* 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]>

Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>

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

fixes Project-MONAI/tutorials#982
fixes Project-MONAI/tutorials#984
fixes Project-MONAI/tutorials#987

### Description
robust mask size and grid

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Current command did not work on my machine:

```batch
M:\Dev\MONAI>python -c 'import monai; monai.config.print_config()'
  File "<string>", line 1
    'import
           ^
SyntaxError: EOL while scanning string literal

M:\Dev\MONAI>python -c "import monai; monai.config.print_config()"
MONAI version: 1.0.0+39.g9355f1c2
Numpy version: 1.23.4
Pytorch version: 1.12.1+cu113
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 9355f1c
MONAI __file__: M:\Dev\MONAI\monai\__init__.py

Optional dependencies:
Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.
Nibabel version: NOT INSTALLED or UNKNOWN VERSION.
scikit-image version: NOT INSTALLED or UNKNOWN VERSION.
Pillow version: 9.2.0
Tensorboard version: NOT INSTALLED or UNKNOWN VERSION.
gdown version: NOT INSTALLED or UNKNOWN VERSION.
TorchVision version: 0.13.1+cu113
tqdm version: NOT INSTALLED or UNKNOWN VERSION.
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: NOT INSTALLED or UNKNOWN VERSION.
pandas version: NOT INSTALLED or UNKNOWN VERSION.
einops version: NOT INSTALLED or UNKNOWN VERSION.
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: NOT INSTALLED or UNKNOWN VERSION.
pynrrd version: NOT INSTALLED or UNKNOWN VERSION.

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies

M:\Dev\MONAI>
```

This adds improvements to SegResNet semantic segmentation to include
deep supervision feature (among other things).

I've decided to add a new network named SegResnetDS instead of replacing
the existing SegResNet, because it would have broken all previously
pretrained model checkpoints.

Please take a look, and if it looks good, I can add unit tests. All the
helper functions, and blocks are inside of the same file (which I
prefer, since it's easier to read) instead of spreading it among other
files (e.g segresnet_ds_block or segresnet_utils).


### Description

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

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

…arge images (#5297)

SlidingWindowInferer: option to adaptively stitch in cpu memory for
large images.

This adds an option to provide maximum input image volume (number of
elements) to dynamically change stitching to cpu memory (to avoid gpu
memory crashes). For example with `cpu_thresh=400*400*400`, all input
images with large volume will be stitched on cpu.

At the moment, a user must decide beforehand, to stitch ALL images on
cpu or gpu (by specifying the 'device' parameter). But in many datasets,
only a few large images require device==cpu, and running inference on
cpu for ALL will be unnecessary slow.

It's related to 
#4625
#4495
#3497
#4726
#4588 


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: myron <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

Fixes MONAI/apps/Auto3DSeg/bundle_gen.py

### Description

Commands ran in subprocess currently cause issues with string formatting
and backslashes not being escaped properly. Changing from Back Flash to
Forward Slash solves the issue.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Maxime <[email protected]>
Signed-off-by: Mingxin Zheng <[email protected]>
Signed-off-by: Mingxin Zheng <[email protected]>
Co-authored-by: Maxime <[email protected]>
Co-authored-by: Mingxin Zheng <[email protected]>
Co-authored-by: Mingxin Zheng <[email protected]>
Co-authored-by: Mingxin Zheng <[email protected]

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

Fixes #5133

### Description
adds a test

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] 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: Wenqi Li <[email protected]>
Signed-off-by: monai-bot <[email protected]>
Co-authored-by: monai-bot <[email protected]>

Ref #5264. Follow-up to #5307. This is a more normal, intuitive variant
of median filtering.

Signed-off-by: Dženan Zukić <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

Fixes Project-MONAI/tutorials#987



### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Fixes #5196, #5316.

### Description

Add api function that allows FL systems to request summary statistics,
i.e. `get_data_stats` in new `ClientStats` class. `MonaiStats` is added
to provide implementation based on Monai bundle.

Utilizes DataAnalyzer functions from Auto3DSeg. Changes to DataAnalyzer
are supposed to not change the behavior.


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>

part of #5284

fixes incorrect ignite version used
https://github.com/Project-MONAI/MONAI/actions/runs/3262265183

fixes autorunner test error:
https://github.com/Project-MONAI/MONAI/actions/runs/3255478854/jobs/5347066136

fixes #5343

### Description
tests are fixed by upgrading dep version and moving
`test_auto3dseg_autorunner` unit test to `test_integration_autorunner`
integration test.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

This adds a DeepSupervisionLoss wrapper class around the main loss
function to accept a list of tensors returned from a deeply supervised
networks. The final loss is computed as the sum of weighted losses for
each of deep supervision levels (accounting for potential differences in
shapes between targets and ds outputs)

The wrapper class is designed to work with arbitrary existing loss,e.g.
```
    loss = DiceCELoss(to_onehot_y=True, softmax=True) 
    ds_loss = DeepSupervisionLoss(loss)
```

Whereas the existing loss accepts the input as a single Tensor, ds_loss
accepts the input as a list of Tensors (for each output of a deeply
supervised network). If only a simple Tensor input is provided, ds_loss
behaves exactly the same as the underlying loss.

I added unit tests too.



### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

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

Fixes #5345

sliding window output should prefer `device` instead of `inputs.device`


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] 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: Wenqi Li <[email protected]>

…n of the linear warmup (#5351)

small enhancement to WarmupCosineSchedule input, to optionally specify
the beginning of the linear warmup from something above 0 ( e.g from a
fraction 0.1 * initial_lr).

a unit test is added too.


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] 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: myron <[email protected]>

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

Fixes #5354.

### Description

Previous output:
```
Current output:
2022-10-18 12:45:59,679 - MonaiAlgo - INFO - Using multi-gpu training on rank 1 (available devices: 2)
2022-10-18 12:45:59,681 - MonaiAlgo - INFO - Using multi-gpu training on rank 0 (available devices: 2)
2022-10-18 12:49:48,790 - ignite.engine.engine.SupervisedTrainer - INFO - Got new best metric of train_accuracy: 0.802879669048168
2022-10-18 12:49:48,790 - ignite.engine.engine.SupervisedTrainer - INFO - Got new best metric of train_accuracy: 0.802879669048168
2022-10-18 12:49:56,579 - ignite.engine.engine.SupervisedEvaluator - INFO - Got new best metric of val_mean_dice: 0.1470419466495514
2022-10-18 12:49:56,579 - ignite.engine.engine.SupervisedEvaluator - INFO - Got new best metric of val_mean_dice: 0.1470419466495514
```
Output after fix:
```
2022-10-18 12:51:05,400 - MonaiAlgo - INFO - Using multi-gpu training on rank 0 (available devices: 2)
2022-10-18 12:51:05,410 - MonaiAlgo - INFO - Using multi-gpu training on rank 1 (available devices: 2)
2022-10-18 12:53:09,889 - ignite.engine.engine.SupervisedTrainer - INFO - Got new best metric of train_accuracy: 0.6750877521656178
2022-10-18 12:53:25,170 - ignite.engine.engine.SupervisedEvaluator - INFO - Got new best metric of val_mean_dice: 0.06980131566524506
```

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] 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: Holger Roth <[email protected]>

A small fix to followup on
#5338
to ensure  ds_loss returns a constant, not an array

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] 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: myron <[email protected]>

)

This adds a utility function str2list to convert a string to a list.
Useful with argparse commandline arguments:
```
        parser.add_argument("--blocks", default=[1,2,3], type=str2list)
        ...
        python mycode.py --blocks=1,2,2,4
```
Unit tests added.

It also includes a small fix for str2bool to accept input as bool (and
return it right away).

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [ x Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x]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: myron <[email protected]>

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

Fixes #5363.

### Description

Update what's new and module description with new Monai FL features.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

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

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

Fixes #5011  .

### Description
Currently, the FlexibleUNet structure only supports the efficient-net
series as the backbone and it is hard to extend to other network
structures. A more extensible and convenient way to add more benchmark
or user-defined backbones will make it more flexible. I plan to make it
by doing steps below

1. A base backbone/encoder class that defines interfaces like the number
of output feature maps, a list of output feature map channels, string
names of backbones and so on.

2. A register that can dynamically register backbones to a dict that will
be used during the flexible unet initialization.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Signed-off-by: Mingxin Zheng
<[email protected]>

Fixes #5201 
Fixes #5332 

### Description

- Remove deprecated meta_dict usage from Auto3DSeg. 
- Fix affine -> spacing conversion
- Update docstring 
- Change "pixel_percentage" to "foreground_percentage" to unify
foreground "pixel"/"voxel" naming

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] In-line docstrings updated.

Signed-off-by: Mingxin Zheng <[email protected]>

### Description
adding tests for python 3.10

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

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

part of #5284


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Fixes #4672 

### Description

Adds the Hovernet Loss, which takes the raw predictions from the
HoverNet net and produces a Loss Tensor.

Hovernet Loss added along with test script that verfies same results as
original TIA version of Hovernet loss. Test script also include
synthetic image generation (fixed to deterministic behaviour)


N.B. Currently does not include a test function for torch script since
the test includes code that torchscipt cannot compile - mainly the
SobelGradient and associated functions. Need to resolve this.



### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] New tests added to cover the changes.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] 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: Behrooz <[email protected]>

Signed-off-by: monai-bot <[email protected]>

Signed-off-by: monai-bot <[email protected]>

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

Fixes #5381

### Description
- non-breaking changes to rename `compute_meandice` to `compute_dice`
- non-breaking changes to rename `compute_meaniou` to `compute_iou`

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] 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: Wenqi Li <[email protected]>

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