- gdcmHeaderEntry *gdcmHeader::GetHeaderEntryByName(std::string tagName) {
- gdcmDictEntry *dictEntry = RefPubDict->GetTagByName(tagName);
- if( dictEntry == NULL)
- return NULL;
-
- return(GetHeaderEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()));
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Checks if a given HeaderEntry (group,number)
- * \ exists in the Public HeaderEntrySet
- * @param Group
- * @param Elem
- * @return boolean
- */
-bool gdcmHeader::CheckIfExistByNumber(guint16 Group, guint16 Elem ) {
- return (PubEntrySet.CheckIfExistByNumber(Group, Elem)>0);
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Gets (from Header) the offset of a 'non string' element value
- * \ (LoadElementValues has already be executed)
- * @param Group
- * @param Elem
- * @return File Offset of the Element Value
- */
-size_t gdcmHeader::GetPubEntryOffsetByNumber(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
- if (!Entry) {
- dbg.Verbose(1, "gdcmHeader::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
- return (size_t)0;
- }
- return Entry->GetOffset();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Gets (from Header) a 'non string' element value
- * \ (LoadElementValues has already be executed)
- * @param Group
- * @param Elem
- * @return Pointer to the 'non string' area
- */
-void * gdcmHeader::GetPubEntryVoidAreaByNumber(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem);
- if (!Entry) {
- dbg.Verbose(1, "gdcmHeader::GetHeaderEntryByNumber",
- "failed to Locate gdcmHeaderEntry");
- return (NULL);
- }
- return Entry->GetVoidArea();
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Loads (from disk) the element content
- * when a string is not suitable
- */
-void * gdcmHeader::LoadEntryVoidArea(guint16 Group, guint16 Elem) {
- gdcmHeaderEntry * Element= GetHeaderEntryByNumber(Group, Elem);
- if ( !Element )
- return NULL;
- size_t o =(size_t)Element->GetOffset();
- fseek(fp, o, SEEK_SET);
- int l=Element->GetLength();
- void * a = malloc(l);
- if(!a) {
- return NULL;
- }
-
- PubEntrySet.SetVoidAreaByNumber(a, Group, Elem);
- // TODO check the result
- size_t l2 = fread(a, 1, l ,fp);
- if(l != l2) {
- free(a);
- return NULL;
- }
- return a;
-}
-
-//-----------------------------------------------------------------------------
-// Private
-/**
- * \ingroup gdcmHeader
- * \brief Loads the element values of all the Header Entries pointed in the
- * public Chained List.
- */
-void gdcmHeader::LoadHeaderEntries(void) {
- rewind(fp);
- for (ListTag::iterator i = GetPubListEntry().begin();
- i != GetPubListEntry().end();
- ++i){
- LoadHeaderEntry(*i);
- }
-
- rewind(fp);
-
- // Load 'non string' values
- std::string PhotometricInterpretation = GetPubEntryByNumber(0x0028,0x0004);
- if( PhotometricInterpretation == "PALETTE COLOR " ){
- LoadEntryVoidArea(0x0028,0x1200); // gray LUT
- LoadEntryVoidArea(0x0028,0x1201); // R LUT
- LoadEntryVoidArea(0x0028,0x1202); // G LUT
- LoadEntryVoidArea(0x0028,0x1203); // B LUT
-
- LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data
- }
-
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to read ACR-LibIDO formated images
- //
- // if recognition code tells us we deal with a LibIDO image
- // we switch lineNumber and columnNumber
- //
- std::string RecCode;
- RecCode = GetPubEntryByNumber(0x0008, 0x0010); // recognition code
- if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
- RecCode == "CANRME_AILIBOD1_1." ) {
- filetype = ACR_LIBIDO;
- std::string rows = GetPubEntryByNumber(0x0028, 0x0010);
- std::string columns = GetPubEntryByNumber(0x0028, 0x0011);
- SetPubEntryByNumber(columns, 0x0028, 0x0010);
- SetPubEntryByNumber(rows , 0x0028, 0x0011);
- }
- // ----------------- End of Special Patch ----------------
-}
-
-/**
- * \ingroup gdcmHeader
- * \brief Loads the element content if it's length is not bigger
- * than the value specified with
- * gdcmHeader::SetMaxSizeLoadElementValue()
- * @param ElVal Header Entry (Dicom Element) to be dealt with
- */
-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){
- //printf("========================= %08x %d\n",FoundLength,FoundLength);
- // sometimes, length seems to be wrong
- //FoundLength =0; // some more clever checking to be done !
- }
-
- 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;
-}