The science behind The Virtual Brain
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
contrib
tvb
.coveragerc
.gitattributes Add .gitattributes file Aug 22, 2013
.gitignore
.travis.yml
AUTHORS
LICENSE
MANIFEST.in
README.rst TVB-1073 Add example of running coverage and excluding tests Dec 14, 2017
bench.py TVB-1731 Change print and (x)range calls for compatibility with Python 3 Aug 1, 2017
setup.py TVB-1073 Complete transition from unittest to pytest. Dec 13, 2017
tvb-package-diagram.jpg Added readme for scientific library. Added contributors setup tutorial. Mar 14, 2013

README.rst

THE VIRTUAL BRAIN SCIENTIFIC LIBRARY

The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains.

"TVB Scientific Library" is the most important scientific contribution of TVB Project, but only a part of our code. In order to use this TVB Python Library (modify/run/test), you are advised to follow the steps described here: http://docs.thevirtualbrain.com/manuals/ContributorsManual/ContributorsManual.html#contributors-manual

The interaction with TVB source code is recommended for advanced users only, for which the concepts proposed by TVB are known and understood, and which also have some programming knowledge.

"TVB Scientific Library" comes in two major forms for code-contributors: as a light-weight Python library, or plugged into TVB framework (including Web interface and Persistence of data layers). Depending on your needs and resources, you could use any of the two available options for contributing and testing new code.

"TVB Scientific Library" is a light-weight, stand-alone Python library that contains all the needed packages in order to run simulations and analysis on data without the need for the entire TVB Framework. This implies that no storage will be provided so data from each session will be lost on close. You need to either persist it yourself in some manner or use the full TVBFramework where HDF5 / database storage is provided as default.

For more details, check: http://www.thevirtualbrain.org/

"TVB Scientific Library" contains the following packages: basic, datatypes, simulator and analyzers. The dependencies between these packages can be seen in tvb-package-diagram.jpg . Following is a short description of each of these packages:

  • tvb.basic

This package is the base of TVB and holds sub-packages that are used by most of the other packages like logging, global settings and the TVB traits package. You should rarely (if at all) need to change code in this package, and should know exactly what you are doing before attempting to change anything from here.

  • tvb.datatypes

The simulator and analyzers packages (as well as uploaders and visualizers in TVB Framework) will need to have a common "language" in order to work with the same data. In TVB architecture, that "common language" is represented by Data Types. TVB Data Types declarations are located in this package.

Most of the datatypes here have a diamond like inheritance structure of the following form:

             DataTypeData
                  |
                 / \\
DataTypeFramework   DataTypeScientific
                 \ /
                  |
               DataType

The DataTypeData holds the actual structure of the datatype. DataTypeScientific holds any methods required from a scientific point of view. DataTypeFramework should just be ignored from a library user point of view as it holds framework related methods and will be removed altogether in the near future. DataType just brings all the above together and is the class you should actually use in your code.

  • tvb.simulator

The Simulation Component is the most important component in The Virtual Brain solution, as it is the component responsible for all the scientific computation related to brain models and data.

You can find various demos of using the simulator under tvb/simulator/demos as well as some nice tutorials under tvb/simulator/doc/tutorials/ .

  • tvb.analyzers

Holds modules that can run various analysis of data resulted from the simulator. There are a few demos which use the PCA analyzer like tvb/simulator/demos/pca_analyse_view_region and tvb/simulator/demos/pca_analyse_view_surface . TVB is not strong in doing data analysis, we barely have a minimum set of analyzers for immediate needs.

NOTE:

To contribute to this repo, you are advised to first fork it under GitHub (through the web ui), and next clone that fork on your machine, and use it as you use any other git repository.

Testing

For testing the package, the Pytest framework is used. Pytest can be installed using pip.

Pytest will run all files in the current directory and its subdirectories of the form test_*.py or *_test.py. More generally, it follows standard test discovery rules

The command for running our tests has two forms. Recommendation when working with a git clone of tvb-library:

cd [folder_where_tvb_library_is]
pytest tvb/test [--junitxml=path]

The second alternative form of running TVB tests, when installing TVB from Pypi, is:

pip install -U tvb-library
pytest --pyargs tvb.tests.library

Coverage

A coverage report can be generated with:

pip install pytest-cov
cd [folder_where_tvb_library_is]
py.test --cov-config .coveragerc --cov=tvb tvb/tests/ --cov-branch --cov-report xml:[file_where_xml_will_be_generated]

Further Resources