CarotidFlowGlyphs.tar

CarotidFlowGlyphs/0000755000076500000240000000000013424703035015433 5ustar  lorensenstaff00000000000000CarotidFlowGlyphs/CarotidFlowGlyphs.py0000755000076500000240000000663013424703035021421 0ustar  lorensenstaff00000000000000#!/usr/bin/env python

import vtk


def main():
    fileName = get_program_parameters()

    colors = vtk.vtkNamedColors()

    ren1 = vtk.vtkRenderer()

    renWin = vtk.vtkRenderWindow()
    renWin.AddRenderer(ren1)

    iren = vtk.vtkRenderWindowInteractor()
    iren.SetRenderWindow(renWin)

    # Create the pipeline.
    #
    reader = vtk.vtkStructuredPointsReader()
    reader.SetFileName(fileName)

    threshold = vtk.vtkThresholdPoints()
    threshold.SetInputConnection(reader.GetOutputPort())
    threshold.ThresholdByUpper(200)

    mask = vtk.vtkMaskPoints()
    mask.SetInputConnection(threshold.GetOutputPort())
    mask.SetOnRatio(5)

    cone = vtk.vtkConeSource()
    cone.SetResolution(11)
    cone.SetHeight(1)
    cone.SetRadius(0.25)

    cones = vtk.vtkGlyph3D()
    cones.SetInputConnection(mask.GetOutputPort())
    cones.SetSourceConnection(cone.GetOutputPort())
    cones.SetScaleFactor(0.4)
    cones.SetScaleModeToScaleByVector()

    lut = vtk.vtkLookupTable()
    lut.SetHueRange(.667, 0.0)
    lut.Build()

    scalarRange = [0] * 2
    cones.Update()
    scalarRange[0] = cones.GetOutput().GetPointData().GetScalars().GetRange()[0]
    scalarRange[1] = cones.GetOutput().GetPointData().GetScalars().GetRange()[1]
    print("range: ", scalarRange[0], ", ", scalarRange[1])

    vectorMapper = vtk.vtkPolyDataMapper()
    vectorMapper.SetInputConnection(cones.GetOutputPort())
    vectorMapper.SetScalarRange(scalarRange[0], scalarRange[1])
    vectorMapper.SetLookupTable(lut)

    vectorActor = vtk.vtkActor()
    vectorActor.SetMapper(vectorMapper)

    # Speed contours.
    iso = vtk.vtkContourFilter()
    iso.SetInputConnection(reader.GetOutputPort())
    iso.SetValue(0, 175)

    isoMapper = vtk.vtkPolyDataMapper()
    isoMapper.SetInputConnection(iso.GetOutputPort())
    isoMapper.ScalarVisibilityOff()

    isoActor = vtk.vtkActor()
    isoActor.SetMapper(isoMapper)
    isoActor.GetProperty().SetRepresentationToWireframe()
    isoActor.GetProperty().SetOpacity(0.25)

    # Outline
    outline = vtk.vtkOutlineFilter()
    outline.SetInputConnection(reader.GetOutputPort())

    outlineMapper = vtk.vtkPolyDataMapper()
    outlineMapper.SetInputConnection(outline.GetOutputPort())

    outlineActor = vtk.vtkActor()
    outlineActor.SetMapper(outlineMapper)
    outlineActor.GetProperty().SetColor(colors.GetColor3d("Black"))

    # Add the actors to the renderer, set the background and size.
    #
    ren1.AddActor(outlineActor)
    ren1.AddActor(vectorActor)
    ren1.AddActor(isoActor)
    ren1.SetBackground(colors.GetColor3d("Wheat"))
    renWin.SetSize(640, 480)

    cam1 = vtk.vtkCamera()
    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()


def get_program_parameters():
    import argparse
    description = 'Visualizing blood flow in human carotid arteries.'
    epilogue = '''
    Cone glyphs indicate flow direction and magnitude. 
    '''
    parser = argparse.ArgumentParser(description=description, epilog=epilogue,
                                     formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('filename', help='carotid.vtk.')
    args = parser.parse_args()
    return args.filename


if __name__ == '__main__':
    main()
CarotidFlowGlyphs/CMakeLists.txt0000644000076500000240000000176013424703035020177 0ustar  lorensenstaff00000000000000
cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

project(CarotidFlowGlyphs)

find_package(VTK COMPONENTS 
  vtkCommonColor
  vtkCommonCore
  vtkCommonDataModel
  vtkFiltersCore
  vtkFiltersModeling
  vtkFiltersSources
  vtkIOLegacy
  vtkInteractionStyle
  vtkRenderingCore
  vtkRenderingFreeType
  vtkRenderingOpenGL2 QUIET)
if (NOT VTK_FOUND)
  message("Skipping CarotidFlowGlyphs: ${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(CarotidFlowGlyphs MACOSX_BUNDLE CarotidFlowGlyphs.cxx )
  target_link_libraries(CarotidFlowGlyphs PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  add_executable(CarotidFlowGlyphs MACOSX_BUNDLE CarotidFlowGlyphs.cxx )
  target_link_libraries(CarotidFlowGlyphs PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS CarotidFlowGlyphs
    MODULES ${VTK_LIBRARIES}
    )
endif () 
CarotidFlowGlyphs/build/0000755000076500000240000000000013424703035016532 5ustar  lorensenstaff00000000000000CarotidFlowGlyphs/CarotidFlowGlyphs.cxx0000644000076500000240000001073213424703035021566 0ustar  lorensenstaff00000000000000#include <vtkActor.h>
#include <vtkCamera.h>
#include <vtkConeSource.h>
#include <vtkContourFilter.h>
#include <vtkGlyph3D.h>
#include <vtkLookupTable.h>
#include <vtkMaskPoints.h>
#include <vtkNamedColors.h>
#include <vtkOutlineFilter.h>
#include <vtkPointData.h>
#include <vtkPolyDataMapper.h>
#include <vtkProperty.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkStructuredPoints.h>
#include <vtkStructuredPointsReader.h>
#include <vtkThresholdPoints.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<vtkThresholdPoints> threshold =
    vtkSmartPointer<vtkThresholdPoints>::New();
  threshold->SetInputConnection(reader->GetOutputPort());
  threshold->ThresholdByUpper(200);

  vtkSmartPointer<vtkMaskPoints> mask =
    vtkSmartPointer<vtkMaskPoints>::New();
  mask->SetInputConnection(threshold->GetOutputPort());
  mask->SetOnRatio(5);

  vtkSmartPointer<vtkConeSource> cone =
    vtkSmartPointer<vtkConeSource>::New();
  cone->SetResolution(11);
  cone->SetHeight(1);
  cone->SetRadius(0.25);

  vtkSmartPointer<vtkGlyph3D> cones =
    vtkSmartPointer<vtkGlyph3D>::New();
  cones->SetInputConnection(mask->GetOutputPort());
  cones->SetSourceConnection(cone->GetOutputPort());
  cones->SetScaleFactor(0.4);
  cones->SetScaleModeToScaleByVector();

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

  double range[2];
  cones->Update();
  range[0] = cones->GetOutput()->GetPointData()->GetScalars()->GetRange()[0];
  range[1] = cones->GetOutput()->GetPointData()->GetScalars()->GetRange()[1];
  std::cout << "range: " << range[0] << ", " << range[1] << std::endl;

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

  vtkSmartPointer<vtkActor> vectorActor =
    vtkSmartPointer<vtkActor>::New();
  vectorActor->SetMapper(vectorMapper);

// 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(vectorActor);
  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;
}