* fixes 4907

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

* fixes flake8

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

* fixes test cases

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

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

* [DLMED] enhance stats

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

* [DLMED] add tests

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

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

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

* [DLMED] fix tests

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

* [DLMED] update according to comments

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

* [DLMED] correct code folder

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

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

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

* [DLMED] keep backward compatible

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

* [DLMED] update according to comments

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

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

Update swin_unetr.py

fixed potential issue with discrepant data types

Signed-off-by: Bardia Khosravi <[email protected]>

Signed-off-by: Bardia Khosravi <[email protected]>

* video dataset

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

* Replace range(len(...)) with enumerate(...)

* add a mean iou handler and the unitest.

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

* add MeanIoUHandler to documentation

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

* add test_handler_mean_iou to min_tests.py

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

* change the metric name in unitest of iou from dice to iou.

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

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

* fixes #4920

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

* workaround #4917

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

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

* Improve FL ExchangeObject printing and summary

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

* add type annotation

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

* testing summary string

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

* typing

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

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

* provide init channel dim

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

* update docstring

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

* provide a default for get

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

* update based on comments

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

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

* Improve data type conversion performance

Signed-off-by: Gigon Bae <[email protected]>

* Update monai/utils/type_conversion.py

Co-authored-by: Gregory Lee <[email protected]>

Signed-off-by: Gigon Bae <[email protected]>
Co-authored-by: Gregory Lee <[email protected]>
Co-authored-by: Behrooz Hashemian <[email protected]>

enhance subprocess tests

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

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

* optional grid for base class api consistency

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

* update docs

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

* update docs

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

* docs update

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

* initial pytorch tests

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

* update tests

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

* update min tests

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

* fixes tests

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

* update dtype

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

* tested compiled

prefer numpy backend for integer interp mode

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

* extend type annotations

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

* update based on comments

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

* fixes a typo

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

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

* Adding __str__ to MetaTensor

Signed-off-by: Eric Kerfoot <[email protected]>

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

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

* Adding docstrings

Signed-off-by: Eric Kerfoot <[email protected]>

* Smooth field meshgrid fix

Signed-off-by: Eric Kerfoot <[email protected]>

Signed-off-by: Eric Kerfoot <[email protected]>

* fixes spatial resample

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

* fixes #4938

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

* skip if no scipy

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

* skip if no cupy

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

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

* Add num_worker for cucim read region

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

* Add unittest for multithread cucim

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

* Update docstring

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

* Minor fix for workflows

Signed-off-by: Eric Kerfoot <[email protected]>

* Minor fix for workflows

Signed-off-by: Eric Kerfoot <[email protected]>

* Minor fix for workflows

Signed-off-by: Eric Kerfoot <[email protected]>

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

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

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

monai env vars

* adds new keyword

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

* fixes #4962

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

* fixes #4964

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

* fixes tests

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

* fixes typo

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

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

* Fix For RandSmoothDeform Component Order

Signed-off-by: Eric Kerfoot <[email protected]>

* Fix For RandSmoothDeform Component Order

Signed-off-by: Eric Kerfoot <[email protected]>

Signed-off-by: Eric Kerfoot <[email protected]>

…tches for 4975, 4979) (#4977)

* fixes #4975

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

* fixes #4971

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

* fixes #4979

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

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

…4986)

Signed-off-by: Sachidanand Alle <[email protected]>

Signed-off-by: Sachidanand Alle <[email protected]>

Two very minor changes to wording.

* enhance worker_init_fn

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

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

Fixes #4993


### Status
**Ready**

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not applicable items -->
- [x] Non-breaking change (fix or new feature that would not break existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing functionality to change).
- [ ] 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: Wenqi Li <[email protected]>

### Description
This defines an abstract dense block class and a convolutional dense block using `Convolution` or `ResidualUnit` classes. A number of existing networks use dense blocks but have their own implementations that should be left as-is since these are reference implementations, but further definitions should use a common definition. I will have a network to submit as a bundle that uses this.

### Status
**Ready**

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not applicable items -->
- [x] Non-breaking change (fix or new feature that would not break existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing functionality to change).
- [x] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`.
- [ ] 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: Eric Kerfoot <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Fixes #5001.

### Description
Raise error if no weights are converted.

### Status
**Ready**

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

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

Fixes #4996 .

### Description
This PR enhanced the `ConfigParser` to support nested new ID.

### 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]>

### Description
Post transform to remove small objects.

Merge Project-MONAI/DocImages#13 when happy.

### Status
**Ready**

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not applicable items -->
- [x] Non-breaking change (fix or new feature that would not break existing functionality).
- [x] New tests added to cover the changes.

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

Fixes #5566 

### 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: PedroFerreiradaCosta <[email protected]>

Fixes #5417 .

### Description

Makes SSIM loss depend on metric instead of the other way around (the
loss was computing the metric).
Returns contrastive sensitivity if the boolean `full` is True when
calling `_compute_metric()`
Adds unit test to `test_ssim_metric.py` to check if contrastive
sensitivity output is working as expected.

### Types of changes
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] New tests added to cover the changes.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Part of #5517.

### Description

When we have a list of transforms, we may want these transforms to do in
random order. Add `RandomOrder` which is a subclass of `Compose` to
provide the ability to apply a list of transformations in random order.

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

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

Part of #5385 .

### Description

This PR added support to override the predefined configs in the
experiment tracking settings.

### 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]>

simpler integration tests

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

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

Fixes # .

### Description

- Make the current nuclick transform tensor enabled.  
- Add option to use Gaussian Filter over user clicks.
- Option to choose initial seed point based on distance transform
instead of random
- Optimize patch/boundary box creation logic for nuclei cells
- The same transform should be useful to create an interactive nuclick
classification model

### 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: Sachidanand Alle <[email protected]>

Signed-off-by: Ben Murray <[email protected]>

### Description

This is part of the work towards #4855. It adds:
 - a lazy `apply` method
 - A transform-like wrapper for `apply` called `Apply`
~- `MetaMatrix` and related functionality to represent abstracted grid
and matrix transforms with metadata~
- A universal `resample` function that can be used to apply grid /
matrix transforms
~- Functional spatial and croppad implementations that define but don't
apply transforms~

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [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: Ben Murray <[email protected]>
Signed-off-by: monai-bot <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>

closes #5581
closes #5582
closes #5583
closes #5584
closes #5586

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

closes #5588
closes #5589 
Signed-off-by: monai-bot <[email protected]>

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

…ls (#5598)

Signed-off-by: Sachidanand Alle <[email protected]>

Fixes # .
Throw error with description when there are no valid user click/signals

### Description
Instead of torch.stack error, provide readable description when the
signal is not valid, and no valid bounding boxes could be created based
on user click points.

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: Sachidanand Alle <[email protected]>

Fixes #5333 .

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Dženan Zukić <[email protected]>
Co-authored-by: Mingxin Zheng <[email protected]>

Making Algo base to have more generic inputs.

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

Fixes #5596
Fixes #5088

### Description
simplify the conda env

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

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

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

Fixes #5611

### Description
skip the padding to make smaller memory footprint when the patch size is
0 or None for a particular dimension

### 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: Wenqi Li <[email protected]>

adds CheckLabelShaped transform under monai.apps.auto3dseg:

- to check if image shape and label shape are the same. Currently, we
usually don't check for it, which results in potentially a
non-descriptive crash later, when computing loss or metric.
- to correct label shape if it is very similar to image shape.
Unfortunately some datasets, such as Hecktor22, has some labels (masks)
with a slightly different shapes (difference in only 1 voxel). And
because of that a user will have to either re-save the whole dataset, or
account for it during the training loop (which is inconvenient). this
utility auto corrects it.

We also already have this auto-correction in DataAnalyzer, and with this
transform, DataAnalyzer logic is simplified.

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

Fixes #5573

When using CacheDataset , and DataLoader num_workers==0, we convert
ProxyList to List in disable_share_memory_cache()

but if we're already inside DDP (DistributedDataParallel), we should not
do such conversion, as it will crash. we should continue using
ProxyList()




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

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

Fixes #5385  .

### Description

This PR is about to enhance the mlflow handler in monai to track more
details in the experiment. Here are a few enhancements
that needs to be added through this PR.

- API for users to add experiment/run name in MLFlow
- API for users to log customized params for each run
- Methods to log result images
- Methods to log optimizer params
- (optional) additional metric_names as a user argument to override the
default engine.state.metrics to instruct MLFlow about metrics to log

After adding these enhancements, some tests listed below should be
excuted.
- Make sure this handler works in multi-gpu environment
- Make sure this handler works in all existed bundles


### 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.
- [x] API for users to add experiment/run name in MLFlow
- [x] API for users to log customized params for each run
- [x] Methods to log result images
- [x] Methods to log optimizer params
- [x] Make sure this handler works in multi-gpu environment
- [ ] Make sure this handler works in all existed bundles

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

Fixes #5613

### Description

- `runtime_cache=False`: the default v1.0.1 behaviour
- `runtime_cache=True` or `"thread"`: single process, for caching cuda
tensors
- `runtime_cache="process"`: single process workflow + multiprocess
dataloader
- `runtime_cache=` user-provided object, could be used to pass a
container shared among processes

I feel in this way the user can determine what to use instead of
guessing and providing an automated solution... let me know what you
think @myron @Nic-Ma, I'm fine if this is eventually merged or not
merged

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

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

Signed-off-by: function2 <[email protected]>

Fixes #5634.


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [ ] 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`.
- [ ] 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: function2 <[email protected]>

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

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

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

part of #5637 


### 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 #5605.

### Description

Fix missing type annotations so `./runtests.sh --mypy` now finds 0
warnings.

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

AutoRunner class improvements

- adds auto-runner option **templates_path_or_url** to optionally accept
a local templates folder location. The default (None) is the same: to
download the release zip e.g.
AutoRunner(templates_path_or_url='/my/local/algorithm_templates')

- enhances **algos** input option to define a subset of algorithm names
to run (e.g. AutoRunner(algos=['segresnet','dints'])

### 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: myron <[email protected]>

Fixes #5616
Fixes #5617

### 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] 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: Behrooz <[email protected]>

### Description

We've had feedback that with MetaTensors, `x.__repr__` is overly
verbose. This is used frequently when debugging with an IDE for example.
The problem is accentuated with e.g., `x.max()`. Here, a single value is
hidden by over 50 lines of text.

Example:

```python
import monai.transforms as mt
loader = mt.LoadImage(image_only=True)
x = loader(x)
print(x.max().__repr__())
```

<details>
  <summary>Output</summary>

```
tensor(2906.1714)
Metadata
	sizeof_hdr: 348
	extents: 0
	session_error: 0
	dim_info: 0
	dim: [  3 161 338  61   1   1   1   1]
	intent_p1: 0.0
	intent_p2: 0.0
	intent_p3: 0.0
	intent_code: 0
	datatype: 16
	bitpix: 32
	slice_start: 0
	pixdim: [1.       1.       1.       2.000296 0.       0.       0.       0.      ]
	vox_offset: 0.0
	scl_slope: nan
	scl_inter: nan
	slice_end: 0
	slice_code: 0
	xyzt_units: 2
	cal_max: 0.0
	cal_min: 0.0
	slice_duration: 0.0
	toffset: 0.0
	glmax: 0
	glmin: 0
	qform_code: 1
	sform_code: 0
	quatern_b: -0.4889228641986847
	quatern_c: 0.5108369588851929
	quatern_d: -0.4703003466129303
	qoffset_x: -77.69402313232422
	qoffset_y: 218.0015411376953
	qoffset_z: -808.5780029296875
	srow_x: [0. 0. 0. 0.]
	srow_y: [0. 0. 0. 0.]
	srow_z: [0. 0. 0. 0.]
	affine: tensor([[ 3.5726e-02, -2.8526e-03,  1.9990e+00, -7.7694e+01],
        [-9.9619e-01,  7.9544e-02,  7.1691e-02,  2.1800e+02],
        [-7.9595e-02, -9.9683e-01,  1.3722e-07, -8.0858e+02],
        [ 0.0000e+00,  0.0000e+00,  0.0000e+00,  1.0000e+00]],
       dtype=torch.float64)
	original_affine: [[ 3.57263708e-02 -2.85262855e-03  1.99901100e+00 -7.76940231e+01]
 [-9.96186848e-01  7.95440337e-02  7.16907652e-02  2.18001541e+02]
 [-7.95951681e-02 -9.96827272e-01  1.37223043e-07 -8.08578003e+02]
 [ 0.00000000e+00  0.00000000e+00  0.00000000e+00  1.00000000e+00]]
	as_closest_canonical: False
	spatial_shape: [161 338  61]
	space: RAS
	original_channel_dim: no_channel
	filename_or_obj: /Users/rich/Downloads/sub-verse004_ct.nii.gz

Applied operations
[]
Is batch?: False
```
</details>

I'm proposing that the `__repr__` and `__str__` match that of
`torch.Tensor`. If users want meta data they can use `x.print_verbose()`
or `print(x.meta)`.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

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

Follow up of issue #5530 #5528 and (closed) PR #5547

### Description

Add test case for a binary classification task in `test_vis_gradcam`

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] New tests added to cover the changes.  
- [x] In-line docstrings updated.

Signed-off-by: Geevarghese George <[email protected]>

Fixes #5649 .

### Description

Add the `auto_close` parameter to mlflow_handler so that it can close
the mlflow run according to given value.
Update the default handler parameter, so that trainer and evaluator
could have `True` value on `auto_close`.

### 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]>

The line `optional_import("cv2")` causes the security light of my macOS
to light up in green, even for the lowest level command e.g., `import
monai`. I was worried I had a virus until I realised what was causing
it! To avoid worrying other users, I suggest we only import when a user
is using the `VideoDataset`.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).

Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>