/*========================================================================= Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ Date: $Date: 2004/11/24 11:17:47 $ Version: $Revision: 1.136 $ 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.html 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: #if defined(_MSC_VER) || defined(__BORLANDC__) #include #else #include #endif namespace gdcm { static const char *TransferSyntaxStrings[] = { // Implicit VR Little Endian "1.2.840.10008.1.2", // Implicit VR Little Endian DLX G.E? "1.2.840.113619.5.2", // Explicit VR Little Endian "1.2.840.10008.1.2.1", // Deflated Explicit VR Little Endian "1.2.840.10008.1.2.1.99", // Explicit VR Big Endian "1.2.840.10008.1.2.2", // JPEG Baseline (Process 1) "1.2.840.10008.1.2.4.50", // JPEG Extended (Process 2 & 4) "1.2.840.10008.1.2.4.51", // JPEG Extended (Process 3 & 5) "1.2.840.10008.1.2.4.52", // JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8) "1.2.840.10008.1.2.4.53", // JPEG Full Progression, Non-Hierarchical (Process 10 & 12) "1.2.840.10008.1.2.4.55", // JPEG Lossless, Non-Hierarchical (Process 14) "1.2.840.10008.1.2.4.57", // JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, [Selection Value 1]) "1.2.840.10008.1.2.4.70", // JPEG 2000 Lossless "1.2.840.10008.1.2.4.90", // JPEG 2000 "1.2.840.10008.1.2.4.91", // RLE Lossless "1.2.840.10008.1.2.5", // Unknown "Unknown Transfer Syntax" }; //----------------------------------------------------------------------------- // Refer to Document::CheckSwap() const unsigned int Document::HEADER_LENGTH_TO_READ = 256; // Refer to Document::SetMaxSizeLoadEntry() const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; //----------------------------------------------------------------------------- // Constructor / Destructor /** * \brief constructor * @param filename file to be opened for parsing */ Document::Document( std::string const & filename ) : ElementSet(-1) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; Initialise(); Fp = 0; if ( !OpenFile() ) { return; } dbg.Verbose(0, "Document::Document: starting parsing of file: ", Filename.c_str()); Fp->seekg( 0, std::ios_base::beg); Fp->seekg(0, std::ios_base::end); long lgt = Fp->tellg(); Fp->seekg( 0, std::ios_base::beg); CheckSwap(); long beg = Fp->tellg(); lgt -= beg; ParseDES( this, beg, lgt, false); // le Load sera fait a la volee Fp->seekg( 0, std::ios_base::beg); // Load 'non string' values std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ) { LoadEntryBinArea(0x0028,0x1200); // gray LUT /// FIXME FIXME FIXME /// The tags refered by the three following lines used to be CORRECTLY /// defined as having an US Value Representation in the public /// dictionnary. BUT the semantics implied by the three following /// lines state that the corresponding tag contents are in fact /// the ones of a BinEntry. /// In order to fix things "Quick and Dirty" the dictionnary was /// altered on PURPOUS but now contains a WRONG value. /// In order to fix things and restore the dictionary to its /// correct value, one needs to decided of the semantics by deciding /// wether the following tags are either: /// - multivaluated US, and hence loaded as ValEntry, but afterwards /// also used as BinEntry, which requires the proper conversion, /// - OW, and hence loaded as BinEntry, but afterwards also used /// as ValEntry, which requires the proper conversion. LoadEntryBinArea(0x0028,0x1201); // R LUT LoadEntryBinArea(0x0028,0x1202); // G LUT LoadEntryBinArea(0x0028,0x1203); // B LUT // Segmented Red Palette Color LUT Data LoadEntryBinArea(0x0028,0x1221); // Segmented Green Palette Color LUT Data LoadEntryBinArea(0x0028,0x1222); // Segmented Blue Palette Color LUT Data LoadEntryBinArea(0x0028,0x1223); } //FIXME later : how to use it? LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent) CloseFile(); // -------------------------------------------------------------- // Specific code to allow gdcm to read ACR-LibIDO formated images // Note: ACR-LibIDO is an extension of the ACR standard that was // used at CREATIS. For the time being (say a couple years) // we keep this kludge to allow a smooth move to gdcm for // CREATIS developpers (sorry folks). // // 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 = ACR_LIBIDO; std::string rows = GetEntryByNumber(0x0028, 0x0010); std::string columns = GetEntryByNumber(0x0028, 0x0011); SetEntryByNumber(columns, 0x0028, 0x0010); SetEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- End of ACR-LibIDO kludge ------------------ PrintLevel = 1; // 'Medium' print level by default } /** * \brief This default constructor doesn't parse the file. You should * then invoke \ref Document::SetFileName and then the parsing. */ Document::Document() : ElementSet(-1) { Fp = 0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); SwapCode = 0; Filetype = ExplicitVR; PrintLevel = 1; // 'Medium' print level by default } /** * \brief Canonical destructor. */ Document::~Document () { RefPubDict = NULL; RefShaDict = NULL; delete RLEInfo; delete JPEGInfo; } //----------------------------------------------------------------------------- // Print /** * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return */ void Document::PrintPubDict(std::ostream & os) { RefPubDict->Print(os); } /** * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ void Document::PrintShaDict(std::ostream & os) { RefShaDict->Print(os); } //----------------------------------------------------------------------------- // Public /** * \brief Get the public dictionary used */ Dict* Document::GetPubDict() { return RefPubDict; } /** * \brief Get the shadow dictionary used */ Dict* Document::GetShaDict() { return RefShaDict; } /** * \brief Set the shadow dictionary used * \param dict dictionary to use in shadow */ bool Document::SetShaDict(Dict *dict) { RefShaDict = dict; return !RefShaDict; } /** * \brief Set the shadow dictionary used * \param dictName name of the dictionary to use in shadow */ bool Document::SetShaDict(DictKey const & dictName) { RefShaDict = Global::GetDicts()->GetDict(dictName); return !RefShaDict; } /** * \brief This predicate, based on hopefully reasonable heuristics, * decides whether or not the current Document was properly parsed * and contains the mandatory information for being considered as * a well formed and usable Dicom/Acr File. * @return true when Document is the one of a reasonable Dicom/Acr file, * false otherwise. */ bool Document::IsReadable() { if( Filetype == Unknown) { dbg.Verbose(0, "Document::IsReadable: wrong filetype"); return false; } if( TagHT.empty() ) { dbg.Verbose(0, "Document::IsReadable: no tags in internal" " hash table."); return false; } return true; } /** * \brief Accessor to the Transfer Syntax (when present) of the * current document (it internally handles reading the * value from disk when only parsing occured). * @return The encountered Transfer Syntax of the current document. */ TransferSyntaxType Document::GetTransferSyntax() { DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); if ( !entry ) { return UnknownTS; } // The entry might be present but not loaded (parsing and loading // happen at different stages): try loading and proceed with check... LoadDocEntrySafe(entry); if (ValEntry* valEntry = dynamic_cast< ValEntry* >(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... if ( transfer.length() == 0 ) { // for brain damaged headers return UnknownTS; } while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { transfer.erase(transfer.length()-1, 1); } for (int i = 0; TransferSyntaxStrings[i] != NULL; i++) { if ( TransferSyntaxStrings[i] == transfer ) { return TransferSyntaxType(i); } } } return UnknownTS; } bool Document::IsJPEGLossless() { TransferSyntaxType r = GetTransferSyntax(); return r == JPEGFullProgressionProcess10_12 || r == JPEGLosslessProcess14 || r == JPEGLosslessProcess14_1; } /** * \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 Document::IsJPEG2000() { TransferSyntaxType r = GetTransferSyntax(); return r == JPEG2000Lossless || r == JPEG2000; } /** * \brief Determines if the Transfer Syntax corresponds to any form * of Jpeg encoded Pixel data. * @return True when any form of JPEG found. False otherwise. */ bool Document::IsJPEG() { TransferSyntaxType r = GetTransferSyntax(); return r == JPEGBaselineProcess1 || r == JPEGExtendedProcess2_4 || r == JPEGExtendedProcess3_5 || r == JPEGSpectralSelectionProcess6_8 || IsJPEGLossless() || IsJPEG2000(); } /** * \brief Determines if the Transfer Syntax corresponds to encapsulated * of encoded Pixel Data (as opposed to native). * @return True when encapsulated. False when native. */ bool Document::IsEncapsulate() { TransferSyntaxType r = GetTransferSyntax(); return IsJPEG() || r == RLELossless; } /** * \brief Predicate for dicom version 3 file. * @return True when the file is a dicom version 3. */ bool Document::IsDicomV3() { // 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 Document::GetFileType() { return Filetype; } /** * \brief Tries to open the file \ref Document::Filename and * checks the preamble when existing. * @return The FILE pointer on success. */ std::ifstream* Document::OpenFile() { if (Filename.length() == 0) return 0; if(Fp) { dbg.Verbose( 0, "Document::OpenFile is already opened when opening: ", Filename.c_str()); } Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); if(!Fp) { dbg.Verbose( 0, "Document::OpenFile cannot open file: ", Filename.c_str()); return 0; } uint16_t zero; Fp->read((char*)&zero, (size_t)2 ); //ACR -- or DICOM with no Preamble; may start with a Shadow Group -- if( zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 || zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 || zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 || zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ) { return Fp; } //DICOM Fp->seekg(126L, std::ios_base::cur); char dicm[4]; Fp->read(dicm, (size_t)4); if( memcmp(dicm, "DICM", 4) == 0 ) { return Fp; } CloseFile(); dbg.Verbose( 0, "Document::OpenFile not DICOM/ACR (missing preamble)", Filename.c_str()); return 0; } /** * \brief closes the file * @return TRUE if the close was successfull */ bool Document::CloseFile() { if( Fp ) { Fp->close(); delete Fp; Fp = 0; } return true; //FIXME how do we detect a non-close ifstream ? } /** * \brief Writes in a file all the Header Entries (Dicom Elements) * @param fp file pointer on an already open file * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ void Document::Write(std::ofstream* fp, FileType filetype) { /// \todo move the following lines (and a lot of others, to be written) /// to a future function CheckAndCorrectHeader /// (necessary if user wants to write a DICOM V3 file /// starting from an ACR-NEMA (V2) Header if (filetype == ImplicitVR) { std::string ts = Util::DicomString( TransferSyntaxStrings[ImplicitVRLittleEndian] ); ReplaceOrCreateByNumber(ts, 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 /// in the following case we have to padd manually with a 0 SetEntryLengthByNumber(18, 0x0002, 0x0010); } if (filetype == ExplicitVR) { std::string ts = Util::DicomString( TransferSyntaxStrings[ExplicitVRLittleEndian] ); ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); //LEAK /// \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 * - 'Group Length' element is optional in DICOM * - but un-updated odd groups lengthes can causes pb * (xmedcon breaker) * * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) ) * UpdateGroupLength(false,filetype); * if ( filetype == ACR) * UpdateGroupLength(true,ACR); */ ElementSet::Write(fp, filetype); // This one is recursive } /** * \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 * @param vr V(alue) R(epresentation) of the Entry -if private Entry- * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ ValEntry* Document::ReplaceOrCreateByNumber( std::string const & value, uint16_t group, uint16_t elem, TagName const & vr ) { ValEntry* valEntry = 0; DocEntry* currentEntry = GetDocEntryByNumber( group, elem); if (!currentEntry) { // check if (group,element) DictEntry exists // if it doesn't, create an entry in DictSet::VirtualEntry // and use it // Find out if the tag we received is in the dictionaries: Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); if (!dictEntry) { currentEntry = NewDocEntryByNumber(group, elem, vr); } else { currentEntry = NewDocEntryByNumber(group, elem); } if (!currentEntry) { dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" " NewDocEntryByNumber failed."); return NULL; } valEntry = new ValEntry(currentEntry); delete currentEntry; if ( !AddEntry(valEntry)) { delete valEntry; dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); return NULL; } } else { valEntry = dynamic_cast< ValEntry* >(currentEntry); if ( !valEntry ) // Euuuuh? It wasn't a ValEntry // then we change it to a ValEntry ? // Shouldn't it be considered as an error ? { // We need to promote the DocEntry to a ValEntry: valEntry = new ValEntry(currentEntry); if (!RemoveEntry(currentEntry)) { delete valEntry; dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" " of previous DocEntry failed."); return NULL; } if ( !AddEntry(valEntry)) { delete valEntry; dbg.Verbose(0, "Document::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. * A copy of the binArea is made to be kept in the Document. * @param binArea (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). */ BinEntry* Document::ReplaceOrCreateByNumber( uint8_t* binArea, int lgth, uint16_t group, uint16_t elem, TagName const & vr ) { BinEntry* binEntry = 0; DocEntry* currentEntry = GetDocEntryByNumber( group, elem); if (!currentEntry) { // check if (group,element) DictEntry exists // if it doesn't, create an entry in DictSet::VirtualEntry // and use it // Find out if the tag we received is in the dictionaries: Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem); if (!dictEntry) { currentEntry = NewDocEntryByNumber(group, elem, vr); } else { currentEntry = NewDocEntryByNumber(group, elem); } if (!currentEntry) { dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" " NewDocEntryByNumber failed."); return NULL; } binEntry = new BinEntry(currentEntry); if ( !AddEntry(binEntry)) { dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); } } else { binEntry = dynamic_cast< BinEntry* >(currentEntry); if ( !binEntry ) // Euuuuh? It wasn't a BinEntry // then we change it to a BinEntry ? // Shouldn't it be considered as an error ? { // We need to promote the DocEntry to a BinEntry: binEntry = new BinEntry(currentEntry); if (!RemoveEntry(currentEntry)) { dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" " of previous DocEntry failed."); return NULL; } if ( !AddEntry(binEntry)) { dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" " promoted BinEntry failed."); return NULL; } } } uint8_t *tmpArea; if (lgth>0 && binArea) { tmpArea = new uint8_t[lgth]; memcpy(tmpArea,binArea,lgth); } else { tmpArea = 0; } if (!SetEntryByNumber(tmpArea, lgth, group, elem)) { if (tmpArea) { delete[] tmpArea; } } return binEntry; } /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it when unexistant. * @param Group Group number of the Entry * @param Elem Element number of the Entry * \return pointer to the modified/created SeqEntry (NULL when creation * failed). */ SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) { SeqEntry* b = 0; DocEntry* a = GetDocEntryByNumber( group, elem); if (!a) { a = NewSeqEntryByNumber(group, elem); if (!a) { return 0; } b = new SeqEntry(a, 1); // FIXME : 1 (Depth) AddEntry(b); } 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 Document::ReplaceIfExistByNumber(std::string const & value, uint16_t group, uint16_t elem ) { SetEntryByNumber(value, 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 true is found */ bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) { const std::string &key = DictEntry::TranslateToKey(group, element ); return TagHT.count(key) != 0; } /** * \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 Document::GetEntryByName(TagName const & tagName) { DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) { 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 Document::GetEntryVRByName(TagName const& tagName) { DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) { return GDCM_UNFOUND; } DocEntry* 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 Document::GetEntryByNumber(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); /// \todo use map methods, instead of multimap JPR if ( !TagHT.count(key)) { return GDCM_UNFOUND; } return ((ValEntry *)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 Document::GetEntryVRByNumber(uint16_t group, uint16_t element) { DocEntry* 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 Document::GetEntryLengthByNumber(uint16_t group, uint16_t element) { DocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) { return -2; //magic number } 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 Document::SetEntryByName( std::string const & content, TagName const & tagName) { DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) { return false; } return SetEntryByNumber(content,dictEntry->GetGroup(), dictEntry->GetElement()); } /** * \brief Accesses an existing DocEntry (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 Document::SetEntryByNumber(std::string const& content, uint16_t group, uint16_t element) { int c; int l; ValEntry* valEntry = GetValEntryByNumber(group, element); if (!valEntry ) { dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding", " ValEntry (try promotion first)."); return false; } // Non even content must be padded with a space (020H)... std::string finalContent = Util::DicomString( content.c_str() ); assert( !(finalContent.size() % 2) ); valEntry->SetValue(finalContent); // Integers have a special treatement for their length: l = finalContent.length(); if ( l != 0) // To avoid to be cheated by 'zero length' integers { VRKey vr = valEntry->GetVR(); if( vr == "US" || vr == "SS" ) { // for multivaluated items c = Util::CountSubstring(content, "\\") + 1; l = c*2; } else if( vr == "UL" || vr == "SL" ) { // for multivaluated items c = Util::CountSubstring(content, "\\") + 1; l = c*4;; } } valEntry->SetLength(l); return true; } /** * \brief Accesses an existing DocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. * @param content new value (void* -> uint8_t*) to substitute with * @param lgth new value length * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ bool Document::SetEntryByNumber(uint8_t*content, int lgth, uint16_t group, uint16_t element) { (void)lgth; //not used TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) { return false; } /* Hope Binary 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? } */ BinEntry* entry = (BinEntry *)TagHT[key]; entry->SetBinArea(content); entry->SetLength(lgth); entry->SetValue(GDCM_BINLOADED); return true; } /** * \brief Accesses an existing DocEntry (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 Document::SetEntryLengthByNumber(uint32_t l, uint16_t group, uint16_t element) { /// \todo use map methods, instead of multimap JPR TagKey key = DictEntry::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 Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) { DocEntry* entry = GetDocEntryByNumber(group, elem); if (!entry) { dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present."); return 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* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) { DocEntry* entry = GetDocEntryByNumber(group, elem); if (!entry) { dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry"); return 0; } if ( BinEntry* binEntry = dynamic_cast(entry) ) { return binEntry->GetBinArea(); } return 0; } /** * \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 Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { // Search the corresponding DocEntry DocEntry *docElement = GetDocEntryByNumber(group, elem); if ( !docElement ) return; BinEntry *binElement = dynamic_cast(docElement); if( !binElement ) return; LoadEntryBinArea(binElement); /* size_t o =(size_t)docElement->GetOffset(); Fp->seekg( o, std::ios_base::beg); size_t l = docElement->GetLength(); uint8_t* a = new uint8_t[l]; if(!a) { dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); return; } // Read the value Fp->read((char*)a, l); if( Fp->fail() || Fp->eof() )//Fp->gcount() == 1 { delete[] a; return; } // Set the value to the DocEntry if( !SetEntryBinAreaByNumber( a, group, elem ) ) { delete[] a; dbg.Verbose(0, "Document::LoadEntryBinArea setting failed."); }*/ } /** * \brief Loads (from disk) the element content * when a string is not suitable * @param element Entry whose binArea is going to be loaded */ void Document::LoadEntryBinArea(BinEntry* element) { bool openFile = !Fp; if(openFile) OpenFile(); size_t o =(size_t)element->GetOffset(); Fp->seekg(o, std::ios_base::beg); size_t l = element->GetLength(); uint8_t* a = new uint8_t[l]; if( !a ) { dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); return; } /// \todo check the result Fp->read((char*)a, l); if( Fp->fail() || Fp->eof()) //Fp->gcount() == 1 { delete[] a; return; } element->SetBinArea(a); if(openFile) CloseFile(); } /** * \brief Sets a 'non string' value to a given Dicom Element * @param area area containing the 'non string' value * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element * @return */ bool Document::SetEntryBinAreaByNumber(uint8_t* area, uint16_t group, uint16_t element) { DocEntry* currentEntry = GetDocEntryByNumber(group, element); if ( !currentEntry ) { return false; } if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) { binEntry->SetBinArea( area ); return true; } return false; } /** * \brief Update the entries with the shadow dictionary. * Only non even entries are analyzed */ void Document::UpdateShaEntries() { //DictEntry *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. */ DocEntry* Document::GetDocEntryByName(TagName const & tagName) { DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) { 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 */ DocEntry* Document::GetDocEntryByNumber(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) { return NULL; } return TagHT.find(key)->second; } /** * \brief Same as \ref Document::GetDocEntryByNumber except it only * returns a result when the corresponding entry is of type * ValEntry. * @return When present, the corresponding ValEntry. */ ValEntry* Document::GetValEntryByNumber(uint16_t group, uint16_t element) { DocEntry* currentEntry = GetDocEntryByNumber(group, element); if ( !currentEntry ) { return 0; } if ( ValEntry* valEntry = dynamic_cast(currentEntry) ) { return valEntry; } dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry."); return 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 Document::LoadDocEntrySafe(DocEntry * entry) { long PositionOnEntry = Fp->tellg(); LoadDocEntry(entry); Fp->seekg(PositionOnEntry, std::ios_base::beg); } /** * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly swaped 32 bits integer. */ uint32_t Document::SwapLong(uint32_t a) { switch (SwapCode) { 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= " << SwapCode << std::endl; dbg.Error(" Document::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. */ uint32_t Document::UnswapLong(uint32_t a) { return SwapLong(a); } /** * \brief Swaps the bytes so they agree with the processor order * @return The properly swaped 16 bits integer. */ uint16_t Document::SwapShort(uint16_t a) { if ( SwapCode == 4321 || SwapCode == 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. */ uint16_t Document::UnswapShort(uint16_t a) { return SwapShort(a); } //----------------------------------------------------------------------------- // Private /** * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) * @return length of the parsed set. */ void Document::ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode) { DocEntry *newDocEntry = 0; while (true) { if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { break; } newDocEntry = ReadNextDocEntry( ); if ( !newDocEntry ) { break; } VRKey vr = newDocEntry->GetVR(); if ( vr != "SQ" ) { if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) ) { /////////////////////// ValEntry ValEntry* newValEntry = new ValEntry( newDocEntry->GetDictEntry() ); //LEAK newValEntry->Copy( newDocEntry ); // When "set" is a Document, then we are at the top of the // hierarchy and the Key is simply of the form ( group, elem )... if (Document* dummy = dynamic_cast< Document* > ( set ) ) { (void)dummy; newValEntry->SetKey( newValEntry->GetKey() ); } // ...but when "set" is a SQItem, we are inserting this new // valEntry in a sequence item. Hence the key has the // generalized form (refer to \ref BaseTagKey): if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newValEntry->SetKey( parentSQItem->GetBaseTagKey() + newValEntry->GetKey() ); } LoadDocEntry( newValEntry ); bool delimitor=newValEntry->IsItemDelimitor(); if( !set->AddEntry( newValEntry ) ) { // If here expect big troubles delete newValEntry; //otherwise mem leak } if (delimitor) { delete newDocEntry; break; } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { delete newDocEntry; break; } } else { if ( ! Global::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) { ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR dbg.Verbose(0, "Document::ParseDES: neither Valentry, " "nor BinEntry. Probably unknown VR."); } //////////////////// BinEntry or UNKOWN VR: /* BinEntry* newBinEntry = new BinEntry( newDocEntry->GetDictEntry() ); //LEAK newBinEntry->Copy( newDocEntry );*/ BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK // When "this" is a Document the Key is simply of the // form ( group, elem )... if (Document* dummy = dynamic_cast< Document* > ( set ) ) { (void)dummy; newBinEntry->SetKey( newBinEntry->GetKey() ); } // but when "this" is a SQItem, we are inserting this new // valEntry in a sequence item, and the kay has the // generalized form (refer to \ref BaseTagKey): if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newBinEntry->SetKey( parentSQItem->GetBaseTagKey() + newBinEntry->GetKey() ); } LoadDocEntry( newBinEntry ); if( !set->AddEntry( newBinEntry ) ) { //Expect big troubles if here delete newBinEntry; } } if ( ( newDocEntry->GetGroup() == 0x7fe0 ) && ( newDocEntry->GetElement() == 0x0010 ) ) { TransferSyntaxType ts = GetTransferSyntax(); if ( ts == RLELossless ) { long PositionOnEntry = Fp->tellg(); Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); ComputeRLEInfo(); Fp->seekg( PositionOnEntry, std::ios_base::beg ); } else if ( IsJPEG() ) { long PositionOnEntry = Fp->tellg(); Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); ComputeJPEGFragmentInfo(); Fp->seekg( PositionOnEntry, std::ios_base::beg ); } } // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); //delete newDocEntry; } else { // VR = "SQ" unsigned long 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 ... SeqEntry* newSeqEntry = new SeqEntry( newDocEntry->GetDictEntry() ); newSeqEntry->Copy( newDocEntry ); newSeqEntry->SetDelimitorMode( delim_mode ); // At the top of the hierarchy, stands a Document. When "set" // is a Document, then we are building the first depth level. // Hence the SeqEntry we are building simply has a depth // level of one: if (Document* dummy = dynamic_cast< Document* > ( set ) ) { (void)dummy; newSeqEntry->SetDepthLevel( 1 ); newSeqEntry->SetKey( newSeqEntry->GetKey() ); } // But when "set" is allready a SQItem, we are building a nested // sequence, and hence the depth level of the new SeqEntry // we are building, is one level deeper: if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); newSeqEntry->SetKey( parentSQItem->GetBaseTagKey() + newSeqEntry->GetKey() ); } if ( l != 0 ) { // Don't try to parse zero-length sequences ParseSQ( newSeqEntry, newDocEntry->GetOffset(), l, delim_mode); } set->AddEntry( newSeqEntry ); if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { delete newDocEntry; break; } } delete newDocEntry; } } /** * \brief Parses a Sequence ( SeqEntry after SeqEntry) * @return parsed length for this level */ void Document::ParseSQ( SeqEntry* seqEntry, long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; bool dlm_mod; while (true) { DocEntry* newDocEntry = ReadNextDocEntry(); if ( !newDocEntry ) { // FIXME Should warn user break; } if( delim_mode ) { if ( newDocEntry->IsSequenceDelimitor() ) { seqEntry->SetSequenceDelimitationItem( newDocEntry ); break; } } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { delete newDocEntry; break; } SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); std::ostringstream newBase; newBase << seqEntry->GetKey() << "/" << SQItemNumber << "#"; itemSQ->SetBaseTagKey( newBase.str() ); unsigned int l = newDocEntry->GetReadLength(); if ( l == 0xffffffff ) { dlm_mod = true; } else { dlm_mod = false; } ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); delete newDocEntry; seqEntry->AddEntry( itemSQ, SQItemNumber ); SQItemNumber++; if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) { break; } } } /** * \brief Loads the element content if its length doesn't exceed * the value specified with Document::SetMaxSizeLoadEntry() * @param entry Header Entry (Dicom Element) to be dealt with */ void Document::LoadDocEntry(DocEntry* entry) { uint16_t group = entry->GetGroup(); std::string vr = entry->GetVR(); uint32_t length = entry->GetLength(); Fp->seekg((long)entry->GetOffset(), std::ios_base::beg); // 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 ! return; } // When the length is zero things are easy: if ( length == 0 ) { ((ValEntry *)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. std::ostringstream s; if (length > MaxSizeLoadEntry) { if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) { //s << "gdcm::NotLoaded (BinEntry)"; s << GDCM_NOTLOADED; s << " Address:" << (long)entry->GetOffset(); s << " Length:" << entry->GetLength(); s << " x(" << std::hex << entry->GetLength() << ")"; binEntryPtr->SetValue(s.str()); } // Be carefull : a BinEntry IS_A ValEntry ... else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { // s << "gdcm::NotLoaded. (ValEntry)"; s << GDCM_NOTLOADED; s << " Address:" << (long)entry->GetOffset(); s << " Length:" << entry->GetLength(); s << " x(" << std::hex << entry->GetLength() << ")"; valEntryPtr->SetValue(s.str()); } else { // fusible std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry " << "nor a ValEntry ?! Should never print that !" << std::endl; } // to be sure we are at the end of the value ... Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), std::ios_base::beg); return; } // When we find a BinEntry not very much can be done : if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) { s << GDCM_BINLOADED; binEntryPtr->SetValue(s.str()); LoadEntryBinArea(binEntryPtr); // last one, not to erase length ! return; } /// \todo Any compacter code suggested (?) if ( IsDocEntryAnInteger(entry) ) { uint32_t NewInt; int nbInt; // When short integer(s) are expected, read and convert the following // n *two characters properly i.e. consider them 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; } } } // See above comment on multiple integers (mutatis mutandis). 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 ((ValEntry *)entry)->SetValue(s.str()); return; } // FIXME: We need an additional byte for storing \0 that is not on disk char *str = new char[length+1]; Fp->read(str, (size_t)length); str[length] = '\0'; //this is only useful when length is odd // Special DicomString call to properly handle \0 and even length std::string newValue; if( length % 2 ) { newValue = Util::DicomString(str, length+1); //dbg.Verbose(0, "Warning: bad length: ", length ); dbg.Verbose(0, "For string :", newValue.c_str()); // Since we change the length of string update it length entry->SetReadLength(length+1); } else { newValue = Util::DicomString(str, length); } delete[] str; if ( ValEntry* valEntry = dynamic_cast(entry) ) { if ( Fp->fail() || Fp->eof())//Fp->gcount() == 1 { dbg.Verbose(1, "Document::LoadDocEntry", "unread element value"); valEntry->SetValue(GDCM_UNREAD); return; } if( vr == "UI" ) { // Because of correspondance with the VR dic valEntry->SetValue(newValue); } else { valEntry->SetValue(newValue); } } else { dbg.Error(true, "Document::LoadDocEntry" "Should have a ValEntry, here !"); } } /** * \brief Find the value Length of the passed Header Entry * @param entry Header Entry whose length of the value shall be loaded. */ void Document::FindDocEntryLength( DocEntry *entry ) throw ( FormatError ) { uint16_t element = entry->GetElement(); std::string vr = entry->GetVR(); uint16_t length16; if ( Filetype == ExplicitVR && !entry->IsImplicitVR() ) { if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" ) { // The following reserved two bytes (see PS 3.5-2003, section // "7.1.2 Data element structure with explicit vr", p 27) must be // skipped before proceeding on reading the length on 4 bytes. Fp->seekg( 2L, std::ios_base::cur); uint32_t length32 = ReadInt32(); if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) { uint32_t lengthOB; try { /// \todo rename that to FindDocEntryLengthOBOrOW since /// the above test is on both OB and OW... lengthOB = FindDocEntryLengthOB(); } catch ( FormatUnexpected ) { // Computing the length failed (this happens with broken // files like gdcm-JPEG-LossLess3a.dcm). We still have a // chance to get the pixels by deciding the element goes // until the end of the file. Hence we artificially fix the // the length and proceed. long currentPosition = Fp->tellg(); Fp->seekg(0L,std::ios_base::end); long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; Fp->seekg(currentPosition, std::ios_base::beg); entry->SetLength(lengthUntilEOF); return; } entry->SetLength(lengthOB); 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 ) { TransferSyntaxType ts = GetTransferSyntax(); if ( ts != ExplicitVRBigEndian ) { throw FormatError( "Document::FindDocEntryLength()", " not explicit VR." ); return; } length16 = 4; SwitchSwapToBigEndian(); // Restore the unproperly loaded values i.e. the group, the element // and the dictionary entry depending on them. uint16_t correctGroup = SwapShort( entry->GetGroup() ); uint16_t correctElem = SwapShort( entry->GetElement() ); DictEntry* 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) { // 0xffff means that we deal with 'Unknown Length' Sequence length16 = 0; } FixDocEntryFoundLength( entry, (uint32_t)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 Document::FindDocEntryVR( DocEntry *entry ) { if ( Filetype != ExplicitVR ) { return; } char vr[3]; long positionOnEntry = Fp->tellg(); // 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. Fp->read (vr, (size_t)2); vr[2] = 0; if( !CheckDocEntryVR(entry, vr) ) { Fp->seekg(positionOnEntry, std::ios_base::beg); // 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 Document::CheckDocEntryVR(DocEntry *entry, VRKey vr) { std::string msg; 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((unsigned char)vr[0]) && !isalpha((unsigned char)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 && !Global::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. msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", entry->GetGroup(), entry->GetElement()); dbg.Verbose(1, "Document::FindVR: ", msg.c_str()); if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000) { // Group length is UL ! DictEntry* 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. DictEntry* 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 entry to tranform * @return Transformed entry value */ std::string Document::GetDocEntryValue(DocEntry *entry) { if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) { std::string val = ((ValEntry *)entry)->GetValue(); std::string vr = entry->GetVR(); uint32_t 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" ) { uint16_t 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" ) { uint32_t 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 ((ValEntry *)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 Entry to reverse transform * @return Reverse transformed entry value */ std::string Document::GetDocEntryUnvalue(DocEntry* entry) { if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) { std::string vr = entry->GetVR(); std::vector tokens; std::ostringstream s; if ( vr == "US" || vr == "SS" ) { uint16_t newInt16; tokens.erase( tokens.begin(), tokens.end()); // clean any previous value Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\"); for (unsigned int i=0; i> 8 ) & 0xFF ); } tokens.clear(); } if ( vr == "UL" || vr == "SL") { uint32_t newInt32; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Util::Tokenize (((ValEntry *)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 ((ValEntry *)entry)->GetValue(); } /** * \brief Skip a given Header Entry * \warning NOT end user intended method ! * @param entry entry to skip */ void Document::SkipDocEntry(DocEntry *entry) { SkipBytes(entry->GetLength()); } /** * \brief Skips to the begining of the next Header Entry * \warning NOT end user intended method ! * @param entry entry to skip */ void Document::SkipToNextDocEntry(DocEntry *entry) { Fp->seekg((long)(entry->GetOffset()), std::ios_base::beg); Fp->seekg( (long)(entry->GetReadLength()), std::ios_base::cur); } /** * \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. * @param entry entry to check * @param foundLength fist assumption about length */ void Document::FixDocEntryFoundLength(DocEntry *entry, uint32_t foundLength) { entry->SetReadLength( foundLength ); // will be updated only if a bug is found if ( foundLength == 0xffffffff) { foundLength = 0; } uint16_t gr = entry->GetGroup(); uint16_t 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 !? } else if ( entry->GetVR() == "SQ" ) { 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 Document::IsDocEntryAnInteger(DocEntry *entry) { uint16_t element = entry->GetElement(); uint16_t group = entry->GetGroup(); const std::string & vr = entry->GetVR(); uint32_t 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; long filePosition = Fp->tellg(); s << "Erroneous Group Length element length on : (" \ << std::hex << group << " , " << element << ") -before- position x(" << filePosition << ")" << "lgt : " << length; dbg.Verbose(0, "Document::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 */ uint32_t Document::FindDocEntryLengthOB() throw( FormatUnexpected ) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. long positionOnEntry = Fp->tellg(); bool foundSequenceDelimiter = false; uint32_t totalLength = 0; while ( !foundSequenceDelimiter ) { uint16_t group; uint16_t elem; try { group = ReadInt16(); elem = ReadInt16(); } catch ( FormatError ) { throw FormatError("Document::FindDocEntryLengthOB()", " group or element not present."); } // We have to decount the group and element we just read totalLength += 4; if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item " "tag nor a Sequence delimiter tag."); Fp->seekg(positionOnEntry, std::ios_base::beg); throw FormatUnexpected("Document::FindDocEntryLengthOB()", "Neither an Item tag nor a Sequence " "delimiter tag."); } if ( elem == 0xe0dd ) { foundSequenceDelimiter = true; } uint32_t itemLength = ReadInt32(); // We add 4 bytes since we just read the ItemLength with ReadInt32 totalLength += itemLength + 4; SkipBytes(itemLength); if ( foundSequenceDelimiter ) { break; } } Fp->seekg( positionOnEntry, std::ios_base::beg); return totalLength; } /** * \brief Reads a supposed to be 16 Bits integer * (swaps it depending on processor endianity) * @return read value */ uint16_t Document::ReadInt16() throw( FormatError ) { uint16_t g; Fp->read ((char*)&g, (size_t)2); if ( Fp->fail() ) { throw FormatError( "Document::ReadInt16()", " file error." ); } if( Fp->eof() ) { throw FormatError( "Document::ReadInt16()", "EOF." ); } g = SwapShort(g); return g; } /** * \brief Reads a supposed to be 32 Bits integer * (swaps it depending on processor endianity) * @return read value */ uint32_t Document::ReadInt32() throw( FormatError ) { uint32_t g; Fp->read ((char*)&g, (size_t)4); if ( Fp->fail() ) { throw FormatError( "Document::ReadInt32()", " file error." ); } if( Fp->eof() ) { throw FormatError( "Document::ReadInt32()", "EOF." ); } g = SwapLong(g); return g; } /** * \brief skips bytes inside the source file * \warning NOT end user intended method ! * @return */ void Document::SkipBytes(uint32_t nBytes) { //FIXME don't dump the returned value Fp->seekg((long)nBytes, std::ios_base::cur); } /** * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ void Document::Initialise() { RefPubDict = Global::GetDicts()->GetDefaultPubDict(); RefShaDict = NULL; RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; } /** * \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 Document::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... uint32_t x = 4; // x : for ntohs bool net2host; // true when HostByteOrder is the same as NetworkByteOrder uint32_t s32; uint16_t s16; char deb[256]; //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". Fp->read(deb, HEADER_LENGTH_TO_READ); char *entCur = deb + 128; if( memcmp(entCur, "DICM", (size_t)4) == 0 ) { dbg.Verbose(1, "Document::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 Document::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? group 0000 { Filetype = ExplicitVR; dbg.Verbose(1, "Document::CheckSwap:", "explicit Value Representation"); } else { Filetype = ImplicitVR; dbg.Verbose(1, "Document::CheckSwap:", "not an explicit Value Representation"); } if ( net2host ) { SwapCode = 4321; dbg.Verbose(1, "Document::CheckSwap:", "HostByteOrder != NetworkByteOrder"); } else { SwapCode = 0; dbg.Verbose(1, "Document::CheckSwap:", "HostByteOrder = NetworkByteOrder"); } // Position the file position indicator at first tag (i.e. // after the file preamble and the "DICM" string). Fp->seekg(0, std::ios_base::beg); Fp->seekg ( 132L, std::ios_base::beg); 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, "Document::CheckSwap:", "not a DICOM Version3 file"); Fp->seekg(0, std::ios_base::beg); // 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 = *((uint32_t *)(entCur)); switch( s32 ) { case 0x00040000 : SwapCode = 3412; Filetype = ACR; return true; case 0x04000000 : SwapCode = 4321; Filetype = ACR; return true; case 0x00000400 : SwapCode = 2143; Filetype = ACR; return true; case 0x00000004 : SwapCode = 0; Filetype = ACR; 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' // in ( 0x0001 .. 0x0008 ) // to determine ' SwapCode' 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 -3, 4, ..., 8-) // the file IS NOT ACR-NEMA nor DICOM V3 // Find a trick to tell it the caller... s16 = *((uint16_t *)(deb)); switch ( s16 ) { case 0x0001 : case 0x0002 : case 0x0003 : case 0x0004 : case 0x0005 : case 0x0006 : case 0x0007 : case 0x0008 : SwapCode = 0; Filetype = ACR; return true; case 0x0100 : case 0x0200 : case 0x0300 : case 0x0400 : case 0x0500 : case 0x0600 : case 0x0700 : case 0x0800 : SwapCode = 4321; Filetype = ACR; return true; default : dbg.Verbose(0, "Document::CheckSwap:", "ACR/NEMA unfound swap info (Really hopeless !)"); Filetype = Unknown; return false; } // Then the only info we have is the net2host one. //if (! net2host ) // SwapCode = 0; //else // SwapCode = 4321; //return; } } /** * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. */ void Document::SwitchSwapToBigEndian() { dbg.Verbose(1, "Document::SwitchSwapToBigEndian", "Switching to BigEndian mode."); if ( SwapCode == 0 ) { SwapCode = 4321; } else if ( SwapCode == 4321 ) { SwapCode = 0; } else if ( SwapCode == 3412 ) { SwapCode = 2143; } else if ( SwapCode == 2143 ) { SwapCode = 3412; } } /** * \brief during parsing, Header Elements too long are not loaded in memory * @param newSize */ void Document::SetMaxSizeLoadEntry(long newSize) { if ( newSize < 0 ) { return; } if ((uint32_t)newSize >= (uint32_t)0xffffffff ) { MaxSizeLoadEntry = 0xffffffff; return; } MaxSizeLoadEntry = newSize; } /** * \brief Header Elements too long will not be printed * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE * @param newSize */ void Document::SetMaxSizePrintEntry(long newSize) { //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME if ( newSize < 0 ) { return; } if ((uint32_t)newSize >= (uint32_t)0xffffffff ) { MaxSizePrintEntry = 0xffffffff; return; } MaxSizePrintEntry = newSize; } /** * \brief Handle broken private tag from Philips NTSCAN * where the endianess is being switch to BigEndian for no * apparent reason * @return no return */ void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) { // Endian reversion. Some files contain groups of tags with reversed endianess. static int reversedEndian = 0; // try to fix endian switching in the middle of headers if ((group == 0xfeff) && (elem == 0x00e0)) { // start endian swap mark for group found reversedEndian++; SwitchSwapToBigEndian(); // fix the tag group = 0xfffe; elem = 0xe000; } else if ((group == 0xfffe) && (elem == 0xe00d) && reversedEndian) { // end of reversed endian group reversedEndian--; SwitchSwapToBigEndian(); } } /** * \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. */ DocEntry* Document::ReadNextDocEntry() { uint16_t group; uint16_t elem; try { group = ReadInt16(); elem = ReadInt16(); } catch ( FormatError e ) { // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. //std::cout << e; return 0; } HandleBrokenEndian(group, elem); DocEntry *newEntry = NewDocEntryByNumber(group, elem); FindDocEntryVR(newEntry); try { FindDocEntryLength(newEntry); } catch ( FormatError e ) { // Call it quits //std::cout << e; delete newEntry; return 0; } newEntry->SetOffset(Fp->tellg()); 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. */ uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group) { for (uint32_t elem = 0; elem < UINT32_MAX; elem++) { TagKey key = DictEntry::TranslateToKey(group, elem); if (TagHT.count(key) == 0) { return elem; } } return UINT32_MAX; } /** * \brief Assuming the internal file pointer \ref Document::Fp * is placed at the beginning of a tag check whether this * tag is (TestGroup, TestElement). * \warning On success the internal file pointer \ref Document::Fp * is modified to point after the tag. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElement) the internal file pointer * \ref Document::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 True on success, false otherwise. */ bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) { long positionOnEntry = Fp->tellg(); long currentPosition = Fp->tellg(); // On debugging purposes //// Read the Item Tag group and element, and make // sure they are what we expected: uint16_t itemTagGroup; uint16_t itemTagElement; try { itemTagGroup = ReadInt16(); itemTagElement = ReadInt16(); } catch ( FormatError e ) { //std::cerr << e << std::endl; return false; } 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, "Document::ReadItemTagLength: wrong Item Tag found:"); dbg.Verbose(0, s.str().c_str()); Fp->seekg(positionOnEntry, std::ios_base::beg); return false; } return true; } /** * \brief Assuming the internal file pointer \ref Document::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 Document::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 Document::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. */ uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement) { long positionOnEntry = Fp->tellg(); (void)positionOnEntry; if ( !ReadTag(testGroup, testElement) ) { return 0; } //// Then read the associated Item Length long currentPosition = Fp->tellg(); uint32_t itemLength = ReadInt32(); { std::ostringstream s; s << "Basic Item Length is: " << itemLength << std::endl; s << " at address: " << (unsigned)currentPosition << std::endl; dbg.Verbose(0, "Document::ReadItemTagLength: ", s.str().c_str()); } return itemLength; } /** * \brief When parsing the Pixel Data of an encapsulated file, read * the basic offset table (when present, and BTW dump it). */ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() { //// Read the Basic Offset Table Item Tag length... uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); // When present, read the basic offset table itself. // Notes: - since the presence of this basic offset table is optional // we can't rely on it for the implementation, and we will simply // trash it's content (when present). // - still, when present, we could add some further checks on the // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 ) { char* basicOffsetTableItemValue = new char[itemLength + 1]; Fp->read(basicOffsetTableItemValue, itemLength); #ifdef GDCM_DEBUG for (unsigned int i=0; i < itemLength; i += 4 ) { uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], uint32_t); std::ostringstream s; s << " Read one length: "; s << std::hex << individualLength << std::endl; dbg.Verbose(0, "Document::ReadAndSkipEncapsulatedBasicOffsetTable: ", s.str().c_str()); } #endif //GDCM_DEBUG delete[] basicOffsetTableItemValue; } } /** * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. * Compute the RLE extra information and store it in \ref RLEInfo * for later pixel retrieval usage. */ void Document::ComputeRLEInfo() { TransferSyntaxType ts = GetTransferSyntax(); if ( ts != RLELossless ) { return; } // Encoded pixel data: for the time being we are only concerned with // Jpeg or RLE Pixel data encodings. // As stated in PS 3.5-2003, section 8.2 p44: // "If sent in Encapsulated Format (i.e. other than the Native Format) the // value representation OB is used". // Hence we expect an OB value representation. Concerning OB VR, // the section PS 3.5-2003, section A.4.c p 58-59, states: // "For the Value Representations OB and OW, the encoding shall meet the // following specifications depending on the Data element tag:" // [...snip...] // - the first item in the sequence of items before the encoded pixel // data stream shall be basic offset table item. The basic offset table // item value, however, is not required to be present" ReadAndSkipEncapsulatedBasicOffsetTable(); // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) // Loop on the individual frame[s] and store the information // on the RLE fragments in a RLEFramesInfo. // Note: - when only a single frame is present, this is a // classical image. // - when more than one frame are present, then we are in // the case of a multi-frame image. long frameLength; while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) ) { // Parse the RLE Header and store the corresponding RLE Segment // Offset Table information on fragments of this current Frame. // Note that the fragment pixels themselves are not loaded // (but just skipped). long frameOffset = Fp->tellg(); uint32_t nbRleSegments = ReadInt32(); if ( nbRleSegments > 16 ) { // There should be at most 15 segments (refer to RLEFrame class) dbg.Verbose(0, "Document::ComputeRLEInfo: too many segments."); } uint32_t rleSegmentOffsetTable[16]; for( int k = 1; k <= 15; k++ ) { rleSegmentOffsetTable[k] = ReadInt32(); } // Deduce from both the RLE Header and the frameLength the // fragment length, and again store this info in a // RLEFramesInfo. long rleSegmentLength[15]; // skipping (not reading) RLE Segments if ( nbRleSegments > 1) { for(unsigned int k = 1; k <= nbRleSegments-1; k++) { rleSegmentLength[k] = rleSegmentOffsetTable[k+1] - rleSegmentOffsetTable[k]; SkipBytes(rleSegmentLength[k]); } } rleSegmentLength[nbRleSegments] = frameLength - rleSegmentOffsetTable[nbRleSegments]; SkipBytes(rleSegmentLength[nbRleSegments]); // Store the collected info RLEFrame* newFrameInfo = new RLEFrame; newFrameInfo->NumberFragments = nbRleSegments; for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) { newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk]; newFrameInfo->Length[uk] = rleSegmentLength[uk]; } RLEInfo->Frames.push_back( newFrameInfo ); } // Make sure that at the end of the item we encounter a 'Sequence // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); dbg.Verbose(0, " item at end of RLE item sequence"); } } /** * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding. * Compute the jpeg extra information (fragment[s] offset[s] and * length) and store it[them] in \ref JPEGInfo for later pixel * retrieval usage. */ void Document::ComputeJPEGFragmentInfo() { // If you need to, look for comments of ComputeRLEInfo(). if ( ! IsJPEG() ) { return; } ReadAndSkipEncapsulatedBasicOffsetTable(); // Loop on the fragments[s] and store the parsed information in a // JPEGInfo. long fragmentLength; while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) { long fragmentOffset = Fp->tellg(); // Store the collected info JPEGFragment* newFragment = new JPEGFragment; newFragment->Offset = fragmentOffset; newFragment->Length = fragmentLength; JPEGInfo->Fragments.push_back( newFragment ); SkipBytes( fragmentLength ); } // Make sure that at the end of the item we encounter a 'Sequence // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); dbg.Verbose(0, " item at end of JPEG item sequence"); } } /** * \brief Walk recursively the given \ref DocEntrySet, and feed * the given hash table (\ref TagDocEntryHT) with all the * \ref DocEntry (Dicom entries) encountered. * This method does the job for \ref BuildFlatHashTable. * @param builtHT Where to collect all the \ref DocEntry encountered * when recursively walking the given set. * @param set The structure to be traversed (recursively). */ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, DocEntrySet* set ) { if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) ) { TagDocEntryHT const & currentHT = elementSet->GetTagHT(); for( TagDocEntryHT::const_iterator i = currentHT.begin(); i != currentHT.end(); ++i) { DocEntry* entry = i->second; if ( SeqEntry* seqEntry = dynamic_cast(entry) ) { const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); item != items.end(); ++item) { BuildFlatHashTableRecurse( builtHT, *item ); } continue; } builtHT[entry->GetKey()] = entry; } return; } if (SQItem* SQItemSet = dynamic_cast< SQItem* > ( set ) ) { const ListDocEntry& currentList = SQItemSet->GetDocEntries(); for (ListDocEntry::const_iterator i = currentList.begin(); i != currentList.end(); ++i) { DocEntry* entry = *i; if ( SeqEntry* seqEntry = dynamic_cast(entry) ) { const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); item != items.end(); ++item) { BuildFlatHashTableRecurse( builtHT, *item ); } continue; } builtHT[entry->GetKey()] = entry; } } } /** * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current * Document. * * The structure used by a Document (through \ref ElementSet), * in order to hold the parsed entries of a Dicom header, is a recursive * one. This is due to the fact that the sequences (when present) * can be nested. Additionaly, the sequence items (represented in * gdcm as \ref SQItem) add an extra complexity to the data * structure. Hence, a gdcm user whishing to visit all the entries of * a Dicom header will need to dig in the gdcm internals (which * implies exposing all the internal data structures to the API). * In order to avoid this burden to the user, \ref BuildFlatHashTable * recursively builds a temporary hash table, which holds all the * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a * std::map<>). * \warning Of course there is NO integrity constrain between the * returned \ref TagDocEntryHT and the \ref ElementSet used * to build it. Hence if the underlying \ref ElementSet is * altered, then it is the caller responsability to invoke * \ref BuildFlatHashTable again... * @return The flat std::map<> we juste build. */ TagDocEntryHT* Document::BuildFlatHashTable() { TagDocEntryHT* FlatHT = new TagDocEntryHT; BuildFlatHashTableRecurse( *FlatHT, this ); return FlatHT; } /** * \brief Compares two documents, according to \ref DicomDir 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 Document::operator<(Document &document) { // Patient Name std::string s1 = GetEntryByNumber(0x0010,0x0010); std::string s2 = document.GetEntryByNumber(0x0010,0x0010); if(s1 < s2) { return true; } else if( s1 > s2 ) { return false; } else { // Patient ID s1 = GetEntryByNumber(0x0010,0x0020); s2 = document.GetEntryByNumber(0x0010,0x0020); if ( s1 < s2 ) { return true; } else if ( s1 > s2 ) { return false; } else { // Study Instance UID s1 = GetEntryByNumber(0x0020,0x000d); s2 = document.GetEntryByNumber(0x0020,0x000d); if ( s1 < s2 ) { return true; } else if( s1 > s2 ) { return false; } else { // Serie Instance UID s1 = GetEntryByNumber(0x0020,0x000e); s2 = document.GetEntryByNumber(0x0020,0x000e); if ( s1 < s2 ) { return true; } else if( s1 > s2 ) { return false; } } } } return false; } } // end namespace gdcm //-----------------------------------------------------------------------------