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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
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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
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- [ ] Quick tests passed locally by running `./runtests.sh --quick
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- [ ] 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]>

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]>