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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<title>ClearMap.IO.VTK — ClearMap 0.9.2 documentation</title>
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<h1>Source code for ClearMap.IO.VTK</h1><div class="highlight"><pre>
<span class="c"># -*- coding: utf-8 -*-</span>
<span class="sd">"""</span>
<span class="sd">Interface to write points to VTK files</span>
<span class="sd">Notes:</span>
<span class="sd"> - points are assumed to be in [x,y,z] coordinates as standard in ClearMap</span>
<span class="sd"> - reading of points not supported at the moment!</span>
<span class="sd">"""</span>
<span class="c">#:copyright: Copyright 2015 by Christoph Kirst, The Rockefeller University, New York City</span>
<span class="c">#:license: GNU, see LICENSE.txt for details.</span>
<span class="c"># Modified from a matlab code by Kannan Umadevi Venkataraju</span>
<span class="c">#from evtk.hl import pointsToVTK </span>
<span class="kn">import</span> <span class="nn">numpy</span><span class="p">;</span>
<span class="kn">import</span> <span class="nn">ClearMap.IO</span> <span class="kn">as</span> <span class="nn">io</span><span class="p">;</span>
<div class="viewcode-block" id="writePoints"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.VTK.writePoints">[docs]</a><span class="k">def</span> <span class="nf">writePoints</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">points</span><span class="p">,</span> <span class="n">labelImage</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">"""Write point data to vtk file</span>
<span class="sd"> </span>
<span class="sd"> Arguments:</span>
<span class="sd"> filename (str): file name</span>
<span class="sd"> points (array): point data</span>
<span class="sd"> labelImage (str, array or None): optional label image to determine point label</span>
<span class="sd"> </span>
<span class="sd"> Returns:</span>
<span class="sd"> str: file name</span>
<span class="sd"> """</span>
<span class="c">#y = points[:,0];</span>
<span class="c">#x = points[:,1];</span>
<span class="c">#z = points[:,2]; </span>
<span class="n">x</span> <span class="o">=</span> <span class="n">points</span><span class="p">[:,</span><span class="mi">0</span><span class="p">];</span>
<span class="n">y</span> <span class="o">=</span> <span class="n">points</span><span class="p">[:,</span><span class="mi">1</span><span class="p">];</span>
<span class="n">z</span> <span class="o">=</span> <span class="n">points</span><span class="p">[:,</span><span class="mi">2</span><span class="p">];</span>
<span class="n">nPoint</span> <span class="o">=</span> <span class="n">x</span><span class="o">.</span><span class="n">size</span><span class="p">;</span>
<span class="c">#print nPoint;</span>
<span class="n">pointLabels</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="n">nPoint</span><span class="p">);</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">labelImage</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">labelImage</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
<span class="n">labelImage</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">readData</span><span class="p">(</span><span class="n">labelImage</span><span class="p">);</span>
<span class="n">dsize</span> <span class="o">=</span> <span class="n">labelImage</span><span class="o">.</span><span class="n">shape</span><span class="p">;</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nPoint</span><span class="p">):</span>
<span class="c">#if y[i] >= 0 and y[i] < dsize[0] and x[i] >= 0 and x[i] < dsize[1] and z[i] >= 0 and z[i] < dsize[2]:</span>
<span class="k">if</span> <span class="n">x</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">>=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">x</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o"><</span> <span class="n">dsize</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">and</span> <span class="n">y</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">>=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">y</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o"><</span> <span class="n">dsize</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">and</span> <span class="n">z</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">>=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">z</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o"><</span> <span class="n">dsize</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span>
<span class="c">#pointLabels[i] = labelImage[y[i], x[i], z[i]];</span>
<span class="n">pointLabels</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">labelImage</span><span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">y</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">z</span><span class="p">[</span><span class="n">i</span><span class="p">]];</span>
<span class="c">#write VTK file</span>
<span class="n">vtkFile</span> <span class="o">=</span> <span class="nb">file</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'# vtk DataFile Version 2.0</span><span class="se">\n</span><span class="s">'</span><span class="p">);</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'Unstructured Grid Example</span><span class="se">\n</span><span class="s">'</span><span class="p">);</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'ASCII</span><span class="se">\n</span><span class="s">'</span><span class="p">);</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'DATASET UNSTRUCTURED_GRID</span><span class="se">\n</span><span class="s">'</span><span class="p">);</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"POINTS "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">nPoint</span><span class="p">)</span> <span class="o">+</span> <span class="s">" float</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">iPoint</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nPoint</span><span class="p">):</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="n">iPoint</span><span class="p">])</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s">'</span><span class="si">%05.20f</span><span class="s">'</span><span class="p">)</span> <span class="o">+</span> <span class="s">" "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">y</span><span class="p">[</span><span class="n">iPoint</span><span class="p">])</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s">'</span><span class="si">%05.20f</span><span class="s">'</span><span class="p">)</span> <span class="o">+</span> <span class="s">" "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">z</span><span class="p">[</span><span class="n">iPoint</span><span class="p">])</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s">'</span><span class="si">%05.20f</span><span class="s">'</span><span class="p">)</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">);</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"CELLS "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">nPoint</span><span class="p">)</span> <span class="o">+</span> <span class="s">" "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">nPoint</span> <span class="o">*</span> <span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">);</span>
<span class="k">for</span> <span class="n">iPoint</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nPoint</span><span class="p">):</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"1 "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">iPoint</span><span class="p">)</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">);</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"CELL_TYPES "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">nPoint</span><span class="p">)</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">);</span>
<span class="k">for</span> <span class="n">iPoint</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nPoint</span><span class="p">):</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"1 </span><span class="se">\n</span><span class="s">"</span><span class="p">);</span>
<span class="c">#vtkFile.write("\n");</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"POINT_DATA "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">nPoint</span><span class="p">)</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">);</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'SCALARS scalars float 1</span><span class="se">\n</span><span class="s">'</span><span class="p">);</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"LOOKUP_TABLE default</span><span class="se">\n</span><span class="s">"</span><span class="p">);</span>
<span class="k">for</span> <span class="n">iLabel</span> <span class="ow">in</span> <span class="n">pointLabels</span><span class="p">:</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">iLabel</span><span class="p">))</span> <span class="o">+</span> <span class="s">" "</span><span class="p">);</span>
<span class="c">#vtkFile.write("1 ")</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">);</span>
<span class="n">vtkFile</span><span class="o">.</span><span class="n">close</span><span class="p">();</span>
<span class="k">return</span> <span class="n">filename</span><span class="p">;</span></div>
<div class="viewcode-block" id="readPoints"><a class="viewcode-back" href="../../../api/ClearMap.IO.html#ClearMap.IO.VTK.readPoints">[docs]</a><span class="k">def</span> <span class="nf">readPoints</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="o">**</span><span class="n">args</span><span class="p">):</span>
<span class="sd">"""Read points form vtk file</span>
<span class="sd"> </span>
<span class="sd"> Notes:</span>
<span class="sd"> - Not implmented yet !</span>
<span class="sd"> """</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">'readPoints for VTK files not implmented!'</span><span class="p">);</span></div>
<span class="c">#%%</span>
<span class="c">############# Stuff -> test above then delete this here//./</span>
<span class="c">#</span>
<span class="c">#if (numel(varargin) >= 2)</span>
<span class="c"># labelList = varargin{2};</span>
<span class="c"># labelIndices = ismember (pointLabels, labelList);</span>
<span class="c"># pointList = pointList (:, labelIndices);</span>
<span class="c"># pointLabels = pointLabels(labelIndices);</span>
<span class="c">#end</span>
<span class="c">#</span>
<span class="c">#nPoint = size (pointList, 2);</span>
<span class="c">#</span>
<span class="c">#%%Swap x and y axis</span>
<span class="c">#pointListx = pointList(2,:);</span>
<span class="c">#pointListy = pointList(1,:);</span>
<span class="c">#pointList(1,:) = pointListx;</span>
<span class="c">#pointList(2,:) = pointListy;</span>
<span class="c">#</span>
<span class="c">#%% Write VTK File</span>
<span class="c">#fp = fopen (vtkFileName, 'w+');</span>
<span class="c">#fprintf (fp, '# vtk DataFile Version 2.0\n');</span>
<span class="c">#fprintf (fp, 'Unstructured Grid Example\n');</span>
<span class="c">#fprintf (fp, 'ASCII\n');</span>
<span class="c">#fprintf (fp, 'DATASET UNSTRUCTURED_GRID\n');</span>
<span class="c">#fprintf (fp, 'POINTS %d float\n', nPoint);</span>
<span class="c">#fprintf (fp, '%05.20f %5.20f %5.20f\n', pointList);</span>
<span class="c">#fprintf (fp, 'CELLS %d %d\n',nPoint, nPoint * 2);</span>
<span class="c">#fprintf (fp, '%d %d\n', [ones(nPoint, 1) [0:nPoint-1]']');</span>
<span class="c">#fprintf (fp, 'CELL_TYPES %d\n', nPoint);</span>
<span class="c">#fprintf (fp, '%d\n', ones (nPoint, 1));</span>
<span class="c">#fprintf (fp, 'POINT_DATA %d\n',nPoint);</span>
<span class="c">#fprintf (fp, 'SCALARS scalars float 1\n');</span>
<span class="c">#fprintf (fp, 'LOOKUP_TABLE default\n');</span>
<span class="c">#fprintf (fp, '%f ', pointLabels);</span>
<span class="c">#fclose (fp);</span>
<span class="c">#</span>
<span class="c">#</span>
<span class="c">#</span>
<span class="c">#</span>
<span class="c">##def writePoints(filename, points, data = None):</span>
<span class="c">## x = points[:,0];</span>
<span class="c">## y = points[:,1];</span>
<span class="c">## z = points[:,2];</span>
<span class="c">## </span>
<span class="c">## pointsToVTK(filename, x, y, z, data = data);</span>
<span class="c"># </span>
<span class="c"># </span>
<span class="c">#def readPoints(filename):</span>
<span class="c"># raise RuntimeError("Reading points from VTK file not implemented yet""")</span>
<span class="c">#</span>
<span class="c"># </span>
<span class="c"># </span>
<span class="c">#</span>
<span class="c"># vtkFileName is the file name to be written</span>
<span class="c"># pointList is the list of x, y, z points to be written</span>
<span class="c"># pointsLabel is the label for each point, it tell which region on brain the cell belongs to</span>
<span class="c">#</span>
<span class="c">#def writeSparsePointsWithLabelVTKFile (vtkFileName, pointList, pointLabels):</span>
<span class="c"># #swap x and y axis</span>
<span class="c"># x = pointList[:,1];</span>
<span class="c"># y = pointList[:,0];</span>
<span class="c"># z = pointList[:,2];</span>
<span class="c"># </span>
<span class="c"># nPoint = x.size;</span>
<span class="c"># </span>
<span class="c"># #write VTK file</span>
<span class="c"># vtkFile = open(vtkFileName, 'w')</span>
<span class="c"># vtkFile.write('# vtk DataFile Version 2.0\n');</span>
<span class="c"># vtkFile.write('Unstructured Grid Example\n');</span>
<span class="c"># vtkFile.write('ASCII\n');</span>
<span class="c"># vtkFile.write('DATASET UNSTRUCTURED_GRID\n');</span>
<span class="c"># vtkFile.write("POINTS " + str(nPoint) + " float\n")</span>
<span class="c"># for iPoint in range(0,nPoint):</span>
<span class="c"># vtkFile.write(str(x[iPoint]).format('%05.20f') + " " + str(y[iPoint]).format('%05.20f') + " " + str(z[iPoint]).format('%05.20f') + "\n"); </span>
<span class="c"># </span>
<span class="c"># vtkFile.write("CELLS " + str(nPoint) + " " + str(nPoint * 2) + "\n");</span>
<span class="c"># for iPoint in range(0, nPoint):</span>
<span class="c"># vtkFile.write("1 " + str(iPoint) + "\n");</span>
<span class="c"># vtkFile.write("CELL_TYPES " + str(nPoint) + "\n");</span>
<span class="c"># for iPoint in range(0, nPoint):</span>
<span class="c"># vtkFile.write("1 \n");</span>
<span class="c"># #vtkFile.write("\n");</span>
<span class="c"># vtkFile.write("POINT_DATA " + str(nPoint) + "\n");</span>
<span class="c"># vtkFile.write('SCALARS scalars float 1\n');</span>
<span class="c"># vtkFile.write("LOOKUP_TABLE default\n");</span>
<span class="c"># for iLabel in pointLabels:</span>
<span class="c"># vtkFile.write(str(int(iLabel)) + " ");</span>
<span class="c"># #vtkFile.write("1 ")</span>
<span class="c"># vtkFile.write("\n");</span>
<span class="c"># vtkFile.close();</span>
<span class="c"># </span>
<span class="c">#"""</span>
<span class="c"># </span>
<span class="c"># </span>
<span class="c">#</span>
<span class="c"># </span>
<span class="c"># vtkFile.close();</span>
<span class="c">#"""</span>
<span class="c">## If the labels are not specified for the cells then all are assigned as one</span>
<span class="c">#def writeSparsePointsVTKFile (vtkFileName, pointList):</span>
<span class="c"># x = pointList[:,1];</span>
<span class="c"># nPoint = x.size;</span>
<span class="c"># pointLabels = numpy.ones([nPoint,1], float)</span>
<span class="c"># writeSparsePointsWithLabelVTKFile (vtkFileName, pointList, pointLabels)</span>
<span class="c">#</span>
<span class="c">#</span>
<span class="c">## sample code of how to use the functions</span>
<span class="c">#vtkFileName = '/Users/kannanuv/Documents/workspace/code/assemblaSVN/idisco/iDISCO/Visualization/test.vtk'</span>
<span class="c">#nPoint = 100;</span>
<span class="c">#pointList = numpy.zeros([nPoint,3], float)</span>
<span class="c">#for iPoint in range(0, nPoint):</span>
<span class="c"># for iCoord in range(0, 3):</span>
<span class="c"># pointList[iPoint,iCoord] = random.random() * 10;</span>
<span class="c">#pointList</span>
<span class="c">#pointLabels = numpy.ones([nPoint,1], dtype=numpy.int)</span>
<span class="c">#writeSparsePointsVTKFile (vtkFileName, pointList)</span>
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