Merged
Conversation
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]>
* fixes tutorial issue 352 Signed-off-by: Wenqi Li <[email protected]> * simplified Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance tensor transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix mypy Signed-off-by: Nic Ma <[email protected]>
…abelClasses`, `RandCropByLabelClassesd` (#2967) Signed-off-by: Richard Brown <[email protected]>
* enhance affinegrid to use torch backend Signed-off-by: Wenqi Li <[email protected]> * style fixes Signed-off-by: Wenqi Li <[email protected]> * codeformat fixes Signed-off-by: Wenqi Li <[email protected]> * backend affien grid Signed-off-by: Wenqi Li <[email protected]> * device support Signed-off-by: Wenqi Li <[email protected]> * less lookup Signed-off-by: Wenqi Li <[email protected]> * create grid with torch backend Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * default to torch create grid Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]> * randaffine with create grid Signed-off-by: Wenqi Li <[email protected]> * create_grid backend change for spatial transforms Signed-off-by: Wenqi Li <[email protected]> * create control grid tensor Signed-off-by: Wenqi Li <[email protected]> * enhance spatial, and crop xforms - Update test_rand_deform_grid.py - center_scale_crop - center_spatial_crop - rand_scale_crop - rand_spatial_crop - rand_spatial_crop_samples Signed-off-by: Wenqi Li <[email protected]> * fixes invert Signed-off-by: Wenqi Li <[email protected]> * tensor resize, unit test fixes Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Behrooz <[email protected]>
* update multimodal doc and model names (Transchex) Signed-off-by: ahatamizadeh <[email protected]>
* remove deprecated Signed-off-by: Wenqi Li <[email protected]> * min-test list Signed-off-by: Wenqi Li <[email protected]> * preserves tests from tests/test_handler_transform_inverter.py Signed-off-by: Wenqi Li <[email protected]>
* enhance nightly test Signed-off-by: Wenqi Li <[email protected]> * print after the test for information Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] enhance not-nan reduction Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
…ks (#3419) * Update segresnet_block.py making the activation function a parameter to the class of the ResBlock * Update segresnet.py * passing activation to the residual blocks * little change * signed Signed-off-by: Patricio Astudillo <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update Signed-off-by: Wenqi Li <[email protected]> * [DLMED] add args and update default (#3418) Signed-off-by: Nic Ma <[email protected]> Signed-off-by: Wenqi Li <[email protected]> * update docstrings Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Patricio Astudillo <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* update vitautoenc Signed-off-by: Wenqi Li <[email protected]> * update based on the comments; compatibility with the previous model weights Signed-off-by: Wenqi Li <[email protected]>
* Update WSIReader level/location/size calculation Signed-off-by: Behrooz <[email protected]> * Update location downsampling Signed-off-by: Behrooz <[email protected]> * Update tests and add a new test case Signed-off-by: Behrooz <[email protected]> * Update few names and logics Signed-off-by: Behrooz <[email protected]> * Fix the dependency issue Signed-off-by: Behrooz <[email protected]> * Check for imagecodecs + tifffile Signed-off-by: Behrooz <[email protected]> * Remove new test case that uses too much memory Signed-off-by: Behrooz <[email protected]> * Add new case and ignore level=0 for TiffFile Signed-off-by: Behrooz <[email protected]> * Address comments Signed-off-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Update TiffFile backend to read only the entire image Signed-off-by: Behrooz <[email protected]>
* [DLMED] extract write logic 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]>
* [DLMED] add dataframe Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance CSV iterable dataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typehints Signed-off-by: Nic Ma <[email protected]> * [DLMED] add comment 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]> * [DLMED] fix file close issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc 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]>
* [DLMED] add BaseWorkflow Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add *args, **kwargs Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] fix deprecated arg 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]>
* enhance dynunet Signed-off-by: Yiheng Wang <[email protected]> * fix black issue Signed-off-by: Yiheng Wang <[email protected]> * use strict=False Signed-off-by: Yiheng Wang <[email protected]> * fix black 21.12 error Signed-off-by: Yiheng Wang <[email protected]> * enhance code and update docstring Signed-off-by: Yiheng Wang <[email protected]>
* fixes deprecated args Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
improve error message if reader nott available
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add dataset generator Signed-off-by: Nic Ma <[email protected]> * [DLMED] add DatasetGenerator 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 wrong test Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove return Signed-off-by: Nic Ma <[email protected]> * [DLMED] update rtol for CI Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] add missing docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] add missing components Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add channel-wise Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip test if before 1.7 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]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add Iteration base class 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: Yiheng Wang <[email protected]>
* [DLMED] support string dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* Update to not include number for the name of the first range Signed-off-by: Behrooz <[email protected]> * Update CuCIM and TorchVision wrappers to include name Signed-off-by: Behrooz <[email protected]> * Update nvtx range to append undelying class for wrapper tranforms Signed-off-by: Behrooz <[email protected]> * Add new test cases to cover changes Signed-off-by: Behrooz <[email protected]> * Update cucim and torchvision check Signed-off-by: Behrooz <[email protected]>
* [DLMED] add missing images Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix 3471 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <[email protected]>
* make bending energy loss invariant to resolution fixes #3485 Signed-off-by: Ebrahim Ebrahim <[email protected]> * set BendingEnergyLoss default normalize to False Maybe it's more important that the default behavior match usage of the term "bending energy" elsewhere, rather than that it be the most convenient behavior. Signed-off-by: Ebrahim Ebrahim <[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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Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.