X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.cxx;h=31bf7bc314d8f9bdaee95eb7f67ba9e4bb551d05;hb=0574f31372f78bf8399e42ee04bd0010e684c440;hp=e9ae38fc4c71c315e2f68879429bb3a6fc330da7;hpb=5d5448482dc2b56be816c48df294af6884746547;p=gdcm.git diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx index e9ae38fc..31bf7bc3 100644 --- a/src/gdcmHeader.cxx +++ b/src/gdcmHeader.cxx @@ -1,1980 +1,269 @@ -// $Header: /cvs/public/gdcm/src/Attic/gdcmHeader.cxx,v 1.117 2003/11/13 18:08:34 jpr Exp $ - +// gdcmHeader.cxx +//----------------------------------------------------------------------------- #include "gdcmHeader.h" #include #include -// For nthos: -#ifdef _MSC_VER -#include -#else -#include -#endif #include // for isalpha -#include + #include "gdcmUtil.h" #include "gdcmTS.h" -// Refer to gdcmHeader::CheckSwap() -#define HEADER_LENGTH_TO_READ 256 -// Refer to gdcmHeader::SetMaxSizeLoadElementValue() -//#define _MaxSizeLoadElementValue_ 1024 -#define _MaxSizeLoadElementValue_ 4096 -/** - * \ingroup gdcmHeader - * \brief - */ -void gdcmHeader::Initialise(void) { - dicom_vr = gdcmGlobal::GetVR(); - dicom_ts = gdcmGlobal::GetTS(); - Dicts = gdcmGlobal::GetDicts(); - RefPubDict = Dicts->GetDefaultPubDict(); - RefShaDict = (gdcmDict*)0; -} - -/** - * \ingroup gdcmHeader - * \brief - * @param InFilename - * @param exception_on_error - */ -gdcmHeader::gdcmHeader(const char *InFilename, - bool exception_on_error, - bool enable_sequences ) { - if (enable_sequences) - enableSequences = 1; - else - enableSequences = 0; - - SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); - filename = InFilename; - Initialise(); - if ( !OpenFile(exception_on_error)) - return; - ParseHeader(); - LoadElements(); - CloseFile(); -} - -/** - * \ingroup gdcmHeader - * \brief - * @param exception_on_error - */ -gdcmHeader::gdcmHeader(bool exception_on_error) { - SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_); - Initialise(); -} - -/** - * \ingroup gdcmHeader - * \brief - * @param exception_on_error - * @return - */ - bool gdcmHeader::OpenFile(bool exception_on_error) - throw(gdcmFileError) { - fp=fopen(filename.c_str(),"rb"); - if(exception_on_error) { - if(!fp) - throw gdcmFileError("gdcmHeader::gdcmHeader(const char *, bool)"); - } - - if ( fp ) { - guint16 zero; - fread(&zero, (size_t)2, (size_t)1, fp); - - //ACR -- or DICOM with no Preamble - if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200) - return true; - //DICOM - fseek(fp, 126L, SEEK_CUR); - char dicm[4]; - fread(dicm, (size_t)4, (size_t)1, fp); - if( memcmp(dicm, "DICM", 4) == 0 ) - return true; - fclose(fp); - dbg.Verbose(0, "gdcmHeader::gdcmHeader not DICOM/ACR", filename.c_str()); - } - else { - dbg.Verbose(0, "gdcmHeader::gdcmHeader cannot open file", filename.c_str()); - } - return false; -} - -/** - * \ingroup gdcmHeader - * \brief - * @return TRUE if the close was successfull - */ -bool gdcmHeader::CloseFile(void) { - int closed = fclose(fp); - fp = (FILE *)0; - if (! closed) - return false; - return true; -} - -/** - * \ingroup gdcmHeader - * \brief Canonical destructor. - */ -gdcmHeader::~gdcmHeader (void) { - dicom_vr = (gdcmVR*)0; - Dicts = (gdcmDictSet*)0; - RefPubDict = (gdcmDict*)0; - RefShaDict = (gdcmDict*)0; - return; -} - -// Fourth semantics: -// -// ---> Warning : This fourth field is NOT part -// of the 'official' Dicom Dictionnary -// and should NOT be used. -// (Not defined for all the groups -// may be removed in a future release) -// -// CMD Command -// META Meta Information -// DIR Directory -// ID -// PAT Patient -// ACQ Acquisition -// REL Related -// IMG Image -// SDY Study -// VIS Visit -// WAV Waveform -// PRC -// DEV Device -// NMI Nuclear Medicine -// MED -// BFS Basic Film Session -// BFB Basic Film Box -// BIB Basic Image Box -// BAB -// IOB -// PJ -// PRINTER -// RT Radio Therapy -// DVH -// SSET -// RES Results -// CRV Curve -// OLY Overlays -// PXL Pixels -// DL Delimiters -// - -/** - * \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 : for 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; -} - -/** - * \ingroup gdcmHeader - * \brief - */ -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; -} - -/** - * \ingroup gdcmHeader - * \brief Find the value representation of the current tag. - * @param ElVal - */ -void gdcmHeader::FindVR( gdcmElValue *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 Determines if the Transfer Syntax was already 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); - std::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 already 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); - std::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 already 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); - std::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 already 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); - std::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 already 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); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.50" ) - return true; - return false; -} - -/** - * \ingroup gdcmHeader - * \brief - * - * @return - */ -bool gdcmHeader::IsJPEGLossless(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - // faire qq chose d'intelligent a la place de ça - 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; - if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true; - - return false; -} - - -/** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already 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); - std::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 already 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); - std::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 already 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); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.4.53" ) - return true; - return false; -} - -/** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a RLE Lossless one. - * - * @return True when RLE Lossless found. False in all - * other cases. - */ -bool gdcmHeader::IsRLELossLessTransferSyntax(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( Transfer == "1.2.840.10008.1.2.5" ) - return true; - return false; -} - -/** - * \ingroup gdcmHeader - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEG200 one.0 - * - * @return True when JPEG2000 (Lossly or LossLess) found. False in all - * other cases. - */ -bool gdcmHeader::IsJPEG2000(void) { - gdcmElValue* Element = PubElValSet.GetElementByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadElementValueSafe(Element); - std::string Transfer = Element->GetValue(); - if ( (Transfer == "1.2.840.10008.1.2.4.90") - || (Transfer == "1.2.840.10008.1.2.4.91") ) - 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) { - - 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') - else if(ElVal->GetGroup() == 0xfffe){ - FoundLength =0; - } - - ElVal->SetUsableLength(FoundLength); -} - -/** - * \ingroup gdcmHeader - * \brief - * - * @return - */ - 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 && g!=0xb00c ) /*for bogus header */ { - char msg[100]; // for sprintf. Sorry - sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n); - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); - errno = 1; - return 0; - } - if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */ - FoundSequenceDelimiter = true; - else if ( n != 0xe000 ){ - char msg[100]; // for sprintf. Sorry - sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n", - n, g,n); - dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",msg); - 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; -} - -/** - * \ingroup gdcmHeader - * \brief - * - * @return - */ - void gdcmHeader::FindLength (gdcmElValue * ElVal) { - guint16 element = ElVal->GetElement(); - guint16 group = ElVal->GetGroup(); - std::string vr = ElVal->GetVR(); - guint16 length16; - if( (element == 0x0010) && (group == 0x7fe0) ) { - dbg.SetDebug(0); - 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(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 - // 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 - } - - 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()); - return; -} - -/** - * \ingroup gdcmHeader - * \brief Swaps back the bytes of 4-byte long integer accordingly to - * processor order. - * @return The properly swaped 32 bits 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); -} - -/** - * \ingroup gdcmHeader - * \brief - * - * @return - */ - void gdcmHeader::SkipBytes(guint32 NBytes) { - //FIXME don't dump the returned value - (void)fseek(fp, (long)NBytes, SEEK_CUR); -} - -/** - * \ingroup gdcmHeader - * \brief - * @param ElVal - * @return - */ - void gdcmHeader::SkipElementValue(gdcmElValue * ElVal) { - SkipBytes(ElVal->GetLength()); -} - -/** - * \ingroup gdcmHeader - * \brief - * @param NewSize - * @return - */ - 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(); - std::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 !!! - - // the test was commented out to 'go inside' the SeQuences - // we don't any longer skip them ! - - // if( vr == "SQ" ) - // 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 an integer is expected, read and convert the following two or - // four bytes properly i.e. as an integer as opposed to a string. - - // Actually, elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - // Any compacter code suggested (?) - - if ( IsAnInteger(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; - } - } - } - s << '\0'; // to avoid oddities on Solaris - 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 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); -} - -/** - * \ingroup gdcmHeader - * \brief Reads a supposed to be 16 Bits integer - * \ (swaps it depending on processor endianity) - * - * @return integer acts as a boolean - */ -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 ) { - // dbg.Verbose(0, "gdcmHeader::ReadInt16", " Failed to read :"); - // if(feof(fp)) - // dbg.Verbose(0, "gdcmHeader::ReadInt16", " End of File encountered"); - if(ferror(fp)) - dbg.Verbose(0, "gdcmHeader::ReadInt16", " File Error"); - errno = 1; - return 0; - } - errno = 0; - g = SwapShort(g); - return g; -} - -/** - * \ingroup gdcmHeader - * \brief Reads a supposed to be 32 Bits integer - * \ (swaps it depending on processor endianity) - * - * @return - */ -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 ) { - //dbg.Verbose(0, "gdcmHeader::ReadInt32", " Failed to read :"); - //if(feof(fp)) - // dbg.Verbose(0, "gdcmHeader::ReadInt32", " End of File encountered"); - if(ferror(fp)) - dbg.Verbose(0, "gdcmHeader::ReadInt32", " File Error"); - errno = 1; - return 0; - } - errno = 0; - g = SwapLong(g); - return g; -} - -/** - * \ingroup gdcmHeader - * \brief - * - * @return - */ - gdcmElValue* gdcmHeader::GetElValueByNumber(guint16 Group, guint16 Elem) { - - gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); - if (!elValue) { - dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", - "failed to Locate gdcmElValue"); - return (gdcmElValue*)0; - } - return elValue; -} - -/** - * \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::NewElValueByNumber(guint16 Group, guint16 Elem) { - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry * NewTag = GetDictEntryByNumber(Group, Elem); - if (!NewTag) - NewTag = new gdcmDictEntry(Group, Elem); - - gdcmElValue* NewElVal = new gdcmElValue(NewTag); - if (!NewElVal) { - dbg.Verbose(1, "gdcmHeader::NewElValueByNumber", - "failed to allocate gdcmElValue"); - return (gdcmElValue*)0; - } - return NewElVal; -} - -/** - * \ingroup gdcmHeader - * \brief TODO - * @param Value - * @param Group - * @param Elem - * \return integer acts as a boolean - */ -int gdcmHeader::ReplaceOrCreateByNumber(std::string Value, - guint16 Group, guint16 Elem ) { - // TODO : FIXME JPRx - // curieux, non ? - // on (je) cree une Elvalue ne contenant pas de valeur - // on l'ajoute au ElValSet - // on affecte une valeur a cette ElValue a l'interieur du ElValSet - // --> devrait pouvoir etre fait + simplement ??? - if (CheckIfExistByNumber(Group, Elem) == 0) { - gdcmElValue* a =NewElValueByNumber(Group, Elem); - if (a == NULL) - return 0; - PubElValSet.Add(a); - } - PubElValSet.SetElValueByNumber(Value, Group, Elem); - return(1); -} - - -/** - * \ingroup gdcmHeader - * \brief Modify (or Creates if not found) an element - * @param Value new value - * @param Group - * @param Elem - * \return integer acts as a boolean - * - */ -int gdcmHeader::ReplaceOrCreateByNumber(char* Value, guint16 Group, guint16 Elem ) { - - gdcmElValue* nvElValue=NewElValueByNumber(Group, Elem); - PubElValSet.Add(nvElValue); - std::string v = Value; - PubElValSet.SetElValueByNumber(v, Group, Elem); - return(1); -} - - -/** - * \ingroup gdcmHeader - * \brief Set a new value if the invoked element exists - * Seems to be useless !!! - * @param Value - * @param Group - * @param Elem - * \return integer acts as a boolean - */ -int gdcmHeader::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) { - - //gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); - std::string v = Value; - PubElValSet.SetElValueByNumber(v, Group, Elem); - return 1; -} - - -/** - * \ingroup gdcmHeader - * \brief Checks if a given ElValue (group,number) - * \ exists in the Public ElValSet - * @param Group - * @param Elem - * @return integer acts as a boolean - */ - -int gdcmHeader::CheckIfExistByNumber(guint16 Group, guint16 Elem ) { - return (PubElValSet.CheckIfExistByNumber(Group, Elem)); - } - -/** - * \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(std::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 = NewElValueByNumber(g, n); - FindVR(NewElVal); - FindLength(NewElVal); - - if (errno == 1) { - // Call it quits - return (gdcmElValue *)0; - } - NewElVal->SetOffset(ftell(fp)); - //if ( (g==0x7fe0) && (n==0x0010) ) - 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 element = ElVal->GetElement(); - 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 { - 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; - std::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 Recover the pixel area length (in Bytes) . - */ -size_t gdcmHeader::GetPixelAreaLength(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; - std::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->GetLength(); - 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::GetDictEntryByNumber(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->GetTagByNumber(group, element); - if (found) - return found; - } - if (RefShaDict) { - found = RefShaDict->GetTagByNumber(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(std::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 ("gdcm::Unfound") otherwise. - */ -std::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 ("gdcm::Unfound") otherwise. - */ -std::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 searched element. - * @return Corresponding element value when it exists, and the string - * GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetPubElValByName(std::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 searched element. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetPubElValRepByName(std::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 searched tag. - * @param element Element of the searched tag. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::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 searched tag. - * @param element Element of the searched tag. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::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 searched element. - * @return Corresponding element value when it exists, and the string - * GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetShaElValByName(std::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 searched element. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetShaElValRepByName(std::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 searched tag. - * @param element Element of the searched tag. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) { - std::string pub = GetPubElValByNumber(group, element); - if (pub.length()) - return pub; - return GetShaElValByNumber(group, element); -} +//----------------------------------------------------------------------------- +// Constructor / Destructor /** * \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 searched tag. - * @param element Element of the searched tag. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. + * \brief + * @param InFilename + * @param exception_on_error + * @param enable_sequences = true to allow the header + * to be parsed *inside* the SeQuences, + * when they have an actual length + * @param ignore_shadow = true if user wants to skip shadow groups + * during parsing, to save memory space */ -std::string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) { - std::string pub = GetPubElValRepByNumber(group, element); - if (pub.length()) - return pub; - return GetShaElValRepByNumber(group, element); +gdcmHeader::gdcmHeader(const char *InFilename, + bool exception_on_error, + bool enable_sequences, + bool ignore_shadow): + gdcmParser(InFilename,exception_on_error,enable_sequences,ignore_shadow) +{ + + // for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010 + // We may encounter the 'RETired' (0x0028, 0x0200) tag + // (Image Location") . This Element contains the number of + // 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. + + // This IS the right place for the code + + std::string ImageLocation = GetEntryByNumber(0x0028, 0x0200); + if ( ImageLocation == GDCM_UNFOUND ) { // Image Location + GrPixel = 0x7fe0; // default value + } else { + GrPixel = (guint16) atoi( ImageLocation.c_str() ); + } + if (GrPixel == 0xe07f) // sometimes Image Location value doesn't follow + GrPixel = 0x7fe0; // the supposed processor endianity. + // see gdcmData/cr172241.dcm + if (GrPixel != 0x7fe0) + // This is a kludge for old dirty Philips imager. + NumPixel = 0x1010; + else + NumPixel = 0x0010; + + TagKey key = gdcmDictEntry::TranslateToKey(GrPixel, NumPixel); + countGrPixel = GetEntry().count(key); } /** * \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 searched element. - * @return Corresponding element value when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. + * \brief Constructor + * @param exception_on_error */ -std::string gdcmHeader::GetElValByName(std::string TagName) { - std::string pub = GetPubElValByName(TagName); - if (pub.length()) - return pub; - return GetShaElValByName(TagName); +gdcmHeader::gdcmHeader(bool exception_on_error) : + gdcmParser(exception_on_error) +{ } /** * \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 searched element. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. + * \brief Canonical destructor. */ -std::string gdcmHeader::GetElValRepByName(std::string TagName) { - std::string pub = GetPubElValRepByName(TagName); - if (pub.length()) - return pub; - return GetShaElValRepByName(TagName); +gdcmHeader::~gdcmHeader (void) { } -/** - * \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(std::string content, guint16 group, - guint16 element) - -//TODO : homogeneiser les noms : SetPubElValByNumber -// qui appelle PubElValSet.SetElValueByNumber -// pourquoi pas SetPubElValueByNumber ?? -{ +//----------------------------------------------------------------------------- +// Print - return ( PubElValSet.SetElValueByNumber (content, group, element) ); -} +// see gdcmParser.cxx +//----------------------------------------------------------------------------- +// Public /** * \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 + * \brief This predicate, based on hopefully reasonable heuristics, + * decides whether or not the current gdcmParser was properly parsed + * and contains the mandatory information for being considered as + * a well formed and usable Dicom/Acr File. + * @return true when gdcmParser is the one of a reasonable Dicom/Acr file, + * false otherwise. */ -int gdcmHeader::SetPubElValByName(std::string content, std::string TagName) { - return ( PubElValSet.SetElValueByName (content, TagName) ); +bool gdcmHeader::IsReadable(void) { + if(!gdcmParser::IsReadable()) { + return(false); + } + std::string res = GetEntryByNumber(0x0028, 0x0005); + if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 ) + return false; // Image Dimensions + if ( !GetHeaderEntryByNumber(0x0028, 0x0100) ) + return false; // "Bits Allocated" + if ( !GetHeaderEntryByNumber(0x0028, 0x0101) ) + return false; // "Bits Stored" + if ( !GetHeaderEntryByNumber(0x0028, 0x0102) ) + return false; // "High Bit" + if ( !GetHeaderEntryByNumber(0x0028, 0x0103) ) + return false; // "Pixel Representation" i.e. 'Sign' + return true; } /** * \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. + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGBaseLineProcess1 one. + * @return True when JPEGBaseLineProcess1found. False in all other cases. */ +bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); -int gdcmHeader::SetPubElValLengthByNumber(guint32 length, guint16 group, - guint16 element) { - return ( PubElValSet.SetElValueLengthByNumber (length, group, element) ); + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.50" ) + return true; + return false; } /** * \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. + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGExtendedProcess2-4 one. + * @return True when JPEGExtendedProcess2-4 found. False in all other cases. */ -int gdcmHeader::SetShaElValByNumber(std::string content, - guint16 group, guint16 element) { - return ( ShaElValSet.SetElValueByNumber (content, group, element) ); +bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); + return ( Element->GetValue() == "1.2.840.10008.1.2.4.51" ); } /** * \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 ShadowTagName name of the tag to be modified + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGExtendeProcess3-5 one. + * @return True when JPEGExtendedProcess3-5 found. False in all other cases. */ -int gdcmHeader::SetShaElValByName(std::string content, std::string ShadowTagName) { - return ( ShaElValSet.SetElValueByName (content, ShadowTagName) ); -} +bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); -/** - * \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); - } + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.52" ) + return true; + return false; } /** * \ingroup gdcmHeader - * \brief This predicate, based on hopefully reasonable 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. + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. + * @return True when JPEGSpectralSelectionProcess6-8 found. False in all + * other cases. */ -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 ) +bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) return false; - return true; + LoadHeaderEntrySafe(Element); + + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.4.53" ) + return true; + return false; } /** * \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. + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a RLE Lossless one. + * @return True when RLE Lossless found. False in all + * other cases. */ -gdcmElValue* gdcmHeader::NewManualElValToPubDict(std::string NewTagName, - std::string VR) { - gdcmElValue* NewElVal = (gdcmElValue*)0; - guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info - guint32 FreeElem = 0; - gdcmDictEntry* NewEntry = (gdcmDictEntry*)0; +bool gdcmHeader::IsRLELossLessTransferSyntax(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); - 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; + std::string Transfer = Element->GetValue(); + if ( Transfer == "1.2.840.10008.1.2.5" ) { + return true; + } + return false; } /** * \ingroup gdcmHeader - * \brief Loads the element values of all the elements present in the - * public tag based hash table. + * \brief Determines if Transfer Syntax was already encountered + * and if it corresponds to a JPEG Lossless one. + * @return True when RLE Lossless found. False in all + * other cases. */ -void gdcmHeader::LoadElements(void) { - rewind(fp); - - // We don't use any longer the HashTable, since a lot a stuff is missing - // when SeQuences were encountered - // - //TagElValueHT ht = PubElValSet.GetTagHt(); - //for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) { - // LoadElementValue(tag->second); - //} - - for (ListTag::iterator i = GetListElem().begin(); - i != GetListElem().end(); - ++i){ - LoadElementValue(*i); - } - - rewind(fp); - - // Load 'non string' values - std::string PhotometricInterpretation = GetPubElValByNumber(0x0028,0x0004); - if( PhotometricInterpretation == "PALETTE COLOR " ){ - LoadElementVoidArea(0x0028,0x1200); // gray LUT - LoadElementVoidArea(0x0028,0x1201); // R LUT - LoadElementVoidArea(0x0028,0x1202); // G LUT - LoadElementVoidArea(0x0028,0x1203); // B LUT - - LoadElementVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data - LoadElementVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data - LoadElementVoidArea(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 = GetPubElValByNumber(0x0008, 0x0010); - if (RecCode == "ACRNEMA_LIBIDO_1.1" || - RecCode == "CANRME_AILIBOD1_1." ) { - filetype = ACR_LIBIDO; - std::string rows = GetPubElValByNumber(0x0028, 0x0010); - std::string columns = GetPubElValByNumber(0x0028, 0x0011); - SetPubElValByNumber(columns, 0x0028, 0x0010); - SetPubElValByNumber(rows , 0x0028, 0x0011); - } - // ----------------- End of Special Patch ---------------- -} - -/** - * \ingroup gdcmHeader - * \brief - * @return - */ -void gdcmHeader::PrintPubElVal(std::ostream & os) { - PubElValSet.Print(os); -} - -/** - * \ingroup gdcmHeader - * \brief - * @return - */ -void gdcmHeader::PrintPubDict(std::ostream & os) { - RefPubDict->Print(os); -} - -/** - * \ingroup gdcmHeader - * \brief - * @return integer, acts as a Boolean - */ -int gdcmHeader::Write(FILE * fp, FileType type) { - - // TODO : move the following lines (and a lot of others, to be written) - // to a future function CheckAndCorrectHeader - - if (type == ImplicitVR) { - std::string implicitVRTransfertSyntax = "1.2.840.10008.1.2"; - ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); - - //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": - // values with a VR of UI shall be padded with a single trailing null - // Dans le cas suivant on doit pader manuellement avec un 0 - - PubElValSet.SetElValueLengthByNumber(18, 0x0002, 0x0010); - } +bool gdcmHeader::IsJPEGLossless(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); + // faire qq chose d'intelligent a la place de ça + if ( !Element ) + return false; + LoadHeaderEntrySafe(Element); - if (type == ExplicitVR) { - std::string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1"; - ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); - - //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": - // values with a VR of UI shall be padded with a single trailing null - // Dans le cas suivant on doit pader manuellement avec un 0 - - PubElValSet.SetElValueLengthByNumber(20, 0x0002, 0x0010); - } + 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; + if (Element->GetValue() == "1.2.840.10008.1.2.4.57") return true; - return PubElValSet.Write(fp, type); + return false; } -// -// ------------------------ 'non string' elements related functions -// - /** - * \ingroup gdcmHeader - * \brief Loads (from disk) the element content - * when a string is not suitable + * \ingroup gdcmHeader + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEG2000 one + * @return True when JPEG2000 (Lossly or LossLess) found. False in all + * other cases. */ -void * gdcmHeader::LoadElementVoidArea(guint16 Group, guint16 Elem) { - gdcmElValue * Element= PubElValSet.GetElementByNumber(Group, Elem); +bool gdcmHeader::IsJPEG2000(void) { + gdcmHeaderEntry* Element = GetHeaderEntryByNumber(0x0002, 0x0010); 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) { - std::cout << "Big Broblem (LoadElementVoidArea, malloc) " - << std::hex << Group << " " << Elem << std::endl; - return NULL; - } - /* int res = */ PubElValSet.SetVoidAreaByNumber(a, Group, Elem); - // TODO check the result - size_t l2 = fread(a, 1, l ,fp); - if(l != l2) { - std::cout << "Big Broblem (LoadElementVoidArea, fread) " - << std::hex << Group << " " << Elem << std::endl; - free(a); - return NULL; - } - return a; -} + return false; + LoadHeaderEntrySafe(Element); -/** - * \ingroup gdcmHeader - * \brief Gets (from Header) the offset of a 'non string' element value - * \ (LoadElementValue has already be executed) - * @param Group - * @param Elem - * @return File Offset of the Element Value - */ - size_t gdcmHeader::GetPubElValOffsetByNumber(guint16 Group, guint16 Elem) { - gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); - if (!elValue) { - dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", - "failed to Locate gdcmElValue"); - return (size_t)0; - } - return elValue->GetOffset(); + std::string Transfer = Element->GetValue(); + if ( (Transfer == "1.2.840.10008.1.2.4.90") + || (Transfer == "1.2.840.10008.1.2.4.91") ) + return true; + return false; } /** * \ingroup gdcmHeader -* \brief Gets (from Header) a 'non string' element value - * \ (LoadElementValue has already be executed) - * @param Group - * @param Elem - * @return Pointer to the 'non string' area - + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. */ - void * gdcmHeader::GetPubElValVoidAreaByNumber(guint16 Group, guint16 Elem) { - gdcmElValue* elValue = PubElValSet.GetElementByNumber(Group, Elem); - if (!elValue) { - dbg.Verbose(1, "gdcmHeader::GetElValueByNumber", - "failed to Locate gdcmElValue"); - return (NULL); - } - return elValue->GetVoidArea(); +bool gdcmHeader::IsDicomV3(void) { + // Checking if Transfert Syntax exists is enough + // Anyway, it's to late check if the 'Preamble' was found ... + // And ... would it be a rich idea to check ? + // (some 'no Preamble' DICOM images exist !) + return (GetHeaderEntryByNumber(0x0002, 0x0010) != NULL); } - -// -// ============================================================================= -// Heuristics based accessors -//============================================================================== -// - -// TODO : move to an other file. - - /** * \ingroup gdcmHeader * \brief Retrieve the number of columns of image. * @return The encountered size when found, 0 by default. + * 0 means the file is NOT USABLE. The caller will have to check */ 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. - std::string StrSize = GetPubElValByNumber(0x0028,0x0011); + std::string StrSize; + StrSize = GetEntryByNumber(0x0028,0x0011); if (StrSize == GDCM_UNFOUND) return 0; return atoi(StrSize.c_str()); @@ -1984,18 +273,17 @@ int gdcmHeader::GetXSize(void) { * \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. + * @return The encountered size when found, 1 by default + * (The ACR-MEMA file contains a Signal, not an Image). */ 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. - std::string StrSize = GetPubElValByNumber(0x0028,0x0010); + std::string StrSize = GetEntryByNumber(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 + // The Rows (0028,0010) entry was optional for ACR/NEMA. It might // hence be a signal (1d image). So we default to 1: return 1; } @@ -2006,20 +294,18 @@ int gdcmHeader::GetYSize(void) { * 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. + * being the ACR-NEMA "Planes" tag content. + * @return The encountered size when found, 1 by default (single image). */ int gdcmHeader::GetZSize(void) { - // Both in DicomV3 and ACR/Nema the consider the "Number of Frames" + // Both DicomV3 and ACR/Nema consider the "Number of Frames" // as the third dimension. - std::string StrSize = GetPubElValByNumber(0x0028,0x0008); + std::string StrSize = GetEntryByNumber(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); + // We then consider the "Planes" entry as the third dimension + StrSize = GetEntryByNumber(0x0028,0x0012); if (StrSize != GDCM_UNFOUND) return atoi(StrSize.c_str()); return 1; @@ -2027,15 +313,16 @@ int gdcmHeader::GetZSize(void) { /** * \ingroup gdcmHeader - * \brief Retrieve the number of Bits Stored + * \brief Retrieve the number of Bits Stored (actually used) * (as opposite to number of Bits Allocated) - * * @return The encountered number of Bits Stored, 0 by default. + * 0 means the file is NOT USABLE. The caller has to check it ! */ -int gdcmHeader::GetBitsStored(void) { - std::string StrSize = GetPubElValByNumber(0x0028,0x0101); +int gdcmHeader::GetBitsStored(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0101); if (StrSize == GDCM_UNFOUND) - return 1; + return 0; // It's supposed to be mandatory + // the caller will have to check return atoi(StrSize.c_str()); } @@ -2043,13 +330,14 @@ int gdcmHeader::GetBitsStored(void) { * \ingroup gdcmHeader * \brief Retrieve the number of Bits Allocated * (8, 12 -compacted ACR-NEMA files, 16, ...) - * * @return The encountered number of Bits Allocated, 0 by default. + * 0 means the file is NOT USABLE. The caller has to check it ! */ -int gdcmHeader::GetBitsAllocated(void) { - std::string StrSize = GetPubElValByNumber(0x0028,0x0100); +int gdcmHeader::GetBitsAllocated(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0100); if (StrSize == GDCM_UNFOUND) - return 1; + return 0; // It's supposed to be mandatory + // the caller will have to check return atoi(StrSize.c_str()); } @@ -2057,13 +345,14 @@ int gdcmHeader::GetBitsAllocated(void) { * \ingroup gdcmHeader * \brief Retrieve the number of Samples Per Pixel * (1 : gray level, 3 : RGB -1 or 3 Planes-) - * * @return The encountered number of Samples Per Pixel, 1 by default. + * (Gray level Pixels) */ -int gdcmHeader::GetSamplesPerPixel(void) { - std::string StrSize = GetPubElValByNumber(0x0028,0x0002); +int gdcmHeader::GetSamplesPerPixel(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0002); if (StrSize == GDCM_UNFOUND) return 1; // Well, it's supposed to be mandatory ... + // but sometimes it's missing : *we* assume Gray pixels return atoi(StrSize.c_str()); } @@ -2071,11 +360,10 @@ int gdcmHeader::GetSamplesPerPixel(void) { * \ingroup gdcmHeader * \brief Retrieve the Planar Configuration for RGB images * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane) - * * @return The encountered Planar Configuration, 0 by default. */ -int gdcmHeader::GetPlanarConfiguration(void) { - std::string StrSize = GetPubElValByNumber(0x0028,0x0006); +int gdcmHeader::GetPlanarConfiguration(void) { + std::string StrSize = GetEntryByNumber(0x0028,0x0006); if (StrSize == GDCM_UNFOUND) return 0; return atoi(StrSize.c_str()); @@ -2084,8 +372,8 @@ int gdcmHeader::GetPlanarConfiguration(void) { /** * \ingroup gdcmHeader * \brief Return the size (in bytes) of a single pixel of data. - * @return The size in bytes of a single pixel of data. - * + * @return The size in bytes of a single pixel of data; 0 by default + * 0 means the file is NOT USABLE; the caller will have to check */ int gdcmHeader::GetPixelSize(void) { std::string PixelType = GetPixelType(); @@ -2095,6 +383,8 @@ int gdcmHeader::GetPixelSize(void) { return 2; if (PixelType == "32U" || PixelType == "32S") return 4; + if (PixelType == "FD") + return 8; dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type"); return 0; } @@ -2109,24 +399,25 @@ int gdcmHeader::GetPixelSize(void) { * - 16S signed 16 bit, * - 32U unsigned 32 bit, * - 32S signed 32 bit, + * - FD floating double 64 bits (Not kosher DICOM, but so usefull!) * \warning 12 bit images appear as 16 bit. * \ 24 bit images appear as 8 bit - * @return + * @return 0S if nothing found. NOT USABLE file. The caller has to check */ -std::string gdcmHeader::GetPixelType(void) { - std::string BitsAlloc; - BitsAlloc = GetElValByName("Bits Allocated"); +std::string gdcmHeader::GetPixelType(void) { + std::string BitsAlloc = GetEntryByNumber(0x0028, 0x0100); // Bits Allocated if (BitsAlloc == GDCM_UNFOUND) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated"); BitsAlloc = std::string("16"); } + if (BitsAlloc == "64") // ) + return ("FD"); if (BitsAlloc == "12") // It will be unpacked BitsAlloc = std::string("16"); else if (BitsAlloc == "24") // (in order no to be messed up BitsAlloc = std::string("8"); // by old RGB images) - std::string Signed; - Signed = GetElValByName("Pixel Representation"); + std::string Signed = GetEntryByNumber(0x0028, 0x0103); // "Pixel Representation" if (Signed == GDCM_UNFOUND) { dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation"); BitsAlloc = std::string("0"); @@ -2134,73 +425,116 @@ std::string gdcmHeader::GetPixelType(void) { if (Signed == "0") Signed = std::string("U"); else - -std::cout << "GetPixelType : " << BitsAlloc + Signed << std::endl; Signed = std::string("S"); return( BitsAlloc + Signed); } + /** - * \ingroup gdcmHeader - * \brief gets the info from 0002,0010 : Transfert Syntax - * \ else 1. - * @return Transfert Syntax Name (as oposite to Transfert Syntax UID) - */ -std::string gdcmHeader::GetTransferSyntaxName(void) { - std::string TransfertSyntax = GetPubElValByNumber(0x0002,0x0010); - if (TransfertSyntax == GDCM_UNFOUND) { - dbg.Verbose(0, "gdcmHeader::GetTransferSyntaxName: unfound Transfert Syntax (0002,0010)"); - return "Uncompressed ACR-NEMA"; - } - // we do it only when we need it - gdcmTS * ts = gdcmGlobal::GetTS(); - std::string tsName=ts->GetValue(TransfertSyntax); - //delete ts; // Seg Fault when deleted ?! - return tsName; + * \ingroup gdcmHeader + * \brief Recover the offset (from the beginning of the file) + * \ of *image* pixels (not *icone image* pixels, if any !) + * @return Pixel Offset + */ +size_t gdcmHeader::GetPixelOffset(void) { + // + // If the element (0x0088,0x0200) 'icone image sequence' is found + // (grPixel,numPixel) is stored twice : the first one for the icon + // the second one for the image ... + // pb : sometimes , (0x0088,0x0200) exists, but doesn't contain *anything* + // see gdcmData/MxTwinLossLess.dcm ... + + //std::string icone = GetEntryByNumber(0x0088,0x0200); //icone image sequence + + IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); + TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); + gdcmHeaderEntry* PixelElement; + if (countGrPixel == 1) + PixelElement = (it.first)->second; + else { + PixelElement = (++it.first)->second; // hope there are no more than 2 ! + } + if (PixelElement) { + return PixelElement->GetOffset(); + } else { + return 0; + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; + } } +// TODO : unify those two (previous one and next one) +/** + * \ingroup gdcmHeader + * \brief Recover the pixel area length (in Bytes) + * @return Pixel Element Length, as stored in the header + * (NOT the memory space necessary to hold the Pixels + * - in case of embeded compressed image-) + * 0 : NOT USABLE file. The caller has to check. + */ +size_t gdcmHeader::GetPixelAreaLength(void) { + + IterHT it = GetHeaderEntrySameNumber(GrPixel,NumPixel); + TagKey key = gdcmDictEntry::TranslateToKey(GrPixel,NumPixel); + gdcmHeaderEntry* PixelElement; + + if (countGrPixel==1) + PixelElement = (it.first)->second; + else + PixelElement = (++it.first)->second; -// -------------------------------- Lookup Table related functions ------------ + if (PixelElement) { + return PixelElement->GetLength(); + } else { + std::cout << "Big trouble : Pixel Element (" + << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" + << std::endl; + return 0; + } +} /** * \ingroup gdcmHeader * \brief tells us if LUT are used - * \warning Right now, Segmented xxx Palette Color Lookup Table Data + * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data' * \ are NOT considered as LUT, since nobody knows - *\ how to deal with them - * @return int acts as a Boolean + * \ how to deal with them + * \ Please warn me if you know sbdy that *does* know ... jprx + * @return true if LUT Descriptors and LUT Tables were found */ - -int gdcmHeader::HasLUT(void) { +bool gdcmHeader::HasLUT(void) { - // Check the presence of the LUT Descriptors - if (GetPubElValByNumber(0x0028,0x1101) == GDCM_UNFOUND) - return 0; + // Check the presence of the LUT Descriptors, and LUT Tables + // LutDescriptorRed + if ( !GetHeaderEntryByNumber(0x0028,0x1101) ) + return false; // LutDescriptorGreen - if (GetPubElValByNumber(0x0028,0x1102) == GDCM_UNFOUND) - return 0; + if ( !GetHeaderEntryByNumber(0x0028,0x1102) ) + return false; // LutDescriptorBlue - if (GetPubElValByNumber(0x0028,0x1103) == GDCM_UNFOUND) - return 0; - // It is not enough - // we check also - if (GetPubElValByNumber(0x0028,0x1201) == GDCM_UNFOUND) - return 0; - if (GetPubElValByNumber(0x0028,0x1202) == GDCM_UNFOUND) - return 0; - if (GetPubElValByNumber(0x0028,0x1203) == GDCM_UNFOUND) - return 0; - return 1; + if ( !GetHeaderEntryByNumber(0x0028,0x1103) ) + return false; + // Red Palette Color Lookup Table Data + if ( !GetHeaderEntryByNumber(0x0028,0x1201) ) + return false; + // Green Palette Color Lookup Table Data + if ( !GetHeaderEntryByNumber(0x0028,0x1202) ) + return false; + // Blue Palette Color Lookup Table Data + if ( !GetHeaderEntryByNumber(0x0028,0x1203) ) + return false; + return true; } /** * \ingroup gdcmHeader * \brief gets the info from 0028,1101 : Lookup Table Desc-Red * \ else 0 - * @return Lookup Table nBit - * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * @return Lookup Table number of Bits , 0 by default + * \ when (0028,0004),Photometric Interpretation = [PALETTE COLOR ] + * @ return bit number of each LUT item */ - int gdcmHeader::GetLUTNbits(void) { std::vector tokens; //int LutLength; @@ -2208,7 +542,7 @@ int gdcmHeader::GetLUTNbits(void) { int LutNbits; //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red = Lookup Table Desc-Blue // Consistency already checked in GetLUTLength - std::string LutDescription = GetPubElValByNumber(0x0028,0x1101); + std::string LutDescription = GetEntryByNumber(0x0028,0x1101); if (LutDescription == GDCM_UNFOUND) return 0; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value @@ -2233,35 +567,30 @@ int gdcmHeader::GetLUTNbits(void) { * \ 0028 1221 Segmented Red Palette Color Lookup Table Data * \ 0028 1222 Segmented Green Palette Color Lookup Table Data * \ 0028 1223 Segmented Blue Palette Color Lookup Table Data - * \ no known Dicom reader deails with them :-( - * @return Lookup Table RGBA + * \ no known Dicom reader deals with them :-( + * @return a RGBA Lookup Table */ - unsigned char * gdcmHeader::GetLUTRGBA(void) { // Not so easy : see // http://www.barre.nom.fr/medical/dicom2/limitations.html#Color%20Lookup%20Tables -// and OT-PAL-8-face.dcm // if Photometric Interpretation # PALETTE COLOR, no LUT to be done - - if (gdcmHeader::GetPubElValByNumber(0x0028,0x0004) != "PALETTE COLOR ") { + if (GetEntryByNumber(0x0028,0x0004) != "PALETTE COLOR ") { return NULL; } - int lengthR, debR, nbitsR; int lengthG, debG, nbitsG; int lengthB, debB, nbitsB; // Get info from Lut Descriptors // (the 3 LUT descriptors may be different) - - std::string LutDescriptionR = GetPubElValByNumber(0x0028,0x1101); + std::string LutDescriptionR = GetEntryByNumber(0x0028,0x1101); if (LutDescriptionR == GDCM_UNFOUND) return NULL; - std::string LutDescriptionG = GetPubElValByNumber(0x0028,0x1102); + std::string LutDescriptionG = GetEntryByNumber(0x0028,0x1102); if (LutDescriptionG == GDCM_UNFOUND) return NULL; - std::string LutDescriptionB = GetPubElValByNumber(0x0028,0x1103); + std::string LutDescriptionB = GetEntryByNumber(0x0028,0x1103); if (LutDescriptionB == GDCM_UNFOUND) return NULL; @@ -2277,86 +606,187 @@ unsigned char * gdcmHeader::GetLUTRGBA(void) { tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (LutDescriptionG, tokens, "\\"); lengthG=atoi(tokens[0].c_str()); // Green LUT length in Bytes - debG =atoi(tokens[1].c_str()); - nbitsG =atoi(tokens[2].c_str()); + debG =atoi(tokens[1].c_str()); // subscript of the first Lut Value + nbitsG =atoi(tokens[2].c_str()); // Lut item size (in Bits) tokens.clear(); tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (LutDescriptionB, tokens, "\\"); lengthB=atoi(tokens[0].c_str()); // Blue LUT length in Bytes - debB =atoi(tokens[1].c_str()); - nbitsB =atoi(tokens[2].c_str()); + debB =atoi(tokens[1].c_str()); // subscript of the first Lut Value + nbitsB =atoi(tokens[2].c_str()); // Lut item size (in Bits) tokens.clear(); -// Load LUTs into memory, (as they were stored on disk) - - unsigned char *lutR =(unsigned char *) - GetPubElValVoidAreaByNumber(0x0028,0x1201); - unsigned char *lutG =(unsigned char *) - GetPubElValVoidAreaByNumber(0x0028,0x1202); - unsigned char *lutB =(unsigned char *) - GetPubElValVoidAreaByNumber(0x0028,0x1203); + // Load LUTs into memory, (as they were stored on disk) + unsigned char *lutR = (unsigned char *) + GetEntryVoidAreaByNumber(0x0028,0x1201); + unsigned char *lutG = (unsigned char *) + GetEntryVoidAreaByNumber(0x0028,0x1202); + unsigned char *lutB = (unsigned char *) + GetEntryVoidAreaByNumber(0x0028,0x1203); if (!lutR || !lutG || !lutB ) { return NULL; } - // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT + // forge the 4 * 8 Bits Red/Green/Blue/Alpha LUT - unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha) - if (!LUTRGBA) { - return NULL; - } - memset(LUTRGBA, 0, 1024); + unsigned char *LUTRGBA = (unsigned char *)calloc(1024,1); // 256 * 4 (R, G, B, Alpha) + if (!LUTRGBA) { + return NULL; + } + memset(LUTRGBA, 0, 1024); // Bits Allocated int nb; - std::string str_nb = GetPubElValByNumber(0x0028,0x0100); + std::string str_nb = GetEntryByNumber(0x0028,0x0100); if (str_nb == GDCM_UNFOUND ) { nb = 16; } else { nb = atoi(str_nb.c_str() ); } - int mult; - - if (nbitsR==16 && nb==8) // when LUT item size is different than pixel size - mult=2; // high byte must be = low byte - else // See PS 3.3-2003 C.11.1.1.2 p 619 - mult=1; - - - // if we get a black image, let's just remove the '+1' - // from 'i*mult+1' and check again - // if it works, we shall have to check the 3 Palettes - // to see which byte is ==0 (first one, or second one) - // and fix the code - // We give up the checking to avoid some overhead - - unsigned char *a; - int i; - a= LUTRGBA+0; - for(i=0;iGetValue(TransfertSyntax); + //delete ts; // Seg Fault when deleted ?! + return tsName; +} + +/** + * \ingroup gdcmHeader + * \brief Sets the Pixel Area size in the Header + * --> not-for-rats function + * @param ImageDataSize new Pixel Area Size + * warning : nothing else is checked + */ +void gdcmHeader::SetImageDataSize(size_t ImageDataSize) { + std::string content1; + char car[20]; + + // Assumes HeaderEntry (GrPixel, NumPixel) is unique ... + // TODO deal with multiplicity (see gdcmData/icone.dcm) + sprintf(car,"%d",ImageDataSize); + gdcmHeaderEntry *a = GetHeaderEntryByNumber(GrPixel, NumPixel); + a->SetLength(ImageDataSize); + + ImageDataSize+=8; + sprintf(car,"%d",ImageDataSize); + content1=car; + SetEntryByNumber(content1, GrPixel, NumPixel); +} + + +/** + * \ingroup gdcmHeader + * \brief compares 2 Headers, according to DICOMDIR rules + * --> not-for-rats function + * \warning does NOT work with ACR-NEMA files + * \todo find a trick to solve the pb (use RET fields ?) + * @param header + * @return true if 'smaller' + */ + bool gdcmHeader::operator<(gdcmHeader &header){ + std::string s1,s2; + + // Patient Name + s1=this->GetEntryByNumber(0x0010,0x0010); + s2=header.GetEntryByNumber(0x0010,0x0010); + if(s1 < s2) + return(true); + else if(s1 > s2) + return(false); + else + { + // Patient ID + s1=this->GetEntryByNumber(0x0010,0x0020); + s2=header.GetEntryByNumber(0x0010,0x0020); + if (s1 < s2) + return(true); + else if (s1 > s2) + return(1); + else + { + // Study Instance UID + s1=this->GetEntryByNumber(0x0020,0x000d); + s2=header.GetEntryByNumber(0x0020,0x000d); + if (s1 < s2) + return(true); + else if(s1 > s2) + return(false); + else + { + // Serie Instance UID + s1=this->GetEntryByNumber(0x0020,0x000e); + s2=header.GetEntryByNumber(0x0020,0x000e); + if (s1 < s2) + return(true); + else if(s1 > s2) + return(false); + } + } + } + return(false); +} + +//----------------------------------------------------------------------------- +// Protected + +//----------------------------------------------------------------------------- +// Private + +//-----------------------------------------------------------------------------