GDCM_NAME_SPACE::DicomDir

GDCM_NAME_SPACE::DicomDir Class Reference

DicomDir defines an object representing a DICOMDIR in memory as a tree-like structure :. More...

#include <gdcmDicomDir.h>

Inheritance diagram for GDCM_NAME_SPACE::DicomDir:

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List of all members.

Public Types

enum  DicomDirType {
  GDCM_DICOMDIR_NONE, GDCM_DICOMDIR_META, GDCM_DICOMDIR_PATIENT, GDCM_DICOMDIR_STUDY,
  GDCM_DICOMDIR_SERIE, GDCM_DICOMDIR_VISIT, GDCM_DICOMDIR_IMAGE, GDCM_DICOMDIR_PRIVATE
}
 Types of the DicomDirObject within the DicomDir. More...
typedef std::list< DicomElement > ListElements

Public Member Functions

bool Load ()
 Loader. use SetFileName(fn) or SetLoadMode(lm) + SetDirectoryName(dn) before !
void Print (std::ostream &os=std::cout, std::string const &indent="")
 Canonical Printer.
void SetDirectoryName (std::string const &dirName)
 Sets the root Directory name to parse, recursively.
virtual void SetFileName (std::string const &fileName)
 Accessor to Filename.
virtual bool IsReadable ()
 This predicate, based on hopefully reasonable heuristics, decides whether or not the current document was properly parsed and contains the mandatory information for being considered as a well formed and usable DicomDir.
DicomDirMeta * NewMeta ()
 adds *the* Meta to a partially created DICOMDIR
DicomDirMeta * GetMeta ()
 Returns a pointer to the DicomDirMeta for this DICOMDIR.
DicomDirPatient * NewPatient ()
 adds a new Patient (with the basic elements) to a partially created DICOMDIR
void ClearPatient ()
 Remove all Patients.
DicomDirPatient * GetFirstPatient ()
 Get the first entry while visiting the DicomDirPatients.
DicomDirPatient * GetNextPatient ()
 Get the next entry while visiting the DicomDirPatients.
int GetNumberOfPatients ()
 returns the number of Patients currently held in the gdcm::DicomDir
void ParseDirectory ()
 fills the whole structure, starting from a root Directory
float GetProgress () const
 GetProgress GetProgress.
void AbortProgress ()
 AbortProgress AbortProgress.
bool IsAborted ()
 IsAborted IsAborted.
bool Write (std::string const &fileName)
 writes on disc a DICOMDIR \ warning does NOT add the missing elements in the header : it's up to the user doing it !
bool Anonymize ()
 Anonymize a DICOMDIR.
virtual void Copy (DocEntrySet *set)
 Copies all the attributes from an other DocEntrySet.
Dict * GetPubDict ()
 Get the public dictionary used.
Dict * GetShaDict ()
 Get the shadow dictionary used.
bool SetShaDict (Dict *dict)
 Set the shadow dictionary used.
bool SetShaDict (DictKey const &dictName)
 Set the shadow dictionary used.
bool IsParsable ()
 This predicate tells us whether or not the current Document was properly parsed and contains at least *one* Dicom Element (and nothing more, sorry).
bool IsDicomV3 ()
 Predicate for dicom version 3 file.
bool IsPapyrus ()
 Predicate for Papyrus file Dedicated to whomsoever it may concern.
FileType GetFileType ()
 returns the File Type (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
std::string GetTransferSyntax ()
 Accessor to the Transfer Syntax (when present) of the current document (it internally handles reading the value from disk when only parsing occured).
std::string GetTransferSyntaxName ()
 Accesses the info from 0002,0010 : Transfer Syntax and TS.
int GetSwapCode ()
 'Swap code' accessor (see SwapCode )
const std::string & GetFileName () const
 Accessor to Filename.
std::ifstream * OpenFile ()
 Tries to open the file Document::Filename and checks the preamble when existing, or if the file starts with an ACR-NEMA look-like element.
bool CloseFile ()
 closes the file
void WriteContent (std::ofstream *fp, FileType type)
 Writes in a file all the Entries (Dicom Elements).
void WriteContent (std::ofstream *fp, FileType filetype, bool insideMetaElements)
 Writes the Header Entries (Dicom Elements) from the H Table.
virtual void LoadEntryBinArea (uint16_t group, uint16_t elem)
 Loads (from disk) the element content when a string is not suitable.
virtual void LoadEntryBinArea (DataEntry *entry)
 Loads (from disk) the element content when a string is not suitable.
void SetMaxSizeLoadEntry (long)
 during parsing, Header Elements too long are not loaded in memory
void AddForceLoadElement (uint16_t group, uint16_t elem)
 Adds a new element we want to load anyway.
bool operator< (Document &document)
 Loads the element while preserving the current underlying file position indicator as opposed to LoadDocEntry that modifies it Compares two documents, according to DicomDir rules.
void SetLoadMode (int mode)
 Sets the LoadMode as a boolean string. LD_NOSEQ, LD_NOSHADOW, LD_NOSHADOWSEQ ... (nothing more, right now) WARNING : before using NO_SHADOW, be sure *all* your files contain accurate values in the 0x0000 element (if any) of *each* Shadow Group. The parser will fail if the size is wrong !
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 std::string GetEntryString (uint16_t group, uint16_t elem)
 Get the "std::string representable" value of the Dicom entry.
virtual void * GetEntryBinArea (uint16_t group, uint16_t elem)
 Gets (from Header) a 'non string' element value.
virtual int GetEntryLength (uint16_t group, uint16_t elem)
 Searches within the DocEntrySet for the value length of a given tag..
DataEntry * GetDataEntry (uint16_t group, uint16_t elem)
 Same as Document::GetDocEntry except it returns a result only when the corresponding entry is of type DataEntry.
SeqEntry * GetSeqEntry (uint16_t group, uint16_t elem)
 Same as Document::GetDocEntry except it returns a result only when the corresponding entry is of type SeqEntry.
bool SetEntryString (std::string const &content, uint16_t group, uint16_t elem)
 Accesses an existing DocEntry (i.e. a Dicom Element) through its (group, element) and modifies its content with the given value.
bool SetEntryString (std::string const &content, DataEntry *entry)
 Accesses an existing DocEntry (i.e. a Dicom Element) and modifies its content with the given value.
bool SetEntryBinArea (uint8_t *content, int lgth, uint16_t group, uint16_t elem)
 Accesses an existing DocEntry (i.e. a Dicom Element) through its (group, element) and modifies its content with the given value.
bool SetEntryBinArea (uint8_t *content, int lgth, DataEntry *entry)
 Accesses an existing DataEntry (i.e. a Dicom Element) and modifies its content with the given value.
DataEntry * InsertEntryString (std::string const &value, uint16_t group, uint16_t elem, VRKey const &vr=GDCM_VRUNKNOWN)
 Modifies the value of a given Doc Entry (Dicom Element) when it exists. Creates it with the given value when unexistant.
DataEntry * InsertEntryBinArea (uint8_t *binArea, int lgth, uint16_t group, uint16_t elem, VRKey const &vr=GDCM_VRUNKNOWN)
 Modifies the value of a given Header Entry (Dicom Element) when it exists. Create it with the given value when unexistant. A copy of the binArea is made to be kept in the Document.
SeqEntry * InsertSeqEntry (uint16_t group, uint16_t elem)
 Creates a new gdcm::SeqEntry and adds it to the current DocEntrySet. (remove any existing entry with same group,elem).
virtual bool CheckIfEntryExist (uint16_t group, uint16_t elem)
 Checks if a given Dicom Element exists within the DocEntrySet.
DataEntry * NewDataEntry (uint16_t group, uint16_t elem, VRKey const &vr=GDCM_VRUNKNOWN)
 Build a new DataEntry from all the low level arguments.
SeqEntry * NewSeqEntry (uint16_t group, uint16_t elem)
 Build a new SeqEntry from all the low level arguments.
void Delete ()
 Delete the object.
void Register ()
 Register the object.
void Unregister ()
 Unregister the object.
const unsigned long & GetRefCount () const
 Get the reference counting.
void SetPrintLevel (int level)
 Sets the print level for the Dicom Header Elements.
int GetPrintLevel ()
 Gets the print level for the Dicom Entries.

Static Public Member Functions

static DicomDir * New ()
 Constructs a DicomDir with a RefCounter.

Protected Member Functions

 DicomDir ()
 Constructor : creates an empty DicomDir.
 ~DicomDir ()
 Constructor Parses recursively the directory and creates the DicomDir or uses an already built DICOMDIR, depending on 'parseDir' value. Canonical destructor.
void CreateDicomDirChainedList (std::string const &path)
 create a Document-like chained list from a root Directory
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 (DicomDir)
void Initialize ()
 Sets all fields to NULL.
void CreateDicomDir ()
 create a 'gdcmDicomDir' from a DICOMDIR Header
bool DoTheLoadingJob ()
 Loader. (DEPRECATED : kept not to break the API) Does the Loading Job (internal use only).
bool AddPatientToEnd (DicomDirPatient *dd)
 AddPatientToEnd.
bool AddStudyToEnd (DicomDirStudy *dd)
 AddStudyToEnd.
bool AddSerieToEnd (DicomDirSerie *dd)
 AddSerieToEnd.
bool AddVisitToEnd (DicomDirVisit *dd)
 AddVisitToEnd.
bool AddImageToEnd (DicomDirImage *dd)
 AddImageToEnd.
bool AddPrivateToEnd (DicomDirPrivate *dd)
 AddPrivateToEnd.
void SetElements (std::string const &path, VectDocument const &list)
 for each Header of the chained list, add/update the Patient/Study/Serie/Image info
void SetElement (std::string const &path, DicomDirType type, Document *header)
 adds to the HTable the Entries (Dicom Elements) corresponding to the given type
void MoveSQItem (DocEntrySet *dst, DocEntrySet *src)
 Move the content of the source SQItem to the destination SQItem Only DocEntry's are moved.

Static Private Member Functions

static bool HeaderLessThan (Document *header1, Document *header2)
 compares two files

Private Attributes

DicomDirMeta * MetaElems
 Pointer on *the* DicomDirObject 'DicomDirMeta Elements'.
ListDicomDirPatient Patients
 Chained list of DicomDirPatient (to be exploited hierarchicaly).
ListDicomDirPatient::iterator ItPatient
bool ParseDir
 value of the ??? for any progress bar

Detailed Description

DicomDir defines an object representing a DICOMDIR in memory as a tree-like structure :.

->DicomDirPatient -> DicomDirStudy -> DicomDirVisit -> DicomDirSerie -> DicomDirImage -> DicomDirPrivate (for Siemens CSA non image)

Definition at line 56 of file gdcmDicomDir.h.

Member Typedef Documentation

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

Definition at line 47 of file gdcmDocument.h.

Member Enumeration Documentation

enum GDCM_NAME_SPACE::DicomDir::DicomDirType
 

Types of the DicomDirObject within the DicomDir.

Enumerator:
GDCM_DICOMDIR_NONE 
GDCM_DICOMDIR_META 
GDCM_DICOMDIR_PATIENT 
GDCM_DICOMDIR_STUDY 
GDCM_DICOMDIR_SERIE 
GDCM_DICOMDIR_VISIT 
GDCM_DICOMDIR_IMAGE 
GDCM_DICOMDIR_PRIVATE 

Definition at line 112 of file gdcmDicomDir.h.

00113    {
00114       GDCM_DICOMDIR_NONE,
00115       GDCM_DICOMDIR_META,
00116       GDCM_DICOMDIR_PATIENT,
00117       GDCM_DICOMDIR_STUDY,
00118       GDCM_DICOMDIR_SERIE,
00119       GDCM_DICOMDIR_VISIT,
00120       GDCM_DICOMDIR_IMAGE,
00121       GDCM_DICOMDIR_PRIVATE
00122    } DicomDirType;

Constructor & Destructor Documentation

GDCM_NAME_SPACE::DicomDir::DicomDir (   )  [protected]
 

Constructor : creates an empty DicomDir.

Definition at line 184 of file gdcmDicomDir.cxx.

References Initialize(), NewMeta(), and ParseDir.

00185 {
00186    Initialize();  // sets all private fields to NULL
00187    ParseDir = false;
00188    NewMeta();
00189 }

GDCM_NAME_SPACE::DicomDir::~DicomDir (   )  [protected]
 

Constructor Parses recursively the directory and creates the DicomDir or uses an already built DICOMDIR, depending on 'parseDir' value. Canonical destructor.

Definition at line 226 of file gdcmDicomDir.cxx.

References ClearPatient(), GDCM_NAME_SPACE::RefCounter::Delete(), and MetaElems.

00227 {
00228    ClearPatient();
00229    if ( MetaElems )
00230    {
00231       MetaElems->Delete();
00232    }
00233 }

Member Function Documentation

void GDCM_NAME_SPACE::DicomDir::AbortProgress (   )  [inline]
 

AbortProgress AbortProgress.

Definition at line 100 of file gdcmDicomDir.h.

00100 { Abort = true; }

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().

00102 {
00103    const TagKey &key = newEntry->GetKey();
00104 
00105    if ( TagHT.count(key) == 1 )
00106    {
00107       gdcmWarningMacro( "Key already present: " << key );
00108       return false;
00109    }
00110    else
00111    {
00112       TagHT.insert(TagDocEntryHT::value_type(newEntry->GetKey(), newEntry));
00113       newEntry->Register();
00114       return true;
00115    }
00116 }

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

Adds a new element we want to load anyway.

Parameters:
group Group number of the target tag.
elem Element number of the target tag.

Definition at line 304 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::DicomElement::Elem, GDCM_NAME_SPACE::DicomElement::Group, and GDCM_NAME_SPACE::Document::UserForceLoadList.

00305 { 
00306    DicomElement el;
00307    el.Group = group;
00308    el.Elem  = elem;
00309    UserForceLoadList.push_back(el); 
00310 }

bool GDCM_NAME_SPACE::DicomDir::AddImageToEnd (  DicomDirImage *  dd  )  [private]
 

AddImageToEnd.

Parameters:
dd SQ Item to enqueue to the DicomDirImage chained List

Definition at line 874 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::DicomDirSerie::AddImage(), GDCM_NAME_SPACE::DicomDirStudy::GetLastSerie(), and Patients.

Referenced by CreateDicomDir(), and SetElement().

00875 {
00876    if ( Patients.size() > 0 )
00877    {
00878       ListDicomDirPatient::iterator itp = Patients.end();
00879       itp--;
00880 
00881       DicomDirStudy *study = (*itp)->GetLastStudy();
00882       if ( study )
00883       {
00884          DicomDirSerie *serie = study->GetLastSerie();
00885          if ( serie )
00886          {
00887             serie->AddImage(dd);
00888             return true;
00889          }
00890       }
00891    }
00892    return false;
00893 }

bool GDCM_NAME_SPACE::DicomDir::AddPatientToEnd (  DicomDirPatient *  dd  )  [private]
 

AddPatientToEnd.

Parameters:
dd SQ Item to enqueue to the DicomPatient chained List

Definition at line 807 of file gdcmDicomDir.cxx.

References Patients.

Referenced by CreateDicomDir(), NewPatient(), and SetElement().

00808 {
00809    Patients.push_back(dd);
00810    return true;
00811 }

bool GDCM_NAME_SPACE::DicomDir::AddPrivateToEnd (  DicomDirPrivate *  dd  )  [private]
 

AddPrivateToEnd.

Parameters:
dd SQ Item to enqueue to the DicomDirPrivate chained List (checked for SIEMENS 'CSA non image')

Definition at line 900 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::DicomDirSerie::AddPrivate(), GDCM_NAME_SPACE::DicomDirStudy::GetLastSerie(), and Patients.

Referenced by CreateDicomDir().

00901 {
00902    if ( Patients.size() > 0 )
00903    {
00904       ListDicomDirPatient::iterator itp = Patients.end();
00905       itp--;
00906 
00907       DicomDirStudy *study = (*itp)->GetLastStudy();
00908       if ( study )
00909       {
00910          DicomDirSerie *serie = study->GetLastSerie();
00911          if ( serie )
00912          {
00913             serie->AddPrivate(dd);
00914             return true;
00915          }
00916       }
00917    }
00918    return false;
00919 }

bool GDCM_NAME_SPACE::DicomDir::AddSerieToEnd (  DicomDirSerie *  dd  )  [private]
 

AddSerieToEnd.

Parameters:
dd SQ Item to enqueue to the DicomDirSerie chained List

Definition at line 833 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::DicomDirStudy::AddSerie(), and Patients.

Referenced by CreateDicomDir(), and SetElement().

00834 {
00835    if ( Patients.size() > 0 )
00836    {
00837       ListDicomDirPatient::iterator itp = Patients.end();
00838       itp--;
00839 
00840       DicomDirStudy *study = (*itp)->GetLastStudy();
00841       if ( study )
00842       {
00843          study->AddSerie(dd);
00844          return true;
00845       }
00846    }
00847    return false;
00848 }

bool GDCM_NAME_SPACE::DicomDir::AddStudyToEnd (  DicomDirStudy *  dd  )  [private]
 

AddStudyToEnd.

Parameters:
dd SQ Item to enqueue to the DicomDirStudy chained List

Definition at line 817 of file gdcmDicomDir.cxx.

References Patients.

Referenced by CreateDicomDir(), and SetElement().

00818 {
00819    if ( Patients.size() > 0 )
00820    {
00821       ListDicomDirPatient::iterator itp = Patients.end();
00822       itp--;
00823       (*itp)->AddStudy(dd);
00824       return true;
00825    }
00826    return false;
00827 }

bool GDCM_NAME_SPACE::DicomDir::AddVisitToEnd (  DicomDirVisit *  dd  )  [private]
 

AddVisitToEnd.

Parameters:
dd SQ Item to enqueue to the DicomDirVisit chained List

Definition at line 854 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::DicomDirStudy::AddVisit(), and Patients.

Referenced by CreateDicomDir().

00855 {
00856    if ( Patients.size() > 0 )
00857    {
00858       ListDicomDirPatient::iterator itp = Patients.end();
00859       itp--;
00860 
00861       DicomDirStudy *study = (*itp)->GetLastStudy();
00862       if ( study )
00863       {
00864          study->AddVisit(dd);
00865          return true;
00866       }
00867    }
00868    return false;
00869 }

bool GDCM_NAME_SPACE::DicomDir::Anonymize (   ) 
 

Anonymize a DICOMDIR.

Returns:
true

Definition at line 527 of file gdcmDicomDir.cxx.

References Patients, and GDCM_NAME_SPACE::DataEntry::SetString().

00528 {
00529    DataEntry *v;
00530    // Something clever to be found to forge the Patient names
00531    std::ostringstream s;
00532    int i = 1;
00533    for(ListDicomDirPatient::iterator cc = Patients.begin();
00534                                      cc!= Patients.end();
00535                                    ++cc)
00536    {
00537       s << i;
00538       v = (*cc)->GetDataEntry(0x0010, 0x0010) ; // Patient's Name
00539       if (v)
00540       {
00541          v->SetString(s.str());
00542       }
00543 
00544       v = (*cc)->GetDataEntry(0x0010, 0x0020) ; // Patient ID
00545       if (v)
00546       {
00547          v->SetString(" ");
00548       }
00549 
00550       v = (*cc)->GetDataEntry(0x0010, 0x0030) ; // Patient's BirthDate
00551       if (v)
00552       {
00553          v->SetString(" ");
00554       }
00555       s << "";
00556       i++;
00557    }
00558    return true;
00559 }

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

CallEndMethod.

Definition at line 1074 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::CMD_ENDPROGRESS, GDCM_NAME_SPACE::CommandManager::ExecuteCommand(), and GDCM_NAME_SPACE::Document::Progress.

01075 {
01076    Progress = 1.0f;
01077    CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
01078 }

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

CallProgressMethod.

Definition at line 1066 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::CMD_PROGRESS, and GDCM_NAME_SPACE::CommandManager::ExecuteCommand().

Referenced by CreateDicomDirChainedList().

01067 {
01068    CommandManager::ExecuteCommand(this,CMD_PROGRESS);
01069 }

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

CallStartMethod.

Definition at line 1056 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::Document::Abort, GDCM_NAME_SPACE::CMD_STARTPROGRESS, GDCM_NAME_SPACE::CommandManager::ExecuteCommand(), and GDCM_NAME_SPACE::Document::Progress.

Referenced by CreateDicomDirChainedList().

01057 {
01058    Progress = 0.0f;
01059    Abort    = false;
01060    CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
01061 }

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().

00413 {
00414    return GetDocEntry(group,elem)!=NULL;
00415 }

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(), CreateDicomDir(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), SetElements(), and GDCM_NAME_SPACE::ElementSet::~ElementSet().

00140 {
00141    for(TagDocEntryHT::iterator cc = TagHT.begin();cc != TagHT.end(); ++cc)
00142    {
00143       if ( cc->second )
00144       {
00145          cc->second->Unregister();
00146       }
00147    }
00148    TagHT.clear();
00149 }

void GDCM_NAME_SPACE::DicomDir::ClearPatient (   ) 
 

Remove all Patients.

Definition at line 420 of file gdcmDicomDir.cxx.

References Patients.

Referenced by Copy(), SetElements(), and ~DicomDir().

00421 {
00422    for(ListDicomDirPatient::iterator cc = Patients.begin();
00423                                      cc!= Patients.end();
00424                                    ++cc)
00425    {
00426       (*cc)->Unregister();
00427    }
00428    Patients.clear();
00429 }

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

closes the file

Returns:
TRUE if the close was successfull

Definition at line 679 of file gdcmDocument.cxx.

Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::File::DoTheLoadingJob(), GDCM_NAME_SPACE::FileHelper::GetRaw(), and GDCM_NAME_SPACE::Document::~Document().

00680 {
00681    if ( Fp )
00682    {
00683       Fp->close();
00684       delete Fp;
00685       Fp = 0;
00686    }
00687    return true;
00688 }

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

Re-computes the length of the Dicom group 0002.

Definition at line 1013 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::DocEntry::GetElement(), GDCM_NAME_SPACE::ElementSet::GetFirstEntry(), GDCM_NAME_SPACE::DocEntry::GetGroup(), GDCM_NAME_SPACE::DocEntry::GetLength(), GDCM_NAME_SPACE::ElementSet::GetNextEntry(), and GDCM_NAME_SPACE::DocEntry::GetVR().

Referenced by GDCM_NAME_SPACE::File::Write().

01014 {
01015    uint16_t gr;
01016    VRKey vr;
01017    
01018    int groupLength = 0;
01019    bool found0002 = false;   
01020   
01021    // for each zero-level Tag in the DCM Header
01022    DocEntry *entry = GetFirstEntry();
01023    while( entry )
01024    {
01025       gr = entry->GetGroup();
01026 
01027       if ( gr == 0x0002 )
01028       {
01029          found0002 = true;
01030 
01031          if ( entry->GetElement() != 0x0000 )
01032          {
01033             vr = entry->GetVR();
01034 
01035             //if ( (vr == "OB")||(vr == "OW")||(vr == "UT")||(vr == "SQ"))
01036             // (no SQ, OW, UT in group 0x0002;)
01037                if ( vr == "OB" ) 
01038                {
01039                   // explicit VR AND (OB, OW, SQ, UT) : 4 more bytes
01040                   groupLength +=  4;
01041                }
01042             groupLength += 2 + 2 + 4 + entry->GetLength();   
01043          }
01044       }
01045       else if (found0002 )
01046          break;
01047 
01048       entry = GetNextEntry();
01049    }
01050    return groupLength; 
01051 }

void GDCM_NAME_SPACE::DicomDir::Copy (  DocEntrySet *  set  )  [virtual]
 

Copies all the attributes from an other DocEntrySet.

Parameters:
set entry to copy from
Remarks:
The contained DocEntries are not copied, only referenced

Reimplemented from GDCM_NAME_SPACE::ElementSet.

Definition at line 566 of file gdcmDicomDir.cxx.

References ClearPatient(), GDCM_NAME_SPACE::ElementSet::Copy(), ItPatient, MetaElems, Patients, and GDCM_NAME_SPACE::RefCounter::Register().

00567 {
00568    // Remove all previous childs
00569    ClearPatient();
00570 
00571    Document::Copy(set);
00572 
00573    DicomDir *dd = dynamic_cast<DicomDir *>(set);
00574    if( dd )
00575    {
00576       if(MetaElems)
00577          MetaElems->Unregister();
00578       MetaElems = dd->MetaElems;
00579       if(MetaElems)
00580          MetaElems->Register();
00581 
00582       Patients = dd->Patients;
00583       for(ItPatient = Patients.begin();ItPatient != Patients.end();++ItPatient)
00584          (*ItPatient)->Register();
00585    }
00586 }

void GDCM_NAME_SPACE::DicomDir::CreateDicomDir (   )  [private]
 

create a 'gdcmDicomDir' from a DICOMDIR Header

do : deal with PRIVATE (not so easy, since PRIVATE appears at different levels ?!? )

Definition at line 666 of file gdcmDicomDir.cxx.

References AddImageToEnd(), AddPatientToEnd(), AddPrivateToEnd(), AddSerieToEnd(), AddStudyToEnd(), AddVisitToEnd(), GDCM_NAME_SPACE::ElementSet::ClearEntry(), GDCM_NAME_SPACE::SQItem::Copy(), gdcmDebugMacro, gdcmErrorMacro, gdcmWarningMacro, GDCM_NAME_SPACE::SQItem::GetDocEntry(), GDCM_NAME_SPACE::ElementSet::GetDocEntry(), GDCM_NAME_SPACE::SeqEntry::GetFirstSQItem(), GDCM_NAME_SPACE::SeqEntry::GetNextSQItem(), GDCM_NAME_SPACE::DicomDirPrivate::New(), GDCM_NAME_SPACE::DicomDirPatient::New(), GDCM_NAME_SPACE::DicomDirStudy::New(), GDCM_NAME_SPACE::DicomDirVisit::New(), GDCM_NAME_SPACE::DicomDirSerie::New(), GDCM_NAME_SPACE::DicomDirImage::New(), and NewMeta().

Referenced by DoTheLoadingJob(), and ParseDirectory().

00667 {
00668    // The SeqEntries of "Directory Record Sequence" are parsed. 
00669    //  When a DicomDir tag ("PATIENT", "STUDY", "SERIE", "IMAGE") is found :
00670    //                    N.B. :  VISIT, PRIVATE not fully dealt with
00671    //  1 - we save the beginning iterator
00672    //  2 - we continue to parse
00673    //  3 - we find an other tag
00674    //       + we create the object for the precedent tag
00675    //       + loop to 1 -
00676    gdcmDebugMacro("Create DicomDir");
00677 
00678    // Directory record sequence
00679    DocEntry *e = GetDocEntry(0x0004, 0x1220);
00680    if ( !e )
00681    {
00682       gdcmWarningMacro( "No Directory Record Sequence (0004,1220) found");
00683       return;         
00684    }
00685    
00686    SeqEntry *s = dynamic_cast<SeqEntry *>(e);
00687    if ( !s )
00688    {
00689       gdcmWarningMacro( "Element (0004,1220) is not a Sequence ?!?");
00690       return;
00691    }
00692 
00693    NewMeta();
00694    
00695    DocEntry *d;
00696    std::string v;
00697    SQItem *si;
00698 
00699    SQItem *tmpSI=s->GetFirstSQItem();
00700    while(tmpSI)
00701    {
00702       d = tmpSI->GetDocEntry(0x0004, 0x1430); // Directory Record Type
00703       if ( DataEntry *dataEntry = dynamic_cast<DataEntry *>(d) )
00704       {
00705          v = dataEntry->GetString();
00706       }
00707       else
00708       {
00709          gdcmWarningMacro( "(0004,1430) not a DataEntry ?!?");
00710          continue;
00711       }
00712 
00713       // A decent DICOMDIR has much more images than series,
00714       // more series than studies, and so on.
00715       // This is the right order to perform the tests
00716 
00717       if ( v == "IMAGE " ) 
00718       {
00719          si = DicomDirImage::New(true); // true = empty
00720          if ( !AddImageToEnd( static_cast<DicomDirImage *>(si)) )
00721          {
00722             si->Delete();
00723             si = NULL;
00724             gdcmErrorMacro( "Add AddImageToEnd failed");
00725          }
00726       }
00727       else if ( v == "SERIES" )
00728       {
00729          si = DicomDirSerie::New(true);  // true = empty
00730          if ( !AddSerieToEnd( static_cast<DicomDirSerie *>(si)) )
00731          {
00732             si->Delete();
00733             si = NULL;
00734             gdcmErrorMacro( "Add AddSerieToEnd failed");
00735          }
00736       }
00737       else if ( v == "VISIT " )
00738       {
00739          si = DicomDirVisit::New(true);  // true = empty
00740          if ( !AddVisitToEnd( static_cast<DicomDirVisit *>(si)) )
00741          {
00742             si->Delete();
00743             si = NULL;
00744             gdcmErrorMacro( "Add AddVisitToEnd failed");
00745          }
00746       }
00747       else if ( v == "STUDY " )
00748       {
00749          si = DicomDirStudy::New(true);  // true = empty
00750          if ( !AddStudyToEnd( static_cast<DicomDirStudy *>(si)) )
00751          {
00752             si->Delete();
00753             si = NULL;
00754             gdcmErrorMacro( "Add AddStudyToEnd failed");
00755          }
00756       }
00757       else if ( v == "PATIENT " )
00758       {
00759          si = DicomDirPatient::New(true);  // true = empty
00760          if ( !AddPatientToEnd( static_cast<DicomDirPatient *>(si)) )
00761          {
00762             si->Delete();
00763             si = NULL;
00764             gdcmErrorMacro( "Add PatientToEnd failed");
00765          }
00766       }
00769       
00770       else if ( v == "PRIVATE " ) // for SIEMENS 'CSA Non Image'      
00771       {
00772       
00773          gdcmWarningMacro( " -------------------------------------------"
00774               << "a PRIVATE SQItem was found : " << v);
00775          si = DicomDirPrivate::New(true);  // true = empty
00776          if ( !AddPrivateToEnd( static_cast<DicomDirPrivate *>(si)) )
00777          {
00778             si->Delete();
00779             si = NULL;
00780             gdcmErrorMacro( "Add PrivateToEnd failed");
00781          }
00782       }      
00783       else
00784       {
00785          // It was neither a 'PATIENT', nor a 'STUDY', nor a 'SERIE',
00786          // nor an 'IMAGE' SQItem. Skip to next item.
00787          gdcmWarningMacro( " -------------------------------------------"
00788          << "a non PATIENT/STUDY/SERIE/IMAGE /VISIT/PRIVATE SQItem was found : "
00789          << v);
00790 
00791         // FIXME : deal with other item types !
00792         tmpSI=s->GetNextSQItem(); // To avoid infinite loop
00793         continue;
00794       }
00795       if ( si )
00796          si->Copy(tmpSI);
00797 
00798       tmpSI=s->GetNextSQItem();
00799    }
00800    ClearEntry();
00801 }

void GDCM_NAME_SPACE::DicomDir::CreateDicomDirChainedList (  std::string const &  path  )  [protected]
 

create a Document-like chained list from a root Directory

Parameters:
path entry point of the tree-like structure

Definition at line 594 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::Document::Abort, GDCM_NAME_SPACE::Document::CallProgressMethod(), GDCM_NAME_SPACE::Document::CallStartMethod(), gdcmDebugMacro, GDCM_NAME_SPACE::DirList::GetFilenames(), GDCM_NAME_SPACE::File::IsReadable(), GDCM_NAME_SPACE::File::Load(), GDCM_NAME_SPACE::Document::LoadMode, GDCM_NAME_SPACE::File::New(), GDCM_NAME_SPACE::Document::Progress, GDCM_NAME_SPACE::Document::SetFileName(), and GDCM_NAME_SPACE::Document::SetLoadMode().

Referenced by ParseDirectory().

00595 {
00596    CallStartMethod();
00597    DirList dirList(path,1); // gets recursively the file list
00598    unsigned int count = 0;
00599    VectDocument list;
00600    File *f;
00601 
00602    DirListType fileList = dirList.GetFilenames();
00603    unsigned int nbFile = fileList.size();
00604    for( DirListType::iterator it  = fileList.begin();
00605                               it != fileList.end();
00606                               ++it )
00607    {
00608       Progress = (float)(count+1)/(float)nbFile;
00609       CallProgressMethod();
00610       if ( Abort )
00611       {
00612          break;
00613       }
00614 
00615       f = File::New( );
00616       f->SetLoadMode(LoadMode); // we allow user not to load Sequences, 
00617                                 //        or Shadow groups, or ......
00618       f->SetFileName( it->c_str() );
00619       f->Load( );
00620 
00621       if ( f->IsReadable() )
00622       {
00623          // Add the file to the chained list:
00624          list.push_back(f);
00625          gdcmDebugMacro( "Readable " << it->c_str() );
00626        }
00627        else
00628        {
00629           f->Delete();
00630        }
00631        count++;
00632    }
00633    // sorts Patient/Study/Serie/
00634    std::sort(list.begin(), list.end(), DicomDir::HeaderLessThan );
00635    
00636    std::string tmp = dirList.GetDirName();      
00637    //for each File of the chained list, add/update the Patient/Study/Serie/Image info
00638    SetElements(tmp, list);
00639    CallEndMethod();
00640 
00641    for(VectDocument::iterator itDoc=list.begin();
00642        itDoc!=list.end();
00643        ++itDoc)
00644    {
00645       dynamic_cast<File *>(*itDoc)->Delete();
00646    }
00647 }

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

Delete the object.

Remarks:
The object is deleted only if its reference counting is to zero

Definition at line 41 of file gdcmRefCounter.h.

Referenced by GDCM_NAME_SPACE::SerieHelper::AddFileName(), GDCM_NAME_SPACE::Document::Backtrack(), GDCM_NAME_SPACE::FileHelper::CheckMandatoryElements(), GDCM_NAME_SPACE::FileHelper::CheckMandatoryEntry(), GDCM_NAME_SPACE::FileHelper::CopyMandatoryEntry(), GDCM_NAME_SPACE::Dict::DoTheLoadingJob(), GDCM_NAME_SPACE::FillDefaultDataDict(), GDCM_NAME_SPACE::DicomDirObject::FillObject(), vtkGdcmReader::GetFileInformation(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryBinArea(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryString(), GDCM_NAME_SPACE::DocEntrySet::InsertSeqEntry(), vtkGdcmReader::LoadFileInformation(), NewMeta(), GDCM_NAME_SPACE::DicomDirStudy::NewVisit(), GDCM_NAME_SPACE::Document::ReadNextDocEntry(), 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(), ~DicomDir(), GDCM_NAME_SPACE::DictSet::~DictSet(), and GDCM_NAME_SPACE::Global::~Global().

00041 { Unregister(); }

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

Loader. (DEPRECATED : kept not to break the API) Does the Loading Job (internal use only).

Returns:
false if file cannot be open or no swap info was found, or no tag was found.

Definition at line 283 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::Document::Abort, CreateDicomDir(), GDCM_NAME_SPACE::Document::Fp, gdcmDebugMacro, gdcmErrorMacro, gdcmWarningMacro, GDCM_NAME_SPACE::ElementSet::GetDocEntry(), GDCM_NAME_SPACE::Document::GetFileName(), GDCM_NAME_SPACE::ElementSet::GetFirstEntry(), GDCM_NAME_SPACE::Document::Load(), NewMeta(), ParseDir, ParseDirectory(), GDCM_NAME_SPACE::Document::Progress, and SetFileName().

Referenced by Load().

00284 {
00285    Progress = 0.0f;
00286    Abort = false;
00287 
00288    if (!ParseDir)
00289    {
00290    // Only if user passed a DICOMDIR
00291    // ------------------------------
00292       Fp = 0;
00293       if (!Document::Load() )
00294       {
00295          return false;
00296       }
00297 
00298       if ( GetFirstEntry() == 0 ) // when user passed a Directory to parse
00299       {
00300          gdcmWarningMacro( "Entry HT empty for file: "<< GetFileName());
00301          return false;
00302       }
00303       // Directory record sequence
00304       DocEntry *e = GetDocEntry(0x0004, 0x1220);
00305       if ( !e )
00306       {
00307          gdcmWarningMacro( "NO 'Directory record sequence' (0x0004,0x1220)"
00308                           << " in file " << GetFileName());
00309          return false;
00310       }
00311       else
00312       {
00313          CreateDicomDir();
00314       }
00315    }
00316    else
00317    {
00318    // Only if user passed a root directory
00319    // ------------------------------------
00320       if ( GetFileName() == "." )
00321       {
00322          // user passed '.' as Name
00323          // we get current directory name
00324          char buf[2048];
00325          const char *cwd = getcwd(buf, 2048);
00326          if( cwd )
00327          {
00328             SetFileName( buf ); // will be converted into a string
00329          }
00330          else
00331          {
00332             gdcmErrorMacro( "Path was too long to fit on 2048 bytes" );
00333          }
00334       }
00335       NewMeta();
00336       gdcmDebugMacro( "Parse directory and create the DicomDir : " 
00337                          << GetFileName() );
00338       ParseDirectory();
00339    }
00340    return true;
00341 }

GDCM_NAME_SPACE::DicomDir::gdcmTypeMacro (  DicomDir   )  [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(), GDCM_NAME_SPACE::Document::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().

00104 {
00105    DocEntry *currentEntry = GetDocEntry(group, elem);
00106    if ( !currentEntry )
00107       return NULL;
00108 
00109    return dynamic_cast<DataEntry*>(currentEntry);
00110 }

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

Searches [both] the public [and the shadow dictionary (when they exist)] for the presence of the DictEntry with given group and element. The public dictionary has precedence on the shadow one(s), if any.

Parameters:
group Group number of the searched DictEntry
elem Element number of the searched DictEntry
Returns:
Corresponding DictEntry when it exists, NULL otherwise.
Remarks:
The returned DictEntry is registered when existing
Todo:
store the DefaultPubDict somwhere, in order not to access the HTable every time ! --> Done!

Definition at line 473 of file gdcmDocEntrySet.cxx.

References gdcmWarningMacro, GDCM_NAME_SPACE::DictSet::GetDefaultPubDict(), GDCM_NAME_SPACE::Global::GetDicts(), GDCM_NAME_SPACE::Dict::GetEntry(), and GDCM_NAME_SPACE::RefCounter::Register().

Referenced by GDCM_NAME_SPACE::Document::ReadNextDocEntry().

00474 {
00475    DictEntry *found = 0;
00478    Dict *pubDict = Global::GetDicts()->GetDefaultPubDict();
00479    if (!pubDict) 
00480    {
00481       gdcmWarningMacro( "We SHOULD have a default dictionary");
00482    }
00483    else
00484    {
00485       found = pubDict->GetEntry(group, elem);
00486       if( found )
00487          found->Register();
00488    }
00489    return found;
00490 }

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(), CreateDicomDir(), GDCM_NAME_SPACE::File::DoTheLoadingJob(), DoTheLoadingJob(), GDCM_NAME_SPACE::File::GetPixelAreaLength(), GDCM_NAME_SPACE::File::GetPixelOffset(), GDCM_NAME_SPACE::Document::GetTransferSyntax(), GDCM_NAME_SPACE::File::HasLUT(), GDCM_NAME_SPACE::Document::IsDicomV3(), GDCM_NAME_SPACE::Document::IsPapyrus(), GDCM_NAME_SPACE::File::IsReadable(), GDCM_NAME_SPACE::Document::LoadEntryBinArea(), GDCM_NAME_SPACE::DocEntryArchive::Push(), and GDCM_NAME_SPACE::DocEntryArchive::Restore().

00187 {
00188    TagKey key = DictEntry::TranslateToKey(group, elem);
00189    TagDocEntryHT::iterator it = TagHT.find(key);
00190 
00191    if ( it!=TagHT.end() )
00192       return it->second;
00193    return NULL;
00194 }

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().

00074 {
00075    DataEntry *entry = GetDataEntry(group, elem);
00076    if ( entry )
00077       return entry->GetBinArea();
00078    return 0;
00079 }

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 SetElement(), and GDCM_NAME_SPACE::File::Write().

00089 {
00090    DocEntry *entry = GetDocEntry(group, elem);
00091    if ( entry )
00092       return entry->GetLength();
00093    return -1;
00094 }

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(), GDCM_NAME_SPACE::Document::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(), GDCM_NAME_SPACE::Document::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(), GDCM_NAME_SPACE::Document::operator<(), and SetElement().

00052 {
00053    DataEntry *entry = dynamic_cast<DataEntry *>(GetDocEntry(group,elem));
00054    if ( entry )
00055    {
00056       if( entry->IsNotLoaded() )
00057          return GDCM_NOTLOADED;
00058       if( entry->IsUnfound() )
00059          return GDCM_UNFOUND;
00060       if( entry->IsUnread() )
00061          return GDCM_UNREAD;
00062       return entry->GetString();
00063    }
00064    return GDCM_UNFOUND;
00065 }

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

Accessor to Filename.

Definition at line 78 of file gdcmDocument.h.

Referenced by DoTheLoadingJob(), GDCM_NAME_SPACE::SerieHelper::FileNameGreaterThan(), GDCM_NAME_SPACE::SerieHelper::FileNameLessThan(), GDCM_NAME_SPACE::Document::IsParsable(), IsReadable(), GDCM_NAME_SPACE::Document::Load(), vtkGdcmReader::LoadImageInMemory(), ParseDirectory(), SetElement(), vtkGdcmReader::TestFileInformation(), and userSuppliedLessThanFunction2().

00078 { return Filename; }

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

returns the File Type (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)

Returns:
the FileType code

Definition at line 417 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::Document::Filetype.

00418 {
00419    return Filetype;
00420 }

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

Get the first entry while visiting *the* 'zero level' DocEntrySet (DocEntries out of any Sequence).

Returns:
The first DocEntry if found, otherwhise NULL

Implements GDCM_NAME_SPACE::DocEntrySet.

Definition at line 156 of file gdcmElementSet.cxx.

References GDCM_NAME_SPACE::ElementSet::ItTagHT, and GDCM_NAME_SPACE::ElementSet::TagHT.

Referenced by GDCM_NAME_SPACE::Document::ComputeGroup0002Length(), DoTheLoadingJob(), NewMeta(), and GDCM_NAME_SPACE::Validator::SetInput().

00157 {
00158    ItTagHT = TagHT.begin();
00159    if (ItTagHT != TagHT.end())
00160       return  ItTagHT->second;
00161    return NULL;
00162 }

DicomDirPatient * GDCM_NAME_SPACE::DicomDir::GetFirstPatient (   ) 
 

Get the first entry while visiting the DicomDirPatients.

Returns:
The first DicomDirPatient if found, otherwhise NULL

Definition at line 435 of file gdcmDicomDir.cxx.

References ItPatient, and Patients.

00436 {
00437    ItPatient = Patients.begin();
00438    if ( ItPatient != Patients.end() )
00439       return *ItPatient;
00440    return NULL;
00441 }

DicomDirMeta* GDCM_NAME_SPACE::DicomDir::GetMeta (   )  [inline]
 

Returns a pointer to the DicomDirMeta for this DICOMDIR.

Definition at line 83 of file gdcmDicomDir.h.

Referenced by Write().

00083 { return MetaElems; }

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

Get the next entry while visiting *the* 'zero level' DocEntrySet (DocEntries out of any Sequence).

Note:
: meaningfull only if GetFirstEntry already called
Returns:
The next DocEntry if found, otherwhise NULL

Implements GDCM_NAME_SPACE::DocEntrySet.

Definition at line 170 of file gdcmElementSet.cxx.

References gdcmAssertMacro, GDCM_NAME_SPACE::ElementSet::ItTagHT, and GDCM_NAME_SPACE::ElementSet::TagHT.

Referenced by GDCM_NAME_SPACE::Document::ComputeGroup0002Length(), and GDCM_NAME_SPACE::Validator::SetInput().

00171 {
00172    gdcmAssertMacro (ItTagHT != TagHT.end());
00173 
00174    ++ItTagHT;
00175    if (ItTagHT != TagHT.end())
00176       return  ItTagHT->second;
00177    return NULL;
00178 }

DicomDirPatient * GDCM_NAME_SPACE::DicomDir::GetNextPatient (   ) 
 

Get the next entry while visiting the DicomDirPatients.

Note:
: meaningfull only if GetFirstEntry already called
Returns:
The next DicomDirPatient if found, otherwhise NULL

Definition at line 448 of file gdcmDicomDir.cxx.

References gdcmAssertMacro, ItPatient, and Patients.

00449 {
00450    gdcmAssertMacro (ItPatient != Patients.end());
00451 
00452    ++ItPatient;
00453    if ( ItPatient != Patients.end() )
00454       return *ItPatient;
00455    return NULL;
00456 }

int GDCM_NAME_SPACE::DicomDir::GetNumberOfPatients (   )  [inline]
 

returns the number of Patients currently held in the gdcm::DicomDir

Definition at line 92 of file gdcmDicomDir.h.

00092 { return Patients.size();}

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

Gets the print level for the Dicom Entries.

Definition at line 50 of file gdcmBase.h.

00050 { return PrintLevel; }

float GDCM_NAME_SPACE::DicomDir::GetProgress (   )  const [inline]
 

GetProgress GetProgress.

Definition at line 98 of file gdcmDicomDir.h.

00098 { return Progress; }

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

Get the public dictionary used.

Definition at line 314 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::Document::RefPubDict.

00315 {
00316    return RefPubDict;
00317 }

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.

00060    {
00061       return RefCount;
00062    }

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

Same as Document::GetDocEntry except it returns a result only when the corresponding entry is of type SeqEntry.

Parameters:
group Group number of the searched Dicom Element
elem Element number of the searched Dicom Element
Returns:
When present, the corresponding SeqEntry.

Definition at line 119 of file gdcmDocEntrySet.cxx.

References GDCM_NAME_SPACE::DocEntrySet::GetDocEntry().

Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::File::GetRescaleSlopeIntercept(), and GDCM_NAME_SPACE::File::GetSpacing().

00120 {
00121    DocEntry *currentEntry = GetDocEntry(group, elem);
00122    if ( !currentEntry )
00123       return NULL;
00124 
00125    return dynamic_cast<SeqEntry*>(currentEntry);
00126 }

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

Get the shadow dictionary used.

Definition at line 322 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::Document::RefShaDict.

00323 {
00324    return RefShaDict;
00325 }

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

'Swap code' accessor (see SwapCode )

Definition at line 74 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile().

00074 { return SwapCode; }

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

Accessor to the Transfer Syntax (when present) of the current document (it internally handles reading the value from disk when only parsing occured).

Returns:
The encountered Transfer Syntax of the current document, if DICOM. GDCM_UNKNOWN for ACR-NEMA files (or broken headers ...)

Definition at line 429 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::GDCM_UNKNOWN, gdcmWarningMacro, and GDCM_NAME_SPACE::ElementSet::GetDocEntry().

Referenced by GDCM_NAME_SPACE::File::ComputeJPEGFragmentInfo(), GDCM_NAME_SPACE::File::ComputeRLEInfo(), GDCM_NAME_SPACE::File::DoTheLoadingJob(), and GDCM_NAME_SPACE::Document::HandleOutOfGroup0002().

00430 {
00431    DocEntry *entry = GetDocEntry(0x0002, 0x0010);
00432    if ( !entry )
00433    {
00434       return GDCM_UNKNOWN;
00435    }
00436 
00437    // The entry might be present but not loaded (parsing and loading
00438    // happen at different stages): try loading and proceed with check...
00439    
00440    // Well ...
00441    // (parsing and loading happen at the very same stage!) 
00442    //LoadDocEntrySafe(entry); //JPRx
00443    if (DataEntry *dataEntry = dynamic_cast<DataEntry *>(entry) )
00444    {
00445       std::string transfer = dataEntry->GetString();
00446       // The actual transfer (as read from disk) might be padded. We
00447       // first need to remove the potential padding. We can make the
00448       // weak assumption that padding was not executed with digits...
00449       if  ( transfer.length() == 0 )
00450       {
00451          // for brain damaged headers
00452          gdcmWarningMacro( "Transfer Syntax has length = 0.");
00453          return GDCM_UNKNOWN;
00454       }
00455       while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
00456       {
00457          transfer.erase(transfer.length()-1, 1);
00458          if  ( transfer.length() == 0 )
00459          {
00460             // for brain damaged headers
00461             gdcmWarningMacro( "Transfer Syntax contains no valid character.");
00462             return GDCM_UNKNOWN;
00463          }
00464       }
00465       return transfer;
00466    }
00467    return GDCM_UNKNOWN;
00468 }

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

Accesses the info from 0002,0010 : Transfer Syntax and TS.

Returns:
The full Transfer Syntax Name (as opposed to Transfer Syntax UID)

Definition at line 474 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::GDCM_NOTLOADED, GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmDebugMacro, gdcmErrorMacro, GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), and GDCM_NAME_SPACE::Global::GetTS().

Referenced by GDCM_NAME_SPACE::Document::HandleOutOfGroup0002().

00475 {
00476    // use the TS (TS : Transfer Syntax)
00477    std::string transferSyntax = GetEntryString(0x0002,0x0010);
00478 
00479    if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) )
00480    {
00481       gdcmErrorMacro( "Transfer Syntax not loaded. " << std::endl
00482                << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" );
00483       return "Uncompressed ACR-NEMA";
00484    }
00485    if ( transferSyntax == GDCM_UNFOUND )
00486    {
00487       gdcmDebugMacro( "Unfound Transfer Syntax (0002,0010)");
00488       return "Uncompressed ACR-NEMA";
00489    }
00490 
00491    // we do it only when we need it
00492    const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax );
00493 
00494    // Global::GetTS() is a global static you shall never try to delete it!
00495    return tsName;
00496 }

bool GDCM_NAME_SPACE::DicomDir::HeaderLessThan (  Document *  header1,
Document *  header2
)  [static, private]
 

compares two files

Definition at line 1208 of file gdcmDicomDir.cxx.

01209 {
01210    return *header1 < *header2;
01211 }

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

Sets all fields to NULL.

Reimplemented from GDCM_NAME_SPACE::Document.

Definition at line 655 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::Document::Abort, MetaElems, and GDCM_NAME_SPACE::Document::Progress.

Referenced by DicomDir().

00656 {
00657    Progress = 0.0;
00658    Abort = false;
00659 
00660    MetaElems = NULL;   
00661 }

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().

00293 {
00294    DataEntry *dataEntry = 0;
00295    DocEntry *currentEntry = GetDocEntry( group, elem );
00296 
00297    // Verify the currentEntry
00298    if (currentEntry)
00299    {
00300       dataEntry = dynamic_cast<DataEntry *>(currentEntry);
00301 
00302       // Verify the VR
00303       if ( dataEntry )
00304          if ( dataEntry->GetVR()!=vr )
00305             dataEntry = NULL;
00306 
00307       // if currentEntry doesn't correspond to the requested dataEntry
00308       if ( !dataEntry)
00309       {
00310          if ( !RemoveEntry(currentEntry) )
00311          {
00312             gdcmWarningMacro( "Removal of previous DocEntry failed.");
00313             return NULL;
00314          }
00315       }
00316    }
00317 
00318    // Create a new dataEntry if necessary
00319    if ( !dataEntry)
00320    {
00321       dataEntry = NewDataEntry(group, elem, vr);
00322 
00323       if ( !AddEntry(dataEntry) )
00324       {
00325          gdcmWarningMacro( "AddEntry failed although this is a creation.");
00326          dataEntry->Delete();
00327          return NULL;
00328       }
00329       dataEntry->Delete();
00330    }
00331 
00332    // Set the dataEntry value
00333    uint8_t *tmpArea;
00334    if ( lgth>0 && binArea )
00335    {
00336       tmpArea = new uint8_t[lgth];
00337       memcpy(tmpArea,binArea,lgth);
00338    }
00339    else
00340    {
00341       tmpArea = 0;
00342    }
00343    if ( !SetEntryBinArea(tmpArea,lgth,dataEntry) )
00344    {
00345       if ( tmpArea )
00346       {
00347          delete[] tmpArea;
00348       }
00349    }
00350    return dataEntry;
00351 }

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().

00219 {
00220    DataEntry *dataEntry = 0;
00221    DocEntry *currentEntry = GetDocEntry( group, elem );
00222    VRKey localVR = vr;
00223    if (currentEntry)
00224    {
00225       dataEntry = dynamic_cast<DataEntry *>(currentEntry);
00226 
00227       // Verify the VR
00228       if ( dataEntry )
00229          if ( dataEntry->GetVR()!=vr )
00230             dataEntry = NULL;
00231 
00232       // if currentEntry doesn't correspond to the requested dataEntry
00233       if ( !dataEntry)
00234       {
00235          if ( !RemoveEntry(currentEntry) )
00236          {
00237             gdcmWarningMacro( "Removal of previous DocEntry failed.");
00238             return NULL;
00239          }
00240       }
00241    }
00242   
00243    else // the 'currentEntry' was not found
00244    {
00245       if ( vr == GDCM_VRUNKNOWN ) // user didn't specify a VR.
00246                                   //  Probabely he trusts the Dicom Dict !
00247       {
00248           DictEntry *e = 
00249             Global::GetDicts()->GetDefaultPubDict()->GetEntry(group, elem);
00250           if ( e )
00251           {
00252              localVR = e->GetVR();  
00253              e->Register(); // ?? JPRx
00254          }
00255       }
00256    }
00257 
00258    // Create a new dataEntry if necessary
00259    if ( !dataEntry )
00260    {
00261       dataEntry = NewDataEntry( group, elem, localVR );
00262 
00263       if ( !AddEntry(dataEntry) )
00264       {
00265          gdcmWarningMacro("AddEntry " << dataEntry->GetKey() 
00266                  << " failed although this is a creation.");
00267          dataEntry->Delete();
00268          return NULL;
00269       }
00270       dataEntry->Delete(); // ?!? JPRx
00271    }
00272 
00273    // Set the dataEntry value
00274    SetEntryString(value, dataEntry); // The std::string value
00275    return dataEntry;
00276 }

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().

00362 {
00363    SeqEntry *seqEntry = 0;
00364    DocEntry *currentEntry = GetDocEntry( group, elem );
00365 
00366    // Verify the currentEntry
00367    if ( currentEntry )
00368    {
00369       seqEntry = dynamic_cast<SeqEntry *>(currentEntry);
00370 
00371       // Verify the VR
00372       if ( seqEntry )
00373          seqEntry = NULL;
00374 
00375       // if currentEntry doesn't correspond to the requested seqEntry
00376       if ( !seqEntry )
00377       {
00378          if (!RemoveEntry(currentEntry))
00379          {
00380             gdcmWarningMacro( "Removal of previous DocEntry failed for ("
00381                <<std::hex << group << "|" << elem <<")" );
00382             return NULL;
00383          }
00384       }
00385    }
00386    // Create a new seqEntry if necessary
00387    if ( !seqEntry )
00388    {
00389       seqEntry = NewSeqEntry(group, elem);
00390 
00391       if ( !AddEntry(seqEntry) )
00392       {
00393          gdcmWarningMacro( "AddEntry failed although this is a creation for ("
00394             <<std::hex << group << "|" << elem <<")" );
00395          seqEntry->Delete();
00396          return NULL;
00397       }
00398       seqEntry->Delete();
00399    }
00400    // Remark :
00401    // SequenceDelimitationItem will be added at the end of the SeqEntry,
00402    // at write time
00403    return seqEntry;
00404 }

bool GDCM_NAME_SPACE::DicomDir::IsAborted (   )  [inline]
 

IsAborted IsAborted.

Definition at line 102 of file gdcmDicomDir.h.

00102 { return Abort; }

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

Predicate for dicom version 3 file.

Returns:
True when the file is a dicom version 3.

Definition at line 386 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::ElementSet::GetDocEntry().

Referenced by GDCM_NAME_SPACE::File::GetYSize(), and GDCM_NAME_SPACE::PixelReadConvert::GrabInformationsFromFile().

00387 {
00388    // Checking if Transfer Syntax exists is enough
00389    // Anyway, it's too late check if the 'Preamble' was found ...
00390    // And ... would it be a rich idea to check ?
00391    // (some 'no Preamble' DICOM images exist !)
00392    return GetDocEntry(0x0002, 0x0010) != NULL;
00393 }

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

Tells us if the ElementSet contains no entry.

Implements GDCM_NAME_SPACE::DocEntrySet.

Definition at line 59 of file gdcmElementSet.h.

Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), and GDCM_NAME_SPACE::Document::IsParsable().

00059 { return TagHT.empty(); }

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

Predicate for Papyrus file Dedicated to whomsoever it may concern.

Returns:
True when the file is a Papyrus file.

Definition at line 400 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::ElementSet::GetDocEntry().

00401 {
00402    // check for Papyrus private Sequence
00403    DocEntry *e = GetDocEntry(0x0041, 0x1050);
00404    if ( !e )
00405       return false;
00406    // check if it's actually a Sequence
00407    if ( !dynamic_cast<SeqEntry*>(e) )
00408       return  false;
00409    return true;
00410 }

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

This predicate tells us whether or not the current Document was properly parsed and contains at least *one* Dicom Element (and nothing more, sorry).

Returns:
false when we're 150 % sure it's NOT a Dicom/Acr file, true otherwise.

Definition at line 354 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::Document::Filetype, gdcmWarningMacro, GDCM_NAME_SPACE::Document::GetFileName(), GDCM_NAME_SPACE::ElementSet::IsEmpty(), and GDCM_NAME_SPACE::Unknown.

Referenced by GDCM_NAME_SPACE::Document::IsReadable().

00355 {
00356    if ( Filetype == Unknown )
00357    {
00358       gdcmWarningMacro( "Wrong filetype for " << GetFileName());
00359       return false;
00360    }
00361 
00362    if ( IsEmpty() )
00363    { 
00364       gdcmWarningMacro( "No tag in internal hash table.");
00365       return false;
00366    }
00367 
00368    return true;
00369 }

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

This predicate, based on hopefully reasonable heuristics, decides whether or not the current document was properly parsed and contains the mandatory information for being considered as a well formed and usable DicomDir.

Returns:
true when Document is the one of a reasonable DicomDir, false otherwise.

Reimplemented from GDCM_NAME_SPACE::Document.

Definition at line 351 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::Document::Filetype, gdcmErrorMacro, gdcmWarningMacro, GDCM_NAME_SPACE::Document::GetFileName(), MetaElems, Patients, and GDCM_NAME_SPACE::Unknown.

00352 {
00353    if ( Filetype == Unknown )
00354    {
00355       gdcmErrorMacro( "Wrong filetype for " << GetFileName());
00356       return false;
00357    }
00358    if ( !MetaElems )
00359    {
00360       gdcmWarningMacro( "Meta Elements missing in DicomDir");
00361       return false;
00362    }
00363    if ( Patients.size() <= 0 )
00364    {
00365       gdcmWarningMacro( "NO Patient in DicomDir");
00366       return false;
00367    }
00368 
00369    return true;
00370 }

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.

00226 {
00227    uint16_t currentGroup;
00228    int codeVR = -1;
00229    int currentCodeVR;
00230    for(TagDocEntryHT::iterator cc = TagHT.begin();cc != TagHT.end(); ++cc)
00231    {
00232       currentGroup = cc->second->GetGroup();
00233 
00234       if ( currentGroup < group )
00235          continue;   
00236       if ( currentGroup > group )
00237          break;
00238       // currentGroup == group
00239       if (codeVR == -1)
00240       {
00241          if (cc->second->IsImplicitVR() )
00242             codeVR = 1;
00243          else 
00244             codeVR = 2;
00245          continue;
00246       }
00247       else
00248       {
00249          if (cc->second->IsImplicitVR() )
00250             currentCodeVR = 1; //Implicit
00251          else 
00252             currentCodeVR = 2; // Explicit  
00253   
00254          if ( currentCodeVR == codeVR )
00255            continue;
00256          else
00257             return -1;    // -1 : not coherent 
00258       }
00259    }   
00260    return codeVR;
00261 }

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

Loader. use SetFileName(fn) or SetLoadMode(lm) + SetDirectoryName(dn) before !

Returns:
false if file cannot be open or no swap info was found, or no tag was found.

Reimplemented from GDCM_NAME_SPACE::Document.

Definition at line 244 of file gdcmDicomDir.cxx.

References DoTheLoadingJob(), and ParseDir.

00245 {
00246    if (!ParseDir)
00247    {
00248       if ( ! this->Document::Load( ) )
00249          return false;
00250    }
00251    return DoTheLoadingJob( );   
00252 }

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

Loads (from disk) the element content when a string is not suitable.

Parameters:
entry Entry whose binArea is going to be loaded

Definition at line 761 of file gdcmDocument.cxx.

References gdcmWarningMacro, GDCM_NAME_SPACE::DataEntry::GetBinArea(), GDCM_NAME_SPACE::DocEntry::GetElement(), GDCM_NAME_SPACE::DocEntry::GetGroup(), GDCM_NAME_SPACE::DocEntry::GetLength(), GDCM_NAME_SPACE::DocEntry::GetOffset(), GDCM_NAME_SPACE::Document::OpenFile(), GDCM_NAME_SPACE::DataEntry::SetState(), and GDCM_NAME_SPACE::DataEntry::STATE_UNREAD.

00762 { 
00763    if( entry->GetBinArea() )
00764       return;
00765 
00766    bool openFile = !Fp;
00767    if ( openFile )
00768       OpenFile();
00769 
00770    //size_t o =(size_t)entry->GetOffset();
00771    Fp->seekg((size_t)entry->GetOffset(), std::ios::beg);  // FIXME : for each DataEntry !
00772 
00773    size_t l = entry->GetLength();
00774    uint8_t *data = new uint8_t[l];
00775    if ( !data )
00776    {
00777       gdcmWarningMacro(  "Cannot allocate DataEntry content for : "
00778                        << std::hex << entry->GetGroup() 
00779                        << "|" << entry->GetElement() );
00780       return;
00781    }
00782 
00783    // Read the data
00784    Fp->read((char*)data, l);
00785    if ( Fp->fail() || Fp->eof() )
00786    {
00787       delete[] data;
00788       entry->SetState(DataEntry::STATE_UNREAD);
00789       return;
00790    }
00791 
00792    // Swap the data content if necessary
00793    uint32_t i;
00794    unsigned short vrLgth = 
00795                         Global::GetVR()->GetAtomicElementLength(entry->GetVR());
00796 
00797 // FIXME : trouble expected if we read an ... OW Entry (LUT, etc ..)
00798 //   if( entry->GetVR() == "OW" )
00799 //      vrLgth = 1;
00800 
00801    switch(vrLgth)
00802    {
00803       case 1:
00804       {
00805          break;
00806       }     
00807       case 2:
00808       {
00809          uint16_t *data16 = (uint16_t *)data;
00810          for(i=0;i<l/vrLgth;i++)
00811             data16[i] = SwapShort(data16[i]);
00812          break;
00813       }
00814       case 4:
00815       {
00816          uint32_t *data32 = (uint32_t *)data;
00817          for(i=0;i<l/vrLgth;i++)
00818             data32[i] = SwapLong(data32[i]);
00819          break;
00820       }
00821       case 8:
00822       {
00823          double *data64 = (double *)data;
00824          for(i=0;i<l/vrLgth;i++)
00825             data64[i] = SwapDouble(data64[i]);
00826          break;
00827       }
00828    }
00829    
00830    entry->SetBinArea(data);
00831 
00832    if ( openFile ) // The file is left in the state (open/close) it was at entrance
00833       CloseFile();
00834 }

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

Loads (from disk) the element content when a string is not suitable.

Parameters:
group group number of the Entry
elem element number of the Entry

Definition at line 736 of file gdcmDocument.cxx.

References gdcmDebugMacro, gdcmWarningMacro, and GDCM_NAME_SPACE::ElementSet::GetDocEntry().

Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), and GDCM_NAME_SPACE::Document::LoadDocEntry().

00737 {
00738    // Search the corresponding DocEntry
00739    DocEntry *docEntry = GetDocEntry(group, elem);
00740    if ( !docEntry )
00741    {
00742       gdcmDebugMacro(std::hex << group << "|" << elem 
00743                        <<  " doesn't exist" );
00744       return;
00745    }
00746    DataEntry *dataEntry = dynamic_cast<DataEntry *>(docEntry);
00747    if ( !dataEntry )
00748    {
00749       gdcmWarningMacro(std::hex << group << "|" << elem 
00750                        <<  " is NOT a DataEntry");
00751       return;
00752    }
00753    LoadEntryBinArea(dataEntry);
00754 }

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().

00071                  { return true; }

void GDCM_NAME_SPACE::DicomDir::MoveSQItem (  DocEntrySet *  dst,
DocEntrySet *  src
)  [private]
 

Move the content of the source SQItem to the destination SQItem Only DocEntry's are moved.

Parameters:
dst destination SQItem
src source SQItem

Definition at line 1190 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::DocEntrySet::AddEntry(), GDCM_NAME_SPACE::DocEntrySet::GetFirstEntry(), and GDCM_NAME_SPACE::DocEntrySet::RemoveEntry().

01191 { 
01192    DocEntry *entry;
01193 // todo : rewrite the whole stuff, without using RemoveEntry an AddEntry,
01194 //        to save time
01195    entry = src->GetFirstEntry();
01196    while(entry)
01197    {
01198       dst->AddEntry(entry);  // use it, *before* removing it!
01199       src->RemoveEntry(entry);
01200       // we destroyed -> the current iterator is not longer valid
01201       entry = src->GetFirstEntry();
01202    }
01203 }

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

Constructs a DicomDir with a RefCounter.

Definition at line 62 of file gdcmDicomDir.h.

00062 {return new DicomDir();}

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

Build a new DataEntry from all the low level arguments.

Parameters:
group Group number of the new Entry
elem Element number of the new Entry
vr V(alue) R(epresentation) of the new Entry
Remarks:
The user of this method must destroy the DataEntry when unused

Definition at line 425 of file gdcmDocEntrySet.cxx.

References gdcmWarningMacro, and GDCM_NAME_SPACE::DataEntry::New().

Referenced by GDCM_NAME_SPACE::FileHelper::CopyDataEntry(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryBinArea(), GDCM_NAME_SPACE::DocEntrySet::InsertEntryString(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

00427 {
00428 
00429    DataEntry *newEntry = DataEntry::New(group, elem, vr);
00430    if (!newEntry) 
00431    {
00432       gdcmWarningMacro( "Failed to allocate DataEntry for ("
00433           <<std::hex << group << "|" << elem <<")" );
00434       return 0;
00435    }
00436    return newEntry;
00437 }

DicomDirMeta * GDCM_NAME_SPACE::DicomDir::NewMeta (   ) 
 

adds *the* Meta to a partially created DICOMDIR

Definition at line 375 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::SQItem::AddEntry(), GDCM_NAME_SPACE::RefCounter::Delete(), GDCM_NAME_SPACE::ElementSet::GetFirstEntry(), MetaElems, GDCM_NAME_SPACE::DicomDirMeta::New(), GDCM_NAME_SPACE::ElementSet::RemoveEntry(), and GDCM_NAME_SPACE::SQItem::SetSQItemNumber().

Referenced by CreateDicomDir(), DicomDir(), and DoTheLoadingJob().

00376 {
00377    if ( MetaElems )
00378    {
00379       MetaElems->Delete();
00380    }
00381    DocEntry *entry = GetFirstEntry();
00382    if ( entry )
00383    { 
00384       MetaElems = DicomDirMeta::New(true); // true = empty
00385 
00386       entry = GetFirstEntry();
00387       while( entry )
00388       {
00389          if ( dynamic_cast<SeqEntry *>(entry) )
00390             break;
00391 
00392          MetaElems->AddEntry(entry);
00393          RemoveEntry(entry);
00394 
00395          entry = GetFirstEntry();
00396       }
00397    }
00398    else  // after root directory parsing
00399    {
00400       MetaElems = DicomDirMeta::New(false); // false = not empty
00401    }
00402    MetaElems->SetSQItemNumber(0); // To avoid further missprinting
00403    return MetaElems;  
00404 }

DicomDirPatient * GDCM_NAME_SPACE::DicomDir::NewPatient (   ) 
 

adds a new Patient (with the basic elements) to a partially created DICOMDIR

Definition at line 410 of file gdcmDicomDir.cxx.

References AddPatientToEnd(), and GDCM_NAME_SPACE::DicomDirPatient::New().

00411 {
00412    DicomDirPatient *dd = DicomDirPatient::New();
00413    AddPatientToEnd( dd );
00414    return dd;
00415 }

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

Build a new SeqEntry from all the low level arguments.

Parameters:
group Group number of the new Entry
elem Element number of the new Entry
Remarks:
The user of this method must destroy the SeqEntry when unused

Definition at line 445 of file gdcmDocEntrySet.cxx.

References gdcmWarningMacro, and GDCM_NAME_SPACE::SeqEntry::New().

Referenced by GDCM_NAME_SPACE::Document::Backtrack(), GDCM_NAME_SPACE::DocEntrySet::InsertSeqEntry(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

00446 {
00447    //DictEntry *dictEntry = GetDictEntry(group, elem, "SQ");
00448 
00449    //SeqEntry *newEntry = SeqEntry::New( dictEntry );
00450    SeqEntry *newEntry = SeqEntry::New( group, elem );
00451    //dictEntry->Unregister(); // GetDictEntry register it
00452    if (!newEntry)
00453    {
00454       gdcmWarningMacro( "Failed to allocate SeqEntry for ("
00455          <<std::hex << group << "|" << elem <<")" );
00456       return 0;
00457    }     
00458    return newEntry;
00459 }

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

Tries to open the file Document::Filename and checks the preamble when existing, or if the file starts with an ACR-NEMA look-like element.

Returns:
The FILE pointer on success, 0 on failure.

Definition at line 590 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::Document::Filename, and GDCM_NAME_SPACE::Document::HasDCMPreamble.

Referenced by GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::File::DoTheLoadingJob(), GDCM_NAME_SPACE::FileHelper::GetRaw(), and GDCM_NAME_SPACE::Document::LoadEntryBinArea().

00591 {
00592    HasDCMPreamble = false;
00593    if (Filename.length() == 0) 
00594    {
00595       return 0;
00596    }
00597 
00598    if ( Fp )
00599    {
00600       gdcmDebugMacro( "File already open: " << Filename.c_str());
00601       CloseFile();
00602    }
00603 
00604    Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
00605    if ( ! *Fp )
00606    {
00607    // Don't user gdcmErrorMacro :
00608    // a spurious message will appear when you use, for instance 
00609    // gdcm::FileHelper *fh = new gdcm::FileHelper( outputFileName );
00610    // to create outputFileName.
00611    
00612    // FIXME : if the upper comment is still usefull 
00613    //         --> the constructor is not so good ...
00614    
00615       gdcmWarningMacro( "Cannot open file: " << Filename.c_str());
00616       delete Fp;
00617       Fp = 0;
00618       return 0;
00619       //exit(1); // No function is allowed to leave the application instead
00620                  // of warning the caller
00621    }
00622  
00623    uint16_t zero = 0;
00624    Fp->read((char*)&zero, (size_t)2);
00625    if ( Fp->eof() )
00626    {
00627       CloseFile();
00628       return 0;
00629    }
00630  
00631    //-- DICOM --
00632    Fp->seekg(126L, std::ios::cur);  // Once per Document
00633    char dicm[4]; // = {' ',' ',' ',' '};
00634    Fp->read(dicm,  (size_t)4);
00635    if ( Fp->eof() )
00636    {
00637       CloseFile();
00638       return 0;
00639    }
00640    
00641    if ( memcmp(dicm, "DICM", 4) == 0 )
00642    {
00643       HasDCMPreamble = true;
00644       return Fp;
00645    }
00646 
00647    //-- Broken ACR or DICOM (?) with no Preamble; may start with a Shadow Group --
00648    // FIXME : We cannot be sure the preable is only zeroes..
00649    //         (see ACUSON-24-YBR_FULL-RLE.dcm )
00650    if ( 
00651        zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 ||
00652        zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 ||
00653        zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 ||
00654        zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ||
00655        zero == 0x0028 || 0x2800    // worse : some ACR-NEMA like files 
00656                                    // start 00028 group ?!?      
00657        )
00658    {
00659       std::string msg = Util::Format(
00660         "ACR/DICOM starting by 0x(%04x) at the beginning of the file\n", zero);
00661       // FIXME : is it a Warning message, or a Debug message?
00662       gdcmWarningMacro( msg.c_str() );
00663       return Fp;
00664    }
00665    
00666    // -- Neither ACR/No Preamble Dicom nor DICOMV3 file
00667    CloseFile();
00668    // Don't user Warning nor Error, not to pollute the output
00669    // while directory recursive parsing ...
00670    gdcmDebugMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
00671                       << Filename.c_str()); 
00672    return 0;
00673 }

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

Loads the element while preserving the current underlying file position indicator as opposed to LoadDocEntry that modifies it Compares two documents, according to DicomDir rules.

Warning:
Does NOT work with ACR-NEMA files
Todo:
Find a trick to solve the pb (use RET fields ?)
Parameters:
document to compare with current one
Returns:
true if 'smaller'

Definition at line 860 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::DocEntrySet::GetEntryString().

00861 {
00862    // Patient Name
00863    std::string s1 = GetEntryString(0x0010,0x0010);
00864    std::string s2 = document.GetEntryString(0x0010,0x0010);
00865    if (s1 < s2)
00866    {
00867       return true;
00868    }
00869    else if ( s1 > s2 )
00870    {
00871       return false;
00872    }
00873    else
00874    {
00875       // Patient ID
00876       s1 = GetEntryString(0x0010,0x0020);
00877       s2 = document.GetEntryString(0x0010,0x0020);
00878       if ( s1 < s2 )
00879       {
00880          return true;
00881       }
00882       else if ( s1 > s2 )
00883       {
00884          return false;
00885       }
00886       else
00887       {
00888          // Study Instance UID
00889          s1 = GetEntryString(0x0020,0x000d);
00890          s2 = document.GetEntryString(0x0020,0x000d);
00891          if ( s1 < s2 )
00892          {
00893             return true;
00894          }
00895          else if ( s1 > s2 )
00896          {
00897             return false;
00898          }
00899          else
00900          {
00901             // Serie Instance UID
00902             s1 = GetEntryString(0x0020,0x000e);
00903             s2 = document.GetEntryString(0x0020,0x000e);    
00904             if ( s1 < s2 )
00905             {
00906                return true;
00907             }
00908             else if ( s1 > s2 )
00909             {
00910                return false;
00911             }
00912          }
00913       }
00914    }
00915    return false;
00916 }

void GDCM_NAME_SPACE::DicomDir::ParseDirectory (   ) 
 

fills the whole structure, starting from a root Directory

Definition at line 461 of file gdcmDicomDir.cxx.

References CreateDicomDir(), CreateDicomDirChainedList(), and GDCM_NAME_SPACE::Document::GetFileName().

Referenced by DoTheLoadingJob().

00462 {
00463    CreateDicomDirChainedList( GetFileName() );
00464    CreateDicomDir();
00465 }

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

Canonical Printer.

Parameters:
os ostream we want to print in
indent Indentation string to be prepended during printing

Reimplemented from GDCM_NAME_SPACE::ElementSet.

Definition at line 1220 of file gdcmDicomDir.cxx.

References MetaElems, Patients, GDCM_NAME_SPACE::DicomDirMeta::Print(), GDCM_NAME_SPACE::Base::PrintLevel, and GDCM_NAME_SPACE::Base::SetPrintLevel().

01221 {
01222    if ( MetaElems )
01223    {
01224       MetaElems->SetPrintLevel(PrintLevel);
01225       MetaElems->Print(os);   
01226    }   
01227    for(ListDicomDirPatient::iterator cc  = Patients.begin();
01228                                      cc != Patients.end();
01229                                    ++cc)
01230    {
01231      (*cc)->SetPrintLevel(PrintLevel);
01232      (*cc)->Print(os);
01233    }
01234 }

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

Reads a supposed to be 16 Bits integer (swaps it depending on processor endianness).

Returns:
read value

Definition at line 946 of file gdcmDocument.cxx.

Referenced by GDCM_NAME_SPACE::File::ReadTag().

00948 {
00949    uint16_t g;
00950    Fp->read ((char*)&g, (size_t)2);
00951    if ( Fp->fail() )
00952    {
00953       throw FormatError( "Document::ReadInt16()", " file error." );
00954    }
00955    if ( Fp->eof() )
00956    {
00957       throw FormatError( "Document::ReadInt16()", "EOF." );
00958    }
00959    g = SwapShort(g); 
00960    return g;
00961 }

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

Reads a supposed to be 32 Bits integer (swaps it depending on processor endianness).

Returns:
read value

Definition at line 980 of file gdcmDocument.cxx.

Referenced by GDCM_NAME_SPACE::File::ComputeRLEInfo(), GDCM_NAME_SPACE::Document::FindDocEntryLengthOBOrOW(), and GDCM_NAME_SPACE::File::ReadTagLength().

00982 {
00983    uint32_t g;
00984    Fp->read ((char*)&g, (size_t)4);
00985    if ( Fp->fail() )
00986    {
00987       throw FormatError( "Document::ReadInt32()", " file error." );
00988    }
00989    if ( Fp->eof() )
00990    {
00991       throw FormatError( "Document::ReadInt32()", "EOF." );
00992    }
00993    g = SwapLong(g);
00994    return g;
00995 }

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(), 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().

00046 { RefCount++; }

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

Clear the hash table from given entry AND delete the entry.

Parameters:
entryToRemove Entry to remove AND delete.

Implements GDCM_NAME_SPACE::DocEntrySet.

Definition at line 122 of file gdcmElementSet.cxx.

References GDCM_NAME_SPACE::DocEntry::GetKey(), GDCM_NAME_SPACE::ElementSet::TagHT, and GDCM_NAME_SPACE::RefCounter::Unregister().

Referenced by GDCM_NAME_SPACE::Document::Backtrack(), NewMeta(), GDCM_NAME_SPACE::DocEntryArchive::Push(), and GDCM_NAME_SPACE::DocEntryArchive::Restore().

00123 {
00124    const TagKey &key = entryToRemove->GetKey();
00125    if ( TagHT.count(key) == 1 )
00126    {
00127       TagHT.erase(key);
00128       entryToRemove->Unregister();
00129       return true;
00130    }
00131 
00132    gdcmWarningMacro( "Key not present : " << key);
00133    return false ;
00134 }

void GDCM_NAME_SPACE::DicomDir::SetDirectoryName (  std::string const &  dirName  )  [inline]
 

Sets the root Directory name to parse, recursively.

Definition at line 69 of file gdcmDicomDir.h.

00070         { ParseDir = true; if (Filename != dirName)
00071                                Filename = dirName, IsDocumentModified = true;}

void GDCM_NAME_SPACE::DicomDir::SetElement (  std::string const &  path,
DicomDirType  type,
Document *  header
)  [private]
 

adds to the HTable the Entries (Dicom Elements) corresponding to the given type

Parameters:
path full path file name (only used when type = GDCM_DICOMDIR_IMAGE
type DicomDirObject type to create (GDCM_DICOMDIR_PATIENT, GDCM_DICOMDIR_STUDY, GDCM_DICOMDIR_SERIE ...)
header Header of the current file

Definition at line 995 of file gdcmDicomDir.cxx.

References AddImageToEnd(), AddPatientToEnd(), AddSerieToEnd(), AddStudyToEnd(), GDCM_NAME_SPACE::RefCounter::Delete(), GDCM_DICOMDIR_IMAGE, GDCM_DICOMDIR_META, GDCM_DICOMDIR_PATIENT, GDCM_DICOMDIR_SERIE, GDCM_DICOMDIR_STUDY, GDCM_NAME_SPACE::GDCM_FILESEPARATOR, GDCM_NAME_SPACE::GDCM_UNFOUND, gdcmErrorMacro, gdcmWarningMacro, GDCM_NAME_SPACE::Global::GetDicomDirElements(), GDCM_NAME_SPACE::DicomDirElement::GetDicomDirImageElements(), GDCM_NAME_SPACE::DicomDirElement::GetDicomDirMetaElements(), GDCM_NAME_SPACE::DicomDirElement::GetDicomDirPatientElements(), GDCM_NAME_SPACE::DicomDirElement::GetDicomDirSerieElements(), GDCM_NAME_SPACE::DicomDirElement::GetDicomDirStudyElements(), GDCM_NAME_SPACE::DocEntrySet::GetEntryLength(), GDCM_NAME_SPACE::DocEntrySet::GetEntryString(), GDCM_NAME_SPACE::Document::GetFileName(), GDCM_NAME_SPACE::Util::GetName(), MetaElems, GDCM_NAME_SPACE::DataEntry::New(), GDCM_NAME_SPACE::DicomDirMeta::New(), GDCM_NAME_SPACE::DicomDirPatient::New(), GDCM_NAME_SPACE::DicomDirStudy::New(), GDCM_NAME_SPACE::DicomDirSerie::New(), GDCM_NAME_SPACE::DicomDirImage::New(), and GDCM_NAME_SPACE::DocEntry::SetOffset().

Referenced by SetElements().

00997 {
00998    ListDicomDirElem elemList;
00999    ListDicomDirElem::const_iterator it;
01000    uint16_t tmpGr, tmpEl;
01001    //DictEntry *dictEntry;
01002    DataEntry *entry;
01003    std::string val;
01004    SQItem *si;
01005    switch( type )
01006    {
01007       case GDCM_DICOMDIR_IMAGE:
01008          elemList = Global::GetDicomDirElements()->GetDicomDirImageElements();
01009          si = DicomDirImage::New(true);
01010          if ( !AddImageToEnd(static_cast<DicomDirImage *>(si)) )
01011          {
01012             si->Delete();
01013             gdcmErrorMacro( "Add ImageToEnd failed");
01014          }
01015          break;
01016       case GDCM_DICOMDIR_SERIE:
01017          elemList = Global::GetDicomDirElements()->GetDicomDirSerieElements();
01018          si = DicomDirSerie::New(true);
01019          if ( !AddSerieToEnd(static_cast<DicomDirSerie *>(si)) )
01020          {
01021             si->Delete();
01022             gdcmErrorMacro( "Add SerieToEnd failed");
01023          }
01024          break;
01025       case GDCM_DICOMDIR_STUDY:
01026          elemList = Global::GetDicomDirElements()->GetDicomDirStudyElements();
01027          si = DicomDirStudy::New(true);
01028          if ( !AddStudyToEnd(static_cast<DicomDirStudy *>(si)) )
01029          {
01030             si->Delete();
01031             gdcmErrorMacro( "Add StudyToEnd failed");
01032          }
01033          break;
01034       case GDCM_DICOMDIR_PATIENT:
01035          elemList = Global::GetDicomDirElements()->GetDicomDirPatientElements();
01036          si = DicomDirPatient::New(true);
01037          if ( !AddPatientToEnd(static_cast<DicomDirPatient *>(si)) )
01038          {
01039             si->Delete();
01040             gdcmErrorMacro( "Add PatientToEnd failed");
01041          }
01042          break;
01043       case GDCM_DICOMDIR_META:  // never used ?!? --> Done within DoTheLoadingJob
01044          if ( MetaElems )
01045          {
01046             MetaElems->Delete();
01047             gdcmErrorMacro( "MetaElements already exist, they will be destroyed");
01048          }
01049          elemList = Global::GetDicomDirElements()->GetDicomDirMetaElements();
01050          MetaElems = DicomDirMeta::New(true);
01051          si = MetaElems;
01052          break;
01053       default:
01054          return;
01055    }
01056 
01057    // FIXME : troubles found when it's a SeqEntry
01058 
01059    // removed all the seems-to-be-useless stuff about Referenced Image Sequence
01060    // to avoid further troubles
01061    // imageElem 0008 1140 "" // Referenced Image Sequence
01062    // imageElem fffe e000 "" // 'no length' item : length to be set to 0xffffffff later
01063    // imageElem 0008 1150 "" // Referenced SOP Class UID    : to be set/forged later
01064    // imageElem 0008 1155 "" // Referenced SOP Instance UID : to be set/forged later
01065    // imageElem fffe e00d "" // Item delimitation : length to be set to ZERO later
01066  
01067    std::string referencedVal;
01068    // for all the relevant elements found in their own spot of the DicomDir.dic
01069    for( it = elemList.begin(); it != elemList.end(); ++it)
01070    {
01071       tmpGr     = it->Group;
01072       tmpEl     = it->Elem;
01073        
01074       entry     = DataEntry::New(tmpGr, tmpEl, it->VR); // dicomelements file was modified, to store VR
01075       entry->SetOffset(0); // just to avoid further missprinting
01076 
01077       if ( header )
01078       {
01079          // NULL when we Build Up (ex nihilo) a DICOMDIR
01080          //   or when we add the META elems
01081          val = header->GetEntryString(tmpGr, tmpEl); 
01082       }
01083       else
01084       {
01085          val = GDCM_UNFOUND;
01086       }
01087 
01088       if ( val == GDCM_UNFOUND) 
01089       {
01090          if ( tmpGr == 0x0004 ) // never present in File !     
01091          {
01092             switch (tmpEl)
01093             {
01094             case 0x1130: // File-set ID
01095                // force to the *end* File Name
01096                val = Util::GetName( path );
01097                break;
01098       
01099             case 0x1500: // Only used for image    
01100                if ( header->GetFileName().substr(0, path.length()) != path )
01101                { 
01102                  gdcmWarningMacro( "The base path of file name is incorrect");
01103                  val = header->GetFileName();
01104                }
01105                else
01106                { 
01107                  // avoid the first '/' in File name !
01108                  if ( header->GetFileName().c_str()[path.length()] 
01109                                                       == GDCM_FILESEPARATOR )
01110                     val = &(header->GetFileName().c_str()[path.length()+1]);
01111                  else  
01112                     val = &(header->GetFileName().c_str()[path.length()]);   
01113                }
01114                break;
01115     
01116              case 0x1510:  // Referenced SOP Class UID in File
01117                referencedVal = header->GetEntryString(0x0008, 0x0016);
01118                // FIXME : probabely something to check
01119                val = referencedVal;
01120                break;
01121        
01122              case 0x1511: // Referenced SOP Instance UID in File
01123                referencedVal = header->GetEntryString(0x0008, 0x0018);
01124                // FIXME : probabely something to check
01125                val = referencedVal;
01126                break;
01127     
01128             case 0x1512: // Referenced Transfer Syntax UID in File
01129                referencedVal = header->GetEntryString(0x0002, 0x0010);
01130                // FIXME : probabely something to check
01131                val = referencedVal;
01132                break;
01133     
01134             default :
01135                val = it->Value;   
01136             } 
01137          }
01138          else
01139          {
01140             // If the entry is not found in the Header, don't write its 'value' in the DICOMDIR !
01141             entry->Delete();
01142             continue;
01143           }
01144       }
01145       else
01146       {
01147          if ( header->GetEntryLength(tmpGr,tmpEl) == 0 )
01148          {
01149             val = it->Value;
01150             // Don't polute the DICOMDIR with empty fields
01151             if (val == "")
01152             {
01153                entry->Delete();
01154                continue;
01155             }  
01156          }    
01157       }
01158 
01159 /* FIX later the pb of creating the 'Implementation Version Name'!
01160 
01161       if (val == GDCM_UNFOUND)
01162          val = "";
01163 
01164       if ( tmpGr == 0x0002 && tmpEl == 0x0013)
01165       { 
01166          // 'Implementation Version Name'
01167          std::string val = "GDCM ";
01168          val += Util::GetVersion();
01169       }
01170 */ 
01171 
01172       entry->SetString( val ); // troubles expected when vr=SQ ...
01173 
01174       if ( type == GDCM_DICOMDIR_META ) // fusible : should never print !
01175       {
01176          gdcmDebugMacro("GDCM_DICOMDIR_META ?!? should never print that");
01177       }
01178       
01179       si->AddEntry(entry);
01180       entry->Delete();
01181    }
01182 }

void GDCM_NAME_SPACE::DicomDir::SetElements (  std::string const &  path,
VectDocument const &  list
)  [private]
 

for each Header of the chained list, add/update the Patient/Study/Serie/Image info

Parameters:
path path of the root directory
list chained list of Headers

Definition at line 927 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::ElementSet::ClearEntry(), ClearPatient(), GDCM_DICOMDIR_IMAGE, GDCM_DICOMDIR_PATIENT, GDCM_DICOMDIR_SERIE, GDCM_DICOMDIR_STUDY, and SetElement().

00928 {
00929    ClearEntry();
00930    ClearPatient();
00931 
00932    std::string patPrevName         = "", patPrevID  = "";
00933    std::string studPrevInstanceUID = "", studPrevID = "";
00934    std::string serPrevInstanceUID  = "", serPrevID  = "";
00935 
00936    std::string patCurName,         patCurID;
00937    std::string studCurInstanceUID, studCurID;
00938    std::string serCurInstanceUID,  serCurID;
00939 
00940    bool first = true;
00941    for( VectDocument::const_iterator it = list.begin();
00942                                      it != list.end(); 
00943                                    ++it )
00944    {
00945       // get the current file characteristics
00946       patCurName         = (*it)->GetEntryString(0x0010,0x0010);
00947       patCurID           = (*it)->GetEntryString(0x0010,0x0011);
00948       studCurInstanceUID = (*it)->GetEntryString(0x0020,0x000d);
00949       studCurID          = (*it)->GetEntryString(0x0020,0x0010);
00950       serCurInstanceUID  = (*it)->GetEntryString(0x0020,0x000e);
00951       serCurID           = (*it)->GetEntryString(0x0020,0x0011);
00952 
00953       if ( patCurName != patPrevName || patCurID != patPrevID || first )
00954       {
00955          SetElement(path, GDCM_DICOMDIR_PATIENT, *it);
00956          first = true;
00957       }
00958 
00959       // if new Study, deal with 'STUDY' Elements   
00960       if ( studCurInstanceUID != studPrevInstanceUID || studCurID != studPrevID 
00961          || first )
00962       {
00963          SetElement(path, GDCM_DICOMDIR_STUDY, *it);
00964          first = true;
00965       }
00966 
00967       // if new Serie, deal with 'SERIE' Elements   
00968       if ( serCurInstanceUID != serPrevInstanceUID || serCurID != serPrevID
00969          || first )
00970       {
00971          SetElement(path, GDCM_DICOMDIR_SERIE, *it);
00972       }
00973       
00974       // Always Deal with 'IMAGE' Elements  
00975       SetElement(path, GDCM_DICOMDIR_IMAGE, *it);
00976 
00977       patPrevName         = patCurName;
00978       patPrevID           = patCurID;
00979       studPrevInstanceUID = studCurInstanceUID;
00980       studPrevID          = studCurID;
00981       serPrevInstanceUID  = serCurInstanceUID;
00982       serPrevID           = serCurID;
00983       first = false;
00984    }
00985 }

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().

00196 {
00197    if (entry)
00198    {
00199       entry->SetLength(lgth);
00200       entry->SetBinArea(content);  
00201       return true;
00202    }
00203    return false;
00204 }

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().

00160 {
00161    DataEntry *entry = GetDataEntry(group, elem);
00162    if (!entry )
00163    {
00164       gdcmWarningMacro( "No corresponding DataEntry " << std::hex << group <<
00165                         "," << elem << " element (try promotion first).");
00166       return false;
00167    }
00168 
00169    return SetEntryBinArea(content,lgth,entry);
00170 }

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().

00179 {
00180    if (entry)
00181    {
00182       entry->SetString(content);
00183       return true;
00184    }
00185    return false;
00186 }

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().

00138 {
00139    DataEntry *entry = GetDataEntry(group, elem);
00140    if (!entry )
00141    {
00142       gdcmWarningMacro( "No corresponding DataEntry " << std::hex << group <<
00143                          "," << elem << " element (try promotion first).");
00144       return false;
00145    }
00146    return SetEntryString(content,entry);
00147 }

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

Accessor to Filename.

Reimplemented from GDCM_NAME_SPACE::Document.

Definition at line 73 of file gdcmDicomDir.h.

Referenced by DoTheLoadingJob().

00074                    { ParseDir = false; if (Filename != fileName)
00075                               Filename = fileName, IsDocumentModified = true;}

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

Sets the LoadMode as a boolean string. LD_NOSEQ, LD_NOSHADOW, LD_NOSHADOWSEQ ... (nothing more, right now) WARNING : before using NO_SHADOW, be sure *all* your files contain accurate values in the 0x0000 element (if any) of *each* Shadow Group. The parser will fail if the size is wrong !

Parameters:
mode Load mode to be used

Definition at line 107 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::SerieHelper::AddFileName(), CreateDicomDirChainedList(), vtkGdcmReader::LoadFileInformation(), and GDCM_NAME_SPACE::FileHelper::SetLoadMode().

00107                                { if (LoadMode != mode) 
00108                                      LoadMode=mode, IsDocumentModified = true; }

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

during parsing, Header Elements too long are not loaded in memory

Parameters:
newSize new size

Definition at line 2182 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::Document::MaxSizeLoadEntry.

Referenced by GDCM_NAME_SPACE::Document::Document().

02183 {
02184    if ( newSize < 0 )
02185    {
02186       return;
02187    }
02188    if ((uint32_t)newSize >= (uint32_t)0xffffffff )
02189    {
02190       MaxSizeLoadEntry = 0xffffffff;
02191       return;
02192    }
02193    MaxSizeLoadEntry = newSize;
02194 }

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 Print().

00047 { PrintLevel = level; }

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

Set the shadow dictionary used.

Parameters:
dictName name of the dictionary to use in shadow

Definition at line 341 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::DictSet::GetDict(), GDCM_NAME_SPACE::Global::GetDicts(), and GDCM_NAME_SPACE::Document::RefShaDict.

00342 {
00343    RefShaDict = Global::GetDicts()->GetDict(dictName);
00344    return !RefShaDict;
00345 }

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

Set the shadow dictionary used.

Parameters:
dict dictionary to use in shadow

Definition at line 331 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::Document::RefShaDict.

00332 {
00333    RefShaDict = dict;
00334    return !RefShaDict;
00335 }

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

skips bytes inside the source file

Definition at line 126 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::File::ComputeJPEGFragmentInfo(), GDCM_NAME_SPACE::File::ComputeRLEInfo(), GDCM_NAME_SPACE::Document::FindDocEntryLengthOBOrOW(), and GDCM_NAME_SPACE::Document::SkipDocEntry().

00126 { Fp->seekg((long)nBytes, std::ios::cur);}

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

Unregister the object.

Remarks:
It decrements the reference counting

Definition at line 50 of file gdcmRefCounter.h.

Referenced by GDCM_NAME_SPACE::Document::ReadNextDocEntry(), GDCM_NAME_SPACE::SQItem::RemoveEntry(), GDCM_NAME_SPACE::ElementSet::RemoveEntry(), and GDCM_NAME_SPACE::FileHelper::~FileHelper().

00051    {
00052 //std::cout <<"================Unreg " << typeid(*this).name() << std::endl;
00053       RefCount--;
00054       if(RefCount<=0)
00055         delete this;
00056    }

bool GDCM_NAME_SPACE::DicomDir::Write (  std::string const &  fileName  ) 
 

writes on disc a DICOMDIR \ warning does NOT add the missing elements in the header : it's up to the user doing it !

Parameters:
fileName file to be written to
Returns:
false only when fail to open

Definition at line 475 of file gdcmDicomDir.cxx.

References GDCM_NAME_SPACE::binary_write(), GDCM_NAME_SPACE::ExplicitVR, gdcmWarningMacro, GetMeta(), and GDCM_NAME_SPACE::DicomDirMeta::WriteContent().

00476 {  
00477    int i;
00478    uint16_t sq[6] = { 0x0004, 0x1220, 0x5153, 0x0000, 0xffff, 0xffff };
00479    uint16_t sqt[4]= { 0xfffe, 0xe0dd, 0x0000, 0x0000 };
00480 
00481    std::ofstream *fp = new std::ofstream(fileName.c_str(),  
00482                                          std::ios::out | std::ios::binary);
00483    if ( !fp ) 
00484    {
00485       gdcmWarningMacro("Failed to open(write) File: " << fileName.c_str());
00486       return false;
00487    }
00488 
00489    char filePreamble[128];
00490    memset(filePreamble, 0, 128);
00491    fp->write(filePreamble, 128);
00492    binary_write( *fp, "DICM");
00493  
00494    DicomDirMeta *ptrMeta = GetMeta();
00495    ptrMeta->WriteContent(fp, ExplicitVR, true);
00496    
00497    // force writing 0004|1220 [SQ ], that CANNOT exist within DicomDirMeta
00498    for(i=0;i<6;++i)
00499    {
00500       binary_write(*fp, sq[i]);
00501    }
00502         
00503    for(ListDicomDirPatient::iterator cc  = Patients.begin();
00504                                      cc != Patients.end();
00505                                    ++cc )
00506    {
00507       (*cc)->WriteContent( fp, ExplicitVR, false );
00508    }
00509    
00510    // force writing Sequence Delimitation Item
00511    for(i=0;i<4;++i)
00512    {
00513       binary_write(*fp, sqt[i]);  // fffe e0dd 0000 0000 
00514    }
00515 
00516    fp->close();
00517    delete fp;
00518 
00519    return true;
00520 }

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

Writes the Header Entries (Dicom Elements) from the H Table.

Parameters:
fp ofstream to write to
filetype ExplicitVR/ImplicitVR/ACR/ACR_LIBIDO/JPEG/JPEG2000/...

Implements GDCM_NAME_SPACE::DocEntrySet.

Definition at line 52 of file gdcmElementSet.cxx.

References GDCM_NAME_SPACE::ACR, GDCM_NAME_SPACE::ACR_LIBIDO, GDCM_NAME_SPACE::ElementSet::MayIWrite(), and GDCM_NAME_SPACE::ElementSet::TagHT.

Referenced by GDCM_NAME_SPACE::Document::WriteContent().

00053 {
00054    bool insideMetaElements     = false;
00055    bool yetOutsideMetaElements = false;
00056    
00057    for (TagDocEntryHT::const_iterator i = TagHT.begin(); 
00058                                      i != TagHT.end(); 
00059                                     ++i)
00060    {
00061         int group = (i->second)->GetGroup();
00062        
00063        if (yetOutsideMetaElements==false && group == 0x0002)
00064           insideMetaElements = true;
00065     
00066        if (insideMetaElements == true && group != 0x0002)
00067        {
00068           yetOutsideMetaElements = true;
00069           insideMetaElements     = false;
00070        }
00071    
00072        // depending on the gdcm::Document type 
00073        // (gdcm::File; gdcm::DicomDir, (more to come ?)
00074        // some groups *cannot* be present.
00075        // We hereby protect gdcm for writting stupid things
00076        // if they were found in the original document. 
00077        if ( !MayIWrite( group ) )
00078           continue;
00079   
00080       // Skip 'Group Length' element, since it may be wrong.
00081       //       except for Group 0x0002
00082       // ( keep it as well for Group 0x0008 of ACR Files, 
00083       //  since some ACR readers *need* it )
00084       
00085        if ( (i->second)->GetElement() != 0x0000 
00086            || 
00087             (  (i->second)->GetGroup() == 0x0002 
00088              ||( (filetype == ACR || filetype == ACR_LIBIDO ) && (i->second)->GetGroup() == 0x0008 ) )
00089         )
00090        {
00091              // There are DocEntries, written recursively
00092              i->second->WriteContent(fp, filetype, insideMetaElements );
00093        }             
00094    } 
00095 }

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

Writes in a file all the Entries (Dicom Elements).

Parameters:
fp file pointer on an already open file (actually: Output File Stream)
filetype Type of the File to be written (ACR-NEMA, ExplicitVR, ImplicitVR)

Definition at line 696 of file gdcmDocument.cxx.

References GDCM_NAME_SPACE::ExplicitVR, GDCM_NAME_SPACE::ImplicitVR, GDCM_NAME_SPACE::JPEG, GDCM_NAME_SPACE::JPEG2000, and GDCM_NAME_SPACE::ElementSet::WriteContent().

Referenced by GDCM_NAME_SPACE::File::Write().

00697 {
00698    // Skip if user wants to write an ACR-NEMA file
00699 
00700    if ( filetype == ImplicitVR || filetype == ExplicitVR ||
00701         filetype == JPEG || filetype == JPEG2000 )
00702    {
00703       // writing Dicom File Preamble
00704       char filePreamble[128];
00705       memset(filePreamble, 0, 128);
00706       fp->write(filePreamble, 128);
00707       fp->write("DICM", 4);
00708    }
00709    /*
00710     * \todo rewrite later, if really usefull
00711     *       - 'Group Length' element is optional in DICOM
00712     *       - but un-updated odd groups lengthes can causes pb
00713     *         (xmedcon breaker)
00714     *
00715     * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) )
00716     *    UpdateGroupLength(false,filetype);
00717     * if ( filetype == ACR)
00718     *    UpdateGroupLength(true,ACR);
00719     *
00720     * --> Computing group length for groups with embeded Sequences
00721     * --> was too much tricky / we were [in a hurry / too lazy]
00722     * --> We don't write the element 0x0000 (group length)
00723     */
00724 
00725    ElementSet::WriteContent(fp, filetype, false); // This one is recursive
00726 }

Member Data Documentation

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

Definition at line 235 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::CallStartMethod(), CreateDicomDirChainedList(), DoTheLoadingJob(), and Initialize().

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

to allow any inner method to know current tag Element number

Definition at line 252 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::ReadNextDocEntry().

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

to allow any inner method to know current tag Group number

Definition at line 250 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::FindDocEntryVR(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

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

Refering underlying filename.

Definition at line 131 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::File::AnonymizeNoLoad(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), and GDCM_NAME_SPACE::Document::OpenFile().

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

ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown.

Definition at line 157 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::CheckSwap(), GDCM_NAME_SPACE::Document::Document(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::Document::FindDocEntryVR(), GDCM_NAME_SPACE::Document::GetFileType(), GDCM_NAME_SPACE::Document::HandleOutOfGroup0002(), GDCM_NAME_SPACE::Document::Initialize(), GDCM_NAME_SPACE::Document::IsParsable(), IsReadable(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

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

File Pointer, opened during Document parsing.

Definition at line 154 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::File::ComputeJPEGFragmentInfo(), GDCM_NAME_SPACE::File::ComputeRLEInfo(), GDCM_NAME_SPACE::Document::Document(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::File::DoTheLoadingJob(), DoTheLoadingJob(), GDCM_NAME_SPACE::File::ReadEncapsulatedBasicOffsetTable(), and GDCM_NAME_SPACE::File::ReadTag().

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

whether we already parsed group 0002 (Meta Elements)

Definition at line 148 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::Document(), GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob(), GDCM_NAME_SPACE::Document::HandleOutOfGroup0002(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

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

whether file has a DCM Preamble

Definition at line 151 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::OpenFile(), and GDCM_NAME_SPACE::Document::ReadNextDocEntry().

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

After opening the file, we read HEADER_LENGTH_TO_READ bytes.

Definition at line 160 of file gdcmDocument.h.

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

Whether the gdcm::Document is already parsed/loaded : False from the creation of the gdcm::Document untill gdcm::Document:Load().

Definition at line 180 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::Document(), and GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob().

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

Whether the gdcm::Document was modified since the last Load().

Definition at line 183 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::Document(), and GDCM_NAME_SPACE::Document::DoTheLoadingDocumentJob().

ListDicomDirPatient::iterator GDCM_NAME_SPACE::DicomDir::ItPatient [private]
 

Definition at line 156 of file gdcmDicomDir.h.

Referenced by Copy(), GetFirstPatient(), and GetNextPatient().

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

Bit string integer (each one considered as a boolean) Bit 0 : Skip Sequences, if possible Bit 1 : Skip Shadow Groups if possible Probabely, some more to add.

Definition at line 175 of file gdcmDocument.h.

Referenced by CreateDicomDirChainedList(), and GDCM_NAME_SPACE::Document::Document().

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

Elements whose value is longer than MAX_SIZE_LOAD_ELEMENT_VALUE are NOT loaded.

Definition at line 163 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::Document().

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

Size threshold above which an element value will NOT be loaded in memory (to avoid loading the image/volume itself). By default, this upper bound is fixed to 1024 bytes (which might look reasonable when one considers the definition of the various VR contents).

Definition at line 247 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::LoadDocEntry(), and GDCM_NAME_SPACE::Document::SetMaxSizeLoadEntry().

DicomDirMeta* GDCM_NAME_SPACE::DicomDir::MetaElems [private]
 

Pointer on *the* DicomDirObject 'DicomDirMeta Elements'.

Definition at line 152 of file gdcmDicomDir.h.

Referenced by Copy(), Initialize(), IsReadable(), NewMeta(), Print(), SetElement(), and ~DicomDir().

bool GDCM_NAME_SPACE::DicomDir::ParseDir [private]
 

value of the ??? for any progress bar

Definition at line 159 of file gdcmDicomDir.h.

Referenced by DicomDir(), DoTheLoadingJob(), and Load().

ListDicomDirPatient GDCM_NAME_SPACE::DicomDir::Patients [private]
 

Chained list of DicomDirPatient (to be exploited hierarchicaly).

Definition at line 155 of file gdcmDicomDir.h.

Referenced by AddImageToEnd(), AddPatientToEnd(), AddPrivateToEnd(), AddSerieToEnd(), AddStudyToEnd(), AddVisitToEnd(), Anonymize(), ClearPatient(), Copy(), GetFirstPatient(), GetNextPatient(), IsReadable(), and Print().

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

To be able to backtrack (Private Sequence, Implicit VR related pb).

Definition at line 128 of file gdcmDocEntrySet.h.

Referenced by GDCM_NAME_SPACE::Document::Backtrack(), and GDCM_NAME_SPACE::DocEntrySet::DocEntrySet().

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

Amount of printed details for each Dicom Entries : 0 : stands for the least detail level.

Definition at line 55 of file gdcmBase.h.

Referenced by GDCM_NAME_SPACE::SeqEntry::Print(), GDCM_NAME_SPACE::FileHelper::Print(), GDCM_NAME_SPACE::ElementSet::Print(), GDCM_NAME_SPACE::DocEntry::Print(), GDCM_NAME_SPACE::DictEntry::Print(), GDCM_NAME_SPACE::DicomDirStudy::Print(), GDCM_NAME_SPACE::DicomDirSerie::Print(), GDCM_NAME_SPACE::DicomDirPatient::Print(), GDCM_NAME_SPACE::DicomDirMeta::Print(), Print(), and GDCM_NAME_SPACE::DataEntry::Print().

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

value of the ??? for any progress bar

Definition at line 234 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::CallEndMethod(), GDCM_NAME_SPACE::Document::CallStartMethod(), CreateDicomDirChainedList(), DoTheLoadingJob(), and Initialize().

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

Public dictionary used to parse this header.

Definition at line 238 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::GetPubDict(), and GDCM_NAME_SPACE::Document::Initialize().

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

Optional "shadow dictionary" (private elements) used to parse this header.

Definition at line 241 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::GetShaDict(), GDCM_NAME_SPACE::Document::Initialize(), and GDCM_NAME_SPACE::Document::SetShaDict().

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

Swap code gives an information on the byte order of a supposed to be an int32, as it's read on disc (depending on the image Transfer Syntax *and* on the processor endianess) as opposed as it should in memory to be dealt as an int32. For instance :

  • a 'Little Endian' image, read with a little endian processor will have a SwapCode= 1234 (the order is OK; nothing to do)
  • a 'Little Endian' image, read with a big endian procesor will have a SwapCode= 4321 (the order is wrong; int32 an int16 must be swapped) note : values 2143, 4321, 3412 remain for the ACR-NEMA time, and the well known 'Bad Big Endian' and 'Bad Little Endian' codes.

Definition at line 145 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::CheckSwap(), GDCM_NAME_SPACE::Document::Document(), GDCM_NAME_SPACE::Document::SwapDouble(), GDCM_NAME_SPACE::Document::SwapLong(), GDCM_NAME_SPACE::Document::SwapShort(), and GDCM_NAME_SPACE::Document::SwitchByteSwapCode().

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

User supplied list of elements to Anonymize.

Definition at line 166 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::File::AddAnonymizeElement(), GDCM_NAME_SPACE::File::AnonymizeFile(), and GDCM_NAME_SPACE::File::AnonymizeNoLoad().

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

User supplied list of elements to force Load.

Definition at line 169 of file gdcmDocument.h.

Referenced by GDCM_NAME_SPACE::Document::AddForceLoadElement().

The documentation for this class was generated from the following files:
Generated on Fri Aug 24 13:01:25 2007 for gdcm by  doxygen 1.4.6