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<!DOCTYPE html>
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<title>mepTracker — meptracker 1.0.1 documentation</title>
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<li><a class="reference internal" href="#">mepTracker</a><ul>
<li><a class="reference internal" href="#install">Install</a></li>
<li><a class="reference internal" href="#usage">Usage</a></li>
<li><a class="reference internal" href="#license">License</a></li>
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<div class="section" id="meptracker">
<h1>mepTracker<a class="headerlink" href="#meptracker" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
<li><strong>Documentation:</strong> <a class="reference external" href="https://yelrew.github.io/m_e_p_t_r_a_c_k_e_r">https://yelrew.github.io/m_e_p_t_r_a_c_k_e_r</a></li>
<li><strong>Source:</strong> <a class="reference external" href="https://github.com/yelrew/meptracker">https://github.com/yelrew/meptracker</a></li>
<li><strong>Bug reports:</strong> <a class="reference external" href="https://github.com/yelrew/meptracker/issues">https://github.com/yelrew/meptracker/issues</a></li>
</ul>
<p>mepTracker is a package for tracking and finding optimal Motor-Evoked Potential (MEPs).
By starting with an initial guess, a path to the region of maximum MEP is determined by
reading the coil responses along an optimized path in a 2D or 3D space.</p>
<p>Currently, an interface to the Simplex vertex-edge optimization method (sve) is available.
The <cite>sve</cite> package is required.
See the <a class="reference external" href="https://github.com/yelrew/sve">SVE page</a> for more information.</p>
<div class="section" id="install">
<h2>Install<a class="headerlink" href="#install" title="Permalink to this headline">¶</a></h2>
<p>The latest version of mepTracker can be installed using pip:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ pip install --user -U git+ssh://git@github.com/yelrew/meptracker
</pre></div>
</div>
<p>or directly from the sources:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ git clone https://github.com/yelrew/meptracker.git && cd meptracker && pip install -e .
</pre></div>
</div>
</div>
<div class="section" id="usage">
<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this headline">¶</a></h2>
<p>The basic mepTracker usage is for determining a 3D path to the region of maximum MEP amplitude
by probing the electromyography at optimal stimulation positions. The scanner function (<code class="docutils literal notranslate"><span class="pre">scanfunc</span></code>)
should return the MEP value probed at the specific coordinates passed as input arguments each iteration.</p>
<p>In this <a class="reference external" href="https://github.com/yelrew/meptracker/blob/master/meptracker/tests/test_tracker_offline_3D.py">example</a>,
<code class="docutils literal notranslate"><span class="pre">scanfunc</span></code> is a <a class="reference external" href="https://github.com/yelrew/meptracker/blob/master/meptracker/tests/test_tracker_offline_scanfunc.py">5th-degree polynomial</a>
in three variables previously fitted from an offline experiment.
The optimal stimulation path is found using the <a class="reference external" href="https://github.com/yelrew/sve">sve</a> method.</p>
<div class="code python highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">import</span> <span class="nn">meptracker</span>
<span class="gp">>>> </span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="gp">>>> </span><span class="kn">from</span> <span class="nn">meptracker.tests.test_tracker_offline_scanfunc</span> <span class="k">import</span> <span class="n">scanfunc</span> <span class="c1"># External scanner function</span>
<span class="go">>>></span>
<span class="gp">>>> </span><span class="c1"># Initial guess and parameters for the sve optimizer</span>
<span class="gp">>>> </span><span class="n">x0</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mf">50.</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mf">100.</span><span class="p">]</span> <span class="c1"># initial guess (average x,y,z from fitted data, in mm)</span>
<span class="gp">>>> </span><span class="n">rMin</span> <span class="o">=</span> <span class="mf">0.0001</span>
<span class="gp">>>> </span><span class="n">rIni</span> <span class="o">=</span> <span class="mi">1</span>
<span class="gp">>>> </span><span class="n">rMax</span> <span class="o">=</span> <span class="mf">116.</span>
<span class="gp">>>> </span><span class="n">stop</span> <span class="o">=</span> <span class="mi">10</span><span class="o">*</span><span class="n">rMin</span>
<span class="go">>>></span>
<span class="gp">>>> </span><span class="c1"># Create the tracker object</span>
<span class="gp">>>> </span><span class="n">tracker</span> <span class="o">=</span> <span class="n">meptracker</span><span class="o">.</span><span class="n">Tracker</span><span class="p">(</span><span class="n">scanfunc</span><span class="p">,</span> <span class="n">dim</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
<span class="go">>>></span>
<span class="gp">>>> </span><span class="c1"># Find the optimal x (the tolerance is the maximum function mismatch)</span>
<span class="gp">>>> </span><span class="n">tracker</span><span class="o">.</span><span class="n">track</span><span class="p">(</span><span class="n">x0</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="s1">'sve'</span><span class="p">,</span> <span class="n">direction</span><span class="o">=</span><span class="s1">'POS'</span><span class="p">,</span>
<span class="gp">>>> </span> <span class="n">rIni</span><span class="o">=</span><span class="n">rIni</span><span class="p">,</span> <span class="n">rMin</span><span class="o">=</span><span class="n">rMin</span><span class="p">,</span> <span class="n">rMax</span><span class="o">=</span><span class="n">rMax</span><span class="p">,</span> <span class="n">stop</span><span class="o">=</span><span class="n">stop</span><span class="p">,</span>
<span class="gp">>>> </span> <span class="n">stop_if_dFx_lt_tol</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">tol_dfx</span> <span class="o">=</span> <span class="o">.</span><span class="mi">1</span><span class="p">)</span>
<span class="go">>>></span>
<span class="gp">>>> </span><span class="n">X</span><span class="p">,</span> <span class="n">Fx</span><span class="p">,</span> <span class="n">v</span><span class="p">,</span> <span class="n">nit</span><span class="p">,</span> <span class="n">nev</span><span class="p">,</span> <span class="n">maxit</span> <span class="o">=</span> <span class="n">tracker</span><span class="o">.</span><span class="n">results</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
<span class="go">>>></span>
<span class="gp">>>> </span><span class="n">np</span><span class="o">.</span><span class="n">set_printoptions</span><span class="p">(</span><span class="n">suppress</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">**********'</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">test_tracker_offline</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s2">"Perform a 3D MEP optimization considering the scanner function "</span><span class="p">,</span> <span class="n">end</span><span class="o">=</span><span class="s1">''</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s2">"as a fitting function obtained from offline MEP data."</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">Problem dimension: "</span><span class="p">,</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s2">"Method used: sve</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s2">"Simplex probe points: "</span><span class="p">,</span> <span class="n">v</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">Results:"</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="se">\n</span><span class="s1">Convergence in'</span><span class="p">,</span> <span class="n">nit</span><span class="p">,</span> <span class="s1">'iterations</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s1">'Summary of the iterative process</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">nit</span><span class="p">,</span> <span class="s1">'iterations'</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="n">nev</span><span class="p">,</span> <span class="s1">'function evaluations'</span><span class="p">)</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">()</span>
<span class="gp">>>> </span><span class="n">n</span> <span class="o">=</span> <span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">(</span><span class="s1">'</span><span class="si">{:^5}{:^12}{:^12}{:^12}{:^12}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s1">'it'</span><span class="p">,</span> <span class="s1">'x1'</span><span class="p">,</span> <span class="s1">'x2'</span><span class="p">,</span> <span class="s1">'x3'</span><span class="p">,</span> <span class="s1">'f(x*)'</span><span class="p">))</span>
<span class="gp">>>> </span><span class="n">fmtr</span> <span class="o">=</span> <span class="s1">'</span><span class="si">{:^5}</span><span class="s1">'</span> <span class="o">+</span> <span class="s1">'</span><span class="si">{:^12.5}</span><span class="s1">'</span><span class="o">*</span><span class="p">(</span><span class="n">n</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
<span class="gp">>>> </span><span class="p">[</span><span class="nb">print</span><span class="p">(</span><span class="n">fmtr</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">X</span><span class="p">[</span><span class="n">i</span><span class="p">,</span><span class="mi">0</span><span class="p">],</span> <span class="n">X</span><span class="p">[</span><span class="n">i</span><span class="p">,</span><span class="mi">1</span><span class="p">],</span> <span class="n">X</span><span class="p">[</span><span class="n">i</span><span class="p">,</span><span class="mi">2</span><span class="p">],</span> <span class="n">Fx</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="o">*</span><span class="nb">range</span><span class="p">(</span><span class="n">nit</span><span class="o">+</span><span class="mi">1</span><span class="p">)]]</span>
<span class="gp">>>> </span><span class="nb">print</span><span class="p">()</span>
</pre></div>
</div>
<p>If <code class="docutils literal notranslate"><span class="pre">map2D</span></code> is <code class="docutils literal notranslate"><span class="pre">True</span></code>, mepTracker will map the 3D input into a 2D polar projection.
The bi-dimensional optimizer output will be converted back to 3D by assuming a fixed radius from the original guess.
See the <a class="reference external" href="https://github.com/yelrew/meptracker/blob/master/meptracker/tests/test_tracker_offline_2D.py">test_tracker_offline_2D</a>
test case for more details.</p>
</div>
<div class="section" id="license">
<h2>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h2>
<div class="line-block">
<div class="line">Neuromat and the mepTracker Developers.</div>
<div class="line">Eduardo Werley <<a class="reference external" href="mailto:ew.angelos%40ieee.org">ew<span>.</span>angelos<span>@</span>ieee<span>.</span>org</a>></div>
<div class="line">Jorge Stolfi <<a class="reference external" href="mailto:stolfi%40ic.unicamp.br">stolfi<span>@</span>ic<span>.</span>unicamp<span>.</span>br</a>></div>
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