merge master by Nic-Ma · Pull Request #434 · Nic-Ma/MONAI

Nic-Ma · 2022-07-20T12:19:26Z

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 <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>

mersad95zd and others added 24 commits July 8, 2022 20:06

4599 mri ssim loss (#4600)

4071750

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>

4655 fixes shape fallback (#4662)

e8672aa

* fixes shape fallback Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #4655 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Fixes pad list data collate (#4670)

51753ab

* 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>

4687 Fix collate issue for ImageDataset (#4688)

fedff1d

[DLMED] fix collate issue Signed-off-by: Nic Ma <nma@nvidia.com>

4693 4696 - fixes swinunetr (#4695)

ec7f9c0

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

def0d90

* 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>

4715 update slicing impl. (#4716)

5fb767c

* update indexing methods Signed-off-by: Wenqi Li <wenqil@nvidia.com> * review attributes Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fix deepedit/nuclick transforms for metatensor (#4719)

345b8ae

* fix deepedit/nuclick transforms for metatensor Signed-off-by: Sachidanand Alle <sachidanand.alle@gmail.com>

4717 Add update API for the ConfigParser (#4721)

ec5376e

[DLMED] add update API for config parser Signed-off-by: Nic Ma <nma@nvidia.com>

4587 mri transforms (#4591)

9fb9d98

4258 Add TCIA dataset (#4610)

422cc6d

* Add TCIA dataset Signed-off-by: Yiheng Wang <vennw@nvidia.com>

4462 dataset summary for metatensor (#4728)

73cd27e

* 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>

Nic-Ma merged commit 47de215 into Nic-Ma:4720-add-track-meta Jul 20, 2022

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merge master#434

merge master#434
Nic-Ma merged 24 commits into
Nic-Ma:4720-add-track-metafrom
Project-MONAI:dev

Nic-Ma commented Jul 20, 2022

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Nic-Ma commented Jul 20, 2022

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