Documentation

Main Page -> Software Documentation

This is the landing page for software documentation, installation instructions, the development workflow, etc.

Mailing lists and collaborative tools

• Project web page: https://www.uib.no/en/ift/142356/medical-physics-bergen-pct-project
• General mailing list: pCT@uib.no
• Slack project

Software installation

• Software tutorial at IFT
• ROOT installation
• Geant 4 installation
• Gate installation
• FLUKA installation
• Insight Toolkit (ITK) installation

  https://itk.org/

  https://github.com/InsightSoftwareConsortium/ITK

• Reconstruction Toolkit (RTK) installation

  http://www.openrtk.org/

  https://github.com/SimonRit/RTK

• DTC Toolkit for reconstruction

  User guide and tutorial

  https://github.com/HelgeEgil/focal (to be merged into gitlab)

  Cluster convolution for GATE

• Visualization Toolkit (VTK) Installation and usage

  http://www.vtk.org/

  https://github.com/Kitware/VTK

• Docker containers

Software repositories

We use the GitLab service hosted by IT of University of Bergen: https://git.app.uib.no/

Get access to the repositories - with UiB account

Open the UiB gitlab web interface.

Log in with your UiB account, then the administrators will give you access to the pCT group. Since authentication goes via Dataporten service, accounts from other Norwegian universities or institutions can be used in the same way.

Get access to the repositories - without UiB account

It is possible to use a github user account to login to the UiB GitLab, however such external users are not allowed to create forks in the GitLab domain. Since forks are mandatory for the development cycle, github logins can effectively only be used for read access. Again the repository administrators need to add you to the pCT group.

Guest accounts for external developers can be set up, get in contact with the group over the general channels

Further information on GitLab in general can by found on the following external webpages:

• Gitlab basics
• Gitlab workflow

The specific instructions how to use the repositories within the pCT project are collected in the following pages:

Getting the code

If you simply need the code, you can download an archive from the GitLab web interface. However, if there is a tiny chance that you might start developing, the recommended way is to clone the repository. See GitLab best practice#Roles.

Development workflow

Every logged-in user can access the main repository, however only a small group of administrators has write access. To contribute, a user creates a fork from the repository. This is a repository copy in the GitLab system where a single developer or a group of developers have full access, see GitLab Developer FAQ#Working with forks.

A local copy of the repository is required on the working machine in order to work on the project. This copy is referred to be a clone, see GitLab Developer FAQ#How can I make a clone of a project in my fork.