std::vector<itk::SmartPointer<BaseData> > NrrdTensorImageReader::Read()
{
std::vector<itk::SmartPointer<mitk::BaseData> > result;
std::string location = GetInputLocation();
if ( location == "")
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename is empty!");
}
else
{
try
{
mitk::LocaleSwitch localeSwitch("C");
try
{
std::string fname3 = mitk::IOUtil::GetTempPath()+"/temp_dti.nii.gz";
int c = 0;
while( itksys::SystemTools::FileExists(fname3) )
{
fname3 = mitk::IOUtil::GetTempPath()+"/temp_dti_" + boost::lexical_cast<std::string>(c) + ".nii.gz";
++c;
}
itksys::SystemTools::CopyAFile(location.c_str(), fname3.c_str());
typedef itk::VectorImage<float,3> ImageType;
itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(fname3);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
TensorImage::ItkTensorImageType::Pointer vecImg = TensorImage::ItkTensorImageType::New();
vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
vecImg->SetDirection( img->GetDirection() ); // Set the image direction
vecImg->SetRegions( img->GetLargestPossibleRegion());
vecImg->Allocate();
itk::ImageRegionIterator<TensorImage::ItkTensorImageType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot.GoToBegin();
itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
it.GoToBegin();
typedef ImageType::PixelType VarPixType;
typedef TensorImage::PixelType FixPixType;
int numComponents = img->GetNumberOfComponentsPerPixel();
if (numComponents==6)
{
MITK_INFO << "Trying to load dti as 6-comp nifti ...";
while (!it.IsAtEnd())
{
VarPixType vec = it.Get();
FixPixType fixVec(vec.GetDataPointer());
TensorImage::PixelType tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(3));
tensor.SetElement(4, vec.GetElement(4));
tensor.SetElement(5, vec.GetElement(5));
fixVec = tensor;
ot.Set(fixVec);
++ot;
++it;
}
}
else if(numComponents==9)
{
MITK_INFO << "Trying to load dti as 9-comp nifti ...";
while (!it.IsAtEnd())
{
VarPixType vec = it.Get();
TensorImage::PixelType tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(4));
tensor.SetElement(4, vec.GetElement(5));
tensor.SetElement(5, vec.GetElement(8));
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
++it;
}
}
else if (numComponents==1)
{
MITK_INFO << "Trying to load dti as 4D nifti ...";
typedef itk::Image<float,4> ImageType;
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(fname3);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
while (!ot.IsAtEnd())
{
TensorImage::PixelType tensor;
ImageType::IndexType idx;
idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
if (size[3]==6)
{
for (unsigned int te=0; te<size[3]; te++)
{
idx[3] = te;
tensor.SetElement(te, img->GetPixel(idx));
}
}
else if (size[3]==9)
{
idx[3] = 0;
tensor.SetElement(0, img->GetPixel(idx));
idx[3] = 1;
tensor.SetElement(1, img->GetPixel(idx));
idx[3] = 2;
tensor.SetElement(2, img->GetPixel(idx));
idx[3] = 4;
tensor.SetElement(3, img->GetPixel(idx));
idx[3] = 5;
tensor.SetElement(4, img->GetPixel(idx));
idx[3] = 8;
tensor.SetElement(5, img->GetPixel(idx));
}
else
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of components for DTI file. Should be 6 or 9!");
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
}
}
OutputType::Pointer resultImage = OutputType::New();
resultImage->InitializeByItk( vecImg.GetPointer() );
resultImage->SetVolume( vecImg->GetBufferPointer() );
result.push_back( resultImage.GetPointer() );
}
catch(...)
{
MITK_INFO << "Trying to load dti as nrrd ...";
typedef itk::VectorImage<float,3> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(location);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
TensorImage::ItkTensorImageType::Pointer vecImg = TensorImage::ItkTensorImageType::New();
vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
vecImg->SetDirection( img->GetDirection() ); // Set the image direction
vecImg->SetRegions( img->GetLargestPossibleRegion());
vecImg->Allocate();
itk::ImageRegionIterator<TensorImage::ItkTensorImageType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot.GoToBegin();
itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
it.GoToBegin();
typedef ImageType::PixelType VarPixType;
typedef TensorImage::PixelType FixPixType;
int numComponents = img->GetNumberOfComponentsPerPixel();
itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();
std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
std::string metaString;
bool readFrame = false;
double xx, xy, xz, yx, yy, yz, zx, zy, zz;
MeasurementFrameType measFrame;
measFrame.SetIdentity();
MeasurementFrameType measFrameTransp;
measFrameTransp.SetIdentity();
for (; itKey != imgMetaKeys.end(); itKey ++)
{
itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
if (itKey->find("measurement frame") != std::string::npos)
{
sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz);
if (xx>10e-10 || xy>10e-10 || xz>10e-10 ||
yx>10e-10 || yy>10e-10 || yz>10e-10 ||
zx>10e-10 || zy>10e-10 || zz>10e-10 )
{
readFrame = true;
measFrame(0,0) = xx;
measFrame(0,1) = xy;
measFrame(0,2) = xz;
measFrame(1,0) = yx;
measFrame(1,1) = yy;
measFrame(1,2) = yz;
measFrame(2,0) = zx;
measFrame(2,1) = zy;
measFrame(2,2) = zz;
measFrameTransp = measFrame.GetTranspose();
}
}
}
if (numComponents==6)
{
while (!it.IsAtEnd())
{
// T'=RTR'
VarPixType vec = it.Get();
FixPixType fixVec(vec.GetDataPointer());
if(readFrame)
{
TensorImage::PixelType tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(3));
tensor.SetElement(4, vec.GetElement(4));
tensor.SetElement(5, vec.GetElement(5));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
fixVec = tensor;
}
ot.Set(fixVec);
++ot;
++it;
}
}
else if(numComponents==9)
{
while (!it.IsAtEnd())
{
VarPixType vec = it.Get();
TensorImage::PixelType tensor;
tensor.SetElement(0, vec.GetElement(0));
tensor.SetElement(1, vec.GetElement(1));
tensor.SetElement(2, vec.GetElement(2));
tensor.SetElement(3, vec.GetElement(4));
tensor.SetElement(4, vec.GetElement(5));
tensor.SetElement(5, vec.GetElement(8));
if(readFrame)
{
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
}
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
++it;
}
}
else if (numComponents==1)
{
typedef itk::Image<float,4> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(location);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
while (!ot.IsAtEnd())
{
TensorImage::PixelType tensor;
ImageType::IndexType idx;
idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
if (size[3]==6)
{
for (unsigned int te=0; te<size[3]; te++)
{
idx[3] = te;
tensor.SetElement(te, img->GetPixel(idx));
}
}
else if (size[3]==9)
{
idx[3] = 0;
tensor.SetElement(0, img->GetPixel(idx));
idx[3] = 1;
tensor.SetElement(1, img->GetPixel(idx));
idx[3] = 2;
tensor.SetElement(2, img->GetPixel(idx));
idx[3] = 4;
tensor.SetElement(3, img->GetPixel(idx));
idx[3] = 5;
tensor.SetElement(4, img->GetPixel(idx));
idx[3] = 8;
tensor.SetElement(5, img->GetPixel(idx));
}
else
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of komponents for DTI file. Should be 6 or 9!");
if(readFrame)
{
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
}
FixPixType fixVec(tensor);
ot.Set(fixVec);
++ot;
}
}
else
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Image has wrong number of pixel components!");
}
OutputType::Pointer resultImage = OutputType::New();
resultImage->InitializeByItk( vecImg.GetPointer() );
resultImage->SetVolume( vecImg->GetBufferPointer() );
result.push_back( resultImage.GetPointer() );
}
}
catch(std::exception& e)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
}
catch(...)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested DTI file!");
}
}
return result;
}
std::vector<itk::SmartPointer<BaseData> > NrrdQBallImageReader::Read()
{
std::vector<itk::SmartPointer<mitk::BaseData> > result;
std::string location = GetInputLocation();
if ( location == "")
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename of the vessel tree to be read is empty!");
}
else
{
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, NULL );
if ( locale.compare(currLocale)!=0 )
{
try
{
setlocale(LC_ALL, locale.c_str());
}
catch(...)
{
MITK_INFO << "Could not set locale " << locale;
}
}
typedef itk::VectorImage<float,3> ImageType;
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
typedef itk::ImageFileReader<ImageType> FileReaderType;
FileReaderType::Pointer reader = FileReaderType::New();
reader->SetImageIO(io);
reader->SetFileName(location);
reader->Update();
ImageType::Pointer img = reader->GetOutput();
typedef itk::Image<itk::Vector<float,QBALL_ODFSIZE>,3> VecImgType;
VecImgType::Pointer vecImg = VecImgType::New();
vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
vecImg->SetDirection( img->GetDirection() ); // Set the image direction
vecImg->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
vecImg->SetBufferedRegion( img->GetLargestPossibleRegion() );
vecImg->Allocate();
itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
ot.GoToBegin();
itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
typedef ImageType::PixelType VarPixType;
typedef VecImgType::PixelType FixPixType;
for (it.GoToBegin(); !it.IsAtEnd(); ++it)
{
VarPixType vec = it.Get();
FixPixType fixVec(vec.GetDataPointer());
ot.Set(fixVec);
++ot;
}
OutputType::Pointer resultImage = OutputType::New();
resultImage->InitializeByItk( vecImg.GetPointer() );
resultImage->SetVolume( vecImg->GetBufferPointer() );
result.push_back( resultImage.GetPointer() );
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
}
catch(std::exception& e)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
}
catch(...)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
}
}
return result;
}