Remove deprecated args and class for v1.3 (#7019)

Fixes #7018.

### Description
- Remove `compute_meaniou`
- Remove `AsChannelFirst`, `AddChannel` and `SplitChannel`
- Remove `create_multigpu_supervised_trainer` and
`create_multigpu_supervised_evaluator`
- deprecated `data_src_cfg_filename` in `AlgoEnsembleBuilder`
- deprecated `runner_id` in `run`
- deprecated `epoch_interval` and `iteration_interval` in
`TensorBoardStatsHandler`
- deprecated `get_validation_stats` in `Evaluator`
- deprecated `get_train_stats` in `Trainer`
- update the default value of `name` to `StatsHandler` in `StatsHandler`
- update the default value of `random_size` to `False` in
`RandSpatialCrop`, `RandScaleCrop`, `RandSpatialCropSamples`
- update the default value of `image_only` to `True` in `LoadImage` and
`SaveImage`
- update `MetaTenor` related deprecation

### 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: KumoLiu <yunl@nvidia.com>

Author: KumoLiu

docs/source/engines.rst

@@ -5,12 +5,6 @@
 Engines
 =======
 
-Multi-GPU data parallel
------------------------
-
-.. automodule:: monai.engines.multi_gpu_supervised_trainer
-  :members:
-
 Workflows
 ---------
 

docs/source/metrics.rst

@@ -61,7 +61,7 @@ Metrics
 
 `Mean IoU`
 ----------
-.. autofunction:: compute_meaniou
+.. autofunction:: compute_iou
 
 .. autoclass:: MeanIoU
     :members:

docs/source/transforms.rst

@@ -996,24 +996,12 @@ Utility
     :members:
     :special-members: __call__
 
-`AsChannelFirst`
-""""""""""""""""
-.. autoclass:: AsChannelFirst
-    :members:
-    :special-members: __call__
-
 `AsChannelLast`
 """""""""""""""
 .. autoclass:: AsChannelLast
     :members:
     :special-members: __call__
 
-`AddChannel`
-""""""""""""
-.. autoclass:: AddChannel
-    :members:
-    :special-members: __call__
-
 `EnsureChannelFirst`
 """"""""""""""""""""
 .. autoclass:: EnsureChannelFirst
@@ -1032,12 +1020,6 @@ Utility
     :members:
     :special-members: __call__
 
-`SplitChannel`
-""""""""""""""
-.. autoclass:: SplitChannel
-    :members:
-    :special-members: __call__
-
 `CastToType`
 """"""""""""
 .. autoclass:: CastToType
@@ -1983,24 +1965,12 @@ Utility (Dict)
     :members:
     :special-members: __call__
 
-`AsChannelFirstd`
-"""""""""""""""""
-.. autoclass:: AsChannelFirstd
-    :members:
-    :special-members: __call__
-
 `AsChannelLastd`
 """"""""""""""""
 .. autoclass:: AsChannelLastd
     :members:
     :special-members: __call__
 
-`AddChanneld`
-"""""""""""""
-.. autoclass:: AddChanneld
-    :members:
-    :special-members: __call__
-
 `EnsureChannelFirstd`
 """""""""""""""""""""
 .. autoclass:: EnsureChannelFirstd
@@ -2019,12 +1989,6 @@ Utility (Dict)
     :members:
     :special-members: __call__
 
-`SplitChanneld`
-"""""""""""""""
-.. autoclass:: SplitChanneld
-    :members:
-    :special-members: __call__
-
 `CastToTyped`
 """""""""""""
 .. autoclass:: CastToTyped

monai/apps/auto3dseg/ensemble_builder.py

@@ -36,7 +36,7 @@
 from monai.bundle import ConfigParser
 from monai.data import partition_dataset
 from monai.transforms import MeanEnsemble, SaveImage, VoteEnsemble
-from monai.utils import RankFilter, deprecated_arg
+from monai.utils import RankFilter
 from monai.utils.enums import AlgoKeys
 from monai.utils.misc import check_kwargs_exist_in_class_init, prob2class
 from monai.utils.module import look_up_option, optional_import
@@ -332,13 +332,6 @@ class AlgoEnsembleBuilder:
 
     """
 
-    @deprecated_arg(
-        "data_src_cfg_filename",
-        since="1.2",
-        removed="1.3",
-        new_name="data_src_cfg_name",
-        msg_suffix="please use `data_src_cfg_name` instead.",
-    )
     def __init__(self, history: Sequence[dict[str, Any]], data_src_cfg_name: str | None = None):
         self.infer_algos: list[dict[AlgoKeys, Any]] = []
         self.ensemble: AlgoEnsemble

monai/apps/deepgrow/transforms.py

@@ -441,8 +441,8 @@ def __call__(self, data):
 
         if np.all(np.less(current_size, self.spatial_size)):
             cropper = SpatialCrop(roi_center=center, roi_size=self.spatial_size)
-            box_start = np.array([s.start for s in cropper.slices])
-            box_end = np.array([s.stop for s in cropper.slices])
+            box_start = np.array([s.start for s in cropper.slices])  # type: ignore[assignment]
+            box_end = np.array([s.stop for s in cropper.slices])  # type: ignore[assignment]
         else:
             cropper = SpatialCrop(roi_start=box_start, roi_end=box_end)
 
@@ -492,9 +492,6 @@ class AddGuidanceFromPointsd(Transform):
             For example, to handle key `image`,  read/write affine matrices from the
             metadata `image_meta_dict` dictionary's `affine` field.
 
-    .. deprecated:: 0.6.0
-        ``dimensions`` is deprecated, use ``spatial_dims`` instead.
-
     """
 
     def __init__(

monai/bundle/scripts.py

@@ -704,7 +704,6 @@ def get_bundle_info(
     return bundle_info[version]  # type: ignore[no-any-return]
 
 
-@deprecated_arg("runner_id", since="1.1", removed="1.3", new_name="run_id", msg_suffix="please use `run_id` instead.")
 def run(
     run_id: str | None = None,
     init_id: str | None = None,
@@ -766,7 +765,7 @@ def run(
             will patch the target config content with `tracking handlers` and the top-level items of `configs`.
             for detailed usage examples, please check the tutorial:
             https://github.com/Project-MONAI/tutorials/blob/main/experiment_management/bundle_integrate_mlflow.ipynb.
-        args_file: a JSON or YAML file to provide default values for `runner_id`, `meta_file`,
+        args_file: a JSON or YAML file to provide default values for `run_id`, `meta_file`,
             `config_file`, `logging`, and override pairs. so that the command line inputs can be simplified.
         override: id-value pairs to override or add the corresponding config content.
             e.g. ``--net#input_chns 42``, ``--net %/data/other.json#net_arg``.

monai/data/dataset.py

@@ -1482,9 +1482,6 @@ class CSVDataset(Dataset):
         kwargs_read_csv: dictionary args to pass to pandas `read_csv` function.
         kwargs: additional arguments for `pandas.merge()` API to join tables.
 
-    .. deprecated:: 0.8.0
-        ``filename`` is deprecated, use ``src`` instead.
-
     """
 
     def __init__(

monai/data/grid_dataset.py

@@ -185,9 +185,6 @@ class GridPatchDataset(IterableDataset):
         transform: a callable data transform operates on the patches.
         with_coordinates: whether to yield the coordinates of each patch, default to `True`.
 
-    .. deprecated:: 0.8.0
-        ``dataset`` is deprecated, use ``data`` instead.
-
     """
 
     def __init__(
@@ -253,9 +250,6 @@ class PatchDataset(Dataset):
 
         >>> torch.Size([2, 1, 3, 3])
 
-    .. deprecated:: 0.8.0
-        ``dataset`` is deprecated, use ``data`` instead.
-
     """
 
     def __init__(

monai/data/image_reader.py

@@ -23,15 +23,15 @@
 import numpy as np
 from torch.utils.data._utils.collate import np_str_obj_array_pattern
 
-from monai.config import DtypeLike, KeysCollection, PathLike
+from monai.config import KeysCollection, PathLike
 from monai.data.utils import (
     affine_to_spacing,
     correct_nifti_header_if_necessary,
     is_no_channel,
     is_supported_format,
     orientation_ras_lps,
 )
-from monai.utils import MetaKeys, SpaceKeys, TraceKeys, deprecated_arg, ensure_tuple, optional_import, require_pkg
+from monai.utils import MetaKeys, SpaceKeys, TraceKeys, ensure_tuple, optional_import, require_pkg
 
 if TYPE_CHECKING:
     import itk
@@ -861,20 +861,17 @@ class NibabelReader(ImageReader):
 
     """
 
-    @deprecated_arg("dtype", since="1.0", msg_suffix="please modify dtype of the returned by ``get_data`` instead.")
     def __init__(
         self,
         channel_dim: str | int | None = None,
         as_closest_canonical: bool = False,
         squeeze_non_spatial_dims: bool = False,
-        dtype: DtypeLike = np.float32,
         **kwargs,
     ):
         super().__init__()
         self.channel_dim = float("nan") if channel_dim == "no_channel" else channel_dim
         self.as_closest_canonical = as_closest_canonical
         self.squeeze_non_spatial_dims = squeeze_non_spatial_dims
-        self.dtype = dtype  # deprecated
         self.kwargs = kwargs
 
     def verify_suffix(self, filename: Sequence[PathLike] | PathLike) -> bool:

monai/data/iterable_dataset.py

@@ -195,9 +195,6 @@ class CSVIterableDataset(IterableDataset):
         kwargs_read_csv: dictionary args to pass to pandas `read_csv` function. Default to ``{"chunksize": chunksize}``.
         kwargs: additional arguments for `pandas.merge()` API to join tables.
 
-    .. deprecated:: 0.8.0
-        ``filename`` is deprecated, use ``src`` instead.
-
     """
 
     def __init__(
@@ -223,8 +220,6 @@ def __init__(
         self.shuffle = shuffle
         self.seed = seed
         self.kwargs_read_csv = kwargs_read_csv or {"chunksize": chunksize}
-        # in case treating deprecated arg `filename` as kwargs, remove it from `kwargs`
-        kwargs.pop("filename", None)
         self.kwargs = kwargs
 
         self.iters: list[Iterable] = self.reset()