Consistent usage of annotation syntax (#5836)

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]>

monai/__init__.py

@@ -9,6 +9,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 import os
 import sys
 

monai/_extensions/__init__.py

@@ -9,4 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 from .loader import load_module

monai/_extensions/loader.py

@@ -9,13 +9,14 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 import platform
 from _thread import interrupt_main
 from contextlib import contextmanager
 from glob import glob
 from os import path
 from threading import Timer
-from typing import Optional
 
 import torch
 
@@ -44,9 +45,7 @@ def timeout(time, message):
                 pass
 
 
-def load_module(
-    module_name: str, defines: Optional[dict] = None, verbose_build: bool = False, build_timeout: int = 300
-):
+def load_module(module_name: str, defines: dict | None = None, verbose_build: bool = False, build_timeout: int = 300):
     """
     Handles the loading of c++ extension modules.
 

monai/apps/__init__.py

@@ -9,6 +9,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 from .datasets import CrossValidation, DecathlonDataset, MedNISTDataset, TciaDataset
 from .mmars import MODEL_DESC, RemoteMMARKeys, download_mmar, get_model_spec, load_from_mmar
 from .utils import SUPPORTED_HASH_TYPES, check_hash, download_and_extract, download_url, extractall, get_logger, logger

monai/apps/auto3dseg/__init__.py

@@ -9,6 +9,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 from .auto_runner import AutoRunner
 from .bundle_gen import BundleAlgo, BundleGen
 from .data_analyzer import DataAnalyzer

monai/apps/auto3dseg/__main__.py

@@ -9,6 +9,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 from monai.apps.auto3dseg.auto_runner import AutoRunner
 from monai.apps.auto3dseg.bundle_gen import BundleAlgo, BundleGen
 from monai.apps.auto3dseg.data_analyzer import DataAnalyzer

monai/apps/auto3dseg/auto_runner.py

@@ -9,12 +9,14 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 import os
 import shutil
 import subprocess
 from copy import deepcopy
 from time import sleep
-from typing import Any, Dict, List, Optional, Union, cast
+from typing import Any, cast
 
 import numpy as np
 import torch
@@ -204,21 +206,21 @@ class AutoRunner:
 
     """
 
-    analyze_params: Optional[Dict]
+    analyze_params: dict | None
 
     def __init__(
         self,
         work_dir: str = "./work_dir",
-        input: Union[Dict[str, Any], str, None] = None,
-        algos: Optional[Union[Dict, List, str]] = None,
-        analyze: Optional[bool] = None,
-        algo_gen: Optional[bool] = None,
-        train: Optional[bool] = None,
+        input: dict[str, Any] | str | None = None,
+        algos: dict | list | str | None = None,
+        analyze: bool | None = None,
+        algo_gen: bool | None = None,
+        train: bool | None = None,
         hpo: bool = False,
         hpo_backend: str = "nni",
         ensemble: bool = True,
         not_use_cache: bool = False,
-        templates_path_or_url: Optional[str] = None,
+        templates_path_or_url: str | None = None,
         **kwargs,
     ):
 
@@ -234,7 +236,7 @@ def __init__(
             input = self.data_src_cfg_name
             logger.info(f"Input config is not provided, using the default {input}")
 
-        if isinstance(input, Dict):
+        if isinstance(input, dict):
             self.data_src_cfg = input
             ConfigParser.export_config_file(
                 config=input, filepath=self.data_src_cfg_name, fmt="yaml", default_flow_style=None, sort_keys=False
@@ -279,14 +281,14 @@ def __init__(
         self.set_num_fold(num_fold=self.num_fold)
 
         self.gpu_customization = False
-        self.gpu_customization_specs: Dict[str, Any] = {}
+        self.gpu_customization_specs: dict[str, Any] = {}
 
         # hpo
         if hpo_backend.lower() != "nni":
             raise NotImplementedError("HPOGen backend only supports NNI")
         self.hpo = hpo and has_nni
         self.set_hpo_params()
-        self.search_space: Dict[str, Dict[str, Any]] = {}
+        self.search_space: dict[str, dict[str, Any]] = {}
         self.hpo_tasks = 0
 
     def read_cache(self):
@@ -336,7 +338,7 @@ def export_cache(self, **kwargs):
         )
 
     def set_gpu_customization(
-        self, gpu_customization: bool = False, gpu_customization_specs: Optional[Dict[str, Any]] = None
+        self, gpu_customization: bool = False, gpu_customization_specs: dict[str, Any] | None = None
     ):
         """
         Set options for GPU-based parameter customization/optimization.
@@ -389,7 +391,7 @@ def set_num_fold(self, num_fold: int = 5):
         if self.ensemble_method_name == "AlgoEnsembleBestByFold":
             self.ensemble_method.n_fold = self.num_fold  # type: ignore
 
-    def set_training_params(self, params: Optional[Dict[str, Any]] = None):
+    def set_training_params(self, params: dict[str, Any] | None = None):
         """
         Set the training params for all algos.
 
@@ -404,7 +406,7 @@ def set_training_params(self, params: Optional[Dict[str, Any]] = None):
         """
         self.train_params = deepcopy(params) if params is not None else {}
 
-    def set_prediction_params(self, params: Optional[Dict[str, Any]] = None):
+    def set_prediction_params(self, params: dict[str, Any] | None = None):
         """
         Set the prediction params for all algos.
 
@@ -420,7 +422,7 @@ def set_prediction_params(self, params: Optional[Dict[str, Any]] = None):
         """
         self.pred_params = deepcopy(params) if params is not None else {}
 
-    def set_analyze_params(self, params: Optional[Dict[str, Any]] = None):
+    def set_analyze_params(self, params: dict[str, Any] | None = None):
         """
         Set the data analysis extra params.
 
@@ -438,7 +440,7 @@ def set_analyze_params(self, params: Optional[Dict[str, Any]] = None):
         else:
             self.analyze_params = deepcopy(params)
 
-    def set_hpo_params(self, params: Optional[Dict[str, Any]] = None):
+    def set_hpo_params(self, params: dict[str, Any] | None = None):
         """
         Set parameters for the HPO module and the algos before the training. It will attempt to (1) override bundle
         templates with the key-value pairs in ``params`` (2) change the config of the HPO module (e.g. NNI) if the
@@ -536,7 +538,7 @@ def set_ensemble_method(self, ensemble_method_name: str = "AlgoEnsembleBestByFol
         else:
             raise NotImplementedError(f"Ensemble method {self.ensemble_method_name} is not implemented.")
 
-    def _train_algo_in_sequence(self, history: List[Dict[str, Any]]):
+    def _train_algo_in_sequence(self, history: list[dict[str, Any]]):
         """
         Train the Algos in a sequential scheme. The order of training is randomized.
 

monai/apps/auto3dseg/bundle_gen.py

@@ -9,17 +9,20 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 import importlib
 import os
 import shutil
 import subprocess
 import sys
 import time
 import warnings
+from collections.abc import Mapping
 from copy import deepcopy
 from pathlib import Path
 from tempfile import TemporaryDirectory
-from typing import Any, Dict, List, Mapping, Optional, Union
+from typing import Any
 from urllib.parse import urlparse
 
 import torch
@@ -369,10 +372,10 @@ class BundleGen(AlgoGen):
     def __init__(
         self,
         algo_path: str = ".",
-        algos: Optional[Union[Dict, List, str]] = None,
-        templates_path_or_url: Optional[str] = None,
-        data_stats_filename: Optional[str] = None,
-        data_src_cfg_name: Optional[str] = None,
+        algos: dict | list | str | None = None,
+        templates_path_or_url: str | None = None,
+        data_stats_filename: str | None = None,
+        data_src_cfg_name: str | None = None,
     ):
 
         if algos is None or isinstance(algos, (list, tuple, str)):
@@ -426,7 +429,7 @@ def __init__(
 
         self.data_stats_filename = data_stats_filename
         self.data_src_cfg_filename = data_src_cfg_name
-        self.history: List[Dict] = []
+        self.history: list[dict] = []
 
     def set_data_stats(self, data_stats_filename: str):
         """
@@ -454,7 +457,7 @@ def get_data_src(self):
         """Get the data source filename"""
         return self.data_src_cfg_filename
 
-    def get_history(self) -> List:
+    def get_history(self) -> list:
         """get the history of the bundleAlgo object with their names/identifiers"""
         return self.history
 
@@ -463,7 +466,7 @@ def generate(
         output_folder=".",
         num_fold: int = 5,
         gpu_customization: bool = False,
-        gpu_customization_specs: Optional[Dict[str, Any]] = None,
+        gpu_customization_specs: dict[str, Any] | None = None,
     ):
         """
         Generate the bundle scripts/configs for each bundleAlgo

monai/apps/auto3dseg/data_analyzer.py

@@ -9,9 +9,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 import warnings
 from os import path
-from typing import Any, Dict, List, Optional, Union, cast
+from typing import Any, cast
 
 import numpy as np
 import torch
@@ -111,18 +113,18 @@ class DataAnalyzer:
 
     def __init__(
         self,
-        datalist: Union[str, Dict],
+        datalist: str | dict,
         dataroot: str = "",
         output_path: str = "./data_stats.yaml",
         average: bool = True,
         do_ccp: bool = False,
-        device: Union[str, torch.device] = "cpu",
+        device: str | torch.device = "cpu",
         worker: int = 2,
         image_key: str = "image",
-        label_key: Optional[str] = "label",
-        hist_bins: Optional[Union[list, int]] = 0,
-        hist_range: Optional[list] = None,
-        fmt: Optional[str] = "yaml",
+        label_key: str | None = "label",
+        hist_bins: list | int | None = 0,
+        hist_range: list | None = None,
+        fmt: str | None = "yaml",
         histogram_only: bool = False,
         **extra_params,
     ):
@@ -146,7 +148,7 @@ def __init__(
         self.extra_params = extra_params
 
     @staticmethod
-    def _check_data_uniformity(keys: List[str], result: Dict):
+    def _check_data_uniformity(keys: list[str], result: dict):
         """
         Check data uniformity since DataAnalyzer provides no support to multi-modal images with different
         affine matrices/spacings due to monai transforms.
@@ -227,7 +229,7 @@ def get_all_case_stats(self, key="training", transform_list=None):
         files, _ = datafold_read(datalist=self.datalist, basedir=self.dataroot, fold=-1, key=key)
         dataset = Dataset(data=files, transform=transform)
         dataloader = DataLoader(dataset, batch_size=1, shuffle=False, num_workers=self.worker, collate_fn=no_collation)
-        result: Dict[DataStatsKeys, Any] = {DataStatsKeys.SUMMARY: {}, DataStatsKeys.BY_CASE: []}
+        result: dict[DataStatsKeys, Any] = {DataStatsKeys.SUMMARY: {}, DataStatsKeys.BY_CASE: []}
 
         if not has_tqdm:
             warnings.warn("tqdm is not installed. not displaying the caching progress.")
@@ -261,7 +263,7 @@ def get_all_case_stats(self, key="training", transform_list=None):
                 )
             result[DataStatsKeys.BY_CASE].append(stats_by_cases)
 
-        result[DataStatsKeys.SUMMARY] = summarizer.summarize(cast(List, result[DataStatsKeys.BY_CASE]))
+        result[DataStatsKeys.SUMMARY] = summarizer.summarize(cast(list, result[DataStatsKeys.BY_CASE]))
 
         if not self._check_data_uniformity([ImageStatsKeys.SPACING], result):
             print("Data spacing is not completely uniform. MONAI transforms may provide unexpected result")

monai/apps/auto3dseg/ensemble_builder.py

@@ -9,10 +9,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from __future__ import annotations
+
 import os
 from abc import ABC, abstractmethod
+from collections.abc import Sequence
 from copy import deepcopy
-from typing import Any, Dict, List, Optional, Sequence, Union
+from typing import Any
 from warnings import warn
 
 import numpy as np
@@ -67,7 +70,7 @@ def get_algo_ensemble(self):
         """
         return self.algo_ensemble
 
-    def set_infer_files(self, dataroot: str, data_list_or_path: Union[str, List], data_key: str = "testing"):
+    def set_infer_files(self, dataroot: str, data_list_or_path: str | list, data_key: str = "testing"):
         """
         Set the files to perform model inference.
 
@@ -78,7 +81,7 @@ def set_infer_files(self, dataroot: str, data_list_or_path: Union[str, List], da
 
         self.infer_files = []
 
-        if isinstance(data_list_or_path, List):
+        if isinstance(data_list_or_path, list):
             self.infer_files = data_list_or_path
         elif isinstance(data_list_or_path, str):
             datalist = ConfigParser.load_config_file(data_list_or_path)
@@ -113,7 +116,7 @@ def ensemble_pred(self, preds, sigmoid=False):
             else:
                 return VoteEnsemble(num_classes=preds[0].shape[0])(classes)
 
-    def __call__(self, pred_param: Optional[Dict[str, Any]] = None):
+    def __call__(self, pred_param: dict[str, Any] | None = None):
         """
         Use the ensembled model to predict result.
 
@@ -233,7 +236,7 @@ def collect_algos(self) -> None:
         self.algo_ensemble = []
         for f_idx in range(self.n_fold):
             best_score = -1.0
-            best_model: Optional[BundleAlgo] = None
+            best_model: BundleAlgo | None = None
             for algo in self.algos:
                 # algorithm folder: {net}_{fold_index}_{other}
                 identifier = algo[AlgoEnsembleKeys.ID].split("_")[1]
@@ -264,8 +267,8 @@ class AlgoEnsembleBuilder:
 
     """
 
-    def __init__(self, history: Sequence[Dict], data_src_cfg_filename: Optional[str] = None):
-        self.infer_algos: List[Dict[AlgoEnsembleKeys, Any]] = []
+    def __init__(self, history: Sequence[dict], data_src_cfg_filename: str | None = None):
+        self.infer_algos: list[dict[AlgoEnsembleKeys, Any]] = []
         self.ensemble: AlgoEnsemble
         self.data_src_cfg = ConfigParser(globals=False)
 
@@ -292,7 +295,7 @@ def __init__(self, history: Sequence[Dict], data_src_cfg_filename: Optional[str]
 
             self.add_inferer(name, gen_algo, best_metric)
 
-    def add_inferer(self, identifier: str, gen_algo: BundleAlgo, best_metric: Optional[float] = None):
+    def add_inferer(self, identifier: str, gen_algo: BundleAlgo, best_metric: float | None = None):
         """
         Add model inferer to the builder.