agisga / duke-dbt-data

duke-dbt-data

A repository with code samples and notebooks for DukeDBT Dataset.

docker

Build docker image:

docker build -t duke-dbt .

Run container bash:

docker run --rm -it \
  -v `pwd`:/duke-dbt \
  -v /path/to/data:/data \
  -p 8889:8889 \
  duke-dbt bash

Replace /path/to/data with a path to the downloaded data folder.

Alexej's command to run docker

docker run --rm --user alexej -it -v `pwd`:/duke-dbt -v /gpfs_projects/alexej.gossmann/BSC-DBT_data/data:/data -p 9999:9999 duke-dbt bash

Note user alexej was added in the Dockerfile to be able to write to the data folder.

jupyter notebook

Serve jupyter notebook from the container:

jupyter notebook --allow-root --ip=0.0.0.0 --port=8889

read dicom image

dcmread_image.ipynb notebook shows how to read image data from a DICOM file in the coordinate system that maches the ground truth bounding boxes.

draw bounding box

draw_box.ipynb notebook shows how to draw a bounding box on the image.

helper functions

To use helper functions from the notebooks, simply copy the duke_dbt_data.py file to your project.