utils.html 26 KB

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  62. <h1>Source code for ipfml.utils</h1><div class="highlight"><pre>
  63. <span></span><span class="sd">&quot;&quot;&quot;</span>
  64. <span class="sd">Utils functions of ipfml package (normalization, integral...)</span>
  65. <span class="sd">&quot;&quot;&quot;</span>
  66. <span class="c1"># main imports</span>
  67. <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
  68. <span class="kn">import</span> <span class="nn">math</span>
  69. <span class="kn">import</span> <span class="nn">sys</span>
  70. <span class="c1"># computation imports</span>
  71. <span class="kn">from</span> <span class="nn">scipy.integrate</span> <span class="k">import</span> <span class="n">simps</span>
  72. <div class="viewcode-block" id="normalize_arr"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.normalize_arr">[docs]</a><span class="k">def</span> <span class="nf">normalize_arr</span><span class="p">(</span><span class="n">arr</span><span class="p">):</span>
  73. <span class="sd">&quot;&quot;&quot;Normalize data of 1D array shape</span>
  74. <span class="sd"> Args:</span>
  75. <span class="sd"> arr: array data of 1D shape</span>
  76. <span class="sd"> Returns:</span>
  77. <span class="sd"> Normalized 1D array</span>
  78. <span class="sd"> Example:</span>
  79. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  80. <span class="sd"> &gt;&gt;&gt; import numpy as np</span>
  81. <span class="sd"> &gt;&gt;&gt; arr = np.arange(11)</span>
  82. <span class="sd"> &gt;&gt;&gt; arr_normalized = utils.normalize_arr(arr)</span>
  83. <span class="sd"> &gt;&gt;&gt; arr_normalized[1]</span>
  84. <span class="sd"> 0.1</span>
  85. <span class="sd"> &quot;&quot;&quot;</span>
  86. <span class="n">output_arr</span> <span class="o">=</span> <span class="p">[]</span>
  87. <span class="n">max_value</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span>
  88. <span class="n">min_value</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span>
  89. <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">arr</span><span class="p">:</span>
  90. <span class="k">try</span><span class="p">:</span>
  91. <span class="n">output_arr</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">v</span> <span class="o">-</span> <span class="n">min_value</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">max_value</span> <span class="o">-</span> <span class="n">min_value</span><span class="p">))</span>
  92. <span class="k">except</span> <span class="ne">ZeroDivisionError</span><span class="p">:</span>
  93. <span class="n">output_arr</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">v</span> <span class="o">-</span> <span class="n">min_value</span><span class="p">)</span> <span class="o">/</span>
  94. <span class="p">(</span><span class="n">max_value</span> <span class="o">-</span> <span class="n">min_value</span> <span class="o">+</span> <span class="n">sys</span><span class="o">.</span><span class="n">float_info</span><span class="o">.</span><span class="n">epsilon</span><span class="p">))</span>
  95. <span class="k">return</span> <span class="n">output_arr</span></div>
  96. <div class="viewcode-block" id="normalize_arr_with_range"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.normalize_arr_with_range">[docs]</a><span class="k">def</span> <span class="nf">normalize_arr_with_range</span><span class="p">(</span><span class="n">arr</span><span class="p">,</span> <span class="nb">min</span><span class="p">,</span> <span class="nb">max</span><span class="p">):</span>
  97. <span class="sd">&#39;&#39;&#39;Normalize data of 1D array shape</span>
  98. <span class="sd"> Args:</span>
  99. <span class="sd"> arr: array data of 1D shape</span>
  100. <span class="sd"> Returns:</span>
  101. <span class="sd"> Normalized 1D Numpy array</span>
  102. <span class="sd"> Example:</span>
  103. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  104. <span class="sd"> &gt;&gt;&gt; import numpy as np</span>
  105. <span class="sd"> &gt;&gt;&gt; arr = np.arange(11)</span>
  106. <span class="sd"> &gt;&gt;&gt; arr_normalized = utils.normalize_arr_with_range(arr, 0, 20)</span>
  107. <span class="sd"> &gt;&gt;&gt; arr_normalized[1]</span>
  108. <span class="sd"> 0.05</span>
  109. <span class="sd"> &#39;&#39;&#39;</span>
  110. <span class="n">output_arr</span> <span class="o">=</span> <span class="p">[]</span>
  111. <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">arr</span><span class="p">:</span>
  112. <span class="k">try</span><span class="p">:</span>
  113. <span class="n">output_arr</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">v</span> <span class="o">-</span> <span class="nb">min</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="nb">max</span> <span class="o">-</span> <span class="nb">min</span><span class="p">))</span>
  114. <span class="k">except</span> <span class="ne">ZeroDivisionError</span><span class="p">:</span>
  115. <span class="n">output_arr</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">v</span> <span class="o">-</span> <span class="nb">min</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="nb">max</span> <span class="o">-</span> <span class="nb">min</span> <span class="o">+</span> <span class="n">sys</span><span class="o">.</span><span class="n">float_info</span><span class="o">.</span><span class="n">epsilon</span><span class="p">))</span>
  116. <span class="k">return</span> <span class="n">output_arr</span></div>
  117. <div class="viewcode-block" id="normalize_2D_arr"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.normalize_2D_arr">[docs]</a><span class="k">def</span> <span class="nf">normalize_2D_arr</span><span class="p">(</span><span class="n">arr</span><span class="p">):</span>
  118. <span class="sd">&quot;&quot;&quot;Return array normalize from its min and max values</span>
  119. <span class="sd"> Args:</span>
  120. <span class="sd"> arr: 2D Numpy array</span>
  121. <span class="sd"> Returns:</span>
  122. <span class="sd"> Normalized 2D Numpy array</span>
  123. <span class="sd"> Example:</span>
  124. <span class="sd"> &gt;&gt;&gt; from PIL import Image</span>
  125. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  126. <span class="sd"> &gt;&gt;&gt; from ipfml.processing import transform</span>
  127. <span class="sd"> &gt;&gt;&gt; img = Image.open(&#39;./images/test_img.png&#39;)</span>
  128. <span class="sd"> &gt;&gt;&gt; img_mscn = transform.rgb_to_mscn(img)</span>
  129. <span class="sd"> &gt;&gt;&gt; img_normalized = utils.normalize_2D_arr(img_mscn)</span>
  130. <span class="sd"> &gt;&gt;&gt; img_normalized.shape</span>
  131. <span class="sd"> (200, 200)</span>
  132. <span class="sd"> &quot;&quot;&quot;</span>
  133. <span class="c1"># getting min and max value from 2D array</span>
  134. <span class="n">max_value</span> <span class="o">=</span> <span class="n">arr</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">max</span><span class="p">()</span>
  135. <span class="n">min_value</span> <span class="o">=</span> <span class="n">arr</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">min</span><span class="p">()</span>
  136. <span class="c1"># normalize each row</span>
  137. <span class="n">output_array</span> <span class="o">=</span> <span class="p">[]</span>
  138. <span class="n">width</span><span class="p">,</span> <span class="n">height</span> <span class="o">=</span> <span class="n">arr</span><span class="o">.</span><span class="n">shape</span>
  139. <span class="k">for</span> <span class="n">row_index</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">height</span><span class="p">):</span>
  140. <span class="n">values</span> <span class="o">=</span> <span class="n">arr</span><span class="p">[</span><span class="n">row_index</span><span class="p">,</span> <span class="p">:]</span>
  141. <span class="n">output_array</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
  142. <span class="n">normalize_arr_with_range</span><span class="p">(</span><span class="n">values</span><span class="p">,</span> <span class="n">min_value</span><span class="p">,</span> <span class="n">max_value</span><span class="p">))</span>
  143. <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">(</span><span class="n">output_array</span><span class="p">)</span></div>
  144. <div class="viewcode-block" id="integral_area_trapz"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.integral_area_trapz">[docs]</a><span class="k">def</span> <span class="nf">integral_area_trapz</span><span class="p">(</span><span class="n">y_values</span><span class="p">,</span> <span class="n">dx</span><span class="p">):</span>
  145. <span class="sd">&quot;&quot;&quot;Returns area under curves from provided data points using Trapezium rule</span>
  146. <span class="sd"> Args:</span>
  147. <span class="sd"> y_values: y values of curve</span>
  148. <span class="sd"> dx: number of unit for x axis</span>
  149. <span class="sd"> Returns:</span>
  150. <span class="sd"> Area under curves obtained from these points</span>
  151. <span class="sd"> Example:</span>
  152. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  153. <span class="sd"> &gt;&gt;&gt; import numpy as np</span>
  154. <span class="sd"> &gt;&gt;&gt; y_values = np.array([5, 20, 4, 18, 19, 18, 7, 4])</span>
  155. <span class="sd"> &gt;&gt;&gt; area = utils.integral_area_trapz(y_values, dx=5)</span>
  156. <span class="sd"> &gt;&gt;&gt; area</span>
  157. <span class="sd"> 452.5</span>
  158. <span class="sd"> &quot;&quot;&quot;</span>
  159. <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">trapz</span><span class="p">(</span><span class="n">y_values</span><span class="p">,</span> <span class="n">dx</span><span class="o">=</span><span class="n">dx</span><span class="p">)</span></div>
  160. <div class="viewcode-block" id="integral_area_simps"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.integral_area_simps">[docs]</a><span class="k">def</span> <span class="nf">integral_area_simps</span><span class="p">(</span><span class="n">y_values</span><span class="p">,</span> <span class="n">dx</span><span class="p">):</span>
  161. <span class="sd">&quot;&quot;&quot;Returns area under curves from provided data points using Simpsons rule</span>
  162. <span class="sd"> Args:</span>
  163. <span class="sd"> y_values: y values of curve</span>
  164. <span class="sd"> dx: number of unit for x axis</span>
  165. <span class="sd"> Returns:</span>
  166. <span class="sd"> Area under curves obtained from these points</span>
  167. <span class="sd"> Example:</span>
  168. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  169. <span class="sd"> &gt;&gt;&gt; import numpy as np</span>
  170. <span class="sd"> &gt;&gt;&gt; y_values = np.array([5, 20, 4, 18, 19, 18, 7, 4])</span>
  171. <span class="sd"> &gt;&gt;&gt; area = utils.integral_area_simps(y_values, dx=5)</span>
  172. <span class="sd"> &gt;&gt;&gt; area</span>
  173. <span class="sd"> 460.0</span>
  174. <span class="sd"> &quot;&quot;&quot;</span>
  175. <span class="k">return</span> <span class="n">simps</span><span class="p">(</span><span class="n">y_values</span><span class="p">,</span> <span class="n">dx</span><span class="o">=</span><span class="n">dx</span><span class="p">)</span></div>
  176. <div class="viewcode-block" id="get_indices_of_highest_values"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.get_indices_of_highest_values">[docs]</a><span class="k">def</span> <span class="nf">get_indices_of_highest_values</span><span class="p">(</span><span class="n">arr</span><span class="p">,</span> <span class="n">n</span><span class="p">):</span>
  177. <span class="sd">&quot;&quot;&quot;Returns indices of n highest values from list or 1D numpy array</span>
  178. <span class="sd"> Args:</span>
  179. <span class="sd"> arr: List of numpy array</span>
  180. <span class="sd"> n: number of highest elements wanted</span>
  181. <span class="sd"> Returns:</span>
  182. <span class="sd"> `n` indices of highest values</span>
  183. <span class="sd"> Example:</span>
  184. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  185. <span class="sd"> &gt;&gt;&gt; import numpy as np</span>
  186. <span class="sd"> &gt;&gt;&gt; arr = np.arange(10)</span>
  187. <span class="sd"> &gt;&gt;&gt; indices = utils.get_indices_of_highest_values(arr, 2)</span>
  188. <span class="sd"> &gt;&gt;&gt; indices</span>
  189. <span class="sd"> array([9, 8])</span>
  190. <span class="sd"> &quot;&quot;&quot;</span>
  191. <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span><span class="o">.</span><span class="n">argsort</span><span class="p">()[</span><span class="o">-</span><span class="n">n</span><span class="p">:][::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span></div>
  192. <div class="viewcode-block" id="get_indices_of_lowest_values"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.get_indices_of_lowest_values">[docs]</a><span class="k">def</span> <span class="nf">get_indices_of_lowest_values</span><span class="p">(</span><span class="n">arr</span><span class="p">,</span> <span class="n">n</span><span class="p">):</span>
  193. <span class="sd">&quot;&quot;&quot;Returns indices of n highest values from list or 1D numpy array</span>
  194. <span class="sd"> Args:</span>
  195. <span class="sd"> arr: List of numpy array</span>
  196. <span class="sd"> n: number of highest elements wanted</span>
  197. <span class="sd"> Returns:</span>
  198. <span class="sd"> `n` indices of highest values</span>
  199. <span class="sd"> Example:</span>
  200. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  201. <span class="sd"> &gt;&gt;&gt; import numpy as np</span>
  202. <span class="sd"> &gt;&gt;&gt; arr = np.arange(10)</span>
  203. <span class="sd"> &gt;&gt;&gt; indices = utils.get_indices_of_lowest_values(arr, 2)</span>
  204. <span class="sd"> &gt;&gt;&gt; indices</span>
  205. <span class="sd"> array([0, 1])</span>
  206. <span class="sd"> &quot;&quot;&quot;</span>
  207. <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span><span class="o">.</span><span class="n">argsort</span><span class="p">()[::</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="o">-</span><span class="n">n</span><span class="p">:][::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span></div>
  208. <div class="viewcode-block" id="get_entropy"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.get_entropy">[docs]</a><span class="k">def</span> <span class="nf">get_entropy</span><span class="p">(</span><span class="n">arr</span><span class="p">):</span>
  209. <span class="sd">&quot;&quot;&quot;Returns the computed entropy from arr</span>
  210. <span class="sd"> Args:</span>
  211. <span class="sd"> arr: numpy array</span>
  212. <span class="sd"> Returns:</span>
  213. <span class="sd"> entropy score computed</span>
  214. <span class="sd"> Example:</span>
  215. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  216. <span class="sd"> &gt;&gt;&gt; import numpy as np</span>
  217. <span class="sd"> &gt;&gt;&gt; arr = np.arange(10)</span>
  218. <span class="sd"> &gt;&gt;&gt; entropy = utils.get_entropy(arr)</span>
  219. <span class="sd"> &gt;&gt;&gt; int(entropy)</span>
  220. <span class="sd"> 0</span>
  221. <span class="sd"> &quot;&quot;&quot;</span>
  222. <span class="n">arr</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span>
  223. <span class="n">eigen_values</span> <span class="o">=</span> <span class="p">[]</span>
  224. <span class="n">sum_eigen_values</span> <span class="o">=</span> <span class="p">(</span><span class="n">arr</span> <span class="o">*</span> <span class="n">arr</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
  225. <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">arr</span><span class="p">:</span>
  226. <span class="n">eigen_values</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">val</span> <span class="o">*</span> <span class="n">val</span><span class="p">)</span>
  227. <span class="n">v</span> <span class="o">=</span> <span class="p">[]</span>
  228. <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">eigen_values</span><span class="p">:</span>
  229. <span class="n">v</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">val</span> <span class="o">/</span> <span class="n">sum_eigen_values</span><span class="p">)</span>
  230. <span class="n">entropy</span> <span class="o">=</span> <span class="mi">0</span>
  231. <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
  232. <span class="k">if</span> <span class="n">val</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
  233. <span class="n">entropy</span> <span class="o">+=</span> <span class="n">val</span> <span class="o">*</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
  234. <span class="n">entropy</span> <span class="o">*=</span> <span class="o">-</span><span class="mi">1</span>
  235. <span class="n">entropy</span> <span class="o">/=</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">v</span><span class="p">))</span>
  236. <span class="k">return</span> <span class="n">entropy</span></div>
  237. <div class="viewcode-block" id="get_entropy_without_i"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.get_entropy_without_i">[docs]</a><span class="k">def</span> <span class="nf">get_entropy_without_i</span><span class="p">(</span><span class="n">arr</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span>
  238. <span class="sd">&quot;&quot;&quot;Returns the computed entropy from arr without contribution of i</span>
  239. <span class="sd"> Args:</span>
  240. <span class="sd"> arr: numpy array</span>
  241. <span class="sd"> i: column index</span>
  242. <span class="sd"> Returns:</span>
  243. <span class="sd"> entropy score computed</span>
  244. <span class="sd"> Example:</span>
  245. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  246. <span class="sd"> &gt;&gt;&gt; import numpy as np</span>
  247. <span class="sd"> &gt;&gt;&gt; arr = np.arange(10)</span>
  248. <span class="sd"> &gt;&gt;&gt; entropy = utils.get_entropy_without_i(arr, 3)</span>
  249. <span class="sd"> &gt;&gt;&gt; int(entropy)</span>
  250. <span class="sd"> 0</span>
  251. <span class="sd"> &quot;&quot;&quot;</span>
  252. <span class="n">arr</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">v</span> <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span> <span class="k">if</span> <span class="n">index</span> <span class="o">!=</span> <span class="n">i</span><span class="p">])</span>
  253. <span class="k">return</span> <span class="n">get_entropy</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span></div>
  254. <div class="viewcode-block" id="get_entropy_contribution_of_i"><a class="viewcode-back" href="../../ipfml/ipfml.utils.html#ipfml.utils.get_entropy_contribution_of_i">[docs]</a><span class="k">def</span> <span class="nf">get_entropy_contribution_of_i</span><span class="p">(</span><span class="n">arr</span><span class="p">,</span> <span class="n">i</span><span class="p">):</span>
  255. <span class="sd">&quot;&quot;&quot;Returns the entropy contribution i column</span>
  256. <span class="sd"> Args:</span>
  257. <span class="sd"> arr: numpy array</span>
  258. <span class="sd"> i: column index</span>
  259. <span class="sd"> Returns:</span>
  260. <span class="sd"> entropy contribution score computed</span>
  261. <span class="sd"> Example:</span>
  262. <span class="sd"> &gt;&gt;&gt; from ipfml import utils</span>
  263. <span class="sd"> &gt;&gt;&gt; import numpy as np</span>
  264. <span class="sd"> &gt;&gt;&gt; arr = np.arange(10)</span>
  265. <span class="sd"> &gt;&gt;&gt; entropy = utils.get_entropy_contribution_of_i(arr, 3)</span>
  266. <span class="sd"> &gt;&gt;&gt; int(entropy)</span>
  267. <span class="sd"> 0</span>
  268. <span class="sd"> &quot;&quot;&quot;</span>
  269. <span class="k">return</span> <span class="n">get_entropy</span><span class="p">(</span><span class="n">arr</span><span class="p">)</span> <span class="o">-</span> <span class="n">get_entropy_without_i</span><span class="p">(</span><span class="n">arr</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span></div>
  270. </pre></div>
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