1) Creating a simple image processing app

Setup

# Create a virtual environment with Python 3.7.
# Skip if you are already in a virtual environment.
# (JupyterLab dropped its support for Python 3.6 since 2021-12-23.
#  See https://github.com/jupyterlab/jupyterlab/pull/11740)
conda create -n monai python=3.7 pytorch torchvision jupyterlab cudatoolkit=11.1 -c pytorch -c conda-forge
conda activate monai

# Launch JupyterLab if you want to work on Jupyter Notebook
jupyter-lab

Executing from Jupyter Notebook

• Creating a Simple Image Processing App with MONAI Deploy App SDK
  • Creating Operators and connecting them in Application class
    • Setup environment
    • Download test input
    • Setup imports
    • Creating Operator classes
      • SobelOperator
      • MedianOperator
      • GaussianOperator
    • Creating Application class
  • Executing app locally
    • sobel_operator.py
    • median_operator.py
    • gaussian_operator.py
    • app.py
    • __main__.py
  • Packaging app
  • Executing packaged app locally

Download 01_simple_app.ipynb

Executing from Shell

# Clone the github project (the latest version of the main branch only)
git clone --branch main --depth 1 https://github.com/Project-MONAI/monai-deploy-app-sdk.git

cd monai-deploy-app-sdk

# Install monai-deploy-app-sdk package
pip install monai-deploy-app-sdk

# Install necessary packages from the app
pip install scikit-image

# Local execution of the app
python examples/apps/simple_imaging_app/app.py -i examples/apps/simple_imaging_app/brain_mr_input.jpg -o output

# Check the output file
ls output

# Package app (creating MAP docker image) using `-l DEBUG` option to see progress.
# This assumes that nvidia docker is installed in the local machine.
# Please see https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#docker to install nvidia-docker2.

monai-deploy package examples/apps/simple_imaging_app -t simple_app:latest -l DEBUG

# Copy a test input file to 'input' folder
mkdir -p input && rm -rf input/*
cp examples/apps/simple_imaging_app/brain_mr_input.jpg input/

# Run the app with docker image and input file locally
monai-deploy run simple_app:latest input output

Tutorials Creating a Simple Image Processing App with MONAI Deploy App SDK