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<li class="navelem"><a class="el" href="dir_b145db2560fed4586389316a9c647f44.html">volumetric</a></li> </ul>
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<div class="title">3dVolMarchingCubes.cpp</div> </div>
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<div class="contents">
<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span>  </div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="preprocessor">#include <queue></span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#include <boost/program_options/options_description.hpp></span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor">#include <boost/program_options/parsers.hpp></span></div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#include <boost/program_options/variables_map.hpp></span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#include <DGtal/kernel/sets/SetPredicate.h></span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor">#include <DGtal/io/readers/VolReader.h></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <DGtal/images/ImageSelector.h></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <DGtal/images/SimpleThresholdForegroundPredicate.h></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <DGtal/images/ImageLinearCellEmbedder.h></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <DGtal/shapes/Shapes.h></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <DGtal/kernel/CanonicEmbedder.h></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <DGtal/helpers/StdDefs.h></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <DGtal/topology/helpers/Surfaces.h></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <DGtal/topology/DigitalSurface.h></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <DGtal/topology/SetOfSurfels.h></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <DGtal/geometry/volumes/KanungoNoise.h></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  </div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#include "CLI11.hpp"</span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  </div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  </div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="keyword">using namespace </span><a class="code" href="namespaceDGtal.html">DGtal</a>;</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="keyword">using namespace </span>Z3i;</div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  </div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="keywordtype">int</span> <a class="code" href="3dHeightMapViewer_8cpp.html#a3c04138a5bfe5d72780bb7e82a18e627">main</a>( <span class="keywordtype">int</span> argc, <span class="keywordtype">char</span>** argv )</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> {</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  </div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="comment">// parse command line using CLI ----------------------------------------------</span></div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  CLI::App app;</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  std::string inputFileName;</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  std::string outputFileName {<span class="stringliteral">"marching-cubes.off"</span>};</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keywordtype">double</span> noise;</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordtype">double</span> threshold {1.0};</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> intAdjacency = 0;</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  </div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  app.description(<span class="stringliteral">"Outputs the isosurface of value <threshold> of the volume <fileName.vol> as an OFF file <output.off>. The <adjacency> (0/1) allows to choose between interior (6,18) and exterior (18,6) adjacency."</span>);</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  app.add_option(<span class="stringliteral">"-i,--input,1"</span>, inputFileName, <span class="stringliteral">"the volume file (.vol)."</span> )</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  ->required()</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  ->check(CLI::ExistingFile);</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  app.add_option(<span class="stringliteral">"--threshold,-t"</span>,threshold, <span class="stringliteral">"the value that defines the isosurface in the image (an integer between 0 and 255)."</span>, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  app.add_option(<span class="stringliteral">"--adjacency,-a"</span>,intAdjacency, <span class="stringliteral">"0: interior adjacency, 1: exterior adjacency"</span>, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  app.add_option(<span class="stringliteral">"-o,--output,2"</span>, outputFileName, <span class="stringliteral">"the output OFF file that represents the geometry of the isosurface"</span>, <span class="keyword">true</span> );</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keyword">auto</span> noiseOpt = app.add_option(<span class="stringliteral">"--noise,-n"</span>, noise, <span class="stringliteral">"Kanungo noise level in ]0,1[. Note that only the largest connected component is considered and that no specific embedder is used."</span>);</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  </div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  app.get_formatter()->column_width(40);</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  CLI11_PARSE(app, argc, argv);</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">// END parse command line using CLI ----------------------------------------------</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  </div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  </div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  </div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordtype">bool</span> addNoise=<span class="keyword">false</span>;</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordflow">if</span> (noiseOpt->count() > 0 )</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  {</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  addNoise=<span class="keyword">true</span>;</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  }</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  </div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a352b7160bf722e2f0bcbee5d0bad6ef3">beginBlock</a>( <span class="stringliteral">"Reading vol file into an image."</span> );</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="keyword">typedef</span> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1ImageContainerBySTLVector.html">ImageSelector < Domain, int>::Type</a> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html">Image</a>;</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html">Image</a> image = <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/structDGtal_1_1VolReader.html#aa4f1ebd956ed345e4c64e78c83da25d2">VolReader<Image>::importVol</a>(inputFileName);</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  </div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keyword">typedef</span> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1functors_1_1SimpleThresholdForegroundPredicate.html">functors::SimpleThresholdForegroundPredicate<Image></a> ThresholdedImage;</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  ThresholdedImage thresholdedImage( image, threshold );</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#afa3a2874289734884107b1ce68ccb93d">endBlock</a>();</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  </div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  </div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a352b7160bf722e2f0bcbee5d0bad6ef3">beginBlock</a>( <span class="stringliteral">"Construct the Khalimsky space from the image domain."</span> );</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1KhalimskySpaceND.html">KSpace</a> ks;</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="keywordtype">bool</span> space_ok =</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  ks.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1KhalimskySpaceND.html#a15dcbcaae831dd1c36090e6336c177d4">init</a>( image.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html#a28a1c55de323d0d0ec62d2db03eaf180">domain</a>().<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1HyperRectDomain.html#a57d51405819b9b13110d7b84d0a154d8">lowerBound</a>(), image.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html#a28a1c55de323d0d0ec62d2db03eaf180">domain</a>().<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1HyperRectDomain.html#a0a1a964e1595dd2651a76e3cfb46fdf4">upperBound</a>(), <span class="keyword">true</span> );</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="keywordflow">if</span> (!space_ok)</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  {</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a1e786a1f3b1047e92b73c82f67e3c295">error</a>() << <span class="stringliteral">"Error in the Khamisky space construction."</span><<std::endl;</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="keywordflow">return</span> 2;</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  }</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#afa3a2874289734884107b1ce68ccb93d">endBlock</a>();</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  </div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keyword">typedef</span> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1SurfelAdjacency.html">SurfelAdjacency<KSpace::dimension></a> MySurfelAdjacency;</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  MySurfelAdjacency surfAdj( intAdjacency ); <span class="comment">// interior in all directions.</span></div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span> <span class="comment"></span> </div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a352b7160bf722e2f0bcbee5d0bad6ef3">beginBlock</a>( <span class="stringliteral">"Extracting boundary by scanning the space. "</span> );</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keyword">typedef</span> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1KhalimskySpaceND.html#a0a02413be83a0f38f23ed5cb45c2bcc4">KSpace::SurfelSet</a> SurfelSet;</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keyword">typedef</span> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1SetOfSurfels.html">SetOfSurfels< KSpace, SurfelSet ></a> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1SetOfSurfels.html">MySetOfSurfels</a>;</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keyword">typedef</span> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1DigitalSurface.html">DigitalSurface< MySetOfSurfels ></a> MyDigitalSurface;</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1SetOfSurfels.html">MySetOfSurfels</a> theSetOfSurfels( ks, surfAdj );</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  </div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="keywordflow">if</span> (addNoise)</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  {</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#ad054990834d2763627166540087a2980">info</a>()<<<span class="stringliteral">"Adding some noise."</span><<std::endl;</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1KanungoNoise.html">KanungoNoise<ThresholdedImage, Z3i::Domain></a> kanungo(thresholdedImage, image.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html#a28a1c55de323d0d0ec62d2db03eaf180">domain</a>(), noise);</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  std::vector< std::vector<SCell > > vectConnectedSCell;</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#ad054990834d2763627166540087a2980">info</a>()<<<span class="stringliteral">"Extracting all connected components."</span><<std::endl;</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Surfaces.html#a19b214170d160153376c4ecf3497de3f">Surfaces<KSpace>::extractAllConnectedSCell</a>( vectConnectedSCell, ks, surfAdj,</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  kanungo, <span class="keyword">false</span>);</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  <span class="keywordflow">if</span>( vectConnectedSCell.size() == 0 )</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  {</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a1e786a1f3b1047e92b73c82f67e3c295">error</a>()<< <span class="stringliteral">"No surface component exists. Please check the vol file --min and --max parameters."</span> << std::endl;</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="keywordflow">return</span> 3;</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  }</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  </div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#ad054990834d2763627166540087a2980">info</a>()<<vectConnectedSCell.size()<<<span class="stringliteral">" components."</span><<std::endl;</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  </div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#ad054990834d2763627166540087a2980">info</a>()<<<span class="stringliteral">"Extracting the largest one."</span><<std::endl;</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="keywordtype">int</span> cc_max_size_idx = -1;</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keyword">auto</span> it_max = std::max_element( vectConnectedSCell.begin(), vectConnectedSCell.end(),</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  [] (std::vector<SCell >& v1, std::vector<SCell >& v2)</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  { return v1.size() < v2.size(); } );</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  cc_max_size_idx = std::distance( vectConnectedSCell.begin(), it_max );</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  theSetOfSurfels.surfelSet().insert( vectConnectedSCell[ cc_max_size_idx ].begin(),</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  vectConnectedSCell[ cc_max_size_idx ].end() );</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  }</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Surfaces.html#af61619b3dbd948aea387202369bddd6f">Surfaces<KSpace>::sMakeBoundary</a>(</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  theSetOfSurfels.surfelSet(), ks, thresholdedImage,</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  image.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html#a28a1c55de323d0d0ec62d2db03eaf180">domain</a>().<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1HyperRectDomain.html#a57d51405819b9b13110d7b84d0a154d8">lowerBound</a>(), image.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html#a28a1c55de323d0d0ec62d2db03eaf180">domain</a>().<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1HyperRectDomain.html#a0a1a964e1595dd2651a76e3cfb46fdf4">upperBound</a>() );</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  </div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  MyDigitalSurface digSurf( theSetOfSurfels );</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#ad054990834d2763627166540087a2980">info</a>() << <span class="stringliteral">"Digital surface has "</span> << digSurf.size() << <span class="stringliteral">" surfels."</span></div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  << std::endl;</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#afa3a2874289734884107b1ce68ccb93d">endBlock</a>();</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  </div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  </div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a352b7160bf722e2f0bcbee5d0bad6ef3">beginBlock</a>( <span class="stringliteral">"Making OFF surface. "</span> );</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  <span class="comment">// Describes how voxels are embedded into Euclidean space.</span></div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <span class="keyword">typedef</span> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/structDGtal_1_1CanonicEmbedder.html">CanonicEmbedder< Space ></a> MyEmbedder;</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="comment">// Describes how the centroid surface elements is placed in-between embedded voxels.</span></div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="keyword">typedef</span> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1ImageLinearCellEmbedder.html">ImageLinearCellEmbedder< KSpace, Image, MyEmbedder ></a> <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/structDGtal_1_1CanonicCellEmbedder.html">CellEmbedder</a>;</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/structDGtal_1_1CanonicCellEmbedder.html">CellEmbedder</a> cellEmbedder;</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  MyEmbedder trivialEmbedder;</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  </div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="comment">// The +0.5 is to avoid isosurface going exactly through a voxel</span></div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <span class="comment">// center, especially for binary volumes.</span></div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  </div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="comment">//Making sure that we probe inside the domain.</span></div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html">Image</a> largerImage( <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal_1_1Z3i.html#a39a69f8da09f1094df563ca067927c61">Domain</a>( image.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html#a28a1c55de323d0d0ec62d2db03eaf180">domain</a>().<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1HyperRectDomain.html#a57d51405819b9b13110d7b84d0a154d8">lowerBound</a>() - <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1PointVector.html#aba9def1d899ca259f6fa532a6eb9a8b5">KSpace::Vector::diagonal</a>(2),</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  image.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html#a28a1c55de323d0d0ec62d2db03eaf180">domain</a>().<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1HyperRectDomain.html#a0a1a964e1595dd2651a76e3cfb46fdf4">upperBound</a>() + <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1PointVector.html#aba9def1d899ca259f6fa532a6eb9a8b5">KSpace::Vector::diagonal</a>(2)));</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keywordflow">for</span>(<span class="keyword">auto</span> p: image.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html#a28a1c55de323d0d0ec62d2db03eaf180">domain</a>())</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  largerImage.setValue( p, image(p));</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  </div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  std::ofstream out( outputFileName.c_str() );</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keywordflow">if</span> (addNoise)</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  {</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="keywordflow">if</span> ( out.good() )</div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  digSurf.exportSurfaceAs3DOFF( out );</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  {</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a1e786a1f3b1047e92b73c82f67e3c295">error</a>()<<<span class="stringliteral">"IO error while opening the output file"</span><<std::endl;</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  exit(2);</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  }</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  }</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  {</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  cellEmbedder.init( ks, image, trivialEmbedder,</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  ( (<span class="keywordtype">double</span>) threshold ) + 0.5 );</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  </div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="keywordflow">if</span> ( out.good() )</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  digSurf.exportEmbeddedSurfaceAs3DOFF( out, cellEmbedder );</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  {</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a1e786a1f3b1047e92b73c82f67e3c295">error</a>()<<<span class="stringliteral">"IO error while opening the output file"</span><<std::endl;</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  exit(2);</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  }</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  }</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  </div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  out.close();</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">trace</a>.<a class="codeRef" href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#afa3a2874289734884107b1ce68ccb93d">endBlock</a>();</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="keywordflow">return</span> 0;</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span> }</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  </div>
<div class="ttc" id="a3dHeightMapViewer_8cpp_html_a3c04138a5bfe5d72780bb7e82a18e627"><div class="ttname"><a href="3dHeightMapViewer_8cpp.html#a3c04138a5bfe5d72780bb7e82a18e627">main</a></div><div class="ttdeci">int main(int argc, char **argv)</div><div class="ttdef"><b>Definition:</b> <a href="3dHeightMapViewer_8cpp_source.html#l00206">3dHeightMapViewer.cpp:206</a></div></div>
<div class="ttc" id="aclassDGtal_1_1DigitalSurface_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1DigitalSurface.html">DGtal::DigitalSurface</a></div></div>
<div class="ttc" id="aclassDGtal_1_1HyperRectDomain_html_a0a1a964e1595dd2651a76e3cfb46fdf4"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1HyperRectDomain.html#a0a1a964e1595dd2651a76e3cfb46fdf4">HyperRectDomain< Space >::upperBound</a></div><div class="ttdeci">const Point & upperBound() const</div></div>
<div class="ttc" id="aclassDGtal_1_1HyperRectDomain_html_a57d51405819b9b13110d7b84d0a154d8"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1HyperRectDomain.html#a57d51405819b9b13110d7b84d0a154d8">HyperRectDomain< Space >::lowerBound</a></div><div class="ttdeci">const Point & lowerBound() const</div></div>
<div class="ttc" id="aclassDGtal_1_1ImageContainerBySTLVector_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1ImageContainerBySTLVector.html">DGtal::ImageContainerBySTLVector</a></div></div>
<div class="ttc" id="aclassDGtal_1_1ImageLinearCellEmbedder_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1ImageLinearCellEmbedder.html">DGtal::ImageLinearCellEmbedder</a></div></div>
<div class="ttc" id="aclassDGtal_1_1Image_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html">DGtal::Image</a></div></div>
<div class="ttc" id="aclassDGtal_1_1Image_html_a28a1c55de323d0d0ec62d2db03eaf180"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Image.html#a28a1c55de323d0d0ec62d2db03eaf180">DGtal::Image::domain</a></div><div class="ttdeci">const Domain & domain() const</div></div>
<div class="ttc" id="aclassDGtal_1_1KanungoNoise_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1KanungoNoise.html">DGtal::KanungoNoise</a></div></div>
<div class="ttc" id="aclassDGtal_1_1KhalimskySpaceND_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1KhalimskySpaceND.html">DGtal::KhalimskySpaceND</a></div></div>
<div class="ttc" id="aclassDGtal_1_1KhalimskySpaceND_html_a0a02413be83a0f38f23ed5cb45c2bcc4"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1KhalimskySpaceND.html#a0a02413be83a0f38f23ed5cb45c2bcc4">DGtal::KhalimskySpaceND::SurfelSet</a></div><div class="ttdeci">std::set< SCell > SurfelSet</div></div>
<div class="ttc" id="aclassDGtal_1_1KhalimskySpaceND_html_a15dcbcaae831dd1c36090e6336c177d4"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1KhalimskySpaceND.html#a15dcbcaae831dd1c36090e6336c177d4">DGtal::KhalimskySpaceND::init</a></div><div class="ttdeci">bool init(const Point &lower, const Point &upper, bool isClosed)</div></div>
<div class="ttc" id="aclassDGtal_1_1PointVector_html_aba9def1d899ca259f6fa532a6eb9a8b5"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1PointVector.html#aba9def1d899ca259f6fa532a6eb9a8b5">PointVector< dim, Integer >::diagonal</a></div><div class="ttdeci">static Self diagonal(Component val=1)</div></div>
<div class="ttc" id="aclassDGtal_1_1SetOfSurfels_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1SetOfSurfels.html">DGtal::SetOfSurfels</a></div></div>
<div class="ttc" id="aclassDGtal_1_1Surfaces_html_a19b214170d160153376c4ecf3497de3f"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Surfaces.html#a19b214170d160153376c4ecf3497de3f">DGtal::Surfaces::extractAllConnectedSCell</a></div><div class="ttdeci">static void extractAllConnectedSCell(std::vector< std::vector< SCell > > &aVectConnectedSCell, const KSpace &aKSpace, const SurfelAdjacency< KSpace::dimension > &aSurfelAdj, const PointPredicate &pp, bool forceOrientCellExterior=false)</div></div>
<div class="ttc" id="aclassDGtal_1_1Surfaces_html_af61619b3dbd948aea387202369bddd6f"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Surfaces.html#af61619b3dbd948aea387202369bddd6f">DGtal::Surfaces::sMakeBoundary</a></div><div class="ttdeci">static void sMakeBoundary(SCellSet &aBoundary, const KSpace &aKSpace, const PointPredicate &pp, const Point &aLowerBound, const Point &aUpperBound)</div></div>
<div class="ttc" id="aclassDGtal_1_1SurfelAdjacency_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1SurfelAdjacency.html">SurfelAdjacency< KSpace::dimension ></a></div></div>
<div class="ttc" id="aclassDGtal_1_1Trace_html_a1e786a1f3b1047e92b73c82f67e3c295"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a1e786a1f3b1047e92b73c82f67e3c295">DGtal::Trace::error</a></div><div class="ttdeci">std::ostream & error()</div></div>
<div class="ttc" id="aclassDGtal_1_1Trace_html_a352b7160bf722e2f0bcbee5d0bad6ef3"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#a352b7160bf722e2f0bcbee5d0bad6ef3">DGtal::Trace::beginBlock</a></div><div class="ttdeci">void beginBlock(const std::string &keyword="")</div></div>
<div class="ttc" id="aclassDGtal_1_1Trace_html_ad054990834d2763627166540087a2980"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#ad054990834d2763627166540087a2980">DGtal::Trace::info</a></div><div class="ttdeci">std::ostream & info()</div></div>
<div class="ttc" id="aclassDGtal_1_1Trace_html_afa3a2874289734884107b1ce68ccb93d"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1Trace.html#afa3a2874289734884107b1ce68ccb93d">DGtal::Trace::endBlock</a></div><div class="ttdeci">double endBlock()</div></div>
<div class="ttc" id="aclassDGtal_1_1functors_1_1SimpleThresholdForegroundPredicate_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/classDGtal_1_1functors_1_1SimpleThresholdForegroundPredicate.html">DGtal::functors::SimpleThresholdForegroundPredicate</a></div></div>
<div class="ttc" id="anamespaceDGtal_1_1Z3i_html_a39a69f8da09f1094df563ca067927c61"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal_1_1Z3i.html#a39a69f8da09f1094df563ca067927c61">DGtal::Z3i::Domain</a></div><div class="ttdeci">HyperRectDomain< Space > Domain</div></div>
<div class="ttc" id="anamespaceDGtal_html"><div class="ttname"><a href="namespaceDGtal.html">DGtal</a></div></div>
<div class="ttc" id="anamespaceDGtal_html_a604c07ec391ad12a1f3fb6479993f112"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/namespaceDGtal.html#a604c07ec391ad12a1f3fb6479993f112">DGtal::trace</a></div><div class="ttdeci">Trace trace(traceWriterTerm)</div></div>
<div class="ttc" id="astructDGtal_1_1CanonicCellEmbedder_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/structDGtal_1_1CanonicCellEmbedder.html">DGtal::CanonicCellEmbedder</a></div></div>
<div class="ttc" id="astructDGtal_1_1CanonicEmbedder_html"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/structDGtal_1_1CanonicEmbedder.html">DGtal::CanonicEmbedder</a></div></div>
<div class="ttc" id="astructDGtal_1_1VolReader_html_aa4f1ebd956ed345e4c64e78c83da25d2"><div class="ttname"><a href="https://dgtal-team.github.io/doc-nightly/structDGtal_1_1VolReader.html#aa4f1ebd956ed345e4c64e78c83da25d2">DGtal::VolReader::importVol</a></div><div class="ttdeci">static ImageContainer importVol(const std::string &filename, const Functor &aFunctor=Functor())</div></div>
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