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Regions.html 24 KB
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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">image_features_extraction</span> <span class="k">import</span> <span class="n">Features</span>
    47. 

  47. 

  48. <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>
    49. 

  49. <span class="kn">from</span> <span class="nn">image_features_extraction</span> <span class="k">import</span> <span class="n">Utils</span>
    50. 

  50. 

  51. <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>
    52. 

  52.     <span class="sd">&quot;&quot;&quot;</span>
    53. 

  53. <span class="sd">    This class represent a collection of regions: segmented image elements</span>
    54. 

  54. <span class="sd">    It cannot be instanced directly. It is returned from the object :class:`Image` through the function</span>
    55. 

  55. <span class="sd">    Regions(...)</span>
    56. 

  56. 

  57. <span class="sd">    :example:</span>
    58. 

  58. <span class="sd">    &gt;&gt;&gt; import image_features_extraction as fe</span>
    59. 

  59. <span class="sd">    &gt;&gt;&gt; imgs = fe.Images(folder_name)</span>
    60. 

  60. <span class="sd">    &gt;&gt;&gt; img = imgs.item(1)</span>
    61. 

  61. <span class="sd">    &gt;&gt;&gt; regs = img.Regions()</span>
    62. 

  62. <span class="sd">    &quot;&quot;&quot;</span>
    63. 

  63. 

  64.     <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>
    65. 

  65.         <span class="k">try</span><span class="p">:</span>
    66. 

  66.              <span class="c1">#self.__iterator_init__()</span>
    67. 

  67.              <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
    68. 

  68.              <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>
    69. 

  69.              <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>
    70. 

  70.              <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>
    71. 

  71.         <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>
    72. 

  72.             <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>
    73. 

  73. 

  74. 

  75.     <span class="k">def</span> <span class="nf">__regions_obj</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
    76. 

  76.         <span class="sd">&quot;&quot;&quot;</span>
    77. 

  77. <span class="sd">        This function returns the Internal object regions. it is used only for debugging</span>
    78. 

  78. <span class="sd">        &quot;&quot;&quot;</span>
    79. 

  79.         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__obj_regions_org</span>
    80. 

  80. 

  81. 

  82. <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>
    83. 

  83.         <span class="sd">&quot;&quot;&quot;</span>
    84. 

  84. <span class="sd">        Item(..) returns the i-th image element  of the regions.</span>
    85. 

  85. 

  86. <span class="sd">        :param i: the i-th element of the collection region</span>
    87. 

  87. <span class="sd">        :type i: int</span>
    88. 

  88. <span class="sd">        :returns: Region</span>
    89. 

  89. <span class="sd">        :rtype: object</span>
    90. 

  90. <span class="sd">        :example:</span>
    91. 

  91. <span class="sd">        &gt;&gt;&gt; import image_features_extraction as fe</span>
    92. 

  92. <span class="sd">        &gt;&gt;&gt; imgs = fe.Images(folder_name)</span>
    93. 

  93. <span class="sd">        &gt;&gt;&gt; img = imgs.item(1)</span>
    94. 

  94. <span class="sd">        &gt;&gt;&gt; regs = img.Regions()</span>
    95. 

  95. <span class="sd">        &gt;&gt;&gt; reg = regs.item(1)</span>
    96. 

  96. <span class="sd">        &quot;&quot;&quot;</span>
    97. 

  97.         <span class="k">try</span><span class="p">:</span>
    98. 

  98.             <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>
    99. 

  99.                 <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>
    100. 

  100. 

  101.             <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>
    102. 

  102.         <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>
    103. 

  103.             <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>
    104. 

  104.             <span class="k">return</span> <span class="kc">None</span></div>
    105. 

  105. 

  106. 

  107. <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>
    108. 

  108.         <span class="sd">&quot;&quot;&quot;</span>
    109. 

  109. <span class="sd">        Measure the values of the specified  property/measure name (e.g., &#39;area&#39;) for all</span>
    110. 

  110. <span class="sd">        elements contained in the object Regions.</span>
    111. 

  111. 

  112. <span class="sd">        :param prop_name: name of the property to measure (e.g, &#39;area&#39;)</span>
    113. 

  113. <span class="sd">        :type prop_name: string</span>
    114. 

  114. <span class="sd">        :returns:  property name  values</span>
    115. 

  115. <span class="sd">        :rtype: List</span>
    116. 

  116. 

  117. <span class="sd">        :example:</span>
    118. 

  118. <span class="sd">        &gt;&gt;&gt; import image_features_extraction as fe</span>
    119. 

  119. <span class="sd">        &gt;&gt;&gt; imgs = fe.Images(folder_name)</span>
    120. 

  120. <span class="sd">        &gt;&gt;&gt; img = imgs.item(1)</span>
    121. 

  121. <span class="sd">        &gt;&gt;&gt; regs = img.Regions()</span>
    122. 

  122. <span class="sd">        &gt;&gt;&gt; areas = regs.prop_values(&#39;area&#39;)</span>
    123. 

  123. 

  124. <span class="sd">        The following properties can be accessed as attributes or keys:</span>
    125. 

  125. 

  126. <span class="sd">        **area** : int</span>
    127. 

  127. <span class="sd">            Number of pixels of region.</span>
    128. 

  128. <span class="sd">        **bbox** : tuple</span>
    129. 

  129. <span class="sd">            Bounding box ``(min_row, min_col, max_row, max_col)``.</span>
    130. 

  130. <span class="sd">            Pixels belonging to the bounding box are in the half-open interval</span>
    131. 

  131. <span class="sd">            ``[min_row; max_row)`` and ``[min_col; max_col)``.</span>
    132. 

  132. <span class="sd">        **bbox_area** : int</span>
    133. 

  133. <span class="sd">            Number of pixels of bounding box.</span>
    134. 

  134. <span class="sd">        **centroid** : array</span>
    135. 

  135. <span class="sd">            Centroid coordinate tuple ``(row, col)``.</span>
    136. 

  136. <span class="sd">        **convex_area** : int</span>
    137. 

  137. <span class="sd">            Number of pixels of convex hull image.</span>
    138. 

  138. <span class="sd">        **convex_image** : (H, J) ndarray</span>
    139. 

  139. <span class="sd">            Binary convex hull image which has the same size as bounding box.</span>
    140. 

  140. <span class="sd">        **coords** : (N, 2) ndarray</span>
    141. 

  141. <span class="sd">            Coordinate list ``(row, col)`` of the region.</span>
    142. 

  142. <span class="sd">        **eccentricity** : float</span>
    143. 

  143. <span class="sd">            Eccentricity of the ellipse that has the same second-moments as the</span>
    144. 

  144. <span class="sd">            region. The eccentricity is the ratio of the focal distance</span>
    145. 

  145. <span class="sd">            (distance between focal points) over the major axis length.</span>
    146. 

  146. <span class="sd">            The value is in the interval [0, 1).</span>
    147. 

  147. <span class="sd">            When it is 0, the ellipse becomes a circle.</span>
    148. 

  148. <span class="sd">        **equivalent_diameter** : float</span>
    149. 

  149. <span class="sd">            The diameter of a circle with the same area as the region.</span>
    150. 

  150. <span class="sd">        **euler_number** : int</span>
    151. 

  151. <span class="sd">            Euler characteristic of region. Computed as number of objects (= 1)</span>
    152. 

  152. <span class="sd">            subtracted by number of holes (8-connectivity).</span>
    153. 

  153. <span class="sd">        **extent** : float</span>
    154. 

  154. <span class="sd">            Ratio of pixels in the region to pixels in the total bounding box.</span>
    155. 

  155. <span class="sd">            Computed as ``area / (rows * cols)``</span>
    156. 

  156. <span class="sd">        **filled_area** : int</span>
    157. 

  157. <span class="sd">            Number of pixels of filled region.</span>
    158. 

  158. <span class="sd">        **filled_image** : (H, J) ndarray</span>
    159. 

  159. <span class="sd">            Binary region image with filled holes which has the same size as</span>
    160. 

  160. <span class="sd">            bounding box.</span>
    161. 

  161. <span class="sd">        **image** : (H, J) ndarray</span>
    162. 

  162. <span class="sd">            Sliced binary region image which has the same size as bounding box.</span>
    163. 

  163. <span class="sd">        **inertia_tensor** : (2, 2) ndarray</span>
    164. 

  164. <span class="sd">            Inertia tensor of the region for the rotation around its mass.</span>
    165. 

  165. <span class="sd">        **inertia_tensor_eigvals** : tuple</span>
    166. 

  166. <span class="sd">            The two eigen values of the inertia tensor in decreasing order.</span>
    167. 

  167. <span class="sd">        **intensity_image** : ndarray</span>
    168. 

  168. <span class="sd">            Image inside region bounding box.</span>
    169. 

  169. <span class="sd">        **label** : int</span>
    170. 

  170. <span class="sd">            The label in the labeled input image.</span>
    171. 

  171. <span class="sd">        **local_centroid** : array</span>
    172. 

  172. <span class="sd">            Centroid coordinate tuple ``(row, col)``, relative to region bounding</span>
    173. 

  173. <span class="sd">            box.</span>
    174. 

  174. <span class="sd">        **major_axis_length** : float</span>
    175. 

  175. <span class="sd">            The length of the major axis of the ellipse that has the same</span>
    176. 

  176. <span class="sd">            normalized second central moments as the region.</span>
    177. 

  177. <span class="sd">        **max_intensity** : float</span>
    178. 

  178. <span class="sd">            Value with the greatest intensity in the region.</span>
    179. 

  179. <span class="sd">        **mean_intensity** : float</span>
    180. 

  180. <span class="sd">            Value with the mean intensity in the region.</span>
    181. 

  181. <span class="sd">        **min_intensity** : float</span>
    182. 

  182. <span class="sd">            Value with the least intensity in the region.</span>
    183. 

  183. <span class="sd">        **minor_axis_length** : float</span>
    184. 

  184. <span class="sd">            The length of the minor axis of the ellipse that has the same</span>
    185. 

  185. <span class="sd">            normalized second central moments as the region.</span>
    186. 

  186. <span class="sd">        **moments** : (3, 3) ndarray</span>
    187. 

  187. <span class="sd">            Spatial moments up to 3rd order::</span>
    188. 

  188. <span class="sd">                m_ji = sum{ array(x, y) * x^j * y^i }</span>
    189. 

  189. <span class="sd">            where the sum is over the `x`, `y` coordinates of the region.</span>
    190. 

  190. <span class="sd">        **moments_central** : (3, 3) ndarray</span>
    191. 

  191. <span class="sd">            Central moments (translation invariant) up to 3rd order::</span>
    192. 

  192. <span class="sd">                mu_ji = sum{ array(x, y) * (x - x_c)^j * (y - y_c)^i }</span>
    193. 

  193. <span class="sd">            where the sum is over the `x`, `y` coordinates of the region,</span>
    194. 

  194. <span class="sd">            and `x_c` and `y_c` are the coordinates of the region&#39;s centroid.</span>
    195. 

  195. <span class="sd">        **moments_hu** : tuple</span>
    196. 

  196. <span class="sd">            Hu moments (translation, scale and rotation invariant).</span>
    197. 

  197. <span class="sd">        **moments_normalized** : (3, 3) ndarray</span>
    198. 

  198. <span class="sd">            Normalized moments (translation and scale invariant) up to 3rd order::</span>
    199. 

  199. <span class="sd">                nu_ji = mu_ji / m_00^[(i+j)/2 + 1]</span>
    200. 

  200. <span class="sd">            where `m_00` is the zeroth spatial moment.</span>
    201. 

  201. <span class="sd">        **orientation** : float</span>
    202. 

  202. <span class="sd">            Angle between the X-axis and the major axis of the ellipse that has</span>
    203. 

  203. <span class="sd">            the same second-moments as the region. Ranging from `-pi/2` to</span>
    204. 

  204. <span class="sd">            `pi/2` in counter-clockwise direction.</span>
    205. 

  205. <span class="sd">        **perimeter** : float</span>
    206. 

  206. <span class="sd">            Perimeter of object which approximates the contour as a line</span>
    207. 

  207. <span class="sd">            through the centers of border pixels using a 4-connectivity.</span>
    208. 

  208. <span class="sd">        **solidity** : float</span>
    209. 

  209. <span class="sd">            Ratio of pixels in the region to pixels of the convex hull image.</span>
    210. 

  210. <span class="sd">        **weighted_centroid** : array</span>
    211. 

  211. <span class="sd">            Centroid coordinate tuple ``(row, col)`` weighted with intensity</span>
    212. 

  212. <span class="sd">            image.</span>
    213. 

  213. <span class="sd">        **weighted_local_centroid** : array</span>
    214. 

  214. <span class="sd">            Centroid coordinate tuple ``(row, col)``, relative to region bounding</span>
    215. 

  215. <span class="sd">            box, weighted with intensity image.</span>
    216. 

  216. <span class="sd">        **weighted_moments** : (3, 3) ndarray</span>
    217. 

  217. <span class="sd">            Spatial moments of intensity image up to 3rd order::</span>
    218. 

  218. <span class="sd">                wm_ji = sum{ array(x, y) * x^j * y^i }</span>
    219. 

  219. <span class="sd">            where the sum is over the `x`, `y` coordinates of the region.</span>
    220. 

  220. <span class="sd">        **weighted_moments_central** : (3, 3) ndarray</span>
    221. 

  221. <span class="sd">            Central moments (translation invariant) of intensity image up to</span>
    222. 

  222. <span class="sd">            3rd order::</span>
    223. 

  223. <span class="sd">                wmu_ji = sum{ array(x, y) * (x - x_c)^j * (y - y_c)^i }</span>
    224. 

  224. <span class="sd">            where the sum is over the `x`, `y` coordinates of the region,</span>
    225. 

  225. <span class="sd">            and `x_c` and `y_c` are the coordinates of the region&#39;s weighted</span>
    226. 

  226. <span class="sd">            centroid.</span>
    227. 

  227. <span class="sd">        **weighted_moments_hu** : tuple</span>
    228. 

  228. <span class="sd">            Hu moments (translation, scale and rotation invariant) of intensity</span>
    229. 

  229. <span class="sd">            image.</span>
    230. 

  230. <span class="sd">        **weighted_moments_normalized** : (3, 3) ndarray</span>
    231. 

  231. <span class="sd">            Normalized moments (translation and scale invariant) of intensity</span>
    232. 

  232. <span class="sd">            image up to 3rd order::</span>
    233. 

  233. <span class="sd">                wnu_ji = wmu_ji / wm_00^[(i+j)/2 + 1]</span>
    234. 

  234. <span class="sd">            where ``wm_00`` is the zeroth spatial moment (intensity-weighted area).</span>
    235. 

  235. 

  236. 

  237. <span class="sd">        .. [1] http://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.regionprops</span>
    238. 

  238. <span class="sd">        &quot;&quot;&quot;</span>
    239. 

  239.         <span class="k">try</span><span class="p">:</span>
    240. 

  240.             <span class="n">vals</span> <span class="o">=</span> <span class="p">[]</span>
    241. 

  241.             <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>
    242. 

  242.                 <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>
    243. 

  243.             <span class="k">return</span> <span class="n">vals</span>
    244. 

  244.         <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
    245. 

  245.             <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>
    246. 

  246.             <span class="k">return</span> <span class="kc">None</span></div>
    247. 

  247. 

  248. 

  249. <div class="viewcode-block" id="Regions.features"><a class="viewcode-back" href="../code.html#Regions.Regions.features">[docs]</a>    <span class="k">def</span> <span class="nf">features</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">feature_list</span><span class="p">):</span>
    250. 

  250.         <span class="sd">&quot;&quot;&quot;</span>
    251. 

  251. <span class="sd">        get_features(...)  returns a table with all  values for the property names given in input, and supplies an</span>
    252. 

  252. <span class="sd">        additional parameter for feature classification</span>
    253. 

  253. 

  254. <span class="sd">        :param features: list of property/measure names (e.g, &#39;area&#39;, &#39;centroid&#39;, etc )</span>
    255. 

  255. <span class="sd">        :type features: List</span>
    256. 

  256. <span class="sd">        :param class_value: classification label</span>
    257. 

  257. <span class="sd">        :type class_value: int, string (default=None)</span>
    258. 

  258. <span class="sd">        : param image_mask: expernal Image mask to be used for the segmentation</span>
    259. 

  259. <span class="sd">        :type image_mask: Image</span>
    260. 

  260. <span class="sd">        :returns: table cointaining all property values (columns) for all elements in the regions object  (rows)</span>
    261. 

  261. <span class="sd">        :rtype: Pandas.DataFrame</span>
    262. 

  262. <span class="sd">        :example:</span>
    263. 

  263. <span class="sd">        &gt;&gt;&gt; import image_features_extraction as fe</span>
    264. 

  264. <span class="sd">        &gt;&gt;&gt; imgs = fe.Images(folder_name)</span>
    265. 

  265. <span class="sd">        &gt;&gt;&gt; img = imgs.item(1)</span>
    266. 

  266. <span class="sd">        &gt;&gt;&gt; regs = img.Regions()</span>
    267. 

  267. <span class="sd">        &gt;&gt;&gt; feature = regs.get_features([&#39;label&#39;, &#39;area&#39;,&#39;perimeter&#39;, &#39;centroid&#39;], class_value=1)</span>
    268. 

  268. <span class="sd">        &gt;&gt;&gt;</span>
    269. 

  269. <span class="sd">        &gt;&gt;&gt; # external image mask</span>
    270. 

  270. <span class="sd">        &gt;&gt;&gt; img_masks = fe.Images(folder_name)</span>
    271. 

  271. <span class="sd">        &gt;&gt;&gt; features = regs.get_features([&#39;label&#39;, &#39;area&#39;,&#39;perimeter&#39;, &#39;centroid&#39;], class_value=1, image_mask=img_masks.item(1))</span>
    272. 

  272. 

  273. <span class="sd">        &quot;&quot;&quot;</span>
    274. 

  274.         <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>
    275. 

  275.         <span class="k">try</span><span class="p">:</span>
    276. 

  276.             <span class="k">for</span> <span class="n">feature_name</span> <span class="ow">in</span> <span class="n">feature_list</span><span class="p">:</span>
    277. 

  277.                 <span class="n">values</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">feature_name</span><span class="p">)</span>
    278. 

  278.                 <span class="n">Utils</span><span class="o">.</span><span class="n">insert_values</span><span class="p">(</span><span class="n">feature_name</span><span class="p">,</span> <span class="n">df</span><span class="p">,</span> <span class="n">values</span><span class="p">)</span>
    279. 

  279.             <span class="k">return</span> <span class="n">Features</span><span class="o">.</span><span class="n">Features</span><span class="p">(</span><span class="n">df</span><span class="p">)</span>
    280. 

  280.         <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
    281. 

  281.             <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>
    282. 

  282.             <span class="k">return</span> <span class="kc">None</span></div></div>
    283. 

  283. </pre></div>
    284. 

  284. 

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  289.         <div class="sphinxsidebarwrapper">
    290. 

  290. <h1 class="logo"><a href="../index.html">Image Features Extraction</a></h1>
    291. 

  291. 

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  299. <h3>Navigation</h3>
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