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itk::GDCMImageIO Class Reference
[Input and Output Filters]

#include <itkGDCMImageIO.h>

Inheritance diagram for itk::GDCMImageIO:

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Collaboration diagram for itk::GDCMImageIO:

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List of all members.

Detailed Description

ImageIO class for reading and writing DICOM V3.0 and ACR/NEMA (V1.0 & V2.0) images This class is only an adaptor to the gdcm library (currently gdcm 1.2.x is used):.

http://creatis-www.insa-lyon.fr/Public/Gdcm/

CREATIS INSA - Lyon 2003-2008 http://www.creatis.insa-lyon.fr

Warning:
There are several restrictions to this current writer: * Basically you always need a DICOM as input to write a proper DICOM image file (As of 12/10/2004 this restriction is solved in GDCM CVS repository) * Eventhough during the writing process you pass in a DICOM file as input The output file may not contains ALL DICOM field from the input file. In particular:

Definition at line 58 of file itkGDCMImageIO.h.
enum  TCompressionType {
  JPEG = 0,
  JPEG2000
}
 itkGetEnumMacro (CompressionType, TCompressionType)
 itkSetEnumMacro (CompressionType, TCompressionType)

Public Types

enum  ByteOrder {
  BigEndian,
  LittleEndian,
  OrderNotApplicable
}
typedef SmartPointer< const
Self
ConstPointer
enum  FileType {
  ASCII,
  Binary,
  TypeNotApplicable
}
enum  IOComponentType {
  UNKNOWNCOMPONENTTYPE,
  UCHAR,
  CHAR,
  USHORT,
  SHORT,
  UINT,
  INT,
  ULONG,
  LONG,
  FLOAT,
  DOUBLE
}
enum  IOPixelType {
  UNKNOWNPIXELTYPE,
  SCALAR,
  RGB,
  RGBA,
  OFFSET,
  VECTOR,
  POINT,
  COVARIANTVECTOR,
  SYMMETRICSECONDRANKTENSOR,
  DIFFUSIONTENSOR3D,
  COMPLEX,
  FIXEDARRAY,
  MATRIX
}
typedef SmartPointer< SelfPointer
typedef GDCMImageIO Self
typedef std::streamoff SizeType
typedef ImageIOBase Superclass

Public Member Functions

virtual void AbortGenerateDataOff ()
virtual void AbortGenerateDataOn ()
virtual bool CanReadFile (const char *)
virtual bool CanStreamRead ()
virtual bool CanStreamWrite ()
virtual bool CanWriteFile (const char *)
virtual LightObject::Pointer CreateAnother () const
virtual void DebugOff () const
virtual void DebugOn () const
virtual void Delete ()
virtual ImageIORegion GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const
virtual const bool & GetAbortGenerateData ()
std::string GetByteOrderAsString (ByteOrder) const
CommandGetCommand (unsigned long tag)
std::string GetComponentTypeAsString (IOComponentType) const
bool GetDebug () const
std::string GetFileTypeAsString (FileType) const
SizeType GetImageSizeInBytes () const
SizeType GetImageSizeInComponents () const
SizeType GetImageSizeInPixels () const
const MetaDataDictionaryGetMetaDataDictionary (void) const
MetaDataDictionaryGetMetaDataDictionary (void)
virtual unsigned long GetMTime () const
virtual const char * GetNameOfClass () const
virtual SizeType GetPixelStride () const
std::string GetPixelTypeAsString (IOPixelType) const
virtual int GetReferenceCount () const
bool GetValueFromTag (const std::string &tag, std::string &value)
bool HasObserver (const EventObject &event) const
void InvokeEvent (const EventObject &) const
void InvokeEvent (const EventObject &)
virtual void Modified () const
void Print (std::ostream &os, Indent indent=0) const
virtual void Read (void *buffer)
virtual void ReadImageInformation ()
virtual void Register () const
void RemoveAllObservers ()
void RemoveObserver (unsigned long tag)
virtual void SetAbortGenerateData (bool _arg)
void SetDebug (bool debugFlag) const
virtual void SetMaxSizeLoadEntry (long _arg)
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual bool SetPixelTypeInfo (const std::type_info &ptype)
virtual void SetReferenceCount (int)
virtual bool SupportsDimension (unsigned long dim)
virtual void UnRegister () const
virtual void UpdateOutputData ()
void UpdateProgress (float amount)
virtual void Write (const void *buffer)
virtual void WriteImageInformation ()
unsigned long AddObserver (const EventObject &event, Command *) const
unsigned long AddObserver (const EventObject &event, Command *)
void GetBodyPart (char *part)
void GetInstitution (char *ins)
void GetManufacturer (char *manu)
void GetModality (char *modality)
void GetModel (char *model)
void GetNumberOfSeriesInStudy (char *series)
void GetNumberOfStudyRelatedSeries (char *series)
void GetPatientAge (char *age)
void GetPatientDOB (char *dob)
void GetPatientID (char *id)
void GetPatientName (char *name)
void GetPatientSex (char *sex)
void GetScanOptions (char *options)
void GetStudyDate (char *date)
void GetStudyDescription (char *desc)
void GetStudyID (char *id)
virtual const std::type_info & GetComponentTypeInfo () const
 itkGetEnumMacro (ComponentType, IOComponentType)
 itkSetEnumMacro (ComponentType, IOComponentType)
virtual unsigned int GetDimensions (unsigned int i) const
virtual void SetDimensions (unsigned int i, unsigned int dim)
virtual std::vector< double > GetDirection (unsigned int i) const
virtual void SetDirection (unsigned int i, vnl_vector< double > &direction)
virtual void SetDirection (unsigned int i, std::vector< double > &direction)
virtual const char * GetFileName () const
virtual void SetFileName (const char *_arg)
virtual const char * GetFrameOfReferenceInstanceUID () const
virtual const char * GetSeriesInstanceUID () const
virtual const char * GetStudyInstanceUID () const
virtual ImageIORegion GetIORegion () const
virtual void SetIORegion (ImageIORegion _arg)
virtual bool GetKeepOriginalUID ()
virtual void KeepOriginalUIDOff ()
virtual void KeepOriginalUIDOn ()
virtual void SetKeepOriginalUID (bool _arg)
virtual bool GetLoadPrivateTags ()
virtual void LoadPrivateTagsOff ()
virtual void LoadPrivateTagsOn ()
virtual void SetLoadPrivateTags (bool _arg)
virtual bool GetLoadSequences ()
virtual void LoadSequencesOff ()
virtual void LoadSequencesOn ()
virtual void SetLoadSequences (bool _arg)
virtual const unsigned int & GetNumberOfComponents ()
virtual void SetNumberOfComponents (unsigned int _arg)
virtual unsigned int GetNumberOfDimensions ()
void SetNumberOfDimensions (unsigned int)
virtual double GetOrigin (unsigned int i) const
virtual void SetOrigin (unsigned int i, double origin)
virtual const float & GetProgress ()
virtual double GetRescaleIntercept ()
virtual double GetRescaleSlope ()
virtual double GetSpacing (unsigned int i) const
virtual void SetSpacing (unsigned int i, double spacing)
virtual const char * GetUIDPrefix () const
virtual void SetUIDPrefix (const char *_arg)
virtual const bool & GetUseCompression ()
virtual void SetUseCompression (bool _arg)
virtual void UseCompressionOff ()
virtual void UseCompressionOn ()
virtual const bool & GetUseStreamedReading ()
virtual void SetUseStreamedReading (bool _arg)
virtual void UseStreamedReadingOff ()
virtual void UseStreamedReadingOn ()
virtual const bool & GetUseStreamedWriting ()
virtual void SetUseStreamedWriting (bool _arg)
virtual void UseStreamedWritingOff ()
virtual void UseStreamedWritingOn ()
 itkGetEnumMacro (ByteOrder, ByteOrder)
 itkSetEnumMacro (ByteOrder, ByteOrder)
void SetByteOrderToBigEndian ()
void SetByteOrderToLittleEndian ()
 itkGetEnumMacro (FileType, FileType)
 itkSetEnumMacro (FileType, FileType)
void SetFileTypeToASCII ()
void SetFileTypeToBinary ()
 itkGetEnumMacro (PixelType, IOPixelType)
 itkSetEnumMacro (PixelType, IOPixelType)
virtual void SetProgress (float _arg)

Static Public Member Functions

static void BreakOnError ()
static bool GetLabelFromTag (const std::string &tag, std::string &labelId)
static Pointer New ()
static bool GetGlobalWarningDisplay ()
static void GlobalWarningDisplayOff ()
static void GlobalWarningDisplayOn ()
static void SetGlobalWarningDisplay (bool flag)
static bool GetLoadPrivateTagsDefault ()
static void LoadPrivateTagsDefaultOff ()
static void LoadPrivateTagsDefaultOn ()
static void SetLoadPrivateTagsDefault (bool b)
static bool GetLoadSequencesDefault ()
static void LoadSequencesDefaultOff ()
static void LoadSequencesDefaultOn ()
static void SetLoadSequencesDefault (bool b)

Protected Member Functions

void ComputeStrides ()
 GDCMImageIO ()
virtual void GenerateData ()
virtual unsigned int GetComponentSize () const
SizeType GetComponentStride () const
virtual unsigned int GetPixelSize () const
SizeType GetRowStride () const
SizeType GetSliceStride () const
void InternalReadImageInformation (std::ifstream &file)
bool OpenGDCMFileForReading (std::ifstream &os, const char *filename)
bool OpenGDCMFileForWriting (std::ofstream &os, const char *filename)
bool PrintObservers (std::ostream &os, Indent indent) const
void PrintSelf (std::ostream &os, Indent indent) const
void ReadBufferAsASCII (std::istream &os, void *buffer, IOComponentType ctype, SizeType numberOfBytesToBeRead)
bool ReadBufferAsBinary (std::istream &os, void *buffer, SizeType numberOfBytesToBeRead)
virtual void Reset (const bool freeDynamic=true)
void Resize (const unsigned int numDimensions, const unsigned int *dimensions)
void WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentType ctype, SizeType numberOfBytesToWrite)
 ~GDCMImageIO ()
virtual void PrintHeader (std::ostream &os, Indent indent) const
virtual void PrintTrailer (std::ostream &os, Indent indent) const

Protected Attributes

ByteOrder m_ByteOrder
IOComponentType m_ComponentType
std::vector< unsigned int > m_Dimensions
std::vector< std::vector<
double > > 
m_Direction
std::string m_FileName
FileType m_FileType
std::string m_FrameOfReferenceInstanceUID
bool m_Initialized
ImageIORegion m_IORegion
bool m_KeepOriginalUID
long m_MaxSizeLoadEntry
unsigned int m_NumberOfComponents
unsigned int m_NumberOfDimensions
std::vector< double > m_Origin
IOPixelType m_PixelType
volatile int m_ReferenceCount
SimpleFastMutexLock m_ReferenceCountLock
double m_RescaleIntercept
double m_RescaleSlope
std::string m_SeriesInstanceUID
std::vector< double > m_Spacing
std::vector< SizeTypem_Strides
std::string m_StudyInstanceUID
std::string m_UIDPrefix
bool m_UseCompression
bool m_UseStreamedReading
bool m_UseStreamedWriting


Member Typedef Documentation

typedef SmartPointer<const Self> itk::LightProcessObject::ConstPointer [inherited]

Reimplemented from itk::Object.

Reimplemented in itk::ImageClassifierBase< TInputImage, TClassifiedImage >, itk::ImageGaussianModelEstimator< TInputImage, TMembershipFunction, TTrainingImage >, itk::ImageKmeansModelEstimator< TInputImage, TMembershipFunction >, itk::ImageModelEstimatorBase< TInputImage, TMembershipFunction >, itk::LevelSetNeighborhoodExtractor< TLevelSet >, itk::LevelSetVelocityNeighborhoodExtractor< TLevelSet, TAuxValue, VAuxDimension >, itk::MetaArrayReader, itk::MetaArrayWriter, itk::Statistics::BackPropagationLayer< TMeasurementVector, TTargetVector >, itk::Statistics::BatchSupervisedTrainingFunction< TSample, TTargetVector, ScalarType >, itk::Statistics::CompletelyConnectedWeightSet< TMeasurementVector, TTargetVector >, itk::Statistics::ErrorBackPropagationLearningFunctionBase< LayerType, TTargetVector >, itk::Statistics::ErrorBackPropagationLearningWithMomentum< LayerType, TTargetVector >, itk::Statistics::IterativeSupervisedTrainingFunction< TSample, TTargetVector, ScalarType >, itk::Statistics::LayerBase< TMeasurementVector, TTargetVector >, itk::Statistics::LearningFunctionBase< LayerType, TTargetVector >, itk::Statistics::QuickPropLearningRule< LayerType, TTargetVector >, itk::Statistics::RBFBackPropagationLearningFunction< LayerType, TTargetVector >, itk::Statistics::RBFLayer< TMeasurementVector, TTargetVector >, itk::Statistics::TrainingFunctionBase< TSample, TTargetVector, ScalarType >, itk::Statistics::WeightSetBase< TMeasurementVector, TTargetVector >, itk::Statistics::SampleClassifier< TSample >, itk::Statistics::SampleClassifierWithMask< TSample, TMaskSample >, and itk::Statistics::LearningFunctionBase< LayerType::LayerInterfaceType, TTargetVector >.

Definition at line 78 of file itkLightProcessObject.h.

typedef SmartPointer<Self> itk::GDCMImageIO::Pointer

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::DicomImageIO.

Definition at line 64 of file itkGDCMImageIO.h.

typedef GDCMImageIO itk::GDCMImageIO::Self

Standard class typedefs.

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::DicomImageIO.

Definition at line 62 of file itkGDCMImageIO.h.

typedef std::streamoff itk::ImageIOBase::SizeType [inherited]

Type for representing size of bytes, and or positions along a file

Definition at line 259 of file itkImageIOBase.h.

typedef ImageIOBase itk::GDCMImageIO::Superclass

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::DicomImageIO.

Definition at line 63 of file itkGDCMImageIO.h.


Member Enumeration Documentation

enum itk::ImageIOBase::ByteOrder [inherited]

Enums used to specify byte order; whether Big Endian or Little Endian. Some subclasses use this, some ignore it.

Enumerator:
BigEndian 
LittleEndian 
OrderNotApplicable 

Definition at line 211 of file itkImageIOBase.h.

enum itk::ImageIOBase::FileType [inherited]

Enums used to specify write style: whether binary or ASCII. Some subclasses use this, some ignore it.

Enumerator:
ASCII 
Binary 
TypeNotApplicable 

Definition at line 207 of file itkImageIOBase.h.

enum itk::ImageIOBase::IOComponentType [inherited]

Enums used to manipulate the component type. The component type refers to the actual storage class associated with either a SCALAR pixel type or elements of a compound pixel.

Enumerator:
UNKNOWNCOMPONENTTYPE 
UCHAR 
CHAR 
USHORT 
SHORT 
UINT 
INT 
ULONG 
LONG 
FLOAT 
DOUBLE 

Definition at line 91 of file itkImageIOBase.h.

enum itk::ImageIOBase::IOPixelType [inherited]

Enums used to manipulate the pixel type. The pixel type provides context for automatic data conversions (for instance, RGB to SCALAR, VECTOR to SCALAR).

Enumerator:
UNKNOWNPIXELTYPE 
SCALAR 
RGB 
RGBA 
OFFSET 
VECTOR 
POINT 
COVARIANTVECTOR 
SYMMETRICSECONDRANKTENSOR 
DIFFUSIONTENSOR3D 
COMPLEX 
FIXEDARRAY 
MATRIX 

Definition at line 83 of file itkImageIOBase.h.

enum itk::GDCMImageIO::TCompressionType

Set/Get a boolean to use the JPEG2000 compression or not.

Enumerator:
JPEG 
JPEG2000 

Definition at line 222 of file itkGDCMImageIO.h.


Constructor & Destructor Documentation

itk::GDCMImageIO::GDCMImageIO (  )  [protected]

itk::GDCMImageIO::~GDCMImageIO (  )  [protected]


Member Function Documentation

virtual void itk::LightProcessObject::AbortGenerateDataOff (  )  [virtual, inherited]

virtual void itk::LightProcessObject::AbortGenerateDataOn (  )  [virtual, inherited]

Turn on and off the AbortGenerateData flag.

unsigned long itk::Object::AddObserver ( const EventObject event,
Command  
) const [inherited]

unsigned long itk::Object::AddObserver ( const EventObject event,
Command  
) [inherited]

Allow people to add/remove/invoke observers (callbacks) to any ITK object. This is an implementation of the subject/observer design pattern. An observer is added by specifying an event to respond to and an itk::Command to execute. It returns an unsigned long tag which can be used later to remove the event or retrieve the command. The memory for the Command becomes the responsibility of this object, so don't pass the same instance of a command to two different objects

static void itk::LightObject::BreakOnError (  )  [static, inherited]

This method is called when itkExceptionMacro executes. It allows the debugger to break on error.

virtual bool itk::GDCMImageIO::CanReadFile ( const char *   )  [virtual]

Determine the file type. Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

virtual bool itk::ImageIOBase::CanStreamRead (  )  [inline, virtual, inherited]

Determine if the ImageIO can stream reading from this file. Default is false.

Reimplemented in itk::MetaImageIO.

Definition at line 283 of file itkImageIOBase.h.

virtual bool itk::ImageIOBase::CanStreamWrite (  )  [inline, virtual, inherited]

Determine if the ImageIO can stream writing to this file. Default is false.

Reimplemented in itk::MetaImageIO.

Definition at line 304 of file itkImageIOBase.h.

virtual bool itk::GDCMImageIO::CanWriteFile ( const char *   )  [virtual]

Determine the file type. Returns true if this ImageIO can write the file specified. GDCM triggers on ".dcm" and ".dicom".

Implements itk::ImageIOBase.

void itk::ImageIOBase::ComputeStrides (  )  [protected, inherited]

Calculates the different strides (distance from one thing to the next). Upon return, strides[0] = bytes to get to the next component of a pixel, strides[1] = bytes to get to the next pixel in x direction, strides[2] = bytes to get to the next row in y direction, strides[3] = bytes to get to the next slice in z direction, etc.

virtual LightObject::Pointer itk::Object::CreateAnother (  )  const [virtual, inherited]

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::LightObject.

virtual void itk::Object::DebugOff (  )  const [virtual, inherited]

Turn debugging output off.

virtual void itk::Object::DebugOn (  )  const [virtual, inherited]

Turn debugging output on.

virtual void itk::LightObject::Delete (  )  [virtual, inherited]

Delete an itk object. This method should always be used to delete an object when the new operator was used to create it. Using the C delete method will not work with reference counting.

virtual void itk::LightProcessObject::GenerateData ( void   )  [inline, protected, virtual, inherited]

This method causes the filter to generate its output.

Reimplemented in itk::ClassifierBase< TDataContainer >, itk::ImageClassifierBase< TInputImage, TClassifiedImage >, itk::ImageGaussianModelEstimator< TInputImage, TMembershipFunction, TTrainingImage >, itk::ImageKmeansModelEstimator< TInputImage, TMembershipFunction >, itk::ImageModelEstimatorBase< TInputImage, TMembershipFunction >, itk::LevelSetNeighborhoodExtractor< TLevelSet >, itk::Statistics::SampleClassifier< TSample >, itk::Statistics::SampleClassifierWithMask< TSample, TMaskSample >, itk::ClassifierBase< TInputImage >, and itk::ClassifierBase< TSample >.

Definition at line 123 of file itkLightProcessObject.h.

virtual ImageIORegion itk::ImageIOBase::GenerateStreamableReadRegionFromRequestedRegion ( const ImageIORegion requested  )  const [virtual, inherited]

Method for supporting streaming. Given a requested region, determine what could be the region that we can read from the file. This is called the streamable region, which will be smaller than the LargestPossibleRegion and greater or equal to the RequestedRegion

Reimplemented in itk::MetaImageIO, and itk::NiftiImageIO.

virtual const bool& itk::LightProcessObject::GetAbortGenerateData (  )  [virtual, inherited]

Get the AbortGenerateData flag for the process object. Process objects may handle premature termination of execution in different ways.

void itk::GDCMImageIO::GetBodyPart ( char *  part  ) 

std::string itk::ImageIOBase::GetByteOrderAsString ( ByteOrder   )  const [inherited]

Convenience method returns the ByteOrder as a string. This can be used for writing output files.

Command* itk::Object::GetCommand ( unsigned long  tag  )  [inherited]

Get the command associated with the given tag. NOTE: This returns a pointer to a Command, but it is safe to asign this to a Command::Pointer. Since Command inherits from LightObject, at this point in the code, only a pointer or a reference to the Command can be used.

virtual unsigned int itk::ImageIOBase::GetComponentSize (  )  const [protected, virtual, inherited]

Compute the size (in bytes) of the components of a pixel. For example, and RGB pixel of unsigned char would have a component size of 1 byte. This method can be invoked only after the component type is set.

Reimplemented in itk::IPLCommonImageIO.

SizeType itk::ImageIOBase::GetComponentStride (  )  const [protected, inherited]

Convenient method for accessing number of bytes to get to the next pixel component. Returns m_Strides[0].

std::string itk::ImageIOBase::GetComponentTypeAsString ( IOComponentType   )  const [inherited]

Convenience method returns the IOComponentType as a string. This can be used for writing output files.

virtual const std::type_info& itk::ImageIOBase::GetComponentTypeInfo (  )  const [virtual, inherited]

Reimplemented in itk::IPLCommonImageIO.

bool itk::Object::GetDebug (  )  const [inherited]

Get the value of the debug flag.

virtual unsigned int itk::ImageIOBase::GetDimensions ( unsigned int  i  )  const [inline, virtual, inherited]

Definition at line 105 of file itkImageIOBase.h.

virtual std::vector<double> itk::ImageIOBase::GetDirection ( unsigned int  i  )  const [inline, virtual, inherited]

Definition at line 131 of file itkImageIOBase.h.

virtual const char* itk::ImageIOBase::GetFileName (  )  const [virtual, inherited]

std::string itk::ImageIOBase::GetFileTypeAsString ( FileType   )  const [inherited]

Convenience method returns the FileType as a string. This can be used for writing output files.

virtual const char* itk::GDCMImageIO::GetFrameOfReferenceInstanceUID (  )  const [virtual]

static bool itk::Object::GetGlobalWarningDisplay (  )  [static, inherited]

SizeType itk::ImageIOBase::GetImageSizeInBytes (  )  const [inherited]

Return the number of bytes in the image.

SizeType itk::ImageIOBase::GetImageSizeInComponents (  )  const [inherited]

Return the number of pixels times the number of components in the image.

SizeType itk::ImageIOBase::GetImageSizeInPixels (  )  const [inherited]

Return the number of pixels in the image.

void itk::GDCMImageIO::GetInstitution ( char *  ins  ) 

virtual ImageIORegion itk::ImageIOBase::GetIORegion (  )  const [virtual, inherited]

virtual bool itk::GDCMImageIO::GetKeepOriginalUID (  )  [virtual]

static bool itk::GDCMImageIO::GetLabelFromTag ( const std::string &  tag,
std::string &  labelId 
) [static]

Method for consulting the DICOM dictionary and recovering the text description of a field using its numeric tag represented as a string. If the tagkey is not found in the dictionary then this static method return false and the value "Unknown " in the labelId. If the tagkey is found then this static method returns true and the actual string descriptor of the tagkey is returned in the variable labelId.

virtual bool itk::GDCMImageIO::GetLoadPrivateTags (  )  [virtual]

static bool itk::GDCMImageIO::GetLoadPrivateTagsDefault (  )  [inline, static]

Definition at line 217 of file itkGDCMImageIO.h.

virtual bool itk::GDCMImageIO::GetLoadSequences (  )  [virtual]

static bool itk::GDCMImageIO::GetLoadSequencesDefault (  )  [inline, static]

Definition at line 201 of file itkGDCMImageIO.h.

void itk::GDCMImageIO::GetManufacturer ( char *  manu  ) 

const MetaDataDictionary& itk::Object::GetMetaDataDictionary ( void   )  const [inherited]

Returns: