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 <[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]>

mersad95zd and others added 24 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]>

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 intoNic-Ma:4720-add-track-metafrom
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Nic-Ma commented Jul 20, 2022

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