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]>

Fixes #6069 .

### Description

This PR adds commonly used default values for `meta_file` and
`logging_file` of `monai.bundle.run` function.

### 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]>

Part of #5991 .

### Description

This PR adds the crop 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).
- [ ] 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]>

Fixes #6066

### Description

prefer the pytorch backend as much as possible

### 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]>

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

---------

Fixes #6049 

### Description
This PR add support to `GridPatch` for both filtering by count and
threshold. When filtering by threshold, the `num_patches` will be
treated as maximum number of patches.

UPDATE: It also removes the deprecated argument of
`skimage.measure.regionprops`, 'coordinates', which was causing some
test to fail.

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

---------

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

)

Part of #5991

### Description
This PR adds the remaining crop 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).
- [ ] 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]>

Fixes #6048


### 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 #5580 

### Description
This PR remove an "unnecessary" array copy in WSITiffFileReader, which
was causing an slow down in loading whole slide images.

### 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]>

### Description
Fixes #6086 remove the channel check
Fixes #6087 internally using `float('nan')` to also represent
`"no_channel"`

### 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: monai-bot <[email protected]>

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

Fixes #6104

### Description

workaround adapted from
https://github.com/pytorch/pytorch/blob/44dac51/torch/_tensor.py#L231-L233

### 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]>

Fixes #6020

### Description

```
pip install cucim
python -c "import cucim"
```
may create a `cufile.log` file in the current working directory (please
see rapidsai/cucim#514)

this PR delays the cucim imports to when the modules are really needed. 

### 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]>

Fixes # 6094.

### Description

Adds the `warn` flag to `RandCropByLabelClasses`. If `True` the behavior
of the class remains unchanged. If `False` the function will not print a
warning if a class is not present in the label.

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

Avoids crashing of the function if `ratios_[i] = 0` cannot be updated

Fixes #6121 

### Description

Adds additional if statement to check if warn is true, so that the
following code can still be executed.

### 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: kbressem <[email protected]>

ClearML is a leading MLOps stack that can supercharge dialogues research
with its state-of-the-art experiment tracking capability. ClearML:
https://clear.ml/

I have added a `clearml_handler.py` which contains ClearMLHandler,
ClearMLStatsHandler, and ClearMLImageHandler class. Basically, clearml
can track everything which is tracked by tensorboard including scalars,
and debug samples, and can also store models, artifacts, and the console
in the ClearML server which can be easily accessed from ClearML WebUI
shown as below:


![Screenshot from 2023-02-16
19-54-36](https://user-images.githubusercontent.com/46783803/219384828-77cb9c4c-4502-4529-95dd-8a95915385eb.png)

![Screenshot from 2023-02-16
19-54-29](https://user-images.githubusercontent.com/46783803/219384810-007ef976-b707-4dae-a31c-e9aba8200967.png)

![Screenshot from 2023-02-16
19-54-18](https://user-images.githubusercontent.com/46783803/219384795-2b5e60ac-fbff-49c7-8d6c-3eb2a34453dd.png)

![Screenshot from 2023-02-16
19-53-32](https://user-images.githubusercontent.com/46783803/219384770-b9b03667-8a12-4887-9049-84318e9a045b.png)
![Screenshot from 2023-02-16
19-53-49](https://user-images.githubusercontent.com/46783803/219384784-436f4ddb-d615-4720-ab62-1dd786a0989c.png)



![Screenshot from 2023-02-16
19-55-29](https://user-images.githubusercontent.com/46783803/219384449-fa41317c-21df-45a9-8605-7c7ed26fa637.png)


ClearMLStatsHandler and ClearMLImageHandler can be used with Pytorch
Trainer just like TensorboardStatsHandler and TensorboardImageHandler.

Use `ClearMLStatsHandler()` & `ClearMLImageHandler(log_dir="./runs/",
batch_transform=from_engine(["image",
"label"]),output_transform=from_engine(["pred"]),)` with any MONAI
example to test its functionality.

Also, please let us where should we put further documentation and
tutorials regarding this MLOps tool in the MONAI.

---------

Signed-off-by: Muhammad Sakib Khan Inan <[email protected]>
Signed-off-by: skinan <[email protected]>
Signed-off-by: Victor Sonck <[email protected]
Signed-off-by: Victor Sonck <[email protected]>

Fixes #6109

### Description
- use tuples for user inputs to avoid changes
- enhance the type checks
- fixes issue of `ratios` in `RandCropByLabelClasses `

### 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 #6124 .

### Description

When running the inference with torchscript wrapped TensorRT models, the
evaluator would give an error. This is caused by the `with
engine.mode()` code run the `training` method of `engine.network`
without checking. In this PR, an attribute check has been added to cover
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: binliu <[email protected]>

### Description
Improve GPU memory efficiency on sliding-window inferer.

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

Fixes #6056 

### Description

This PR enable to instantiate `WSIReader` classes with default values
for `mode` and `dtype`. It also accepts `torch.dtype` as dtype and if
`torch.dtype` is provided, the output will be a `torch.Tensor` to avoid
additional step to convert the output for inference.

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

---------

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

A part of #5991  .

### Description

Ready

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

---------

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

### Description

This PR should fix the memory issue with quick test instances for
running wsireader tests by using a lower resolution images for testing.

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

for slightly different affine (atol < 1e-3) the shape output might be
different
```
sum([1.49999991e+00 1.44128689e-04] * [237. 144.]) = sum([3.55499980e+02 2.07545313e-02]) = 355.52073414989167

sum([ 1.49999989e+00 -6.16167492e-10] * [237. 144.]) = sum([ 3.55499975e+02 -8.87281188e-08]) = 355.4999748785736
```

- increase the stability of affine inv
- check affine floating point types
- ensure same shape when there's only tiny difference in pixdim 


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

---------

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

Fixes #5821 .

### Description

The main idea of this PR is to solve 3 pain points of the current bundle
training or inference workflow:
1. Training or inference is defined in a "rigid" `training` or
`evaluation` list, so 3rd party package can't flexibly initialize and
run the workflows separately, see:
Project-MONAI/model-zoo#294. This PR splits it
into `initialize`, `run` and `finalize`, and still compatible with
current existing bundles.
2. 3rd party packages need to access the bundle config directly with
specifed keys based on `ConfigParser`, but some developers of bundles
don't want to write JSON or YAML configs. This PR implemented the
interface to support both config-based and python-based workflows.
3. MONAI Label, MONAI deploy, MONAI-FL require many fixed properties of
a training or inference workflow, but we don't have definition for them
in the code, just described in the developer guide doc of model-zoo.
This PR implemented the `TrainProperties` and `inferenceProperties`
interfaces and check tool.

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

Fixes Project-MONAI/tutorials#1250.
Fixes #6149

### Description
Now when `Resize` accept the same spatial_size with the original shape
and `set_track_meta(False)`, it will only return meta information.

https://github.com/Project-MONAI/MONAI/blob/9fd6d4ced3efb344cf3b24c51d899d8fafc882d5/monai/transforms/spatial/functional.py#L297-L301

In fast_training_tutorial.ipynb, when in "fast" mode, it will
`set_track_meta(False)` which causes error when doing `Resize`
This pr change `sliding_window_inference` to only `Resize` when the
shape is different.

https://github.com/Project-MONAI/MONAI/blob/a2ec3752f54bfc3b40e7952234fbeb5452ed63e3/monai/inferers/utils.py#L253

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

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

Fixes #5972 .

### Description
Fix and New Feature included:
- fix cache rate:
Project-MONAI/research-contributions#173
- typo fix
Project-MONAI/research-contributions#178
- scheduler step fix
Project-MONAI/research-contributions#182
- enhancement
Project-MONAI/research-contributions#184
- Fixed pretrain weight loading
Project-MONAI/research-contributions#202

### 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] `python tests/test_integration_autorunner.py` succeeded locally

---------

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

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

---------

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

Adds several improvements to DataAnalyzer, including

- Calculates image sizes in mm and their summaries (in additional to
shapes and spacing)
- Saves the datastats.yaml file as 2 files, the summary and the
statistics by case. The datastats.yaml will have only summaries, to be
able to load it faster. Otherwise for a large datasets (with many
labels) YAML loading takes over 2minutes.


### 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: myron <[email protected]>