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<h1>Coverage for <b>navipy/io/ivfile.py</b> :
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</td>
<td class="text">
<p id="t1" class="stm mis"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span><span class="strut"> </span></p>
<p id="t2" class="stm mis"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span><span class="strut"> </span></p>
<p id="t3" class="pln"><span class="strut"> </span></p>
<p id="t4" class="pln"><span class="strut"> </span></p>
<p id="t5" class="stm mis"><span class="key">def</span> <span class="nam">load</span><span class="op">(</span><span class="nam">filename_tra</span><span class="op">,</span> <span class="nam">separator</span><span class="op">=</span><span class="str">' '</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t6" class="pln"> <span class="str">"""</span><span class="strut"> </span></p>
<p id="t7" class="pln"><span class="str"> Read a trajectory file created by ivTrace</span><span class="strut"> </span></p>
<p id="t8" class="pln"><span class="str"> The separator in the file is repeated such,</span><span class="strut"> </span></p>
<p id="t9" class="pln"><span class="str"> that columns are alligned in a text editor.</span><span class="strut"> </span></p>
<p id="t10" class="pln"><span class="strut"> </span></p>
<p id="t11" class="pln"><span class="str"> :param filename_tra: filename of the trajectory to load</span><span class="strut"> </span></p>
<p id="t12" class="pln"><span class="str"> :type filename_tra: string</span><span class="strut"> </span></p>
<p id="t13" class="pln"><span class="str"> :param separator:(optional, default a space), \</span><span class="strut"> </span></p>
<p id="t14" class="pln"><span class="str">the separator in the tra file</span><span class="strut"> </span></p>
<p id="t15" class="pln"><span class="str"> :type separator: string</span><span class="strut"> </span></p>
<p id="t16" class="pln"><span class="str"> :return: a pandas dataframe</span><span class="strut"> </span></p>
<p id="t17" class="pln"><span class="str"> """</span><span class="strut"> </span></p>
<p id="t18" class="stm mis"> <span class="nam">name_param_ellipse</span> <span class="op">=</span> <span class="nam">get_ellipse_param</span><span class="op">(</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t19" class="stm mis"> <span class="nam">nbcolumn</span> <span class="op">=</span> <span class="op">-</span><span class="nam">np</span><span class="op">.</span><span class="nam">inf</span><span class="strut"> </span></p>
<p id="t20" class="pln"> <span class="com"># Count the number of separators</span><span class="strut"> </span></p>
<p id="t21" class="stm mis"> <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">filename_tra</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">f</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t22" class="stm mis"> <span class="key">for</span> <span class="nam">line_i</span><span class="op">,</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">f</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t23" class="stm mis"> <span class="nam">nbcol</span> <span class="op">=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="nam">separator</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t24" class="stm mis"> <span class="key">if</span> <span class="nam">nbcol</span> <span class="op">></span> <span class="nam">nbcolumn</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t25" class="stm mis"> <span class="nam">nbcolumn</span> <span class="op">=</span> <span class="nam">nbcol</span><span class="strut"> </span></p>
<p id="t26" class="pln"> <span class="com"># print(line_i,nbcolumn)</span><span class="strut"> </span></p>
<p id="t27" class="stm mis"> <span class="nam">nb_line</span> <span class="op">=</span> <span class="nam">line_i</span><span class="strut"> </span></p>
<p id="t28" class="pln"> <span class="com"># print(nb_line)</span><span class="strut"> </span></p>
<p id="t29" class="pln"><span class="strut"> </span></p>
<p id="t30" class="pln"> <span class="com"># Create a dataframe with the number of detected columns and lines</span><span class="strut"> </span></p>
<p id="t31" class="stm mis"> <span class="nam">data</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="nam">index</span><span class="op">=</span><span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">nb_line</span><span class="op">)</span><span class="op">,</span> <span class="nam">columns</span><span class="op">=</span><span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">nbcol</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t32" class="pln"> <span class="com"># Populate the dataframe with the data</span><span class="strut"> </span></p>
<p id="t33" class="pln"> <span class="com"># Empty columns are skipped in the following manner:</span><span class="strut"> </span></p>
<p id="t34" class="pln"> <span class="com"># if 1st column is empty in the file, and the 2nd is not,</span><span class="strut"> </span></p>
<p id="t35" class="pln"> <span class="com"># the 2nd column will be at the first column of data</span><span class="strut"> </span></p>
<p id="t36" class="stm mis"> <span class="key">import</span> <span class="nam">re</span><span class="strut"> </span></p>
<p id="t37" class="stm mis"> <span class="nam">nums</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="str">r"[+-]?\d+(?:\.\d+)?"</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t38" class="stm mis"> <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">filename_tra</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">f</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t39" class="stm mis"> <span class="key">for</span> <span class="nam">line_i</span><span class="op">,</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">f</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t40" class="pln"> <span class="com"># print(line_i)</span><span class="strut"> </span></p>
<p id="t41" class="stm mis"> <span class="nam">m</span> <span class="op">=</span> <span class="nam">nums</span><span class="op">.</span><span class="nam">search</span><span class="op">(</span><span class="nam">line</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t42" class="stm mis"> <span class="nam">frame_i</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">m</span><span class="op">.</span><span class="nam">group</span><span class="op">(</span><span class="num">0</span><span class="op">)</span><span class="op">)</span> <span class="com"># '{:7d}'</span><span class="strut"> </span></p>
<p id="t43" class="stm mis"> <span class="nam">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="op">(</span><span class="nam">line</span><span class="op">.</span><span class="nam">find</span><span class="op">(</span><span class="nam">m</span><span class="op">.</span><span class="nam">group</span><span class="op">(</span><span class="num">0</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> <span class="nam">len</span><span class="op">(</span><span class="nam">m</span><span class="op">.</span><span class="nam">group</span><span class="op">(</span><span class="num">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">:</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t44" class="stm mis"> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">line_i</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="nam">frame_i</span><span class="strut"> </span></p>
<p id="t45" class="stm mis"> <span class="nam">col_i</span> <span class="op">=</span> <span class="num">1</span><span class="strut"> </span></p>
<p id="t46" class="stm mis"> <span class="key">while</span> <span class="nam">len</span><span class="op">(</span><span class="nam">line</span><span class="op">)</span> <span class="op">></span> <span class="num">39</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t47" class="stm mis"> <span class="nam">cline</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="op">:</span><span class="num">8</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t48" class="stm mis"> <span class="key">if</span> <span class="nam">cline</span> <span class="op">==</span> <span class="str">' '</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t49" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="strut"> </span></p>
<p id="t50" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t51" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">float</span><span class="op">(</span><span class="nam">cline</span><span class="op">)</span> <span class="com"># ' {:7.2f}'</span><span class="strut"> </span></p>
<p id="t52" class="stm mis"> <span class="nam">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">8</span><span class="op">:</span><span class="op">]</span> <span class="com"># Truncate line it is easier to process later</span><span class="strut"> </span></p>
<p id="t53" class="stm mis"> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">line_i</span><span class="op">,</span> <span class="nam">col_i</span><span class="op">]</span> <span class="op">=</span> <span class="nam">field</span><span class="strut"> </span></p>
<p id="t54" class="stm mis"> <span class="nam">col_i</span> <span class="op">+=</span> <span class="num">1</span><span class="strut"> </span></p>
<p id="t55" class="stm mis"> <span class="nam">cline</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="op">:</span><span class="num">8</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t56" class="stm mis"> <span class="key">if</span> <span class="nam">cline</span> <span class="op">==</span> <span class="str">' '</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t57" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="strut"> </span></p>
<p id="t58" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t59" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">float</span><span class="op">(</span><span class="nam">cline</span><span class="op">)</span> <span class="com"># ' {:7.2f}'</span><span class="strut"> </span></p>
<p id="t60" class="stm mis"> <span class="nam">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">8</span><span class="op">:</span><span class="op">]</span> <span class="com"># Truncate line it is easier to process later</span><span class="strut"> </span></p>
<p id="t61" class="stm mis"> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">line_i</span><span class="op">,</span> <span class="nam">col_i</span><span class="op">]</span> <span class="op">=</span> <span class="nam">field</span><span class="strut"> </span></p>
<p id="t62" class="stm mis"> <span class="nam">col_i</span> <span class="op">+=</span> <span class="num">1</span><span class="strut"> </span></p>
<p id="t63" class="stm mis"> <span class="nam">cline</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="op">:</span><span class="num">10</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t64" class="stm mis"> <span class="key">if</span> <span class="nam">cline</span> <span class="op">==</span> <span class="str">' '</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t65" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="strut"> </span></p>
<p id="t66" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t67" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">float</span><span class="op">(</span><span class="nam">cline</span><span class="op">)</span> <span class="com"># ' {:7.2f}'</span><span class="strut"> </span></p>
<p id="t68" class="stm mis"> <span class="nam">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">10</span><span class="op">:</span><span class="op">]</span> <span class="com"># Truncate line it is easier to process later</span><span class="strut"> </span></p>
<p id="t69" class="stm mis"> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">line_i</span><span class="op">,</span> <span class="nam">col_i</span><span class="op">]</span> <span class="op">=</span> <span class="nam">field</span><span class="strut"> </span></p>
<p id="t70" class="stm mis"> <span class="nam">col_i</span> <span class="op">+=</span> <span class="num">1</span><span class="strut"> </span></p>
<p id="t71" class="stm mis"> <span class="nam">cline</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="op">:</span><span class="num">6</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t72" class="stm mis"> <span class="key">if</span> <span class="nam">cline</span> <span class="op">==</span> <span class="str">' '</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t73" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="strut"> </span></p>
<p id="t74" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t75" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">cline</span><span class="op">)</span> <span class="com"># ' {:7.2f}'</span><span class="strut"> </span></p>
<p id="t76" class="stm mis"> <span class="nam">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">6</span><span class="op">:</span><span class="op">]</span> <span class="com"># Truncate line it is easier to process later</span><span class="strut"> </span></p>
<p id="t77" class="stm mis"> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">line_i</span><span class="op">,</span> <span class="nam">col_i</span><span class="op">]</span> <span class="op">=</span> <span class="nam">field</span><span class="strut"> </span></p>
<p id="t78" class="stm mis"> <span class="nam">col_i</span> <span class="op">+=</span> <span class="num">1</span><span class="strut"> </span></p>
<p id="t79" class="stm mis"> <span class="nam">cline</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="op">:</span><span class="num">7</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t80" class="stm mis"> <span class="key">if</span> <span class="nam">cline</span> <span class="op">==</span> <span class="str">' '</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t81" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="strut"> </span></p>
<p id="t82" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t83" class="stm mis"> <span class="nam">field</span> <span class="op">=</span> <span class="nam">float</span><span class="op">(</span><span class="nam">cline</span><span class="op">)</span> <span class="com"># ' {:7.2f}'</span><span class="strut"> </span></p>
<p id="t84" class="stm mis"> <span class="nam">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">7</span><span class="op">:</span><span class="op">]</span> <span class="com"># Truncate line it is easier to process later</span><span class="strut"> </span></p>
<p id="t85" class="stm mis"> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">line_i</span><span class="op">,</span> <span class="nam">col_i</span><span class="op">]</span> <span class="op">=</span> <span class="nam">field</span><span class="strut"> </span></p>
<p id="t86" class="stm mis"> <span class="nam">col_i</span> <span class="op">+=</span> <span class="num">1</span><span class="strut"> </span></p>
<p id="t87" class="pln"> <span class="com"># We remove unecessary columns:</span><span class="strut"> </span></p>
<p id="t88" class="stm mis"> <span class="nam">data_2</span> <span class="op">=</span> <span class="nam">data</span><span class="op">.</span><span class="nam">set_index</span><span class="op">(</span><span class="nam">keys</span><span class="op">=</span><span class="num">0</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t89" class="stm mis"> <span class="nam">data_2</span><span class="op">.</span><span class="nam">index</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">'frame'</span><span class="strut"> </span></p>
<p id="t90" class="stm mis"> <span class="nam">data_2</span> <span class="op">=</span> <span class="nam">data_2</span><span class="op">.</span><span class="nam">dropna</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">,</span> <span class="nam">how</span><span class="op">=</span><span class="str">'all'</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t91" class="stm mis"> <span class="nam">data_2</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">data_2</span><span class="op">.</span><span class="nam">index</span><span class="op">.</span><span class="nam">astype</span><span class="op">(</span><span class="nam">int</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t92" class="stm mis"> <span class="nam">data_2</span> <span class="op">=</span> <span class="nam">data_2</span><span class="op">.</span><span class="nam">astype</span><span class="op">(</span><span class="nam">float</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t93" class="pln"> <span class="com"># Calculate the number of ellipses</span><span class="strut"> </span></p>
<p id="t94" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">mod</span><span class="op">(</span><span class="nam">data_2</span><span class="op">.</span><span class="nam">shape</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">name_param_ellipse</span><span class="op">)</span><span class="op">)</span> <span class="op">!=</span> <span class="num">0</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t95" class="stm mis"> <span class="nam">msg</span> <span class="op">=</span> <span class="str">"Wrong number of ellipses read from files"</span><span class="strut"> </span></p>
<p id="t96" class="stm mis"> <span class="nam">msg</span> <span class="op">+=</span> <span class="str">"{} not devisable by {}"</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">data_2</span><span class="op">.</span><span class="nam">shape</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">,</span><span class="strut"> </span></p>
<p id="t97" class="pln"> <span class="nam">len</span><span class="op">(</span><span class="nam">name_param_ellipse</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t98" class="stm mis"> <span class="key">raise</span> <span class="nam">IOError</span><span class="op">(</span><span class="nam">msg</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t99" class="pln"> <span class="com"># Name nicely the data</span><span class="strut"> </span></p>
<p id="t100" class="stm mis"> <span class="nam">columns</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t101" class="stm mis"> <span class="key">for</span> <span class="nam">mark_i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">data_2</span><span class="op">.</span><span class="nam">shape</span><span class="op">[</span><span class="num">1</span><span class="op">]</span> <span class="op">//</span> <span class="nam">len</span><span class="op">(</span><span class="nam">name_param_ellipse</span><span class="op">)</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t102" class="stm mis"> <span class="key">for</span> <span class="nam">label</span> <span class="key">in</span> <span class="nam">name_param_ellipse</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t103" class="stm mis"> <span class="nam">columns</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="op">(</span><span class="nam">mark_i</span><span class="op">,</span> <span class="nam">label</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t104" class="stm mis"> <span class="nam">data_2</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">MultiIndex</span><span class="op">.</span><span class="nam">from_tuples</span><span class="op">(</span><span class="nam">columns</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t105" class="stm mis"> <span class="nam">data_2</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">names</span> <span class="op">=</span> <span class="op">[</span><span class="str">'marker'</span><span class="op">,</span> <span class="str">'ellipse_param'</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t106" class="stm mis"> <span class="nam">data_2</span><span class="op">.</span><span class="nam">head</span><span class="op">(</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t107" class="stm mis"> <span class="key">return</span> <span class="nam">data_2</span><span class="strut"> </span></p>
<p id="t108" class="pln"><span class="strut"> </span></p>
<p id="t109" class="pln"><span class="strut"> </span></p>
<p id="t110" class="stm mis"><span class="key">def</span> <span class="nam">get_nbmarker</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t111" class="stm mis"> <span class="key">return</span> <span class="nam">len</span><span class="op">(</span><span class="nam">data</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">levels</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t112" class="pln"><span class="strut"> </span></p>
<p id="t113" class="pln"><span class="strut"> </span></p>
<p id="t114" class="stm mis"><span class="key">def</span> <span class="nam">get_ellipse_param</span><span class="op">(</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t115" class="stm mis"> <span class="key">return</span> <span class="op">[</span><span class="str">'x'</span><span class="op">,</span> <span class="str">'y'</span><span class="op">,</span> <span class="str">'orientation'</span><span class="op">,</span> <span class="str">'size'</span><span class="op">,</span> <span class="str">'roundness'</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t116" class="pln"><span class="strut"> </span></p>
<p id="t117" class="pln"><span class="strut"> </span></p>
<p id="t118" class="stm mis"><span class="key">def</span> <span class="nam">append</span><span class="op">(</span><span class="nam">tra_file</span><span class="op">,</span> <span class="nam">frame_i</span><span class="op">,</span> <span class="nam">ellipses</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t119" class="pln"> <span class="str">""" Append a line in a ivtrace files</span><span class="strut"> </span></p>
<p id="t120" class="pln"><span class="str"> an ascii file reconstructing the format ivTrace writes.</span><span class="strut"> </span></p>
<p id="t121" class="pln"><span class="strut"> </span></p>
<p id="t122" class="pln"><span class="str"> line format:</span><span class="strut"> </span></p>
<p id="t123" class="pln"><span class="str"> '{:7d} {:7.2f} {:7.2f} {:9.5f} {:5d} {:6.2f} {:7.2f} {:7.2f} {:9.5f} ... '</span><span class="strut"> </span></p>
<p id="t124" class="pln"><span class="str"> ^ ^ ^ ^ ^ ^ | ^ ^ ^</span><span class="strut"> </span></p>
<p id="t125" class="pln"><span class="str"> | | | | | | | | | |</span><span class="strut"> </span></p>
<p id="t126" class="pln"><span class="str"> Frame# | | angle | eccentricity | | angle</span><span class="strut"> </span></p>
<p id="t127" class="pln"><span class="str"> | x y area | x y</span><span class="strut"> </span></p>
<p id="t128" class="pln"><span class="str"> |<---------------Ellipse #1 ------------->| |<--------Ellipse #2 --->...</span><span class="strut"> </span></p>
<p id="t129" class="pln"><span class="strut"> </span></p>
<p id="t130" class="pln"><span class="strut"> </span></p>
<p id="t131" class="pln"><span class="str"> :param file: file to append the line</span><span class="strut"> </span></p>
<p id="t132" class="pln"><span class="str"> :type file: file</span><span class="strut"> </span></p>
<p id="t133" class="pln"><span class="str"> :param frame_i: frame number</span><span class="strut"> </span></p>
<p id="t134" class="pln"><span class="str"> :type frame_i: integer</span><span class="strut"> </span></p>
<p id="t135" class="pln"><span class="str"> :param ellipses: a Nx5 array containing x,y,Ma,ma,angle of an\</span><span class="strut"> </span></p>
<p id="t136" class="pln"><span class="str">ellipse</span><span class="strut"> </span></p>
<p id="t137" class="pln"><span class="str"> :type ellipses: a numpy array</span><span class="strut"> </span></p>
<p id="t138" class="pln"><span class="str"> """</span><span class="strut"> </span></p>
<p id="t139" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'{:7d}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">frame_i</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t140" class="pln"> <span class="com"># for each region write 5 fields...</span><span class="strut"> </span></p>
<p id="t141" class="stm mis"> <span class="key">for</span> <span class="nam">ell</span> <span class="key">in</span> <span class="nam">ellipses</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t142" class="stm mis"> <span class="nam">ell_x</span> <span class="op">=</span> <span class="nam">ell</span><span class="op">.</span><span class="nam">x</span><span class="strut"> </span></p>
<p id="t143" class="stm mis"> <span class="nam">ell_y</span> <span class="op">=</span> <span class="nam">ell</span><span class="op">.</span><span class="nam">y</span><span class="strut"> </span></p>
<p id="t144" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">any</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="op">[</span><span class="nam">ell</span><span class="op">.</span><span class="nam">width</span><span class="op">,</span> <span class="nam">ell</span><span class="op">.</span><span class="nam">height</span><span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t145" class="stm mis"> <span class="nam">ell_area</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="strut"> </span></p>
<p id="t146" class="stm mis"> <span class="nam">ell_ecc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="strut"> </span></p>
<p id="t147" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t148" class="stm mis"> <span class="nam">ell_area</span> <span class="op">=</span> <span class="nam">ell</span><span class="op">.</span><span class="nam">area</span><span class="strut"> </span></p>
<p id="t149" class="stm mis"> <span class="key">if</span> <span class="nam">ell</span><span class="op">.</span><span class="nam">width</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t150" class="stm mis"> <span class="nam">ell_ecc</span> <span class="op">=</span> <span class="num">1</span><span class="strut"> </span></p>
<p id="t151" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t152" class="stm mis"> <span class="nam">ell_ecc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">ell</span><span class="op">.</span><span class="nam">roundness</span><span class="op">)</span><span class="op">**</span><span class="num">2</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t153" class="stm mis"> <span class="nam">ell_angle</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">deg2rad</span><span class="op">(</span><span class="nam">ell</span><span class="op">.</span><span class="nam">angle</span><span class="op">)</span> <span class="op">+</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">2</span> <span class="com"># Because ivTrace</span><span class="strut"> </span></p>
<p id="t154" class="pln"><span class="strut"> </span></p>
<p id="t155" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">ell_x</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t156" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t157" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t158" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:7.2f}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">ell_x</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t159" class="pln"><span class="strut"> </span></p>
<p id="t160" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">ell_y</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t161" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t162" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t163" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:7.2f}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">ell_y</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t164" class="pln"><span class="strut"> </span></p>
<p id="t165" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">ell_angle</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t166" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t167" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t168" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:9.5f}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">ell_angle</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t169" class="pln"><span class="strut"> </span></p>
<p id="t170" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">ell_area</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t171" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t172" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t173" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:5d}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">round</span><span class="op">(</span><span class="nam">ell_area</span><span class="op">)</span><span class="op">.</span><span class="nam">astype</span><span class="op">(</span><span class="nam">int</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t174" class="pln"><span class="strut"> </span></p>
<p id="t175" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">ell_ecc</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t176" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t177" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t178" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:6.2f}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">ell_ecc</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t179" class="pln"> <span class="com"># append end of line</span><span class="strut"> </span></p>
<p id="t180" class="stm mis"> <span class="nam">tra_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'\n'</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t181" class="pln"><span class="strut"> </span></p>
<p id="t182" class="pln"><span class="strut"> </span></p>
<p id="t183" class="stm mis"><span class="key">def</span> <span class="nam">save</span><span class="op">(</span><span class="nam">traFile</span><span class="op">,</span> <span class="nam">data</span><span class="op">,</span> <span class="nam">mode</span><span class="op">=</span><span class="str">'w'</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t184" class="pln"> <span class="str">"""</span><span class="strut"> </span></p>
<p id="t185" class="pln"><span class="str"> write_tra - write trajectory data into an ivtrace file</span><span class="strut"> </span></p>
<p id="t186" class="pln"><span class="str"> write_tra (traFile, traData) writes the trajectory data in traData into</span><span class="strut"> </span></p>
<p id="t187" class="pln"><span class="str"> an ascii file reconstructing the format ivTrace writes.</span><span class="strut"> </span></p>
<p id="t188" class="pln"><span class="strut"> </span></p>
<p id="t189" class="pln"><span class="str"> :param traFile: filename of the trajectory</span><span class="strut"> </span></p>
<p id="t190" class="pln"><span class="str"> :type traFile: string</span><span class="strut"> </span></p>
<p id="t191" class="pln"><span class="str"> :param traData: Dataframe with index the frame number</span><span class="strut"> </span></p>
<p id="t192" class="pln"><span class="str"> :type traData: pandas dataframe</span><span class="strut"> </span></p>
<p id="t193" class="pln"><span class="strut"> </span></p>
<p id="t194" class="pln"><span class="str"> >>write_tra_file('trajectory.tra', data);</span><span class="strut"> </span></p>
<p id="t195" class="pln"><span class="str"> """</span><span class="strut"> </span></p>
<p id="t196" class="pln"> <span class="com"># Convert dataframe to matrix</span><span class="strut"> </span></p>
<p id="t197" class="stm mis"> <span class="nam">nb_markers</span> <span class="op">=</span> <span class="nam">get_nbmarker</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t198" class="stm mis"> <span class="nam">name_param_ellipse</span> <span class="op">=</span> <span class="nam">get_ellipse_param</span><span class="op">(</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t199" class="pln"> <span class="com"># Save</span><span class="strut"> </span></p>
<p id="t200" class="stm mis"> <span class="nam">file</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">traFile</span><span class="op">,</span> <span class="nam">mode</span><span class="op">,</span> <span class="nam">newline</span><span class="op">=</span><span class="str">'\n'</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t201" class="stm mis"> <span class="key">for</span> <span class="nam">frame_i</span> <span class="key">in</span> <span class="nam">data</span><span class="op">.</span><span class="nam">index</span><span class="op">.</span><span class="nam">values</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t202" class="pln"> <span class="com"># print index field of the line</span><span class="strut"> </span></p>
<p id="t203" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'{:7d}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">int</span><span class="op">(</span><span class="nam">frame_i</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t204" class="pln"> <span class="com"># for each region write 5 fields...</span><span class="strut"> </span></p>
<p id="t205" class="stm mis"> <span class="key">for</span> <span class="nam">mark_i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">nb_markers</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t206" class="stm mis"> <span class="nam">val</span> <span class="op">=</span> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">frame_i</span><span class="op">,</span> <span class="op">(</span><span class="nam">mark_i</span><span class="op">,</span> <span class="nam">name_param_ellipse</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">)</span><span class="op">]</span> <span class="com"># x</span><span class="strut"> </span></p>
<p id="t207" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t208" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t209" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t210" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:7.2f}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t211" class="pln"><span class="strut"> </span></p>
<p id="t212" class="stm mis"> <span class="nam">val</span> <span class="op">=</span> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">frame_i</span><span class="op">,</span> <span class="op">(</span><span class="nam">mark_i</span><span class="op">,</span> <span class="nam">name_param_ellipse</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span><span class="op">]</span> <span class="com"># y</span><span class="strut"> </span></p>
<p id="t213" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t214" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t215" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t216" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:7.2f}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t217" class="pln"><span class="strut"> </span></p>
<p id="t218" class="pln"> <span class="com"># orientation</span><span class="strut"> </span></p>
<p id="t219" class="stm mis"> <span class="nam">val</span> <span class="op">=</span> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">frame_i</span><span class="op">,</span> <span class="op">(</span><span class="nam">mark_i</span><span class="op">,</span> <span class="nam">name_param_ellipse</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">)</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t220" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t221" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t222" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t223" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:9.5f}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t224" class="pln"><span class="strut"> </span></p>
<p id="t225" class="stm mis"> <span class="nam">val</span> <span class="op">=</span> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">frame_i</span><span class="op">,</span> <span class="op">(</span><span class="nam">mark_i</span><span class="op">,</span> <span class="nam">name_param_ellipse</span><span class="op">[</span><span class="num">3</span><span class="op">]</span><span class="op">)</span><span class="op">]</span> <span class="com"># size</span><span class="strut"> </span></p>
<p id="t226" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t227" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t228" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t229" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:5d}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">int</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t230" class="pln"><span class="strut"> </span></p>
<p id="t231" class="pln"> <span class="com"># roundness</span><span class="strut"> </span></p>
<p id="t232" class="stm mis"> <span class="nam">val</span> <span class="op">=</span> <span class="nam">data</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">frame_i</span><span class="op">,</span> <span class="op">(</span><span class="nam">mark_i</span><span class="op">,</span> <span class="nam">name_param_ellipse</span><span class="op">[</span><span class="num">4</span><span class="op">]</span><span class="op">)</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t233" class="stm mis"> <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">isnan</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t234" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t235" class="pln"> <span class="key">else</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t236" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">' {:6.2f}'</span><span class="op">.</span><span class="nam">format</span><span class="op">(</span><span class="nam">val</span><span class="op">)</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t237" class="pln"> <span class="com"># append end of line</span><span class="strut"> </span></p>
<p id="t238" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">'\n'</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t239" class="stm mis"> <span class="nam">file</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t240" class="pln"><span class="strut"> </span></p>
<p id="t241" class="pln"><span class="strut"> </span></p>
<p id="t242" class="stm mis"><span class="key">def</span> <span class="nam">manhattan</span><span class="op">(</span><span class="nam">filename</span><span class="op">,</span> <span class="nam">corner_th</span><span class="op">=</span><span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t243" class="pln"> <span class="str">"""Load a manhattan clicked on ivTrace</span><span class="strut"> </span></p>
<p id="t244" class="pln"><span class="strut"> </span></p>
<p id="t245" class="pln"><span class="str"> The points within the top left corner will be set to NaN</span><span class="strut"> </span></p>
<p id="t246" class="pln"><span class="str"> The corner region is: [[0, corner_th],[0, corner_th]]</span><span class="strut"> </span></p>
<p id="t247" class="pln"><span class="strut"> </span></p>
<p id="t248" class="pln"><span class="str"> :param filename: the ivTrace file (.tra file)</span><span class="strut"> </span></p>
<p id="t249" class="pln"><span class="str"> :type filename: str</span><span class="strut"> </span></p>
<p id="t250" class="pln"><span class="str"> :param corner_th: threshold to ignore points</span><span class="strut"> </span></p>
<p id="t251" class="pln"><span class="str"> :type corner_th: numeric</span><span class="strut"> </span></p>
<p id="t252" class="pln"><span class="str"> :returns: A x,y manhattan with index i, the i-th tower</span><span class="strut"> </span></p>
<p id="t253" class="pln"><span class="str"> :rtype: pd.DataFrame</span><span class="strut"> </span></p>
<p id="t254" class="pln"><span class="str"> """</span><span class="strut"> </span></p>
<p id="t255" class="pln"><span class="strut"> </span></p>
<p id="t256" class="stm mis"> <span class="nam">df</span> <span class="op">=</span> <span class="nam">load</span><span class="op">(</span><span class="nam">filename</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t257" class="stm mis"> <span class="nam">manhattan_2d</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="nam">index</span><span class="op">=</span><span class="nam">range</span><span class="op">(</span><span class="nam">get_nbmarker</span><span class="op">(</span><span class="nam">df</span><span class="op">)</span><span class="op">)</span><span class="op">,</span><span class="strut"> </span></p>
<p id="t258" class="pln"> <span class="nam">columns</span><span class="op">=</span><span class="op">[</span><span class="str">'x'</span><span class="op">,</span> <span class="str">'y'</span><span class="op">]</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t259" class="pln"><span class="strut"> </span></p>
<p id="t260" class="stm mis"> <span class="nam">df</span> <span class="op">=</span> <span class="nam">df</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="num">0</span><span class="op">,</span> <span class="op">:</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t261" class="stm mis"> <span class="key">for</span> <span class="nam">mark_i</span> <span class="key">in</span> <span class="nam">manhattan_2d</span><span class="op">.</span><span class="nam">index</span><span class="op">:</span><span class="strut"> </span></p>
<p id="t262" class="stm mis"> <span class="nam">manhattan_2d</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">mark_i</span><span class="op">,</span> <span class="str">'x'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">df</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="op">(</span><span class="nam">mark_i</span><span class="op">,</span> <span class="str">'x'</span><span class="op">)</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t263" class="stm mis"> <span class="nam">manhattan_2d</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">mark_i</span><span class="op">,</span> <span class="str">'y'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">df</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="op">(</span><span class="nam">mark_i</span><span class="op">,</span> <span class="str">'y'</span><span class="op">)</span><span class="op">]</span><span class="strut"> </span></p>
<p id="t264" class="stm mis"> <span class="nam">topleft_corner</span> <span class="op">=</span> <span class="op">(</span><span class="nam">manhattan_2d</span><span class="op">.</span><span class="nam">x</span> <span class="op"><</span> <span class="nam">corner_th</span><span class="op">)</span> <span class="xx">\</span><span class="strut"> </span></p>
<p id="t265" class="pln"> <span class="op">&</span> <span class="op">(</span><span class="nam">manhattan_2d</span><span class="op">.</span><span class="nam">y</span> <span class="op"><</span> <span class="nam">corner_th</span><span class="op">)</span><span class="strut"> </span></p>
<p id="t266" class="stm mis"> <span class="nam">manhattan_2d</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">topleft_corner</span><span class="op">,</span> <span class="op">:</span><span class="op">]</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="strut"> </span></p>
<p id="t267" class="stm mis"> <span class="key">return</span> <span class="nam">manhattan_2d</span><span class="strut"> </span></p>
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