X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=8437264ba6268cf28f9d21c8eb86fb132f8a95a7;hb=0ad9dae4659b21bfd5c834c1af724eab4dcdf4f6;hp=289bf43a91cfda4485f484d61f48c769f40c5848;hpb=05f4ffeadc3beb5ff48fd88e7342d9287c18a27b;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 289bf43a..8437264b 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/11/09 21:55:55 $ - Version: $Revision: 1.119 $ + Date: $Date: 2005/01/23 10:12:33 $ + Version: $Revision: 1.204 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,55 +23,32 @@ #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" +#include "gdcmTS.h" +#include "gdcmException.h" +#include "gdcmDictSet.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" +#include "gdcmDocEntrySet.h" +#include "gdcmSQItem.h" #include #include // For nthos: -#if defined(_MSC_VER) || defined(__BORLANDC__) +#if defined(_MSC_VER) || defined(__BORLANDC__) || defined(__MINGW32__) #include -#else +#endif + +#ifdef CMAKE_HAVE_NETINET_IN_H #include #endif namespace gdcm { -static const char *TransferSyntaxStrings[] = { - // Implicit VR Little Endian - "1.2.840.10008.1.2", - // 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; +//const unsigned int Document::HEADER_LENGTH_TO_READ = 256; // Refer to Document::SetMaxSizeLoadEntry() const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 @@ -82,52 +59,58 @@ const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; /** * \brief constructor - * @param filename file to be opened for parsing + * @param filename 'Document' (File or DicomDir) to be opened for parsing */ -Document::Document( std::string const & filename ) : ElementSet(-1) +Document::Document( std::string const &filename ) : ElementSet(-1) { + RLEInfo = NULL; + JPEGInfo = NULL; + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; - Initialise(); + Initialize(); + Fp = 0; if ( !OpenFile() ) { return; } - dbg.Verbose(0, "Document::Document: starting parsing of file: ", - Filename.c_str()); - Fp->seekg( 0, std::ios_base::beg); + Group0002Parsed = false; + + gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str()); + // Fp->seekg( 0, std::ios::beg); - Fp->seekg(0, std::ios_base::end); + Fp->seekg(0, std::ios::end); long lgt = Fp->tellg(); - Fp->seekg( 0, std::ios_base::beg); + Fp->seekg( 0, std::ios::beg); + CheckSwap(); long beg = Fp->tellg(); lgt -= beg; - ParseDES( this, beg, lgt, false); // le Load sera fait a la volee + ParseDES( this, beg, lgt, false); // Loading is done during parsing - Fp->seekg( 0, std::ios_base::beg); + Fp->seekg( 0, std::ios::beg); // 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 /// 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 + /// dictionary. 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 "Quick and Dirty" the dictionary was + /// 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: + /// whether 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 @@ -159,20 +142,18 @@ 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 (RET) 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 } /** @@ -181,9 +162,16 @@ Document::Document( std::string const & filename ) : ElementSet(-1) */ Document::Document() : ElementSet(-1) { + RLEInfo = NULL; + JPEGInfo = NULL; + + Fp = 0; + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - Initialise(); - PrintLevel = 1; // 'Medium' print level by default + Initialize(); + SwapCode = 1234; + Filetype = ExplicitVR; + Group0002Parsed = false; } /** @@ -194,15 +182,10 @@ Document::~Document () RefPubDict = NULL; RefShaDict = NULL; - // Recursive clean up of sequences - for (TagDocEntryHT::const_iterator it = TagHT.begin(); - it != TagHT.end(); ++it ) - { - //delete it->second; //temp remove - } - TagHT.clear(); - delete RLEInfo; - delete JPEGInfo; + if( RLEInfo ) + delete RLEInfo; + if( JPEGInfo ) + delete JPEGInfo; } //----------------------------------------------------------------------------- @@ -212,8 +195,9 @@ 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); } @@ -221,8 +205,9 @@ 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); } @@ -231,7 +216,7 @@ void Document::PrintShaDict(std::ostream & os) /** * \brief Get the public dictionary used */ -Dict* Document::GetPubDict() +Dict *Document::GetPubDict() { return RefPubDict; } @@ -239,14 +224,14 @@ 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) { @@ -256,9 +241,9 @@ 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; @@ -276,41 +261,38 @@ 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."); + //if( TagHT.empty() ) + if ( IsEmpty() ) + { + gdcmVerboseMacro( "No tag in internal hash table."); return false; } return true; } - /** - * \brief Internal function that checks whether the Transfer Syntax given - * as argument is the one present in the current document. - * @param syntaxToCheck The transfert syntax we need to check against. - * @return True when SyntaxToCheck corresponds to the Transfer Syntax of - * the current document. False either when the document contains - * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match. + * \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() +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 @@ -319,68 +301,15 @@ TransferSyntaxType Document::GetTransferSyntax() if ( transfer.length() == 0 ) { // for brain damaged headers - return UnknownTS; + return GDCM_UNKNOWN; } - while ( !isdigit(transfer[transfer.length()-1]) ) + 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; } /** @@ -389,11 +318,28 @@ 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; +} + +/** + * \brief Predicate for Papyrus file + * Dedicated to whomsoever it may concern + * @return True when the file is a Papyrus file. + */ +bool Document::IsPapyrus() +{ + // check for Papyrus private Sequence + DocEntry *e = GetDocEntry(0x0041, 0x1050); + if ( !e ) + return false; + // check if it's actually a Sequence + if ( !dynamic_cast(e) ) + return false; + return true; } /** @@ -411,40 +357,67 @@ FileType Document::GetFileType() * checks the preamble when existing. * @return The FILE pointer on success. */ -std::ifstream* Document::OpenFile() +std::ifstream *Document::OpenFile() { - Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); - if(!Fp) + HasDCMPreamble = false; + if (Filename.length() == 0) + { + return 0; + } + + if(Fp) + { + 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; } uint16_t zero; - Fp->read((char*)&zero, (size_t)2 ); - - //ACR -- or DICOM with no Preamble -- - if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 ) + Fp->read((char*)&zero, (size_t)2); + if( Fp->eof() ) { + CloseFile(); + return 0; + } + + //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 ) + { + std::string msg + = Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero); + gdcmVerboseMacro( msg.c_str() ); return Fp; } //DICOM - Fp->seekg(126L, std::ios_base::cur); + Fp->seekg(126L, std::ios::cur); char dicm[4]; Fp->read(dicm, (size_t)4); + if( Fp->eof() ) + { + CloseFile(); + return 0; + } if( memcmp(dicm, "DICM", 4) == 0 ) { + HasDCMPreamble = true; return Fp; } - Fp->close(); - dbg.Verbose( 0, - "Document::OpenFile not DICOM/ACR (missing preamble)", - Filename.c_str()); + CloseFile(); + gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str()); return 0; } @@ -455,55 +428,39 @@ std::ifstream* Document::OpenFile() */ bool Document::CloseFile() { - Fp->close(); - delete Fp; - Fp = 0; + if( Fp ) + { + Fp->close(); + delete Fp; + Fp = 0; + } - return true; //FIXME how do we detect a non-close ifstream ? + return true; //FIXME how do we detect a non-closed ifstream ? } /** * \brief Writes in a file all the Header Entries (Dicom Elements) - * @param fp file pointer on an already open file + * @param fp file pointer on an already open file (actually: Output File Stream) * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -void Document::Write(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 /// (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) + if ( filetype == ImplicitVR || 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); + // writing Dicom File Preamble + char filePreamble[128]; + memset(filePreamble, 0, 128); + fp->write(filePreamble, 128); + fp->write("DICM", 4); } - + /** * \todo rewrite later, if really usefull * - 'Group Length' element is optional in DICOM @@ -516,199 +473,193 @@ void Document::Write(std::ofstream* fp, FileType filetype) * UpdateGroupLength(true,ACR); */ - ElementSet::Write(fp, filetype); // This one is recursive - + ElementSet::WriteContent(fp, filetype); // This one is recursive } /** - * \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 * @param elem Element number of the Entry - * @param VR V(alue) R(epresentation) of the Entry -if private 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); +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) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; - } - valEntry = new ValEntry(currentEntry); - if ( !AddEntry(valEntry)) - { - delete valEntry; - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); - } - // This is the reason why NewDocEntryByNumber are a real - // bad habit !!! FIXME - delete currentEntry; - } - 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 ? + // if currentEntry doesn't correspond to the requested valEntry + if( !valEntry) { - // 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."); + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + return NULL; } } } - SetEntryByNumber(value, group, elem); + // 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; + return NULL; + } + } + + // Set the binEntry value + SetEntry(value, valEntry); 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 + * @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 + // Verify the currentEntry + if (currentEntry) + { + binEntry = dynamic_cast< BinEntry* >(currentEntry); - // Find out if the tag we received is in the dictionaries: - Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); - DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem); + // Verify the VR + if( binEntry ) + if( binEntry->GetVR()!=vr ) + binEntry=NULL; - if (!dictEntry) + // if currentEntry doesn't correspond to the requested valEntry + if( !binEntry) { - currentEntry = NewDocEntryByNumber(group, elem, vr); - } - else - { - currentEntry = NewDocEntryByNumber(group, elem); - } - if (!currentEntry) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; + if (!RemoveEntry(currentEntry)) + { + gdcmVerboseMacro( "Removal of previous DocEntry failed."); + + return NULL; + } } - binEntry = new BinEntry(currentEntry); + } + + // Create a new binEntry if necessary + if (!binEntry) + { + binEntry = NewBinEntry(group, elem, vr); + if ( !AddEntry(binEntry)) { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); + + delete binEntry; + return NULL; } } + + // Set the binEntry value + uint8_t *tmpArea; + if (lgth>0 && binArea) + { + tmpArea = new uint8_t[lgth]; + memcpy(tmpArea,binArea,lgth); + } 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 ? + tmpArea = 0; + } + if (!SetEntry(tmpArea,lgth,binEntry)) + { + if (tmpArea) { - // 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; - } + delete[] tmpArea; } } - SetEntryByNumber(binArea, lgth, group, elem); - 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 + * @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 *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; + } } + } + // Create a new seqEntry if necessary + if (!seqEntry) + { + seqEntry = NewSeqEntry(group, elem); - b = new SeqEntry(a, 1); // FIXME : 1 (Depth) - AddEntry(b); - } - return b; + if ( !AddEntry(seqEntry)) + { + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); + + delete seqEntry; + return NULL; + } + } + return seqEntry; } /** @@ -719,10 +670,10 @@ 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; } @@ -730,143 +681,45 @@ bool Document::ReplaceIfExistByNumber(std::string const & value, //----------------------------------------------------------------------------- // 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. + * @param group Group number of the searched tag. + * @param elem 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) +std::string Document::GetEntryVR(uint16_t group, uint16_t elem) { - DocEntry* elem = GetDocEntryByNumber(group, element); - if ( !elem ) + DocEntry *element = GetDocEntry(group, elem); + if ( !element ) { return GDCM_UNFOUND; } - return elem->GetVR(); + return element->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. + * @param group Group number of the searched tag. + * @param elem 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 elem) { - DocEntry* elem = GetDocEntryByNumber(group, element); - if ( !elem ) + DocEntry *element = GetDocEntry(group, elem); + if ( !element ) { 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()); + return element->GetLength(); } /** @@ -874,48 +727,19 @@ bool Document::SetEntryByName(std::string const & content, * 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 + * @param group group number of the Dicom Element to modify + * @param elem 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 elem) { - int c; - int l; - - ValEntry* valEntry = GetValEntryByNumber(group, element); - if (!valEntry ) + ValEntry *entry = GetValEntry(group, elem); + 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)... - 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; + return SetEntry(content,entry); } /** @@ -924,79 +748,62 @@ bool Document::SetEntryByNumber(std::string const& content, * 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 + * @param group group number of the Dicom Element to modify + * @param elem 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 elem) { - (void)lgth; //not used - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key)) + BinEntry *entry = GetBinEntry(group, elem); + 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? - } -*/ - BinEntry* a = (BinEntry *)TagHT[key]; - a->SetBinArea(content); - a->SetLength(lgth); - a->SetValue(GDCM_BINLOADED); - - return true; + return SetEntry(content,lgth,entry); } /** * \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. + * 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::SetEntryLengthByNumber(uint32_t l, - uint16_t group, uint16_t element) +bool Document::SetEntry(std::string const &content, ValEntry *entry) { - /// \todo use map methods, instead of multimap JPR - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key) ) + if(entry) { - return false; - } - if ( l % 2 ) - { - l++; // length must be even + entry->SetValue(content); + return true; } - ( ((TagHT.equal_range(key)).first)->second )->SetLength(l); - - return true ; + return false; } /** - * \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 + * \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 */ -size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) +bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry) { - DocEntry* entry = GetDocEntryByNumber(group, elem); - if (!entry) + if(entry) { - dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present."); - return 0; + // 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 entry->GetOffset(); + return false; } /** @@ -1006,15 +813,15 @@ size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) * @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(); } @@ -1023,211 +830,105 @@ void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) } /** - * \brief Loads (from disk) the element content - * when a string is not suitable + * \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) +void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { - DocEntry *docElement = GetDocEntryByNumber(group, elem); + // Search the corresponding DocEntry + DocEntry *docElement = GetDocEntry(group, elem); if ( !docElement ) - { - return NULL; - } - 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 NULL; - } - Fp->read((char*)a, l); - if( Fp->fail() || Fp->eof() )//Fp->gcount() == 1 - { - delete[] a; - return NULL; - } - /// \todo Drop any already existing void area! JPR - if( !SetEntryBinAreaByNumber( a, group, elem ) ) - { - dbg.Verbose(0, "Document::LoadEntryBinArea setting failed."); - } - return a; -} -/** - * \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) -{ - 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 NULL; - } - element->SetBinArea((uint8_t*)a); - /// \todo check the result - Fp->read((char*)a, l); - if( Fp->fail() || Fp->eof()) //Fp->gcount() == 1 - { - delete[] a; - return NULL; - } - - return a; -} - -/** - * \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 true; -} - -/** - * \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(); + return; - (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling - if(entry){ - // Set the new entry and the new value - (*it)->SetDictEntry(entry); - CheckDocEntryVR(*it,vr); + BinEntry *binElement = dynamic_cast(docElement); + if( !binElement ) + return; - (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling - - } - else - { - // Remove precedent value transformation - (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr)); - } - } -*/ + LoadEntryBinArea(binElement); } /** - * \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. + * \brief Loads (from disk) the element content + * when a string is not suitable + * @param elem Entry whose binArea is going to be loaded */ -DocEntry* Document::GetDocEntryByName(TagName const & tagName) +void Document::LoadEntryBinArea(BinEntry *elem) { - DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) + if(elem->GetBinArea()) + return; + + bool openFile = !Fp; + if(openFile) + OpenFile(); + + size_t o =(size_t)elem->GetOffset(); + Fp->seekg(o, std::ios::beg); + + size_t l = elem->GetLength(); + uint8_t *a = new uint8_t[l]; + if( !a ) { - return NULL; + gdcmVerboseMacro( "Cannot allocate BinEntry content"); + return; } - 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)) + /// \todo check the result + Fp->read((char*)a, l); + if( Fp->fail() || Fp->eof()) { - return NULL; + delete[] a; + return; } - return TagHT.find(key)->second; + + elem->SetBinArea(a); + + if(openFile) + CloseFile(); } /** - * \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. + * \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 elem Element number of the searched Dicom Element + * @return */ -ValEntry* Document::GetValEntryByNumber(uint16_t group, uint16_t element) +/*bool Document::SetEntryBinArea(uint8_t *area, + uint16_t group, uint16_t elem) { - DocEntry* currentEntry = GetDocEntryByNumber(group, element); + DocEntry *currentEntry = GetDocEntry(group, elem); if ( !currentEntry ) { - return 0; + return false; } - if ( ValEntry* valEntry = dynamic_cast(currentEntry) ) + + if ( BinEntry *binEntry = dynamic_cast(currentEntry) ) { - return valEntry; + binEntry->SetBinArea( area ); + return true; } - dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry."); - return 0; -} + return false; +}*/ + /** - * \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. + * \brief Loads the element while preserving the current + * underlying file position indicator as opposed to + * LoadDocEntry that modifies it. + * @param entry Header Entry whose value will be loaded. * @return */ -void Document::LoadDocEntrySafe(DocEntry * entry) +void Document::LoadDocEntrySafe(DocEntry *entry) { - long PositionOnEntry = Fp->tellg(); - LoadDocEntry(entry); - Fp->seekg(PositionOnEntry, std::ios_base::beg); + if(Fp) + { + long PositionOnEntry = Fp->tellg(); + LoadDocEntry(entry); + Fp->seekg(PositionOnEntry, std::ios::beg); + } } /** @@ -1239,23 +940,20 @@ 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; @@ -1304,111 +1002,130 @@ 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) - { - if ( !delim_mode && (Fp->tellg()-offset) >= l_max) + { + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { 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 ( Filetype == ExplicitVR && ! 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 ( dynamic_cast< Document* > ( set ) ) + { + newBinEntry->SetKey( newBinEntry->GetKey() ); + } + // but when "this" is a SQItem, we are inserting this new + // valEntry in a sequence item, and the key 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() ); - 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 ( 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 ) ) + if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newValEntry->SetKey( parentSQItem->GetBaseTagKey() + newValEntry->GetKey() ); } - set->AddEntry( newValEntry ); LoadDocEntry( newValEntry ); - if (newValEntry->IsItemDelimitor()) + bool delimitor=newValEntry->IsItemDelimitor(); + if( !set->AddEntry( newValEntry ) ) { - break; - } - if ( !delim_mode && (Fp->tellg()-offset) >= l_max) - { - break; + // If here expect big troubles + //delete newValEntry; //otherwise mem leak + used=false; } - } - 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 ); - // When "this" is a Document the Key is simply of the - // form ( group, elem )... - if (Document* dummy = dynamic_cast< Document* > ( set ) ) + if (delimitor) { - (void)dummy; - newBinEntry->SetKey( newBinEntry->GetKey() ); + if(!used) + delete newDocEntry; + break; } - // 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 ) ) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - newBinEntry->SetKey( parentSQItem->GetBaseTagKey() - + newBinEntry->GetKey() ); + if(!used) + delete newDocEntry; + break; } - - set->AddEntry( newBinEntry ); - LoadDocEntry( 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(); - Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); + long positionOnEntry = Fp->tellg(); + Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeRLEInfo(); - Fp->seekg( PositionOnEntry, std::ios_base::beg ); + Fp->seekg( positionOnEntry, std::ios::beg ); } - else if ( IsJPEG() ) + else if ( Global::GetTS()->IsJPEG(ts) ) { - long PositionOnEntry = Fp->tellg(); - Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); + long positionOnEntry = Fp->tellg(); + Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeJPEGFragmentInfo(); - Fp->seekg( PositionOnEntry, std::ios_base::beg ); + Fp->seekg( positionOnEntry, std::ios::beg ); } } - + // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); } @@ -1428,25 +1145,22 @@ 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; + //(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() @@ -1460,12 +1174,14 @@ void Document::ParseDES(DocEntrySet *set, long offset, l, delim_mode); } set->AddEntry( newSeqEntry ); - if ( !delim_mode && (Fp->tellg()-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { break; } } - delete newDocEntry; + + if(!used) + delete newDocEntry; } } @@ -1473,15 +1189,18 @@ 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; bool dlm_mod; + long offsetStartCurrentSQItem = offset; while (true) { - DocEntry* newDocEntry = ReadNextDocEntry(); + // the first time, we read the fff0,e000 of the first SQItem + DocEntry *newDocEntry = ReadNextDocEntry(); + if ( !newDocEntry ) { // FIXME Should warn user @@ -1491,15 +1210,16 @@ void Document::ParseSQ( SeqEntry* seqEntry, { if ( newDocEntry->IsSequenceDelimitor() ) { - seqEntry->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetDelimitationItem( newDocEntry ); break; } } - if ( !delim_mode && (Fp->tellg()-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - break; + delete newDocEntry; + break; } - + // create the current SQItem SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); std::ostringstream newBase; newBase << seqEntry->GetKey() @@ -1517,12 +1237,25 @@ void Document::ParseSQ( SeqEntry* seqEntry, { dlm_mod = false; } - - ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); - - seqEntry->AddEntry( itemSQ, SQItemNumber ); + // FIXME, TODO + // when we're here, element fffe,e000 is already passed. + // it's lost for the SQItem we're going to process !! + + //ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); + //delete newDocEntry; // FIXME well ... it's too late to use it ! + + // Let's try :------------ + // remove fff0,e000, created out of the SQItem + delete newDocEntry; + Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); + // fill up the current SQItem, starting at the beginning of fff0,e000 + ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod); + offsetStartCurrentSQItem = Fp->tellg(); + // end try ----------------- + + seqEntry->AddSQItem( itemSQ, SQItemNumber ); SQItemNumber++; - if ( !delim_mode && ( Fp->tellg() - offset ) >= l_max ) + if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) { break; } @@ -1534,13 +1267,13 @@ 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(); uint32_t length = entry->GetLength(); - Fp->seekg((long)entry->GetOffset(), std::ios_base::beg); + Fp->seekg((long)entry->GetOffset(), std::ios::beg); // A SeQuence "contains" a set of Elements. // (fffe e000) tells us an Element is beginning @@ -1566,7 +1299,7 @@ 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; @@ -1575,8 +1308,8 @@ void Document::LoadDocEntry(DocEntry* entry) 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) ) + // Be carefull : a BinEntry IS_A ValEntry ... + else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { // s << "gdcm::NotLoaded. (ValEntry)"; s << GDCM_NOTLOADED; @@ -1588,25 +1321,25 @@ 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 ... Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), - std::ios_base::beg); + std::ios::beg); return; } // 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) ) { @@ -1665,10 +1398,10 @@ 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 { @@ -1676,12 +1409,11 @@ 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; } @@ -1698,8 +1430,7 @@ void Document::LoadDocEntry(DocEntry* entry) } else { - dbg.Error(true, "Document::LoadDocEntry" - "Should have a ValEntry, here !"); + gdcmErrorMacro( "Should have a ValEntry, here !"); } } @@ -1711,7 +1442,6 @@ 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; @@ -1722,7 +1452,7 @@ void Document::FindDocEntryLength( DocEntry *entry ) // 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); + Fp->seekg( 2L, std::ios::cur); uint32_t length32 = ReadInt32(); if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) @@ -1730,9 +1460,7 @@ 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 ) { @@ -1742,12 +1470,16 @@ void Document::FindDocEntryLength( DocEntry *entry ) // 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 = Fp->tellg() - currentPosition; - Fp->seekg(currentPosition, std::ios_base::beg); + 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; } @@ -1757,6 +1489,14 @@ 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 @@ -1777,6 +1517,8 @@ 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 @@ -1785,37 +1527,39 @@ 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(); - // 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 ( 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 = GetDictEntry( 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 ); +// } + + // 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 ); @@ -1829,6 +1573,9 @@ void Document::FindDocEntryLength( DocEntry *entry ) // 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. + + // Well ... group 0002 is always coded in 'Explicit VR Litle Endian' + // even if Transfer Syntax is 'Implicit VR ...' FixDocEntryFoundLength( entry, ReadInt32() ); return; @@ -1837,16 +1584,12 @@ 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 @@ -1856,105 +1599,34 @@ 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_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(); + Fp->seekg(positionOnEntry, std::ios::beg); + 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(vr[0]) && !isalpha(vr[1]) ) - { - realExplicit = false; - } - // CLEANME searching the dicom_vr at each occurence is expensive. // PostPone this test in an optional integrity check at the end // of parsing or only in debug mode. - if ( realExplicit && !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; } @@ -2042,7 +1714,7 @@ 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() ) { @@ -2103,12 +1775,13 @@ 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_base::beg); - Fp->seekg( (long)(entry->GetReadLength()), std::ios_base::cur); + Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg); + if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb + Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur); } /** @@ -2116,7 +1789,7 @@ 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) @@ -2127,30 +1800,25 @@ 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 !? @@ -2161,9 +1829,7 @@ 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 !? @@ -2177,7 +1843,7 @@ 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 @@ -2188,7 +1854,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, } } - entry->SetUsableLength(foundLength); + entry->SetLength(foundLength); } /** @@ -2199,15 +1865,15 @@ 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 ) { @@ -2222,21 +1888,18 @@ 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; } @@ -2246,7 +1909,7 @@ 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. @@ -2265,8 +1928,8 @@ 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 @@ -2274,12 +1937,13 @@ 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."); - Fp->seekg(positionOnEntry, std::ios_base::beg); - throw FormatUnexpected("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( "Neither an Item tag nor a Sequence delimiter tag."); } if ( elem == 0xe0dd ) @@ -2297,7 +1961,7 @@ uint32_t Document::FindDocEntryLengthOB() break; } } - Fp->seekg( positionOnEntry, std::ios_base::beg); + Fp->seekg( positionOnEntry, std::ios::beg); return totalLength; } @@ -2353,19 +2017,20 @@ uint32_t Document::ReadInt32() void Document::SkipBytes(uint32_t nBytes) { //FIXME don't dump the returned value - Fp->seekg((long)nBytes, std::ios_base::cur); + Fp->seekg((long)nBytes, std::ios::cur); } /** * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ -void Document::Initialise() +void Document::Initialize() { RefPubDict = Global::GetDicts()->GetDefaultPubDict(); RefShaDict = NULL; RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; + Filetype = Unknown; } /** @@ -2388,7 +2053,7 @@ bool Document::CheckSwap() uint32_t s32; uint16_t s16; - char deb[256]; //HEADER_LENGTH_TO_READ]; + char deb[256]; // First, compare HostByteOrder and NetworkByteOrder in order to // determine if we shall need to swap bytes (i.e. the Endian type). @@ -2401,25 +2066,24 @@ 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". - Fp->read(deb, HEADER_LENGTH_TO_READ); + // 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, @@ -2427,56 +2091,52 @@ 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). - Fp->seekg(0, std::ios_base::beg); - Fp->seekg ( 132L, std::ios_base::beg); + // 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; } // 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); + 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. // By clean we mean that the length of the first tag is written down. @@ -2488,7 +2148,7 @@ bool Document::CheckSwap() // representation of a 32 bits integer. Hence the following dirty // trick : s32 = *((uint32_t *)(entCur)); - + switch( s32 ) { case 0x00040000 : @@ -2504,7 +2164,7 @@ bool Document::CheckSwap() Filetype = ACR; return true; case 0x00000004 : - SwapCode = 0; + SwapCode = 1234; Filetype = ACR; return true; default : @@ -2513,13 +2173,13 @@ bool Document::CheckSwap() // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA, // i.e. the 'group length' element is not present : - // check the supposed to be 'group number' - // 0x0002 or 0x0004 or 0x0008 + // 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 -4, 8-) + // 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... @@ -2527,48 +2187,49 @@ bool Document::CheckSwap() switch ( s16 ) { + case 0x0001 : case 0x0002 : + case 0x0003 : case 0x0004 : - case 0x0008 : - SwapCode = 0; + case 0x0005 : + case 0x0006 : + case 0x0007 : + case 0x0008 : + SwapCode = 1234; Filetype = ACR; return true; + case 0x0100 : case 0x0200 : + case 0x0300 : case 0x0400 : - case 0x0800 : + 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; + 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 ) { @@ -2606,7 +2267,6 @@ void Document::SetMaxSizeLoadEntry(long newSize) */ void Document::SetMaxSizePrintEntry(long newSize) { - //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME if ( newSize < 0 ) { return; @@ -2621,14 +2281,111 @@ void Document::SetMaxSizePrintEntry(long 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++; + SwitchByteSwapCode(); + // fix the tag + group = 0xfffe; + elem = 0xe000; + } + else if (group == 0xfffe && elem == 0xe00d && reversedEndian) + { + // end of reversed endian group + reversedEndian--; + SwitchByteSwapCode(); + } +} + +/** + * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS + * @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; + } + + // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..." + + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian ) + { + Filetype = ImplicitVR; + } + + // 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; @@ -2646,8 +2403,47 @@ DocEntry* Document::ReadNextDocEntry() return 0; } - DocEntry *newEntry = NewDocEntryByNumber(group, elem); - FindDocEntryVR(newEntry); + // Sometimes file contains groups of tags with reversed endianess. + HandleBrokenEndian(group, elem); + +// 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. + if ( newEntry->GetGroup() != 0xfffe ) + { + std::string msg; + msg = Util::Format("Entry (%04x,%04x) should be Explicit VR\n", + newEntry->GetGroup(), newEntry->GetElement()); + gdcmVerboseMacro( msg.c_str() ); + } + } + newEntry->SetImplicitVR(); + } try { @@ -2666,25 +2462,25 @@ DocEntry* Document::ReadNextDocEntry() return newEntry; } - +//GenerateFreeTagKeyInGroup? What was it designed for ?!? /** * \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; -} +//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 @@ -2720,16 +2516,14 @@ 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()); - Fp->seekg(positionOnEntry, std::ios_base::beg); + 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; } @@ -2752,8 +2546,6 @@ bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) */ uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement) { - long positionOnEntry = Fp->tellg(); - (void)positionOnEntry; if ( !ReadTag(testGroup, testElement) ) { @@ -2764,11 +2556,9 @@ 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; } @@ -2790,7 +2580,7 @@ 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 @@ -2798,12 +2588,8 @@ 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 @@ -2818,8 +2604,8 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() */ void Document::ComputeRLEInfo() { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts != RLELossless ) + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsRLELossless(ts) ) { return; } @@ -2860,10 +2646,10 @@ 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[15]; + uint32_t rleSegmentOffsetTable[16]; for( int k = 1; k <= 15; k++ ) { rleSegmentOffsetTable[k] = ReadInt32(); @@ -2889,7 +2675,7 @@ 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++ ) { @@ -2903,8 +2689,7 @@ 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"); } } @@ -2917,7 +2702,8 @@ 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; } @@ -2932,7 +2718,7 @@ 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 ); @@ -2944,12 +2730,11 @@ 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"); } } -/** +/* * \brief Walk recursively the given \ref DocEntrySet, and feed * the given hash table (\ref TagDocEntryHT) with all the * \ref DocEntry (Dicom entries) encountered. @@ -2958,18 +2743,18 @@ 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(); @@ -2985,15 +2770,15 @@ 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(); @@ -3008,14 +2793,14 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, } } -} +}*/ -/** +/* * \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 old the parsed entries of a Dicom header, is a recursive + * 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 @@ -3033,12 +2818,12 @@ 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; -} +}*/ @@ -3052,8 +2837,8 @@ 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; @@ -3065,8 +2850,8 @@ 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; @@ -3078,8 +2863,8 @@ 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; @@ -3091,8 +2876,8 @@ 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; @@ -3107,6 +2892,49 @@ 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 = GetFirstEntry(); + 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 //-----------------------------------------------------------------------------