Fixes #5776 


### 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 #5793 .

### Description

This PR provides a workaround for the incompatible sphinx 6.0.0

### 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: Wenqi Li <[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]>

VarAutoEncoder.__init__() got an unexpected keyword argument
'dimensions' because now it is called spatial_dims.

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

Fixes #5775 .

### Description

This PR fixes the issue of `_get_latest_bundle_version` on Windows
(`os.path.join` will produce backslash which will create a wrong url)
Thanks @SachidanandAlle for finding this issue.

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

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

<!--pre-commit.ci start-->
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.3.0 →
v4.4.0](pre-commit/pre-commit-hooks@v4.3.0...v4.4.0)
- [github.com/asottile/pyupgrade: v2.38.2 →
v3.3.1](asottile/pyupgrade@v2.38.2...v3.3.1)
- [github.com/hadialqattan/pycln: v2.1.1 →
v2.1.2](hadialqattan/pycln@v2.1.1...v2.1.2)
<!--pre-commit.ci end-->

fixes #5805

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

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

Fixes #3178

### Description
As discussed in #3178, this PR adds a more general interface to apply
simple convolutions to images. This PR (re-)implements 2D and 3D
versions for mean filtering, edge detection, outline detection, mask
dilatation and image sharpening.

### Detailed description
The main transform is `ImageFilter`. It comes with some preset filters
that can be initialized using a string. Available presets are `["mean",
"laplace", "elliptical", "sobel", "sharpen", "median", "gauss",
"savitzky_golay"]`. For example, a transformation for mean filtering can
be created with:

```python
mean_filter = ImageFilter("mean", 3)
```
`ImageFilter` automatically detects whether the input is 2D or 3D and
creates the appropriate filter on the first call. This filter will then
be used in future calls of the transformation, so switching between 2D
and 3D images is not supported.

The initialization form string is only a convenience function. All
preset filters are also available in
`monai.networks.layers.simplelayers` as `nn.Module` subclasses.
ImageFilter` can also be created directly from an `nn.Module`. For
example, to create a transformation for mean filtering, the following is
also possible:

```python
filter_3d = MeanFilter(spatial_dims=3, size=3)
mean_filter = ImageFilter(filter_3d)
```

In this example, however, the filter size is predefined and is not
automatically derived from the input.
In addition, it is also possible to use custom filters with
`ImageFilter` using a `torch.Tensor` or `numpy.ndarray`. For example:

```python
filter_3d = torch.ones(3,3,3)
mean_filter = ImageFilter(filter_3d)
```

`RandImageFilter` is a randomizable variant of `ImageFilter` that
executes with probability `p` on each call. Both `ImageFilter` and
`RandImageFilter` also have dictionary versions.



### 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: kbressem <[email protected]>

Fixes #5653.

### Description

A new utility decorator that enables us to warn users of a changing
default argument.
Current implementation does the following:
- If version < since no warning will be printed.
- If the default argument is explicitly set by the caller no warning
will be printed.
- If since <= version < replaced a warning like this will be printed:
"Default of argument `{name}` has been deprecated since version
`{since}` from `{old_default}` to `{new_default}`. It will be changed in
version `{replaced}`."
- If replaced <= version a warning like this will be printed: "Default
of argument `{name}` was changed in version `{changed}` from
`{old_default}` to `{new_default}`."
- It doesn't validate the `old_default`, so you can even use this in
scenarios where the default is actually `None` but set later in the
function. This also enables us to set `old_default` to any string if the
default is e.g. not printable.
- The only validation that will throw an error is, if the `new_default`
== the actual default and version < replaced. Which means, that somebody
replaced the value already, before the version was incremented. Apart
from that also any value for `new_default` can be set, giving the same
advantages as for the `old_default`.

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

Signed-off-by: Felix Schnabel <[email protected]>

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

Fixes #5782

### Description
- adds 'mode' and 'align_corners' options to the blocks and nets
- fixes a few typos

### 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 #5624 
Fixes #5816 

### Description

- undo the workaround
(29a34ad)
- smaller test case tests/test_auto3dseg_ensemble.py

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

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

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

Fixes #5609.

### Description
Update the docstring for `HoVerNet` and `UpSample`.

### 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]>

…5813)

part of #5804.

### Description

This adds a simple attribute access for ConfigParser so

```python
from monai.bundle import ConfigParser
parser = ConfigParser({"a":"b"})
a = parser.get_parsed_content("a")
```
can be rewritten to
```python
from monai.bundle import ConfigParser
parser = ConfigParser({"a":"b"})
a = parser.a
```
This only works for variables/methods that are not included in
ConfigParser so e.g. `parser.config` would still get the whole config.
This PR only supports shallow attribute accesses, since the returned
value will be a `dict` where you need to use `["key"]` to get the
content.

### 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`.

Signed-off-by: Felix Schnabel <[email protected]>

running the test cases

### 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).

Fixes #5823.

### Description
This PR types following decorators:
- `deprecated`
- `deprecated_arg`
- `deprecated_arg_default`

Found
[here](https://github.com/Project-MONAI/MONAI/blob/dev/monai/utils/deprecate_utils.py).
It also fixes any typing issues that occurred because of the additional
typing.

Secondly, it fixes untyped decorator usage of the `ignite` library
(because of `optional_import`) for
[Workflow](https://github.com/Project-MONAI/MONAI/blob/34d713f9887a85f140630a75e9261b89f0005c84/monai/engines/workflow.py#L45)
and
[IgniteMetric](https://github.com/Project-MONAI/MONAI/blob/f9d472af05ceb56513771ea2faccebb79edc1a7a/monai/handlers/ignite_metric.py#L36).

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

Signed-off-by: Felix Schnabel <[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]>

Fixes #5833


### 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: Wenqi Li <[email protected]>

Fixes #5835.

### Description
Use `from __future__ import annotations` in all source files using
annotations, so we have consistent usage (and not only in ~5 files).
The new annotations are also more readable e.g.
`Optional[Union[List[str], str]]` vs. `list[str] | str | None`.

Secondly, this issue includes changing `from typing import Callable,
Sequence, ...` to `from collections.abc import Callable, Sequence, ...`
since the ones in the `typing` module are deprecated. They are
interchangeable even for `isinstance` checks (see also [this
stackoverflow
thread](https://stackoverflow.com/questions/62547848/should-isinstance-check-against-typing-or-collections-abc)).

### 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] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.

Signed-off-by: Felix Schnabel <[email protected]>

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

fixes #5779

### 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.


review torch 1.12 tests and upgrade to the latest (1.13+)

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

### Description

This PR exclude `CuCIM`, `CuCIMD`, `RandCuCIM`, and `RandCuCIMD` wrapper
transfrom from `get_transform_backends` as they are not supposed to
support torch or numpy necessarily.

### 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: Mikael Brudfors
[[email protected]](mailto:[email protected])

part of #5740

### Description


Makes the binary and categorical metrics from MetricsReloaded available
in MONAI via a wrapper module (`monai/metrics/wrapper.py`).

This module allows to use the MetricsReloaded metrics as, e.g.:
```py
import torch
from monai.metrics import MetricsReloadedBinary

metric_name = "Cohens Kappa"
metric = MetricsReloadedBinary(metric_name=metric_name)

# first iteration
# shape [batch=1, channel=1, 2, 2]
y_pred = torch.tensor([[[[1.0, 0.0], [0.0, 1.0]]]])
y = torch.tensor([[[[1.0, 0.0], [1.0, 1.0]]]])
print(metric(y_pred, y))

# second iteration
# shape [batch=1, channel=1, 2, 2]
y_pred = torch.tensor([[[[1.0, 0.0], [0.0, 0.0]]]])
y = torch.tensor([[[[1.0, 0.0], [1.0, 1.0]]]])
print(metric(y_pred, y))

# aggregate
# shape ([batch=2, channel=1])
print(metric.aggregate(reduction="none"))  # tensor([[0.5], [0.2]])

# reset
metric.reset()
```

Tests of all metrics are in `tests/test_metrics_reloaded.py`.

Note that MetricsReloaded is an optional dependency of MONAI; so in
order to use the wrapper, MONAI needs to be installed with:
```sh
pip install '.[metricsreloaded]'
```

### 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: Mikael Brudfors <[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: Mikael Brudfors <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: monai-bot <[email protected]>

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

Fixes #5844

- improves the error message when slicing data with inconsistent
metadata
- fixes an indexing case:
```
x = MetaTensor(np.zeros((10, 3, 4)))
x[slice(1, 0)]  # should return zero length data
```

### 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 #5855

### 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.


Test pre-merge pipeline only!

### Description

We noted it was possible to instantiate classes derived from DenseNet
only if spatial_dims, in_channels, and out_channels parameters were
passed by keywords.
Passing them via positional scheme was not working.
This small bug should be fixed now.

### Example:
Before my fix:
```
import monai
net = monai.networks.nets.DenseNet(3,1,2) # Working
net = monai.networks.nets.DenseNet121(3,1,2) # NOT woking
net = monai.networks.nets.DenseNet121(spatial_dims=3, in_channels=1, out_channels=2) # Woking
```

After my fix:
```
import monai
net = monai.networks.nets.DenseNet121(3,1,2) # Woking
```

Thanks to @robsver for pointing this issue 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`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Fixes #5852

### Description
1. the following partial instantiate doesn't work
```py
config = {"import statements": "$import math", 
          "calc": {"_target_": "math.isclose", "a": 0.001, "b": 0.001}}
print(ConfigParser(config).calc())
```
with an error message:
```
Component to instantiate must represent a valid class or function, but got math.isclose.
Traceback (most recent call last):
  File "test.py", line 4, in <module>
    print(ConfigParser(config).calc())
TypeError: isclose() missing required argument 'a' (pos 1)
```

because `math.isclose` is a builtin type but not a function:

```py
import inspect
inspect.isfunction(math.isclose)  # False
inspect.isbuiltin(math.isclose)  # True
```

the `partial` should support `callable` including builtin functions


2. also this PR supports `_target_` of reference object's methods such
as partial init:
```py
"forward": {"_target_": "$@model().forward", "x": "$torch.rand(1, 3, 256, 256)"}
```

### 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]>

Add ITK to the list of optional dependencies.

### Types of changes
- [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: Dženan Zukić <[email protected]>

Fixes #1840 .

### Description

I integrated the trainable bilateral filter layer (TBF) in the MONAI
repository as a new PyTorch filter layer. The TBF contains an analytical
gradient derivation toward its filter parameters and its noisy input
image which enables gradient-based optimization within the PyTorch
graph. See [here](https://doi.org/10.1002/mp.15718) for more details on
the gradient derivation. Unit tests were added that check the filter
output as well as the gradient computation.

### 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: Fabian Wagner <[email protected]>

Fixes #5862.

### Description

if `untyped_storage()` is present (pytorch 2) use it, else use
`storage()`.

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

Fixes #5865 

### Description

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

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

Signed-off-by: Suraj Pai <[email protected]>

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

Fixes #5875 .

### Description

Add warning in `RandHistogramShift` when the image's intensity is a
single value.

### 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]>

#5965)

Fixes #5964

### Description

Added callable options for iteration_log and epoch_log in StatsHandler.

Ref:
#5958 (reply in thread)


### 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: vfdev-5 <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: vfdev <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Eric Kerfoot <[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: Wenqi Li <[email protected]>

Fixes #5902

### Description
the source image in ResampleToMatch may not have a `filename_or_obj`
when the source image is not created from `LoadImage`

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

---------

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

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


Fixes #5983 
Fixes #5696 

### Description
- torch.inverse was less stable across different base image versions
- there's a bug for loading the module
pytorch/pytorch#90613
this therefore also closes
#5696

this PR tries to move away from the torch.linalg APIs for small inverse
tasks where there's no need for making them differentiable
![Screenshot 2023-02-09 at 23 42
15](https://user-images.githubusercontent.com/831580/217963728-7c96733d-8570-4643-8fe1-2b8867e8e511.png)

![Screenshot 2023-02-13 at 14 47
50](https://user-images.githubusercontent.com/831580/218489820-578ff684-6173-4d46-9603-779b0e2e2fe2.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).
- [ ] 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: binliu <[email protected]>

Fixes #5971  .

### Description
There is a mismatch shape between the conv weight and input shape in
`FlexibleUNet`, if using `pixelshuffle` upsampling method. This is
caused by the wrong initialized `pre_conv` parameter in the decoder,
which should be `default` instead of `None`. Fixed this question in this
PR by changing it to `default` and adding some test cases.

### 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: YanxuanLiu <[email protected]>

Fixes #5912  .

### Description

1. removed 22.02 and 22.10 from cron
2. add 22.09 and 22.11 to blossom jobs

### 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: YanxuanLiu <[email protected]>

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

Fixes #5957


### 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: Wenqi Li <[email protected]>

…g transforms (#5993)

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

Fixes #5652 

### Description
by default random_size=True is somewhat unexpected

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

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

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

Fixes #5978

### Description
necessary logic for flexible test cases of algo templates auto3dseg

### 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]>

### Description

This adds a dependabot workflow to update github actions versions as I
have noticed deprecations in some of the recent runs here in
https://github.com/Project-MONAI/MONAI/actions.

This is like what was integrated at
Project-MONAI/MONAILabel@2ee812a
which resulted in automatically created PRs to update outdated github
actions in Project-MONAI/MONAILabel#1310 and
Project-MONAI/MONAILabel#1311.

Once this is integrated, auto created PRs by dependabot will be opened.

### 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.

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to
3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/checkout/releases">actions/checkout's
releases</a>.</em></p>
<blockquote>
<h2>v3.0.0</h2>
<ul>
<li>Updated to the node16 runtime by default
<ul>
<li>This requires a minimum <a
href="https://github.com/actions/runner/releases/tag/v2.285.0">Actions
Runner</a> version of v2.285.0 to run, which is by default available in
GHES 3.4 or later.</li>
</ul>
</li>
</ul>
<h2>v2.6.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Add backports to v2 branch by <a
href="https://github.com/cory-miller"><code>@​cory-miller</code></a> in
<a
href="https://github-redirect.dependabot.com/actions/checkout/pull/1040">actions/checkout#1040</a>
<ul>
<li>Includes backports from the following changes: <a
href="https://github-redirect.dependabot.com/actions/checkout/pull/964">actions/checkout#964</a>,
<a
href="https://github-redirect.dependabot.com/actions/checkout/pull/1002">actions/checkout#1002</a>,
<a
href="https://github-redirect.dependabot.com/actions/checkout/pull/1029">actions/checkout#1029</a></li>
<li>Upgraded the licensed version to match what is used in v3.</li>
</ul>
</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v2.5.0...v2.6.0">https://github.com/actions/checkout/compare/v2.5.0...v2.6.0</a></p>
<h2>v2.5.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Update <code>@​actions/core</code> to 1.10.0 by <a
href="https://github.com/rentziass"><code>@​rentziass</code></a> in <a
href="https://github-redirect.dependabot.com/actions/checkout/pull/962">actions/checkout#962</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v2...v2.5.0">https://github.com/actions/checkout/compare/v2...v2.5.0</a></p>
<h2>v2.4.2</h2>
<h2>What's Changed</h2>
<ul>
<li>Add set-safe-directory input to allow customers to take control. (<a
href="https://github-redirect.dependabot.com/actions/checkout/issues/770">#770</a>)
by <a
href="https://github.com/TingluoHuang"><code>@​TingluoHuang</code></a>
in <a
href="https://github-redirect.dependabot.com/actions/checkout/pull/776">actions/checkout#776</a></li>
<li>Prepare changelog for v2.4.2. by <a
href="https://github.com/TingluoHuang"><code>@​TingluoHuang</code></a>
in <a
href="https://github-redirect.dependabot.com/actions/checkout/pull/778">actions/checkout#778</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v2...v2.4.2">https://github.com/actions/checkout/compare/v2...v2.4.2</a></p>
<h2>v2.4.1</h2>
<ul>
<li>Fixed an issue where checkout failed to run in container jobs due to
the new git setting <code>safe.directory</code></li>
</ul>
<h2>v2.4.0</h2>
<ul>
<li>Convert SSH URLs like <code>org-&lt;ORG_ID&gt;@github.com:</code> to
<code>https://github.com/</code> - <a
href="https://github-redirect.dependabot.com/actions/checkout/pull/621">pr</a></li>
</ul>
<h2>v2.3.5</h2>
<p>Update dependencies</p>
<h2>v2.3.4</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/379">Add
missing <code>await</code>s</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/360">Swap
to Environment Files</a></li>
</ul>
<h2>v2.3.3</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/345">Remove
Unneeded commit information from build logs</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/326">Add
Licensed to verify third party dependencies</a></li>
</ul>
<h2>v2.3.2</h2>
<p><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/320">Add
Third Party License Information to Dist Files</a></p>
<h2>v2.3.1</h2>
<p><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/284">Fix
default branch resolution for .wiki and when using SSH</a></p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/actions/checkout/blob/main/CHANGELOG.md">actions/checkout's
changelog</a>.</em></p>
<blockquote>
<h1>Changelog</h1>
<h2>v3.1.0</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/939">Use
<code>@​actions/core</code> <code>saveState</code> and
<code>getState</code></a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/922">Add
<code>github-server-url</code> input</a></li>
</ul>
<h2>v3.0.2</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/770">Add
input <code>set-safe-directory</code></a></li>
</ul>
<h2>v3.0.1</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/762">Fixed
an issue where checkout failed to run in container jobs due to the new
git setting <code>safe.directory</code></a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/744">Bumped
various npm package versions</a></li>
</ul>
<h2>v3.0.0</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/689">Update
to node 16</a></li>
</ul>
<h2>v2.3.1</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/284">Fix
default branch resolution for .wiki and when using SSH</a></li>
</ul>
<h2>v2.3.0</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/278">Fallback
to the default branch</a></li>
</ul>
<h2>v2.2.0</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/258">Fetch
all history for all tags and branches when fetch-depth=0</a></li>
</ul>
<h2>v2.1.1</h2>
<ul>
<li>Changes to support GHES (<a
href="https://github-redirect.dependabot.com/actions/checkout/pull/236">here</a>
and <a
href="https://github-redirect.dependabot.com/actions/checkout/pull/248">here</a>)</li>
</ul>
<h2>v2.1.0</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/191">Group
output</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/199">Changes
to support GHES alpha release</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/184">Persist
core.sshCommand for submodules</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/163">Add
support ssh</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/179">Convert
submodule SSH URL to HTTPS, when not using SSH</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/157">Add
submodule support</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/144">Follow
proxy settings</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/141">Fix
ref for pr closed event when a pr is merged</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/128">Fix
issue checking detached when git less than 2.22</a></li>
</ul>
<h2>v2.0.0</h2>
<ul>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/108">Do
not pass cred on command line</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/107">Add
input persist-credentials</a></li>
<li><a
href="https://github-redirect.dependabot.com/actions/checkout/pull/104">Fallback
to REST API to download repo</a></li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/actions/checkout/commit/ac593985615ec2ede58e132d2e21d2b1cbd6127c"><code>ac59398</code></a>
Fix comment typos (that got added in <a
href="https://github-redirect.dependabot.com/actions/checkout/issues/770">#770</a>)
(<a
href="https://github-redirect.dependabot.com/actions/checkout/issues/1057">#1057</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/3ba5ee6fac7e0e30e2ea884e236f282d3a775891"><code>3ba5ee6</code></a>
Add in explicit reference to private checkout options (<a
href="https://github-redirect.dependabot.com/actions/checkout/issues/1050">#1050</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/885641592076c27bfb56c028cd5612cdad63e16d"><code>8856415</code></a>
Implement branch list using callbacks from exec function (<a
href="https://github-redirect.dependabot.com/actions/checkout/issues/1045">#1045</a>)</li>
<li><a
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3.2.0 (<a
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Update <code>@​actions/io</code> to 1.1.2 (<a
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wrap pipeline commands for submoduleForeach in quotes (<a
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<li><a
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Replace datadog/squid with ubuntu/squid Docker image (<a
href="https://github-redirect.dependabot.com/actions/checkout/issues/1002">#1002</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/1f9a0c22da41e6ebfa534300ef656657ea2c6707"><code>1f9a0c2</code></a>
README - fix status badge (<a
href="https://github-redirect.dependabot.com/actions/checkout/issues/967">#967</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/8230315d06ad95c617244d2f265d237a1682d445"><code>8230315</code></a>
Add workflow to update a main version (<a
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Prepare release v3.1.0 (<a
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Bumps
[actions/upload-artifact](https://github.com/actions/upload-artifact)
from 2 to 3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/upload-artifact/releases">actions/upload-artifact's
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<blockquote>
<h2>v3.0.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Update default runtime to node16 (<a
href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/293">#293</a>)</li>
<li>Update package-lock.json file version to 2 (<a
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</ul>
<h3>Breaking Changes</h3>
<p>With the update to Node 16, all scripts will now be run with Node 16
rather than Node 12.</p>
<h2>v2.3.1</h2>
<p>Fix for empty fails on Windows failing on upload <a
href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/281">#281</a></p>
<h2>v2.3.0 Upload Artifact</h2>
<ul>
<li>Optimizations for faster uploads of larger files that are already
compressed</li>
<li>Significantly improved logging when there are chunked uploads</li>
<li>Clarifications in logs around the upload size and prohibited
characters that aren't allowed in the artifact name or any uploaded
files</li>
<li>Various other small bugfixes &amp; optimizations</li>
</ul>
<h2>v2.2.4</h2>
<ul>
<li>Retry on HTTP 500 responses from the service</li>
</ul>
<h2>v2.2.3</h2>
<ul>
<li>Fixes for proxy related issues</li>
</ul>
<h2>v2.2.2</h2>
<ul>
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<h2>v2.2.1</h2>
<ul>
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<h2>v2.2.0</h2>
<ul>
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<h2>v2.1.4</h2>
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<h2>v2.1.1</h2>
<ul>
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directories before starting uploads</li>
</ul>
<h2>v2.1.0</h2>
<ul>
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<li><a
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ci(github): update action/download-artifact from v1 to v3 (<a
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Create devcontainer for codespaces + update all dev dependencies (<a
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Bump Actions NPM dependencies (<a
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ci(github): update action/checkout from v2 to v3 (<a
href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/315">#315</a>)</li>
<li><a
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README: Bump actions/checkout to v3 (<a
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<li><a
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Update to latest <code>actions/publish-action</code> (<a
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<li><a
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Bump actions-core to v1.10.0 (<a
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Merge pull request <a
href="https://github-redirect.dependabot.com/actions/upload-artifact/issues/327">#327</a>
from actions/robherley/artifact-1.1.0</li>
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nvm use 12 &amp; npm run release</li>
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recompile with correct ncc version</li>
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Fixes #6002



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

---------

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

Fixes #6007

### Description
- reverse_indexing = False:
to support consistency with PIL/torchvision
```py
img = LoadImage(image_only=True, ensure_channel_first=True, reverse_indexing=False)("MONAI-logo_color.png")  # PILReader
torchvision.utils.save_image(img, "MONAI-logo_color_torchvision.png", normalize=True)
```
- reverse_indexing = True:
to support consistency with other backends in monai
```py
img = LoadImage(image_only=True, ensure_channel_first=True, reader="PILReader", reverse_indexing=True)(filename)  # PIL backend
img_1 = LoadImage(image_only=True, ensure_channel_first=True, reader="ITKReader")(filename)  # itk backend
np.testing.assert_allclose(img, img_1)  # true
```

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

---------

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

### Description
Improve sliding-window inference with enhanced GPU memory efficiency.

### Types of changes
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applicable items -->
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existing functionality).
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--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

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

Part of #5991 .

### Description

This PR adds the minor utility enhancements from #5860 relate to lazy
resampling, and it belongs to the first part mentioned in
#5991

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applicable items -->
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--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]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Fixes #6018

### Description
removes deprecated apt install

### 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 #5708
Fixes #4117

### Description

This is a migration of the PR (by @ntatsisk https://github.com/ntatsisk)
InsightSoftwareConsortium/itk-torch-transform-bridge#6
into MONAI.

### 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: Felix Schnabel <[email protected]>

… and MLFlow (#5976)

Follow-up PR on extending `iteration_log`/`epoch_log` functionality

### Description

> Could you please help also enable this feature for other very similar
handlers? Like:

https://github.com/Project-MONAI/MONAI/blob/dev/monai/handlers/tensorboard_handlers.py#L94
And:

https://github.com/Project-MONAI/MONAI/blob/dev/monai/handlers/mlflow_handler.py#L101

-
#5965 (review)

### 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
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- [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.

Fixes #6033 


### 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.
- [ ] 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 #5864 #5871 #5872 

### Description

This PR implements `PatchInferer` according to #5837, the base classes
for `Splitter` and `Merger` along with few concrete classes
`SlidingWindowSplitter` and `AvgMerger`. This can provide a sliding
window inference for tensor inputs.

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

---------

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

### Description

Improve GPU utilization rate of DiNTS network.

### 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: dongy <[email protected]>

### Description

This PR removes `map_level` from `SlidingPatchWSIDataset`, which seems
to be left from the previous changes and has not used anywhere. Also it
updates the outdated docstring.

### 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: Behrooz <[email protected]>

Improve GPU utilization of dints network

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

Part of #5991.
### Description

This PR adds the pad transforms from
#5860 relate to lazy
resampling, and it belongs to the second part mentioned in
#5991

### 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]>

A part of #5991 .

### Description

This PR adds the changes of `SpatialResample` from #5860 .

### 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]>

Add citation URL to README.

Signed-off-by: Richard Brown <[email protected]>
Co-authored-by: Eric Kerfoot <[email protected]>

### Description

The recommendation in `StatsHandler` of setting the global logging
config may not work in some cases (e.g. google colab and
#5960)
https://docs.python.org/3/library/logging.html#logging.basicConfig


https://github.com/Project-MONAI/MONAI/blob/3eef61e82883e9bc6c08d26954fc86286df7d1b3/monai/handlers/stats_handler.py#L55

in general we shouldn't recommend changing the root logger directly.

This PR changes the message to tune the module level loggers, updated
example message will be:
```
.the effective log level of ignite.engine.engine.Engine higher than INFO, StatsHandler may not generate logs,
please use the following code before running the engine to enable it: 
                                                                                
import logging                                                              
logging.getLogger('ignite.engine.engine.Engine').setLevel(logging.INFO) 
```

the updated commands are tested in the colab example:

https://colab.research.google.com/drive/1boqy7ENpKrqaJoxFlbHIBnIODAs1Ih1T

### 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]>