if ( !OpenFile(exception_on_error))
return;
+
+ rewind(fp);
+ //if (!CheckSwap())
+ // return false; // to go on compiling
+
+ fseek(fp,0L,SEEK_END);
+ long lgt = ftell(fp);
+
+ rewind(fp);
+ CheckSwap();
+ long beg = ftell(fp);
+ lgt -= beg;
+
+ //std::cout << "beg, lgt : " << beg << " " << lgt << std::endl;
- //LoadHeaderEntries();
- long l=ParseES( (gdcmDocEntrySet *)this, 120L, 0x7fffffff, false);
- // TODO : find the right values
+ long l=ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
CloseFile();
printLevel = 1; // 'Medium' print level by default
//-----------------------------------------------------------------------------
// Print
/**
- * \brief Prints the Header 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
* false otherwise.
*/
bool gdcmDocument::IsReadable(void) {
- if(filetype==Unknown) {
+ if(filetype==gdcmUnknown) {
return(false);
}
if(listEntries.size()<=0) {
/// a moins de se livrer a un tres complique ajout des champs manquants.
/// faire un CheckAndCorrectHeader (?)
- if (type == ImplicitVR)
+ if (type == gdcmImplicitVR)
{
std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2;
ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
SetEntryLengthByNumber(18, 0x0002, 0x0010);
}
- if (type == ExplicitVR)
+ if (type == gdcmExplicitVR)
{
std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1;
ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
a =NewDocEntryByNumber(Group, Elem);
if (a == NULL)
return NULL;
- AddDocEntry(a);
+ AddEntry(a);
}
SetEntryByNumber(Value, Group, Elem);
//a->SetValue(Value);
gdcmDictEntry * tagZ = new gdcmDictEntry(gr_bid, 0x0000, "UL");
elemZ = new gdcmDocEntry(tagZ);
elemZ->SetLength(4);
- AddDocEntry(elemZ); // create it
+ AddEntry(elemZ); // create it
}
else
{
fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group
fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
- if ( type == ExplicitVR ) {
+ if ( type == gdcmExplicitVR ) {
// Special case of delimiters:
if (group == 0xfffe) {
tag2 != listEntries.end();
++tag2)
{
- if ( type == ACR ){
+ if ( type == gdcmACR ){
if ((*tag2)->GetGroup() < 0x0008)
// Ignore pure DICOM V3 groups
continue;
for (TagDocEntryHT::iterator tag2=tagHT.begin();
tag2 != tagHT.end();
++tag2){
- if ( type == ACR ){
+ 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
a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
break;
default :
+ std::cout << "swapCode= " << sw << std::endl;
dbg.Error(" gdcmDocument::SwapLong : unset swap code");
a=0;
}
* @return false if file is not ACR-NEMA / PAPYRUS / DICOM
*/
-long gdcmDocument::ParseES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
+long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
gdcmValEntry *vl;
+ gdcmBinEntry *bn;
gdcmSeqEntry *sq;
+ string vr;
long l;
while (true) {
NewDocEntry = ReadNextDocEntry( );
if (!NewDocEntry)
break;
- if (NewDocEntry->GetVR() !="SQ") {
- vl= new gdcmValEntry(NewDocEntry->GetDictEntry());
- vl->Copy(NewDocEntry);
- delete NewDocEntry;
- set->AddEntry(vl);
- if (!delim_mode && vl->isItemDelimitor())
- break;
+
+ std::cout << hex << NewDocEntry->GetGroup()
+ << " "
+ << NewDocEntry->GetElement()
+ << " "
+ << NewDocEntry->GetVR()
+ << " "
+ << NewDocEntry->GetReadLength()
+ << " "
+ << NewDocEntry->GetOffset()
+ << std::endl;
+
+ vr = NewDocEntry->GetVR();
+ if (vr!="SQ") {
+
+ if (vr == "AE" || vr == "AS" || vr == "DA" || vr == "PN" ||
+ vr == "UI" || vr == "TM" || vr == "SH" || vr == "LO" ||
+ vr == "CS" || vr == "IS" || vr == "LO" || vr == "LT" ||
+ vr == "SH" || vr == "ST" ||
+ vr == "SL" || vr == "SS" || vr == "UL" || vr == "US"
+ ) {
+ // --- ValEntry
+ vl= new gdcmValEntry(NewDocEntry->GetDictEntry());
+ vl->Copy(NewDocEntry);
+ set->AddEntry(vl);
+ LoadDocEntry(vl);
+ std::cout << "value [" << vl->GetValue() << "]" << std::endl;
+ if (!delim_mode && vl->isItemDelimitor())
+ break;
+ } else { // BinEntry
+
+ // Hope the following VR *do* correspond to a BinEntry
+
+ //AT Attribute Tag; // 2 16-bit unsigned short integers
+ //FL Floating Point Single; // 32-bit IEEE 754:1985 float
+ //FD Floating Point Double; // 64-bit IEEE 754:1985 double
+ //UN Unknown; // Any length of bytes
+ //UT Unlimited Text; // At most 2^32 -1 chars
+ //OB Other Byte String; // String of bytes (VR independant)
+ //OW Other Word String; // String of 16-bit words (VR dependant)
+
+ bn = new gdcmBinEntry(NewDocEntry->GetDictEntry());
+ bn->Copy(NewDocEntry);
+ LoadDocEntry(bn);
+ std::cout << "value [" << "Bin Entry, in voidArea" << "]" << std::endl;
+ }
+
+ SkipToNextDocEntry(NewDocEntry); // to be sure to be at the beginning
+ l = NewDocEntry->GetFullLength();
+
+ } else { // VR = "SQ"
- } else { // VR = "SQ"
- l=NewDocEntry->GetReadLength();
- if (l == 0xffffffff)
- delim_mode = true;
- else
- delim_mode = false;
- sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry());
- sq->Copy(NewDocEntry);
- long lgt = ParseSQ((gdcmDocEntrySet *)sq, offset, l, delim_mode);
- set->AddEntry(sq);
- if ( !delim_mode && ftell(fp)-offset >= l_max)
- break;
+ //SkipDocEntry(NewDocEntry);
+
+ std::cout << "gdcmDocument::ParseDES : SQ found " << std::endl;
+ l=NewDocEntry->GetReadLength();
+ if (l == 0xffffffff)
+ delim_mode = true;
+ else
+ delim_mode = false;
+ sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry());
+ sq->Copy(NewDocEntry);
+ sq->SetDelimitorMode(delim_mode);
+ long lgt = ParseSQ((gdcmDocEntrySet *)sq, offset, l, delim_mode);
+ // FIXME : on en fait quoi, de lgt ?
+ set->AddEntry(sq);
+ if ( !delim_mode && ftell(fp)-offset >= l_max)
+ break;
}
- }
+ }
+ cout << endl;
+ delete NewDocEntry;
return l; // ??
}
+/**
+ * \brief Parses a Sequence ( SeqEntry after SeqEntry)
+ * @return parsed length for this level
+ */
+
long gdcmDocument::ParseSQ(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
+ std::cout << "Entree ds gdcmDocument::ParseSQ" << std::endl;
+
gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
gdcmSQItem *itemSQ;
bool dlm_mod;
int lgr, l, lgth;
+ cout << "=============== on entre ds une Sequence" <<endl;
while (true) {
+ std::cout << "gdcmDocument::ParseSQ on itere" << std::endl;
+
if(delim_mode) {
NewDocEntry = ReadNextDocEntry();
- if (NewDocEntry->isSequenceDelimitor())
- // =====> ATTENTION : il faudra tout de meme ajouter
- // le Sequence Delimiter ?!?
- //set.Add(???);
+ if (NewDocEntry->isSequenceDelimitor()) {
+ // add the Sequence Delimitor // TODO : find the trick to put it proprerly !
+ // ((gdcmSeqEntry *)set)->SetSequenceDelimitationItem(NewDocEntry);
break;
+ }
}
if (!delim_mode && (ftell(fp)-offset) >= l_max){
break;
}
itemSQ = new gdcmSQItem();
-
+ itemSQ->AddEntry(NewDocEntry); // no value, no voidArea. Think of it while printing !
l= NewDocEntry->GetLength();
if (l ==0xffffffff)
dlm_mod = true;
else
dlm_mod=false;
- lgr=ParseES(itemSQ, offset, l, dlm_mod);
+ lgr=ParseDES(itemSQ, offset, l, dlm_mod);
((gdcmSeqEntry *)set)->AddEntry(itemSQ);
}
- //Update(lgth); // TODO // to go on compiling
+ //Update(lgth);
+ lgth = ftell(fp) - offset;
+ cout << "=============== lgr Sequence :" << lgth <<endl;
return(lgth);
}
while ( (newDocEntry = ReadNextDocEntry()) ) {
SkipDocEntry(newDocEntry);
if ( (ignoreShadow==0) || (newDocEntry->GetGroup()%2) == 0) {
- AddDocEntry(newDocEntry);
+ AddEntry(newDocEntry);
}
}
rewind(fp);
((gdcmValEntry *)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 newDocEntry
- */
-void gdcmDocument::AddDocEntry(gdcmDocEntry *newDocEntry) {
- tagHT.insert( PairHT( newDocEntry->GetKey(),newDocEntry) );
- listEntries.push_back(newDocEntry);
-}
/**
* \brief Find the value Length of the passed Header Entry
guint16 length16;
- if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) )
+ if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) )
{
if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") )
{
*/
void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry)
{
- if (filetype != ExplicitVR)
+ if (filetype != gdcmExplicitVR)
return;
char VR[3];
*/
void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry)
{
- SkipBytes(entry->GetLength());
+ SkipBytes(entry->GetLength());
}
+/**
+ * \brief Skips to the begining of the next Header Entry
+ * \warning NOT end user intended method !
+ * @param entry
+ */
+void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry)
+{
+ (void)fseek(fp, (long)(entry->GetOffset()), SEEK_SET);
+ (void)fseek(fp, (long)(entry->GetReadLength()), SEEK_CUR);
+}
+
+/**
+ * \brief Loads the value for a a given VLEntry
+ * \warning NOT end user intended method !
+ * @param entry
+ */
+void gdcmDocument::LoadVLEntry(gdcmDocEntry *entry)
+{
+ //SkipBytes(entry->GetLength());
+ LoadDocEntry(entry);
+}
/**
* \brief When the length of an element value is obviously wrong (because
* the parser went Jabberwocky) one can hope improving things by
// Use gdcmDocument::dicom_vr to test all the possibilities
// instead of just checking for UL, OB and UI !? group 0000
{
- filetype = ExplicitVR;
+ filetype = gdcmExplicitVR;
dbg.Verbose(1, "gdcmDocument::CheckSwap:",
"explicit Value Representation");
}
else
{
- filetype = ImplicitVR;
+ filetype = gdcmImplicitVR;
dbg.Verbose(1, "gdcmDocument::CheckSwap:",
"not an explicit Value Representation");
}
switch (s32) {
case 0x00040000 :
sw = 3412;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
case 0x04000000 :
sw = 4321;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
case 0x00000400 :
sw = 2143;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
case 0x00000004 :
sw = 0;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
default :
case 0x0004 :
case 0x0008 :
sw = 0;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
case 0x0200 :
case 0x0400 :
case 0x0800 :
sw = 4321;
- filetype = ACR;
+ filetype = gdcmACR;
return true;
default :
dbg.Verbose(0, "gdcmDocument::CheckSwap:",
"ACR/NEMA unfound swap info (Really hopeless !)");
- filetype = Unknown;
+ filetype = gdcmUnknown;
return false;
}
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
+ * (read the 'Group Number', the 'Element Number',
+ * gets the Dict Entry
+ * gets the VR, gets the length, gets the offset value)
* @return On succes the newly created DocEntry, NULL on failure.
*/
gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) {
if (errno == 1) {
// Call it quits
+ delete NewEntry;
return NULL;
}
NewEntry->SetOffset(ftell(fp));
// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem,
// VR, "GDCM", NewTagName);
// NewEntry = new gdcmDocEntry(DictEntry);
-// AddDocEntry(NewEntry);
+// AddEntry(NewEntry);
// return NewEntry;
//}
return UINT32_MAX;
}
+
+/**
+ * \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;
+}
+
+
+
//-----------------------------------------------------------------------------
#include "gdcmDictSet.h"
#include "gdcmDocEntry.h"
#include "gdcmDocEntrySet.h"
+#include "gdcmElementSet.h"
#include <map>
#include <list>
/**
* \brief used by both gdcmHeader and gdcmDicomDir
*/
-class GDCM_EXPORT gdcmDocument
+class GDCM_EXPORT gdcmDocument : public gdcmElementSet
{
private:
/// Public dictionary used to parse this header
/// in order no to polute the screen output. By default, this upper bound
/// is fixed to 64 bytes.
guint32 MaxSizePrintEntry;
+
+
protected:
/// Refering underlying filename.
// Print
- /// Canonical Printing method (see also gdcmDocument::SetPrintLevel)
- virtual void Print (std::ostream &os = std::cout)
- {PrintEntry(os);};
- virtual void PrintEntry (std::ostream &os = std::cout);
+ // Canonical Printing method (see also gdcmDocument::SetPrintLevel)
+ // virtual void Print (std::ostream &os = std::cout);
+ // {PrintEntry(os);};
+
+ // no more Print method for gdcmDocument (inherits from gdcmElementSet
+ // virtual void PrintEntry (std::ostream &os = std::cout)
+ // { return Print(os);};
// the 2 following will be merged
virtual void PrintPubDict (std::ostream &os = std::cout);
bool ReplaceIfExistByNumber (char *Value, guint16 Group, guint16 Elem);
virtual void *LoadEntryVoidArea (guint16 Group, guint16 Element);
-
+ void LoadVLEntry (gdcmDocEntry *entry);
+
// System access
guint16 SwapShort(guint16); // needed by gdcmFile
guint32 SwapLong(guint32); // needed by gdcmFile
//void UpdateGroupLength(bool SkipSequence = false,
// FileType type = ImplicitVR);
- void AddDocEntry (gdcmDocEntry *);
+ //void AddDocEntry (gdcmDocEntry *);
private:
// Read
//bool LoadHeaderEntries(bool exception_on_error = false) throw(gdcmFormatError);
- // remplacé par ParseES.
+ // remplacé par ParseDES.
// What about exception_on_error ?
- long ParseES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode);
+ long ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode);
long ParseSQ(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode);
std::string GetDocEntryUnvalue(gdcmDocEntry *);
void SkipDocEntry (gdcmDocEntry *);
+ void SkipToNextDocEntry (gdcmDocEntry *);
+
void FixDocEntryFoundLength(gdcmDocEntry *, guint32);
bool IsDocEntryAnInteger (gdcmDocEntry *);
void SetMaxSizeLoadEntry(long);
void SetMaxSizePrintEntry(long);
- // DictEntry related utilities
+ // DictEntry related utilities
+
gdcmDictEntry *GetDictEntryByName (std::string Name);
gdcmDictEntry *GetDictEntryByNumber(guint16, guint16);
gdcmDictEntry *NewVirtualDictEntry(guint16 group,
std::string vr = "unkn",
std::string fourth = "unkn",
std::string name = "unkn");
- //gdcmDictEntry *NewVirtualDictEntry(gdcmDocEntry *); // never defined
+ //gdcmDictEntry *NewVirtualDictEntry(gdcmDocEntry *); // never defined
// DocEntry related utilities
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff