radarad-device-axivity

This project presents a test environment for the parser developed by Biobank Accelerometer Analysis. The test environment consists of a Dockerified ubuntu OS with a JDK installed. The source code of Biobank Accelerometer Analysis is mounted under the directory workdir. To have the test environment please follow the commands below.

Clone this github project

git clone https://github.com/halilagin/radarad-device-axivity.git

Change directory in the project

cd radarad-device-axivity

Change directory in workdir directory

cd workdir

Download the Biobank Accelerometer Analysis project.

git clone https://github.com/activityMonitoring/biobankAccelerometerAnalysis.git

Delete the .git of the Biobank Accelerometer Analysis project.

rm -rf biobankAccelerometerAnalysis/.git

Introduce a JDK to the docker container.

To introduce a JDK to docker container, you need to download a JDK and and update the mount path of the JDK in docker-compoe.yml file. First, go to the root directory of this project and follow the commands below.

Downlaod JDK

sh download.java.sh

UnTar JDK

Use tar command to untar the downloaded file.

Create a directory named "containers-programs".

The downloaded JDK should be in the directory "containers-programs". Normally you will have that file in the project repository as a symbolic link. Remove that symbolic link file and create a directory with the same name.

rm containers-programs #remove the symbolic link
mkdir containers-programs

Move untarred JDK into containers-programs with the directory name jdk

The final home directory of the JDK should have the name jdk because it is introduced in docker-compose.yml with that name.

mv  {UNTARRED JDK DIRECTORY} containers-programs/jdk

Run Docker instance

sh dcup.sh

Connect to the docker instance via terminal

sh dcterminal.sh

In docker environment, test the code as introduced in the project Biobank Accelerometer Analysis

This commands are taken from the project Biobank Accelerometer Analysis. Please see their home page for further information.

Follow the commands below.

cd workdir/biobankAccelerometerAnalysis
sh utilities/downloadDataModels.sh
javac -cp java/JTransforms-3.1-with-dependencies.jar java/*.java
python3 accProcess.py data/sample.cwa.gz
python3 accPlot.py data/sample-timeSeries.csv.gz data/sample-plot.png

Validatation

If you see the file data/sample-plot.png under biobankAccelerometerAnalysis project folder which is similar to the one below it means that everything is working as expected.