GDCM_NAME_SPACE::File Class Reference

DICOM elements and their corresponding values (and additionaly the corresponding DICOM dictionary entry) of the header of a DICOM file. More...

#include <gdcmFile.h>

Inheritance diagram for GDCM_NAME_SPACE::File:

[legend]Collaboration diagram for GDCM_NAME_SPACE::File:

[legend]List of all members.

Public Types
typedef std::list< DicomElement >	ListElements
Public Member Functions
bool	Load ()
	Loader.
bool	IsReadable ()
	This predicate, based on hopefully reasonable heuristics, decides whether or not the current File was properly parsed and contains the mandatory information for being considered as a well formed and usable Dicom/Acr File.
void	SetFourthDimensionLocation (uint16_t group, uint16_t elem)
int	GetImageNumber ()
	gets the info from 0020,0013 : Image Number else 0.
ModalityType	GetModality ()
	gets the info from 0008,0060 : Modality
int	GetXSize ()
	Retrieve the number of columns of image.
int	GetYSize ()
	Retrieve the number of lines of image.
int	GetZSize ()
	Retrieve the number of planes of volume or the number of frames of a multiframe.
int	GetTSize ()
	Retrieve the -unnormalized- number of 'times' of '4D image'. User has to tell gdcm the location of this '4th Dimension component' using SetFourthDimensionLocation() method before.
bool	GetSpacing (float &xspacing, float &yspacing, float &zspacing)
float	GetXSpacing ()
	gets the info from 0018,1164 : ImagerPixelSpacing then 0028,0030 : Pixel Spacing else 1.0
float	GetYSpacing ()
	gets the info from 0018,1164 : ImagerPixelSpacing then from 0028,0030 : Pixel Spacing else 1.0
float	GetZSpacing ()
	gets the info from 0018,0088 : Space Between Slices else from 0018,0050 : Slice Thickness else 1.0
float	GetXOrigin ()
	gets the info from 0020,0032 : Image Position Patient else from 0020,0030 : Image Position (RET) else 0.
float	GetYOrigin ()
	gets the info from 0020,0032 : Image Position Patient else from 0020,0030 : Image Position (RET) else 0.
float	GetZOrigin ()
	gets the info from 0020,0032 : Image Position Patient else from 0020,0030 : Image Position (RET) else from 0020,1041 : Slice Location else from 0020,0050 : Location else 0.
float	GetXCosineOnX ()
	gets the cosine of image X axis, against patient X axis (Sorry, but Python needs it :-( )
float	GetXCosineOnY ()
	gets the cosine of image X axis, against patient Y axis (Sorry, but Python needs it :-( )
float	GetXCosineOnZ ()
	gets the cosine of image X axis, against patient Z axis (Sorry, but Python needs it :-( )
float	GetYCosineOnX ()
	gets the cosine of image Y axis, against patient X axis (Sorry, but Python needs it :-( )
float	GetYCosineOnY ()
	gets the cosine of image Y axis, against patient Y axis (Sorry, but Python needs it :-( )
float	GetYCosineOnZ ()
	gets the cosine of image Y axis, against patient Z axis (Sorry, but Python needs it :-( )
bool	GetImageOrientationPatient (float iop[6])
	gets the info from 0020,0037 : Image Orientation Patient or from 0020 0035 : Image Orientation (RET)
bool	GetImagePositionPatient (float ipp[3])
	gets the info from 0020,0032 : Image Position Patient or from 0020 0030 : Image Position (RET)
int	GetBitsStored ()
	Retrieve the number of Bits Stored (actually used) (as opposed to number of Bits Allocated).
int	GetBitsAllocated ()
	Retrieve the number of Bits Allocated (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,).
int	GetHighBitPosition ()
	Retrieve the high bit position.
int	GetSamplesPerPixel ()
	Retrieve the number of Samples Per Pixel (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-).
int	GetPlanarConfiguration ()
	Retrieve the Planar Configuration for RGB images (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane).
int	GetPixelSize ()
	Return the size (in bytes) of a single pixel of data.
std::string	GetPixelType ()
	Build the Pixel Type of the image. Possible values are: 8U unsigned 8 bit, 8S signed 8 bit, 16U unsigned 16 bit, 16S signed 16 bit, 32U unsigned 32 bit, 32S signed 32 bit, FD floating double 64 bits (Not kosher DICOM, but so usefull!).
bool	IsSignedPixelData ()
	Check whether the pixels are signed (1) or UNsigned (0) data.
bool	IsMonochrome ()
	Check whether this a monochrome picture (gray levels) or not, using "Photometric Interpretation" tag (0x0028,0x0004).
bool	IsMonochrome1 ()
	Check whether this a MONOCHROME1 picture (high values = dark) or not using "Photometric Interpretation" tag (0x0028,0x0004).
bool	IsPaletteColor ()
	Check whether this a "PALETTE COLOR" picture or not by accessing the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
bool	IsYBRFull ()
	Check whether this a "YBR_FULL" color picture or not by accessing the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
bool	HasLUT ()
	tells us if LUT are used
int	GetLUTNbits ()
	gets the info from 0028,1101 : Lookup Table Desc-Red else 0
bool	GetRescaleSlopeIntercept (double &slope, double &intercept)
double	GetRescaleIntercept ()
	gets the info from 0028,1052 : Rescale Intercept
double	GetRescaleSlope ()
	gets the info from 0028,1053 : Rescale Slope
int	GetNumberOfScalarComponents ()
	This function is intended to user who doesn't want to have to manage a LUT and expects to get an RBG Pixel image (or a monochrome one, if no LUT found ...).
int	GetNumberOfScalarComponentsRaw ()
	This function is intended to user that DOESN'T want to get RGB pixels image when it's stored as a PALETTE COLOR image the (vtk) user is supposed to know how deal with LUTs -.
uint16_t	GetGrPixel ()
	Accessor to File::GrPixel.
uint16_t	GetNumPixel ()
	Accessor to File::NumPixel.
size_t	GetPixelOffset ()
	Recover the offset (from the beginning of the file) of *image* pixels (not *icone image* pixels, if any !).
size_t	GetPixelAreaLength ()
	Recover the pixel area length (in Bytes).
RLEFramesInfo *	GetRLEInfo ()
	returns the RLE info
JPEGFragmentsInfo *	GetJPEGInfo ()
	Returns the JPEG Fragments info.
void	AddAnonymizeElement (uint16_t group, uint16_t elem, std::string const &value)
	Adds the characteristics of a new element we want to anonymize.
void	ClearAnonymizeList ()
	Clears the list of elements to be anonymized.
void	AnonymizeNoLoad ()
	Overwrites in the file the values of the DicomElements held in the list.
bool	AnonymizeFile ()
	anonymize a File (remove Patient's personal info passed with AddAnonymizeElement()
bool	Write (std::string fileName, FileType filetype)
	Performs some consistency checking on various 'File related' (as opposed to 'DicomDir related') entries then writes in a file all the (Dicom Elements) included the Pixels.
Dict *	GetPubDict ()
	Get the public dictionary used.
Dict *	GetShaDict ()
	Get the shadow dictionary used.
bool	SetShaDict (Dict *dict)
	Set the shadow dictionary used.
bool	SetShaDict (DictKey const &dictName)
	Set the shadow dictionary used.
bool	IsParsable ()
	This predicate tells us whether or not the current Document was properly parsed and contains at least *one* Dicom Element (and nothing more, sorry).
bool	IsDicomV3 ()
	Predicate for dicom version 3 file.
bool	IsPapyrus ()
	Predicate for Papyrus file Dedicated to whomsoever it may concern.
FileType	GetFileType ()
	returns the File Type (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
std::string	GetTransferSyntax ()
	Accessor to the Transfer Syntax (when present) of the current document (it internally handles reading the value from disk when only parsing occured).
std::string	GetTransferSyntaxName ()
	Accesses the info from 0002,0010 : Transfer Syntax and TS.
int	GetSwapCode ()
	'Swap code' accessor (see SwapCode )
const std::string &	GetFileName () const
	Accessor to Filename.
virtual void	SetFileName (std::string const &fileName)
	Accessor to Filename.
std::ifstream *	OpenFile ()
	Tries to open the file Document::Filename and checks the preamble when existing, or if the file starts with an ACR-NEMA look-like element.
bool	CloseFile ()
	closes the file
void	WriteContent (std::ofstream *fp, FileType type)
	Writes in a file all the Entries (Dicom Elements).
void	WriteContent (std::ofstream *fp, FileType filetype, bool insideMetaElements)
	Writes the Header Entries (Dicom Elements) from the H Table.
virtual void	LoadEntryBinArea (uint16_t group, uint16_t elem)
	Loads (from disk) the element content when a string is not suitable.
virtual void	LoadEntryBinArea (DataEntry *entry)
	Loads (from disk) the element content when a string is not suitable.
void	SetMaxSizeLoadEntry (long)
	during parsing, Header Elements too long are not loaded in memory
void	AddForceLoadElement (uint16_t group, uint16_t elem)
	Adds a new element we want to load anyway.
bool	operator< (Document &document)
	Loads the element while preserving the current underlying file position indicator as opposed to LoadDocEntry that modifies it Compares two documents, according to DicomDir rules.
void	SetLoadMode (int mode)
	Sets the LoadMode as a boolean string. LD_NOSEQ, LD_NOSHADOW, LD_NOSHADOWSEQ ... (nothing more, right now) WARNING : before using NO_SHADOW, be sure *all* your files contain accurate values in the 0x0000 element (if any) of *each* Shadow Group. The parser will fail if the size is wrong !
virtual void	Print (std::ostream &os=std::cout, std::string const &indent="")
	Prints the Header Entries (Dicom Elements) from the H Table.
bool	AddEntry (DocEntry *Entry)
	add a new Dicom Element pointer to the H Table
bool	RemoveEntry (DocEntry *EntryToRemove)
	Clear the hash table from given entry AND delete the entry.
void	ClearEntry ()
	delete all entries in the ElementSet
DocEntry *	GetFirstEntry ()
	Get the first entry while visiting *the* 'zero level' DocEntrySet (DocEntries out of any Sequence).
DocEntry *	GetNextEntry ()
	Get the next entry while visiting *the* 'zero level' DocEntrySet (DocEntries out of any Sequence).
DocEntry *	GetDocEntry (uint16_t group, uint16_t elem)
	retrieves a Dicom Element using (group, element)
bool	IsEmpty ()
	Tells us if the ElementSet contains no entry.
int	IsVRCoherent (uint16_t group)
	Checks whether *all* the DataEntries of the group have all the same type for VR (ImplicitVR or ExplicitVR).
virtual void	Copy (DocEntrySet *set)
	Copies all the attributes from an other DocEntrySet.
virtual std::string	GetEntryString (uint16_t group, uint16_t elem)
	Get the "std::string representable" value of the Dicom entry.
virtual void *	GetEntryBinArea (uint16_t group, uint16_t elem)
	Gets (from Header) a 'non string' element value.
virtual int	GetEntryLength (uint16_t group, uint16_t elem)
	Searches within the DocEntrySet for the value length of a given tag..
DataEntry *	GetDataEntry (uint16_t group, uint16_t elem)
	Same as Document::GetDocEntry except it returns a result only when the corresponding entry is of type DataEntry.
SeqEntry *	GetSeqEntry (uint16_t group, uint16_t elem)
	Same as Document::GetDocEntry except it returns a result only when the corresponding entry is of type SeqEntry.
bool	SetEntryString (std::string const &content, uint16_t group, uint16_t elem)
	Accesses an existing DocEntry (i.e. a Dicom Element) through its (group, element) and modifies its content with the given value.
bool	SetEntryString (std::string const &content, DataEntry *entry)
	Accesses an existing DocEntry (i.e. a Dicom Element) and modifies its content with the given value.
bool	SetEntryBinArea (uint8_t *content, int lgth, uint16_t group, uint16_t elem)
	Accesses an existing DocEntry (i.e. a Dicom Element) through its (group, element) and modifies its content with the given value.
bool	SetEntryBinArea (uint8_t *content, int lgth, DataEntry *entry)
	Accesses an existing DataEntry (i.e. a Dicom Element) and modifies its content with the given value.
DataEntry *	InsertEntryString (std::string const &value, uint16_t group, uint16_t elem, VRKey const &vr=GDCM_VRUNKNOWN)
	Modifies the value of a given Doc Entry (Dicom Element) when it exists. Creates it with the given value when unexistant.
DataEntry *	InsertEntryBinArea (uint8_t *binArea, int lgth, uint16_t group, uint16_t elem, VRKey const &vr=GDCM_VRUNKNOWN)
	Modifies the value of a given Header Entry (Dicom Element) when it exists. Create it with the given value when unexistant. A copy of the binArea is made to be kept in the Document.
SeqEntry *	InsertSeqEntry (uint16_t group, uint16_t elem)
	Creates a new gdcm::SeqEntry and adds it to the current DocEntrySet. (remove any existing entry with same group,elem).
virtual bool	CheckIfEntryExist (uint16_t group, uint16_t elem)
	Checks if a given Dicom Element exists within the DocEntrySet.
DataEntry *	NewDataEntry (uint16_t group, uint16_t elem, VRKey const &vr=GDCM_VRUNKNOWN)
	Build a new DataEntry from all the low level arguments.
SeqEntry *	NewSeqEntry (uint16_t group, uint16_t elem)
	Build a new SeqEntry from all the low level arguments.
void	Delete ()
	Delete the object.
void	Register ()
	Register the object.
void	Unregister ()
	Unregister the object.
const unsigned long &	GetRefCount () const
	Get the reference counting.
void	SetPrintLevel (int level)
	Sets the print level for the Dicom Header Elements.
int	GetPrintLevel ()
	Gets the print level for the Dicom Entries.
Static Public Member Functions
static File *	New ()
Protected Member Functions
	File ()
	Constructor used when we want to generate dicom files from scratch.
virtual	~File ()
	Canonical destructor.
bool	MayIWrite (uint16_t group)
	Protect the Writer from writing illegal groups.
virtual void	CallStartMethod ()
	CallStartMethod.
virtual void	CallProgressMethod ()
	CallProgressMethod.
virtual void	CallEndMethod ()
	CallEndMethod.
uint16_t	ReadInt16 () throw ( FormatError )
	Reads a supposed to be 16 Bits integer (swaps it depending on processor endianness).
uint32_t	ReadInt32 () throw ( FormatError )
	Reads a supposed to be 32 Bits integer (swaps it depending on processor endianness).
void	SkipBytes (uint32_t nBytes)
	skips bytes inside the source file
int	ComputeGroup0002Length ()
	Re-computes the length of the Dicom group 0002.
DictEntry *	GetDictEntry (uint16_t group, uint16_t elem)
	Searches [both] the public [and the shadow dictionary (when they exist)] for the presence of the DictEntry with given group and element. The public dictionary has precedence on the shadow one(s), if any.
Protected Attributes
RLEFramesInfo *	RLEInfo
	Store the RLE frames info obtained during parsing of pixels.
JPEGFragmentsInfo *	JPEGInfo
	Store the JPEG fragments info obtained during parsing of pixels.
uint16_t	NumPixel
	In some cases (e.g. for some ACR-NEMA images) the Entry Element Number of the 'Pixel Element' is *not* found at 0x0010. In order to make things easier the parser shall store the proper value in NumPixel to provide a unique access facility.
uint16_t	GrPixel
	In some cases (e.g. for some ACR-NEMA images) the header entry for the group of pixels is *not* found at 0x7fe0. In order to make things easier the parser shall store the proper value in GrPixel to provide a unique access facility.
TagKey	FourthDimensionLocation
	allows user to tell gdcm in which DataElement is stored the -unnormalized- 4th Dimension
std::string	Filename
	Refering underlying filename.
int	SwapCode
	Swap code gives an information on the byte order of a supposed to be an int32, as it's read on disc (depending on the image Transfer Syntax *and* on the processor endianess) as opposed as it should in memory to be dealt as an int32. For instance : a 'Little Endian' image, read with a little endian processor will have a SwapCode= 1234 (the order is OK; nothing to do) a 'Little Endian' image, read with a big endian procesor will have a SwapCode= 4321 (the order is wrong; int32 an int16 must be swapped) note : values 2143, 4321, 3412 remain for the ACR-NEMA time, and the well known 'Bad Big Endian' and 'Bad Little Endian' codes.
bool	Group0002Parsed
	whether we already parsed group 0002 (Meta Elements)
bool	HasDCMPreamble
	whether file has a DCM Preamble
std::ifstream *	Fp
	File Pointer, opened during Document parsing.
FileType	Filetype
	ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown.
ListElements	UserAnonymizeList
	User supplied list of elements to Anonymize.
ListElements	UserForceLoadList
	User supplied list of elements to force Load.
int	LoadMode
	Bit string integer (each one considered as a boolean) Bit 0 : Skip Sequences, if possible Bit 1 : Skip Shadow Groups if possible Probabely, some more to add.
bool	IsDocumentAlreadyLoaded
	Whether the gdcm::Document is already parsed/loaded : False from the creation of the gdcm::Document untill gdcm::Document:Load().
bool	IsDocumentModified
	Whether the gdcm::Document was modified since the last Load().
float	Progress
	value of the ??? for any progress bar
bool	Abort
Dict *	RefPubDict
	Public dictionary used to parse this header.
Dict *	RefShaDict
	Optional "shadow dictionary" (private elements) used to parse this header.
uint32_t	MaxSizeLoadEntry
	Size threshold above which an element value will NOT be loaded in memory (to avoid loading the image/volume itself). By default, this upper bound is fixed to 1024 bytes (which might look reasonable when one considers the definition of the various VR contents).
uint16_t	CurrentGroup
	to allow any inner method to know current tag Group number
uint16_t	CurrentElem
	to allow any inner method to know current tag Element number
DocEntry *	PreviousDocEntry
	To be able to backtrack (Private Sequence, Implicit VR related pb).
int	PrintLevel
	Amount of printed details for each Dicom Entries : 0 : stands for the least detail level.
Static Protected Attributes
static const unsigned int	HEADER_LENGTH_TO_READ
	After opening the file, we read HEADER_LENGTH_TO_READ bytes.
static const unsigned int	MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff
	Elements whose value is longer than MAX_SIZE_LOAD_ELEMENT_VALUE are NOT loaded.
Private Member Functions
	gdcmTypeMacro (File)
bool	DoTheLoadingJob ()
	Does the Loading Job (internal use only).
void	ComputeRLEInfo ()
	Parse pixel data from disk of [multi-]fragment RLE encoding. Compute the RLE extra information and store it in RLEInfo for later pixel retrieval usage.
void	ComputeJPEGFragmentInfo ()
	Parse pixel data from disk of [multi-]fragment Jpeg encoding. Compute the jpeg extra information (fragment[s] offset[s] and length) and store it[them] in JPEGInfo for later pixel retrieval usage.
bool	ReadTag (uint16_t, uint16_t)
	Assuming the internal file pointer Document::Fp is placed at the beginning of a tag, check whether this tag is (TestGroup, TestElem).
uint32_t	ReadTagLength (uint16_t, uint16_t)
	Assuming the internal file pointer Document::Fp is placed at the beginning of a tag (TestGroup, TestElement), read the length associated to the Tag.
void	ReadEncapsulatedBasicOffsetTable ()
	When parsing the Pixel Data of an encapsulated file, read the basic offset table (when present, and BTW dump it).
Private Attributes
uint32_t *	BasicOffsetTableItemValue

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Detailed Description

DICOM elements and their corresponding values (and additionaly the corresponding DICOM dictionary entry) of the header of a DICOM file.

The typical usage of instances of class File is to classify a set of dicom files according to header information e.g. to create a file hierarchy reflecting the Patient/Study/Serie informations, or extracting a given SerieId. Accessing the content (image[s] or volume[s]) is beyond the functionality of this class and belongs to gdcm::FileHelper.

Note:

The various entries of the explicit value representation (VR) shall be managed within a dictionary which is shared by all File instances.

The File::Set*Tag* family members cannot be defined as protected due to Swig limitations for as Has_a dependency between File and FileHelper.

Definition at line 99 of file gdcmFile.h.

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Member Typedef Documentation

typedef std::list<DicomElement> GDCM_NAME_SPACE::Document::ListElements [inherited]

Definition at line 47 of file gdcmDocument.h.

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Constructor & Destructor Documentation

GDCM_NAME_SPACE::File::File (   )  [protected]

Constructor used when we want to generate dicom files from scratch. Definition at line 114 of file gdcmFile.cxx. References BasicOffsetTableItemValue, FourthDimensionLocation, GrPixel, JPEGInfo, NumPixel, and RLEInfo. : Document() { RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; GrPixel = 0x7fe0; // to avoid further troubles NumPixel = 0x0010; BasicOffsetTableItemValue = 0; FourthDimensionLocation = TagKey(0,0); }

GDCM_NAME_SPACE::File::~File (   )  [protected, virtual]

Canonical destructor. Definition at line 129 of file gdcmFile.cxx. References BasicOffsetTableItemValue, JPEGInfo, and RLEInfo. { if ( RLEInfo ) delete RLEInfo; if ( JPEGInfo ) delete JPEGInfo; delete[] BasicOffsetTableItemValue; }

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Member Function Documentation

void GDCM_NAME_SPACE::File::AddAnonymizeElement (  uint16_t  group, uint16_t  elem, std::string const &  value )

Adds the characteristics of a new element we want to anonymize. Parameters: group  Group number of the target tag. elem  Element number of the target tag. value  new value (string) to substitute with Definition at line 1793 of file gdcmFile.cxx. References GDCM_NAME_SPACE::DicomElement::Elem, GDCM_NAME_SPACE::DicomElement::Group, GDCM_NAME_SPACE::Document::UserAnonymizeList, and GDCM_NAME_SPACE::DicomElement::Value. { DicomElement el; el.Group = group; el.Elem = elem; el.Value = value; UserAnonymizeList.push_back(el); }

bool GDCM_NAME_SPACE::ElementSet::AddEntry (  DocEntry *  newEntry  )  [virtual, inherited]

add a new Dicom Element pointer to the H Table Parameters: newEntry  entry to add Implements GDCM_NAME_SPACE::DocEntrySet. Definition at line 101 of file gdcmElementSet.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntry::GetKey(), and GDCM_NAME_SPACE::ElementSet::TagHT. Referenced by GDCM_NAME_SPACE::DocEntryArchive::Push(), and GDCM_NAME_SPACE::DocEntryArchive::Restore(). { const TagKey &key = newEntry->GetKey(); if ( TagHT.count(key) == 1 ) { gdcmWarningMacro( "Key already present: " << key ); return false; } else { TagHT.insert(TagDocEntryHT::value_type(newEntry->GetKey(), newEntry)); newEntry->Register(); return true; } }

void GDCM_NAME_SPACE::Document::AddForceLoadElement (  uint16_t  group, uint16_t  elem )  [inherited]

Adds a new element we want to load anyway. Parameters: group  Group number of the target tag. elem  Element number of the target tag. Definition at line 304 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::DicomElement::Elem, GDCM_NAME_SPACE::DicomElement::Group, and GDCM_NAME_SPACE::Document::UserForceLoadList. { DicomElement el; el.Group = group; el.Elem = elem; UserForceLoadList.push_back(el); }

bool GDCM_NAME_SPACE::File::AnonymizeFile (   )

anonymize a File (remove Patient's personal info passed with AddAnonymizeElement() Note: You cannot Anonymize a DataEntry (to be fixed) Definition at line 1863 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, GDCM_NAME_SPACE::ElementSet::GetDocEntry(), GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GDCM_NAME_SPACE::DocEntrySet::SetEntryString(), and GDCM_NAME_SPACE::Document::UserAnonymizeList. { // If Anonymisation list is empty, let's perform some basic anonymization if ( UserAnonymizeList.begin() == UserAnonymizeList.end() ) { // If exist, replace by spaces SetEntryString(" ",0x0010, 0x2154); // Telephone SetEntryString(" ",0x0010, 0x1040); // Adress SetEntryString(" ",0x0010, 0x0020); // Patient ID DocEntry *patientNameHE = GetDocEntry (0x0010, 0x0010); if ( patientNameHE ) // we replace it by Study Instance UID (why not ?) { std::string studyInstanceUID = GetEntryString (0x0020, 0x000d); if ( studyInstanceUID != GDCM_UNFOUND ) { SetEntryString(studyInstanceUID, 0x0010, 0x0010); } else { SetEntryString("anonymized", 0x0010, 0x0010); } } } else { GDCM_NAME_SPACE::DocEntry *d; for (ListElements::iterator it = UserAnonymizeList.begin(); it != UserAnonymizeList.end(); ++it) { d = GetDocEntry( (*it).Group, (*it).Elem); if ( d == NULL) continue; if ( dynamic_cast<SeqEntry *>(d) ) { gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; } if ( dynamic_cast<DataEntry *>(d) ) { gdcmWarningMacro( "To 'Anonymize' a DataEntry, better use AnonymizeNoLoad (FIXME) "); continue; } else SetEntryString ((*it).Value, (*it).Group, (*it).Elem); } } // In order to make definitively impossible any further identification // remove or replace all the stuff that contains a Date //0008 0012 DA ID Instance Creation Date //0008 0020 DA ID Study Date //0008 0021 DA ID Series Date //0008 0022 DA ID Acquisition Date //0008 0023 DA ID Content Date //0008 0024 DA ID Overlay Date //0008 0025 DA ID Curve Date //0008 002a DT ID Acquisition Datetime //0018 9074 DT ACQ Frame Acquisition Datetime //0018 9151 DT ACQ Frame Reference Datetime //0018 a002 DT ACQ Contribution Date Time //0020 3403 SH REL Modified Image Date (RET) //0032 0032 DA SDY Study Verified Date //0032 0034 DA SDY Study Read Date //0032 1000 DA SDY Scheduled Study Start Date //0032 1010 DA SDY Scheduled Study Stop Date //0032 1040 DA SDY Study Arrival Date //0032 1050 DA SDY Study Completion Date //0038 001a DA VIS Scheduled Admission Date //0038 001c DA VIS Scheduled Discharge Date //0038 0020 DA VIS Admitting Date //0038 0030 DA VIS Discharge Date //0040 0002 DA PRC Scheduled Procedure Step Start Date //0040 0004 DA PRC Scheduled Procedure Step End Date //0040 0244 DA PRC Performed Procedure Step Start Date //0040 0250 DA PRC Performed Procedure Step End Date //0040 2004 DA PRC Issue Date of Imaging Service Request //0040 4005 DT PRC Scheduled Procedure Step Start Date and Time //0040 4011 DT PRC Expected Completion Date and Time //0040 a030 DT PRC Verification Date Time //0040 a032 DT PRC Observation Date Time //0040 a120 DT PRC DateTime //0040 a121 DA PRC Date //0040 a13a DT PRC Referenced Datetime //0070 0082 DA ??? Presentation Creation Date //0100 0420 DT ??? SOP Autorization Date and Time //0400 0105 DT ??? Digital Signature DateTime //2100 0040 DA PJ Creation Date //3006 0008 DA SSET Structure Set Date //3008 0024 DA ??? Treatment Control Point Date //3008 0054 DA ??? First Treatment Date //3008 0056 DA ??? Most Recent Treatment Date //3008 0162 DA ??? Safe Position Exit Date //3008 0166 DA ??? Safe Position Return Date //3008 0250 DA ??? Treatment Date //300a 0006 DA RT RT Plan Date //300a 022c DA RT Air Kerma Rate Reference Date //300e 0004 DA RT Review Date return true; }

void GDCM_NAME_SPACE::File::AnonymizeNoLoad (   )

Overwrites in the file the values of the DicomElements held in the list. Definition at line 1807 of file gdcmFile.cxx. References GDCM_NAME_SPACE::Document::Filename, gdcmWarningMacro, GDCM_NAME_SPACE::ElementSet::GetDocEntry(), and GDCM_NAME_SPACE::Document::UserAnonymizeList. { std::fstream *fp = new std::fstream(Filename.c_str(), std::ios::in | std::ios::out | std::ios::binary); GDCM_NAME_SPACE::DocEntry *d; uint32_t offset; uint32_t lgth; uint32_t valLgth = 0; std::string *spaces; for (ListElements::iterator it = UserAnonymizeList.begin(); it != UserAnonymizeList.end(); ++it) { //std::cout << "File::AnonymizeNoLoad -------" << std::hex <<(*it).Group <<"|"<< // (*it).Elem // << "[" << (*it).Value << "] "<< std::dec << std::endl; d = GetDocEntry( (*it).Group, (*it).Elem); if ( d == NULL) continue; if ( dynamic_cast<SeqEntry *>(d) ) { gdcmWarningMacro( "You cannot 'Anonymize' a SeqEntry "); continue; } valLgth = (*it).Value.size(); if (valLgth == 0) continue; offset = d->GetOffset(); lgth = d->GetLength(); //std::cout << "lgth " << lgth << " valLgth " << valLgth << std::endl; if (valLgth < lgth) { spaces = new std::string( lgth-valLgth, ' '); (*it).Value = (*it).Value + *spaces; //std::cout << "[" << (*it).Value << "] " << lgth << std::endl; delete spaces; } fp->seekp( offset, std::ios::beg ); fp->write( (*it).Value.c_str(), lgth ); } fp->close(); delete fp; }

void GDCM_NAME_SPACE::Document::CallEndMethod (   )  [protected, virtual, inherited]

CallEndMethod. Definition at line 1074 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::CMD_ENDPROGRESS, GDCM_NAME_SPACE::CommandManager::ExecuteCommand(), and GDCM_NAME_SPACE::Document::Progress. { Progress = 1.0f; CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS); }

void GDCM_NAME_SPACE::Document::CallProgressMethod (   )  [protected, virtual, inherited]

CallProgressMethod. Definition at line 1066 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::CMD_PROGRESS, and GDCM_NAME_SPACE::CommandManager::ExecuteCommand(). Referenced by GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(). { CommandManager::ExecuteCommand(this,CMD_PROGRESS); }

void GDCM_NAME_SPACE::Document::CallStartMethod (   )  [protected, virtual, inherited]

CallStartMethod. Definition at line 1056 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::Document::Abort, GDCM_NAME_SPACE::CMD_STARTPROGRESS, GDCM_NAME_SPACE::CommandManager::ExecuteCommand(), and GDCM_NAME_SPACE::Document::Progress. Referenced by GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(). { Progress = 0.0f; Abort = false; CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS); }

bool GDCM_NAME_SPACE::DocEntrySet::CheckIfEntryExist (  uint16_t  group, uint16_t  elem )  [virtual, inherited]

Checks if a given Dicom Element exists within the DocEntrySet. Parameters: group  Group number of the searched Dicom Element elem  Element number of the searched Dicom Element Returns: true is found Definition at line 412 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetDocEntry(). { return GetDocEntry(group,elem)!=NULL; }

void GDCM_NAME_SPACE::File::ClearAnonymizeList (   )  [inline]

Clears the list of elements to be anonymized. Definition at line 184 of file gdcmFile.h. { UserAnonymizeList.clear(); }

void GDCM_NAME_SPACE::ElementSet::ClearEntry (   )  [virtual, inherited]

delete all entries in the ElementSet Implements GDCM_NAME_SPACE::DocEntrySet. Definition at line 139 of file gdcmElementSet.cxx. References GDCM_NAME_SPACE::ElementSet::TagHT. Referenced by GDCM_NAME_SPACE::ElementSet::Copy(), GDCM_NAME_SPACE::DicomDir::CreateDicomDir(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::DicomDir::SetElements(), and GDCM_NAME_SPACE::ElementSet::~ElementSet(). { for(TagDocEntryHT::iterator cc = TagHT.begin();cc != TagHT.end(); ++cc) { if ( cc->second ) { cc->second->Unregister(); } } TagHT.clear(); }

bool GDCM_NAME_SPACE::Document::CloseFile (   )  [inherited]

closes the file Returns: TRUE if the close was successfull Definition at line 679 of file gdcmDocument.cxx. Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), DoTheLoadingJob(), GDCM_NAME_SPACE::FileHelper::GetRaw(), and GDCM_NAME_SPACE::Document::~Document(). { if ( Fp ) { Fp->close(); delete Fp; Fp = 0; } return true; }

int GDCM_NAME_SPACE::Document::ComputeGroup0002Length (   )  [protected, inherited]

Re-computes the length of the Dicom group 0002. Definition at line 1013 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::DocEntry::GetElement(), GDCM_NAME_SPACE::ElementSet::GetFirstEntry(), GDCM_NAME_SPACE::DocEntry::GetGroup(), GDCM_NAME_SPACE::DocEntry::GetLength(), GDCM_NAME_SPACE::ElementSet::GetNextEntry(), and GDCM_NAME_SPACE::DocEntry::GetVR(). Referenced by Write(). { uint16_t gr; VRKey vr; int groupLength = 0; bool found0002 = false; // for each zero-level Tag in the DCM Header DocEntry *entry = GetFirstEntry(); while( entry ) { gr = entry->GetGroup(); if ( gr == 0x0002 ) { found0002 = true; if ( entry->GetElement() != 0x0000 ) { vr = entry->GetVR(); //if ( (vr == "OB")||(vr == "OW")||(vr == "UT")||(vr == "SQ")) // (no SQ, OW, UT in group 0x0002;) if ( vr == "OB" ) { // explicit VR AND (OB, OW, SQ, UT) : 4 more bytes groupLength += 4; } groupLength += 2 + 2 + 4 + entry->GetLength(); } } else if (found0002 ) break; entry = GetNextEntry(); } return groupLength; }

void GDCM_NAME_SPACE::File::ComputeJPEGFragmentInfo (   )  [private]

Parse pixel data from disk of [multi-]fragment Jpeg encoding. Compute the jpeg extra information (fragment[s] offset[s] and length) and store it[them] in JPEGInfo for later pixel retrieval usage. Definition at line 2142 of file gdcmFile.cxx. References GDCM_NAME_SPACE::JPEGFragmentsInfo::AddFragment(), BasicOffsetTableItemValue, GDCM_NAME_SPACE::Document::Fp, gdcmWarningMacro, GDCM_NAME_SPACE::Document::GetTransferSyntax(), GDCM_NAME_SPACE::Global::GetTS(), JPEGInfo, ReadEncapsulatedBasicOffsetTable(), ReadTag(), ReadTagLength(), GDCM_NAME_SPACE::JPEGFragment::SetLength(), GDCM_NAME_SPACE::JPEGFragment::SetOffset(), and GDCM_NAME_SPACE::Document::SkipBytes(). Referenced by DoTheLoadingJob(). { // If you need to, look for comments of ComputeRLEInfo(). std::string ts = GetTransferSyntax(); if ( ! Global::GetTS()->IsJPEG(ts) ) { return; } ReadEncapsulatedBasicOffsetTable(); // Loop on the fragments[s] and store the parsed information in a // JPEGInfo. long fragmentLength; int i=0; uint32_t sum = 0; while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) { // Since we have read the basic offset table, let's check the value were correct // or else produce a warning: // A.4 Transfer syntaxes for encapsulation of encoded pixel data: // When the Item Value is present, the Basic Offset Table Item Value shall contain // concatenated 32-bit unsigned integer values that are byte offsets to the first // byte of the Item Tag of the first fragment for each frame in the Sequence of // Items. These offsets are measured from the first byte of the first Item Tag // following the Basic Offset Table item (See Table A.4-2). if ( BasicOffsetTableItemValue ) { // If a BasicOffsetTableItemValue was read uint32_t individualLength = BasicOffsetTableItemValue[i]; //assert( individualLength == sum ); // Seems like 00191113.dcm is off by one ?? if( individualLength != sum ) { gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght:" << individualLength << " != " << sum ); } sum += fragmentLength + 8; i++; } long fragmentOffset = Fp->tellg(); // Once per fragment // Store the collected info JPEGFragment *newFragment = new JPEGFragment; newFragment->SetOffset(fragmentOffset); newFragment->SetLength(fragmentLength); JPEGInfo->AddFragment(newFragment); SkipBytes(fragmentLength); } // Make sure that we encounter a 'Sequence Delimiter Item' // at the end of the item : if ( !ReadTag(0xfffe, 0xe0dd) ) { gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence"); } }

void GDCM_NAME_SPACE::File::ComputeRLEInfo (   )  [private]

Parse pixel data from disk of [multi-]fragment RLE encoding. Compute the RLE extra information and store it in RLEInfo for later pixel retrieval usage. Definition at line 2030 of file gdcmFile.cxx. References BasicOffsetTableItemValue, GDCM_NAME_SPACE::Document::Fp, gdcmWarningMacro, GDCM_NAME_SPACE::Document::GetTransferSyntax(), GDCM_NAME_SPACE::Global::GetTS(), ReadEncapsulatedBasicOffsetTable(), GDCM_NAME_SPACE::Document::ReadInt32(), ReadTagLength(), and GDCM_NAME_SPACE::Document::SkipBytes(). Referenced by DoTheLoadingJob(). { std::string ts = GetTransferSyntax(); if ( !Global::GetTS()->IsRLELossless(ts) ) { return; } // Encoded pixel data: for the time being we are only concerned with // Jpeg or RLE Pixel data encodings. // As stated in PS 3.5-2003, section 8.2 p44: // "If sent in Encapsulated Format (i.e. other than the Native Format) the // value representation OB is used". // Hence we expect an OB value representation. Concerning OB VR, // the section PS 3.5-2003, section A.4.c p 58-59, states: // "For the Value Representations OB and OW, the encoding shall meet the // following specifications depending on the Data element tag:" // [...snip...] // - the first item in the sequence of items before the encoded pixel // data stream shall be basic offset table item. The basic offset table // item value, however, is not required to be present" ReadEncapsulatedBasicOffsetTable(); // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) // Loop on the individual frame[s] and store the information // on the RLE fragments in a RLEFramesInfo. // Note: - when only a single frame is present, this is a // classical image. // - when more than one frame are present, then we are in // the case of a multi-frame image. long frameLength; int i=0; uint32_t sum = 0; while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) != 0 ) { // Since we have read the basic offset table, let's check the value were correct // or else produce a warning: if ( BasicOffsetTableItemValue ) { // If a BasicOffsetTableItemValue was read uint32_t individualLength = BasicOffsetTableItemValue[i]; assert( individualLength == sum ); // REMOVE that if this is a problem if( individualLength != sum ) { gdcmWarningMacro( "BasicOffsetTableItemValue differs from the fragment lenght" ); } sum += frameLength + 8; i++; } // Parse the RLE Header and store the corresponding RLE Segment // Offset Table information on fragments of this current Frame. // Note that the fragment pixels themselves are not loaded // (but just skipped). long frameOffset = Fp->tellg(); // once per fragment uint32_t nbRleSegments = ReadInt32(); if ( nbRleSegments > 16 ) { // There should be at most 15 segments (refer to RLEFrame class) gdcmWarningMacro( "Too many segments."); } uint32_t rleSegmentOffsetTable[16]; for( int k = 1; k <= 15; k++ ) { rleSegmentOffsetTable[k] = ReadInt32(); } // Deduce from both RLE Header and frameLength // the fragment length, and again store this info // in a RLEFramesInfo. long rleSegmentLength[15]; // skipping (not reading) RLE Segments if ( nbRleSegments > 1) { for(unsigned int k = 1; k <= nbRleSegments-1; k++) { rleSegmentLength[k] = rleSegmentOffsetTable[k+1] - rleSegmentOffsetTable[k]; SkipBytes(rleSegmentLength[k]); } } rleSegmentLength[nbRleSegments] = frameLength - rleSegmentOffsetTable[nbRleSegments]; SkipBytes(rleSegmentLength[nbRleSegments]); // Store the collected info RLEFrame *newFrame = new RLEFrame; newFrame->SetNumberOfFragments(nbRleSegments); for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) { newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]); newFrame->SetLength(uk,rleSegmentLength[uk]); } RLEInfo->AddFrame(newFrame); } // Make sure that we encounter a 'Sequence Delimiter Item' // at the end of the item : if ( !ReadTag(0xfffe, 0xe0dd) ) // once per RLE File { gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence"); } }

void GDCM_NAME_SPACE::ElementSet::Copy (  DocEntrySet *  set  )  [virtual, inherited]

Copies all the attributes from an other DocEntrySet. Parameters: set  entry to copy from Remarks: The contained DocEntries a not copied, only referenced Reimplemented from GDCM_NAME_SPACE::DocEntrySet. Reimplemented in GDCM_NAME_SPACE::DicomDir. Definition at line 201 of file gdcmElementSet.cxx. References GDCM_NAME_SPACE::ElementSet::ClearEntry(), GDCM_NAME_SPACE::DocEntrySet::Copy(), GDCM_NAME_SPACE::ElementSet::ItTagHT, and GDCM_NAME_SPACE::ElementSet::TagHT. Referenced by GDCM_NAME_SPACE::DicomDir::Copy(). { // Remove all previous entries ClearEntry(); DocEntrySet::Copy(set); ElementSet *eltSet = dynamic_cast<ElementSet *>(set); if( eltSet ) { TagHT = eltSet->TagHT; for(ItTagHT = TagHT.begin();ItTagHT != TagHT.end();++ItTagHT) { (ItTagHT->second)->Register(); } } }

void GDCM_NAME_SPACE::RefCounter::Delete (   )  [inline, inherited]

Delete the object. Remarks: The object is deleted only if its reference counting is to zero Definition at line 41 of file gdcmRefCounter.h. Referenced by GDCM_NAME_SPACE::SerieHelper::AddFileName(), GDCM_NAME_SPACE::Document::Backtrack(), GDCM_NAME_SPACE::FileHelper::CheckMandatoryElements(), GDCM_NAME_SPACE::FileHelper::CheckMandatoryEntry(), GDCM_NAME_SPACE::FileHelper::CopyMandatoryEntry(), GDCM_NAME_SPACE::Dict::DoTheLoadingJob(), GDCM_NAME_SPACE::FillDefaultDataDict(), GDCM_NAME_SPACE::DicomDirObject::FillObject(), vtkGdcmReader::GetFileInformation(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryBinArea(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryString(), GDCM_NAME_SPACE::DocEntrySet::InsertSeqEntry(), vtkGdcmReader::LoadFileInformation(), GDCM_NAME_SPACE::DicomDir::NewMeta(), GDCM_NAME_SPACE::DicomDirStudy::NewVisit(), GDCM_NAME_SPACE::Document::ReadNextDocEntry(), GDCM_NAME_SPACE::DicomDir::SetElement(), GDCM_NAME_SPACE::FileHelper::SetMandatoryEntry(), GDCM_NAME_SPACE::FileHelper::SetWriteFileTypeToExplicitVR(), GDCM_NAME_SPACE::FileHelper::SetWriteFileTypeToImplicitVR(), GDCM_NAME_SPACE::FileHelper::SetWriteFileTypeToJPEG(), GDCM_NAME_SPACE::FileHelper::SetWriteFileTypeToJPEG2000(), GDCM_NAME_SPACE::FileHelper::SetWriteToLibido(), GDCM_NAME_SPACE::DicomDir::~DicomDir(), GDCM_NAME_SPACE::DictSet::~DictSet(), and GDCM_NAME_SPACE::Global::~Global(). { Unregister(); }

bool GDCM_NAME_SPACE::File::DoTheLoadingJob (   )  [private]

Does the Loading Job (internal use only). Returns: false if file cannot be open or no swap info was found, or no tag was found. Definition at line 158 of file gdcmFile.cxx. References GDCM_NAME_SPACE::Document::CloseFile(), ComputeJPEGFragmentInfo(), ComputeRLEInfo(), GDCM_NAME_SPACE::Document::Fp, GDCM_NAME_SPACE::GDCM_UNFOUND, GetBitsAllocated(), GDCM_NAME_SPACE::ElementSet::GetDocEntry(), GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GDCM_NAME_SPACE::DocEntry::GetOffset(), GDCM_NAME_SPACE::Document::GetTransferSyntax(), GDCM_NAME_SPACE::Global::GetTS(), GDCM_NAME_SPACE::DocEntry::GetVR(), GrPixel, NumPixel, GDCM_NAME_SPACE::Document::OpenFile(), and GDCM_NAME_SPACE::DocEntry::SetVR(). Referenced by Load(). { // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 // We may encounter the 'RETired' (0x0028, 0x0200) tag // (Image Location") . This entry contains the number of // the group that contains the pixel data (hence the "Pixel Data" // is found by indirection through the "Image Location"). // Inside the group pointed by "Image Location" the searched element // is conventionally the element 0x0010 (when the norm is respected). // When the "Image Location" is missing we default to group 0x7fe0. // Note: this IS the right place for the code // Image Location const std::string &imgLocation = GetEntryString(0x0028, 0x0200); if ( imgLocation == GDCM_UNFOUND ) { // default value GrPixel = 0x7fe0; } else { GrPixel = (uint16_t) atoi( imgLocation.c_str() ); } // sometimes Image Location value doesn't follow // the supposed processor endianness. // see gdcmData/cr172241.dcm if ( GrPixel == 0xe07f ) { GrPixel = 0x7fe0; } if ( GrPixel != 0x7fe0 ) { // This is a kludge for old dirty Philips imager. NumPixel = 0x1010; } else { NumPixel = 0x0010; } // Now, we know GrPixel and NumPixel. // Let's create a VirtualDictEntry to allow a further VR modification // and force VR to match with BitsAllocated. DocEntry *entry = GetDocEntry(GrPixel, NumPixel); if ( entry != 0 ) { // Compute the RLE or JPEG info OpenFile(); const std::string &ts = GetTransferSyntax(); Fp->seekg( entry->GetOffset(), std::ios::beg ); if ( Global::GetTS()->IsRLELossless(ts) ) ComputeRLEInfo(); else if ( Global::GetTS()->IsJPEG(ts) ) ComputeJPEGFragmentInfo(); CloseFile(); // Create a new DataEntry to change the DictEntry // The changed DictEntry will have // - a correct PixelVR OB or OW) // - the name to "Pixel Data" //==>Take it easy! //==> Just change the VR ! /* DataEntry *oldEntry = dynamic_cast<DataEntry *>(entry); if (oldEntry) { VRKey PixelVR; // 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB) // more than 8 (i.e 12, 16) is a 'O Words' if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) PixelVR = "OB"; else PixelVR = "OW"; // Change only made if usefull if ( PixelVR != oldEntry->GetVR() ) { //DictEntry* newDict = DictEntry::New(GrPixel,NumPixel, // PixelVR,"1","Pixel Data"); //DataEntry *newEntry = DataEntry::New(newDict); //newDict->Delete(); //newEntry->Copy(entry); //newEntry->SetBinArea(oldEntry->GetBinArea(),oldEntry->IsSelfArea()); //oldEntry->SetSelfArea(false); //RemoveEntry(oldEntry); //AddEntry(newEntry); //newEntry->Delete(); } } */ VRKey PixelVR; // 8 bits allocated is a 'OB(ytes)' , as well as 24 (old ACR-NEMA RGB) // more than 8 (i.e 12, 16) is a 'OW(ords)' if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 ) PixelVR = "OB"; else PixelVR = "OW"; // Change only made if usefull if ( PixelVR != entry->GetVR() ) { entry->SetVR(PixelVR); } } return true; }

GDCM_NAME_SPACE::File::gdcmTypeMacro (  File   )  [private]

int GDCM_NAME_SPACE::File::GetBitsAllocated (   )

Retrieve the number of Bits Allocated (8, 12 -compacted ACR-NEMA files-, 16, 24 -old RGB ACR-NEMA files-,). Returns: The encountered Number of Bits Allocated, 0 by default. 0 means the file is NOT USABLE. The caller has to check it ! Definition at line 1230 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), and GDCM_NAME_SPACE::DataEntry::GetValue(). Referenced by GDCM_NAME_SPACE::FileHelper::CheckWriteIntegrity(), GDCM_NAME_SPACE::FileHelper::ConvertFixGreyLevels(), DoTheLoadingJob(), GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(), GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEG2000UserData(), and GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEGUserData(). { DataEntry *entry = GetDataEntry(0x0028,0x0100); if( !entry ) { gdcmWarningMacro("BitsAllocated (0028,0100) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); }

int GDCM_NAME_SPACE::File::GetBitsStored (   )

Retrieve the number of Bits Stored (actually used) (as opposed to number of Bits Allocated). Returns: The encountered number of Bits Stored, 0 by default. 0 means the file is NOT USABLE. The caller has to check it ! Definition at line 1213 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), and GDCM_NAME_SPACE::DataEntry::GetValue(). Referenced by GDCM_NAME_SPACE::FileHelper::ConvertFixGreyLevels(), and GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(). { DataEntry *entry = GetDataEntry(0x0028,0x0101); if( !entry ) { gdcmWarningMacro("BitsStored (0028,0101) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); }

DataEntry * GDCM_NAME_SPACE::DocEntrySet::GetDataEntry (  uint16_t  group, uint16_t  elem )  [inherited]

Same as Document::GetDocEntry except it returns a result only when the corresponding entry is of type DataEntry. Parameters: group  Group number of the searched Dicom Element elem  Element number of the searched Dicom Element Returns: When present, the corresponding DataEntry. Definition at line 103 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetDocEntry(). Referenced by GDCM_NAME_SPACE::FileHelper::CheckMandatoryElements(), GDCM_NAME_SPACE::FileHelper::CheckMandatoryEntry(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GetBitsAllocated(), GetBitsStored(), GDCM_NAME_SPACE::DocEntrySet::GetEntryBinArea(), GetHighBitPosition(), GetPlanarConfiguration(), GetRescaleIntercept(), GetSamplesPerPixel(), GetTSize(), GetXOrigin(), GetXSize(), GetXSpacing(), GetYOrigin(), GetYSize(), GetYSpacing(), GetZOrigin(), GetZSize(), GetZSpacing(), IsSignedPixelData(), GDCM_NAME_SPACE::ElementSet::Print(), GDCM_NAME_SPACE::DocEntrySet::SetEntryBinArea(), GDCM_NAME_SPACE::DocEntrySet::SetEntryString(), GDCM_NAME_SPACE::FileHelper::SetWriteToLibido(), GDCM_NAME_SPACE::FileHelper::SetWriteToNoLibido(), GDCM_NAME_SPACE::FileHelper::Write(), Write(), and GDCM_NAME_SPACE::DicomDirMeta::WriteContent(). { DocEntry *currentEntry = GetDocEntry(group, elem); if ( !currentEntry ) return NULL; return dynamic_cast<DataEntry*>(currentEntry); }

DictEntry * GDCM_NAME_SPACE::DocEntrySet::GetDictEntry (  uint16_t  group, uint16_t  elem )  [protected, inherited]

Searches [both] the public [and the shadow dictionary (when they exist)] for the presence of the DictEntry with given group and element. The public dictionary has precedence on the shadow one(s), if any. Parameters: group  Group number of the searched DictEntry elem  Element number of the searched DictEntry Returns: Corresponding DictEntry when it exists, NULL otherwise. Remarks: The returned DictEntry is registered when existing Todo: store the DefaultPubDict somwhere, in order not to access the HTable every time ! --> Done! Definition at line 473 of file gdcmDocEntrySet.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DictSet::GetDefaultPubDict(), GDCM_NAME_SPACE::Global::GetDicts(), GDCM_NAME_SPACE::Dict::GetEntry(), and GDCM_NAME_SPACE::RefCounter::Register(). Referenced by GDCM_NAME_SPACE::Document::ReadNextDocEntry(). { DictEntry *found = 0; Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); if (!pubDict) { gdcmWarningMacro( "We SHOULD have a default dictionary"); } else { found = pubDict->GetEntry(group, elem); if( found ) found->Register(); } return found; }

DocEntry * GDCM_NAME_SPACE::ElementSet::GetDocEntry (  uint16_t  group, uint16_t  elem )  [virtual, inherited]

retrieves a Dicom Element using (group, element) Parameters: group  Group number of the searched Dicom Element elem  Element number of the searched Dicom Element Returns: Implements GDCM_NAME_SPACE::DocEntrySet. Definition at line 186 of file gdcmElementSet.cxx. References GDCM_NAME_SPACE::ElementSet::TagHT, and GDCM_NAME_SPACE::DictEntry::TranslateToKey(). Referenced by AnonymizeFile(), AnonymizeNoLoad(), GDCM_NAME_SPACE::FileHelper::CopyDataEntry(), GDCM_NAME_SPACE::DicomDir::CreateDicomDir(), DoTheLoadingJob(), GDCM_NAME_SPACE::DicomDir::DoTheLoadingJob(), GetPixelAreaLength(), GetPixelOffset(), GDCM_NAME_SPACE::Document::GetTransferSyntax(), HasLUT(), GDCM_NAME_SPACE::Document::IsDicomV3(), GDCM_NAME_SPACE::Document::IsPapyrus(), IsReadable(), GDCM_NAME_SPACE::Document::LoadEntryBinArea(), GDCM_NAME_SPACE::DocEntryArchive::Push(), and GDCM_NAME_SPACE::DocEntryArchive::Restore(). { TagKey key = DictEntry::TranslateToKey(group, elem); TagDocEntryHT::iterator it = TagHT.find(key); if ( it!=TagHT.end() ) return it->second; return NULL; }

void * GDCM_NAME_SPACE::DocEntrySet::GetEntryBinArea (  uint16_t  group, uint16_t  elem )  [virtual, inherited]

Gets (from Header) a 'non string' element value. Parameters: group  group number of the Entry elem  element number of the Entry Returns: Pointer to the 'non string' area Definition at line 73 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DataEntry::GetBinArea(), and GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(). { DataEntry *entry = GetDataEntry(group, elem); if ( entry ) return entry->GetBinArea(); return 0; }

int GDCM_NAME_SPACE::DocEntrySet::GetEntryLength (  uint16_t  group, uint16_t  elem )  [virtual, inherited]

Searches within the DocEntrySet for the value length of a given tag.. Parameters: group  Group number of the searched tag. elem  Element number of the searched tag. Returns: Corresponding element length; -1 if not found Definition at line 88 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetDocEntry(), and GDCM_NAME_SPACE::DocEntry::GetLength(). Referenced by GDCM_NAME_SPACE::DicomDir::SetElement(), and Write(). { DocEntry *entry = GetDocEntry(group, elem); if ( entry ) return entry->GetLength(); return -1; }

std::string GDCM_NAME_SPACE::DocEntrySet::GetEntryString (  uint16_t  group, uint16_t  elem )  [virtual, inherited]

Get the "std::string representable" value of the Dicom entry. Parameters: group  Group number of the searched tag. elem  Element number of the searched tag. Returns: Corresponding element value when it exists, and the string GDCM_UNFOUND otherwise. Definition at line 51 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::GDCM_NOTLOADED, GDCM_NAME_SPACE::GDCM_UNFOUND, GDCM_NAME_SPACE::GDCM_UNREAD, GDCM_NAME_SPACE::DocEntrySet::GetDocEntry(), GDCM_NAME_SPACE::DataEntry::GetString(), GDCM_NAME_SPACE::DataEntry::IsNotLoaded(), GDCM_NAME_SPACE::DataEntry::IsUnfound(), and GDCM_NAME_SPACE::DataEntry::IsUnread(). Referenced by GDCM_NAME_SPACE::SerieHelper::AddFile(), AnonymizeFile(), GDCM_NAME_SPACE::FileHelper::CheckMandatoryElements(), GDCM_NAME_SPACE::SerieHelper::CreateUniqueSeriesIdentifier(), GDCM_NAME_SPACE::SerieHelper::CreateUserDefinedFileIdentifier(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), DoTheLoadingJob(), GDCM_NAME_SPACE::DirList::Explore(), GetImageNumber(), GetImageOrientationPatient(), GetImagePositionPatient(), GetLUTNbits(), GetModality(), GetNumberOfScalarComponents(), GetNumberOfScalarComponentsRaw(), GetPixelSize(), GetPixelType(), GetRescaleSlope(), GetRescaleSlopeIntercept(), GetSpacing(), GDCM_NAME_SPACE::Document::GetTransferSyntaxName(), GetXSpacing(), GetYSpacing(), IsMonochrome(), IsMonochrome1(), IsPaletteColor(), IsReadable(), IsYBRFull(), GDCM_NAME_SPACE::Document::operator<(), and GDCM_NAME_SPACE::DicomDir::SetElement(). { DataEntry *entry = dynamic_cast<DataEntry *>(GetDocEntry(group,elem)); if ( entry ) { if( entry->IsNotLoaded() ) return GDCM_NOTLOADED; if( entry->IsUnfound() ) return GDCM_UNFOUND; if( entry->IsUnread() ) return GDCM_UNREAD; return entry->GetString(); } return GDCM_UNFOUND; }

const std::string& GDCM_NAME_SPACE::Document::GetFileName (   )  const [inline, inherited]

Accessor to Filename. Definition at line 78 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::DicomDir::DoTheLoadingJob(), GDCM_NAME_SPACE::SerieHelper::FileNameGreaterThan(), GDCM_NAME_SPACE::SerieHelper::FileNameLessThan(), GDCM_NAME_SPACE::Document::IsParsable(), GDCM_NAME_SPACE::DicomDir::IsReadable(), GDCM_NAME_SPACE::Document::Load(), vtkGdcmReader::LoadImageInMemory(), GDCM_NAME_SPACE::DicomDir::ParseDirectory(), GDCM_NAME_SPACE::DicomDir::SetElement(), vtkGdcmReader::TestFileInformation(), and userSuppliedLessThanFunction2(). { return Filename; }

FileType GDCM_NAME_SPACE::Document::GetFileType (   )  [inherited]

returns the File Type (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) Returns: the FileType code Definition at line 417 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::Document::Filetype. { return Filetype; }

DocEntry * GDCM_NAME_SPACE::ElementSet::GetFirstEntry (   )  [virtual, inherited]

Get the first entry while visiting *the* 'zero level' DocEntrySet (DocEntries out of any Sequence). Returns: The first DocEntry if found, otherwhise NULL Implements GDCM_NAME_SPACE::DocEntrySet. Definition at line 156 of file gdcmElementSet.cxx. References GDCM_NAME_SPACE::ElementSet::ItTagHT, and GDCM_NAME_SPACE::ElementSet::TagHT. Referenced by GDCM_NAME_SPACE::Document::ComputeGroup0002Length(), GDCM_NAME_SPACE::DicomDir::DoTheLoadingJob(), GDCM_NAME_SPACE::DicomDir::NewMeta(), and GDCM_NAME_SPACE::Validator::SetInput(). { ItTagHT = TagHT.begin(); if (ItTagHT != TagHT.end()) return ItTagHT->second; return NULL; }

uint16_t GDCM_NAME_SPACE::File::GetGrPixel (   )  [inline]

Accessor to File::GrPixel. Definition at line 168 of file gdcmFile.h. { return GrPixel; }

int GDCM_NAME_SPACE::File::GetHighBitPosition (   )

Retrieve the high bit position. Warning: The method defaults to 0 when information is missing. The responsability of checking this value is left to the caller. Returns: The high bit position when present. 0 when missing. Definition at line 1247 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), and GDCM_NAME_SPACE::DataEntry::GetValue(). Referenced by GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(). { DataEntry *entry = GetDataEntry(0x0028,0x0102); if( !entry ) { gdcmWarningMacro("HighBitPosition (0028,0102) is supposed to be mandatory"); return 0; } return (int)entry->GetValue(0); }

int GDCM_NAME_SPACE::File::GetImageNumber (   )

gets the info from 0020,0013 : Image Number else 0. Returns: image number Definition at line 338 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, and GDCM_NAME_SPACE::DocEntrySet::GetEntryString(). Referenced by GDCM_NAME_SPACE::SerieHelper::ImageNumberGreaterThan(), and GDCM_NAME_SPACE::SerieHelper::ImageNumberLessThan(). { //0020 0013 : Image Number std::string strImNumber = GetEntryString(0x0020,0x0013); if ( strImNumber != GDCM_UNFOUND ) { return atoi( strImNumber.c_str() ); } return 0; //Hopeless }

bool GDCM_NAME_SPACE::File::GetImageOrientationPatient (  float  iop[6]  )

gets the info from 0020,0037 : Image Orientation Patient or from 0020 0035 : Image Orientation (RET) (needed to organize DICOM files based on their x,y,z position) Parameters: iop  adress of the (6)float array to receive values. (defaulted as 1.,0.,0.,0.,1.,0. if nothing -or inconsistent stuff- is found. Returns: true when one of the tag -with consistent values- is found false when nothing or inconsistent stuff - is found Definition at line 1056 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmWarningMacro, and GDCM_NAME_SPACE::DocEntrySet::GetEntryString(). Referenced by GDCM_NAME_SPACE::Orientation::GetOrientation(), GDCM_NAME_SPACE::Orientation::GetOrientationType(), GetXCosineOnX(), GetXCosineOnY(), GetXCosineOnZ(), GetYCosineOnX(), GetYCosineOnY(), and GetYCosineOnZ(). { std::string strImOriPat; //iop is supposed to be float[6] iop[0] = iop[4] = 1.; iop[1] = iop[2] = iop[3] = iop[5] = 0.; // 0020 0037 DS REL Image Orientation (Patient) if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND ) { if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)." << " Less than 6 values were found." ); return false; } return true; } //For ACR-NEMA // 0020 0035 DS REL Image Orientation (RET) else if ( (strImOriPat = GetEntryString(0x0020,0x0035)) != GDCM_UNFOUND ) { if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ", &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 ) { gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). " << "Less than 6 values were found." ); return false; } return true; } return false; }

bool GDCM_NAME_SPACE::File::GetImagePositionPatient (  float  ipp[3]  )

gets the info from 0020,0032 : Image Position Patient or from 0020 0030 : Image Position (RET) Parameters: ipp  adress of the (3)float array to receive values. (defaulted as 0.,0.,0. if nothing -or inconsistent stuff- is found. Returns: true when one of the tag -with consistent values- is found false when nothing or inconsistent stuff - is found Definition at line 1172 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmWarningMacro, and GDCM_NAME_SPACE::DocEntrySet::GetEntryString(). { std::string strImPosiPat; //ipp is supposed to be float[3] ipp[0] = ipp[1] = ipp[2] = 0.; // 0020 0032 DS REL Image Position (Patient) strImPosiPat = GetEntryString(0x0020,0x0032); if ( strImPosiPat != GDCM_UNFOUND ) { if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ", &ipp[0], &ipp[1], &ipp[2]) != 3 ) { gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)." << " Less than 3 values were found." ); return false; } return true; } //For ACR-NEMA // 0020 0030 DS REL Image Position (RET) else if ( (strImPosiPat = GetEntryString(0x0020,0x0030)) != GDCM_UNFOUND ) { if ( sscanf( strImPosiPat.c_str(), "%f \\ %f \\%f ", &ipp[0], &ipp[1], &ipp[2]) != 3 ) { gdcmWarningMacro( "wrong Image Position Patient (0020,0030). " << "Less than 3 values were found." ); return false; } return true; } return false; }

JPEGFragmentsInfo* GDCM_NAME_SPACE::File::GetJPEGInfo (   )  [inline]

Returns the JPEG Fragments info. Definition at line 178 of file gdcmFile.h. { return JPEGInfo; }

int GDCM_NAME_SPACE::File::GetLUTNbits (   )

gets the info from 0028,1101 : Lookup Table Desc-Red else 0 Returns: Lookup Table number of Bits , 0 by default when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] @ return bit number of each LUT item Definition at line 1538 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), and GDCM_NAME_SPACE::Util::Tokenize(). { std::vector<std::string> tokens; int lutNbits; //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red // = Lookup Table Desc-Blue // Consistency already checked in GetLUTLength std::string lutDescription = GetEntryString(0x0028,0x1101); if ( lutDescription == GDCM_UNFOUND ) { return 0; } tokens.clear(); // clean any previous value Util::Tokenize ( lutDescription, tokens, "\\" ); //LutLength=atoi(tokens[0].c_str()); //LutDepth=atoi(tokens[1].c_str()); lutNbits = atoi( tokens[2].c_str() ); tokens.clear(); return lutNbits; }

ModalityType GDCM_NAME_SPACE::File::GetModality (   )

gets the info from 0008,0060 : Modality Returns: Modality Type Todo: throw error return value ??? specified <> unknown in our database Definition at line 353 of file gdcmFile.cxx. References GDCM_NAME_SPACE::AS, GDCM_NAME_SPACE::AU, GDCM_NAME_SPACE::BI, GDCM_NAME_SPACE::CF, GDCM_NAME_SPACE::CP, GDCM_NAME_SPACE::CR, GDCM_NAME_SPACE::CS, GDCM_NAME_SPACE::CT, GDCM_NAME_SPACE::DD, GDCM_NAME_SPACE::DF, GDCM_NAME_SPACE::DG, GDCM_NAME_SPACE::DM, GDCM_NAME_SPACE::DS, GDCM_NAME_SPACE::DX, GDCM_NAME_SPACE::ECG, GDCM_NAME_SPACE::EPS, GDCM_NAME_SPACE::FA, GDCM_NAME_SPACE::FS, GDCM_NAME_SPACE::GDCM_UNFOUND, GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GDCM_NAME_SPACE::HC, GDCM_NAME_SPACE::HD, GDCM_NAME_SPACE::LP, GDCM_NAME_SPACE::LS, GDCM_NAME_SPACE::MA, GDCM_NAME_SPACE::MR, GDCM_NAME_SPACE::NM, GDCM_NAME_SPACE::OT, GDCM_NAME_SPACE::PT, GDCM_NAME_SPACE::RF, GDCM_NAME_SPACE::RG, GDCM_NAME_SPACE::RTDOSE, GDCM_NAME_SPACE::RTIMAGE, GDCM_NAME_SPACE::RTPLAN, GDCM_NAME_SPACE::RTSTRUCT, GDCM_NAME_SPACE::SM, GDCM_NAME_SPACE::ST, GDCM_NAME_SPACE::TG, GDCM_NAME_SPACE::Unknow, GDCM_NAME_SPACE::US, GDCM_NAME_SPACE::VF, GDCM_NAME_SPACE::XA, and GDCM_NAME_SPACE::XC. { // 0008 0060 : Modality std::string strModality = GetEntryString(0x0008,0x0060); if ( strModality != GDCM_UNFOUND ) { if ( strModality.find("AU") < strModality.length()) return AU; else if ( strModality.find("AS") < strModality.length()) return AS; else if ( strModality.find("BI") < strModality.length()) return BI; else if ( strModality.find("CF") < strModality.length()) return CF; else if ( strModality.find("CP") < strModality.length()) return CP; else if ( strModality.find("CR") < strModality.length()) return CR; else if ( strModality.find("CT") < strModality.length()) return CT; else if ( strModality.find("CS") < strModality.length()) return CS; else if ( strModality.find("DD") < strModality.length()) return DD; else if ( strModality.find("DF") < strModality.length()) return DF; else if ( strModality.find("DG") < strModality.length()) return DG; else if ( strModality.find("DM") < strModality.length()) return DM; else if ( strModality.find("DS") < strModality.length()) return DS; else if ( strModality.find("DX") < strModality.length()) return DX; else if ( strModality.find("ECG") < strModality.length()) return ECG; else if ( strModality.find("EPS") < strModality.length()) return EPS; else if ( strModality.find("FA") < strModality.length()) return FA; else if ( strModality.find("FS") < strModality.length()) return FS; else if ( strModality.find("HC") < strModality.length()) return HC; else if ( strModality.find("HD") < strModality.length()) return HD; else if ( strModality.find("LP") < strModality.length()) return LP; else if ( strModality.find("LS") < strModality.length()) return LS; else if ( strModality.find("MA") < strModality.length()) return MA; else if ( strModality.find("MR") < strModality.length()) return MR; else if ( strModality.find("NM") < strModality.length()) return NM; else if ( strModality.find("OT") < strModality.length()) return OT; else if ( strModality.find("PT") < strModality.length()) return PT; else if ( strModality.find("RF") < strModality.length()) return RF; else if ( strModality.find("RG") < strModality.length()) return RG; else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE; else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE; else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN; else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT; else if ( strModality.find("SM") < strModality.length()) return SM; else if ( strModality.find("ST") < strModality.length()) return ST; else if ( strModality.find("TG") < strModality.length()) return TG; else if ( strModality.find("US") < strModality.length()) return US; else if ( strModality.find("VF") < strModality.length()) return VF; else if ( strModality.find("XA") < strModality.length()) return XA; else if ( strModality.find("XC") < strModality.length()) return XC; else { return Unknow; } } return Unknow; }

DocEntry * GDCM_NAME_SPACE::ElementSet::GetNextEntry (   )  [virtual, inherited]

Get the next entry while visiting *the* 'zero level' DocEntrySet (DocEntries out of any Sequence). Note: : meaningfull only if GetFirstEntry already called Returns: The next DocEntry if found, otherwhise NULL Implements GDCM_NAME_SPACE::DocEntrySet. Definition at line 170 of file gdcmElementSet.cxx. References gdcmAssertMacro, GDCM_NAME_SPACE::ElementSet::ItTagHT, and GDCM_NAME_SPACE::ElementSet::TagHT. Referenced by GDCM_NAME_SPACE::Document::ComputeGroup0002Length(), and GDCM_NAME_SPACE::Validator::SetInput(). { gdcmAssertMacro (ItTagHT != TagHT.end()); ++ItTagHT; if (ItTagHT != TagHT.end()) return ItTagHT->second; return NULL; }

int GDCM_NAME_SPACE::File::GetNumberOfScalarComponents (   )

This function is intended to user who doesn't want to have to manage a LUT and expects to get an RBG Pixel image (or a monochrome one, if no LUT found ...). Warning: to be used with GetImagePixels() Returns: 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*) Definition at line 1682 of file gdcmFile.cxx. References GDCM_NAME_SPACE::Util::DicomStringEqual(), GDCM_NAME_SPACE::GDCM_UNFOUND, GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GetSamplesPerPixel(), and HasLUT(). Referenced by IsMonochrome(), vtkGdcmReader::LoadImageInMemory(), GDCM_NAME_SPACE::FileHelper::SetWriteToRaw(), GDCM_NAME_SPACE::FileHelper::SetWriteToRGB(), and vtkGdcmReader::TestFileInformation(). { if ( GetSamplesPerPixel() == 3 ) { return 3; } // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) if ( GetEntryString(0x0028,0x0100) == "24" ) { return 3; } std::string strPhotometricInterpretation = GetEntryString(0x0028,0x0004); if ( ( strPhotometricInterpretation == "PALETTE COLOR ") ) { if ( HasLUT() )// PALETTE COLOR is NOT enough { return 3; } else { return 1; } } // beware of trailing space at end of string // DICOM tags are never of odd length if ( strPhotometricInterpretation == GDCM_UNFOUND || Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") || Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") ) { return 1; } else { // we assume that *all* kinds of YBR are dealt with return 3; } }

int GDCM_NAME_SPACE::File::GetNumberOfScalarComponentsRaw (   )

This function is intended to user that DOESN'T want to get RGB pixels image when it's stored as a PALETTE COLOR image the (vtk) user is supposed to know how deal with LUTs -. Warning: to be used with GetImagePixelsRaw() Returns: 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -) Definition at line 1732 of file gdcmFile.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), and GetSamplesPerPixel(). Referenced by vtkGdcmReader::GetFileInformation(), vtkGdcmReader::LoadImageInMemory(), and vtkGdcmReader::TestFileInformation(). { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old RGB images) if ( File::GetEntryString(0x0028,0x0100) == "24" ) { return 3; } // we assume that *all* kinds of YBR are dealt with return GetSamplesPerPixel(); }

uint16_t GDCM_NAME_SPACE::File::GetNumPixel (   )  [inline]

Accessor to File::NumPixel. Definition at line 170 of file gdcmFile.h. { return NumPixel; }

size_t GDCM_NAME_SPACE::File::GetPixelAreaLength (   )

Recover the pixel area length (in Bytes). Returns: Pixel Element Length, as stored in the header (NOT the memory space necessary to hold the Pixels -in case of embeded compressed image-) 0 : NOT USABLE file. The caller has to check. Definition at line 1772 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::ElementSet::GetDocEntry(), GDCM_NAME_SPACE::DocEntry::GetLength(), GrPixel, and NumPixel. { DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); if ( pxlElement ) { return pxlElement->GetLength(); } else { gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } }

size_t GDCM_NAME_SPACE::File::GetPixelOffset (   )

Recover the offset (from the beginning of the file) of *image* pixels (not *icone image* pixels, if any !). Returns: Pixel Offset Definition at line 1750 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::ElementSet::GetDocEntry(), GDCM_NAME_SPACE::DocEntry::GetOffset(), GrPixel, and NumPixel. { DocEntry *pxlElement = GetDocEntry(GrPixel, NumPixel); if ( pxlElement ) { return pxlElement->GetOffset(); } else { gdcmWarningMacro( "Big trouble : Pixel Element (" << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" ); return 0; } }

int GDCM_NAME_SPACE::File::GetPixelSize (   )

Return the size (in bytes) of a single pixel of data. Returns: The size in bytes of a single pixel of data; 0 by default 0 means the file is NOT USABLE; the caller will have to check Definition at line 1296 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), and GetPixelType(). Referenced by vtkGdcmReader::GetFileInformation(), vtkGdcmReader::LoadImageInMemory(), and vtkGdcmReader::TestFileInformation(). { // 0028 0100 US IMG Bits Allocated // (in order no to be messed up by old ACR-NEMA RGB images) assert( !(GetEntryString(0x0028,0x0100) == "24") ); std::string pixelType = GetPixelType(); if ( pixelType == "8U" || pixelType == "8S" ) { return 1; } if ( pixelType == "16U" || pixelType == "16S") { return 2; } if ( pixelType == "32U" || pixelType == "32S") { return 4; } if ( pixelType == "FD" ) { return 8; } gdcmWarningMacro( "Unknown pixel type: " << pixelType); return 0; }

std::string GDCM_NAME_SPACE::File::GetPixelType (   )

Build the Pixel Type of the image. Possible values are: 8U unsigned 8 bit, 8S signed 8 bit, 16U unsigned 16 bit, 16S signed 16 bit, 32U unsigned 32 bit, 32S signed 32 bit, FD floating double 64 bits (Not kosher DICOM, but so usefull!). Warning: 12 bit images appear as 16 bit. 24 bit images appear as 8 bit + photochromatic interp ="RGB " + Planar Configuration = 0 Returns: 0S if nothing found. NOT USABLE file. The caller has to check Definition at line 1338 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), and IsSignedPixelData(). Referenced by vtkGdcmReader::GetFileInformation(), and GetPixelSize(). { std::string bitsAlloc = GetEntryString(0x0028, 0x0100); // Bits Allocated if ( bitsAlloc == GDCM_UNFOUND ) { gdcmWarningMacro( "Bits Allocated (0028,0100) supposed to be mandatory"); bitsAlloc = "16"; // default and arbitrary value, not to polute the output } else if ( bitsAlloc == "64" ) { return "FD"; } // useless since we have to bypass a bug ( >8 && < 16) else if ( bitsAlloc == "12" ) { // It will be unpacked bitsAlloc = "16"; } else if ( bitsAlloc == "24" ) { // (in order no to be messed up by old RGB images) bitsAlloc = "8"; } int i= atoi(bitsAlloc.c_str()); // fix a bug in some headers if ( i > 8 && i < 16 ) { bitsAlloc = "16"; } std::string sign; if( IsSignedPixelData() ) { sign = "S"; } else { sign = "U"; } return bitsAlloc + sign; }

int GDCM_NAME_SPACE::File::GetPlanarConfiguration (   )

Retrieve the Planar Configuration for RGB images (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane). Returns: The encountered Planar Configuration, 0 by default. Definition at line 1281 of file gdcmFile.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), and GDCM_NAME_SPACE::DataEntry::GetValue(). { DataEntry *entry = GetDataEntry(0x0028,0x0006); if( !entry ) { return 0; } return (int)entry->GetValue(0); }

int GDCM_NAME_SPACE::Base::GetPrintLevel (   )  [inline, inherited]

Gets the print level for the Dicom Entries. Definition at line 50 of file gdcmBase.h. { return PrintLevel; }

Dict * GDCM_NAME_SPACE::Document::GetPubDict (   )  [inherited]

Get the public dictionary used. Definition at line 314 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::Document::RefPubDict. { return RefPubDict; }

const unsigned long& GDCM_NAME_SPACE::RefCounter::GetRefCount (   )  const [inline, inherited]

Get the reference counting. Returns: Reference count Definition at line 59 of file gdcmRefCounter.h. { return RefCount; }

double GDCM_NAME_SPACE::File::GetRescaleIntercept (   )

gets the info from 0028,1052 : Rescale Intercept Returns: Rescale Intercept. defaulted to 0.0 if not found or empty Definition at line 1636 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), and GDCM_NAME_SPACE::DataEntry::GetValue(). { // 0028 1052 DS IMG Rescale Intercept DataEntry *entry = GetDataEntry(0x0028, 0x1052); if( !entry ) { gdcmWarningMacro( "Missing Rescale Intercept (0028,1052)"); return 0.0f; } return (float)entry->GetValue(0); }

double GDCM_NAME_SPACE::File::GetRescaleSlope (   )

gets the info from 0028,1053 : Rescale Slope Returns: Rescale Slope. defaulted to 1.0 if not found or empty Definition at line 1653 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), and GetRescaleSlopeIntercept(). { double resInter = 0.; double resSlope = 1.; if ( GetRescaleSlopeIntercept(resSlope, resInter) ) { return resSlope; } //0028 1053 DS IMG Rescale Slope std::string strRescSlope = GetEntryString(0x0028,0x1053); if ( strRescSlope != GDCM_UNFOUND ) { if ( sscanf( strRescSlope.c_str(), "%lf ", &resSlope) != 1 ) { // bug in the element 0x0028,0x1053 gdcmWarningMacro( "Rescale Slope (0028,1053) is empty."); } } return resSlope; }

bool GDCM_NAME_SPACE::File::GetRescaleSlopeIntercept (  double &  slope, double &  intercept )

Definition at line 1565 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmWarningMacro, GDCM_NAME_SPACE::SQItem::GetDocEntry(), GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GDCM_NAME_SPACE::SeqEntry::GetFirstSQItem(), GDCM_NAME_SPACE::SeqEntry::GetNumberOfSQItems(), GDCM_NAME_SPACE::DocEntrySet::GetSeqEntry(), GDCM_NAME_SPACE::DataEntry::GetString(), and GDCM_NAME_SPACE::Global::GetTS(). Referenced by GetRescaleSlope(). { slope = 1.0; intercept = 0.0; TS *ts = Global::GetTS(); std::string sopclassuid_used; // D 0002|0002 [UI] [Media Storage SOP Class UID] const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002); const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str); //D 0008|0016 [UI] [SOP Class UID] const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016); const std::string &sopclassuid = ts->GetValue(sopclassuid_str); if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND ) { return false; } else { if( mediastoragesopclassuid == sopclassuid ) { sopclassuid_used = mediastoragesopclassuid; } else { gdcmWarningMacro( "Inconsistant SOP Class UID: " << mediastoragesopclassuid << " and " << sopclassuid ); return false; } } // ok we have now the correc SOP Class UID if( sopclassuid_used == "Enhanced MR Image Storage" ) { SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230); unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems(); if( !n ) return false; SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem(); DocEntry *p = item1->GetDocEntry(0x0028,0x9145); if( !p ) return false; SeqEntry *seq = dynamic_cast<SeqEntry*>(p); unsigned int n1 = seq->GetNumberOfSQItems(); if( !n1 ) return false; SQItem *item2 = seq->GetFirstSQItem(); // D 0028|1052 [DS] [Rescale Intercept] [0 ] DocEntry *p2 = item2->GetDocEntry(0x0028,0x1052); if( !p2 ) return false; DataEntry *entry = dynamic_cast<DataEntry *>(p2); std::string intercept_str = entry->GetString(); if ( sscanf( intercept_str.c_str(), "%lf", &intercept) != 1 ) { intercept = 0.; return false; } // D 0028|1053 [DS] [Rescale Slope] [5.65470085470085] DocEntry *p3 = item2->GetDocEntry(0x0028,0x1053); if( !p3 ) return false; DataEntry *entry2 = dynamic_cast<DataEntry *>(p3); std::string slope_str = entry2->GetString(); if ( sscanf( slope_str.c_str(), "%lf", &slope) != 1 ) { slope = 1.; return false; } return true; } return false; }

RLEFramesInfo* GDCM_NAME_SPACE::File::GetRLEInfo (   )  [inline]

returns the RLE info Definition at line 176 of file gdcmFile.h. { return RLEInfo; }

int GDCM_NAME_SPACE::File::GetSamplesPerPixel (   )

Retrieve the number of Samples Per Pixel (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-). Returns: The encountered number of Samples Per Pixel, 1 by default. (we assume Gray level Pixels) Definition at line 1264 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), and GDCM_NAME_SPACE::DataEntry::GetValue(). Referenced by GDCM_NAME_SPACE::FileHelper::CheckWriteIntegrity(), GetNumberOfScalarComponents(), GetNumberOfScalarComponentsRaw(), GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(), GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEG2000UserData(), and GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEGUserData(). { DataEntry *entry = GetDataEntry(0x0028,0x0002); if( !entry ) { gdcmWarningMacro("SamplesPerPixel (0028,0002) is supposed to be mandatory"); return 1; // Well, it's supposed to be mandatory ... // but sometimes it's missing : *we* assume Gray pixels } return (int)entry->GetValue(0); }

SeqEntry * GDCM_NAME_SPACE::DocEntrySet::GetSeqEntry (  uint16_t  group, uint16_t  elem )  [inherited]

Same as Document::GetDocEntry except it returns a result only when the corresponding entry is of type SeqEntry. Parameters: group  Group number of the searched Dicom Element elem  Element number of the searched Dicom Element Returns: When present, the corresponding SeqEntry. Definition at line 119 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetDocEntry(). Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GetRescaleSlopeIntercept(), and GetSpacing(). { DocEntry *currentEntry = GetDocEntry(group, elem); if ( !currentEntry ) return NULL; return dynamic_cast<SeqEntry*>(currentEntry); }

Dict * GDCM_NAME_SPACE::Document::GetShaDict (   )  [inherited]

Get the shadow dictionary used. Definition at line 322 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::Document::RefShaDict. { return RefShaDict; }

bool GDCM_NAME_SPACE::File::GetSpacing (  float &  xspacing, float &  yspacing, float &  zspacing )

Definition at line 475 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmWarningMacro, GDCM_NAME_SPACE::SQItem::GetDocEntry(), GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GDCM_NAME_SPACE::SeqEntry::GetFirstSQItem(), GDCM_NAME_SPACE::SeqEntry::GetNumberOfSQItems(), GDCM_NAME_SPACE::DocEntrySet::GetSeqEntry(), GDCM_NAME_SPACE::DataEntry::GetString(), and GDCM_NAME_SPACE::Global::GetTS(). Referenced by GetXSpacing(), GetYSpacing(), and GetZSpacing(). { xspacing = yspacing = zspacing = 1.0; TS *ts = Global::GetTS(); std::string sopclassuid_used; // D 0002|0002 [UI] [Media Storage SOP Class UID] //const std::string &mediastoragesopclassuid_str = GetEntryValue(0x0002,0x0002); const std::string &mediastoragesopclassuid_str = GetEntryString(0x0002,0x0002); const std::string &mediastoragesopclassuid = ts->GetValue(mediastoragesopclassuid_str); //D 0008|0016 [UI] [SOP Class UID] const std::string &sopclassuid_str = GetEntryString(0x0008,0x0016); const std::string &sopclassuid = ts->GetValue(sopclassuid_str); if ( mediastoragesopclassuid == GDCM_UNFOUND && sopclassuid == GDCM_UNFOUND ) { return false; } else { if( mediastoragesopclassuid == sopclassuid ) { sopclassuid_used = mediastoragesopclassuid; } else { gdcmWarningMacro( "Inconsistant SOP Class UID: " << mediastoragesopclassuid << " and " << sopclassuid ); return false; } } // ok we have now the correc SOP Class UID if( sopclassuid_used == "Enhanced MR Image Storage" ) { SeqEntry *PerframeFunctionalGroupsSequence = GetSeqEntry(0x5200,0x9230); unsigned int n = PerframeFunctionalGroupsSequence->GetNumberOfSQItems(); if( !n ) return false; SQItem *item1 = PerframeFunctionalGroupsSequence->GetFirstSQItem(); DocEntry *p = item1->GetDocEntry(0x0028,0x9110); if( !p ) return false; SeqEntry *seq = dynamic_cast<SeqEntry*>(p); unsigned int n1 = seq->GetNumberOfSQItems(); if( !n1 ) return false; SQItem *item2 = seq->GetFirstSQItem(); // D 0028|0030 [DS] [Pixel Spacing] [0.83333331346511\0.83333331346511 ] DocEntry *p2 = item2->GetDocEntry(0x0028,0x0030); if( !p2 ) return false; DataEntry *entry = dynamic_cast<DataEntry *>(p2); std::string spacing = entry->GetString(); if ( sscanf( spacing.c_str(), "%f\\%f", &yspacing, &xspacing) != 2 ) { xspacing = yspacing = 1.; return false; } // D 0018|0050 [DS] [Slice Thickness] [1 ] DocEntry *p3 = item2->GetDocEntry(0x0018,0x0050); if( !p3 ) return false; DataEntry *entry2 = dynamic_cast<DataEntry *>(p3); std::string thickness = entry2->GetString(); if ( sscanf( thickness.c_str(), "%f", &zspacing) != 1 ) { zspacing = 1.; return false; } return true; } return false; }

int GDCM_NAME_SPACE::Document::GetSwapCode (   )  [inline, inherited]

'Swap code' accessor (see SwapCode ) Definition at line 74 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(). { return SwapCode; }

std::string GDCM_NAME_SPACE::Document::GetTransferSyntax (   )  [inherited]

Accessor to the Transfer Syntax (when present) of the current document (it internally handles reading the value from disk when only parsing occured). Returns: The encountered Transfer Syntax of the current document, if DICOM. GDCM_UNKNOWN for ACR-NEMA files (or broken headers ...) Definition at line 429 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::GDCM_UNKNOWN, gdcmWarningMacro, and GDCM_NAME_SPACE::ElementSet::GetDocEntry(). Referenced by ComputeJPEGFragmentInfo(), ComputeRLEInfo(), DoTheLoadingJob(), and GDCM_NAME_SPACE::Document::HandleOutOfGroup0002(). { DocEntry *entry = GetDocEntry(0x0002, 0x0010); if ( !entry ) { return GDCM_UNKNOWN; } // The entry might be present but not loaded (parsing and loading // happen at different stages): try loading and proceed with check... // Well ... // (parsing and loading happen at the very same stage!) //LoadDocEntrySafe(entry); //JPRx if (DataEntry *dataEntry = dynamic_cast<DataEntry *>(entry) ) { std::string transfer = dataEntry->GetString(); // The actual transfer (as read from disk) might be padded. We // first need to remove the potential padding. We can make the // weak assumption that padding was not executed with digits... if ( transfer.length() == 0 ) { // for brain damaged headers gdcmWarningMacro( "Transfer Syntax has length = 0."); return GDCM_UNKNOWN; } while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { transfer.erase(transfer.length()-1, 1); if ( transfer.length() == 0 ) { // for brain damaged headers gdcmWarningMacro( "Transfer Syntax contains no valid character."); return GDCM_UNKNOWN; } } return transfer; } return GDCM_UNKNOWN; }

std::string GDCM_NAME_SPACE::Document::GetTransferSyntaxName (   )  [inherited]

Accesses the info from 0002,0010 : Transfer Syntax and TS. Returns: The full Transfer Syntax Name (as opposed to Transfer Syntax UID) Definition at line 474 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::GDCM_NOTLOADED, GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmDebugMacro, gdcmErrorMacro, GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), and GDCM_NAME_SPACE::Global::GetTS(). Referenced by GDCM_NAME_SPACE::Document::HandleOutOfGroup0002(). { // use the TS (TS : Transfer Syntax) std::string transferSyntax = GetEntryString(0x0002,0x0010); if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) ) { gdcmErrorMacro( "Transfer Syntax not loaded. " << std::endl << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" ); return "Uncompressed ACR-NEMA"; } if ( transferSyntax == GDCM_UNFOUND ) { gdcmDebugMacro( "Unfound Transfer Syntax (0002,0010)"); return "Uncompressed ACR-NEMA"; } // we do it only when we need it const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax ); // Global::GetTS() is a global static you shall never try to delete it! return tsName; }

int GDCM_NAME_SPACE::File::GetTSize (   )

Retrieve the -unnormalized- number of 'times' of '4D image'. User has to tell gdcm the location of this '4th Dimension component' using SetFourthDimensionLocation() method before. Warning: The defaulted value is 1. Returns: The encountered size when found, 1 by default (The file doesn't contain a '4D image'.). Definition at line 551 of file gdcmFile.cxx. References FourthDimensionLocation, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::TagKey::GetElement(), GDCM_NAME_SPACE::TagKey::GetGroup(), and GDCM_NAME_SPACE::DataEntry::GetValue(). Referenced by GDCM_NAME_SPACE::FileHelper::CheckWriteIntegrity(), and GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(). { if (FourthDimensionLocation == TagKey(0,0) )// 4D location is not set : not a 4D object return 1; DataEntry *entry = GetDataEntry(FourthDimensionLocation.GetGroup(), FourthDimensionLocation.GetElement() ); if( !entry ) { gdcmWarningMacro( " FourthDimensionLocation not found at : " << std::hex << FourthDimensionLocation.GetGroup() << "|" << FourthDimensionLocation.GetElement()); return 1; } else { return (int)entry->GetValue(0); } }

float GDCM_NAME_SPACE::File::GetXCosineOnX (   )

gets the cosine of image X axis, against patient X axis (Sorry, but Python needs it :-( ) Returns: cosine of image X axis, against patient X axis Definition at line 1096 of file gdcmFile.cxx. References GetImageOrientationPatient(). { float iop[6]; GetImageOrientationPatient( iop ); return(iop[0]); }

float GDCM_NAME_SPACE::File::GetXCosineOnY (   )

gets the cosine of image X axis, against patient Y axis (Sorry, but Python needs it :-( ) Returns: cosine of image X axis, against patient Y axis Definition at line 1108 of file gdcmFile.cxx. References GetImageOrientationPatient(). { float iop[6]; GetImageOrientationPatient( iop ); return(iop[1]); }

float GDCM_NAME_SPACE::File::GetXCosineOnZ (   )

gets the cosine of image X axis, against patient Z axis (Sorry, but Python needs it :-( ) Returns: cosine of image X axis, against patient Z axis Definition at line 1120 of file gdcmFile.cxx. References GetImageOrientationPatient(). { float iop[6]; GetImageOrientationPatient( iop ); return(iop[2]); }

float GDCM_NAME_SPACE::File::GetXOrigin (   )

gets the info from 0020,0032 : Image Position Patient else from 0020,0030 : Image Position (RET) else 0. Returns: up-left image corner X position Definition at line 915 of file gdcmFile.cxx. References gdcmErrorMacro, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::DataEntry::GetValueCount(), and GDCM_NAME_SPACE::DataEntry::IsValueCountValid(). { DataEntry *entry = GetDataEntry(0x0020,0x0032); if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); entry = GetDataEntry(0x0020,0x0030); if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); return 0.0f; } } if( entry->GetValueCount() == 3 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(0); } return 0.0f; }

int GDCM_NAME_SPACE::File::GetXSize (   )

Retrieve the number of columns of image. Returns: The encountered size when found, 0 by default. 0 means the file is NOT USABLE. The caller will have to check Definition at line 419 of file gdcmFile.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), and GDCM_NAME_SPACE::DataEntry::GetValue(). Referenced by GDCM_NAME_SPACE::FileHelper::CheckWriteIntegrity(), vtkGdcmReader::GetFileInformation(), GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(), vtkGdcmReader::LoadImageInMemory(), GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEG2000UserData(), GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEGUserData(), and vtkGdcmReader::TestFileInformation(). { DataEntry *entry = GetDataEntry(0x0028,0x0011); if( entry ) return (int)entry->GetValue(0); return 0; }

float GDCM_NAME_SPACE::File::GetXSpacing (   )

gets the info from 0018,1164 : ImagerPixelSpacing then 0028,0030 : Pixel Spacing else 1.0 Returns: X dimension of a pixel Todo: check the various SOP Class to get the Pixel Spacing at the proper location Todo: find images to check if it *actually* works Definition at line 579 of file gdcmFile.cxx. References GDCM_NAME_SPACE::Util::DicomStringEqual(), gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GetSpacing(), GDCM_NAME_SPACE::DataEntry::GetValue(), and GDCM_NAME_SPACE::DataEntry::GetValueCount(). Referenced by vtkGdcmReader::GetFileInformation(). { float xspacing = 1.0; float yspacing = 1.0; float zspacing = 1.0; uint32_t nbValue; DataEntry *entry; bool ok = false; if ( GetSpacing(xspacing,yspacing,zspacing) ) { return xspacing; } // else fallback /* From:David Clunie - view profile Date:Wed, May 24 2006 1:12 pm Email:David Clunie <dclu...@dclunie.com> Groups:comp.protocols.dicom The short answer is that: - (0018,1164) describes a spacing equivalent to that which would be measured off a film in projection radiography - (0018,7022) does not describe the image pixels themselves, since detector elements may have been binned to produce pixels - (0018,7020) may be different from (0018,7022) since there may be non-sensitive material separating individual detectors (i.e. the size is smaller than the spacing between centers) Only (0018,1164) is relevant when measuring things; the detector-specific attributes are there to describe the acquisition. David PS. For ultrasound you need to use Region Calibration. */ /* It *SHOULD* first find the IOD and then deduce which tags to read Eg: Cross section this is in Pixel Spacing (0028,0030) CR is in Imager Pixel Spacing (0018,1164) US is in Pixel Aspect Ratio (0028,0034) RT is in : (3002,0011) Image Plane Pixel Spacing (3002,0012) RT Image Position and (3004,000c) for deducing Z spacing */ std::string SOPClassUID = GetEntryString(0x0008,0x0016); if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") // Ultrasound Image Storage (Retired) || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") // Ultrasound Image Storage || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") // Ultrasound Multi-Frame Storage (Retired) || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) // Ultrasound Multi-FrameImage Storage { // - check if SOPClassUID contains 2 parts (e.g. "4\3") // - guess how to deduce the spacing (FOV ?, ??) entry = GetDataEntry(0x0028,0x0034); if ( entry ) { nbValue = entry->GetValueCount(); if( nbValue !=2 ) { gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " << "has a wrong number of values :" << nbValue); } xspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... ok = true; } if (ok) return xspacing; } /* if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.1") ) // Computed Radiography Image Storage // CR is in Imager Pixel Spacing (0018,1164)// */ // go on with old method ... // --------------------- // To follow David Clunie's advice, we first check ImagerPixelSpacing entry = GetDataEntry(0x0018,0x1164); if( entry ) { nbValue = entry->GetValueCount(); // Can't use IsValueCountValid because of the complex heuristic. if( nbValue !=2 ) gdcmWarningMacro("ImagerPixelSpacing (0x0018,0x1164) " << "has a wrong number of values :" << nbValue); if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); else if( nbValue >= 2 ) xspacing = (float)entry->GetValue(1); else xspacing = (float)entry->GetValue(0); if ( xspacing == 0.0 ) xspacing = 1.0; return xspacing; } else { gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } entry = GetDataEntry(0x0028,0x0030); if( entry ) { nbValue = entry->GetValueCount(); if( nbValue !=2 ) gdcmWarningMacro("PixelSpacing (0x0018,0x0030) " << "has a wrong number of values :" << nbValue); if( nbValue >= 3 ) xspacing = (float)entry->GetValue(2); else if( nbValue >= 2 ) xspacing = (float)entry->GetValue(1); else xspacing = (float)entry->GetValue(0); if ( xspacing == 0.0 ) xspacing = 1.0; return xspacing; } else { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } return xspacing; }

float GDCM_NAME_SPACE::File::GetYCosineOnX (   )

gets the cosine of image Y axis, against patient X axis (Sorry, but Python needs it :-( ) Returns: cosine of image Y axis, against patient X axis Definition at line 1132 of file gdcmFile.cxx. References GetImageOrientationPatient(). { float iop[6]; GetImageOrientationPatient( iop ); return(iop[3]); }

float GDCM_NAME_SPACE::File::GetYCosineOnY (   )

gets the cosine of image Y axis, against patient Y axis (Sorry, but Python needs it :-( ) Returns: cosine of image Y axis, against patient Y axis Definition at line 1144 of file gdcmFile.cxx. References GetImageOrientationPatient(). { float iop[6]; GetImageOrientationPatient( iop ); return(iop[4]); }

float GDCM_NAME_SPACE::File::GetYCosineOnZ (   )

gets the cosine of image Y axis, against patient Z axis (Sorry, but Python needs it :-( ) Returns: cosine of image Y axis, against patient Z axis Definition at line 1156 of file gdcmFile.cxx. References GetImageOrientationPatient(). { float iop[6]; GetImageOrientationPatient( iop ); return(iop[5]); }

float GDCM_NAME_SPACE::File::GetYOrigin (   )

gets the info from 0020,0032 : Image Position Patient else from 0020,0030 : Image Position (RET) else 0. Returns: up-left image corner Y position Definition at line 946 of file gdcmFile.cxx. References gdcmErrorMacro, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::DataEntry::GetValueCount(), and GDCM_NAME_SPACE::DataEntry::IsValueCountValid(). { DataEntry *entry = GetDataEntry(0x0020,0x0032); if( !entry ) { gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)"); entry = GetDataEntry(0x0020,0x0030); if( !entry ) { gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)"); return 0.0f; } } if( entry->GetValueCount() == 3 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(1); } return 0.0f; }

int GDCM_NAME_SPACE::File::GetYSize (   )

Retrieve the number of lines of image. Warning: The defaulted value is 1 as opposed to File::GetXSize() Returns: The encountered size when found, 1 by default (The ACR-NEMA file contains a Signal, not an Image). Definition at line 433 of file gdcmFile.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::DataEntry::GetValue(), and GDCM_NAME_SPACE::Document::IsDicomV3(). Referenced by GDCM_NAME_SPACE::FileHelper::CheckWriteIntegrity(), vtkGdcmReader::GetFileInformation(), GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(), vtkGdcmReader::LoadImageInMemory(), GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEG2000UserData(), GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEGUserData(), and vtkGdcmReader::TestFileInformation(). { DataEntry *entry = GetDataEntry(0x0028,0x0010); if( entry ) return (int)entry->GetValue(0); if ( IsDicomV3() ) { return 0; } // The Rows (0028,0010) entry was optional for ACR/NEMA. // (at least some images didn't have it.) // It might hence be a signal (1D image). So we default to 1: return 1; }

float GDCM_NAME_SPACE::File::GetYSpacing (   )

gets the info from 0018,1164 : ImagerPixelSpacing then from 0028,0030 : Pixel Spacing else 1.0 Returns: Y dimension of a pixel Todo: check the various SOP Class to get the Pixel Spacing at the proper location Todo: find images to check if it *actually* works Definition at line 737 of file gdcmFile.cxx. References GDCM_NAME_SPACE::Util::DicomStringEqual(), gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GetSpacing(), GDCM_NAME_SPACE::DataEntry::GetValue(), and GDCM_NAME_SPACE::DataEntry::GetValueCount(). Referenced by vtkGdcmReader::GetFileInformation(). { float xspacing = 1., yspacing = 1.0, zspacing = 1.; uint32_t nbValue; DataEntry *entry; bool ok = false; if ( GetSpacing(xspacing,yspacing,zspacing) ) { return yspacing; } // else fallback std::string SOPClassUID = GetEntryString(0x0008,0x0016); if (Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6") // Ultrasound Image Storage (Retired) || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.6.1") // Ultrasound Image Storage || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3") // Ultrasound Multi-Frame Storage (Retired) || Util::DicomStringEqual( SOPClassUID,"1.2.840.10008.5.1.4.1.1.3.1") ) // Ultrasound Multi-FrameImage Storage { // - check if SOPClassUID contains 2 parts (e.g. "4\3") // - no way to deduce the spacing/ entry = GetDataEntry(0x0028,0x0034); if ( entry ) { nbValue = entry->GetValueCount(); if( nbValue ==2 ) { yspacing = (float)entry->GetValue(0)/(float)entry->GetValue(1); //std::cout << "ys " << yspacing << std::endl; ok = true; } else { gdcmWarningMacro("PixelAspectRatio (0x0028,0x0034) " << "has a wrong number of values :" << nbValue); if (nbValue == 0 ) { ok = false; } else if (nbValue == 1 ) { yspacing = 1.0; // We get Pixel Aspect Ratio, not Spacing ... ok = true; } } } if (ok) return yspacing; } // go on with old method ... // --------------------- // To follow David Clunie's advice, we first check ImagerPixelSpacing yspacing = 1.0; // To follow David Clunie's advice, we first check ImagerPixelSpacing entry = GetDataEntry(0x0018,0x1164); if( entry ) { yspacing = (float)entry->GetValue(0); if ( yspacing == 0.0 ) yspacing = 1.0; return yspacing; } else { gdcmWarningMacro( "Unfound Imager Pixel Spacing (0018,1164)" ); } entry = GetDataEntry(0x0028,0x0030); if( entry ) { yspacing = (float)entry->GetValue(0); if ( yspacing == 0.0 ) yspacing = 1.0; return yspacing; } else { gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" ); } return yspacing; }

float GDCM_NAME_SPACE::File::GetZOrigin (   )

gets the info from 0020,0032 : Image Position Patient else from 0020,0030 : Image Position (RET) else from 0020,1041 : Slice Location else from 0020,0050 : Location else 0. Returns: up-left image corner Z position Definition at line 979 of file gdcmFile.cxx. References gdcmErrorMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::DataEntry::GetValue(), GDCM_NAME_SPACE::DataEntry::GetValueCount(), and GDCM_NAME_SPACE::DataEntry::IsValueCountValid(). { DataEntry *entry = GetDataEntry(0x0020,0x0032); if( entry ) { if( entry->GetValueCount() == 3 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(2); } gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)"); return 0.0f; } entry = GetDataEntry(0x0020,0x0030); if( entry ) { if( entry->GetValueCount() == 3 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(2); } gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)"); return 0.0f; } // for *very* old ACR-NEMA images entry = GetDataEntry(0x0020,0x1041); if( entry ) { if( entry->GetValueCount() == 1 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(0); // VM=1 ! } gdcmWarningMacro( "Wrong Slice Location (0020,1041)"); return 0.0f; } entry = GetDataEntry(0x0020,0x0050); if( entry ) { if( entry->GetValueCount() == 1 ) { if (!entry->IsValueCountValid() ) { gdcmErrorMacro( "Invalid Value Count" ); } return (float)entry->GetValue(0); } gdcmWarningMacro( "Wrong Location (0020,0050)"); return 0.0f; } return 0.; // Hopeless }

int GDCM_NAME_SPACE::File::GetZSize (   )

Retrieve the number of planes of volume or the number of frames of a multiframe. Warning: When present we consider the "Number of Frames" as the third dimension. When missing we consider the third dimension as being the ACR-NEMA "Planes" tag content. Returns: The encountered size when found, 1 by default (single image). Definition at line 458 of file gdcmFile.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), and GDCM_NAME_SPACE::DataEntry::GetValue(). Referenced by GDCM_NAME_SPACE::FileHelper::CheckWriteIntegrity(), vtkGdcmReader::GetFileInformation(), GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(), vtkGdcmReader::LoadImageInMemory(), GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEG2000UserData(), GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEGUserData(), vtkGdcmReader::TestFileInformation(), userSuppliedMirrorFunction(), userSuppliedTopDownFunction(), and userSuppliedUpsideDownFunction(). { // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. DataEntry *entry = GetDataEntry(0x0028,0x0008); if( entry ) return (int)entry->GetValue(0); // We then consider the "Planes" entry as the third dimension entry = GetDataEntry(0x0028,0x0012); if( entry ) return (int)entry->GetValue(0); return 1; }

float GDCM_NAME_SPACE::File::GetZSpacing (   )

gets the info from 0018,0088 : Space Between Slices else from 0018,0050 : Slice Thickness else 1.0 When an element is missing, we suppose slices join together (no overlapping, no interslice gap) but we have no way to check it ! For *Dicom* images, ZSpacing *should be* calculated using XOrigin, YOrigin, ZOrigin (of the top left image corner) of 2 consecutive images, and the Orientation Computing ZSpacing on a single image is not really meaningfull ! Returns: Z dimension of a voxel-to be Definition at line 845 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GetSpacing(), and GDCM_NAME_SPACE::DataEntry::GetValue(). Referenced by vtkGdcmReader::GetFileInformation(). { float xspacing = 1.0; float yspacing = 1.0; float zspacing = 1.0; if ( GetSpacing(xspacing,yspacing,zspacing) ) { return zspacing; } // Spacing Between Slices : distance between the middle of 2 slices // Slices may be : // jointives (Spacing between Slices = Slice Thickness) // overlapping (Spacing between Slices < Slice Thickness) // disjointes (Spacing between Slices > Slice Thickness) // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal // It only concerns the MRI guys, not people wanting to visualize volumes // If Spacing Between Slices is missing, // we suppose slices joint together DataEntry *entry = GetDataEntry(0x0018,0x0088); if( entry ) { zspacing = (float)entry->GetValue(0); if ( zspacing == 0.0 ) zspacing = 1.0; return zspacing; } else gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)"); // if no 'Spacing Between Slices' is found, // we assume slices join together // (no overlapping, no interslice gap) entry = GetDataEntry(0x0018,0x0050); if( entry ) { zspacing = (float)entry->GetValue(0); if ( zspacing == 0.0 ) zspacing = 1.0; return zspacing; } else gdcmWarningMacro("Unfound Slice Thickness (0018,0050)"); // if no 'Spacing Between Slices' is found, // we assume slices join together // (no overlapping, no interslice gap) entry = GetDataEntry(0x3004,0x000c); if( entry ) { float z1 = (float)entry->GetValue(0); float z2 = (float)entry->GetValue(1); zspacing = z2 - z1; // can be negative... if ( zspacing == 0.0 ) zspacing = 1.0; return zspacing; } return zspacing; }

bool GDCM_NAME_SPACE::File::HasLUT (   )

tells us if LUT are used Warning: Right now, 'Segmented xxx Palette Color Lookup Table Data' are NOT considered as LUT, since nobody knows how to deal with them Please warn me if you know sbdy that *does* know ... jprx Returns: true if LUT Descriptors and LUT Tables were found Definition at line 1492 of file gdcmFile.cxx. References GDCM_NAME_SPACE::ElementSet::GetDocEntry(). Referenced by GDCM_NAME_SPACE::FileHelper::CheckWriteIntegrity(), vtkGdcmReader::GetFileInformation(), GetNumberOfScalarComponents(), vtkGdcmReader::LoadImageInMemory(), GDCM_NAME_SPACE::FileHelper::SetWriteToRaw(), and vtkGdcmReader::TestFileInformation(). { // Check the presence of the LUT Descriptors, and LUT Tables // LutDescriptorRed if ( !GetDocEntry(0x0028,0x1101) ) { return false; } // LutDescriptorGreen if ( !GetDocEntry(0x0028,0x1102) ) { return false; } // LutDescriptorBlue if ( !GetDocEntry(0x0028,0x1103) ) { return false; } // Red Palette Color Lookup Table Data if ( !GetDocEntry(0x0028,0x1201) ) { return false; } // Green Palette Color Lookup Table Data if ( !GetDocEntry(0x0028,0x1202) ) { return false; } // Blue Palette Color Lookup Table Data if ( !GetDocEntry(0x0028,0x1203) ) { return false; } // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent) // NOT taken into account, but we don't know how to use it ... return true; }

DataEntry * GDCM_NAME_SPACE::DocEntrySet::InsertEntryBinArea (  uint8_t *  binArea, int  lgth, uint16_t  group, uint16_t  elem, VRKey const &  vr = GDCM_VRUNKNOWN )  [inherited]

Modifies the value of a given Header Entry (Dicom Element) when it exists. Create it with the given value when unexistant. A copy of the binArea is made to be kept in the Document. Parameters: binArea  (binary) value to be set lgth  length of the Bin Area we want to set group  Group number of the Entry elem  Element number of the Entry vr  V(alue) R(epresentation) of the Entry -if private Entry- Returns: pointer to the modified/created Header Entry (NULL when creation failed). Definition at line 290 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DocEntrySet::AddEntry(), GDCM_NAME_SPACE::RefCounter::Delete(), gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDocEntry(), GDCM_NAME_SPACE::DocEntry::GetVR(), GDCM_NAME_SPACE::DocEntrySet::NewDataEntry(), GDCM_NAME_SPACE::DocEntrySet::RemoveEntry(), and GDCM_NAME_SPACE::DocEntrySet::SetEntryBinArea(). Referenced by GDCM_NAME_SPACE::FileHelper::InsertEntryBinArea(). { DataEntry *dataEntry = 0; DocEntry *currentEntry = GetDocEntry( group, elem ); // Verify the currentEntry if (currentEntry) { dataEntry = dynamic_cast<DataEntry *>(currentEntry); // Verify the VR if ( dataEntry ) if ( dataEntry->GetVR()!=vr ) dataEntry = NULL; // if currentEntry doesn't correspond to the requested dataEntry if ( !dataEntry) { if ( !RemoveEntry(currentEntry) ) { gdcmWarningMacro( "Removal of previous DocEntry failed."); return NULL; } } } // Create a new dataEntry if necessary if ( !dataEntry) { dataEntry = NewDataEntry(group, elem, vr); if ( !AddEntry(dataEntry) ) { gdcmWarningMacro( "AddEntry failed although this is a creation."); dataEntry->Delete(); return NULL; } dataEntry->Delete(); } // Set the dataEntry value uint8_t *tmpArea; if ( lgth>0 && binArea ) { tmpArea = new uint8_t[lgth]; memcpy(tmpArea,binArea,lgth); } else { tmpArea = 0; } if ( !SetEntryBinArea(tmpArea,lgth,dataEntry) ) { if ( tmpArea ) { delete[] tmpArea; } } return dataEntry; }

DataEntry * GDCM_NAME_SPACE::DocEntrySet::InsertEntryString (  std::string const &  value, uint16_t  group, uint16_t  elem, VRKey const &  vr = GDCM_VRUNKNOWN )  [inherited]

Modifies the value of a given Doc Entry (Dicom Element) when it exists. Creates it with the given value when unexistant. Parameters: value  (string) Value to be set group  Group number of the Entry elem  Element number of the Entry vr  V(alue) R(epresentation) of the Entry -if private Entry- Returns: pointer to the modified/created Header Entry (NULL when creation failed). Definition at line 216 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DocEntrySet::AddEntry(), GDCM_NAME_SPACE::RefCounter::Delete(), GDCM_NAME_SPACE::GDCM_VRUNKNOWN, gdcmWarningMacro, GDCM_NAME_SPACE::DictSet::GetDefaultPubDict(), GDCM_NAME_SPACE::Global::GetDicts(), GDCM_NAME_SPACE::DocEntrySet::GetDocEntry(), GDCM_NAME_SPACE::Dict::GetEntry(), GDCM_NAME_SPACE::DocEntry::GetKey(), GDCM_NAME_SPACE::DictEntry::GetVR(), GDCM_NAME_SPACE::DocEntry::GetVR(), GDCM_NAME_SPACE::DocEntrySet::NewDataEntry(), GDCM_NAME_SPACE::RefCounter::Register(), GDCM_NAME_SPACE::DocEntrySet::RemoveEntry(), and GDCM_NAME_SPACE::DocEntrySet::SetEntryString(). Referenced by GDCM_NAME_SPACE::FileHelper::InsertEntryString(), GDCM_NAME_SPACE::FileHelper::Write(), and Write(). { DataEntry *dataEntry = 0; DocEntry *currentEntry = GetDocEntry( group, elem ); VRKey localVR = vr; if (currentEntry) { dataEntry = dynamic_cast<DataEntry *>(currentEntry); // Verify the VR if ( dataEntry ) if ( dataEntry->GetVR()!=vr ) dataEntry = NULL; // if currentEntry doesn't correspond to the requested dataEntry if ( !dataEntry) { if ( !RemoveEntry(currentEntry) ) { gdcmWarningMacro( "Removal of previous DocEntry failed."); return NULL; } } } else // the 'currentEntry' was not found { if ( vr == GDCM_VRUNKNOWN ) // user didn't specify a VR. // Probabely he trusts the Dicom Dict ! { DictEntry *e = Global::GetDicts()->GetDefaultPubDict()->GetEntry(group, elem); if ( e ) { localVR = e->GetVR(); e->Register(); // ?? JPRx } } } // Create a new dataEntry if necessary if ( !dataEntry ) { dataEntry = NewDataEntry( group, elem, localVR ); if ( !AddEntry(dataEntry) ) { gdcmWarningMacro("AddEntry " << dataEntry->GetKey() << " failed although this is a creation."); dataEntry->Delete(); return NULL; } dataEntry->Delete(); // ?!? JPRx } // Set the dataEntry value SetEntryString(value, dataEntry); // The std::string value return dataEntry; }

SeqEntry * GDCM_NAME_SPACE::DocEntrySet::InsertSeqEntry (  uint16_t  group, uint16_t  elem )  [inherited]

Creates a new gdcm::SeqEntry and adds it to the current DocEntrySet. (remove any existing entry with same group,elem). Parameters: group  Group number of the Entry elem  Element number of the Entry Returns: pointer to the created SeqEntry (NULL when creation failed). Definition at line 361 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DocEntrySet::AddEntry(), GDCM_NAME_SPACE::RefCounter::Delete(), gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDocEntry(), GDCM_NAME_SPACE::DocEntrySet::NewSeqEntry(), and GDCM_NAME_SPACE::DocEntrySet::RemoveEntry(). Referenced by GDCM_NAME_SPACE::FileHelper::InsertSeqEntry(). { SeqEntry *seqEntry = 0; DocEntry *currentEntry = GetDocEntry( group, elem ); // Verify the currentEntry if ( currentEntry ) { seqEntry = dynamic_cast<SeqEntry *>(currentEntry); // Verify the VR if ( seqEntry ) seqEntry = NULL; // if currentEntry doesn't correspond to the requested seqEntry if ( !seqEntry ) { if (!RemoveEntry(currentEntry)) { gdcmWarningMacro( "Removal of previous DocEntry failed for (" <<std::hex << group << "|" << elem <<")" ); return NULL; } } } // Create a new seqEntry if necessary if ( !seqEntry ) { seqEntry = NewSeqEntry(group, elem); if ( !AddEntry(seqEntry) ) { gdcmWarningMacro( "AddEntry failed although this is a creation for (" <<std::hex << group << "|" << elem <<")" ); seqEntry->Delete(); return NULL; } seqEntry->Delete(); } // Remark : // SequenceDelimitationItem will be added at the end of the SeqEntry, // at write time return seqEntry; }

bool GDCM_NAME_SPACE::Document::IsDicomV3 (   )  [inherited]

Predicate for dicom version 3 file. Returns: True when the file is a dicom version 3. Definition at line 386 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::ElementSet::GetDocEntry(). Referenced by GetYSize(), and GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(). { // Checking if Transfer Syntax exists is enough // Anyway, it's too late check if the 'Preamble' was found ... // And ... would it be a rich idea to check ? // (some 'no Preamble' DICOM images exist !) return GetDocEntry(0x0002, 0x0010) != NULL; }

bool GDCM_NAME_SPACE::ElementSet::IsEmpty (   )  [inline, virtual, inherited]

Tells us if the ElementSet contains no entry. Implements GDCM_NAME_SPACE::DocEntrySet. Definition at line 59 of file gdcmElementSet.h. Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), and GDCM_NAME_SPACE::Document::IsParsable(). { return TagHT.empty(); }

bool GDCM_NAME_SPACE::File::IsMonochrome (   )

Check whether this a monochrome picture (gray levels) or not, using "Photometric Interpretation" tag (0x0028,0x0004). Returns: true when "MONOCHROME1" or "MONOCHROME2". False otherwise. Definition at line 1407 of file gdcmFile.cxx. References GDCM_NAME_SPACE::Util::DicomStringEqual(), GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), and GetNumberOfScalarComponents(). { const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { gdcmWarningMacro( "Photometric Interpretation (0028,0004) supposed to be " << "mandatory"); // to deal with old ACR-NEMA images if (GetNumberOfScalarComponents() == 1) return true; } return false; }

bool GDCM_NAME_SPACE::File::IsMonochrome1 (   )

Check whether this a MONOCHROME1 picture (high values = dark) or not using "Photometric Interpretation" tag (0x0028,0x0004). Returns: true when "MONOCHROME1" . False otherwise. Definition at line 1431 of file gdcmFile.cxx. References GDCM_NAME_SPACE::Util::DicomStringEqual(), GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmWarningMacro, and GDCM_NAME_SPACE::DocEntrySet::GetEntryString(). { const std::string &PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1") ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { gdcmWarningMacro( "Photometric Interpretation (0028,0004) : supposed to" << " be mandatory! "); } return false; }

bool GDCM_NAME_SPACE::File::IsPaletteColor (   )

Check whether this a "PALETTE COLOR" picture or not by accessing the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). Returns: true when "PALETTE COLOR". False otherwise. Definition at line 1451 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmDebugMacro, and GDCM_NAME_SPACE::DocEntrySet::GetEntryString(). { std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "PALETTE COLOR " ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { gdcmDebugMacro( "Not found : Palette color (0028,0004)"); } return false; }

bool GDCM_NAME_SPACE::Document::IsPapyrus (   )  [inherited]

Predicate for Papyrus file Dedicated to whomsoever it may concern. Returns: True when the file is a Papyrus file. Definition at line 400 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::ElementSet::GetDocEntry(). { // check for Papyrus private Sequence DocEntry *e = GetDocEntry(0x0041, 0x1050); if ( !e ) return false; // check if it's actually a Sequence if ( !dynamic_cast<SeqEntry*>(e) ) return false; return true; }

bool GDCM_NAME_SPACE::Document::IsParsable (   )  [inherited]

This predicate tells us whether or not the current Document was properly parsed and contains at least *one* Dicom Element (and nothing more, sorry). Returns: false when we're 150 % sure it's NOT a Dicom/Acr file, true otherwise. Definition at line 354 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::Document::Filetype, gdcmWarningMacro, GDCM_NAME_SPACE::Document::GetFileName(), GDCM_NAME_SPACE::ElementSet::IsEmpty(), and GDCM_NAME_SPACE::Unknown. Referenced by GDCM_NAME_SPACE::Document::IsReadable(). { if ( Filetype == Unknown ) { gdcmWarningMacro( "Wrong filetype for " << GetFileName()); return false; } if ( IsEmpty() ) { gdcmWarningMacro( "No tag in internal hash table."); return false; } return true; }

bool GDCM_NAME_SPACE::File::IsReadable (   )  [virtual]

This predicate, based on hopefully reasonable heuristics, decides whether or not the current File was properly parsed and contains the mandatory information for being considered as a well formed and usable Dicom/Acr File. Returns: true when File is the one of a reasonable Dicom/Acr file, false otherwise. Reimplemented from GDCM_NAME_SPACE::Document. Definition at line 277 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmWarningMacro, GDCM_NAME_SPACE::ElementSet::GetDocEntry(), GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GrPixel, GDCM_NAME_SPACE::Document::IsReadable(), and NumPixel. Referenced by GDCM_NAME_SPACE::SerieHelper::AddFileName(), GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(), GDCM_NAME_SPACE::SerieHelper::CreateUniqueSeriesIdentifier(), GDCM_NAME_SPACE::FileHelper::FileHelper(), vtkGdcmReader::LoadFileInformation(), and GDCM_NAME_SPACE::FileHelper::Print(). { if ( !Document::IsReadable() ) { return false; } const std::string &res = GetEntryString(0x0028, 0x0005); if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) { gdcmWarningMacro("Wrong Image Dimensions" << res); return false; // Image Dimensions } bool b0028_0100 = true; if ( !GetDocEntry(0x0028, 0x0100) ) { gdcmWarningMacro("Bits Allocated (0028|0100) not found"); //return false; // "Bits Allocated" b0028_0100 = false; } bool b0028_0101 = true; if ( !GetDocEntry(0x0028, 0x0101) ) { gdcmWarningMacro("Bits Stored (0028|0101) not found"); //return false; // "Bits Stored" b0028_0101 = false; } bool b0028_0102 = true; if ( !GetDocEntry(0x0028, 0x0102) ) { gdcmWarningMacro("Hight Bit (0028|0102) not found"); //return false; // "High Bit" b0028_0102 = false; } bool b0028_0103 = true; if ( !GetDocEntry(0x0028, 0x0103) ) { gdcmWarningMacro("Pixel Representation (0028|0103) not found"); //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed) b0028_0103 = false; } if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103) { gdcmWarningMacro("Too much mandatory Tags missing !"); return false; } if ( !GetDocEntry(GrPixel, NumPixel) ) { gdcmWarningMacro("Pixel Dicom Element " << std::hex << GrPixel << "|" << NumPixel << "not found"); return false; // Pixel Dicom Element not found :-( } return true; }

bool GDCM_NAME_SPACE::File::IsSignedPixelData (   )

Check whether the pixels are signed (1) or UNsigned (0) data. Warning: The method defaults to false (UNsigned) when tag 0028|0103 is missing. The responsability of checking this value is left to the caller (NO transformation is performed on the pixels to make then >0) Returns: True when signed, false when UNsigned Definition at line 1390 of file gdcmFile.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), and GDCM_NAME_SPACE::DataEntry::GetValue(). Referenced by GDCM_NAME_SPACE::FileHelper::ConvertFixGreyLevels(), GetPixelType(), GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile(), and GDCM_NAME_SPACE::PixelWriteConvert::SetCompressJPEG2000UserData(). { DataEntry *entry = GetDataEntry(0x0028, 0x0103);//"Pixel Representation" if( !entry ) { gdcmWarningMacro( "Pixel Representation (0028,0103) supposed to be " << "mandatory"); return false; } return entry->GetValue(0) != 0; }

int GDCM_NAME_SPACE::ElementSet::IsVRCoherent (  uint16_t  group  )  [inherited]

Checks whether *all* the DataEntries of the group have all the same type for VR (ImplicitVR or ExplicitVR). Parameters: group  group number to be checked Returns: 1:ImplicitVR 2:ExplicitVR -1:NotCoherent Definition at line 225 of file gdcmElementSet.cxx. References GDCM_NAME_SPACE::ElementSet::TagHT. { uint16_t currentGroup; int codeVR = -1; int currentCodeVR; for(TagDocEntryHT::iterator cc = TagHT.begin();cc != TagHT.end(); ++cc) { currentGroup = cc->second->GetGroup(); if ( currentGroup < group ) continue; if ( currentGroup > group ) break; // currentGroup == group if (codeVR == -1) { if (cc->second->IsImplicitVR() ) codeVR = 1; else codeVR = 2; continue; } else { if (cc->second->IsImplicitVR() ) currentCodeVR = 1; //Implicit else currentCodeVR = 2; // Explicit if ( currentCodeVR == codeVR ) continue; else return -1; // -1 : not coherent } } return codeVR; }

bool GDCM_NAME_SPACE::File::IsYBRFull (   )

Check whether this a "YBR_FULL" color picture or not by accessing the "Photometric Interpretation" tag ( 0x0028, 0x0004 ). Returns: true when "YBR_FULL". False otherwise. Definition at line 1470 of file gdcmFile.cxx. References GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmDebugMacro, and GDCM_NAME_SPACE::DocEntrySet::GetEntryString(). { std::string PhotometricInterp = GetEntryString( 0x0028, 0x0004 ); if ( PhotometricInterp == "YBR_FULL" ) { return true; } if ( PhotometricInterp == GDCM_UNFOUND ) { gdcmDebugMacro( "Not found : YBR Full (0028,0004)"); } return false; }

bool GDCM_NAME_SPACE::File::Load (   )  [virtual]

Loader. Returns: false if file cannot be open or no swap info was found, or no tag was found. Reimplemented from GDCM_NAME_SPACE::Document. Definition at line 145 of file gdcmFile.cxx. References DoTheLoadingJob(). Referenced by GDCM_NAME_SPACE::SerieHelper::AddFileName(), GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(), GDCM_NAME_SPACE::FileHelper::Load(), and vtkGdcmReader::LoadFileInformation(). { if ( ! this->Document::Load( ) ) return false; return DoTheLoadingJob( ); }

void GDCM_NAME_SPACE::Document::LoadEntryBinArea (  DataEntry *  entry  )  [virtual, inherited]

Loads (from disk) the element content when a string is not suitable. Parameters: entry  Entry whose binArea is going to be loaded Definition at line 761 of file gdcmDocument.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DataEntry::GetBinArea(), GDCM_NAME_SPACE::DocEntry::GetElement(), GDCM_NAME_SPACE::DocEntry::GetGroup(), GDCM_NAME_SPACE::DocEntry::GetLength(), GDCM_NAME_SPACE::DocEntry::GetOffset(), GDCM_NAME_SPACE::Document::OpenFile(), GDCM_NAME_SPACE::DataEntry::SetState(), and GDCM_NAME_SPACE::DataEntry::STATE_UNREAD. { if( entry->GetBinArea() ) return; bool openFile = !Fp; if ( openFile ) OpenFile(); //size_t o =(size_t)entry->GetOffset(); Fp->seekg((size_t)entry->GetOffset(), std::ios::beg); // FIXME : for each DataEntry ! size_t l = entry->GetLength(); uint8_t *data = new uint8_t[l]; if ( !data ) { gdcmWarningMacro( "Cannot allocate DataEntry content for : " << std::hex << entry->GetGroup() << "|" << entry->GetElement() ); return; } // Read the data Fp->read((char*)data, l); if ( Fp->fail() || Fp->eof() ) { delete[] data; entry->SetState(DataEntry::STATE_UNREAD); return; } // Swap the data content if necessary uint32_t i; unsigned short vrLgth = Global::GetVR()->GetAtomicElementLength(entry->GetVR()); // FIXME : trouble expected if we read an ... OW Entry (LUT, etc ..) // if( entry->GetVR() == "OW" ) // vrLgth = 1; switch(vrLgth) { case 1: { break; } case 2: { uint16_t *data16 = (uint16_t *)data; for(i=0;i<l/vrLgth;i++) data16[i] = SwapShort(data16[i]); break; } case 4: { uint32_t *data32 = (uint32_t *)data; for(i=0;i<l/vrLgth;i++) data32[i] = SwapLong(data32[i]); break; } case 8: { double *data64 = (double *)data; for(i=0;i<l/vrLgth;i++) data64[i] = SwapDouble(data64[i]); break; } } entry->SetBinArea(data); if ( openFile ) // The file is left in the state (open/close) it was at entrance CloseFile(); }

void GDCM_NAME_SPACE::Document::LoadEntryBinArea (  uint16_t  group, uint16_t  elem )  [virtual, inherited]

Loads (from disk) the element content when a string is not suitable. Parameters: group  group number of the Entry elem  element number of the Entry Definition at line 736 of file gdcmDocument.cxx. References gdcmDebugMacro, gdcmWarningMacro, and GDCM_NAME_SPACE::ElementSet::GetDocEntry(). Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), and GDCM_NAME_SPACE::Document::LoadDocEntry(). { // Search the corresponding DocEntry DocEntry *docEntry = GetDocEntry(group, elem); if ( !docEntry ) { gdcmDebugMacro(std::hex << group << "|" << elem << " doesn't exist" ); return; } DataEntry *dataEntry = dynamic_cast<DataEntry *>(docEntry); if ( !dataEntry ) { gdcmWarningMacro(std::hex << group << "|" << elem << " is NOT a DataEntry"); return; } LoadEntryBinArea(dataEntry); }

bool GDCM_NAME_SPACE::File::MayIWrite (  uint16_t  group  )  [inline, protected]

Protect the Writer from writing illegal groups. Reimplemented from GDCM_NAME_SPACE::ElementSet. Definition at line 195 of file gdcmFile.h. { if (group < 8 && group !=2 ) return false; else return true; }

static File* GDCM_NAME_SPACE::File::New (   )  [inline, static]

Definition at line 104 of file gdcmFile.h. Referenced by GDCM_NAME_SPACE::SerieHelper::AddFileName(), GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(), GDCM_NAME_SPACE::FileHelper::FileHelper(), and vtkGdcmReader::LoadFileInformation(). {return new File();}

DataEntry * GDCM_NAME_SPACE::DocEntrySet::NewDataEntry (  uint16_t  group, uint16_t  elem, VRKey const &  vr = GDCM_VRUNKNOWN )  [inherited]

Build a new DataEntry from all the low level arguments. Parameters: group  Group number of the new Entry elem  Element number of the new Entry vr  V(alue) R(epresentation) of the new Entry Remarks: The user of this method must destroy the DataEntry when unused Definition at line 425 of file gdcmDocEntrySet.cxx. References gdcmWarningMacro, and GDCM_NAME_SPACE::DataEntry::New(). Referenced by GDCM_NAME_SPACE::FileHelper::CopyDataEntry(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryBinArea(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryString(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry(). { DataEntry *newEntry = DataEntry::New(group, elem, vr); if (!newEntry) { gdcmWarningMacro( "Failed to allocate DataEntry for (" <<std::hex << group << "|" << elem <<")" ); return 0; } return newEntry; }

SeqEntry * GDCM_NAME_SPACE::DocEntrySet::NewSeqEntry (  uint16_t  group, uint16_t  elem )  [inherited]

Build a new SeqEntry from all the low level arguments. Parameters: group  Group number of the new Entry elem  Element number of the new Entry Remarks: The user of this method must destroy the SeqEntry when unused Definition at line 445 of file gdcmDocEntrySet.cxx. References gdcmWarningMacro, and GDCM_NAME_SPACE::SeqEntry::New(). Referenced by GDCM_NAME_SPACE::Document::Backtrack(), GDCM_NAME_SPACE::DocEntrySet::InsertSeqEntry(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry(). { //DictEntry *dictEntry = GetDictEntry(group, elem, "SQ"); //SeqEntry *newEntry = SeqEntry::New( dictEntry ); SeqEntry *newEntry = SeqEntry::New( group, elem ); //dictEntry->Unregister(); // GetDictEntry register it if (!newEntry) { gdcmWarningMacro( "Failed to allocate SeqEntry for (" <<std::hex << group << "|" << elem <<")" ); return 0; } return newEntry; }

std::ifstream * GDCM_NAME_SPACE::Document::OpenFile (   )  [inherited]

Tries to open the file Document::Filename and checks the preamble when existing, or if the file starts with an ACR-NEMA look-like element. Returns: The FILE pointer on success, 0 on failure. Definition at line 590 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::Document::Filename, and GDCM_NAME_SPACE::Document::HasDCMPreamble. Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), DoTheLoadingJob(), GDCM_NAME_SPACE::FileHelper::GetRaw(), and GDCM_NAME_SPACE::Document::LoadEntryBinArea(). { HasDCMPreamble = false; if (Filename.length() == 0) { return 0; } if ( Fp ) { gdcmDebugMacro( "File already open: " << Filename.c_str()); CloseFile(); } Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); if ( ! *Fp ) { // Don't user gdcmErrorMacro : // a spurious message will appear when you use, for instance // gdcm::FileHelper *fh = new gdcm::FileHelper( outputFileName ); // to create outputFileName. // FIXME : if the upper comment is still usefull // --> the constructor is not so good ... gdcmWarningMacro( "Cannot open file: " << Filename.c_str()); delete Fp; Fp = 0; return 0; //exit(1); // No function is allowed to leave the application instead // of warning the caller } uint16_t zero = 0; Fp->read((char*)&zero, (size_t)2); if ( Fp->eof() ) { CloseFile(); return 0; } //-- DICOM -- Fp->seekg(126L, std::ios::cur); // Once per Document char dicm[4]; // = {' ',' ',' ',' '}; Fp->read(dicm, (size_t)4); if ( Fp->eof() ) { CloseFile(); return 0; } if ( memcmp(dicm, "DICM", 4) == 0 ) { HasDCMPreamble = true; return Fp; } //-- Broken ACR or DICOM (?) with no Preamble; may start with a Shadow Group -- // FIXME : We cannot be sure the preable is only zeroes.. // (see ACUSON-24-YBR_FULL-RLE.dcm ) if ( zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 || zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 || zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 || zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 || zero == 0x0028 || 0x2800 // worse : some ACR-NEMA like files // start 00028 group ?!? ) { std::string msg = Util::Format( "ACR/DICOM starting by 0x(%04x) at the beginning of the file\n", zero); // FIXME : is it a Warning message, or a Debug message? gdcmWarningMacro( msg.c_str() ); return Fp; } // -- Neither ACR/No Preamble Dicom nor DICOMV3 file CloseFile(); // Don't user Warning nor Error, not to pollute the output // while directory recursive parsing ... gdcmDebugMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: " << Filename.c_str()); return 0; }

bool GDCM_NAME_SPACE::Document::operator< (  Document &  document  )  [inherited]

Loads the element while preserving the current underlying file position indicator as opposed to LoadDocEntry that modifies it Compares two documents, according to DicomDir rules. Warning: Does NOT work with ACR-NEMA files Todo: Find a trick to solve the pb (use RET fields ?) Parameters: document  to compare with current one Returns: true if 'smaller' Definition at line 860 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::DocEntrySet::GetEntryString(). { // Patient Name std::string s1 = GetEntryString(0x0010,0x0010); std::string s2 = document.GetEntryString(0x0010,0x0010); if (s1 < s2) { return true; } else if ( s1 > s2 ) { return false; } else { // Patient ID s1 = GetEntryString(0x0010,0x0020); s2 = document.GetEntryString(0x0010,0x0020); if ( s1 < s2 ) { return true; } else if ( s1 > s2 ) { return false; } else { // Study Instance UID s1 = GetEntryString(0x0020,0x000d); s2 = document.GetEntryString(0x0020,0x000d); if ( s1 < s2 ) { return true; } else if ( s1 > s2 ) { return false; } else { // Serie Instance UID s1 = GetEntryString(0x0020,0x000e); s2 = document.GetEntryString(0x0020,0x000e); if ( s1 < s2 ) { return true; } else if ( s1 > s2 ) { return false; } } } } return false; }

void GDCM_NAME_SPACE::ElementSet::Print (  std::ostream &  os = std::cout, std::string const &  indent = "" )  [virtual, inherited]

Prints the Header Entries (Dicom Elements) from the H Table. Parameters: os  ostream to write to indent  Indentation string to be prepended during printing Reimplemented from GDCM_NAME_SPACE::Base. Reimplemented in GDCM_NAME_SPACE::DicomDir. Definition at line 277 of file gdcmElementSet.cxx. References GDCM_NAME_SPACE::DataEntry::FLAG_PIXELDATA, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::Base::PrintLevel, GDCM_NAME_SPACE::DataEntry::SetFlag(), and GDCM_NAME_SPACE::ElementSet::TagHT. Referenced by GDCM_NAME_SPACE::FileHelper::Print(). { // Let's change the 'warning value' for Pixel Data, // to avoid human reader to be confused by 'gdcm::NotLoaded'. DataEntry *pixelElement = GetDataEntry(0x7fe0,0x0010); if ( pixelElement != 0 ) { pixelElement->SetFlag( DataEntry::FLAG_PIXELDATA ); } for( TagDocEntryHT::const_iterator i = TagHT.begin(); i != TagHT.end(); ++i) { DocEntry *entry = i->second; entry->SetPrintLevel(PrintLevel); entry->Print(os); if ( dynamic_cast<SeqEntry*>(entry) ) { // Avoid the newline for a sequence: continue; } os << std::endl; } }

void GDCM_NAME_SPACE::File::ReadEncapsulatedBasicOffsetTable (   )  [private]

When parsing the Pixel Data of an encapsulated file, read the basic offset table (when present, and BTW dump it). Definition at line 2297 of file gdcmFile.cxx. References BasicOffsetTableItemValue, GDCM_NAME_SPACE::Document::Fp, gdcmDebugMacro, and ReadTagLength(). Referenced by ComputeJPEGFragmentInfo(), and ComputeRLEInfo(). { uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); // When present, read the basic offset table itself. // Notes: - since the presence of this basic offset table is optional // we can't rely on it for the implementation, and we will simply // trash its content (when present). // - still, when present, we could add some further checks on the // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 ) { char *charBasicOffsetTableItemValue = new char[itemLength]; Fp->read(charBasicOffsetTableItemValue, itemLength); unsigned int nbEntries = itemLength/4; assert( nbEntries*4 == itemLength); // Make sure this is a multiple BasicOffsetTableItemValue = new uint32_t[nbEntries]; for (unsigned int i=0; i < nbEntries; i++ ) { BasicOffsetTableItemValue[i] = *((uint32_t*)(&charBasicOffsetTableItemValue[4*i])); #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION) uint32_t val = BasicOffsetTableItemValue[i]; BasicOffsetTableItemValue[i] = ( (val<<24) | ((val<<8) & 0x00ff0000) | ( (val>>8) & 0x0000ff00) | (val>>24) ); #endif gdcmDebugMacro( "Read one length for: " << std::hex << BasicOffsetTableItemValue[i] ); } delete[] charBasicOffsetTableItemValue; } }

uint16_t GDCM_NAME_SPACE::Document::ReadInt16 (   )  throw ( FormatError ) [protected, inherited]

Reads a supposed to be 16 Bits integer (swaps it depending on processor endianness). Returns: read value Definition at line 946 of file gdcmDocument.cxx. Referenced by ReadTag(). { uint16_t g; Fp->read ((char*)&g, (size_t)2); if ( Fp->fail() ) { throw FormatError( "Document::ReadInt16()", " file error." ); } if ( Fp->eof() ) { throw FormatError( "Document::ReadInt16()", "EOF." ); } g = SwapShort(g); return g; }

uint32_t GDCM_NAME_SPACE::Document::ReadInt32 (   )  throw ( FormatError ) [protected, inherited]

Reads a supposed to be 32 Bits integer (swaps it depending on processor endianness). Returns: read value Definition at line 980 of file gdcmDocument.cxx. Referenced by ComputeRLEInfo(), GDCM_NAME_SPACE::Document::FindDocEntryLengthOBOrOW(), and ReadTagLength(). { uint32_t g; Fp->read ((char*)&g, (size_t)4); if ( Fp->fail() ) { throw FormatError( "Document::ReadInt32()", " file error." ); } if ( Fp->eof() ) { throw FormatError( "Document::ReadInt32()", "EOF." ); } g = SwapLong(g); return g; }

bool GDCM_NAME_SPACE::File::ReadTag (  uint16_t  testGroup, uint16_t  testElem )  [private]

Assuming the internal file pointer Document::Fp is placed at the beginning of a tag, check whether this tag is (TestGroup, TestElem). Warning: On success the internal file pointer Document::Fp is modified to point after the tag. On failure (i.e. when the tag wasn't the expected tag (TestGroup, TestElem) the internal file pointer Document::Fp is restored to its original position. Parameters: testGroup  The expected group of the tag. testElem  The expected Element of the tag. Returns: True on success, false otherwise. Definition at line 2214 of file gdcmFile.cxx. References GDCM_NAME_SPACE::Document::Fp, gdcmErrorMacro, gdcmWarningMacro, GDCM_NAME_SPACE::Document::ReadInt16(), and GDCM_NAME_SPACE::DictEntry::TranslateToKey(). Referenced by ComputeJPEGFragmentInfo(), and ReadTagLength(). { long positionOnEntry = Fp->tellg(); // Only when reading fragments //long currentPosition = positionOnEntry; // On debugging purposes // Read the Item Tag group and element, and make // sure they are what we expected: uint16_t itemTagGroup; uint16_t itemTagElem; try { itemTagGroup = ReadInt16(); itemTagElem = ReadInt16(); } catch ( FormatError ) { gdcmErrorMacro( "Can not read tag for " << " We should have found tag (" << DictEntry::TranslateToKey(testGroup,testElem) << ")" ) ; return false; } if ( itemTagGroup != testGroup || itemTagElem != testElem ) { // in order not to pollute output we don't warn on 'delimitors' if (itemTagGroup != 0xfffe || testGroup != 0xfffe ) gdcmWarningMacro( "Wrong Item Tag found:" << " We should have found tag (" << DictEntry::TranslateToKey(testGroup,testElem) << ")" << std::endl << " but instead we encountered tag (" << DictEntry::TranslateToKey(itemTagGroup,itemTagElem) << ")" << " at address: " << " 0x(" << std::hex << (unsigned int)positionOnEntry << std::dec << ")" ) ; Fp->seekg(positionOnEntry, std::ios::beg); return false; } return true; }

uint32_t GDCM_NAME_SPACE::File::ReadTagLength (  uint16_t  testGroup, uint16_t  testElem )  [private]

Assuming the internal file pointer Document::Fp is placed at the beginning of a tag (TestGroup, TestElement), read the length associated to the Tag. Warning: On success the internal file pointer Document::Fp is modified to point after the tag and its length. On failure (i.e. when the tag wasn't the expected tag (TestGroup, TestElement) the internal file pointer Document::Fp is restored to its original position. Parameters: testGroup  The expected Group of the tag. testElem  The expected Element of the tag. Returns: On success returns the length associated to the tag. On failure returns 0. Definition at line 2270 of file gdcmFile.cxx. References gdcmDebugMacro, gdcmErrorMacro, GDCM_NAME_SPACE::Document::ReadInt32(), ReadTag(), and GDCM_NAME_SPACE::DictEntry::TranslateToKey(). Referenced by ComputeJPEGFragmentInfo(), ComputeRLEInfo(), and ReadEncapsulatedBasicOffsetTable(). { if ( !ReadTag(testGroup, testElem) ) { // Avoid polutting output if ( testGroup != 0xfffe ) gdcmErrorMacro( "ReadTag did not succeed for (" << DictEntry::TranslateToKey(testGroup,testElem) << ")..." ); return 0; } // long currentPosition = Fp->tellg(); // save time // JPRx uint32_t itemLength = ReadInt32(); gdcmDebugMacro( "Basic Item Length is: " << itemLength // << " at address: " << std::hex << (unsigned int)currentPosition ); return itemLength; }

void GDCM_NAME_SPACE::RefCounter::Register (   )  [inline, inherited]

Register the object. Remarks: It increments the reference counting Definition at line 46 of file gdcmRefCounter.h. Referenced by GDCM_NAME_SPACE::SQItem::AddEntry(), GDCM_NAME_SPACE::SeqEntry::AddSQItem(), GDCM_NAME_SPACE::SeqEntry::Copy(), GDCM_NAME_SPACE::DicomDir::Copy(), GDCM_NAME_SPACE::FileHelper::FileHelper(), GDCM_NAME_SPACE::DocEntrySet::GetDictEntry(), GDCM_NAME_SPACE::DocEntry::GetName(), GDCM_NAME_SPACE::DocEntry::GetVM(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryString(), GDCM_NAME_SPACE::CommandManager::InSetCommand(), GDCM_NAME_SPACE::DocEntryArchive::Push(), and GDCM_NAME_SPACE::SeqEntry::SetDelimitationItem(). { RefCount++; }

bool GDCM_NAME_SPACE::ElementSet::RemoveEntry (  DocEntry *  entryToRemove  )  [virtual, inherited]

Clear the hash table from given entry AND delete the entry. Parameters: entryToRemove  Entry to remove AND delete. Implements GDCM_NAME_SPACE::DocEntrySet. Definition at line 122 of file gdcmElementSet.cxx. References GDCM_NAME_SPACE::DocEntry::GetKey(), GDCM_NAME_SPACE::ElementSet::TagHT, and GDCM_NAME_SPACE::RefCounter::Unregister(). Referenced by GDCM_NAME_SPACE::Document::Backtrack(), GDCM_NAME_SPACE::DicomDir::NewMeta(), GDCM_NAME_SPACE::DocEntryArchive::Push(), and GDCM_NAME_SPACE::DocEntryArchive::Restore(). { const TagKey &key = entryToRemove->GetKey(); if ( TagHT.count(key) == 1 ) { TagHT.erase(key); entryToRemove->Unregister(); return true; } gdcmWarningMacro( "Key not present : " << key); return false ; }

bool GDCM_NAME_SPACE::DocEntrySet::SetEntryBinArea (  uint8_t *  content, int  lgth, DataEntry *  entry )  [inherited]

Accesses an existing DataEntry (i.e. a Dicom Element) and modifies its content with the given value. Parameters: content  new value (void* -> uint8_t*) to substitute with entry  Entry to be modified lgth  new value length Definition at line 195 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DataEntry::SetBinArea(), and GDCM_NAME_SPACE::DocEntry::SetLength(). { if (entry) { entry->SetLength(lgth); entry->SetBinArea(content); return true; } return false; }

bool GDCM_NAME_SPACE::DocEntrySet::SetEntryBinArea (  uint8_t *  content, int  lgth, uint16_t  group, uint16_t  elem )  [inherited]

Accesses an existing DocEntry (i.e. a Dicom Element) through its (group, element) and modifies its content with the given value. Parameters: content  new value (void* -> uint8_t*) to substitute with lgth  new value length group  group number of the Dicom Element to modify elem  element number of the Dicom Element to modify Definition at line 158 of file gdcmDocEntrySet.cxx. References gdcmWarningMacro, and GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(). Referenced by GDCM_NAME_SPACE::DocEntrySet::InsertEntryBinArea(), and GDCM_NAME_SPACE::FileHelper::SetEntryBinArea(). { DataEntry *entry = GetDataEntry(group, elem); if (!entry ) { gdcmWarningMacro( "No corresponding DataEntry " << std::hex << group << "," << elem << " element (try promotion first)."); return false; } return SetEntryBinArea(content,lgth,entry); }

bool GDCM_NAME_SPACE::DocEntrySet::SetEntryString (  std::string const &  content, DataEntry *  entry )  [inherited]

Accesses an existing DocEntry (i.e. a Dicom Element) and modifies its content with the given value. Parameters: content  new value (string) to substitute with entry  Entry to be modified Definition at line 178 of file gdcmDocEntrySet.cxx. References GDCM_NAME_SPACE::DataEntry::SetString(). { if (entry) { entry->SetString(content); return true; } return false; }

bool GDCM_NAME_SPACE::DocEntrySet::SetEntryString (  std::string const &  content, uint16_t  group, uint16_t  elem )  [inherited]

Accesses an existing DocEntry (i.e. a Dicom Element) through its (group, element) and modifies its content with the given value. Parameters: content  new value (string) to substitute with group  group number of the Dicom Element to modify elem  element number of the Dicom Element to modify Definition at line 136 of file gdcmDocEntrySet.cxx. References gdcmWarningMacro, and GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(). Referenced by AnonymizeFile(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryString(), and GDCM_NAME_SPACE::FileHelper::SetEntryString(). { DataEntry *entry = GetDataEntry(group, elem); if (!entry ) { gdcmWarningMacro( "No corresponding DataEntry " << std::hex << group << "," << elem << " element (try promotion first)."); return false; } return SetEntryString(content,entry); }

virtual void GDCM_NAME_SPACE::Document::SetFileName (  std::string const &  fileName  )  [inline, virtual, inherited]

Accessor to Filename. Reimplemented in GDCM_NAME_SPACE::DicomDir. Definition at line 80 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::SerieHelper::AddFileName(), GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(), GDCM_NAME_SPACE::Document::Document(), vtkGdcmReader::LoadFileInformation(), and GDCM_NAME_SPACE::FileHelper::SetFileName(). { if (Filename != fileName) Filename = fileName, IsDocumentModified = true; }

void GDCM_NAME_SPACE::File::SetFourthDimensionLocation (  uint16_t  group, uint16_t  elem )  [inline]

Definition at line 112 of file gdcmFile.h. { FourthDimensionLocation = TagKey(group, elem); }

void GDCM_NAME_SPACE::Document::SetLoadMode (  int  mode  )  [inline, inherited]

Sets the LoadMode as a boolean string. LD_NOSEQ, LD_NOSHADOW, LD_NOSHADOWSEQ ... (nothing more, right now) WARNING : before using NO_SHADOW, be sure *all* your files contain accurate values in the 0x0000 element (if any) of *each* Shadow Group. The parser will fail if the size is wrong ! Parameters: mode  Load mode to be used Definition at line 107 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::SerieHelper::AddFileName(), GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(), vtkGdcmReader::LoadFileInformation(), and GDCM_NAME_SPACE::FileHelper::SetLoadMode(). { if (LoadMode != mode) LoadMode=mode, IsDocumentModified = true; }

void GDCM_NAME_SPACE::Document::SetMaxSizeLoadEntry (  long  newSize  )  [inherited]

during parsing, Header Elements too long are not loaded in memory Parameters: newSize  new size Definition at line 2182 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::Document::MaxSizeLoadEntry. Referenced by GDCM_NAME_SPACE::Document::Document(). { if ( newSize < 0 ) { return; } if ((uint32_t)newSize >= (uint32_t)0xffffffff ) { MaxSizeLoadEntry = 0xffffffff; return; } MaxSizeLoadEntry = newSize; }

void GDCM_NAME_SPACE::Base::SetPrintLevel (  int  level  )  [inline, inherited]

Sets the print level for the Dicom Header Elements. Note: 0 for Light Print; 1 for 'medium' Print, 2 for Heavy Print Definition at line 47 of file gdcmBase.h. Referenced by GDCM_NAME_SPACE::FileHelper::Print(), and GDCM_NAME_SPACE::DicomDir::Print(). { PrintLevel = level; }

bool GDCM_NAME_SPACE::Document::SetShaDict (  DictKey const &  dictName  )  [inherited]

Set the shadow dictionary used. Parameters: dictName  name of the dictionary to use in shadow Definition at line 341 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::DictSet::GetDict(), GDCM_NAME_SPACE::Global::GetDicts(), and GDCM_NAME_SPACE::Document::RefShaDict. { RefShaDict = Global::GetDicts()->GetDict(dictName); return !RefShaDict; }

bool GDCM_NAME_SPACE::Document::SetShaDict (  Dict *  dict  )  [inherited]

Set the shadow dictionary used. Parameters: dict  dictionary to use in shadow Definition at line 331 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::Document::RefShaDict. { RefShaDict = dict; return !RefShaDict; }

void GDCM_NAME_SPACE::Document::SkipBytes (  uint32_t  nBytes  )  [inline, protected, inherited]

skips bytes inside the source file Definition at line 126 of file gdcmDocument.h. Referenced by ComputeJPEGFragmentInfo(), ComputeRLEInfo(), GDCM_NAME_SPACE::Document::FindDocEntryLengthOBOrOW(), and GDCM_NAME_SPACE::Document::SkipDocEntry(). { Fp->seekg((long)nBytes, std::ios::cur);}

void GDCM_NAME_SPACE::RefCounter::Unregister (   )  [inline, inherited]

Unregister the object. Remarks: It decrements the reference counting Definition at line 50 of file gdcmRefCounter.h. Referenced by GDCM_NAME_SPACE::Document::ReadNextDocEntry(), GDCM_NAME_SPACE::SQItem::RemoveEntry(), GDCM_NAME_SPACE::ElementSet::RemoveEntry(), and GDCM_NAME_SPACE::FileHelper::~FileHelper(). { //std::cout <<"================Unreg " << typeid(*this).name() << std::endl; RefCount--; if(RefCount<=0) delete this; }

bool GDCM_NAME_SPACE::File::Write (  std::string  fileName, FileType  writetype )

Performs some consistency checking on various 'File related' (as opposed to 'DicomDir related') entries then writes in a file all the (Dicom Elements) included the Pixels. Parameters: fileName  file name to write to writetype  type of the file to be written (ACR, ExplicitVR, ImplicitVR) Todo: FIXME : Derma?.dcm does not have it...let's remove it ?!? JPRx Definition at line 1979 of file gdcmFile.cxx. References GDCM_NAME_SPACE::Document::ComputeGroup0002Length(), GDCM_NAME_SPACE::Util::DicomString(), GDCM_NAME_SPACE::Util::Format(), gdcmDebugMacro, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::DocEntrySet::GetEntryLength(), GrPixel, GDCM_NAME_SPACE::DocEntrySet::InsertEntryString(), GDCM_NAME_SPACE::JPEG, NumPixel, GDCM_NAME_SPACE::DataEntry::SetString(), and GDCM_NAME_SPACE::Document::WriteContent(). Referenced by GDCM_NAME_SPACE::FileHelper::Write(). { gdcmDebugMacro(" File::Write "); std::ofstream *fp = new std::ofstream(fileName.c_str(), std::ios::out | std::ios::binary); if (*fp == NULL) { gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str()); return false; } // Entry : 0002|0000 = group length -> recalculated DataEntry *e0000 = GetDataEntry(0x0002,0x0000); if ( e0000 ) { std::ostringstream sLen; sLen << ComputeGroup0002Length( ); e0000->SetString(sLen.str()); } if( writetype != JPEG ) { int i_lgPix = GetEntryLength(GrPixel, NumPixel); if (i_lgPix != -2) { // no (GrPixel, NumPixel) element std::string s_lgPix = Util::Format("%d", i_lgPix+12); s_lgPix = Util::DicomString( s_lgPix.c_str() ); InsertEntryString(s_lgPix,GrPixel, 0x0000, "UL"); } } Document::WriteContent(fp, writetype); fp->close(); delete fp; return true; }

void GDCM_NAME_SPACE::ElementSet::WriteContent (  std::ofstream *  fp, FileType  filetype, bool  dummy )  [virtual, inherited]

Writes the Header Entries (Dicom Elements) from the H Table. Parameters: fp  ofstream to write to filetype  ExplicitVR/ImplicitVR/ACR/ACR_LIBIDO/JPEG/JPEG2000/... Implements GDCM_NAME_SPACE::DocEntrySet. Definition at line 52 of file gdcmElementSet.cxx. References GDCM_NAME_SPACE::ACR, GDCM_NAME_SPACE::ACR_LIBIDO, GDCM_NAME_SPACE::ElementSet::MayIWrite(), and GDCM_NAME_SPACE::ElementSet::TagHT. Referenced by GDCM_NAME_SPACE::Document::WriteContent(). { bool insideMetaElements = false; bool yetOutsideMetaElements = false; for (TagDocEntryHT::const_iterator i = TagHT.begin(); i != TagHT.end(); ++i) { int group = (i->second)->GetGroup(); if (yetOutsideMetaElements==false && group == 0x0002) insideMetaElements = true; if (insideMetaElements == true && group != 0x0002) { yetOutsideMetaElements = true; insideMetaElements = false; } // depending on the gdcm::Document type // (gdcm::File; gdcm::DicomDir, (more to come ?) // some groups *cannot* be present. // We hereby protect gdcm for writting stupid things // if they were found in the original document. if ( !MayIWrite( group ) ) continue; // Skip 'Group Length' element, since it may be wrong. // except for Group 0x0002 // ( keep it as well for Group 0x0008 of ACR Files, // since some ACR readers *need* it ) if ( (i->second)->GetElement() != 0x0000 || ( (i->second)->GetGroup() == 0x0002 ||( (filetype == ACR || filetype == ACR_LIBIDO ) && (i->second)->GetGroup() == 0x0008 ) ) ) { // There are DocEntries, written recursively i->second->WriteContent(fp, filetype, insideMetaElements ); } } }

void GDCM_NAME_SPACE::Document::WriteContent (  std::ofstream *  fp, FileType  filetype )  [inherited]

Writes in a file all the Entries (Dicom Elements). Parameters: fp  file pointer on an already open file (actually: Output File Stream) filetype  Type of the File to be written (ACR-NEMA, ExplicitVR, ImplicitVR) Definition at line 696 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::ExplicitVR, GDCM_NAME_SPACE::ImplicitVR, GDCM_NAME_SPACE::JPEG, GDCM_NAME_SPACE::JPEG2000, and GDCM_NAME_SPACE::ElementSet::WriteContent(). Referenced by Write(). { // Skip if user wants to write an ACR-NEMA file if ( filetype == ImplicitVR || filetype == ExplicitVR || filetype == JPEG || filetype == JPEG2000 ) { // writing Dicom File Preamble char filePreamble[128]; memset(filePreamble, 0, 128); fp->write(filePreamble, 128); fp->write("DICM", 4); } /* * \todo rewrite later, if really usefull * - 'Group Length' element is optional in DICOM * - but un-updated odd groups lengthes can causes pb * (xmedcon breaker) * * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) ) * UpdateGroupLength(false,filetype); * if ( filetype == ACR) * UpdateGroupLength(true,ACR); * * --> Computing group length for groups with embeded Sequences * --> was too much tricky / we were [in a hurry / too lazy] * --> We don't write the element 0x0000 (group length) */ ElementSet::WriteContent(fp, filetype, false); // This one is recursive }

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Member Data Documentation

bool GDCM_NAME_SPACE::Document::Abort [mutable, protected, inherited]

Definition at line 235 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::CallStartMethod(), GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(), GDCM_NAME_SPACE::DicomDir::DoTheLoadingJob(), and GDCM_NAME_SPACE::DicomDir::Initialize().

uint32_t* GDCM_NAME_SPACE::File::BasicOffsetTableItemValue [private]

Definition at line 224 of file gdcmFile.h. Referenced by ComputeJPEGFragmentInfo(), ComputeRLEInfo(), File(), ReadEncapsulatedBasicOffsetTable(), and ~File().

uint16_t GDCM_NAME_SPACE::Document::CurrentElem [protected, inherited]

to allow any inner method to know current tag Element number Definition at line 252 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::ReadNextDocEntry().

uint16_t GDCM_NAME_SPACE::Document::CurrentGroup [protected, inherited]

to allow any inner method to know current tag Group number Definition at line 250 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::FindDocEntryVR(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

std::string GDCM_NAME_SPACE::Document::Filename [protected, inherited]

Refering underlying filename. Definition at line 131 of file gdcmDocument.h. Referenced by AnonymizeNoLoad(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), and GDCM_NAME_SPACE::Document::OpenFile().

FileType GDCM_NAME_SPACE::Document::Filetype [protected, inherited]

ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown. Definition at line 157 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::CheckSwap(), GDCM_NAME_SPACE::Document::Document(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::Document::FindDocEntryVR(), GDCM_NAME_SPACE::Document::GetFileType(), GDCM_NAME_SPACE::Document::HandleOutOfGroup0002(), GDCM_NAME_SPACE::Document::Initialize(), GDCM_NAME_SPACE::Document::IsParsable(), GDCM_NAME_SPACE::DicomDir::IsReadable(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

TagKey GDCM_NAME_SPACE::File::FourthDimensionLocation [protected]

allows user to tell gdcm in which DataElement is stored the -unnormalized- 4th Dimension Definition at line 215 of file gdcmFile.h. Referenced by File(), and GetTSize().

std::ifstream* GDCM_NAME_SPACE::Document::Fp [protected, inherited]

File Pointer, opened during Document parsing. Definition at line 154 of file gdcmDocument.h. Referenced by ComputeJPEGFragmentInfo(), ComputeRLEInfo(), GDCM_NAME_SPACE::Document::Document(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), DoTheLoadingJob(), GDCM_NAME_SPACE::DicomDir::DoTheLoadingJob(), ReadEncapsulatedBasicOffsetTable(), and ReadTag().

bool GDCM_NAME_SPACE::Document::Group0002Parsed [protected, inherited]

whether we already parsed group 0002 (Meta Elements) Definition at line 148 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::Document(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::Document::HandleOutOfGroup0002(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

uint16_t GDCM_NAME_SPACE::File::GrPixel [protected]

In some cases (e.g. for some ACR-NEMA images) the header entry for the group of pixels is *not* found at 0x7fe0. In order to make things easier the parser shall store the proper value in GrPixel to provide a unique access facility. Definition at line 212 of file gdcmFile.h. Referenced by DoTheLoadingJob(), File(), GetPixelAreaLength(), GetPixelOffset(), IsReadable(), and Write().

bool GDCM_NAME_SPACE::Document::HasDCMPreamble [protected, inherited]

whether file has a DCM Preamble Definition at line 151 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::OpenFile(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

const unsigned int GDCM_NAME_SPACE::Document::HEADER_LENGTH_TO_READ [static, protected, inherited]

After opening the file, we read HEADER_LENGTH_TO_READ bytes. Definition at line 160 of file gdcmDocument.h.

bool GDCM_NAME_SPACE::Document::IsDocumentAlreadyLoaded [protected, inherited]

Whether the gdcm::Document is already parsed/loaded : False from the creation of the gdcm::Document untill gdcm::Document:Load(). Definition at line 180 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::Document(), and GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob().

bool GDCM_NAME_SPACE::Document::IsDocumentModified [protected, inherited]

Whether the gdcm::Document was modified since the last Load(). Definition at line 183 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::Document(), and GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob().

JPEGFragmentsInfo* GDCM_NAME_SPACE::File::JPEGInfo [protected]

Store the JPEG fragments info obtained during parsing of pixels. Definition at line 201 of file gdcmFile.h. Referenced by ComputeJPEGFragmentInfo(), File(), and ~File().

int GDCM_NAME_SPACE::Document::LoadMode [protected, inherited]

Bit string integer (each one considered as a boolean) Bit 0 : Skip Sequences, if possible Bit 1 : Skip Shadow Groups if possible Probabely, some more to add. Definition at line 175 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(), and GDCM_NAME_SPACE::Document::Document().

const unsigned int GDCM_NAME_SPACE::Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff [static, protected, inherited]

Elements whose value is longer than MAX_SIZE_LOAD_ELEMENT_VALUE are NOT loaded. Definition at line 163 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::Document().

uint32_t GDCM_NAME_SPACE::Document::MaxSizeLoadEntry [protected, inherited]

Size threshold above which an element value will NOT be loaded in memory (to avoid loading the image/volume itself). By default, this upper bound is fixed to 1024 bytes (which might look reasonable when one considers the definition of the various VR contents). Definition at line 247 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::LoadDocEntry(), and GDCM_NAME_SPACE::Document::SetMaxSizeLoadEntry().

uint16_t GDCM_NAME_SPACE::File::NumPixel [protected]

In some cases (e.g. for some ACR-NEMA images) the Entry Element Number of the 'Pixel Element' is *not* found at 0x0010. In order to make things easier the parser shall store the proper value in NumPixel to provide a unique access facility. Definition at line 207 of file gdcmFile.h. Referenced by DoTheLoadingJob(), File(), GetPixelAreaLength(), GetPixelOffset(), IsReadable(), and Write().

DocEntry* GDCM_NAME_SPACE::DocEntrySet::PreviousDocEntry [protected, inherited]

To be able to backtrack (Private Sequence, Implicit VR related pb). Definition at line 128 of file gdcmDocEntrySet.h. Referenced by GDCM_NAME_SPACE::Document::Backtrack(), and GDCM_NAME_SPACE::DocEntrySet::DocEntrySet().

int GDCM_NAME_SPACE::Base::PrintLevel [protected, inherited]

Amount of printed details for each Dicom Entries : 0 : stands for the least detail level. Definition at line 55 of file gdcmBase.h. Referenced by GDCM_NAME_SPACE::SeqEntry::Print(), GDCM_NAME_SPACE::FileHelper::Print(), GDCM_NAME_SPACE::ElementSet::Print(), GDCM_NAME_SPACE::DocEntry::Print(), GDCM_NAME_SPACE::DictEntry::Print(), GDCM_NAME_SPACE::DicomDirStudy::Print(), GDCM_NAME_SPACE::DicomDirSerie::Print(), GDCM_NAME_SPACE::DicomDirPatient::Print(), GDCM_NAME_SPACE::DicomDirMeta::Print(), GDCM_NAME_SPACE::DicomDir::Print(), and GDCM_NAME_SPACE::DataEntry::Print().

float GDCM_NAME_SPACE::Document::Progress [protected, inherited]

value of the ??? for any progress bar Definition at line 234 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::CallEndMethod(), GDCM_NAME_SPACE::Document::CallStartMethod(), GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList(), GDCM_NAME_SPACE::DicomDir::DoTheLoadingJob(), and GDCM_NAME_SPACE::DicomDir::Initialize().

Dict* GDCM_NAME_SPACE::Document::RefPubDict [protected, inherited]

Public dictionary used to parse this header. Definition at line 238 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::GetPubDict(), and GDCM_NAME_SPACE::Document::Initialize().

Dict* GDCM_NAME_SPACE::Document::RefShaDict [protected, inherited]

Optional "shadow dictionary" (private elements) used to parse this header. Definition at line 241 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::GetShaDict(), GDCM_NAME_SPACE::Document::Initialize(), and GDCM_NAME_SPACE::Document::SetShaDict().

RLEFramesInfo* GDCM_NAME_SPACE::File::RLEInfo [protected]

Store the RLE frames info obtained during parsing of pixels. Definition at line 199 of file gdcmFile.h. Referenced by File(), and ~File().

int GDCM_NAME_SPACE::Document::SwapCode [protected, inherited]

Swap code gives an information on the byte order of a supposed to be an int32, as it's read on disc (depending on the image Transfer Syntax *and* on the processor endianess) as opposed as it should in memory to be dealt as an int32. For instance : a 'Little Endian' image, read with a little endian processor will have a SwapCode= 1234 (the order is OK; nothing to do) a 'Little Endian' image, read with a big endian procesor will have a SwapCode= 4321 (the order is wrong; int32 an int16 must be swapped) note : values 2143, 4321, 3412 remain for the ACR-NEMA time, and the well known 'Bad Big Endian' and 'Bad Little Endian' codes. Definition at line 145 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::CheckSwap(), GDCM_NAME_SPACE::Document::Document(), GDCM_NAME_SPACE::Document::SwapDouble(), GDCM_NAME_SPACE::Document::SwapLong(), GDCM_NAME_SPACE::Document::SwapShort(), and GDCM_NAME_SPACE::Document::SwitchByteSwapCode().

ListElements GDCM_NAME_SPACE::Document::UserAnonymizeList [protected, inherited]

User supplied list of elements to Anonymize. Definition at line 166 of file gdcmDocument.h. Referenced by AddAnonymizeElement(), AnonymizeFile(), and AnonymizeNoLoad().

ListElements GDCM_NAME_SPACE::Document::UserForceLoadList [protected, inherited]

User supplied list of elements to force Load. Definition at line 169 of file gdcmDocument.h. Referenced by GDCM_NAME_SPACE::Document::AddForceLoadElement().

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

• gdcmFile.h
• gdcmFile.cxx

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