merge master#61
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Nic-Ma merged 124 commits intoNic-Ma:1905-enhance-brats-transformfrom Mar 31, 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]>
* 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]>
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]>
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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.