[ITK-users] [ITK] Vector field not shown correctly on VTK

[Nicolas Gallego]

Hi Jose Ignacio
Have you visualized your data on paraview for example?
hope that helps
-- 
Nicolás Gallego Ortiz

2014-05-12 21:50 GMT+02:00 Jose Ignacio Prieto <joseignacio.prieto at gmail.com
>:

> Hi all, I am sending this to both lists, ITK and VTK. I have trouble
> loading three velocity dicom images (X, Y and Z axis). The problem is that
> when displaying the vector field as a Glyph3D, the arrows are aligned only
> in one axis. I have tried to check through iterators after the itk to vtk
> filter and the output shows the vector is fine. Then I don't know if the
> problem is in the glyph3d config or in the vtk data type. I attach all my
> code if someone could give me a hand.
>
> Thank you very much.
>
>
>
>
> typedef short    ShortPixelType;
> typedef itk::Image<ShortPixelType, 4> ImageType4D; // ITK Image
> typedef itk::Image<ShortPixelType, 3> ImageType3D; // ITK Image
> typedef itk::Image< itk::CovariantVector< ShortPixelType, 3>, 4 >
> VectorImageType4D;
> typedef itk::Image< itk::CovariantVector< ShortPixelType, 3>, 3 >
> VectorImageType3D;
> typedef itk::itkImageSeriesReader< ImageType4D>        ReaderType;
> typedef itk::ImageFileWriter< VectorImageType3D>  WriterType3D;
> typedef itk::ImageFileWriter< VectorImageType4D>  WriterType4D;
> typedef itk::ExtractImageFilter<VectorImageType4D, VectorImageType3D>
> ReductorType;
> typedef itk::ImageToVTKImageFilter<VectorImageType3D>       ConnectorType;
> typedef itk::ComposeImageFilter< ImageType4D, VectorImageType4D >
> Vector4DComposer;
> typedef itk::ImageFileReader< VectorImageType4D>  ReaderType4D;
>
>
>
>     std::vector< ReaderType::Pointer > reader;
>     std::vector< NamesGeneratorType::Pointer > nameGenerator;
>     std::vector< ImageIOType::Pointer > dicomIO;
>     reader.resize(3);
>     nameGenerator.resize(3);
>     dicomIO.resize(3);
>     Vector4DComposer::Pointer vecComposer = Vector4DComposer::New();
>     VectorImageType4D::Pointer m_vectorImage;
>
>    for (int i = 0 ; i < 3 ; i++)
>    {
>        reader[i] = ReaderType::New();
>        nameGenerator[i] = NamesGeneratorType::New();
>        dicomIO[i] = ImageIOType::New();
>        nameGenerator[i]->SetDirectory( argv[i + 1]);
>        reader[i]->SetFileNames(nameGenerator[i]->GetInputFileNames());
>        reader[i]->SetImageIO( dicomIO[i] );
>        reader[i]->Update();
>        vecComposer->SetInput(i,reader[i]->GetOutput());
>    }
>
>    vecComposer->UpdateLargestPossibleRegion();
>    ImageType4D::SizeType size =
> vecComposer->GetOutput()->GetLargestPossibleRegion().GetSize();
>
>    int nframes =
> vecComposer->GetOutput()->GetLargestPossibleRegion().GetSize()[3];
>    int dim_eliminada=3;
>    size[dim_eliminada]=0;
>    VectorImageType4D::IndexType start =
> vecComposer->GetOutput()->GetLargestPossibleRegion().GetIndex();
>    start[dim_eliminada] = 30;
>    VectorImageType4D::RegionType desiredRegion;
>    desiredRegion.SetSize(  size  );
>    desiredRegion.SetIndex( start );
>
>    ReductorType::Pointer reductor = ReductorType::New();
>    reductor->InPlaceOn();
>    reductor->SetDirectionCollapseToSubmatrix();
>    reductor->SetExtractionRegion( desiredRegion );
>    reductor->SetInput(vecComposer->GetOutput());
>    reductor->Update();
>
>
>    ConnectorType::Pointer m_connector = ConnectorType::New();
>    m_connector->SetInput(reductor->GetOutput());
>    m_connector->UpdateLargestPossibleRegion();
>    m_connector->Update();
>
>   std::cout << "image start " << std::endl;
>    for (int i = 0; i < m_connector->GetOutput()->GetDimensions()[0]; i++)
>    {
>        for (int j = 0; j < m_connector->GetOutput()->GetDimensions()[1];
> j++)
>        {
>            for (int k = 0; k <
> m_connector->GetOutput()->GetDimensions()[2]; k++)
>            {
>                myfile<< "On point " << "i, j, k: " << i<<", "<< j<<", "<<
> k<<
>                         " Component 0: "<<
> m_connector->GetOutput()->GetScalarComponentAsDouble(i, j, k, 0) <<
>                         " Component 1: "<<
> m_connector->GetOutput()->GetScalarComponentAsDouble(i, j, k, 1) <<
>                         " Component 2: "<<
> m_connector->GetOutput()->GetScalarComponentAsDouble(i, j, k, 2) <<
>                          "\n";
>            }
>        }
>    }
>
>    vtkSmartPointer< vtkImageDataGeometryFilter > vtkConverter =
> vtkSmartPointer< vtkImageDataGeometryFilter >::New();
>    vtkConverter->SetInput(m_connector->GetOutput());
>    vtkConverter->UpdateWholeExtent();
>
>    vtkSmartPointer< vtkArrowSource > m_arrows = vtkSmartPointer<
> vtkArrowSource >::New();
>    m_arrows->SetTipLength(.1);
>    m_arrows->SetTipResolution(5);
>    m_arrows->SetTipRadius(.05);
>    m_arrows->SetShaftResolution(5);
>    m_arrows->SetShaftRadius(.015);
>    m_arrows->Update();
>
>    vtkSmartPointer< vtkGlyph3D > m_glyphs = vtkSmartPointer< vtkGlyph3D
> >::New();
> //   m_glyphs->SetSourceConnection(m_connector->GetOutput());
> //   m_glyphs->SetInput(m_connector->GetOutput());
> //   m_glyphs->SetInputConnection(m_connector->GetOutput() ());
>    m_glyphs->SetInputConnection(vtkConverter->GetOutputPort());
> //   m_glyphs->SetSource(m_arrows->GetOutput());
>    m_glyphs->SetSourceConnection(m_arrows->GetOutputPort());
>    m_glyphs->OrientOn();
> //   m_glyphs->OrientOff();
> //   m_glyphs->SetVectorModeToVectorRotationOff();
>    m_glyphs->SetVectorModeToUseVector();
> //   m_glyphs->SetVectorModeToUseNormal();
> //   m_glyphs->SetScaleModeToDataScalingOn();
> //   m_glyphs->SetScaleModeToDataScalingOff();
> //   m_glyphs->SetColorModeToColorByVector();
> //   m_glyphs->SetScaleModeToScaleByVector();
> //   m_glyphs->SetColorModeToColorByScalar();
>    m_glyphs->SetColorModeToColorByScale();
>    m_glyphs->SetScaleFactor(0.2);
> //   m_glyphs->SetIndexModeToVector();
> //   m_glyphs->SetScaleModeToDataScalingOff();
> //   m_glyphs->SetScaleFactor(.5);
>    m_glyphs->Update();
>
>    vtkSmartPointer< vtkOpenGLPolyDataMapper > glyphPolyData =
> vtkSmartPointer< vtkOpenGLPolyDataMapper >::New();
>    glyphPolyData->SetInputConnection(m_glyphs->GetOutputPort());
>    vtkSmartPointer< vtkOpenGLActor > glyphActor = vtkSmartPointer<
> vtkOpenGLActor >::New();
>    glyphActor->SetMapper(glyphPolyData);
>
>    vtkSmartPointer< vtkWin32OpenGLRenderWindow >  renWin =
> vtkSmartPointer< vtkWin32OpenGLRenderWindow>::New();
>
>    vtkSmartPointer< vtkOpenGLRenderer>  ren1 = vtkSmartPointer<
> vtkOpenGLRenderer> ::New();
>    renWin->AddRenderer(ren1);
>    ren1->AddActor(glyphActor);
>
>    vtkSmartPointer< vtkRenderWindowInteractor > rwi = vtkSmartPointer<
> vtkRenderWindowInteractor >::New();
>    vtkSmartPointer<MouseInteractorStyle> styleActor =
> vtkSmartPointer<MouseInteractorStyle>::New();
>    rwi->SetInteractorStyle(styleActor);
>
>    rwi->SetRenderWindow(renWin);
>    rwi->SetSize(640, 480);
>    rwi->Initialize();
>    renWin->Render();
>    rwi->Start();
>
>
> --
> José Ignacio Prieto
> Software developer
> Biomedical Imaging Center
> Pontificia Universidad Catolica de Chile
>
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