Format code with isort

- Update license year if needed
- Fix some typing issues in core module
- Add `is_module_installed()` method in importutil.py

Author: gigony

examples/apps/ai_spleen_seg_app/__init__.py

@@ -1,5 +1,6 @@
 import os
 import sys
+
 _current_dir = os.path.abspath(os.path.dirname(__file__))
 if sys.path and os.path.abspath(sys.path[0]) != _current_dir:
     sys.path.insert(0, _current_dir)

examples/apps/ai_spleen_seg_app/app.py

@@ -10,12 +10,15 @@
 # limitations under the License.
 
 import logging
+
+from spleen_seg_operator import SpleenSegOperator
+
 from monai.deploy.core import Application, resource
 from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
+from monai.deploy.operators.dicom_seg_writer_operator import DICOMSegmentationWriterOperator
 from monai.deploy.operators.dicom_series_selector_operator import DICOMSeriesSelectorOperator
 from monai.deploy.operators.dicom_series_to_volume_operator import DICOMSeriesToVolumeOperator
-from monai.deploy.operators.dicom_seg_writer_operator import DICOMSegmentationWriterOperator
-from spleen_seg_operator import SpleenSegOperator
+
 
 @resource(cpu=1, gpu=1, memory="7Gi")
 # pip_packages can be a string that is a path(str) to requirements.txt file or a list of packages.

examples/apps/ai_spleen_seg_app/spleen_seg_operator.py

@@ -11,33 +11,22 @@
 
 import logging
 
+from monai.deploy.core import ExecutionContext, Image, InputContext, IOType, Operator, OutputContext, env, input, output
+from monai.deploy.operators.monai_seg_inference_operator import InMemImageReader, MonaiSegInferenceOperator
 from monai.transforms import (
     Activationsd,
     AsDiscreted,
     Compose,
+    CropForegroundd,
     EnsureChannelFirstd,
     Invertd,
     LoadImaged,
-    Spacingd,
     SaveImaged,
     ScaleIntensityRanged,
-    CropForegroundd,
-    ToTensord
-)
-
-from monai.deploy.core import (
-    ExecutionContext,
-    Image,
-    InputContext,
-    IOType,
-    Operator,
-    OutputContext,
-    input,
-    output,
-    env
+    Spacingd,
+    ToTensord,
 )
 
-from monai.deploy.operators.monai_seg_inference_operator import MonaiSegInferenceOperator, InMemImageReader
 
 @input("image", Image, IOType.IN_MEMORY)
 @output("seg_image", Image, IOType.IN_MEMORY)

examples/apps/dicom_series_to_image_app/__init__.py

@@ -1,5 +1,6 @@
 import os
 import sys
+
 _current_dir = os.path.abspath(os.path.dirname(__file__))
 if sys.path and os.path.abspath(sys.path[0]) != _current_dir:
     sys.path.insert(0, _current_dir)

examples/apps/simple_imaging_app/__init__.py

@@ -1,5 +1,6 @@
 import os
 import sys
+
 _current_dir = os.path.abspath(os.path.dirname(__file__))
 if sys.path and os.path.abspath(sys.path[0]) != _current_dir:
     sys.path.insert(0, _current_dir)

examples/apps/simple_imaging_app/median_operator.py

@@ -49,7 +49,6 @@ def compute(self, input: InputContext, output: OutputContext, context: Execution
 
         # `context.input.get().path` (Path) is the file/folder path of the input data from the application's context.
         # `context.output.get().path` (Path) is the file/folder path of the output data from the application's context.
-
         # `context.models.get(model_name)` returns a model instance
         #  (a null model would be returned if model is not available)
         # If model_name is not specified and only one model exists, it returns that model.

monai/deploy/__init__.py

@@ -1,3 +1,14 @@
+# Copyright 2021 MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 from . import _version
+
 __version__ = _version.get_versions()['version']

monai/deploy/cli/__init__.py

@@ -1 +1,18 @@
-from .main import main
+# Copyright 2021 MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os
+import sys
+
+_current_dir = os.path.abspath(os.path.dirname(__file__))
+if sys.path and os.path.abspath(sys.path[0]) != _current_dir:
+    sys.path.insert(0, _current_dir)
+del _current_dir

monai/deploy/cli/__main__.py

@@ -1,4 +1,4 @@
-# Copyright 2020 - 2021 MONAI Consortium
+# Copyright 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -10,7 +10,7 @@
 # limitations under the License.
 
 
-from . import main
+from main import main
 
 if __name__ == "__main__":
-    main.main()
+    main()

monai/deploy/core/application.py

@@ -53,7 +53,7 @@ class Application(ABC):
     # This is needed to identify Application class across different environments (e.g. by `runpy.run_path()`).
     _class_id: str = "monai.application"
 
-    _env: "ApplicationEnv" = None
+    _env: Optional["ApplicationEnv"] = None
 
     def __init__(
         self,
@@ -179,7 +179,7 @@ def add_operator(self, operator: Operator):
         self._graph.add_operator(operator)
 
     def add_flow(
-        self, upstream_op: Operator, downstream_op: Operator, io_map: Optional[Dict[str, Union[str, Set]]] = None
+        self, upstream_op: Operator, downstream_op: Operator, io_map: Optional[Dict[str, Union[str, Set[str]]]] = None
     ):
         """Adds a flow from upstream to downstream.
 
@@ -189,8 +189,8 @@ def add_flow(
         Args:
             upstream_op (Operator): An instance of the upstream operator of type Operator.
             downstream_op (Operator): An instance of the downstream operator of type Operator.
-            io_map (Optional[Dict[str, str]]): A dictionary of mapping from the source operator's label to the
-                                               destination operator's label.
+            io_map (Optional[Dict[str, Union[str, Set[str]]]]): A dictionary of mapping from the source operator's label
+                                                                 to the destination operator's label(s).
         """
 
         # Ensure that the upstream and downstream operators are valid
@@ -213,12 +213,13 @@ def add_flow(
             io_map = {"": {""}}
 
         # Convert io_map's values to the set of strings.
+        io_maps : Dict[str, Set[str]] = io_map  # type: ignore
         for k, v in io_map.items():
             if isinstance(v, str):
-                io_map[k] = {v}
+                io_maps[k] = {v}
 
         # Verify that the upstream & downstream operator have the input and output ports specified by the io_map
-        output_labels = list(io_map.keys())
+        output_labels = list(io_maps.keys())
 
         if len(op_output_labels) == 1 and len(output_labels) != 1:
             raise IOMappingError(
@@ -231,17 +232,17 @@ def add_flow(
             if output_label not in op_output_labels:
                 if len(op_output_labels) == 1 and len(output_labels) == 1 and output_label == "":
                     # Set the default output port label.
-                    io_map[next(iter(op_output_labels))] = io_map[output_label]
-                    del io_map[output_label]
+                    io_maps[next(iter(op_output_labels))] = io_maps[output_label]
+                    del io_maps[output_label]
                     break
                 raise IOMappingError(
                     f"The upstream operator({upstream_op.name}) has no output port with label '{output_label}'. "
                     f"It should be one of ({', '.join(op_output_labels)})."
                 )
 
-        output_labels = list(io_map.keys())  # re-evaluate output_labels
+        output_labels = list(io_maps.keys())  # re-evaluate output_labels
         for output_label in output_labels:
-            input_labels = io_map[output_label]
+            input_labels = io_maps[output_label]
 
             if len(op_input_labels) == 1 and len(input_labels) != 1:
                 raise IOMappingError(
@@ -262,7 +263,7 @@ def add_flow(
                         f"It should be one of ({', '.join(op_input_labels)})."
                     )
 
-        self._graph.add_flow(upstream_op, downstream_op, io_map)
+        self._graph.add_flow(upstream_op, downstream_op, io_maps)
 
     def get_package_info(self, model_path: Union[str, Path] = "") -> Dict:
         """Returns the package information of this application.

monai/deploy/core/datastores/memory.py

@@ -1,10 +1,21 @@
+# Copyright 2021 MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 from typing import Any, Dict, Hashable, KeysView, Optional
 
 from .datastore import Datastore
 
 
 class MemoryDatastore(Datastore):
-    def __init__(self):
+    def __init__(self, **kwargs: Dict):
         self._storage: Dict = {}
 
     def get(self, key: Hashable, def_val: Optional[Any] = None) -> Any:

monai/deploy/core/domain/dicom_series.py

@@ -1,4 +1,4 @@
-# Copyright 2020 - 2021 MONAI Consortium
+# Copyright 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -9,8 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-import math
 from .dicom_sop_instance import DICOMSOPInstance
 from .domain import Domain
 

monai/deploy/core/domain/image.py

@@ -1,4 +1,4 @@
-# Copyright 2020 - 2021 MONAI Consortium
+# Copyright 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +12,7 @@
 from typing import Any, Dict, Optional, Union
 
 try:
-    from numpy.typing import ArrayLike
+    from numpy.typing import ArrayLike  # type: ignore
 except ImportError:
     ArrayLike = Any
 

monai/deploy/core/execution_context.py

@@ -17,7 +17,6 @@
     from .operator import Operator
 
 from .datastores import Datastore, MemoryDatastore
-from .domain import NamedDataPath
 from .io_context import InputContext, OutputContext
 from .models import Model
 
@@ -42,7 +41,7 @@ def __init__(
         models: Optional[Model] = None,
     ):
         if datastore is None:
-            self._storage = MemoryDatastore()
+            self._storage: Datastore = MemoryDatastore()
         else:
             self._storage = datastore
 

monai/deploy/core/executors/executor.py

@@ -10,7 +10,7 @@
 # limitations under the License.
 
 from abc import ABC, abstractmethod
-from typing import TYPE_CHECKING, Optional
+from typing import TYPE_CHECKING, Dict, Optional
 
 if TYPE_CHECKING:
     from monai.deploy.core import Application
@@ -21,7 +21,7 @@
 class Executor(ABC):
     """This is the base class that enables execution of an application."""
 
-    def __init__(self, app: "Application", datastore: Optional[Datastore] = None):
+    def __init__(self, app: "Application", datastore: Optional[Datastore] = None, **kwargs: Dict):
         """Constructor of the class.
 
         Given an application it invokes the compose method on the app, which

monai/deploy/core/graphs/graph.py

@@ -1,4 +1,4 @@
-# Copyright 2020 - 2021 MONAI Consortium
+# Copyright 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -10,7 +10,7 @@
 # limitations under the License.
 
 from abc import ABC, abstractmethod
-from typing import Dict, Generator, Optional
+from typing import Dict, Generator, Optional, Set
 
 from monai.deploy.core.operator import Operator
 
@@ -24,24 +24,26 @@ def add_operator(self, op: Operator):
         pass
 
     @abstractmethod
-    def add_flow(self, op_u: Operator, op_v: Operator, io_map: Dict[str, str]):
+    def add_flow(self, op_u: Operator, op_v: Operator, io_map: Dict[str, Set[str]]):
         """Add an edge to the graph.
 
         Args:
             op_u (Operator): A source operator.
             op_v (Operator): A destination operator.
-            io_map (Dict[str, str]): A dictionary of mapping from the source operator's label to the destination operator's label.
+            io_map (Dict[str, Set[str]]): A dictionary of mapping from the source operator's label to the destination
+                                          operator's label(s).
         """
         pass
 
     @abstractmethod
-    def get_io_map(self, op_u: Operator, op_v) -> Dict[str, str]:
+    def get_io_map(self, op_u: Operator, op_v) -> Dict[str, Set[str]]:
         """Get a mapping from the source operator's output label to the destination operator's input label.
         Args:
             op_u (Operator): A source operator.
             op_v (Operator): A destination operator.
         Returns:
-            A dictionary of mapping from the source operator's output label to the destination operator's input label.
+            A dictionary of mapping from the source operator's output label to the destination operator's
+            input label(s).
         """
         pass