Package: nixodmlconverter
odML ↔️ NIX metadata conversion toolThis tool reads inodML/NIXfiles and writes the metadata structure to newly
created NIX / odML files. When run as a script from the command line, it prints
information regarding the number of Sections and Properties that were read, written,
or skipped for various reasons.For more information on the odML and NIX data formats, please check the sections below.InstallationYou can easily install the converter via the Python package managerpip.pip install nixodmlconverterUsageAfter installing the package, you can use theconvert.pyscript found in the
directory 'nix-odML-converter/nixodmlconverter' that acts as a command line tool.You can use it to a) import the content of an existing odML file into a NIX file or
b) to export the odML content of a NIX file into a new odML file.Import of odML into a NIX fileFrom the command line use theconvert.pyscript to import the contents of an existing
odML file into a NIX file:python nix-odML-convert/nixodmlconverter/convert.py odmlfile.xml nixfile.nixThe odML file has to be provided in XML format.Export odML from a NIX fileFrom the command line use theconvert.pyscript to export the contents of an existing
NIX file to a new odML file:python nix-odML-convert/nixodmlconverter/convert.py nixfile.nix newodmlfile.xmlUsage notesFor compatibility with the NIX metadata format, which differs slightly from the
odML format, the following modifications occur when converting from odML to NIX:If a Section has areferencecreate a property calledreferenceIf a Property has areferenceput the reference in the Property's valuesValues of typeURL,person, andtextare treated as stringsValues of typedatetime,date, andtimeare converted to string representationsValues of typebinaryare discardedBuilding from sourceYou can also install the package by cloning the github repository and
installing from source.git clone https://github.com/G-Node/nix-odML-converter.git
cd nix-odML-converter
python setup.py installDependenciesPython 3.6+Python packages:odml (>=1.4.5)nixio (>=1.5.0b3)These dependency packages can be manually installed via the python package managerpip:pip install "odml>=1.4.5" "nixio>=1.5.0b3"or by manually installing the nix-odML-converter from the repository root:python setup.py installPython 2 has reached end of life. Future versions of nixodmlconverter will no longer support Python 2.  We further recommend using a Python version >= 3.6.NIX (Neuroscience information exchange) formatThe NIX data model allows to store fully annotated scientific datasets, i.e. the
data together with its metadata within the same container. Our aim is to achieve
standardization by providing a common/generic data structure for a multitude of
data types.The source code of the core python library is freely available onGitHuband can be installed via the
Python package managerpipby typingpip install nixio.More information about the project including related projects as well as tutorials and
examples can be found at our odMLproject page.odML (Open metaData Markup Language) formatThe open metadata Markup Language is a file based format (XML, JSON, YAML) for storing
metadata in an organised human- and machine-readable way. odML is an initiative to define
and establish an open, flexible, and easy-to-use format to transport metadata.The source code of the core library is freely available onGitHuband can be installed via the
Python package managerpipby typingpip install odml.More information about the project including related projects as well as tutorials and
examples can be found at our odMLproject page.