#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"
+#define UI1_1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5"
-typedef struct {
- guint32 totalSQlength;
- guint32 alreadyParsedlength;
-} pileElem;
+#define str2num(str, typeNum) *((typeNum *)(str))
//-----------------------------------------------------------------------------
// Refer to gdcmDocument::CheckSwap()
gdcmDocument::gdcmDocument(const char *inFilename,
bool exception_on_error,
bool enable_sequences,
- bool ignore_shadow) {
+ bool ignore_shadow)
+ : gdcmElementSet(-1) {
enableSequences=enable_sequences;
ignoreShadow =ignore_shadow;
long beg = ftell(fp);
lgt -= beg;
- //std::cout << "beg, lgt : " << beg << " " << lgt << std::endl;
-
+ SQDepthLevel=0;
+
long l=ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
- CloseFile();
-
- /* TO DO : uncomment when everything else is OK
+ CloseFile();
// --------------------------------------------------------------
// Special Patch to allow gdcm to read ACR-LibIDO formated images
RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
// with "little-endian strings"
{
- filetype = ACR_LIBIDO;
+ 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 ----------------
- */
-
printLevel = 1; // 'Medium' print level by default
}
* \brief constructor
* @param exception_on_error
*/
-gdcmDocument::gdcmDocument(bool exception_on_error) {
- (void)exception_on_error;
+gdcmDocument::gdcmDocument(bool exception_on_error)
+ :gdcmElementSet(-1) {
+ (void)exception_on_error;
enableSequences=0;
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
*/
bool gdcmDocument::IsReadable(void) {
if(filetype==gdcmUnknown) {
+ std::cout << "wrong filetype" <<std::endl;
return(false);
}
- if(listEntries.size()<=0) {
+ if(!tagHT.empty()<=0) {
+ std::cout << "wrong tagHT size "<< tagHT.size() <<std::endl;
return(false);
}
return false;
LoadDocEntrySafe(Element);
- std::string Transfer = Element->GetValue();
+ std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
if ( Transfer == UI1_2_840_10008_1_2 )
return true;
return false;
return false;
LoadDocEntrySafe(Element);
- std::string Transfer = Element->GetValue();
+ std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
if ( Transfer == UI1_2_840_10008_1_2_1 )
return true;
return false;
return false;
LoadDocEntrySafe(Element);
- std::string Transfer = Element->GetValue();
+ std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
if ( Transfer == UI1_2_840_10008_1_2_1_99 )
return true;
return false;
return false;
LoadDocEntrySafe(Element);
- std::string Transfer = Element->GetValue();
+ std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier !
return true;
return false;
/// ==============
/// 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)
+/// (so we shall remove the Group*HT from the gdcmDocument)
/// To be checked
/// =============
return GDCM_UNFOUND;
gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
+ dictEntry->GetElement());
return elem->GetVR();
}
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHT.count(key))
return GDCM_UNFOUND;
- return tagHT.find(key)->second->GetValue();
+ return ((gdcmValEntry *)tagHT.find(key)->second)->GetValue();
}
/**
}
gdcmDocEntry * a;
- IterHT p;
- TagDocEntryHT::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 :
-
- // Oops ! this was for multimap, right ?
- a = ((tagHT.equal_range(key)).first)->second;
-
+ a = tagHT[key];
+
((gdcmValEntry*)a)->SetValue(content);
std::string vr = a->GetVR();
void gdcmDocument::UpdateShaEntries(void) {
gdcmDictEntry *entry;
std::string vr;
-
+
+ // TODO : if still any use (?) explore recursively the whole structure
+/*
for(ListTag::iterator it=listEntries.begin();
it!=listEntries.end();
++it)
else
vr=(*it)->GetVR();
- //(*it)->SetValue(GetDocEntryUnvalue(*it));
- // to go on compiling
+ (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling
if(entry){
// Set the new entry and the new value
(*it)->SetDictEntry(entry);
CheckDocEntryVR(*it,vr);
- //(*it)->SetValue(GetDocEntryValue(*it));
- // to go on compiling
+ (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling
}
else
(*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr));
}
}
+*/
}
/**
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::GetDocEntrySameNumber(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
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, ...)
- */
-
- /* Probabely useless, now !
-
-void gdcmDocument::UpdateGroupLength(bool SkipSequence, FileType type) {
- guint16 gr, el;
- std::string vr;
-
- gdcmDocEntry *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;
-
- gdcmDocEntry *elemZ;
-
- // for each Tag in the DCM Header
-
- for (TagDocEntryHT::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 gdcmDocEntry(tagZ);
- elemZ->SetLength(4);
- AddEntry(elemZ); // create it
- }
- else
- {
- elemZ=GetDocEntryByNumber(gr_bid, 0x0000);
- }
- sprintf(trash ,"%d",g->second);
- str_trash=trash;
- //elemZ->SetValue(str_trash); // to go on compiling
- }
-}
-
-*/
/**
* \brief Writes in a file (according to the requested format)
return;
void *voidArea;
- // voidArea = tag->GetVoidArea();
- // to go on compiling
+ // voidArea = tag->GetVoidArea(); // to go on compiling
if (voidArea != NULL)
{ // there is a 'non string' LUT, overlay, etc
fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
// 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, "\\");
+ Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
guint16 val_uint16 = atoi(tokens[i].c_str());
{
std::vector<std::string> tokens;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (tag->GetValue(), tokens, "\\");
+ Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
guint32 val_uint32 = atoi(tokens[i].c_str());
tokens.clear();
return;
}
- fwrite (tag->GetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value
+ fwrite (((gdcmValEntry *)tag)->GetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value
}
/**
// bytes. When this is not the case, pad with an additional byte:
if(length%2==1)
{
-// tag->SetValue(tag->GetValue()+"\0");
-// to go on compiling
+// tag->SetValue(tag->GetValue()+"\0"); // to go on compiling
tag->SetLength(tag->GetReadLength()+1);
}
*/
bool gdcmDocument::WriteEntries(FILE *_fp,FileType type)
-{
+{
+
+// FIXME : explore recursively the whole structure...
+
/// \todo (?) check write failures (after *each* fwrite)
- for (ListTag::iterator tag2=listEntries.begin();
- tag2 != listEntries.end();
- ++tag2)
+ for (TagDocEntryHT::iterator tag2=tagHT.begin();
+ tag2 != tagHT.end();
+ ++tag2)
{
if ( type == gdcmACR ){
- if ((*tag2)->GetGroup() < 0x0008)
+ if ((*tag2).second->GetGroup() < 0x0008)
// Ignore pure DICOM V3 groups
continue;
- if ((*tag2)->GetElement() %2)
+ if ((*tag2).second->GetElement() %2)
// Ignore the "shadow" groups
continue;
- if ((*tag2)->GetVR() == "SQ" ) // ignore Sequences
+ if ((*tag2).second->GetVR() == "SQ" ) // ignore Sequences
continue;
- if ((*tag2)->GetSQDepthLevel() != 0) // Not only ignore the SQ element
+ if ((*tag2).second->GetSQDepthLevel() != 0) // Not only ignore the SQ element
continue;
}
- if (! WriteEntry(*tag2,_fp,type) )
+ if (! WriteEntry((*tag2).second,_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 (TagDocEntryHT::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
//-----------------------------------------------------------------------------
// Private
-
-
/**
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
* @return false if file is not ACR-NEMA / PAPYRUS / DICOM
gdcmSeqEntry *sq;
string vr;
long l;
- cout << hex << "offset " << offset
- << " l_max "<< l_max
- << " ftell a l'entree " << ftell(fp)
- << endl;
+ int depth;
+
+ depth = set->GetDepthLevel();
while (true) {
+
+ if ( !delim_mode && ftell(fp)-offset >= l_max) {
+ break;
+ }
NewDocEntry = ReadNextDocEntry( );
if (!NewDocEntry)
break;
-
- std::cout << hex
- << " gr "
- << NewDocEntry->GetGroup()
- << " el "
- << NewDocEntry->GetElement()
- << " vr "
- << NewDocEntry->GetVR()
- << " lgt "
- << NewDocEntry->GetReadLength()
- << " off "
- << 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 == "SH" || vr == "ST" || vr == "DS" ||
vr == "SL" || vr == "SS" || vr == "UL" || vr == "US"
) {
// --- ValEntry
vl= new gdcmValEntry(NewDocEntry->GetDictEntry());
- vl->Copy(NewDocEntry);
- set->AddEntry(vl);
+ vl->Copy(NewDocEntry);
+ vl->SetDepthLevel(depth),
+ set->AddEntry(vl);
LoadDocEntry(vl);
- std::cout << "value [" << vl->GetValue() << "]" << std::endl;
if (/*!delim_mode && */vl->isItemDelimitor())
break;
- cout << hex
- << " l_max = "<< l_max
- << " offset = " << offset
- << " ftell(fp) = " << ftell(fp)
- << endl;
- if ( !delim_mode && ftell(fp)-offset >= l_max)
- break;
+ if ( !delim_mode && ftell(fp)-offset >= l_max) {
+ break;
+ }
} else { // BinEntry
// Hope the following VR *do* correspond to a BinEntry
bn = new gdcmBinEntry(NewDocEntry->GetDictEntry());
bn->Copy(NewDocEntry);
+ set->AddEntry(bn);
LoadDocEntry(bn);
- std::cout << "value [" << "Bin Entry, in voidArea" << "]" << std::endl;
}
-
- SkipToNextDocEntry(NewDocEntry); // to be sure we are at the beginning
- l = NewDocEntry->GetFullLength();
-
+ if (NewDocEntry->GetGroup() == 0x7fe0 &&
+ NewDocEntry->GetElement() == 0x0010 ) {
+ if (NewDocEntry->GetLength()==0xffffffff)
+ // Broke US.3405.1.dcm
+
+ Parse7FE0(); // to skip the pixels
+ // (multipart JPEG/RLE are trouble makers)
+ } else {
+ SkipToNextDocEntry(NewDocEntry); // to be sure we are at the beginning
+ l = NewDocEntry->GetFullLength();
+ }
} else { // VR = "SQ"
-
- 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());
+
+ l=NewDocEntry->GetReadLength();
+ if (l != 0) // don't mess the delim_mode for zero-length sequence
+ if (l == 0xffffffff)
+ delim_mode = true;
+ else
+ delim_mode = false;
+ // no other way to create it ...
+ sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry(),set->GetDepthLevel());
sq->Copy(NewDocEntry);
sq->SetDelimitorMode(delim_mode);
+ sq->SetDepthLevel(depth);
- if (l != 0) { // Don't try to parse zero-length sequences
- long lgt = ParseSQ((gdcmDocEntrySet *)sq,
- //NewDocEntry->GetOffset(),
- offset, // marche pour DICOMDIR, plante sur 3...dcm
+ if (l != 0) { // Don't try to parse zero-length sequences
+
+ long lgt = ParseSQ( sq,
+ NewDocEntry->GetOffset(),
l, delim_mode);
- }
+ }
// FIXME : on en fait quoi, de lgt ?
set->AddEntry(sq);
- cout << " l_max = " << l_max
- << " offset = " << offset
- << "ftell(fp) = " << ftell(fp)
- << endl;
- if ( !delim_mode && ftell(fp)-offset >= l_max)
+ 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) {
-
- cout << "=================== gdcmDocument::ParseSQ on entre ds une Sequence"
- << hex
- << " offset " << offset
- << " l_max " << l_max
- << " delim_mode " << delim_mode
- <<endl;
+long gdcmDocument::ParseSQ(gdcmSeqEntry *set, long offset, long l_max, bool delim_mode) {
int SQItemNumber = 0;
gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
gdcmSQItem *itemSQ;
bool dlm_mod;
int lgr, l, lgth;
-
+ int depth = set->GetDepthLevel();
while (true) {
- std::cout << " ===== gdcmDocument::ParseSQ on itere "
- << "sur les SQ Items : num "
- << SQItemNumber << std::endl;
- NewDocEntry = ReadNextDocEntry();
-cout << "=============================== isSequenceDelimitor "
- << NewDocEntry->isSequenceDelimitor()
- << endl;
+ NewDocEntry = ReadNextDocEntry();
if(delim_mode) {
if (NewDocEntry->isSequenceDelimitor()) {
- cout << " SequenceDelimitationItem found" << endl;
- // add the Sequence Delimitor // TODO : find the trick to put it proprerly !
- // ((gdcmSeqEntry *)set)->SetSequenceDelimitationItem(NewDocEntry);
+ //add the Sequence Delimitor // TODO : find the trick to put it properly !
+ set->SetSequenceDelimitationItem(NewDocEntry);
break;
}
}
if (!delim_mode && (ftell(fp)-offset) >= l_max) {
- cout << hex
- << " offset " << offset
- << " l_max " << l_max
- << " ftell " << ftell(fp)
- << endl;
- cout << "depasse ou atteint : on sort " << endl;
break;
- }
- itemSQ = new gdcmSQItem();
+ }
+ itemSQ = new gdcmSQItem(set->GetDepthLevel());
itemSQ->AddEntry(NewDocEntry); // no value, no voidArea. Think of it while printing !
l= NewDocEntry->GetReadLength();
- cout << "NewDocEntry->GetReadLength() " << l << endl;
+
if (l ==0xffffffff)
dlm_mod = true;
else
dlm_mod=false;
-cout << "================================ appel ParseDES :dlm_mod = " << dlm_mod <<endl;
+
lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod);
- ((gdcmSeqEntry *)set)->AddEntry(itemSQ);
-cout << "================================ sortie ParseDES " << endl;
- SQItemNumber ++;
+
+ set->AddEntry(itemSQ);
+ SQItemNumber ++; // a voir
+ if (!delim_mode && (ftell(fp)-offset) >= l_max) {
+ break;
+ }
}
- //Update(lgth);
lgth = ftell(fp) - offset;
- cout << "=============== lgr Sequence :" << lgth <<endl;
return(lgth);
}
-
-/**
- * \brief Parses the header of the file and load element values.
- * @return false if file is not ACR-NEMA / PAPYRUS / DICOM
- */
-
-/* =======================================================================
-// Replaced by ParseSQ
-
-bool gdcmDocument::LoadHeaderEntries(bool exception_on_error) throw(gdcmFormatError) {
- (void)exception_on_error;
- rewind(fp);
- if (!CheckSwap())
- return false;
-
- gdcmDocEntry *newDocEntry = (gdcmDocEntry *)0;
- while ( (newDocEntry = ReadNextDocEntry()) ) {
- SkipDocEntry(newDocEntry);
- if ( (ignoreShadow==0) || (newDocEntry->GetGroup()%2) == 0) {
- AddEntry(newDocEntry);
- }
- }
- rewind(fp);
- // Be carefull : merging this two loops may cause troubles ...
- for (ListTag::iterator i = GetListEntry().begin();
- i != GetListEntry().end();
- ++i)
- {
- LoadDocEntry(*i);
- }
- rewind(fp);
-
- // Load 'non string' values
-
-
- // --------------------------------------------------------------
- // 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 = ACR_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 gdcmDocument::SetMaxSizeLoadEntry()
// 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() << ")";
((gdcmValEntry *)Entry)->SetValue(s.str());
+ // to be sure we are at the end of the value ...
+ fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET);
+
return;
}
{
if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) )
{
- std::string val=Entry->GetValue();
+ std::string val=((gdcmValEntry *)Entry)->GetValue();
std::string vr=Entry->GetVR();
guint32 length = Entry->GetLength();
std::ostringstream s;
return(s.str());
}
- return(Entry->GetValue());
+ return(((gdcmValEntry *)Entry)->GetValue());
}
/**
guint16 NewInt16;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (Entry->GetValue(), tokens, "\\");
+ Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
NewInt16 = atoi(tokens[i].c_str());
guint32 NewInt32;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (Entry->GetValue(), tokens, "\\");
+ Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
NewInt32 = atoi(tokens[i].c_str());
return(s.str());
}
- return(Entry->GetValue());
+ return(((gdcmValEntry *)Entry)->GetValue());
}
/**
}
+/**
+ * \ingroup gdcmDocument
+ * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files
+ * \ No other way so 'skip' the Data
+ *
+ */
+void gdcmDocument::Parse7FE0 (void) {
+
+ gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
+ if ( !Element )
+ return;
+
+ std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
+ if (Transfer == UI1_2_840_10008_1_2 )
+ return;
+ if ( Transfer == UI1_2_840_10008_1_2_1 )
+ return;
+ if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier !
+ return;
+ if ( Transfer == UI1_2_840_10008_1_2_1_99 )
+ return;
+
+ int nb;
+ std::string str_nb=GetEntryByNumber(0x0028,0x0100);
+ if (str_nb == GDCM_UNFOUND ) {
+ nb = 16;
+ } else {
+ nb = atoi(str_nb.c_str() );
+ if (nb == 12) nb =16;
+ }
+
+ guint16 ItemTagGr,ItemTagEl;
+ int ln;
+ long ftellRes;
+
+ // -------------------- for Parsing : Position on begining of Jpeg/RLE Pixels
+
+ if ( Transfer != UI1_1_2_840_10008_1_2_5 ) { // !RLELossLessTransferSyntax
+ // JPEG Image
+ ftellRes=ftell(fp);
+ fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
+ (unsigned)ftellRes,ItemTagGr,ItemTagEl );
+ ftellRes=ftell(fp);
+ fread(&ln,4,1,fp);
+ if(GetSwapCode())
+ ln=SwapLong(ln); // Basic Offset Table Item Length
+ printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n",
+ (unsigned)ftellRes,ln,ln);
+ if (ln != 0) {
+ // What is it used for ??
+ char * BasicOffsetTableItemValue= new char[ln+1];
+ fread(BasicOffsetTableItemValue,ln,1,fp);
+ guint32 a;
+ for (int i=0;i<ln;i+=4){
+ a=str2num(&BasicOffsetTableItemValue[i],guint32);
+ printf(" x(%08x) %d\n",a,a);
+ }
+ }
+
+ ftellRes=ftell(fp);
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+ (unsigned)ftellRes,ItemTagGr,ItemTagEl );
+
+ while ( ( ItemTagGr==0xfffe) && (ItemTagEl!=0xe0dd) ) { // Parse fragments
+
+ ftellRes=ftell(fp);
+ fread(&ln,4,1,fp);
+ if(GetSwapCode())
+ ln=SwapLong(ln); // length
+ printf(" at %x : fragment length %d x(%08x)\n",
+ (unsigned)ftellRes, ln,ln);
+
+ // ------------------------
+ fseek(fp,ln,SEEK_CUR); // skipping (not reading) fragment pixels
+ // ------------------------
+
+ ftellRes=ftell(fp);
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+ (unsigned)ftellRes,ItemTagGr,ItemTagEl );
+ }
+
+ } else {
+
+ // RLE Image
+ long RleSegmentLength[15],fragmentLength;
+ guint32 nbRleSegments;
+ guint32 RleSegmentOffsetTable[15];
+ ftellRes=ftell(fp);
+ // Basic Offset Table with Item Value
+ // Item Tag
+ fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
+ (unsigned)ftellRes,ItemTagGr,ItemTagEl );
+ // Item Length
+ ftellRes=ftell(fp);
+ fread(&ln,4,1,fp);
+ if(GetSwapCode())
+ ln=SwapLong(ln); // Basic Offset Table Item Length
+ printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n",
+ (unsigned)ftellRes,ln,ln);
+ if (ln != 0) {
+ // What is it used for ??
+ char * BasicOffsetTableItemValue= new char[ln+1];
+ fread(BasicOffsetTableItemValue,ln,1,fp);
+ guint32 a;
+ for (int i=0;i<ln;i+=4){
+ a=str2num(&BasicOffsetTableItemValue[i],guint32);
+ printf(" x(%08x) %d\n",a,a);
+ }
+ }
+
+ ftellRes=ftell(fp);
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+ (unsigned)ftellRes,ItemTagGr,ItemTagEl );
+
+ // while 'Sequence Delimiter Item' (fffe,e0dd) not found
+ while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
+ // Parse fragments of the current Fragment (Frame)
+ ftellRes=ftell(fp);
+ fread(&fragmentLength,4,1,fp);
+ if(GetSwapCode())
+ fragmentLength=SwapLong(fragmentLength); // length
+ printf(" at %x : 'fragment' length %d x(%08x)\n",
+ (unsigned)ftellRes, (unsigned)fragmentLength,(unsigned)fragmentLength);
+
+ //------------------ scanning (not reading) fragment pixels
+
+ fread(&nbRleSegments,4,1,fp); // Reading : Number of RLE Segments
+ if(GetSwapCode())
+ nbRleSegments=SwapLong(nbRleSegments);
+ printf(" Nb of RLE Segments : %d\n",nbRleSegments);
+
+ for(int k=1; k<=15; k++) { // Reading RLE Segments Offset Table
+ ftellRes=ftell(fp);
+ fread(&RleSegmentOffsetTable[k],4,1,fp);
+ if(GetSwapCode())
+ RleSegmentOffsetTable[k]=SwapLong(RleSegmentOffsetTable[k]);
+ printf(" at : %x Offset Segment %d : %d (%x)\n",
+ (unsigned)ftellRes,k,RleSegmentOffsetTable[k],
+ RleSegmentOffsetTable[k]);
+ }
+
+ if (nbRleSegments>1) { // skipping (not reading) RLE Segments
+ for(unsigned int k=1; k<=nbRleSegments-1; k++) {
+ RleSegmentLength[k]= RleSegmentOffsetTable[k+1]
+ - RleSegmentOffsetTable[k];
+ ftellRes=ftell(fp);
+ printf (" Segment %d : Length = %d x(%x) Start at %x\n",
+ k,(unsigned)RleSegmentLength[k],(unsigned)RleSegmentLength[k], (unsigned)ftellRes);
+ fseek(fp,RleSegmentLength[k],SEEK_CUR);
+ }
+ }
+ RleSegmentLength[nbRleSegments]= fragmentLength
+ - RleSegmentOffsetTable[nbRleSegments];
+ ftellRes=ftell(fp);
+ printf (" Segment %d : Length = %d x(%x) Start at %x\n",
+ nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments],
+ (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes);
+
+ fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR);
+
+ // ------------------ end of scanning fragment pixels
+
+ ftellRes=ftell(fp);
+ fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
+ fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
+ if(GetSwapCode()) {
+ ItemTagGr=SwapShort(ItemTagGr);
+ ItemTagEl=SwapShort(ItemTagEl);
+ }
+ printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
+ (unsigned)ftellRes,ItemTagGr,ItemTagEl );
+ }
+ }
+ return;
+}
+
+
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff