X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=79bad798db30be47bc330d1abf1e21ec16419ded;hb=bd217557a398371d5d0a27c5aa6e09e47eb65652;hp=e5e627e436fe4b9390379491fc5f5c4a84e05339;hpb=922095a0dd56f24d651b36f62256690020937d9a;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index e5e627e4..79bad798 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/12/10 13:49:07 $ - Version: $Revision: 1.150 $ + Date: $Date: 2005/01/13 09:23:27 $ + Version: $Revision: 1.187 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -43,42 +43,7 @@ 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; @@ -94,7 +59,7 @@ const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; * \brief constructor * @param filename file to be opened for parsing */ -Document::Document( std::string const & filename ) : ElementSet(-1) +Document::Document( std::string const &filename ) : ElementSet(-1) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; @@ -106,14 +71,16 @@ Document::Document( std::string const & filename ) : ElementSet(-1) return; } - dbg.Verbose(0, "Document::Document: starting parsing of file: ", - Filename.c_str()); - Fp->seekg( 0, std::ios::beg); + Group0002Parsed = false; + + gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str()); + // Fp->seekg( 0, std::ios::beg); Fp->seekg(0, std::ios::end); long lgt = Fp->tellg(); Fp->seekg( 0, std::ios::beg); + CheckSwap(); long beg = Fp->tellg(); lgt -= beg; @@ -124,7 +91,7 @@ Document::Document( std::string const & filename ) : ElementSet(-1) // Load 'non string' values - std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + std::string PhotometricInterpretation = GetEntry(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ) { LoadEntryBinArea(0x0028,0x1200); // gray LUT @@ -135,7 +102,7 @@ Document::Document( std::string const & filename ) : ElementSet(-1) /// 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. + /// altered on PURPOSE 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: @@ -170,20 +137,18 @@ Document::Document( std::string const & filename ) : ElementSet(-1) // we switch lineNumber and columnNumber // std::string RecCode; - RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code + RecCode = GetEntry(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); + std::string rows = GetEntry(0x0028, 0x0010); + std::string columns = GetEntry(0x0028, 0x0011); + SetEntry(columns, 0x0028, 0x0010); + SetEntry(rows , 0x0028, 0x0011); } // ----------------- End of ACR-LibIDO kludge ------------------ - - PrintLevel = 1; // 'Medium' print level by default } /** @@ -196,9 +161,9 @@ Document::Document() : ElementSet(-1) SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); - SwapCode = 0; + SwapCode = 1234; Filetype = ExplicitVR; - PrintLevel = 1; // 'Medium' print level by default + Group0002Parsed = false; } /** @@ -220,8 +185,9 @@ Document::~Document () * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return */ -void Document::PrintPubDict(std::ostream & os) +void Document::PrintPubDict(std::ostream &os) { + RefPubDict->SetPrintLevel(PrintLevel); RefPubDict->Print(os); } @@ -229,8 +195,9 @@ void Document::PrintPubDict(std::ostream & os) * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ -void Document::PrintShaDict(std::ostream & os) +void Document::PrintShaDict(std::ostream &os) { + RefShaDict->SetPrintLevel(PrintLevel); RefShaDict->Print(os); } @@ -239,7 +206,7 @@ void Document::PrintShaDict(std::ostream & os) /** * \brief Get the public dictionary used */ -Dict* Document::GetPubDict() +Dict *Document::GetPubDict() { return RefPubDict; } @@ -247,14 +214,14 @@ Dict* Document::GetPubDict() /** * \brief Get the shadow dictionary used */ -Dict* Document::GetShaDict() +Dict *Document::GetShaDict() { return RefShaDict; } /** * \brief Set the shadow dictionary used - * \param dict dictionary to use in shadow + * @param dict dictionary to use in shadow */ bool Document::SetShaDict(Dict *dict) { @@ -264,9 +231,9 @@ bool Document::SetShaDict(Dict *dict) /** * \brief Set the shadow dictionary used - * \param dictName name of the dictionary to use in shadow + * @param dictName name of the dictionary to use in shadow */ -bool Document::SetShaDict(DictKey const & dictName) +bool Document::SetShaDict(DictKey const &dictName) { RefShaDict = Global::GetDicts()->GetDict(dictName); return !RefShaDict; @@ -284,14 +251,13 @@ bool Document::IsReadable() { if( Filetype == Unknown) { - dbg.Verbose(0, "Document::IsReadable: wrong filetype"); + gdcmVerboseMacro( "Wrong filetype"); return false; } if( TagHT.empty() ) { - dbg.Verbose(0, "Document::IsReadable: no tags in internal" - " hash table."); + gdcmVerboseMacro( "No tags in internal hash table."); return false; } @@ -304,18 +270,18 @@ bool Document::IsReadable() * value from disk when only parsing occured). * @return The encountered Transfer Syntax of the current document. */ -TransferSyntaxType Document::GetTransferSyntax() +std::string Document::GetTransferSyntax() { - DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); + DocEntry *entry = GetDocEntry(0x0002, 0x0010); if ( !entry ) { - return UnknownTS; + return GDCM_UNKNOWN; } // 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) ) + if (ValEntry *valEntry = dynamic_cast< ValEntry* >(entry) ) { std::string transfer = valEntry->GetValue(); // The actual transfer (as read from disk) might be padded. We @@ -324,68 +290,15 @@ TransferSyntaxType Document::GetTransferSyntax() if ( transfer.length() == 0 ) { // for brain damaged headers - return UnknownTS; + return GDCM_UNKNOWN; } 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 transfer; } - 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; + return GDCM_UNKNOWN; } /** @@ -394,11 +307,11 @@ bool Document::IsEncapsulate() */ bool Document::IsDicomV3() { - // Checking if Transfert Syntax exists is enough + // Checking if Transfer 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; + return GetDocEntry(0x0002, 0x0010) != NULL; } /** @@ -416,8 +329,10 @@ FileType Document::GetFileType() * checks the preamble when existing. * @return The FILE pointer on success. */ -std::ifstream* Document::OpenFile() +std::ifstream *Document::OpenFile() { + + HasDCMPreamble = false; if (Filename.length() == 0) { return 0; @@ -425,17 +340,13 @@ std::ifstream* Document::OpenFile() if(Fp) { - dbg.Verbose( 0, - "Document::OpenFile is already opened when opening: ", - Filename.c_str()); + gdcmVerboseMacro( "File already open: " << 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()); + gdcmDebugMacro( "Cannot open file: " << Filename.c_str()); delete Fp; Fp = 0; return 0; @@ -456,6 +367,9 @@ std::ifstream* Document::OpenFile() zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 || zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ) { + std::string msg + = Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero); + gdcmVerboseMacro( msg.c_str() ); return Fp; } @@ -470,13 +384,12 @@ std::ifstream* Document::OpenFile() } if( memcmp(dicm, "DICM", 4) == 0 ) { + HasDCMPreamble = true; return Fp; } CloseFile(); - dbg.Verbose( 0, - "Document::OpenFile not DICOM/ACR (missing preamble)", - Filename.c_str()); + gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str()); return 0; } @@ -504,7 +417,7 @@ bool Document::CloseFile() * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -void Document::WriteContent(std::ofstream* fp, FileType filetype) +void Document::WriteContent(std::ofstream *fp, FileType filetype) { /// \todo move the following lines (and a lot of others, to be written) /// to a future function CheckAndCorrectHeader @@ -536,7 +449,7 @@ void Document::WriteContent(std::ofstream* fp, FileType filetype) } /** - * \brief Modifies the value of a given Header Entry (Dicom Element) + * \brief Modifies the value of a given Doc 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 @@ -545,79 +458,51 @@ void Document::WriteContent(std::ofstream* fp, FileType filetype) * \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); +ValEntry *Document::ReplaceOrCreate(std::string const &value, + uint16_t group, + uint16_t elem, + TagName const &vr ) +{ + ValEntry *valEntry = 0; + DocEntry *currentEntry = GetDocEntry( group, elem); - if (!currentEntry) + if (currentEntry) { - // check if (group,element) DictEntry exists - // if it doesn't, create an entry in DictSet::VirtualEntry - // and use it + valEntry = dynamic_cast< ValEntry* >(currentEntry); - // 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); - } + // Verify the VR + if( valEntry ) + if( valEntry->GetVR()!=vr ) + valEntry=NULL; - if (!currentEntry) + // if currentEntry doesn't correspond to the requested valEntry + if( !valEntry) { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; + if (!RemoveEntry(currentEntry)) + { + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + + return NULL; + } } + } - valEntry = new ValEntry(currentEntry); - delete currentEntry; + // Create a new valEntry if necessary + if (!valEntry) + { + valEntry = NewValEntry(group, elem, vr); if ( !AddEntry(valEntry)) { + gdcmVerboseMacro("AddEntry failed although this is a creation."); + 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); + // Set the binEntry value + SetEntry(value, valEntry); return valEntry; } @@ -628,75 +513,56 @@ ValEntry* Document::ReplaceOrCreateByNumber( * @param binArea (binary) 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). */ -BinEntry* Document::ReplaceOrCreateByNumber( - uint8_t* binArea, - int lgth, - uint16_t group, - uint16_t elem, - TagName const & vr ) +BinEntry *Document::ReplaceOrCreate(uint8_t *binArea, + int lgth, + uint16_t group, + uint16_t elem, + TagName const &vr ) { - BinEntry* binEntry = 0; - DocEntry* currentEntry = GetDocEntryByNumber( group, elem); - if (!currentEntry) - { + BinEntry *binEntry = 0; + DocEntry *currentEntry = GetDocEntry( group, elem); - // 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."); - } - delete currentEntry; - } - else + // Verify the currentEntry + if (currentEntry) { 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 ? + + // Verify the VR + if( binEntry ) + if( binEntry->GetVR()!=vr ) + binEntry=NULL; + + // if currentEntry doesn't correspond to the requested valEntry + if( !binEntry) { - // 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."); + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + return NULL; } } } + // Create a new binEntry if necessary + if (!binEntry) + { + binEntry = NewBinEntry(group, elem, vr); + + if ( !AddEntry(binEntry)) + { + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); + + delete binEntry; + return NULL; + } + } + + // Set the binEntry value uint8_t *tmpArea; if (lgth>0 && binArea) { @@ -707,7 +573,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( { tmpArea = 0; } - if (!SetEntryByNumber(tmpArea, lgth, group, elem)) + if (!SetEntry(tmpArea,lgth,binEntry)) { if (tmpArea) { @@ -718,7 +584,6 @@ BinEntry* Document::ReplaceOrCreateByNumber( return binEntry; } - /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it when unexistant. @@ -727,22 +592,48 @@ BinEntry* Document::ReplaceOrCreateByNumber( * \return pointer to the modified/created SeqEntry (NULL when creation * failed). */ -SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) +SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem) { - SeqEntry* b = 0; - DocEntry* a = GetDocEntryByNumber( group, elem); - if (!a) + SeqEntry *seqEntry = 0; + DocEntry *currentEntry = GetDocEntry( group, elem); + + // Verify the currentEntry + if (currentEntry) { - a = NewSeqEntryByNumber(group, elem); - if (!a) + seqEntry = dynamic_cast< SeqEntry* >(currentEntry); + + // Verify the VR + if( seqEntry ) + if( seqEntry->GetVR()!="SQ" ) + seqEntry=NULL; + + // if currentEntry doesn't correspond to the requested valEntry + if( !seqEntry) { - return 0; + if (!RemoveEntry(currentEntry)) + { + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + + return NULL; + } } + } - b = new SeqEntry(a, 1); // FIXME : 1 (Depth) - AddEntry(b); - } - return b; + // Create a new seqEntry if necessary + if (!seqEntry) + { + seqEntry = NewSeqEntry(group, elem); + + if ( !AddEntry(seqEntry)) + { + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); + + delete seqEntry; + return NULL; + } + } + + return seqEntry; } /** @@ -753,19 +644,14 @@ SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) * @param elem element number of the Entry * \return boolean */ -bool Document::ReplaceIfExistByNumber(std::string const & value, - uint16_t group, uint16_t elem ) +bool Document::ReplaceIfExist(std::string const &value, + uint16_t group, uint16_t elem ) { - SetEntryByNumber(value, group, elem); + SetEntry(value, group, elem); return true; } -std::string Document::GetTransferSyntaxValue(TransferSyntaxType type) -{ - return TransferSyntaxStrings[type]; -} - //----------------------------------------------------------------------------- // Protected @@ -775,57 +661,12 @@ std::string Document::GetTransferSyntaxValue(TransferSyntaxType type) * @param element Element number of the searched Dicom Element * @return true is found */ -bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) +bool Document::CheckIfEntryExist(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 @@ -836,7 +677,7 @@ std::string Document::GetEntryVRByName(TagName const& tagName) * @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) +std::string Document::GetEntry(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) @@ -861,9 +702,9 @@ std::string Document::GetEntryByNumber(uint16_t group, uint16_t element) * @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) +std::string Document::GetEntryVR(uint16_t group, uint16_t element) { - DocEntry* elem = GetDocEntryByNumber(group, element); + DocEntry *elem = GetDocEntry(group, element); if ( !elem ) { return GDCM_UNFOUND; @@ -879,33 +720,15 @@ std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element) * @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) +int Document::GetEntryLength(uint16_t group, uint16_t element) { - DocEntry* elem = GetDocEntryByNumber(group, element); + DocEntry *elem = GetDocEntry(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) @@ -915,19 +738,16 @@ bool Document::SetEntryByName( std::string const & content, * @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) +bool Document::SetEntry(std::string const& content, + uint16_t group, uint16_t element) { - ValEntry* valEntry = GetValEntryByNumber(group, element); - if (!valEntry ) + ValEntry *entry = GetValEntry(group, element); + if (!entry ) { - dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding", - " ValEntry (try promotion first)."); + gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); return false; } - // Non even content must be padded with a space (020H)... - valEntry->SetValue(content); - return true; + return SetEntry(content,entry); } /** @@ -939,30 +759,60 @@ bool Document::SetEntryByNumber(std::string const& content, * @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) +bool Document::SetEntry(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)) + BinEntry *entry = GetBinEntry(group, element); + if (!entry ) { + gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); 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? + return SetEntry(content,lgth,entry); +} + +/** + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) + * and modifies it's content with the given value. + * @param content new value (string) to substitute with + * @param entry Entry to be modified + */ +bool Document::SetEntry(std::string const &content,ValEntry *entry) +{ + if(entry) + { + entry->SetValue(content); + return true; } -*/ - BinEntry* entry = (BinEntry *)TagHT[key]; - entry->SetBinArea(content); - entry->SetLength(lgth); - entry->SetValue(GDCM_BINLOADED); + return false; +} - return true; -} +/** + * \brief Accesses an existing BinEntry (i.e. a Dicom Element) + * and modifies it's content with the given value. + * @param content new value (void* -> uint8_t*) to substitute with + * @param entry Entry to be modified + * @param lgth new value length + */ +bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry) +{ + if(entry) + { + // 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? + }*/ + + entry->SetBinArea(content); + entry->SetLength(lgth); + entry->SetValue(GDCM_BINLOADED); + return true; + } + return false; +} /** * \brief Gets (from Header) a 'non string' element value @@ -971,15 +821,15 @@ bool Document::SetEntryByNumber(uint8_t*content, int lgth, * @param elem element number of the Entry * @return Pointer to the 'non string' area */ -void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) +void *Document::GetEntryBinArea(uint16_t group, uint16_t elem) { - DocEntry* entry = GetDocEntryByNumber(group, elem); + DocEntry *entry = GetDocEntry(group, elem); if (!entry) { - dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry"); + gdcmVerboseMacro( "No entry"); return 0; } - if ( BinEntry* binEntry = dynamic_cast(entry) ) + if ( BinEntry *binEntry = dynamic_cast(entry) ) { return binEntry->GetBinArea(); } @@ -996,7 +846,7 @@ void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { // Search the corresponding DocEntry - DocEntry *docElement = GetDocEntryByNumber(group, elem); + DocEntry *docElement = GetDocEntry(group, elem); if ( !docElement ) return; @@ -1012,7 +862,7 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) * when a string is not suitable * @param element Entry whose binArea is going to be loaded */ -void Document::LoadEntryBinArea(BinEntry* element) +void Document::LoadEntryBinArea(BinEntry *element) { if(element->GetBinArea()) return; @@ -1025,16 +875,16 @@ void Document::LoadEntryBinArea(BinEntry* element) Fp->seekg(o, std::ios::beg); size_t l = element->GetLength(); - uint8_t* a = new uint8_t[l]; + uint8_t *a = new uint8_t[l]; if( !a ) { - dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); + gdcmVerboseMacro( "Cannot allocate a"); return; } /// \todo check the result Fp->read((char*)a, l); - if( Fp->fail() || Fp->eof()) //Fp->gcount() == 1 + if( Fp->fail() || Fp->eof()) { delete[] a; return; @@ -1053,16 +903,16 @@ void Document::LoadEntryBinArea(BinEntry* element) * @param element Element number of the searched Dicom Element * @return */ -/*bool Document::SetEntryBinAreaByNumber(uint8_t* area, - uint16_t group, uint16_t element) +/*bool Document::SetEntryBinArea(uint8_t *area, + uint16_t group, uint16_t element) { - DocEntry* currentEntry = GetDocEntryByNumber(group, element); + DocEntry *currentEntry = GetDocEntry(group, element); if ( !currentEntry ) { return false; } - if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) + if ( BinEntry *binEntry = dynamic_cast(currentEntry) ) { binEntry->SetBinArea( area ); return true; @@ -1071,72 +921,6 @@ void Document::LoadEntryBinArea(BinEntry* element) 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 @@ -1147,7 +931,7 @@ DocEntry* Document::GetDocEntryByName(TagName const & tagName) * @param element Element number of the searched Dicom Element * @return */ -DocEntry* Document::GetDocEntryByNumber(uint16_t group, uint16_t element) +DocEntry *Document::GetDocEntry(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) @@ -1158,35 +942,57 @@ DocEntry* Document::GetDocEntryByNumber(uint16_t group, uint16_t element) } /** - * \brief Same as \ref Document::GetDocEntryByNumber except it only + * \brief Same as \ref Document::GetDocEntry 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) +ValEntry *Document::GetValEntry(uint16_t group, uint16_t element) { - DocEntry* currentEntry = GetDocEntryByNumber(group, element); + DocEntry *currentEntry = GetDocEntry(group, element); if ( !currentEntry ) { return 0; } - if ( ValEntry* valEntry = dynamic_cast(currentEntry) ) + if ( ValEntry *entry = dynamic_cast(currentEntry) ) { - return valEntry; + return entry; } - dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry."); + gdcmVerboseMacro( "Unfound ValEntry."); + + return 0; +} + +/** + * \brief Same as \ref Document::GetDocEntry except it only + * returns a result when the corresponding entry is of type + * BinEntry. + * @return When present, the corresponding BinEntry. + */ +BinEntry *Document::GetBinEntry(uint16_t group, uint16_t element) +{ + DocEntry *currentEntry = GetDocEntry(group, element); + if ( !currentEntry ) + { + return 0; + } + if ( BinEntry *entry = dynamic_cast(currentEntry) ) + { + return entry; + } + gdcmVerboseMacro( "Unfound BinEntry."); return 0; } /** * \brief Loads the element while preserving the current - * underlying file position indicator as opposed to + * underlying file position indicator as opposed to * to LoadDocEntry that modifies it. - * @param entry Header Entry whose value shall be loaded. + * @param entry Header Entry whose value will be loaded. * @return */ -void Document::LoadDocEntrySafe(DocEntry * entry) +void Document::LoadDocEntrySafe(DocEntry *entry) { if(Fp) { @@ -1205,23 +1011,20 @@ uint32_t Document::SwapLong(uint32_t a) { switch (SwapCode) { - case 0 : + case 1234 : break; case 4321 : a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) ); - break; - + break; case 3412 : a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) ); - break; - + break; case 2143 : a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); - break; + break; default : - //std::cout << "swapCode= " << SwapCode << std::endl; - dbg.Error(" Document::SwapLong : unset swap code"); + gdcmErrorMacro( "Unset swap code:" << SwapCode ); a = 0; } return a; @@ -1270,6 +1073,11 @@ void Document::ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode) { DocEntry *newDocEntry = 0; + ValEntry *newValEntry; + BinEntry *newBinEntry; + SeqEntry *newSeqEntry; + VRKey vr; + bool used=false; while (true) { @@ -1277,26 +1085,63 @@ void Document::ParseDES(DocEntrySet *set, long offset, { break; } + + used=true; newDocEntry = ReadNextDocEntry( ); if ( !newDocEntry ) { break; } - VRKey vr = newDocEntry->GetVR(); - if ( vr != "SQ" ) + vr = newDocEntry->GetVR(); + newValEntry = dynamic_cast(newDocEntry); + newBinEntry = dynamic_cast(newDocEntry); + newSeqEntry = dynamic_cast(newDocEntry); + + if ( newValEntry || newBinEntry ) { - - if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) ) + if ( newBinEntry ) + { + if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) ) + { + ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR + gdcmVerboseMacro( std::hex << newDocEntry->GetGroup() + << "|" << newDocEntry->GetElement() + << " : Neither Valentry, nor BinEntry." + "Probably unknown VR."); + } + + //////////////////// BinEntry or UNKOWN VR: + // 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; + used=false; + } + } + else { /////////////////////// 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 ) ) + if (Document *dummy = dynamic_cast< Document* > ( set ) ) { (void)dummy; newValEntry->SetKey( newValEntry->GetKey() ); @@ -1304,7 +1149,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, // ...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 ) ) + if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newValEntry->SetKey( parentSQItem->GetBaseTagKey() + newValEntry->GetKey() ); @@ -1315,79 +1160,46 @@ void Document::ParseDES(DocEntrySet *set, long offset, if( !set->AddEntry( newValEntry ) ) { // If here expect big troubles - delete newValEntry; //otherwise mem leak + //delete newValEntry; //otherwise mem leak + used=false; } if (delimitor) { - delete newDocEntry; + if(!used) + delete newDocEntry; break; } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - delete newDocEntry; + if(!used) + 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 ); //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 ) + std::string ts = GetTransferSyntax(); + if ( Global::GetTS()->IsRLELossless(ts) ) { - long PositionOnEntry = Fp->tellg(); + long positionOnEntry = Fp->tellg(); Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeRLEInfo(); - Fp->seekg( PositionOnEntry, std::ios::beg ); + Fp->seekg( positionOnEntry, std::ios::beg ); } - else if ( IsJPEG() ) + else if ( Global::GetTS()->IsJPEG(ts) ) { - long PositionOnEntry = Fp->tellg(); + long positionOnEntry = Fp->tellg(); Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeJPEGFragmentInfo(); - Fp->seekg( PositionOnEntry, std::ios::beg ); + Fp->seekg( positionOnEntry, std::ios::beg ); } } - + // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); - //delete newDocEntry; } else { @@ -1405,25 +1217,22 @@ void Document::ParseDES(DocEntrySet *set, long offset, } } // 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 ) ) + 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 + // But when "set" is already 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 ) ) + if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); newSeqEntry->SetKey( parentSQItem->GetBaseTagKey() @@ -1439,11 +1248,12 @@ void Document::ParseDES(DocEntrySet *set, long offset, set->AddEntry( newSeqEntry ); if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - delete newDocEntry; break; } } - delete newDocEntry; + + if(!used) + delete newDocEntry; } } @@ -1451,7 +1261,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, * \brief Parses a Sequence ( SeqEntry after SeqEntry) * @return parsed length for this level */ -void Document::ParseSQ( SeqEntry* seqEntry, +void Document::ParseSQ( SeqEntry *seqEntry, long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; @@ -1459,7 +1269,7 @@ void Document::ParseSQ( SeqEntry* seqEntry, while (true) { - DocEntry* newDocEntry = ReadNextDocEntry(); + DocEntry *newDocEntry = ReadNextDocEntry(); if ( !newDocEntry ) { // FIXME Should warn user @@ -1514,7 +1324,7 @@ void Document::ParseSQ( SeqEntry* seqEntry, * the value specified with Document::SetMaxSizeLoadEntry() * @param entry Header Entry (Dicom Element) to be dealt with */ -void Document::LoadDocEntry(DocEntry* entry) +void Document::LoadDocEntry(DocEntry *entry) { uint16_t group = entry->GetGroup(); std::string vr = entry->GetVR(); @@ -1546,7 +1356,7 @@ void Document::LoadDocEntry(DocEntry* entry) std::ostringstream s; if (length > MaxSizeLoadEntry) { - if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) + if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) ) { //s << "gdcm::NotLoaded (BinEntry)"; s << GDCM_NOTLOADED; @@ -1556,7 +1366,7 @@ void Document::LoadDocEntry(DocEntry* entry) binEntryPtr->SetValue(s.str()); } // Be carefull : a BinEntry IS_A ValEntry ... - else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) ) + else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { // s << "gdcm::NotLoaded. (ValEntry)"; s << GDCM_NOTLOADED; @@ -1568,8 +1378,8 @@ void Document::LoadDocEntry(DocEntry* entry) else { // fusible - std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry " - << "nor a ValEntry ?! Should never print that !" << std::endl; + gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry " + << "nor a ValEntry ?! Should never print that !" ); } // to be sure we are at the end of the value ... @@ -1579,14 +1389,14 @@ void Document::LoadDocEntry(DocEntry* entry) } // When we find a BinEntry not very much can be done : - if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) + 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) ) { @@ -1645,10 +1455,10 @@ void Document::LoadDocEntry(DocEntry* entry) if( length % 2 ) { newValue = Util::DicomString(str, length+1); - //dbg.Verbose(0, "Warning: bad length: ", length ); - dbg.Verbose(0, "For string :", newValue.c_str()); + gdcmVerboseMacro("Warning: bad length: " << length << + ",For string :" << newValue.c_str()); // Since we change the length of string update it length - entry->SetReadLength(length+1); + //entry->SetReadLength(length+1); } else { @@ -1656,12 +1466,11 @@ void Document::LoadDocEntry(DocEntry* entry) } delete[] str; - if ( ValEntry* valEntry = dynamic_cast(entry) ) + if ( ValEntry *valEntry = dynamic_cast(entry) ) { - if ( Fp->fail() || Fp->eof())//Fp->gcount() == 1 + if ( Fp->fail() || Fp->eof()) { - dbg.Verbose(1, "Document::LoadDocEntry", - "unread element value"); + gdcmVerboseMacro("Unread element value"); valEntry->SetValue(GDCM_UNREAD); return; } @@ -1678,8 +1487,7 @@ void Document::LoadDocEntry(DocEntry* entry) } else { - dbg.Error(true, "Document::LoadDocEntry" - "Should have a ValEntry, here !"); + gdcmErrorMacro( "Should have a ValEntry, here !"); } } @@ -1691,7 +1499,6 @@ void Document::LoadDocEntry(DocEntry* entry) void Document::FindDocEntryLength( DocEntry *entry ) throw ( FormatError ) { - uint16_t element = entry->GetElement(); std::string vr = entry->GetVR(); uint16_t length16; @@ -1710,9 +1517,7 @@ void Document::FindDocEntryLength( DocEntry *entry ) uint32_t lengthOB; try { - /// \todo rename that to FindDocEntryLengthOBOrOW since - /// the above test is on both OB and OW... - lengthOB = FindDocEntryLengthOB(); + lengthOB = FindDocEntryLengthOBOrOW(); } catch ( FormatUnexpected ) { @@ -1723,11 +1528,15 @@ void Document::FindDocEntryLength( DocEntry *entry ) // the length and proceed. long currentPosition = Fp->tellg(); Fp->seekg(0L,std::ios::end); + long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; Fp->seekg(currentPosition, std::ios::beg); + + entry->SetReadLength(lengthUntilEOF); entry->SetLength(lengthUntilEOF); return; } + entry->SetReadLength(lengthOB); entry->SetLength(lengthOB); return; } @@ -1737,6 +1546,14 @@ void Document::FindDocEntryLength( DocEntry *entry ) // Length is encoded on 2 bytes. length16 = ReadInt16(); + + // FIXME : This heuristic supposes that the first group following + // group 0002 *has* and element 0000. + // BUT ... Element 0000 is optionnal :-( + + + // Fixed using : HandleOutOfGroup0002() + // (first hereafter strategy ...) // We can tell the current file is encoded in big endian (like // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag @@ -1757,6 +1574,8 @@ void Document::FindDocEntryLength( DocEntry *entry ) // 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. + //---> Unfortunately, element 0000 is optional. + //---> This will not work when missing! // 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 @@ -1765,37 +1584,40 @@ void Document::FindDocEntryLength( DocEntry *entry ) // 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(); + + // + // if ( element == 0x0000 && length16 == 0x0400 ) + // { + // std::string ts = GetTransferSyntax(); + // if ( Global::GetTS()->GetSpecialTransferSyntax(ts) + // != TS::ExplicitVRBigEndian ) + // { + // throw FormatError( "Document::FindDocEntryLength()", + // " not explicit VR." ); + // return; + // } + // length16 = 4; + // SwitchByteSwapCode(); + // 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 ) - { +// uint16_t correctGroup = SwapShort( entry->GetGroup() ); +// uint16_t correctElem = SwapShort( entry->GetElement() ); +// DictEntry *newTag = GetDictEntry( correctGroup, correctElem ); if ( !newTag ) +// { // This correct tag is not in the dictionary. Create a new one. - newTag = NewVirtualDictEntry(correctGroup, correctElem); - } +// 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. +// entry->SetDictEntry( newTag ); +// } + + + // 0xffff means that we deal with 'No Length' Sequence + // or 'No Length' SQItem if ( length16 == 0xffff) - { - // 0xffff means that we deal with 'Unknown Length' Sequence + { length16 = 0; } FixDocEntryFoundLength( entry, (uint32_t)length16 ); @@ -1817,16 +1639,12 @@ void Document::FindDocEntryLength( DocEntry *entry ) /** * \brief Find the Value Representation of the current Dicom Element. - * @param entry + * @return Value Representation of the current Entry */ -void Document::FindDocEntryVR( DocEntry *entry ) +std::string Document::FindDocEntryVR() { if ( Filetype != ExplicitVR ) - { - return; - } - - char vr[3]; + return GDCM_UNKNOWN; long positionOnEntry = Fp->tellg(); // Warning: we believe this is explicit VR (Value Representation) because @@ -1836,104 +1654,34 @@ void Document::FindDocEntryVR( DocEntry *entry ) // 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. + + char vr[3]; Fp->read (vr, (size_t)2); vr[2] = 0; - if( !CheckDocEntryVR(entry, vr) ) + if( !CheckDocEntryVR(vr) ) { Fp->seekg(positionOnEntry, std::ios::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(); + return GDCM_UNKNOWN; } + return vr; } /** * \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) +bool Document::CheckDocEntryVR(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 ); - } + if ( !Global::GetVR()->IsValidVR(vr) ) 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; } @@ -2021,7 +1769,7 @@ std::string Document::GetDocEntryValue(DocEntry *entry) * @param entry Entry to reverse transform * @return Reverse transformed entry value */ -std::string Document::GetDocEntryUnvalue(DocEntry* entry) +std::string Document::GetDocEntryUnvalue(DocEntry *entry) { if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) { @@ -2082,12 +1830,12 @@ void Document::SkipDocEntry(DocEntry *entry) /** * \brief Skips to the begining of the next Header Entry * \warning NOT end user intended method ! - * @param entry entry to skip + * @param currentDocEntry entry to skip */ -void Document::SkipToNextDocEntry(DocEntry *entry) +void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) { - Fp->seekg((long)(entry->GetOffset()), std::ios::beg); - Fp->seekg( (long)(entry->GetReadLength()), std::ios::cur); + Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg); + Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur); } /** @@ -2095,7 +1843,7 @@ void Document::SkipToNextDocEntry(DocEntry *entry) * the parser went Jabberwocky) one can hope improving things by * applying some heuristics. * @param entry entry to check - * @param foundLength fist assumption about length + * @param foundLength first assumption about length */ void Document::FixDocEntryFoundLength(DocEntry *entry, uint32_t foundLength) @@ -2106,30 +1854,25 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, foundLength = 0; } - uint16_t gr = entry->GetGroup(); - uint16_t el = entry->GetElement(); + uint16_t gr = entry->GetGroup(); + uint16_t elem = 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()); + gdcmVerboseMacro( "Warning : Tag with uneven length " << foundLength + << " in x(" << std::hex << gr << "," << elem <<")"); } //////// 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)... + // are no longer in use (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 ) ) + if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) ) { foundLength = 10; entry->SetReadLength(10); /// \todo a bug is to be fixed !? @@ -2140,9 +1883,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, // 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 ) ) + else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) ) { foundLength = 4; entry->SetReadLength(4); /// \todo a bug is to be fixed !? @@ -2156,7 +1897,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, //////// 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 ) + else if( gr == 0xfffe ) { // According to the norm, fffe|0000 shouldn't exist. BUT the Philips // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to @@ -2167,7 +1908,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, } } - entry->SetUsableLength(foundLength); + entry->SetLength(foundLength); } /** @@ -2178,15 +1919,15 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, */ bool Document::IsDocEntryAnInteger(DocEntry *entry) { - uint16_t element = entry->GetElement(); + uint16_t elem = entry->GetElement(); uint16_t group = entry->GetGroup(); - const std::string & vr = entry->GetVR(); + 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 ( elem == 0 ) // This is the group length of the group { if ( length == 4 ) { @@ -2201,21 +1942,18 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) // 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 + gdcmVerboseMacro( "Erroneous Group Length element length on : (" + << std::hex << group << " , " << elem << ") -before- position x(" << filePosition << ")" - << "lgt : " << length; - dbg.Verbose(0, "Document::IsDocEntryAnInteger", s.str().c_str() ); + << "lgt : " << length ); } } if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" ) { return true; - } - + } return false; } @@ -2225,7 +1963,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) * @return */ -uint32_t Document::FindDocEntryLengthOB() +uint32_t Document::FindDocEntryLengthOBOrOW() throw( FormatUnexpected ) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. @@ -2244,8 +1982,8 @@ uint32_t Document::FindDocEntryLengthOB() } catch ( FormatError ) { - throw FormatError("Document::FindDocEntryLengthOB()", - " group or element not present."); + throw FormatError("Unexpected end of file encountered during ", + "Document::FindDocEntryLengthOBOrOW()"); } // We have to decount the group and element we just read @@ -2253,12 +1991,13 @@ uint32_t Document::FindDocEntryLengthOB() if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { - dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item " - "tag nor a Sequence delimiter tag."); + long filePosition = Fp->tellg(); + gdcmVerboseMacro( "Neither an Item tag nor a Sequence delimiter tag on :" + << std::hex << group << " , " << elem + << ") -before- position x(" << filePosition << ")" ); + Fp->seekg(positionOnEntry, std::ios::beg); - throw FormatUnexpected("Document::FindDocEntryLengthOB()", - "Neither an Item tag nor a Sequence " - "delimiter tag."); + throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag."); } if ( elem == 0xe0dd ) @@ -2381,25 +2120,24 @@ bool Document::CheckSwap() 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". + // The easiest case is the one of a 'true' DICOM header, we just have + // to look for the string "DICM" inside the file preamble. Fp->read(deb, 256); char *entCur = deb + 128; if( memcmp(entCur, "DICM", (size_t)4) == 0 ) { - dbg.Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3"); + gdcmVerboseMacro( "Looks like DICOM Version3 (preamble + DCM)" ); - // 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) -, + // Group 0002 should always be VR, and the first element 0000 + // Let's be carefull (so many wrong headers ...) + // and 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, @@ -2407,46 +2145,42 @@ bool Document::CheckSwap() // 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 !- + // group 0x0002 *is always* Explicit VR Sometimes , + // even if elem 0002,0010 (Transfer Syntax) tells us the file is + // *Implicit* VR (see former 'gdcmData/icone.dcm') 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* + // 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"); + gdcmVerboseMacro( "Group 0002 : Explicit Value Representation"); } else { Filetype = ImplicitVR; - dbg.Verbose(1, "Document::CheckSwap:", - "not an explicit Value Representation"); + gdcmVerboseMacro( "Group 0002 :Not an explicit Value Representation;" + << "Looks like a bugged Header!"); } if ( net2host ) { SwapCode = 4321; - dbg.Verbose(1, "Document::CheckSwap:", - "HostByteOrder != NetworkByteOrder"); + gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder"); } else { - SwapCode = 0; - dbg.Verbose(1, "Document::CheckSwap:", - "HostByteOrder = NetworkByteOrder"); + SwapCode = 1234; + gdcmVerboseMacro( "HostByteOrder = NetworkByteOrder"); } - // Position the file position indicator at first tag (i.e. - // after the file preamble and the "DICM" string). + // Position the file position indicator at first tag + // (i.e. after the file preamble and the "DICM" string). Fp->seekg(0, std::ios::beg); Fp->seekg ( 132L, std::ios::beg); return true; @@ -2455,7 +2189,7 @@ bool Document::CheckSwap() // 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"); + gdcmVerboseMacro( "Not a DICOM Version3 file"); Fp->seekg(0, std::ios::beg); // Our next best chance would be to be considering a 'clean' ACR/NEMA file. @@ -2484,7 +2218,7 @@ bool Document::CheckSwap() Filetype = ACR; return true; case 0x00000004 : - SwapCode = 0; + SwapCode = 1234; Filetype = ACR; return true; default : @@ -2515,7 +2249,7 @@ bool Document::CheckSwap() case 0x0006 : case 0x0007 : case 0x0008 : - SwapCode = 0; + SwapCode = 1234; Filetype = ACR; return true; case 0x0100 : @@ -2530,37 +2264,28 @@ bool Document::CheckSwap() Filetype = ACR; return true; default : - dbg.Verbose(0, "Document::CheckSwap:", - "ACR/NEMA unfound swap info (Really hopeless !)"); + gdcmVerboseMacro( "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. + * \brief Change the Byte Swap code. */ -void Document::SwitchSwapToBigEndian() +void Document::SwitchByteSwapCode() { - dbg.Verbose(1, "Document::SwitchSwapToBigEndian", - "Switching to BigEndian mode."); - if ( SwapCode == 0 ) + gdcmVerboseMacro( "Switching Byte Swap code from "<< SwapCode); + if ( SwapCode == 1234 ) { SwapCode = 4321; } else if ( SwapCode == 4321 ) { - SwapCode = 0; + SwapCode = 1234; } else if ( SwapCode == 3412 ) { @@ -2619,7 +2344,7 @@ void Document::SetMaxSizePrintEntry(long newSize) * apparent reason * @return no return */ -void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) +void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) { // Endian reversion. Some files contain groups of tags with reversed endianess. static int reversedEndian = 0; @@ -2628,27 +2353,90 @@ void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) { // start endian swap mark for group found reversedEndian++; - SwitchSwapToBigEndian(); + SwitchByteSwapCode(); // fix the tag group = 0xfffe; elem = 0xe000; } - else if ((group == 0xfffe) && (elem == 0xe00d) && reversedEndian) + else if (group == 0xfffe && elem == 0xe00d && reversedEndian) { // end of reversed endian group reversedEndian--; - SwitchSwapToBigEndian(); + SwitchByteSwapCode(); + } +} + +/** + * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS + * else 1. + * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID) + */ +std::string Document::GetTransferSyntaxName() +{ + // use the TS (TS : Transfer Syntax) + std::string transferSyntax = GetEntry(0x0002,0x0010); + + if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) ) + { + gdcmErrorMacro( "Transfer Syntax not loaded. " << std::endl + << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" ); + return "Uncompressed ACR-NEMA"; + } + if ( transferSyntax == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Unfound Transfer Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; + } + + // we do it only when we need it + const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax ); + + // Global::GetTS() is a global static you shall never try to delete it! + return tsName; +} + +/** + * \brief Group 0002 is always coded Little Endian + * whatever Transfer Syntax is + * @return no return + */ +void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) +{ + // Endian reversion. Some files contain groups of tags with reversed endianess. + if ( !Group0002Parsed && group != 0x0002) + { + Group0002Parsed = true; + // we just came out of group 0002 + // if Transfer syntax is Big Endian we have to change CheckSwap + + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsTransferSyntax(ts) ) + { + gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts ); + return; + } + + // FIXME Strangely, this works with + //'Implicit VR Transfer Syntax (GE Private) + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian ) + { + gdcmVerboseMacro("Transfer Syntax Name = [" + << GetTransferSyntaxName() << "]" ); + SwitchByteSwapCode(); + group = SwapShort(group); + elem = SwapShort(elem); + } } } /** * \brief Read the next tag but WITHOUT loading it's value * (read the 'Group Number', the 'Element Number', - * gets the Dict Entry + * 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() +DocEntry *Document::ReadNextDocEntry() { uint16_t group; uint16_t elem; @@ -2666,9 +2454,44 @@ DocEntry* Document::ReadNextDocEntry() return 0; } + // Sometimes file contains groups of tags with reversed endianess. HandleBrokenEndian(group, elem); - DocEntry *newEntry = NewDocEntryByNumber(group, elem); - FindDocEntryVR(newEntry); + +// In 'true DICOM' files Group 0002 is always little endian + if ( HasDCMPreamble ) + HandleOutOfGroup0002(group, elem); + + std::string vr = FindDocEntryVR(); + std::string realVR = vr; + + if( vr == GDCM_UNKNOWN) + { + DictEntry *dictEntry = GetDictEntry(group,elem); + if( dictEntry ) + realVR = dictEntry->GetVR(); + } + + DocEntry *newEntry; + if( Global::GetVR()->IsVROfSequence(realVR) ) + newEntry = NewSeqEntry(group, elem); + else if( Global::GetVR()->IsVROfStringRepresentable(realVR) ) + newEntry = NewValEntry(group, elem,vr); + else + newEntry = NewBinEntry(group, elem,vr); + + if( vr == GDCM_UNKNOWN ) + { + if( Filetype == ExplicitVR ) + { + // We thought this was explicit VR, but we end up with an + // implicit VR tag. Let's backtrack. + std::string msg; + msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", + newEntry->GetGroup(), newEntry->GetElement()); + gdcmVerboseMacro( msg.c_str() ); + } + newEntry->SetImplicitVR(); + } try { @@ -2741,15 +2564,13 @@ bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) } 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()); + gdcmVerboseMacro( "Wrong Item Tag found:" + << " We should have found tag (" + << std::hex << testGroup << "," << testElement << ")" << std::endl + << " but instead we encountered tag (" + << std::hex << itemTagGroup << "," << itemTagElement << ")" + << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" + ) ; Fp->seekg(positionOnEntry, std::ios::beg); return false; @@ -2785,11 +2606,9 @@ uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement) 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()); + gdcmVerboseMacro( "Basic Item Length is: " + << itemLength << std::endl + << " at address: " << std::hex << (unsigned int)currentPosition); } return itemLength; } @@ -2811,7 +2630,7 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 ) { - char* basicOffsetTableItemValue = new char[itemLength + 1]; + char *basicOffsetTableItemValue = new char[itemLength + 1]; Fp->read(basicOffsetTableItemValue, itemLength); #ifdef GDCM_DEBUG @@ -2819,12 +2638,8 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() { 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()); + gdcmVerboseMacro( "Read one length: " << + std::hex << individualLength ); } #endif //GDCM_DEBUG @@ -2839,8 +2654,8 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() */ void Document::ComputeRLEInfo() { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts != RLELossless ) + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsRLELossless(ts) ) { return; } @@ -2881,7 +2696,7 @@ void Document::ComputeRLEInfo() if ( nbRleSegments > 16 ) { // There should be at most 15 segments (refer to RLEFrame class) - dbg.Verbose(0, "Document::ComputeRLEInfo: too many segments."); + gdcmVerboseMacro( "Too many segments."); } uint32_t rleSegmentOffsetTable[16]; @@ -2910,7 +2725,7 @@ void Document::ComputeRLEInfo() SkipBytes(rleSegmentLength[nbRleSegments]); // Store the collected info - RLEFrame* newFrameInfo = new RLEFrame; + RLEFrame *newFrameInfo = new RLEFrame; newFrameInfo->NumberFragments = nbRleSegments; for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) { @@ -2924,8 +2739,7 @@ void Document::ComputeRLEInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); - dbg.Verbose(0, " item at end of RLE item sequence"); + gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence"); } } @@ -2938,7 +2752,8 @@ void Document::ComputeRLEInfo() void Document::ComputeJPEGFragmentInfo() { // If you need to, look for comments of ComputeRLEInfo(). - if ( ! IsJPEG() ) + std::string ts = GetTransferSyntax(); + if ( ! Global::GetTS()->IsJPEG(ts) ) { return; } @@ -2953,7 +2768,7 @@ void Document::ComputeJPEGFragmentInfo() long fragmentOffset = Fp->tellg(); // Store the collected info - JPEGFragment* newFragment = new JPEGFragment; + JPEGFragment *newFragment = new JPEGFragment; newFragment->Offset = fragmentOffset; newFragment->Length = fragmentLength; JPEGInfo->Fragments.push_back( newFragment ); @@ -2965,8 +2780,7 @@ void Document::ComputeJPEGFragmentInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); - dbg.Verbose(0, " item at end of JPEG item sequence"); + gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence"); } } @@ -2979,18 +2793,18 @@ void Document::ComputeJPEGFragmentInfo() * when recursively walking the given set. * @param set The structure to be traversed (recursively). */ -void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, - DocEntrySet* set ) +void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, + DocEntrySet *set ) { - if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) ) + if (ElementSet *elementSet = dynamic_cast< ElementSet* > ( set ) ) { - TagDocEntryHT const & currentHT = elementSet->GetTagHT(); + TagDocEntryHT const ¤tHT = elementSet->GetTagHT(); for( TagDocEntryHT::const_iterator i = currentHT.begin(); i != currentHT.end(); ++i) { - DocEntry* entry = i->second; - if ( SeqEntry* seqEntry = dynamic_cast(entry) ) + DocEntry *entry = i->second; + if ( SeqEntry *seqEntry = dynamic_cast(entry) ) { const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); @@ -3006,15 +2820,15 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, return; } - if (SQItem* SQItemSet = dynamic_cast< SQItem* > ( set ) ) + 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) ) + DocEntry *entry = *i; + if ( SeqEntry *seqEntry = dynamic_cast(entry) ) { const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); @@ -3054,9 +2868,9 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, * \ref BuildFlatHashTable again... * @return The flat std::map<> we juste build. */ -TagDocEntryHT* Document::BuildFlatHashTable() +TagDocEntryHT *Document::BuildFlatHashTable() { - TagDocEntryHT* FlatHT = new TagDocEntryHT; + TagDocEntryHT *FlatHT = new TagDocEntryHT; BuildFlatHashTableRecurse( *FlatHT, this ); return FlatHT; } @@ -3073,8 +2887,8 @@ TagDocEntryHT* Document::BuildFlatHashTable() bool Document::operator<(Document &document) { // Patient Name - std::string s1 = GetEntryByNumber(0x0010,0x0010); - std::string s2 = document.GetEntryByNumber(0x0010,0x0010); + std::string s1 = GetEntry(0x0010,0x0010); + std::string s2 = document.GetEntry(0x0010,0x0010); if(s1 < s2) { return true; @@ -3086,8 +2900,8 @@ bool Document::operator<(Document &document) else { // Patient ID - s1 = GetEntryByNumber(0x0010,0x0020); - s2 = document.GetEntryByNumber(0x0010,0x0020); + s1 = GetEntry(0x0010,0x0020); + s2 = document.GetEntry(0x0010,0x0020); if ( s1 < s2 ) { return true; @@ -3099,8 +2913,8 @@ bool Document::operator<(Document &document) else { // Study Instance UID - s1 = GetEntryByNumber(0x0020,0x000d); - s2 = document.GetEntryByNumber(0x0020,0x000d); + s1 = GetEntry(0x0020,0x000d); + s2 = document.GetEntry(0x0020,0x000d); if ( s1 < s2 ) { return true; @@ -3112,8 +2926,8 @@ bool Document::operator<(Document &document) else { // Serie Instance UID - s1 = GetEntryByNumber(0x0020,0x000e); - s2 = document.GetEntryByNumber(0x0020,0x000e); + s1 = GetEntry(0x0020,0x000e); + s2 = document.GetEntry(0x0020,0x000e); if ( s1 < s2 ) { return true; @@ -3128,6 +2942,52 @@ bool Document::operator<(Document &document) return false; } + +/** + * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader + * @param filetype Type of the File to be written + */ +int Document::ComputeGroup0002Length( FileType filetype ) +{ + uint16_t gr, el; + std::string vr; + + int groupLength = 0; + bool found0002 = false; + + // for each zero-level Tag in the DCM Header + DocEntry *entry; + + Initialize(); + entry = GetNextEntry(); + while(entry) + { + gr = entry->GetGroup(); + + if (gr == 0x0002) + { + found0002 = true; + + el = entry->GetElement(); + vr = entry->GetVR(); + + if (filetype == ExplicitVR) + { + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) + { + groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes + } + } + groupLength += 2 + 2 + 4 + entry->GetLength(); + } + else if (found0002 ) + break; + + entry = GetNextEntry(); + } + return groupLength; +} + } // end namespace gdcm //-----------------------------------------------------------------------------