pfdcm 1.1.0

Path and File DICOM

Table of Contents

• Overview
  • pfdcm
• Installation
  • Python Virtual Environment
  • Using the fnndsc/ubuntu-python3 dock
  • Using the fnndsc/pfdcm dock
• Usage
  • pfdcm usage

Overview

This repository provides pfdcm – a controlling service that speaks to a PACS and handles DICOM data management. This is the bleeding edge dev branch.

pfdcm

Most simply, pfdcm provides a REST-type interface to querying a PACS as well as managing DICOM data received from a PACS.

Installation

Installation is relatively straightforward, and we recommend using either python virtual environments or docker.

Python Virtual Environment

On Ubuntu, install the Python virtual environment creator

sudo apt install virtualenv

Then, create a directory for your virtual environments e.g.:

mkdir ~/python-envs

You might want to add to your .bashrc file these two lines:

export WORKON_HOME=~/python-envs
source /usr/local/bin/virtualenvwrapper.sh

Then you can source your .bashrc and create a new Python3 virtual environment:

source .bashrc
mkvirtualenv --python=python3 python_env

To activate or “enter” the virtual env:

workon python_env

To deactivate virtual env:

deactivate

Using the fnndsc/ubuntu-python3 dock

We provide a slim docker image with python3 based off Ubuntu. If you want to play inside this dock and install pman manually, do

docker pull fnndsc/ubuntu-python3

This docker has an entry point python3. To enter the dock at a different entry and install your own stuff:

docker run -ti --entrypoint /bin/bash fnndsc/ubuntu-python3

Now,

apt update && \
apt install -y libssl-dev libcurl4-openssl-dev librtmp-dev && \
pip install pfdcm

If you do the above, remember to commit your changes to the docker image otherwise they’ll be lost when you remove the dock instance!

 docker commit <container-ID> local/ubuntu-python3-pfdcm

where ``<container-ID>`` is the ID of the above container.

Using the fnndsc/pfdcm dock

The easiest option however, is to just use the fnndsc/pfdcm dock.

docker pull fnndsc/pfdcm

and then run

docker run --name pfdcm -v /home:/Users --rm -ti fnndsc/pfdcm --forever --httpResponse

Usage

For usage of pfdcm, consult the relevant wiki pages.

pfdcm usage

For pfdcm detailed information, see the pfdcm wiki page.