alkino/brion

Blue Brain C++ File IO Library

Brion

Welcome to Brion, a C++ project for read and write access to Blue Brain data structures, including BlueConfig/CircuitConfig, Circuit, CompartmentReport, Mesh, Morphology, Synapse and Target files.

Brion can be retrieved by cloning the source code. The [latest API documentation] (http://bluebrain.github.io/Brion-1.9/index.html) can be found on bluebrain.github.io. Additional documentation exists for the [Python wrapping of Brain] (python/index.html).

To keep track of the changes between releases check the [changelog](@ref Changelog).

Features

Brion provides two libraries Brion and Brain. The former is a collection of file readers and writers intended for low level access to the data model. The latter is a set of higher level classes that wrap low level data objects with a use-case oriented API.

IO library

This is the core library provided by Brion. It includes classes for reading and writing files which store the Blue Brain data model.

• Fast and low-overhead read access to:
  • Blue configs (brion::BlueConfig)
  • Circuit description (brion::Circuit)
  • H5 Synapses data (brion::SynapseSummary, brion::Synapse)
  • Target (brion::Target)
  • BBP binary meshes (brion::Mesh)
  • BBP H5 morphologies and SWC morphologies (brion::Morphology)
  • Compartment reports (brion::CompartmentReport)
  • Spike reports (brion::SpikeReport)
• Fast and low-overhead write access to:
  • Compartment reports (brion::CompartmentReport)
  • BBP binary meshes (brion::Mesh)
  • BBP H5 morphologies (brion::Morphology)
  • Spike reports (brion::SpikeReport)
• Basic [data types](@ref brion/types.h) to work with the loaded data using Boost, Lunchbox, vmmlib.

High level library

The higher level library is called Brain and it provides:

• brain::Circuit to facilitate loading information about cells, morphologies (in local and global circuit coordinates) and synapses.
• brain::neuron::Morphology with higher level functions to deal with morphologies.
• brain::Synapses and brain::Synapse for array and object access to synapses.

Building

Brion is a cross-platform library, designed to run on any modern operating system, including all Unix variants. Brion uses CMake to create a platform-specific build environment. The following platforms and build environments are tested:

• Linux: Ubuntu 16.04, RHEL 6.8 (Makefile, Ninja)

Building from source is as simple as:

git clone --recursive https://github.com/BlueBrain/Brion.git
mkdir Brion/build
cd Brion/build
cmake -GNinja -DCLONE_SUBPROJECTS=ON ..
ninja