstring Signed-off-by: Behrooz <[email protected]> * Update length of the smartcache dataset Signed-off-by: Behrooz <[email protected]> * Add unittest for SmartCachePatchWSIDataset Signed-off-by: Behrooz <[email protected]> * Minor changes and fixes Signed-off-by: Behrooz <[email protected]> * Add unnittest for OpenSlide option Signed-off-by: Behrooz <[email protected]> * Add new line Signed-off-by: Behrooz <[email protected]> * Remove SmartCachePatchWSIDataset test to fix it Signed-off-by: Behrooz <[email protected]> * move init docstring to class docstring Signed-off-by: Richard Brown <[email protected]>
* Implement fully convolutional version of torchvision models Signed-off-by: Behrooz <[email protected]> * Update networks init with TorchVisionFullyConvModel Signed-off-by: Behrooz <[email protected]> * Add unittests for TorchVisionFullyConvModel Signed-off-by: Behrooz <[email protected]> * Add another test case Signed-off-by: Behrooz <[email protected]> * Upate docs for TorchVisionFullyConvModel Signed-off-by: Behrooz <[email protected]> * Make torchvision import optional Signed-off-by: Behrooz <[email protected]> * Skip the tests if torchvision not available Signed-off-by: Behrooz <[email protected]> * Improve the model based on comments Signed-off-by: Behrooz <[email protected]> * Update and add test cases Signed-off-by: Behrooz <[email protected]>
* Add label dimensions to be compatible with changes in model output Signed-off-by: Behrooz <[email protected]> * Update test case outputs and add new test case Signed-off-by: Behrooz <[email protected]>
* fixes init affinehead Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
Status
Ready/Work in progress/Hold
Types of changes
./runtests.sh --codeformat --coverage../runtests.sh --quick.make htmlcommand in thedocs/folder.