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;
}
double Mesh::computeStandardDeviationFromPixelsInside(ImageType::Pointer image)
{
MeshTypeB::Pointer mesh = MeshTypeB::New();
typedef itk::Point< double, 3 > PointType;
PointType pnt;
ImageType::IndexType index;
CVector3 p, n, min(10000,10000,10000), max;
for (unsigned int i=0; i<points_.size(); i++) {
p = points_[i]->getPosition();
pnt[0] = p[0]; pnt[1] = p[1]; pnt[2] = p[2];
mesh->SetPoint(i,pnt);
image->TransformPhysicalPointToIndex(pnt, index);
if (index[0]<min[0]) min[0]=index[0];
if (index[1]<min[1]) min[1]=index[1];
if (index[2]<min[2]) min[2]=index[2];
if (index[0]>max[0]) max[0]=index[0];
if (index[1]>max[1]) max[1]=index[1];
if (index[2]>max[2]) max[2]=index[2];
}
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);
}
CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput(image);
BinaryImageType::Pointer im = castFilter->GetOutput();
BinaryImageType::IndexType indexRegion;
BinaryImageType::SizeType sizeRegion;
sizeRegion[0] = max[0]-min[0]+5; // adding two pixels at each side to be sure
sizeRegion[1] = max[1]-min[1]+5;
sizeRegion[2] = max[2]-min[2]+5;
indexRegion[0] = min[0]-2;
indexRegion[1] = min[1]-2;
indexRegion[2] = min[2]-2;
BinaryImageType::RegionType region(indexRegion,sizeRegion);
im->SetRegions(region);
MeshFilterType::Pointer meshFilter = MeshFilterType::New();
meshFilter->SetInput(mesh);
meshFilter->SetInfoImage(im);
/*meshFilter->SetDirection(image->GetDirection());
meshFilter->SetSpacing(image->GetSpacing());
meshFilter->SetOrigin(image->GetOrigin());
meshFilter->SetSize(sizeRegion);
meshFilter->SetIndex(indexRegion);*/
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;
}
MeshFilterType::OutputImageType::Pointer binary = meshFilter->GetOutput();
vector<double> valueVoxels;
typedef ImageType::IndexType IndexType;
IndexType ind;
ImageIterator it( binary, binary->GetRequestedRegion() );
it.GoToBegin();
while(!it.IsAtEnd())
{
if (it.Get()==true)
{
ind = it.GetIndex();
valueVoxels.push_back(image->GetPixel(ind));
}
++it;
}
double mean = 0.0, sum = 0.0, std = 0.0, nbVoxels = valueVoxels.size();
for (int i=0; i<nbVoxels; i++)
mean += valueVoxels[i];
mean /= nbVoxels;
for (int i=0; i<nbVoxels; i++) {
sum += valueVoxels[i]*valueVoxels[i];
}
std = sqrt(sum/nbVoxels-mean*mean);
/*ofstream myfile;
myfile.open("StandardDeviation.txt", ios_base::app);
myfile << ind[1] << " " << mean << " " << std << endl;
myfile.close();*/
return mean;
}
void mitk::SurfaceStampImageFilter::SurfaceStampProcessing(itk::Image<TPixel, 3> *input, MeshType *mesh)
{
typedef itk::Image<TPixel, 3> ImageType;
typedef itk::Image<unsigned char, 3> BinaryImageType;
typedef itk::TriangleMeshToBinaryImageFilter<mitk::SurfaceStampImageFilter::MeshType, BinaryImageType> FilterType;
BinaryImageType::Pointer binaryInput = BinaryImageType::New();
binaryInput->SetSpacing(input->GetSpacing());
binaryInput->SetOrigin(input->GetOrigin());
binaryInput->SetDirection(input->GetDirection());
binaryInput->SetRegions(input->GetLargestPossibleRegion());
binaryInput->Allocate();
binaryInput->FillBuffer(0);
FilterType::Pointer filter = FilterType::New();
filter->SetInput(mesh);
filter->SetInfoImage(binaryInput);
filter->SetInsideValue(1);
filter->SetOutsideValue(0);
filter->Update();
BinaryImageType::Pointer resultImage = filter->GetOutput();
resultImage->DisconnectPipeline();
mitk::Image::Pointer outputImage = this->GetOutput();
typename ImageType::Pointer itkOutputImage;
mitk::CastToItkImage(outputImage, itkOutputImage);
typedef itk::ImageRegionConstIterator<BinaryImageType> BinaryIteratorType;
typedef itk::ImageRegionConstIterator<ImageType> InputIteratorType;
typedef itk::ImageRegionIterator<ImageType> OutputIteratorType;
BinaryIteratorType sourceIter(resultImage, resultImage->GetLargestPossibleRegion());
sourceIter.GoToBegin();
InputIteratorType inputIter(input, input->GetLargestPossibleRegion());
inputIter.GoToBegin();
OutputIteratorType outputIter(itkOutputImage, itkOutputImage->GetLargestPossibleRegion());
outputIter.GoToBegin();
typename ImageType::PixelType inputValue;
unsigned char sourceValue;
auto fgValue = static_cast<typename ImageType::PixelType>(m_ForegroundValue);
auto bgValue = static_cast<typename ImageType::PixelType>(m_BackgroundValue);
while (!sourceIter.IsAtEnd())
{
sourceValue = static_cast<unsigned char>(sourceIter.Get());
inputValue = static_cast<typename ImageType::PixelType>(inputIter.Get());
if (sourceValue != 0)
outputIter.Set(fgValue);
else if (m_OverwriteBackground)
outputIter.Set(bgValue);
else
outputIter.Set(inputValue);
++sourceIter;
++inputIter;
++outputIter;
}
}