GetMeshAndTopology.cxx

#include "antsUtilities.h"
#include <algorithm>

#include <string>

#include <math.h>
#include <time.h>
#include "itkVTKPolyDataWriter.h"
#include "vtkSTLWriter.h"
#include "vtkXMLPolyDataWriter.h"
#include "itkImage.h"

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIterator.h"
#include "itkMesh.h"
#include "itkSphereMeshSource.h"
#include "itkBinaryMask3DMeshSource.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "vtkPolyData.h"
#include "vtkCellData.h"
#include "vtkPolyDataConnectivityFilter.h"
#include "vtkExtractEdges.h"
#include "vtkPolyDataReader.h"

#include "BinaryImageToMeshFilter.h"
#include "vtkUnstructuredGrid.h"
#include "vtkCallbackCommand.h"
#include "vtkPointPicker.h"
#include "vtkCellPicker.h"
#include "vtkPolyDataWriter.h"
#include "vtkPolyDataReader.h"
#include "vtkRenderWindow.h"
#include "vtkRenderer.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkDataSetMapper.h"
#include <vtkPolyDataMapper.h>
#include <vtkActor.h>
#include <vtkRenderWindow.h>
#include <vtkRenderer.h>
#include <vtkPolyData.h>
#include <vtkSmartPointer.h>
#include <vtkSphereSource.h>
#include <vtkWindowToImageFilter.h>
#include <vtkPNGWriter.h>
#include <vtkGraphicsFactory.h>
#include "ReadWriteData.h"
#include "itkRescaleIntensityImageFilter.h"
#include "vtkDelaunay2D.h"
#include "vtkFloatArray.h"
#include <vtkSmartPointer.h>
#include <vtkWindowedSincPolyDataFilter.h>

#include "vtkVolume16Reader.h"
#include "vtkImageReader2.h"
#include "vtkPolyDataMapper.h"
#include "vtkActor.h"
#include "vtkOutlineFilter.h"
#include "vtkCamera.h"
#include "vtkProperty.h"
#include "vtkPolyData.h"
#include "vtkPolyVertex.h"
#include "vtkPointData.h"
#include "vtkExtractEdges.h"
#include "vtkPolyDataNormals.h"
#include "vtkMarchingCubes.h"
#include "vtkImageGaussianSmooth.h"
#include "vtkDecimatePro.h"
#include "vtkContourFilter.h"
#include "vtkPolyDataConnectivityFilter.h"

#include "vtkSmoothPolyDataFilter.h"
#include "vtkSTLWriter.h"
#include "itkSurfaceImageCurvature.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkImageRegionIterator.h"
#include "itkPointSet.h"
#include <vtkLookupTable.h>
#include <vtkScalarBarActor.h>


namespace ants
{

void Display(vtkUnstructuredGrid* vtkgrid, std::string offscreen, bool secondwin = false, bool delinter = true )
{

  vtkSmartPointer<vtkPolyDataNormals> normalGenerator = vtkSmartPointer<vtkPolyDataNormals>::New();
  normalGenerator->SetInputData(vtkgrid);
  normalGenerator->ComputePointNormalsOn();
  normalGenerator->ComputeCellNormalsOff();
  normalGenerator->Update();

  vtkSmartPointer<vtkGraphicsFactory> graphics_factory =
    vtkSmartPointer<vtkGraphicsFactory>::New();
  if ( offscreen.length() > 4 ) graphics_factory->SetOffScreenOnlyMode( 1);
  graphics_factory->SetUseMesaClasses( 1 );

  vtkRenderer*     ren1 = vtkRenderer::New();
  vtkRenderer*     ren2 = vtkRenderer::New();
  vtkRenderWindow* renWin = vtkRenderWindow::New();
  renWin->AddRenderer(ren1);
  if( secondwin )
    {
    renWin->AddRenderer(ren2);
    }
  vtkRenderWindowInteractor* inter = vtkRenderWindowInteractor::New();
  inter->SetRenderWindow(renWin);
  vtkCallbackCommand *cbc = vtkCallbackCommand::New();
  ren1->AddObserver(vtkCommand::KeyPressEvent, cbc);

  vtkDataSetMapper* mapper = vtkDataSetMapper::New();
  mapper->SetInputData(  normalGenerator->GetOutput() );

 // Create a lookup table to map cell data to colors
  vtkSmartPointer<vtkLookupTable> lut =
    vtkSmartPointer<vtkLookupTable>::New();
  int tableSize = std::max( 10, 10);
  lut->SetNumberOfTableValues(tableSize);
  lut->Build();
  lut->SetTableRange( 0 , 1 );
  lut->SetTableValue(0     , 1     , 1     , 1, 1);  //Black
  lut->SetTableValue(1, 0.8900, 0.8100, 0.3400, 1); // Banana
  lut->SetTableValue(2, 1.0000, 0.3882, 0.2784, 1); // Tomato
  lut->SetTableValue(3, 0.9608, 0.8706, 0.7020, 1); // Wheat
  lut->SetTableValue(4, 0.9020, 0.9020, 0.9804, 1); // Lavender
  lut->SetTableValue(5, 1.0000, 0.4900, 0.2500, 1); // Flesh
  lut->SetTableValue(6, 0.5300, 0.1500, 0.3400, 1); // Raspberry
  lut->SetTableValue(7, 0.9804, 0.5020, 0.4471, 1); // Salmon
  lut->SetTableValue(8, 0.7400, 0.9900, 0.7900, 1); // Mint
  lut->SetTableValue(9, 0.2000, 0.6300, 0.7900, 1); // Peacock
  mapper->SetLookupTable(lut);
  mapper->ScalarVisibilityOn();
  mapper->SetScalarRange(0, 1);
  //  mapper->SetScalarModeToUsePointData();
  //  mapper->SetColorModeToMapScalars();

  vtkActor* actor = vtkActor::New();
  actor->SetMapper(mapper);
  vtkSmartPointer<vtkScalarBarActor> scalarBar =
    vtkSmartPointer<vtkScalarBarActor>::New();
  scalarBar->SetLookupTable(mapper->GetLookupTable());
  scalarBar->SetTitle("F(x)");
  scalarBar->SetNumberOfLabels(4);
// Create a lookup table to share between the mapper and the scalarbar
  vtkSmartPointer<vtkLookupTable> hueLut =
    vtkSmartPointer<vtkLookupTable>::New();
  hueLut->SetTableRange (0, 1);
  hueLut->SetHueRange (0, 1);
  hueLut->SetSaturationRange (1, 1);
  hueLut->SetValueRange (1, 1);
  hueLut->Build();

  //  mapper->SetLookupTable( hueLut );
  scalarBar->SetLookupTable( lut );
  vtkDataSetMapper* mapper2 = vtkDataSetMapper::New();
  if( secondwin )
    {
    mapper2->SetInputData(vtkgrid);
    }
  if( secondwin )
    {
    mapper2->SetScalarRange(0, 255);
    }
  vtkActor* actor2 = vtkActor::New();
  if( secondwin )
    {
    actor2->SetMapper(mapper2);
    }
  if( secondwin )
    {
    ren1->SetViewport(0.0, 0.0, 0.5, 1.0);
    ren2->SetViewport(0.5, 0.0, 1.0, 1.0);
    }
  else
    {
    ren1->SetViewport(0.0, 0.0, 1.0, 1.0);
    }
  if( secondwin )
    {
    ren2->AddActor(actor2);
    }
  // add the actor and start the render loop
  // see http://www.vtk.org/doc/nightly/html/classvtkProperty.html
  actor->GetProperty()->SetInterpolationToFlat();
  actor->GetProperty()->SetInterpolationToGouraud();
  actor->GetProperty()->ShadingOff();
  ren1->AddActor(actor);
  ren1->SetBackground(1,1,1); // Background color
  ren1->AddActor2D(scalarBar);
  renWin->Render();

  if ( offscreen.length() > 4 )
    {
    vtkSmartPointer<vtkWindowToImageFilter> windowToImageFilter =
    vtkSmartPointer<vtkWindowToImageFilter>::New();
    windowToImageFilter->SetInput(renWin);
    windowToImageFilter->SetMagnification( 4 );
    windowToImageFilter->Update();

    vtkSmartPointer<vtkPNGWriter> writer =
      vtkSmartPointer<vtkPNGWriter>::New();
    writer->SetFileName( offscreen.c_str()  );
    writer->SetInputConnection(windowToImageFilter->GetOutputPort());
    writer->Write();
    }
  if (  offscreen.length() < 5 )  inter->Start();
  mapper->Delete();
  actor->Delete();
  ren1->Delete();
  mapper2->Delete();
  actor2->Delete();
  ren2->Delete();
  renWin->Delete();
  if( delinter )
    {
    inter->Delete();
    }
}

float ComputeGenus(vtkPolyData* pd1)
{
  vtkExtractEdges* edgeex = vtkExtractEdges::New();

  edgeex->SetInputData(pd1);
  edgeex->Update();
  vtkPolyData* edg1 = edgeex->GetOutput();

  vtkIdType nedg = edg1->GetNumberOfCells();
  vtkIdType vers = pd1->GetNumberOfPoints();
  int       nfac = pd1->GetNumberOfPolys();

  float g = 0.5 * (2.0 - vers + nedg - nfac);
  std::cout << " Genus " << g << std::endl;

  std::cout << " face " << nfac << " edg " << nedg <<  " vert " << vers << std::endl;

  return g;
}


float vtkComputeTopology(vtkPolyData* pd)
{
  // Marching cubes
//    std::cout << " Marching Cubes ";
//    vtkMarchingCubes *marchingCubes = vtkMarchingCubes::New();
//    vtkContourFilter *marchingCubes = vtkContourFilter::New();
//    vtkKitwareContourFilter *marchingCubes = vtkKitwareContourFilter::New();
//    marchingCubes->SetInput((vtkDataSet*) vds);
//    marchingCubes->SetValue(0, hithresh);
//    int nc;
//    std::cout << " Input #conts "; std::cin >> nc;
//    marchingCubes->SetNumberOfContours(2);
//    marchingCubes->SetComputeScalars(false);
//    marchingCubes->SetComputeGradients(false);
//    marchingCubes->SetComputeNormals(false);
  vtkPolyDataConnectivityFilter* con = vtkPolyDataConnectivityFilter::New();

  con->SetExtractionModeToLargestRegion();
//    con->SetInput(marchingCubes->GetOutput());
  con->SetInputData(pd);
  con->Update();
  float g = ComputeGenus(con->GetOutput() );
  return g;
#if 0
  int inputNumberOfPoints = con->GetOutput()->GetNumberOfPoints();
  int inputNumberOfPolys = con->GetOutput()->GetNumberOfPolys();

  vtkPolyDataConnectivityFilter *polyDataConnectivityFilter =
    vtkPolyDataConnectivityFilter::New();
  polyDataConnectivityFilter->SetInputData( con->GetOutput() );
  polyDataConnectivityFilter->SetExtractionModeToAllRegions();
  polyDataConnectivityFilter->SetExtractionModeToLargestRegion();
  polyDataConnectivityFilter->Update();

  int connectivityNumberOfExtractedRegions = polyDataConnectivityFilter->
    GetNumberOfExtractedRegions();

  polyDataConnectivityFilter->Delete();

  vtkExtractEdges *extractEdges = vtkExtractEdges::New();
  extractEdges->SetInputData( con->GetOutput() );
  extractEdges->Update();

  int extractNumberOfLines = extractEdges->GetOutput()->GetNumberOfLines();

  extractEdges->Delete();

  int EulerCharacteristic = inputNumberOfPoints - extractNumberOfLines
    + inputNumberOfPolys;

  double genus = 0.5 * ( 2 * connectivityNumberOfExtractedRegions
                         - EulerCharacteristic );

  std::cout << "EulerCharacteristic " << EulerCharacteristic << std::endl;
  std::cout << "genus " << genus << std::endl;

  return genus;
#endif
}

template <class TImage>
void GetValueMesh(typename TImage::Pointer image, typename TImage::Pointer image2,  std::string outfn,
                  const char* paramname, float scaledata,
                  float aaParm, std::string offscreen , unsigned int inflate )
{
  //  std::cout << " parname " << std::string(paramname) << std::endl;
  typedef TImage      ImageType;

  typedef BinaryImageToMeshFilter<ImageType> FilterType;
  typename  FilterType::Pointer fltMesh = FilterType::New();
  fltMesh->SetInput( image );
  fltMesh->SetAntiAliasMaxRMSError( aaParm ); // to do nothing, set negative
  fltMesh->SetSmoothingIterations( 0 );
  fltMesh->SetDecimateFactor( 0.0 );
  fltMesh->Update();
  vtkPolyData* vtkmesh = fltMesh->GetMesh();
// assign scalars to the original surface mesh
//  std::string offsc=std::string("");
//  Display((vtkUnstructuredGrid*)vtkmesh, offsc );
  vtkSmartPointer<vtkWindowedSincPolyDataFilter> smoother =
    vtkSmartPointer<vtkWindowedSincPolyDataFilter>::New();
  smoother->SetInputData(vtkmesh);
  smoother->SetNumberOfIterations(25);
  smoother->BoundarySmoothingOff();
  smoother->FeatureEdgeSmoothingOff();
  smoother->SetFeatureAngle(120.0);
  smoother->SetPassBand(.01);
  smoother->NonManifoldSmoothingOn();
  smoother->NormalizeCoordinatesOn();
  smoother->Update();
  vtkmesh = smoother->GetOutput();

  std::cout << " Genus " << vtkComputeTopology(vtkmesh) << std::endl;

  vtkPoints* vtkpoints = vtkmesh->GetPoints();
  int        numPoints = vtkpoints->GetNumberOfPoints();
  float      mx = 0, mn = 9.e9, meank = 0;
  for( int i = 0; i < numPoints; i++ )
    {
    typename ImageType::IndexType index;
    typename ImageType::PointType point;
    for( int j = 0; j < 3; j++ )
      {
      point[j] = (vtkpoints->GetPoint(i)[j]);
      }
    image2->TransformPhysicalPointToIndex(point, index);
    float temp = image2->GetPixel(index);
    if( fabs(temp) > mx )
      {
      mx = fabs(temp);
      }
    if( fabs(temp) < mn && mn > 0 )
      {
      mn = fabs(temp);
      }
    meank += fabs(temp);
    }
  std::cout << " max kap " << mx << " mn k " << mn <<  std::endl;
  meank /= numPoints;
//  mx=1.3;
//  mx=2.0;
  float localscaledata = scaledata;
  localscaledata = 1;
  // while (!done)
    {
    vtkFloatArray* param = vtkFloatArray::New();
    param->SetName(paramname);
    float dif = (mx - mn) * localscaledata;
    const float mx2 = meank + dif;
    const float mn2 = meank - dif;
    dif = mx2 - mn2;
    for( int i = 0; i < (numPoints); i++ )
      {
      typename ImageType::IndexType index;
      typename ImageType::PointType point;
      for( int j = 0; j < 3; j++ )
        {
        point[j] = (vtkpoints->GetPoint(i)[j]);
        }
      image2->TransformPhysicalPointToIndex(point, index);
      float temp = image2->GetPixel(index);
      //    param->InsertNextValue(temp);
      //    float temp=surfk->CurvatureAtIndex(index);
      if( i % 1000 == 0 )
        {
        std::cout << " kappa " << temp << std::endl;
        }
      // =fabs(manifoldIntegrator->GetGraphNode(i)->GetTotalCost());

      temp = fabs(temp);
      float vvv = (temp - mn2) * 255. / dif;
      vvv = (temp - mn) / dif;
      /*
      if (vvv > 128)
        {
      float dif=255-vvv;
      vvv = 128 - dif;
        }
      else
        {
      float dif=128-vvv;
      vvv = 128 + dif;
      }*/
      param->InsertNextValue(vvv);
      }
    vtkmesh->GetPointData()->SetScalars(param);
    }
  std::cout <<" Now display to " << offscreen << std::endl;
  vtkSmartPointer<vtkWindowedSincPolyDataFilter> inflater =
    vtkSmartPointer<vtkWindowedSincPolyDataFilter>::New();
  inflater->SetInputData(vtkmesh);
  inflater->SetNumberOfIterations( inflate );
  inflater->BoundarySmoothingOn();
  inflater->FeatureEdgeSmoothingOff();
  inflater->SetFeatureAngle(180.0);
  inflater->SetEdgeAngle(180.0);
  inflater->SetPassBand( 0.001 ); // smaller values increase smoothing
  inflater->NonManifoldSmoothingOn();
  inflater->NormalizeCoordinatesOff();
  if ( inflate > 0 ) {
    inflater->Update();
    vtkmesh = inflater->GetOutput();
  }
  if ( offscreen.length() > 2 ) Display((vtkUnstructuredGrid*)vtkmesh, offscreen );
  std::cout << " done with mesh map ";
  /*
  typedef itk::VTKPolyDataWriter<MeshType> WriterType;
  WriterType::Pointer writer = WriterType::New();
  writer->SetInputData( vtkmesh );
  writer->SetFileName( outfn.c_str() );
  writer->Update();
  */
  vtkSTLWriter *writer = vtkSTLWriter::New();
  writer->SetInputData( vtkmesh );
  std::cout << " writing " << outfn << std::endl;
  writer->SetFileName( outfn.c_str() );
  writer->Write();
  std::cout << " done writing ";
  inflater->Delete();
  smoother->Delete();
  std::cout << " done writing2 ";
  return;
}

template <class TImage>
float GetImageTopology(typename TImage::Pointer image)
{
  typedef TImage      ImageType;

  double aaParm = 0.024;
  typedef BinaryImageToMeshFilter<ImageType> FilterType;
  typename  FilterType::Pointer fltMesh = FilterType::New();
  fltMesh->SetInput(image);
  fltMesh->SetAntiAliasMaxRMSError(aaParm);
  fltMesh->SetAntiAliasMaxRMSError( -1000.0 );   // to do nothing
  fltMesh->Update();
  vtkPolyData* vtkmesh = fltMesh->GetMesh();
// assign scalars to the original surface mesh
//  Display((vtkUnstructuredGrid*)vtkmesh);

  float genus =  vtkComputeTopology(vtkmesh);
  std::cout << " Genus " << genus << std::endl;

  return genus;
}

// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int GetMeshAndTopology( std::vector<std::string> args, std::ostream*  )
{
  // put the arguments coming in as 'args' into standard (argc,argv) format;
  // 'args' doesn't have the command name as first, argument, so add it manually;
  // 'args' may have adjacent arguments concatenated into one argument,
  // which the parser should handle
  args.insert( args.begin(), "GetMeshAndTopology" );

  int     argc = args.size();
  char* * argv = new char *[args.size() + 1];
  for( unsigned int i = 0; i < args.size(); ++i )
    {
    // allocate space for the string plus a null character
    argv[i] = new char[args[i].length() + 1];
    std::strncpy( argv[i], args[i].c_str(), args[i].length() );
    // place the null character in the end
    argv[i][args[i].length()] = '\0';
    }
  argv[argc] = 0;
  // class to automatically cleanup argv upon destruction
  class Cleanup_argv
  {
public:
    Cleanup_argv( char* * argv_, int argc_plus_one_ ) : argv( argv_ ), argc_plus_one( argc_plus_one_ )
    {
    }

    ~Cleanup_argv()
    {
      for( unsigned int i = 0; i < argc_plus_one; ++i )
        {
        delete[] argv[i];
        }
      delete[] argv;
    }

private:
    char* *      argv;
    unsigned int argc_plus_one;
  };
  Cleanup_argv cleanup_argv( argv, argc + 1 );

  // antscout->set_stream( out_stream );

  if( argc < 2 )
    {
    std::cout << argv[0] << " binaryimage valueimage  out paramname ValueScale AntiaAliasParm=0.001 offscreen.png  inflation-interations " << std::endl;
    std::cout << " outputs vtk version of input image -- assumes object is defined by non-zero values " << std::endl;
    std::cout << " mesh is colored by the value of the image voxel " << std::endl;
    std::cout <<  " the AntiaAliasParm could cause topo problems but makes nicer meshes  " << std::endl;
    std::cout <<  " the offscreen param will render to screen if set to win, 0 means no rendering " << std::endl;
    std::cout << " ValueScale controls contrast in image appearance - lower increaseses contrast -- should be <= 1 "
             << std::endl;
    return EXIT_FAILURE;
    }

  // Define the dimension of the images
  const unsigned int Dimension = 3;
  typedef float PixelType;
  // Declare the types of the output images
  typedef itk::Image<PixelType, Dimension> ImageType;

  // Declare the type of the Mesh

  std::string outfn = std::string(argv[3]);

  ImageType::Pointer image;
  ReadImage<ImageType>(image, argv[1]);
  ImageType::Pointer image2;
  ReadImage<ImageType>(image2, argv[2]);

  ImageType::DirectionType fmat = image->GetDirection();
  fmat.SetIdentity();
  image->SetDirection(fmat);
  image2->SetDirection(fmat);

  // Save the mesh
  float       aaParm = 0.03;
  const char* paramname = std::string("f(x)").c_str();
  if( argc > 4 )
    {
    paramname = (argv[4]);
    }
  float scaledata = 0.5;
  if( argc > 5 )
    {
    scaledata = atof(argv[5]);
    }
  if( argc > 6 )
    {
    aaParm = atof(argv[6]);
    }
  std::cout << "aaParm " << aaParm << std::endl;
  std::string offscreen="win";
  if( argc > 7 )
    {
    offscreen = std::string( argv[7] );
    }
  unsigned int inflate = 0;
  if( argc > 8 )
    {
    inflate = atoi(argv[8]);
    }
  GetValueMesh<ImageType>(image, image2, outfn, paramname, scaledata, aaParm, offscreen, inflate );
  //  GetImageTopology<ImageType>(image);
  return EXIT_SUCCESS;
}
} // namespace ants