#include <itkGDCMImageIO.h>

Inheritance diagram for itk::GDCMImageIO:

Collaboration diagram for itk::GDCMImageIO:

Public Types
typedef SmartPointer< Self >	Pointer
typedef GDCMImageIO	Self
typedef ImageIOBase	Superclass
Public Member Functions
virtual bool	CanReadFile (const char *)
virtual bool	CanWriteFile (const char *)
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
void	GetBodyPart (char *part)
void	GetInstitution (char *ins)
virtual IOComponentType	GetInternalComponentType () const
void	GetManufacturer (char *manu)
void	GetModality (char *modality)
void	GetModel (char *model)
virtual const char *	GetNameOfClass () const
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)
bool	GetValueFromTag (const std::string &tag, std::string &value)
virtual void	Read (void *buffer)
virtual void	ReadImageInformation ()
virtual void	SetMaxSizeLoadEntry (const long)
virtual void	Write (const void *buffer)
virtual void	WriteImageInformation ()

virtual double	GetRescaleSlope () const
virtual double	GetRescaleIntercept () const

virtual const char *	GetUIDPrefix () const
virtual void	SetUIDPrefix (const char *_arg)

virtual const char *	GetStudyInstanceUID () const
virtual const char *	GetSeriesInstanceUID () const
virtual const char *	GetFrameOfReferenceInstanceUID () const

virtual void	SetKeepOriginalUID (bool _arg)
virtual bool	GetKeepOriginalUID () const
virtual void	KeepOriginalUIDOn ()
virtual void	KeepOriginalUIDOff ()

virtual void	SetLoadSequences (const bool)
virtual bool	GetLoadSequences () const
virtual void	LoadSequencesOn ()
virtual void	LoadSequencesOff ()

virtual void	SetLoadPrivateTags (const bool)
virtual bool	GetLoadPrivateTags () const
virtual void	LoadPrivateTagsOn ()
virtual void	LoadPrivateTagsOff ()
Static Public Member Functions
static bool	GetLabelFromTag (const std::string &tag, std::string &labelId)
static Pointer	New ()

static void	SetLoadSequencesDefault (bool)
static void	LoadSequencesDefaultOn ()
static void	LoadSequencesDefaultOff ()
static bool	GetLoadSequencesDefault ()

static void	SetLoadPrivateTagsDefault (bool)
static void	LoadPrivateTagsDefaultOn ()
static void	LoadPrivateTagsDefaultOff ()
static bool	GetLoadPrivateTagsDefault ()
Protected Member Functions
	GDCMImageIO ()
void	InternalReadImageInformation (std::ifstream &file)
bool	OpenGDCMFileForReading (std::ifstream &os, const char *filename)
bool	OpenGDCMFileForWriting (std::ofstream &os, const char *filename)
void	PrintSelf (std::ostream &os, Indent indent) const
	~GDCMImageIO ()
Protected Attributes
std::string	m_FrameOfReferenceInstanceUID
bool	m_KeepOriginalUID
double	m_RescaleIntercept
double	m_RescaleSlope
std::string	m_SeriesInstanceUID
std::string	m_StudyInstanceUID
std::string	m_UIDPrefix
Private Member Functions
	GDCMImageIO (const Self &)
void	operator= (const Self &)
Private Attributes
std::string	m_BodyPart
TCompressionType	m_CompressionType
InternalHeader *	m_DICOMHeader
unsigned int	m_GlobalNumberOfDimensions
std::string	m_Institution
ImageIOBase::IOComponentType	m_InternalComponentType
std::string	m_Manufacturer
std::string	m_Modality
std::string	m_Model
std::string	m_NumberOfSeriesInStudy
std::string	m_NumberOfStudyRelatedSeries
std::string	m_PatientAge
std::string	m_PatientDOB
std::string	m_PatientID
std::string	m_PatientName
std::string	m_PatientSex
std::string	m_ScanOptions
std::string	m_StudyDate
std::string	m_StudyDescription
std::string	m_StudyID
enum	TCompressionType { JPEG = 0, JPEG2000, JPEGLS, RLE }
virtual void	SetCompressionType (const TCompressionType _arg)
virtual TCompressionType	GetCompressionType () const

Detailed Description

ImageIO class for reading and writing DICOM V3.0 and ACR/NEMA 1&2 uncompressed images This class is only an adaptor to the gdcm library (currently gdcm 1.2.x is used by default):

GDCM 1.2 can be found at: http://www.creatis.insa-lyon.fr/software/public/Gdcm/

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

Using the CMake variable: ITK_USE_SYSTEM_GDCM it is now possible to use a system installed GDCM 2.x release. GDCM 2.x is now being developped on sourceforge.net :

http://gdcm.sourceforge.net

Documentation:

Warning:

There are several restrictions to this current writer:

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:
- The SeQuence DICOM field (SQ).
- Fields from Private Dictionary
Some very long (>0xfff) binary fields are not loaded (typically 0029|0010), you need to explicitely set the maximum length of elements to load to be bigger (see Get/SetMaxSizeLoadEntry)
GDCMImageIO was not handling rescale slope/intercept properly. This is fixed as of 11/12/2007
In DICOM some field are stored directly using there binary representation. When loaded into the MetaDataDict some fields are converted to ASCII (only VR: OB/OW/OF and UN are encoded as mime64).

Wiki Examples:

All Examples

Resample a DICOM series

Definition at line 86 of file itkGDCMImageIO.h.

Member Typedef Documentation

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

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::DicomImageIO.

Definition at line 92 of file itkGDCMImageIO.h.

typedef GDCMImageIO itk::GDCMImageIO::Self

Standard class typedefs.

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::DicomImageIO.

Definition at line 90 of file itkGDCMImageIO.h.

typedef ImageIOBase itk::GDCMImageIO::Superclass

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::DicomImageIO.

Definition at line 91 of file itkGDCMImageIO.h.

Member Enumeration Documentation

enum itk::GDCMImageIO::TCompressionType

Set/Get a compression type to use.

Enumerator:

JPEG
JPEG2000
JPEGLS
RLE

Definition at line 277 of file itkGDCMImageIO.h.

Constructor & Destructor Documentation

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

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

itk::GDCMImageIO::GDCMImageIO ( const Self & ) [private]

Member Function Documentation

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::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.

virtual::itk::LightObject::Pointer itk::GDCMImageIO::CreateAnother ( void ) const [virtual]

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::LightProcessObject.

Reimplemented in itk::DicomImageIO.

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

virtual TCompressionType itk::GDCMImageIO::GetCompressionType ( ) const [virtual]

Set/Get a compression type to use.

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

Access the generated DICOM UID's.

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

virtual IOComponentType itk::GDCMImageIO::GetInternalComponentType ( ) const [virtual]

Get the original component type of the image. This differs from ComponentType which may change as a function of rescale slope and intercept.

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

Preserve the original DICOM UID of the input files

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 ( ) const [inline, virtual]

Parse any private tags in the DICOM file. Defaults to the value of LoadPrivateTagsDefault. Loading DICOM files is faster when private tags are not needed.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 242 of file itkGDCMImageIO.h.

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

Global method to define the default value for LoadPrivateTags. When instances of GDCMImageIO are created, the ivar LoadPrivateTags is initialized to the value of LoadPrivateTagsDefault. This method is useful when relying on the IO factory mechanism to load images rather than specifying a particular ImageIO object on the readers. Default is false.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 272 of file itkGDCMImageIO.h.

virtual bool itk::GDCMImageIO::GetLoadSequences ( ) const [inline, virtual]

Parse any sequences in the DICOM file. Defaults to the value of LoadSequencesDefault. Loading DICOM files is faster when sequences are not needed.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 231 of file itkGDCMImageIO.h.

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

Global method to define the default value for LoadSequences. When instances of GDCMImageIO are created, the ivar LoadSequences is initialized to the value of LoadSequencesDefault. This method is useful when relying on the IO factory mechanism to load images rather than specifying a particular ImageIO object on the readers. Default is false.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 258 of file itkGDCMImageIO.h.

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

void itk::GDCMImageIO::GetModality ( char * modality )

void itk::GDCMImageIO::GetModel ( char * model )

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

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::DicomImageIO.

void itk::GDCMImageIO::GetNumberOfSeriesInStudy ( char * series )

void itk::GDCMImageIO::GetNumberOfStudyRelatedSeries ( char * series )

void itk::GDCMImageIO::GetPatientAge ( char * age )

void itk::GDCMImageIO::GetPatientDOB ( char * dob )

void itk::GDCMImageIO::GetPatientID ( char * id )

void itk::GDCMImageIO::GetPatientName ( char * name )

Convenience methods to query patient information and scanner information. These methods are here for compatibility with the DICOMImageIO2 class and as such should not be used in any new code. They rely on properly preallocated buffer, which is not a good practice. Instead user are encourage to use directly the GetValueFromTag function

void itk::GDCMImageIO::GetPatientSex ( char * sex )

virtual double itk::GDCMImageIO::GetRescaleIntercept ( ) const [virtual]

Macro to access Rescale Slope and Rescale Intercept. Which are needed to rescale properly image when needed. User then need to Always check those value when access value from the DICOM header

virtual double itk::GDCMImageIO::GetRescaleSlope ( ) const [virtual]

Macro to access Rescale Slope and Rescale Intercept. Which are needed to rescale properly image when needed. User then need to Always check those value when access value from the DICOM header

void itk::GDCMImageIO::GetScanOptions ( char * options )

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

Access the generated DICOM UID's.

void itk::GDCMImageIO::GetStudyDate ( char * date )

void itk::GDCMImageIO::GetStudyDescription ( char * desc )

void itk::GDCMImageIO::GetStudyID ( char * id )

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

Access the generated DICOM UID's.

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

Macro to access the DICOM UID prefix. By default this is the ITK root id. This default can be overriden if the exam is for example part of an existing study.

bool itk::GDCMImageIO::GetValueFromTag	(	const std::string &	tag,
		std::string &	value
	)

More general method to retrieve an arbitrary DICOM value based on a DICOM Tag (eg "0123|4567"). WARNING: You need to use the lower case for hex 0x[a-f], for instance: "0020|000d" instead of "0020|000D" (the latter won't work)

void itk::GDCMImageIO::InternalReadImageInformation ( std::ifstream & file ) [protected]

virtual void itk::GDCMImageIO::KeepOriginalUIDOff ( ) [virtual]

Preserve the original DICOM UID of the input files

virtual void itk::GDCMImageIO::KeepOriginalUIDOn ( ) [virtual]

Preserve the original DICOM UID of the input files

static void itk::GDCMImageIO::LoadPrivateTagsDefaultOff ( ) [inline, static]

Global method to define the default value for LoadPrivateTags. When instances of GDCMImageIO are created, the ivar LoadPrivateTags is initialized to the value of LoadPrivateTagsDefault. This method is useful when relying on the IO factory mechanism to load images rather than specifying a particular ImageIO object on the readers. Default is false.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 271 of file itkGDCMImageIO.h.

static void itk::GDCMImageIO::LoadPrivateTagsDefaultOn ( ) [inline, static]

Global method to define the default value for LoadPrivateTags. When instances of GDCMImageIO are created, the ivar LoadPrivateTags is initialized to the value of LoadPrivateTagsDefault. This method is useful when relying on the IO factory mechanism to load images rather than specifying a particular ImageIO object on the readers. Default is false.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 270 of file itkGDCMImageIO.h.

virtual void itk::GDCMImageIO::LoadPrivateTagsOff ( ) [inline, virtual]

Parse any private tags in the DICOM file. Defaults to the value of LoadPrivateTagsDefault. Loading DICOM files is faster when private tags are not needed.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 244 of file itkGDCMImageIO.h.

virtual void itk::GDCMImageIO::LoadPrivateTagsOn ( ) [inline, virtual]

Parse any private tags in the DICOM file. Defaults to the value of LoadPrivateTagsDefault. Loading DICOM files is faster when private tags are not needed.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 243 of file itkGDCMImageIO.h.

static void itk::GDCMImageIO::LoadSequencesDefaultOff ( ) [inline, static]

Global method to define the default value for LoadSequences. When instances of GDCMImageIO are created, the ivar LoadSequences is initialized to the value of LoadSequencesDefault. This method is useful when relying on the IO factory mechanism to load images rather than specifying a particular ImageIO object on the readers. Default is false.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 257 of file itkGDCMImageIO.h.

static void itk::GDCMImageIO::LoadSequencesDefaultOn ( ) [inline, static]

Global method to define the default value for LoadSequences. When instances of GDCMImageIO are created, the ivar LoadSequences is initialized to the value of LoadSequencesDefault. This method is useful when relying on the IO factory mechanism to load images rather than specifying a particular ImageIO object on the readers. Default is false.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 256 of file itkGDCMImageIO.h.

virtual void itk::GDCMImageIO::LoadSequencesOff ( ) [inline, virtual]

Parse any sequences in the DICOM file. Defaults to the value of LoadSequencesDefault. Loading DICOM files is faster when sequences are not needed.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 233 of file itkGDCMImageIO.h.

virtual void itk::GDCMImageIO::LoadSequencesOn ( ) [inline, virtual]

Parse any sequences in the DICOM file. Defaults to the value of LoadSequencesDefault. Loading DICOM files is faster when sequences are not needed.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 232 of file itkGDCMImageIO.h.

static Pointer itk::GDCMImageIO::New ( ) [static]

Method for creation through the object factory.

Reimplemented from itk::LightProcessObject.

Reimplemented in itk::DicomImageIO.

bool itk::GDCMImageIO::OpenGDCMFileForReading	(	std::ifstream &	os,
		const char *	filename
	)		`[protected]`

bool itk::GDCMImageIO::OpenGDCMFileForWriting	(	std::ofstream &	os,
		const char *	filename
	)		`[protected]`

void itk::GDCMImageIO::operator= ( const Self & ) [private]

This method causes the filter to generate its output.

Reimplemented from itk::ImageIOBase.

Reimplemented in itk::DicomImageIO.

void itk::GDCMImageIO::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const `[protected, virtual]`

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::ImageIOBase.

virtual void itk::GDCMImageIO::Read ( void * buffer ) [virtual]

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::GDCMImageIO::ReadImageInformation ( ) [virtual]

Set the spacing and dimesion information for the current filename.

Implements itk::ImageIOBase.

virtual void itk::GDCMImageIO::SetCompressionType ( const TCompressionType _arg ) [virtual]

Set/Get a compression type to use.

virtual void itk::GDCMImageIO::SetKeepOriginalUID ( bool _arg ) [virtual]

Preserve the original DICOM UID of the input files

virtual void itk::GDCMImageIO::SetLoadPrivateTags ( const bool ) [inline, virtual]

Parse any private tags in the DICOM file. Defaults to the value of LoadPrivateTagsDefault. Loading DICOM files is faster when private tags are not needed.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 241 of file itkGDCMImageIO.h.

static void itk::GDCMImageIO::SetLoadPrivateTagsDefault ( bool ) [inline, static]

Global method to define the default value for LoadPrivateTags. When instances of GDCMImageIO are created, the ivar LoadPrivateTags is initialized to the value of LoadPrivateTagsDefault. This method is useful when relying on the IO factory mechanism to load images rather than specifying a particular ImageIO object on the readers. Default is false.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 269 of file itkGDCMImageIO.h.

virtual void itk::GDCMImageIO::SetLoadSequences ( const bool ) [inline, virtual]

Parse any sequences in the DICOM file. Defaults to the value of LoadSequencesDefault. Loading DICOM files is faster when sequences are not needed.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 230 of file itkGDCMImageIO.h.

static void itk::GDCMImageIO::SetLoadSequencesDefault ( bool ) [inline, static]

Global method to define the default value for LoadSequences. When instances of GDCMImageIO are created, the ivar LoadSequences is initialized to the value of LoadSequencesDefault. This method is useful when relying on the IO factory mechanism to load images rather than specifying a particular ImageIO object on the readers. Default is false.

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 255 of file itkGDCMImageIO.h.

virtual void itk::GDCMImageIO::SetMaxSizeLoadEntry ( const long ) [inline, virtual]

A DICOM file can contains multiple binary stream that can be very long For example an Overlay on the image. Most of the time user do not want to load this binary structure in memory since it can consume lot of memory. Therefore any field that is bigger than the default value 0xfff is discarded and just seek'd This method allow advanced user to force the reading of such field

Warning:: this is a GDCM 1.x only option, no effect on GDCM 2.x

Definition at line 223 of file itkGDCMImageIO.h.

virtual void itk::GDCMImageIO::SetUIDPrefix ( const char * _arg ) [virtual]

Macro to access the DICOM UID prefix. By default this is the ITK root id. This default can be overriden if the exam is for example part of an existing study.

virtual void itk::GDCMImageIO::Write ( const void * buffer ) [virtual]

Writes the data to disk from the memory buffer provided. Make sure that the IORegion has been set properly.

Implements itk::ImageIOBase.

virtual void itk::GDCMImageIO::WriteImageInformation ( ) [virtual]

Writes the spacing and dimentions of the image. Assumes SetFileName has been called with a valid file name.

Implements itk::ImageIOBase.