merge master#259
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Nic-Ma merged 129 commits intoNic-Ma:3189-extra-prepare-batchfrom Oct 26, 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]>
Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* [DLMED] add state attr Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix integration test Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add integration test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more random test 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]>
…gLabel (#3129) Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* add alias tests Signed-off-by: Wenqi Li <[email protected]> * monai.losses.dice Signed-off-by: Wenqi Li <[email protected]> * monai.utils.deprecated Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.senet Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.dynunet Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.unet Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.densenet Signed-off-by: Wenqi Li <[email protected]> * monai.networks.nets.ahnet Signed-off-by: Wenqi Li <[email protected]> * only check for the existing modules Signed-off-by: Wenqi Li <[email protected]> * fixes docs Signed-off-by: Wenqi Li <[email protected]>
* upgrade torch image to 2109 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * more time for fast training Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit a5b4447. Signed-off-by: Wenqi Li <[email protected]>
* add griddistortion Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix pre-commit ci black error Signed-off-by: Yiheng Wang <[email protected]> * add unittest Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* [DLMED] add metric example Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* update rand grid distortion Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes formatting and errors Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add Tensor to CropForegroundd transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance data conversion Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests and fix convert tensor issue Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
…tatement (#3147) * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement * black --skip-magic-trailing-comma Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]>
* update versioning Signed-off-by: Wenqi Li <[email protected]> * build docker Signed-off-by: Wenqi Li <[email protected]> * install docker Signed-off-by: Wenqi Li <[email protected]> * remove selfhosted Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * ubuntu cpu tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * test docker options Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * exclude open slide tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * temp checkout Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 error Signed-off-by: Wenqi Li <[email protected]> * skip weights downloading when http error out Signed-off-by: Wenqi Li <[email protected]>
* temp tests Signed-off-by: Wenqi Li <[email protected]> * adds doker Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * check branches Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes cmp Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add tutorial link Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] update spacing and orientation transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] update others Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>
* update to torch 1.10 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes for torch 1.10 Signed-off-by: Wenqi Li <[email protected]> * fixes coverage tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * type fixes Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit cb3e0c7. Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * fixes for windows Signed-off-by: Wenqi Li <[email protected]> * fixes integration Signed-off-by: Wenqi Li <[email protected]> * fixes #3171 Signed-off-by: Wenqi Li <[email protected]> * temp fix windows Signed-off-by: Wenqi Li <[email protected]>
…3158) * [DLMED] add example in doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] add example about copy_cache Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments 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]> Co-authored-by: monai-bot <[email protected]>
* revise docstrings Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes windows tests Signed-off-by: Wenqi Li <[email protected]>
* adds util logger Signed-off-by: Wenqi Li <[email protected]> * update based on comments 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]>
* [DLMED] add scale_datalist 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]>
* [DLMED] add utitlity 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] fix CI for old PyTorch Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI issue Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
) * Torch `BoundingRect`, `FillHoles`, VoteEnsemble` Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * skip test_fill_holesd Signed-off-by: Richard Brown <[email protected]> * merge fix Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * np->np/pt->pt Signed-off-by: Richard Brown <[email protected]> * no type check Signed-off-by: Richard Brown <[email protected]> * return ndarrayortensor Signed-off-by: Richard Brown <[email protected]> * MeanEnsemble Signed-off-by: Richard Brown <[email protected]>
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Fixes # .
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./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.