CarotidFlow

VTKEx/Cxx/VisualizationAlgorithms/CarotidFlow

Description

This example generates streamtubes of blood velocity. an isosurface of speed provides context. The starting positions for the streamtubes were determined by experimenting with the data. Because of the way the data was measured and the resolution of the velocity field, many streamers travel outside the artery. This is because the boundary layer of the blood flow is not captured due to limitations in data resolution. Consequently, as the blood flows around curves, there is a component of the velocity field that directs the streamtube outside the artery. As a result it is hard to find starting positions for the streamtubes that yield interesting results. The examples uses the source object vtkPointSource in combination with vtkThresholdPoints to work around this problem. vtkPointSource generates random points centered around a sphere of a specified radius. We need only find an approximate position for the starting points of the streamtubes and then generate a cloud of random seed points. vtkThresholdPoints is used to cull points that may be generated outside the regions of high flow velocity.

Cite

See 3D Phase Contrast MRI of Cerebral Blood Flow and Surface Anatomy for background.

Info

See Figure 6-44 in Chapter 6 the VTK Textbook.

Other languages

See (Python)

Question

If you have a simple question about this example contact us at VTKExProject If your question is more complex and may require extended discussion, please use the VTK Discourse Forum

Code

CarotidFlow.cxx

#include <vtkActor.h>
#include <vtkCamera.h>
#include <vtkContourFilter.h>
#include <vtkLookupTable.h>
#include <vtkNamedColors.h>
#include <vtkOutlineFilter.h>
#include <vtkPointData.h>
#include <vtkPointSource.h>
#include <vtkPolyDataMapper.h>
#include <vtkProperty.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkStreamTracer.h>
#include <vtkStructuredPointsReader.h>
#include <vtkThresholdPoints.h>
#include <vtkTubeFilter.h>

int main (int argc, char *argv[])
{
  if (argc < 2)
  {
    std::cout << "Usage: " << argv[0] << " carotid.vtk" << std::endl;
    return EXIT_FAILURE;
  }

  vtkSmartPointer<vtkNamedColors> colors =
    vtkSmartPointer<vtkNamedColors>::New();

  vtkSmartPointer<vtkRenderer> ren1 =
    vtkSmartPointer<vtkRenderer>::New();

  vtkSmartPointer<vtkRenderWindow> renWin =
    vtkSmartPointer<vtkRenderWindow>::New();
  renWin->AddRenderer(ren1);

  vtkSmartPointer<vtkRenderWindowInteractor> iren =
    vtkSmartPointer<vtkRenderWindowInteractor>::New();
  iren->SetRenderWindow(renWin);

// create pipeline
//
  vtkSmartPointer<vtkStructuredPointsReader> reader =
    vtkSmartPointer<vtkStructuredPointsReader>::New();
  reader->SetFileName(argv[1]);

  vtkSmartPointer<vtkPointSource> psource =
    vtkSmartPointer<vtkPointSource>::New();
  psource->SetNumberOfPoints(25);
  psource->SetCenter(133.1, 116.3, 5.0);
  psource->SetRadius(2.0);

  vtkSmartPointer<vtkThresholdPoints> threshold =
    vtkSmartPointer<vtkThresholdPoints>::New();
  threshold->SetInputConnection(reader->GetOutputPort());
  threshold->ThresholdByUpper(275);

  vtkSmartPointer<vtkStreamTracer> streamers =
    vtkSmartPointer<vtkStreamTracer>::New();
  streamers->SetInputConnection(reader->GetOutputPort());
  streamers->SetSourceConnection(psource->GetOutputPort());
//  streamers->SetMaximumPropagationUnitToTimeUnit();
  streamers->SetMaximumPropagation(100.0);
//  streamers->SetInitialIntegrationStepUnitToCellLengthUnit();
  streamers->SetInitialIntegrationStep(0.2);
  streamers->SetTerminalSpeed(.01);
  streamers->Update();
  double range[2];
  range[0] = streamers->GetOutput()->GetPointData()->GetScalars()->GetRange()[0];
  range[1] = streamers->GetOutput()->GetPointData()->GetScalars()->GetRange()[1];

  vtkSmartPointer<vtkTubeFilter> tubes =
    vtkSmartPointer<vtkTubeFilter>::New();
  tubes->SetInputConnection(streamers->GetOutputPort());
  tubes->SetRadius(0.3);
  tubes->SetNumberOfSides(6);
  tubes->SetVaryRadius(0);

  vtkSmartPointer<vtkLookupTable> lut =
    vtkSmartPointer<vtkLookupTable>::New();
  lut->SetHueRange(.667, 0.0);
  lut->Build();

  vtkSmartPointer<vtkPolyDataMapper> streamerMapper =
    vtkSmartPointer<vtkPolyDataMapper>::New();
  streamerMapper->SetInputConnection(tubes->GetOutputPort());
  streamerMapper->SetScalarRange(range[0], range[1]);
  streamerMapper->SetLookupTable(lut);

  vtkSmartPointer<vtkActor> streamerActor =
    vtkSmartPointer<vtkActor>::New();
  streamerActor->SetMapper(streamerMapper);

// contours of speed
  vtkSmartPointer<vtkContourFilter> iso =
    vtkSmartPointer<vtkContourFilter>::New();
  iso->SetInputConnection(reader->GetOutputPort());
  iso->SetValue(0, 175);

  vtkSmartPointer<vtkPolyDataMapper> isoMapper =
    vtkSmartPointer<vtkPolyDataMapper>::New();
  isoMapper->SetInputConnection(iso->GetOutputPort());
  isoMapper->ScalarVisibilityOff();

  vtkSmartPointer<vtkActor> isoActor =
    vtkSmartPointer<vtkActor>::New();
  isoActor->SetMapper(isoMapper);
  isoActor->GetProperty()->SetRepresentationToWireframe();
  isoActor->GetProperty()->SetOpacity(0.25);

// outline
  vtkSmartPointer<vtkOutlineFilter> outline =
    vtkSmartPointer<vtkOutlineFilter>::New();
  outline->SetInputConnection(reader->GetOutputPort());

  vtkSmartPointer<vtkPolyDataMapper> outlineMapper =
    vtkSmartPointer<vtkPolyDataMapper>::New();
  outlineMapper->SetInputConnection(outline->GetOutputPort());

  vtkSmartPointer<vtkActor> outlineActor =
    vtkSmartPointer<vtkActor>::New();
  outlineActor->SetMapper(outlineMapper);
  outlineActor->GetProperty()->SetColor(colors->GetColor3d("Black").GetData());

// Add the actors to the renderer, set the background and size
//
  ren1->AddActor(outlineActor);
  ren1->AddActor(streamerActor);
  ren1->AddActor(isoActor);
  ren1->SetBackground(colors->GetColor3d("Wheat").GetData());
  renWin->SetSize(640, 480);

  vtkSmartPointer<vtkCamera> cam1 =
    vtkSmartPointer<vtkCamera>::New();
  cam1->SetClippingRange(17.4043, 870.216);
  cam1->SetFocalPoint(136.71, 104.025, 23);
  cam1->SetPosition(204.747, 258.939, 63.7925);
  cam1->SetViewUp(-0.102647, -0.210897, 0.972104);
  cam1->Zoom(1.6);
  ren1->SetActiveCamera(cam1);

// render the image
//
  renWin->Render();
  iren->Start();

  return EXIT_SUCCESS;
}

CMakeLists.txt

cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

project(CarotidFlow)

find_package(VTK COMPONENTS 
  vtkvtkCommonColor
  vtkvtkCommonCore
  vtkvtkCommonDataModel
  vtkvtkFiltersCore
  vtkvtkFiltersFlowPaths
  vtkvtkFiltersModeling
  vtkvtkFiltersSources
  vtkvtkIOLegacy
  vtkvtkInteractionStyle
  vtkvtkRenderingContextOpenGL2
  vtkvtkRenderingCore
  vtkvtkRenderingFreeType
  vtkvtkRenderingGL2PSOpenGL2
  vtkvtkRenderingOpenGL2 QUIET)
if (NOT VTK_FOUND)
  message("Skipping CarotidFlow: ${VTK_NOT_FOUND_MESSAGE}")
  return ()
endif()
message (STATUS "VTK_VERSION: ${VTK_VERSION}")
if (VTK_VERSION VERSION_LESS "8.90.0")
  # old system
  include(${VTK_USE_FILE})
  add_executable(CarotidFlow MACOSX_BUNDLE CarotidFlow.cxx )
  target_link_libraries(CarotidFlow PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  add_executable(CarotidFlow MACOSX_BUNDLE CarotidFlow.cxx )
  target_link_libraries(CarotidFlow PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS CarotidFlow
    MODULES ${VTK_LIBRARIES}
    )
endif ()

Download and Build CarotidFlow

Click here to download CarotidFlow and its CMakeLists.txt file. Once the tarball CarotidFlow.tar has been downloaded and extracted,

cd CarotidFlow/build

If VTK is installed:

cmake ..

If VTK is not installed but compiled on your system, you will need to specify the path to your VTK build:

cmake -DVTK_DIR:PATH=/home/me/vtk_build ..

Build the project:

make

and run it:

./CarotidFlow

WINDOWS USERS

Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.