/*========================================================================= Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ Date: $Date: 2004/06/21 04:18:25 $ Version: $Revision: 1.20 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "gdcmDocument.h" #include "gdcmValEntry.h" #include "gdcmBinEntry.h" #include "gdcmSeqEntry.h" #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" #include #include // For nthos: #ifdef _MSC_VER #include #else #include #endif # include // Implicit VR Little Endian #define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" // Explicit VR Little Endian #define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1" // Deflated Explicit VR Little Endian #define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" // Explicit VR Big Endian #define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2" // JPEG Baseline (Process 1) #define UI1_2_840_10008_1_2_4_50 "1.2.840.10008.1.2.4.50" // JPEG Extended (Process 2 & 4) #define UI1_2_840_10008_1_2_4_51 "1.2.840.10008.1.2.4.51" // JPEG Extended (Process 3 & 5) #define UI1_2_840_10008_1_2_4_52 "1.2.840.10008.1.2.4.52" // JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8) #define UI1_2_840_10008_1_2_4_53 "1.2.840.10008.1.2.4.53" // JPEG Full Progression, Non-Hierarchical (Process 10 & 12) #define UI1_2_840_10008_1_2_4_55 "1.2.840.10008.1.2.4.55" // JPEG Lossless, Non-Hierarchical (Process 14) #define UI1_2_840_10008_1_2_4_57 "1.2.840.10008.1.2.4.57" // JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, // [Selection Value 1]) #define UI1_2_840_10008_1_2_4_70 "1.2.840.10008.1.2.4.70" // JPEG 2000 Lossless #define UI1_2_840_10008_1_2_4_90 "1.2.840.10008.1.2.4.90" // JPEG 2000 #define UI1_2_840_10008_1_2_4_91 "1.2.840.10008.1.2.4.91" // RLE Lossless #define UI1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5" #define str2num(str, typeNum) *((typeNum *)(str)) //----------------------------------------------------------------------------- // Refer to gdcmDocument::CheckSwap() const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256; // Refer to gdcmDocument::SetMaxSizeLoadEntry() const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096; const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief constructor * @param inFilename file to be opened for parsing * @param exception_on_error whether we throw an exception or not * @param enable_sequences = true to allow the header * to be parsed *inside* the SeQuences, * when they have an actual length * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files * @param ignore_shadow to allow skipping the shadow elements, * to save memory space. * \warning The TRUE value for this param has to be used * with a FALSE value for the 'enable_sequence' param. * ('public elements' may be embedded in 'shadow Sequences') */ gdcmDocument::gdcmDocument(std::string const & inFilename, bool exception_on_error, bool enable_sequences, bool ignore_shadow) : gdcmElementSet(-1) { enableSequences=enable_sequences; IgnoreShadow =ignore_shadow; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = inFilename; Initialise(); if ( !OpenFile(exception_on_error)) return; dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ", Filename.c_str()); rewind(fp); fseek(fp,0L,SEEK_END); long lgt = ftell(fp); rewind(fp); CheckSwap(); long beg = ftell(fp); lgt -= beg; SQDepthLevel=0; long l=ParseDES( this, beg, lgt, false); // le Load sera fait a la volee (void)l; //is l used anywhere ? CloseFile(); // -------------------------------------------------------------- // 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 = GetEntryByNumber(0x0008, 0x0010); // recognition code if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { Filetype = gdcmACR_LIBIDO; std::string rows = GetEntryByNumber(0x0028, 0x0010); std::string columns = GetEntryByNumber(0x0028, 0x0011); SetEntryByNumber(columns, 0x0028, 0x0010); SetEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- End of Special Patch ---------------- printLevel = 1; // 'Medium' print level by default } /** * \brief constructor * @param exception_on_error */ gdcmDocument::gdcmDocument(bool exception_on_error) :gdcmElementSet(-1) { (void)exception_on_error; enableSequences=0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); printLevel = 1; // 'Medium' print level by default } /** * \brief Canonical destructor. */ gdcmDocument::~gdcmDocument (void) { RefPubDict = NULL; RefShaDict = NULL; // Recursive clean up of sequences for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it ) { delete (it->second); } tagHT.clear(); } //----------------------------------------------------------------------------- // Print /** * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return */ void gdcmDocument::PrintPubDict(std::ostream & os) { RefPubDict->Print(os); } /** * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ void gdcmDocument::PrintShaDict(std::ostream & os) { RefShaDict->Print(os); } //----------------------------------------------------------------------------- // Public /** * \brief Get the public dictionary used */ gdcmDict *gdcmDocument::GetPubDict(void) { return(RefPubDict); } /** * \brief Get the shadow dictionary used */ gdcmDict *gdcmDocument::GetShaDict(void) { return(RefShaDict); } /** * \brief Set the shadow dictionary used * \param dict dictionary to use in shadow */ bool gdcmDocument::SetShaDict(gdcmDict *dict){ RefShaDict=dict; return(!RefShaDict); } /** * \brief Set the shadow dictionary used * \param dictName name of the dictionary to use in shadow */ bool gdcmDocument::SetShaDict(DictKey dictName){ RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName); return(!RefShaDict); } /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current gdcmDocument was properly parsed * and contains the mandatory information for being considered as * a well formed and usable Dicom/Acr File. * @return true when gdcmDocument is the one of a reasonable Dicom/Acr file, * false otherwise. */ bool gdcmDocument::IsReadable(void) { if(Filetype==gdcmUnknown) { dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype"); return(false); } if(!tagHT.empty()<=0) { dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal" " hash table."); return(false); } return(true); } /** * \brief Internal function that checks whether the Transfer Syntax given * as argument is the one present in the current document. * @param SyntaxToCheck The transfert syntax we need to check against. * @return True when SyntaxToCheck corresponds to the Transfer Syntax of * the current document. False either when the document contains * no Transfer Syntax, or when the Tranfer Syntaxes don't match. */ bool gdcmDocument::IsGivenTransferSyntax(const std::string & SyntaxToCheck) { gdcmDocEntry *Entry = GetDocEntryByNumber(0x0002, 0x0010); if ( !Entry ) return false; // The entry might be present but not loaded (parsing and loading // happen at differente stages): try loading and proceed with check... LoadDocEntrySafe(Entry); if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(Entry) ) { std::string Transfer = ValEntry->GetValue(); // The actual transfer (as read from disk) might be padded. We // first need to remove the potential padding. We can make the // weak assumption that padding was not executed with digits... while ( ! isdigit(Transfer[Transfer.length()-1]) ) { Transfer.erase(Transfer.length()-1, 1); } if ( Transfer == SyntaxToCheck ) return true; } return false; } /** * \brief Determines if the Transfer Syntax of the present document * corresponds to a Implicit Value Representation of * Little Endian. * \sa \ref gdcmDocument::IsGivenTransferSyntax. * @return True when ImplicitVRLittleEndian found. False in all other cases. */ bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) { return IsGivenTransferSyntax(UI1_2_840_10008_1_2); } /** * \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 gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1); } /** * \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 gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99); } /** * \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 gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2); } /** * \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 gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax(void) { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50); } /** * \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 gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax(void) { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51); } /** * \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 gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax(void) { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52); } /** * \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 gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53); } /** * \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 gdcmDocument::IsRLELossLessTransferSyntax(void) { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); } /** * \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. */ bool gdcmDocument::IsJPEGLossless(void) { return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55) || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57) || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) ); } /** * \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. */ bool gdcmDocument::IsJPEG2000(void) { return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); } /** * \brief Predicate for dicom version 3 file. * @return True when the file is a dicom version 3. */ bool gdcmDocument::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 (GetDocEntryByNumber(0x0002, 0x0010) != NULL); } /** * \brief returns the File Type * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) * @return the FileType code */ FileType gdcmDocument::GetFileType(void) { return Filetype; } /** * \brief opens the file * @param exception_on_error * @return */ FILE *gdcmDocument::OpenFile(bool exception_on_error) throw(gdcmFileError) { fp=fopen(Filename.c_str(),"rb"); if(!fp) { if(exception_on_error) throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)"); else { dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ", Filename.c_str()); return NULL; } } 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 fp; //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 fp; fclose(fp); dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", Filename.c_str()); } else { dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", Filename.c_str()); } return NULL; } /** * \brief closes the file * @return TRUE if the close was successfull */ bool gdcmDocument::CloseFile(void) { int closed = fclose(fp); fp = (FILE *)0; if (! closed) return false; return true; } /** * \brief Writes in a file all the Header Entries (Dicom Elements) * of the Chained List * @param fp file pointer on an already open file * @param type Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ bool gdcmDocument::Write(FILE *fp, FileType type) { /// \todo /// ============== /// The stuff will have to be rewritten using the SeQuence based /// tree-like stucture instead of the chained list . /// (so we shall remove the Group*HT from the gdcmDocument) /// To be checked /// ============= /// \todo move the following lines (and a lot of others, to be written) /// to a future function CheckAndCorrectHeader /// \todo /// Question : /// Comment pourrait-on savoir si le DcmHeader vient d'un fichier /// DicomV3 ou non (FileType est un champ de gdcmDocument ...) /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA /// no way /// a moins de se livrer a un tres complique ajout des champs manquants. /// faire un CheckAndCorrectHeader (?) if (type == gdcmImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); /// \todo 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 SetEntryLengthByNumber(18, 0x0002, 0x0010); } if (type == gdcmExplicitVR) { std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); /// \todo 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 SetEntryLengthByNumber(20, 0x0002, 0x0010); } /** * \todo rewrite later, if really usefull * * --> Warning : un-updated odd groups lengths can causes pb * --> (xmedcon breaks) * --> to be re- written with future org. * * if ( (type == ImplicitVR) || (type == ExplicitVR) ) * UpdateGroupLength(false,type); * if ( type == ACR) * UpdateGroupLength(true,ACR); */ WriteEntries(fp,type); return true; } /** * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. * @param Value (string) Value to be set * @param Group Group number of the Entry * @param Elem Element number of the Entry * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( std::string Value, guint16 Group, guint16 Elem ) { gdcmDocEntry* CurrentEntry; gdcmValEntry* ValEntry; CurrentEntry = GetDocEntryByNumber( Group, Elem); if (!CurrentEntry) { // The entry wasn't present and we simply create the required ValEntry: CurrentEntry = NewDocEntryByNumber(Group, Elem); if (!CurrentEntry) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" " NewDocEntryByNumber failed."); return NULL; } ValEntry = new gdcmValEntry(CurrentEntry); if ( !AddEntry(ValEntry)) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); } } else { ValEntry = dynamic_cast< gdcmValEntry* >(CurrentEntry); if ( !ValEntry ) { // We need to promote the gdcmDocEntry to a gdcmValEntry: ValEntry = new gdcmValEntry(CurrentEntry); if (!RemoveEntry(CurrentEntry)) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" " of previous DocEntry failed."); return NULL; } if ( !AddEntry(ValEntry)) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" " promoted ValEntry failed."); return NULL; } } } SetEntryByNumber(Value, Group, Elem); return ValEntry; } /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. * @param voidArea (binary) value to be set * @param Group Group number of the Entry * @param Elem Element number of the Entry * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( void *voidArea, int lgth, guint16 Group, guint16 Elem) { gdcmDocEntry* a; gdcmBinEntry* b; a = GetDocEntryByNumber( Group, Elem); if (a == NULL) { a =NewBinEntryByNumber(Group, Elem); if (a == NULL) return NULL; b = new gdcmBinEntry(a); AddEntry(b); } SetEntryByNumber(voidArea, lgth, Group, Elem); b->SetVoidArea(voidArea); return b; } /** * \brief Set a new value if the invoked element exists * Seems to be useless !!! * @param Value new element value * @param Group group number of the Entry * @param Elem element number of the Entry * \return boolean */ bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) { std::string v = Value; SetEntryByNumber(v, Group, Elem); return true; } //----------------------------------------------------------------------------- // Protected /** * \brief Checks if a given Dicom Element exists within the H table * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element * @return number of occurences */ int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { std::string key = gdcmDictEntry::TranslateToKey(group, element ); return tagHT.count(key); } /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value of a given tag. * \warning Don't use any longer : use GetPubEntryByName * @param tagName name of the searched element. * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ std::string gdcmDocument::GetEntryByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); } /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * 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 gdcmDocument::GetEntryVRByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), dictEntry->GetElement()); return elem->GetVR(); } /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag. * @param group Group number of the searched tag. * @param element Element number of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){ TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return GDCM_UNFOUND; return ((gdcmValEntry *)tagHT.find(key)->second)->GetValue(); } /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * 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 number of the searched tag. * @param element Element number of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ std::string gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) { gdcmDocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) return GDCM_UNFOUND; return elem->GetVR(); } /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the value length of a given tag.. * @param group Group number of the searched tag. * @param element Element number of the searched tag. * @return Corresponding element length; -2 if not found */ int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) { gdcmDocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) return -2; return elem->GetLength(); } /** * \brief Sets the value (string) of the Header Entry (Dicom Element) * @param content string value of the Dicom Element * @param tagName name of the searched Dicom Element. * @return true when found */ bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return false; return SetEntryByNumber(content,dictEntry->GetGroup(), dictEntry->GetElement()); } /** * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. * @param content new value (string) to substitute with * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ bool gdcmDocument::SetEntryByNumber(std::string content, guint16 group, guint16 element) { gdcmValEntry* ValEntry = GetValEntryByNumber(group, element); if (!ValEntry) { dbg.Verbose(0, "gdcmDocument::SetEntryByNumber: no corresponding", " ValEntry (try promotion first)."); return false; } // Non even content must be padded with a space (020H). if((content.length())%2) content = content + '\0'; ValEntry->SetValue(content); // Integers have a special treatement for their length: VRKey vr = ValEntry->GetVR(); if( (vr == "US") || (vr == "SS") ) ValEntry->SetLength(2); else if( (vr == "UL") || (vr == "SL") ) ValEntry->SetLength(4); else ValEntry->SetLength(content.length()); return true; } /** * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. * @param content new value (void *) to substitute with * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ bool gdcmDocument::SetEntryByNumber(void *content, int lgth, guint16 group, guint16 element) { (void)lgth; //not used TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; /* Hope Binray field length is never wrong if(lgth%2) // Non even length are padded with a space (020H). { lgth++; //content = content + '\0'; // fing a trick to enlarge a binary field? } */ gdcmBinEntry * a; a = (gdcmBinEntry *)tagHT[key]; a->SetVoidArea(content); //a->SetLength(lgth); // ??? return true; } /** * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) * in the PubDocEntrySet of this instance * through it's (group, element) and modifies it's length with * the given value. * \warning Use with extreme caution. * @param l new length to substitute with * @param group group number of the Entry to modify * @param element element number of the Entry to modify * @return true on success, false otherwise. */ bool gdcmDocument::SetEntryLengthByNumber(guint32 l, guint16 group, guint16 element) { TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; if (l%2) l++; // length must be even ( ((tagHT.equal_range(key)).first)->second )->SetLength(l); return true ; } /** * \brief Gets (from Header) the offset of a 'non string' element value * (LoadElementValues has already be executed) * @param Group group number of the Entry * @param Elem element number of the Entry * @return File Offset of the Element Value */ size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) { gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem); if (!Entry) { dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber", "failed to Locate gdcmDocEntry"); return (size_t)0; } return Entry->GetOffset(); } /** * \brief Gets (from Header) a 'non string' element value * (LoadElementValues has already be executed) * @param Group group number of the Entry * @param Elem element number of the Entry * @return Pointer to the 'non string' area */ void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) { gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem); if (!Entry) { dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber", "failed to Locate gdcmDocEntry"); return (NULL); } return ((gdcmBinEntry *)Entry)->GetVoidArea(); } /** * \brief Loads (from disk) the element content * when a string is not suitable * @param Group group number of the Entry * @param Elem element number of the Entry */ void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem) { gdcmDocEntry * Element= GetDocEntryByNumber(Group, Elem); if ( !Element ) return NULL; size_t o =(size_t)Element->GetOffset(); fseek(fp, o, SEEK_SET); size_t l = Element->GetLength(); char* a = new char[l]; if(!a) { dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); return NULL; } SetEntryVoidAreaByNumber(a, Group, Elem); /// \todo check the result size_t l2 = fread(a, 1, l ,fp); if(l != l2) { delete[] a; return NULL; } return a; } /** * \brief Sets a 'non string' value to a given Dicom Element * @param area * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element * @return */ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, guint16 group, guint16 element) { TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; // This was for multimap ? (( gdcmBinEntry *)( ((tagHT.equal_range(key)).first)->second ))->SetVoidArea(area); return true; } /** * \brief Update the entries with the shadow dictionary. * Only non even entries are analyzed */ void gdcmDocument::UpdateShaEntries(void) { //gdcmDictEntry *entry; std::string vr; /// \todo TODO : still any use to explore recursively the whole structure? /* for(ListTag::iterator it=listEntries.begin(); it!=listEntries.end(); ++it) { // Odd group => from public dictionary if((*it)->GetGroup()%2==0) continue; // Peer group => search the corresponding dict entry if(RefShaDict) entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement()); else entry=NULL; if((*it)->IsImplicitVR()) vr="Implicit"; else vr=(*it)->GetVR(); (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling if(entry){ // Set the new entry and the new value (*it)->SetDictEntry(entry); CheckDocEntryVR(*it,vr); (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling } else { // Remove precedent value transformation (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr)); } } */ } /** * \brief Searches within the Header Entries for a Dicom Element of * a given tag. * @param tagName name of the searched Dicom Element. * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ gdcmDocEntry *gdcmDocument::GetDocEntryByName(std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return NULL; return(GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); } /** * \brief retrieves a Dicom Element (the first one) using (group, element) * \warning (group, element) IS NOT an identifier inside the Dicom Header * if you think it's NOT UNIQUE, check the count number * and use iterators to retrieve ALL the Dicoms Elements within * a given couple (group, element) * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element * @return */ gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element) { TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return NULL; return tagHT.find(key)->second; } /** * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only * returns a result when the corresponding entry is of type * ValEntry. * @return When present, the corresponding ValEntry. */ gdcmValEntry* gdcmDocument::GetValEntryByNumber(guint16 group, guint16 element) { gdcmDocEntry* CurrentEntry = GetDocEntryByNumber(group, element); if (! CurrentEntry) return (gdcmValEntry*)0; if ( gdcmValEntry* ValEntry = dynamic_cast(CurrentEntry) ) { return ValEntry; } dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry."); return (gdcmValEntry*)0; } /** * \brief Loads the element while preserving the current * underlying file position indicator as opposed to * to LoadDocEntry that modifies it. * @param entry Header Entry whose value shall be loaded. * @return */ void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) { long PositionOnEntry = ftell(fp); LoadDocEntry(entry); fseek(fp, PositionOnEntry, SEEK_SET); } /** * \brief Writes in a file (according to the requested format) * the group, the element, the value representation and the length * of a single gdcmDocEntry passed as argument. * @param tag pointer on the gdcmDocEntry to be written * @param _fp already open file pointer * @param type type of the File to be written */ void gdcmDocument::WriteEntryTagVRLength(gdcmDocEntry *tag, FILE *_fp, FileType type) { guint16 group = tag->GetGroup(); VRKey vr = tag->GetVR(); guint16 el = tag->GetElement(); guint32 lgr = tag->GetReadLength(); if ( (group == 0xfffe) && (el == 0x0000) ) // Fix in order to make some MR PHILIPS images e-film readable // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm: // we just *always* ignore spurious fffe|0000 tag ! return; fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element if ( type == gdcmExplicitVR ) { // Special case of delimiters: if (group == 0xfffe) { // Delimiters have NO Value Representation and have NO length. // Hence we skip writing the VR and length and we pad by writing // 0xffffffff int ff=0xffffffff; fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp); return; } guint16 z=0; guint16 shortLgr = lgr; if (vr == "unkn") { // Unknown was 'written' // deal with Little Endian fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); } else { fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp); if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) { fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); } else { fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); } } } else // IMPLICIT VR { fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); } } /** * \brief Writes in a file (according to the requested format) * the value of a single gdcmDocEntry passed as argument. * @param tag Pointer on the gdcmDocEntry to be written * @param _fp Already open file pointer * @param type type of the File to be written */ // \todo TODO : to be re -written recursively ! void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type) { (void)type; guint16 group = tag->GetGroup(); VRKey vr = tag->GetVR(); guint32 lgr = tag->GetReadLength(); if (vr == "SQ") // SeQuences have no value: return; if (group == 0xfffe) // Delimiters have no associated value: return; //-------------------------------- // // FIXME :right now, both value and voidArea belong to gdcmValue // // ------------------------------- // if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) ) { void *voidArea; gdcmBinEntry *BinEntry= (gdcmBinEntry *)tag;; voidArea = BinEntry->GetVoidArea(); if (voidArea != NULL) { // there is a 'non string' LUT, overlay, etc fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value return; } // } if (vr == "US" || vr == "SS") { // some 'Short integer' fields may be mulivaluated // each single value is separated from the next one by '\' // we split the string and write each value as a short int std::vector tokens; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\"); for (unsigned int i=0; i tokens; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\"); for (unsigned int i=0; iGetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value } /** * \brief Writes in a file (according to the requested format) * a single gdcmDocEntry passed as argument. * \sa WriteEntryValue, WriteEntryTagVRLength. * @param tag Pointer on the gdcmDocEntry to be written * @param _fp Already open file pointer * @param type type of the File to be written */ bool gdcmDocument::WriteEntry(gdcmDocEntry *tag, FILE *_fp,FileType type) { guint32 length = tag->GetLength(); if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(tag) ) { // The value of a tag MUST (see the DICOM norm) be an odd number of // bytes. When this is not the case, pad with an additional byte: if(length%2==1) { ValEntry->SetValue(ValEntry->GetValue()+"\0"); ValEntry->SetLength(ValEntry->GetReadLength()+1); } WriteEntryTagVRLength(ValEntry, _fp, type); WriteEntryValue(ValEntry, _fp, type); return true; } if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) ) { (void)BinEntry; //not used /// \todo FIXME : when voidArea belong to gdcmBinEntry only, fix /// voidArea length // // The value of a tag MUST (see the DICOM norm) be an odd number of // bytes. When this is not the case, pad with an additional byte: /* if(length%2==1) { tag->SetValue(tag->GetValue()+"\0"); tag->SetLength(tag->GetReadLength()+1); } */ WriteEntryTagVRLength(tag, _fp, type); WriteEntryValue(tag, _fp, type); return true; } return false; //default behavior ? } /** * \brief writes on disc according to the requested format * (ACR-NEMA, ExplicitVR, ImplicitVR) the image * using the Chained List * \warning does NOT add the missing elements in the header : * it's up to the user doing it ! * (function CheckHeaderCoherence to be written) * \warning DON'T try, right now, to write a DICOM image * from an ACR Header (meta elements will be missing!) * @param type type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) * @param _fp already open file pointer */ bool gdcmDocument::WriteEntries(FILE *_fp,FileType type) { /// \todo FIXME : explore recursively the whole structure... /// \todo (?) check write failures (after *each* fwrite) dbg.Verbose(0, "gdcmDocument::WriteEntries: entering."); for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it ) { gdcmDocEntry * entry = it->second; if ( type == gdcmACR ){ if (entry->GetGroup() < 0x0008) // Ignore pure DICOM V3 groups continue; if (entry->GetGroup() %2) // Ignore the "shadow" groups continue; if (entry->GetVR() == "SQ" ) // ignore Sequences continue; } if (! WriteEntry(entry, _fp, type) ) { dbg.Verbose(0, "gdcmDocument::WriteEntries: write failure."); return false; } } return true; } /** * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly swaped 32 bits integer. */ guint32 gdcmDocument::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 : std::cout << "swapCode= " << sw << std::endl; dbg.Error(" gdcmDocument::SwapLong : unset swap code"); a=0; } return(a); } /** * \brief Unswaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly unswaped 32 bits integer. */ guint32 gdcmDocument::UnswapLong(guint32 a) { return (SwapLong(a)); } /** * \brief Swaps the bytes so they agree with the processor order * @return The properly swaped 16 bits integer. */ guint16 gdcmDocument::SwapShort(guint16 a) { if ( (sw==4321) || (sw==2143) ) a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff)); return (a); } /** * \brief Unswaps the bytes so they agree with the processor order * @return The properly unswaped 16 bits integer. */ guint16 gdcmDocument::UnswapShort(guint16 a) { return (SwapShort(a)); } //----------------------------------------------------------------------------- // Private /** * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) * @return false if file is not ACR-NEMA / PAPYRUS / DICOM */ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) { gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; gdcmValEntry *NewValEntry = (gdcmValEntry *)0; gdcmBinEntry *bn; gdcmSeqEntry *sq; VRKey vr; unsigned long l; int depth; depth = set->GetDepthLevel(); while (true) { if ( !delim_mode && ftell(fp)-offset >= l_max) { break; } NewDocEntry = ReadNextDocEntry( ); if (!NewDocEntry) break; vr = NewDocEntry->GetVR(); if (vr!="SQ") { if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) ) { /////// ValEntry NewValEntry = new gdcmValEntry(NewDocEntry->GetDictEntry()); NewValEntry->Copy(NewDocEntry); NewValEntry->SetDepthLevel(depth); set->AddEntry(NewValEntry); LoadDocEntry(NewValEntry); if (/*!delim_mode && */NewValEntry->isItemDelimitor()) break; if ( !delim_mode && ftell(fp)-offset >= l_max) { break; } } else { if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) { ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, " "nor BinEntry. Probably unknown VR."); } ////// BinEntry or UNKOWN VR: bn = new gdcmBinEntry(NewDocEntry->GetDictEntry()); bn->Copy(NewDocEntry); set->AddEntry(bn); LoadDocEntry(bn); } if (NewDocEntry->GetGroup() == 0x7fe0 && NewDocEntry->GetElement() == 0x0010 ) { if (NewDocEntry->GetLength()==0xffffffff) // Broken US.3405.1.dcm Parse7FE0(); // to skip the pixels // (multipart JPEG/RLE are trouble makers) } else { // to be sure we are at the beginning SkipToNextDocEntry(NewDocEntry); l = NewDocEntry->GetFullLength(); } } else { // VR = "SQ" l=NewDocEntry->GetReadLength(); if (l != 0) // don't mess the delim_mode for zero-length sequence if (l == 0xffffffff) delim_mode = true; else delim_mode = false; // no other way to create it ... sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry(), set->GetDepthLevel()); sq->Copy(NewDocEntry); sq->SetDelimitorMode(delim_mode); sq->SetDepthLevel(depth); if (l != 0) { // Don't try to parse zero-length sequences long lgt = ParseSQ( sq, NewDocEntry->GetOffset(), l, delim_mode); (void)lgt; //not used... } // FIXME : on en fait quoi, de lgt ? set->AddEntry(sq); if ( !delim_mode && ftell(fp)-offset >= l_max) { break; } } delete NewDocEntry; } return l; // ?? } /** * \brief Parses a Sequence ( SeqEntry after SeqEntry) * @return parsed length for this level */ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; gdcmSQItem *itemSQ; bool dlm_mod; int lgr, lgth; unsigned int l; int depth = set->GetDepthLevel(); (void)depth; //not used while (true) { NewDocEntry = ReadNextDocEntry(); if(delim_mode) { if (NewDocEntry->isSequenceDelimitor()) { /// \todo add the Sequence Delimitor /// \todo find the trick to put it properly ! set->SetSequenceDelimitationItem(NewDocEntry); break; } } if (!delim_mode && (ftell(fp)-offset) >= l_max) { break; } itemSQ = new gdcmSQItem(set->GetDepthLevel()); itemSQ->AddEntry(NewDocEntry); /// \todo no value, no voidArea. Think of it while printing ! l= NewDocEntry->GetReadLength(); if (l == 0xffffffff) dlm_mod = true; else dlm_mod=false; lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod); set->AddEntry(itemSQ,SQItemNumber); SQItemNumber ++; if (!delim_mode && (ftell(fp)-offset) >= l_max) { break; } } lgth = ftell(fp) - offset; return(lgth); } /** * \brief Loads the element content if its length doesn't exceed * the value specified with gdcmDocument::SetMaxSizeLoadEntry() * @param Entry Header Entry (Dicom Element) to be dealt with */ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) { size_t item_read; guint16 group = Entry->GetGroup(); std::string vr= Entry->GetVR(); guint32 length = Entry->GetLength(); fseek(fp, (long)Entry->GetOffset(), SEEK_SET); // 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 ) { // NO more value field for SQ ! //Entry->SetValue("gdcm::Skipped"); // appel recursif de Load Value // (meme pb que pour le parsing) return; } // When the length is zero things are easy: if ( length == 0 ) { ((gdcmValEntry *)Entry)->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 > MaxSizeLoadEntry) { if (gdcmValEntry* ValEntryPtr = dynamic_cast< gdcmValEntry* >(Entry) ) { std::ostringstream s; s << "gdcm::NotLoaded."; s << " Address:" << (long)Entry->GetOffset(); s << " Length:" << Entry->GetLength(); s << " x(" << std::hex << Entry->GetLength() << ")"; ValEntryPtr->SetValue(s.str()); } // to be sure we are at the end of the value ... fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET); return; } // Any compacter code suggested (?) if ( IsDocEntryAnInteger(Entry) ) { guint32 NewInt; std::ostringstream s; int nbInt; // When short integer(s) are expected, read and convert the following // n *two characters properly i.e. as short integers as opposed to strings. // Elements with Value Multiplicity > 1 // contain a set of integers (not a single one) 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; } } } // When integer(s) are expected, read and convert the following // n * four characters properly i.e. as integers as opposed to strings. // Elements with Value Multiplicity > 1 // contain a set of integers (not a single one) else if (vr == "UL" || vr == "SL") { nbInt = length / 4; NewInt = ReadInt32(); s << NewInt; if (nbInt > 1) { for (int i=1; i < nbInt; i++) { s << '\\'; NewInt = ReadInt32(); s << NewInt; } } } #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM ((gdcmValEntry *)Entry)->SetValue(s.str()); return; } // We need an additional byte for storing \0 that is not on disk std::string NewValue(length,0); item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp); if ( item_read != 1 ) { dbg.Verbose(1, "gdcmDocument::LoadElementValue","unread element value"); ((gdcmValEntry *)Entry)->SetValue("gdcm::UnRead"); return; } if( (vr == "UI") ) // Because of correspondance with the VR dic ((gdcmValEntry *)Entry)->SetValue(NewValue.c_str()); else ((gdcmValEntry *)Entry)->SetValue(NewValue); } /** * \brief Find the value Length of the passed Header Entry * @param Entry Header Entry whose length of the value shall be loaded. */ void gdcmDocument::FindDocEntryLength (gdcmDocEntry *Entry) { guint16 element = Entry->GetElement(); //guint16 group = Entry->GetGroup(); //FIXME std::string vr = Entry->GetVR(); guint16 length16; if ( (Filetype == gdcmExplicitVR) && (! Entry->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) ) { Entry->SetLength(FindDocEntryLengthOB()); return; } FixDocEntryFoundLength(Entry, 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, "gdcmDocument::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(Entry->GetGroup()); guint16 CorrectElem = SwapShort(Entry->GetElement()); gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup, CorrectElem); if (!NewTag) { // This correct tag is not in the dictionary. Create a new one. NewTag = NewVirtualDictEntry(CorrectGroup, CorrectElem); } // FIXME this can create a memory leaks on the old entry that be // left unreferenced. Entry->SetDictEntry(NewTag); } // Heuristic: well some files are really ill-formed. if ( length16 == 0xffff) { length16 = 0; //dbg.Verbose(0, "gdcmDocument::FindLength", // "Erroneous element length fixed."); // Actually, length= 0xffff means that we deal with // Unknown Sequence Length } FixDocEntryFoundLength(Entry, (guint32)length16); return; } else { // Either implicit VR or a non DICOM conformal (see note 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. FixDocEntryFoundLength(Entry, ReadInt32()); return; } } /** * \brief Find the Value Representation of the current Dicom Element. * @param Entry */ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry) { if (Filetype != gdcmExplicitVR) return; char VR[3]; 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. (void)fread (&VR, (size_t)2,(size_t)1, fp); VR[2]=0; if(!CheckDocEntryVR(Entry,VR)) { 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 ( Entry->IsVRUnknown() ) Entry->SetVR("Implicit"); Entry->SetImplicitVR(); } } /** * \brief Check the correspondance between the VR of the header entry * and the taken VR. If they are different, the header entry is * updated with the new VR. * @param Entry Header Entry to check * @param vr Dicom Value Representation * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, VRKey vr) { char msg[100]; // for sprintf bool RealExplicit = true; // 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 && !gdcmGlobal::GetVR()->Count(vr) ) RealExplicit= false; if ( !RealExplicit ) { // 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", Entry->GetGroup(),Entry->GetElement()); dbg.Verbose(1, "gdcmDocument::FindVR: ",msg); if (Entry->GetGroup()%2 && Entry->GetElement() == 0x0000) { // Group length is UL ! gdcmDictEntry* NewEntry = NewVirtualDictEntry( Entry->GetGroup(),Entry->GetElement(), "UL","FIXME","Group Length"); Entry->SetDictEntry(NewEntry); } return(false); } if ( Entry->IsVRUnknown() ) { // When not a dictionary entry, we can safely overwrite the VR. if (Entry->GetElement() == 0x0000) { // Group length is UL ! Entry->SetVR("UL"); } else { Entry->SetVR(vr); } } else if ( Entry->GetVR() != vr ) { // 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* NewEntry = NewVirtualDictEntry( Entry->GetGroup(),Entry->GetElement(), vr,"FIXME",Entry->GetName()); Entry->SetDictEntry(NewEntry); } return(true); } /** * \brief Get the transformed value of the header entry. The VR value * is used to define the transformation to operate on the value * \warning NOT end user intended method ! * @param Entry * @return Transformed entry value */ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry) { if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) { std::string val=((gdcmValEntry *)Entry)->GetValue(); std::string vr=Entry->GetVR(); guint32 length = Entry->GetLength(); std::ostringstream s; int nbInt; // When short integer(s) are expected, read and convert the following // n * 2 bytes properly i.e. as a multivaluated strings // (each single value is separated fromthe next one by '\' // as usual for standard multivaluated filels // Elements with Value Multiplicity > 1 // contain a set of short integers (not a single one) if (vr == "US" || vr == "SS") { guint16 NewInt16; nbInt = length / 2; for (int i=0; i < nbInt; i++) { if(i!=0) s << '\\'; NewInt16 = (val[2*i+0]&0xFF)+((val[2*i+1]&0xFF)<<8); NewInt16 = SwapShort(NewInt16); s << NewInt16; } } // When integer(s) are expected, read and convert the following // n * 4 bytes properly i.e. as a multivaluated strings // (each single value is separated fromthe next one by '\' // as usual for standard multivaluated filels // Elements with Value Multiplicity > 1 // contain a set of integers (not a single one) else if (vr == "UL" || vr == "SL") { guint32 NewInt32; nbInt = length / 4; for (int i=0; i < nbInt; i++) { if(i!=0) s << '\\'; NewInt32= (val[4*i+0]&0xFF)+((val[4*i+1]&0xFF)<<8)+ ((val[4*i+2]&0xFF)<<16)+((val[4*i+3]&0xFF)<<24); NewInt32=SwapLong(NewInt32); s << NewInt32; } } #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM return(s.str()); } return(((gdcmValEntry *)Entry)->GetValue()); } /** * \brief Get the reverse transformed value of the header entry. The VR * value is used to define the reverse transformation to operate on * the value * \warning NOT end user intended method ! * @param Entry * @return Reverse transformed entry value */ std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry) { if ( (IsDocEntryAnInteger(Entry)) && (Entry->IsImplicitVR()) ) { std::string vr=Entry->GetVR(); std::ostringstream s; std::vector tokens; if (vr == "US" || vr == "SS") { guint16 NewInt16; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\"); for (unsigned int i=0; i>8)&0xFF); } tokens.clear(); } if (vr == "UL" || vr == "SL") { guint32 NewInt32; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\"); for (unsigned int i=0; i>8)&0xFF) <<(char)((NewInt32>>16)&0xFF)<<(char)((NewInt32>>24)&0xFF); } tokens.clear(); } #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM return(s.str()); } return(((gdcmValEntry *)Entry)->GetValue()); } /** * \brief Skip a given Header Entry * \warning NOT end user intended method ! * @param entry */ void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry) { SkipBytes(entry->GetLength()); } /** * \brief Skips to the begining of the next Header Entry * \warning NOT end user intended method ! * @param entry */ void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) { (void)fseek(fp, (long)(entry->GetOffset()), SEEK_SET); (void)fseek(fp, (long)(entry->GetReadLength()), SEEK_CUR); } /** * \brief Loads the value for a a given VLEntry * \warning NOT end user intended method ! * @param entry */ void gdcmDocument::LoadVLEntry(gdcmDocEntry *entry) { //SkipBytes(entry->GetLength()); LoadDocEntry(entry); } /** * \brief When the length of an element value is obviously wrong (because * the parser went Jabberwocky) one can hope improving things by * applying some heuristics. */ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, guint32 FoundLength) { Entry->SetReadLength(FoundLength); // will be updated only if a bug is found if ( FoundLength == 0xffffffff) { FoundLength = 0; } guint16 gr =Entry->GetGroup(); guint16 el =Entry->GetElement(); if (FoundLength%2) { std::ostringstream s; s << "Warning : Tag with uneven length " << FoundLength << " in x(" << std::hex << gr << "," << el <<")" << std::dec; dbg.Verbose(0, s.str().c_str()); } //////// Fix for some naughty General Electric images. // Allthough not recent many such GE corrupted images are still present // on Creatis hard disks. Hence this fix shall remain when such images // are no longer in user (we are talking a few years, here)... // Note: XMedCom probably uses such a trick since it is able to read // those pesky GE images ... if (FoundLength == 13) { // Only happens for this length ! if ( (Entry->GetGroup() != 0x0008) || ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ) { FoundLength = 10; Entry->SetReadLength(10); /// \todo a bug is to be fixed !? } } //////// Fix for some brain-dead 'Leonardo' Siemens images. // Occurence of such images is quite low (unless one leaves close to a // 'Leonardo' source. Hence, one might consider commenting out the // following fix on efficiency reasons. else if ( (Entry->GetGroup() == 0x0009) && ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ) { FoundLength = 4; Entry->SetReadLength(4); /// \todo a bug is to be fixed !? } //////// Deal with sequences, but only on users request: else if ( ( Entry->GetVR() == "SQ") && enableSequences) { FoundLength = 0; // ReadLength is unchanged } //////// We encountered a 'delimiter' element i.e. a tag of the form // "fffe|xxxx" which is just a marker. Delimiters length should not be // taken into account. else if(Entry->GetGroup() == 0xfffe) { // According to the norm, fffe|0000 shouldn't exist. BUT the Philips // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to // causes extra troubles... if( Entry->GetElement() != 0x0000 ) { FoundLength = 0; } } Entry->SetUsableLength(FoundLength); } /** * \brief Apply some heuristics to predict whether the considered * element value contains/represents an integer or not. * @param Entry The element value on which to apply the predicate. * @return The result of the heuristical predicate. */ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { guint16 element = Entry->GetElement(); guint16 group = Entry->GetGroup(); std::string vr = Entry->GetVR(); guint32 length = Entry->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 { // Allthough this should never happen, still some images have a // corrupted group length [e.g. have a glance at offset x(8336) of // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm]. // Since for dicom compliant and well behaved headers, the present // test is useless (and might even look a bit paranoid), when we // encounter such an ill-formed image, we simply display a warning // message and proceed on parsing (while crossing fingers). std::ostringstream s; int filePosition = ftell(fp); s << "Erroneous Group Length element length on : (" \ << std::hex << group << " , " << element << ") -before- position x(" << filePosition << ")" << "lgt : " << length; dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() ); } } if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) return true; return false; } /** * \brief Find the Length till the next sequence delimiter * \warning NOT end user intended method ! * @return */ guint32 gdcmDocument::FindDocEntryLengthOB(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, "gdcmDocument::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, "gdcmDocument::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; } /** * \brief Reads a supposed to be 16 Bits integer * (swaps it depending on processor endianity) * @return read value */ guint16 gdcmDocument::ReadInt16() { guint16 g; size_t item_read; item_read = fread (&g, (size_t)2,(size_t)1, fp); if ( item_read != 1 ) { if(ferror(fp)) dbg.Verbose(0, "gdcmDocument::ReadInt16", " File Error"); errno = 1; return 0; } errno = 0; g = SwapShort(g); return g; } /** * \brief Reads a supposed to be 32 Bits integer * (swaps it depending on processor endianity) * @return read value */ guint32 gdcmDocument::ReadInt32() { guint32 g; size_t item_read; item_read = fread (&g, (size_t)4,(size_t)1, fp); if ( item_read != 1 ) { if(ferror(fp)) dbg.Verbose(0, "gdcmDocument::ReadInt32", " File Error"); errno = 1; return 0; } errno = 0; g = SwapLong(g); return g; } /** * \brief skips bytes inside the source file * \warning NOT end user intended method ! * @return */ void gdcmDocument::SkipBytes(guint32 NBytes) { //FIXME don't dump the returned value (void)fseek(fp, (long)NBytes, SEEK_CUR); } /** * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ void gdcmDocument::Initialise(void) { RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); RefShaDict = NULL; } /** * \brief Discover what the swap code is (among little endian, big endian, * bad little endian, bad big endian). * sw is set * @return false when we are absolutely sure * it's neither ACR-NEMA nor DICOM * true when we hope ours assuptions are OK */ bool gdcmDocument::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 x=4; // x : for ntohs bool net2host; // true when HostByteOrder is the same as NetworkByteOrder guint32 s32; guint16 s16; 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, "gdcmDocument::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 : FIXME: // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR, // but elem 0002,0010 (Transfert Syntax) tells us the file is // *Implicit* VR. -and it is !- if( (memcmp(entCur, "UL", (size_t)2) == 0) || (memcmp(entCur, "OB", (size_t)2) == 0) || (memcmp(entCur, "UI", (size_t)2) == 0) || (memcmp(entCur, "CS", (size_t)2) == 0) ) // CS, to remove later // when Write DCM *adds* // FIXME // Use gdcmDocument::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? group 0000 { Filetype = gdcmExplicitVR; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "explicit Value Representation"); } else { Filetype = gdcmImplicitVR; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not an explicit Value Representation"); } if (net2host) { sw = 4321; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "HostByteOrder != NetworkByteOrder"); } else { sw = 0; dbg.Verbose(1, "gdcmDocument::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 true; } // 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, "gdcmDocument::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 : s32 = *((guint32 *)(entCur)); switch (s32) { case 0x00040000 : sw = 3412; Filetype = gdcmACR; return true; case 0x04000000 : sw = 4321; Filetype = gdcmACR; return true; case 0x00000400 : sw = 2143; Filetype = gdcmACR; return true; case 0x00000004 : sw = 0; Filetype = gdcmACR; return true; default : // 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 check if this file wouldn't happen to be 'dirty' ACR/NEMA, // i.e. the 'group length' element is not present : // check the supposed to be 'group number' // 0x0002 or 0x0004 or 0x0008 // to determine ' sw' value . // Only 0 or 4321 will be possible // (no oportunity to check for the formerly well known // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian' // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -4, 8-) // the file IS NOT ACR-NEMA nor DICOM V3 // Find a trick to tell it the caller... s16 = *((guint16 *)(deb)); switch (s16) { case 0x0002 : case 0x0004 : case 0x0008 : sw = 0; Filetype = gdcmACR; return true; case 0x0200 : case 0x0400 : case 0x0800 : sw = 4321; Filetype = gdcmACR; return true; default : dbg.Verbose(0, "gdcmDocument::CheckSwap:", "ACR/NEMA unfound swap info (Really hopeless !)"); Filetype = gdcmUnknown; return false; } // Then the only info we have is the net2host one. //if (! net2host ) // sw = 0; //else // sw = 4321; //return; } } /** * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. */ void gdcmDocument::SwitchSwapToBigEndian(void) { dbg.Verbose(1, "gdcmDocument::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; } /** * \brief during parsing, Header Elements too long are not loaded in memory * @param NewSize */ void gdcmDocument::SetMaxSizeLoadEntry(long NewSize) { if (NewSize < 0) return; if ((guint32)NewSize >= (guint32)0xffffffff) { MaxSizeLoadEntry = 0xffffffff; return; } MaxSizeLoadEntry = NewSize; } /** * \brief Header Elements too long will not be printed * \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE * @param NewSize */ void gdcmDocument::SetMaxSizePrintEntry(long NewSize) { if (NewSize < 0) return; if ((guint32)NewSize >= (guint32)0xffffffff) { MaxSizePrintEntry = 0xffffffff; return; } MaxSizePrintEntry = NewSize; } /** * \brief Read the next tag but WITHOUT loading it's value * (read the 'Group Number', the 'Element Number', * gets the Dict Entry * gets the VR, gets the length, gets the offset value) * @return On succes the newly created DocEntry, NULL on failure. */ gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) { guint16 g,n; gdcmDocEntry *NewEntry; g = ReadInt16(); n = ReadInt16(); if (errno == 1) // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. return (gdcmDocEntry *)0; NewEntry = NewDocEntryByNumber(g, n); FindDocEntryVR(NewEntry); FindDocEntryLength(NewEntry); if (errno == 1) { // Call it quits delete NewEntry; return NULL; } NewEntry->SetOffset(ftell(fp)); return NewEntry; } /** * \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 */ gdcmDocEntry *gdcmDocument::NewDocEntryByName(std::string Name) { gdcmDictEntry *NewTag = GetDictEntryByName(Name); if (!NewTag) NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name); gdcmDocEntry* NewEntry = new gdcmDocEntry(NewTag); if (!NewEntry) { dbg.Verbose(1, "gdcmDocument::ObtainDocEntryByName", "failed to allocate gdcmDocEntry"); return (gdcmDocEntry *)0; } return NewEntry; } /** * \brief Request a new virtual dict entry to the dict set * @param group group number of the underlying DictEntry * @param element element number of the underlying DictEntry * @param vr VR of the underlying DictEntry * @param fourth owner group * @param name english name */ gdcmDictEntry *gdcmDocument::NewVirtualDictEntry(guint16 group, guint16 element, std::string vr, std::string fourth, std::string name) { return gdcmGlobal::GetDicts()->NewVirtualDictEntry(group,element,vr,fourth,name); } /** * \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 number of the underlying DictEntry * @param Elem element number of the underlying DictEntry */ gdcmDocEntry* gdcmDocument::NewDocEntryByNumber(guint16 Group, guint16 Elem) { // Find out if the tag we encountered is in the dictionaries: gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); if (!DictEntry) DictEntry = NewVirtualDictEntry(Group, Elem); gdcmDocEntry *NewEntry = new gdcmDocEntry(DictEntry); if (!NewEntry) { dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber", "failed to allocate gdcmDocEntry"); return (gdcmDocEntry*)0; } return NewEntry; } /** * \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 number of the underlying DictEntry * @param Elem element number of the underlying DictEntry */ gdcmValEntry *gdcmDocument::NewValEntryByNumber(guint16 Group, guint16 Elem) { // Find out if the tag we encountered is in the dictionaries: gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); if (!DictEntry) DictEntry = NewVirtualDictEntry(Group, Elem); gdcmValEntry *NewEntry = new gdcmValEntry(DictEntry); if (!NewEntry) { dbg.Verbose(1, "gdcmDocument::NewValEntryByNumber", "failed to allocate gdcmValEntry"); return NULL; } return NewEntry; } /** * \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 number of the underlying DictEntry * @param Elem element number of the underlying DictEntry */ gdcmBinEntry *gdcmDocument::NewBinEntryByNumber(guint16 Group, guint16 Elem) { // Find out if the tag we encountered is in the dictionaries: gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); if (!DictEntry) DictEntry = NewVirtualDictEntry(Group, Elem); gdcmBinEntry *NewEntry = new gdcmBinEntry(DictEntry); if (!NewEntry) { dbg.Verbose(1, "gdcmDocument::NewBinEntryByNumber", "failed to allocate gdcmBinEntry"); return NULL; } return NewEntry; } /** * \brief Generate a free TagKey i.e. a TagKey that is not present * in the TagHt dictionary. * @param group The generated tag must belong to this group. * @return The element of tag with given group which is fee. */ guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group) { for (guint32 elem = 0; elem < UINT32_MAX; elem++) { TagKey key = gdcmDictEntry::TranslateToKey(group, elem); if (tagHT.count(key) == 0) return elem; } return UINT32_MAX; } /** * \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 *gdcmDocument::GetDictEntryByName(std::string Name) { gdcmDictEntry *found = (gdcmDictEntry *)0; if (!RefPubDict && !RefShaDict) { dbg.Verbose(0, "gdcmDocument::GetDictEntry", "we SHOULD have a default dictionary"); } if (RefPubDict) { found = RefPubDict->GetDictEntryByName(Name); if (found) return found; } if (RefShaDict) { found = RefShaDict->GetDictEntryByName(Name); if (found) return found; } return found; } /** * \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 number of the searched DictEntry * @param element element number of the searched DictEntry * @return Corresponding DictEntry when it exists, NULL otherwise. */ gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element) { gdcmDictEntry *found = (gdcmDictEntry *)0; if (!RefPubDict && !RefShaDict) { dbg.Verbose(0, "gdcmDocument::GetDictEntry", "we SHOULD have a default dictionary"); } if (RefPubDict) { found = RefPubDict->GetDictEntryByNumber(group, element); if (found) return found; } if (RefShaDict) { found = RefShaDict->GetDictEntryByNumber(group, element); if (found) return found; } return found; } /** * \brief Assuming the internal file pointer \ref gdcmDocument::fp * is placed at the beginning of a tag (TestGroup, TestElement), * read the length associated to the Tag. * \warning On success the internal file pointer \ref gdcmDocument::fp * is modified to point after the tag and it's length. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElement) the internal file pointer * \ref gdcmDocument::fp is restored to it's original position. * @param TestGroup The expected group of the tag. * @param TestElement The expected Element of the tag. * @return On success returns the length associated to the tag. On failure * returns 0. */ guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement) { guint16 ItemTagGroup; guint16 ItemTagElement; long PositionOnEntry = ftell(fp); long CurrentPosition = ftell(fp); // On debugging purposes //// Read the Item Tag group and element, and make // sure they are respectively 0xfffe and 0xe000: ItemTagGroup = ReadInt16(); ItemTagElement = ReadInt16(); if ( (ItemTagGroup != TestGroup) || (ItemTagElement != TestElement ) ) { std::ostringstream s; s << " We should have found tag ("; s << std::hex << TestGroup << "," << TestElement << ")" << std::endl; s << " but instead we encountered tag ("; s << std::hex << ItemTagGroup << "," << ItemTagElement << ")" << std::endl; s << " at address: " << (unsigned)CurrentPosition << std::endl; dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:"); dbg.Verbose(0, s.str().c_str()); fseek(fp, PositionOnEntry, SEEK_SET); return 0; } //// Then read the associated Item Length CurrentPosition=ftell(fp); guint32 ItemLength; ItemLength = ReadInt32(); { std::ostringstream s; s << "Basic Item Length is: " << ItemLength << std::endl; s << " at address: " << (unsigned)CurrentPosition << std::endl; dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: ", s.str().c_str()); } return ItemLength; } /** * \brief Read the length of an exptected Item tag i.e. (0xfffe, 0xe000). * \sa \ref gdcmDocument::ReadTagLength * \warning See warning of \ref gdcmDocument::ReadTagLength * @return On success returns the length associated to the item tag. * On failure returns 0. */ guint32 gdcmDocument::ReadItemTagLength(void) { return ReadTagLength(0xfffe, 0xe000); } /** * \brief Read the length of an exptected Sequence Delimiter tag i.e. * (0xfffe, 0xe0dd). * \sa \ref gdcmDocument::ReadTagLength * \warning See warning of \ref gdcmDocument::ReadTagLength * @return On success returns the length associated to the Sequence * Delimiter tag. On failure returns 0. */ guint32 gdcmDocument::ReadSequenceDelimiterTagLength(void) { return ReadTagLength(0xfffe, 0xe0dd); } /** * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files * No other way so 'skip' the Data * */ void gdcmDocument::Parse7FE0 (void) { gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return; if ( IsImplicitVRLittleEndianTransferSyntax() || IsExplicitVRLittleEndianTransferSyntax() || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier ! || IsDeflatedExplicitVRLittleEndianTransferSyntax() ) return; // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels //// Read the Basic Offset Table Item Tag length... guint32 ItemLength = ReadItemTagLength(); //// ... and then read length[s] itself[themselves]. We don't use // the values read (BTW what is the purpous of those lengths ?) if (ItemLength != 0) { // BTW, what is the purpous of those length anyhow !? char * BasicOffsetTableItemValue = new char[ItemLength + 1]; fread(BasicOffsetTableItemValue, ItemLength, 1, fp); for (unsigned int i=0; i < ItemLength; i += 4){ guint32 IndividualLength; IndividualLength = str2num(&BasicOffsetTableItemValue[i],guint32); std::ostringstream s; s << " Read one length: "; s << std::hex << IndividualLength << std::endl; dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str()); } } if ( ! IsRLELossLessTransferSyntax() ) { // JPEG Image //// We then skip (not reading them) all the fragments of images: while ( (ItemLength = ReadItemTagLength()) ) { SkipBytes(ItemLength); } } else { // RLE Image long ftellRes; long RleSegmentLength[15], fragmentLength; // while 'Sequence Delimiter Item' (fffe,e0dd) not found while ( (fragmentLength = ReadSequenceDelimiterTagLength()) ) { // Parse fragments of the current Fragment (Frame) //------------------ scanning (not reading) fragment pixels guint32 nbRleSegments = ReadInt32(); printf(" Nb of RLE Segments : %d\n",nbRleSegments); //// Reading RLE Segments Offset Table guint32 RleSegmentOffsetTable[15]; for(int k=1; k<=15; k++) { ftellRes=ftell(fp); RleSegmentOffsetTable[k] = ReadInt32(); printf(" at : %x Offset Segment %d : %d (%x)\n", (unsigned)ftellRes,k,RleSegmentOffsetTable[k], RleSegmentOffsetTable[k]); } // skipping (not reading) RLE Segments if (nbRleSegments>1) { for(unsigned int k=1; k<=nbRleSegments-1; k++) { RleSegmentLength[k]= RleSegmentOffsetTable[k+1] - RleSegmentOffsetTable[k]; ftellRes=ftell(fp); printf (" Segment %d : Length = %d x(%x) Start at %x\n", k,(unsigned)RleSegmentLength[k], (unsigned)RleSegmentLength[k], (unsigned)ftellRes); SkipBytes(RleSegmentLength[k]); } } RleSegmentLength[nbRleSegments]= fragmentLength - RleSegmentOffsetTable[nbRleSegments]; ftellRes=ftell(fp); printf (" Segment %d : Length = %d x(%x) Start at %x\n", nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments], (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes); SkipBytes(RleSegmentLength[nbRleSegments]); } } } /** * \brief Compares two documents, according to \ref gdcmDicomDir rules * \warning Does NOT work with ACR-NEMA files * \todo Find a trick to solve the pb (use RET fields ?) * @param document * @return true if 'smaller' */ bool gdcmDocument::operator<(gdcmDocument &document) { std::string s1,s2; // Patient Name s1=this->GetEntryByNumber(0x0010,0x0010); s2=document.GetEntryByNumber(0x0010,0x0010); if(s1 < s2) return true; else if(s1 > s2) return false; else { // Patient ID s1=this->GetEntryByNumber(0x0010,0x0020); s2=document.GetEntryByNumber(0x0010,0x0020); if (s1 < s2) return true; else if (s1 > s2) return true; else { // Study Instance UID s1=this->GetEntryByNumber(0x0020,0x000d); s2=document.GetEntryByNumber(0x0020,0x000d); if (s1 < s2) return true; else if(s1 > s2) return false; else { // Serie Instance UID s1=this->GetEntryByNumber(0x0020,0x000e); s2=document.GetEntryByNumber(0x0020,0x000e); if (s1 < s2) return true; else if(s1 > s2) return false; } } } return false; } //-----------------------------------------------------------------------------