// do the work
void mitk::PhilipsDicomDiffusionImageHeaderReader::Update()
{
// check if there are filenames
if(m_DicomFilenames.size())
{
ReadPublicTags();
ReadPublicTags2();
TransformGradients();
}
}
// do the work
void mitk::SiemensDicomDiffusionImageHeaderReader::Update()
{
// check if there are filenames
if(m_DicomFilenames.size())
{
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;
}
}
// adapted from slicer
// DicomToNrrdConverter.cxx
VolumeReaderType::DictionaryArrayRawPointer
inputDict = m_VolumeReader->GetMetaDataDictionaryArray();
ReadPublicTags();
float x0, y0, z0;
float x1, y1, z1;
std::string tag;
tag.clear();
itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0020|0032", tag );
sscanf( tag.c_str(), "%f\\%f\\%f", &x0, &y0, &z0 );
//MITK_INFO << "Slice 0: " << tag << std::endl;
tag.clear();
// assume volume interleaving, i.e. the second dicom file stores
// the second slice in the same volume as the first dicom file
if((*inputDict).size() > 1)
{
itk::ExposeMetaData<std::string> ( *(*inputDict)[1], "0020|0032", tag );
sscanf( tag.c_str(), "%f\\%f\\%f", &x1, &y1, &z1 );
//MITK_INFO << "Slice 1: " << tag << std::endl;
x1 -= x0; y1 -= y0; z1 -= z0;
x0 = x1*this->m_Output->xSlice + y1*this->m_Output->ySlice + z1*this->m_Output->zSlice;
if (x0 < 0)
{
m_SliceOrderIS = false;
}
}
ReadPublicTags2();
int nStride = 1;
this->m_Output->nSliceInVolume = m_sliceLocations.size();
nStride = this->m_Output->nSliceInVolume;
MITK_INFO << m_DicomFilenames[0] << std::endl;
MITK_INFO << "Dims " << this->m_Output->nRows << "x"
<< this->m_Output->nCols << "x" << this->m_Output->nSliceInVolume << " " << std::endl;
for (int k = 0; k < m_nSlice; k += nStride )
{
gdcm::ImageReader reader;
reader.SetFileName( m_DicomFilenames[k].c_str() );
if( !reader.Read() )
{
itkExceptionMacro(<< "Cannot read requested file");
}
const gdcm::File &f = reader.GetFile();
const gdcm::DataSet &ds = f.GetDataSet();
// gdcm::DataSet ds = header0->GetDataSet();
gdcm::DataSet::ConstIterator it = ds.Begin();
// Copy of the header->content
// copy information stored in 0029,1010 into a string for parsing
for(; it != ds.End(); ++it)
{
const gdcm::DataElement &ref = *it;
if (ref.GetTag() == gdcm::Tag(0x0029,0x1010)) {
tag = std::string(ref.GetByteValue()->GetPointer(),ref.GetByteValue()->GetLength());
}
}
// parse B_value from 0029,1010 tag
std::vector<double> valueArray(0);
vnl_vector_fixed<double, 3> vect3d;
int nItems = ExtractSiemensDiffusionInformation(tag, "B_value", valueArray);
if (nItems != 1 || valueArray[0] == 0) // did not find enough information
{
tag.clear();
MITK_INFO << "Reading diffusion info from 0019|100c and 0019|100e tags" << std::endl;
bool success = false;
for(it = ds.Begin(); it != ds.End(); ++it)
{
const gdcm::DataElement &ref = *it;
if (ref.GetTag() == gdcm::Tag(0x0019,0x100c)) {
tag = std::string(ref.GetByteValue()->GetPointer(),ref.GetByteValue()->GetLength());
this->m_Output->bValue = atof( tag.c_str() );
success = true;
}
}
tag.clear();
if(success)
{
if(this->m_Output->bValue == 0)
{
MITK_INFO << "BV: 0 (Baseline image)";
continue;
}
success = false;
for(it = ds.Begin(); it != ds.End(); ++it)
{
const gdcm::DataElement &ref = *it;
if (ref.GetTag() == gdcm::Tag(0x0019,0x100e)) {
tag = std::string(ref.GetByteValue()->GetPointer(),ref.GetByteValue()->GetLength());
success = true;
}
}
if(success)
{
memcpy( &vect3d[0], tag.c_str()+0, 8 );
memcpy( &vect3d[1], tag.c_str()+8, 8 );
memcpy( &vect3d[2], tag.c_str()+16, 8 );
vect3d.normalize();
this->m_Output->DiffusionVector = vect3d;
TransformGradients();
MITK_INFO << "BV: " << this->m_Output->bValue;
MITK_INFO << " GD: " << this->m_Output->DiffusionVector;
continue;
}
}
}
else
{
MITK_INFO << "Reading diffusion info from 0029,1010 tag" << std::endl;
this->m_Output->bValue = valueArray[0];
if(this->m_Output->bValue == 0)
{
MITK_INFO << "BV: 0 (Baseline image)";
continue;
}
valueArray.resize(0);
nItems = ExtractSiemensDiffusionGradientInformation(tag, "DiffusionGradientDirection", valueArray);
if (nItems == 3)
{
vect3d[0] = valueArray[0];
vect3d[1] = valueArray[1];
vect3d[2] = valueArray[2];
vect3d.normalize();
this->m_Output->DiffusionVector = vect3d;
TransformGradients();
MITK_INFO << "BV: " << this->m_Output->bValue;
MITK_INFO << " GD: " << this->m_Output->DiffusionVector;
continue;
}
}
MITK_ERROR << "No diffusion info found, forcing to BASELINE image." << std::endl;
this->m_Output->bValue = 0.0;
vect3d.fill( 0.0 );
this->m_Output->DiffusionVector = vect3d;
}
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
}
// do the work
void mitk::GEDicomDiffusionImageHeaderReader::Update()
{
// check if there are filenames
if(m_DicomFilenames.size())
{
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;
}
}
// adapted from namic-sandbox
// DicomToNrrdConverter.cxx
VolumeReaderType::DictionaryArrayRawPointer inputDict
= m_VolumeReader->GetMetaDataDictionaryArray();
ReadPublicTags();
float x0, y0, z0;
float x1, y1, z1;
std::string tag;
tag.clear();
itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0020|0032", tag );
sscanf( tag.c_str(), "%f\\%f\\%f", &x0, &y0, &z0 );
std::cout << "Slice 0: " << tag << std::endl;
tag.clear();
// assume volume interleaving, i.e. the second dicom file stores
// the second slice in the same volume as the first dicom file
itk::ExposeMetaData<std::string> ( *(*inputDict)[1], "0020|0032", tag );
sscanf( tag.c_str(), "%f\\%f\\%f", &x1, &y1, &z1 );
std::cout << "Slice 1: " << tag << std::endl;
x1 -= x0; y1 -= y0; z1 -= z0;
x0 = x1*this->m_Output->xSlice + y1*this->m_Output->ySlice + z1*this->m_Output->zSlice;
if (x0 < 0)
{
m_SliceOrderIS = false;
}
ReadPublicTags2();
int nSliceInVolume;
int nVolume;
nSliceInVolume = m_sliceLocations.size();
nVolume = m_nSlice/nSliceInVolume;
// assume volume interleaving
std::cout << "Number of Slices: " << m_nSlice << std::endl;
std::cout << "Number of Volume: " << nVolume << std::endl;
std::cout << "Number of Slices in each volume: " << nSliceInVolume << std::endl;
for (int k = 0; k < m_nSlice; k += nSliceInVolume)
{
tag.clear();
bool exist = itk::ExposeMetaData<std::string> ( *(*inputDict)[k], "0043|1039", tag);
float b = atof( tag.c_str() );
this->m_Output->bValue = b;
vnl_vector_fixed<double, 3> vect3d;
if (!exist || b == 0)
{
vect3d.fill( 0 );
this->m_Output->DiffusionVector = vect3d;
continue;
}
vect3d.fill( 0 );
tag.clear();
itk::ExposeMetaData<std::string> ( *(*inputDict)[k], "0019|10bb", tag);
vect3d[0] = atof( tag.c_str() );
tag.clear();
itk::ExposeMetaData<std::string> ( *(*inputDict)[k], "0019|10bc", tag);
vect3d[1] = atof( tag.c_str() );
tag.clear();
itk::ExposeMetaData<std::string> ( *(*inputDict)[k], "0019|10bd", tag);
vect3d[2] = atof( tag.c_str() );
vect3d.normalize();
this->m_Output->DiffusionVector = vect3d;
}
TransformGradients();
try
{
setlocale(LC_ALL, currLocale.c_str());
}
catch(...)
{
MITK_INFO << "Could not reset locale " << currLocale;
}
}
}
