GDCM_NAME_SPACE::Document Class Reference

Derived by both gdcm::File and gdcm::DicomDir. More...

#include <gdcmDocument.h>

Inheritance diagram for GDCM_NAME_SPACE::Document:

[legend]Collaboration diagram for GDCM_NAME_SPACE::Document:

[legend]List of all members.

Public Types
typedef std::list< DicomElement >	ListElements
Public Member Functions
virtual bool	Load ()
	Loader. use SetLoadMode(), SetFileName() before !
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).
virtual bool	IsReadable ()
	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).
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.
void	WriteContent (std::ofstream *fp, FileType filetype, bool insideMetaElements)
	Writes 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.
Protected Member Functions
	Document ()
	This default constructor neither loads nor parses the file. You should then invoke Document::Load.
virtual	~Document ()
	Canonical destructor.
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.
bool	MayIWrite (uint16_t)
	Some group are illegal withing some Dicom Documents Only the Document knows it.
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
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 (Document)
void	Initialize ()
	Loads all the needed Dictionaries.
bool	DoTheLoadingDocumentJob ()
	Loader. (DEPRECATED : not to break the API) Performs the Loading Job (internal use only).
void	ReadBegBuffer (size_t l) throw ( FormatError )
	Reads a given length of bytes (in order to avoid to many CPU time-consuming fread-s).
uint16_t	SwapShort (uint16_t)
	Swaps the bytes so they agree with the processor order.
uint32_t	SwapLong (uint32_t)
	Swaps back the bytes of 4-byte long integer accordingly to processor order.
double	SwapDouble (double)
	Swaps back the bytes of 8-byte long 'double' accordingly to processor order.
uint16_t	UnswapShort (uint16_t a)
	Unswaps back the bytes of 2-bytes long integer so they agree with the processor order.
uint32_t	UnswapLong (uint32_t a)
	Unswaps back the bytes of 4-byte long integer so they agree with the processor order.
void	ParseDES (DocEntrySet *set, long offset, long l_max, bool delim_mode)
	Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries).
bool	ParseSQ (SeqEntry *seq, long offset, long l_max, bool delim_mode)
	Parses a Sequence ( SeqEntry after SeqEntry).
void	LoadDocEntry (DocEntry *e, bool forceLoad=false)
	Loads (or not) the element content depending if its length exceeds or not the value specified with Document::SetMaxSizeLoadEntry().
void	FindDocEntryLength (DocEntry *e) throw ( FormatError )
	Find the value Length of the passed Doc Entry.
uint32_t	FindDocEntryLengthOBOrOW () throw ( FormatUnexpected )
	Find the Length till the next sequence delimiter.
VRKey	FindDocEntryVR ()
	Find the Value Representation of the current Dicom Element.
bool	CheckDocEntryVR (const VRKey &k)
	Check the correspondance between the VR of the header entry and the taken VR. If they are different, the header entry is updated with the new VR.
void	SkipDocEntry (DocEntry *entry)
	Skip a given Header Entry.
void	SkipToNextDocEntry (DocEntry *entry)
	Skips to the beginning of the next Header Entry.
void	FixDocEntryFoundLength (DocEntry *entry, uint32_t l)
	When the length of an element value is obviously wrong (because the parser went Jabberwocky) one can hope improving things by applying some heuristics.
bool	IsDocEntryAnInteger (DocEntry *entry)
	Apply some heuristics to predict whether the considered element value contains/represents an integer or not.
bool	CheckSwap ()
	Discover what the swap code is (among little endian, big endian, bad little endian, bad big endian). sw is set.
void	SwitchByteSwapCode ()
	Change the Byte Swap code.
DocEntry *	ReadNextDocEntry ()
	Read the next tag WITHOUT loading it's value (read the 'Group Number', the 'Element Number', gets the Dict Entry gets the VR, gets the length, gets the offset value).
uint16_t	GetInt16 ()
	Gets from BegBuffer a supposed to be 16 Bits integer (swaps it depending on processor endianness).
uint32_t	GetInt32 ()
	Gets from BegBuffer a supposed to be 32 Bits integer (swaps it depending on processor endianness).
void	HandleBrokenEndian (uint16_t &group, uint16_t &elem)
	Handle broken private tag from Philips NTSCAN where the endianess is being switched to BigEndian for no apparent reason.
void	HandleOutOfGroup0002 (uint16_t &group, uint16_t &elem)
	Group 0002 is always coded Little Endian whatever Transfer Syntax is.
DocEntry *	Backtrack (DocEntry *docEntry)
	When a private Sequence + Implicit VR is encountered we cannot guess it's a Sequence till we find the first Item Starter. We then backtrack to do the job.
Private Attributes
char	BegBuffer [8]
	buffer to avoid some freads
char *	PtrBegBuffer
size_t	CurrentOffsetPosition
	to avoid time consuming ftellg
bool	changeFromUN
	to indicate if last supposed to be UN DataElement is not (according to a private Dicom dictionary)
bool	UnexpectedEOF
	whether an unexpected EOF was encountered

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Detailed Description

Derived by both gdcm::File and gdcm::DicomDir.

Definition at line 42 of file gdcmDocument.h.

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Member Typedef Documentation

typedef std::list<DicomElement> GDCM_NAME_SPACE::Document::ListElements

Definition at line 47 of file gdcmDocument.h.

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Constructor & Destructor Documentation

GDCM_NAME_SPACE::Document::Document (   )  [protected]

This default constructor neither loads nor parses the file. You should then invoke Document::Load. Definition at line 56 of file gdcmDocument.cxx. References changeFromUN, CurrentOffsetPosition, GDCM_NAME_SPACE::ExplicitVR, Filetype, Fp, Group0002Parsed, Initialize(), IsDocumentAlreadyLoaded, IsDocumentModified, GDCM_NAME_SPACE::LD_ALL, LoadMode, MAX_SIZE_LOAD_ELEMENT_VALUE, SetFileName(), SetMaxSizeLoadEntry(), SwapCode, and UnexpectedEOF. :ElementSet() { Fp = 0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialize(); SwapCode = 1234; Filetype = ExplicitVR; CurrentOffsetPosition = 0; // Load will set it to true if sucessfull Group0002Parsed = false; IsDocumentAlreadyLoaded = false; IsDocumentModified = true; LoadMode = LD_ALL; // default : load everything, later SetFileName(""); changeFromUN=false; UnexpectedEOF=false; }

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

Canonical destructor. Definition at line 80 of file gdcmDocument.cxx. References CloseFile(). { CloseFile(); }

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Member Function Documentation

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 )

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 UserForceLoadList. { DicomElement el; el.Group = group; el.Elem = elem; UserForceLoadList.push_back(el); }

DocEntry * GDCM_NAME_SPACE::Document::Backtrack (  DocEntry *  docEntry  )  [private]

When a private Sequence + Implicit VR is encountered we cannot guess it's a Sequence till we find the first Item Starter. We then backtrack to do the job. Parameters: docEntry  Item Starter that warned us Definition at line 1408 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::RefCounter::Delete(), gdcmDebugMacro, GDCM_NAME_SPACE::DocEntry::GetElement(), GDCM_NAME_SPACE::DocEntry::GetGroup(), GDCM_NAME_SPACE::DocEntry::GetLength(), GDCM_NAME_SPACE::DocEntry::GetOffset(), GDCM_NAME_SPACE::DocEntrySet::NewSeqEntry(), GDCM_NAME_SPACE::DocEntrySet::PreviousDocEntry, GDCM_NAME_SPACE::ElementSet::RemoveEntry(), GDCM_NAME_SPACE::DocEntry::SetLength(), and GDCM_NAME_SPACE::DocEntry::SetOffset(). Referenced by ParseDES(). { // delete the Item Starter, built erroneously out of any Sequence // it's not yet in the HTable/chained list docEntry->Delete(); // Get all info we can from PreviousDocEntry uint16_t group = PreviousDocEntry->GetGroup(); uint16_t elem = PreviousDocEntry->GetElement(); uint32_t lgt = PreviousDocEntry->GetLength(); long offset = PreviousDocEntry->GetOffset(); gdcmDebugMacro( "Backtrack :" << std::hex << group << "|" << elem << " at offset 0x(" <<offset << ")" ); RemoveEntry( PreviousDocEntry ); // forge the Seq Entry DocEntry *newEntry = NewSeqEntry(group, elem); newEntry->SetLength(lgt); newEntry->SetOffset(offset); // Move back to the beginning of the Sequence Fp->seekg(offset, std::ios::beg); // Only for Shadow Implicit VR SQ return newEntry; }

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

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

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

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]

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

bool GDCM_NAME_SPACE::Document::CheckDocEntryVR (  const VRKey &  vr  )  [private]

Check the correspondance between the VR of the header entry and the taken VR. If they are different, the header entry is updated with the new VR. Parameters: vr  Dicom Value Representation Returns: false if the VR is incorrect or if the VR isn't referenced otherwise, it returns true Definition at line 1735 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::Global::GetVR(), and GDCM_NAME_SPACE::VR::IsValidVR(). { return Global::GetVR()->IsValidVR(vr); }

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; }

bool GDCM_NAME_SPACE::Document::CheckSwap (   )  [private]

Discover what the swap code is (among little endian, big endian, bad little endian, bad big endian). sw is set. Returns: false when we are absolutely sure it's neither ACR-NEMA nor DICOM true when we hope ours assuptions are OK Definition at line 1912 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::ACR, CurrentOffsetPosition, GDCM_NAME_SPACE::ExplicitVR, Filetype, gdcmDebugMacro, gdcmWarningMacro, GDCM_NAME_SPACE::ImplicitVR, GDCM_NAME_SPACE::Util::IsCurrentProcessorBigEndian(), SwapCode, and GDCM_NAME_SPACE::Unknown. Referenced by DoTheLoadingDocumentJob(). { uint32_t s32; uint16_t s16; char deb[256]; // First, compare HostByteOrder and NetworkByteOrder in order to // determine if we shall need to swap bytes (i.e. the Endian type). bool net2host = Util::IsCurrentProcessorBigEndian(); // The easiest case is the one of a 'true' DICOM header, we just have // to look for the string "DICM" inside the file preamble. Fp->read(deb, 256); char *entCur = deb + 128; if ( memcmp(entCur, "DICM", (size_t)4) == 0 ) { gdcmDebugMacro( "Looks like DICOM Version3 (preamble + DCM)" ); // Group 0002 should always be VR, and the first element 0000 // Let's be carefull (so many wrong headers ...) // and determine the value representation (VR) : // Let's skip to the first element (0002,0000) and check there if we find // "UL" - or "OB" if the 1st one is (0002,0001) -, // in which case we (almost) know it is explicit VR. // WARNING: if it happens to be implicit VR then what we will read // is the length of the group. If this ascii representation of this // length happens to be "UL" then we shall believe it is explicit VR. // We need to skip : // * the 128 bytes of File Preamble (often padded with zeroes), // * the 4 bytes of "DICM" string, // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001) // i.e. a total of 136 bytes. entCur = deb + 136; // group 0x0002 *is always* Explicit VR Sometimes, // even if elem 0002,0010 (Transfer Syntax) tells us the file is // *Implicit* VR (see former 'gdcmData/icone.dcm') if ( memcmp(entCur, "UL", (size_t)2) == 0 || memcmp(entCur, "OB", (size_t)2) == 0 || memcmp(entCur, "UI", (size_t)2) == 0 || memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later // when Write DCM *adds* // FIXME // Use Document::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? group 0000 { Filetype = ExplicitVR; gdcmDebugMacro( "Group 0002 : Explicit Value Representation"); } else { Filetype = ImplicitVR; gdcmWarningMacro( "Group 0002 :Not an explicit Value Representation;" << "Looks like a bugged Header!"); } // Here, we assume that the file IS kosher Dicom ! // (The meta elements - group 0x0002 - ARE little endian !) if ( net2host ) { SwapCode = 4321; gdcmDebugMacro( "HostByteOrder != NetworkByteOrder, SwapCode = 4321"); } else { SwapCode = 1234; gdcmDebugMacro( "HostByteOrder = NetworkByteOrder, SwapCode = 1234"); } // Position the file position indicator at first tag // (i.e. after the file preamble and the "DICM" string). Fp->seekg ( 132L, std::ios::beg); // Once per Document CurrentOffsetPosition = 132; return true; } // ------------------------------- End of DicomV3 ---------------- // Alas, this is not a DicomV3 file and whatever happens there is no file // preamble. We can reset the file position indicator to where the data // is (i.e. the beginning of the file). gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)"); Fp->seekg(0, std::ios::beg); // Once per ACR-NEMA Document CurrentOffsetPosition = 0; // Let's check 'No Preamble Dicom File' : // Should start with group 0x0002 // and be Explicit Value Representation s16 = *((uint16_t *)(deb)); SwapCode = 0; switch ( s16 ) { case 0x0002 : SwapCode = 1234; entCur = deb + 4; break; case 0x0200 : SwapCode = 4321; entCur = deb + 6; } if ( SwapCode != 0 ) { if ( memcmp(entCur, "UL", (size_t)2) == 0 || memcmp(entCur, "OB", (size_t)2) == 0 || memcmp(entCur, "UI", (size_t)2) == 0 || memcmp(entCur, "SH", (size_t)2) == 0 || memcmp(entCur, "AE", (size_t)2) == 0 || memcmp(entCur, "OB", (size_t)2) == 0 ) { Filetype = ExplicitVR; // FIXME : not enough to say it's Explicit // Wait untill reading Transfer Syntax gdcmDebugMacro( "Group 0002 : Explicit Value Representation"); return true; } } // ------------------------------- End of 'No Preamble' DicomV3 ------------- // Our next best chance would be to be considering a 'clean' ACR/NEMA file. // By clean we mean that the length of the first group is written down. // If this is the case and since the length of the first group HAS to be // four (bytes), then determining the proper swap code is straightforward. entCur = deb + 4; // We assume the array of char we are considering contains the binary // representation of a 32 bits integer. Hence the following dirty // trick : s32 = *((uint32_t *)(entCur)); switch( s32 ) { case 0x00040000 : SwapCode = 3412; Filetype = ACR; return true; case 0x04000000 : SwapCode = 4321; Filetype = ACR; return true; case 0x00000400 : SwapCode = 2143; Filetype = ACR; return true; case 0x00000004 : SwapCode = 1234; Filetype = ACR; return true; default : // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file. // It is time for despaired wild guesses. // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA, // i.e. the 'group length' element is not present : // check the supposed-to-be 'group number' // in ( 0x0001 .. 0x0008 ) // to determine ' SwapCode' value . // Only 0 or 4321 will be possible // (no oportunity to check for the formerly well known // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian' // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc-3, 4, ..., 8-) // the file IS NOT ACR-NEMA nor DICOM V3 // Find a trick to tell it the caller... s16 = *((uint16_t *)(deb)); gdcmDebugMacro("not a DicomV3 nor a 'clean' ACR/NEMA;" << " (->despaired wild guesses !)"); switch ( s16 ) { case 0x0001 : case 0x0002 : case 0x0003 : case 0x0004 : case 0x0005 : case 0x0006 : case 0x0007 : case 0x0008 : case 0x0028 : SwapCode = 1234; Filetype = ACR; return true; case 0x0100 : case 0x0200 : case 0x0300 : case 0x0400 : case 0x0500 : case 0x0600 : case 0x0700 : case 0x0800 : case 0x2800 : SwapCode = 4321; Filetype = ACR; return true; default : s16 = *((uint16_t *)(deb)); if (s16 != 0x0000) return false; s16 = *((uint16_t *)(deb+2)); Fp->seekg ( 0L, std::ios::beg); // Once per Document CurrentOffsetPosition = 0; switch(s16) // try an other trick! // -> to be able to decode 0029|1010 DataElement // -> and be not less cleaver than dcmdump ;-) { case 0x0004 : SwapCode = 1234; break; case 0x0400 : SwapCode = 3412; break; default: gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)"); Filetype = Unknown; return false; } // Check if next 2 bytes are a VR // Probabely something more time-consuming exists with std::string const char VRvalues[] = "AEASCSDADSFLFDISLOLTPNSHSLSSSTTMUIULUSUTOBOWOFATUNSQ"; int nbVal = 26; const char *pt = VRvalues; for (int i=0;i<nbVal;i++) { if(*(deb+4) == *pt++) if(*(deb+5) == *pt++) { Filetype = ExplicitVR; return true; } } Filetype = ImplicitVR; return true; } } }

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(), 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 (   )

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

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

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 GDCM_NAME_SPACE::File::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::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(), 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(), 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::Document::DoTheLoadingDocumentJob (   )  [private]

Loader. (DEPRECATED : not to break the API) Performs the Loading Job (internal use only). Returns: false if file cannot be open or no swap info was found, or no tag was found. FIXME --> FIXME : The difference between BinEntry and DataEntry --> no longer exists, but the alteration of Dicom Dictionary remains. --> Old comment restored on purpose. --> New one (replacing both BinEntry and ValEntry by DataEntry) --> had absolutely no meaning. --> The whole comment will be removed when the stuff is cleaned ! --> The tags refered by the three following lines used to be CORRECTLY defined as having an US Value Representation in the public dictionary. BUT the semantics implied by the three following lines state that the corresponding tag contents are in fact the ones of a BinEntry. In order to fix things "Quick and Dirty" the dictionary was altered on PURPOSE but now contains a WRONG value. In order to fix things and restore the dictionary to its correct value, one needs to decide of the semantics by deciding whether the following tags are either : multivaluated US, and hence loaded as ValEntry, but afterwards also used as BinEntry, which requires the proper conversion, OW, and hence loaded as BinEntry, but afterwards also used as ValEntry, which requires the proper conversion. Definition at line 124 of file gdcmDocument.cxx. References CheckSwap(), GDCM_NAME_SPACE::ElementSet::ClearEntry(), CloseFile(), Filename, Filetype, Fp, gdcmDebugMacro, gdcmErrorMacro, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDataEntry(), GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GDCM_NAME_SPACE::SeqEntry::GetFirstSQItem(), GDCM_NAME_SPACE::DocEntry::GetLength(), GDCM_NAME_SPACE::DocEntrySet::GetSeqEntry(), Group0002Parsed, IsDocumentAlreadyLoaded, IsDocumentModified, GDCM_NAME_SPACE::ElementSet::IsEmpty(), LoadEntryBinArea(), OpenFile(), ParseDES(), and GDCM_NAME_SPACE::Unknown. Referenced by Load(). { if ( ! IsDocumentModified ) // Nothing to do ! return true; ClearEntry(); Fp = 0; if ( !OpenFile() ) { // warning already performed in OpenFile() Filetype = Unknown; return false; } Group0002Parsed = false; gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str()); // Computes the total length of the file Fp->seekg(0, std::ios::end); // Once per Document ! long lgt = Fp->tellg(); // Once per Document ! Fp->seekg(0, std::ios::beg); // Once per Document ! // CheckSwap returns a boolean // (false if no swap info of any kind was found) if (! CheckSwap() ) { gdcmWarningMacro( "Neither a DICOM V3 nor an ACR-NEMA file: " << Filename.c_str()); CloseFile(); return false; } long beg = Fp->tellg(); // just after DICOM preamble (if any) lgt -= beg; // remaining length to parse // Recursive call. // Loading is done during parsing ParseDES( this, beg, lgt, false); // delim_mode is first defaulted to false if ( IsEmpty() ) { gdcmErrorMacro( "No tag in internal hash table for: " << Filename.c_str()); CloseFile(); return false; } IsDocumentAlreadyLoaded = true; //Fp->seekg(0, std::ios::beg); // Once per Document! // Load 'non string' values std::string PhotometricInterpretation = GetEntryString(0x0028,0x0004); if ( PhotometricInterpretation == "PALETTE COLOR " ) { // FIXME // Probabely this line should be outside the 'if' // Try to find an image sample holding a 'gray LUT' LoadEntryBinArea(0x0028,0x1200); // gray LUT // --> OB (byte aray) or OW (short int aray) // The actual VR has to be deduced from other entries. // Our way of loading them may fail in some cases : // We must or not SwapByte depending on other field values. LoadEntryBinArea(0x0028,0x1201); // R LUT LoadEntryBinArea(0x0028,0x1202); // G LUT LoadEntryBinArea(0x0028,0x1203); // B LUT // Segmented Red Palette Color LUT Data LoadEntryBinArea(0x0028,0x1221); // Segmented Green Palette Color LUT Data LoadEntryBinArea(0x0028,0x1222); // Segmented Blue Palette Color LUT Data LoadEntryBinArea(0x0028,0x1223); } //FIXME later : how to use it? SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000); // Modality LUT Sequence if ( modLutSeq !=0 ) { SQItem *sqi= modLutSeq->GetFirstSQItem(); if ( sqi != 0 ) { DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006); // LUT Data if ( dataEntry != 0 ) { if ( dataEntry->GetLength() != 0 ) { // FIXME : CTX dependent means : contexted dependant. // see upper comment. LoadEntryBinArea(dataEntry); //LUT Data (CTX dependent) } } } } // Force Loading some more elements if user asked to. GDCM_NAME_SPACE::DocEntry *d; for (ListElements::iterator it = UserForceLoadList.begin(); it != UserForceLoadList.end(); ++it) { gdcmDebugMacro( "Force Load " << std::hex << (*it).Group << "|" <<(*it).Elem ); d = GetDocEntry( (*it).Group, (*it).Elem); if ( d == NULL) { gdcmWarningMacro( "You asked to ForceLoad " << std::hex << (*it).Group <<"|"<< (*it).Elem << " that doesn't exist" ); continue; } LoadDocEntry(d, true); } CloseFile(); // ---------------------------- // Specific code to allow gdcm to read ACR-LibIDO formated images // Note: ACR-LibIDO is an extension of the ACR standard that was // used at CREATIS. For the time being (say a couple of years) // we keep this kludge to allow CREATIS users // reading their old images. // // if recognition code tells us we deal with a LibIDO image // we switch lineNumber and columnNumber // std::string RecCode; RecCode = GetEntryString(0x0008, 0x0010); // recognition code (RET) if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { Filetype = ACR_LIBIDO; std::string rows = GetEntryString(0x0028, 0x0010); std::string columns = GetEntryString(0x0028, 0x0011); SetEntryString(columns, 0x0028, 0x0010); SetEntryString(rows , 0x0028, 0x0011); } // --- End of ACR-LibIDO kludge --- return true; }

void GDCM_NAME_SPACE::Document::FindDocEntryLength (  DocEntry *  entry  )  throw ( FormatError ) [private]

Find the value Length of the passed Doc Entry. Parameters: entry  Header Entry whose length of the value shall be loaded. Definition at line 1508 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::ExplicitVR, and gdcmWarningMacro. Referenced by ReadNextDocEntry(). { const VRKey &vr = entry->GetVR(); uint16_t length16; if ( Filetype == ExplicitVR && !entry->IsImplicitVR() ) { // WARNING : // // For some images, length of UN elements is coded on 2 bytes (instead of 4) // There are *not* readable ! // You can make a quick and dirty patch, commenting out //| vr == "UN" // in the following line. // (the 'straight' images will no longer be readable ...) if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT" || vr == "UN" || changeFromUN == true) { changeFromUN = false; // The following reserved two bytes (see PS 3.5-2003, section // "7.1.2 Data element structure with explicit vr", p 27) must be // skipped before proceeding on reading the length on 4 bytes. //Fp->seekg( 2L, std::ios::cur); // Once per OW,OB,SQ DocEntry uint32_t length32 = ReadInt32(); // Once per OW,OB,SQ DocEntry CurrentOffsetPosition+=4; if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) { uint32_t lengthOB; try { lengthOB = FindDocEntryLengthOBOrOW();// for encapsulation of encoded pixel } catch ( FormatUnexpected ) { // Computing the length failed (this happens with broken // files like gdcm-JPEG-LossLess3a.dcm). We still have a // chance to get the pixels by deciding the element goes // until the end of the file. Hence we artificially fix the // the length and proceed. gdcmWarningMacro( " Computing the length failed for " << entry->GetKey() <<" in " <<GetFileName()); long currentPosition = Fp->tellg(); // Only for gdcm-JPEG-LossLess3a.dcm-like Fp->seekg(0L,std::ios::end); // Only for gdcm-JPEG-LossLess3a.dcm-like long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; // Only for gdcm-JPEG-LossLess3a.dcm-like Fp->seekg(currentPosition, std::ios::beg); // Only for gdcm-JPEG-LossLess3a.dcm-like entry->SetReadLength(lengthUntilEOF); entry->SetLength(lengthUntilEOF); return; } entry->SetReadLength(lengthOB); entry->SetLength(lengthOB); return; } FixDocEntryFoundLength(entry, length32); return; } // Length is encoded on 2 bytes. //length16 = ReadInt16(); length16 = GetInt16(); // 0xffff means that we deal with 'No Length' Sequence // or 'No Length' SQItem if ( length16 == 0xffff) { length16 = 0; } FixDocEntryFoundLength( entry, (uint32_t)length16 ); return; } else { // Either implicit VR or a non DICOM conformal (see note below) explicit // VR that ommited the VR of (at least) this element. Farts happen. // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25 // on Data elements "Implicit and Explicit VR Data Elements shall // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. // Well ... group 0002 is always coded in 'Explicit VR Litle Endian' // even if Transfer Syntax is 'Implicit VR ...' // --> Except for 'Implicit VR Big Endian Transfer Syntax GE Private' // where Group 0x0002 is *also* encoded in Implicit VR ! FixDocEntryFoundLength( entry, GetInt32() /*ReadInt32()*/ ); return; } }

uint32_t GDCM_NAME_SPACE::Document::FindDocEntryLengthOBOrOW (   )  throw ( FormatUnexpected ) [private]

Find the Length till the next sequence delimiter. Warning: NOT end user intended method ! Returns: Definition at line 1606 of file gdcmDocument.cxx. References gdcmWarningMacro, GetInt16(), ReadBegBuffer(), ReadInt32(), and SkipBytes(). { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. long positionOnEntry = Fp->tellg(); // Only for OB,OW DataElements bool foundSequenceDelimiter = false; uint32_t totalLength = 0; while ( !foundSequenceDelimiter ) { uint16_t group; uint16_t elem; try { //group = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements //elem = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements ReadBegBuffer(4); // Once per fragment (if any) of OB,OW DataElements } catch ( FormatError ) { throw FormatError("Unexpected end of file encountered during ", "Document::FindDocEntryLengthOBOrOW()"); } group = GetInt16(); elem = GetInt16(); // We have to decount the group and element we just read totalLength += 4; if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { gdcmWarningMacro( "Neither an Item tag nor a Sequence delimiter tag on :" << std::hex << group << " , " << elem << ")" ); Fp->seekg(positionOnEntry, std::ios::beg); // Once per fragment (if any) of OB,OW DataElements throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag."); } if ( elem == 0xe0dd ) { foundSequenceDelimiter = true; } uint32_t itemLength = ReadInt32(); // Once per fragment (if any) of OB,OW DataElements // We add 4 bytes since we just read the ItemLength with ReadInt32 totalLength += itemLength + 4; SkipBytes(itemLength); if ( foundSequenceDelimiter ) { break; } } Fp->seekg( positionOnEntry, std::ios::beg); // Only once for OB,OW DataElements return totalLength; }

VRKey GDCM_NAME_SPACE::Document::FindDocEntryVR (   )  [private]

Find the Value Representation of the current Dicom Element. Returns: Value Representation of the current Entry Definition at line 1670 of file gdcmDocument.cxx. References CurrentGroup, CurrentOffsetPosition, GDCM_NAME_SPACE::ExplicitVR, Filetype, GDCM_NAME_SPACE::GDCM_VRUNKNOWN, gdcmWarningMacro, GDCM_NAME_SPACE::Global::GetVR(), and PtrBegBuffer. Referenced by ReadNextDocEntry(). { if ( Filetype != ExplicitVR ) { return GDCM_VRUNKNOWN; } // Delimiters (0xfffe), are not explicit VR ... if ( CurrentGroup == 0xfffe ) return GDCM_VRUNKNOWN; //long positionOnEntry; //if( Debug::GetWarningFlag() ) // positionOnEntry = Fp->tellg(); // Only in Warning Mode // Warning: we believe this is explicit VR (Value Representation) because // we used a heuristic that found "UL" in the first tag and/or // 'Transfer Syntax' told us it is. // Alas this doesn't guarantee that all the tags will be in explicit VR. // In some cases one finds implicit VR tags mixed within an explicit VR file // Well... // 'Normaly' the only case is : group 0002 Explicit, and other groups Implicit // // Hence we make sure the present tag is in explicit VR and try to fix things // if it happens not to be the case. VRKey vr; //Fp->read(&(vr[0]),(size_t)2); vr[0] = *PtrBegBuffer++; vr[1] = *PtrBegBuffer++; //if ( !CheckDocEntryVR(vr) ) // avoid useless function call if ( !Global::GetVR()->IsValidVR(vr) ) { /* // std::cout << "================================================================Unknown VR" << std::hex << "0x(" << (unsigned int)vr[0] << "|" << (unsigned int)vr[1] << ")" << "for : " << CurrentGroup << " at offset : 0x(" << positionOnEntry << ")" << std::endl; */ gdcmWarningMacro( "Unknown VR " << std::hex << "0x(" << (unsigned int)vr[0] << "|" << (unsigned int)vr[1] << ")" << " at offset : 0x(" << CurrentOffsetPosition-4<< ") for group " << CurrentGroup ); //Fp->seekg(positionOnEntry, std::ios::beg); //JPRx //Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?) //see :MR_Philips_Intera_PrivateSequenceExplicitVR.dcm PtrBegBuffer-=2; return GDCM_VRUNKNOWN; } return vr; }

void GDCM_NAME_SPACE::Document::FixDocEntryFoundLength (  DocEntry *  entry, uint32_t  foundLength )  [private]

When the length of an element value is obviously wrong (because the parser went Jabberwocky) one can hope improving things by applying some heuristics. Parameters: entry  entry to check foundLength  first assumption about length (before bug fix, or set to zero if =0xffffffff) Definition at line 1773 of file gdcmDocument.cxx. References gdcmErrorMacro, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntry::GetElement(), GDCM_NAME_SPACE::DocEntry::GetGroup(), GDCM_NAME_SPACE::DocEntry::GetVR(), GDCM_NAME_SPACE::DocEntry::SetLength(), and GDCM_NAME_SPACE::DocEntry::SetReadLength(). { entry->SetReadLength( foundLength );// will be updated only if a bug is found if ( foundLength == 0xffffffff) { //foundLength = 0; //entry->SetLength(foundLength); entry->SetLength(0); return; // return ASAP; don't waist time on useless tests } uint16_t gr = entry->GetGroup(); uint16_t elem = entry->GetElement(); if ( foundLength % 2) { gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength << " in x(" << std::hex << gr << "," << elem <<")"); } // Allthough not recent many such GE corrupted images are still present // on Creatis hard disks. Hence this fix shall remain when such images // are no longer in use (we are talking a few years, here)... // Note: XMedCon probably uses such a trick since it is able to read // those pesky GE images ... if ( foundLength == 13) { // Only happens for this length ! if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) ) { foundLength = 10; entry->SetReadLength(10); // a bug is to be fixed !? } } // Occurence of such images is quite low (unless one leaves close to a // 'Leonardo' source. Hence, one might consider commenting out the // following fix on efficiency reasons. else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) ) { // Ideally we should check we are in Explicit and double check // that VR=UL... this is done properly in gdcm2 if( foundLength == 6 ) { gdcmWarningMacro( "Replacing Length from 6 into 4" ); foundLength = 4; entry->SetReadLength(4); // a bug is to be fixed ! } else if ( foundLength%4 ) { gdcmErrorMacro( "This looks like to a buggy Siemens DICOM file." "The length of this tag seems to be wrong" ); } } else if ( entry->GetVR() == "SQ" ) { foundLength = 0; // ReadLength is unchanged } // "fffe|xxxx" which is just a marker. Delimiters length should not be // taken into account. else if ( gr == 0xfffe ) { // According to the norm, fffe|0000 shouldn't exist. BUT the Philips // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to // causes extra troubles... if ( elem != 0x0000 ) { foundLength = 0; } else { foundLength=12; // to skip the mess that follows this bugged Tag ! } } entry->SetLength(foundLength); }

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

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(), DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::File::GetBitsAllocated(), GDCM_NAME_SPACE::File::GetBitsStored(), GDCM_NAME_SPACE::DocEntrySet::GetEntryBinArea(), GDCM_NAME_SPACE::File::GetHighBitPosition(), GDCM_NAME_SPACE::File::GetPlanarConfiguration(), GDCM_NAME_SPACE::File::GetRescaleIntercept(), GDCM_NAME_SPACE::File::GetSamplesPerPixel(), GDCM_NAME_SPACE::File::GetTSize(), GDCM_NAME_SPACE::File::GetXOrigin(), GDCM_NAME_SPACE::File::GetXSize(), GDCM_NAME_SPACE::File::GetXSpacing(), GDCM_NAME_SPACE::File::GetYOrigin(), GDCM_NAME_SPACE::File::GetYSize(), GDCM_NAME_SPACE::File::GetYSpacing(), GDCM_NAME_SPACE::File::GetZOrigin(), GDCM_NAME_SPACE::File::GetZSize(), GDCM_NAME_SPACE::File::GetZSpacing(), GDCM_NAME_SPACE::File::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(), GDCM_NAME_SPACE::File::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 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 GDCM_NAME_SPACE::File::AnonymizeFile(), GDCM_NAME_SPACE::File::AnonymizeNoLoad(), GDCM_NAME_SPACE::FileHelper::CopyDataEntry(), GDCM_NAME_SPACE::DicomDir::CreateDicomDir(), GDCM_NAME_SPACE::File::DoTheLoadingJob(), GDCM_NAME_SPACE::DicomDir::DoTheLoadingJob(), GDCM_NAME_SPACE::File::GetPixelAreaLength(), GDCM_NAME_SPACE::File::GetPixelOffset(), GetTransferSyntax(), GDCM_NAME_SPACE::File::HasLUT(), IsDicomV3(), IsPapyrus(), GDCM_NAME_SPACE::File::IsReadable(), 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 GDCM_NAME_SPACE::File::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(), GDCM_NAME_SPACE::File::AnonymizeFile(), GDCM_NAME_SPACE::FileHelper::CheckMandatoryElements(), GDCM_NAME_SPACE::SerieHelper::CreateUniqueSeriesIdentifier(), GDCM_NAME_SPACE::SerieHelper::CreateUserDefinedFileIdentifier(), DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::File::DoTheLoadingJob(), GDCM_NAME_SPACE::DirList::Explore(), GDCM_NAME_SPACE::File::GetImageNumber(), GDCM_NAME_SPACE::File::GetImageOrientationPatient(), GDCM_NAME_SPACE::File::GetImagePositionPatient(), GDCM_NAME_SPACE::File::GetLUTNbits(), GDCM_NAME_SPACE::File::GetModality(), GDCM_NAME_SPACE::File::GetNumberOfScalarComponents(), GDCM_NAME_SPACE::File::GetNumberOfScalarComponentsRaw(), GDCM_NAME_SPACE::File::GetPixelSize(), GDCM_NAME_SPACE::File::GetPixelType(), GDCM_NAME_SPACE::File::GetRescaleSlope(), GDCM_NAME_SPACE::File::GetRescaleSlopeIntercept(), GDCM_NAME_SPACE::File::GetSpacing(), GetTransferSyntaxName(), GDCM_NAME_SPACE::File::GetXSpacing(), GDCM_NAME_SPACE::File::GetYSpacing(), GDCM_NAME_SPACE::File::IsMonochrome(), GDCM_NAME_SPACE::File::IsMonochrome1(), GDCM_NAME_SPACE::File::IsPaletteColor(), GDCM_NAME_SPACE::File::IsReadable(), GDCM_NAME_SPACE::File::IsYBRFull(), 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]

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(), IsParsable(), GDCM_NAME_SPACE::DicomDir::IsReadable(), 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 (   )

returns the File Type (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) Returns: the FileType code Definition at line 417 of file gdcmDocument.cxx. References 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 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::Document::GetInt16 (   )  [private]

Gets from BegBuffer a supposed to be 16 Bits integer (swaps it depending on processor endianness). Returns: read value Definition at line 968 of file gdcmDocument.cxx. References PtrBegBuffer, and SwapShort(). Referenced by FindDocEntryLengthOBOrOW(), and ReadNextDocEntry(). { uint16_t g = *((uint16_t*)PtrBegBuffer); g = SwapShort(g); PtrBegBuffer+=2; return g; }

uint32_t GDCM_NAME_SPACE::Document::GetInt32 (   )  [private]

Gets from BegBuffer a supposed to be 32 Bits integer (swaps it depending on processor endianness). Returns: read value Definition at line 1002 of file gdcmDocument.cxx. References PtrBegBuffer, and SwapLong(). { uint32_t g = *((uint32_t*)PtrBegBuffer); g = SwapLong(g); PtrBegBuffer+=4; return g; }

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 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::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 (   )

Get the public dictionary used. Definition at line 314 of file gdcmDocument.cxx. References 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; }

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 DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::File::GetRescaleSlopeIntercept(), and GDCM_NAME_SPACE::File::GetSpacing(). { DocEntry *currentEntry = GetDocEntry(group, elem); if ( !currentEntry ) return NULL; return dynamic_cast<SeqEntry*>(currentEntry); }

Dict * GDCM_NAME_SPACE::Document::GetShaDict (   )

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

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

'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 (   )

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 GDCM_NAME_SPACE::File::ComputeJPEGFragmentInfo(), GDCM_NAME_SPACE::File::ComputeRLEInfo(), GDCM_NAME_SPACE::File::DoTheLoadingJob(), and 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 (   )

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(), GDCM_NAME_SPACE::Global::GetTS(), and GDCM_NAME_SPACE::TS::GetValue(). Referenced by 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; }

void GDCM_NAME_SPACE::Document::HandleBrokenEndian (  uint16_t &  group, uint16_t &  elem )  [private]

Handle broken private tag from Philips NTSCAN where the endianess is being switched to BigEndian for no apparent reason. Returns: no return Definition at line 2349 of file gdcmDocument.cxx. References gdcmDebugMacro, gdcmWarningMacro, and SwitchByteSwapCode(). Referenced by ReadNextDocEntry(). { // for strange PMS Gyroscan Intera images // Item 'starter' has a tag : 0x3f3f,0x3f00, for no apparent reason // --- Feel free to remove this test *on your own coy of gdcm* // if you are sure you'll never face this problem. if ((group == 0x3f3f) && (elem == 0x3f00)) { // start endian swap mark for group found gdcmDebugMacro( " delimiter 0x3f3f found." ); // fix the tag group = 0xfffe; elem = 0xe000; return; } // --- End of removable code // Endian reversion. // Some files contain groups of tags with reversed endianess. static int reversedEndian = 0; // try to fix endian switching in the middle of headers if ((group == 0xfeff) && (elem == 0x00e0)) { // start endian swap mark for group found gdcmDebugMacro( "Start endian swap mark found." ); reversedEndian++; SwitchByteSwapCode(); // fix the tag group = 0xfffe; elem = 0xe000; } else if (group == 0xfffe && elem == 0xe00d && reversedEndian) { // end of reversed endian group gdcmDebugMacro( "End of reversed endian." ); reversedEndian--; SwitchByteSwapCode(); } else if (group == 0xfeff && elem == 0xdde0) { // reversed Sequence Terminator found // probabely a bug in the header ! // Do what you want, it breaks ! //reversedEndian--; //SwitchByteSwapCode(); gdcmWarningMacro( "Should never get here! reversed Sequence Terminator!" ); // fix the tag group = 0xfffe; elem = 0xe0dd; } else if (group == 0xfffe && elem == 0xe0dd) { gdcmDebugMacro( "Straight Sequence Terminator." ); } }

void GDCM_NAME_SPACE::Document::HandleOutOfGroup0002 (  uint16_t &  group, uint16_t &  elem )  [private]

Group 0002 is always coded Little Endian whatever Transfer Syntax is. Returns: no return Todo: find a trick to warn user and stop processing Definition at line 2412 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::TS::DeflatedExplicitVRLittleEndian, Filetype, GDCM_NAME_SPACE::GDCM_UNKNOWN, gdcmDebugMacro, gdcmWarningMacro, GDCM_NAME_SPACE::TS::GetSpecialTransferSyntax(), GetTransferSyntax(), GetTransferSyntaxName(), GDCM_NAME_SPACE::Global::GetTS(), Group0002Parsed, GDCM_NAME_SPACE::ImplicitVR, GDCM_NAME_SPACE::TS::ImplicitVRBigEndianPrivateGE, GDCM_NAME_SPACE::TS::ImplicitVRLittleEndian, SwapShort(), and SwitchByteSwapCode(). Referenced by ReadNextDocEntry(). { // Endian reversion. // Some files contain groups of tags with reversed endianess. Group0002Parsed = true; // we just came out of group 0002 // if Transfer Syntax is Big Endian we have to change CheckSwap std::string ts = GetTransferSyntax(); TS::SpecialType s = Global::GetTS()->GetSpecialTransferSyntax(ts); // Group 0002 is always 'Explicit ...' // even when Transfer Syntax says 'Implicit ..." if ( s == TS::ImplicitVRLittleEndian || s == TS::ImplicitVRBigEndianPrivateGE ) { Filetype = ImplicitVR; } // FIXME Strangely, this works with //'Implicit VR BigEndian Transfer Syntax' (GE Private) // // --> Probabely normal, since we considered we never have // to trust manufacturers. // (we often find 'Implicit VR' tag, // even when Transfer Syntax tells us it's Explicit ... // NEVER trust the meta elements! // (see what ezDICOM does ...) /* if ( s == TS::ExplicitVRBigEndian ) { gdcmDebugMacro("Transfer Syntax Name = [" << GetTransferSyntaxName() << "]" ); SwitchByteSwapCode(); group = SwapShort(group); elem = SwapShort(elem); } */ //-- Broken ACR may start with a Shadow Group -- // worse : some ACR-NEMA like files start 00028 group ?!? if ( !( (group >= 0x0001 && group <= 0x0008) || group == 0x0028 ) ) { // We trust what we see. SwitchByteSwapCode(); group = SwapShort(group); elem = SwapShort(elem); // not what we where told (by meta elements) ! gdcmDebugMacro("Transfer Syntax Name = [" << GetTransferSyntaxName() << "]" ); } if ( s == TS::DeflatedExplicitVRLittleEndian) { gdcmWarningMacro("Transfer Syntax [" << GetTransferSyntaxName() << "] :" << " not yet dealt with "); return; } // The following shouldn't occur very often // Let's check at the very end. if ( ts == GDCM_UNKNOWN ) { gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " ); return; } if ( !Global::GetTS()->IsTransferSyntax(ts) ) { gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: [" << ts << "]"); return; } }

void GDCM_NAME_SPACE::Document::Initialize (   )  [private]

Loads all the needed Dictionaries. Warning: NOT end user intended method ! Reimplemented in GDCM_NAME_SPACE::DicomDir. Definition at line 1086 of file gdcmDocument.cxx. References Filetype, GDCM_NAME_SPACE::DictSet::GetDefaultPubDict(), GDCM_NAME_SPACE::Global::GetDicts(), RefPubDict, RefShaDict, and GDCM_NAME_SPACE::Unknown. Referenced by Document(). { RefPubDict = Global::GetDicts()->GetDefaultPubDict(); RefShaDict = NULL; Filetype = Unknown; }

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 GDCM_NAME_SPACE::File::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 (   )

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 GDCM_NAME_SPACE::File::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::Document::IsDocEntryAnInteger (  DocEntry *  entry  )  [private]

Apply some heuristics to predict whether the considered element value contains/represents an integer or not. Parameters: entry  The element value on which to apply the predicate. Returns: The result of the heuristical predicate. Definition at line 1863 of file gdcmDocument.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntry::GetElement(), GDCM_NAME_SPACE::DocEntry::GetGroup(), GDCM_NAME_SPACE::DocEntry::GetLength(), and GDCM_NAME_SPACE::DocEntry::GetVR(). { uint16_t elem = entry->GetElement(); uint16_t group = entry->GetGroup(); const VRKey &vr = entry->GetVR(); uint32_t length = entry->GetLength(); // When we have some semantics on the element we just read, and if we // a priori know we are dealing with an integer, then we shall be // able to swap its element value properly. if ( elem == 0 ) // This is the group length of the group { if ( length == 4 ) { return true; } else { // Although this should never happen, still some images have a // corrupted group length [e.g. have a glance at offset x(8336) of // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm. // Since for dicom compliant and well behaved headers, the present // test is useless (and might even look a bit paranoid), when we // encounter such an ill-formed image, we simply display a warning // message and proceed on parsing (while crossing fingers). long filePosition = Fp->tellg(); // Only when elem 0x0000 length is not 4 (?!?) (void)filePosition; gdcmWarningMacro( "Erroneous Group Length element length on : (" << std::hex << group << " , " << elem << ") -before- position x(" << filePosition << ")" << "lgt : " << length ); } } if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" ) { return true; } return false; }

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 DoTheLoadingDocumentJob(), and IsParsable(). { return TagHT.empty(); }

bool GDCM_NAME_SPACE::Document::IsPapyrus (   )

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 (   )

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 Filetype, gdcmWarningMacro, GetFileName(), GDCM_NAME_SPACE::ElementSet::IsEmpty(), and GDCM_NAME_SPACE::Unknown. Referenced by 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::Document::IsReadable (   )  [virtual]

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. Reimplemented in GDCM_NAME_SPACE::DicomDir, and GDCM_NAME_SPACE::File. Definition at line 377 of file gdcmDocument.cxx. References IsParsable(). Referenced by GDCM_NAME_SPACE::File::IsReadable(). { return IsParsable(); }

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::Document::Load (   )  [virtual]

Loader. use SetLoadMode(), SetFileName() before ! Returns: false if file cannot be open or no swap info was found, or no tag was found. Reimplemented in GDCM_NAME_SPACE::DicomDir, and GDCM_NAME_SPACE::File. Definition at line 92 of file gdcmDocument.cxx. References DoTheLoadingDocumentJob(), gdcmWarningMacro, and GetFileName(). Referenced by GDCM_NAME_SPACE::DicomDir::DoTheLoadingJob(). { if ( GetFileName() == "" ) { gdcmWarningMacro( "Use SetFileName, before !" ); return false; } return DoTheLoadingDocumentJob( ); }

void GDCM_NAME_SPACE::Document::LoadDocEntry (  DocEntry *  entry, bool  forceLoad = false )  [private]

Loads (or not) the element content depending if its length exceeds or not the value specified with Document::SetMaxSizeLoadEntry(). Parameters: entry  Header Entry (Dicom Element) to be dealt with forceLoad  whether you want to force loading of 'long' elements Todo: : a method that *doesn't* load anything (maybe with MaxSizeLoadEntry=0 ?) + a ForceLoad call on the +/- 20 'usefull' fields Allow user to tell the fields he wants to ForceLoad during initial stage. Later, a GetString or GetBinArea will load the value from disk, if not loaded + a method that load *everything* that's not yet loaded Definition at line 1442 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::DocEntry::GetElement(), GDCM_NAME_SPACE::DocEntry::GetGroup(), GDCM_NAME_SPACE::DocEntry::GetLength(), GDCM_NAME_SPACE::DocEntry::GetVR(), LoadEntryBinArea(), MaxSizeLoadEntry, GDCM_NAME_SPACE::DataEntry::SetBinArea(), GDCM_NAME_SPACE::DataEntry::SetState(), and GDCM_NAME_SPACE::DataEntry::STATE_NOTLOADED. { uint16_t group = entry->GetGroup(); uint16_t elem = entry->GetElement(); const VRKey &vr = entry->GetVR(); uint32_t length = entry->GetLength(); // Fp->seekg((long)entry->GetOffset(), std::ios::beg); // JPRx // A SeQuence "contains" a set of Elements. // (fffe e000) tells us an Element is beginning // (fffe e00d) tells us an Element just ended // (fffe e0dd) tells us the current SeQuence just ended // (fffe 0000) is an 'impossible' tag value, // found in MR-PHILIPS-16-Multi-Seq.dcm if ( (group == 0xfffe && elem != 0x0000 ) || vr == "SQ" ) { // NO more value field for SQ ! return; } DataEntry *dataEntryPtr = dynamic_cast< DataEntry* >(entry); if( !dataEntryPtr ) { return; } // When the length is zero things are easy: if ( length == 0 ) { dataEntryPtr->SetBinArea(NULL,true); return; } // The elements whose length is bigger than the specified upper bound // are not loaded. if (!forceLoad) { if (length > MaxSizeLoadEntry) { dataEntryPtr->SetBinArea(NULL,true); dataEntryPtr->SetState(DataEntry::STATE_NOTLOADED); // to be sure we are at the end of the value ... // Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), // std::ios::beg); //JPRx return; } } LoadEntryBinArea(dataEntryPtr); // last one, not to erase length ! }

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

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(), 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]

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 DoTheLoadingDocumentJob(), and 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::ElementSet::MayIWrite (  uint16_t   )  [inline, protected, inherited]

Some group are illegal withing some Dicom Documents Only the Document knows it. Reimplemented in GDCM_NAME_SPACE::File. Definition at line 70 of file gdcmElementSet.h. Referenced by GDCM_NAME_SPACE::ElementSet::WriteContent(). { return true; }

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 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 Backtrack(), GDCM_NAME_SPACE::DocEntrySet::InsertSeqEntry(), and 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 (   )

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 Filename, and HasDCMPreamble. Referenced by DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::File::DoTheLoadingJob(), GDCM_NAME_SPACE::FileHelper::GetRaw(), and 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  )

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::Document::ParseDES (  DocEntrySet *  set, long  offset, long  l_max, bool  delim_mode )  [private]

Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries). Parameters: set  DocEntrySet we are going to parse ('zero level' or a SQItem) offset  start of parsing l_max  length to parse (meaningless when we are in 'delimitor mode') delim_mode  : whether we are in 'delimitor mode' (l=0xffffff) or not Todo: FIXME : On 64 bits processors, tellg gives unexpected results after a while ? Probabely a bug in gdcm code somwhere (some memory erased ?) Definition at line 1100 of file gdcmDocument.cxx. References Backtrack(), gdcmDebugMacro, GDCM_NAME_SPACE::Debug::GetDebugFlag(), GDCM_NAME_SPACE::DocEntry::GetKey(), GDCM_NAME_SPACE::DocEntry::GetVR(), GDCM_NAME_SPACE::DocEntry::IsItemStarter(), and ReadNextDocEntry(). Referenced by DoTheLoadingDocumentJob(). { DocEntry *newDocEntry; DataEntry *newDataEntry; SeqEntry *newSeqEntry; //VRKey vr; bool used; // will be set to false when something wrong happens to an Entry. // (Entry will then be deleted) bool delim_mode_intern = delim_mode; bool first = true; gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode << " at offset " << std::hex << "0x(" << offset << ")" ); while (true) { // Uncomment to track the bug /* if( Debug::GetDebugFlag() ) std::cout << std::dec <<"(long)(Fp->tellg()) " << (long)(Fp->tellg()) // in Debug mode << std::hex << " 0x(" <<(long)(Fp->tellg()) << ")" << std::endl; */ // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry if ( !delim_mode ) // 'and then' doesn't exist in C++ :-( if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry, when no delim mode { break; } newDocEntry = ReadNextDocEntry( ); if ( !newDocEntry ) { break; } // Uncoment this cerr line to be able to 'follow' the DocEntries // when something *very* strange happens if( Debug::GetDebugFlag() ) std::cerr<<newDocEntry->GetKey()<<" "<<newDocEntry->GetVR()<<std::endl; // an Item Starter found elsewhere but in the first position // of a SeqEntry means previous entry was a Sequence // but we didn't get it (private Sequence + Implicit VR) // we have to backtrack. if ( !first && newDocEntry->IsItemStarter() ) { // Debug message within the method ! newDocEntry = Backtrack(newDocEntry); } else { PreviousDocEntry = newDocEntry; } used = true; newDataEntry = dynamic_cast<DataEntry*>(newDocEntry); if ( newDataEntry ) { //vr = newDocEntry->GetVR(); // useless ? if ( !set->AddEntry( newDataEntry ) ) { gdcmDebugMacro( "in ParseDES : cannot add a DataEntry " << newDataEntry->GetKey() << " (at offset : 0x(" << newDataEntry->GetOffset() << ") )" ); used=false; } else { newDataEntry->Delete(); // Load only if we can add (not a duplicate key) LoadDocEntry( newDataEntry ); } if ( newDataEntry->GetElement() == 0x0000 ) // if on group length { if ( newDataEntry->GetGroup()%2 != 0 ) // if Shadow Group { if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr { std::string strLgrGroup = newDataEntry->GetString(); int lgrGroup; //if ( newDataEntry->IsUnfound() ) /?!? JPR { lgrGroup = atoi(strLgrGroup.c_str()); Fp->seekg(lgrGroup, std::ios::cur); // Once per Shadow group, when NOSHADOW RemoveEntry( newDocEntry ); // Remove and delete continue; } } } } bool delimitor = newDataEntry->IsItemDelimitor(); bool outOfBounds = false; if (!delim_mode ) if ( ((long)(Fp->tellg())-offset) >= l_max ) //Once per DataEntry when no delim mode outOfBounds = true; // 'and then', 'or else' don't exist in C++ :-( // if ( (delimitor) || // (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) // Once per DataEntry if ( delimitor || outOfBounds ) { if ( !used ) newDocEntry->Delete(); break; } // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); // FIXME : once per DocEntry, segfault if commented out } else { unsigned long l = newDocEntry->GetReadLength(); if ( l != 0 ) // don't mess the delim_mode for 'zero-length sequence' { if ( l == 0xffffffff ) { delim_mode_intern = true; } else { delim_mode_intern = false; } } if ( (LoadMode & LD_NOSHADOWSEQ) && ! delim_mode_intern ) { // User asked to skip SeQuences *only* if they belong to Shadow Group if ( newDocEntry->GetGroup()%2 != 0 ) { Fp->seekg( l, std::ios::cur); // once per SQITEM, when NOSHADOWSEQ newDocEntry->Delete(); // Delete, not in the set continue; } } if ( (LoadMode & LD_NOSEQ) && ! delim_mode_intern ) { // User asked to skip *any* SeQuence Fp->seekg( l, std::ios::cur); // Once per SQ, when NOSEQ newDocEntry->Delete(); // Delete, not in the set continue; } // delay the dynamic cast as late as possible newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry); // no other way to create the Delimitor ... newSeqEntry->SetDelimitorMode( delim_mode_intern ); // At the top of the hierarchy, stands a Document. When "set" // is a Document, then we are building the first depth level. // Hence the SeqEntry we are building simply has a depth // level of one: if ( set == this ) // ( dynamic_cast< Document* > ( set ) ) { newSeqEntry->SetDepthLevel( 1 ); } // But when "set" is already a SQItem, we are building a nested // sequence, and hence the depth level of the new SeqEntry // we are building, is one level deeper: // time waste hunting else if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); } if ( l != 0 ) { // Don't try to parse zero-length sequences gdcmDebugMacro( "Entry in ParseSQ, delim " << delim_mode_intern << " at offset 0x(" << std::hex << newDocEntry->GetOffset() << ")"); bool res = ParseSQ( newSeqEntry, newDocEntry->GetOffset(), l, delim_mode_intern); gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern << " -->return : " << res); } if ( !set->AddEntry( newSeqEntry ) ) { gdcmWarningMacro( "in ParseDES : cannot add a SeqEntry " << newSeqEntry->GetKey() << " (at offset : 0x(" << newSeqEntry->GetOffset() << ") )" ); used = false; } else { newDocEntry->Delete(); } // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry if ( !delim_mode ) // 'and then' doesn't exist in C++ :-( if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry when no delim mode { if ( !used ) newDocEntry->Delete(); break; } } // end SeqEntry : VR = "SQ" if ( !used ) { newDocEntry->Delete(); } first = false; if (UnexpectedEOF) // some terminator was missing break; } // end While gdcmDebugMacro( "Exit from ParseDES, delim-mode " << delim_mode ); }

bool GDCM_NAME_SPACE::Document::ParseSQ (  SeqEntry *  seqEntry, long  offset, long  l_max, bool  delim_mode )  [private]

Parses a Sequence ( SeqEntry after SeqEntry). Returns: false if expected fff0,e000 not found Definition at line 1334 of file gdcmDocument.cxx. References gdcmWarningMacro, GDCM_NAME_SPACE::DocEntry::IsSequenceDelimitor(), ReadNextDocEntry(), GDCM_NAME_SPACE::SeqEntry::SetDelimitationItem(), and UnexpectedEOF. { int SQItemNumber = 0; bool dlm_mod; long offsetStartCurrentSQItem = offset; while (true) { // the first time, we read the fff0,e000 of the first SQItem DocEntry *newDocEntry = ReadNextDocEntry(); if ( !newDocEntry ) { // The most frequent is when a SQ terminator is missing (?!?) gdcmWarningMacro("in ParseSQ : should never get here!"); UnexpectedEOF = true; return false; } if ( delim_mode ) { if ( newDocEntry->IsSequenceDelimitor() ) { seqEntry->SetDelimitationItem( newDocEntry ); newDocEntry->Delete(); break; } } else // ! delim_mode { if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SQItem when no delim mode { newDocEntry->Delete(); break; } } // create the current SQItem SQItem *itemSQ = SQItem::New( seqEntry->GetDepthLevel() ); unsigned int l = newDocEntry->GetReadLength(); if ( l == 0xffffffff ) { dlm_mod = true; } else { dlm_mod = false; } // fill up the current SQItem, starting at the beginning of fff0,e000 Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); // Once per SQItem ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod); offsetStartCurrentSQItem = Fp->tellg(); // Once per SQItem seqEntry->AddSQItem( itemSQ, SQItemNumber ); itemSQ->Delete(); newDocEntry->Delete(); SQItemNumber++; //if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) //JPRx if ( !delim_mode && (offsetStartCurrentSQItem-offset ) >= l_max ) { break; } } return true; }

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::Document::ReadBegBuffer (  size_t  l  )  throw ( FormatError ) [private]

Reads a given length of bytes (in order to avoid to many CPU time-consuming fread-s). Parameters: l  length to read Definition at line 926 of file gdcmDocument.cxx. Referenced by FindDocEntryLengthOBOrOW(), and ReadNextDocEntry(). { Fp->read (BegBuffer, (size_t)l); if ( Fp->fail() ) { throw FormatError( "Document::ReadBegBuffer()", " file error." ); } if ( Fp->eof() ) { throw FormatError( "Document::ReadBegBuffer()", "EOF." ); } PtrBegBuffer = BegBuffer; CurrentOffsetPosition+=l; }

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

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 GDCM_NAME_SPACE::File::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]

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 GDCM_NAME_SPACE::File::ComputeRLEInfo(), FindDocEntryLengthOBOrOW(), and GDCM_NAME_SPACE::File::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; }

DocEntry * GDCM_NAME_SPACE::Document::ReadNextDocEntry (   )  [private]

Read the next tag WITHOUT loading it's value (read the 'Group Number', the 'Element Number', gets the Dict Entry gets the VR, gets the length, gets the offset value). Returns: On succes : the newly created DocEntry, NULL on failure. Todo: : fixme If inside a supposed to be UN DataElement (but SQ according to a private dictionnary) there is some more supposed to be UN DataElements, it will probabely fail. --> find a -non time consuming- trick to store changeFromUN info at DataElement level, not at the Document level. Definition at line 2203 of file gdcmDocument.cxx. References changeFromUN, CurrentElem, CurrentGroup, GDCM_NAME_SPACE::RefCounter::Delete(), GDCM_NAME_SPACE::ExplicitVR, Filetype, FindDocEntryLength(), FindDocEntryVR(), GDCM_NAME_SPACE::GDCM_VRUNKNOWN, gdcmWarningMacro, GDCM_NAME_SPACE::DocEntrySet::GetDictEntry(), GetInt16(), GDCM_NAME_SPACE::DocEntry::GetKey(), GDCM_NAME_SPACE::DictEntry::GetVR(), Group0002Parsed, HandleBrokenEndian(), HandleOutOfGroup0002(), HasDCMPreamble, GDCM_NAME_SPACE::DocEntrySet::NewDataEntry(), GDCM_NAME_SPACE::DocEntrySet::NewSeqEntry(), ReadBegBuffer(), GDCM_NAME_SPACE::DocEntry::SetImplicitVR(), GDCM_NAME_SPACE::DocEntry::SetOffset(), GDCM_NAME_SPACE::DataEntry::STATE_NOTLOADED, and GDCM_NAME_SPACE::RefCounter::Unregister(). Referenced by ParseDES(), and ParseSQ(). { try { ReadBegBuffer(8); // Avoid to many time consuming freads //CurrentGroup = ReadInt16(); //CurrentElem = ReadInt16(); } catch ( FormatError ) { // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. return 0; } changeFromUN = false; CurrentGroup = GetInt16(); CurrentElem = GetInt16(); // In 'true DICOM' files Group 0002 is always little endian if ( HasDCMPreamble ) { if ( !Group0002Parsed && CurrentGroup != 0x0002) // avoid calling a function when useless HandleOutOfGroup0002(CurrentGroup, CurrentElem); else // Sometimes file contains groups of tags with reversed endianess. HandleBrokenEndian(CurrentGroup, CurrentElem); } VRKey vr = FindDocEntryVR(); VRKey realVR = vr; if ( vr == GDCM_VRUNKNOWN ) { if ( CurrentElem == 0x0000 ) // Group Length { realVR = "UL"; // must be UL } else if (CurrentGroup == 0xfffe) // Don't get DictEntry for Delimitors { realVR = "UL"; } // Was commented out in order not to generate 'Shadow Groups' where some // Data Elements are Explicit VR and some other ones Implicit VR // -> Better we fix the problem at Write time else if (CurrentGroup%2 == 1 ) { if (CurrentElem >= 0x0010 && CurrentElem <=0x00ff ) // DICOM PS 3-5 7.8.1 a) states that : // Private Creator Data Elements numbered (gggg,0010-00FF) (gggg is odd) // attributes have to be LO (Long String) and the VM shall be equal to 1 realVR = "LO"; // Seems not to be true // Still in gdcmtk, David Clunnie disagrees, Marco Eichelberg says it's OK ... // We let it for a while? //(We should check length==4, for more security, but we don't have it yet !) else if ( CurrentElem == 0x0001) realVR = "UL"; // Private Group Length To End } else { DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);//only when ImplicitVR if ( dictEntry ) { realVR = dictEntry->GetVR(); dictEntry->Unregister(); // GetDictEntry registered it } } } // if UN found, let's check the dictionary, and trust it! // (maybe a private dictionary exists?) else if (vr == "UN") { DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem); if ( dictEntry ) { realVR = dictEntry->GetVR(); dictEntry->Unregister(); // GetDictEntry registered it // for VR = "UN", length is always stored on 4 bytes. changeFromUN=true; } } DocEntry *newEntry; //if ( Global::GetVR()->IsVROfSequence(realVR) ) if (realVR == "SQ") { newEntry = NewSeqEntry(CurrentGroup, CurrentElem); } else { newEntry = NewDataEntry(CurrentGroup, CurrentElem, realVR); static_cast<DataEntry *>(newEntry)->SetState(DataEntry::STATE_NOTLOADED); } if ( vr == GDCM_VRUNKNOWN ) { if ( Filetype == ExplicitVR ) { // We thought this was explicit VR, but we end up with an // implicit VR tag. Let's backtrack. //if ( newEntry->GetGroup() != 0xfffe ) if (CurrentGroup != 0xfffe) { int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x(" << offset << ") should be Explicit VR"); } } newEntry->SetImplicitVR(); } try { FindDocEntryLength(newEntry); } catch ( FormatError ) { // Call it quits newEntry->Delete(); return 0; } newEntry->SetOffset(Fp->tellg()); // for each DocEntry return newEntry; }

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 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 GDCM_NAME_SPACE::File::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]

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(), Document(), vtkGdcmReader::LoadFileInformation(), and GDCM_NAME_SPACE::FileHelper::SetFileName(). { if (Filename != fileName) Filename = fileName, IsDocumentModified = true; }

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

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  )

during parsing, Header Elements too long are not loaded in memory Parameters: newSize  new size Definition at line 2182 of file gdcmDocument.cxx. References MaxSizeLoadEntry. Referenced by 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  )

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 RefShaDict. { RefShaDict = Global::GetDicts()->GetDict(dictName); return !RefShaDict; }

bool GDCM_NAME_SPACE::Document::SetShaDict (  Dict *  dict  )

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

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

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

void GDCM_NAME_SPACE::Document::SkipDocEntry (  DocEntry *  entry  )  [private]

Skip a given Header Entry. Parameters: entry  entry to skip Definition at line 1744 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::DocEntry::GetLength(), and SkipBytes(). { SkipBytes(entry->GetLength()); }

void GDCM_NAME_SPACE::Document::SkipToNextDocEntry (  DocEntry *  currentDocEntry  )  [private]

Skips to the beginning of the next Header Entry. Parameters: currentDocEntry  entry to skip Definition at line 1753 of file gdcmDocument.cxx. References GDCM_NAME_SPACE::DocEntry::GetGroup(), GDCM_NAME_SPACE::DocEntry::GetOffset(), and GDCM_NAME_SPACE::DocEntry::GetReadLength(). { long l = currentDocEntry->GetReadLength(); if ( l == -1 ) // length = 0xffff shouldn't appear here ... // ... but PMS imagers happen ! return; Fp->seekg((size_t)(currentDocEntry->GetOffset()), std::ios::beg); //FIXME :each DocEntry if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb { Fp->seekg( l,std::ios::cur); //FIXME :each DocEntry } }

double GDCM_NAME_SPACE::Document::SwapDouble (  double  a  )  [private]

Swaps back the bytes of 8-byte long 'double' accordingly to processor order. Returns: The properly swaped 64 bits double. Definition at line 551 of file gdcmDocument.cxx. References gdcmErrorMacro, and SwapCode. { switch (SwapCode) { // There were no 'double' at ACR-NEMA time. // We just have to deal with 'straight Little Endian' and // 'straight Big Endian' case 1234 : break; case 4321 : { char *beg = (char *)&a; char *end = beg + 7; char t; for (unsigned int i = 0; i<7; i++) { t = *beg; *beg = *end; *end = t; beg++, end--; } } break; default : gdcmErrorMacro( "Unexpected swap code:" << SwapCode ); a = 0.; } return a; }

uint32_t GDCM_NAME_SPACE::Document::SwapLong (  uint32_t  a  )  [private]

Swaps back the bytes of 4-byte long integer accordingly to processor order. Returns: The properly swaped 32 bits integer. Definition at line 519 of file gdcmDocument.cxx. References gdcmErrorMacro, and SwapCode. Referenced by GetInt32(). { switch (SwapCode) { case 1234 : break; case 4321 : // a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | // ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) ); // save CPU time a=( ( a<<24) | ((a<<8) & 0x00ff0000) | ((a>>8) & 0x0000ff00) | (a>>24) ); break; case 3412 : // a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) ); a=( (a<<16) | (a>>16) ); break; case 2143 : a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); break; default : gdcmErrorMacro( "Unexpected swap code:" << SwapCode ); a = 0; } return a; }

uint16_t GDCM_NAME_SPACE::Document::SwapShort (  uint16_t  a  )  [private]

Swaps the bytes so they agree with the processor order. Returns: The properly swaped 16 bits integer. Definition at line 503 of file gdcmDocument.cxx. References SwapCode. Referenced by GetInt16(), and HandleOutOfGroup0002(). { if ( SwapCode == 4321 || SwapCode == 2143 ) { //a = ((( a << 8 ) & 0xff00 ) | (( a >> 8 ) & 0x00ff ) ); // Save CPU time a = ( a << 8 ) | ( a >> 8 ); } return a; }

void GDCM_NAME_SPACE::Document::SwitchByteSwapCode (   )  [private]

Change the Byte Swap code. Definition at line 2155 of file gdcmDocument.cxx. References gdcmDebugMacro, and SwapCode. Referenced by HandleBrokenEndian(), and HandleOutOfGroup0002(). { gdcmDebugMacro( "Switching Byte Swap code from "<< SwapCode << " at: 0x" << std::hex << Fp->tellg() ); // Only when DEBUG if ( SwapCode == 1234 ) { SwapCode = 4321; } else if ( SwapCode == 4321 ) { SwapCode = 1234; } else if ( SwapCode == 3412 ) { SwapCode = 2143; } else if ( SwapCode == 2143 ) { SwapCode = 3412; } gdcmDebugMacro( " Into: "<< SwapCode ); }

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 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; }

uint32_t GDCM_NAME_SPACE::Document::UnswapLong (  uint32_t  a  )  [inline, private]

Unswaps back the bytes of 4-byte long integer so they agree with the processor order. Definition at line 200 of file gdcmDocument.h. { return SwapLong(a);}

uint16_t GDCM_NAME_SPACE::Document::UnswapShort (  uint16_t  a  )  [inline, private]

Unswaps back the bytes of 2-bytes long integer so they agree with the processor order. Definition at line 197 of file gdcmDocument.h. { return SwapShort(a);}

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 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 )

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 GDCM_NAME_SPACE::File::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]

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

char GDCM_NAME_SPACE::Document::BegBuffer[8] [private]

buffer to avoid some freads Definition at line 260 of file gdcmDocument.h.

bool GDCM_NAME_SPACE::Document::changeFromUN [private]

to indicate if last supposed to be UN DataElement is not (according to a private Dicom dictionary) Definition at line 266 of file gdcmDocument.h. Referenced by Document(), and ReadNextDocEntry().

uint16_t GDCM_NAME_SPACE::Document::CurrentElem [protected]

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

uint16_t GDCM_NAME_SPACE::Document::CurrentGroup [protected]

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

size_t GDCM_NAME_SPACE::Document::CurrentOffsetPosition [private]

to avoid time consuming ftellg Definition at line 263 of file gdcmDocument.h. Referenced by CheckSwap(), Document(), and FindDocEntryVR().

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

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

FileType GDCM_NAME_SPACE::Document::Filetype [protected]

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

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

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

bool GDCM_NAME_SPACE::Document::Group0002Parsed [protected]

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

bool GDCM_NAME_SPACE::Document::HasDCMPreamble [protected]

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

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

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]

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 Document(), and DoTheLoadingDocumentJob().

bool GDCM_NAME_SPACE::Document::IsDocumentModified [protected]

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

int GDCM_NAME_SPACE::Document::LoadMode [protected]

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 Document().

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

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

uint32_t GDCM_NAME_SPACE::Document::MaxSizeLoadEntry [protected]

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 LoadDocEntry(), and SetMaxSizeLoadEntry().

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 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]

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

char* GDCM_NAME_SPACE::Document::PtrBegBuffer [private]

Definition at line 261 of file gdcmDocument.h. Referenced by FindDocEntryVR(), GetInt16(), and GetInt32().

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

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

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

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

int GDCM_NAME_SPACE::Document::SwapCode [protected]

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 CheckSwap(), Document(), SwapDouble(), SwapLong(), SwapShort(), and SwitchByteSwapCode().

bool GDCM_NAME_SPACE::Document::UnexpectedEOF [private]

whether an unexpected EOF was encountered Definition at line 268 of file gdcmDocument.h. Referenced by Document(), and ParseSQ().

ListElements GDCM_NAME_SPACE::Document::UserAnonymizeList [protected]

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

ListElements GDCM_NAME_SPACE::Document::UserForceLoadList [protected]

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

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

• gdcmDocument.h
• gdcmDocument.cxx

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