merge master by Nic-Ma · Pull Request #440 · Nic-Ma/MONAI

Nic-Ma · 2022-08-26T00:34:28Z

Fixes # .

Description

A few sentences describing the changes proposed in this pull request.

Status

Ready/Work in progress/Hold

Types of changes

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.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

Signed-off-by: mersad95zd <[email protected]>

* bc nonbreaking tests Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]> * compatible collate Signed-off-by: Wenqi Li <[email protected]> * adds flag Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * fixes min tests Signed-off-by: Wenqi Li <[email protected]> * integration Signed-off-by: Wenqi Li <[email protected]> * default to metatensor Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * update baesd on comments, refactoring, more tests Signed-off-by: Wenqi Li <[email protected]> * debug typing Signed-off-by: Wenqi Li <[email protected]> * debug typing Signed-off-by: Wenqi Li <[email protected]> * debug typing Signed-off-by: Wenqi Li <[email protected]> * simplify, more tests Signed-off-by: Wenqi Li <[email protected]> * multisamples cropping Signed-off-by: Wenqi Li <[email protected]> * simplified utilities, docstrings Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * exclude in min Signed-off-by: Wenqi Li <[email protected]>

* Create meaniou.py Signed-off-by: Yashika Jain <[email protected]> * Create test_compute_meaniou.py Signed-off-by: Yashika Jain <[email protected]> * Update __init__.py Signed-off-by: Yashika Jain <[email protected]> * Update metrics.rst Signed-off-by: Yashika Jain <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Yashika Jain <[email protected]> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <[email protected]> * Update meaniou.py Signed-off-by: Yashika Jain <[email protected]> * Update metrics.rst Signed-off-by: Yashika Jain <[email protected]> * Update __init__.py Signed-off-by: Yashika Jain <[email protected]> * Update meaniou.py Signed-off-by: Yashika Jain <[email protected]> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <[email protected]> * Update metrics.rst Signed-off-by: Yashika Jain <[email protected]> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <[email protected]> * Update test_compute_meaniou.py Signed-off-by: Yashika Jain <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <[email protected]>

* fixes shape fallback Signed-off-by: Wenqi Li <[email protected]> * fixes #4655 Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] enhance metrics doc with example Signed-off-by: Nic Ma <[email protected]> * [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 <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* fixes pad-collate Signed-off-by: Wenqi Li <[email protected]> * adds tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* blend_images: voxel-wise alpha Signed-off-by: Richard Brown <[email protected]> * linting is wrong Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]>

* enhance verify metadata and dynunet docstring Signed-off-by: Yiheng Wang <[email protected]> * reverse dynunet changes and fix flake8 error Signed-off-by: Yiheng Wang <[email protected]> * fix flake8 error Signed-off-by: Yiheng Wang <[email protected]>

[DLMED] fix collate issue Signed-off-by: Nic Ma <[email protected]>

* adds __array_function__ impl. Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update ufunc Signed-off-by: Wenqi Li <[email protected]> * pt1.7 Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * more checking Signed-off-by: Wenqi Li <[email protected]>

* mri utils added Signed-off-by: mersad95zd <[email protected]> * fft_utils with its unit test added Signed-off-by: mersad95zd <[email protected]> * fft_utils updated with monai data converter Signed-off-by: mersad95zd <[email protected]> * updated fft_util's docstring Signed-off-by: mersad95zd <[email protected]> * apps.rst updated with fft_utils docstrings under the reconstruction module Signed-off-by: mersad95zd <[email protected]> * fft_utils docstring updated by adding dimension hins Signed-off-by: mersad95zd <[email protected]> * fft_utils docstring updated by removing redundant output type Signed-off-by: mersad95zd <[email protected]> * test_fft_utils.py moved to the tests folder Signed-off-by: mersad95zd <[email protected]> * created fft_utils_t, the torch-only version of fft_utils Signed-off-by: mersad95zd <[email protected]> * [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 <[email protected]> * docs/source/networks.rst updated with fft_utils_t Signed-off-by: mersad95zd <[email protected]> * [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 <[email protected]> * initial mri_transforms added under apps/reconstruction Signed-off-by: mersad95zd <[email protected]> * with PR1 files to avoid error Signed-off-by: mersad95zd <[email protected]> * PR1 included Signed-off-by: mersad95zd <[email protected]> * PR1 files finally removed Signed-off-by: mersad95zd <[email protected]> * putting test_mri_transforms under apps for now Signed-off-by: mersad95zd <[email protected]> * isort fixed Signed-off-by: mersad95zd <[email protected]> * ignore this commit, still in progress Signed-off-by: mersad95zd <[email protected]> * [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 <[email protected]> * completing transform arrays and dicts plus mri_utils and the unit tests Signed-off-by: mersad95zd <[email protected]> * [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 <[email protected]> * fixed docs and tests Signed-off-by: mersad95zd <[email protected]> * added unittests for DetailedNormalizeIntensityd and TargetBasedSpatialCropd and fixed unbiased issue of torch.std Signed-off-by: mersad95zd <[email protected]> * fixed random seed; added enum keys; corrected docs format; corrected typos Signed-off-by: mersad95zd <[email protected]> * rss name corrected Signed-off-by: mersad95zd <[email protected]> * minor issues fixed; todos are __init__ and decide upon randomize Signed-off-by: mersad95zd <[email protected]> * added __init__ Signed-off-by: mersad95zd <[email protected]> * fixed file names Signed-off-by: mersad95zd <[email protected]> * added more notes to InputTargetNormalizeIntensity Signed-off-by: mersad95zd <[email protected]> * added more clarifications to InputTargetNormalizeIntensityd Signed-off-by: mersad95zd <[email protected]> * made ReferenceBasedNormalizeIntensityd and ReferenceBasedSpatialCropd consistent with other monai transforms Signed-off-by: mersad95zd <[email protected]> * minor updates to kspace masks Signed-off-by: mersad95zd <[email protected]> * new utils added: complex_mul and complex_conj Signed-off-by: mersad95zd <[email protected]> * mypy issue with mri_utils unittest resolved Signed-off-by: mersad95zd <[email protected]> * a separate PR for mri_utils Signed-off-by: mersad95zd <[email protected]> * minor update to enum keys Signed-off-by: mersad95zd <[email protected]> * minor docstring fix Signed-off-by: mersad95zd <[email protected]> * separated complex utils Signed-off-by: mersad95zd <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docs updated Signed-off-by: mersad95zd <[email protected]> * docs updated Signed-off-by: mersad95zd <[email protected]> * compelx_utils docstring updated Signed-off-by: mersad95zd <[email protected]> Co-authored-by: Can Zhao <[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]>

* mri utils added Signed-off-by: mersad95zd <[email protected]> * fft_utils with its unit test added Signed-off-by: mersad95zd <[email protected]> * fft_utils updated with monai data converter Signed-off-by: mersad95zd <[email protected]> * updated fft_util's docstring Signed-off-by: mersad95zd <[email protected]> * apps.rst updated with fft_utils docstrings under the reconstruction module Signed-off-by: mersad95zd <[email protected]> * fft_utils docstring updated by adding dimension hins Signed-off-by: mersad95zd <[email protected]> * fft_utils docstring updated by removing redundant output type Signed-off-by: mersad95zd <[email protected]> * test_fft_utils.py moved to the tests folder Signed-off-by: mersad95zd <[email protected]> * created fft_utils_t, the torch-only version of fft_utils Signed-off-by: mersad95zd <[email protected]> * [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 <[email protected]> * docs/source/networks.rst updated with fft_utils_t Signed-off-by: mersad95zd <[email protected]> * [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 <[email protected]> * initial mri_transforms added under apps/reconstruction Signed-off-by: mersad95zd <[email protected]> * with PR1 files to avoid error Signed-off-by: mersad95zd <[email protected]> * PR1 included Signed-off-by: mersad95zd <[email protected]> * PR1 files finally removed Signed-off-by: mersad95zd <[email protected]> * putting test_mri_transforms under apps for now Signed-off-by: mersad95zd <[email protected]> * isort fixed Signed-off-by: mersad95zd <[email protected]> * ignore this commit, still in progress Signed-off-by: mersad95zd <[email protected]> * [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 <[email protected]> * completing transform arrays and dicts plus mri_utils and the unit tests Signed-off-by: mersad95zd <[email protected]> * [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 <[email protected]> * fixed docs and tests Signed-off-by: mersad95zd <[email protected]> * fast-mri-reader initial commit; todo is the unittest Signed-off-by: mersad95zd <[email protected]> * unittest added Signed-off-by: mersad95zd <[email protected]> * remove unncessary packages from the reader Signed-off-by: mersad95zd <[email protected]> * manual installation of h5py added Signed-off-by: mersad95zd <[email protected]> * enum keys added Signed-off-by: mersad95zd <[email protected]> * h5py added to requirements-dev.txt Signed-off-by: mersad95zd <[email protected]> * optional import of h5py Signed-off-by: mersad95zd <[email protected]> * fixed h5py dependency Signed-off-by: mersad95zd <[email protected]> * fixed h5py dependency again Signed-off-by: mersad95zd <[email protected]> * fixed docstring; fixed import issue Signed-off-by: mersad95zd <[email protected]> * added h5py to relevant requirement files; updated fastmri_reader Signed-off-by: mersad95zd <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docs updated Signed-off-by: mersad95zd <[email protected]> * fixed os.path.basename Signed-off-by: mersad95zd <[email protected]> Co-authored-by: Can Zhao <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* get/set array Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 Signed-off-by: Wenqi Li <[email protected]> * update docstrings Signed-off-by: Wenqi Li <[email protected]> * more tests Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 Signed-off-by: Wenqi Li <[email protected]> * update according to comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * fixes #4699 Signed-off-by: Wenqi Li <[email protected]>

…support 0.9.1* (#4692) * Fix nuclick transform for meta tensor Signed-off-by: SACHIDANAND ALLE <[email protected]> * Fix deepgrow transform for metatensor Signed-off-by: Sachidanand Alle <[email protected]>

* fixes swinunetr Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * less changes Signed-off-by: Wenqi Li <[email protected]> * review docs Signed-off-by: Wenqi Li <[email protected]>

* preserve key order Signed-off-by: KumoLiu <[email protected]> * fixes integration Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* fixes #4708 Signed-off-by: Wenqi Li <[email protected]> * shallow copy Signed-off-by: Wenqi Li <[email protected]> * update device affine Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * update copy Signed-off-by: Wenqi Li <[email protected]>

* update indexing methods Signed-off-by: Wenqi Li <[email protected]> * review attributes Signed-off-by: Wenqi Li <[email protected]>

* using copy() Signed-off-by: Wenqi Li <[email protected]> * simple copy attr Signed-off-by: Wenqi Li <[email protected]> * simple copy Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * update util Signed-off-by: Wenqi Li <[email protected]> * update default Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * update data converting to have is_batch Signed-off-by: Wenqi Li <[email protected]> * update attr copying Signed-off-by: Wenqi Li <[email protected]> * refactoring Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * remove deepcopy Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * shape different assign Signed-off-by: Wenqi Li <[email protected]>

* fix deepedit/nuclick transforms for metatensor Signed-off-by: Sachidanand Alle <[email protected]>

[DLMED] add update API for config parser Signed-off-by: Nic Ma <[email protected]>

* Add TCIA dataset Signed-off-by: Yiheng Wang <[email protected]>

* dataset summary for metatensor Signed-off-by: Wenqi Li <[email protected]> * dataset summary support metatensor Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]>

* fix metatensor for detection Signed-off-by: Can Zhao <[email protected]> * fix mypy Signed-off-by: Can Zhao <[email protected]>

* update detection transforms for metatensor Signed-off-by: Wenqi Li <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]> * more tests about applied operations Signed-off-by: Wenqi Li <[email protected]>

* optional final Tanh Signed-off-by: Wenqi Li <[email protected]> * update param name Signed-off-by: Wenqi Li <[email protected]>

* add user warnings in AsChannelFirst and AddChannel Signed-off-by: KumoLiu <[email protected]> * change warning to deprecated Signed-off-by: KumoLiu <[email protected]> * change since0.9 to 0.8 Signed-off-by: KumoLiu <[email protected]> * add use MetaTensor data type Signed-off-by: KumoLiu <[email protected]> * fix pep8 Signed-off-by: KumoLiu <[email protected]>

* support block type string in resnet, senet Signed-off-by: KumoLiu <[email protected]> * fix docstring Signed-off-by: KumoLiu <[email protected]> * fix docstring in resnet Signed-off-by: KumoLiu <[email protected]> Co-authored-by: Yiheng Wang <[email protected]>

* [DLMED] add track_meta option Signed-off-by: Nic Ma <[email protected]>

* 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 <[email protected]> * [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 <[email protected]> * Add flexible unet to monai's documentation and modify the docstring of flexible unet Signed-off-by: binliunls <[email protected]> * change the input size in unit test of flexible unet for CI/CD Signed-off-by: binliunls <[email protected]> * modify the unit test file of flexible unet to make it works on CI/CD Signed-off-by: binliunls <[email protected]> * add pretrain weight check in flexible unet unitest. Signed-off-by: binliunls <[email protected]> * 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 <[email protected]> * [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 <[email protected]> * delete the useless legacy pool in init functin of FlexibleUNet, change the dim parameter of segmentation head to spatial_dims. Signed-off-by: binliu <[email protected]> * modify the hints of features in unet_decoder forward function Signed-off-by: binliu <[email protected]> * add a is_pad parameter to decided whether pad the upsampling features to fit encoder features Signed-off-by: binliu <[email protected]> * delete the useless pool input Signed-off-by: binliu <[email protected]> Signed-off-by: binliu <[email protected]> Signed-off-by: binliunls <[email protected]> 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 <[email protected]> * initial commit of e2e-varnet Signed-off-by: mersad95zd <[email protected]> * docstrings updated; model attributes changed and polished according to monai style Signed-off-by: mersad95zd <[email protected]> * added docs Signed-off-by: mersad95zd <[email protected]> * reformatted varnet Signed-off-by: mersad95zd <[email protected]> * fixed varnet forward Signed-off-by: mersad95zd <[email protected]> * major update to utils and modules to make them jit script compatible Signed-off-by: mersad95zd <[email protected]> * [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 <[email protected]> * made fft_utils_t compatible with pytorch==1.7.1 jit rules Signed-off-by: mersad95zd <[email protected]> * removed redundancy between _t and normal funcs Signed-off-by: mersad95zd <[email protected]> Signed-off-by: mersad95zd <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* add dummy filter Signed-off-by: Holger Roth <[email protected]> * [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 <[email protected]> * rename filter example Signed-off-by: Holger Roth <[email protected]> * add license header Signed-off-by: Holger Roth <[email protected]> Signed-off-by: Holger Roth <[email protected]>

* fixes 4907 Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 Signed-off-by: Wenqi Li <[email protected]> * fixes test cases Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] enhance stats Signed-off-by: Nic Ma <[email protected]> * [DLMED] add tests Signed-off-by: Nic Ma <[email protected]> * [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 <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] correct code folder Signed-off-by: Nic Ma <[email protected]> * [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 <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Signed-off-by: Nic Ma <[email protected]> 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 <[email protected]> Signed-off-by: Bardia Khosravi <[email protected]>

* video dataset Signed-off-by: Richard Brown <[email protected]>

* Replace range(len(...)) with enumerate(...)

* add a mean iou handler and the unitest. Signed-off-by: binliu <[email protected]> * add MeanIoUHandler to documentation Signed-off-by: binliu <[email protected]> * add test_handler_mean_iou to min_tests.py Signed-off-by: binliu <[email protected]> * change the metric name in unitest of iou from dice to iou. Signed-off-by: binliu <[email protected]> Signed-off-by: binliu <[email protected]>

* fixes #4920 Signed-off-by: Wenqi Li <[email protected]> * workaround #4917 Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

* Improve FL ExchangeObject printing and summary Signed-off-by: Holger Roth <[email protected]> * add type annotation Signed-off-by: Holger Roth <[email protected]> * testing summary string Signed-off-by: Wenqi Li <[email protected]> * typing Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Holger Roth <[email protected]>

* provide init channel dim Signed-off-by: Wenqi Li <[email protected]> * update docstring Signed-off-by: Wenqi Li <[email protected]> * provide a default for get Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

* Improve data type conversion performance Signed-off-by: Gigon Bae <[email protected]> * Update monai/utils/type_conversion.py Co-authored-by: Gregory Lee <[email protected]> Signed-off-by: Gigon Bae <[email protected]> Co-authored-by: Gregory Lee <[email protected]> Co-authored-by: Behrooz Hashemian <[email protected]>

enhance subprocess tests Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

* optional grid for base class api consistency Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * docs update Signed-off-by: Wenqi Li <[email protected]> * initial pytorch tests Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * update min tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * update dtype Signed-off-by: Wenqi Li <[email protected]> * tested compiled prefer numpy backend for integer interp mode Signed-off-by: Wenqi Li <[email protected]> * extend type annotations Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes a typo Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

* Adding __str__ to MetaTensor Signed-off-by: Eric Kerfoot <[email protected]> * [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 <[email protected]> * Smooth field meshgrid fix Signed-off-by: Eric Kerfoot <[email protected]> Signed-off-by: Eric Kerfoot <[email protected]>

* fixes spatial resample Signed-off-by: Wenqi Li <[email protected]> * fixes #4938 Signed-off-by: Wenqi Li <[email protected]> * skip if no scipy Signed-off-by: Wenqi Li <[email protected]> * skip if no cupy Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

* Add num_worker for cucim read region Signed-off-by: Behrooz <[email protected]> * Add unittest for multithread cucim Signed-off-by: Behrooz <[email protected]> * Update docstring Signed-off-by: Behrooz <[email protected]>

* Minor fix for workflows Signed-off-by: Eric Kerfoot <[email protected]> * Minor fix for workflows Signed-off-by: Eric Kerfoot <[email protected]> * Minor fix for workflows Signed-off-by: Eric Kerfoot <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Signed-off-by: Eric Kerfoot <[email protected]> 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 <[email protected]> * fixes #4962 Signed-off-by: Wenqi Li <[email protected]> * fixes #4964 Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * fixes typo Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

* Fix For RandSmoothDeform Component Order Signed-off-by: Eric Kerfoot <[email protected]> * Fix For RandSmoothDeform Component Order Signed-off-by: Eric Kerfoot <[email protected]> Signed-off-by: Eric Kerfoot <[email protected]>

…tches for 4975, 4979) (#4977) * fixes #4975 Signed-off-by: Wenqi Li <[email protected]> * fixes #4971 Signed-off-by: Wenqi Li <[email protected]> * fixes #4979 Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

…4986) Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

Two very minor changes to wording.

* enhance worker_init_fn Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Holger Roth <[email protected]>

Fixes #4993 ### Status **Ready** ### Types of changes  - [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 <[email protected]>

### 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  - [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 <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

mersad95zd and others added 30 commits July 8, 2022 20:06

4599 mri ssim loss (#4600)

4071750

Signed-off-by: mersad95zd <[email protected]>

4655 fixes shape fallback (#4662)

e8672aa

* fixes shape fallback Signed-off-by: Wenqi Li <[email protected]> * fixes #4655 Signed-off-by: Wenqi Li <[email protected]>

Fixes pad list data collate (#4670)

51753ab

* fixes pad-collate Signed-off-by: Wenqi Li <[email protected]> * adds tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

blend_images: voxel-wise alpha (#4679)

b390b09

* blend_images: voxel-wise alpha Signed-off-by: Richard Brown <[email protected]> * linting is wrong Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]>

4687 Fix collate issue for ImageDataset (#4688)

fedff1d

[DLMED] fix collate issue Signed-off-by: Nic Ma <[email protected]>

MONAILabel needed changes for DeepEdit/Deepgrow/NuClick Transform to …

7a5de8b

…support 0.9.1* (#4692) * Fix nuclick transform for meta tensor Signed-off-by: SACHIDANAND ALLE <[email protected]> * Fix deepgrow transform for metatensor Signed-off-by: Sachidanand Alle <[email protected]>

4693 4696 - fixes swinunetr (#4695)

ec7f9c0

* fixes swinunetr Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * less changes Signed-off-by: Wenqi Li <[email protected]> * review docs Signed-off-by: Wenqi Li <[email protected]>

Preserve ordering of input dict's keys in crop transforms (#4707)

def0d90

* preserve key order Signed-off-by: KumoLiu <[email protected]> * fixes integration Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

4715 update slicing impl. (#4716)

5fb767c

* update indexing methods Signed-off-by: Wenqi Li <[email protected]> * review attributes Signed-off-by: Wenqi Li <[email protected]>

fix deepedit/nuclick transforms for metatensor (#4719)

345b8ae

* fix deepedit/nuclick transforms for metatensor Signed-off-by: Sachidanand Alle <[email protected]>

4717 Add update API for the ConfigParser (#4721)

ec5376e

[DLMED] add update API for config parser Signed-off-by: Nic Ma <[email protected]>

4587 mri transforms (#4591)

9fb9d98

4258 Add TCIA dataset (#4610)

422cc6d

* Add TCIA dataset Signed-off-by: Yiheng Wang <[email protected]>

4462 dataset summary for metatensor (#4728)

73cd27e

* dataset summary for metatensor Signed-off-by: Wenqi Li <[email protected]> * dataset summary support metatensor Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]>

fix meta_tensor for box_ops (#4666)

fed6fc7

* fix metatensor for detection Signed-off-by: Can Zhao <[email protected]> * fix mypy Signed-off-by: Can Zhao <[email protected]>

4462 update detection transforms for metatensor (#4729)

953c7d4

* update detection transforms for metatensor Signed-off-by: Wenqi Li <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]> * more tests about applied operations Signed-off-by: Wenqi Li <[email protected]>

4581 optional final Tanh (#4736)

5048752

* optional final Tanh Signed-off-by: Wenqi Li <[email protected]> * update param name Signed-off-by: Wenqi Li <[email protected]>

4720 Add track_meta option to the ToTensor transform (#4733)

b9d39d4

* [DLMED] add track_meta option Signed-off-by: Nic Ma <[email protected]>

binliunls and others added 29 commits August 12, 2022 09:20

4907 invertd for resizing same spatial shapes (#4908)

535c6f1

* fixes 4907 Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 Signed-off-by: Wenqi Li <[email protected]> * fixes test cases Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

Issue with half precision training (#4913)

342f4aa

Update swin_unetr.py fixed potential issue with discrepant data types Signed-off-by: Bardia Khosravi <[email protected]> Signed-off-by: Bardia Khosravi <[email protected]>

Video dataset (#4767)

7be203d

* video dataset Signed-off-by: Richard Brown <[email protected]>

Replace range(len(...)) with enumerate(...) (#4918)

695507d

* Replace range(len(...)) with enumerate(...)

4920 integration test fixes (#4921)

55caf94

* fixes #4920 Signed-off-by: Wenqi Li <[email protected]> * workaround #4917 Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

4929 - enhance the subprocess tests to have detailed outputs (#4937)

2e2cae0

enhance subprocess tests Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

Multithread WSIReader for cucim backend (#4943)

f2bd04b

* Add num_worker for cucim read region Signed-off-by: Behrooz <[email protected]> * Add unittest for multithread cucim Signed-off-by: Behrooz <[email protected]> * Update docstring Signed-off-by: Behrooz <[email protected]>

monai env vars (#4952)

eb18504

monai env vars

Fix For RandSmoothDeform Component Order (#4973)

32af32c

* Fix For RandSmoothDeform Component Order Signed-off-by: Eric Kerfoot <[email protected]> * Fix For RandSmoothDeform Component Order Signed-off-by: Eric Kerfoot <[email protected]> Signed-off-by: Eric Kerfoot <[email protected]>

Support multiple click interactions per batch for DeepEdit training (#…

d9c80b9

…4986) Signed-off-by: Sachidanand Alle <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

Update index.rst (#4989)

6c5cfd2

Two very minor changes to wording.

4990 enhance worker_init_fn (#4991)

e343575

* enhance worker_init_fn Signed-off-by: Wenqi Li <[email protected]>

Improve MonaiAlgo (#4985)

aa93129

Signed-off-by: Holger Roth <[email protected]>

Nic-Ma merged commit d9ccbf1 into Nic-Ma:4996-configparser-newset Aug 26, 2022

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merge master#440

merge master#440
Nic-Ma merged 105 commits intoNic-Ma:4996-configparser-newsetfrom
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Nic-Ma commented Aug 26, 2022

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