+void gdcmHeader::LoadHeaderEntry(gdcmHeaderEntry * ElVal) {
+ size_t item_read;
+ guint16 group = ElVal->GetGroup();
+ std::string vr= ElVal->GetVR();
+ guint32 length = ElVal->GetLength();
+ bool SkipLoad = false;
+
+ fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
+
+ // the test was commented out to 'go inside' the SeQuences
+ // we don't any longer skip them !
+
+ // if( vr == "SQ" ) // (DO NOT remove this comment)
+ // SkipLoad = true;
+
+ // A SeQuence "contains" a set of Elements.
+ // (fffe e000) tells us an Element is beginning
+ // (fffe e00d) tells us an Element just ended
+ // (fffe e0dd) tells us the current SeQuence just ended
+ if( group == 0xfffe )
+ SkipLoad = true;
+
+ if ( SkipLoad ) {
+ ElVal->SetLength(0);
+ ElVal->SetValue("gdcm::Skipped");
+ return;
+ }
+
+ // When the length is zero things are easy:
+ if ( length == 0 ) {
+ ElVal->SetValue("");
+ return;
+ }
+
+ // The elements whose length is bigger than the specified upper bound
+ // are not loaded. Instead we leave a short notice of the offset of
+ // the element content and it's length.
+ if (length > MaxSizeLoadElementValue) {
+ std::ostringstream s;
+ s << "gdcm::NotLoaded.";
+ s << " Address:" << (long)ElVal->GetOffset();
+ s << " Length:" << ElVal->GetLength();
+ s << " x(" << std::hex << ElVal->GetLength() << ")";
+ ElVal->SetValue(s.str());
+ return;
+ }
+
+ // When integer(s) are expected, read and convert the following
+ // n *(two or four bytes)
+ // properly i.e. as integers as opposed to a strings.
+ // Elements with Value Multiplicity > 1
+ // contain a set of integers (not a single one)
+
+ // Any compacter code suggested (?)
+ if ( IsHeaderEntryAnInteger(ElVal) ) {
+ guint32 NewInt;
+ std::ostringstream s;
+ int nbInt;
+ if (vr == "US" || vr == "SS") {
+ nbInt = length / 2;
+ NewInt = ReadInt16();
+ s << NewInt;
+ if (nbInt > 1) {
+ for (int i=1; i < nbInt; i++) {
+ s << '\\';
+ NewInt = ReadInt16();
+ s << NewInt;
+ }
+ }
+
+ } else if (vr == "UL" || vr == "SL") {
+ nbInt = length / 4;
+ NewInt = ReadInt32();
+ s << NewInt;
+ if (nbInt > 1) {
+ for (int i=1; i < nbInt; i++) {
+ s << '\\';
+ NewInt = ReadInt32();
+ s << NewInt;
+ }
+ }
+ }
+#ifdef GDCM_NO_ANSI_STRING_STREAM
+ s << std::ends; // to avoid oddities on Solaris
+#endif //GDCM_NO_ANSI_STRING_STREAM
+ ElVal->SetValue(s.str());
+ return;
+ }
+
+ // We need an additional byte for storing \0 that is not on disk
+ char* NewValue = (char*)malloc(length+1);
+ if( !NewValue) {
+ dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue");
+ return;
+ }
+ NewValue[length]= 0;
+
+ item_read = fread(NewValue, (size_t)length, (size_t)1, fp);
+ if ( item_read != 1 ) {
+ free(NewValue);
+ dbg.Verbose(1, "gdcmHeader::LoadElementValue","unread element value");
+ ElVal->SetValue("gdcm::UnRead");
+ return;
+ }
+ ElVal->SetValue(NewValue);
+ free(NewValue);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Loads the element while preserving the current
+ * underlying file position indicator as opposed to
+ * to LoadHeaderEntry that modifies it.
+ * @param entry Header Entry whose value shall be loaded.
+ * @return
+ */
+void gdcmHeader::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) {
+ long PositionOnEntry = ftell(fp);
+ LoadHeaderEntry(entry);
+ fseek(fp, PositionOnEntry, SEEK_SET);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief
+ * @param entry Header Entry whose value shall be loaded.
+
+ * @return
+ */
+ void gdcmHeader::FindHeaderEntryLength (gdcmHeaderEntry * ElVal) {
+ guint16 element = ElVal->GetElement();
+ guint16 group = ElVal->GetGroup();
+ std::string vr = ElVal->GetVR();
+ guint16 length16;
+ if( (element == 0x0010) && (group == 0x7fe0) ) {
+ dbg.SetDebug(-1);
+ dbg.Verbose(2, "gdcmHeader::FindLength: ",
+ "we reached 7fe0 0010");
+ }
+
+ 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(FindHeaderEntryLengthOB());
+ return;
+ }
+ FixHeaderEntryFoundLength(ElVal, length32);
+ return;
+ }
+
+ // 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 consists 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
+ // encounter 1024 (0x0400) chances are the encoding changed and we
+ // found a group with big endian encoding.
+ // We shall use this second strategy. In order to 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 already 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 have got our
+ // hands on a big endian encoded file: we switch the swap code to
+ // big endian and proceed...
+ if ( (element == 0x0000) && (length16 == 0x0400) ) {
+ if ( ! IsExplicitVRBigEndianTransferSyntax() ) {
+ dbg.Verbose(0, "gdcmHeader::FindLength", "not explicit VR");
+ errno = 1;
+ return;
+ }
+ 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 = GetDictEntryByNumber(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.");
+ // Actually, length= 0xffff means that we deal with
+ // Unknown Sequence Length
+ }
+
+ FixHeaderEntryFoundLength(ElVal, (guint32)length16);
+ return;
+ }
+
+ // 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.
+ FixHeaderEntryFoundLength(ElVal, ReadInt32());
+ return;
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Find the Value Representation of the current Dicom Element.
+ * @param ElVal
+ */
+void gdcmHeader::FindHeaderEntryVR( gdcmHeaderEntry *ElVal) {
+ if (filetype != ExplicitVR)
+ return;
+
+ char VR[3];
+ std::string vr;
+ int lgrLue;
+ char msg[100]; // for sprintf. Sorry
+
+ 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;
+
+ lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
+ VR[2]=0;
+ vr = std::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.
+
+ sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
+ ElVal->GetGroup(),ElVal->GetElement());
+ dbg.Verbose(1, "gdcmHeader::FindVR: ",msg);
+
+ 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
+ * @param ElVal
+ * @return
+ */
+void gdcmHeader::SkipHeaderEntry(gdcmHeaderEntry * entry) {
+ SkipBytes(entry->GetLength());
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief When the length of an element value is obviously wrong (because
+ * the parser went Jabberwocky) one can hope improving things by
+ * applying this heuristic.
+ */
+void gdcmHeader::FixHeaderEntryFoundLength(gdcmHeaderEntry * ElVal, guint32 FoundLength) {
+
+ ElVal->SetReadLength(FoundLength); // will be updated only if a bug is found
+
+ if ( FoundLength == 0xffffffff) {
+ FoundLength = 0;
+ }
+
+ // Sorry for the patch!
+ // XMedCom did the trick to read some nasty GE images ...
+ else if (FoundLength == 13) {
+ // The following 'if' will be removed when there is no more
+ // images on Creatis HDs with a 13 length for Manufacturer...
+ if ( (ElVal->GetGroup() != 0x0008) ||
+ ( (ElVal->GetElement() != 0x0070) && (ElVal->GetElement() != 0x0080) ) ) {
+ // end of remove area
+ FoundLength =10;
+ ElVal->SetReadLength(10); // a bug is to be fixed
+ }
+ }
+ // to fix some garbage 'Leonardo' Siemens images
+ // May be commented out to avoid overhead
+ else if ( (ElVal->GetGroup() == 0x0009) &&
+ ( (ElVal->GetElement() == 0x1113) || (ElVal->GetElement() == 0x1114) ) ){
+ FoundLength =4;
+ ElVal->SetReadLength(4); // a bug is to be fixed
+ }
+ // end of fix
+
+ // to try to 'go inside' SeQuences (with length), and not to skip them
+ else if ( ElVal->GetVR() == "SQ") {
+ if (enableSequences) // only if the user does want to !
+ FoundLength =0;
+ }
+
+ // a SeQuence Element is beginning
+ // Let's forget it's length
+ // (we want to 'go inside')
+
+ // Pb : *normaly* fffe|e000 is just a marker, its length *should be* zero
+ // in gdcm-MR-PHILIPS-16-Multi-Seq.dcm we find lengthes as big as 28800
+ // if we set the length to zero IsHeaderEntryAnInteger() breaks...
+ // if we don't, we lost 28800 characters from the Header :-(
+
+ else if(ElVal->GetGroup() == 0xfffe){
+ // sometimes, length seems to be wrong
+ FoundLength =0; // some more clever checking to be done !
+ // I give up!
+ // only gdcm-MR-PHILIPS-16-Multi-Seq.dcm
+ // causes troubles :-(
+ }
+
+ ElVal->SetUsableLength(FoundLength);
+}
+
+/**
+ * \ingroup gdcmHeader
+ * \brief Apply some heuristics to predict wether the considered
+ * element value contains/represents an integer or not.
+ * @param ElVal The element value on which to apply the predicate.
+ * @return The result of the heuristical predicate.
+ */
+bool gdcmHeader::IsHeaderEntryAnInteger(gdcmHeaderEntry * ElVal) {
+ guint16 element = ElVal->GetElement();
+ guint16 group = ElVal->GetGroup();
+ std::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 {
+ std::ostringstream s;
+ s << "Erroneous Group Length element length on :" \
+ << std::hex << group << " , " << element;
+ dbg.Error("gdcmHeader::IsAnInteger",
+ s.str().c_str());
+ }
+ }
+ if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
+ return true;
+
+ return false;