VolumeBase* MultiVolumeReader::read(const VolumeURL& origin)
throw (tgt::FileException, std::bad_alloc)
{
std::string path = extractPurePathFromFileName(origin.getPath());
std::string refFile = origin.getSearchParameter("file");
if (refFile == "")
throw tgt::FileException("'file' parameter missing in URL", origin.getURL());
VolumeURL refOrigin(path + refFile);
LINFO("Loading file " + refOrigin.getPath());
VolumeBase* handle = 0;
if (populator_)
handle = populator_->getVolumeSerializer()->read(refOrigin);
else {
VolumeSerializerPopulator populator;
handle = populator.getVolumeSerializer()->read(refOrigin);
}
if (handle)
handle->setOrigin(origin);
return handle;
}
// ------------------------------------------------------------------------
void NormaliseImage(const ImageType::Pointer &input,
const ImageType::Pointer &reference,
ImageType::Pointer &output,
SeriesTransform &trans)
{
// flip the x and y axis
typedef itk::PermuteAxesImageFilter<ImageType> FlipperType;
FlipperType::Pointer flipper = FlipperType::New();
itk::FixedArray<unsigned int, 3> order;
order[0] = 1;
order[1] = 0;
order[2] = 2;
flipper->SetOrder(order);
flipper->SetInput(input);
flipper->Update();
output = flipper->GetOutput();
// get the reference offset
vnl_vector<double> refOrigin(3);
refOrigin[0] = reference->GetOrigin()[0];// + trans.translation[0];
refOrigin[1] = reference->GetOrigin()[1];// + trans.translation[1];
refOrigin[2] = reference->GetOrigin()[2];// + trans.translation[2];
vnl_matrix<double> refRot = reference->GetDirection().GetVnlMatrix();
vnl_matrix<double> refRotInv = vnl_inverse(refRot);
vnl_vector<double> refOffset = refRotInv * refOrigin;
// get the image origin
vnl_vector<double> origin(3);
origin[0] = output->GetOrigin()[0];
origin[1] = output->GetOrigin()[1];
origin[2] = output->GetOrigin()[2];
// apply the rotation to the origin
origin = refRotInv * origin;
// apply the offset to the origin
origin = origin - refOffset;
// apply the scaling
origin /= reference->GetSpacing()[0];
// put the values into the output image
ImageType::PointType itkOrigin;
itkOrigin[0] = origin[0];
itkOrigin[1] = origin[1];
itkOrigin[2] = origin[2];
ImageType::SpacingType spacing;
spacing.Fill(output->GetSpacing()[0] / reference->GetSpacing()[0]);
// get the new direction
ImageType::DirectionType dirOut = output->GetDirection();
dirOut = reference->GetDirection().GetInverse() * dirOut.GetVnlMatrix();
output->SetSpacing(spacing);
output->SetDirection(dirOut);
output->SetOrigin(itkOrigin);
}
