merge master#291
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Nic-Ma merged 192 commits intoNic-Ma:3346-simplify-asdiscretefrom Nov 17, 2021
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* 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]>
* 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]>
* update clang-format download Signed-off-by: Wenqi Li <[email protected]> * fixes unit test 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]>
* MIL component to extract patches Signed-off-by: myron <[email protected]> * MIL component to extract patches Signed-off-by: myron <[email protected]> * random flag, minor fixes Signed-off-by: myron <[email protected]> * minor fixes for padding Signed-off-by: myron <[email protected]> * improve tests Signed-off-by: myron <[email protected]> Co-authored-by: Behrooz <[email protected]>
* 3251 Add dependency check in WSIReader (#3312) * [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: myron <[email protected]> * [DLMED] MILmodel PR Signed-off-by: myron <[email protected]> * small updates Signed-off-by: myron <[email protected]> * fix jit issues Signed-off-by: myron <[email protected]> * jit fix attempt Signed-off-by: myron <[email protected]> * removing Enum Signed-off-by: myron <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: Behrooz <[email protected]>
* update pathlike obj Signed-off-by: Wenqi Li <[email protected]> * support of pathlike obj Signed-off-by: Wenqi Li <[email protected]> * review path obj Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * autofix Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes dep issue Signed-off-by: Wenqi Li <[email protected]>
…_keys is True (#3325) * [DLMED] enhance no keys for allow_missing_keys 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] update according to comments Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[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 -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.