--- /dev/null
+// gdcmDocument.cxx
+//-----------------------------------------------------------------------------
+
+#include "gdcmDocument.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 gdcmDocument::CheckSwap()
+const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256;
+
+// Refer to gdcmDocument::SetMaxSizeLoadEntry()
+const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096;
+
+const unsigned int gdcmDocument::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')
+ */
+gdcmDocument::gdcmDocument(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;
+
+ LoadDocEntries();
+ 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
+ */
+gdcmDocument::gdcmDocument(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.
+ */
+gdcmDocument::~gdcmDocument (void) {
+ RefPubDict = NULL;
+ RefShaDict = NULL;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+/**
+ * \brief Prints the Doc Entries (Dicom Elements)
+ * from the chained list
+ * @return
+ */
+void gdcmDocument::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 gdcmDocument::PrintPubDict(std::ostream & os) {
+ RefPubDict->Print(os);
+}
+
+/**
+ * \brief Prints The Dict Entries of THE shadow Dicom Dictionary
+ * @return
+ */
+void gdcmDocument::PrintShaDict(std::ostream & os) {
+ RefShaDict->Print(os);
+}
+
+//-----------------------------------------------------------------------------
+// Public
+/**
+ * \brief Get the public dictionary used
+ */
+gdcmDict *gdcmDocument::GetPubDict(void) {
+ return(RefPubDict);
+}
+
+/**
+ * \brief Get the shadow dictionary used
+ */
+gdcmDict *gdcmDocument::GetShaDict(void) {
+ return(RefShaDict);
+}
+
+/**
+ * \brief Set the shadow dictionary used
+ * \param dict dictionary to use in shadow
+ */
+bool gdcmDocument::SetShaDict(gdcmDict *dict){
+ RefShaDict=dict;
+ return(!RefShaDict);
+}
+
+/**
+ * \brief Set the shadow dictionary used
+ * \param dictName name of the dictionary to use in shadow
+ */
+bool gdcmDocument::SetShaDict(DictKey dictName){
+ RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName);
+ return(!RefShaDict);
+}
+
+/**
+ * \brief This predicate, based on hopefully reasonable heuristics,
+ * decides whether or not the current gdcmDocument was properly parsed
+ * and contains the mandatory information for being considered as
+ * a well formed and usable Dicom/Acr File.
+ * @return true when gdcmDocument is the one of a reasonable Dicom/Acr file,
+ * false otherwise.
+ */
+bool gdcmDocument::IsReadable(void) {
+ if(filetype==Unknown) {
+ 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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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, Unknown)
+ * @return the FileType code
+ */
+FileType gdcmDocument::GetFileType(void) {
+ return(filetype);
+}
+
+/**
+ * \brief opens the file
+ * @param exception_on_error
+ * @return
+ */
+FILE *gdcmDocument::OpenFile(bool exception_on_error)
+ throw(gdcmFileError)
+{
+ fp=fopen(filename.c_str(),"rb");
+ if(exception_on_error)
+ {
+ if(!fp)
+ throw gdcmFileError("gdcmDocument::gdcmDocument(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, "gdcmDocument::OpenFile not DICOM/ACR", filename.c_str());
+ }
+ else {
+ dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", filename.c_str());
+ }
+ return(NULL);
+}
+
+/**
+ * \brief closes the file
+ * @return TRUE if the close was successfull
+ */
+bool gdcmDocument::CloseFile(void) {
+ int closed = fclose(fp);
+ fp = (FILE *)0;
+ if (! closed)
+ return false;
+ return true;
+}
+
+/**
+ * \brief Writes in a file all the Doc 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 gdcmDocument::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 gdcmDocument)
+/// 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 gdcmDocument ...)
+ /// 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 == ImplicitVR)
+ {
+ 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 == ExplicitVR)
+ {
+ 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 * gdcmDocument::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 gdcmDocument::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 gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) {
+ std::string key = gdcmDictEntry::TranslateToKey(group, element );
+ return (tagHT.count(key));
+}
+
+/**
+ * \brief Searches within Doc 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 gdcmDocument::GetEntryByName(std::string tagName) {
+ gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
+ if( dictEntry == NULL)
+ return GDCM_UNFOUND;
+
+ return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
+}
+
+/**
+ * \brief Searches within Doc 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 gdcmDocument::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 Doc 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 gdcmDocument::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 Doc 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 gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) {
+ gdcmHeaderEntry* elem = GetHeaderEntryByNumber(group, element);
+ if ( !elem )
+ return GDCM_UNFOUND;
+ return elem->GetVR();
+}
+
+/**
+ * \brief Searches within Doc 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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem)
+{
+ gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
+ if (!Entry)
+ {
+ dbg.Verbose(1, "gdcmDocument::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 * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem)
+{
+ gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
+ if (!Entry)
+ {
+ dbg.Verbose(1, "gdcmDocument::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 *gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 Doc 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 *gdcmDocument::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* gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 == ExplicitVR)
+ {
+ 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 gdcmDocument::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 == ExplicitVR ) {
+
+ // 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") { // Unknown 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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::WriteEntries(FILE *_fp,FileType type)
+{
+ /// \todo (?) check write failures (after *each* fwrite)
+
+ for (ListTag::iterator tag2=listEntries.begin();
+ tag2 != listEntries.end();
+ ++tag2)
+ {
+ if ( type == ACR ){
+ 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 gdcmDocument::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 == ACR ){
+ 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 gdcmDocument::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(" gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::UnswapShort(guint16 a) {
+ return (SwapShort(a));
+}
+
+//-----------------------------------------------------------------------------
+// Private
+
+/**
+ * \brief Loads the element content if its length doesn't exceed
+ * the value specified with gdcmDocument::SetMaxSizeLoadEntry()
+ * @param Entry Header Entry (Dicom Element) to be dealt with
+ */
+void gdcmDocument::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, "gdcmDocument::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 gdcmDocument::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 gdcmDocument::FindHeaderEntryLength (gdcmHeaderEntry *Entry) {
+ guint16 element = Entry->GetElement();
+ //guint16 group = Entry->GetGroup(); //FIXME
+ std::string vr = Entry->GetVR();
+ guint16 length16;
+
+
+ if ( (filetype == ExplicitVR) && (! 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, "gdcmDocument::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, "gdcmDocument::FindLength",
+ // "Erroneous element length fixed.");
+ // Actually, length= 0xffff means that we deal with
+ // Unknown 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 gdcmDocument::FindHeaderEntryVR( gdcmHeaderEntry *Entry)
+{
+ if (filetype != ExplicitVR)
+ 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 gdcmDocument::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, "gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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("gdcmDocument::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 gdcmDocument::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, "gdcmDocument::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, "gdcmDocument::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 gdcmDocument::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, "gdcmDocument::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 gdcmDocument::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, "gdcmDocument::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 gdcmDocument::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 gdcmDocument::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 gdcmDocument::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, "gdcmDocument::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 gdcmDocument::dicom_vr to test all the possibilities
+ // instead of just checking for UL, OB and UI !? group 0000
+ {
+ filetype = ExplicitVR;
+ dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ "explicit Value Representation");
+ }
+ else
+ {
+ filetype = ImplicitVR;
+ dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ "not an explicit Value Representation");
+ }
+
+ if (net2host)
+ {
+ sw = 4321;
+ dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ "HostByteOrder != NetworkByteOrder");
+ }
+ else
+ {
+ sw = 0;
+ dbg.Verbose(1, "gdcmDocument::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, "gdcmDocument::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 = ACR;
+ return true;
+ case 0x04000000 :
+ sw = 4321;
+ filetype = ACR;
+ return true;
+ case 0x00000400 :
+ sw = 2143;
+ filetype = ACR;
+ return true;
+ case 0x00000004 :
+ sw = 0;
+ filetype = ACR;
+ return true;
+ default :
+
+ // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
+ // It is time for despaired wild guesses.
+ // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA,
+ // i.e. the 'group length' element is not present :
+
+ // check the supposed to be 'group number'
+ // 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 = ACR;
+ return true;
+ case 0x0200 :
+ case 0x0400 :
+ case 0x0800 :
+ sw = 4321;
+ filetype = ACR;
+ return true;
+ default :
+ dbg.Verbose(0, "gdcmDocument::CheckSwap:",
+ "ACR/NEMA unfound swap info (Really hopeless !)");
+ filetype = Unknown;
+ 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 gdcmDocument::SwitchSwapToBigEndian(void)
+{
+ dbg.Verbose(1, "gdcmDocument::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 gdcmDocument::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 gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE
+ * @param NewSize
+ */
+void gdcmDocument::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 *gdcmDocument::GetDictEntryByName(std::string Name)
+{
+ gdcmDictEntry *found = (gdcmDictEntry *)0;
+ if (!RefPubDict && !RefShaDict)
+ {
+ dbg.Verbose(0, "gdcmDocument::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 *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element)
+{
+ gdcmDictEntry *found = (gdcmDictEntry *)0;
+ if (!RefPubDict && !RefShaDict)
+ {
+ dbg.Verbose(0, "gdcmDocument::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 *gdcmDocument::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 *gdcmDocument::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, "gdcmDocument::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 *gdcmDocument::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 *gdcmDocument::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, "gdcmDocument::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 *gdcmDocument::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 gdcmDocument::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