Reader to read raw image files. More...

#include <mitkRawImageFileReader.h>

Inheritance diagram for mitk::RawImageFileReader:

Collaboration diagram for mitk::RawImageFileReader:

Public Types
enum	IOPixelType { UCHAR, SCHAR, USHORT, SSHORT, UINT, SINT, FLOAT, DOUBLE }
enum	EndianityType { LITTLE, BIG }
typedef RawImageFileReader	Self
typedef FileReader	Superclass
typedef itk::SmartPointer< Self >	Pointer
typedef itk::SmartPointer < const Self >	ConstPointer
Public Member Functions
virtual const char *	GetClassName () const
virtual void	SetFileName (std::string _arg)
virtual void	SetFileName (const char *_arg)
	Specify the file to load.
virtual std::string	GetFileName ()
virtual const char *	GetFileName () const
	Get the specified the file to load.
virtual void	SetFilePrefix (std::string _arg)
virtual void	SetFilePrefix (const char *_arg)
	Specify file prefix for the file(s) to load.
virtual std::string	GetFilePrefix ()
virtual const char *	GetFilePrefix () const
	Get the specified file prefix for the file(s) to load.
virtual void	SetFilePattern (std::string _arg)
virtual void	SetFilePattern (const char *_arg)
	Specified file pattern for the file(s) to load. The sprintf format used to build filename from FilePrefix and number.
virtual std::string	GetFilePattern ()
virtual 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.
virtual void	SetPixelType (IOPixelType _arg)
virtual void	SetEndianity (EndianityType _arg)
virtual void	SetDimensionality (int _arg)
virtual int	GetDimensionality ()
void	SetDimensions (unsigned int i, unsigned int dim)
unsigned int	GetDimensions (unsigned int i) const
Static Public Member Functions
static Pointer	New ()
static bool	CanReadFile (const std::string filename, const std::string filePrefix, const std::string filePattern)
Protected Member Functions
	RawImageFileReader ()
	~RawImageFileReader ()
virtual void	GenerateData ()
	A version of GenerateData() specific for image processing filters.
template<typename TPixel , unsigned int VImageDimensions>
void	TypedGenerateData ()
Protected Attributes
std::string	m_FileName
std::string	m_FilePrefix
std::string	m_FilePattern
IOPixelType	m_PixelType
int	m_Dimensionality
EndianityType	m_Endianity
itk::Vector< int, 3 >	m_Dimensions

Detailed Description

Reader to read raw image files.

The user must set the dimensionality, the dimensions and the pixel type. If they are incorrect, the image will not be opened or the visualization will be incorrect.

Definition at line 33 of file mitkRawImageFileReader.h.

Member Typedef Documentation

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

Definition at line 36 of file mitkRawImageFileReader.h.

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

Definition at line 36 of file mitkRawImageFileReader.h.

typedef RawImageFileReader mitk::RawImageFileReader::Self

Definition at line 36 of file mitkRawImageFileReader.h.

typedef FileReader mitk::RawImageFileReader::Superclass

Definition at line 36 of file mitkRawImageFileReader.h.

Member Enumeration Documentation

enum mitk::RawImageFileReader::EndianityType

Endianity of bits.

Enumerator:

LITTLE
BIG

Definition at line 61 of file mitkRawImageFileReader.h.

{LITTLE, BIG} EndianityType;

enum mitk::RawImageFileReader::IOPixelType

Supported pixel types.

Enumerator:

UCHAR
SCHAR
USHORT
SSHORT
UINT
SINT
FLOAT
DOUBLE

Definition at line 57 of file mitkRawImageFileReader.h.

{UCHAR,SCHAR,USHORT,SSHORT, UINT, SINT, FLOAT, DOUBLE} IOPixelType;

Constructor & Destructor Documentation

mitk::RawImageFileReader::RawImageFileReader ( ) [protected]

Definition at line 26 of file mitkRawImageFileReader.cpp.

    : m_FileName(""), m_FilePrefix(""), m_FilePattern("")
{
}

mitk::RawImageFileReader::~RawImageFileReader ( ) [protected]

Definition at line 31 of file mitkRawImageFileReader.cpp.

{
}

Member Function Documentation

bool mitk::RawImageFileReader::CanReadFile	(	const std::string	filename,
		const std::string	filePrefix,
		const std::string	filePattern
	)		`[static]`

Definition at line 51 of file mitkRawImageFileReader.cpp.

{
  // First check the extension
  if(  filename == "" )
    return false;

  // check if image is serie
  if( filePattern != "" && filePrefix != "" )
    return false;

  return true;
}

void mitk::RawImageFileReader::GenerateData ( ) [protected, virtual]

A version of GenerateData() specific for image processing filters.

This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See also:: ThreadedGenerateData()

Reimplemented from mitk::ImageSource.

Definition at line 64 of file mitkRawImageFileReader.cpp.

References MITK_INFO.

{
  mitk::Image::Pointer output = this->GetOutput();
  
  if (this->GetOutput()==NULL)
  {
    MITK_INFO << "Error" << std::endl;
  }

  // Check to see if we can read the file given the name or prefix
  if ( m_FileName == "" )
  {
    itkWarningMacro( << "File Type not supported!" );
    return ;
  }

  // check file dimensionality and pixel type and perform reading according to it
  if (m_Dimensionality == 2)
  {
         if (m_PixelType == SCHAR) TypedGenerateData<signed char, 2 >();
    else if (m_PixelType == UCHAR) TypedGenerateData<unsigned char, 2 >();
    else if (m_PixelType == SSHORT) TypedGenerateData<signed short int, 2 >();
    else if (m_PixelType == USHORT) TypedGenerateData<unsigned short int, 2 >();
    else if (m_PixelType == UINT)   TypedGenerateData<unsigned int, 2 >();
    else if (m_PixelType == SINT)   TypedGenerateData<signed int, 2 >();
    else if (m_PixelType == FLOAT)  TypedGenerateData<float, 2 >();
    else if (m_PixelType == DOUBLE) TypedGenerateData<double, 2 >();
    else
    {
      MITK_INFO << "Error while reading raw file: Dimensionality or pixel type not supported or not properly set" << std::endl;
      return;
    }
   }
  else if (m_Dimensionality==3)
  {
         if (m_PixelType == SCHAR) TypedGenerateData<signed char, 3 >();
    else if (m_PixelType == UCHAR) TypedGenerateData<unsigned char, 3 >();
    else if (m_PixelType == SSHORT) TypedGenerateData<signed short int, 3 >();
    else if (m_PixelType == USHORT) TypedGenerateData<unsigned short int, 3 >();
    else if (m_PixelType == UINT)   TypedGenerateData<unsigned int, 3 >();
    else if (m_PixelType == SINT)   TypedGenerateData<signed int, 3 >();
    else if (m_PixelType == FLOAT)  TypedGenerateData<float, 3 >();
    else if (m_PixelType == DOUBLE) TypedGenerateData<double, 3 >();
    else
    {
      MITK_INFO << "Error while reading raw file: Dimensionality or pixel type not supported or not properly set" << std::endl;
      return;
    }
  }  
  else
  {
    MITK_INFO << "Error while reading raw file: Dimensionality not supported" << std::endl;
    return;
      
  }   
      
  MITK_INFO << "...reading raw finished!" << std::endl;
}

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

virtual int mitk::RawImageFileReader::GetDimensionality ( ) [virtual]

unsigned int mitk::RawImageFileReader::GetDimensions ( unsigned int i ) const

Definition at line 44 of file mitkRawImageFileReader.cpp.

{
  if ( i > 2 ) return 0;

  return m_Dimensions[i];
}

virtual std::string mitk::RawImageFileReader::GetFileName ( ) [virtual]

virtual const char* mitk::RawImageFileReader::GetFileName ( ) const [virtual]

Get the specified the file to load.

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

Implements mitk::FileReader.

virtual std::string mitk::RawImageFileReader::GetFilePattern ( ) [virtual]

virtual const char* mitk::RawImageFileReader::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.

virtual std::string mitk::RawImageFileReader::GetFilePrefix ( ) [virtual]

virtual const char* mitk::RawImageFileReader::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.

static Pointer mitk::RawImageFileReader::New ( ) [static]

Method for creation through the object factory.

Reimplemented from mitk::ImageSource.

Referenced by mitkRawImageFileReaderTest().

virtual void mitk::RawImageFileReader::SetDimensionality ( int _arg ) [virtual]

void mitk::RawImageFileReader::SetDimensions	(	unsigned int	i,
		unsigned int	dim
	)

Image dimensions must be set one by one, starting from dimension 0.

Definition at line 35 of file mitkRawImageFileReader.cpp.

{ 
  if ( i > 2 ) return;

  this->Modified();               // TODO: this order (first modified, then set the variable) is intended??
  m_Dimensions[i] = dim;
}

virtual void mitk::RawImageFileReader::SetEndianity ( EndianityType _arg ) [virtual]

virtual void mitk::RawImageFileReader::SetFileName ( const char * aFileName ) [virtual]

Specify the file to load.

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

Implements mitk::FileReader.

virtual void mitk::RawImageFileReader::SetFileName ( std::string _arg ) [virtual]

virtual void mitk::RawImageFileReader::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.

virtual void mitk::RawImageFileReader::SetFilePattern ( std::string _arg ) [virtual]

virtual void mitk::RawImageFileReader::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.

virtual void mitk::RawImageFileReader::SetFilePrefix ( std::string _arg ) [virtual]

virtual void mitk::RawImageFileReader::SetPixelType ( IOPixelType _arg ) [virtual]

template<typename TPixel , unsigned int VImageDimensions>

void mitk::RawImageFileReader::TypedGenerateData ( ) [protected]

Definition at line 124 of file mitkRawImageFileReader.cpp.

References mitk::CastToMitkImage(), MITK_ERROR, MITK_INFO, and mitk::Image::New().

{
  mitk::Image::Pointer output = this->GetOutput();
  
  if (this->GetOutput()==NULL)
  {
    MITK_INFO << "Error" << std::endl;
  }
  
  MITK_INFO << "loading " << m_FileName << " via itk::ImageIOFactory... " << std::endl;

  // Check to see if we can read the file given the name or prefix
  if ( m_FileName == "" )
  {
    itkWarningMacro( << "File Type not supported!" );
    return ;
  }

  typedef itk::Image< TPixel, VImageDimensions > ImageType;
  typedef itk::ImageFileReader< ImageType > ReaderType;
  typedef itk::RawImageIO< TPixel, VImageDimensions >  IOType;
  
  typename ReaderType::Pointer reader = ReaderType::New();
  typename IOType::Pointer io = IOType::New();

  io->SetFileDimensionality(VImageDimensions);
  
  for (unsigned short int dim = 0; dim < VImageDimensions; ++dim)
  { 
    io->SetDimensions(dim, m_Dimensions[dim] );
  }

  if (m_Endianity == LITTLE)
  {
    io->SetByteOrderToLittleEndian();
  }
  else if (m_Endianity == BIG)
  {
    io->SetByteOrderToBigEndian();
  }
  else
  {
    MITK_INFO << "Warning: endianity not properly set. Resulting image might be incorrect";
  }

  reader->SetImageIO( io );
  reader->SetFileName(m_FileName.c_str());

  try
  {
    reader->Update();
  }
  catch( itk::ExceptionObject & err )
  {
    MITK_ERROR <<"An error occurred during the raw image reading process: ";
    MITK_INFO << err << std::endl;
  }

  mitk::Image::Pointer image = mitk::Image::New();
  mitk::CastToMitkImage(reader->GetOutput(), image);
  output->Initialize( image );
  output->SetVolume(  reader->GetOutput()->GetBufferPointer());
}