PineRootConnectivity

auto NumberofTriangles = [](auto *pd)

def NumberOfTriangles(pd):

#include <vtkActor.h>
#include <vtkCamera.h>
#include <vtkDataSetMapper.h>
#include <vtkMCubesReader.h>
#include <vtkNamedColors.h>
#include <vtkOutlineFilter.h>
#include <vtkPolyData.h>
#include <vtkPolyDataConnectivityFilter.h>
#include <vtkPolyDataMapper.h>
#include <vtkProperty.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>

int main(int argc, char* argv[])
{
  if (argc < 2)
  {
    std::cout << "Usage: " << argv[0] << " filename [noConnectivity]"
              << std::endl;
    std::cout << "where: filename is pine_root.tri." << std::endl;
    std::cout << "       if noConnectivity is nonzero then the connectivity "
                 "filter is ignored."
              << std::endl;
    return EXIT_FAILURE;
  }

  /**
  * Count the triangles in the polydata.
  * @param pd: vtkPolyData.
  * @return The number of triangles.
  */
  auto NumberofTriangles = [](vtkPolyData* pd) {
    vtkCellArray* cells = pd->GetPolys();
    vtkIdType npts = 0;
    vtkIdType* pts;
    auto numOfTriangles = 0;
    for (auto i = 0; i < pd->GetNumberOfPolys(); ++i)
    {
      int c = cells->GetNextCell(npts, pts);
      if (c == 0)
      {
        break;
      }
      // If a cell has three points it is a triangle.
      if (npts == 3)
      {
        numOfTriangles++;
      }
    }
    return numOfTriangles;
  };

  std::string fileName = argv[1];
  auto noConnectivity = false;
  if (argc > 2)
  {
    noConnectivity = atoi(argv[2]) != 0;
  }

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

  // Create the pipeline.
  vtkSmartPointer<vtkMCubesReader> reader =
    vtkSmartPointer<vtkMCubesReader>::New();
  reader->SetFileName(fileName.c_str());
  reader->FlipNormalsOff();
  if (!noConnectivity)
  {
    reader->Update();
    std::cout << "Before Connectivity." << std::endl;
    std::cout << "There are: " << NumberofTriangles(reader->GetOutput())
              << " triangles." << std::endl;
  }

  vtkSmartPointer<vtkPolyDataConnectivityFilter> connect =
    vtkSmartPointer<vtkPolyDataConnectivityFilter>::New();
  connect->SetInputConnection(reader->GetOutputPort());
  connect->SetExtractionModeToLargestRegion();
  if (!noConnectivity)
  {
    connect->Update();
    std::cout << "After Connectivity." << std::endl;
    // Note the use of vtkPolyData::SafeDownCast here.
    std::cout << "There are: " << NumberofTriangles(vtkPolyData::SafeDownCast(
                                    connect->GetOutput()))
              << " triangles." << std::endl;
  }

  vtkSmartPointer<vtkDataSetMapper> isoMapper =
    vtkSmartPointer<vtkDataSetMapper>::New();
  if (noConnectivity)
  {
    isoMapper->SetInputConnection(reader->GetOutputPort());
  }
  else
  {
    isoMapper->SetInputConnection(connect->GetOutputPort());
  }
  isoMapper->ScalarVisibilityOff();
  vtkSmartPointer<vtkActor> isoActor = vtkSmartPointer<vtkActor>::New();
  isoActor->SetMapper(isoMapper);
  isoActor->GetProperty()->SetColor(colors->GetColor3d("raw_sienna").GetData());

  // Get an outline of the data set for context.
  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());

  // Create the Renderer, RenderWindow and RenderWindowInteractor.
  vtkSmartPointer<vtkRenderer> ren = vtkSmartPointer<vtkRenderer>::New();
  vtkSmartPointer<vtkRenderWindow> renWin =
    vtkSmartPointer<vtkRenderWindow>::New();
  renWin->AddRenderer(ren);
  vtkSmartPointer<vtkRenderWindowInteractor> iren =
    vtkSmartPointer<vtkRenderWindowInteractor>::New();
  iren->SetRenderWindow(renWin);

  // Add the actors to the renderer, set the background and size.
  ren->AddActor(outlineActor);
  ren->AddActor(isoActor);
  // renWin->SetSize(750, 750);
  renWin->SetSize(512, 512);
  ren->SetBackground(colors->GetColor3d("SlateGray").GetData());

  vtkCamera* cam = ren->GetActiveCamera();
  cam->SetFocalPoint(40.6018, 37.2813, 50.1953);
  cam->SetPosition(40.6018, -280.533, 47.0172);
  cam->ComputeViewPlaneNormal();
  cam->SetClippingRange(26.1073, 1305.36);
  cam->SetViewAngle(20.9219);
  cam->SetViewUp(0.0, 0.0, 1.0);

  iren->Initialize();
  renWin->Render();
  iren->Start();

  return EXIT_SUCCESS;
}

cmake_minimum_required(VERSION 2.8)

PROJECT(PineRootConnectivity)

find_package(VTK REQUIRED)
include(${VTK_USE_FILE})

add_executable(PineRootConnectivity MACOSX_BUNDLE PineRootConnectivity.cxx )

target_link_libraries(PineRootConnectivity ${VTK_LIBRARIES})

cd PineRootConnectivity/build 

cmake ..

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

make

./PineRootConnectivity