<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello, <div><br></div><div>I have a 3D image which is the output of the itk::ScalarImageKmeansImageFilter. The image contains a surface extracted from an object, and the voxels have values evenly distributed between 0 and 255, assigned by the k-means algorithm. I would like to visualize this surface showing the k-means clusters as patches of different colors.</div><div><br></div><div>Currently, I am reading the image using ITK, converting it to a VTK image, and using the vtkImageDataGeometryFilter to get polydata. I then display the polydata. However, the color of the voxels which are background is dark blue, so that I cannot see the rest of the image. Do I need to change the color mapping, or is my approach incorrect?</div><div><br></div><div>I converted the image data to polydata because I was following some of the VTK display examples. But maybe there is a better way to do this? My code is below.</div><div><br></div><div>Thanks,</div><div>Sara</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span style="color: #aa0d91">int</span> main(<span style="color: #aa0d91">int</span> argc, <span style="color: #aa0d91">char</span> * argv [] )</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; ">{ </div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span><span style="color: #aa0d91">if</span>( argc < <span style="color: #1c00cf">2</span> )</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "> {</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>std::cerr << <span style="color: #c41a16">"Missing parameters"</span> << std::endl;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>std::cerr << <span style="color: #c41a16">"Usage: "</span> << argv[<span style="color: #1c00cf">0</span>] << <span style="color: #c41a16">" inputImageFilename "</span> << std::endl;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(170, 13, 145); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>return<span style="color: #000000"> </span><span style="color: #1c00cf">1</span><span style="color: #000000">;</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "> }</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "> <span style="color: #aa0d91">const</span> <span style="color: #aa0d91">unsigned</span> <span style="color: #aa0d91">int</span> Dimension = <span style="color: #1c00cf">3</span>;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span><span style="color: #aa0d91">typedef</span> <span style="color: #aa0d91">signed</span> <span style="color: #aa0d91">short</span> InputPixelType;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span><span style="color: #aa0d91">typedef</span> itk::Image< InputPixelType, Dimension > InputImageType;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span><span style="color: #aa0d91">typedef</span> itk::ImageFileReader< InputImageType > ReaderType;</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>ReaderType::Pointer reader = ReaderType::New();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>reader->SetFileName( argv[<span style="color: #1c00cf">1</span>] );</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>reader->Update();</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(0, 116, 0); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>// Obtain center of the input image</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>InputImageType::Pointer inputImage = reader->GetOutput();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>InputImageType::SizeType size = inputImage->GetBufferedRegion().GetSize();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>InputImageType::IndexType start = inputImage->GetBufferedRegion().GetIndex();</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(0, 116, 0); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>// Create the itk::VTKImageExport </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span><span style="color: #aa0d91">typedef</span> itk::VTKImageExport< InputImageType > ExportFilter1Type;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>ExportFilter1Type::Pointer itkExporter1 = ExportFilter1Type::New();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>itkExporter1->SetInput( reader->GetOutput() );</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(0, 116, 0); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>// Create the vtkImageImport and connect it to the itk::VTKImageExport </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkImageImport* vtkImporter1 = vtkImageImport::New(); </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>ConnectPipelines(itkExporter1, vtkImporter1);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkImporter1->Update();</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(0, 116, 0); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>// Convert the image to a polydata</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkImageDataGeometryFilter * imageDataGeometryFilter = vtkImageDataGeometryFilter::New();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>imageDataGeometryFilter->SetInputConnection(vtkImporter1->GetOutputPort());<span class="Apple-tab-span" style="white-space:pre"> </span></div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(0, 116, 0); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>// Create a renderer, render window, and render window interactor <span class="Apple-tab-span" style="white-space:pre"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkRenderer* renderer = vtkRenderer::New();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkRenderWindow* renWin = vtkRenderWindow::New();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkRenderWindowInteractor* iren = vtkRenderWindowInteractor::New();</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>renWin->SetSize(<span style="color: #1c00cf">500</span>, <span style="color: #1c00cf">500</span>);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>renWin->AddRenderer(renderer);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>iren->SetRenderWindow(renWin);</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(0, 116, 0); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>// Set visualization properties</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>renderer->SetBackground(<span style="color: #1c00cf">0.4392</span>, <span style="color: #1c00cf">0.5020</span>, <span style="color: #1c00cf">0.5647</span>);</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkPolyDataMapper * polyMapper = vtkPolyDataMapper::New();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkActor * polyActor = vtkActor::New();</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>polyActor->SetMapper( polyMapper );</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>polyMapper->SetInput( imageDataGeometryFilter->GetOutput() );</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>polyMapper->ScalarVisibilityOn();</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkProperty * property = vtkProperty::New();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>property->SetAmbient(<span style="color: #1c00cf">0.1</span>);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>property->SetDiffuse(<span style="color: #1c00cf">0.1</span>);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>property->SetSpecular(<span style="color: #1c00cf">0.5</span>);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>property->SetColor(<span style="color: #1c00cf">1.0</span>,<span style="color: #1c00cf">0.0</span>,<span style="color: #1c00cf">0.0</span>);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>property->SetLineWidth(<span style="color: #1c00cf">2.0</span>);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>property->SetRepresentationToSurface();</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>polyActor->SetProperty( property );</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>renderer->AddActor( polyActor );</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(0, 116, 0); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>// Bring up the render window and begin interaction.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>renderer->ResetCamera();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>renWin->Render();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>iren->Start();</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(0, 116, 0); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>// Release VTK components</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>polyActor->Delete();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>vtkImporter1->Delete();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>property->Delete();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>polyMapper->Delete();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>renWin->Delete();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>renderer->Delete();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>iren->Delete();</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; "><span class="Apple-tab-span" style="white-space:pre"> </span>imageDataGeometryFilter->Delete();</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Monaco; min-height: 14.0px"><span class="Apple-tab-span" style="white-space:pre"> </span><br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; color: rgb(170, 13, 145); "><span style="color: #000000"><span class="Apple-tab-span" style="white-space:pre"> </span></span>return<span style="color: #000000"> </span><span style="color: #1c00cf">0</span><span style="color: #000000">;</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; ">}</div></div></body></html>