merge master by Nic-Ma · Pull Request #439 · Nic-Ma/MONAI

Nic-Ma · 2022-08-10T14:31:22Z

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]>

* 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]> * support for multi-channel inputs Signed-off-by: mersad95zd <[email protected]> * docstring fixed Signed-off-by: mersad95zd <[email protected]> * minor argument fix 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]>

* Implement GridSplit using torch.as_strided Signed-off-by: Behrooz <[email protected]>

added YanxuanLiu as blossom trigger user Signed-off-by: YanxuanLiu <[email protected]> Co-authored-by: YanxuanLiu <[email protected]>

fixes #4774 Signed-off-by: Wenqi Li <[email protected]>

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

fixes docstring Signed-off-by: Wenqi Li <[email protected]>

* adds meta[space] Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]>

* Change from round to floor Signed-off-by: Behrooz <[email protected]> * Explicit conversion to tuple for locs Signed-off-by: Behrooz <[email protected]>

* Update patch merging with a for loop Signed-off-by: function2 <[email protected]> * Make patch merging order backward compatible for 2D Signed-off-by: function2 <[email protected]>

…ime (#4800) * fixes #4799 Signed-off-by: Wenqi Li <[email protected]> * removes flake8-pyi Signed-off-by: Wenqi Li <[email protected]> * update warning message Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] adapt to affine Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

* set no ops id Signed-off-by: Wenqi Li <[email protected]> * make reset optional in datasets 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]> * 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]> * initial e2e-varnet commit Signed-off-by: mersad95zd <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed sensitivitymodel docstring Signed-off-by: mersad95zd <[email protected]> * removed varnet from this PR; improved complex_unet, coil_sensitivity_model, varnetblock Signed-off-by: mersad95zd <[email protected]> * changed BasicUnet to BasicUNet in complex_unet.py Signed-off-by: mersad95zd <[email protected]> * removed assert; changed basic_unet import Signed-off-by: mersad95zd <[email protected]> * complex_unet and utils updated Signed-off-by: mersad95zd <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * major update to utils and complex_unet; unittest added; minor fix in ssim_loss docstring Signed-off-by: mersad95zd <[email protected]> * minor fix to unittest Signed-off-by: mersad95zd <[email protected]> * minor typing fix in utils Signed-off-by: mersad95zd <[email protected]> * removed inverse_complex_normalize Signed-off-by: mersad95zd <[email protected]> * fixed padding Signed-off-by: mersad95zd <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mri_utils formatted Signed-off-by: mersad95zd <[email protected]> * add more inline comments to complex_unet 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>

Signed-off-by: YanxuanLiu <[email protected]> Co-authored-by: YanxuanLiu <[email protected]>

* prune metadata keys 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]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update to 22.07 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test error Signed-off-by: Nic Ma <[email protected]> * Update box_utils.py Co-authored-by: Can Zhao <[email protected]>

* inital commit, it's a draft Signed-off-by: mersad95zd <[email protected]> * dummy commit Signed-off-by: mersad95zd <[email protected]> * add model functionality to sens model and complex_unet; polished sens model Signed-off-by: mersad95zd <[email protected]> * added docstring and unit tests; added inline comments to sens model forward Signed-off-by: mersad95zd <[email protected]> * fixed minor formatting issues; ready to review Signed-off-by: mersad95zd <[email protected]> * added a feature to check input and output channels of user-defined networks Signed-off-by: mersad95zd <[email protected]> * checking input channels, leaving output channels for future Signed-off-by: mersad95zd <[email protected]>

…4826) update installation instructions Signed-off-by: Wenqi Li <[email protected]>

* add Metatenosr support in ConcatItemd Signed-off-by: KumoLiu <[email protected]> * fix flake8 error Signed-off-by: KumoLiu <[email protected]> * fix flake8 error Signed-off-by: KumoLiu <[email protected]> * remove deprecated class in EnsureChannelFirst Signed-off-by: KumoLiu <[email protected]> * fix flake8 error Signed-off-by: KumoLiu <[email protected]> * update channel operation Signed-off-by: KumoLiu <[email protected]> * fix flake8 error Signed-off-by: KumoLiu <[email protected]> * fix deepgrow channel bug Signed-off-by: KumoLiu <[email protected]> * remove unuse line Signed-off-by: KumoLiu <[email protected]>

* Adding profiling manager Signed-off-by: Eric Kerfoot <[email protected]> * Adding profiling manager Signed-off-by: Eric Kerfoot <[email protected]> * Update tests Signed-off-by: eric <[email protected]> * Fixes 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 * Fix 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 * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Darwin fix Signed-off-by: Eric Kerfoot <[email protected]> * Remove multiprocessing test and update documentation 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 Co-authored-by: eric <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Refactor the comparison involving `not` * Refactor `if` expression (#4835) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove methods with unnecessary super delegation. (#4834) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * Remove assert statement from non-test files (#4836) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>

…nsforms (#4842) * Change to EnsureChannelFirst to include behaviour from deprecated transforms Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]>

* Add client_algo.py, monai_algo.py and exchange_object.py (#4612) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add client_algo.py, monai_algo.py and exchange_object.py Signed-off-by: Warvito <[email protected]> * add train test * test predict and get_weights * add test for exchange object * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix formatting * fixes style issues Signed-off-by: Wenqi Li <[email protected]> * fixes style and doc Signed-off-by: Wenqi Li <[email protected]> * fixes style issue Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * combine config files using one parser; use evaluate instead of predict to be closer with moani terminology * fix default return ids * allow standardized usage of bundle * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove comments * remove local path from configs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Holger Roth <[email protected]> Co-authored-by: Holger Roth <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]>

* initial varnetblock commit Signed-off-by: mersad95zd <[email protected]> * initial varnetblock commit Signed-off-by: mersad95zd <[email protected]> * still an initial commit Signed-off-by: mersad95zd <[email protected]> * added block utils and updated varnetblock Signed-off-by: mersad95zd <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed flake errors Signed-off-by: mersad95zd <[email protected]> * added docstrings; added block utils unittests Signed-off-by: mersad95zd <[email protected]> * corrected some namings in utils Signed-off-by: mersad95zd <[email protected]> * did a minor fix to coil sensitivity model Signed-off-by: mersad95zd <[email protected]> * did a minor fix to coil sensitivity model Signed-off-by: mersad95zd <[email protected]> * did a minor fix to coil sensitivity model Signed-off-by: mersad95zd <[email protected]>

fixes shuffle buffer Signed-off-by: Wenqi Li <[email protected]>

* test cuda Signed-off-by: Wenqi Li <[email protected]> * testing devices Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update test cases Signed-off-by: Wenqi Li <[email protected]> * fixes #4848 Signed-off-by: Wenqi Li <[email protected]> * fixes #4718 Signed-off-by: Wenqi Li <[email protected]> * skip tests for previous pt Signed-off-by: Wenqi Li <[email protected]>

* Deprecate pathology datasets Signed-off-by: Behrooz <[email protected]> * Update min test exclusion Signed-off-by: Behrooz <[email protected]> * Update test file names for deprecated component and update prob map deprecation Signed-off-by: Behrooz <[email protected]>

* Update DeepEdit transform Signed-off-by: Andres <[email protected]> * Update transform arg type Signed-off-by: Andres <[email protected]> * Update metatensor attribute Signed-off-by: Andres <[email protected]> * Add check for compatibility Signed-off-by: Andres <[email protected]> * Change to numpy array Signed-off-by: Andres <[email protected]>

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

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]>

mersad95zd and others added 29 commits July 26, 2022 08:40

Implement GridSplit using torch.as_strided (#4768)

4831909

* Implement GridSplit using torch.as_strided Signed-off-by: Behrooz <[email protected]>

[CICD] Add YanxuanLiu as blossom trigger user (#4780)

83ec156

added YanxuanLiu as blossom trigger user Signed-off-by: YanxuanLiu <[email protected]> Co-authored-by: YanxuanLiu <[email protected]>

4774 dtype-percentile (#4775)

a400cda

fixes #4774 Signed-off-by: Wenqi Li <[email protected]>

4772 adds test cases (#4773)

5f019d7

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

4779 fixes docstring (#4785)

46d9026

fixes docstring Signed-off-by: Wenqi Li <[email protected]>

4789 adds a space type metadata field to metatensor (#4790)

c1eaf42

* adds meta[space] Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]>

Fix ProbMap locations (#4796)

2c89142

* Change from round to floor Signed-off-by: Behrooz <[email protected]> * Explicit conversion to tuple for locs Signed-off-by: Behrooz <[email protected]>

Update patch merging with a for loop (#4793)

288edee

* Update patch merging with a for loop Signed-off-by: function2 <[email protected]> * Make patch merging order backward compatible for 2D Signed-off-by: function2 <[email protected]>

4799 change deprecation warning category to provide more info at runt…

4ae41e8

…ime (#4800) * fixes #4799 Signed-off-by: Wenqi Li <[email protected]> * removes flake8-pyi Signed-off-by: Wenqi Li <[email protected]> * update warning message Signed-off-by: Wenqi Li <[email protected]>

4791 Adapt affine arg to the Spacing transform (#4792)

30d592c

* [DLMED] adapt to affine Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

4769 adds a util to reset applied operations id (#4778)

3a8c421

* set no ops id Signed-off-by: Wenqi Li <[email protected]> * make reset optional in datasets Signed-off-by: Wenqi Li <[email protected]>

correct blossom trigger list format (#4821)

9317d14

Signed-off-by: YanxuanLiu <[email protected]> Co-authored-by: YanxuanLiu <[email protected]>

4814 Update PyTorch base docker to 22.07 (#4815)

ef05b24

* [DLMED] update to 22.07 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test error Signed-off-by: Nic Ma <[email protected]> * Update box_utils.py Co-authored-by: Can Zhao <[email protected]>

4206 4621 4811 update c++/cuda extension installation instructions (#…

f317aeb

…4826) update installation instructions Signed-off-by: Wenqi Li <[email protected]>

4841 shuffle buffer for multiple epochs (#4847)

e8d7c96

fixes shuffle buffer Signed-off-by: Wenqi Li <[email protected]>

4854 fixes percentile (#4877)

38bc8fa

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

Nic-Ma merged commit d6d9ad6 into Nic-Ma:4862-enhance-docstring Aug 10, 2022

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

merge master#439

merge master#439
Nic-Ma merged 69 commits intoNic-Ma:4862-enhance-docstringfrom
Project-MONAI:dev

Nic-Ma commented Aug 10, 2022

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

14 participants

Conversation

Nic-Ma commented Aug 10, 2022

Description

Status

Types of changes

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

14 participants