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====
pybv
====
``pybv`` is a lightweight I/O utility for the BrainVision data format.
The BrainVision data format is a recommended data format for use in the
`Brain Imaging Data Structure <https://bids.neuroimaging.io>`_.
The documentation can be found under the following links:
- for the `stable release <https://pybv.rtfd.io/en/stable/>`_
- for the `latest (development) version <https://pybv.rtfd.io/en/latest/>`_
About the BrainVision data format
=================================
BrainVision is the name of a file format commonly used for storing electrophysiology data.
Originally, it was put forward by the company `Brain Products <https://www.brainproducts.com>`_,
however the simplicity of the format has allowed for a diversity of tools reading from and
writing to the format.
The format consists of three separate files:
1. A text header file (``.vhdr``) containing meta data
2. A text marker file (``.vmrk``) containing information about events in the
data
3. A binary data file (``.eeg``) containing the voltage values of the EEG
Both text files are based on the
`Microsoft Windows INI format <https://en.wikipedia.org/wiki/INI_file>`_
consisting of:
- sections marked as ``[square brackets]``
- comments marked as ``; comment``
- key-value pairs marked as ``key=value``
The binary ``.eeg`` data file is written in little-endian format without a Byte Order
Mark (BOM), in accordance with the specification by Brain Products.
This ensures that the data file is uniformly written irrespective of the
native system architecture.
A documentation for the BrainVision file format is provided by Brain Products.
You can `view the specification <https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/>`_
as hosted by Brain Products.
Installation
============
``pybv`` runs on Python version 3.7 or higher.
``pybv``'s only dependency is ``numpy``.
However, we currently recommend that you install MNE-Python for reading BrainVision data.
See their `installation instructions <https://mne.tools/stable/install/index.html>`_.
After you have a working installation of MNE-Python (or only ``numpy`` if you
do not want to read data and only write it), you can install ``pybv`` through
the following:
- ``pip install --upgrade pybv``
or if you use `conda <https://docs.conda.io/en/latest/miniconda.html>`_:
- ``conda install --channel conda-forge pybv``
Contributing
============
The development of ``pybv`` is taking place on
`GitHub <https://github.com/bids-standard/pybv>`_.
For more information, please see
`CONTRIBUTING.md <https://github.com/bids-standard/pybv/blob/main/.github/CONTRIBUTING.md>`_
Usage
=====
Writing BrainVision files
-------------------------
The primary functionality provided by ``pybv`` is the ``write_brainvision``
function. This writes a numpy array of data and provided metadata into a
collection of BrainVision files on disk.
.. code-block:: python
from pybv import write_brainvision
# for further parameters see our API documentation
write_brainvision(data=data, sfreq=sfreq, ch_names=ch_names,
fname_base=fname, folder_out=tmpdir,
events=events)
Reading BrainVision files
-------------------------
Currently, ``pybv`` recommends using `MNE-Python <https://mne.tools>`_
for reading BrainVision files.
Here is an example of the MNE-Python code required to read BrainVision data:
.. code-block:: python
import mne
# Import the BrainVision data into an MNE Raw object
raw = mne.io.read_raw_brainvision('tmp/test.vhdr', preload=True)
# Reconstruct the original events from our Raw object
events, event_ids = mne.events_from_annotations(raw)
Alternatives
============
The BrainVision data format is very popular and accordingly there are many
software packages to read this format, or write to it.
The following table is intended as a quick overview of packages similar to
`pybv <https://github.com/bids-standard/pybv>`_.
Please let us know if you know of additional packages that should be listed here.
+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| Name of software | Language | Notes |
+=============================================================================+======================+=============================================================================================================================================+
| `BioSig Project <http://biosig.sourceforge.net/index.html>`_ | miscellaneous | Reading and writing capabilities depend on bindings used, see their `overview <https://pub.ist.ac.at/~schloegl/biosig/TESTED>`_ |
+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| `Brainstorm <https://neuroimage.usc.edu/brainstorm/>`_ | MATLAB | Read and write, search for ``brainamp`` in their `io functions <https://github.com/brainstorm-tools/brainstorm3/tree/master/toolbox/io>`_ |
+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| `BrainVision Analyzer <https://www.brainproducts.com/downloads.php?kid=9>`_ | n/a, GUI for Windows | Read and write, by Brain Products, requires commercial license |
+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| `brainvisionloader.jl <https://github.com/agricolab/brainvisionloader.jl>`_ | Julia | Read |
+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| `EEGLAB <https://sccn.ucsd.edu/eeglab/index.php>`_ | MATLAB / Octave | Read and write via `BVA-IO <https://github.com/arnodelorme/bva-io>`_ |
+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| `FieldTrip <https://www.fieldtriptoolbox.org>`_ | MATLAB | Read and write, search for ``brainvision`` in their `fileio functions <https://github.com/fieldtrip/fieldtrip/tree/master/fileio/private>`_ |
+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| `MNE-Python <https://mne.tools>`_ | Python | Read (writing via ``pybv``) |
+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
Acknowledgements
================
This package was originally adapted from the
`Philistine package <https://gitlab.com/palday/philistine>`_ by
`palday <https://phillipalday.com/>`_.
It copies much of the BrainVision exporting code, but removes the dependence on MNE.
Several features have been added, such as support for individual units for each channel.
Raw data
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A text header file (``.vhdr``) containing meta data\n2. A text marker file (``.vmrk``) containing information about events in the\n data\n3. 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This writes a numpy array of data and provided metadata into a\ncollection of BrainVision files on disk.\n\n.. code-block:: python\n\n from pybv import write_brainvision\n\n # for further parameters see our API documentation\n write_brainvision(data=data, sfreq=sfreq, ch_names=ch_names,\n fname_base=fname, folder_out=tmpdir,\n events=events)\n\nReading BrainVision files\n-------------------------\n\nCurrently, ``pybv`` recommends using `MNE-Python <https://mne.tools>`_\nfor reading BrainVision files.\n\nHere is an example of the MNE-Python code required to read BrainVision data:\n\n.. code-block:: python\n\n import mne\n\n # Import the BrainVision data into an MNE Raw object\n raw = mne.io.read_raw_brainvision('tmp/test.vhdr', preload=True)\n\n # Reconstruct the original events from our Raw object\n events, event_ids = mne.events_from_annotations(raw)\n\nAlternatives\n============\n\nThe BrainVision data format is very popular and accordingly there are many\nsoftware packages to read this format, or write to it.\nThe following table is intended as a quick overview of packages similar to\n`pybv <https://github.com/bids-standard/pybv>`_.\nPlease let us know if you know of additional packages that should be listed here.\n\n+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+\n| Name of software | Language | Notes |\n+=============================================================================+======================+=============================================================================================================================================+\n| `BioSig Project <http://biosig.sourceforge.net/index.html>`_ | miscellaneous | Reading and writing capabilities depend on bindings used, see their `overview <https://pub.ist.ac.at/~schloegl/biosig/TESTED>`_ |\n+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+\n| `Brainstorm <https://neuroimage.usc.edu/brainstorm/>`_ | MATLAB | Read and write, search for ``brainamp`` in their `io functions <https://github.com/brainstorm-tools/brainstorm3/tree/master/toolbox/io>`_ |\n+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+\n| `BrainVision Analyzer <https://www.brainproducts.com/downloads.php?kid=9>`_ | n/a, GUI for Windows | Read and write, by Brain Products, requires commercial license |\n+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+\n| `brainvisionloader.jl <https://github.com/agricolab/brainvisionloader.jl>`_ | Julia | Read |\n+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+\n| `EEGLAB <https://sccn.ucsd.edu/eeglab/index.php>`_ | MATLAB / Octave | Read and write via `BVA-IO <https://github.com/arnodelorme/bva-io>`_ |\n+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+\n| `FieldTrip <https://www.fieldtriptoolbox.org>`_ | MATLAB | Read and write, search for ``brainvision`` in their `fileio functions <https://github.com/fieldtrip/fieldtrip/tree/master/fileio/private>`_ |\n+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+\n| `MNE-Python <https://mne.tools>`_ | Python | Read (writing via ``pybv``) |\n+-----------------------------------------------------------------------------+----------------------+---------------------------------------------------------------------------------------------------------------------------------------------+\n\nAcknowledgements\n================\n\nThis package was originally adapted from the\n`Philistine package <https://gitlab.com/palday/philistine>`_ by\n`palday <https://phillipalday.com/>`_.\nIt copies much of the BrainVision exporting code, but removes the dependence on MNE.\nSeveral features have been added, such as support for individual units for each channel.\n",
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