deploy: d4c8e2a

.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 990981d2d6449dcefbca3b44c94306e0
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/index.rst.txt

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+Virtual Brain Inference (VBI)
+##############################
+
+
+Installation
+============
+
+Requirements
+============
+
+- Python3
+- Matplotlib
+- Scipy
+- numpy
+- C++ >= 11
+
+.. code-block:: bash
+
+
+    conda env create --file environment.yml --name vbi
+    conda activate vbi
+
+    # gpu support
+    # conda install -c conda-forge cupy cudatoolkit=11.3
+    # conda install -c conda-forge pytorch-gpu
+
+    # If you need to use models implemented in C++ :
+    cd vbi/CPPModels
+    make  
+    # you need to install swig if you get an error and probably write the version of 
+    # python you are using at makefile
+    PYTHON_VERSION = 3.8 # or whatever version you have
+
+
+`swig` need to be installed for using models implemented in C++ .
+
+.. code-block:: bash
+
+    sudo apt-get install swig
+    sudo apt-get install python3-dev # or [python3.9-dev] depends the default version of python on your machine.
+    # unless you get an error which says: fatal error,  Python.h not found.
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+Modules
+########
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   neural_mass
+

_sources/neural_mass.rst.txt

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+
+Damp Oscillator
+---------------
+
+.. automodule:: vbi.models.cpp.damp_oscillator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+Jansen-Rit Neural Mass Model
+----------------------------
+
+.. math::
+    :nowrap:
+
+    \begin{align*}
+    \dot{y_0(t)} &= y_3(t) \\
+    \dot{y_1(t)} &= y_4(t) \\
+    \dot{y_2(t)} &= y_5(t) \\
+    \dot{y_3(t)} &= Aa\, \sigma(y_1(t)-y_2(t)) - 2ay_3(t) - a^2 y_0(t)\\
+    \dot{y_4(t)} &= Aa\Big[ P(t) +C_2 \, \sigma(C_1 y_0(t)) \Big] - 2a y_4(t) -a^2 y_1(t) \\
+    \dot{y_5(t)} &= Bb \Big[ C_4\, \sigma(C_3 y_0(t)) \Big] -2by_5(t) -b^2 y_2(t) \\
+    \sigma(v) &= \frac{v_{max}}{1+\exp(r(v_0-v))} \\
+    \end{align*}
+
+
+.. automodule:: vbi.models.cpp.jansen_rit 
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+