*/
void gdcmParser::PrintEntry(std::ostream & os) {
std::ostringstream s;
-
+
for (ListTag::iterator i = listEntries.begin();
- i != listEntries.end();
- ++i)
+ i != listEntries.end();
+ ++i)
{
- (*i)->SetPrintLevel(printLevel);
- (*i)->Print(os);
+ (*i)->SetPrintLevel(printLevel);
+ (*i)->Print(os);
}
os<<s.str();
}
// TODO : move the following lines (and a lot of others, to be written)
// to a future function CheckAndCorrectHeader
- // Question :
- // Comment pourrait-on savoir si le DcmHeader vient d'un fichier DicomV3 ou non
- // (FileType est un champ de gdcmParser ...)
- // WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA
- // no way
- // a moins de se livrer a un tres complique ajout des champs manquants.
- // faire un CheckAndCorrectHeader (?)
-
+ // Question :
+ // Comment pourrait-on savoir si le DcmHeader vient d'un fichier
+ // DicomV3 ou non (FileType est un champ de gdcmParser ...)
+ // WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA
+ // no way
+ // a moins de se livrer a un tres complique ajout des champs manquants.
+ // faire un CheckAndCorrectHeader (?)
if (type == ImplicitVR)
{
gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber(
std::string Value,
guint16 Group,
- guint16 Elem ){
+ guint16 Elem ){
gdcmHeaderEntry* a;
- a = GetHeaderEntryByNumber( Group, Elem);
+ a = GetHeaderEntryByNumber( Group, Elem);
if (a == NULL) {
gdcmHeaderEntry *a =NewHeaderEntryByNumber(Group, Elem);
if (a == NULL)
AddHeaderEntry(nvHeaderEntry);
- std::string v = Value;
+ std::string v = Value;
SetEntryByNumber(v, Group, Elem);
return(nvHeaderEntry);
}
*/
bool gdcmParser::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem )
{
- std::string v = Value;
+ std::string v = Value;
SetEntryByNumber(v, Group, Elem);
return true;
}
* @return number of occurences
*/
int gdcmParser::CheckIfEntryExistByNumber(guint16 group, guint16 element ) {
- std::string key = gdcmDictEntry::TranslateToKey(group, element );
- return (tagHT.count(key));
+ std::string key = gdcmDictEntry::TranslateToKey(group, element );
+ return (tagHT.count(key));
}
/**
return GDCM_UNFOUND;
gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(),
- dictEntry->GetElement());
+ dictEntry->GetElement());
return elem->GetVR();
}
bool gdcmParser::SetEntryByName(std::string content,std::string tagName) {
gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
- return false;
+ return false;
return(SetEntryByNumber(content,dictEntry->GetGroup(),
dictEntry->GetElement()));
else if( (vr == "UL") || (vr == "SL") )
lgr = 4;
else
- lgr = l;
+ lgr = l;
a->SetLength(lgr);
return true;
-}
+}
/**
* \ingroup gdcmParser
*/
bool gdcmParser::SetEntryLengthByNumber(guint32 l,
guint16 group,
- guint16 element)
+ 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 ;
+ ( ((tagHT.equal_range(key)).first)->second )->SetLength(l);
+
+ return true ;
}
/**
*/
size_t gdcmParser::GetEntryOffsetByNumber(guint16 Group, guint16 Elem)
{
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
+ gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
if (!Entry)
{
dbg.Verbose(1, "gdcmParser::GetHeaderEntryByNumber",
*/
void * gdcmParser::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem)
{
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
+ gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
if (!Entry)
{
dbg.Verbose(1, "gdcmParser::GetHeaderEntryByNumber",
int l=Element->GetLength();
void * a = malloc(l);
if(!a)
- return NULL;
+ return NULL;
SetEntryVoidAreaByNumber(a, Group, Elem);
// TODO check the result
size_t l2 = fread(a, 1, l ,fp);
if(l != l2)
{
- free(a);
- return NULL;
+ free(a);
+ return NULL;
}
return a;
*/
bool gdcmParser::SetEntryVoidAreaByNumber(void * area,
guint16 group,
- guint16 element)
+ guint16 element)
{
TagKey key = gdcmDictEntry::TranslateToKey(group, element);
if ( ! tagHT.count(key))
return false;
- ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area);
+ ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area);
return true;
}
vr = elem->GetVR();
sprintf(trash, "%04x", gr);
- key = trash; // generate 'group tag'
+ 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 ( 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
+ {
+ groupHt[key] = 0; // initialize group length
}
else
{
// FIXME: g++ -Wall -Wstrict-prototypes reports on following line:
// warning: unsigned int format, different type arg
sscanf(g->first.c_str(),"%x",&gr_bid);
- tk = g->first + "|0000"; // generate the element full tag
+ 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
+ AddHeaderEntry(elemZ); // create it
}
else
{
int compte =0;
itsTimeToWritePixels = false;
- gr = tag->GetGroup();
- el = tag->GetElement();
- lgr = tag->GetReadLength();
- val = tag->GetValue().c_str();
- vr = tag->GetVR();
- voidArea = tag->GetVoidArea();
+ gr = tag->GetGroup();
+ el = tag->GetElement();
+ lgr = tag->GetReadLength();
+ val = tag->GetValue().c_str();
+ vr = tag->GetVR();
+ voidArea = tag->GetVoidArea();
- // === Deal with the length
- // --------------------
- if((tag->GetLength())%2==1)
- {
- tag->SetValue(tag->GetValue()+"\0");
- tag->SetLength(tag->GetReadLength()+1);
- }
+ // === Deal with the length
+ // --------------------
+ if((tag->GetLength())%2==1)
+ {
+ tag->SetValue(tag->GetValue()+"\0");
+ tag->SetLength(tag->GetReadLength()+1);
+ }
- if ( type == ACR )
- {
- if (gr < 0x0008) return; // ignore pure DICOM V3 groups
- if (gr %2) return; // ignore shadow groups
- if (vr == "SQ" ) return; // ignore Sequences
- // TODO : find a trick to *skip* the SeQuences !
- // Not only ignore the SQ element
- if (gr == 0xfffe ) return; // ignore delimiters
- }
+ if ( type == ACR )
+ {
+ if (gr < 0x0008) return; // ignore pure DICOM V3 groups
+ if (gr %2) return; // ignore shadow groups
+ if (vr == "SQ" ) return; // ignore Sequences
+ // TODO : find a trick to *skip* the SeQuences !
+ // Not only ignore the SQ element
+ if (gr == 0xfffe ) return; // ignore delimiters
+ }
- fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group
- fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
+ fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group
+ fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element
- if ( (type == ExplicitVR) || (type == DICOMDIR) ) {
- // EXPLICIT VR
- guint16 z=0, shortLgr;
-
- if (gr == 0xfffe) { // NO Value Representation for 'delimiters'
- // no length : write ffffffff
-
- // special patch to make some MR PHILIPS
- if (el == 0x0000) return; // images e-film readable // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm
- // from Hospital Guy de Chauliac,
- // Montpellier
- // we just ignore spurious fffe|0000 tag !
-
- fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp);
- return; // NO value for 'delimiters'
- }
-
- shortLgr=lgr;
- if (vr == "unkn") { // Unknown was 'written'
- // deal with Little Endian
- fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
+ if ( (type == ExplicitVR) || (type == DICOMDIR) ) {
+ // EXPLICIT VR
+ guint16 z=0, shortLgr;
+
+ if (gr == 0xfffe) { // NO Value Representation for 'delimiters'
+ // no length : write ffffffff
+
+ // special patch to make some MR PHILIPS images e-film readable
+ // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm
+ // from Hospital Guy de Chauliac, Montpellier
+ // we just ignore spurious fffe|0000 tag !
+ if (el == 0x0000) return;
+
+ fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp);
+ return; // NO value for 'delimiters'
+ }
+
+ 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 (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);
- }
+ fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
}
- }
- else // IMPLICIT VR
- {
- fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
}
+ }
+ else // IMPLICIT VR
+ {
+ fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
+ }
- // === Deal with the value
- // -------------------
- if (vr == "SQ") return; // no "value" to write for the SEQuences
- if (gr == 0xfffe)return; // no "value" to write for the delimiters
+ // === Deal with the value
+ // -------------------
+ if (vr == "SQ") return; // no "value" to write for the SEQuences
+ if (gr == 0xfffe)return; // no "value" to write for the delimiters
- if (voidArea != NULL)
- { // there is a 'non string' LUT, overlay, etc
- fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
- return;
- }
+ 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")
+ if (vr == "US" || vr == "SS")
+ {
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (tag->GetValue(), tokens, "\\");
+ for (unsigned int i=0; i<tokens.size();i++)
{
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (tag->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- val_uint16 = atoi(tokens[i].c_str());
- ptr = &val_uint16;
- fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- return;
+ val_uint16 = atoi(tokens[i].c_str());
+ ptr = &val_uint16;
+ fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
}
- if (vr == "UL" || vr == "SL")
+ tokens.clear();
+ return;
+ }
+
+ if (vr == "UL" || vr == "SL")
+ {
+ tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+ Tokenize (tag->GetValue(), tokens, "\\");
+ for (unsigned int i=0; i<tokens.size();i++)
{
- tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (tag->GetValue(), tokens, "\\");
- for (unsigned int i=0; i<tokens.size();i++)
- {
- val_uint32 = atoi(tokens[i].c_str());
- ptr = &val_uint32;
- fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
- }
- tokens.clear();
- return;
- }
+ val_uint32 = atoi(tokens[i].c_str());
+ ptr = &val_uint32;
+ fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
+ }
+ tokens.clear();
+ return;
+ }
- // Pixels are never loaded in the element !
- // we stop writting when Pixel are processed
- // FIX : we loose trailing elements (RAB, right now)
+ // Pixels are never loaded in the element !
+ // we stop writting when Pixel are processed
+ // FIX : we loose trailing elements (RAB, right now)
- if ((gr == GrPixel) && (el == NumPixel) ) {
- compte++;
- if (compte == countGrPixel) {// we passed *all* the GrPixel,NumPixel
- itsTimeToWritePixels = true;
- return;
- }
- }
- fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
+ if ((gr == GrPixel) && (el == NumPixel) ) {
+ compte++;
+ if (compte == countGrPixel) {// we passed *all* the GrPixel,NumPixel
+ itsTimeToWritePixels = true;
+ return;
+ }
+ }
+ fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
}
/**
SkipHeaderEntry(newHeaderEntry);
if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) {
AddHeaderEntry(newHeaderEntry);
- }
+ }
}
return true;
}
// if recognition code tells us we deal with a LibIDO image
// we switch lineNumber and columnNumber
//
- std::string RecCode;
+ std::string RecCode;
RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code
if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
RecCode == "CANRME_AILIBOD1_1." )
// When integer(s) are expected, read and convert the following
// n *(two or four bytes)
- // properly i.e. as integers as opposed to strings.
+ // properly i.e. as integers as opposed to strings.
// Elements with Value Multiplicity > 1
// contain a set of integers (not a single one)
-
+
// Any compacter code suggested (?)
if ( IsHeaderEntryAnInteger(Entry) ) {
guint32 NewInt;
NewInt = ReadInt16();
s << NewInt;
}
- }
+ }
}
else if (vr == "UL" || vr == "SL") {
nbInt = length / 4;
#endif //GDCM_NO_ANSI_STRING_STREAM
Entry->SetValue(s.str());
- return;
+ return;
}
// We need an additional byte for storing \0 that is not on disk
gdcmDictEntry* NewEntry = NewVirtualDictEntry(
Entry->GetGroup(),Entry->GetElement(),
"UL","FIXME","Group Length");
- Entry->SetDictEntry(NewEntry);
+ Entry->SetDictEntry(NewEntry);
}
return(false);
}
void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 FoundLength)
{
Entry->SetReadLength(FoundLength); // will be updated only if a bug is found
-
+
if ( FoundLength == 0xffffffff) {
FoundLength = 0;
}
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
+ FoundLength =0; // ReadLength is unchanged
}
// a SeQuence Element is beginning
{
// *normally, fffe|0000 doesn't exist !
if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm
- // causes extra troubles :-(
+ // causes extra troubles :-(
FoundLength =0;
}
Entry->SetUsableLength(FoundLength);
else
{
std::ostringstream s;
- int filePosition = ftell(fp);
+ int filePosition = ftell(fp);
s << "Erroneous Group Length element length on : (" \
<< std::hex << group << " , " << element
- << ") -before- position x(" << filePosition << ")"
- << "lgt : " << length;
- // These 2 lines commented out : a *very dirty* patch
- // to go on PrintHeader'ing gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
- // have a glance at offset x(8336) ...
- // For *regular* headers, the test is useless..
- // lets's print a warning message and go on,
- // instead of giving up with an error message
-
- //std::cout << s.str().c_str() << std::endl;
-
- // dbg.Error("gdcmParser::IsHeaderEntryAnInteger",
- // s.str().c_str());
+ << ") -before- position x(" << filePosition << ")"
+ << "lgt : " << length;
+ // These 2 lines commented out : a *very dirty* patch
+ // to go on PrintHeader'ing gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
+ // have a glance at offset x(8336) ...
+ // For *regular* headers, the test is useless..
+ // lets's print a warning message and go on,
+ // instead of giving up with an error message
+
+ //std::cout << s.str().c_str() << std::endl;
+ // dbg.Error("gdcmParser::IsHeaderEntryAnInteger",
+ // s.str().c_str());
}
}
if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
// 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 !-
+ // 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*
+ (memcmp(entCur, "OB", (size_t)2) == 0) ||
+ (memcmp(entCur, "UI", (size_t)2) == 0) ||
+ (memcmp(entCur, "CS", (size_t)2) == 0) ) // CS, to remove later
+ // when Write DCM *adds*
// FIXME
// Use gdcmParser::dicom_vr to test all the possibilities
- // instead of just checking for UL, OB and UI !? // group 0000
-
+ // instead of just checking for UL, OB and UI !? group 0000
{
filetype = ExplicitVR;
dbg.Verbose(1, "gdcmParser::CheckSwap:",
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,
case 0x0800 :
sw = 4321;
filetype = ACR;
- return true;
+ return true;
default :
dbg.Verbose(0, "gdcmParser::CheckSwap:",
"ACR/NEMA unfound swap info (Really hopeless !)");
filetype = Unknown;
return false;
}
-
- // Then the only info we have is the net2host one.
- //if (! net2host )
+
+ // Then the only info we have is the net2host one.
+ //if (! net2host )
// sw = 0;
//else
// sw = 4321;
- //return;
+ //return;
}
}
NewEntry = NewHeaderEntryByNumber(g, n);
FindHeaderEntryVR(NewEntry);
FindHeaderEntryLength(NewEntry);
-
+
if (errno == 1) {
// Call it quits
return NULL;
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff