Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes

mitk::DicomDiffusionImageHeaderReader Class Reference

#include <mitkDicomDiffusionImageHeaderReader.h>

Inheritance diagram for mitk::DicomDiffusionImageHeaderReader:
Inheritance graph
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List of all members.

Public Types

enum  SupportedVendors {
  SV_SIEMENS, SV_SIEMENS_MOSAIC, SV_PHILIPS, SV_GE,
  SV_UNKNOWN_VENDOR
}
typedef
DicomDiffusionImageHeaderReader 		Self
typedef itk::Object Superclass
typedef itk::SmartPointer< Self > Pointer
typedef itk::SmartPointer
< const Self > 		ConstPointer
typedef std::vector< std::string > FileNamesContainer
typedef short PixelValueType
typedef itk::OrientedImage
< PixelValueType, 2 > 		SliceType
typedef itk::OrientedImage
< PixelValueType, 3 > 		VolumeType
typedef itk::ImageSeriesReader
< VolumeType > 		VolumeReaderType
typedef itk::ImageFileReader
< SliceType > 		SliceReaderType
typedef itk::GDCMImageIO ImageIOType

Public Member Functions

virtual const char * GetClassName () const
void SetSeriesDicomFilenames (FileNamesContainer dicomFilenames)
void SetGdcmIO (ImageIOType::Pointer gdcmIO)
void SetVolumeReader (VolumeReaderType::Pointer volumeReader)
void SetOutputPointer (DiffusionImageHeaderInformation::Pointer output)
virtual void Update ()
DiffusionImageHeaderInformation::Pointer GetOutput ()
SupportedVendors GetVendorID ()

Static Public Member Functions

static Pointer New ()

Protected Member Functions

 DicomDiffusionImageHeaderReader ()
virtual ~DicomDiffusionImageHeaderReader ()
void ReadPublicTags ()
void ReadPublicTags2 ()
void TransformGradients ()

Protected Attributes

FileNamesContainer m_DicomFilenames
DiffusionImageHeaderInformation::Pointer m_Output
ImageIOType::Pointer m_GdcmIO
VolumeReaderType::Pointer m_VolumeReader
bool m_SliceOrderIS
bool m_SingleSeries
int m_nSlice
std::vector< float > m_sliceLocations

Detailed Description

Definition at line 34 of file mitkDicomDiffusionImageHeaderReader.h.

Member Typedef Documentation

typedef itk::SmartPointer<const Self> mitk::DicomDiffusionImageHeaderReader::ConstPointer

Reimplemented in mitk::GEDicomDiffusionImageHeaderReader, mitk::PhilipsDicomDiffusionImageHeaderReader, mitk::SiemensDicomDiffusionImageHeaderReader, and mitk::SiemensMosaicDicomDiffusionImageHeaderReader.

Definition at line 38 of file mitkDicomDiffusionImageHeaderReader.h.

typedef std::vector< std::string > mitk::DicomDiffusionImageHeaderReader::FileNamesContainer

Definition at line 49 of file mitkDicomDiffusionImageHeaderReader.h.

typedef itk::GDCMImageIO mitk::DicomDiffusionImageHeaderReader::ImageIOType

Definition at line 56 of file mitkDicomDiffusionImageHeaderReader.h.

typedef short mitk::DicomDiffusionImageHeaderReader::PixelValueType

Definition at line 51 of file mitkDicomDiffusionImageHeaderReader.h.

typedef itk::SmartPointer<Self> mitk::DicomDiffusionImageHeaderReader::Pointer

Reimplemented in mitk::GEDicomDiffusionImageHeaderReader, mitk::PhilipsDicomDiffusionImageHeaderReader, mitk::SiemensDicomDiffusionImageHeaderReader, and mitk::SiemensMosaicDicomDiffusionImageHeaderReader.

Definition at line 38 of file mitkDicomDiffusionImageHeaderReader.h.

typedef DicomDiffusionImageHeaderReader mitk::DicomDiffusionImageHeaderReader::Self

Reimplemented in mitk::GEDicomDiffusionImageHeaderReader, mitk::PhilipsDicomDiffusionImageHeaderReader, mitk::SiemensDicomDiffusionImageHeaderReader, and mitk::SiemensMosaicDicomDiffusionImageHeaderReader.

Definition at line 38 of file mitkDicomDiffusionImageHeaderReader.h.

typedef itk::ImageFileReader< SliceType > mitk::DicomDiffusionImageHeaderReader::SliceReaderType

Definition at line 55 of file mitkDicomDiffusionImageHeaderReader.h.

typedef itk::OrientedImage< PixelValueType, 2 > mitk::DicomDiffusionImageHeaderReader::SliceType

Definition at line 52 of file mitkDicomDiffusionImageHeaderReader.h.

typedef itk::Object mitk::DicomDiffusionImageHeaderReader::Superclass

Reimplemented in mitk::GEDicomDiffusionImageHeaderReader, mitk::PhilipsDicomDiffusionImageHeaderReader, mitk::SiemensDicomDiffusionImageHeaderReader, and mitk::SiemensMosaicDicomDiffusionImageHeaderReader.

Definition at line 38 of file mitkDicomDiffusionImageHeaderReader.h.

typedef itk::ImageSeriesReader< VolumeType > mitk::DicomDiffusionImageHeaderReader::VolumeReaderType

Definition at line 54 of file mitkDicomDiffusionImageHeaderReader.h.

typedef itk::OrientedImage< PixelValueType, 3 > mitk::DicomDiffusionImageHeaderReader::VolumeType

Definition at line 53 of file mitkDicomDiffusionImageHeaderReader.h.

Member Enumeration Documentation

enum mitk::DicomDiffusionImageHeaderReader::SupportedVendors
Enumerator:
SV_SIEMENS 
SV_SIEMENS_MOSAIC 
SV_PHILIPS 
SV_GE 
SV_UNKNOWN_VENDOR 

Definition at line 41 of file mitkDicomDiffusionImageHeaderReader.h.

                         { 
      SV_SIEMENS,
      SV_SIEMENS_MOSAIC,
      SV_PHILIPS,
      SV_GE,
      SV_UNKNOWN_VENDOR
    };

Constructor & Destructor Documentation

mitk::DicomDiffusionImageHeaderReader::DicomDiffusionImageHeaderReader (  ) [protected]

Definition at line 49 of file mitkDicomDiffusionImageHeaderReader.cpp.

References m_SingleSeries, and m_SliceOrderIS.

{
  m_SliceOrderIS = true;
  m_SingleSeries = true;
}
mitk::DicomDiffusionImageHeaderReader::~DicomDiffusionImageHeaderReader (  ) [protected, virtual]

Definition at line 55 of file mitkDicomDiffusionImageHeaderReader.cpp.

{
}

Member Function Documentation

virtual const char* mitk::DicomDiffusionImageHeaderReader::GetClassName (  ) const [virtual]

Reimplemented in mitk::GEDicomDiffusionImageHeaderReader, mitk::PhilipsDicomDiffusionImageHeaderReader, mitk::SiemensDicomDiffusionImageHeaderReader, and mitk::SiemensMosaicDicomDiffusionImageHeaderReader.

mitk::DiffusionImageHeaderInformation::Pointer mitk::DicomDiffusionImageHeaderReader::GetOutput ( void   )

Definition at line 200 of file mitkDicomDiffusionImageHeaderReader.cpp.

{
  return m_Output;
}
mitk::DicomDiffusionImageHeaderReader::SupportedVendors mitk::DicomDiffusionImageHeaderReader::GetVendorID (  )

Definition at line 60 of file mitkDicomDiffusionImageHeaderReader.cpp.

{
  // adapted from namic-sandbox
  // DicomToNrrdConverter.cxx

  m_GdcmIO = ImageIOType::New();
  m_GdcmIO->LoadPrivateTagsOn();
  m_GdcmIO->SetMaxSizeLoadEntry( 65536 );

  m_VolumeReader = VolumeReaderType::New();
  m_VolumeReader->SetImageIO( m_GdcmIO );
  m_VolumeReader->SetFileNames( m_DicomFilenames );

  try
  {
    m_VolumeReader->Update();
  }
  catch (itk::ExceptionObject &excp)
  {
    std::cerr << "Exception thrown while reading slice" << std::endl;
    std::cerr << excp << std::endl;
    return SV_UNKNOWN_VENDOR;
  }

  VolumeReaderType::DictionaryArrayRawPointer inputDict 
    = m_VolumeReader->GetMetaDataDictionaryArray();

  std::string vendor;
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0008|0070", vendor );
  // std::cout << vendor << std::endl;

  std::string ImageType;
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0008|0008", ImageType );
  //std::cout << ImageType << std::endl;

  if ( vendor.find("GE") != std::string::npos )
  {
    // for GE data
    return SV_GE;
  }
  else if( vendor.find("SIEMENS") != std::string::npos )
  {
    if ( ImageType.find("MOSAIC") != std::string::npos )
    {
      // for Siemens MOSAIC
      return SV_SIEMENS_MOSAIC;
    }
    else
    {
      // for Siemens SPLIT
      return SV_SIEMENS;
    }
  }
  else if( vendor.find("PHILIPS") != std::string::npos )
  {
    // for philips data
    return SV_PHILIPS;
  }
  else
  {
    // for unrecognized vendors
    return SV_UNKNOWN_VENDOR;
  }
}
static Pointer mitk::DicomDiffusionImageHeaderReader::New (  ) [static]

Reimplemented in mitk::GEDicomDiffusionImageHeaderReader, mitk::PhilipsDicomDiffusionImageHeaderReader, mitk::SiemensDicomDiffusionImageHeaderReader, and mitk::SiemensMosaicDicomDiffusionImageHeaderReader.

Referenced by QmitkDiffusionDicomImport::DicomLoadStartLoad().

void mitk::DicomDiffusionImageHeaderReader::ReadPublicTags (  ) [protected]

Definition at line 205 of file mitkDicomDiffusionImageHeaderReader.cpp.

References InsertUnique().

{
  VolumeReaderType::DictionaryArrayRawPointer inputDict 
    = m_VolumeReader->GetMetaDataDictionaryArray();

  // load in all public tags
  m_nSlice = inputDict->size();   
  std::string tag;

  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0008|103e", tag );
  this->m_Output->seriesDescription = tag.c_str();

  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0020|0011", tag );
  this->m_Output->seriesNumber = atoi(tag.c_str());

  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0010|0010", tag );
  this->m_Output->patientName = tag.c_str();

  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0028|0010", tag );
  this->m_Output->nRows = atoi( tag.c_str() );

  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0028|0011", tag );
  this->m_Output->nCols = atoi( tag.c_str() );

  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0028|0030", tag );
  sscanf( tag.c_str(), "%f\\%f", &this->m_Output->xRes, &this->m_Output->yRes );

  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0020|0032", tag );
  sscanf( tag.c_str(), "%f\\%f\\%f", &this->m_Output->xOrigin, &this->m_Output->yOrigin, &this->m_Output->zOrigin );

  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0018|0050", tag );
  this->m_Output->sliceThickness = atof( tag.c_str() );

  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0018|0088", tag );
  this->m_Output->sliceSpacing = atof( tag.c_str() );

  // figure out how many slices are there in a volume, each unique
  // SliceLocation represent one slice 
  for (int k = 0; k < m_nSlice; k++)
  {
    tag.clear();
    itk::ExposeMetaData<std::string> ( *(*inputDict)[k], "0020|1041",  tag);
    float sliceLocation = atof( tag.c_str() );
    InsertUnique( m_sliceLocations, sliceLocation );
  }    

  // check ImageOrientationPatient and figure out slice direction in
  // L-P-I (right-handed) system.
  // In Dicom, the coordinate frame is L-P by default. Look at
  // http://medical.nema.org/dicom/2007/07_03pu.pdf ,  page 301
  tag.clear();
  itk::ExposeMetaData<std::string> ( *(*inputDict)[0], "0020|0037", tag );
  float xRow, yRow, zRow, xCol, yCol, zCol, xSlice, ySlice, zSlice /*, orthoSliceSpacing*/;
  sscanf( tag.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", &xRow, &yRow, &zRow, &xCol, &yCol, &zCol );
  //std::cout << "ImageOrientationPatient (0020:0037): ";
  //std::cout << xRow << ", " << yRow << ", " << zRow << "; ";
  //std::cout << xCol << ", " << yCol << ", " << zCol << "\n";

  // In Dicom, the measurement frame is L-P by default. Look at
  // http://medical.nema.org/dicom/2007/07_03pu.pdf ,  page 301, in
  // order to make this compatible with Slicer's RAS frame, we
  // multiply the direction cosines by the negatives of the resolution
  // (resolution is required by nrrd format). Direction cosine is not
  // affacted since the resulting frame is still a right-handed frame.
  xRow = -xRow;
  yRow = -yRow;

  xCol = -xCol;
  yCol = -yCol;

  // Cross product, this gives I-axis direction
  xSlice = (yRow*zCol-zRow*yCol)*this->m_Output->sliceSpacing;
  ySlice = (zRow*xCol-xRow*zCol)*this->m_Output->sliceSpacing;
  zSlice = (xRow*yCol-yRow*xCol)*this->m_Output->sliceSpacing;

  xRow *= this->m_Output->xRes;
  yRow *= this->m_Output->xRes;
  zRow *= this->m_Output->xRes;

  xCol *= this->m_Output->yRes;
  yCol *= this->m_Output->yRes;
  zCol *= this->m_Output->yRes;

  this->m_Output->xRow = xRow;
  this->m_Output->yRow = yRow;
  this->m_Output->zRow = zRow;
  this->m_Output->xCol = xCol;
  this->m_Output->yCol = yCol;
  this->m_Output->zCol = zCol;
  this->m_Output->xSlice = xSlice;
  this->m_Output->ySlice = ySlice;
  this->m_Output->zSlice = zSlice;

}
void mitk::DicomDiffusionImageHeaderReader::ReadPublicTags2 (  ) [protected]

Definition at line 314 of file mitkDicomDiffusionImageHeaderReader.cpp.

{

  if (!m_SliceOrderIS)
  {
    this->m_Output->xSlice = -this->m_Output->xSlice;
    this->m_Output->ySlice = -this->m_Output->ySlice;
    this->m_Output->zSlice = -this->m_Output->zSlice;
  }

  //std::cout << "Row: " << this->m_Output->xRow << ", " << this->m_Output->yRow << ", " << this->m_Output->zRow << std::endl;
  //std::cout << "Col: " << this->m_Output->xCol << ", " << this->m_Output->yCol << ", " << this->m_Output->zCol << std::endl;
  //std::cout << "Sli: " << this->m_Output->xSlice << ", " << this->m_Output->ySlice << ", " << this->m_Output->zSlice << std::endl;

  //orthoSliceSpacing = fabs(zSlice);

  //int nVolume;

  //float maxBvalue = 0;
  //int nBaseline = 0;

}
void mitk::DicomDiffusionImageHeaderReader::SetGdcmIO ( ImageIOType::Pointer  gdcmIO ) [inline]

Definition at line 62 of file mitkDicomDiffusionImageHeaderReader.h.

    { this->m_GdcmIO = gdcmIO; }
void mitk::DicomDiffusionImageHeaderReader::SetOutputPointer ( DiffusionImageHeaderInformation::Pointer  output ) [inline]

Definition at line 68 of file mitkDicomDiffusionImageHeaderReader.h.

    { this->m_Output = output; }
void mitk::DicomDiffusionImageHeaderReader::SetSeriesDicomFilenames ( FileNamesContainer  dicomFilenames ) [inline]

Definition at line 59 of file mitkDicomDiffusionImageHeaderReader.h.

    { this->m_DicomFilenames = dicomFilenames; }
void mitk::DicomDiffusionImageHeaderReader::SetVolumeReader ( VolumeReaderType::Pointer  volumeReader ) [inline]

Definition at line 65 of file mitkDicomDiffusionImageHeaderReader.h.

    { this->m_VolumeReader = volumeReader; }
void mitk::DicomDiffusionImageHeaderReader::TransformGradients (  ) [protected]

Definition at line 337 of file mitkDicomDiffusionImageHeaderReader.cpp.

{
  // transform gradient directions into RAS frame 
    if ( !m_SliceOrderIS )
    {
      this->m_Output->DiffusionVector[2] = -this->m_Output->DiffusionVector[2];  // I -> S
    }
}
void mitk::DicomDiffusionImageHeaderReader::Update (  ) [virtual]

Reimplemented in mitk::GEDicomDiffusionImageHeaderReader, mitk::PhilipsDicomDiffusionImageHeaderReader, mitk::SiemensDicomDiffusionImageHeaderReader, and mitk::SiemensMosaicDicomDiffusionImageHeaderReader.

Definition at line 126 of file mitkDicomDiffusionImageHeaderReader.cpp.

References mitk::PhilipsDicomDiffusionImageHeaderReader::New(), mitk::SiemensMosaicDicomDiffusionImageHeaderReader::New(), mitk::SiemensDicomDiffusionImageHeaderReader::New(), mitk::GEDicomDiffusionImageHeaderReader::New(), and mitk::DiffusionImageHeaderInformation::New().

{

  // check if there are filenames
  if(m_DicomFilenames.size())
  {

    m_Output = mitk::DiffusionImageHeaderInformation::New();
    m_Output->m_DicomFilenames = m_DicomFilenames;

    // create correct reader
    switch(GetVendorID())
    {
    case(SV_GE):
      {
        GEDicomDiffusionImageHeaderReader::Pointer reader
          = GEDicomDiffusionImageHeaderReader::New();
        reader->SetSeriesDicomFilenames(this->m_DicomFilenames);
        reader->SetGdcmIO(this->m_GdcmIO);
        reader->SetVolumeReader(this->m_VolumeReader);
        reader->SetOutputPointer(this->m_Output);
        reader->Update();
        this->m_Output = reader->GetOutput();
        break;
      }
    case(SV_SIEMENS):
      {
        SiemensDicomDiffusionImageHeaderReader::Pointer reader
          = SiemensDicomDiffusionImageHeaderReader::New();
        reader->SetSeriesDicomFilenames(this->m_DicomFilenames);
        reader->SetGdcmIO(this->m_GdcmIO);
        reader->SetVolumeReader(this->m_VolumeReader);
        reader->SetOutputPointer(this->m_Output);
        reader->Update();
        this->m_Output = reader->GetOutput();
        break;
      }
    case(SV_SIEMENS_MOSAIC):
      {

        SiemensMosaicDicomDiffusionImageHeaderReader::Pointer reader
          = SiemensMosaicDicomDiffusionImageHeaderReader::New();
        reader->SetSeriesDicomFilenames(this->m_DicomFilenames);
        reader->SetGdcmIO(this->m_GdcmIO);
        reader->SetVolumeReader(this->m_VolumeReader);
        reader->SetOutputPointer(this->m_Output);
        reader->Update();
        this->m_Output = reader->GetOutput();
        break;
      }
    case(SV_PHILIPS):
      {

        PhilipsDicomDiffusionImageHeaderReader::Pointer reader
          = PhilipsDicomDiffusionImageHeaderReader::New();
        reader->SetSeriesDicomFilenames(this->m_DicomFilenames);
        reader->SetGdcmIO(this->m_GdcmIO);
        reader->SetVolumeReader(this->m_VolumeReader);
        reader->SetOutputPointer(this->m_Output);
        reader->Update();
        this->m_Output = reader->GetOutput();
        break;
      }
    case(SV_UNKNOWN_VENDOR):
      {
        std::cerr << "diffusion header reader: unknown vendor" << std::endl;
        break;
      }
    }
  }
}

Member Data Documentation

FileNamesContainer mitk::DicomDiffusionImageHeaderReader::m_DicomFilenames [protected]

Definition at line 96 of file mitkDicomDiffusionImageHeaderReader.h.

ImageIOType::Pointer mitk::DicomDiffusionImageHeaderReader::m_GdcmIO [protected]

Definition at line 99 of file mitkDicomDiffusionImageHeaderReader.h.

int mitk::DicomDiffusionImageHeaderReader::m_nSlice [protected]

Definition at line 104 of file mitkDicomDiffusionImageHeaderReader.h.

DiffusionImageHeaderInformation::Pointer mitk::DicomDiffusionImageHeaderReader::m_Output [protected]

Definition at line 97 of file mitkDicomDiffusionImageHeaderReader.h.

bool mitk::DicomDiffusionImageHeaderReader::m_SingleSeries [protected]

Definition at line 103 of file mitkDicomDiffusionImageHeaderReader.h.

Referenced by DicomDiffusionImageHeaderReader().

std::vector<float> mitk::DicomDiffusionImageHeaderReader::m_sliceLocations [protected]

Definition at line 105 of file mitkDicomDiffusionImageHeaderReader.h.

bool mitk::DicomDiffusionImageHeaderReader::m_SliceOrderIS [protected]

Definition at line 102 of file mitkDicomDiffusionImageHeaderReader.h.

Referenced by DicomDiffusionImageHeaderReader().

VolumeReaderType::Pointer mitk::DicomDiffusionImageHeaderReader::m_VolumeReader [protected]

Definition at line 100 of file mitkDicomDiffusionImageHeaderReader.h.

The documentation for this class was generated from the following files:
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