merge master #284
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merge master #284
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* ndim -> spatial_dims Signed-off-by: Wenqi Li <wenqil@nvidia.com> * dimensions -> spatial_dims Signed-off-by: Wenqi Li <wenqil@nvidia.com> * deprecated arg with auto replacement Signed-off-by: Wenqi Li
* [DLMED] merge LocalPatchShuffle Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Torch RandRotate
* Add cupy to tensor Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittest for cupy>tensor Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] enhance the pad mode Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update all the tensor pad related Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix error tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix GPU tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Nic Ma <nma@nvidia.com>
* con1_padding -> conv1_padding Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simpler init. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes 2715 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds 3d tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 error Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* ThresholdIntensity, ThresholdIntensityd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* Add dropout arg in DynUNet init Signed-off-by: Andres <diazandr3s@gmail.com>
* [DLMED] add device option Signed-off-by: Nic Ma <nma@nvidia.com> * look up options for types Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
…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 <33289025+rijobro@users.noreply.github.com> * Affine, RandAffine, Affined, RandAffined Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * deprecate as_tensor_output Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * remove plotting Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * Rand2dElastic, Rand3dElastic, Rand2dElasticd, Rand3dElasticd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * CropForeground Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Invertd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* transforms convert to the necessary type Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* Add dtype to ToCuPy Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittests to include dtype Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Implement convert_to_cupy Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Addressed all comments Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Addressed all comments Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add dtype for Sequence Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
* [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove unnecessary arg Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix style issue Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] enhance type conversion Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com>
* fixes tutorial 353 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adding type tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * improves type checks Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes as channel first Signed-off-by: Wenqi Li <wenqil@nvidia.com> * type test option Signed-off-by: Wenqi Li <wenqil@nvidia.com> * ndarray suuport Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * bash option for windows test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * enhance norm intensity tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes merge tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Nic Ma <nma@nvidia.com>
* add multimodal transformers Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>
…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 <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* Update with cupy.ndarray Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change to use has_cp Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change the format Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix a bug Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
* Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* Adding ViT Autoencoder * Fixing Debug print statement Signed-off-by: vnath <vnath@nvidia.com> * Truncating Classification Related Code snippets Signed-off-by: vnath <vnath@nvidia.com> * Added explanation for input arguments Signed-off-by: vnath <vnath@nvidia.com> * Added explanation for input arguments Signed-off-by: vnath <vnath@nvidia.com> * Changed Class Name for vit autoencoder Signed-off-by: vnath <vnath@nvidia.com> * Changed Class Name for vit autoencoder Signed-off-by: vnath <vnath@nvidia.com> * Addressed Wenqi comments for test cases Signed-off-by: vnath <vnath@nvidia.com> * Removed the flag for same as input size for cleaner code Signed-off-by: vnath <vnath@nvidia.com> * Test cases for loop removed, much more polishing done of the code Signed-off-by: vnath <vnath@nvidia.com> * Doc changes added Signed-off-by: vnath <vnath@nvidia.com> * Fixed rst formatting a raising error and also added raising error for 2D inputs Signed-off-by: vnath <vnath@nvidia.com> * Modified the ViTAutoEnc to adapt for version 1.6 of pytorch for backward comptability Signed-off-by: vnath <vnath@nvidia.com> * Variable name changed for test case file Signed-off-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* adds backend for largest cc Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] enhance rescale Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] add check missing files Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance PILReader doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add root dir Signed-off-by: Nic Ma <nma@nvidia.com>
* Add level argument to __init__ for WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change reader_lib to backend Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update some comments Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstring Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
…our) (#3254) * fixes docstring typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * label to contour Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes dtype Signed-off-by: Wenqi Li <wenqil@nvidia.com> * tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update filtering Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes backends Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update postprocessing steps Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Nic Ma <nma@nvidia.com>
* Unify wsireader unittests and add new tests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove variant of wsireader unittests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix import Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change the logic to skip Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Ignore N802 for setUpModule Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Skip if no tifffile Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * exclude test_wsireader form min tests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove trailing comma Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change WSIReaderTests base class Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Nic Ma <nma@nvidia.com>
…3255) * [DLMED] fix spatial size collate issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add channel_dim Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
* adds an option to skip renorm Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update intensity scale range/percentile Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [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 <wenqil@nvidia.com> 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 <nma@nvidia.com> * [DLMED] add RGB color GIF Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add support to handlers Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add optional import Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] format code Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8≈ Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typing Signed-off-by: Nic Ma <nma@nvidia.com> * [DLEMD] test python 3.6 Signed-off-by: Nic Ma <nma@nvidia.com> * test remove typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix tests Signed-off-by: Nic Ma <nma@nvidia.com> * temp fix Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] remove moviepy Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
* revise metrics and cumulative Signed-off-by: Wenqi Li <wenqil@nvidia.com> * updated based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* enhance dynunet based on brats21 1st solution Signed-off-by: Yiheng Wang <vennw@nvidia.com> * add act_name argument Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove v1 and change error type Signed-off-by: Yiheng Wang <vennw@nvidia.com> * skip torchscript check before pt 1.6 for dynunet Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] Add metric Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add metric Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update for latest API Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix min tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix test typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
* [DLMED] add cross validation datalist Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add doc and tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove nifti test Signed-off-by: Nic Ma <nma@nvidia.com>
* fixes #2213 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* add b-spline result to unit-test Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * style fix Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * to exclude in min_tests
… is True (#3305) * [DLMED] fix keys issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit test Signed-off-by: Nic Ma <nma@nvidia.com>
* [DLMED] update DiceLoss doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>
* Add tifffile support to WSIReader Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update unittests Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix a typo Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstring Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstring Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix the backend name Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix a typo Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add test for multiple get_data call Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Change to context manager for tifffile object Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
* update to 2110 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update integration results Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 02b3acc. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 1356e8e. Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Contrastive Loss added, first draft Signed-off-by: vnath <vnath@nvidia.com> * Almost all requirements covered Signed-off-by: vnath <vnath@nvidia.com> * Review Ready Signed-off-by: vnath <vnath@nvidia.com> * CL Loss needs negative mask to be on the device, fix commited Signed-off-by: vnath <vnath@nvidia.com> * Cuda test added to CL loss test file Signed-off-by: vnath <vnath@nvidia.com> * Fix for tests failing on PT16 due to device mismatch Signed-off-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <vnath@nvidia.com> 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 <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>
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Fixes # .
Description
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./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.