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How to run the app

Get Code

Check out this repository

Prepare input data

Health Data

Patient health data needs to be provided in a csv file. It needs the following columns:

  • date (eg. 15.12.17)
  • time (eg. 13:59)
  • bgValue
  • cgmValue
  • basalValue
  • bolusValue
  • mealValue
  • glucoseAnnotation

Go to Folder cd data/csv

Add file called data.csv

Start with a file containing about 5 days of history and see how fast the computation is.

Autotune config files

Go to Folder cd data/input (call it from root of project)

Add your profile.json and profile.pump.json files

Use a Docker container to run the python and nodejs code

Build Docker image

Build the docker image from the provided Dockerfile

docker build -t t1d-pred:latest . (call from root of project)

Run Docker image

You need to mount your local files and input data to the docker container

docker run --rm -v <absoulute path to root of project (should end with /t1d-prediction)>:/t1d t1d-pred:latest

Inside the docker container the python/main.py will be called.

Run Docker image with autowatch

Nodemon will watch inside the docker container for file changes (only .py) and will restart the main.py docker run --rm -v <absoulute path to root of project>:/t1d t1d-pred:latest nodemon --exec python python/main.py -e py -L

To stop running containers with autowatch

docker stop $(docker ps -a -q --filter ancestor=t1d-pred:latest --format="{{.ID}}")

Change code

To change code, open the python directory with your editor of choice. For rapid development start the docker container with autowatch. It will rerun the code everytime you change a python file.

After the first run, autotune has created all necessary files and run_autotune in python/main.py can be set to False for a faster runtime.

Run keras in docker

Build

docker build -t t1d-pred-ml:latest -f Dockerfile-ML .

RUN

docker run --rm -v ~/code/t1d-prediction:/t1d t1d-pred-ml:latest

RUN AND BUILD

docker build -t t1d-pred-ml:latest -f Dockerfile-ML . && docker run --runtime=nvidia --rm -v ~/code/t1d-prediction:/t1d t1d-pred-ml:latest