merge master#440
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Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
* bc nonbreaking tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * compatible collate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds flag Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes min tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * integration Signed-off-by: Wenqi Li <wenqil@nvidia.com> * default to metatensor Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update baesd on comments, refactoring, more tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * debug typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * debug typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * debug typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplify, more tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * multisamples cropping Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified utilities, docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * exclude in min Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Create meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Create test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update __init__.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update metrics.rst Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update metrics.rst Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update __init__.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update metrics.rst Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <yashikajain201@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com>
* fixes shape fallback Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4655 Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] enhance metrics doc with example Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* fixes pad-collate Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* blend_images: voxel-wise alpha Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * linting is wrong Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* enhance verify metadata and dynunet docstring Signed-off-by: Yiheng Wang <vennw@nvidia.com> * reverse dynunet changes and fix flake8 error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix flake8 error Signed-off-by: Yiheng Wang <vennw@nvidia.com>
[DLMED] fix collate issue Signed-off-by: Nic Ma <nma@nvidia.com>
* adds __array_function__ impl. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update ufunc Signed-off-by: Wenqi Li <wenqil@nvidia.com> * pt1.7 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more checking Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* mri utils added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils with its unit test added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils updated with monai data converter Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * updated fft_util's docstring Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * apps.rst updated with fft_utils docstrings under the reconstruction module Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by adding dimension hins Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by removing redundant output type Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * test_fft_utils.py moved to the tests folder Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * created fft_utils_t, the torch-only version of fft_utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fft_utils_t updated with type ignore for mypy Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docs/source/networks.rst updated with fft_utils_t Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * manual fix for fft_utils_t output data types Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial mri_transforms added under apps/reconstruction Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * with PR1 files to avoid error Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 included Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 files finally removed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * putting test_mri_transforms under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * isort fixed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * ignore this commit, still in progress Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * created utils, array, and dictionary; still a very early-stage commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * completing transform arrays and dicts plus mri_utils and the unit tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move tests under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docs and tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added unittests for DetailedNormalizeIntensityd and TargetBasedSpatialCropd and fixed unbiased issue of torch.std Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed random seed; added enum keys; corrected docs format; corrected typos Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * rss name corrected Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor issues fixed; todos are __init__ and decide upon randomize Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added __init__ Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed file names Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added more notes to InputTargetNormalizeIntensity Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added more clarifications to InputTargetNormalizeIntensityd Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * made ReferenceBasedNormalizeIntensityd and ReferenceBasedSpatialCropd consistent with other monai transforms Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor updates to kspace masks Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * new utils added: complex_mul and complex_conj Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * mypy issue with mri_utils unittest resolved Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * a separate PR for mri_utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor update to enum keys Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * minor docstring fix Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * separated complex utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docs updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docs updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * compelx_utils docstring updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Co-authored-by: Can Zhao <69829124+Can-Zhao@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>
* mri utils added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils with its unit test added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils updated with monai data converter Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * updated fft_util's docstring Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * apps.rst updated with fft_utils docstrings under the reconstruction module Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by adding dimension hins Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fft_utils docstring updated by removing redundant output type Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * test_fft_utils.py moved to the tests folder Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * created fft_utils_t, the torch-only version of fft_utils Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fft_utils_t updated with type ignore for mypy Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docs/source/networks.rst updated with fft_utils_t Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * manual fix for fft_utils_t output data types Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial mri_transforms added under apps/reconstruction Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * with PR1 files to avoid error Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 included Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * PR1 files finally removed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * putting test_mri_transforms under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * isort fixed Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * ignore this commit, still in progress Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * created utils, array, and dictionary; still a very early-stage commit Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * completing transform arrays and dicts plus mri_utils and the unit tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move tests under apps for now Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docs and tests Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fast-mri-reader initial commit; todo is the unittest Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * unittest added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * remove unncessary packages from the reader Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * manual installation of h5py added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * enum keys added Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * h5py added to requirements-dev.txt Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * optional import of h5py Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed h5py dependency Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed h5py dependency again Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed docstring; fixed import issue Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added h5py to relevant requirement files; updated fastmri_reader Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docs updated Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed os.path.basename Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Co-authored-by: Can Zhao <69829124+Can-Zhao@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* get/set array Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update according to comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4699 Signed-off-by: Wenqi Li <wenqil@nvidia.com>
…support 0.9.1* (#4692) * Fix nuclick transform for meta tensor Signed-off-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com> * Fix deepgrow transform for metatensor Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>
* fixes swinunetr Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * less changes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * review docs Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* preserve key order Signed-off-by: KumoLiu <yunl@nvidia.com> * fixes integration Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
* fixes #4708 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * shallow copy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update device affine Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update copy Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* update indexing methods Signed-off-by: Wenqi Li <wenqil@nvidia.com> * review attributes Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* using copy() Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simple copy attr Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simple copy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update util Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update default Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update data converting to have is_batch Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update attr copying Signed-off-by: Wenqi Li <wenqil@nvidia.com> * refactoring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove deepcopy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * shape different assign Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* fix deepedit/nuclick transforms for metatensor Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>
[DLMED] add update API for config parser Signed-off-by: Nic Ma <nma@nvidia.com>
* Add TCIA dataset Signed-off-by: Yiheng Wang <vennw@nvidia.com>
* dataset summary for metatensor Signed-off-by: Wenqi Li <wenqil@nvidia.com> * dataset summary support metatensor Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* fix metatensor for detection Signed-off-by: Can Zhao <canz@nvidia.com> * fix mypy Signed-off-by: Can Zhao <canz@nvidia.com>
* update detection transforms for metatensor Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes mypy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more tests about applied operations Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* optional final Tanh Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update param name Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* add user warnings in AsChannelFirst and AddChannel Signed-off-by: KumoLiu <yunl@nvidia.com> * change warning to deprecated Signed-off-by: KumoLiu <yunl@nvidia.com> * change since0.9 to 0.8 Signed-off-by: KumoLiu <yunl@nvidia.com> * add use MetaTensor data type Signed-off-by: KumoLiu <yunl@nvidia.com> * fix pep8 Signed-off-by: KumoLiu <yunl@nvidia.com>
* support block type string in resnet, senet Signed-off-by: KumoLiu <yunl@nvidia.com> * fix docstring Signed-off-by: KumoLiu <yunl@nvidia.com> * fix docstring in resnet Signed-off-by: KumoLiu <yunl@nvidia.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>
* [DLMED] add track_meta option Signed-off-by: Nic Ma <nma@nvidia.com>
* Add flexible unet. A flexible U-Net implements an encoder-decoder network. This network uses U-Net as decoder and efficientnet-V1 family as encoder. The encoder type can be set by passing parameters 'efficientnet-b0, ..., efficientnet-b7, efficientnet-l2' to the initialize function. Signed-off-by: binliu <binliu@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix feature_channel name issue and input parameters issue. add a unit test file for flexible unet. Signed-off-by: binliunls <binliu@nvidia.com> * Add flexible unet to monai's documentation and modify the docstring of flexible unet Signed-off-by: binliunls <binliu@nvidia.com> * change the input size in unit test of flexible unet for CI/CD Signed-off-by: binliunls <binliu@nvidia.com> * modify the unit test file of flexible unet to make it works on CI/CD Signed-off-by: binliunls <binliu@nvidia.com> * add pretrain weight check in flexible unet unitest. Signed-off-by: binliunls <binliu@nvidia.com> * fix bias, dim, flexible_unet doc string problem, add @skip_if_quick to unitest since the download may cost a lot of time. Signed-off-by: binliunls <binliu@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix the if branch of adv_prop model to a simple equation. Signed-off-by: binliu <binliu@nvidia.com> * delete the useless legacy pool in init functin of FlexibleUNet, change the dim parameter of segmentation head to spatial_dims. Signed-off-by: binliu <binliu@nvidia.com> * modify the hints of features in unet_decoder forward function Signed-off-by: binliu <binliu@nvidia.com> * add a is_pad parameter to decided whether pad the upsampling features to fit encoder features Signed-off-by: binliu <binliu@nvidia.com> * delete the useless pool input Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: binliunls <binliu@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* initial commit of e2e-varnet Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * initial commit of e2e-varnet Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * docstrings updated; model attributes changed and polished according to monai style Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * added docs Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * reformatted varnet Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * fixed varnet forward Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * major update to utils and modules to make them jit script compatible Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reformat fft_utils_t Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * made fft_utils_t compatible with pytorch==1.7.1 jit rules Signed-off-by: mersad95zd <m.zalbagi@gmail.com> * removed redundancy between _t and normal funcs Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Signed-off-by: mersad95zd <m.zalbagi@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* add dummy filter Signed-off-by: Holger Roth <hroth@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * adds docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * rename filter example Signed-off-by: Holger Roth <hroth@nvidia.com> * add license header Signed-off-by: Holger Roth <hroth@nvidia.com> Signed-off-by: Holger Roth <hroth@nvidia.com>
* fixes 4907 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes flake8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes test cases Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* [DLMED] enhance stats Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add tests Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] fix tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] correct code folder Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] keep backward compatible Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Update swin_unetr.py fixed potential issue with discrepant data types Signed-off-by: Bardia Khosravi <bardiakhosravi95@gmail.com> Signed-off-by: Bardia Khosravi <bardiakhosravi95@gmail.com>
* video dataset Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* Replace range(len(...)) with enumerate(...)
* add a mean iou handler and the unitest. Signed-off-by: binliu <binliu@nvidia.com> * add MeanIoUHandler to documentation Signed-off-by: binliu <binliu@nvidia.com> * add test_handler_mean_iou to min_tests.py Signed-off-by: binliu <binliu@nvidia.com> * change the metric name in unitest of iou from dice to iou. Signed-off-by: binliu <binliu@nvidia.com> Signed-off-by: binliu <binliu@nvidia.com>
* Improve FL ExchangeObject printing and summary Signed-off-by: Holger Roth <hroth@nvidia.com> * add type annotation Signed-off-by: Holger Roth <hroth@nvidia.com> * testing summary string Signed-off-by: Wenqi Li <wenqil@nvidia.com> * typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Holger Roth <hroth@nvidia.com>
* provide init channel dim Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * provide a default for get 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>
* Improve data type conversion performance Signed-off-by: Gigon Bae <gbae@nvidia.com> * Update monai/utils/type_conversion.py Co-authored-by: Gregory Lee <grlee77@gmail.com> Signed-off-by: Gigon Bae <gbae@nvidia.com> Co-authored-by: Gregory Lee <grlee77@gmail.com> Co-authored-by: Behrooz Hashemian <3968947+drbeh@users.noreply.github.com>
enhance subprocess tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* optional grid for base class api consistency Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * docs update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * initial pytorch tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update min tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update dtype Signed-off-by: Wenqi Li <wenqil@nvidia.com> * tested compiled prefer numpy backend for integer interp mode Signed-off-by: Wenqi Li <wenqil@nvidia.com> * extend type annotations Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes a typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Adding __str__ to MetaTensor Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Adding docstrings Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Smooth field meshgrid fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
* fixes spatial resample Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4938 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip if no scipy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip if no cupy Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Add num_worker for cucim read region Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add unittest for multithread cucim Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update docstring Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
* Minor fix for workflows Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Minor fix for workflows Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Minor fix for workflows Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
monai env vars
* adds new keyword Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4962 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4964 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* Fix For RandSmoothDeform Component Order Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Fix For RandSmoothDeform Component Order Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
…4986) Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com> Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>
Two very minor changes to wording.
* enhance worker_init_fn Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Holger Roth <hroth@nvidia.com>
Fixes #4993 ### Status **Ready** ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [x] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Wenqi Li <wenqil@nvidia.com>
### Description This defines an abstract dense block class and a convolutional dense block using `Convolution` or `ResidualUnit` classes. A number of existing networks use dense blocks but have their own implementations that should be left as-is since these are reference implementations, but further definitions should use a common definition. I will have a network to submit as a bundle that uses this. ### Status **Ready** ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [x] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [x] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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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 --disttests.make htmlcommand in thedocs/folder.