merge master

merge master

merge master

merge master

merge master

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

Fixes Project-MONAI#5090

### Description
update version numbers

### 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]>

…ONAI#5182)

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

Fixes Project-MONAI#5176.

### Description
Remove batch dim in `SobelGradients` and `SobelGradientsd` to make it
consistent with other post transforms.

### 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: KumoLiu <[email protected]>

…t-MONAI#5183)

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

Fixes Project-MONAI#5177.

### Description

Add channel dim in `ComputeHoVerMaps` and `ComputeHoVerMapsd` to make it
consistent with other transforms.

### 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: KumoLiu <[email protected]>
Co-authored-by: Behrooz Hashemian <[email protected]>

Fixes Project-MONAI#5031.

### Description
Update federated learning figure. Using SVG format. Also removes from
svg from gitignore.

### 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: KumoLiu <[email protected]>

Fixes Project-MONAI#5209.

### Description
Fix typo in `RandScaleIntensityd`

### 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: KumoLiu <[email protected]>

fixes Project-MONAI#5193 
fixes Project-MONAI#5204

### Description

revise the import error messages and ignore a torchaudio warning.

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

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

…ey()` default (Project-MONAI#5213)

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

Fixes Project-MONAI#5211
Fixes Project-MONAI#5214

### Description
- set device based on the first item:
```py
device = self.rand_2d_elastic.device
if device is None and isinstance(d[first_key], torch.Tensor):
    device = d[first_key].device  # type: ignore
    self.rand_2d_elastic.set_device(device)
```

- simplied transform `first_key()` default to a tuple

### 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]>

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

Fixes Project-MONAI#3844

### Description
adding the flexibility for skipping the transform if the pixdim is in
the specified range

### 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: Yiheng Wang <[email protected]>

Fixes Project-MONAI#4264 .

### Description

This PR adds the antialiasing option for `Resized` transform.

### 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]>

…les (Project-MONAI#5224)

### Description

Some users may have models that take adjoint information. This PR allows
the adjoint information to be passed through the visualisation classes
to the model via `**kwargs`.

Also combined the test files of GradCAM and GradCAM++ as they were the
same.

### 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] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.

Signed-off-by: Richard Brown <[email protected]>

### Description

We should be using `PY_EXE` in runtests as opposed to raw `pip`.

### 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: Richard Brown <[email protected]>

Fixes Project-MONAI#5232 .

### Description

According to user's feedback, this PR enhanced the MONAI bundle doc page
to include tutorial examples and model-zoo info.

### 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: Wenqi Li <[email protected]>

Fixes Project-MONAI#5163

### Description

enhance metatensor compatibility for `OneOf`

### 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]>

Fixes Project-MONAI#5233 .

### Description

This PR added file existing check for the logging config, requested by
@holgerroth .

### 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: Wenqi Li <[email protected]>

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

Fixes Project-MONAI#5225 .

### Description
1. fix 1d data error in `VarAutoEncoder`
2. add `use_sigmoid` flag

### 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: KumoLiu <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

1. Fix the issue Project-MONAI#5227 
2. fix a small code flaw

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

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

Fixes Project-MONAI#5195.

### Description

Add support for MonaiAlgo to be run with torchrun for multi-gpu
training.

### 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: Holger Roth <[email protected]>

Fixes Project-MONAI#5218 

### Description

This PR moves `HoVerNet` Mode and Branch outside of the module and make
them independent `StrEnums`.

### 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] 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>

…#5230)

### Description

Occlusion sensitivity currently works by setting the logits at the
center of the occluded region. Even though neighbouring voxels are
occluded at the same time, this is not recorded. A better way to do it
would be to do an average each time a voxel is occluded. This is taken
care of by switching to using `sliding_window_inference`.

We had to do a bit of hacking to get this to work.
`sliding_window_inference` normally takes a subset of the whole image
and infers that. We want `sliding_window_inference` to tell us which
part of the image we should occlude, then we occlude it and infer the
**whole** image. To that end, we use a meshgrid to tell us the
coordinates of the region `sliding_window_inference` wants us to
occlude. We occlude, infer and then crop back to the size of the region
that was requested by `sliding_window_inference`.

This PR also allows for different occlusion kernels. We currently have:
- gaussian (actually inverse gaussian): the center of the occluded
region is zero, and towards the edge of the image is unchanged. This
doesn't introduce hard edges into the image, which might undermine the
visualisation process.
- mean_patch: the occluded region is replaced with the mean of the patch
it is occluding.
- mean_img: the occluded region is replaced with the mean of the whole
image (current implementation).

## Changes to input arguments
This PR is backwards incompatible, as using `sliding_window_inference`
means changing the API significantly.
    - pad_val: now determined by `mode`
    - stride: `overlap` used instead
    - per_channel: all channels are done simultaneously
    - upsampler: image is no longer downsampled

## Changes to output
Output previously had the shape `B,C,H,W,[D],N` where `C` and `N` were
the number of input and output channels of the network, respectively.
Now, we output the shape `B,N,H,W,[D]` as the `per_channel` feature is
no longer present.

Columns 2-4 are occlusion sensitivity done with Gaussian, mean of patch
and mean of image:


![vis](https://user-images.githubusercontent.com/33289025/193261000-b879bce8-3aab-433b-af6c-cbb9c885d0a3.png)

### 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).
- [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: Richard Brown <[email protected]>

### Description

Adds (optional) kernel_size parameter to UpSample, used for deconv
(convolution transpose up-sampling).

This allows to upsample, e.g to upscale to 2x with a kernel_size 3.
(currently the default is to upscale to 2x with a kernel size 2)

if this parameter is not set, the behavior is the same as before


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

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

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

Fixes Project-MONAI#5251

### Description
replace `None` with `"none"` in the readers

### 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: Can Zhao <[email protected]>

Fixes Project-MONAI#5250.

### Description

Fixed bug that allow_low_quality_matches in set_regular_matcher was
always set to True and it's not using value from the argument, in
retinanet.

### 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: Can Zhao <[email protected]>
Signed-off-by: monai-bot <[email protected]>
Co-authored-by: monai-bot <[email protected]>

…-MONAI#5256)

<!--pre-commit.ci start-->
updates:
- [github.com/asottile/pyupgrade: v2.34.0 →
v2.38.2](asottile/pyupgrade@v2.34.0...v2.38.2)
- [github.com/asottile/yesqa: v1.3.0 →
v1.4.0](asottile/yesqa@v1.3.0...v1.4.0)
- [github.com/hadialqattan/pycln: v1.3.5 →
v2.1.1](hadialqattan/pycln@v1.3.5...v2.1.1)
<!--pre-commit.ci end-->

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: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <[email protected]>

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

Fixes Project-MONAI#5253 

### Description
enhance computing offset for spacing

### 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]>