Creating Application class

Application Class

The Application class is perhaps the most important class that MONAI Deploy App developers will interact with. A developer will inherit a new Application from the monai.deploy.core.Application base class. The base application class provides support for chaining up operators, as well as a mechanism to execute the application. The compose() method of this class needs to be implemented in the inherited class to instantiate Operators and connect them to form a Directed Acyclic Graph.

The following code shows an example Application (app.py) code:

An Application class definition example (app.py)

from monai.deploy.core import Application, env, resource


@resource(cpu=1, gpu=1, memory="2Gi")
# pip_packages can be a string that is a path(str) to requirements.txt file or a list of packages.
@env(pip_packages=["scikit-image >= 0.17.2"])
class App(Application):
    """This is a very basic application.

    This showcases the MONAI Deploy application framework.
    """

    # App's name. <class name>('App') if not specified.
    name = "my_app"
    # App's description. <class docstring> if not specified.
    description = "This is a reference application."
    # App's version. <git version tag> or '0.0.0' if not specified.
    version = "0.1.0"

    def compose(self):
        # Execute `self.add_flow()` or `self.add_operator()` methods here.
        pass

if __name__ == "__main__":
    App(do_run=True)

Decorators

The resource requirements (such as cpu, memory, and gpu) for the application can be specified by using @resource decorator. This information is used only when the packaged app (Docker image) is executed.

@env accepts pip_packages parameter as a string that is a path to requirements.txt file or a list of packages to install. If pip_packages is specified, the definition will be aggregated with the package dependency list of other operators. The aggregated requirement definitions are stored as a “requirements.txt” file and it would be installed in packaging time.

compose() method

In compose() method, operators are instantiated and connected through self.add_flow().

add_flow(upstream_op, downstream_op, io_map=None)

io_map is a dictionary of mapping from the source operator’s label to the destination operator’s label(s) and its type is Dict[str, str|Set[str]].

We can skip specifying io_map if both the number of upstream_op’s outputs and the number of downstream_op’s inputs are one. For example, if Operators named task1 and task2 has only one input and output (with the label image), self.add_flow(task1, task2) is same with self.add_flow(task1, task2, {"image": "image"}) or self.add_flow(task1, task2, {"image": {"image"}}).

    def compose(self):
        task1 = Task1()
        task2 = Task2()

        self.add_flow(task1, task2)
        # self.add_flow(task1, task2, {"image": "image"})
        # self.add_flow(task1, task2, {"image": {"image"}})

add_operator(operator)

If an operator in the workflow graph is both a root node and a leaf node, you can execute self.add_operator() for adding the operator to the workflow graph of the application.

    def compose(self):
        single_op = SingleOperator()
        self.add_operator(single_op)

if __name__ == “__main__”:

if __name__ == "__main__":
    App(do_run=True)

The above lines in app.py are needed to execute the application code by using python interpreter.

__main__.py file

__main__.py file is needed for MONAI Application Packager to detect main application code (app.py) when the application is executed with the application folder path (e.g., python app_folder/).

__main__.py file example (assuming that ‘App’ class is available in ‘app.py’ file)

from app import App

if __name__ == "__main__":
    App(do_run=True)

Creating a Reusable Application

Like Operator class, an Application class can be implemented in a way that the common Application class can be reusable.

Complex compose() Example

%%{init: {"theme": "base", "themeVariables": { "fontSize": "16px"}} }%% classDiagram direction TB Reader1 --|> Processor1 : image...{image1,image2}\nmetadata...metadata Reader2 --|> Processor2 : roi...roi Processor1 --|> Processor2 : image...image Processor2 --|> Processor3 : image...image Processor2 --|> Notifier : image...image Processor1 --|> Writer : image...image Processor3 --|> Writer : seg_image...seg_image class Reader1 { <in>input_path : DISK image(out) IN_MEMORY metadata(out) IN_MEMORY } class Reader2 { <in>input_path : DISK roi(out) IN_MEMORY } class Processor1 { <in>image1 : IN_MEMORY <in>image2 : IN_MEMORY <in>metadata : IN_MEMORY image(out) IN_MEMORY } class Processor2 { <in>image : IN_MEMORY <in>roi : IN_MEMORY image(out) IN_MEMORY } class Processor3 { <in>image : IN_MEMORY seg_image(out) IN_MEMORY } class Writer { <in>image : IN_MEMORY <in>seg_image : IN_MEMORY output_image(out) DISK } class Notifier { <in>image : IN_MEMORY }

⠀⠀A complex workflow

The above workflow can be expressed like below

    def compose(self):
        reader1 = Reader1()
        reader2 = Reader2()
        processor1 = Processor1()
        processor2 = Processor2()
        processor3 = Processor3()
        notifier = Notifier()
        writer = Writer()

        self.add_flow(reader1, processor1, {"image": {"image1", "image2"},
                                            "metadata": "metadata"})
        self.add_flow(reader2, processor2, {"roi": "roi"})
        self.add_flow(processor1, processor2, {"image": "image"})
        self.add_flow(processor1, writer, {"image": "image"})
        self.add_flow(processor2, notifier)
        self.add_flow(processor2, processor3)
        self.add_flow(processor3, writer, {"seg_image": "seg_image"})

Creating Operator classes Executing app locally