-#include "gdcmlib.h"
-extern "C" {
-#include "glib.h"
-}
+// gdcmHeader.cxx
+
+#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 HEADER_LENGTH_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) {
+ SetMaxSizeLoadElementValue(1024);
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;
}
return;
}
VRHT *vr = new VRHT;
- (*vr)["AE"] = "Application Entity"; // 16 car max
- (*vr)["AS"] = "Age String"; // 4 car fixe
- (*vr)["AT"] = "Attribute Tag"; // 2 unsigned short int
- (*vr)["CS"] = "Code String"; // 16 car max
- (*vr)["DA"] = "Date"; // 8 car fixe
- (*vr)["DS"] = "Decimal String"; // Decimal codé Binaire 16 max
- (*vr)["DT"] = "Date Time"; // 26 car max
- (*vr)["FL"] = "Floating Point Single"; // 4 octets IEEE 754:1985
- (*vr)["FD"] = "Floating Point Double"; // 8 octets IEEE 754:1985
- (*vr)["IS"] = "Integer String"; // en format externe 12 max
- (*vr)["LO"] = "Long String"; // 64 octets max
- (*vr)["LT"] = "Long Text"; // 10240 max
- (*vr)["OB"] = "Other Byte String";
- (*vr)["OW"] = "Other Word String";
- (*vr)["PN"] = "Person Name";
- (*vr)["SH"] = "Short String"; // 16 car max
- (*vr)["SL"] = "Signed Long";
+ (*vr)["AE"] = "Application Entity"; // At most 16 bytes
+ (*vr)["AS"] = "Age String"; // Exactly 4 bytes
+ (*vr)["AT"] = "Attribute Tag"; // 2 16-bit unsigned short integers
+ (*vr)["CS"] = "Code String"; // At most 16 bytes
+ (*vr)["DA"] = "Date"; // Exactly 8 bytes
+ (*vr)["DS"] = "Decimal String"; // At most 16 bytes
+ (*vr)["DT"] = "Date Time"; // At most 26 bytes
+ (*vr)["FL"] = "Floating Point Single"; // 32-bit IEEE 754:1985 float
+ (*vr)["FD"] = "Floating Point Double"; // 64-bit IEEE 754:1985 double
+ (*vr)["IS"] = "Integer String"; // At most 12 bytes
+ (*vr)["LO"] = "Long String"; // At most 64 chars
+ (*vr)["LT"] = "Long Text"; // At most 10240 chars
+ (*vr)["OB"] = "Other Byte String"; // String of bytes (vr independant)
+ (*vr)["OW"] = "Other Word String"; // String of 16-bit words (vr dep)
+ (*vr)["PN"] = "Person Name"; // At most 64 chars
+ (*vr)["SH"] = "Short String"; // At most 16 chars
+ (*vr)["SL"] = "Signed Long"; // Exactly 4 bytes
(*vr)["SQ"] = "Sequence of Items"; // Not Applicable
- (*vr)["SS"] = "Signed Short"; // 2 octets
- (*vr)["ST"] = "Short Text"; // 1024 car max
- (*vr)["TM"] = "Time"; // 16 car max
- (*vr)["UI"] = "Unique Identifier"; // 64 car max
- (*vr)["UN"] = "Unknown";
- (*vr)["UT"] = "Unlimited Text"; // 2 puissance 32 -1 car max
- (*vr)["UL"] = "Unsigned Long "; // 4 octets fixe
- (*vr)["US"] = "Unsigned Short "; // 2 octets fixe
+ (*vr)["SS"] = "Signed Short"; // Exactly 2 bytes
+ (*vr)["ST"] = "Short Text"; // At most 1024 chars
+ (*vr)["TM"] = "Time"; // At most 16 bytes
+ (*vr)["UI"] = "Unique Identifier"; // At most 64 bytes
+ (*vr)["UL"] = "Unsigned Long "; // Exactly 4 bytes
+ (*vr)["UN"] = "Unknown"; // Any length of bytes
+ (*vr)["US"] = "Unsigned Short "; // Exactly 2 bytes
+ (*vr)["UT"] = "Unlimited Text"; // At most 2^32 -1 chars
dicom_vr = vr;
}
/**
* \ingroup gdcmHeader
- * \brief La seule maniere sure que l'on aie pour determiner
- * si on est en LITTLE_ENDIAN, BIG-ENDIAN,
- * BAD-LITTLE-ENDIAN, BAD-BIG-ENDIAN
- * est de trouver l'element qui donne la longueur d'un 'GROUP'
- * (on sait que la longueur de cet element vaut 0x00000004)
- * et de regarder comment cette longueur est codee en memoire
- *
- * Le probleme vient de ce que parfois, il n'y en a pas ...
- *
- * On fait alors le pari qu'on a a faire a du LITTLE_ENDIAN propre.
- * (Ce qui est la norme -pas respectee- depuis ACR-NEMA)
- * Si ce n'est pas le cas, on ne peut rien faire.
+ * \brief Discover what the swap code is (among little endian, big endian,
+ * bad little endian, bad big endian).
*
- * (il faudrait avoir des fonctions auxquelles
- * on passe le code Swap en parametre, pour faire des essais 'manuels')
*/
void gdcmHeader::CheckSwap()
{
+ // The only guaranted way of finding the swap code is to find a
+ // group tag since we know it's length has to be of four bytes i.e.
+ // 0x00000004. Finding the swap code in then straigthforward. Trouble
+ // occurs when we can't find such group...
guint32 s;
guint32 x=4; // x : pour ntohs
bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
int lgrLue;
char * entCur;
- char deb[HEADER_LENGHT_TO_READ];
+ char deb[HEADER_LENGTH_TO_READ];
// First, compare HostByteOrder and NetworkByteOrder in order to
// determine if we shall need to swap bytes (i.e. the Endian type).
// 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);
+ lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp);
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) {
entCur = deb + 136;
if(memcmp(entCur, "UL", (size_t)2) == 0) {
filetype = ExplicitVR;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
"explicit Value Representation");
} else {
filetype = ImplicitVR;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
"not an explicit Value Representation");
}
if (net2host) {
sw = 4321;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
"HostByteOrder != NetworkByteOrder");
} else {
sw = 0;
- dbg.Verbose(0, "gdcmHeader::CheckSwap:",
+ dbg.Verbose(1, "gdcmHeader::CheckSwap:",
"HostByteOrder = NetworkByteOrder");
}
// four (bytes), then determining the proper swap code is straightforward.
entCur = deb + 4;
- s = str2num(entCur, int);
+ s = str2num(entCur, guint32);
switch (s) {
case 0x00040000 :
- sw=3412;
+ sw = 3412;
filetype = ACR;
return;
case 0x04000000 :
- sw=4321;
+ sw = 4321;
filetype = ACR;
return;
case 0x00000400 :
- sw=2143;
+ sw = 2143;
filetype = ACR;
return;
case 0x00000004 :
- sw=0;
+ sw = 0;
filetype = ACR;
return;
default :
dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "ACE/NEMA unfound swap info (time to raise bets)");
+ "ACR/NEMA unfound swap info (time to raise bets)");
}
// 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
+ // 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 (! net2host )
sw = 0;
else
return;
}
+void gdcmHeader::SwitchSwapToBigEndian(void) {
+ dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian",
+ "Switching to BigEndian mode.");
+ if ( sw == 0 ) {
+ sw = 4321;
+ return;
+ }
+ if ( sw == 4321 ) {
+ sw = 0;
+ return;
+ }
+ if ( sw == 3412 ) {
+ sw = 2143;
+ return;
+ }
+ if ( sw == 2143 )
+ sw = 3412;
+}
+
+void gdcmHeader::GetPixels(size_t lgrTotale, void* Pixels) {
+ size_t pixelsOffset;
+ pixelsOffset = GetPixelOffset();
+ fseek(fp, pixelsOffset, SEEK_SET);
+ fread(Pixels, 1, lgrTotale, fp);
+}
+
/**
* \ingroup gdcmHeader
- * \brief recupere la longueur d'un champ DICOM.
- * Preconditions:
- * 1/ le fichier doit deja avoir ete ouvert,
- * 2/ CheckSwap() doit avoir ete appele
- * 3/ la partie 'group' ainsi que la partie 'elem'
- * de l'acr_element doivent avoir ete lues.
- *
- * ACR-NEMA : we allways get
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ElementSize (4 Octets)
- * DICOM en implicit Value Representation :
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ElementSize (4 Octets)
- *
- * DICOM en explicit Value Representation :
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ValueRepresentation (2 Octets)
- * ElementSize (2 Octets)
- *
- * ATTENTION : dans le cas ou ValueRepresentation = OB, OW, SQ, UN
- * GroupNumber (2 Octets)
- * ElementNumber (2 Octets)
- * ValueRepresentation (2 Octets)
- * zone reservee (2 Octets)
- * ElementSize (4 Octets)
+ * \brief Find the value representation of the current tag.
*
* @param sw code swap
* @param skippedLength pointeur sur nombre d'octets que l'on a saute qd
* @return longueur retenue pour le champ
*/
-void gdcmHeader::FindVR( ElValue *pleCourant) {
- char VR[3];
- int lgrLue;
- long PositionOnEntry = ftell(fp);
-
+void gdcmHeader::FindVR( ElValue *ElVal) {
if (filetype != ExplicitVR)
return;
- lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
- VR[2]=0;
-
+ 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
// 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);
+ bool RealExplicit = true;
+
+ 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++ implementations 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() ) {
+ // When not a dictionary entry, we can safely overwrite the vr.
+ ElVal->SetVR(vr);
+ return;
+ }
+ if ( ElVal->GetVR() == vr ) {
+ // The vr we just read and the dictionary agree. Nothing to do.
+ return;
+ }
+ // The vr present in the file and the dictionary disagree. We assume
+ // the file writer knew best and use the vr of the file. Since it would
+ // be unwise to overwrite the vr of a dictionary (since it would
+ // compromise it's next user), we need to clone the actual DictEntry
+ // and change the vr for the read one.
+ gdcmDictEntry* NewTag = new gdcmDictEntry(ElVal->GetGroup(),
+ ElVal->GetElement(),
+ vr,
+ "FIXME",
+ ElVal->GetName());
+ ElVal->SetDictEntry(NewTag);
return;
}
// We thought this was explicit VR, but we end up with an
// implicit VR tag. Let's backtrack.
- pleCourant->SetVR("Implicit");
+ 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();
}
-void gdcmHeader::FindLength( ElValue *pleCourant) {
- int lgrLue;
- guint32 l_gr;
- unsigned short int l_gr_2;
-
- string vr = pleCourant->GetVR();
+/**
+ * \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.GetElementByNumber(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);
+}
+
+guint32 gdcmHeader::FindLengthOB(void) {
+ // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
+ guint16 g;
+ guint16 n;
+ long PositionOnEntry = ftell(fp);
+ bool FoundSequenceDelimiter = false;
+ guint32 TotalLength = 0;
+ guint32 ItemLength;
+
+ while ( ! FoundSequenceDelimiter) {
+ g = ReadInt16();
+ n = ReadInt16();
+ TotalLength += 4; // We even have to decount the group and element
+ if ( g != 0xfffe ) {
+ dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
+ "wrong group for an item sequence.");
+ throw Error::FileReadError(fp, "gdcmHeader::FindLengthOB");
+ }
+ if ( n == 0xe0dd )
+ FoundSequenceDelimiter = true;
+ else if ( n != 0xe000) {
+ dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
+ "wrong element for an item sequence.");
+ throw Error::FileReadError(fp, "gdcmHeader::FindLengthOB");
+ }
+ ItemLength = ReadInt32();
+ TotalLength += ItemLength + 4; // We add 4 bytes since we just read
+ // the ItemLength with ReadInt32
+ SkipBytes(ItemLength);
+ }
+ fseek(fp, PositionOnEntry, SEEK_SET);
+ return TotalLength;
+}
+
+void gdcmHeader::FindLength(ElValue * ElVal) {
+ guint16 element = ElVal->GetElement();
+ string vr = ElVal->GetVR();
+ guint16 length16;
- if ( (filetype == ExplicitVR) && (vr != "Implicit") ) {
- if ( ( 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);
-
- } else {
- // Length is encoded on 2 bytes.
- 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;
- } else {
- l_gr = l_gr_2;
+ if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) {
+
+ if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) {
+ // The following reserved two bytes (see PS 3.5-2001, section
+ // 7.1.2 Data element structure with explicit vr p27) must be
+ // skipped before proceeding on reading the length on 4 bytes.
+ fseek(fp, 2L, SEEK_CUR);
+ guint32 length32 = ReadInt32();
+ if ( (vr == "OB") && (length32 == 0xffffffff) ) {
+ ElVal->SetLength(FindLengthOB());
+ return;
}
+ FixFoundLength(ElVal, length32);
+ return;
}
- } else {
- // Either implicit VR or an explicit VR that (at least for this
- // element) lied a little bit. Length is on 4 bytes.
- lgrLue=fread (&l_gr, (size_t)4,(size_t)1, fp);
- l_gr= SwapLong((long)l_gr);
+
+ // Length is encoded on 2 bytes.
+ length16 = ReadInt16();
+
+ // 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 big 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 in waiting 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 == 0x000) && (length16 == 0x0400) ) {
+ 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);
+ }
+ // FIXME this can create a memory leaks on the old entry that be
+ // left unreferenced.
+ ElVal->SetDictEntry(NewTag);
+ }
+
+ // 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;
}
- // Traitement des curiosites sur la longueur
- if ( l_gr == 0xffffffff)
- l_gr=0;
-
- pleCourant->SetLength(l_gr);
+ // Either implicit VR or a non DICOM conformal (see not below) explicit
+ // VR that ommited the VR of (at least) this element. Farts happen.
+ // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25
+ // on Data elements "Implicit and Explicit VR Data Elements shall
+ // not coexist in a Data Set and Data Sets nested within it".]
+ // 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::SwapLong(guint32 a) {
// FIXME: il pourrait y avoir un pb pour les entiers negatifs ...
/**
* \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::SwapShort(short int a) {
+guint16 gdcmHeader::SwapShort(guint16 a) {
if ( (sw==4321) || (sw==2143) )
a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
return (a);
}
+void gdcmHeader::SkipBytes(guint32 NBytes) {
+ //FIXME don't dump the returned value
+ (void)fseek(fp, (long)NBytes, SEEK_CUR);
+}
+
+void gdcmHeader::SkipElementValue(ElValue * ElVal) {
+ SkipBytes(ElVal->GetLength());
+}
+
+void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
+ if (NewSize < 0)
+ return;
+ if ((guint32)NewSize >= (guint32)0xffffffff) {
+ MaxSizeLoadElementValue = 0xffffffff;
+ return;
+ }
+ MaxSizeLoadElementValue = NewSize;
+}
+
/**
* \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
*/
-
-ElValue * gdcmHeader::ReadNextElement(void) {
- guint16 g;
- guint16 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();
+ bool SkipLoad = false;
+
+ fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
- if (feof(fp)) {
- dbg.Verbose(1, "ReadNextElement: EOF encountered");
- return (NULL);
+ // Sequences not treated yet !
+ //
+ // Ne faudrait-il pas au contraire trouver immediatement
+ // une maniere 'propre' de traiter les sequences (vr = SQ)
+ // car commencer par les ignorer risque de conduire a qq chose
+ // qui pourrait ne pas etre generalisable
+ //
+ 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 ) {
+ // FIXME the following skip is not necessary
+ SkipElementValue(ElVal);
+ ElVal->SetLength(0);
+ ElVal->SetValue("gdcm::Skipped");
+ return;
}
- if (ferror(fp)){
- dbg.Verbose(1, "ReadNextElement: failed to read NumGr");
- return (NULL);
+
+ // When the length is zero things are easy:
+ if ( length == 0 ) {
+ ElVal->SetValue("");
+ return;
+ }
+
+ // Values bigger than specified are not loaded.
+ //
+ // En fait, c'est les elements dont la longueur est superieure
+ // a celle fixee qui ne sont pas charges
+ //
+ if (length > MaxSizeLoadElementValue) {
+ ostringstream s;
+ s << "gdcm::NotLoaded.";
+ s << " Address:" << (long)ElVal->GetOffset();
+ s << " Length:" << ElVal->GetLength();
+ //mesg += " Length:" + ElVal->GetLength();
+ ElVal->SetValue(s.str());
+ return;
}
- if (sw) g= SwapShort(((short)g));
-
- // ------------------------- Lecture Num Elem : n
- lgrLue=fread (&n, (size_t)2,(size_t)1, fp);
+ // 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;
+ }
- 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*)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;
+
+ item_read = fread(NewValue, (size_t)length, (size_t)1, fp);
+ if ( item_read != 1 ) {
+ 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);
+}
+
+
+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);
- 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;
}
- FindVR(nouvDcmElem);
- FindLength(nouvDcmElem);
- nouvDcmElem->SetOffset(ftell(fp));
- l = nouvDcmElem->GetLength();
+ FindVR(NewElVal);
+ try { FindLength(NewElVal); }
+ catch ( Error::FileReadError ) { // Call it quits
+ return (ElValue *)0;
+ }
+ NewElVal->SetOffset(ftell(fp));
+ return NewElVal;
+}
- //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);
+bool gdcmHeader::IsAnInteger(ElValue * ElVal) {
+ guint16 group = ElVal->GetGroup();
+ guint16 element = ElVal->GetElement();
+ string vr = ElVal->GetVR();
+ guint32 length = ElVal->GetLength();
- // Une sequence contient un ensemble de group element repetes n fois
- // et g=fffe indique la fin (contient une longueur bidon).
- if(g==0xfffe) l=0; // pour sauter les indicateurs de 'SQ'
-
-
- // ------------------------- Lecture Valeur element
-
- // 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);
- }
-
- // 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 ( IsAnInteger(g, n, NewTag->GetVR(), l) ) {
- // CLEANME THe following is really UGLY !
- if( l == 4 ) {
- *(guint32 *) NewValue = SwapLong ((*(guint32 *) NewValue));
- } else {
- if( l == 2 )
- *(guint16 *) NewValue = SwapShort ((*(guint16 *)NewValue));
- }
- //FIXME: don't we have to distinguish guin16 and guint32
- //FIXME: make the following an util fonction
- ostringstream s;
- s << *(guint32 *) NewValue;
- nouvDcmElem->value = s.str();
- g_free(NewValue);
- } else
- nouvDcmElem->value = NewValue;
- return nouvDcmElem;
-}
-
-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.
+ // 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)
- dbg.Error("gdcmHeader::ShouldBeSwaped", "should be four");
- return true;
+ if (length == 4)
+ return true;
+ else
+ dbg.Error("gdcmHeader::IsAnInteger",
+ "Erroneous Group Length element length.");
}
if ( group % 2 != 0 )
if ( (group == 0x0028) && (element == 0x0005) )
// This tag is retained from ACR/NEMA
// CHECKME Why should "Image Dimensions" be a single integer ?
+ //
+ // "Image Dimensions", c'est en fait le 'nombre de dimensions'
+ // de l'objet ACR-NEMA stocké
+ // 1 : Signal
+ // 2 : Image
+ // 3 : Volume
+ // 4 : Sequence
+ //
+ // DICOM V3 ne retient pas cette information
+ // Par defaut, tout est 'Image',
+ // C'est a l'utilisateur d'explorer l'ensemble des entetes
+ // pour savoir à quoi il a a faire
+ //
+ // Le Dicom Multiframe peut etre utilise pour stocker,
+ // dans un seul fichier, une serie temporelle (cardio vasculaire GE, p.ex)
+ // ou un volume (medecine Nucleaire, p.ex)
+ //
return true;
if ( (group == 0x0028) && (element == 0x0200) )
/**
* \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) {
- // 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.
- cout << "aaaaaaaaaaaaaaaaaaaaa";
- // PubElVals.PrintByName(cout);
- ostringstream val;
- val << hex << GetPubElValByName("Image Location");
- cout << GetPubElValByName("Image Location") << endl;
- cout <<hex << GetPubElValByName("Image Location") << dec << endl;
- cout << "aaaa" << hex << val << dec << endl;
- if (val)
- //grPixel = val.hex().str();
- grPixel = 0;
- else
- grPixel = 0x7FE0;
- return;
-
- 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->GetLength()+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.GetElementByNumber(grPixel, numPixel);
+ if (PixelElement)
+ return PixelElement->GetOffset();
+ else
+ return 0;
}
gdcmDictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) {
+ //
+ // Y a-t-il une raison de lui passer des guint32
+ // alors que group et element sont des guint16?
+ //
gdcmDictEntry * found = (gdcmDictEntry*)0;
if (!RefPubDict && !RefShaDict) {
//FIXME build a default dictionary !
return found;
}
+list<string> * gdcmHeader::GetPubTagNames(void) {
+ list<string> * Result = new list<string>;
+ TagHT entries = RefPubDict->GetEntries();
+
+ for (TagHT::iterator tag = entries.begin(); tag != entries.end(); ++tag){
+ Result->push_back( tag->second->GetName() );
+ }
+ return Result;
+}
+
+map<string, list<string> > * gdcmHeader::GetPubTagNamesByCategory(void) {
+ map<string, list<string> > * Result = new map<string, list<string> >;
+ TagHT entries = RefPubDict->GetEntries();
+
+ for (TagHT::iterator tag = entries.begin(); tag != entries.end(); ++tag){
+ (*Result)[tag->second->GetFourth()].push_back(tag->second->GetName());
+ }
+ return Result;
+}
+
string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
- return PubElVals.GetElValue(group, element);
+ return PubElVals.GetElValueByNumber(group, element);
+}
+
+string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) {
+ ElValue* elem = PubElVals.GetElementByNumber(group, element);
+ if ( !elem )
+ return "gdcm::Unfound";
+ return elem->GetVR();
}
string gdcmHeader::GetPubElValByName(string TagName) {
- return PubElVals.GetElValue(TagName);
+ return PubElVals.GetElValueByName(TagName);
+}
+
+string gdcmHeader::GetPubElValRepByName(string TagName) {
+ ElValue* elem = PubElVals.GetElementByName(TagName);
+ if ( !elem )
+ return "gdcm::Unfound";
+ return elem->GetVR();
+}
+
+string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) {
+ return ShaElVals.GetElValueByNumber(group, element);
+}
+
+string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) {
+ ElValue* elem = ShaElVals.GetElementByNumber(group, element);
+ if ( !elem )
+ return "gdcm::Unfound";
+ return elem->GetVR();
+}
+
+string gdcmHeader::GetShaElValByName(string TagName) {
+ return ShaElVals.GetElValueByName(TagName);
+}
+
+string gdcmHeader::GetShaElValRepByName(string TagName) {
+ ElValue* elem = ShaElVals.GetElementByName(TagName);
+ if ( !elem )
+ return "gdcm::Unfound";
+ return elem->GetVR();
+}
+
+
+string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) {
+ string pub = GetPubElValByNumber(group, element);
+ if (pub.length())
+ return pub;
+ return GetShaElValByNumber(group, element);
+}
+
+string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) {
+ string pub = GetPubElValRepByNumber(group, element);
+ if (pub.length())
+ return pub;
+ return GetShaElValRepByNumber(group, element);
+}
+
+string gdcmHeader::GetElValByName(string TagName) {
+ string pub = GetPubElValByName(TagName);
+ if (pub.length())
+ return pub;
+ return GetShaElValByName(TagName);
+}
+
+string gdcmHeader::GetElValRepByName(string TagName) {
+ string pub = GetPubElValRepByName(TagName);
+ if (pub.length())
+ return pub;
+ return GetShaElValRepByName(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);
CheckSwap();
while ( (newElValue = ReadNextElement()) ) {
+ SkipElementValue(newElValue);
PubElVals.Add(newElValue);
}
- SetAsidePixelData((ElValue*)0);
+}
+
+/**
+ * \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) {
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff