GitHub - BlueBrain/MVDTool at v2.4.4 (original) (raw)

MVD-tool

Information

A simple C++ parser and tool for the MVD3 and Sonata neuroscience file formats

provide a tool to convert MVD2 to MVD3
provide a tool to export MVD to CSV
provide a simple header base parser for MVD2
provide a parser based on the HighFive library for MVD3 and Sonata

It also provides a high level Python API for parsing MVD3 and Sonata files.

Compilation

Prerequisites

CMake >= 3.0
GCC >= 4.9
BOOST >= 1.41
HighFive
libSONATA

Compile and Install the C++ parser

mkdir build; pushd build cmake ../ -DCMAKE_INSTALL_PREFIX= make make install

Compile and Install the Python API

Examples with the Python API

Reading Sonata files

import mvdtool node = mvdtool.open("tests/nodes.h5")

retrieve data for the full range

node.morphologies()

retrieve data for a certain range

node.morphologies([0, 1, 3])

Reading MVD3 files

import mvdtool mvd = mvdtool.open("tests/circuit.mvd3") mvd.morphologies()

Certain attributes in MVD files require the information from the mecombo file. In this case, it's strictly necessary that the mecombo file contains all combos from the MVD file.

mvd_tsv = mvdtool.open("tests/circuit_tsv.mvd3") mvd_tsv.open_combo_tsv("tests/mecombo_emodel.tsv") mvd_tsv.emodels()

Funding & Acknowledgment

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.

License

LGPLv2.1+