mitk::SurfaceInterpolationController::ContourPositionInformation CreateContourPositionInformation(mitk::Surface::Pointer contour)
{
mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
contourInfo.contour = contour;
double n[3];
double p[3];
contour->GetVtkPolyData()->GetPoints()->GetPoint(0, p);
vtkPolygon::ComputeNormal(contour->GetVtkPolyData()->GetPoints(), n);
contourInfo.contourNormal = n;
contourInfo.contourPoint = p;
return contourInfo;
}
mitk::Surface::Pointer mitk::SurfaceModifier::DeepCopy(mitk::Surface::Pointer originalSurface)
{
mitk::Surface::Pointer clonedSurface = mitk::Surface::New();
vtkSmartPointer<vtkPolyData> clonedPolyData = vtkPolyData::New();
clonedPolyData->DeepCopy(originalSurface->GetVtkPolyData());
clonedSurface->SetVtkPolyData(clonedPolyData);
return clonedSurface;
}
void mitk::SurfaceInterpolationController::AddNewContour (mitk::Surface::Pointer newContour)
{
if( newContour->GetVtkPolyData()->GetNumberOfPoints() > 0)
{
ContourPositionInformation contourInfo = CreateContourPositionInformation(newContour);
this->AddToInterpolationPipeline(contourInfo);
this->Modified();
}
}
bool CompareSurfacePointPositions(mitk::Surface::Pointer s1, mitk::Surface::Pointer s2)
{
vtkPoints* p1 = s1->GetVtkPolyData()->GetPoints();
vtkPoints* p2 = s2->GetVtkPolyData()->GetPoints();
if(p1->GetNumberOfPoints() != p2->GetNumberOfPoints())
return false;
for(int i = 0; i < p1->GetNumberOfPoints(); ++i)
{
if(p1->GetPoint(i)[0] != p2->GetPoint(i)[0] ||
p1->GetPoint(i)[1] != p2->GetPoint(i)[1] ||
p1->GetPoint(i)[2] != p2->GetPoint(i)[2] )
{
return true;
}
}
return false;
}
bool mitk::SurfaceModifier::AddOutlierToSurface(mitk::Surface::Pointer surface, double varianceX, double varianceY, double varianceZ, double outlierChance)
{
vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
points->ShallowCopy(surface->GetVtkPolyData()->GetPoints());
for(unsigned int i = 0; i < points->GetNumberOfPoints(); i++)
{
double p[3];
points->GetPoint(i, p);
mitk::Point3D point;
point[0] = p[0];
point[1] = p[1];
point[2] = p[2];
if((outlierChance-vtkMath::Random(0,1))>0) point = PerturbePoint(point,varianceX,varianceY,varianceZ);
p[0] = point[0];
p[1] = point[1];
p[2] = point[2];
points->SetPoint(i, p);
}
surface->GetVtkPolyData()->SetPoints(points);
return true;
}
bool mitk::SurfaceModifier::PerturbeSurface(mitk::Surface::Pointer surface, double varianceX, double varianceY, double varianceZ, double maxNoiseVectorLenght)
{
vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
points->ShallowCopy(surface->GetVtkPolyData()->GetPoints());
for(unsigned int i = 0; i < points->GetNumberOfPoints(); i++)
{
double p[3];
points->GetPoint(i, p);
mitk::Point3D point;
point[0] = p[0];
point[1] = p[1];
point[2] = p[2];
point = PerturbePoint(point,varianceX,varianceY,varianceZ,maxNoiseVectorLenght);
p[0] = point[0];
p[1] = point[1];
p[2] = point[2];
points->SetPoint(i, p);
}
surface->GetVtkPolyData()->SetPoints(points);
return true;
}
bool mitk::SurfaceModifier::TransformSurface(mitk::Surface::Pointer surface, itk::Matrix<double,3,3> TransformationR, itk::Vector<double,3> TransformationT)
{
//apply transformation
vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
points->ShallowCopy(surface->GetVtkPolyData()->GetPoints());
for(unsigned int i = 0; i < points->GetNumberOfPoints(); i++)
{
double p[3];
points->GetPoint(i, p);
mitk::Point3D point;
point[0] = p[0];
point[1] = p[1];
point[2] = p[2];
point = TransformPoint(point,TransformationR,TransformationT);
p[0] = point[0];
p[1] = point[1];
p[2] = point[2];
points->SetPoint(i, p);
}
surface->GetVtkPolyData()->SetPoints(points);
return true;
}
void mitk::SurfaceInterpolationController::ReinitializeInterpolation(mitk::Surface::Pointer contours)
{
// 1. detect coplanar contours
// 2. merge coplanar contours into a single surface
// 4. add contour to pipeline
// Split the surface into separate polygons
vtkSmartPointer<vtkCellArray> existingPolys;
vtkSmartPointer<vtkPoints> existingPoints;
existingPolys = contours->GetVtkPolyData()->GetPolys();
existingPoints = contours->GetVtkPolyData()->GetPoints();
existingPolys->InitTraversal();
vtkSmartPointer<vtkIdList> ids = vtkSmartPointer<vtkIdList>::New();
typedef std::pair<mitk::Vector3D, mitk::Point3D> PointNormalPair;
std::vector<ContourPositionInformation> list;
std::vector<vtkSmartPointer<vtkPoints> > pointsList;
int count (0);
for( existingPolys->InitTraversal(); existingPolys->GetNextCell(ids);)
{
// Get the points
vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
existingPoints->GetPoints(ids, points);
++count;
pointsList.push_back(points);
PointNormalPair p_n;
double n[3];
vtkPolygon::ComputeNormal(points, n);
p_n.first = n;
double p[3];
existingPoints->GetPoint(ids->GetId(0), p);
p_n.second = p;
ContourPositionInformation p_info;
p_info.contourNormal = n;
p_info.contourPoint = p;
list.push_back(p_info);
continue;
}
// Detect and sort coplanar polygons
auto outer = list.begin();
std::vector< std::vector< vtkSmartPointer<vtkPoints> > > relatedPoints;
while (outer != list.end())
{
auto inner = outer;
++inner;
std::vector< vtkSmartPointer<vtkPoints> > rel;
auto pointsIter = pointsList.begin();
rel.push_back((*pointsIter));
pointsIter = pointsList.erase(pointsIter);
while (inner != list.end())
{
if(ContoursCoplanar((*outer),(*inner)))
{
inner = list.erase(inner);
rel.push_back((*pointsIter));
pointsIter = pointsList.erase(pointsIter);
}
else
{
++inner;
++pointsIter;
}
}
relatedPoints.push_back(rel);
++outer;
}
// Build the separate surfaces again
std::vector<mitk::Surface::Pointer> finalSurfaces;
for (unsigned int i = 0; i < relatedPoints.size(); ++i)
{
vtkSmartPointer<vtkPolyData> contourSurface = vtkSmartPointer<vtkPolyData>::New();
vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
vtkSmartPointer<vtkCellArray> polygons = vtkSmartPointer<vtkCellArray>::New();
unsigned int pointId (0);
for (unsigned int j = 0; j < relatedPoints.at(i).size(); ++j)
{
unsigned int numPoints = relatedPoints.at(i).at(j)->GetNumberOfPoints();
vtkSmartPointer<vtkPolygon> polygon = vtkSmartPointer<vtkPolygon>::New();
polygon->GetPointIds()->SetNumberOfIds(numPoints);
polygon->GetPoints()->SetNumberOfPoints(numPoints);
vtkSmartPointer<vtkPoints> currentPoints = relatedPoints.at(i).at(j);
for (unsigned k = 0; k < numPoints; ++k)
{
points->InsertPoint(pointId, currentPoints->GetPoint(k));
polygon->GetPointIds()->SetId(k, pointId);
++pointId;
}
polygons->InsertNextCell(polygon);
}
contourSurface->SetPoints(points);
contourSurface->SetPolys(polygons);
contourSurface->BuildLinks();
mitk::Surface::Pointer surface = mitk::Surface::New();
surface->SetVtkPolyData(contourSurface);
finalSurfaces.push_back(surface);
}
// Add detected contours to interpolation pipeline
this->AddNewContours(finalSurfaces);
}
mitk::Surface::Pointer mitk::ACVD::Remesh(mitk::Surface::Pointer surface, int numVertices, double gradation, int subsampling, double edgeSplitting, int optimizationLevel, bool forceManifold, bool boundaryFixing)
{
MITK_INFO << "Start remeshing...";
vtkSmartPointer<vtkPolyData> surfacePolyData = vtkSmartPointer<vtkPolyData>::New();
surfacePolyData->DeepCopy(surface->GetVtkPolyData());
vtkSmartPointer<vtkSurface> mesh = vtkSmartPointer<vtkSurface>::New();
mesh->CreateFromPolyData(surfacePolyData);
mesh->GetCellData()->Initialize();
mesh->GetPointData()->Initialize();
mesh->DisplayMeshProperties();
if (edgeSplitting != 0.0)
mesh->SplitLongEdges(edgeSplitting);
vtkSmartPointer<vtkIsotropicDiscreteRemeshing> remesher = vtkSmartPointer<vtkIsotropicDiscreteRemeshing>::New();
remesher->GetMetric()->SetGradation(gradation);
remesher->SetBoundaryFixing(boundaryFixing);
remesher->SetConsoleOutput(1);
remesher->SetForceManifold(forceManifold);
remesher->SetInput(mesh);
remesher->SetNumberOfClusters(numVertices);
remesher->SetNumberOfThreads(vtkMultiThreader::GetGlobalDefaultNumberOfThreads());
remesher->SetSubsamplingThreshold(subsampling);
remesher->Remesh();
if (optimizationLevel != 0)
{
ClustersQuadrics clustersQuadrics(numVertices);
vtkSmartPointer<vtkIdList> faceList = vtkSmartPointer<vtkIdList>::New();
vtkSmartPointer<vtkIntArray> clustering = remesher->GetClustering();
vtkSmartPointer<vtkSurface> remesherInput = remesher->GetInput();
int clusteringType = remesher->GetClusteringType();
int numItems = remesher->GetNumberOfItems();
int numMisclassifiedItems = 0;
for (int i = 0; i < numItems; ++i)
{
int cluster = clustering->GetValue(i);
if (cluster >= 0 && cluster < numVertices)
{
if (clusteringType != 0)
{
remesherInput->GetVertexNeighbourFaces(i, faceList);
int numIds = static_cast<int>(faceList->GetNumberOfIds());
for (int j = 0; j < numIds; ++j)
vtkQuadricTools::AddTriangleQuadric(clustersQuadrics.Elements[cluster], remesherInput, faceList->GetId(j), false);
}
else
{
vtkQuadricTools::AddTriangleQuadric(clustersQuadrics.Elements[cluster], remesherInput, i, false);
}
}
else
{
++numMisclassifiedItems;
}
}
if (numMisclassifiedItems != 0)
std::cout << numMisclassifiedItems << " items with wrong cluster association" << std::endl;
vtkSmartPointer<vtkSurface> remesherOutput = remesher->GetOutput();
double point[3];
for (int i = 0; i < numVertices; ++i)
{
remesherOutput->GetPoint(i, point);
vtkQuadricTools::ComputeRepresentativePoint(clustersQuadrics.Elements[i], point, optimizationLevel);
remesherOutput->SetPointCoordinates(i, point);
}
std::cout << "After quadrics post-processing:" << std::endl;
remesherOutput->DisplayMeshProperties();
}
vtkSmartPointer<vtkPolyDataNormals> normals = vtkSmartPointer<vtkPolyDataNormals>::New();
normals->SetInput(remesher->GetOutput());
normals->AutoOrientNormalsOn();
normals->ComputeCellNormalsOff();
normals->ComputePointNormalsOn();
normals->ConsistencyOff();
normals->FlipNormalsOff();
normals->NonManifoldTraversalOff();
normals->SplittingOff();
normals->Update();
Surface::Pointer remeshedSurface = Surface::New();
remeshedSurface->SetVtkPolyData(normals->GetOutput());
MITK_INFO << "Finished remeshing";
return remeshedSurface;
}