Merged
Conversation
* ndim -> spatial_dims Signed-off-by: Wenqi Li <[email protected]> * dimensions -> spatial_dims Signed-off-by: Wenqi Li <[email protected]> * deprecated arg with auto replacement Signed-off-by: Wenqi Li
* [DLMED] merge LocalPatchShuffle Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
Torch RandRotate
* Add cupy to tensor Signed-off-by: Behrooz <[email protected]> * Add unittest for cupy>tensor Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] enhance the pad mode Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the tensor pad related Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix error tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix GPU tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* con1_padding -> conv1_padding Signed-off-by: Wenqi Li <[email protected]> * simpler init. Signed-off-by: Wenqi Li <[email protected]> * fixes 2715 Signed-off-by: Wenqi Li <[email protected]> * adds 3d tests Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 error Signed-off-by: Wenqi Li <[email protected]>
* ThresholdIntensity, ThresholdIntensityd Signed-off-by: Richard Brown <[email protected]>
* Add dropout arg in DynUNet init Signed-off-by: Andres <[email protected]>
* [DLMED] add device option Signed-off-by: Nic Ma <[email protected]> * look up options for types Signed-off-by: Wenqi Li <[email protected]> * adds unit tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
…iles, ScaleIntensityRangePercentilesd (#2943) ScaleIntensityRange, ScaleIntensityRanged, ScaleIntensityRangePercentiles, ScaleIntensityRangePercentilesd
Rotate, Rotated, RandRotate, RandRotated
…ndAffined, Rand2dElastic, Rand3dElastic, Rand2dElasticd, Rand3dElasticd (#2922) * AffineGrid, RandAffineGrid, Resample Signed-off-by: Richard Brown <[email protected]> * Affine, RandAffine, Affined, RandAffined Signed-off-by: Richard Brown <[email protected]> * deprecate as_tensor_output Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * remove plotting Signed-off-by: Richard Brown <[email protected]> * Rand2dElastic, Rand3dElastic, Rand2dElasticd, Rand3dElasticd Signed-off-by: Richard Brown <[email protected]> * CropForeground Signed-off-by: Richard Brown <[email protected]> * fix Invertd Signed-off-by: Richard Brown <[email protected]>
* transforms convert to the necessary type Signed-off-by: Richard Brown <[email protected]>
* Add dtype to ToCuPy Signed-off-by: Behrooz <[email protected]> * Add unittests to include dtype Signed-off-by: Behrooz <[email protected]> * Implement convert_to_cupy Signed-off-by: Behrooz <[email protected]> * Addressed all comments Signed-off-by: Behrooz <[email protected]> * Addressed all comments Signed-off-by: Behrooz <[email protected]> * Add dtype for Sequence Signed-off-by: Behrooz <[email protected]>
* [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove unnecessary arg Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix style issue Signed-off-by: Nic Ma <[email protected]>
* [DLMED] enhance type conversion Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>
* fixes tutorial 353 Signed-off-by: Wenqi Li <[email protected]> * adding type tests Signed-off-by: Wenqi Li <[email protected]> * improves type checks Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 Signed-off-by: Wenqi Li <[email protected]> * fixes as channel first Signed-off-by: Wenqi Li <[email protected]> * type test option Signed-off-by: Wenqi Li <[email protected]> * ndarray suuport Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]> update Signed-off-by: Wenqi Li <[email protected]> * bash option for windows test Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]> * enhance norm intensity tests Signed-off-by: Wenqi Li <[email protected]> * fixes merge tests Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* add multimodal transformers Signed-off-by: ahatamizadeh <[email protected]>
…op_centers`, `generate_pos_neg_label_crop_centers`, `generate_label_classes_crop_centers` (#2958) torch map_binary_to_indices, map_classes_to_indices, correct_crop_centers, generate_pos_neg_label_crop_centers, generate_label_classes_crop_centers
* Implement CuCIM wrapper transfrom Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Richard Brown <[email protected]>
* Update with cupy.ndarray Signed-off-by: Behrooz <[email protected]> * Change to use has_cp Signed-off-by: Behrooz <[email protected]> * Change the format Signed-off-by: Behrooz <[email protected]> * Fix a bug Signed-off-by: Behrooz <[email protected]>
* Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]>
* Add level argument to __init__ for WSIReader Signed-off-by: Behrooz <[email protected]> * Change reader_lib to backend Signed-off-by: Behrooz <[email protected]> * Update some comments Signed-off-by: Behrooz <[email protected]> * Update docstring Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Behrooz <[email protected]>
…our) (#3254) * fixes docstring typos Signed-off-by: Wenqi Li <[email protected]> * label to contour Signed-off-by: Wenqi Li <[email protected]> * fixes dtype Signed-off-by: Wenqi Li <[email protected]> * tests Signed-off-by: Wenqi Li <[email protected]> * docstring Signed-off-by: Wenqi Li <[email protected]> * update filtering Signed-off-by: Wenqi Li <[email protected]> * fixes backends Signed-off-by: Wenqi Li <[email protected]> * adds tests Signed-off-by: Wenqi Li <[email protected]> * update postprocessing steps Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* Unify wsireader unittests and add new tests Signed-off-by: Behrooz <[email protected]> * Remove variant of wsireader unittests Signed-off-by: Behrooz <[email protected]> * Fix import Signed-off-by: Behrooz <[email protected]> * Change the logic to skip Signed-off-by: Behrooz <[email protected]> * Ignore N802 for setUpModule Signed-off-by: Behrooz <[email protected]> * Skip if no tifffile Signed-off-by: Behrooz <[email protected]> * exclude test_wsireader form min tests Signed-off-by: Behrooz <[email protected]> * Remove trailing comma Signed-off-by: Behrooz <[email protected]> * Change WSIReaderTests base class Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
…3255) * [DLMED] fix spatial size collate issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add channel_dim Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* adds an option to skip renorm Signed-off-by: Wenqi Li <[email protected]> * update intensity scale range/percentile Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update based on comments Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* [DLMED] add support for both TensorBoard and TensorBoardX Signed-off-by: Nic Ma <[email protected]> * [DLMED] add RGB color GIF Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support to handlers Signed-off-by: Nic Ma <[email protected]> * [DLMED] add optional import Signed-off-by: Nic Ma <[email protected]> * [DLMED] format code Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8≈ Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typing Signed-off-by: Nic Ma <[email protected]> * [DLEMD] test python 3.6 Signed-off-by: Nic Ma <[email protected]> * test remove typing Signed-off-by: Wenqi Li <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tests Signed-off-by: Nic Ma <[email protected]> * temp fix Signed-off-by: Wenqi Li <[email protected]> * [DLMED] remove moviepy Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* revise metrics and cumulative Signed-off-by: Wenqi Li <[email protected]> * updated based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* enhance dynunet based on brats21 1st solution Signed-off-by: Yiheng Wang <[email protected]> * add act_name argument Signed-off-by: Yiheng Wang <[email protected]> * remove v1 and change error type Signed-off-by: Yiheng Wang <[email protected]> * skip torchscript check before pt 1.6 for dynunet Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] Add metric Signed-off-by: Nic Ma <[email protected]> * [DLMED] add metric Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update for latest API Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix min tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] add cross validation datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] add doc and tests 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] remove nifti test Signed-off-by: Nic Ma <[email protected]>
* fixes #2213 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* add b-spline result to unit-test Signed-off-by: kate-sann5100 <[email protected]> * style fix Signed-off-by: kate-sann5100 <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * to exclude in min_tests
… is True (#3305) * [DLMED] fix keys issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit test Signed-off-by: Nic Ma <[email protected]>
* [DLMED] update DiceLoss doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* Add tifffile support to WSIReader Signed-off-by: Behrooz <[email protected]> * Update unittests Signed-off-by: Behrooz <[email protected]> * Fix a typo Signed-off-by: Behrooz <[email protected]> * Update docstring Signed-off-by: Behrooz <[email protected]> * Update docstring Signed-off-by: Behrooz <[email protected]> * Fix the backend name Signed-off-by: Behrooz <[email protected]> * Fix a typo Signed-off-by: Behrooz <[email protected]> * Add test for multiple get_data call Signed-off-by: Behrooz <[email protected]> * Change to context manager for tifffile object Signed-off-by: Behrooz <[email protected]>
* update to 2110 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * update integration results Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 02b3acc. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 1356e8e. Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Archit <[email protected]> Co-authored-by: Archit <[email protected]>
* Contrastive Loss added, first draft Signed-off-by: vnath <[email protected]> * Almost all requirements covered Signed-off-by: vnath <[email protected]> * Review Ready Signed-off-by: vnath <[email protected]> * CL Loss needs negative mask to be on the device, fix commited Signed-off-by: vnath <[email protected]> * Cuda test added to CL loss test file Signed-off-by: vnath <[email protected]> * Fix for tests failing on PT16 due to device mismatch Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* [DLMED] add dep check Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo 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]>
Signed-off-by: Sebastian Penhouet <[email protected]> Co-authored-by: Sebastian Penhouet <[email protected]> Co-authored-by: Nic Ma <[email protected]>
… API (#3295) * adds traceable API Signed-off-by: Wenqi Li <[email protected]> * drop peek Signed-off-by: Wenqi Li <[email protected]> * deprecate inversekeys Signed-off-by: Wenqi Li <[email protected]> * inversekeys -> tracekeys Signed-off-by: Wenqi Li <[email protected]> * update trace_key Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add affine to dict transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]>
* torch version check Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * additional cases Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * update unit test names Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes codeformat Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
17 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
Status
Ready/Work in progress/Hold
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.