Fix all type errors in existing code

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

Author: gigony

examples/apps/ai_spleen_seg_app/spleen_seg_operator.py

@@ -12,6 +12,7 @@
 import logging
 
 from monai.deploy.core import ExecutionContext, Image, InputContext, IOType, Operator, OutputContext, env, input, output
+from monai.deploy.core.domain.monai_types import ComposeInterface
 from monai.deploy.operators.monai_seg_inference_operator import InMemImageReader, MonaiSegInferenceOperator
 from monai.transforms import (
     Activationsd,
@@ -81,7 +82,7 @@ def compute(self, input: InputContext, output: OutputContext, context: Execution
             # Now let the built-in operator handles the work with the I/O spec and execution context.
             infer_operator.compute(input, output, context)
 
-    def pre_process(self, img_reader) -> Compose:
+    def pre_process(self, img_reader) -> ComposeInterface:
         """Composes transforms for preprocessing input before predicting on a model."""
 
         my_key = self._input_dataset_key
@@ -96,7 +97,7 @@ def pre_process(self, img_reader) -> Compose:
             ]
         )
 
-    def post_process(self, pre_transforms: Compose, out_dir: str = "./infer_output") -> Compose:
+    def post_process(self, pre_transforms: ComposeInterface, out_dir: str = "./infer_output") -> ComposeInterface:
         """Composes transforms for postprocessing the prediction results."""
 
         pred_key = self._pred_dataset_key

monai/deploy/cli/__main__.py

@@ -10,7 +10,7 @@
 # limitations under the License.
 
 
-from main import main
+from main import main  # type: ignore # for pytype
 
 if __name__ == "__main__":
     main()

monai/deploy/core/domain/dicom_series.py

@@ -9,6 +9,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from typing import Any
+
 from .dicom_sop_instance import DICOMSOPInstance
 from .domain import Domain
 
@@ -21,6 +23,23 @@ def __init__(self, series_instance_uid):
         self._series_instance_uid = series_instance_uid
         self._sop_instances = []
 
+        self._series_date: Any = None
+        self._series_time: Any = None
+        self._modality: Any = None
+        self._series_description: Any = None
+        self._body_part_examined: Any = None
+        self._patient_position: Any = None
+        self._series_number: Any = None
+        self._laterality: Any = None
+        self._row_pixel_spacing: Any = None
+        self._col_pixel_spacing: Any = None
+        self._depth_pixel_spacing: Any = None
+        self._row_direction_cosine: Any = None
+        self._col_direction_cosine: Any = None
+        self._depth_direction_cosine: Any = None
+        self._dicom_affine_transform: Any = None
+        self._nifti_affine_transform: Any = None
+
     def get_series_instance_uid(self):
         return self._series_instance_uid
 
@@ -33,131 +52,131 @@ def get_sop_instances(self):
 
     @property
     def series_date(self):
-        return self.__series_date
+        return self._series_date
 
     @series_date.setter
     def series_date(self, val):
-        self.__series_date = val
+        self._series_date = val
 
     @property
     def series_time(self):
-        return self.__series_time
+        return self._series_time
 
     @series_time.setter
     def series_time(self, val):
-        self.__series_time = val
+        self._series_time = val
 
     @property
     def modality(self):
-        return self.__modality
+        return self._modality
 
     @modality.setter
     def modality(self, val):
-        self.__modality = val
+        self._modality = val
 
     @property
     def series_description(self):
-        return self.__series_description
+        return self._series_description
 
     @series_description.setter
     def series_description(self, val):
-        self.__series_description = val
+        self._series_description = val
 
     @property
     def body_part_examined(self):
-        return self.__body_part_examined
+        return self._body_part_examined
 
     @body_part_examined.setter
     def body_part_examined(self, val):
-        self.__body_part_examined = val
+        self._body_part_examined = val
 
     @property
     def patient_position(self):
-        return self.__patient_position
+        return self._patient_position
 
     @patient_position.setter
     def patient_position(self, val):
-        self.__patient_position = val
+        self._patient_position = val
 
     @property
     def series_number(self):
-        return self.__series_number
+        return self._series_number
 
     @series_number.setter
     def series_number(self, val):
-        self.__series_number = val
+        self._series_number = val
 
     @property
     def laterality(self):
-        return self.__laterality
+        return self._laterality
 
     @laterality.setter
     def laterality(self, val):
-        self.__laterality = val
+        self._laterality = val
 
     @property
     def row_pixel_spacing(self):
-        return self.__row_pixel_spacing
+        return self._row_pixel_spacing
 
     @row_pixel_spacing.setter
     def row_pixel_spacing(self, val):
-        self.__row_pixel_spacing = val
+        self._row_pixel_spacing = val
 
     @property
     def col_pixel_spacing(self):
-        return self.__col_pixel_spacing
+        return self._col_pixel_spacing
 
     @col_pixel_spacing.setter
     def col_pixel_spacing(self, val):
-        self.__col_pixel_spacing = val
+        self._col_pixel_spacing = val
 
     @property
     def depth_pixel_spacing(self):
-        return self.__depth_pixel_spacing
+        return self._depth_pixel_spacing
 
     @depth_pixel_spacing.setter
     def depth_pixel_spacing(self, val):
-        self.__depth_pixel_spacing = val
+        self._depth_pixel_spacing = val
 
     @property
     def row_direction_cosine(self):
-        return self.__row_direction_cosine
+        return self._row_direction_cosine
 
     @row_direction_cosine.setter
     def row_direction_cosine(self, val):
-        self.__row_direction_cosine = val
+        self._row_direction_cosine = val
 
     @property
     def col_direction_cosine(self):
-        return self.__col_direction_cosine
+        return self._col_direction_cosine
 
     @col_direction_cosine.setter
     def col_direction_cosine(self, val):
-        self.__col_direction_cosine = val
+        self._col_direction_cosine = val
 
     @property
     def depth_direction_cosine(self):
-        return self.__depth_direction_cosine
+        return self._depth_direction_cosine
 
     @depth_direction_cosine.setter
     def depth_direction_cosine(self, val):
-        self.__depth_direction_cosine = val
+        self._depth_direction_cosine = val
 
     @property
     def dicom_affine_transform(self):
-        return self.__dicom_affine_transform
+        return self._dicom_affine_transform
 
     @dicom_affine_transform.setter
     def dicom_affine_transform(self, val):
-        self.__dicom_affine_transform = val
+        self._dicom_affine_transform = val
 
     @property
     def nifti_affine_transform(self):
-        return self.__nifti_affine_transform
+        return self._nifti_affine_transform
 
     @nifti_affine_transform.setter
     def nifti_affine_transform(self, val):
-        self.__nifti_affine_transform = val
+        self._nifti_affine_transform = val
 
     def __str__(self):
         result = "---------------" + "\n"

monai/deploy/core/domain/dicom_sop_instance.py

@@ -9,34 +9,33 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from typing import Union
+from typing import Generic
 
 from monai.deploy.utils.importutil import optional_import
 
+from .dicom_types import SopInstance_KT, SopInstance_VT, SopInstanceInterface
 from .domain import Domain
 
 DataElement, _ = optional_import("pydicom", name="DataElement")
 Dataset, _ = optional_import("pydicom", name="Dataset")
-Tag, _ = optional_import("pydicom.tag", name="Tag")
-BaseTag, _ = optional_import("pydicom.tag", name="BaseTag")
-tag_in_exception, _ = optional_import("pydicom.tag", name="tag_in_exception")
-TagType, _ = optional_import("pydicom.tag", name="TagType")
+TagType, _ = optional_import("pydicom.tag")
 
 
-class DICOMSOPInstance(Domain):
+# Ignore type for Generic: https://github.com/google/pytype/issues/704
+class DICOMSOPInstance(Domain, Generic[SopInstance_KT, SopInstance_VT]):  # type: ignore
     """This class representes a SOP Instance.
 
     An attribute can be looked up with a slice ([group_number, element number]).
     """
 
     def __init__(self, native_sop):
         super().__init__(None)
-        self._sop = native_sop
+        self._sop: SopInstanceInterface = native_sop
 
     def get_native_sop_instance(self):
         return self._sop
 
-    def __getitem__(self, key: Union[int, slice, "TagType"]) -> Union["Dataset", "DataElement"]:
+    def __getitem__(self, key: SopInstance_KT) -> SopInstance_VT:
         return self._sop.__getitem__(key)
 
     def get_pixel_array(self):

monai/deploy/core/domain/dicom_study.py

@@ -10,6 +10,8 @@
 # limitations under the License.
 
 
+from typing import Any
+
 from .domain import Domain
 
 
@@ -24,6 +26,12 @@ def __init__(self, study_instance_uid):
         self._study_instance_uid = study_instance_uid
         self._series_dict = {}
 
+        self._study_id: Any = None
+        self._study_date: Any = None
+        self._study_time: Any = None
+        self._study_description: Any = None
+        self._accession_number: Any = None
+
     def get_study_instance_uid(self):
         return self._study_instance_uid
 
@@ -35,43 +43,43 @@ def get_all_series(self):
 
     @property
     def study_id(self):
-        return self.__study_id
+        return self._study_id
 
     @study_id.setter
     def study_id(self, val):
-        self.__study_id = val
+        self._study_id = val
 
     @property
     def study_date(self):
-        return self.__study_date
+        return self._study_date
 
     @study_date.setter
     def study_date(self, val):
-        self.__study_date = val
+        self._study_date = val
 
     @property
     def study_time(self):
-        return self.__study_time
+        return self._study_time
 
     @study_time.setter
     def study_time(self, val):
-        self.__study_time = val
+        self._study_time = val
 
     @property
     def study_description(self):
-        return self.__study_description
+        return self._study_description
 
     @study_description.setter
     def study_description(self, val):
-        self.__study_description = val
+        self._study_description = val
 
     @property
     def accession_number(self):
-        return self.__accession_number
+        return self._accession_number
 
     @accession_number.setter
     def accession_number(self, val):
-        self.__accession_number = val
+        self._accession_number = val
 
     def __str__(self):
         result = "---------------" + "\n"

monai/deploy/core/domain/dicom_types.py

@@ -0,0 +1,37 @@
+# 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, TypeVar
+
+from typing_extensions import Protocol
+
+
+class TagTypeInterface(Protocol):
+    pass
+
+
+class DatasetInterface(Protocol):
+    pass
+
+
+class DataElementInterface(Protocol):
+    pass
+
+
+SopInstance_KT = TypeVar("SopInstance_KT", int, slice, TagTypeInterface)
+SopInstance_VT = TypeVar("SopInstance_VT", DatasetInterface, DataElementInterface)
+
+
+class SopInstanceInterface(Protocol):
+    pixel_array: Any
+
+    def __getitem__(self, key: SopInstance_KT) -> SopInstance_VT:
+        ...

monai/deploy/core/domain/domain.py

@@ -29,5 +29,5 @@ def __init__(self, metadata: Optional[Dict] = None):
         else:
             self._metadata = {}
 
-    def metadata(self) -> Optional[Dict]:
+    def metadata(self) -> Dict:
         return self._metadata