* 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]>

* Adding __str__ to MetaTensor

Signed-off-by: Eric Kerfoot <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Adding docstrings

Signed-off-by: Eric Kerfoot <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Signed-off-by: Eric Kerfoot <[email protected]>

* fixes torchvision fc models

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]>

* flexible fc layer search

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

* support identity layer

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

* update to use torchivision utils

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

* update docstrings

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

* update docstrings

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

* fixes typo

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

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

* set up a backward compatibility policy

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]>

* update based on comments

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

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

* [DLMED] enhance docstring

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

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

Fixes #5485

### Description
compatibility torchscript for netadapter

also fixes #5487

### 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]>

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

part of #5394


### 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.


cc @rijobro

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

Fixes #5344 .

### Description

This PR implements the metric of Panoptic Quality.


### 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.
- [ ] 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: Yiheng Wang <[email protected]>
Co-authored-by: Behrooz Hashemian <[email protected]>
Co-authored-by: Dženan Zukić <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

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


### Description

adds a paper ref

### 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]>

Fixes #5308 .

### Description

This PR added runtime cache support in the `CacheDataset`.

### 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]>

Fixes #5028.

### Description
Since the output for HoVerNet is a dictionary, `from_engine` can't meet
the requirements. This PR is to extend `from_engine` to work with
HoVerNet.

### 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.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Signed-off-by: Roland Kica <[email protected]>

### Description

Implementing F beta score based on Confusion matrix metric

### 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: Roland Kica <[email protected]>

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

Signed-off-by: Yiheng Wang <[email protected]>

Fixes #5497 .

### Description

This PR updates the init bundle function to match up with
https://github.com/Project-MONAI/model-zoo/blob/dev/CONTRIBUTING.md

### 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.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Yiheng Wang <[email protected]>

Fixes #5498

### Description

simply add arguments (reduction and get_not_nans) for parent class and
update ssim loss function to inherit loss, not nn.module.

### 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: Joeycho <[email protected]>

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

Fixes #5505

### Description
- provides an option to preserve the input dtype when:
  - `LoadImge(dtype=None, ...)`
  - `SaveImage(output_dtype=None, ...)`

- deprecate `dtype` in `NibabelReader`, so the readers always preserve
the dtype

### 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`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

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

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

Fixes #5510

### Description
this makes `device` and `post_func` optional 

### 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`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

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

### Description

This PR added the `MLFlow` support the bundle script.
It refers to the `patched_fit` implementation of MLFlow + Lightning:

https://github.com/mlflow/mlflow/blob/master/mlflow/pytorch/_pytorch_autolog.py#L328-L338

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

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

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

Signed-off-by: Yiheng Wang <[email protected]>

Fixes #5515  .

### Description

This PR adjusts the freeze encoder function, and also fix the issue of
un-trigger some of the unit tests.

### 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: Yiheng Wang <[email protected]>

Signed-off-by: Geevarghese George <[email protected]>

### Description

This is a simple fix following #5465. 
The downsampling layer is not expected to have a bias term. The previous
implementation did not explicitly set `bias=False` and defaulted to
PyTorch Conv3D/2D where `bias=True`. With this change, the correct
number (62 for resnet18) of parameter groups are returned:
```python
from torchvision import models 
from monai.networks import nets
d2net_torch = models.resnet18()
d2net_monai = nets.resnet18(spatial_dims=2)
d3net_monai = nets.resnet18(spatial_dims=3)
len(list(d2net_torch.parameters())), len(list(d2net_monai.parameters())), len(list(d3net_monai.parameters())) 
# 62, 62, 62
# before: 62 65 65 
```
Other deeper 2D ResNet architectures are also comparable to the PyTorch
implementation; the `pretrained`/`weights` parameter can be allowed for
these networks. Currently, it raises a `NotImplemetedError` with
`pretrained=True` even for 2D ResNets.

### 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: Geevarghese George <[email protected]>

### Description

Fix Project-MONAI/tutorials#1040

### 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: Nic Ma <[email protected]>

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

Fixes #5517.

### Description

Add a `new_key` argument, it will create a new key for the output and
keep the value of the key intact when `overwrite` is set to False.

### 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.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

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

Fixes #5180.

### Description
For the post-process in HoVerNet, now we have PR #5173 to process the
segmentation output(which has been merged) and PR #5186 to process the
classification output(which is under review now). We want a whole
transform containing these two components which can be easily used in
the MONAI model zoo bundle. Here has a draft version of how to combine
these components, if anyone has any suggestions, please feel free to
take it out.

### 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`.
- [x] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: KumoLiu <[email protected]>
Signed-off-by: yunliu <[email protected]>
Co-authored-by: Behrooz Hashemian <[email protected]>

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

### Description
this PR includes a few minor improvements
- allow string input, such as `device="cuda:1"` for Workflow
- skip stats key metric if `key_metric_name` is None
(monai/handlers/stats_handler.py)
- print incompatible metric values in the warning message
(CheckpointSaver)
- adds a `epochs` parameter for `ShuffleBuffer`
(#5488)
- adds a `output_name_formatter` for `SaveImage`
(#5508)
- simplify torch version in bundle init
(#5529)

### 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: Nic Ma <[email protected]>
Co-authored-by: Nic Ma <[email protected]>

Fixes #5500 

### Description

Update `HoVerNetLoss` with the improvements and changes in
`SobelGradients`.

### 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).

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

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

Fixes #3694

### Description
adds a wrapper for loss function:
```py
dice_loss = DiceLoss(include_background=True)
loss_metric = LossMetric(loss_fn=dice_loss)
```
so that `loss_metric` it can be used as a metric in:

https://github.com/Project-MONAI/MONAI/blob/b030839e98e6a00c1ab0e53545f60b62dc4da4a4/monai/handlers/ignite_metric.py#L32

### 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`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

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

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

Fixes #5532 

### Description
returns early if it's torch.Size

### 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.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Fixes #5521 

### Description

This PR implement `SlidingWindowHoVerNetInferer` that with HoVerNet
model, where the output size is different than the input but cannot be
scaled and should be padded and then cropped.

### 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.

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

Fixes #5542 

### 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).
- [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`.
- [x] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: kate-sann5100 <[email protected]>
Signed-off-by: monai-bot <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: monai-bot <[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]>

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

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

This adds several non-breaking fixes to DataAnalyzer

- do_ccp option defaults to False (as we don't currently use it, and
it's pretty slow)
- on GPU, dataloading is in parallel (num_workers = self.workers),
previously it was only synchronous
- when label for one case is completely empty (no foreground), it
crashes, so this PR fixes, by putting all zeros in label status

this PR partially addresses
#5430

### 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>