merge master#316
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Nic-Ma merged 247 commits intoNic-Ma:3465-support-string-dtypefrom Dec 10, 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]>
* update changelog for v0.8.0 Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* [DLMED] update highlights for v0.8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] add tutorial link Signed-off-by: Nic Ma <[email protected]> * [DLMED] add MLFlow related Signed-off-by: Nic Ma <[email protected]> * [DLMED] update description and charts Signed-off-by: Nic Ma <[email protected]> * [DLMED] update chart name Signed-off-by: Nic Ma <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * update dints link Signed-off-by: Wenqi Li <[email protected]> * update highlights Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* fixes typos Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* fixes crop types Signed-off-by: Wenqi Li <[email protected]> * fixes dtypes Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] update based on Yiheng's comments Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add channel dim Signed-off-by: Nic Ma <[email protected]> * [DLMED] add RGB support Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add support for other pickle Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 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]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] test flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] test flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* fixes pickle mod Signed-off-by: Wenqi Li <[email protected]> * update pickle Signed-off-by: Wenqi Li <[email protected]> * docstring 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]>
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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.