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API and documentation
=====================


C++ models
-------------------------

**Parameter Flexibility:** Many parameters in C++ models can be specified as either scalar values (applied uniformly across all brain regions) or vectors/arrays (allowing region-specific values). When a parameter description indicates "scalar|vector" type, it means the parameter can be heterogeneous across regions. For example, excitability parameters can vary between brain regions to model regional differences in neural properties.

vbi.models.cpp.base
~~~~~~~~~~~~~~~~~~~~~~~~~ 
    .. automodule:: vbi.models.cpp.base 
        :members: :undoc-members:
        :undoc-members:

vbi.models.cpp.jansen_rit
~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cpp.jansen_rit
        :members:
        :undoc-members:

vbi.models.cpp.km
~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cpp.km
        :members:
        :undoc-members:

vbi.models.cpp.mpr 
~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cpp.mpr
        :members:
        :undoc-members:

vbi.models.cpp.vep 
~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cpp.vep
        :members:
        :undoc-members:

vbi.models.cpp.wc 
~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cpp.wc
        :members:
        :undoc-members:

vbi.models.cpp.damp_oscillator
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cpp.damp_oscillator
        :members:
        :undoc-members:


Cupy models 
-----------

vbi.models.cupy.base
~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.base
        :members:
        :undoc-members:

vbi.models.cupy.mpr 
~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.mpr
        :members:
        :undoc-members:

vbi.models.cupy.ghb
~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.ghb
        :members:
        :undoc-members:

vbi.models.cupy.jansen_rit
~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.jansen_rit
        :members:
        :undoc-members:

vbi.models.cupy.utils 
~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.utils
        :members:
        :undoc-members:

vbi.models.cupy.bold
~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.bold
        :members:
        :undoc-members:

vbi.models.cupy.km
~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.km
        :members:
        :undoc-members:

vbi.models.cupy.mpr_modified_bold
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.mpr_modified_bold
        :members:
        :undoc-members:

.. vbi.models.cupy.mpr_multi_gpu
.. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
..     .. automodule:: vbi.models.cupy.mpr_multi_gpu
..         :members:
..         :undoc-members:

vbi.models.cupy.wilson_cowan
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.wilson_cowan
        :members:
        :undoc-members:

vbi.models.cupy.ww
~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.cupy.ww
        :members:
        :undoc-members:


Numba models 
------------

vbi.models.numba.base
~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.numba.base
        :members:
        :undoc-members:

vbi.models.numba.damp_oscillator
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.numba.damp_oscillator
        :members:
        :undoc-members:

vbi.models.numba.ghb
~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.numba.ghb
        :members:
        :undoc-members:

vbi.models.numba.jansen_rit
~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.numba.jansen_rit
        :members:
        :undoc-members:

vbi.models.numba.mpr
~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.numba.mpr
        :members:
        :undoc-members:

vbi.models.numba.vep
~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.numba.vep
        :members:
        :undoc-members:

vbi.models.numba.wilson_cowan
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.numba.wilson_cowan
        :members:
        :undoc-members:

vbi.models.numba.sl
~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.numba.sl
        :members:
        :undoc-members:

vbi.models.numba.ww
~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.numba.ww
        :members:
        :undoc-members:


PyTorch models 
--------------

vbi.models.pytorch.rww_sde_kong
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.pytorch.rww_sde_kong
        :members:
        :undoc-members:


TVB-K models 
------------

vbi.models.tvbk.tvbk_wrapper
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.tvbk.tvbk_wrapper
        :members:
        :undoc-members:

vbi.models.tvbk.utils
~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.models.tvbk.utils
        :members:
        :undoc-members:


Core VBI modules
----------------

vbi.cde
~~~~~~~
    .. automodule:: vbi.cde
        :members:
        :undoc-members:

vbi.inference
~~~~~~~~~~~~~
    .. automodule:: vbi.inference
        :members:
        :undoc-members:

vbi.utils
~~~~~~~~~
    .. automodule:: vbi.utils
        :members:
        :undoc-members:

vbi.optional_deps
~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.optional_deps
        :members:
        :undoc-members:


Feature extraction
------------------

vbi.feature_extraction.calc_features
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.feature_extraction.calc_features
        :members:
        :undoc-members:

vbi.feature_extraction.features
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.feature_extraction.features
        :members:
        :undoc-members:

vbi.feature_extraction.features_settings
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.feature_extraction.features_settings
        :members:
        :undoc-members:

vbi.feature_extraction.features_utils
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.feature_extraction.features_utils
        :members:
        :undoc-members:

vbi.feature_extraction.utility
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.feature_extraction.utility
        :members:
        :undoc-members:


Dataset
-------------------------

vbi.dataset
~~~~~~~~~~~~~~~~~~~~~~~~~
    .. automodule:: vbi.dataset
        :members:
        :undoc-members: