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Module feast
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<h1 class="epydoc">Source Code for <a href="feast-module.html">Module feast</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">'''</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"> The FEAST module provides an interface between the C-library</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring"> for feature selection to Python. </tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring"> References: </tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"> 1) G. Brown, A. Pocock, M.-J. Zhao, and M. Lujan, "Conditional</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"> likelihood maximization: A unifying framework for information</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"> theoretic feature selection," Journal of Machine Learning </tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"> Research, vol. 13, pp. 27-66, 2012.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">'''</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-name">__author__</tt> <tt class="py-op">=</tt> <tt class="py-string">"Calvin Morrison"</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-name">__copyright__</tt> <tt class="py-op">=</tt> <tt class="py-string">"Copyright 2013, EESI Laboratory"</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable feast.__credits__=feast-module.html#__credits__"><a title="feast.__credits__" class="py-name" href="#" onclick="return doclink('link-0', '__credits__', 'link-0');">__credits__</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"Calvin Morrison"</tt><tt class="py-op">,</tt> <tt class="py-string">"Gregory Ditzler"</tt><tt class="py-op">]</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-name">__license__</tt> <tt class="py-op">=</tt> <tt class="py-string">"GPL"</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-name">__version__</tt> <tt class="py-op">=</tt> <tt class="py-string">"0.2.0"</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable feast.__maintainer__=feast-module.html#__maintainer__"><a title="feast.__maintainer__" class="py-name" href="#" onclick="return doclink('link-1', '__maintainer__', 'link-1');">__maintainer__</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Calvin Morrison"</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable feast.__email__=feast-module.html#__email__"><a title="feast.__email__" class="py-name" href="#" onclick="return doclink('link-2', '__email__', 'link-2');">__email__</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"mutantturkey@gmail.com"</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable feast.__status__=feast-module.html#__status__"><a title="feast.__status__" class="py-name" href="#" onclick="return doclink('link-3', '__status__', 'link-3');">__status__</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Release"</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">as</tt> <tt class="py-name">np</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">ctypes</tt> <tt class="py-keyword">as</tt> <tt class="py-name">c</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable feast.libFSToolbox=feast-module.html#libFSToolbox"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-4', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">CDLL</tt><tt class="py-op">(</tt><tt class="py-string">"libFSToolbox.so"</tt><tt class="py-op">)</tt><tt class="py-op">;</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">(</tt><tt class="py-string">"Error: could not load libFSToolbox.so"</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> </tt>
<a name="BetaGamma"></a><div id="BetaGamma-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <a class="py-toggle" href="#" id="BetaGamma-toggle" onclick="return toggle('BetaGamma');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#BetaGamma">BetaGamma</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">,</tt> <tt class="py-param">beta</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-param">gamma</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BetaGamma-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BetaGamma-expanded"><a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> This algorithm implements conditional mutual information </tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> feature select, such that beta and gamma control the </tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> weight attached to the redundant mutual and conditional</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> mutual information, respectively. </tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> @param data: data in a Numpy array such that len(data) = </tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> (REQUIRED)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy list with </tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> (REQUIRED)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select. (REQUIRED)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> @param beta: penalty attacted to I(X_j;X_k) </tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> @type beta: float between 0 and 1.0 </tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> @param gamma: positive weight attached to the conditional</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> redundancy term I(X_k;X_j|Y)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> @type gamma: float between 0 and 1.0 </tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> @return: features in the order they were selected. </tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name" targets="Function feast.check_data()=feast-module.html#check_data"><a title="feast.check_data" class="py-name" href="#" onclick="return doclink('link-5', 'check_data', 'link-5');">check_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-comment"># python values</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">n_observations</tt><tt class="py-op">,</tt> <tt class="py-name">n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-comment"># cast as C types</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_observations</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">c_n_select</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_features</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">c_beta</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">(</tt><tt class="py-name">beta</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">c_gamma</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">(</tt><tt class="py-name">gamma</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-6', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Function feast.BetaGamma()=feast-module.html#BetaGamma"><a title="feast.BetaGamma" class="py-name" href="#" onclick="return doclink('link-7', 'BetaGamma', 'link-7');">BetaGamma</a></tt><tt class="py-op">.</tt><tt class="py-name">restype</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt> <tt class="py-op">*</tt> <tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">features</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-8', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="feast.BetaGamma" class="py-name" href="#" onclick="return doclink('link-9', 'BetaGamma', 'link-7');">BetaGamma</a></tt><tt class="py-op">(</tt><tt class="py-name">c_n_select</tt><tt class="py-op">,</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt><tt class="py-op">,</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt><tt class="py-op">,</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">labels</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">c_beta</tt><tt class="py-op">,</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">c_gamma</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-comment"># turn our output into a list</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">features</tt><tt class="py-op">.</tt><tt class="py-name">contents</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-comment"># recall that feast was implemented with Matlab in mind, so the </tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-comment"># authors assumed the indexing started a one; however, in Python </tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-comment"># the indexing starts at zero. </tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">i</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">selected_features</tt> </tt>
</div><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="CIFE"></a><div id="CIFE-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="CIFE-toggle" onclick="return toggle('CIFE');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#CIFE">CIFE</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CIFE-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CIFE-expanded"><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> This function implements the Condred feature selection algorithm.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> beta = 1; gamma = 1;</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> @param data: A Numpy array such that len(data) = </tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy list with </tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select.</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> @return selected_features: features in the order they were selected. </tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-10" class="py-name"><a title="feast.BetaGamma" class="py-name" href="#" onclick="return doclink('link-10', 'BetaGamma', 'link-7');">BetaGamma</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">,</tt> <tt class="py-name">n_select</tt><tt class="py-op">,</tt> <tt class="py-name">beta</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">,</tt> <tt class="py-name">gamma</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> </tt>
<a name="CMIM"></a><div id="CMIM-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="CMIM-toggle" onclick="return toggle('CMIM');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#CMIM">CMIM</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CMIM-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CMIM-expanded"><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> This function implements the conditional mutual information</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> maximization feature selection algorithm. Note that this </tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> implementation does not allow for the weighting of the </tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> redundancy terms that BetaGamma will allow you to do.</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> @param data: A Numpy array such that len(data) = </tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy array with </tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select.</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> @return: features in the order that they were selected. </tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="feast.check_data" class="py-name" href="#" onclick="return doclink('link-11', 'check_data', 'link-5');">check_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-comment"># python values</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">n_observations</tt><tt class="py-op">,</tt> <tt class="py-name">n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-comment"># cast as C types</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_observations</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">c_n_select</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_features</tt><tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt id="link-12" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-12', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Function feast.CMIM()=feast-module.html#CMIM"><a title="feast.CMIM" class="py-name" href="#" onclick="return doclink('link-13', 'CMIM', 'link-13');">CMIM</a></tt><tt class="py-op">.</tt><tt class="py-name">restype</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt> <tt class="py-op">*</tt> <tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">features</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-14', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="feast.CMIM" class="py-name" href="#" onclick="return doclink('link-15', 'CMIM', 'link-13');">CMIM</a></tt><tt class="py-op">(</tt><tt class="py-name">c_n_select</tt><tt class="py-op">,</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt><tt class="py-op">,</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt><tt class="py-op">,</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">labels</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-comment"># turn our output into a list</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">features</tt><tt class="py-op">.</tt><tt class="py-name">contents</tt><tt class="py-op">:</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-comment"># recall that feast was implemented with Matlab in mind, so the </tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-comment"># authors assumed the indexing started a one; however, in Python </tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-comment"># the indexing starts at zero. </tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">i</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">selected_features</tt> </tt>
</div><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="CondMI"></a><div id="CondMI-def"><a name="L167"></a><tt class="py-lineno">167</tt> <a class="py-toggle" href="#" id="CondMI-toggle" onclick="return toggle('CondMI');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#CondMI">CondMI</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CondMI-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CondMI-expanded"><a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> This function implements the conditional mutual information</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> maximization feature selection algorithm. </tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"> @param data: data in a Numpy array such that len(data) = n_observations,</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> and len(data.transpose()) = n_features</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: represented in a numpy list with </tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select.</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring"> @return: features in the order they were selected. </tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"> @rtype list</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="feast.check_data" class="py-name" href="#" onclick="return doclink('link-16', 'check_data', 'link-5');">check_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-comment"># python values</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">n_observations</tt><tt class="py-op">,</tt> <tt class="py-name">n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-comment"># cast as C types</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_observations</tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">c_n_select</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_features</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-17', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Function feast.CondMI()=feast-module.html#CondMI"><a title="feast.CondMI" class="py-name" href="#" onclick="return doclink('link-18', 'CondMI', 'link-18');">CondMI</a></tt><tt class="py-op">.</tt><tt class="py-name">restype</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt> <tt class="py-op">*</tt> <tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">features</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-19', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="feast.CondMI" class="py-name" href="#" onclick="return doclink('link-20', 'CondMI', 'link-18');">CondMI</a></tt><tt class="py-op">(</tt><tt class="py-name">c_n_select</tt><tt class="py-op">,</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt><tt class="py-op">,</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt><tt class="py-op">,</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">labels</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-comment"># turn our output into a list</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">features</tt><tt class="py-op">.</tt><tt class="py-name">contents</tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-comment"># recall that feast was implemented with Matlab in mind, so the </tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-comment"># authors assumed the indexing started a one; however, in Python </tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-comment"># the indexing starts at zero. </tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">i</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">selected_features</tt> </tt>
</div><a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> </tt>
<a name="Condred"></a><div id="Condred-def"><a name="L216"></a><tt class="py-lineno">216</tt> <a class="py-toggle" href="#" id="Condred-toggle" onclick="return toggle('Condred');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#Condred">Condred</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Condred-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Condred-expanded"><a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-docstring"> This function implements the Condred feature selection algorithm.</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> beta = 0; gamma = 1;</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-docstring"> @param data: data in a Numpy array such that len(data) = </tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy list with </tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select.</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-docstring"> @return: the features in the order they were selected. </tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="feast.check_data" class="py-name" href="#" onclick="return doclink('link-21', 'check_data', 'link-5');">check_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-22" class="py-name"><a title="feast.BetaGamma" class="py-name" href="#" onclick="return doclink('link-22', 'BetaGamma', 'link-7');">BetaGamma</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">,</tt> <tt class="py-name">n_select</tt><tt class="py-op">,</tt> <tt class="py-name">beta</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt><tt class="py-op">,</tt> <tt class="py-name">gamma</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> </tt>
<a name="DISR"></a><div id="DISR-def"><a name="L239"></a><tt class="py-lineno">239</tt> <a class="py-toggle" href="#" id="DISR-toggle" onclick="return toggle('DISR');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#DISR">DISR</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DISR-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DISR-expanded"><a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-docstring"> This function implements the double input symmetrical relevance</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"> feature selection algorithm. </tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-docstring"> @param data: data in a Numpy array such that len(data) = </tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy list with </tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select. (REQUIRED)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-docstring"> @return: the features in the order they were selected. </tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="feast.check_data" class="py-name" href="#" onclick="return doclink('link-23', 'check_data', 'link-5');">check_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-comment"># python values</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">n_observations</tt><tt class="py-op">,</tt> <tt class="py-name">n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-comment"># cast as C types</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_observations</tt><tt class="py-op">)</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">c_n_select</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_features</tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-24', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Function feast.DISR()=feast-module.html#DISR"><a title="feast.DISR" class="py-name" href="#" onclick="return doclink('link-25', 'DISR', 'link-25');">DISR</a></tt><tt class="py-op">.</tt><tt class="py-name">restype</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt> <tt class="py-op">*</tt> <tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">features</tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-26', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="feast.DISR" class="py-name" href="#" onclick="return doclink('link-27', 'DISR', 'link-25');">DISR</a></tt><tt class="py-op">(</tt><tt class="py-name">c_n_select</tt><tt class="py-op">,</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt><tt class="py-op">,</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt><tt class="py-op">,</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">labels</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-comment"># turn our output into a list</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">features</tt><tt class="py-op">.</tt><tt class="py-name">contents</tt><tt class="py-op">:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-comment"># recall that feast was implemented with Matlab in mind, so the </tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-comment"># authors assumed the indexing started a one; however, in Python </tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-comment"># the indexing starts at zero. </tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">i</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">selected_features</tt> </tt>
</div><a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> </tt>
<a name="ICAP"></a><div id="ICAP-def"><a name="L290"></a><tt class="py-lineno">290</tt> <a class="py-toggle" href="#" id="ICAP-toggle" onclick="return toggle('ICAP');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#ICAP">ICAP</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ICAP-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ICAP-expanded"><a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-docstring"> This function implements the interaction capping feature </tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-docstring"> selection algorithm. </tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"> @param data: data in a Numpy array such that len(data) = </tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy list with </tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select. (REQUIRED)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-docstring"> @return: the features in the order they were selected. </tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="feast.check_data" class="py-name" href="#" onclick="return doclink('link-28', 'check_data', 'link-5');">check_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">)</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-comment"># python values</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">n_observations</tt><tt class="py-op">,</tt> <tt class="py-name">n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-comment"># cast as C types</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_observations</tt><tt class="py-op">)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">c_n_select</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_features</tt><tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt id="link-29" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-29', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Function feast.ICAP()=feast-module.html#ICAP"><a title="feast.ICAP" class="py-name" href="#" onclick="return doclink('link-30', 'ICAP', 'link-30');">ICAP</a></tt><tt class="py-op">.</tt><tt class="py-name">restype</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt> <tt class="py-op">*</tt> <tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">features</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-31', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="feast.ICAP" class="py-name" href="#" onclick="return doclink('link-32', 'ICAP', 'link-30');">ICAP</a></tt><tt class="py-op">(</tt><tt class="py-name">c_n_select</tt><tt class="py-op">,</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt><tt class="py-op">,</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt><tt class="py-op">,</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-name">labels</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-comment"># turn our output into a list</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">features</tt><tt class="py-op">.</tt><tt class="py-name">contents</tt><tt class="py-op">:</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-comment"># recall that feast was implemented with Matlab in mind, so the </tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-comment"># authors assumed the indexing started a one; however, in Python </tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-comment"># the indexing starts at zero. </tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">i</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">selected_features</tt> </tt>
</div><a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> </tt>
<a name="JMI"></a><div id="JMI-def"><a name="L342"></a><tt class="py-lineno">342</tt> <a class="py-toggle" href="#" id="JMI-toggle" onclick="return toggle('JMI');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#JMI">JMI</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="JMI-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="JMI-expanded"><a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt class="py-docstring"> This function implements the joint mutual information feature</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-docstring"> selection algorithm. </tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-docstring"> @param data: data in a Numpy array such that len(data) = </tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy list with </tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select. (REQUIRED)</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-docstring"> @return: the features in the order they were selected. </tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="feast.check_data" class="py-name" href="#" onclick="return doclink('link-33', 'check_data', 'link-5');">check_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">)</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-comment"># python values</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-name">n_observations</tt><tt class="py-op">,</tt> <tt class="py-name">n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-comment"># cast as C types</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_observations</tt><tt class="py-op">)</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">c_n_select</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_features</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt id="link-34" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-34', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Function feast.JMI()=feast-module.html#JMI"><a title="feast.JMI" class="py-name" href="#" onclick="return doclink('link-35', 'JMI', 'link-35');">JMI</a></tt><tt class="py-op">.</tt><tt class="py-name">restype</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt> <tt class="py-op">*</tt> <tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">features</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-36', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="feast.JMI" class="py-name" href="#" onclick="return doclink('link-37', 'JMI', 'link-35');">JMI</a></tt><tt class="py-op">(</tt><tt class="py-name">c_n_select</tt><tt class="py-op">,</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt><tt class="py-op">,</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt><tt class="py-op">,</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-name">labels</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-comment"># turn our output into a list</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">features</tt><tt class="py-op">.</tt><tt class="py-name">contents</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-comment"># recall that feast was implemented with Matlab in mind, so the </tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-comment"># authors assumed the indexing started a one; however, in Python </tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-comment"># the indexing starts at zero. </tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">i</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">selected_features</tt> </tt>
</div><a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> </tt>
<a name="MIFS"></a><div id="MIFS-def"><a name="L392"></a><tt class="py-lineno">392</tt> <a class="py-toggle" href="#" id="MIFS-toggle" onclick="return toggle('MIFS');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#MIFS">MIFS</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MIFS-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MIFS-expanded"><a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-docstring"> This function implements the MIFS algorithm.</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-docstring"> beta = 1; gamma = 0;</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"><tt class="py-docstring"> @param data: data in a Numpy array such that len(data) = </tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy list with </tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select. (REQUIRED)</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-docstring"> @return: the features in the order they were selected. </tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-38" class="py-name"><a title="feast.BetaGamma" class="py-name" href="#" onclick="return doclink('link-38', 'BetaGamma', 'link-7');">BetaGamma</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">,</tt> <tt class="py-name">n_select</tt><tt class="py-op">,</tt> <tt class="py-name">beta</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt><tt class="py-op">,</tt> <tt class="py-name">gamma</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> </tt>
<a name="MIM"></a><div id="MIM-def"><a name="L413"></a><tt class="py-lineno">413</tt> <a class="py-toggle" href="#" id="MIM-toggle" onclick="return toggle('MIM');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#MIM">MIM</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MIM-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MIM-expanded"><a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-docstring"> This function implements the MIM algorithm.</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-docstring"> beta = 0; gamma = 0;</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-docstring"> @param data: data in a Numpy array such that len(data) = </tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy list with </tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select. (REQUIRED)</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"><tt class="py-docstring"> @return: the features in the order they were selected. </tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name"><a title="feast.check_data" class="py-name" href="#" onclick="return doclink('link-39', 'check_data', 'link-5');">check_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-40" class="py-name"><a title="feast.BetaGamma" class="py-name" href="#" onclick="return doclink('link-40', 'BetaGamma', 'link-7');">BetaGamma</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">,</tt> <tt class="py-name">n_select</tt><tt class="py-op">,</tt> <tt class="py-name">beta</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt><tt class="py-op">,</tt> <tt class="py-name">gamma</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> </tt>
<a name="mRMR"></a><div id="mRMR-def"><a name="L436"></a><tt class="py-lineno">436</tt> <a class="py-toggle" href="#" id="mRMR-toggle" onclick="return toggle('mRMR');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#mRMR">mRMR</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">,</tt> <tt class="py-param">n_select</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="mRMR-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="mRMR-expanded"><a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"><tt class="py-docstring"> This funciton implements the max-relevance min-redundancy feature</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"><tt class="py-docstring"> selection algorithm. </tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"><tt class="py-docstring"> @param data: data in a Numpy array such that len(data) = </tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"><tt class="py-docstring"> n_observations, and len(data.transpose()) = n_features</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"><tt class="py-docstring"> @type data: ndarray</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: labels represented in a numpy list with </tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-docstring"> n_observations as the number of elements. That is </tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-docstring"> len(labels) = len(data) = n_observations.</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-docstring"> @type labels: ndarray</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"><tt class="py-docstring"> @param n_select: number of features to select. (REQUIRED)</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"><tt class="py-docstring"> @type n_select: integer</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-docstring"> @return: the features in the order they were selected. </tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: list</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="feast.check_data" class="py-name" href="#" onclick="return doclink('link-41', 'check_data', 'link-5');">check_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">labels</tt><tt class="py-op">)</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt class="py-comment"># python values</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-name">n_observations</tt><tt class="py-op">,</tt> <tt class="py-name">n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-comment"># cast as C types</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_observations</tt><tt class="py-op">)</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-name">c_n_select</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_int</tt><tt class="py-op">(</tt><tt class="py-name">n_features</tt><tt class="py-op">)</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-42', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt class="py-name">mRMR_D</tt><tt class="py-op">.</tt><tt class="py-name">restype</tt> <tt class="py-op">=</tt> <tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt> <tt class="py-op">*</tt> <tt class="py-name">n_select</tt><tt class="py-op">)</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">features</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="feast.libFSToolbox" class="py-name" href="#" onclick="return doclink('link-43', 'libFSToolbox', 'link-4');">libFSToolbox</a></tt><tt class="py-op">.</tt><tt class="py-name">mRMR_D</tt><tt class="py-op">(</tt><tt class="py-name">c_n_select</tt><tt class="py-op">,</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-name">c_n_observations</tt><tt class="py-op">,</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-name">c_n_features</tt><tt class="py-op">,</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-name">labels</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">ctypes</tt><tt class="py-op">.</tt><tt class="py-name">data_as</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">POINTER</tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">.</tt><tt class="py-name">c_double</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-comment"># turn our output into a list</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">features</tt><tt class="py-op">.</tt><tt class="py-name">contents</tt><tt class="py-op">:</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-comment"># recall that feast was implemented with Matlab in mind, so the </tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-comment"># authors assumed the indexing started a one; however, in Python </tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-comment"># the indexing starts at zero. </tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-name">selected_features</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">i</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">selected_features</tt> </tt>
</div><a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> </tt>
<a name="check_data"></a><div id="check_data-def"><a name="L484"></a><tt class="py-lineno">484</tt> <a class="py-toggle" href="#" id="check_data-toggle" onclick="return toggle('check_data');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="feast-module.html#check_data">check_data</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">labels</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="check_data-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="check_data-expanded"><a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"><tt class="py-docstring"> Check dimensions of the data and the labels. Raise and exception</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"><tt class="py-docstring"> if there is a problem.</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"><tt class="py-docstring"> Data and Labels are automatically cast as doubles before calling the </tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"><tt class="py-docstring"> feature selection functions</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"><tt class="py-docstring"> @param data: the data </tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"><tt class="py-docstring"> @param labels: the labels</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-docstring"> @return (data, labels): ndarray of floats</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: tuple</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ndarray</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">False</tt><tt class="py-op">:</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">(</tt><tt class="py-string">"data must be an numpy ndarray."</tt><tt class="py-op">)</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">labels</tt><tt class="py-op">,</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ndarray</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">False</tt><tt class="py-op">:</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">(</tt><tt class="py-string">"labels must be an numpy ndarray."</tt><tt class="py-op">)</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">labels</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">(</tt><tt class="py-string">"data and labels must be the same length"</tt><tt class="py-op">)</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1.0</tt><tt class="py-op">*</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">*</tt><tt class="py-name">labels</tt> </tt>
</div><a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> </tt><script type="text/javascript">
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