// gdcmHeader.cxx #include #include // For nthos: #ifdef _MSC_VER #include #else #include #endif #include // for isalpha #include #include "gdcmUtil.h" #include "gdcmHeader.h" #include "iddcmjpeg.h" // Refer to gdcmHeader::CheckSwap() #define HEADER_LENGTH_TO_READ 256 // Refer to gdcmHeader::SetMaxSizeLoadElementValue() #define _MaxSizeLoadElementValue_ 1024 VRHT * gdcmHeader::dicom_vr = (VRHT*)0; void gdcmHeader::Initialise(void) { if (!gdcmHeader::dicom_vr) InitVRDict(); Dicts = new gdcmDictSet(); RefPubDict = Dicts->GetDefaultPubDict(); RefShaDict = (gdcmDict*)0; } gdcmHeader::gdcmHeader(const char *InFilename, bool exception_on_error) throw(gdcmFileError) { SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); filename = InFilename; Initialise(); fp=fopen(InFilename,"rb"); if(exception_on_error) { if(!fp) throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)"); } else dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename); ParseHeader(); LoadElements(); } gdcmHeader::~gdcmHeader (void) { //FIXME obviously there is much to be done here ! fclose(fp); return; } void gdcmHeader::InitVRDict (void) { if (dicom_vr) { dbg.Verbose(0, "gdcmHeader::InitVRDict:", "VR dictionary allready set"); return; } VRHT *vr = new VRHT; (*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"; // 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 Discover what the swap code is (among little endian, big endian, * bad little endian, bad big endian). * */ 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_LENGTH_TO_READ]; // 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 net2host = false; // The easiest case is the one of a DICOM header, since it possesses a // file preamble where it suffice to look for the string "DICM". lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp); entCur = deb + 128; if(memcmp(entCur, "DICM", (size_t)4) == 0) { dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3"); // Next, determine the value representation (VR). Let's skip to the // first element (0002, 0000) and check there if we find "UL" // - or "OB" if the 1st one is (0002,0001) -, // 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),or (0002, 0001) // i.e. a total of 136 bytes. entCur = deb + 136; // FIXME // Use gdcmHeader::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? if( (memcmp(entCur, "UL", (size_t)2) == 0) || (memcmp(entCur, "OB", (size_t)2) == 0) || (memcmp(entCur, "UI", (size_t)2) == 0) ) { filetype = ExplicitVR; dbg.Verbose(1, "gdcmHeader::CheckSwap:", "explicit Value Representation"); } else { filetype = ImplicitVR; dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not an explicit Value Representation"); } if (net2host) { sw = 4321; 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); return; } // End of DicomV3 // 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). dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 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; // We assume the array of char we are considering contains the binary // representation of a 32 bits integer. Hence the following dirty // trick : s = *((guint32 *)(entCur)); switch (s) { case 0x00040000 : sw = 3412; filetype = ACR; return; case 0x04000000 : sw = 4321; filetype = ACR; return; case 0x00000400 : sw = 2143; filetype = ACR; return; case 0x00000004 : sw = 0; filetype = ACR; return; default : dbg.Verbose(0, "gdcmHeader::CheckSwap:", "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 is // not present. Then the only info we have is the net2host one. filetype = Unknown; if (! net2host ) sw = 0; else sw = 4321; 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); if (IsJPEGLossless()) { _Pixels=_IdDcmJpegRead(fp); } else { fread(_Pixels, 1, lgrTotale, fp); } } /** * \ingroup gdcmHeader * \brief Find the value representation of the current tag. */ void gdcmHeader::FindVR( gdcmElValue *ElVal) { if (filetype != ExplicitVR) return; 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; 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. 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 ImplicitVRLittleEndian one. * * @return True when ImplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2" ) return true; return false; } /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was allready encountered * and if it corresponds to a ExplicitVRLittleEndian one. * * @return True when ExplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.1" ) return true; return false; } /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was allready encountered * and if it corresponds to a DeflatedExplicitVRLittleEndian one. * * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.1.99" ) return true; return false; } /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was allready encountered * and if it corresponds to a Explicit VR Big Endian one. * * @return True when big endian found. False in all other cases. */ bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.2" ) //1.2.2 ??? A verifier ! return true; return false; } /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was allready encountered * and if it corresponds to a JPEGBaseLineProcess1 one. * * @return True when JPEGBaseLineProcess1found. False in all other cases. */ bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.50" ) return true; return false; } // faire qq chose d'intelligent a la place de ça bool gdcmHeader::IsJPEGLossless(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); const char * Transfert = Element->GetValue().c_str(); if ( memcmp(Transfert+strlen(Transfert)-2 ,"70",2)==0) return true; if ( memcmp(Transfert+strlen(Transfert)-2 ,"55",2)==0) return true; return false; } /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was allready encountered * and if it corresponds to a JPEGExtendedProcess2-4 one. * * @return True when JPEGExtendedProcess2-4 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.51" ) return true; return false; } /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was allready encountered * and if it corresponds to a JPEGExtendeProcess3-5 one. * * @return True when JPEGExtendedProcess3-5 found. False in all other cases. */ bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.52" ) return true; return false; } /** * \ingroup gdcmHeader * \brief Determines if the Transfer Syntax was allready encountered * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. * * @return True when JPEGSpectralSelectionProcess6-8 found. False in all * other cases. */ bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); if ( !Element ) return false; LoadElementValueSafe(Element); string Transfer = Element->GetValue(); if ( Transfer == "1.2.840.10008.1.2.4.53" ) return true; return false; } /** * \ingroup gdcmHeader * \brief Predicate for dicom version 3 file. * @return True when the file is a dicom version 3. */ bool gdcmHeader::IsDicomV3(void) { if ( (filetype == ExplicitVR) || (filetype == ImplicitVR) ) return true; return false; } /** * \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::FixFoundLength(gdcmElValue * ElVal, guint32 FoundLength) { if ( FoundLength == 0xffffffff) FoundLength = 0; ElVal->SetLength(FoundLength); } 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(); if (errno == 1) return 0; 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."); errno = 1; return 0; } if ( n == 0xe0dd ) FoundSequenceDelimiter = true; else if ( n != 0xe000) { dbg.Verbose(1, "gdcmHeader::FindLengthOB: ", "wrong element for an item sequence."); errno = 1; return 0; } 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(gdcmElValue * ElVal) { guint16 element = ElVal->GetElement(); string vr = ElVal->GetVR(); guint16 length16; 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; } // 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 // 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 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 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 have 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 ( ! 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 = GetDictEntryByKey(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; } // 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 Swaps back the bytes of 4-byte long integer accordingly to * processor order. * * @return The suggested integer. */ guint32 gdcmHeader::SwapLong(guint32 a) { switch (sw) { case 0 : break; case 4321 : a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) ); break; case 3412 : a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) ); break; case 2143 : a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); break; default : dbg.Error(" gdcmHeader::SwapLong : unset swap code"); a=0; } return(a); } /** * \ingroup gdcmHeader * \brief Swaps the bytes so they agree with the processor order * @return The properly swaped 16 bits integer. */ 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(gdcmElValue * 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 Loads the element content if it's length is not bigger * than the value specified with * gdcmHeader::SetMaxSizeLoadElementValue() */ void gdcmHeader::LoadElementValue(gdcmElValue * 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); // FIXME 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 // Well, I'm expecting your code !!! 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; 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) { ostringstream s; s << "gdcm::NotLoaded."; s << " Address:" << (long)ElVal->GetOffset(); s << " Length:" << ElVal->GetLength(); ElVal->SetValue(s.str()); return; } // 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. // pour les elements de Value Multiplicity > 1 // on aura en fait une serie d'entiers // on devrait pouvoir faire + compact (?) if ( IsAnInteger(ElVal) ) { guint32 NewInt; 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; } } } ElVal->SetValue(s.str()); return; } // 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; } 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); } /** * \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(gdcmElValue * 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); errno = 0; if ( item_read != 1 ) { dbg.Verbose(1, "gdcmHeader::ReadInt16", " File read error"); errno = 1; return 0; } 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); errno = 0; if ( item_read != 1 ) { dbg.Verbose(1, "gdcmHeader::ReadInt32", " File read error"); errno = 1; return 0; } g = SwapLong(g); return g; } // // TODO : JPR Pour des raisons d'homogeneité de noms, // remplacer les quelques GetxxxByKey // par des GetxxxByNumber, lorsqu'on passe gr, el en param. // il peut etre interessant de rajouter des GetxxxByKey, auxquels on passe *vraiment* une TagKey // /** * \ingroup gdcmHeader * \brief Build a new Element Value from all the low level arguments. * Check for existence of dictionary entry, and build * a default one when absent. * @param Group group of the underlying DictEntry * @param Elem element of the underlying DictEntry */ gdcmElValue* gdcmHeader::NewElValueByKey(guint16 Group, guint16 Elem) { // Find out if the tag we encountered is in the dictionaries: gdcmDictEntry * NewTag = GetDictEntryByKey(Group, Elem); if (!NewTag) NewTag = new gdcmDictEntry(Group, Elem); gdcmElValue* NewElVal = new gdcmElValue(NewTag); if (!NewElVal) { dbg.Verbose(1, "gdcmHeader::NewElValueByKey", "failed to allocate gdcmElValue"); return (gdcmElValue*)0; } return NewElVal; } /** * \ingroup gdcmHeader * \brief TODO * @param */ int gdcmHeader::ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Elem ) { gdcmElValue* nvElValue=NewElValueByKey(Group, Elem); PubElValSet.Add(nvElValue); PubElValSet.SetElValueByNumber(Value, Group, Elem); return(1); } /** * \ingroup gdcmHeader * \brief Build a new Element Value from all the low level arguments. * Check for existence of dictionary entry, and build * a default one when absent. * @param Name Name of the underlying DictEntry */ gdcmElValue* gdcmHeader::NewElValueByName(string Name) { gdcmDictEntry * NewTag = GetDictEntryByName(Name); if (!NewTag) NewTag = new gdcmDictEntry(0xffff, 0xffff, "LO", "Unknown", Name); gdcmElValue* NewElVal = new gdcmElValue(NewTag); if (!NewElVal) { dbg.Verbose(1, "gdcmHeader::ObtainElValueByName", "failed to allocate gdcmElValue"); return (gdcmElValue*)0; } return NewElVal; } /** * \ingroup gdcmHeader * \brief Read the next tag but WITHOUT loading it's value * @return On succes the newly created ElValue, NULL on failure. */ gdcmElValue * gdcmHeader::ReadNextElement(void) { guint16 g,n; gdcmElValue * NewElVal; g = ReadInt16(); n = ReadInt16(); if (errno == 1) // We reached the EOF (or an error occured) and header parsing // has to be considered as finished. return (gdcmElValue *)0; NewElVal = NewElValueByKey(g, n); FindVR(NewElVal); FindLength(NewElVal); if (errno == 1) // Call it quits return (gdcmElValue *)0; NewElVal->SetOffset(ftell(fp)); return NewElVal; } /** * \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::IsAnInteger(gdcmElValue * 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 { printf("Erroneous Group Length element length %d\n",length); dbg.Error("gdcmHeader::IsAnInteger", "Erroneous Group Length element length."); } } if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) return true; return false; } /** * \ingroup gdcmHeader * \brief Recover the offset (from the beginning of the file) of the pixels. */ 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 == "gdcm::Unfound" ) { grPixel = 0x7fe0; } else { grPixel = (guint16) atoi( ImageLocation.c_str() ); } if (grPixel != 0x7fe0) // This is a kludge for old dirty Philips imager. numPixel = 0x1010; else numPixel = 0x0010; gdcmElValue* PixelElement = PubElValSet.GetElementByNumber(grPixel, numPixel); if (PixelElement) return PixelElement->GetOffset(); else return 0; } /** * \ingroup gdcmHeader * \brief Searches both the public and the shadow dictionary (when they * exist) for the presence of the DictEntry with given * group and element. The public dictionary has precedence on the * shadow one. * @param group group of the searched DictEntry * @param element element of the searched DictEntry * @return Corresponding DictEntry when it exists, NULL otherwise. */ gdcmDictEntry * gdcmHeader::GetDictEntryByKey(guint16 group, guint16 element) { gdcmDictEntry * found = (gdcmDictEntry*)0; if (!RefPubDict && !RefShaDict) { dbg.Verbose(0, "gdcmHeader::GetDictEntry", "we SHOULD have a default dictionary"); } if (RefPubDict) { found = RefPubDict->GetTagByKey(group, element); if (found) return found; } if (RefShaDict) { found = RefShaDict->GetTagByKey(group, element); if (found) return found; } return found; } /** * \ingroup gdcmHeader * \brief Searches both the public and the shadow dictionary (when they * exist) for the presence of the DictEntry with given name. * The public dictionary has precedence on the shadow one. * @param Name name of the searched DictEntry * @return Corresponding DictEntry when it exists, NULL otherwise. */ gdcmDictEntry * gdcmHeader::GetDictEntryByName(string Name) { gdcmDictEntry * found = (gdcmDictEntry*)0; if (!RefPubDict && !RefShaDict) { dbg.Verbose(0, "gdcmHeader::GetDictEntry", "we SHOULD have a default dictionary"); } if (RefPubDict) { found = RefPubDict->GetTagByName(Name); if (found) return found; } if (RefShaDict) { found = RefShaDict->GetTagByName(Name); if (found) return found; } return found; } /** * \ingroup gdcmHeader * \brief Searches within the public dictionary for element value of * a given tag. * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value when it exists, and the string * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) { return PubElValSet.GetElValueByNumber(group, element); } /** * \ingroup gdcmHeader * \brief Searches within the public dictionary for element value * representation of a given tag. * * Obtaining the VR (Value Representation) might be needed by caller * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) { gdcmElValue* elem = PubElValSet.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); } /** * \ingroup gdcmHeader * \brief Searches within the public dictionary for element value of * a given tag. * @param TagName name of the researched element. * @return Corresponding element value when it exists, and the string * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValByName(string TagName) { return PubElValSet.GetElValueByName(TagName); } /** * \ingroup gdcmHeader * \brief Searches within the elements parsed with the public dictionary for * the element value representation of a given tag. * * Obtaining the VR (Value Representation) might be needed by caller * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. * @param TagName name of the researched element. * @return Corresponding element value representation when it exists, * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetPubElValRepByName(string TagName) { gdcmElValue* elem = PubElValSet.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); } /** * \ingroup gdcmHeader * \brief Searches within elements parsed with the SHADOW dictionary * for the element value of a given tag. * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) { return ShaElValSet.GetElValueByNumber(group, element); } /** * \ingroup gdcmHeader * \brief Searches within the elements parsed with the SHADOW dictionary * for the element value representation of a given tag. * * Obtaining the VR (Value Representation) might be needed by caller * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) { gdcmElValue* elem = ShaElValSet.GetElementByNumber(group, element); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); } /** * \ingroup gdcmHeader * \brief Searches within the elements parsed with the shadow dictionary * for an element value of given tag. * @param TagName name of the researched element. * @return Corresponding element value when it exists, and the string * "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValByName(string TagName) { return ShaElValSet.GetElValueByName(TagName); } /** * \ingroup gdcmHeader * \brief Searches within the elements parsed with the shadow dictionary for * the element value representation of a given tag. * * Obtaining the VR (Value Representation) might be needed by caller * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. * @param TagName name of the researched element. * @return Corresponding element value representation when it exists, * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetShaElValRepByName(string TagName) { gdcmElValue* elem = ShaElValSet.GetElementByName(TagName); if ( !elem ) return "gdcm::Unfound"; return elem->GetVR(); } /** * \ingroup gdcmHeader * \brief Searches within elements parsed with the public dictionary * and then within the elements parsed with the shadow dictionary * for the element value of a given tag. * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) { string pub = GetPubElValByNumber(group, element); if (pub.length()) return pub; return GetShaElValByNumber(group, element); } /** * \ingroup gdcmHeader * \brief Searches within elements parsed with the public dictionary * and then within the elements parsed with the shadow dictionary * for the element value representation of a given tag. * * Obtaining the VR (Value Representation) might be needed by caller * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. * @param group Group of the researched tag. * @param element Element of the researched tag. * @return Corresponding element value representation when it exists, * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) { string pub = GetPubElValRepByNumber(group, element); if (pub.length()) return pub; return GetShaElValRepByNumber(group, element); } /** * \ingroup gdcmHeader * \brief Searches within elements parsed with the public dictionary * and then within the elements parsed with the shadow dictionary * for the element value of a given tag. * @param TagName name of the researched element. * @return Corresponding element value when it exists, * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetElValByName(string TagName) { string pub = GetPubElValByName(TagName); if (pub.length()) return pub; return GetShaElValByName(TagName); } /** * \ingroup gdcmHeader * \brief Searches within elements parsed with the public dictionary * and then within the elements parsed with the shadow dictionary * for the element value representation of a given tag. * * Obtaining the VR (Value Representation) might be needed by caller * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. * @param TagName name of the researched element. * @return Corresponding element value representation when it exists, * and the string "gdcm::Unfound" otherwise. */ string gdcmHeader::GetElValRepByName(string TagName) { string pub = GetPubElValRepByName(TagName); if (pub.length()) return pub; return GetShaElValRepByName(TagName); } /** * \ingroup gdcmHeader * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance * through it's (group, element) and modifies it's content with * the given value. * @param content new value to substitute with * @param group group of the ElVal to modify * @param element element of the ElVal to modify */ int gdcmHeader::SetPubElValByNumber(string content, guint16 group, guint16 element) { return ( PubElValSet.SetElValueByNumber (content, group, element) ); } /** * \ingroup gdcmHeader * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance * through tag name and modifies it's content with the given value. * @param content new value to substitute with * @param TagName name of the tag to be modified */ int gdcmHeader::SetPubElValByName(string content, string TagName) { return ( PubElValSet.SetElValueByName (content, TagName) ); } /** * \ingroup gdcmHeader * \brief Accesses an existing gdcmElValue in the PubElValSet of this instance * through it's (group, element) and modifies it's length with * the given value. * \warning Use with extreme caution. * @param length new length to substitute with * @param group group of the ElVal to modify * @param element element of the ElVal to modify * @return 1 on success, 0 otherwise. */ int gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group, guint16 element) { return ( PubElValSet.SetElValueLengthByNumber (length, group, element) ); } /** * \ingroup gdcmHeader * \brief Accesses an existing gdcmElValue in the ShaElValSet of this instance * through it's (group, element) and modifies it's content with * the given value. * @param content new value to substitute with * @param group group of the ElVal to modify * @param element element of the ElVal to modify * @return 1 on success, 0 otherwise. */ int gdcmHeader::SetShaElValByNumber(string content, guint16 group, guint16 element) { return ( ShaElValSet.SetElValueByNumber (content, group, element) ); } /** * \ingroup gdcmHeader * \brief Accesses an existing gdcmElValue in the ShaElValSet of this instance * through tag name and modifies it's content with the given value. * @param content new value to substitute with * @param TagName name of the tag to be modified */ int gdcmHeader::SetShaElValByName(string content, string TagName) { return ( ShaElValSet.SetElValueByName (content, TagName) ); } /** * \ingroup gdcmHeader * \brief Parses the header of the file but WITHOUT loading element values. */ void gdcmHeader::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { gdcmElValue * newElValue = (gdcmElValue *)0; rewind(fp); CheckSwap(); while ( (newElValue = ReadNextElement()) ) { SkipElementValue(newElValue); PubElValSet.Add(newElValue); } } /** * \ingroup gdcmHeader * \brief Retrieve the number of columns of image. * @return The encountered size when found, 0 by default. */ int gdcmHeader::GetXSize(void) { // We cannot check for "Columns" because the "Columns" tag is present // both in IMG (0028,0011) and OLY (6000,0011) sections of the dictionary. string StrSize = GetPubElValByNumber(0x0028,0x0011); if (StrSize == "gdcm::Unfound") return 0; return atoi(StrSize.c_str()); } /** * \ingroup gdcmHeader * \brief Retrieve the number of lines of image. * \warning The defaulted value is 1 as opposed to gdcmHeader::GetXSize() * @return The encountered size when found, 1 by default. */ int gdcmHeader::GetYSize(void) { // We cannot check for "Rows" because the "Rows" tag is present // both in IMG (0028,0010) and OLY (6000,0010) sections of the dictionary. string StrSize = GetPubElValByNumber(0x0028,0x0010); if (StrSize != "gdcm::Unfound") return atoi(StrSize.c_str()); if ( IsDicomV3() ) return 0; else // The Rows (0028,0010) entry is optional for ACR/NEMA. It might // hence be a signal (1d image). So we default to 1: return 1; } /** * \ingroup gdcmHeader * \brief Retrieve the number of planes of volume or the number * of frames of a multiframe. * \warning When present we consider the "Number of Frames" as the third * dimension. When absent we consider the third dimension as * being the "Planes" tag content. * @return The encountered size when found, 1 by default. */ int gdcmHeader::GetZSize(void) { // Both in DicomV3 and ACR/Nema the consider the "Number of Frames" // as the third dimension. string StrSize = GetPubElValByNumber(0x0028,0x0008); if (StrSize != "gdcm::Unfound") return atoi(StrSize.c_str()); // We then consider the "Planes" entry as the third dimension [we // cannot retrieve by name since "Planes tag is present both in // IMG (0028,0012) and OLY (6000,0012) sections of the dictionary]. StrSize = GetPubElValByNumber(0x0028,0x0012); if (StrSize != "gdcm::Unfound") return atoi(StrSize.c_str()); return 1; } /** * \ingroup gdcmHeader * \brief Build the Pixel Type of the image. * Possible values are: * - U8 unsigned 8 bit, * - S8 signed 8 bit, * - U16 unsigned 16 bit, * - S16 signed 16 bit, * - U32 unsigned 32 bit, * - S32 signed 32 bit, * \warning 12 bit images appear as 16 bit. * @return */ string gdcmHeader::GetPixelType(void) { string BitsAlloc; BitsAlloc = GetElValByName("Bits Allocated"); if (BitsAlloc == "gdcm::Unfound") { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); BitsAlloc = string("16"); } if (BitsAlloc == "12") BitsAlloc = string("16"); string Signed; Signed = GetElValByName("Pixel Representation"); if (Signed == "gdcm::Unfound") { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); BitsAlloc = string("0"); } if (Signed == "0") Signed = string("U"); else Signed = string("S"); return( BitsAlloc + Signed); } /** * \ingroup gdcmHeader * \brief This predicate, based on hopefully reasonnable heuristics, * decides whether or not the current gdcmHeader was properly parsed * and contains the mandatory information for being considered as * a well formed and usable image. * @return true when gdcmHeader is the one of a reasonable Dicom file, * false otherwise. */ bool gdcmHeader::IsReadable(void) { if ( GetElValByName("Image Dimensions") != "gdcm::Unfound" && atoi(GetElValByName("Image Dimensions").c_str()) > 4 ) { return false; } if ( GetElValByName("Bits Allocated") == "gdcm::Unfound" ) return false; if ( GetElValByName("Bits Stored") == "gdcm::Unfound" ) return false; if ( GetElValByName("High Bit") == "gdcm::Unfound" ) return false; if ( GetElValByName("Pixel Representation") == "gdcm::Unfound" ) return false; return true; } /** * \ingroup gdcmHeader * \brief Small utility function that creates a new manually crafted * (as opposed as read from the file) gdcmElValue with user * specified name and adds it to the public tag hash table. * \note A fake TagKey is generated so the PubDict can keep it's coherence. * @param NewTagName The name to be given to this new tag. * @param VR The Value Representation to be given to this new tag. * @ return The newly hand crafted Element Value. */ gdcmElValue* gdcmHeader::NewManualElValToPubDict(string NewTagName, string VR) { gdcmElValue* NewElVal = (gdcmElValue*)0; guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info guint32 FreeElem = 0; gdcmDictEntry* NewEntry = (gdcmDictEntry*)0; FreeElem = PubElValSet.GenerateFreeTagKeyInGroup(StuffGroup); if (FreeElem == UINT32_MAX) { dbg.Verbose(1, "gdcmHeader::NewManualElValToPubDict", "Group 0xffff in Public Dict is full"); return (gdcmElValue*)0; } NewEntry = new gdcmDictEntry(StuffGroup, FreeElem, VR, "GDCM", NewTagName); NewElVal = new gdcmElValue(NewEntry); PubElValSet.Add(NewElVal); return NewElVal; } /** * \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 = PubElValSet.GetTagHt(); for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { LoadElementValue(tag->second); } } void gdcmHeader::PrintPubElVal(ostream & os) { PubElValSet.Print(os); } void gdcmHeader::PrintPubDict(ostream & os) { RefPubDict->Print(os); } int gdcmHeader::Write(FILE * fp, FileType type) { return PubElValSet.Write(fp, type); }