#include <mitkNrrdDiffusionImageReader.h>

Inheritance diagram for mitk::NrrdDiffusionImageReader< TPixelType >:

Collaboration diagram for mitk::NrrdDiffusionImageReader< TPixelType >:

Public Types
typedef mitk::DiffusionImage < TPixelType >	OutputType
typedef itk::VectorImage < TPixelType, 3 >	ImageType
typedef DiffusionImageSource < TPixelType >	DiffVolSourceType
typedef vnl_vector_fixed < double, 3 >	GradientDirectionType
typedef itk::VectorContainer < unsigned int, GradientDirectionType >	GradientDirectionContainerType
typedef NrrdDiffusionImageReader	Self
typedef DiffVolSourceType	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer < const Self >	ConstPointer
Public Member Functions
virtual const char *	GetClassName () const
const char *	GetFileName () const
	Get the specified the file to load.
void	SetFileName (const char *aFileName)
	Specify the file to load.
const char *	GetFilePrefix () const
	Get the specified file prefix for the file(s) to load.
void	SetFilePrefix (const char *aFilePrefix)
	Specify file prefix for the file(s) to load.
const char *	GetFilePattern () const
	Get the specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.
void	SetFilePattern (const char *aFilePattern)
	Specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.
Static Public Member Functions
static Pointer	New ()
	Method for creation through the object factory.
static bool	CanReadFile (const std::string filename, const std::string filePrefix, const std::string filePattern)
Protected Member Functions
virtual void	GenerateData ()
virtual void	GenerateOutputInformation ()
Protected Attributes
std::string	m_FileName
std::string	m_FilePrefix
std::string	m_FilePattern
OutputType::Pointer	m_OutputCache
itk::TimeStamp	m_CacheTime
GradientDirectionContainerType::Pointer	m_DiffusionVectors
float	m_B_Value

Detailed Description

template<class TPixelType>
class mitk::NrrdDiffusionImageReader< TPixelType >

Definition at line 35 of file mitkNrrdDiffusionImageReader.h.

Member Typedef Documentation

template<class TPixelType >

typedef itk::SmartPointer<const Self> mitk::NrrdDiffusionImageReader< TPixelType >::ConstPointer

Reimplemented from mitk::DiffusionImageSource< TPixelType >.

Definition at line 46 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

typedef DiffusionImageSource<TPixelType> mitk::NrrdDiffusionImageReader< TPixelType >::DiffVolSourceType

Definition at line 41 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

typedef itk::VectorContainer< unsigned int, GradientDirectionType > mitk::NrrdDiffusionImageReader< TPixelType >::GradientDirectionContainerType

Definition at line 44 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

typedef vnl_vector_fixed< double, 3 > mitk::NrrdDiffusionImageReader< TPixelType >::GradientDirectionType

Definition at line 42 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

typedef itk::VectorImage<TPixelType,3> mitk::NrrdDiffusionImageReader< TPixelType >::ImageType

Definition at line 40 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

typedef mitk::DiffusionImage<TPixelType> mitk::NrrdDiffusionImageReader< TPixelType >::OutputType

Reimplemented from mitk::DiffusionImageSource< TPixelType >.

Definition at line 39 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

typedef itk::SmartPointer<Self> mitk::NrrdDiffusionImageReader< TPixelType >::Pointer

Reimplemented from mitk::DiffusionImageSource< TPixelType >.

Definition at line 46 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

typedef NrrdDiffusionImageReader mitk::NrrdDiffusionImageReader< TPixelType >::Self

Reimplemented from mitk::DiffusionImageSource< TPixelType >.

Definition at line 46 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

typedef DiffVolSourceType mitk::NrrdDiffusionImageReader< TPixelType >::Superclass

Reimplemented from mitk::DiffusionImageSource< TPixelType >.

Definition at line 46 of file mitkNrrdDiffusionImageReader.h.

Member Function Documentation

template<class TPixelType >

bool mitk::NrrdDiffusionImageReader< TPixelType >::CanReadFile	(	const std::string	filename,
		const std::string	filePrefix,
		const std::string	filePattern
	)		`[static]`

Definition at line 201 of file mitkNrrdDiffusionImageReader.cpp.

  {
    // First check the extension
    if(  filename == "" )
    {
      return false;
    }
    std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
    ext = itksys::SystemTools::LowerCase(ext);

    if (ext == ".hdwi" || ext == ".dwi")
    {
      itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();

      typedef itk::ImageFileReader<ImageType> FileReaderType;
      typename FileReaderType::Pointer reader = FileReaderType::New();
      reader->SetImageIO(io);
      reader->SetFileName(filename);
      reader->Update();
      typename ImageType::Pointer img = reader->GetOutput();
      itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();    
      std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
      std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
      std::string metaString;

      for (; itKey != imgMetaKeys.end(); itKey ++)
      {
        itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
        if (itKey->find("modality") != std::string::npos)
        {
          if (metaString.find("DWMRI") != std::string::npos) 
          {
            return true;
          }
        }
      }
    }
    return false;
  }

template<class TPixelType >

void mitk::NrrdDiffusionImageReader< TPixelType >::GenerateData ( ) [protected, virtual]

Does the real work.

Reimplemented from mitk::ImageSource.

Definition at line 32 of file mitkNrrdDiffusionImageReader.cpp.

  {

    // Since everything is completely read in GenerateOutputInformation() it is stored
    // in a cache variable. A timestamp is associated.
    // If the timestamp of the cache variable is newer than the MTime, we only need to
    // assign the cache variable to the DataObject.
    // Otherwise, the tree must be read again from the file and OuputInformation must 
    // be updated!
    if ( ( ! m_OutputCache ) || ( this->GetMTime( ) > m_CacheTime.GetMTime( ) ) )
    {
      this->GenerateOutputInformation();
      itkWarningMacro("Cache regenerated!");    
    }

    if (!m_OutputCache)
    {
      itkWarningMacro("Tree cache is empty!");    
    }

    static_cast<OutputType*>(this->GetOutput())
      ->SetVectorImage(m_OutputCache->GetVectorImage());
    static_cast<OutputType*>(this->GetOutput())
      ->SetB_Value(m_OutputCache->GetB_Value());
    static_cast<OutputType*>(this->GetOutput())
      ->SetDirections(m_OutputCache->GetDirections());
    static_cast<OutputType*>(this->GetOutput())
      ->InitializeFromVectorImage();
  }

template<class TPixelType >

void mitk::NrrdDiffusionImageReader< TPixelType >::GenerateOutputInformation ( void ) [protected, virtual]

Definition at line 63 of file mitkNrrdDiffusionImageReader.cpp.

  {
    typename OutputType::Pointer outputForCache = OutputType::New();
    if ( m_FileName == "") 
    {
      throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename to be read is empty!");
    }
    else
    {
      try
      {
        itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
        typedef itk::ImageFileReader<ImageType> FileReaderType;
        typename FileReaderType::Pointer reader = FileReaderType::New();
        reader->SetImageIO(io);
        reader->SetFileName(this->m_FileName);
        reader->Update();

        typename ImageType::Pointer img = reader->GetOutput();

        itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();    
        std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
        std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
        std::string metaString;

        GradientDirectionType vect3d;
        m_DiffusionVectors = GradientDirectionContainerType::New();

        int numberOfImages = 0;
        int numberOfGradientImages = 0;
        bool readb0 = false;

        for (; itKey != imgMetaKeys.end(); itKey ++)
        {
          double x,y,z;

          itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
          if (itKey->find("DWMRI_gradient") != std::string::npos)
          { 
            std::cout << *itKey << " ---> " << metaString << std::endl;      
            sscanf(metaString.c_str(), "%lf %lf %lf\n", &x, &y, &z);
            vect3d[0] = x; vect3d[1] = y; vect3d[2] = z;
            m_DiffusionVectors->InsertElement( numberOfImages, vect3d );
            ++numberOfImages;
            // If the direction is 0.0, this is a reference image
            if (vect3d[0] == 0.0 &&
              vect3d[1] == 0.0 &&
              vect3d[2] == 0.0)
            {
              continue;
            }
            ++numberOfGradientImages;;
          }
          else if (itKey->find("DWMRI_b-value") != std::string::npos)
          {
            std::cout << *itKey << " ---> " << metaString << std::endl;      
            readb0 = true;
            m_B_Value = atof(metaString.c_str());
          }
        }

        std::cout << "Number of gradient images: "
          << numberOfGradientImages
          << " and Number of reference images: "
          << numberOfImages - numberOfGradientImages
          << std::endl;

        if(!readb0)
        {
          std::cerr << "BValue not specified in header file" << std::endl;
        }

        // This call updates the output information of the associated VesselTreeData
        outputForCache->SetVectorImage(img);
        outputForCache->SetB_Value(m_B_Value);
        outputForCache->SetDirections(m_DiffusionVectors);

        // Since we have already read the tree, we can store it in a cache variable
        // so that it can be assigned to the DataObject in GenerateData();
        m_OutputCache = outputForCache;
        m_CacheTime.Modified();
      }
      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!");
      }
    }
  }

template<class TPixelType >

virtual const char* mitk::NrrdDiffusionImageReader< TPixelType >::GetClassName ( ) const [virtual]

Reimplemented from mitk::DiffusionImageSource< TPixelType >.

template<class TPixelType >

const char * mitk::NrrdDiffusionImageReader< TPixelType >::GetFileName ( ) const [virtual]

Get the specified the file to load.

Either the FileName or FilePrefix plus FilePattern are used to read.

Implements mitk::FileReader.

Definition at line 159 of file mitkNrrdDiffusionImageReader.cpp.

  {
    return m_FileName.c_str();
  }

template<class TPixelType >

const char * mitk::NrrdDiffusionImageReader< TPixelType >::GetFilePattern ( ) const [virtual]

Get the specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

Definition at line 187 of file mitkNrrdDiffusionImageReader.cpp.

  {
    return m_FilePattern.c_str();
  }

template<class TPixelType >

const char * mitk::NrrdDiffusionImageReader< TPixelType >::GetFilePrefix ( ) const [virtual]

Get the specified file prefix for the file(s) to load.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

Definition at line 173 of file mitkNrrdDiffusionImageReader.cpp.

  {
    return m_FilePrefix.c_str();
  }

template<class TPixelType >

static Pointer mitk::NrrdDiffusionImageReader< TPixelType >::New ( ) [static]

Method for creation through the object factory.

Reimplemented from mitk::DiffusionImageSource< TPixelType >.

template<class TPixelType >

void mitk::NrrdDiffusionImageReader< TPixelType >::SetFileName ( const char * aFileName ) [virtual]

Specify the file to load.

Either the FileName or FilePrefix plus FilePattern are used to read.

Implements mitk::FileReader.

Definition at line 166 of file mitkNrrdDiffusionImageReader.cpp.

  {
    m_FileName = aFileName;
  }

template<class TPixelType >

void mitk::NrrdDiffusionImageReader< TPixelType >::SetFilePattern ( const char * aFilePattern ) [virtual]

Specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

Definition at line 194 of file mitkNrrdDiffusionImageReader.cpp.

  {
    m_FilePattern = aFilePattern;
  }

template<class TPixelType >

void mitk::NrrdDiffusionImageReader< TPixelType >::SetFilePrefix ( const char * aFilePrefix ) [virtual]

Specify file prefix for the file(s) to load.

You should specify either a FileName or FilePrefix. Use FilePrefix if the data is stored in multiple files.

Implements mitk::FileReader.

Definition at line 180 of file mitkNrrdDiffusionImageReader.cpp.

  {
    m_FilePrefix = aFilePrefix;
  }

Member Data Documentation

template<class TPixelType >

float mitk::NrrdDiffusionImageReader< TPixelType >::m_B_Value [protected]

Definition at line 72 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

itk::TimeStamp mitk::NrrdDiffusionImageReader< TPixelType >::m_CacheTime [protected]

Definition at line 69 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

GradientDirectionContainerType::Pointer mitk::NrrdDiffusionImageReader< TPixelType >::m_DiffusionVectors [protected]

Definition at line 71 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

std::string mitk::NrrdDiffusionImageReader< TPixelType >::m_FileName [protected]

Definition at line 64 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

std::string mitk::NrrdDiffusionImageReader< TPixelType >::m_FilePattern [protected]

Definition at line 66 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

std::string mitk::NrrdDiffusionImageReader< TPixelType >::m_FilePrefix [protected]

Definition at line 65 of file mitkNrrdDiffusionImageReader.h.

template<class TPixelType >

OutputType::Pointer mitk::NrrdDiffusionImageReader< TPixelType >::m_OutputCache [protected]

Definition at line 68 of file mitkNrrdDiffusionImageReader.h.

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

mitk::NrrdDiffusionImageReader< TPixelType > Class Template Reference

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<class TPixelType> class mitk::NrrdDiffusionImageReader< TPixelType >

Member Typedef Documentation

Member Function Documentation

Member Data Documentation

template<class TPixelType>
class mitk::NrrdDiffusionImageReader< TPixelType >