Axon python libraries API documentation¶
Axon python API is used by BrainVISA software. It includes modules to manage BrainVISA toolboxes, processes, databases, graphical user interface, etc.
Axon libraries rely on soma.base and soma.qtgui modules.
- It may use soma.workflow to generate workflows for parallel execution on a cluster
- It may also use of soma.aims if available, for files conversion and identification.
- and of anatomist if available, for viewers.
- This API can be used in several contexts:
- in a BrainVISA IPython shell started with brainvisa --shell or start shell menu
- in a BrainVISA process
- in a script executed from brainvisa in batch mode: brainvisa -b -e myScript.py
- in a Python script where Brainvisa is loaded using the module brainvisa.axon
Modules organization¶
A part of the API is in the form of classical python modules under the main brainvisa module while another part of the API (the older one) is in a brainvisa directory that is not in the python path and thus not accessible without running BrainVISA.
- Modules under the main brainvisa directory: main module executed at Brainvisa startup, modules about the processes and data ontology.
- brainvisa.* modules: toolboxes, preferences, databases.
Examples¶
- Setting a database: brainvisaSetDatabase.py
- A process with a dynamic signature: DynamicSignature.py
- Processes : Any process available in BrainVISA may be used as an example to help in developing new processes. The source code of each process is available directly from BrainVISA inline documentation: just click on the file name in the technical information part of the process documentation.
