.. currentmodule:: brian

.. index::
   pair: example usage; NeuronGroup
   pair: example usage; run
   pair: example usage; raster_plot
   pair: example usage; Connection
   pair: example usage; PoissonGroup
   pair: example usage; SpikeMonitor

.. _example-misc_topographic_map2:

Example: topographic_map2 (misc)
================================

Topographic map - an example of complicated connections.
Two layers of neurons.
The first layer is connected randomly to the second one in a
topographical way.
The second layer has random lateral connections.
Each neuron has a position x[i].

::

    from brian import *
    
    N = 100
    tau = 10 * ms
    tau_e = 2 * ms # AMPA synapse
    eqs = '''
    dv/dt=(I-v)/tau : volt
    dI/dt=-I/tau_e : volt
    '''
    
    rates = zeros(N) * Hz
    rates[N / 2 - 10:N / 2 + 10] = ones(20) * 30 * Hz
    layer1 = PoissonGroup(N, rates=rates)
    layer1.x = linspace(0., 1., len(layer1)) # abstract position between 0 and 1
    layer2 = NeuronGroup(N, model=eqs, threshold=10 * mV, reset=0 * mV)
    layer2.x = linspace(0., 1., len(layer2))
    
    # Generic connectivity function
    topomap = lambda i, j, x, y, sigma: exp(-abs(x[i] - y[j]) / sigma)
    
    feedforward = Connection(layer1, layer2, sparseness=.5,
                               weight=lambda i, j:topomap(i, j, layer1.x, layer2.x, .3) * 3 * mV)
    
    recurrent = Connection(layer2, layer2, sparseness=.5,
                             weight=lambda i, j:topomap(i, j, layer1.x, layer2.x, .2) * .5 * mV)
    
    spikes = SpikeMonitor(layer2)
    
    run(1 * second)
    subplot(211)
    raster_plot(spikes)
    subplot(223)
    imshow(feedforward.W.todense(), interpolation='nearest', origin='lower')
    title('Feedforward connection strengths')
    subplot(224)
    imshow(recurrent.W.todense(), interpolation='nearest', origin='lower')
    title('Recurrent connection strengths')
    show()