Make the contructor of the derived operators explictly requiring fragment as arg.

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

Author: MMelQin

examples/apps/simple_imaging_app/__main__.py

@@ -1,13 +1,5 @@
-from pathlib import Path
-
 from app import App
 
 if __name__ == "__main__":
-    app = App()
-
-    # If there exists the named config file, use it to configure the objects which support it.
-    config_file = Path(__file__).parent.absolute() / "simple_imaing_app.yaml"
-    if config_file.exists():
-        app.config(config_file)
+    App().run()
 
-    app.run()

examples/apps/simple_imaging_app/app.py

@@ -47,6 +47,10 @@ def compose(self):
         output_data_path = Path(app_context.output_path)
         print(f"sample_data_path: {sample_data_path}")
 
+        # Please note that the Application object, self, is passed as the first positonal argument
+        # and the others as kwargs.
+        # Also note the CountCondition of 1 on the first operator, indicating to the application executor
+        # to invoke this operator, hence the pipleline, only once.
         sobel_op = SobelOperator(self, CountCondition(self, 1), input_folder=sample_data_path, name="sobel_op")
         median_op = MedianOperator(self, name="median_op")
         gaussian_op = GaussianOperator(self, output_folder=output_data_path, name="gaussian_op")
@@ -56,7 +60,7 @@ def compose(self):
             {
                 ("out1", "in1"),
             },
-        )  # Using port name is optional for single port cases
+        )
         self.add_flow(
             median_op,
             gaussian_op,
@@ -66,16 +70,9 @@ def compose(self):
                     "in1",
                 )
             },
-        )
+        )  # Using port name is optional for single port cases
 
 
 if __name__ == "__main__":
     load_env_log_level()
-    app = App()
-
-    # If there exists the named config file, use it to configure the objects which support it.
-    config_file = Path(__file__).parent.absolute() / "simple_imaing_app.yaml"
-    if config_file.exists():
-        app.config(config_file)
-
-    app.run()
+    App().run()

examples/apps/simple_imaging_app/gaussian_operator.py

@@ -14,7 +14,7 @@
 from skimage.filters import gaussian
 from skimage.io import imsave
 
-from monai.deploy.core import ConditionType, Operator, OperatorSpec
+from monai.deploy.core import ConditionType, Fragment, Operator, OperatorSpec
 
 
 # If `pip_packages` is specified, the definition will be aggregated with the package dependency list of other
@@ -23,12 +23,24 @@
 class GaussianOperator(Operator):
     """This Operator implements a smoothening based on Gaussian.
 
-    It ingests a single input, an array, but emits none, instead it saves a file in the output folder.
+    It has the following input and output:
+        single input:
+          an image array object
+        single output:
+          an image arrary object, without enforcing a downsteam receiver
+
+    Besides, this operator also saves the image file in the given output folder.
     """
 
     DEFAULT_OUTPUT_FOLDER = Path.cwd() / "output"
 
-    def __init__(self, *args, output_folder: Path, **kwargs):
+    def __init__(self, fragment: Fragment, *args, output_folder: Path, **kwargs):
+        """Create an instance to be part of the given application (fragment).
+
+        Args:
+            fragment (Fragment): The instance of Application class which is derived from Fragment
+            output_folder (Path): The folder to save the output file.
+        """
         self.output_folder = output_folder if output_folder else GaussianOperator.DEFAULT_OUTPUT_FOLDER
         self.index = 0
 
@@ -40,11 +52,11 @@ def __init__(self, *args, output_folder: Path, **kwargs):
         self.channel_axis = 2
 
         # Need to call the base class constructor last
-        super().__init__(*args, **kwargs)
+        super().__init__(fragment, *args, **kwargs)
 
     def setup(self, spec: OperatorSpec):
         spec.input("in1")
-        spec.output("out1").condition(ConditionType.NONE)  # This condition type allows for no or not-ready receiver.
+        spec.output("out1").condition(ConditionType.NONE)  # Condition is for no or not-ready receiver ports.
         spec.param("sigma_default", 0.2)
         spec.param("channel_axis", 2)
 

examples/apps/simple_imaging_app/median_operator.py

@@ -11,7 +11,7 @@
 
 from skimage.filters import median
 
-from monai.deploy.core import Operator, OperatorSpec
+from monai.deploy.core import Fragment, Operator, OperatorSpec
 
 
 # If `pip_packages` is specified, the definition will be aggregated with the package dependency list of other
@@ -21,15 +21,21 @@ class MedianOperator(Operator):
     """This Operator implements a noise reduction.
 
     The algorithm is based on the median operator.
-    It ingests a single input and provides a single output, both are of type in-memory array
+    It ingests a single input and provides a single output, both are in-memory image arrays
     """
 
     # Define __init__ method with super().__init__() if you want to override the default behavior.
-    def __init__(self, *args, **kwargs):
+    def __init__(self, fragment: Fragment, *args, **kwargs):
+        """Create an instance to be part of the given application (fragment).
+
+        Args:
+            fragment (Fragment): The instance of Application class which is derived from Fragment
+        """
+
         self.index = 0
 
         # Need to call the base class constructor last
-        super().__init__(*args, **kwargs)
+        super().__init__(fragment, *args, **kwargs)
 
     def setup(self, spec: OperatorSpec):
         spec.input("in1")

examples/apps/simple_imaging_app/sobel_operator.py

@@ -11,7 +11,7 @@
 
 from pathlib import Path
 
-from monai.deploy.core import Operator, OperatorSpec
+from monai.deploy.core import Fragment, Operator, OperatorSpec
 
 
 # # If `pip_packages` is specified, the definition will be aggregated with the package dependency list of other
@@ -29,7 +29,13 @@ class SobelOperator(Operator):
 
     DEFAULT_INPUT_FOLDER = Path.cwd() / "input"
 
-    def __init__(self, *args, input_folder: Path, **kwargs):
+    def __init__(self, fragment: Fragment, *args, input_folder: Path, **kwargs):
+        """Create an instance to be part of the given application (fragment).
+
+        Args:
+            fragment (Fragment): An instance of the Application class which is derived from Fragment
+            input_folder (Path): The folder to read the image file from
+        """
         self.index = 0
 
         # May want to validate the path, but it should really be validated when the compute function is called, also,
@@ -39,7 +45,7 @@ def __init__(self, *args, input_folder: Path, **kwargs):
         )
 
         # Need to call the base class constructor last
-        super().__init__(*args, **kwargs)
+        super().__init__(fragment, *args, **kwargs)
 
     def setup(self, spec: OperatorSpec):
         spec.output("out1")