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odML Editor

The odML-Editor is a standalone GUI application used for working with the odML Documents. The Python odML library is available on GitHub. If you are not familiar with the version control system git, but still want to use it, have a look at the documentation available on the git-scm website.

Breaking changes

odML Version 1.4+ introduced breaking format and API changes compared to the previous versions of odML. Files saved in a previous format version can be automatically converted into the new format via "File - Import". The import will create a new file and will not overwrite the original file.

Be aware that the value dtype binary has been removed. Incorporating binary data into odML files is discouraged, provide references to the original files using the URL dtype instead.

For details regarding the introduced changes please check the github release notes.

Release Versions

All released versions are distributed via the Python Package Index and can be installed using pip:

pip install odml-ui

Once installed, the program can be activated via the command line:

odmlui

Note: It might be required to install the external GTK3 dependencies first.

Dependencies

The odML-Editor makes use of the Gtk 3+ library for the GUI, and the python-odml library. The following dependencies need to be installed for the odML-Editor.

  • Python 3.6+
  • odml v1.5.1+ (pip install odml)

An installation using the conda package manager is highly recommended. Please also note, that Python 2 is no longer supported.

For Ubuntu-based distributions

  • sudo apt-get install libgtk-3-0
  • sudo apt-get install gobject-introspection
  • sudo apt-get install python3-gi

For Fedora-based distributions

  • sudo dnf install gtk3
  • sudo dnf install pygobject3
  • sudo dnf install python3-gobject

Anaconda Dependencies

Anaconda environments require only the following packages before installing the odML-Editor:

  • Python 3.6+.

  • Install the following packages in the following order:

      conda install -c pkgw/label/superseded gtk3
  conda install -c conda-forge pygobject
  conda install -c conda-forge gdk-pixbuf
  conda install -c pkgw-forge adwaita-icon-theme

NOTE: These packages currently only work on Linux out of the box!

The macOS installation of these 3rd party dependencies contain a bug which causes the opening of any window selecting files to crash the application.

If you still want to use odmlui with conda on macOS, you currently need to apply a manual fix at the start of your session in your active conda environment to avert this crash:

export GSETTINGS_SCHEMA_DIR=$CONDA_PREFIX/share/glib-2.0/schemas

You can also add scripts to your conda environment that always automatically sets up the required environment variable at the start of a conda session as described in the conda documentation.

macOS using homebrew

For Python 3

  • brew install gtk+3
  • brew install pygobject3
  • brew install gnome-icon-theme
  • brew install gobject-introspection

Windows with Anaconda

Dependencies

Installation

  • Install Anaconda
  • Create a new environment with Python 2.7+
  • Install PyGObject for Windows - base package and GTK+ 3.18.9 package

Select portable Python installation -> add path to virtual env Python default: C:\Users\userName\Anacaonda\envs\nameOfEnv\

  • Start Anaconda prompt
  • install odml (pip install odml)
  • install odml-ui (python setup.py install)
  • run with (odmlui)

Windows Warning

Windows of odml-ui cannot be moved (only maximized) - movement or resize of the windows crashes the application.

Installation from source

The most straightforward way to get to the odML-Editor source from the command line is to use git and clone the repository from GitHub into your directory of choice:

cd /home/usr/toolbox/
git clone https://github.com/G-Node/odml-ui.git

If you don't want to use git, download the ZIP file also provided on GitHub to your computer (e.g. as above on your home directory under a "toolbox" folder).

To install the odML-Editor, enter the corresponding directory and run:

cd /home/usr/toolbox/odml-ui/
python setup.py install

Note: pip install gi will lead to a namespace conflict with the required GObject introspection library.

Documentation

More information about the project including related projects as well as tutorials and examples can be found at our odML project page.

Bugs & Questions

Should you find a behaviour that is likely a bug or feel there is something missing, just create an issue over at the GitHub odML-Editor issue tracker.