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Regions.html

Regions.html 15 KB
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  8.     <title>Regions &#8212; image features extraction 1.0.0 documentation</title>
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    40. 

  40.             
    41. 

  41.   <h1>Source code for Regions</h1><div class="highlight"><pre>
    42. 

  42. <span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
    43. 

  43. <span class="kn">from</span> <span class="nn">image_features_extraction</span> <span class="k">import</span> <span class="n">my_iterator</span>
    44. 

  44. <span class="kn">from</span> <span class="nn">image_features_extraction</span> <span class="k">import</span> <span class="n">Region</span>
    45. 

  45. <span class="kn">from</span> <span class="nn">image_features_extraction</span> <span class="k">import</span> <span class="n">MyException</span>
    46. 

  46. <span class="kn">from</span> <span class="nn">skimage.measure</span> <span class="k">import</span> <span class="n">label</span><span class="p">,</span> <span class="n">regionprops</span>
    47. 

  47. 

  48. 

  49. <div class="viewcode-block" id="Regions"><a class="viewcode-back" href="../code.html#Regions.Regions">[docs]</a><span class="k">class</span> <span class="nc">Regions</span><span class="p">(</span><span class="n">my_iterator</span><span class="o">.</span><span class="n">my_iterator</span><span class="p">):</span>
    50. 

  50.     <span class="sd">&quot;&quot;&quot;</span>
    51. 

  51. <span class="sd">    This class represent a collection of regions: segmented image elements</span>
    52. 

  52. <span class="sd">    It cannot be instanced directly. It is returned from the object :class:`Image` through the function</span>
    53. 

  53. <span class="sd">    Regions(...)</span>
    54. 

  54. 

  55. <span class="sd">    :example:</span>
    56. 

  56. <span class="sd">    &gt;&gt;&gt; import image_features_extraction as fe</span>
    57. 

  57. <span class="sd">    &gt;&gt;&gt; imgs = fe.Images(folder_name)</span>
    58. 

  58. <span class="sd">    &gt;&gt;&gt; img = imgs.item(1)</span>
    59. 

  59. <span class="sd">    &gt;&gt;&gt; regs = img.Regions()</span>
    60. 

  60. <span class="sd">    &quot;&quot;&quot;</span>
    61. 

  61. 

  62.     <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj_regions</span><span class="p">):</span>
    63. 

  63.         <span class="k">try</span><span class="p">:</span>
    64. 

  64.              <span class="bp">self</span><span class="o">.</span><span class="n">__iterator_init__</span><span class="p">()</span>
    65. 

  65.              <span class="bp">self</span><span class="o">.</span><span class="n">__obj_regions_org</span> <span class="o">=</span> <span class="n">obj_regions</span>
    66. 

  66.              <span class="bp">self</span><span class="o">.</span><span class="n">__obj_regions</span> <span class="o">=</span> <span class="n">regionprops</span><span class="p">(</span><span class="n">obj_regions</span><span class="p">)</span> <span class="c1"># used regionprops from skimage</span>
    67. 

  67.              <span class="bp">self</span><span class="o">.</span><span class="n">count_update</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__obj_regions</span><span class="p">))</span>
    68. 

  68.         <span class="k">except</span> <span class="n">MyException</span><span class="o">.</span><span class="n">MyException</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
    69. 

  69.             <span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">args</span><span class="p">)</span>
    70. 

  70. 

  71. 

  72.     <span class="k">def</span> <span class="nf">__regions_obj</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
    73. 

  73.         <span class="sd">&quot;&quot;&quot;</span>
    74. 

  74. <span class="sd">        This function returns the Internal object regions. it is used only for debugging</span>
    75. 

  75. <span class="sd">        &quot;&quot;&quot;</span>
    76. 

  76.         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__obj_regions_org</span>
    77. 

  77. 

  78. 

  79. <div class="viewcode-block" id="Regions.item"><a class="viewcode-back" href="../code.html#Regions.Regions.item">[docs]</a>    <span class="k">def</span> <span class="nf">item</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span>
    80. 

  80.         <span class="sd">&quot;&quot;&quot;</span>
    81. 

  81. <span class="sd">        Item(..) returns the i-th image element  of the regions.</span>
    82. 

  82. 

  83. <span class="sd">        :param i: the i-th element of the collection region</span>
    84. 

  84. <span class="sd">        :type i: int</span>
    85. 

  85. <span class="sd">        :returns: Region</span>
    86. 

  86. <span class="sd">        :rtype: object</span>
    87. 

  87. <span class="sd">        :example:</span>
    88. 

  88. <span class="sd">        &gt;&gt;&gt; import image_features_extraction as fe</span>
    89. 

  89. <span class="sd">        &gt;&gt;&gt; imgs = fe.Images(folder_name)</span>
    90. 

  90. <span class="sd">        &gt;&gt;&gt; img = imgs.item(1)</span>
    91. 

  91. <span class="sd">        &gt;&gt;&gt; regs = img.Regions()</span>
    92. 

  92. <span class="sd">        &gt;&gt;&gt; reg = regs.item(1)</span>
    93. 

  93. <span class="sd">        &quot;&quot;&quot;</span>
    94. 

  94.         <span class="k">try</span><span class="p">:</span>
    95. 

  95.             <span class="k">if</span> <span class="n">i</span> <span class="o">&gt;=</span> <span class="bp">self</span><span class="o">.</span><span class="n">count</span><span class="p">():</span>
    96. 

  96.                 <span class="k">raise</span> <span class="n">MyException</span><span class="o">.</span><span class="n">MyException</span><span class="p">(</span><span class="s2">&quot;error: index out of bound&quot;</span><span class="p">)</span>
    97. 

  97. 

  98.             <span class="k">return</span> <span class="n">Region</span><span class="o">.</span><span class="n">Region</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__obj_regions</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
    99. 

  99.         <span class="k">except</span> <span class="n">MyException</span><span class="o">.</span><span class="n">MyException</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
    100. 

  100.             <span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">args</span><span class="p">)</span>
    101. 

  101.             <span class="k">return</span> <span class="kc">None</span></div>
    102. 

  102. 

  103. 

  104. <div class="viewcode-block" id="Regions.prop_values"><a class="viewcode-back" href="../code.html#Regions.Regions.prop_values">[docs]</a>    <span class="k">def</span> <span class="nf">prop_values</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">prop_name</span><span class="p">):</span>
    105. 

  105.         <span class="sd">&quot;&quot;&quot;</span>
    106. 

  106. <span class="sd">        prop_values(...) returns the values of the specified  property/measure name (e.g., &#39;area&#39;) for all image</span>
    107. 

  107. <span class="sd">        elements contained in the object Regions. For a list of property names refer to &quot;regionprops  &lt;http://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.regionprops&gt;&quot;_.</span>
    108. 

  108. 

  109. <span class="sd">        :param prop_name: name of the property to measure (e.g, &#39;area&#39;)</span>
    110. 

  110. <span class="sd">        :type prop_name: string</span>
    111. 

  111. <span class="sd">        :returns: values of the property name in input</span>
    112. 

  112. <span class="sd">        :rtype: List</span>
    113. 

  113. 

  114. <span class="sd">        :example:</span>
    115. 

  115. <span class="sd">        &gt;&gt;&gt; import image_features_extraction as fe</span>
    116. 

  116. <span class="sd">        &gt;&gt;&gt; imgs = fe.Images(folder_name)</span>
    117. 

  117. <span class="sd">        &gt;&gt;&gt; img = imgs.item(1)</span>
    118. 

  118. <span class="sd">        &gt;&gt;&gt; regs = img.Regions()</span>
    119. 

  119. <span class="sd">        &gt;&gt;&gt; areas = regs.prop_values(&#39;area&#39;)</span>
    120. 

  120. <span class="sd">        &quot;&quot;&quot;</span>
    121. 

  121.         <span class="k">try</span><span class="p">:</span>
    122. 

  122. 

  123.             <span class="n">vals</span> <span class="o">=</span> <span class="p">[]</span>
    124. 

  124.             <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">__obj_regions</span><span class="p">:</span>
    125. 

  125.                 <span class="n">vals</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">prop_name</span><span class="p">))</span>
    126. 

  126.             <span class="k">return</span> <span class="n">vals</span>
    127. 

  127. 

  128.         <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
    129. 

  129.             <span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">args</span><span class="p">)</span>
    130. 

  130.             <span class="k">return</span> <span class="kc">None</span></div>
    131. 

  131. 

  132. 

  133. <div class="viewcode-block" id="Regions.get_features"><a class="viewcode-back" href="../code.html#Regions.Regions.get_features">[docs]</a>    <span class="k">def</span> <span class="nf">get_features</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">features</span><span class="p">,</span> <span class="n">class_value</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">class_name</span><span class="o">=</span><span class="s1">&#39;class_name&#39;</span><span class="p">):</span>
    134. 

  134.         <span class="sd">&quot;&quot;&quot;</span>
    135. 

  135. <span class="sd">        get_features(...)  returns a table with all  values for the property names given in input, and supplies an</span>
    136. 

  136. <span class="sd">        additional parameter for feature classification</span>
    137. 

  137. 

  138. <span class="sd">        :param features: list of property/measure names (e.g, &#39;area&#39;, &#39;centroid&#39;, etc )</span>
    139. 

  139. <span class="sd">        :type features: List</span>
    140. 

  140. <span class="sd">        :param class_value: classification label</span>
    141. 

  141. <span class="sd">        :type class_value: int, string (default=None)</span>
    142. 

  142. <span class="sd">        :returns: table cointaining all property values (columns) for all elements in the regions object  (rows)</span>
    143. 

  143. <span class="sd">        :rtype: Pandas.DataFrame</span>
    144. 

  144. <span class="sd">        :example:</span>
    145. 

  145. <span class="sd">        &gt;&gt;&gt; import image_features_extraction as fe</span>
    146. 

  146. <span class="sd">        &gt;&gt;&gt; imgs = fe.Images(folder_name)</span>
    147. 

  147. <span class="sd">        &gt;&gt;&gt; img = imgs.item(1)</span>
    148. 

  148. <span class="sd">        &gt;&gt;&gt; regs = img.Regions()</span>
    149. 

  149. <span class="sd">        &gt;&gt;&gt; df = regs.get_features([&#39;label&#39;, &#39;area&#39;,&#39;perimeter&#39;, &#39;centroid&#39;], class_value=1)</span>
    150. 

  150. 

  151. <span class="sd">        &quot;&quot;&quot;</span>
    152. 

  152.         <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">()</span>
    153. 

  153.         <span class="k">try</span><span class="p">:</span>
    154. 

  154.             <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">features</span><span class="p">:</span>
    155. 

  155.                 <span class="n">df</span><span class="p">[</span><span class="n">f</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">prop_values</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
    156. 

  156.             <span class="k">if</span> <span class="n">class_value</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
    157. 

  157.                 <span class="n">df</span><span class="p">[</span><span class="n">class_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">class_value</span>
    158. 

  158.             <span class="k">return</span> <span class="n">df</span>
    159. 

  159.         <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
    160. 

  160.             <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;one or more input labels might be wrong:</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
    161. 

  161.             <span class="k">return</span> <span class="kc">None</span></div></div>
    162. 

  162. </pre></div>
    163. 

  163. 

  164.           </div>
    165. 

  165.         </div>
    166. 

  166.       </div>
    167. 

  167.       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
    168. 

  168.         <div class="sphinxsidebarwrapper">
    169. 

  169. <h1 class="logo"><a href="../index.html">image features extraction</a></h1>
    170. 

  170. 

  171. 

  172. 

  173. 

  174. 

  175. 

  176. 

  177. 

  178. <h3>Navigation</h3>
    179. 

  179. <p class="caption"><span class="caption-text">Contents:</span></p>
    180. 

  180. <ul>
    181. 

  181. <li class="toctree-l1"><a class="reference internal" href="../intro.html">Introduction</a></li>
    182. 

  182. <li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Tutorial</a></li>
    183. 

  183. <li class="toctree-l1"><a class="reference internal" href="../code.html">Classes/Modules</a></li>
    184. 

  184. </ul>
    185. 

  185. 

  186. <div class="relations">
    187. 

  187. <h3>Related Topics</h3>
    188. 

  188. <ul>
    189. 

  189.   <li><a href="../index.html">Documentation overview</a><ul>
    190. 

  190.   <li><a href="index.html">Module code</a><ul>
    191. 

  191.   </ul></li>
    192. 

  192.   </ul></li>
    193. 

  193. </ul>
    194. 

  194. </div>
    195. 

  195. <div id="searchbox" style="display: none" role="search">
    196. 

  196.   <h3>Quick search</h3>
    197. 

  197.     <form class="search" action="../search.html" method="get">
    198. 

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    199. 

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    202. 

  202.     </form>
    203. 

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    204. 

  204. <script type="text/javascript">$('#searchbox').show(0);</script>
    205. 

  205.         </div>
    206. 

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    207. 

  207.       <div class="clearer"></div>
    208. 

  208.     </div>
    209. 

  209.     <div class="footer">
    210. 

  210.       &copy;2017, Remigio Picone.
    211. 

  211.       
    212. 

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    213. 

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    214. 

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    215. 

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    217. 

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    221. 

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    222. 

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    223.