{
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    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
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      "outputs": [],
      "source": [
        "%matplotlib inline"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n# A spatial network in 3D\n\nHans Ekkehard Plesser, UMB\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "import nest\nimport matplotlib.pyplot as plt\nfrom mpl_toolkits.mplot3d import Axes3D\n\nnest.ResetKernel()\n\npos = nest.spatial.free(nest.random.uniform(-0.5, 0.5), extent=[1.5, 1.5, 1.5])\n\nl1 = nest.Create('iaf_psc_alpha', 1000, positions=pos)\n\n# visualize\n\n# extract position information, transpose to list of x, y and z positions\nxpos, ypos, zpos = zip(*nest.GetPosition(l1))\nfig = plt.figure()\nax = fig.add_subplot(111, projection='3d')\nax.scatter(xpos, ypos, zpos, s=15, facecolor='b')\n\n# full connections in box volume [-0.2,0.2]**3\nnest.Connect(l1, l1,\n             {'rule': 'pairwise_bernoulli',\n              'p': 1.,\n              'allow_autapses': False,\n              'mask': {'box': {'lower_left': [-0.2, -0.2, -0.2],\n                               'upper_right': [0.2, 0.2, 0.2]}}})\n\n# show connections from center element\n# sender shown in red, targets in green\nctr = nest.FindCenterElement(l1)\nxtgt, ytgt, ztgt = zip(*nest.GetTargetPositions(ctr, l1)[0])\nxctr, yctr, zctr = nest.GetPosition(ctr)\nax.scatter([xctr], [yctr], [zctr], s=40, facecolor='r')\nax.scatter(xtgt, ytgt, ztgt, s=40, facecolor='g', edgecolor='g')\n\ntgts = nest.GetTargetNodes(ctr, l1)[0]\ndistances = nest.Distance(ctr, l1)\ntgt_distances = [d for i, d in enumerate(distances) if i + 1 in tgts]\n\nplt.figure()\nplt.hist(tgt_distances, 25)\nplt.show()"
      ]
    }
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      "file_extension": ".py",
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