brats_deploy.py

from monai.deploy.core import (
    Application,
)
from utils.transforms import post_trans, test_transform
from utils.operators import MonaiSegInferenceBRATSOperator, SaveAsNiftiOperator, GetModelsOperator, GetImagePathsOperator


class BratsApp(Application):
    # Define workflow of the application
    # This class will be called on execution
    def compose(self):
        # Define needed Operators
        get_models_op = GetModelsOperator()
        get_image_paths_op = GetImagePathsOperator()
        seg_inference_op = MonaiSegInferenceBRATSOperator(
            pre_transforms=test_transform,
            post_transforms=post_trans
        )
        save_as_nifti_op = SaveAsNiftiOperator()

        # Construct workflow
        self.add_flow(
            get_image_paths_op,
            seg_inference_op,
            io_map={"image": "image"}
        )
        self.add_flow(
            get_models_op,
            seg_inference_op,
            io_map={"model": "model"}
        )
        self.add_flow(
            seg_inference_op,
            save_as_nifti_op,
            io_map={"seg_image": "seg_image"}
        )

if __name__ == "__main__":
    # Will be called when the file is executed
    BratsApp(do_run=True)