-#include "gdcmlib.h"
+#include "gdcm.h"
extern "C" {
#include "glib.h"
}
#define HEADER_LENGHT_TO_READ 256 // on ne lit plus que le debut
+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))
void gdcmHeader::Initialise(void) {
if (!gdcmHeader::dicom_vr)
InitVRDict();
- PixelPosition = (size_t)0;
- PixelsTrouves = false;
RefPubDict = gdcmHeader::Dicts->GetDefaultPublicDict();
RefShaDict = (gdcmDict*)0;
}
-gdcmHeader::gdcmHeader (char* InFilename) {
+gdcmHeader::gdcmHeader (const char* InFilename) {
filename = InFilename;
Initialise();
fp=fopen(InFilename,"rw");
dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename);
- BuildHeader();
- fclose(fp);
+ ParseHeader();
}
gdcmHeader::~gdcmHeader (void) {
+ fclose(fp);
return;
}
entCur = deb + 128;
if(memcmp(entCur, "DICM", (size_t)4) == 0) {
filetype = TrueDicom;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
} else {
filetype = Unknown;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
}
if(filetype == TrueDicom) {
* @return longueur retenue pour le champ
*/
-void gdcmHeader::FindVR( ElValue *pleCourant) {
+void gdcmHeader::FindVR( ElValue *ElVal) {
char VR[3];
int lgrLue;
long PositionOnEntry = ftell(fp);
// first extraction by calling proper method.
VRAtr FoundVR = dicom_vr->find(string(VR))->first;
if ( ! FoundVR.empty()) {
- pleCourant->SetVR(FoundVR);
+ ElVal->SetVR(FoundVR);
return;
}
// We thought this was explicit VR, but we end up with an
// implicit VR tag. Let's backtrack.
- pleCourant->SetVR("Implicit");
+ ElVal->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();
+void gdcmHeader::FindLength( ElValue * ElVal) {
+ guint32 length32;
+ guint16 length16;
- if ( (filetype == ExplicitVR) && (vr != "Implicit") ) {
- if ( ( vr == "OB" ) || ( vr == "OW" )
- || ( vr == "SQ" ) || ( vr == "UN" ) ) {
+ if (filetype == ExplicitVR) {
+ string vr = ElVal->GetVR();
+ if ( (vr != "Implicit")
+ && ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) ) {
// 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);
- lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp);
- l_gr = SwapLong((guint32)l_gr);
+ length32 = ReadInt32();
} else {
- //on lit la lgr sur DEUX octets
- lgrLue=fread (&l_gr_2, (size_t)2,(size_t)1, fp);
-
- l_gr_2 = SwapShort((unsigned short)l_gr_2);
-
- if ( l_gr_2 == 0xffff) {
- l_gr = 0;
+ // Length is encoded on 2 bytes.
+ length16 = ReadInt16();
+
+ if ( length16 == 0xffff) {
+ length32 = 0;
} else {
- l_gr = l_gr_2;
+ length32 = length16;
}
}
} 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);
+ // Either implicit VR or an explicit VR that (at least for this
+ // element) lied a little bit. Length is on 4 bytes.
+ length32 = ReadInt32();
}
-
+
// Traitement des curiosites sur la longueur
- if ( (int)l_gr == 0xffffffff)
- l_gr=0;
+ if ( length32 == 0xffffffff)
+ length32=0;
- pleCourant->SetLgrElem(l_gr);
+ ElVal->SetLength(length32);
}
+
/**
* \ingroup gdcmHeader
* \brief remet les octets dans un ordre compatible avec celui du processeur
* @return longueur retenue pour le champ
*/
-short int gdcmHeader::SwapShort(short int a) {
+guint16 gdcmHeader::SwapShort(guint16 a) {
if ( (sw==4321) || (sw==2143) )
a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
return (a);
}
-/**
- * \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.
- */
+void gdcmHeader::SkipElementValue(ElValue * ElVal) {
+ //FIXME don't dump the returned value
+ (void)fseek(fp, (long)ElVal->GetLength(), SEEK_CUR);
+}
-ElValue * gdcmHeader::ReadNextElement(void) {
- unsigned short g;
- unsigned short n;
- guint32 l;
- size_t lgrLue;
- ElValue * nouvDcmElem;
-
- // ------------------------- Lecture Num group : g
- lgrLue=fread (&g, (size_t)2,(size_t)1, fp);
+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();
+ fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
- if (feof(fp)) {
- dbg.Verbose(1, "ReadNextElement: EOF encountered");
- return (NULL);
+ // Sequences not treated yet !
+ if( vr == "SQ" ) {
+ SkipElementValue(ElVal);
+ ElVal->SetLength(0);
+ return;
}
- if (ferror(fp)){
- dbg.Verbose(1, "ReadNextElement: failed to read NumGr");
- return (NULL);
+ // 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) {
+ SkipElementValue(ElVal);
+ ElVal->SetLength(0);
+ return;
}
- if (sw) g= SwapShort(((short)g));
-
- // ------------------------- Lecture Num Elem : n
- lgrLue=fread (&n, (size_t)2,(size_t)1, fp);
+ if ( IsAnInteger(group, elem, vr, length) ) {
+ 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;
+ }
- if (feof(fp)) {
- dbg.Verbose(1, "ReadNextElement: EOF encountered");
- return (NULL);
+ // 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;
}
- if (ferror(fp)){
- dbg.Verbose(1, "ReadNextElement: failed to read NumElem");
- return (NULL);
+ 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);
+}
+
+
+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(sw) n= SwapShort(((short)n));
+ try {
+ g = ReadInt16();
+ n = ReadInt16();
+ }
+ catch ( Error::FileReadError ) {
+ // We reached the EOF (or an error occured) and header parsing
+ // has to be considered as finished.
+ return (ElValue *)0;
+ }
// Find out if the tag we encountered is in the dictionaries:
gdcmDictEntry * NewTag = IsInDicts(g, n);
if (!NewTag)
- NewTag = new gdcmDictEntry(g, n, "Unknown", "Unknown", "Unkown");
+ NewTag = new gdcmDictEntry(g, n, "Unknown", "Unknown", "Unknown");
- nouvDcmElem = new ElValue(NewTag);
- if (!nouvDcmElem) {
+ NewElVal = new ElValue(NewTag);
+ if (!NewElVal) {
dbg.Verbose(1, "ReadNextElement: failed to allocate ElValue");
- return(NULL);
+ return (ElValue*)0;
}
- // ------------------------- Lecture longueur element : l
-
- 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);
-
+ FindVR(NewElVal);
+ FindLength(NewElVal);
+ NewElVal->SetOffset(ftell(fp));
+ return NewElVal;
+}
- if(g==0xfffe) l=0; // pour sauter les indicateurs de 'SQ'
+bool gdcmHeader::IsAnInteger(guint16 group, guint16 element,
+ string vr, guint32 length ) {
+ // When we have some semantics on the element we just read, and we
+ // a priori now we are dealing with an integer, then we can swap it's
+ // element value properly.
+ if ( element == 0 ) { // This is the group length of the group
+ if (length != 4)
+ dbg.Error("gdcmHeader::ShouldBeSwaped", "should be four");
+ return true;
+ }
+ if ( group % 2 != 0 )
+ // We only have some semantics on documented elements, which are
+ // the even ones.
+ return false;
- // ------------------------- 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 {
- 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;
-
- // ------------------------- 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 = SwapLong ((*(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
-
- // 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 =
- SwapLong ((*(guint32 *) NewValue));
- } else {
- if(l==2)
- *(unsigned short *) NewValue =
- SwapShort ((*(unsigned short *)NewValue));
- }
- }
- } /* fin if l==2 ==4 */
- } /* fin if g pair */
- } /* fin sw */
- }
- nouvDcmElem->value = NewValue;
- 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 is.
- 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;
- }
- } 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 (grPixel != 0x7FE0) // Vieux pb Philips
- numPixel = 0x1010; // encore utile ??
- else
- numPixel = 0x0010;
- }
- }
- }
- } else { // on vient de trouver les pixels
- if (g == grPixel) {
- if (n == numPixel) {
- PixelPosition = elem->Offset;
- PixelsTrouves = true;
- dbg.Verbose(0, "gdcmHeader::SetAsidePixelData:",
- "Pixel data found");
- }
- }
+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;
}
gdcmDictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) {
return found;
}
-string gdcmHeader::GetPubElValByNumber(unsigned short, unsigned short) {
+string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
+ return PubElVals.GetElValue(group, element);
+}
+
+string gdcmHeader::GetPubElValByName(string TagName) {
+ return PubElVals.GetElValue(TagName);
}
/**
- * \ingroup gdcmHeader
- * \brief renvoie un pointeur sur le ID_DCM_HDR correspondant au fichier
- * @param filename Nom du fichier ACR / LibIDO / DICOM
- * @return le ID_DCM_HDR
+ * \ingroup gdcmHeader
+ * \brief Parses the header of the file but does NOT load element values.
*/
-
-void gdcmHeader::BuildHeader(void) {
+void gdcmHeader::ParseHeader(void) {
ElValue * newElValue = (ElValue *)0;
- rewind(fp);
rewind(fp);
CheckSwap();
while ( (newElValue = ReadNextElement()) ) {
+ SkipElementValue(newElValue);
PubElVals.Add(newElValue);
}
}
-int gdcmHeader::PrintPubElVal(ostream & os) {
- return PubElVals.Print(os);
+/**
+ * \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) {
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff