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* Add TCIA dataset

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* dataset summary for metatensor

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* Makes self.data mutable

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* add allow_missing_keys in EnsureChannelFirstd

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* fix flake8 error

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[DLMED] enhance spacing and orientation

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* add Metatenosr support in ConcatItemd

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* fixes #4747 padding

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* permanent dataset hashes transforms

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* fixes

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* documentation

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* default to no hash

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* update changelog

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* update patch merging

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* update v0.9.1

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

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

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* docs/source/networks.rst updated with fft_utils_t

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

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

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* initial mri_transforms added under apps/reconstruction

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* with PR1 files to avoid error

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* PR1 included

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* PR1 files finally removed

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* putting test_mri_transforms under apps for now

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* isort fixed

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* ignore this commit, still in progress

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

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

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

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

* move tests under apps for now

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* remove unncessary packages from the reader

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* enum keys added

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* h5py added to requirements-dev.txt

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* optional import of h5py

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* fixed h5py dependency

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* fixed h5py dependency again

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* fixed docstring; fixed import issue

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* added h5py to relevant requirement files; updated fastmri_reader

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

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

* docs updated

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* fixed os.path.basename

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* support for multi-channel inputs

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* docstring fixed

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* minor argument fix

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Co-authored-by: Can Zhao <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <[email protected]>

* Implement GridSplit using torch.as_strided

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added YanxuanLiu as blossom trigger user

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

fixes #4774

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* update test cases

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* fixes flake8

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* fixes tests

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fixes docstring

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* adds meta[space]

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* fixes unit test

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* Change from round to floor

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* Explicit conversion to tuple for locs

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* Update patch merging with a for loop

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* Make patch merging order backward compatible for 2D

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

Fixes #5413

### Description
excluding background shouldn't be done before softmax

### 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]>

Fixes #5422

### Description
the kernel size and strides are hard-coded:

https://github.com/Project-MONAI/MONAI/blob/a209b06438343830e561a0afd41b1025516a8977/monai/networks/nets/attentionunet.py#L151

this PR makes the values tunable.

`level` parameter is not used and removed in this PR.

### 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]>

Fixes #5425

tested: https://github.com/Project-MONAI/MONAI/actions/runs/3344552788

### 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: Ben Murray <[email protected]>

Fixes # .

### 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.
- [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: Ben Murray <[email protected]>

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

Fixes #5432 
Fixes Project-MONAI/MONAILabel#1064

### Description
convert potential itk types in `img.GetMetaDataDictionary()` to numpy
arrays

### 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: Wenqi Li <[email protected]>

follow-up of #4922

### Description
- minimal interface to track the pending transforms via metatensor
- transforms.Flip is modified as an example for discussion
- discussion points:
- maintaining `pending_operations` and `applied_operations`
independently?
- the data structure for `pending_operations` element is a python
dictionary
  - transform "functional" refactoring

### 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]>

Fixes #5390 .

### Description

This PR simplified the `hash key` caching mode in the `CacheDataset` to
use `list` as cache type, same as regular cache.

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

This refactors CumulativeAverage() by removing subclassing from
Cumulative() to have much less overhead, and adds additionan
functionality to specify count.
(as discussed here #5380)

CumulativeAverage previously was not used almost anywhere, except for
MIL tutorial. Name of class methods .aggregate() and .append() are
preserved, so it should work the same way as before (non-breaking).

New tests are added (especially to test in multi-gpu DDP)


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

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

Fixes #5427 .

### 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] In-line docstrings updated.

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

Fixes #5188 

### Description

This PR reimplement `SobelGradients` and `SobelGradientsd` using
separable kernels and generalize it to images with any spatial dimension
(2D, 3D, etc.) and option to calculate the gradient along any given
axis.

### 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]>

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

fixes #5444

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

Fixes #3881 
Follow-up of Project-MONAI/tutorials#481

### Description
following
https://github.com/InsightSoftwareConsortium/ITK/blob/15aa8d58a01a1279e1fafa2214c82edd80b17e92/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx#L2174-L2176

### Status
**Ready**

### 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: Wenqi Li <[email protected]>

Fixes #5310 .

### Description
Add a post transform to process NP branch output(an output branch in
HoVerNet) which turns the probability map from the network into the
instance segmentation result.


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

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

- auto style fixing
- bump versioneer to 0.23 from 0.19

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

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

it's not easy to always keep the dco signing-off line when the pull
requests have many commits and rebasing. And the current instructions of
rebasing commits for DCO don't work properly in many cases
([example](https://github.com/Project-MONAI/MONAI/pull/5377/checks?check_run_id=9245758301)).
This PR set the option
https://github.com/dcoapp/app#individual-remediation-commit-support so
that the signing-off could be done via follow-up commits retroactively.

the new instructions for signing the PR will be provided similarly to
this testing example:
https://github.com/gr2m/sandbox/runs/4221328432 

### 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: Lee Newberg <[email protected]>

### Description

Re-writes version numbers as strings rather than numbers because 3.1 !=
3.10, etc. Nothing is broken at present but in the future as, e.g., the
Python version for some things goes from 3.8 to 3.9 to 3.10, this could
end up being an unexpected problem.

### 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: Lee Newberg <[email protected]>

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

Fixes #5028.

### Description
Since the output for HoVerNet is a dictionary, we already have
`PrepareBatchExtraInput` to support extra input data for the network,
but it still can't meet the requirements. This PR is to extend
`PrepareBatchExtraInput` to make the label can be a dictionary.

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

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

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

Fixes #5466.

### Description
In `GeneralizedDiceLoss`, now it do channel reduction before reduction,
remove channel reduction in this PR.

https://github.com/Project-MONAI/MONAI/blob/c38d503a587f1779914bd071a1b2d66a6d9080c2/monai/losses/dice.py#L360-L363

### 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: KumoLiu <[email protected]>

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

### Description
allow `config_file=None` when running `python -m monai.bundle run`,

this enables convenient quick runs via CLI, for example:
```bash
python -m monai.bundle run my_test --my_test="$print('hello')"
```

```bash
python -m monai.bundle run my_test --my_test="{_target_: LoadImage}"
```

output after this PR:
```
`config_file` not provided for 'monai.bundle run'.
2022-11-04 12:16:42,463 - INFO - --- input summary of monai.bundle.scripts.run ---
2022-11-04 12:16:42,463 - INFO - > runner_id: 'my_test'
2022-11-04 12:16:42,463 - INFO - > my_test: {'_target_': 'LoadImage'}
2022-11-04 12:16:42,463 - INFO - ---


<monai.transforms.io.array.LoadImage object at 0x7f80e2d05790>
```

### 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 #5469  

### Description

For CrossEntropy, PyTorch v1.10+ allows target values to be either class
probabilities or indices, whereas v1.9- only allows for class indices,
so class indices are now used. This should provide a better solution for
#5393 and remove the need for #5401


### 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: JHancox <[email protected]>
Signed-off-by: Behrooz <[email protected]>
Co-authored-by: Behrooz <[email protected]>

Fixes #3803

### Description

- fixes lncc loss
- adds a cache of the reference grid for `warp`

### 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: KumoLiu <[email protected]>

Fixes #5180.

### Description
Add classification post-process script for 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).
- [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: KumoLiu <[email protected]>
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: monai-bot <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Behrooz <[email protected]>
Co-authored-by: monai-bot <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

Fixes #5431 
Fixes #5452

### Description
- deprecating pytorch 1.7 tests
- adds pytorch 1.13 tests
- upgrade base image to pytorch 22.10

### 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.
- [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: Wenqi Li <[email protected]>

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

Fixes #5386 #5387 .

### Description

This PR modifies HoverNet via change the kernel size and padding size in
order to be consistent with the reference source.

This PR also enables to output same shape as the input when using fast
mode (takes the conic branch version (see:
https://github.com/vqdang/hover_net/tree/conic) for reference).

What's more, the functionality of loading pretrained weights is added,
users need to add the url which contains the weights that follow the
format of the encoder.

Finally, this PR adds the `np_out_channels` arg to control the output
channels of the nucleus prediction branch.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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]>
Co-authored-by: Behrooz Hashemian <[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]>