# PineRootDecimation

VTKExamples/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

### Code¶

PineRootDecimation.cxx

#include <vtkActor.h>
#include <vtkCamera.h>
#include <vtkConnectivityFilter.h>
#include <vtkDataSetMapper.h>
#include <vtkDecimatePro.h>
#include <vtkNamedColors.h>
#include <vtkOutlineFilter.h>
#include <vtkPolyData.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" << 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;
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];

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

// Create the pipeline.
std::cout << "Before Decimation." << std::endl;
std::cout << "There are: " << NumberofTriangles(reader->GetOutput())
<< " triangles." << std::endl;

vtkSmartPointer<vtkDecimatePro> deci = vtkSmartPointer<vtkDecimatePro>::New();
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;

vtkSmartPointer<vtkConnectivityFilter> connect =
vtkSmartPointer<vtkConnectivityFilter>::New();
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;

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

// Add the actors to the renderer, set the background and size.
// 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;
}


### CMakeLists.txt¶

cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

project(PineRootDecimation)

find_package(VTK COMPONENTS
vtkCommonColor
vtkCommonDataModel
vtkFiltersCore
vtkFiltersModeling
vtkIOGeometry
vtkInteractionStyle
vtkRenderingContextOpenGL2
vtkRenderingCore
vtkRenderingFreeType
vtkRenderingGL2PSOpenGL2
vtkRenderingOpenGL2 QUIET)
if (NOT VTK_FOUND)
message("Skipping PineRootDecimation: ${VTK_NOT_FOUND_MESSAGE}") return () endif() message (STATUS "VTK_VERSION:${VTK_VERSION}")
if (VTK_VERSION VERSION_LESS "8.90.0")
# old system
include(${VTK_USE_FILE}) add_executable(PineRootDecimation MACOSX_BUNDLE PineRootDecimation.cxx ) target_link_libraries(PineRootDecimation PRIVATE${VTK_LIBRARIES})
else ()
# include all components
target_link_libraries(PineRootDecimation PRIVATE ${VTK_LIBRARIES}) # vtk_module_autoinit is needed vtk_module_autoinit( TARGETS PineRootDecimation MODULES${VTK_LIBRARIES}
)
endif ()


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.