X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=9c12f0ce8a8aa4f97e5210cd1c9dfec6311580ac;hb=25c9af365d9221bd45f3fbe27275ff0f66a265b1;hp=f1322ac53c5c0966d8d179b82eeff6ac9fe7dccc;hpb=251590eb8bbe0635858d05909052d11c6a7ba490;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index f1322ac5..9c12f0ce 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2005/01/06 13:35:38 $ - Version: $Revision: 1.155 $ + Date: $Date: 2005/02/07 09:51:03 $ + Version: $Revision: 1.225 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -24,61 +24,25 @@ #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 +#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", - // Implicit VR Little Endian DLX G.E? - "1.2.840.113619.5.2", - // Explicit VR Little Endian - "1.2.840.10008.1.2.1", - // Deflated Explicit VR Little Endian - "1.2.840.10008.1.2.1.99", - // Explicit VR Big Endian - "1.2.840.10008.1.2.2", - // JPEG Baseline (Process 1) - "1.2.840.10008.1.2.4.50", - // JPEG Extended (Process 2 & 4) - "1.2.840.10008.1.2.4.51", - // JPEG Extended (Process 3 & 5) - "1.2.840.10008.1.2.4.52", - // JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8) - "1.2.840.10008.1.2.4.53", - // JPEG Full Progression, Non-Hierarchical (Process 10 & 12) - "1.2.840.10008.1.2.4.55", - // JPEG Lossless, Non-Hierarchical (Process 14) - "1.2.840.10008.1.2.4.57", - // JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, [Selection Value 1]) - "1.2.840.10008.1.2.4.70", - // JPEG 2000 Lossless - "1.2.840.10008.1.2.4.90", - // JPEG 2000 - "1.2.840.10008.1.2.4.91", - // RLE Lossless - "1.2.840.10008.1.2.5", - // Unknown - "Unknown Transfer Syntax" -}; - //----------------------------------------------------------------------------- // Refer to Document::CheckSwap() //const unsigned int Document::HEADER_LENGTH_TO_READ = 256; @@ -89,16 +53,17 @@ const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; //----------------------------------------------------------------------------- // Constructor / Destructor - +// Constructors and destructors are protected to avoid user to invoke directly /** * \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) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; - Initialise(); + Initialize(); Fp = 0; if ( !OpenFile() ) @@ -106,39 +71,41 @@ Document::Document( std::string const & filename ) : ElementSet(-1) return; } - dbg.Verbose(0, "Document::Document: starting parsing of file: ", - Filename.c_str()); - Fp->seekg( 0, std::ios::beg); + Group0002Parsed = false; + + gdcmWarningMacro( "Starting parsing of file: " << Filename.c_str()); + // Fp->seekg( 0, std::ios::beg); - Fp->seekg(0, std::ios::end); + Fp->seekg(0, std::ios::end); long lgt = Fp->tellg(); - Fp->seekg( 0, std::ios::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::beg); // Load 'non string' values - std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + std::string PhotometricInterpretation = GetEntryValue(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 @@ -159,7 +126,7 @@ Document::Document( std::string const & filename ) : ElementSet(-1) CloseFile(); - // -------------------------------------------------------------- + // ---------------------------- // Specific code to allow gdcm to read ACR-LibIDO formated images // Note: ACR-LibIDO is an extension of the ACR standard that was // used at CREATIS. For the time being (say a couple years) @@ -170,32 +137,34 @@ Document::Document( std::string const & filename ) : ElementSet(-1) // we switch lineNumber and columnNumber // std::string RecCode; - RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code + RecCode = GetEntryValue(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 = GetEntryValue(0x0028, 0x0010); + std::string columns = GetEntryValue(0x0028, 0x0011); + SetValEntry(columns, 0x0028, 0x0010); + SetValEntry(rows , 0x0028, 0x0011); } - // ----------------- End of ACR-LibIDO kludge ------------------ + // --- End of ACR-LibIDO kludge --- } /** * \brief This default constructor doesn't parse the file. You should * then invoke \ref Document::SetFileName and then the parsing. */ -Document::Document() : ElementSet(-1) +Document::Document() + :ElementSet(-1) { Fp = 0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - Initialise(); - SwapCode = 0; + Initialize(); + SwapCode = 1234; Filetype = ExplicitVR; + Group0002Parsed = false; } /** @@ -205,32 +174,6 @@ Document::~Document () { RefPubDict = NULL; RefShaDict = NULL; - - delete RLEInfo; - delete JPEGInfo; -} - -//----------------------------------------------------------------------------- -// Print - -/** - * \brief Prints The Dict Entries of THE public Dicom Dictionary - * @return - */ -void Document::PrintPubDict(std::ostream & os) -{ - RefPubDict->SetPrintLevel(PrintLevel); - RefPubDict->Print(os); -} - -/** - * \brief Prints The Dict Entries of THE shadow Dicom Dictionary - * @return - */ -void Document::PrintShaDict(std::ostream & os) -{ - RefShaDict->SetPrintLevel(PrintLevel); - RefShaDict->Print(os); } //----------------------------------------------------------------------------- @@ -238,7 +181,7 @@ void Document::PrintShaDict(std::ostream & os) /** * \brief Get the public dictionary used */ -Dict* Document::GetPubDict() +Dict *Document::GetPubDict() { return RefPubDict; } @@ -246,14 +189,14 @@ 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) { @@ -263,9 +206,9 @@ 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; @@ -283,38 +226,77 @@ bool Document::IsReadable() { if( Filetype == Unknown) { - dbg.Verbose(0, "Document::IsReadable: wrong filetype"); + gdcmWarningMacro( "Wrong filetype"); return false; } - if( TagHT.empty() ) - { - dbg.Verbose(0, "Document::IsReadable: no tags in internal" - " hash table."); + if ( IsEmpty() ) + { + gdcmWarningMacro( "No tag in internal hash table."); return false; } return true; } +/** + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. + */ +bool Document::IsDicomV3() +{ + // 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 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; +} + +/** + * \brief returns the File Type + * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) + * @return the FileType code + */ +FileType Document::GetFileType() +{ + return Filetype; +} + /** * \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 @@ -323,100 +305,97 @@ TransferSyntaxType Document::GetTransferSyntax() if ( transfer.length() == 0 ) { // for brain damaged headers - return UnknownTS; + return GDCM_UNKNOWN; } while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { transfer.erase(transfer.length()-1, 1); } - for (int i = 0; TransferSyntaxStrings[i] != NULL; i++) - { - if ( TransferSyntaxStrings[i] == transfer ) - { - return TransferSyntaxType(i); - } - } + return transfer; } - return UnknownTS; + return GDCM_UNKNOWN; } -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. + * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS + * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID) */ -bool Document::IsJPEG2000() +std::string Document::GetTransferSyntaxName() { - TransferSyntaxType r = GetTransferSyntax(); - return r == JPEG2000Lossless || r == JPEG2000; -} + // use the TS (TS : Transfer Syntax) + std::string transferSyntax = GetEntryValue(0x0002,0x0010); -/** - * \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(); -} + 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 ) + { + gdcmWarningMacro( "Unfound Transfer Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; + } -/** - * \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; -} + // 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; +} +// +// --------------- Swap Code ------------------ /** - * \brief Predicate for dicom version 3 file. - * @return True when the file is a dicom version 3. + * \brief Swaps the bytes so they agree with the processor order + * @return The properly swaped 16 bits integer. */ -bool Document::IsDicomV3() +uint16_t Document::SwapShort(uint16_t a) { - // Checking if Transfert Syntax exists is enough - // Anyway, it's to late check if the 'Preamble' was found ... - // And ... would it be a rich idea to check ? - // (some 'no Preamble' DICOM images exist !) - return GetDocEntryByNumber(0x0002, 0x0010) != NULL; + if ( SwapCode == 4321 || SwapCode == 2143 ) + { + a = ((( a << 8 ) & 0xff00 ) | (( a >> 8 ) & 0x00ff ) ); + } + return a; } /** - * \brief returns the File Type - * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) - * @return the FileType code + * \brief Swaps back the bytes of 4-byte long integer accordingly to + * processor order. + * @return The properly swaped 32 bits integer. */ -FileType Document::GetFileType() +uint32_t Document::SwapLong(uint32_t a) { - return Filetype; -} + switch (SwapCode) + { + case 1234 : + break; + case 4321 : + a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | + ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) ); + break; + case 3412 : + a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) ); + break; + case 2143 : + a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); + break; + default : + gdcmErrorMacro( "Unset swap code:" << SwapCode ); + a = 0; + } + return a; +} +// +// -----------------File I/O --------------- /** * \brief Tries to open the file \ref Document::Filename and * checks the preamble when existing. * @return The FILE pointer on success. */ -std::ifstream* Document::OpenFile() +std::ifstream *Document::OpenFile() { + HasDCMPreamble = false; if (Filename.length() == 0) { return 0; @@ -424,23 +403,20 @@ std::ifstream* Document::OpenFile() if(Fp) { - dbg.Verbose( 0, - "Document::OpenFile is already opened when opening: ", - Filename.c_str()); + gdcmWarningMacro( "File already open: " << Filename.c_str()); + CloseFile(); } 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; + uint16_t zero = 0; Fp->read((char*)&zero, (size_t)2); if( Fp->eof() ) { @@ -455,12 +431,15 @@ std::ifstream* Document::OpenFile() zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 || zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ) { + std::string msg + = Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero); + gdcmWarningMacro( msg.c_str() ); return Fp; } //DICOM Fp->seekg(126L, std::ios::cur); - char dicm[4]; + char dicm[4] = {' ',' ',' ',' '}; Fp->read(dicm, (size_t)4); if( Fp->eof() ) { @@ -469,13 +448,12 @@ std::ifstream* Document::OpenFile() } if( memcmp(dicm, "DICM", 4) == 0 ) { + HasDCMPreamble = true; return Fp; } CloseFile(); - dbg.Verbose( 0, - "Document::OpenFile not DICOM/ACR (missing preamble)", - Filename.c_str()); + gdcmWarningMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str()); return 0; } @@ -492,23 +470,23 @@ bool Document::CloseFile() 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. + * @return Always true. */ -void Document::WriteContent(std::ofstream* fp, FileType filetype) +void Document::WriteContent(std::ofstream *fp, FileType filetype) { - /// \todo move the following lines (and a lot of others, to be written) - /// to a future function CheckAndCorrectHeader - /// (necessary if user wants to write a DICOM V3 file - /// starting from an ACR-NEMA (V2) Header + // \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 || filetype == ExplicitVR ) { @@ -519,700 +497,278 @@ void Document::WriteContent(std::ofstream* fp, FileType filetype) fp->write("DICM", 4); } -/** - * \todo rewrite later, if really usefull - * - 'Group Length' element is optional in DICOM - * - but un-updated odd groups lengthes can causes pb - * (xmedcon breaker) - * - * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) ) - * UpdateGroupLength(false,filetype); - * if ( filetype == ACR) - * UpdateGroupLength(true,ACR); - */ - + /* + * \todo rewrite later, if really usefull + * - 'Group Length' element is optional in DICOM + * - but un-updated odd groups lengthes can causes pb + * (xmedcon breaker) + * + * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) ) + * UpdateGroupLength(false,filetype); + * if ( filetype == ACR) + * UpdateGroupLength(true,ACR); + */ + ElementSet::WriteContent(fp, filetype); // This one is recursive } +// ----------------------------------------- +// Content entries /** - * \brief Modifies the value of a given Header Entry (Dicom Element) - * when it exists. Create it with the given value when unexistant. - * @param value (string) Value to be set - * @param group Group number of the Entry - * @param elem Element number of the Entry - * @param vr V(alue) R(epresentation) of the Entry -if private Entry- - * \return pointer to the modified/created Header Entry (NULL when creation - * failed). - */ -ValEntry* Document::ReplaceOrCreateByNumber( - std::string const & value, - uint16_t group, - uint16_t elem, - TagName const & vr ) + * \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) { - ValEntry* valEntry = 0; - DocEntry* currentEntry = GetDocEntryByNumber( group, elem); - - if (!currentEntry) - { - // check if (group,element) DictEntry exists - // if it doesn't, create an entry in DictSet::VirtualEntry - // and use it - - // Find out if the tag we received is in the dictionaries: - Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); - DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); - if (!dictEntry) - { - currentEntry = NewDocEntryByNumber(group, elem, vr); - } - else - { - currentEntry = NewDocEntryByNumber(group, elem); - } - - if (!currentEntry) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; - } - - valEntry = new ValEntry(currentEntry); - delete currentEntry; - - if ( !AddEntry(valEntry)) - { - delete valEntry; - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); - return NULL; - } - } - else - { - valEntry = dynamic_cast< ValEntry* >(currentEntry); - if ( !valEntry ) // Euuuuh? It wasn't a ValEntry - // then we change it to a ValEntry ? - // Shouldn't it be considered as an error ? - { - // We need to promote the DocEntry to a ValEntry: - valEntry = new ValEntry(currentEntry); - if (!RemoveEntry(currentEntry)) - { - delete valEntry; - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); - return NULL; - } - if ( !AddEntry(valEntry)) - { - delete valEntry; - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" - " promoted ValEntry failed."); - return NULL; - } - } - } + // Search the corresponding DocEntry + DocEntry *docElement = GetDocEntry(group, elem); + if ( !docElement ) + return; - SetEntryByNumber(value, group, elem); + BinEntry *binElement = dynamic_cast(docElement); + if( !binElement ) + return; - return valEntry; -} + LoadEntryBinArea(binElement); +} -/* - * \brief Modifies the value of a given Header Entry (Dicom Element) - * when it exists. Create it with the given value when unexistant. - * A copy of the binArea is made to be kept in the Document. - * @param binArea (binary) value to be set - * @param Group Group number of the Entry - * @param Elem Element number of the Entry - * \return pointer to the modified/created Header Entry (NULL when creation - * failed). +/** + * \brief Loads (from disk) the element content + * when a string is not suitable + * @param elem Entry whose binArea is going to be loaded */ -BinEntry* Document::ReplaceOrCreateByNumber( - uint8_t* binArea, - int lgth, - uint16_t group, - uint16_t elem, - TagName const & vr ) +void Document::LoadEntryBinArea(BinEntry *elem) { - BinEntry* binEntry = 0; - DocEntry* currentEntry = GetDocEntryByNumber( group, elem); - if (!currentEntry) - { + if(elem->GetBinArea()) + return; - // check if (group,element) DictEntry exists - // if it doesn't, create an entry in DictSet::VirtualEntry - // and use it + bool openFile = !Fp; + if(openFile) + OpenFile(); - // Find out if the tag we received is in the dictionaries: - Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); - DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem); + size_t o =(size_t)elem->GetOffset(); + Fp->seekg(o, std::ios::beg); - if (!dictEntry) - { - currentEntry = NewDocEntryByNumber(group, elem, vr); - } - else - { - currentEntry = NewDocEntryByNumber(group, elem); - } - if (!currentEntry) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; - } - binEntry = new BinEntry(currentEntry); - if ( !AddEntry(binEntry)) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); - } - delete currentEntry; - } - else + size_t l = elem->GetLength(); + uint8_t *a = new uint8_t[l]; + if( !a ) { - binEntry = dynamic_cast< BinEntry* >(currentEntry); - if ( !binEntry ) // Euuuuh? It wasn't a BinEntry - // then we change it to a BinEntry ? - // Shouldn't it be considered as an error ? - { - // We need to promote the DocEntry to a BinEntry: - binEntry = new BinEntry(currentEntry); - if (!RemoveEntry(currentEntry)) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); - return NULL; - } - if ( !AddEntry(binEntry)) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" - " promoted BinEntry failed."); - return NULL; - } - } + gdcmWarningMacro( "Cannot allocate BinEntry content"); + return; } - uint8_t *tmpArea; - if (lgth>0 && binArea) - { - tmpArea = new uint8_t[lgth]; - memcpy(tmpArea,binArea,lgth); - } - else - { - tmpArea = 0; - } - if (!SetEntryByNumber(tmpArea, lgth, group, elem)) + /// \todo check the result + Fp->read((char*)a, l); + if( Fp->fail() || Fp->eof()) { - if (tmpArea) - { - delete[] tmpArea; - } + delete[] a; + return; } - return binEntry; -} - - -/* - * \brief Modifies the value of a given Header Entry (Dicom Element) - * when it exists. Create it when unexistant. - * @param Group Group number of the Entry - * @param Elem Element number of the Entry - * \return pointer to the modified/created SeqEntry (NULL when creation - * failed). - */ -SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) -{ - SeqEntry* b = 0; - DocEntry* a = GetDocEntryByNumber( group, elem); - if (!a) - { - a = NewSeqEntryByNumber(group, elem); - if (!a) - { - return 0; - } - - b = new SeqEntry(a, 1); // FIXME : 1 (Depth) - AddEntry(b); - } - return b; -} - -/** - * \brief Set a new value if the invoked element exists - * Seems to be useless !!! - * @param value new element value - * @param group group number of the Entry - * @param elem element number of the Entry - * \return boolean - */ -bool Document::ReplaceIfExistByNumber(std::string const & value, - uint16_t group, uint16_t elem ) -{ - SetEntryByNumber(value, group, elem); - - return true; -} - -std::string Document::GetTransferSyntaxValue(TransferSyntaxType type) -{ - return TransferSyntaxStrings[type]; -} - -//----------------------------------------------------------------------------- -// Protected + elem->SetBinArea(a); -/** - * \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; + if(openFile) + CloseFile(); } /** - * \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. + * \brief Loads the element while preserving the current + * underlying file position indicator as opposed to + * LoadDocEntry that modifies it. + * @param entry DocEntry whose value will be loaded. */ -std::string Document::GetEntryByName(TagName const & tagName) +void Document::LoadDocEntrySafe(DocEntry *entry) { - DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) + if(Fp) { - return GDCM_UNFOUND; + long PositionOnEntry = Fp->tellg(); + LoadDocEntry(entry); + Fp->seekg(PositionOnEntry, std::ios::beg); } - - 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. + * \brief Compares two documents, according to \ref DicomDir rules + * \warning Does NOT work with ACR-NEMA files + * \todo Find a trick to solve the pb (use RET fields ?) + * @param document to compare with current one + * @return true if 'smaller' */ -std::string Document::GetEntryVRByName(TagName const& tagName) +bool Document::operator<(Document &document) { - DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) + // Patient Name + std::string s1 = GetEntryValue(0x0010,0x0010); + std::string s2 = document.GetEntryValue(0x0010,0x0010); + if(s1 < s2) { - return GDCM_UNFOUND; + return true; } - - 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); - if ( !TagHT.count(key)) + else if( s1 > s2 ) { - return GDCM_UNFOUND; + return false; } - - return ((ValEntry *)TagHT.find(key)->second)->GetValue(); -} - -/** - * \brief Searches within Header Entries (Dicom Elements) parsed with - * the public and private dictionaries - * for the element value representation of a given tag.. - * - * Obtaining the VR (Value Representation) might be needed by caller - * to convert the string typed content to caller's native type - * (think of C++ vs Python). The VR is actually of a higher level - * of semantics than just the native C++ type. - * @param group Group number of the searched tag. - * @param element Element number of the searched tag. - * @return Corresponding element value representation when it exists, - * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. - */ -std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element) -{ - DocEntry* elem = GetDocEntryByNumber(group, element); - if ( !elem ) + else { - return GDCM_UNFOUND; - } - return elem->GetVR(); -} - -/** - * \brief Searches within Header Entries (Dicom Elements) parsed with - * the public and private dictionaries - * for the value length of a given tag.. - * @param group Group number of the searched tag. - * @param element Element number of the searched tag. - * @return Corresponding element length; -2 if not found - */ -int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element) -{ - DocEntry* elem = GetDocEntryByNumber(group, element); - if ( !elem ) - { - return -2; //magic number - } - return elem->GetLength(); -} -/** - * \brief Sets the value (string) of the Header Entry (Dicom Element) - * @param content string value of the Dicom Element - * @param tagName name of the searched Dicom Element. - * @return true when found - */ -bool Document::SetEntryByName( std::string const & content, - TagName const & tagName) -{ - DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) - { - return false; - } - - return SetEntryByNumber(content,dictEntry->GetGroup(), - dictEntry->GetElement()); -} - -/** - * \brief Accesses an existing DocEntry (i.e. a Dicom Element) - * through it's (group, element) and modifies it's content with - * the given value. - * @param content new value (string) to substitute with - * @param group group number of the Dicom Element to modify - * @param element element number of the Dicom Element to modify - */ -bool Document::SetEntryByNumber(std::string const& content, - uint16_t group, uint16_t element) -{ - ValEntry* valEntry = GetValEntryByNumber(group, element); - if (!valEntry ) - { - dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding", - " ValEntry (try promotion first)."); - return false; - } - // Non even content must be padded with a space (020H)... - valEntry->SetValue(content); - return true; -} - -/** - * \brief Accesses an existing DocEntry (i.e. a Dicom Element) - * through it's (group, element) and modifies it's content with - * the given value. - * @param content new value (void* -> uint8_t*) to substitute with - * @param lgth new value length - * @param group group number of the Dicom Element to modify - * @param element element number of the Dicom Element to modify - */ -bool Document::SetEntryByNumber(uint8_t*content, int lgth, - uint16_t group, uint16_t element) -{ - (void)lgth; //not used - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key)) - { - return false; - } - -/* Hope Binary field length is *never* wrong - if(lgth%2) // Non even length are padded with a space (020H). - { - lgth++; - //content = content + '\0'; // fing a trick to enlarge a binary field? - } -*/ - BinEntry* entry = (BinEntry *)TagHT[key]; - entry->SetBinArea(content); - entry->SetLength(lgth); - entry->SetValue(GDCM_BINLOADED); - - return true; -} - -/** - * \brief Gets (from Header) a 'non string' element value - * (LoadElementValues has already be executed) - * @param group group number of the Entry - * @param elem element number of the Entry - * @return Pointer to the 'non string' area - */ -void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) -{ - DocEntry* entry = GetDocEntryByNumber(group, elem); - if (!entry) - { - dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry"); - return 0; - } - if ( BinEntry* binEntry = dynamic_cast(entry) ) - { - return binEntry->GetBinArea(); + // Patient ID + s1 = GetEntryValue(0x0010,0x0020); + s2 = document.GetEntryValue(0x0010,0x0020); + if ( s1 < s2 ) + { + return true; + } + else if ( s1 > s2 ) + { + return false; + } + else + { + // Study Instance UID + s1 = GetEntryValue(0x0020,0x000d); + s2 = document.GetEntryValue(0x0020,0x000d); + if ( s1 < s2 ) + { + return true; + } + else if( s1 > s2 ) + { + return false; + } + else + { + // Serie Instance UID + s1 = GetEntryValue(0x0020,0x000e); + s2 = document.GetEntryValue(0x0020,0x000e); + if ( s1 < s2 ) + { + return true; + } + else if( s1 > s2 ) + { + return false; + } + } + } } - - return 0; -} - -/** - * \brief Loads (from disk) the element content - * when a string is not suitable - * @param group group number of the Entry - * @param elem element number of the Entry - */ -void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) -{ - // Search the corresponding DocEntry - DocEntry *docElement = GetDocEntryByNumber(group, elem); - if ( !docElement ) - return; - - BinEntry *binElement = dynamic_cast(docElement); - if( !binElement ) - return; - - LoadEntryBinArea(binElement); + return false; } +//----------------------------------------------------------------------------- +// Protected /** - * \brief Loads (from disk) the element content - * when a string is not suitable - * @param element Entry whose binArea is going to be loaded + * \brief Reads a supposed to be 16 Bits integer + * (swaps it depending on processor endianness) + * @return read value */ -void Document::LoadEntryBinArea(BinEntry* element) +uint16_t Document::ReadInt16() + throw( FormatError ) { - if(element->GetBinArea()) - return; - - bool openFile = !Fp; - if(openFile) - OpenFile(); - - size_t o =(size_t)element->GetOffset(); - Fp->seekg(o, std::ios::beg); - - size_t l = element->GetLength(); - uint8_t* a = new uint8_t[l]; - if( !a ) + uint16_t g; + Fp->read ((char*)&g, (size_t)2); + if ( Fp->fail() ) { - dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); - return; + throw FormatError( "Document::ReadInt16()", " file error." ); } - - /// \todo check the result - Fp->read((char*)a, l); - if( Fp->fail() || Fp->eof()) //Fp->gcount() == 1 + if( Fp->eof() ) { - delete[] a; - return; + throw FormatError( "Document::ReadInt16()", "EOF." ); } - - element->SetBinArea(a); - - if(openFile) - CloseFile(); + g = SwapShort(g); + return g; } /** - * \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 + * \brief Reads a supposed to be 32 Bits integer + * (swaps it depending on processor endianness) + * @return read value */ -/*bool Document::SetEntryBinAreaByNumber(uint8_t* area, - uint16_t group, uint16_t element) +uint32_t Document::ReadInt32() + throw( FormatError ) { - DocEntry* currentEntry = GetDocEntryByNumber(group, element); - if ( !currentEntry ) - { - return false; - } - - if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) + uint32_t g; + Fp->read ((char*)&g, (size_t)4); + if ( Fp->fail() ) { - binEntry->SetBinArea( area ); - return true; + throw FormatError( "Document::ReadInt32()", " file error." ); } - - return false; -}*/ - -/** - * \brief Searches within the Header Entries for a Dicom Element of - * a given tag. - * @param tagName name of the searched Dicom Element. - * @return Corresponding Dicom Element when it exists, and NULL - * otherwise. - */ -DocEntry* Document::GetDocEntryByName(TagName const & tagName) -{ - DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( !dictEntry ) + if( Fp->eof() ) { - return NULL; + throw FormatError( "Document::ReadInt32()", "EOF." ); } - - return GetDocEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); + g = SwapLong(g); + return g; } /** - * \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 + * \brief skips bytes inside the source file + * \warning NOT end user intended method ! + * @return */ -DocEntry* Document::GetDocEntryByNumber(uint16_t group, uint16_t element) +void Document::SkipBytes(uint32_t nBytes) { - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key)) - { - return NULL; - } - return TagHT.find(key)->second; + //FIXME don't dump the returned value + Fp->seekg((long)nBytes, std::ios::cur); } /** - * \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 Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader + * @param filetype Type of the File to be written */ -ValEntry* Document::GetValEntryByNumber(uint16_t group, uint16_t element) +int Document::ComputeGroup0002Length( FileType filetype ) { - DocEntry* currentEntry = GetDocEntryByNumber(group, element); - if ( !currentEntry ) - { - return 0; - } - if ( ValEntry* valEntry = dynamic_cast(currentEntry) ) + uint16_t gr; + std::string vr; + + int groupLength = 0; + bool found0002 = false; + + // for each zero-level Tag in the DCM Header + DocEntry *entry = GetFirstEntry(); + while( entry ) { - return valEntry; - } - dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry."); - - return 0; -} + gr = entry->GetGroup(); -/** - * \brief Loads the element while preserving the current - * underlying file position indicator as opposed to - * to LoadDocEntry that modifies it. - * @param entry Header Entry whose value shall be loaded. - * @return - */ -void Document::LoadDocEntrySafe(DocEntry * entry) -{ - if(Fp) - { - long PositionOnEntry = Fp->tellg(); - LoadDocEntry(entry); - Fp->seekg(PositionOnEntry, std::ios::beg); - } -} + if( gr == 0x0002 ) + { + found0002 = true; -/** - * \brief Swaps back the bytes of 4-byte long integer accordingly to - * processor order. - * @return The properly swaped 32 bits integer. - */ -uint32_t Document::SwapLong(uint32_t a) -{ - switch (SwapCode) - { - case 0 : - break; - case 4321 : - a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | - ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) ); - break; - - case 3412 : - a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) ); - break; - - case 2143 : - a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); + if( entry->GetElement() != 0x0000 ) + { + vr = entry->GetVR(); + + if( filetype == ExplicitVR ) + { + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) + { + // explicit VR AND OB, OW, SQ : 4 more bytes + groupLength += 4; + } + } + groupLength += 2 + 2 + 4 + entry->GetLength(); + } + } + else if (found0002 ) break; - default : - //std::cout << "swapCode= " << SwapCode << std::endl; - dbg.Error(" Document::SwapLong : unset swap code"); - a = 0; - } - return a; -} - -/** - * \brief Unswaps back the bytes of 4-byte long integer accordingly to - * processor order. - * @return The properly unswaped 32 bits integer. - */ -uint32_t Document::UnswapLong(uint32_t a) -{ - return SwapLong(a); -} -/** - * \brief Swaps the bytes so they agree with the processor order - * @return The properly swaped 16 bits integer. - */ -uint16_t Document::SwapShort(uint16_t a) -{ - if ( SwapCode == 4321 || SwapCode == 2143 ) - { - a = ((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) ); + entry = GetNextEntry(); } - return a; + return groupLength; } +//----------------------------------------------------------------------------- +// Private /** - * \brief Unswaps the bytes so they agree with the processor order - * @return The properly unswaped 16 bits integer. + * \brief Loads all the needed Dictionaries + * \warning NOT end user intended method ! */ -uint16_t Document::UnswapShort(uint16_t a) +void Document::Initialize() { - return SwapShort(a); + RefPubDict = Global::GetDicts()->GetDefaultPubDict(); + RefShaDict = NULL; + Filetype = Unknown; } -//----------------------------------------------------------------------------- -// Private - /** * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) * @return length of the parsed set. @@ -1221,6 +777,11 @@ void Document::ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode) { DocEntry *newDocEntry = 0; + ValEntry *newValEntry; + BinEntry *newBinEntry; + SeqEntry *newSeqEntry; + VRKey vr; + bool used = false; while (true) { @@ -1228,34 +789,71 @@ void Document::ParseDES(DocEntrySet *set, long offset, { break; } + + used = true; newDocEntry = ReadNextDocEntry( ); + if ( !newDocEntry ) { break; } - VRKey vr = newDocEntry->GetVR(); - if ( vr != "SQ" ) - { - - if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) ) + vr = newDocEntry->GetVR(); + newValEntry = dynamic_cast(newDocEntry); + newBinEntry = dynamic_cast(newDocEntry); + newSeqEntry = dynamic_cast(newDocEntry); + + if ( newValEntry || newBinEntry ) + { + if ( newBinEntry ) + { + if ( Filetype == ExplicitVR && + !Global::GetVR()->IsVROfBinaryRepresentable(vr) ) + { + ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR + gdcmWarningMacro( 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() ); //LEAK - newValEntry->Copy( newDocEntry ); - // When "set" is a Document, then we are at the top of the // hierarchy and the Key is simply of the form ( group, elem )... - if (Document* dummy = dynamic_cast< Document* > ( set ) ) + if ( 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() ); @@ -1266,79 +864,26 @@ void Document::ParseDES(DocEntrySet *set, long offset, if( !set->AddEntry( newValEntry ) ) { // If here expect big troubles - delete newValEntry; //otherwise mem leak + //delete newValEntry; //otherwise mem leak + used=false; } if (delimitor) { - delete newDocEntry; + if(!used) + delete newDocEntry; break; } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - delete newDocEntry; + if(!used) + delete newDocEntry; break; } } - else - { - if ( ! Global::GetVR()->IsVROfGdcmBinaryRepresentable(vr) ) - { - ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR - dbg.Verbose(0, "Document::ParseDES: neither Valentry, " - "nor BinEntry. Probably unknown VR."); - } - - //////////////////// BinEntry or UNKOWN VR: - BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK - - // When "this" is a Document the Key is simply of the - // form ( group, elem )... - if (Document* dummy = dynamic_cast< Document* > ( set ) ) - { - (void)dummy; - newBinEntry->SetKey( newBinEntry->GetKey() ); - } - // but when "this" is a SQItem, we are inserting this new - // valEntry in a sequence item, and the kay has the - // generalized form (refer to \ref BaseTagKey): - if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) ) - { - newBinEntry->SetKey( parentSQItem->GetBaseTagKey() - + newBinEntry->GetKey() ); - } - - LoadDocEntry( newBinEntry ); - if( !set->AddEntry( newBinEntry ) ) - { - //Expect big troubles if here - delete newBinEntry; - } - } - if ( ( newDocEntry->GetGroup() == 0x7fe0 ) - && ( newDocEntry->GetElement() == 0x0010 ) ) - { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts == RLELossless ) - { - long PositionOnEntry = Fp->tellg(); - Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); - ComputeRLEInfo(); - Fp->seekg( PositionOnEntry, std::ios::beg ); - } - else if ( IsJPEG() ) - { - long PositionOnEntry = Fp->tellg(); - Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); - ComputeJPEGFragmentInfo(); - Fp->seekg( PositionOnEntry, std::ios::beg ); - } - } - // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); - //delete newDocEntry; } else { @@ -1356,25 +901,22 @@ 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() @@ -1387,14 +929,20 @@ void Document::ParseDES(DocEntrySet *set, long offset, newDocEntry->GetOffset(), l, delim_mode); } - set->AddEntry( newSeqEntry ); + if( !set->AddEntry( newSeqEntry ) ) + { + used = false; + } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - delete newDocEntry; + if( !used ) + delete newDocEntry; break; } } - delete newDocEntry; + + if( !used ) + delete newDocEntry; } } @@ -1402,15 +950,18 @@ 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 @@ -1420,7 +971,7 @@ void Document::ParseSQ( SeqEntry* seqEntry, { if ( newDocEntry->IsSequenceDelimitor() ) { - seqEntry->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetDelimitationItem( newDocEntry ); break; } } @@ -1429,7 +980,7 @@ void Document::ParseSQ( SeqEntry* seqEntry, delete newDocEntry; break; } - + // create the current SQItem SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); std::ostringstream newBase; newBase << seqEntry->GetKey() @@ -1447,11 +998,23 @@ void Document::ParseSQ( SeqEntry* seqEntry, { dlm_mod = false; } - - ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); + // 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; - - seqEntry->AddEntry( itemSQ, SQItemNumber ); + 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 && ((long)(Fp->tellg())-offset ) >= l_max ) { @@ -1461,11 +1024,11 @@ void Document::ParseSQ( SeqEntry* seqEntry, } /** - * \brief Loads the element content if its length doesn't exceed - * the value specified with Document::SetMaxSizeLoadEntry() - * @param entry Header Entry (Dicom Element) to be dealt with + * \brief Loads the element content if its length doesn't exceed + * the value specified with Document::SetMaxSizeLoadEntry() + * @param entry Header Entry (Dicom Element) to be dealt with */ -void Document::LoadDocEntry(DocEntry* entry) +void Document::LoadDocEntry(DocEntry *entry) { uint16_t group = entry->GetGroup(); std::string vr = entry->GetVR(); @@ -1497,7 +1060,7 @@ 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; @@ -1507,7 +1070,7 @@ void Document::LoadDocEntry(DocEntry* entry) binEntryPtr->SetValue(s.str()); } // Be carefull : a BinEntry IS_A ValEntry ... - else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) ) + else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { // s << "gdcm::NotLoaded. (ValEntry)"; s << GDCM_NOTLOADED; @@ -1519,8 +1082,8 @@ void Document::LoadDocEntry(DocEntry* entry) else { // fusible - std::cout<< "MaxSizeLoadEntry exceeded, neither a BinEntry " - << "nor a ValEntry ?! Should never print that !" << std::endl; + gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry " + << "nor a ValEntry ?! Should never print that !" ); } // to be sure we are at the end of the value ... @@ -1530,14 +1093,14 @@ void Document::LoadDocEntry(DocEntry* entry) } // When we find a BinEntry not very much can be done : - if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) ) + if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) ) { s << GDCM_BINLOADED; binEntryPtr->SetValue(s.str()); LoadEntryBinArea(binEntryPtr); // last one, not to erase length ! return; } - + /// \todo Any compacter code suggested (?) if ( IsDocEntryAnInteger(entry) ) { @@ -1596,10 +1159,10 @@ 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()); + gdcmWarningMacro("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 { @@ -1607,12 +1170,11 @@ 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"); + gdcmWarningMacro("Unread element value"); valEntry->SetValue(GDCM_UNREAD); return; } @@ -1629,12 +1191,10 @@ void Document::LoadDocEntry(DocEntry* entry) } else { - dbg.Error(true, "Document::LoadDocEntry" - "Should have a ValEntry, here !"); + gdcmErrorMacro( "Should have a ValEntry, here !"); } } - /** * \brief Find the value Length of the passed Header Entry * @param entry Header Entry whose length of the value shall be loaded. @@ -1642,7 +1202,6 @@ 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; @@ -1661,9 +1220,7 @@ 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 ) { @@ -1674,11 +1231,15 @@ void Document::FindDocEntryLength( DocEntry *entry ) // the length and proceed. long currentPosition = Fp->tellg(); Fp->seekg(0L,std::ios::end); + long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; Fp->seekg(currentPosition, std::ios::beg); + + entry->SetReadLength(lengthUntilEOF); entry->SetLength(lengthUntilEOF); return; } + entry->SetReadLength(lengthOB); entry->SetLength(lengthOB); return; } @@ -1688,6 +1249,14 @@ 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 @@ -1708,6 +1277,8 @@ 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 @@ -1716,37 +1287,39 @@ 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 ); @@ -1760,20 +1333,80 @@ 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; } } +/** + * \brief Find the Length till the next sequence delimiter + * \warning NOT end user intended method ! + * @return + */ +uint32_t Document::FindDocEntryLengthOBOrOW() + throw( FormatUnexpected ) +{ + // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. + long positionOnEntry = Fp->tellg(); + bool foundSequenceDelimiter = false; + uint32_t totalLength = 0; + + while ( !foundSequenceDelimiter ) + { + uint16_t group; + uint16_t elem; + try + { + group = ReadInt16(); + elem = ReadInt16(); + } + catch ( FormatError ) + { + throw FormatError("Unexpected end of file encountered during ", + "Document::FindDocEntryLengthOBOrOW()"); + } + // We have to decount the group and element we just read + totalLength += 4; + if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) + { + long filePosition = Fp->tellg(); + gdcmWarningMacro( "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 ) + { + foundSequenceDelimiter = true; + } + uint32_t itemLength = ReadInt32(); + // We add 4 bytes since we just read the ItemLength with ReadInt32 + totalLength += itemLength + 4; + SkipBytes(itemLength); + + if ( foundSequenceDelimiter ) + { + break; + } + } + Fp->seekg( positionOnEntry, std::ios::beg); + return totalLength; +} + /** * \brief Find the Value Representation of the current Dicom Element. - * @param entry + * @return Value Representation of the current Entry */ std::string Document::FindDocEntryVR() { if ( Filetype != ExplicitVR ) - return(GDCM_UNKNOWN); + return GDCM_UNKNOWN; long positionOnEntry = Fp->tellg(); // Warning: we believe this is explicit VR (Value Representation) because @@ -1791,25 +1424,21 @@ std::string Document::FindDocEntryVR() if( !CheckDocEntryVR(vr) ) { Fp->seekg(positionOnEntry, std::ios::beg); - return(GDCM_UNKNOWN); + return GDCM_UNKNOWN; } - return(vr); + 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(VRKey vr) { - // 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 ( !Global::GetVR()->IsValidVR(vr) ) return false; @@ -1887,7 +1516,6 @@ std::string Document::GetDocEntryValue(DocEntry *entry) #endif //GDCM_NO_ANSI_STRING_STREAM return s.str(); } - return ((ValEntry *)entry)->GetValue(); } @@ -1899,7 +1527,7 @@ 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() ) { @@ -1958,14 +1586,15 @@ void Document::SkipDocEntry(DocEntry *entry) } /** - * \brief Skips to the begining of the next Header Entry + * \brief Skips to the beginning of the next Header Entry * \warning NOT end user intended method ! - * @param entry entry to skip + * @param currentDocEntry entry to skip */ -void Document::SkipToNextDocEntry(DocEntry *entry) +void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) { - Fp->seekg((long)(entry->GetOffset()), std::ios::beg); - Fp->seekg( (long)(entry->GetReadLength()), std::ios::cur); + Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg); + if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb + Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur); } /** @@ -1973,7 +1602,7 @@ 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) @@ -1984,30 +1613,25 @@ 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()); + gdcmWarningMacro( "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 !? @@ -2018,9 +1642,7 @@ 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 !? @@ -2034,7 +1656,7 @@ 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 @@ -2043,9 +1665,8 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, { foundLength = 0; } - } - - entry->SetUsableLength(foundLength); + } + entry->SetLength(foundLength); } /** @@ -2056,15 +1677,15 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, */ bool Document::IsDocEntryAnInteger(DocEntry *entry) { - uint16_t element = entry->GetElement(); - uint16_t group = entry->GetGroup(); - const std::string & vr = entry->GetVR(); - uint32_t length = entry->GetLength(); + uint16_t elem = entry->GetElement(); + uint16_t group = entry->GetGroup(); + const std::string &vr = entry->GetVR(); + uint32_t length = entry->GetLength(); // When we have some semantics on the element we just read, and if we // a priori know we are dealing with an integer, then we shall be // able to swap it's element value properly. - if ( element == 0 ) // This is the group length of the group + if ( elem == 0 ) // This is the group length of the group { if ( length == 4 ) { @@ -2079,150 +1700,19 @@ 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 + gdcmWarningMacro( "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() ); - } - } - - if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" ) - { - return true; - } - return false; -} - -/** - * \brief Find the Length till the next sequence delimiter - * \warning NOT end user intended method ! - * @return - */ - -uint32_t Document::FindDocEntryLengthOB() - throw( FormatUnexpected ) -{ - // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. - long positionOnEntry = Fp->tellg(); - bool foundSequenceDelimiter = false; - uint32_t totalLength = 0; - - while ( !foundSequenceDelimiter ) - { - uint16_t group; - uint16_t elem; - try - { - group = ReadInt16(); - elem = ReadInt16(); - } - catch ( FormatError ) - { - throw FormatError("Document::FindDocEntryLengthOB()", - " group or element not present."); - } - - // We have to decount the group and element we just read - totalLength += 4; - - if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) - { - dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item " - "tag nor a Sequence delimiter tag."); - Fp->seekg(positionOnEntry, std::ios::beg); - throw FormatUnexpected("Document::FindDocEntryLengthOB()", - "Neither an Item tag nor a Sequence " - "delimiter tag."); - } - - if ( elem == 0xe0dd ) - { - foundSequenceDelimiter = true; - } - - uint32_t itemLength = ReadInt32(); - // We add 4 bytes since we just read the ItemLength with ReadInt32 - totalLength += itemLength + 4; - SkipBytes(itemLength); - - if ( foundSequenceDelimiter ) - { - break; + << "lgt : " << length ); } } - Fp->seekg( positionOnEntry, std::ios::beg); - return totalLength; -} - -/** - * \brief Reads a supposed to be 16 Bits integer - * (swaps it depending on processor endianity) - * @return read value - */ -uint16_t Document::ReadInt16() - throw( FormatError ) -{ - uint16_t g; - Fp->read ((char*)&g, (size_t)2); - if ( Fp->fail() ) - { - throw FormatError( "Document::ReadInt16()", " file error." ); - } - if( Fp->eof() ) - { - throw FormatError( "Document::ReadInt16()", "EOF." ); - } - g = SwapShort(g); - return g; -} - -/** - * \brief Reads a supposed to be 32 Bits integer - * (swaps it depending on processor endianity) - * @return read value - */ -uint32_t Document::ReadInt32() - throw( FormatError ) -{ - uint32_t g; - Fp->read ((char*)&g, (size_t)4); - if ( Fp->fail() ) - { - throw FormatError( "Document::ReadInt32()", " file error." ); - } - if( Fp->eof() ) - { - throw FormatError( "Document::ReadInt32()", "EOF." ); - } - g = SwapLong(g); - return g; -} - -/** - * \brief skips bytes inside the source file - * \warning NOT end user intended method ! - * @return - */ -void Document::SkipBytes(uint32_t nBytes) -{ - //FIXME don't dump the returned value - Fp->seekg((long)nBytes, std::ios::cur); -} - -/** - * \brief Loads all the needed Dictionaries - * \warning NOT end user intended method ! - */ -void Document::Initialise() -{ - RefPubDict = Global::GetDicts()->GetDefaultPubDict(); - RefShaDict = NULL; - RLEInfo = new RLEFramesInfo; - JPEGInfo = new JPEGFragmentsInfo; - Filetype = Unknown; + + if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" ) + { + return true; + } + return false; } /** @@ -2258,25 +1748,24 @@ bool Document::CheckSwap() net2host = false; } - // The easiest case is the one of a DICOM header, since it possesses a - // file preamble where it suffice to look for the string "DICM". + // The easiest case is the one of a 'true' DICOM header, we just have + // to look for the string "DICM" inside the file preamble. Fp->read(deb, 256); char *entCur = deb + 128; if( memcmp(entCur, "DICM", (size_t)4) == 0 ) { - dbg.Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3"); + gdcmWarningMacro( "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, @@ -2284,46 +1773,42 @@ bool Document::CheckSwap() // i.e. a total of 136 bytes. entCur = deb + 136; - // FIXME : FIXME: - // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR, - // but elem 0002,0010 (Transfert Syntax) tells us the file is - // *Implicit* VR. -and it is !- + // group 0x0002 *is always* Explicit VR Sometimes , + // even if elem 0002,0010 (Transfer Syntax) tells us the file is + // *Implicit* VR (see former 'gdcmData/icone.dcm') if( memcmp(entCur, "UL", (size_t)2) == 0 || memcmp(entCur, "OB", (size_t)2) == 0 || memcmp(entCur, "UI", (size_t)2) == 0 || memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later - // when Write DCM *adds* + // when Write DCM *adds* // FIXME // Use Document::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? group 0000 { Filetype = ExplicitVR; - dbg.Verbose(1, "Document::CheckSwap:", - "explicit Value Representation"); + gdcmWarningMacro( "Group 0002 : Explicit Value Representation"); } else { Filetype = ImplicitVR; - dbg.Verbose(1, "Document::CheckSwap:", - "not an explicit Value Representation"); + gdcmWarningMacro( "Group 0002 :Not an explicit Value Representation;" + << "Looks like a bugged Header!"); } if ( net2host ) { SwapCode = 4321; - dbg.Verbose(1, "Document::CheckSwap:", - "HostByteOrder != NetworkByteOrder"); + gdcmWarningMacro( "HostByteOrder != NetworkByteOrder"); } else { - SwapCode = 0; - dbg.Verbose(1, "Document::CheckSwap:", - "HostByteOrder = NetworkByteOrder"); + SwapCode = 1234; + gdcmWarningMacro( "HostByteOrder = NetworkByteOrder"); } - // Position the file position indicator at first tag (i.e. - // after the file preamble and the "DICM" string). + // Position the file position indicator at first tag + // (i.e. after the file preamble and the "DICM" string). Fp->seekg(0, std::ios::beg); Fp->seekg ( 132L, std::ios::beg); return true; @@ -2332,7 +1817,7 @@ bool Document::CheckSwap() // Alas, this is not a DicomV3 file and whatever happens there is no file // preamble. We can reset the file position indicator to where the data // is (i.e. the beginning of the file). - dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file"); + gdcmWarningMacro( "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. @@ -2361,7 +1846,7 @@ bool Document::CheckSwap() Filetype = ACR; return true; case 0x00000004 : - SwapCode = 0; + SwapCode = 1234; Filetype = ACR; return true; default : @@ -2392,7 +1877,7 @@ bool Document::CheckSwap() case 0x0006 : case 0x0007 : case 0x0008 : - SwapCode = 0; + SwapCode = 1234; Filetype = ACR; return true; case 0x0100 : @@ -2407,37 +1892,26 @@ bool Document::CheckSwap() Filetype = ACR; return true; default : - dbg.Verbose(0, "Document::CheckSwap:", - "ACR/NEMA unfound swap info (Really hopeless !)"); + gdcmWarningMacro( "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 ) + gdcmWarningMacro( "Switching Byte Swap code from "<< SwapCode); + if ( SwapCode == 1234 ) { SwapCode = 4321; } else if ( SwapCode == 4321 ) { - SwapCode = 0; + SwapCode = 1234; } else if ( SwapCode == 3412 ) { @@ -2467,7 +1941,6 @@ void Document::SetMaxSizeLoadEntry(long newSize) MaxSizeLoadEntry = newSize; } - /** * \brief Header Elements too long will not be printed * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE @@ -2475,7 +1948,6 @@ void Document::SetMaxSizeLoadEntry(long newSize) */ void Document::SetMaxSizePrintEntry(long newSize) { - //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME if ( newSize < 0 ) { return; @@ -2489,43 +1961,14 @@ 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++; - SwitchSwapToBigEndian(); - // fix the tag - group = 0xfffe; - elem = 0xe000; - } - else if ((group == 0xfffe) && (elem == 0xe00d) && reversedEndian) - { - // end of reversed endian group - reversedEndian--; - SwitchSwapToBigEndian(); - } -} - /** * \brief Read the next tag but WITHOUT loading it's value * (read the 'Group Number', the 'Element Number', - * gets the Dict Entry + * gets the 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; @@ -2539,24 +1982,47 @@ DocEntry* Document::ReadNextDocEntry() { // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. - //std::cout << e; return 0; } + // Sometimes file contains groups of tags with reversed endianess. HandleBrokenEndian(group, elem); - std::string vr=FindDocEntryVR(); - DocEntry *newEntry = NewDocEntryByNumber(group, elem, vr); + // In 'true DICOM' files Group 0002 is always little endian + if ( HasDCMPreamble ) + HandleOutOfGroup0002(group, elem); + + std::string vr = FindDocEntryVR(); + std::string realVR = vr; + + if( vr == GDCM_UNKNOWN) + { + DictEntry *dictEntry = GetDictEntry(group,elem); + if( dictEntry ) + realVR = dictEntry->GetVR(); + } + + DocEntry *newEntry; + if( Global::GetVR()->IsVROfSequence(realVR) ) + newEntry = NewSeqEntry(group, elem); + else if( Global::GetVR()->IsVROfStringRepresentable(realVR) ) + newEntry = NewValEntry(group, elem,vr); + else + newEntry = NewBinEntry(group, elem,vr); + if( vr == GDCM_UNKNOWN ) { if( Filetype == ExplicitVR ) { // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - std::string msg; - msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", - newEntry->GetGroup(), newEntry->GetElement()); - dbg.Verbose(1, "Document::FindVR: ", msg.c_str()); + // 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()); + gdcmWarningMacro( msg.c_str() ); + } } newEntry->SetImplicitVR(); } @@ -2578,493 +2044,77 @@ DocEntry* Document::ReadNextDocEntry() return newEntry; } - -/** - * \brief Generate a free TagKey i.e. a TagKey that is not present - * in the TagHt dictionary. - * @param group The generated tag must belong to this group. - * @return The element of tag with given group which is fee. - */ -uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group) -{ - for (uint32_t elem = 0; elem < UINT32_MAX; elem++) - { - TagKey key = DictEntry::TranslateToKey(group, elem); - if (TagHT.count(key) == 0) - { - return elem; - } - } - return UINT32_MAX; -} - -/** - * \brief Assuming the internal file pointer \ref Document::Fp - * is placed at the beginning of a tag check whether this - * tag is (TestGroup, TestElement). - * \warning On success the internal file pointer \ref Document::Fp - * is modified to point after the tag. - * On failure (i.e. when the tag wasn't the expected tag - * (TestGroup, TestElement) the internal file pointer - * \ref Document::Fp is restored to it's original position. - * @param testGroup The expected group of the tag. - * @param testElement The expected Element of the tag. - * @return True on success, false otherwise. - */ -bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) -{ - long positionOnEntry = Fp->tellg(); - long currentPosition = Fp->tellg(); // On debugging purposes - - //// Read the Item Tag group and element, and make - // sure they are what we expected: - uint16_t itemTagGroup; - uint16_t itemTagElement; - try - { - itemTagGroup = ReadInt16(); - itemTagElement = ReadInt16(); - } - catch ( FormatError e ) - { - //std::cerr << e << std::endl; - return false; - } - if ( itemTagGroup != testGroup || itemTagElement != testElement ) - { - std::ostringstream s; - s << " We should have found tag ("; - s << std::hex << testGroup << "," << testElement << ")" << std::endl; - s << " but instead we encountered tag ("; - s << std::hex << itemTagGroup << "," << itemTagElement << ")" - << std::endl; - s << " at address: " << (unsigned)currentPosition << std::endl; - dbg.Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:"); - dbg.Verbose(0, s.str().c_str()); - Fp->seekg(positionOnEntry, std::ios::beg); - - return false; - } - return true; -} - -/** - * \brief Assuming the internal file pointer \ref Document::Fp - * is placed at the beginning of a tag (TestGroup, TestElement), - * read the length associated to the Tag. - * \warning On success the internal file pointer \ref Document::Fp - * is modified to point after the tag and it's length. - * On failure (i.e. when the tag wasn't the expected tag - * (TestGroup, TestElement) the internal file pointer - * \ref Document::Fp is restored to it's original position. - * @param testGroup The expected group of the tag. - * @param testElement The expected Element of the tag. - * @return On success returns the length associated to the tag. On failure - * returns 0. - */ -uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement) -{ - long positionOnEntry = Fp->tellg(); - (void)positionOnEntry; - - if ( !ReadTag(testGroup, testElement) ) - { - return 0; - } - - //// Then read the associated Item Length - long currentPosition = Fp->tellg(); - uint32_t itemLength = ReadInt32(); - { - std::ostringstream s; - s << "Basic Item Length is: " - << itemLength << std::endl; - s << " at address: " << (unsigned)currentPosition << std::endl; - dbg.Verbose(0, "Document::ReadItemTagLength: ", s.str().c_str()); - } - return itemLength; -} - -/** - * \brief When parsing the Pixel Data of an encapsulated file, read - * the basic offset table (when present, and BTW dump it). - */ -void Document::ReadAndSkipEncapsulatedBasicOffsetTable() -{ - //// Read the Basic Offset Table Item Tag length... - uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); - - // When present, read the basic offset table itself. - // Notes: - since the presence of this basic offset table is optional - // we can't rely on it for the implementation, and we will simply - // trash it's content (when present). - // - still, when present, we could add some further checks on the - // lengths, but we won't bother with such fuses for the time being. - if ( itemLength != 0 ) - { - char* basicOffsetTableItemValue = new char[itemLength + 1]; - Fp->read(basicOffsetTableItemValue, itemLength); - -#ifdef GDCM_DEBUG - for (unsigned int i=0; i < itemLength; i += 4 ) - { - uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], - uint32_t); - std::ostringstream s; - s << " Read one length: "; - s << std::hex << individualLength << std::endl; - dbg.Verbose(0, - "Document::ReadAndSkipEncapsulatedBasicOffsetTable: ", - s.str().c_str()); - } -#endif //GDCM_DEBUG - - delete[] basicOffsetTableItemValue; - } -} - /** - * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. - * Compute the RLE extra information and store it in \ref RLEInfo - * for later pixel retrieval usage. + * \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::ComputeRLEInfo() +void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts != RLELossless ) + // 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)) { - return; - } - - // Encoded pixel data: for the time being we are only concerned with - // Jpeg or RLE Pixel data encodings. - // As stated in PS 3.5-2003, section 8.2 p44: - // "If sent in Encapsulated Format (i.e. other than the Native Format) the - // value representation OB is used". - // Hence we expect an OB value representation. Concerning OB VR, - // the section PS 3.5-2003, section A.4.c p 58-59, states: - // "For the Value Representations OB and OW, the encoding shall meet the - // following specifications depending on the Data element tag:" - // [...snip...] - // - the first item in the sequence of items before the encoded pixel - // data stream shall be basic offset table item. The basic offset table - // item value, however, is not required to be present" - - ReadAndSkipEncapsulatedBasicOffsetTable(); - - // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G) - // Loop on the individual frame[s] and store the information - // on the RLE fragments in a RLEFramesInfo. - // Note: - when only a single frame is present, this is a - // classical image. - // - when more than one frame are present, then we are in - // the case of a multi-frame image. - long frameLength; - while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) ) - { - // Parse the RLE Header and store the corresponding RLE Segment - // Offset Table information on fragments of this current Frame. - // Note that the fragment pixels themselves are not loaded - // (but just skipped). - long frameOffset = Fp->tellg(); - - uint32_t nbRleSegments = ReadInt32(); - if ( nbRleSegments > 16 ) - { - // There should be at most 15 segments (refer to RLEFrame class) - dbg.Verbose(0, "Document::ComputeRLEInfo: too many segments."); - } - - uint32_t rleSegmentOffsetTable[16]; - for( int k = 1; k <= 15; k++ ) - { - rleSegmentOffsetTable[k] = ReadInt32(); - } - - // Deduce from both the RLE Header and the frameLength the - // fragment length, and again store this info in a - // RLEFramesInfo. - long rleSegmentLength[15]; - // skipping (not reading) RLE Segments - if ( nbRleSegments > 1) - { - for(unsigned int k = 1; k <= nbRleSegments-1; k++) - { - rleSegmentLength[k] = rleSegmentOffsetTable[k+1] - - rleSegmentOffsetTable[k]; - SkipBytes(rleSegmentLength[k]); - } - } - - rleSegmentLength[nbRleSegments] = frameLength - - rleSegmentOffsetTable[nbRleSegments]; - SkipBytes(rleSegmentLength[nbRleSegments]); - - // Store the collected info - RLEFrame* newFrameInfo = new RLEFrame; - newFrameInfo->NumberFragments = nbRleSegments; - for( unsigned int uk = 1; uk <= nbRleSegments; uk++ ) - { - newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk]; - newFrameInfo->Length[uk] = rleSegmentLength[uk]; - } - RLEInfo->Frames.push_back( newFrameInfo ); - } - - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': - if ( !ReadTag(0xfffe, 0xe0dd) ) + // start endian swap mark for group found + reversedEndian++; + SwitchByteSwapCode(); + // fix the tag + group = 0xfffe; + elem = 0xe000; + } + else if (group == 0xfffe && elem == 0xe00d && reversedEndian) { - dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); - dbg.Verbose(0, " item at end of RLE item sequence"); + // end of reversed endian group + reversedEndian--; + SwitchByteSwapCode(); } } /** - * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding. - * Compute the jpeg extra information (fragment[s] offset[s] and - * length) and store it[them] in \ref JPEGInfo for later pixel - * retrieval usage. + * \brief Group 0002 is always coded Little Endian + * whatever Transfer Syntax is + * @return no return */ -void Document::ComputeJPEGFragmentInfo() +void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) { - // If you need to, look for comments of ComputeRLEInfo(). - if ( ! IsJPEG() ) - { - return; - } - - ReadAndSkipEncapsulatedBasicOffsetTable(); - - // Loop on the fragments[s] and store the parsed information in a - // JPEGInfo. - long fragmentLength; - while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) - { - long fragmentOffset = Fp->tellg(); - - // Store the collected info - JPEGFragment* newFragment = new JPEGFragment; - newFragment->Offset = fragmentOffset; - newFragment->Length = fragmentLength; - JPEGInfo->Fragments.push_back( newFragment ); - - SkipBytes( fragmentLength ); - } - - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': - if ( !ReadTag(0xfffe, 0xe0dd) ) + // Endian reversion. Some files contain groups of tags with reversed endianess. + if ( !Group0002Parsed && group != 0x0002) { - dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); - dbg.Verbose(0, " item at end of JPEG item sequence"); - } -} - -/** - * \brief Walk recursively the given \ref DocEntrySet, and feed - * the given hash table (\ref TagDocEntryHT) with all the - * \ref DocEntry (Dicom entries) encountered. - * This method does the job for \ref BuildFlatHashTable. - * @param builtHT Where to collect all the \ref DocEntry encountered - * when recursively walking the given set. - * @param set The structure to be traversed (recursively). - */ -void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, - DocEntrySet* set ) -{ - if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) ) - { - TagDocEntryHT const & currentHT = elementSet->GetTagHT(); - for( TagDocEntryHT::const_iterator i = currentHT.begin(); - i != currentHT.end(); - ++i) - { - DocEntry* entry = i->second; - if ( SeqEntry* seqEntry = dynamic_cast(entry) ) - { - const ListSQItem& items = seqEntry->GetSQItems(); - for( ListSQItem::const_iterator item = items.begin(); - item != items.end(); - ++item) - { - BuildFlatHashTableRecurse( builtHT, *item ); - } - continue; - } - builtHT[entry->GetKey()] = entry; - } - return; - } + Group0002Parsed = true; + // we just came out of group 0002 + // if Transfer syntax is Big Endian we have to change CheckSwap - if (SQItem* SQItemSet = dynamic_cast< SQItem* > ( set ) ) - { - const ListDocEntry& currentList = SQItemSet->GetDocEntries(); - for (ListDocEntry::const_iterator i = currentList.begin(); - i != currentList.end(); - ++i) + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsTransferSyntax(ts) ) { - DocEntry* entry = *i; - if ( SeqEntry* seqEntry = dynamic_cast(entry) ) - { - const ListSQItem& items = seqEntry->GetSQItems(); - for( ListSQItem::const_iterator item = items.begin(); - item != items.end(); - ++item) - { - BuildFlatHashTableRecurse( builtHT, *item ); - } - continue; - } - builtHT[entry->GetKey()] = entry; + gdcmWarningMacro("True DICOM File, with NO Tansfer Syntax: " << ts ); + return; } - } -} - -/** - * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current - * Document. - * - * The structure used by a Document (through \ref ElementSet), - * in order to hold the parsed entries of a Dicom header, is a recursive - * one. This is due to the fact that the sequences (when present) - * can be nested. Additionaly, the sequence items (represented in - * gdcm as \ref SQItem) add an extra complexity to the data - * structure. Hence, a gdcm user whishing to visit all the entries of - * a Dicom header will need to dig in the gdcm internals (which - * implies exposing all the internal data structures to the API). - * In order to avoid this burden to the user, \ref BuildFlatHashTable - * recursively builds a temporary hash table, which holds all the - * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a - * std::map<>). - * \warning Of course there is NO integrity constrain between the - * returned \ref TagDocEntryHT and the \ref ElementSet used - * to build it. Hence if the underlying \ref ElementSet is - * altered, then it is the caller responsability to invoke - * \ref BuildFlatHashTable again... - * @return The flat std::map<> we juste build. - */ -TagDocEntryHT* Document::BuildFlatHashTable() -{ - TagDocEntryHT* FlatHT = new TagDocEntryHT; - BuildFlatHashTableRecurse( *FlatHT, this ); - return FlatHT; -} - + // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..." - -/** - * \brief Compares two documents, according to \ref DicomDir rules - * \warning Does NOT work with ACR-NEMA files - * \todo Find a trick to solve the pb (use RET fields ?) - * @param document - * @return true if 'smaller' - */ -bool Document::operator<(Document &document) -{ - // Patient Name - std::string s1 = GetEntryByNumber(0x0010,0x0010); - std::string s2 = document.GetEntryByNumber(0x0010,0x0010); - if(s1 < s2) - { - return true; - } - else if( s1 > s2 ) - { - return false; - } - else - { - // Patient ID - s1 = GetEntryByNumber(0x0010,0x0020); - s2 = document.GetEntryByNumber(0x0010,0x0020); - if ( s1 < s2 ) - { - return true; - } - else if ( s1 > s2 ) - { - return false; - } - else - { - // Study Instance UID - s1 = GetEntryByNumber(0x0020,0x000d); - s2 = document.GetEntryByNumber(0x0020,0x000d); - if ( s1 < s2 ) - { - return true; - } - else if( s1 > s2 ) - { - return false; - } - else + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian ) { - // Serie Instance UID - s1 = GetEntryByNumber(0x0020,0x000e); - s2 = document.GetEntryByNumber(0x0020,0x000e); - if ( s1 < s2 ) - { - return true; - } - else if( s1 > s2 ) - { - return false; - } + Filetype = ImplicitVR; } - } - } - return false; -} - - -/** - * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader - * @param filetype Type of the File to be written - */ -int Document::ComputeGroup0002Length( FileType filetype ) -{ - uint16_t gr, el; - std::string vr; - - int groupLength = 0; - bool found0002 = false; - - // for each zero-level Tag in the DCM Header - DocEntry *entry; - - Initialize(); - entry = GetNextEntry(); - while(entry) - { - gr = entry->GetGroup(); - - if (gr == 0x0002) + + // FIXME Strangely, this works with + //'Implicit VR Transfer Syntax (GE Private) + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian ) { - 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(); + gdcmWarningMacro("Transfer Syntax Name = [" + << GetTransferSyntaxName() << "]" ); + SwitchByteSwapCode(); + group = SwapShort(group); + elem = SwapShort(elem); } - else if (found0002 ) - break; - - entry = GetNextEntry(); } - return groupLength; } -} // end namespace gdcm +//----------------------------------------------------------------------------- +// Print //----------------------------------------------------------------------------- +} // end namespace gdcm