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| <!DOCTYPE html> | ||
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| <html lang="en" data-content_root="../../"> | ||
| <head> | ||
| <meta charset="utf-8" /> | ||
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| <title>examples.00_intro — vbjax v0.0.10 documentation</title> | ||
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| <li class="nav-item nav-item-this"><a href="">examples.00_intro</a></li> | ||
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| <h1>Source code for examples.00_intro</h1><div class="highlight"><pre> | ||
| <span></span><span class="sd">""" </span> | ||
| <span class="sd">**Example 1**: A simple network of coupled Montbrio model nodes.</span> | ||
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| <span class="sd">Starting with a few imports</span> | ||
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| <span class="sd">.. literalinclude:: ../../vbjax/examples/00_intro.py</span> | ||
| <span class="sd"> :start-after: example-st\u0061rt</span> | ||
| <span class="sd"> :lines: 1-2</span> | ||
| <span class="sd"> :caption:</span> | ||
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| <span class="sd">This example shows how to use the `vbjax` library to simulate a network of</span> | ||
| <span class="sd">Montbrio model nodes. The network is defined by the function `network` which</span> | ||
| <span class="sd">takes as arguments the state of the network and the parameters of the model.</span> | ||
| <span class="sd">The function returns the time derivative of the state of the network. The</span> | ||
| <span class="sd">function `make_sde` is used to create a function `loop` that simulates the</span> | ||
| <span class="sd">network for a given time interval and a given set of initial conditions.</span> | ||
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| <span class="sd">The function `vb.randn` is used to generate a set of noise samples. </span> | ||
| <span class="sd">The dimesions are `(time, state, node)`. The first noise sample is used as the</span> | ||
| <span class="sd">initial condition of the network. The remaining noise samples are used to</span> | ||
| <span class="sd">generate the noise term of the stochastic differential equation.</span> | ||
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| <span class="sd">The function `loop` takes as arguments the initial conditions of the network,</span> | ||
| <span class="sd">vector of noise samples, and the parameters of the model. The function returns</span> | ||
| <span class="sd">the state of the network at each time step.</span> | ||
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| <span class="sd">The function `vb.plot_states` is used to plot the state of the network. The</span> | ||
| <span class="sd">function takes as arguments the state of the network, the format of the plot,</span> | ||
| <span class="sd">and the name of the output file.</span> | ||
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| <span class="sd">"""</span> | ||
| <span class="c1"># example-start</span> | ||
| <span class="kn">import</span> <span class="nn">vbjax</span> <span class="k">as</span> <span class="nn">vb</span> | ||
| <span class="kn">import</span> <span class="nn">jax.numpy</span> <span class="k">as</span> <span class="nn">np</span> | ||
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| <div class="viewcode-block" id="network"> | ||
| <a class="viewcode-back" href="../../tutorial.html#examples.00_intro.network">[docs]</a> | ||
| <span class="k">def</span> <span class="nf">network</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">p</span><span class="p">):</span> | ||
| <span class="n">c</span> <span class="o">=</span> <span class="mf">0.03</span><span class="o">*</span><span class="n">x</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> | ||
| <span class="k">return</span> <span class="n">vb</span><span class="o">.</span><span class="n">mpr_dfun</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">p</span><span class="p">)</span></div> | ||
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| <span class="n">_</span><span class="p">,</span> <span class="n">loop</span> <span class="o">=</span> <span class="n">vb</span><span class="o">.</span><span class="n">make_sde</span><span class="p">(</span><span class="n">dt</span><span class="o">=</span><span class="mf">0.01</span><span class="p">,</span> <span class="n">dfun</span><span class="o">=</span><span class="n">network</span><span class="p">,</span> <span class="n">gfun</span><span class="o">=</span><span class="mf">0.1</span><span class="p">)</span> | ||
| <span class="n">zs</span> <span class="o">=</span> <span class="n">vb</span><span class="o">.</span><span class="n">randn</span><span class="p">(</span><span class="mi">500</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">32</span><span class="p">)</span> | ||
| <span class="n">xs</span> <span class="o">=</span> <span class="n">loop</span><span class="p">(</span><span class="n">zs</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">zs</span><span class="p">[</span><span class="mi">1</span><span class="p">:],</span> <span class="n">vb</span><span class="o">.</span><span class="n">mpr_default_theta</span><span class="p">)</span> | ||
| <span class="n">vb</span><span class="o">.</span><span class="n">plot_states</span><span class="p">(</span><span class="n">xs</span><span class="p">,</span> <span class="s1">'rV'</span><span class="p">,</span> <span class="n">jpg</span><span class="o">=</span><span class="s1">'example1'</span><span class="p">,</span> <span class="n">show</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> | ||
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| <span class="c1"># example-end</span> | ||
| </pre></div> | ||
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| <div class="clearer"></div> | ||
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| <div class="clearer"></div> | ||
| </div> | ||
| <div class="related" role="navigation" aria-label="related navigation"> | ||
| <h3>Navigation</h3> | ||
| <ul> | ||
| <li class="right" style="margin-right: 10px"> | ||
| <a href="../../genindex.html" title="General Index" | ||
| >index</a></li> | ||
| <li class="right" > | ||
| <a href="../../py-modindex.html" title="Python Module Index" | ||
| >modules</a> |</li> | ||
| <li class="nav-item nav-item-0"><a href="../../index.html">vbjax v0.0.10 documentation</a> »</li> | ||
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| © Copyright 2023, Marmaduke Woodman. | ||
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| neural_mass | ||
| ----------- | ||
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| .. automodule:: vbjax.neural_mass | ||
| :members: | ||
| :undoc-members: | ||
| :show-inheritance: | ||
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| monitor | ||
| -------- | ||
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| .. automodule:: vbjax.monitor | ||
| :members: | ||
| :undoc-members: | ||
| :show-inheritance: | ||
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| loops | ||
| ----- | ||
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| .. automodule:: vbjax.loops | ||
| :members: | ||
| :undoc-members: | ||
| :show-inheritance: | ||
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| connectome | ||
| ---------- | ||
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| .. automodule:: vbjax.connectome | ||
| :members: | ||
| :undoc-members: | ||
| :show-inheritance: | ||
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| layers | ||
| ------ | ||
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| .. automodule:: vbjax.layers | ||
| :members: | ||
| :undoc-members: | ||
| :show-inheritance: | ||
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| sparse | ||
| ------ | ||
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| .. automodule:: vbjax.sparse | ||
| :members: | ||
| :undoc-members: | ||
| :show-inheritance: | ||
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| util | ||
| ---- | ||
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| .. automodule:: vbjax.util | ||
| :members: | ||
| :undoc-members: | ||
| :show-inheritance: | ||
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| shtlc | ||
| ----- | ||
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| .. automodule:: vbjax.shtlc | ||
| :members: | ||
| :undoc-members: | ||
| :show-inheritance: |
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| Tutorial | ||
| *************** | ||
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| This is some test text. | ||
| .. automodule:: examples.00_intro | ||
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