Merged
Conversation
* 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]>
* 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]>
* [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]>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
20 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
Status
Ready/Work in progress/Hold
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.