void Image3D::TransformMeshToBinaryImage(Mesh* m, string filename, OrientationType orient, bool sub_segmentation, bool cropUpDown, CVector3* upperSlicePoint, CVector3* upperSliceNormal, CVector3* downSlicePoint, CVector3* downSliceNormal)
{
//m->subdivision(2);
MeshTypeB::Pointer mesh;
MeshFilterType::Pointer meshFilter = MeshFilterType::New();
if (cropUpDown)
{
mesh = MeshTypeB::New();
vtkSmartPointer<vtkPolyData> polyData;
try {
polyData = m->reduceMeshUpAndDown(*upperSlicePoint, *upperSliceNormal, *downSlicePoint, *downSliceNormal);
}
catch (const exception& e) {
cout << e.what() << endl;
}
vtkSmartPointer<vtkFillHolesFilter> fillHolesFilter = vtkSmartPointer<vtkFillHolesFilter>::New();
fillHolesFilter->SetInputData(polyData);
fillHolesFilter->SetHoleSize(1000.0);
fillHolesFilter->Update();
// Make the triangle windong order consistent
vtkSmartPointer<vtkPolyDataNormals> normals = vtkSmartPointer<vtkPolyDataNormals>::New();
normals->SetInputData(fillHolesFilter->GetOutput());
normals->ConsistencyOn();
normals->SplittingOff();
normals->Update();
// Restore the original normals
normals->GetOutput()->GetPointData()->SetNormals(polyData->GetPointData()->GetNormals());
polyData = normals->GetOutput();
//
// Transfer the points from the vtkPolyData into the itk::Mesh
//
const unsigned int numberOfPoints = polyData->GetNumberOfPoints();
vtkPoints * vtkpoints = polyData->GetPoints();
mesh->GetPoints()->Reserve( numberOfPoints );
for(unsigned int p =0; p < numberOfPoints; p++)
{
double * apoint = vtkpoints->GetPoint( p );
mesh->SetPoint( p, MeshTypeB::PointType( apoint ));
}
//
// Transfer the cells from the vtkPolyData into the itk::Mesh
//
vtkCellArray * triangleStrips = polyData->GetStrips();
vtkIdType * cellPoints;
vtkIdType numberOfCellPoints;
//
// First count the total number of triangles from all the triangle strips.
//
unsigned int numberOfTriangles = 0;
triangleStrips->InitTraversal();
while( triangleStrips->GetNextCell( numberOfCellPoints, cellPoints ) )
{
numberOfTriangles += numberOfCellPoints-2;
}
vtkCellArray * polygons = polyData->GetPolys();
polygons->InitTraversal();
while( polygons->GetNextCell( numberOfCellPoints, cellPoints ) )
{
if( numberOfCellPoints == 3 )
{
numberOfTriangles ++;
}
}
//
// Reserve memory in the itk::Mesh for all those triangles
//
mesh->GetCells()->Reserve( numberOfTriangles );
//
// Copy the triangles from vtkPolyData into the itk::Mesh
//
//
typedef MeshTypeB::CellType CellType;
typedef itk::TriangleCell< CellType > TriangleCellType;
int cellId = 0;
// first copy the triangle strips
triangleStrips->InitTraversal();
while( triangleStrips->GetNextCell( numberOfCellPoints, cellPoints ) )
{
unsigned int numberOfTrianglesInStrip = numberOfCellPoints - 2;
unsigned long pointIds[3];
pointIds[0] = cellPoints[0];
pointIds[1] = cellPoints[1];
pointIds[2] = cellPoints[2];
for( unsigned int t=0; t < numberOfTrianglesInStrip; t++ )
{
MeshTypeB::CellAutoPointer c;
TriangleCellType * tcell = new TriangleCellType;
tcell->SetPointIds( pointIds );
c.TakeOwnership( tcell );
mesh->SetCell( cellId, c );
cellId++;
pointIds[0] = pointIds[1];
pointIds[1] = pointIds[2];
pointIds[2] = cellPoints[t+3];
}
}
// then copy the normal triangles
polygons->InitTraversal();
while( polygons->GetNextCell( numberOfCellPoints, cellPoints ) )
{
if( numberOfCellPoints !=3 ) // skip any non-triangle.
{
continue;
}
MeshTypeB::CellAutoPointer c;
TriangleCellType * t = new TriangleCellType;
t->SetPointIds( (unsigned long*)cellPoints );
c.TakeOwnership( t );
mesh->SetCell( cellId, c );
cellId++;
}
meshFilter->SetInput(mesh);
}
else
{
mesh = MeshTypeB::New();
vector<Vertex*> points = m->getListPoints();
PointType pnt;
CVector3 p, n;
for (unsigned int i=0; i<points.size(); i++) {
p = points[i]->getPosition();
n = points[i]->getNormal();
pnt[0] = p[0]; pnt[1] = p[1]; pnt[2] = p[2];
mesh->SetPoint(i,pnt);
}
vector<int> triangles = m->getListTriangles();
for (unsigned int i=0; i<triangles.size(); i+=3)
{
CellTypeB::CellAutoPointer triangle;
triangle.TakeOwnership(new CellTypeB);
triangle->SetPointId(0,triangles[i]);
triangle->SetPointId(1,triangles[i+1]);
triangle->SetPointId(2,triangles[i+2]);
mesh->SetCell((int)(i+1)/3,triangle);
}
meshFilter->SetInput(mesh);
}
meshFilter->SetOrigin(imageOriginale_->GetOrigin());
meshFilter->SetSpacing(imageOriginale_->GetSpacing());
meshFilter->SetSize(imageOriginale_->GetLargestPossibleRegion().GetSize());
meshFilter->SetDirection(imageOriginale_->GetDirection());
meshFilter->SetIndex(imageOriginale_->GetLargestPossibleRegion().GetIndex());
//meshFilter->SetTolerance(1.0);
meshFilter->SetInsideValue(1.0);
meshFilter->SetOutsideValue(0.0);
try {
meshFilter->Update();
}
catch( itk::ExceptionObject & e )
{
cout << "Exception thrown ! " << endl;
cout << "An error ocurred during creating binary image" << endl;
cout << "Location = " << e.GetLocation() << endl;
cout << "Description = " << e.GetDescription() << endl;
}
BinaryImageType::Pointer im = meshFilter->GetOutput();
if (!sub_segmentation)
{
imageSegmentation_ = im;
}
else
{
BinaryImageType::RegionType region = im->GetLargestPossibleRegion();
itk::ImageRegionConstIterator<BinaryImageType> imageIterator(im,region);
unsigned char pixel, pixel_seg;
BinaryIndexType index;
while(!imageIterator.IsAtEnd())
{
index = imageIterator.GetIndex();
pixel = imageIterator.Get();
pixel_seg = imageSegmentation_->GetPixel(index);
im->SetPixel(index,pixel && !pixel_seg);
++imageIterator;
}
}
OrientImage<BinaryImageType> orientationFilter;
orientationFilter.setInputImage(im);
orientationFilter.orientation(orient);
im = orientationFilter.getOutputImage();
// Write the image
typedef itk::ImageFileWriter< BinaryImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
writer->SetImageIO(io);
writer->SetFileName(filename);
writer->SetInput(im);
try {
writer->Update();
}
catch( itk::ExceptionObject & e )
{
cout << "Exception thrown ! " << endl;
cout << "An error ocurred during Writing" << endl;
cout << "Location = " << e.GetLocation() << endl;
cout << "Description = " << e.GetDescription() << endl;
}
}
void Initialisation::savePointAsBinaryImage(ImageType::Pointer initialImage, string filename, OrientationType orientation)
{
if (points_.size() > 0)
{
typedef itk::Image< unsigned char, 3 > BinaryImageType;
BinaryImageType::Pointer binary = BinaryImageType::New();
ImageType::RegionType region;
ImageType::IndexType start;
start[0] = 0; start[1] = 0; start[2] = 0;
ImageType::SizeType size, imSize = initialImage->GetLargestPossibleRegion().GetSize();
size[0] = imSize[0]; size[1] = imSize[1]; size[2] = imSize[2];
region.SetSize(size);
region.SetIndex(start);
binary->CopyInformation(initialImage);
binary->SetRegions(region);
binary->Allocate();
binary->FillBuffer(false);
typedef ImageType::IndexType IndexType;
ContinuousIndex ind;
IndexType ind2;
unsigned int pSize = points_.size();
unsigned int indexMiddle = 0;
for (unsigned int i=0; i<pSize; i++) {
if (points_[i][1] == startSlice_)
indexMiddle = i;
}
ind[0] = points_[indexMiddle][0]; ind[1] = points_[indexMiddle][1]; ind[2] = points_[indexMiddle][2];
PointType pt;
inputImage_->TransformContinuousIndexToPhysicalPoint(ind, pt);
initialImage->TransformPhysicalPointToIndex(pt, ind2);
binary->SetPixel(ind2,true);
OrientImage<BinaryImageType> orientationFilter;
orientationFilter.setInputImage(binary);
orientationFilter.orientation(orientation);
binary = orientationFilter.getOutputImage();
ImageIterator it( binary, binary->GetRequestedRegion() );
it.GoToBegin();
while(!it.IsAtEnd())
{
if (it.Get()==true)
{
ind2 = it.GetIndex();
break;
}
++it;
}
if (verbose_) cout << "Center of spinal cord saved on pixel : " << ind2 << endl;
WriterBinaryType::Pointer writer = WriterBinaryType::New();
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
writer->SetImageIO(io);
writer->SetFileName(filename);
writer->SetInput(binary);
try {
writer->Write();
} catch( itk::ExceptionObject & e ) {
std::cerr << "Exception caught while writing image " << std::endl;
std::cerr << e << std::endl;
}
}
else cout << "Error: Spinal cord center not detected" << endl;
}