# PineRootDecimation

vtk-examples/Cxx/VisualizationAlgorithms/PineRootDecimation

### Description¶

Demonstrates how to apply the decimation filter to get a reduced data size and then the connectivity filter to remove noisy isosurfaces. The data is from the root system of a pine tree.

To count the number of triangles in the polydata we do the following:

#### C++¶

We use a lambda function

auto NumberofTriangles = [](auto *pd)


#### Python¶

We just implement:

def NumberOfTriangles(pd):


within the scope of the calling function.

Info

See Figure 9-52 in Chapter 9 in the VTK Textbook.

Other languages

See (Python)

Question

If you have a question about this example, please use the VTK Discourse Forum

### Code¶

PineRootDecimation.cxx

#include <vtkActor.h>
#include <vtkCamera.h>
#include <vtkCellArray.h>
#include <vtkConnectivityFilter.h>
#include <vtkDataSetMapper.h>
#include <vtkDecimatePro.h>
#include <vtkMCubesReader.h>
#include <vtkNamedColors.h>
#include <vtkNew.h>
#include <vtkOutlineFilter.h>
#include <vtkPolyData.h>
#include <vtkPolyDataMapper.h>
#include <vtkProperty.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#ifdef VTK_CELL_ARRAY_V2
#include <vtkCellArrayIterator.h>
#endif // VTK_CELL_ARRAY_V2

int main(int argc, char* argv[])
{
if (argc < 2)
{
std::cout << "Usage: " << argv[0] << " filename" << std::endl;
std::cout << "where: filename is pine_root.tri." << 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;
auto numOfTriangles = 0;
#ifdef VTK_CELL_ARRAY_V2

// Newer versions of vtkCellArray prefer local iterators:
std::cout << pd->GetNumberOfPolys() << std::endl;
auto cellIter = vtk::TakeSmartPointer(cells->NewIterator());
for (cellIter->GoToFirstCell(); !cellIter->IsDoneWithTraversal();
cellIter->GoToNextCell())
{
auto cell = cellIter->GetCurrentCell();
if (cell == nullptr)
{
break;
}
// If a cell has three points it is a triangle.
if (cell->GetNumberOfIds() == 3)
{
numOfTriangles++;
}
}

#else  // VTK_CELL_ARRAY_V2

// Older implementations of vtkCellArray use internal iterator APIs (not
// thread safe):
vtkIdType* pts;
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++;
}
}
#endif // VTK_CELL_ARRAY_V2

return numOfTriangles;
};
///**
//* 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];

vtkNew<vtkNamedColors> colors;

// Create the pipeline.
vtkNew<vtkMCubesReader> reader;
reader->SetFileName(fileName.c_str());
reader->FlipNormalsOff();
reader->Update();
std::cout << "Before Decimation." << std::endl;
std::cout << "There are: " << NumberofTriangles(reader->GetOutput())
<< " triangles." << std::endl;

vtkNew<vtkDecimatePro> deci;
deci->SetInputConnection(reader->GetOutputPort());
deci->SetTargetReduction(0.9);
deci->SetAbsoluteError(0.0005);
deci->SetFeatureAngle(30);
deci->SetErrorIsAbsolute(1);
deci->AccumulateErrorOn();
// deci->SplittingOff();
deci->Update();
std::cout << "After Decimation." << std::endl;
std::cout << "There are: " << NumberofTriangles(deci->GetOutput())
<< " triangles." << std::endl;

vtkNew<vtkConnectivityFilter> connect;
connect->SetInputConnection(deci->GetOutputPort());
connect->SetExtractionModeToLargestRegion();
connect->Update();
std::cout << "After Connectivity." << std::endl;
// Note the use of dynamic_cast<vtkPolyData*> here.
std::cout << "There are: "
<< NumberofTriangles(
dynamic_cast<vtkPolyData*>(connect->GetOutput()))
<< " triangles." << std::endl;

vtkNew<vtkDataSetMapper> isoMapper;
isoMapper->SetInputConnection(connect->GetOutputPort());
isoMapper->ScalarVisibilityOff();
vtkNew<vtkActor> isoActor;
isoActor->SetMapper(isoMapper);
isoActor->GetProperty()->SetColor(colors->GetColor3d("raw_sienna").GetData());

// Get an outline of the data set for context.
vtkNew<vtkOutlineFilter> outline;
outline->SetInputConnection(reader->GetOutputPort());
vtkNew<vtkPolyDataMapper> outlineMapper;
outlineMapper->SetInputConnection(outline->GetOutputPort());
vtkNew<vtkActor> outlineActor;
outlineActor->SetMapper(outlineMapper);
outlineActor->GetProperty()->SetColor(colors->GetColor3d("Black").GetData());

// Create the Renderer, RenderWindow and RenderWindowInteractor.
vtkNew<vtkRenderer> ren;
vtkNew<vtkRenderWindow> renWin;
renWin->AddRenderer(ren);
vtkNew<vtkRenderWindowInteractor> iren;
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);
renWin->SetWindowName("PineRootDecimation");

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;
}


### CMakeLists.txt¶

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(PineRootDecimation)

find_package(VTK COMPONENTS
CommonColor
CommonCore
CommonDataModel
FiltersCore
FiltersModeling
IOGeometry
InteractionStyle
RenderingContextOpenGL2
RenderingCore
RenderingFreeType
RenderingGL2PSOpenGL2
RenderingOpenGL2
)

if (NOT VTK_FOUND)
message(FATAL_ERROR "PineRootDecimation: Unable to find the VTK build folder.")
endif()

# Prevent a "command line is too long" failure in Windows.
set(CMAKE_NINJA_FORCE_RESPONSE_FILE "ON" CACHE BOOL "Force Ninja to use response files.")
add_executable(PineRootDecimation MACOSX_BUNDLE PineRootDecimation.cxx )
target_link_libraries(PineRootDecimation PRIVATE ${VTK_LIBRARIES} ) # vtk_module_autoinit is needed vtk_module_autoinit( TARGETS PineRootDecimation MODULES${VTK_LIBRARIES}
)


### Download and Build PineRootDecimation¶

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

cd PineRootDecimation/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:

./PineRootDecimation


WINDOWS USERS

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