-#include "gdcmlib.h"
-extern "C" {
-#include "glib.h"
-}
+#include "gdcm.h"
#include <stdio.h>
// For nthos:
#ifdef _MSC_VER
#else
#include <netinet/in.h>
#endif
+#include <cctype> // for isalpha
#include <map>
+#include <sstream>
+#include "gdcmUtil.h"
+
+#define HEADER_LENGHT_TO_READ 256 // on ne lit plus que le debut
-#define LGR_ENTETE_A_LIRE 256 // on ne lit plus que le debut
-#define DEBUG 1
+namespace Error {
+ struct FileReadError {
+ FileReadError(FILE* fp, const char* Mesg) {
+ if (feof(fp))
+ dbg.Verbose(1, "EOF encountered :", Mesg);
+ if (ferror(fp))
+ dbg.Verbose(1, "Error on reading :", Mesg);
+ }
+ };
+}
//FIXME: this looks dirty to me...
#define str2num(str, typeNum) *((typeNum *)(str))
VRHT * gdcmHeader::dicom_vr = (VRHT*)0;
+gdcmDictSet* gdcmHeader::Dicts = new gdcmDictSet();
-gdcmHeader::gdcmHeader () {
+void gdcmHeader::Initialise(void) {
if (!gdcmHeader::dicom_vr)
InitVRDict();
- bool grPixelTrouve = false;
- PixelPosition = (size_t)0;
- PixelsTrouves = false;
+ RefPubDict = gdcmHeader::Dicts->GetDefaultPublicDict();
+ RefShaDict = (gdcmDict*)0;
+}
+
+gdcmHeader::gdcmHeader (const char* InFilename) {
+ filename = InFilename;
+ Initialise();
+ fp=fopen(InFilename,"rw");
+ dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename);
+ ParseHeader();
+}
+
+gdcmHeader::~gdcmHeader (void) {
+ fclose(fp);
+ return;
}
void gdcmHeader::InitVRDict (void) {
- if (dicom_vr && DEBUG) {
- printf ("InitVRDict : VR dictionary allready set\n");
+ if (dicom_vr) {
+ dbg.Verbose(0, "gdcmHeader::InitVRDict:", "VR dictionary allready set");
return;
}
VRHT *vr = new VRHT;
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;
- if (DEBUG) printf ("_IdDcmCheckSwap : C est du DICOM actuel \n");
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
} else {
filetype = Unknown;
- if (DEBUG) printf ("_IdDcmCheckSwap : Ce n'est PAS du DICOM actuel\n");
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
}
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;
- if (DEBUG) printf ("_IdDcmCheckSwap : Explicit VR\n");
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
+ "explicit Value Representation");
} else {
filetype = ImplicitVR;
- if (DEBUG) printf ("_IdDcmCheckSwap : PAS Explicit VR\n");
+ dbg.Verbose(1, "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
- if (DEBUG) printf("HostByteOrder = NetworkByteOrder\n");
- } else { /* on est sur une Sun ou une SGI */
+
+ if (net2host) {
sw = 4321;
- if (DEBUG) printf("HostByteOrder != NetworkByteOrder\n");
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
+ "HostByteOrder != NetworkByteOrder");
+ } else {
+ sw = 0;
+ dbg.Verbose(1, "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, guint32);
switch (s) {
case 0x00040000 :
- sw=3412; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
+ sw = 3412;
filetype = ACR;
- break;
+ return;
case 0x04000000 :
- sw=4321; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
+ sw = 4321;
filetype = ACR;
- break;
+ return;
case 0x00000400 :
- sw=2143; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
- filetype = ACR;
- break;
+ sw = 2143;
+ filetype = ACR;
+ return;
case 0x00000004 :
- sw=0; if(DEBUG) printf("s : %08x sw : %d\n",s,sw);
+ sw = 0;
filetype = ACR;
- break;
- default :
- sw = -1;
- if (DEBUG) printf (" Pas trouve l info de Swap; On va parier\n");
- }
- if(sw!=-1) {
- rewind(fp); // les info commencent au debut
- offsetCourant=0;
return;
+ default :
+ dbg.Verbose(0, "gdcmHeader::CheckSwap:",
+ "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
-
- // 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
- if (DEBUG) printf("On force la chance \n");
+ // 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 is
+ // not present. Then the only info we have is the net2host one.
+ //FIXME Si c'est du RAW, ca degagera + tard
- 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;
+void gdcmHeader::SwitchSwapToBigEndian(void) {
+ dbg.Verbose(0, "gdcmHeader::FindLength", "Switching to BigEndian mode.");
+ if ( sw == 0 ) {
+ sw = 4321;
+ return;
}
- return;
+ if ( sw == 4321 ) {
+ sw = 0;
+ return;
+ }
+ if ( sw == 3412 ) {
+ sw = 2143;
+ return;
+ }
+ if ( sw == 2143 )
+ sw = 3412;
}
/**
* @return longueur retenue pour le champ
*/
-// FIXME sw n'est plus un argument necessaire
-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 *ElVal) {
+ char VR[3];
+ string vr;
int lgrLue;
+ 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.
+ bool RealExplicit = true;
+
+ if (filetype != ExplicitVR)
+ return;
+
+ lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
+ VR[2]=0;
+ vr = string(VR);
+
+ // 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++ implentations 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 && !dicom_vr->count(vr) )
+ RealExplicit = false;
+
+ if ( RealExplicit ) {
+ if ( ElVal->IsVrUnknown() )
+ ElVal->SetVR(vr);
+ return;
+ }
- // FIX ME
- // ATTENTION : nbCode correspond au nombre d'elements dans la table
- // de type DICOM_VR. A nettoyer.
- //
- int nbCode=26;
+ // We thought this was explicit VR, but we end up with an
+ // implicit VR tag. Let's backtrack.
+ dbg.Verbose(1, "gdcmHeader::FindVR:", "Falsely explicit vr file");
+ 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 ( ElVal->IsVrUnknown() )
+ ElVal->SetVR("Implicit");
+ ElVal->SetImplicitVr();
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Determines if the Transfer Syntax was allready encountered
+ * and if it corresponds to a Big Endian one.
+ *
+ * @return True when big endian found. False in all other cases.
+ */
+bool gdcmHeader::IsBigEndianTransferSyntax(void) {
+ ElValue* Element = PubElVals.GetElement(0x0002, 0x0010);
+ if ( !Element )
+ return false;
+ LoadElementValueSafe(Element);
+ string Transfer = Element->GetValue();
+ if ( Transfer == "1.2.840.10008.1.2.2" )
+ return true;
+ return false;
+}
+
+void gdcmHeader::FixFoundLength(ElValue * ElVal, guint32 FoudLength) {
+ // Heuristic: a final fix.
+ if ( FoudLength == 0xffffffff)
+ FoudLength = 0;
+ ElVal->SetLength(FoudLength);
+}
+
+void gdcmHeader::FindLength( ElValue * ElVal) {
+ guint16 element = ElVal->GetElement();
+ string vr = ElVal->GetVR();
+ guint16 length16;
- 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
+ if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) {
+ if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) {
- if(DEBUG)
- printf("IdDcmRecupLgr : Explicit VR, mais pas de code connu\n");
- memcpy(&l_gr, VR,(size_t)2);
-
- lgrLue=fread ( ((char*)&l_gr)+2, (size_t)2, (size_t)1, fp);
-
- l_gr = SWAP_LONG((guint32)l_gr);
-
- if(DEBUG)
- printf("IdDcmRecupLgr : lgr deduite : %08x , %d\n",l_gr,l_gr);
-
- pleCourant->SetLgrLue(l_gr);
- if ( (int)l_gr == -1)
- l_gr=0;
-
- *skippedLength = 4;
- if (DEBUG)
- printf(" 1 : lgr %08x (%d )skippedLength %d\n",
- l_gr,l_gr, *skippedLength);
- return(l_gr);
- }
-
- // On repart dans la sequence 'sensee'
-
- if(DEBUG)
- printf("VR : [%01x , %01x] (%c%c) en position %d du tableau\n",
- VR[0],VR[1],VR[0],VR[1],i);
-
- 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 )) ) {
-
- // les 2 octets suivants sont reserves: on les saute
- if(DEBUG)
- printf("IdDcmRecupLgr : les 2 octets suivants sont reserves\n");
+ // 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 = SWAP_LONG((guint32)l_gr);
- *skippedLength = 8;
+ FixFoundLength(ElVal, ReadInt32());
+ return;
+ }
+
+ // Length is encoded on 2 bytes.
+ length16 = ReadInt16();
- } 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 = SWAP_SHORT((unsigned short)l_gr_2);
-
- pleCourant->SetLgrLue(l_gr_2);
-
-
- if ( l_gr_2 == 0xffff) {
- l_gr = 0;
- } else {
- l_gr = l_gr_2;
+ // 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 bie 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 consist to wait 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
+ // encouter 1024 (0x0400) chances are the encoding changed and we
+ // found a group with big endian encoding.
+ // We shall use this second strategy. In order 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 allready 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 got our
+ // hands on a big endian encoded file: we switch the swap code to
+ // big endian and proceed...
+ if ( (element == 0) && (length16 == 1024) ) {
+ if ( ! IsBigEndianTransferSyntax() )
+ throw Error::FileReadError(fp, "gdcmHeader::FindLength");
+ length16 = 4;
+ SwitchSwapToBigEndian();
+ // Restore the unproperly loaded values i.e. the group, the element
+ // and the dictionary entry depending on them.
+ guint16 CorrectGroup = SwapShort(ElVal->GetGroup());
+ guint16 CorrectElem = SwapShort(ElVal->GetElement());
+ gdcmDictEntry * NewTag = IsInDicts(CorrectGroup, CorrectElem);
+ if (!NewTag) {
+ // This correct tag is not in the dictionary. Create a new one.
+ NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem);
}
- *skippedLength = 4;
+ // FIXME this can create a memory leaks on the old entry that be
+ // left unreferenced.
+ ElVal->SetDictEntry(NewTag);
}
- } else {
- // Explicit VR = 0
- //on lit la lgr sur QUATRE octets
-
- lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp);
-
- l_gr= SWAP_LONG((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
- if (DEBUG) printf(" SQ trouve : lgr %d \n",l_gr);
+
+ // Heuristic: well some files are really ill-formed.
+ if ( length16 == 0xffff) {
+ length16 = 0;
+ dbg.Verbose(0, "gdcmHeader::FindLength",
+ "Erroneous element length fixed.");
+ }
+ FixFoundLength(ElVal, (guint32)length16);
+ return;
}
-
- if (DEBUG)
- printf(" 2 : lgr %08x (%d) skippedLength %d\n",l_gr,l_gr, *skippedLength);
- return(l_gr);
+
+ // Either implicit VR or an explicit VR that (at least for this
+ // element) lied a little bit. Length is on 4 bytes.
+ FixFoundLength(ElVal, ReadInt32());
}
+
/**
* \ingroup gdcmHeader
- * \brief remet les octets dans un ordre compatible avec celui du processeur
-
- * @return longueur retenue pour le champ
+ * \brief Swaps back the bytes of 4-byte long integer accordingly to
+ * processor order.
+ *
+ * @return The suggested integer.
*/
-guint32 gdcmHeader::SWAP_LONG(guint32 a) {
+guint32 gdcmHeader::SwapLong(guint32 a) {
// FIXME: il pourrait y avoir un pb pour les entiers negatifs ...
switch (sw) {
+ case 0 :
+ break;
case 4321 :
a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
break;
default :
- printf("\n\n\n *******\n erreur code swap ?!?\n\n\n");
+ dbg.Error(" gdcmHeader::SwapLong : unset swap code");
a=0;
}
return(a);
/**
* \ingroup gdcmHeader
- * \brief remet les octets dans un ordre compatible avec celui du processeur
-
- * @return longueur retenue pour le champ
+ * \brief Swaps the bytes so they agree with the processor order
+ * @return The properly swaped 16 bits integer.
*/
-short int gdcmHeader::SWAP_SHORT(short int a) {
+guint16 gdcmHeader::SwapShort(guint16 a) {
if ( (sw==4321) || (sw==2143) )
a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
return (a);
}
+void gdcmHeader::SkipElementValue(ElValue * ElVal) {
+ //FIXME don't dump the returned value
+ (void)fseek(fp, (long)ElVal->GetLength(), SEEK_CUR);
+}
+
/**
* \ingroup gdcmHeader
- * \brief lit le dicom_element suivant.
- * (le fichier doit deja avoir ete ouvert,
- * _IdAcrCheckSwap(ID_DCM_HDR *e) avoir ete appele)
- * @param e ID_DCM_HDR dans lequel effectuer la recherche.
- * @param sw code swap.
- * @return En cas de succes, 1
- * 0 en cas d'echec.
+ * \brief Loads the element if it's size is not to big.
+ * @param ElVal Element whose value shall be loaded.
+ * @param MaxSize Size treshold above which the element value is not
+ * loaded in memory. The element value is allways loaded
+ * when MaxSize is equal to UINT32_MAX.
+ * @return
*/
+void gdcmHeader::LoadElementValue(ElValue * ElVal) {
+ size_t item_read;
+ guint16 group = ElVal->GetGroup();
+ guint16 elem = ElVal->GetElement();
+ string vr = ElVal->GetVR();
+ guint32 length = ElVal->GetLength();
+ bool SkipLoad = false;
-ElValue * gdcmHeader::ReadNextElement(void) {
- unsigned short g;
- unsigned short n;
- guint32 l;
- long int posFich;
- int skL;
- size_t lgrLue;
- //CLEANME DICOM_ELEMENTS *t;
- ElValue * nouvDcmElem;
-
- if (DEBUG) printf(" ===> entree ds _IdDcmReadNextElement\n");
-
- // 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
- if (DEBUG) printf(" On a atteint la fin du fichier\n");
- return(NULL);
- } else {
- if (DEBUG) {
- posFich = ftell(fp);
- printf("lgrFich %f positionDsFich %f offset courant %f\n",
- (float)taille_fich,
- (float)posFich,
- (float)offsetCourant);
- }
- }
+ fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
- // ------------------------- Lecture Num group : g
- lgrLue=fread (&g, (size_t)2,(size_t)1, fp);
-
- if (feof(fp)) {
- if (DEBUG) printf("_IdDcmReadNextElement : eof trouve\n");
- return (NULL);
+ // Sequences not treated yet !
+ if( vr == "SQ" )
+ SkipLoad = true;
+
+ // Heuristic : a sequence "contains" a set of tags (called items). It looks
+ // like the last tag of a sequence (the one that terminates the sequence)
+ // has a group of 0xfffe (with a dummy length).
+ if( group == 0xfffe )
+ SkipLoad = true;
+
+ // The group length doesn't represent data to be loaded in memory, since
+ // each element of the group shall be loaded individualy.
+ if( elem == 0 )
+ SkipLoad = true;
+
+ if ( SkipLoad ) {
+ SkipElementValue(ElVal);
+ ElVal->SetLength(0);
+ ElVal->SetValue("gdcm::Skipped");
+ return;
}
- if (ferror(fp)){
- if (DEBUG) printf(" IdDcmReadNextElement : echec lecture NumGr\n");
- return (NULL);
+
+ // When the length is zero things are easy:
+ if ( length == 0 ) {
+ ElVal->SetValue("");
+ return;
}
- if (DEBUG) printf("_IdDcmReadNextElement : gr %04x\n",g );
-
- if (sw) g= SWAP_SHORT(((short)g));
+ // When an integer is expected, read and convert the following two or
+ // four bytes properly i.e. as an integer as opposed to a string.
+ if ( IsAnInteger(ElVal) ) {
+ guint32 NewInt;
+ if( length == 2 ) {
+ NewInt = ReadInt16();
+ } else if( length == 4 ) {
+ NewInt = ReadInt32();
+ } else
+ dbg.Error(true, "LoadElementValue: Inconsistency when reading Int.");
+
+ //FIXME: make the following an util fonction
+ ostringstream s;
+ s << NewInt;
+ ElVal->SetValue(s.str());
+ return;
+ }
- //CLEANME nouvDcmElem->Gr=g;
- //FIXME this might be usefull for detecting at parse time that
- //something is screwy in the file
- //e->__NumeroGroupePrecedent =g;
+ // FIXME The exact size should be length if we move to strings or whatever
+ char* NewValue = (char*)g_malloc(length+1);
+ if( !NewValue) {
+ dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue");
+ return;
+ }
+ NewValue[length]= 0;
+ // FIXME les elements trop long (seuil a fixer a la main) ne devraient
+ // pas etre charge's !!!! Voir TODO.
+ item_read = fread(NewValue, (size_t)length, (size_t)1, fp);
+ if ( item_read != 1 ) {
+ g_free(NewValue);
+ Error::FileReadError(fp, "gdcmHeader::LoadElementValue");
+ ElVal->SetValue("gdcm::UnRead");
+ return;
+ }
+ ElVal->SetValue(NewValue);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Loads the element while preserving the current
+ * underlying file position indicator as opposed to
+ * to LoadElementValue that modifies it.
+ * @param ElVal Element whose value shall be loaded.
+ * @return
+ */
+void gdcmHeader::LoadElementValueSafe(ElValue * ElVal) {
+ long PositionOnEntry = ftell(fp);
+ LoadElementValue(ElVal);
+ fseek(fp, PositionOnEntry, SEEK_SET);
+}
+
- // ------------------------- Lecture Num Elem : n
- lgrLue=fread (&n, (size_t)2,(size_t)1, fp);
+guint16 gdcmHeader::ReadInt16(void) {
+ guint16 g;
+ size_t item_read;
+ item_read = fread (&g, (size_t)2,(size_t)1, fp);
+ if ( item_read != 1 )
+ throw Error::FileReadError(fp, "gdcmHeader::ReadInt16");
+ g = SwapShort(g);
+ return g;
+}
+
+guint32 gdcmHeader::ReadInt32(void) {
+ guint32 g;
+ size_t item_read;
+ item_read = fread (&g, (size_t)4,(size_t)1, fp);
+ if ( item_read != 1 )
+ throw Error::FileReadError(fp, "gdcmHeader::ReadInt32");
+ g = SwapLong(g);
+ return g;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Read the next tag without loading it's value
+ * @return On succes the newly created ElValue, NULL on failure.
+ */
+
+ElValue * gdcmHeader::ReadNextElement(void) {
+ guint16 g;
+ guint16 n;
+ ElValue * NewElVal;
- if (feof(fp)) {
- if (DEBUG) printf("_IdDcmReadNextElement : eof trouve\n");
- return (NULL);
+ try {
+ g = ReadInt16();
+ n = ReadInt16();
}
- if (ferror(fp)){
- if (DEBUG) printf(" IdDcmReadNextElement : echec lecture NumElem\n");
- return (NULL);
+ catch ( Error::FileReadError ) {
+ // We reached the EOF (or an error occured) and header parsing
+ // has to be considered as finished.
+ return (ElValue *)0;
}
-
- if (DEBUG) printf("_IdDcmReadNextElement : num %04x\n",n );
-
- if(sw) n= SWAP_SHORT(((short)n));
- //CLEANMEnouvDcmElem->Num=n;
// Find out if the tag we encountered is in the dictionaries:
- DictEntry * NewTag = IsInDicts(g, n);
+ gdcmDictEntry * NewTag = IsInDicts(g, n);
if (!NewTag)
- NewTag = new DictEntry(g, n, "Unknown", "Unknown");
+ NewTag = new gdcmDictEntry(g, n);
- nouvDcmElem = new ElValue(NewTag);
- if (!nouvDcmElem) {
- printf("Echec alloc ElValue *nouvDcmElem\n");
- return(NULL);
+ NewElVal = new ElValue(NewTag);
+ if (!NewElVal) {
+ dbg.Verbose(1, "ReadNextElement: failed to allocate ElValue");
+ return (ElValue*)0;
}
- // ------------------------- Lecture longueur element : l
-
- l = RecupLgr(nouvDcmElem, &skL);
-
- if(g==0xfffe) l=0; // pour sauter les indicateurs de 'SQ'
+ FindVR(NewElVal);
+ try { FindLength(NewElVal); }
+ catch ( Error::FileReadError ) { // Call it quits
+ return (ElValue *)0;
+ }
+ NewElVal->SetOffset(ftell(fp));
+ return NewElVal;
+}
+
+bool gdcmHeader::IsAnInteger(ElValue * ElVal) {
+ guint16 group = ElVal->GetGroup();
+ guint16 element = ElVal->GetElement();
+ string vr = ElVal->GetVR();
+ guint32 length = ElVal->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
+ dbg.Error("gdcmHeader::IsAnInteger",
+ "Erroneous Group Length element length.");
+ }
- nouvDcmElem->LgrElem=l;
+ if ( group % 2 != 0 )
+ // We only have some semantics on documented elements, which are
+ // the even ones.
+ return false;
- if (DEBUG)
- if (n!=0)
- printf("_IdDcmReadNextElement : "
- " gr %04x\tnum %04x\tlong %08x (%d)\n", g,n,l,l);
-
- // ------------------------- Lecture Valeur element
+ if ( (length != 4) && ( length != 2) )
+ // Swapping only make sense on integers which are 2 or 4 bytes long.
+ return false;
- // FIXME The exact size should be l if we move to strings or whatever
- // CLEAN ME NEWValue used to be nouvDcmElem->valeurElem
- char* NewValue = (char*)g_malloc(l+1);
- if(NewValue) {
- NewValue[l]= 0;
- } else {
- if (DEBUG)
- printf(" IdDcmReadNextElement : echec Alloc valeurElem lgr : %d\n",l);
- return (NULL);
- }
+ if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
+ return true;
- // FIXME les elements trop long (seuil a fixer a la main) ne devraient
- // pas etre charge's !!!! Voir TODO.
- lgrLue=fread (NewValue, (size_t)l,(size_t)1, fp);
+ if ( (group == 0x0028) && (element == 0x0005) )
+ // This tag is retained from ACR/NEMA
+ // CHECKME Why should "Image Dimensions" be a single integer ?
+ return true;
- offsetCourant += 2 + 2 + skL; // gr + num + lgr
- nouvDcmElem->Offset = offsetCourant;
- offsetCourant += l; // debut elem suivant
-
- // ------------------------- Doit-on le Swapper ?
+ if ( (group == 0x0028) && (element == 0x0200) )
+ // This tag is retained from ACR/NEMA
+ return true;
- if ((n==0) && sw) { // n=0 : lgr du groupe : guint32
- *(guint32 *) NewValue = SWAP_LONG ((*(guint32 *) NewValue));
- } else {
- if(sw) {
- if ( (g/2)*2-g==0) { /* on ne teste pas les groupes impairs */
-
- if ((l==4)||(l==2)) { // pour eviter de swapper les chaines
- // de lgr 2 ou 4
- if (DEBUG)
- printf("Consultation Dictionary DICOM g %04x n %0xx l %d\n",
- g,n,l);
-
- // FIXME make reference to nouvDcmElem->GetTag
- string VR = NewTag->GetVR();
- if ( (VR == "UL") || (VR == "US")
- || (VR == "SL") || (VR == "SS")
- || (g == 0x0028 && ( n == 0x0005 || n == 0x0200) )) {
- // seuls (28,5) de vr RET et (28,200) sont des entiers
- // ... jusqu'a preuve du contraire
-
- if(l==4) {
- *(guint32 *) NewValue =
- SWAP_LONG ((*(guint32 *) NewValue));
- } else {
- if(l==2)
- *(unsigned short *) NewValue =
- SWAP_SHORT ((*(unsigned short *)NewValue));
- }
- }
- } /* fin if l==2 ==4 */
- } /* fin if g pair */
- } /* fin sw */
- }
- nouvDcmElem->value = NewValue;
- SetAsidePixelData(nouvDcmElem);
- return nouvDcmElem;
+ return false;
}
/**
* \ingroup gdcmHeader
- * \brief If we encountered the offset of the pixels in the file
- * (Pixel Data) then keep the info aside.
+ * \brief Recover the offset (from the beginning of the file) of the pixels.
*/
-void gdcmHeader::SetAsidePixelData(ElValue* elem) {
- /// FIXME this wall process is bizarre:
- // on peut pas lire pixel data et pixel location puis
- // a la fin de la lecture aller interpreter ce qui existe ?
- // penser a nettoyer les variables globales associes genre
- // PixelsTrouve ou grPixelTrouve...
- //
- // They are two cases :
- // * the pixel data (i.e. the image or the volume) is pointed by it's
- // default official tag (0x7fe0,0x0010),
- // * the writer of this file decided to put the image "address" (i.e the
- // offset from the begining of the file) at a different tag.
- // Then the "Pixel Data" offset might be found by indirection through
- // the "Image Location" tag (0x0028, 0x0200). In other terms the Image
- // Location tag contains the group where the "Pixel Data" offset is and
- // inside this group the element is conventionally at element 0x0010
- // (when the norm is respected).
- //
- // Hence getting our hands on the Pixel Data is a two stage process:
- // 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.
- guint16 g;
- guint16 n;
- g = elem->GetGroup();
- n = elem->GetElement();
- if (!grPixelTrouve) { // on n a pas encore trouve les pixels
- if (g > 0x0028) {
- if (n > 0x0200 || g == 0x7FE0 ) { // on a depasse (28,200)
- grPixel = 0x7FE0;
- numPixel = 0x0010;
- grPixelTrouve = true;
- if (DEBUG)
- printf("------------------------grPixel %04x numPixel %04x\n",
- grPixel,numPixel);
- }
- } else { // on est sur (28,200)
- if (g == 0x0028) {
- if (n == 0x0200) {
- grPixelTrouve = 1;
- char* NewValue = (char*)g_malloc(elem->GetLgrElem()+1);
- // FIXME: not very elegant conversion
- for(int i=0;i<4;i++)
- *((char*)(&grPixel)+i) = *(NewValue+i);
- elem->SetValue(NewValue);
-
- if (DEBUG)
- printf("------------------------GrPixel %04x\n", grPixel);
-
- if (grPixel != 0x7FE0) // Vieux pb Philips
- numPixel = 0x1010; // encore utile ??
- else
- numPixel = 0x0010;
- if (DEBUG)
- printf("------------------------grPixel %04x numPixel %04x\n",
- grPixel,numPixel);
- }
- }
- }
- } else { // on vient de trouver les pixels
- if (g == grPixel) {
- if (n == numPixel) {
- PixelPosition = elem->Offset;
- PixelsTrouves = true;
- if (DEBUG)
- printf(" \t===> Pixels Trouves\n");
- }
- }
+size_t gdcmHeader::GetPixelOffset(void) {
+ // If this file complies with the norm we should encounter the
+ // "Image Location" tag (0x0028, 0x0200). This tag contains the
+ // the group that contains the pixel data (hence the "Pixel Data"
+ // is found by indirection through the "Image Location").
+ // Inside the group pointed by "Image Location" the searched element
+ // is conventionally the element 0x0010 (when the norm is respected).
+ // When the "Image Location" is absent we default to group 0x7fe0.
+ guint16 grPixel;
+ guint16 numPixel;
+ string ImageLocation = GetPubElValByName("Image Location");
+ if ( ImageLocation == "UNFOUND" ) {
+ grPixel = 0x7FE0;
+ } else {
+ grPixel = (guint16) atoi( ImageLocation.c_str() );
}
+ if (grPixel != 0x7fe0)
+ // FIXME is this still necessary ?
+ // Now, this looks like an old dirty fix for Philips imager
+ numPixel = 0x1010;
+ else
+ numPixel = 0x0010;
+ ElValue* PixelElement = PubElVals.GetElement(grPixel, numPixel);
+ if (PixelElement)
+ return PixelElement->GetOffset();
+ else
+ return 0;
}
-DictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) {
- DictEntry * found = (DictEntry*)0;
+gdcmDictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) {
+ gdcmDictEntry * found = (gdcmDictEntry*)0;
if (!RefPubDict && !RefShaDict) {
//FIXME build a default dictionary !
printf("FIXME in gdcmHeader::IsInDicts\n");
}
return found;
}
+
+string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
+ return PubElVals.GetElValue(group, element);
+}
+
+string gdcmHeader::GetPubElValByName(string TagName) {
+ return PubElVals.GetElValue(TagName);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Parses the header of the file but does NOT load element values.
+ */
+void gdcmHeader::ParseHeader(void) {
+ ElValue * newElValue = (ElValue *)0;
+
+ rewind(fp);
+ CheckSwap();
+ while ( (newElValue = ReadNextElement()) ) {
+ SkipElementValue(newElValue);
+ PubElVals.Add(newElValue);
+ }
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Loads the element values of all the elements present in the
+ * public tag based hash table.
+ */
+void gdcmHeader::LoadElements(void) {
+ rewind(fp);
+ TagElValueHT ht = PubElVals.GetTagHt();
+ for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag)
+ LoadElementValue(tag->second);
+}
+
+void gdcmHeader::PrintPubElVal(ostream & os) {
+ PubElVals.Print(os);
+}
+
+void gdcmHeader::PrintPubDict(ostream & os) {
+ RefPubDict->Print(os);
+}