#include <sstream>
#include "gdcmUtil.h"
-#define LGR_ENTETE_A_LIRE 256 // on ne lit plus que le debut
+#define HEADER_LENGHT_TO_READ 256 // on ne lit plus que le debut
//FIXME: this looks dirty to me...
#define str2num(str, typeNum) *((typeNum *)(str))
void gdcmHeader::Initialise(void) {
if (!gdcmHeader::dicom_vr)
InitVRDict();
- bool grPixelTrouve = false;
PixelPosition = (size_t)0;
PixelsTrouves = false;
RefPubDict = gdcmHeader::Dicts->GetDefaultPublicDict();
int lgrLue;
char * entCur;
- char deb[LGR_ENTETE_A_LIRE];
+ char deb[HEADER_LENGHT_TO_READ];
- // On teste le processeur
- if (x==ntohs(x)) {
+ // 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 {
+ else
net2host = false;
- }
- // On commence par verifier si c'est du DICOM 'actuel'
- // -------------
- lgrLue = fread(deb,1,LGR_ENTETE_A_LIRE, fp);
+ // The easiest case is the one of a DICOM header, since it possesses a
+ // file preamble where it suffice to look for the sting "DICM".
+ lgrLue = fread(deb, 1, HEADER_LENGHT_TO_READ, fp);
- entCur = deb+128;
+ entCur = deb + 128;
if(memcmp(entCur, "DICM", (size_t)4) == 0) {
filetype = TrueDicom;
dbg.Verbose(0, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
}
if(filetype == TrueDicom) {
- // on saute le File Preamble (souvent a ZERO) : 128 Octets
- // + le DICM (4), et le (0002, 0000) soit 4 (136 = 128 + 4 + 4)
- entCur = deb+136;
+ // Next, determine the value representation (VR). Let's skip to the
+ // first element (0002, 0000) and check there if we find "UL", 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),
+ // i.e. a total of 136 bytes.
+ entCur = deb + 136;
if(memcmp(entCur, "UL", (size_t)2) == 0) {
- // les 2 premiers octets de la lgr peuvent valoir UL --> Explicit VR
filetype = ExplicitVR;
dbg.Verbose(0, "gdcmHeader::CheckSwap:",
"explicit Value Representation");
dbg.Verbose(0, "gdcmHeader::CheckSwap:",
"not an explicit Value Representation");
}
-
- if (net2host) { // HostByteOrder is different from NetworkByteOrder
- sw = 0; // on est sur PC ou DEC --> LITTLE-ENDIAN -> Rien a faire
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "HostByteOrder = NetworkByteOrder");
- } else { /* on est sur une Sun ou une SGI */
+
+ if (net2host) {
sw = 4321;
dbg.Verbose(0, "gdcmHeader::CheckSwap:",
"HostByteOrder != NetworkByteOrder");
+ } else {
+ sw = 0;
+ dbg.Verbose(0, "gdcmHeader::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); //On se positionne sur le debut des info
- offsetCourant=132;
+ fseek (fp, 132L, SEEK_SET);
+ return;
} // End of TrueDicom
- // Pas du TrueDicom : permiere hypothese c'est de l'ACR 'propre', auquel
- // cas la lgr du premier element du groupe est FORCEMENT 4
- entCur=deb + 4;
- s=str2num(entCur,int);
+ // 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).
+ 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;
+ s = str2num(entCur, int);
switch (s) {
case 0x00040000 :
sw=3412;
filetype = ACR;
- break;
+ return;
case 0x04000000 :
sw=4321;
filetype = ACR;
- break;
+ return;
case 0x00000400 :
sw=2143;
- filetype = ACR;
- break;
+ filetype = ACR;
+ return;
case 0x00000004 :
sw=0;
filetype = ACR;
- break;
+ return;
default :
- sw = -1;
dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "unfound swap info (time to raise bets)");
- }
- if(sw!=-1) {
- rewind(fp); // les info commencent au debut
- offsetCourant=0;
- return;
+ "ACE/NEMA unfound swap info (time to raise bets)");
}
- // Deuxieme hypothese : c'est de l'ACR 'pas propre' i.e. il manque
- // la lgr du groupe
+ // 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 assume this file
+ // happens to be 'dirty' ACR/NEMA, i.e. the length of the group it
+ // not present. Then the only info we have is the net2host one.
+ //FIXME Si c'est du RAW, ca degagera + tard
- // On n'a pas trouve l'info de swap.
- // Si c'est du VRAI ACR NEMA et
- // * si on est sur une DEC ou un PC alors swap=0,
- // * si on est sur SUN ou SGI, alors swap=4321
- // Si c'est du RAW, ca degagera + tard
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "time for wild guesses...");
-
- if (x!=ntohs(x)) // HostByteOrder is different from NetworkByteOrder
- // on est sur PC ou DEC --> LITTLE-ENDIAN -> Rien a faire
+ if (! net2host )
sw = 0;
else
- // on est sur Sun ou SGI
sw = 4321;
- rewind(fp); // les info commencent au debut
- offsetCourant=0;
- return;
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Pour les fichiers non TrueDicom, si le recognition
- * code (0008,0010) s'avere etre "ACR_LIBIDO", alors
- * valide la reconnaissance du fichier en positionnant
- * filetype.
- */
-void gdcmHeader::setAcrLibido() {
- string RecCode;
-
- if ( filetype != TrueDicom) {
- printf("_setAcrLibido expects a presumably ACR file\n");
- // Recognition Code --> n'existe plus en DICOM V3 ...
- RecCode = GetPubElValByNumber(0x0008, 0x0010);
- // FIXME NOW
- if (RecCode == "ACRNEMA_LIBIDO" ||
- RecCode == "CANRME_AILIBOD" )
- filetype = ACR_LIBIDO;
- else
- filetype = ACR;
- }
return;
}
* @return longueur retenue pour le champ
*/
-long int gdcmHeader::RecupLgr( ElValue *pleCourant, int *skippedLength) {
- guint32 l_gr;
- unsigned short int l_gr_2;
- int i;
- char VR[5];
+void gdcmHeader::FindVR( ElValue *pleCourant) {
+ char VR[3];
int lgrLue;
+ long PositionOnEntry = ftell(fp);
- // FIX ME
- // ATTENTION : nbCode correspond au nombre d'elements dans la table
- // de type DICOM_VR. A nettoyer.
- //
- int nbCode=26;
-
- if (filetype == ExplicitVR) {
- lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
- VR[2]=0;
-
- // 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.
-
- // FIXME There should be only one occurence returned. Avoid the
- // first extraction by calling proper method.
- VRAtr FoundVR = dicom_vr->find(string(VR))->first;
- if (FoundVR.empty()) {
- pleCourant->SetVR(FoundVR);
- } else {
-
- // On est mal : implicit VR repere
- // mais ce n'est pas un code connu ...
- // On reconstitue la longueur
-
- dbg.Verbose(1, "gdcmHeader::RecupLgr:",
- "Explicit VR, but no known code");
- memcpy(&l_gr, VR,(size_t)2);
- lgrLue=fread ( ((char*)&l_gr)+2, (size_t)2, (size_t)1, fp);
- l_gr = SwapLong((guint32)l_gr);
- pleCourant->SetLgrLue(l_gr);
- if ( (int)l_gr == -1)
- l_gr=0;
-
- *skippedLength = 4;
- return(l_gr);
- }
+ if (filetype != ExplicitVR)
+ return;
+
+ lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
+ VR[2]=0;
- // On repart dans la sequence 'sensee'
- if ( (!memcmp( VR,"OB",(size_t)2 )) ||
- (!memcmp( VR,"OW",(size_t)2 )) ||
- (!memcmp( VR,"SQ",(size_t)2 )) ||
- (!memcmp( VR,"UN",(size_t)2 )) ) {
+ // 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.
+
+ // FIXME There should be only one occurence returned. Avoid the
+ // first extraction by calling proper method.
+ VRAtr FoundVR = dicom_vr->find(string(VR))->first;
+ if ( ! FoundVR.empty()) {
+ pleCourant->SetVR(FoundVR);
+ return;
+ }
+
+ // We thought this was explicit VR, but we end up with an
+ // implicit VR tag. Let's backtrack.
+ pleCourant->SetVR("Implicit");
+ fseek(fp, PositionOnEntry, SEEK_SET);
+}
+
+void gdcmHeader::RecupLgr( ElValue *pleCourant) {
+ int lgrLue;
+ guint32 l_gr;
+ unsigned short int l_gr_2;
+
+ string vr = pleCourant->GetVR();
+
+ if ( (filetype == ExplicitVR) && (vr != "Implicit") ) {
+ if ( ( vr == "OB" ) || ( vr == "OW" )
+ || ( vr == "SQ" ) || ( vr == "UN" ) ) {
- // les 2 octets suivants sont reserves: on les saute
+ // The following two bytes are reserved, so we skip them,
+ // and we proceed on reading the length on 4 bytes.
fseek(fp, 2L,SEEK_CUR);
-
- //on lit la lgr sur QUATRE octets
lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp);
l_gr = SwapLong((guint32)l_gr);
- *skippedLength = 8;
-
+
} else {
//on lit la lgr sur DEUX octets
lgrLue=fread (&l_gr_2, (size_t)2,(size_t)1, fp);
- if(sw) l_gr_2 = SwapShort((unsigned short)l_gr_2);
-
- pleCourant->SetLgrLue(l_gr_2);
+ l_gr_2 = SwapShort((unsigned short)l_gr_2);
if ( l_gr_2 == 0xffff) {
l_gr = 0;
} else {
l_gr = l_gr_2;
}
- *skippedLength = 4;
}
} else {
// Explicit VR = 0
//on lit la lgr sur QUATRE octets
-
lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp);
-
l_gr= SwapLong((long)l_gr);
- *skippedLength = 4;
}
-
- pleCourant->SetLgrLue(l_gr);
-
+
// Traitement des curiosites sur la longueur
-
if ( (int)l_gr == 0xffffffff)
l_gr=0;
- if(!memcmp( VR,"SQ",(size_t)2 )) { // ca annonce une SEQUENCE d'items ?!
- l_gr=0; // on lira donc les items de la sequence
- }
-
- return(l_gr);
+ pleCourant->SetLgrElem(l_gr);
}
/**
unsigned short g;
unsigned short n;
guint32 l;
- long int posFich;
- int skL;
size_t lgrLue;
- //CLEANME DICOM_ELEMENTS *t;
ElValue * nouvDcmElem;
- // FIXME la probabilte pour depasser sans s'en rendre compte
- // est grande avec le test d'egalite' suivant !
- if(offsetCourant == taille_fich) { // On a atteint la fin du fichier
- dbg.Verbose(1, "ReadNextElement: EOF reached");
- return(NULL);
- }
-
// ------------------------- Lecture Num group : g
lgrLue=fread (&g, (size_t)2,(size_t)1, fp);
// ------------------------- Lecture longueur element : l
- l = RecupLgr(nouvDcmElem, &skL);
-
+ FindVR(nouvDcmElem);
+ RecupLgr(nouvDcmElem);
+ nouvDcmElem->SetOffset(ftell(fp));
+ l = nouvDcmElem->GetLgrElem();
+
+ //FIXMEif(!memcmp( VR,"SQ",(size_t)2 )) { // ca annonce une SEQUENCE d'items ?!
+ //FIXME l_gr=0; // on lira donc les items de la sequence
+ //FIXME}
+ //FIXMEreturn(l_gr);
+
+
if(g==0xfffe) l=0; // pour sauter les indicateurs de 'SQ'
- nouvDcmElem->LgrElem=l;
// ------------------------- Lecture Valeur element
// pas etre charge's !!!! Voir TODO.
lgrLue=fread (NewValue, (size_t)l,(size_t)1, fp);
- offsetCourant += 2 + 2 + skL; // gr + num + lgr
- nouvDcmElem->Offset = offsetCourant;
- offsetCourant += l; // debut elem suivant
// ------------------------- Doit-on le Swapper ?
} /* fin sw */
}
nouvDcmElem->value = NewValue;
- // CLEAN ME: simply trash the following line and postpone the process !
- // SetAsidePixelData(nouvDcmElem);
return nouvDcmElem;
}
// 1/ * find if the "Pixel Data" tag exists.
// * if it does not exist, look for the "Pixel Location" tag.
// 2/ look at the proper tag ("Pixel Data" or "Pixel Location" when
- // it exists) what the offset it.
+ // it exists) what the offset is.
guint16 g;
guint16 n;
g = elem->GetGroup();
ElValue * newElValue = (ElValue *)0;
rewind(fp);
- fseek(fp, 0L, SEEK_END);
- /*
- * obtains the current value of the file-position
- * indicator for the stream pointed to by stream
- */
- taille_fich = ftell(fp);
rewind(fp);
CheckSwap();
while ( (newElValue = ReadNextElement()) ) {
PubElVals.Add(newElValue);
}
- setAcrLibido();
}
int gdcmHeader::PrintPubElVal(ostream & os) {
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