Migrated the simple nii loader

Signed-off-by: M Q <mingmelvinq@nvidia.com>

Author: MMelQin

monai/deploy/operators/nii_data_loader_operator.py

@@ -1,56 +1,91 @@
-# # Copyright 2021-2022 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.
+# Copyright 2021-2023 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 numpy as np
+from pathlib import Path
 
-# import monai.deploy.core as md
-# from monai.deploy.core import DataPath, ExecutionContext, InputContext, IOType, Operator, OutputContext
-# from monai.deploy.utils.importutil import optional_import
+import numpy as np
 
-# SimpleITK, _ = optional_import("SimpleITK")
+import monai.deploy.core as md
+from monai.deploy.core import ConditionType, Fragment, Operator, OperatorSpec
+from monai.deploy.utils.importutil import optional_import
+
+SimpleITK, _ = optional_import("SimpleITK")
 
 
 # @md.input("image_path", DataPath, IOType.DISK)
 # @md.output("image", np.ndarray, IOType.IN_MEMORY)
 # @md.env(pip_packages=["SimpleITK>=2.0.2"])
-# class NiftiDataLoader(Operator):
-#     """
-#     This operator reads a nifti image, extracts the numpy array and forwards it to the next operator
-#     """
+class NiftiDataLoader(Operator):
+    """
+    This operator reads a nifti image, extracts the numpy array and forwards it to the next operator
+
+    Named input:
+        image_path: Path to the image file, optional, used to override the path set in the object.
+
+    Named output:
+        image: A Numpy object in memory. Downstream receiver optional.
+    """
+
+    def __init__(self, fragment: Fragment, *args, input_path: Path, **kwargs) -> None:
+        """Creates an instance with the file path to load image from.
+
+        Args:
+            fragment (Fragment): An instance of the Application class which is derived from Fragment.
+            input_path (Path): The Path to read the image file from, overriden by the named input.
+        """
+        self.input_path = input_path  # Allow to be None, to be overridden when compute is called.
+        self.input_name_path = "image_path"
+        self.output_name_image = "image"
+
+        # Need to call the base class constructor last
+        super().__init__(fragment, *args, **kwargs)
+
+    def setup(self, spec: OperatorSpec):
+        spec.input(self.input_name_path).condition(ConditionType.NONE)
+        spec.output(self.output_name_image).condition(ConditionType.NONE)  # Fine for no or not-ready receiver ports.
+
+    def compute(self, op_input, op_output, context):
+        input_path = None
+        try:
+            input_path = op_input.receive(self.input_name_path)
+        except Exception:
+            if self.input_path and not self.input_path.is_file():
+                input_path = self.input_path
+            else:
+                raise ValueError("No path given to load image from.")
 
-#     def compute(self, op_input: InputContext, op_output: OutputContext, context: ExecutionContext):
-#         input_path = op_input.get().path
-#         image_np = self.convert_and_save(input_path)
-#         op_output.set(image_np)
+        image_np = self.convert_and_save(input_path)
+        op_output.emit(image_np, self.output_name_image)
 
-#     def convert_and_save(self, nii_path):
-#         """
-#         reads the nifti image and
-#         """
-#         image_reader = SimpleITK.ImageFileReader()
-#         image_reader.SetFileName(str(nii_path))
-#         image = image_reader.Execute()
-#         image_np = np.transpose(SimpleITK.GetArrayFromImage(image), [2, 1, 0])
-#         return image_np
+    def convert_and_save(self, nii_path):
+        """
+        reads the nifti image and returns a numpy image array
+        """
+        image_reader = SimpleITK.ImageFileReader()
+        image_reader.SetFileName(str(nii_path))
+        image = image_reader.Execute()
+        image_np = np.transpose(SimpleITK.GetArrayFromImage(image), [2, 1, 0])
+        return image_np
 
 
-# def test():
-#     filepath = "/home/gupta/Documents/mni_icbm152_nlin_sym_09a/mni_icbm152_gm_tal_nlin_sym_09a.nii"
-#     nii_operator = NiftiDataLoader()
-#     _ = nii_operator.convert_and_save(filepath)
+def test():
+    filepath = "/home/mqin/src/monai-deploy-app-sdk/inputs/lung_seg_ct/nii/volume-covid19-A-0001.nii"  #  "/home/gupta/Documents/mni_icbm152_nlin_sym_09a/mni_icbm152_gm_tal_nlin_sym_09a.nii"
+    fragment = Fragment()
+    nii_operator = NiftiDataLoader(fragment, input_path=filepath)
+    _ = nii_operator.convert_and_save(filepath)
 
 
-# def main():
-#     test()
+def main():
+    test()
 
 
-# if __name__ == "__main__":
-#     main()
+if __name__ == "__main__":
+    main()