int testRepresenterForVectorImage(const std::string& datadir) {
typedef itk::StandardImageRepresenter<itk::Vector<float, 2>, 2> RepresenterType;
typedef GenericRepresenterTest<RepresenterType> RepresenterTestType;
const std::string referenceFilename = datadir + "/hand_dfs/df-hand-1.vtk";
const std::string testDatasetFilename = datadir + "/hand_dfs/df-hand-2.vtk";
RepresenterType::Pointer representer = RepresenterType::New();
VectorImageType::Pointer reference = loadVectorImage(referenceFilename);
representer->SetReference(reference);
// choose a test dataset, a point and its associate pixel value
VectorImageType::Pointer testDataset = loadVectorImage(testDatasetFilename);
VectorImageType::IndexType idx;
idx.Fill(0);
VectorImageType::PointType testPt;
reference->TransformIndexToPhysicalPoint(idx, testPt);
VectorImageType::PixelType testValue = testDataset->GetPixel(idx);
RepresenterTestType representerTest(representer, testDataset, std::make_pair(testPt, testValue));
return (representerTest.runAllTests() == true);
}
mitk::TbssImage::Pointer mitk::TbssImporter::ImportMeta()
{
mitk::TbssImage::Pointer tbssImg = mitk::TbssImage::New();
m_Data = DataImageType::New();
std::vector< std::pair<mitk::TbssImage::MetaDataFunction, int> > metaInfo;
// Gradient images are vector images, so they will add more dimensions to the vector
int vecLength = m_MetaFiles.size();
//Check if there is a gradient image
for(int i=0; i < m_MetaFiles.size(); i++)
{
std::pair<std::string, std::string> p = m_MetaFiles.at(i);
if(RetrieveTbssFunction(p.first) == mitk::TbssImage::GRADIENT_X)
{
vecLength += 2;
}
}
int currIndex = 0;
for(int i=0; i < m_MetaFiles.size(); i++)
{
std::pair<std::string, std::string> p = m_MetaFiles.at(i);
std::string function = p.first;
std::string file = p.second;
// Add to metainfo to give the tbss image a function-index pair
std::pair<mitk::TbssImage::MetaDataFunction, int> pair;
pair.first = RetrieveTbssFunction(function);
pair.second = i;
if(pair.first == mitk::TbssImage::GRADIENT_X)
{
metaInfo.push_back(std::pair<mitk::TbssImage::MetaDataFunction, int>(mitk::TbssImage::GRADIENT_X, i));
metaInfo.push_back(std::pair<mitk::TbssImage::MetaDataFunction, int>(mitk::TbssImage::GRADIENT_Y, i+1));
metaInfo.push_back(std::pair<mitk::TbssImage::MetaDataFunction, int>(mitk::TbssImage::GRADIENT_Z, i+2));
VectorReaderType::Pointer fileReader = VectorReaderType::New();
fileReader->SetFileName(file);
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
fileReader->SetImageIO(io);
fileReader->Update();
VectorImageType::Pointer img = fileReader->GetOutput();
VectorImageType::SizeType size = img->GetLargestPossibleRegion().GetSize();
if(i==0)
{
// First image in serie. Properties should be used to initialize m_Data
m_Data->SetRegions(img->GetLargestPossibleRegion().GetSize());
m_Data->SetSpacing(img->GetSpacing());
m_Data->SetOrigin(img->GetOrigin());
m_Data->SetDirection(img->GetDirection());
m_Data->SetVectorLength(vecLength);
m_Data->Allocate();
}
/* Dealing with a gradient image, so the size of the vector need to be increased by 2
since this image contains 3 volumes. Old data should not be deleted*/
for(int x=0; x<size[0]; x++)
{
for(int y=0; y<size[1]; y++)
{
for(int z=0; z<size[2]; z++)
{
itk::Index<3> ix;
ix[0] = x;
ix[1] = y;
ix[2] = z;
itk::VariableLengthVector<int> vec = img->GetPixel(ix);
itk::VariableLengthVector<float> pixel = m_Data->GetPixel(ix);
for(int j=0; j<vec.Size(); j++)
{
int pos = currIndex+j;
float f = vec.GetElement(j);
pixel.SetElement(pos, f);
}
m_Data->SetPixel(ix, pixel);
}
}
}
currIndex += img->GetVectorLength();
tbssImg->SetContainsGradient(true);
// Read vector image and add to m_Data
}
else {
metaInfo.push_back(pair);
FileReaderType3D::Pointer fileReader = FileReaderType3D::New();
fileReader->SetFileName(file);
fileReader->Update();
FloatImage3DType::Pointer img = fileReader->GetOutput();
FloatImage3DType::SizeType size = img->GetLargestPossibleRegion().GetSize();
if(i==0)
{
// First image in serie. Properties should be used to initialize m_Data
m_Data->SetRegions(img->GetLargestPossibleRegion().GetSize());
m_Data->SetSpacing(img->GetSpacing());
m_Data->SetOrigin(img->GetOrigin());
m_Data->SetDirection(img->GetDirection());
m_Data->SetVectorLength(vecLength);
m_Data->Allocate();
}
for(int x=0; x<size[0]; x++)
{
for(int y=0; y<size[1]; y++)
{
for(int z=0; z<size[2]; z++)
{
itk::Index<3> ix;
ix[0] = x;
ix[1] = y;
ix[2] = z;
float f = img->GetPixel(ix);
itk::VariableLengthVector<float> pixel = m_Data->GetPixel(ix);
pixel.SetElement(currIndex, f);
m_Data->SetPixel(ix, pixel);
}
}
}
}
if(pair.first == mitk::TbssImage::MEAN_FA_SKELETON)
{
tbssImg->SetContainsMeanSkeleton(true);
}
else if(pair.first == mitk::TbssImage::MEAN_FA_SKELETON_MASK)
{
tbssImg->SetContainsSkeletonMask(true);
}
else if(pair.first == mitk::TbssImage::DISTANCE_MAP)
{
tbssImg->SetContainsDistanceMap(true);
}
currIndex++;
}
tbssImg->SetIsMeta(true);
tbssImg->SetImage(m_Data);
tbssImg->SetMetaInfo(metaInfo);
tbssImg->InitializeFromVectorImage();
return tbssImg;
}