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.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/csa_spatial_example.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_csa_spatial_example.py>`
        to download the full example code

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.. _sphx_glr_auto_examples_csa_spatial_example.py:


Using CSA with spatial populations
----------------------------------

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----

 Run this example as a Jupyter notebook:

  .. card::
    :width: 25%
    :margin: 2
    :text-align: center
    :link: https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fnest%2Fnest-simulator-examples&urlpath=lab%2Ftree%2Fnest-simulator-examples%2Fnotebooks%2Fnotebooks%2Fcsa_spatial_example.ipynb&branch=main
    :link-alt: JupyterHub service

    .. image:: https://nest-simulator.org/TryItOnEBRAINS.png


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   :padding: 0 0 2 0

   .. grid-item::
     :class: sd-text-muted
     :margin: 0 0 3 0
     :padding: 0 0 3 0
     :columns: 4

     See :ref:`our guide <run_jupyter>` for more information and troubleshooting.

----


This example shows a brute-force way of specifying connections between
NEST populations with spatial data using Connection Set Algebra instead of
the built-in connection routines.

Using the CSA requires NEST to be compiled with support for
libneurosim. For details, see [1]_.

See Also
~~~~~~~~

:doc:`csa_example`

References
~~~~~~~~~~

.. [1] Djurfeldt M, Davison AP and Eppler JM (2014). Efficient generation of
       connectivity in neuronal networks from simulator-independent
       descriptions. Front. Neuroinform.
       https://doi.org/10.3389/fninf.2014.00043

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First, we import all necessary modules.

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.. code-block:: Python


    import matplotlib.pyplot as plt
    import nest


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Next, we check for the availability of the CSA Python module. If it does
not import, we exit with an error message.

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.. code-block:: Python


    try:
        import csa

        haveCSA = True
    except ImportError:
        print(
            "This example requires CSA to be installed in order to run.\n"
            + "Please make sure you compiled NEST using\n"
            + "  -Dwith-libneurosim=[OFF|ON|</path/to/libneurosim>]\n"
            + "and CSA and libneurosim are available."
        )
        import sys

        sys.exit(1)


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We define a factory that returns a CSA-style geometry function for
the given layer. The function returned will return for each CSA-index
the position in space of the given neuron as a 2- or 3-element list.

This function stores a copy of the neuron positions internally, entailing
memory overhead.

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.. code-block:: Python



    def geometryFunction(population):
        positions = nest.GetPosition(population)

        def geometry_function(idx):
            return positions[idx]

        return geometry_function



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We create two spatial populations that have 20x20 neurons of type
``iaf_psc_alpha``.

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.. code-block:: Python


    pop1 = nest.Create("iaf_psc_alpha", positions=nest.spatial.grid([20, 20]))
    pop2 = nest.Create("iaf_psc_alpha", positions=nest.spatial.grid([20, 20]))


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For each population, we create a CSA-style geometry function and a CSA metric
based on them.

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.. code-block:: Python


    g1 = geometryFunction(pop1)
    g2 = geometryFunction(pop2)
    d = csa.euclidMetric2d(g1, g2)


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The connection set `cg` describes a Gaussian connectivity profile with
``sigma = 0.2`` and cutoff at 0.5, and two values (10000.0 and 1.0) used as
``weight`` and ``delay``, respectively.

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.. code-block:: Python


    cg = csa.cset(csa.random * (csa.gaussian(0.2, 0.5) * d), 10000.0, 1.0)


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We can now connect the populations using the ``Connect`` function
with the ``conngen`` rule. It takes the IDs of pre- and postsynaptic
neurons (``pop1`` and ``pop2``), the connection set (``cg``) and a
dictionary that map the parameters weight and delay to positions in
the value set associated with the connection set (``params_map``).

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.. code-block:: Python


    params_map = {"weight": 0, "delay": 1}
    connspec = {"rule": "conngen", "cg": cg, "params_map": params_map}
    nest.Connect(pop1, pop2, connspec)


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Finally, we use the ``PlotTargets`` function to show all targets in `pop2`
starting at the center neuron of `pop1`.

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.. code-block:: Python


    cntr = nest.FindCenterElement(pop1)
    nest.PlotTargets(cntr, pop2)
    plt.show()


.. _sphx_glr_download_auto_examples_csa_spatial_example.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: csa_spatial_example.ipynb <csa_spatial_example.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: csa_spatial_example.py <csa_spatial_example.py>`


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 .. rst-class:: sphx-glr-signature

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