ReadSLC

VTKExamples/Cxx/IO/ReadSLC

Description

In this example you will familiarize yourself with the stages required to read a .slc file and create a visualization pipeline in VTK. Following is the three step procedure:

  1. Read the data from .slc file using vtkSLCReader

  2. Implement Marching cubes Algorithm using vtkContourFilter

  3. Create Visualization pipeline to visualize data using an actor, mapper and rendering window

Cite

This example was provided by Bharatesh Chakravarthi from Virtual Environment Lab, Chung-Ang University, Seoul, South Korea

Other Languages

See (Python), (Java)

Code

ReadSLC.cxx

#include <vtkSmartPointer.h>
#include <vtkSLCReader.h>

#include <vtkPolyData.h>
#include <vtkPolyDataMapper.h>
#include <vtkActor.h>
#include <vtkCamera.h>
#include <vtkRenderWindow.h>
#include <vtkRenderer.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkContourFilter.h>
#include <vtkProperty.h>
#include <vtkExtractVOI.h>
#include <vtkOutlineFilter.h>
#include <vtkNamedColors.h>


//Author: Bharatesh Chakravarthi 
//Affiliation: Virtual Environment Lab, Chung-Ang University, Seoul, South Korea

int main(int argc, char *argv[])
{
  if (argc < 2)
  {
    //Pass the filename (<filename>.slc) as parameter to read .slc file 
    std::cout << "Required parameters: Filename" << std::endl;
    return EXIT_FAILURE;
  }

  double isoValue = 72.0;
  if (argc < 3)
  {
    isoValue = 72.0;
  }
  else
  {
    isoValue = std::atof(argv[2]);
  }
  std::string inputFilename = argv[1];

  //Using vtkSLCReader to read Volumetric file format(<filename.slc>) 
  vtkSmartPointer<vtkSLCReader> reader =
    vtkSmartPointer<vtkSLCReader>::New();
  reader->SetFileName(inputFilename.c_str());
  reader->Update();

  // Implementing Marching Cubes Algorithm to create the surface using
  // vtkContourFilter object 
  vtkSmartPointer<vtkContourFilter> cFilter =
    vtkSmartPointer<vtkContourFilter>::New();
  cFilter->SetInputConnection(reader->GetOutputPort());

  // Change the range(2nd and 3rd Paramater) based on your
  // requirement. recomended value for 1st parameter is above 1
//  cFilter->GenerateValues(5, 80.0, 100.0); 
  cFilter->SetValue(0, isoValue);
  cFilter->Update();

  //Adding the outliner using vtkOutlineFilter object
  vtkSmartPointer<vtkOutlineFilter> outliner =
    vtkSmartPointer<vtkOutlineFilter>::New();
  outliner->SetInputConnection(reader->GetOutputPort());
  outliner->Update();

  // Visualize
  vtkSmartPointer<vtkPolyDataMapper> mapper =
    vtkSmartPointer<vtkPolyDataMapper>::New();
  mapper->SetInputConnection(cFilter->GetOutputPort());
  mapper->SetScalarVisibility(0);

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

  vtkSmartPointer<vtkActor> actor =
    vtkSmartPointer<vtkActor>::New();
  actor->SetMapper(mapper);
  actor->GetProperty()->SetDiffuse(.8);
  actor->GetProperty()->SetDiffuseColor(colors->GetColor3d("Ivory").GetData());
  actor->GetProperty()->SetSpecular(.8);
  actor->GetProperty()->SetSpecularPower(120.0);

  //extractVOI is used to fix the problem of subsampling of data and reduce slow interaction and increase loading speed
  vtkSmartPointer<vtkExtractVOI> extractVOI =
    vtkSmartPointer<vtkExtractVOI>::New();
  extractVOI->SetInputConnection(reader->GetOutputPort());
  extractVOI->SetSampleRate(2, 2, 2);
  extractVOI->Update();

  vtkSmartPointer<vtkRenderer> renderer =
    vtkSmartPointer<vtkRenderer>::New();
  vtkSmartPointer<vtkRenderWindow> renderWindow =
    vtkSmartPointer<vtkRenderWindow>::New();
  renderWindow->AddRenderer(renderer);
  renderWindow->SetSize(640, 512);

  vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor
    = vtkSmartPointer<vtkRenderWindowInteractor>::New();
  renderWindowInteractor->SetRenderWindow(renderWindow);

  renderer->AddActor(actor);
  renderer->SetBackground(colors->GetColor3d("SlateGray").GetData());
  renderWindow->Render();

  // Pick a good view
  vtkCamera *cam1 = renderer->GetActiveCamera();
  cam1->SetFocalPoint(0.0, 0.0, 0.0);
  cam1->SetPosition(0.0, -1.0, 0.0);
  cam1->SetViewUp(0.0, 0.0, -1.0);
  cam1->Azimuth(30.0);
  renderer->ResetCamera();
  renderer->ResetCameraClippingRange();

  renderWindow->Render();
  renderWindowInteractor->Start();

  return EXIT_SUCCESS;
}

CMakeLists.txt

cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

project(ReadSLC)

find_package(VTK COMPONENTS 
  vtkCommonColor
  vtkCommonCore
  vtkCommonDataModel
  vtkFiltersCore
  vtkFiltersModeling
  vtkIOImage
  vtkImagingCore
  vtkInteractionStyle
  vtkRenderingCore
  vtkRenderingFreeType
  vtkRenderingOpenGL2 QUIET)
if (NOT VTK_FOUND)
  message("Skipping ReadSLC: ${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(ReadSLC MACOSX_BUNDLE ReadSLC.cxx )
  target_link_libraries(ReadSLC PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  add_executable(ReadSLC MACOSX_BUNDLE ReadSLC.cxx )
  target_link_libraries(ReadSLC PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS ReadSLC
    MODULES ${VTK_LIBRARIES}
    )
endif ()

Download and Build ReadSLC

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

cd ReadSLC/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:

./ReadSLC

WINDOWS USERS

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