+++ /dev/null
-// gdcmParser.cxx
-//-----------------------------------------------------------------------------
-//#define UINT32_MAX (4294967295U)
-
-
-#include "gdcmParser.h"
-#include "gdcmGlobal.h"
-#include "gdcmUtil.h"
-#include "gdcmDebug.h"
-
-#include <errno.h>
-#include <vector>
-
-// For nthos:
-#ifdef _MSC_VER
- #include <winsock.h>
-#else
- #include <netinet/in.h>
-#endif
-
-# include <iomanip>
-
-#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2"
-#define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1"
-#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2"
-#define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99"
-
-typedef struct {
- guint32 totalSQlength;
- guint32 alreadyParsedlength;
-} pileElem;
-
-//-----------------------------------------------------------------------------
-// Refer to gdcmParser::CheckSwap()
-const unsigned int gdcmParser::HEADER_LENGTH_TO_READ = 256;
-
-// Refer to gdcmParser::SetMaxSizeLoadEntry()
-const unsigned int gdcmParser::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
-
-const unsigned int gdcmParser::MAX_SIZE_PRINT_ELEMENT_VALUE = 64;
-
-//-----------------------------------------------------------------------------
-// Constructor / Destructor
-
-/**
- * \brief constructor
- * @param inFilename file to be opened for parsing
- * @param exception_on_error whether we throw an exception or not
- * @param enable_sequences = true to allow the header
- * to be parsed *inside* the SeQuences,
- * when they have an actual length
- * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files
- * @param ignore_shadow to allow skipping the shadow elements,
- * to save memory space.
- * \warning The TRUE value for this param has to be used
- * with a FALSE value for the 'enable_sequence' param.
- * ('public elements' may be embedded in 'shadow Sequences')
- */
-gdcmParser::gdcmParser(const char *inFilename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow) {
- enableSequences=enable_sequences;
- ignoreShadow =ignore_shadow;
-
- SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- filename = inFilename;
- Initialise();
-
- if ( !OpenFile(exception_on_error))
- return;
-
- LoadHeaderEntries();
- CloseFile();
-
- wasUpdated = 0; // will be set to 1 if user adds an entry
- printLevel = 1; // 'Medium' print level by default
-}
-
-/**
- * \brief constructor
- * @param exception_on_error
- */
-gdcmParser::gdcmParser(bool exception_on_error) {
- (void)exception_on_error;
- enableSequences=0;
-
- SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
- Initialise();
-
- wasUpdated = 0; // will be set to 1 if user adds an entry
- printLevel = 1; // 'Medium' print level by default
-}
-
-/**
- * \brief Canonical destructor.
- */
-gdcmParser::~gdcmParser (void) {
- RefPubDict = NULL;
- RefShaDict = NULL;
-}
-
-//-----------------------------------------------------------------------------
-// Print
-/**
- * \brief Prints the Header Entries (Dicom Elements)
- * from the chained list
- * @return
- */
-void gdcmParser::PrintEntry(std::ostream & os) {
-
- for (ListTag::iterator i = listEntries.begin();
- i != listEntries.end();
- ++i)
- {
- (*i)->SetPrintLevel(printLevel);
- (*i)->Print(os);
- }
-}
-
-
-/**
- * \brief Prints The Dict Entries of THE public Dicom Dictionary
- * @return
- */
-void gdcmParser::PrintPubDict(std::ostream & os) {
- RefPubDict->Print(os);
-}
-
-/**
- * \brief Prints The Dict Entries of THE shadow Dicom Dictionary
- * @return
- */
-void gdcmParser::PrintShaDict(std::ostream & os) {
- RefShaDict->Print(os);
-}
-
-//-----------------------------------------------------------------------------
-// Public
-/**
- * \brief Get the public dictionary used
- */
-gdcmDict *gdcmParser::GetPubDict(void) {
- return(RefPubDict);
-}
-
-/**
- * \brief Get the shadow dictionary used
- */
-gdcmDict *gdcmParser::GetShaDict(void) {
- return(RefShaDict);
-}
-
-/**
- * \brief Set the shadow dictionary used
- * \param dict dictionary to use in shadow
- */
-bool gdcmParser::SetShaDict(gdcmDict *dict){
- RefShaDict=dict;
- return(!RefShaDict);
-}
-
-/**
- * \brief Set the shadow dictionary used
- * \param dictName name of the dictionary to use in shadow
- */
-bool gdcmParser::SetShaDict(DictKey dictName){
- RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName);
- return(!RefShaDict);
-}
-
-/**
- * \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current gdcmParser was properly parsed
- * and contains the mandatory information for being considered as
- * a well formed and usable Dicom/Acr File.
- * @return true when gdcmParser is the one of a reasonable Dicom/Acr file,
- * false otherwise.
- */
-bool gdcmParser::IsReadable(void) {
- if(filetype==gdcmUnknown) {
- return(false);
- }
- if(listEntries.size()<=0) {
- return(false);
- }
-
- return(true);
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a ImplicitVRLittleEndian one.
- * @return True when ImplicitVRLittleEndian found. False in all other cases.
- */
-bool gdcmParser::IsImplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry *Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2 )
- return true;
- return false;
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a ExplicitVRLittleEndian one.
- * @return True when ExplicitVRLittleEndian found. False in all other cases.
- */
-bool gdcmParser::IsExplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2_1 )
- return true;
- return false;
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a DeflatedExplicitVRLittleEndian one.
- * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
- */
-bool gdcmParser::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2_1_99 )
- return true;
- return false;
-}
-
-/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a Explicit VR Big Endian one.
- * @return True when big endian found. False in all other cases.
- */
-bool gdcmParser::IsExplicitVRBigEndianTransferSyntax(void) {
- gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadHeaderEntrySafe(Element);
-
- std::string Transfer = Element->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier !
- return true;
- return false;
-}
-
-/**
- * \brief returns the File Type
- * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unfound)
- * @return the FileType code
- */
-FileType gdcmParser::GetFileType(void) {
- return(filetype);
-}
-
-/**
- * \brief opens the file
- * @param exception_on_error
- * @return
- */
-FILE *gdcmParser::OpenFile(bool exception_on_error)
- throw(gdcmFileError)
-{
- fp=fopen(filename.c_str(),"rb");
- if(exception_on_error)
- {
- if(!fp)
- throw gdcmFileError("gdcmParser::gdcmParser(const char *, bool)");
- }
-
- if ( fp )
- {
- guint16 zero;
- fread(&zero, (size_t)2, (size_t)1, fp);
-
- //ACR -- or DICOM with no Preamble --
- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200)
- return(fp);
-
- //DICOM
- fseek(fp, 126L, SEEK_CUR);
- char dicm[4];
- fread(dicm, (size_t)4, (size_t)1, fp);
- if( memcmp(dicm, "DICM", 4) == 0 )
- return(fp);
-
- fclose(fp);
- dbg.Verbose(0, "gdcmParser::OpenFile not DICOM/ACR", filename.c_str());
- }
- else {
- dbg.Verbose(0, "gdcmParser::OpenFile cannot open file", filename.c_str());
- }
- return(NULL);
-}
-
-/**
- * \brief closes the file
- * @return TRUE if the close was successfull
- */
-bool gdcmParser::CloseFile(void) {
- int closed = fclose(fp);
- fp = (FILE *)0;
- if (! closed)
- return false;
- return true;
-}
-
-/**
- * \brief Writes in a file all the Header Entries (Dicom Elements)
- * of the Chained List
- * @param fp file pointer on an already open file
- * @param type Type of the File to be written
- * (ACR-NEMA, ExplicitVR, ImplicitVR)
- * \return Always true.
- */
-bool gdcmParser::Write(FILE *fp, FileType type) {
-/// \todo
-/// ==============
-/// The stuff will have to be rewritten using the SeQuence based
-/// tree-like stucture instead of the chained list .
-/// (so we shall remove the GroupHT from the gdcmParser)
-/// To be checked
-/// =============
-
- /// \todo move the following lines (and a lot of others, to be written)
- /// to a future function CheckAndCorrectHeader
-
- /// \todo
- /// Question :
- /// Comment pourrait-on savoir si le DcmHeader vient d'un fichier
- /// DicomV3 ou non (FileType est un champ de gdcmParser ...)
- /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA
- /// no way
- /// a moins de se livrer a un tres complique ajout des champs manquants.
- /// faire un CheckAndCorrectHeader (?)
-
- if (type == gdcmImplicitVR)
- {
- std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2;
- ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
-
- /// \todo Refer to standards on page 21, chapter 6.2
- /// "Value representation": values with a VR of UI shall be
- /// padded with a single trailing null
- /// Dans le cas suivant on doit pader manuellement avec un 0
-
- SetEntryLengthByNumber(18, 0x0002, 0x0010);
- }
-
- if (type == gdcmExplicitVR)
- {
- std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1;
- ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
-
- /// \todo Refer to standards on page 21, chapter 6.2
- /// "Value representation": values with a VR of UI shall be
- /// padded with a single trailing null
- /// Dans le cas suivant on doit pader manuellement avec un 0
-
- SetEntryLengthByNumber(20, 0x0002, 0x0010);
- }
-
-/**
- * \todo rewrite later, if really usefull
- *
- * --> Warning : un-updated odd groups lengths can causes pb
- * --> (xmedcon breaks)
- * --> to be re- written with future org.
- *
- * if ( (type == ImplicitVR) || (type == ExplicitVR) )
- * UpdateGroupLength(false,type);
- * if ( type == ACR)
- * UpdateGroupLength(true,ACR);
- */
-
- WriteEntries(fp,type);
- return(true);
-}
-
-/**
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * \warning Adds the Header Entry to the HTable, NOT to the chained List
- * @param Value Value to be set
- * @param Group Group of the Entry
- * @param Elem Element of the Entry
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
- */
-gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber(
- std::string Value,
- guint16 Group,
- guint16 Elem ){
- gdcmHeaderEntry* a;
- a = GetHeaderEntryByNumber( Group, Elem);
- if (a == NULL) {
- a =NewHeaderEntryByNumber(Group, Elem);
- if (a == NULL)
- return NULL;
- AddHeaderEntry(a);
- }
- //CLEANME SetEntryByNumber(Value, Group, Elem);
- a->SetValue(Value);
- return(a);
-}
-
-/**
- * \brief Set a new value if the invoked element exists
- * Seems to be useless !!!
- * @param Value new element value
- * @param Group group of the Entry
- * @param Elem element of the Entry
- * \return boolean
- */
-bool gdcmParser::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem )
-{
- std::string v = Value;
- SetEntryByNumber(v, Group, Elem);
- return true;
-}
-
-//-----------------------------------------------------------------------------
-// Protected
-
-/**
- * \brief Checks if a given Dicom Element exists
- * within the H table
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return number of occurences
- */
-int gdcmParser::CheckIfEntryExistByNumber(guint16 group, guint16 element ) {
- std::string key = gdcmDictEntry::TranslateToKey(group, element );
- return (tagHT.count(key));
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value of a given tag.
- * \warning Don't use any longer : use GetPubEntryByName
- * @param tagName name of the searched element.
- * @return Corresponding element value when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmParser::GetEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return GDCM_UNFOUND;
-
- return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param tagName name of the searched element.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmParser::GetEntryVRByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return GDCM_UNFOUND;
-
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
- return elem->GetVR();
-}
-
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag.
- * @param group Group of the searched tag.
- * @param element Element of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmParser::GetEntryByNumber(guint16 group, guint16 element){
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return GDCM_UNFOUND;
- return tagHT.find(key)->second->GetValue();
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the element value representation of a given tag..
- *
- * Obtaining the VR (Value Representation) might be needed by caller
- * to convert the string typed content to caller's native type
- * (think of C++ vs Python). The VR is actually of a higher level
- * of semantics than just the native C++ type.
- * @param group Group of the searched tag.
- * @param element Element of the searched tag.
- * @return Corresponding element value representation when it exists,
- * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
- */
-std::string gdcmParser::GetEntryVRByNumber(guint16 group, guint16 element) {
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
- if ( !elem )
- return GDCM_UNFOUND;
- return elem->GetVR();
-}
-
-/**
- * \brief Searches within Header Entries (Dicom Elements) parsed with
- * the public and private dictionaries
- * for the value length of a given tag..
- * @param group Group of the searched tag.
- * @param element Element of the searched tag.
- * @return Corresponding element length; -2 if not found
- */
-int gdcmParser::GetEntryLengthByNumber(guint16 group, guint16 element) {
- gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
- if ( !elem )
- return -2;
- return elem->GetLength();
-}
-/**
- * \brief Sets the value (string) of the Header Entry (Dicom Element)
- * @param content string value of the Dicom Element
- * @param tagName name of the searched Dicom Element.
- * @return true when found
- */
-bool gdcmParser::SetEntryByName(std::string content,std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return false;
-
- return(SetEntryByNumber(content,dictEntry->GetGroup(),
- dictEntry->GetElement()));
-}
-
-/**
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
- * \warning Don't use any longer : use SetPubEntryByNumber
- * @param content new value to substitute with
- * @param group group of the Dicom Element to modify
- * @param element element of the Dicom Element to modify
- */
-bool gdcmParser::SetEntryByNumber(std::string content,
- guint16 group,
- guint16 element)
-{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return false;
- int l = content.length();
- if(l%2) // Non even length are padded with a space (020H).
- {
- l++;
- content = content + '\0';
- }
-
- gdcmHeaderEntry * a;
- IterHT p;
- TagHeaderEntryHT::iterator p2;
- // DO NOT remove the following lines : they explain the stuff
- //p= tagHT.equal_range(key); // get a pair of iterators first-last synonym
- //p2=p.first; // iterator on the first synonym
- //a=p2->second; // H Table target column (2-nd col)
-
- // or, easier :
- a = ((tagHT.equal_range(key)).first)->second;
-
- a-> SetValue(content);
-
- std::string vr = a->GetVR();
-
- guint32 lgr;
- if( (vr == "US") || (vr == "SS") )
- lgr = 2;
- else if( (vr == "UL") || (vr == "SL") )
- lgr = 4;
- else
- lgr = l;
-
- a->SetLength(lgr);
- return true;
-}
-
-/**
- * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element)
- * in the PubHeaderEntrySet of this instance
- * through it's (group, element) and modifies it's length with
- * the given value.
- * \warning Use with extreme caution.
- * @param l new length to substitute with
- * @param group group of the Entry to modify
- * @param element element of the Entry to modify
- * @return true on success, false otherwise.
- */
-bool gdcmParser::SetEntryLengthByNumber(guint32 l,
- guint16 group,
- guint16 element)
-{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return false;
- if (l%2) l++; // length must be even
- ( ((tagHT.equal_range(key)).first)->second )->SetLength(l);
-
- return true ;
-}
-
-/**
- * \brief Gets (from Header) the offset of a 'non string' element value
- * (LoadElementValues has already be executed)
- * @param Group group of the Entry
- * @param Elem element of the Entry
- * @return File Offset of the Element Value
- */
-size_t gdcmParser::GetEntryOffsetByNumber(guint16 Group, guint16 Elem)
-{
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
- if (!Entry)
- {
- dbg.Verbose(1, "gdcmParser::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
- return (size_t)0;
- }
- return Entry->GetOffset();
-}
-
-/**
- * \brief Gets (from Header) a 'non string' element value
- * (LoadElementValues has already be executed)
- * @param Group group of the Entry
- * @param Elem element of the Entry
- * @return Pointer to the 'non string' area
- */
-void * gdcmParser::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem)
-{
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
- if (!Entry)
- {
- dbg.Verbose(1, "gdcmParser::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
- return (NULL);
- }
- return Entry->GetVoidArea();
-}
-
-/**
- * \brief Loads (from disk) the element content
- * when a string is not suitable
- * @param Group group of the Entry
- * @param Elem element of the Entry
- */
-void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem)
-{
- gdcmHeaderEntry * Element= GetHeaderEntryByNumber(Group, Elem);
- if ( !Element )
- return NULL;
- size_t o =(size_t)Element->GetOffset();
- fseek(fp, o, SEEK_SET);
- size_t l=Element->GetLength();
- char* a = new char[l];
- if(!a)
- return NULL;
-
- SetEntryVoidAreaByNumber(a, Group, Elem);
- /// \todo check the result
- size_t l2 = fread(a, 1, l ,fp);
- if(l != l2)
- {
- delete[] a;
- return NULL;
- }
-
- return a;
-}
-
-/**
- * \brief Sets a 'non string' value to a given Dicom Element
- * @param area
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return
- */
-bool gdcmParser::SetEntryVoidAreaByNumber(void * area,
- guint16 group,
- guint16 element)
-{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return false;
- ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area);
- return true;
-}
-
-/**
- * \brief Update the entries with the shadow dictionary.
- * Only non even entries are analyzed
- */
-void gdcmParser::UpdateShaEntries(void) {
- gdcmDictEntry *entry;
- std::string vr;
-
- for(ListTag::iterator it=listEntries.begin();
- it!=listEntries.end();
- ++it)
- {
- // Odd group => from public dictionary
- if((*it)->GetGroup()%2==0)
- continue;
-
- // Peer group => search the corresponding dict entry
- if(RefShaDict)
- entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement());
- else
- entry=NULL;
-
- if((*it)->IsImplicitVR())
- vr="Implicit";
- else
- vr=(*it)->GetVR();
-
- (*it)->SetValue(GetHeaderEntryUnvalue(*it));
- if(entry){
- // Set the new entry and the new value
- (*it)->SetDictEntry(entry);
- CheckHeaderEntryVR(*it,vr);
-
- (*it)->SetValue(GetHeaderEntryValue(*it));
- }
- else
- {
- // Remove precedent value transformation
- (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr));
- }
- }
-}
-
-/**
- * \brief Searches within the Header Entries for a Dicom Element of
- * a given tag.
- * @param tagName name of the searched Dicom Element.
- * @return Corresponding Dicom Element when it exists, and NULL
- * otherwise.
- */
- gdcmHeaderEntry *gdcmParser::GetHeaderEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
- if( dictEntry == NULL)
- return NULL;
-
- return(GetHeaderEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
-}
-
-/**
- * \brief retrieves a Dicom Element (the first one) using (group, element)
- * \warning (group, element) IS NOT an identifier inside the Dicom Header
- * if you think it's NOT UNIQUE, check the count number
- * and use iterators to retrieve ALL the Dicoms Elements within
- * a given couple (group, element)
- * @param group Group number of the searched Dicom Element
- * @param element Element number of the searched Dicom Element
- * @return
- */
-gdcmHeaderEntry* gdcmParser::GetHeaderEntryByNumber(guint16 group, guint16 element)
-{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
- return NULL;
- return tagHT.find(key)->second;
-}
-
-/**
- * \brief retrieves the Dicom Elements (all of them) using (group, element)
- * @param group Group number of the searched Dicom Element.
- * @param element Element number of the searched Dicom Element.
- * @return a range (i.e.pair<,>) containing all elements whose key is group|element)
- */
-
-IterHT gdcmParser::GetHeaderEntrySameNumber(guint16 group, guint16 element){
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- return (tagHT.equal_range(key));
-}
-
-/**
- * \brief Loads the element while preserving the current
- * underlying file position indicator as opposed to
- * to LoadHeaderEntry that modifies it.
- * @param entry Header Entry whose value shall be loaded.
- * @return
- */
-void gdcmParser::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) {
- long PositionOnEntry = ftell(fp);
- LoadHeaderEntry(entry);
- fseek(fp, PositionOnEntry, SEEK_SET);
-}
-
-/**
- * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
- * \warning : to be re-written using the chained list instead of the H table.
- * \warning : DO NOT use (doesn't work any longer because of the multimap)
- * \todo : to be re-written using the chained list instead of the H table
- * @param SkipSequence TRUE if we don't want to write Sequences (ACR-NEMA Files)
- * @param type Type of the File (ExplicitVR,ImplicitVR, ACR, ...)
- */
-void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) {
- guint16 gr, el;
- std::string vr;
-
- gdcmHeaderEntry *elem;
- char trash[10];
- std::string str_trash;
-
- GroupKey key;
- GroupHT groupHt; // to hold the length of each group
- TagKey tk;
- // remember :
- // typedef std::map<GroupKey, int> GroupHT;
-
- gdcmHeaderEntry *elemZ;
-
- // for each Tag in the DCM Header
-
- for (TagHeaderEntryHT::iterator tag2 = tagHT.begin();
- tag2 != tagHT.end();
- ++tag2)
- {
- elem = tag2->second;
- gr = elem->GetGroup();
- el = elem->GetElement();
- vr = elem->GetVR();
-
- sprintf(trash, "%04x", gr);
- key = trash; // generate 'group tag'
-
- // if the caller decided not to take SEQUENCEs into account
- // e.g : he wants to write an ACR-NEMA File
-
- if (SkipSequence && vr == "SQ")
- continue;
-
- // Still unsolved problem :
- // we cannot find the 'Sequence Delimitation Item'
- // since it's at the end of the Hash Table
- // (fffe,e0dd)
-
- // there is SEQUENCE in ACR-NEMA
- // WARNING :
- // --> la descente a l'interieur' des SQ
- // devrait etre faite avec une liste chainee, pas avec une HTable...
-
- if ( groupHt.count(key) == 0) // we just read the first elem of a given group
- {
- if (el == 0x0000) // the first elem is 0x0000
- {
- groupHt[key] = 0; // initialize group length
- }
- else
- {
- groupHt[key] = 2 + 2 + 4 + elem->GetLength(); // non 0x0000 first group elem
- }
- }
- else // any elem but the first
- {
- if (type == gdcmExplicitVR)
- {
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
- {
- groupHt[key] += 4; // explicit VR AND OB, OW, SQ : 4 more bytes
- }
- }
- groupHt[key] += 2 + 2 + 4 + elem->GetLength();
- }
- }
-
- unsigned short int gr_bid;
-
- for (GroupHT::iterator g = groupHt.begin(); // for each group we found
- g != groupHt.end();
- ++g)
- {
- // FIXME: g++ -Wall -Wstrict-prototypes reports on following line:
- // warning: unsigned int format, different type arg
- sscanf(g->first.c_str(),"%x",&gr_bid); //FIXME
- tk = g->first + "|0000"; // generate the element full tag
-
- if ( tagHT.count(tk) == 0) // if element 0x0000 not found
- {
- gdcmDictEntry * tagZ = new gdcmDictEntry(gr_bid, 0x0000, "UL");
- elemZ = new gdcmHeaderEntry(tagZ);
- elemZ->SetLength(4);
- AddHeaderEntry(elemZ); // create it
- }
- else
- {
- elemZ=GetHeaderEntryByNumber(gr_bid, 0x0000);
- }
- sprintf(trash ,"%d",g->second);
- str_trash=trash;
- elemZ->SetValue(str_trash);
- }
-}
-
-/**
- * \brief Writes in a file (according to the requested format)
- * the group, the element, the value representation and the length
- * of a single gdcmHeaderEntry passed as argument.
- * @param tag pointer on the gdcmHeaderEntry to be written
- * @param _fp already open file pointer
- * @param type type of the File to be written
- */
-void gdcmParser::WriteEntryTagVRLength(gdcmHeaderEntry *tag,
- FILE *_fp,
- FileType type)
-{
- guint16 group = tag->GetGroup();
- std::string vr = tag->GetVR();
- guint16 el = tag->GetElement();
- guint32 lgr = tag->GetReadLength();
-
- if ( (group == 0xfffe) && (el == 0x0000) )
- // Fix in order to make some MR PHILIPS images e-film readable
- // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm:
- // we just *always* ignore spurious fffe|0000 tag !
- return;
-
- fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group
- fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
-
- if ( type == gdcmExplicitVR ) {
-
- // Special case of delimiters:
- if (group == 0xfffe) {
- // Delimiters have NO Value Representation and have NO length.
- // Hence we skip writing the VR and length and we pad by writing
- // 0xffffffff
-
- int ff=0xffffffff;
- fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp);
- return;
- }
-
- guint16 z=0;
- guint16 shortLgr = lgr;
- if (vr == "unkn") { // Unfound was 'written'
- // deal with Little Endian
- fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
- fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
- } else {
- fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp);
- if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") )
- {
- fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp);
- fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
- } else {
- fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
- }
- }
- }
- else // IMPLICIT VR
- {
- fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
- }
-}
-
-/**
- * \brief Writes in a file (according to the requested format)
- * the value of a single gdcmHeaderEntry passed as argument.
- * @param tag Pointer on the gdcmHeaderEntry to be written
- * @param _fp Already open file pointer
- * @param type type of the File to be written
- */
-void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
-{
- (void)type;
- guint16 group = tag->GetGroup();
- std::string vr = tag->GetVR();
- guint32 lgr = tag->GetReadLength();
-
- if (vr == "SQ")
- // SeQuences have no value:
- return;
- if (group == 0xfffe)
- // Delimiters have no associated value:
- return;
-
- void *voidArea;
- voidArea = tag->GetVoidArea();
- if (voidArea != NULL)
- { // there is a 'non string' LUT, overlay, etc
- fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
- return;
- }
-
- if (vr == "US" || vr == "SS")
- {
- // some 'Short integer' fields may be mulivaluated
- // each single value is separated from the next one by '\'
- // we split the string and write each value as a short int
- std::vector<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (tag->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- guint16 val_uint16 = atoi(tokens[i].c_str());
- void *ptr = &val_uint16;
- fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- return;
- }
- // some 'Integer' fields may be mulivaluated
- // each single value is separated from the next one by '\'
- // we split the string and write each value as an int
- if (vr == "UL" || vr == "SL")
- {
- std::vector<std::string> tokens;
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (tag->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- guint32 val_uint32 = atoi(tokens[i].c_str());
- void *ptr = &val_uint32;
- fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- return;
- }
- fwrite (tag->GetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value
-}
-
-/**
- * \brief Writes in a file (according to the requested format)
- * a single gdcmHeaderEntry passed as argument.
- * \sa WriteEntryValue, WriteEntryTagVRLength.
- * @param tag Pointer on the gdcmHeaderEntry to be written
- * @param _fp Already open file pointer
- * @param type type of the File to be written
- */
-
-bool gdcmParser::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type)
-{
- guint32 length = tag->GetLength();
-
- // The value of a tag MUST (see the DICOM norm) be an odd number of
- // bytes. When this is not the case, pad with an additional byte:
- if(length%2==1)
- {
- tag->SetValue(tag->GetValue()+"\0");
- tag->SetLength(tag->GetReadLength()+1);
- }
-
- WriteEntryTagVRLength(tag, _fp, type);
- WriteEntryValue(tag, _fp, type);
- return true;
-}
-
-/**
- * \brief writes on disc according to the requested format
- * (ACR-NEMA, ExplicitVR, ImplicitVR) the image
- * using the Chained List
- * \warning does NOT add the missing elements in the header :
- * it's up to the user doing it !
- * (function CheckHeaderCoherence to be written)
- * \warning DON'T try, right now, to write a DICOM image
- * from an ACR Header (meta elements will be missing!)
- * \sa WriteEntriesDeprecated (Special temporary method for Theralys)
- * @param type type of the File to be written
- * (ACR-NEMA, ExplicitVR, ImplicitVR)
- * @param _fp already open file pointer
- */
-
-bool gdcmParser::WriteEntries(FILE *_fp,FileType type)
-{
- /// \todo (?) check write failures (after *each* fwrite)
-
- for (ListTag::iterator tag2=listEntries.begin();
- tag2 != listEntries.end();
- ++tag2)
- {
- if ( type == gdcmACR ){
- if ((*tag2)->GetGroup() < 0x0008)
- // Ignore pure DICOM V3 groups
- continue;
- if ((*tag2)->GetElement() %2)
- // Ignore the "shadow" groups
- continue;
- if ((*tag2)->GetVR() == "SQ" ) // ignore Sequences
- continue;
- if ((*tag2)->GetSQDepthLevel() != 0) // Not only ignore the SQ element
- continue;
- }
- if (! WriteEntry(*tag2,_fp,type) )
- return false;
- }
- return true;
-}
-
-/**
- * \brief writes on disc according to the requested format
- * (ACR-NEMA, ExplicitVR, ImplicitVR) the image,
- * using only the last synonym of each mutimap H Table post.
- * \warning Uses the H Table, instead of the Chained List
- * in order to be compliant with the old way to proceed
- * (added elements taken in to account)
- * Only THERALYS, during a transitory phase is supposed
- * to use this method !!!
- * \warning DON'T try, right now, to write a DICOM image
- * from an ACR Header (meta elements will be missing!)
- * \sa WriteEntries
- * @param _fp already open file pointer
- * @param type type of the File to be written
- * (ACR-NEMA, ExplicitVR, ImplicitVR)
- */
-void gdcmParser::WriteEntriesDeprecated(FILE *_fp,FileType type) {
-
- // restent a tester les echecs en ecriture (apres chaque fwrite)
-
- for (TagHeaderEntryHT::iterator tag2=tagHT.begin();
- tag2 != tagHT.end();
- ++tag2){
- if ( type == gdcmACR ){
- if ((*tag2->second).GetGroup() < 0x0008) continue; // ignore pure DICOM V3 groups
- if ((*tag2->second).GetElement() %2) continue; // ignore shadow groups
- if ((*tag2->second).GetVR() == "SQ" ) continue; // ignore Sequences
- if ((*tag2->second).GetSQDepthLevel() != 0) continue; // Not only ignore the SQ element
- }
- if ( ! WriteEntry(tag2->second,_fp,type))
- break;
- }
-}
-
-/**
- * \brief Swaps back the bytes of 4-byte long integer accordingly to
- * processor order.
- * @return The properly swaped 32 bits integer.
- */
-guint32 gdcmParser::SwapLong(guint32 a) {
- switch (sw) {
- case 0 :
- break;
- case 4321 :
- a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
- ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
- break;
-
- case 3412 :
- a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
- break;
-
- case 2143 :
- a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
- break;
- default :
- dbg.Error(" gdcmParser::SwapLong : unset swap code");
- a=0;
- }
- return(a);
-}
-
-/**
- * \brief Unswaps back the bytes of 4-byte long integer accordingly to
- * processor order.
- * @return The properly unswaped 32 bits integer.
- */
-guint32 gdcmParser::UnswapLong(guint32 a) {
- return (SwapLong(a));
-}
-
-/**
- * \brief Swaps the bytes so they agree with the processor order
- * @return The properly swaped 16 bits integer.
- */
-guint16 gdcmParser::SwapShort(guint16 a) {
- if ( (sw==4321) || (sw==2143) )
- a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
- return (a);
-}
-
-/**
- * \brief Unswaps the bytes so they agree with the processor order
- * @return The properly unswaped 16 bits integer.
- */
-guint16 gdcmParser::UnswapShort(guint16 a) {
- return (SwapShort(a));
-}
-
-//-----------------------------------------------------------------------------
-// Private
-/**
- * \brief Parses the header of the file and load element values.
- * @return false if file is not ACR-NEMA / PAPYRUS / DICOM
- */
-bool gdcmParser::LoadHeaderEntries(bool exception_on_error) throw(gdcmFormatError) {
- (void)exception_on_error;
- rewind(fp);
- if (!CheckSwap())
- return false;
-
- gdcmHeaderEntry *newHeaderEntry = (gdcmHeaderEntry *)0;
- while ( (newHeaderEntry = ReadNextHeaderEntry()) ) {
- SkipHeaderEntry(newHeaderEntry);
- if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) {
- AddHeaderEntry(newHeaderEntry);
- }
- }
- rewind(fp);
- // Be carefull : merging this two loops may cause troubles ...
- for (ListTag::iterator i = GetListEntry().begin();
- i != GetListEntry().end();
- ++i)
- {
- LoadHeaderEntry(*i);
- }
- rewind(fp);
-
- // Load 'non string' values
-
- std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
- if( PhotometricInterpretation == "PALETTE COLOR " ) {
- LoadEntryVoidArea(0x0028,0x1200); // gray LUT
- LoadEntryVoidArea(0x0028,0x1201); // R LUT
- LoadEntryVoidArea(0x0028,0x1202); // G LUT
- LoadEntryVoidArea(0x0028,0x1203); // B LUT
-
- LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data
- }
- //FIXME later : how to use it?
- LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent)
-
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to read ACR-LibIDO formated images
- //
- // if recognition code tells us we deal with a LibIDO image
- // we switch lineNumber and columnNumber
- //
- std::string RecCode;
- RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code
- if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
- RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
- // with "little-endian strings"
- {
- filetype = gdcmACR_LIBIDO;
- std::string rows = GetEntryByNumber(0x0028, 0x0010);
- std::string columns = GetEntryByNumber(0x0028, 0x0011);
- SetEntryByNumber(columns, 0x0028, 0x0010);
- SetEntryByNumber(rows , 0x0028, 0x0011);
- }
- // ----------------- End of Special Patch ----------------
- return true;
-}
-
-/**
- * \brief Loads the element content if its length doesn't exceed
- * the value specified with gdcmParser::SetMaxSizeLoadEntry()
- * @param Entry Header Entry (Dicom Element) to be dealt with
- */
-void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) {
- size_t item_read;
- guint16 group = Entry->GetGroup();
- std::string vr= Entry->GetVR();
- guint32 length = Entry->GetLength();
-
- fseek(fp, (long)Entry->GetOffset(), SEEK_SET);
-
- // A SeQuence "contains" a set of Elements.
- // (fffe e000) tells us an Element is beginning
- // (fffe e00d) tells us an Element just ended
- // (fffe e0dd) tells us the current SeQuence just ended
- if( group == 0xfffe ) {
- Entry->SetValue("gdcm::Skipped");
- return;
- }
-
- // When the length is zero things are easy:
- if ( length == 0 ) {
- Entry->SetValue("");
- return;
- }
-
- // The elements whose length is bigger than the specified upper bound
- // are not loaded. Instead we leave a short notice of the offset of
- // the element content and it's length.
- if (length > MaxSizeLoadEntry) {
- std::ostringstream s;
- s << "gdcm::NotLoaded.";
- s << " Address:" << (long)Entry->GetOffset();
- s << " Length:" << Entry->GetLength();
- s << " x(" << std::hex << Entry->GetLength() << ")";
- Entry->SetValue(s.str());
- return;
- }
-
- // Any compacter code suggested (?)
- if ( IsHeaderEntryAnInteger(Entry) ) {
- guint32 NewInt;
- std::ostringstream s;
- int nbInt;
- // When short integer(s) are expected, read and convert the following
- // n *two characters properly i.e. as short integers as opposed to strings.
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- if (vr == "US" || vr == "SS") {
- nbInt = length / 2;
- NewInt = ReadInt16();
- s << NewInt;
- if (nbInt > 1){
- for (int i=1; i < nbInt; i++) {
- s << '\\';
- NewInt = ReadInt16();
- s << NewInt;
- }
- }
- }
- // When integer(s) are expected, read and convert the following
- // n * four characters properly i.e. as integers as opposed to strings.
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- else if (vr == "UL" || vr == "SL") {
- nbInt = length / 4;
- NewInt = ReadInt32();
- s << NewInt;
- if (nbInt > 1) {
- for (int i=1; i < nbInt; i++) {
- s << '\\';
- NewInt = ReadInt32();
- s << NewInt;
- }
- }
- }
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
-
- Entry->SetValue(s.str());
- return;
- }
-
- // We need an additional byte for storing \0 that is not on disk
- std::string NewValue(length,0);
- item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp);
- if ( item_read != 1 ) {
- dbg.Verbose(1, "gdcmParser::LoadElementValue","unread element value");
- Entry->SetValue("gdcm::UnRead");
- return;
- }
-
- if( (vr == "UI") ) // Because of correspondance with the VR dic
- Entry->SetValue(NewValue.c_str());
- else
- Entry->SetValue(NewValue);
-}
-
-/**
- * \brief add a new Dicom Element pointer to
- * the H Table and at the end of the chained List
- * \warning push_bash in listEntries ONLY during ParseHeader
- * \todo something to allow further Elements addition,
- * (at their right place in the chained list)
- * when position to be taken care of
- * @param newHeaderEntry
- */
-void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) {
- tagHT.insert( PairHT( newHeaderEntry->GetKey(),newHeaderEntry) );
- listEntries.push_back(newHeaderEntry);
- wasUpdated = 1;
-}
-
-/**
- * \brief Find the value Length of the passed Header Entry
- * @param Entry Header Entry whose length of the value shall be loaded.
- */
- void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry *Entry) {
- guint16 element = Entry->GetElement();
- //guint16 group = Entry->GetGroup(); //FIXME
- std::string vr = Entry->GetVR();
- guint16 length16;
-
-
- if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) )
- {
- if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") )
- {
- // The following reserved two bytes (see PS 3.5-2001, section
- // 7.1.2 Data element structure with explicit vr p27) must be
- // skipped before proceeding on reading the length on 4 bytes.
- fseek(fp, 2L, SEEK_CUR);
- guint32 length32 = ReadInt32();
-
- if ( (vr == "OB") && (length32 == 0xffffffff) )
- {
- Entry->SetLength(FindHeaderEntryLengthOB());
- return;
- }
- FixHeaderEntryFoundLength(Entry, length32);
- return;
- }
-
- // Length is encoded on 2 bytes.
- length16 = ReadInt16();
-
- // We can tell the current file is encoded in big endian (like
- // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag
- // and it's value is the one of the encoding of a big endian file.
- // In order to deal with such big endian encoded files, we have
- // (at least) two strategies:
- // * when we load the "Transfer Syntax" tag with value of big endian
- // encoding, we raise the proper flags. Then we wait for the end
- // of the META group (0x0002) among which is "Transfer Syntax",
- // before switching the swap code to big endian. We have to postpone
- // the switching of the swap code since the META group is fully encoded
- // in little endian, and big endian coding only starts at the next
- // group. The corresponding code can be hard to analyse and adds
- // many additional unnecessary tests for regular tags.
- // * the second strategy consists in waiting for trouble, that shall
- // appear when we find the first group with big endian encoding. This
- // is easy to detect since the length of a "Group Length" tag (the
- // ones with zero as element number) has to be of 4 (0x0004). When we
- // encounter 1024 (0x0400) chances are the encoding changed and we
- // found a group with big endian encoding.
- // We shall use this second strategy. In order to make sure that we
- // can interpret the presence of an apparently big endian encoded
- // length of a "Group Length" without committing a big mistake, we
- // add an additional check: we look in the already parsed elements
- // for the presence of a "Transfer Syntax" whose value has to be "big
- // endian encoding". When this is the case, chances are we have got our
- // hands on a big endian encoded file: we switch the swap code to
- // big endian and proceed...
- if ( (element == 0x0000) && (length16 == 0x0400) )
- {
- if ( ! IsExplicitVRBigEndianTransferSyntax() )
- {
- dbg.Verbose(0, "gdcmParser::FindLength", "not explicit VR");
- errno = 1;
- return;
- }
- length16 = 4;
- SwitchSwapToBigEndian();
- // Restore the unproperly loaded values i.e. the group, the element
- // and the dictionary entry depending on them.
- guint16 CorrectGroup = SwapShort(Entry->GetGroup());
- guint16 CorrectElem = SwapShort(Entry->GetElement());
- gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup,
- CorrectElem);
- if (!NewTag)
- {
- // This correct tag is not in the dictionary. Create a new one.
- NewTag = NewVirtualDictEntry(CorrectGroup, CorrectElem);
- }
- // FIXME this can create a memory leaks on the old entry that be
- // left unreferenced.
- Entry->SetDictEntry(NewTag);
- }
-
- // Heuristic: well some files are really ill-formed.
- if ( length16 == 0xffff)
- {
- length16 = 0;
- //dbg.Verbose(0, "gdcmParser::FindLength",
- // "Erroneous element length fixed.");
- // Actually, length= 0xffff means that we deal with
- // Unfound Sequence Length
- }
- FixHeaderEntryFoundLength(Entry, (guint32)length16);
- return;
- }
- else
- {
- // Either implicit VR or a non DICOM conformal (see note below) explicit
- // VR that ommited the VR of (at least) this element. Farts happen.
- // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25
- // on Data elements "Implicit and Explicit VR Data Elements shall
- // not coexist in a Data Set and Data Sets nested within it".]
- // Length is on 4 bytes.
-
- FixHeaderEntryFoundLength(Entry, ReadInt32());
- return;
- }
-}
-
-/**
- * \brief Find the Value Representation of the current Dicom Element.
- * @param Entry
- */
-void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry)
-{
- if (filetype != gdcmExplicitVR)
- return;
-
- char VR[3];
-
- long PositionOnEntry = ftell(fp);
- // Warning: we believe this is explicit VR (Value Representation) because
- // we used a heuristic that found "UL" in the first tag. Alas this
- // doesn't guarantee that all the tags will be in explicit VR. In some
- // cases (see e-film filtered files) one finds implicit VR tags mixed
- // within an explicit VR file. Hence we make sure the present tag
- // is in explicit VR and try to fix things if it happens not to be
- // the case.
-
- (void)fread (&VR, (size_t)2,(size_t)1, fp);
- VR[2]=0;
- if(!CheckHeaderEntryVR(Entry,VR))
- {
- fseek(fp, PositionOnEntry, SEEK_SET);
- // When this element is known in the dictionary we shall use, e.g. for
- // the semantics (see the usage of IsAnInteger), the VR proposed by the
- // dictionary entry. Still we have to flag the element as implicit since
- // we know now our assumption on expliciteness is not furfilled.
- // avoid .
- if ( Entry->IsVRUnknown() )
- Entry->SetVR("Implicit");
- Entry->SetImplicitVR();
- }
-}
-
-/**
- * \brief Check the correspondance between the VR of the header entry
- * and the taken VR. If they are different, the header entry is
- * updated with the new VR.
- * @param Entry Header Entry to check
- * @param vr Dicom Value Representation
- * @return false if the VR is incorrect of if the VR isn't referenced
- * otherwise, it returns true
-*/
-bool gdcmParser::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr)
-{
- char msg[100]; // for sprintf
- bool RealExplicit = true;
-
- // Assume we are reading a falsely explicit VR file i.e. we reached
- // a tag where we expect reading a VR but are in fact we read the
- // first to bytes of the length. Then we will interogate (through find)
- // the dicom_vr dictionary with oddities like "\004\0" which crashes
- // both GCC and VC++ implementations of the STL map. Hence when the
- // expected VR read happens to be non-ascii characters we consider
- // we hit falsely explicit VR tag.
-
- if ( (!isalpha(vr[0])) && (!isalpha(vr[1])) )
- RealExplicit = false;
-
- // CLEANME searching the dicom_vr at each occurence is expensive.
- // PostPone this test in an optional integrity check at the end
- // of parsing or only in debug mode.
- if ( RealExplicit && !gdcmGlobal::GetVR()->Count(vr) )
- RealExplicit= false;
-
- if ( !RealExplicit )
- {
- // We thought this was explicit VR, but we end up with an
- // implicit VR tag. Let's backtrack.
- sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
- Entry->GetGroup(),Entry->GetElement());
- dbg.Verbose(1, "gdcmParser::FindVR: ",msg);
- if (Entry->GetGroup()%2 && Entry->GetElement() == 0x0000) { // Group length is UL !
- gdcmDictEntry* NewEntry = NewVirtualDictEntry(
- Entry->GetGroup(),Entry->GetElement(),
- "UL","FIXME","Group Length");
- Entry->SetDictEntry(NewEntry);
- }
- return(false);
- }
-
- if ( Entry->IsVRUnknown() )
- {
- // When not a dictionary entry, we can safely overwrite the VR.
- if (Entry->GetElement() == 0x0000) { // Group length is UL !
- Entry->SetVR("UL");
- } else {
- Entry->SetVR(vr);
- }
- }
- else if ( Entry->GetVR() != vr )
- {
- // The VR present in the file and the dictionary disagree. We assume
- // the file writer knew best and use the VR of the file. Since it would
- // be unwise to overwrite the VR of a dictionary (since it would
- // compromise it's next user), we need to clone the actual DictEntry
- // and change the VR for the read one.
- gdcmDictEntry* NewEntry = NewVirtualDictEntry(
- Entry->GetGroup(),Entry->GetElement(),
- vr,"FIXME",Entry->GetName());
- Entry->SetDictEntry(NewEntry);
- }
- return(true);
-}
-
-/**
- * \brief Get the transformed value of the header entry. The VR value
- * is used to define the transformation to operate on the value
- * \warning NOT end user intended method !
- * @param Entry
- * @return Transformed entry value
- */
-std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry)
-{
- if ( (IsHeaderEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
- {
- std::string val=Entry->GetValue();
- std::string vr=Entry->GetVR();
- guint32 length = Entry->GetLength();
- std::ostringstream s;
- int nbInt;
-
- // When short integer(s) are expected, read and convert the following
- // n * 2 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // as usual for standard multivaluated filels
- // Elements with Value Multiplicity > 1
- // contain a set of short integers (not a single one)
-
- if (vr == "US" || vr == "SS")
- {
- guint16 NewInt16;
-
- nbInt = length / 2;
- for (int i=0; i < nbInt; i++)
- {
- if(i!=0)
- s << '\\';
- NewInt16 = (val[2*i+0]&0xFF)+((val[2*i+1]&0xFF)<<8);
- NewInt16 = SwapShort(NewInt16);
- s << NewInt16;
- }
- }
-
- // When integer(s) are expected, read and convert the following
- // n * 4 bytes properly i.e. as a multivaluated strings
- // (each single value is separated fromthe next one by '\'
- // as usual for standard multivaluated filels
- // Elements with Value Multiplicity > 1
- // contain a set of integers (not a single one)
- else if (vr == "UL" || vr == "SL")
- {
- guint32 NewInt32;
-
- nbInt = length / 4;
- for (int i=0; i < nbInt; i++)
- {
- if(i!=0)
- s << '\\';
- NewInt32= (val[4*i+0]&0xFF)+((val[4*i+1]&0xFF)<<8)+
- ((val[4*i+2]&0xFF)<<16)+((val[4*i+3]&0xFF)<<24);
- NewInt32=SwapLong(NewInt32);
- s << NewInt32;
- }
- }
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- return(s.str());
- }
-
- return(Entry->GetValue());
-}
-
-/**
- * \brief Get the reverse transformed value of the header entry. The VR
- * value is used to define the reverse transformation to operate on
- * the value
- * \warning NOT end user intended method !
- * @param Entry
- * @return Reverse transformed entry value
- */
-std::string gdcmParser::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry)
-{
- if ( (IsHeaderEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
- {
- std::string vr=Entry->GetVR();
- std::ostringstream s;
- std::vector<std::string> tokens;
-
- if (vr == "US" || vr == "SS")
- {
- guint16 NewInt16;
-
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (Entry->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- NewInt16 = atoi(tokens[i].c_str());
- s<<(NewInt16&0xFF)<<((NewInt16>>8)&0xFF);
- }
- tokens.clear();
- }
- if (vr == "UL" || vr == "SL")
- {
- guint32 NewInt32;
-
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (Entry->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- NewInt32 = atoi(tokens[i].c_str());
- s<<(char)(NewInt32&0xFF)<<(char)((NewInt32>>8)&0xFF)
- <<(char)((NewInt32>>16)&0xFF)<<(char)((NewInt32>>24)&0xFF);
- }
- tokens.clear();
- }
-
-#ifdef GDCM_NO_ANSI_STRING_STREAM
- s << std::ends; // to avoid oddities on Solaris
-#endif //GDCM_NO_ANSI_STRING_STREAM
- return(s.str());
- }
-
- return(Entry->GetValue());
-}
-
-/**
- * \brief Skip a given Header Entry
- * \warning NOT end user intended method !
- * @param entry
- */
-void gdcmParser::SkipHeaderEntry(gdcmHeaderEntry *entry)
-{
- SkipBytes(entry->GetLength());
-}
-
-/**
- * \brief When the length of an element value is obviously wrong (because
- * the parser went Jabberwocky) one can hope improving things by
- * applying this heuristic.
- */
-void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 FoundLength)
-{
- Entry->SetReadLength(FoundLength); // will be updated only if a bug is found
- if ( FoundLength == 0xffffffff) {
- FoundLength = 0;
- }
-
- guint16 gr =Entry->GetGroup();
- guint16 el =Entry->GetElement();
-
- if (FoundLength%2) {
- std::ostringstream s;
- s << "Warning : Tag with uneven length " << FoundLength
- << " in x(" << std::hex << gr << "," << el <<")" << std::dec;
- dbg.Verbose(0,s.str().c_str());
- }
-
- // Sorry for the patch!
- // XMedCom did the trick to read some naughty GE images ...
- if (FoundLength == 13) {
- // The following 'if' will be removed when there is no more
- // images on Creatis HDs with a 13 length for Manufacturer...
- if ( (Entry->GetGroup() != 0x0008) ||
- ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){
- // end of remove area
- FoundLength =10;
- Entry->SetReadLength(10); // a bug is to be fixed
- }
- }
-
- // to fix some garbage 'Leonardo' Siemens images
- // May be commented out to avoid overhead
- else if ( (Entry->GetGroup() == 0x0009) &&
- ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){
- FoundLength =4;
- Entry->SetReadLength(4); // a bug is to be fixed
- }
- // end of fix
-
- // to try to 'go inside' SeQuences (with length), and not to skip them
- else if ( Entry->GetVR() == "SQ")
- {
- if (enableSequences) // only if the user does want to !
- FoundLength =0; // ReadLength is unchanged
- }
-
- // we found a 'delimiter' element
- // fffe|xxxx is just a marker, we don't take its length into account
- else if(Entry->GetGroup() == 0xfffe)
- {
- // *normally, fffe|0000 doesn't exist !
- if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm
- // causes extra troubles :-(
- FoundLength =0;
- }
-
- Entry->SetUsableLength(FoundLength);
-}
-
-/**
- * \brief Apply some heuristics to predict whether the considered
- * element value contains/represents an integer or not.
- * @param Entry The element value on which to apply the predicate.
- * @return The result of the heuristical predicate.
- */
-bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) {
- guint16 element = Entry->GetElement();
- guint16 group = Entry->GetGroup();
- std::string vr = Entry->GetVR();
- guint32 length = Entry->GetLength();
- // When we have some semantics on the element we just read, and if we
- // a priori know we are dealing with an integer, then we shall be
- // able to swap it's element value properly.
- if ( element == 0 ) // This is the group length of the group
- {
- if (length == 4)
- return true;
- else
- {
- std::ostringstream s;
- int filePosition = ftell(fp);
- s << "Erroneous Group Length element length on : (" \
- << std::hex << group << " , " << element
- << ") -before- position x(" << filePosition << ")"
- << "lgt : " << length;
- // These 2 lines commented out : a *very dirty* patch
- // to go on PrintHeader'ing gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
- // have a glance at offset x(8336) ...
- // For *regular* headers, the test is useless..
- // lets's print a warning message and go on,
- // instead of giving up with an error message
-
- //std::cout << s.str().c_str() << std::endl;
- // dbg.Error("gdcmParser::IsHeaderEntryAnInteger",
- // s.str().c_str());
- }
- }
- if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
- return true;
-
- return false;
-}
-/**
- * \brief Find the Length till the next sequence delimiter
- * \warning NOT end user intended method !
- * @return
- */
-
- guint32 gdcmParser::FindHeaderEntryLengthOB(void) {
- // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
- guint16 g;
- guint16 n;
- long PositionOnEntry = ftell(fp);
- bool FoundSequenceDelimiter = false;
- guint32 TotalLength = 0;
- guint32 ItemLength;
-
- while ( ! FoundSequenceDelimiter)
- {
- g = ReadInt16();
- n = ReadInt16();
- if (errno == 1)
- return 0;
- TotalLength += 4; // We even have to decount the group and element
-
- if ( g != 0xfffe && g!=0xb00c ) //for bogus header
- {
- char msg[100]; // for sprintf. Sorry
- sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n);
- dbg.Verbose(1, "gdcmParser::FindLengthOB: ",msg);
- errno = 1;
- return 0;
- }
- if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) // for bogus header
- FoundSequenceDelimiter = true;
- else if ( n != 0xe000 )
- {
- char msg[100]; // for sprintf. Sorry
- sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n",
- n, g,n);
- dbg.Verbose(1, "gdcmParser::FindLengthOB: ",msg);
- errno = 1;
- return 0;
- }
- ItemLength = ReadInt32();
- TotalLength += ItemLength + 4; // We add 4 bytes since we just read
- // the ItemLength with ReadInt32
- SkipBytes(ItemLength);
- }
- fseek(fp, PositionOnEntry, SEEK_SET);
- return TotalLength;
-}
-
-/**
- * \brief Reads a supposed to be 16 Bits integer
- * (swaps it depending on processor endianity)
- * @return read value
- */
-guint16 gdcmParser::ReadInt16(void) {
- guint16 g;
- size_t item_read;
- item_read = fread (&g, (size_t)2,(size_t)1, fp);
- if ( item_read != 1 ) {
- if(ferror(fp))
- dbg.Verbose(0, "gdcmParser::ReadInt16", " File Error");
- errno = 1;
- return 0;
- }
- errno = 0;
- g = SwapShort(g);
- return g;
-}
-
-/**
- * \brief Reads a supposed to be 32 Bits integer
- * (swaps it depending on processor endianity)
- * @return read value
- */
-guint32 gdcmParser::ReadInt32(void) {
- guint32 g;
- size_t item_read;
- item_read = fread (&g, (size_t)4,(size_t)1, fp);
- if ( item_read != 1 ) {
- if(ferror(fp))
- dbg.Verbose(0, "gdcmParser::ReadInt32", " File Error");
- errno = 1;
- return 0;
- }
- errno = 0;
- g = SwapLong(g);
- return g;
-}
-
-/**
- * \brief skips bytes inside the source file
- * \warning NOT end user intended method !
- * @return
- */
-void gdcmParser::SkipBytes(guint32 NBytes) {
- //FIXME don't dump the returned value
- (void)fseek(fp, (long)NBytes, SEEK_CUR);
-}
-
-/**
- * \brief Loads all the needed Dictionaries
- * \warning NOT end user intended method !
- */
-void gdcmParser::Initialise(void)
-{
- RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
- RefShaDict = (gdcmDict*)0;
-}
-
-/**
- * \brief Discover what the swap code is (among little endian, big endian,
- * bad little endian, bad big endian).
- * sw is set
- * @return false when we are absolutely sure
- * it's neither ACR-NEMA nor DICOM
- * true when we hope ours assuptions are OK
- */
-bool gdcmParser::CheckSwap() {
-
- // The only guaranted way of finding the swap code is to find a
- // group tag since we know it's length has to be of four bytes i.e.
- // 0x00000004. Finding the swap code in then straigthforward. Trouble
- // occurs when we can't find such group...
-
- guint32 x=4; // x : for ntohs
- bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
- guint32 s32;
- guint16 s16;
-
- int lgrLue;
- char *entCur;
- char deb[HEADER_LENGTH_TO_READ];
-
- // First, compare HostByteOrder and NetworkByteOrder in order to
- // determine if we shall need to swap bytes (i.e. the Endian type).
- if (x==ntohs(x))
- net2host = true;
- else
- net2host = false;
-
- // The easiest case is the one of a DICOM header, since it possesses a
- // file preamble where it suffice to look for the string "DICM".
- lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp);
-
- entCur = deb + 128;
- if(memcmp(entCur, "DICM", (size_t)4) == 0) {
- dbg.Verbose(1, "gdcmParser::CheckSwap:", "looks like DICOM Version3");
-
- // Next, determine the value representation (VR). Let's skip to the
- // first element (0002, 0000) and check there if we find "UL"
- // - or "OB" if the 1st one is (0002,0001) -,
- // in which case we (almost) know it is explicit VR.
- // WARNING: if it happens to be implicit VR then what we will read
- // is the length of the group. If this ascii representation of this
- // length happens to be "UL" then we shall believe it is explicit VR.
- // FIXME: in order to fix the above warning, we could read the next
- // element value (or a couple of elements values) in order to make
- // sure we are not commiting a big mistake.
- // We need to skip :
- // * the 128 bytes of File Preamble (often padded with zeroes),
- // * the 4 bytes of "DICM" string,
- // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001)
- // i.e. a total of 136 bytes.
- entCur = deb + 136;
-
- // FIXME : FIXME:
- // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR,
- // but elem 0002,0010 (Transfert Syntax) tells us the file is
- // *Implicit* VR. -and it is !-
-
- if( (memcmp(entCur, "UL", (size_t)2) == 0) ||
- (memcmp(entCur, "OB", (size_t)2) == 0) ||
- (memcmp(entCur, "UI", (size_t)2) == 0) ||
- (memcmp(entCur, "CS", (size_t)2) == 0) ) // CS, to remove later
- // when Write DCM *adds*
- // FIXME
- // Use gdcmParser::dicom_vr to test all the possibilities
- // instead of just checking for UL, OB and UI !? group 0000
- {
- filetype = gdcmExplicitVR;
- dbg.Verbose(1, "gdcmParser::CheckSwap:",
- "explicit Value Representation");
- }
- else
- {
- filetype = gdcmImplicitVR;
- dbg.Verbose(1, "gdcmParser::CheckSwap:",
- "not an explicit Value Representation");
- }
-
- if (net2host)
- {
- sw = 4321;
- dbg.Verbose(1, "gdcmParser::CheckSwap:",
- "HostByteOrder != NetworkByteOrder");
- }
- else
- {
- sw = 0;
- dbg.Verbose(1, "gdcmParser::CheckSwap:",
- "HostByteOrder = NetworkByteOrder");
- }
-
- // Position the file position indicator at first tag (i.e.
- // after the file preamble and the "DICM" string).
- rewind(fp);
- fseek (fp, 132L, SEEK_SET);
- return true;
- } // End of DicomV3
-
- // Alas, this is not a DicomV3 file and whatever happens there is no file
- // preamble. We can reset the file position indicator to where the data
- // is (i.e. the beginning of the file).
- dbg.Verbose(1, "gdcmParser::CheckSwap:", "not a DICOM Version3 file");
- rewind(fp);
-
- // Our next best chance would be to be considering a 'clean' ACR/NEMA file.
- // By clean we mean that the length of the first tag is written down.
- // If this is the case and since the length of the first group HAS to be
- // four (bytes), then determining the proper swap code is straightforward.
-
- entCur = deb + 4;
- // We assume the array of char we are considering contains the binary
- // representation of a 32 bits integer. Hence the following dirty
- // trick :
- s32 = *((guint32 *)(entCur));
-
- switch (s32) {
- case 0x00040000 :
- sw = 3412;
- filetype = gdcmACR;
- return true;
- case 0x04000000 :
- sw = 4321;
- filetype = gdcmACR;
- return true;
- case 0x00000400 :
- sw = 2143;
- filetype = gdcmACR;
- return true;
- case 0x00000004 :
- sw = 0;
- filetype = gdcmACR;
- return true;
- default :
-
- // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
- // It is time for despaired wild guesses.
- // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA,
- // i.e. the 'group length' element is not present :
-
- // check the supposed to be 'group number'
- // 0x0002 or 0x0004 or 0x0008
- // to determine ' sw' value .
- // Only 0 or 4321 will be possible
- // (no oportunity to check for the formerly well known
- // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
- // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -4, 8-)
- // the file IS NOT ACR-NEMA nor DICOM V3
- // Find a trick to tell it the caller...
-
- s16 = *((guint16 *)(deb));
-
- switch (s16) {
- case 0x0002 :
- case 0x0004 :
- case 0x0008 :
- sw = 0;
- filetype = gdcmACR;
- return true;
- case 0x0200 :
- case 0x0400 :
- case 0x0800 :
- sw = 4321;
- filetype = gdcmACR;
- return true;
- default :
- dbg.Verbose(0, "gdcmParser::CheckSwap:",
- "ACR/NEMA unfound swap info (Really hopeless !)");
- filetype = gdcmUnknown;
- return false;
- }
-
- // Then the only info we have is the net2host one.
- //if (! net2host )
- // sw = 0;
- //else
- // sw = 4321;
- //return;
- }
-}
-
-/**
- * \brief Restore the unproperly loaded values i.e. the group, the element
- * and the dictionary entry depending on them.
- */
-void gdcmParser::SwitchSwapToBigEndian(void)
-{
- dbg.Verbose(1, "gdcmParser::SwitchSwapToBigEndian",
- "Switching to BigEndian mode.");
- if ( sw == 0 )
- {
- sw = 4321;
- return;
- }
- if ( sw == 4321 )
- {
- sw = 0;
- return;
- }
- if ( sw == 3412 )
- {
- sw = 2143;
- return;
- }
- if ( sw == 2143 )
- sw = 3412;
-}
-
-/**
- * \brief during parsing, Header Elements too long are not loaded in memory
- * @param NewSize
- */
-void gdcmParser::SetMaxSizeLoadEntry(long NewSize)
-{
- if (NewSize < 0)
- return;
- if ((guint32)NewSize >= (guint32)0xffffffff)
- {
- MaxSizeLoadEntry = 0xffffffff;
- return;
- }
- MaxSizeLoadEntry = NewSize;
-}
-
-
-/**
- * \brief Header Elements too long will not be printed
- * \todo See comments of \ref gdcmParser::MAX_SIZE_PRINT_ELEMENT_VALUE
- * @param NewSize
- */
-void gdcmParser::SetMaxSizePrintEntry(long NewSize)
-{
- if (NewSize < 0)
- return;
- if ((guint32)NewSize >= (guint32)0xffffffff)
- {
- MaxSizePrintEntry = 0xffffffff;
- return;
- }
- MaxSizePrintEntry = NewSize;
-}
-
-/**
- * \brief Searches both the public and the shadow dictionary (when they
- * exist) for the presence of the DictEntry with given name.
- * The public dictionary has precedence on the shadow one.
- * @param Name name of the searched DictEntry
- * @return Corresponding DictEntry when it exists, NULL otherwise.
- */
-gdcmDictEntry *gdcmParser::GetDictEntryByName(std::string Name)
-{
- gdcmDictEntry *found = (gdcmDictEntry *)0;
- if (!RefPubDict && !RefShaDict)
- {
- dbg.Verbose(0, "gdcmParser::GetDictEntry",
- "we SHOULD have a default dictionary");
- }
- if (RefPubDict)
- {
- found = RefPubDict->GetDictEntryByName(Name);
- if (found)
- return found;
- }
- if (RefShaDict)
- {
- found = RefShaDict->GetDictEntryByName(Name);
- if (found)
- return found;
- }
- return found;
-}
-
-/**
- * \brief 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.
- * @param group group of the searched DictEntry
- * @param element element of the searched DictEntry
- * @return Corresponding DictEntry when it exists, NULL otherwise.
- */
-gdcmDictEntry *gdcmParser::GetDictEntryByNumber(guint16 group,guint16 element)
-{
- gdcmDictEntry *found = (gdcmDictEntry *)0;
- if (!RefPubDict && !RefShaDict)
- {
- dbg.Verbose(0, "gdcmParser::GetDictEntry",
- "we SHOULD have a default dictionary");
- }
- if (RefPubDict)
- {
- found = RefPubDict->GetDictEntryByNumber(group, element);
- if (found)
- return found;
- }
- if (RefShaDict)
- {
- found = RefShaDict->GetDictEntryByNumber(group, element);
- if (found)
- return found;
- }
- return found;
-}
-
-/**
- * \brief Read the next tag but WITHOUT loading it's value
- * @return On succes the newly created HeaderEntry, NULL on failure.
- */
-gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) {
- guint16 g,n;
- gdcmHeaderEntry *NewEntry;
- g = ReadInt16();
- n = ReadInt16();
-
- if (errno == 1)
- // We reached the EOF (or an error occured) therefore
- // header parsing has to be considered as finished.
- return (gdcmHeaderEntry *)0;
-
-// Pb : how to propagate the element length (used in SkipHeaderEntry)
-// direct call to SkipBytes ?
-
-// if (ignoreShadow == 1 && g%2 ==1)
- // if user wants to skip shadow groups
- // and current element *is* a shadow element
- // we don't create anything
-// return (gdcmHeaderEntry *)1; // to tell caller it's NOT finished
-
- NewEntry = NewHeaderEntryByNumber(g, n);
- FindHeaderEntryVR(NewEntry);
- FindHeaderEntryLength(NewEntry);
-
- if (errno == 1) {
- // Call it quits
- return NULL;
- }
- NewEntry->SetOffset(ftell(fp));
- return NewEntry;
-}
-
-/**
- * \brief Build a new Element Value from all the low level arguments.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Name Name of the underlying DictEntry
- */
-gdcmHeaderEntry *gdcmParser::NewHeaderEntryByName(std::string Name)
-{
- gdcmDictEntry *NewTag = GetDictEntryByName(Name);
- if (!NewTag)
- NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name);
-
- gdcmHeaderEntry* NewEntry = new gdcmHeaderEntry(NewTag);
- if (!NewEntry)
- {
- dbg.Verbose(1, "gdcmParser::ObtainHeaderEntryByName",
- "failed to allocate gdcmHeaderEntry");
- return (gdcmHeaderEntry *)0;
- }
- return NewEntry;
-}
-
-/**
- * \brief Request a new virtual dict entry to the dict set
- * @param group group of the underlying DictEntry
- * @param element element of the underlying DictEntry
- * @param vr VR of the underlying DictEntry
- * @param fourth owner group
- * @param name english name
- */
-gdcmDictEntry *gdcmParser::NewVirtualDictEntry(guint16 group, guint16 element,
- std::string vr,
- std::string fourth,
- std::string name)
-{
- return gdcmGlobal::GetDicts()->NewVirtualDictEntry(group,element,vr,fourth,name);
-}
-
-/**
- * \brief Build a new Element Value from all the low level arguments.
- * Check for existence of dictionary entry, and build
- * a default one when absent.
- * @param Group group of the underlying DictEntry
- * @param Elem element of the underlying DictEntry
- */
-gdcmHeaderEntry *gdcmParser::NewHeaderEntryByNumber(guint16 Group, guint16 Elem)
-{
- // Find out if the tag we encountered is in the dictionaries:
- gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
- if (!DictEntry)
- DictEntry = NewVirtualDictEntry(Group, Elem);
-
- gdcmHeaderEntry *NewEntry = new gdcmHeaderEntry(DictEntry);
- if (!NewEntry)
- {
- dbg.Verbose(1, "gdcmParser::NewHeaderEntryByNumber",
- "failed to allocate gdcmHeaderEntry");
- return NULL;
- }
- return NewEntry;
-}
-
-/// \todo Never used; commented out, waiting for removal.
-/**
- * \brief Small utility function that creates a new manually crafted
- * (as opposed as read from the file) gdcmHeaderEntry with user
- * specified name and adds it to the public tag hash table.
- * \note A fake TagKey is generated so the PubDict can keep it's coherence.
- * @param NewTagName The name to be given to this new tag.
- * @param VR The Value Representation to be given to this new tag.
- * @return The newly hand crafted Element Value.
- */
-//gdcmHeaderEntry *gdcmParser::NewManualHeaderEntryToPubDict(std::string NewTagName,
-// std::string VR)
-//{
-// gdcmHeaderEntry *NewEntry = NULL;
-// guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
-// guint32 FreeElem = 0;
-// gdcmDictEntry *DictEntry = NULL;
-//
-// FreeElem = GenerateFreeTagKeyInGroup(StuffGroup);
-// if (FreeElem == UINT32_MAX)
-// {
-// dbg.Verbose(1, "gdcmHeader::NewManualHeaderEntryToPubDict",
-// "Group 0xffff in Public Dict is full");
-// return NULL;
-// }
-//
-// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem,
-// VR, "GDCM", NewTagName);
-// NewEntry = new gdcmHeaderEntry(DictEntry);
-// AddHeaderEntry(NewEntry);
-// return NewEntry;
-//}
-
-/**
- * \brief Generate a free TagKey i.e. a TagKey that is not present
- * in the TagHt dictionary.
- * @param group The generated tag must belong to this group.
- * @return The element of tag with given group which is fee.
- */
-guint32 gdcmParser::GenerateFreeTagKeyInGroup(guint16 group)
-{
- for (guint32 elem = 0; elem < UINT32_MAX; elem++)
- {
- TagKey key = gdcmDictEntry::TranslateToKey(group, elem);
- if (tagHT.count(key) == 0)
- return elem;
- }
- return UINT32_MAX;
-}
-
-//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff