#include <mitkSiemensMosaicDicomDiffusionImageHeaderReader.h>
Public Types | |
| typedef SiemensMosaicDicomDiffusionImageHeaderReader | Self |
| typedef DicomDiffusionImageHeaderReader | Superclass |
| typedef itk::SmartPointer< Self > | Pointer |
| typedef itk::SmartPointer < const Self > | ConstPointer |
Public Member Functions | |
| virtual const char * | GetClassName () const |
| int | ExtractSiemensDiffusionInformation (std::string tagString, std::string nameString, std::vector< double > &valueArray) |
| virtual void | Update () |
Static Public Member Functions | |
| static Pointer | New () |
Protected Member Functions | |
| SiemensMosaicDicomDiffusionImageHeaderReader () | |
| virtual | ~SiemensMosaicDicomDiffusionImageHeaderReader () |
Definition at line 26 of file mitkSiemensMosaicDicomDiffusionImageHeaderReader.h.
| typedef itk::SmartPointer<const Self> mitk::SiemensMosaicDicomDiffusionImageHeaderReader::ConstPointer |
Reimplemented from mitk::DicomDiffusionImageHeaderReader.
Definition at line 30 of file mitkSiemensMosaicDicomDiffusionImageHeaderReader.h.
| typedef itk::SmartPointer<Self> mitk::SiemensMosaicDicomDiffusionImageHeaderReader::Pointer |
Reimplemented from mitk::DicomDiffusionImageHeaderReader.
Definition at line 30 of file mitkSiemensMosaicDicomDiffusionImageHeaderReader.h.
| typedef SiemensMosaicDicomDiffusionImageHeaderReader mitk::SiemensMosaicDicomDiffusionImageHeaderReader::Self |
Reimplemented from mitk::DicomDiffusionImageHeaderReader.
Definition at line 30 of file mitkSiemensMosaicDicomDiffusionImageHeaderReader.h.
| typedef DicomDiffusionImageHeaderReader mitk::SiemensMosaicDicomDiffusionImageHeaderReader::Superclass |
Reimplemented from mitk::DicomDiffusionImageHeaderReader.
Definition at line 30 of file mitkSiemensMosaicDicomDiffusionImageHeaderReader.h.
| mitk::SiemensMosaicDicomDiffusionImageHeaderReader::SiemensMosaicDicomDiffusionImageHeaderReader | ( | ) | [protected] |
Definition at line 49 of file mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp.
{
}
| mitk::SiemensMosaicDicomDiffusionImageHeaderReader::~SiemensMosaicDicomDiffusionImageHeaderReader | ( | ) | [protected, virtual] |
Definition at line 53 of file mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp.
{
}
| int mitk::SiemensMosaicDicomDiffusionImageHeaderReader::ExtractSiemensDiffusionInformation | ( | std::string | tagString, |
| std::string | nameString, | ||
| std::vector< double > & | valueArray | ||
| ) |
Definition at line 57 of file mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp.
{
std::string::size_type atPosition = tagString.find( nameString );
if ( atPosition == std::string::npos)
{
return 0;
}
else
{
std::string infoAsString = tagString.substr( atPosition, tagString.size()-atPosition+1 );
const char * infoAsCharPtr = infoAsString.c_str();
int vm = *(infoAsCharPtr+64);
std::string vr = infoAsString.substr( 68, 4 );
//int syngodt = *(infoAsCharPtr+72);
//int nItems = *(infoAsCharPtr+76);
//int localDummy = *(infoAsCharPtr+80);
int offset = 84;
for (int k = 0; k < vm; k++)
{
int itemLength = *(infoAsCharPtr+offset+4);
int strideSize = static_cast<int> (ceil(static_cast<double>(itemLength)/4) * 4);
std::string valueString = infoAsString.substr( offset+16, itemLength );
valueArray.push_back( atof(valueString.c_str()) );
offset += 16+strideSize;
}
return vm;
}
}
| virtual const char* mitk::SiemensMosaicDicomDiffusionImageHeaderReader::GetClassName | ( | ) | const [virtual] |
Reimplemented from mitk::DicomDiffusionImageHeaderReader.
| static Pointer mitk::SiemensMosaicDicomDiffusionImageHeaderReader::New | ( | ) | [static] |
Reimplemented from mitk::DicomDiffusionImageHeaderReader.
Referenced by mitk::DicomDiffusionImageHeaderReader::Update().
| void mitk::SiemensMosaicDicomDiffusionImageHeaderReader::Update | ( | ) | [virtual] |
Reimplemented from mitk::DicomDiffusionImageHeaderReader.
Definition at line 89 of file mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp.
References MITK_ERROR, MITK_INFO, SiemensDictBValue(), SiemensDictDiffusionDirection(), SiemensDictDiffusionMatrix(), SiemensDictNMosiac(), SiemensDictShadowInfo(), SiemensMosiacParameters(), and QuadProgPP::sqrt().
{
// check if there are filenames
if(m_DicomFilenames.size())
{
// adapted from namic-sandbox
// DicomToNrrdConverter.cxx
VolumeReaderType::DictionaryArrayRawPointer inputDict
= m_VolumeReader->GetMetaDataDictionaryArray();
#ifndef DGDCM2
if(gdcm::Global::GetDicts()->GetDefaultPubDict()->GetEntry(SiemensMosiacParameters.GetKey()) == 0)
gdcm::Global::GetDicts()->GetDefaultPubDict()->AddEntry(SiemensMosiacParameters);
if(gdcm::Global::GetDicts()->GetDefaultPubDict()->GetEntry(SiemensDictNMosiac.GetKey()) == 0)
gdcm::Global::GetDicts()->GetDefaultPubDict()->AddEntry(SiemensDictNMosiac);
if(gdcm::Global::GetDicts()->GetDefaultPubDict()->GetEntry(SiemensDictBValue.GetKey()) == 0)
gdcm::Global::GetDicts()->GetDefaultPubDict()->AddEntry(SiemensDictBValue);
if(gdcm::Global::GetDicts()->GetDefaultPubDict()->GetEntry(SiemensDictDiffusionDirection.GetKey()) == 0)
gdcm::Global::GetDicts()->GetDefaultPubDict()->AddEntry(SiemensDictDiffusionDirection);
if(gdcm::Global::GetDicts()->GetDefaultPubDict()->GetEntry(SiemensDictDiffusionMatrix.GetKey()) == 0)
gdcm::Global::GetDicts()->GetDefaultPubDict()->AddEntry(SiemensDictDiffusionMatrix);
if(gdcm::Global::GetDicts()->GetDefaultPubDict()->GetEntry(SiemensDictShadowInfo.GetKey()) == 0)
gdcm::Global::GetDicts()->GetDefaultPubDict()->AddEntry(SiemensDictShadowInfo);
#endif
ReadPublicTags();
int mMosaic = 0; // number of raws in each mosaic block;
int nMosaic = 0; // number of columns in each mosaic block
std::cout << "Siemens SliceMosaic......" << std::endl;
m_SliceOrderIS = false;
// for siemens mosaic image, figure out mosaic slice order from 0029|1010
std::string tag;
tag.clear();
#ifndef DGDCM2
gdcm::File *header0 = new gdcm::File;
gdcm::BinEntry* binEntry;
header0->SetMaxSizeLoadEntry(65536);
header0->SetFileName( m_DicomFilenames[0] );
header0->SetLoadMode( gdcm::LD_ALL );
header0->Load();
// copy information stored in 0029,1010 into a string for parsing
gdcm::DocEntry* docEntry = header0->GetFirstEntry();
while(docEntry)
{
if ( docEntry->GetKey() == "0029|1010" )
{
binEntry = dynamic_cast<gdcm::BinEntry*> ( docEntry );
int binLength = binEntry->GetFullLength();
tag.resize( binLength );
uint8_t * tagString = binEntry->GetBinArea();
for (int n = 0; n < binLength; n++)
{
tag[n] = *(tagString+n);
}
break;
}
docEntry = header0->GetNextEntry();
}
#else
gdcm::ImageReader reader;
reader.SetFileName( m_DicomFilenames[0].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());
}
}
#endif
// parse SliceNormalVector from 0029,1010 tag
std::vector<double> valueArray(0);
int nItems = ExtractSiemensDiffusionInformation(tag, "SliceNormalVector", valueArray);
if (nItems != 3) // did not find enough information
{
std::cout << "Warning: Cannot find complete information on SliceNormalVector in 0029|1010\n";
std::cout << " Slice order may be wrong.\n";
}
else if (valueArray[2] > 0)
{
m_SliceOrderIS = true;
}
// parse NumberOfImagesInMosaic from 0029,1010 tag
valueArray.resize(0);
nItems = ExtractSiemensDiffusionInformation(tag, "NumberOfImagesInMosaic", valueArray);
if (nItems == 0) // did not find enough information
{
std::cout << "Warning: Cannot find complete information on NumberOfImagesInMosaic in 0029|1010\n";
std::cout << " Resulting image may contain empty slices.\n";
}
else
{
this->m_Output->nSliceInVolume = static_cast<int>(valueArray[0]);
mMosaic = static_cast<int> (ceil(sqrt(valueArray[0])));
nMosaic = mMosaic;
}
std::cout << "Mosaic in " << mMosaic << " X " << nMosaic << " blocks (total number of blocks = " << valueArray[0] << ").\n";
ReadPublicTags2();
int nStride = 1;
std::cout << "Data in Siemens Mosaic Format\n";
//nVolume = nSlice;
//std::cout << "Number of Volume: " << nVolume << std::endl;
std::cout << "Number of Slices in each volume: " << this->m_Output->nSliceInVolume << std::endl;
nStride = 1;
for (int k = 0; k < m_nSlice; k += nStride )
{
#ifndef DGDCM2
gdcm::File *header0 = new gdcm::File;
gdcm::BinEntry* binEntry;
header0->SetMaxSizeLoadEntry(65536);
header0->SetFileName( m_DicomFilenames[0] );
header0->SetLoadMode( gdcm::LD_ALL );
header0->Load();
// copy information stored in 0029,1010 into a string for parsing
gdcm::DocEntry* docEntry = header0->GetFirstEntry();
while(docEntry)
{
if ( docEntry->GetKey() == "0029|1010" )
{
binEntry = dynamic_cast<gdcm::BinEntry*> ( docEntry );
int binLength = binEntry->GetFullLength();
tag.resize( binLength );
uint8_t * tagString = binEntry->GetBinArea();
for (int n = 0; n < binLength; n++)
{
tag[n] = *(tagString+n);
}
break;
}
docEntry = header0->GetNextEntry();
}
#else
gdcm::ImageReader reader;
reader.SetFileName( m_DicomFilenames[0].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());
}
}
#endif
// 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
{
MITK_INFO << "Reading diffusion info from 0019|100c and 0019|100e tags";
tag.clear();
bool success = itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0019|100c", tag );
if(success)
{
this->m_Output->bValue = atof( tag.c_str() );
tag.clear();
success = itk::ExposeMetaData<std::string> ( *(*inputDict)[k], "0019|100e", tag);
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 << std::endl;
continue;
}
}
}
else
{
MITK_INFO << "Reading diffusion info from 0029|1010 tags";
this->m_Output->bValue = valueArray[0];
// parse DiffusionGradientDirection from 0029,1010 tag
valueArray.resize(0);
nItems = ExtractSiemensDiffusionInformation(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, assuming BASELINE" << std::endl;
this->m_Output->bValue = 0.0;
vect3d.fill( 0.0 );
this->m_Output->DiffusionVector = vect3d;
}
}
}
1.7.2