X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=8437264ba6268cf28f9d21c8eb86fb132f8a95a7;hb=0ad9dae4659b21bfd5c834c1af724eab4dcdf4f6;hp=313cee7ae760a6a61a9873a0415a5fb8a5c18bdb;hpb=9ca4fd0ccbfea12ed7760856de3a8faf41625869;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 313cee7a..8437264b 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2005/01/07 16:45:51 $ - Version: $Revision: 1.164 $ + Date: $Date: 2005/01/23 10:12:33 $ + Version: $Revision: 1.204 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -35,49 +35,16 @@ #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 Big 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() @@ -92,13 +59,16 @@ const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; /** * \brief constructor - * @param filename file to be opened for parsing + * @param filename 'Document' (File or DicomDir) to be opened for parsing */ Document::Document( std::string const &filename ) : ElementSet(-1) { + RLEInfo = NULL; + JPEGInfo = NULL; + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; - Initialise(); + Initialize(); Fp = 0; if ( !OpenFile() ) @@ -106,39 +76,41 @@ Document::Document( std::string const &filename ) : ElementSet(-1) return; } - Debug::Verbose(0, "Document::Document: starting parsing of file: ", - Filename.c_str()); - Fp->seekg( 0, std::ios::beg); + Group0002Parsed = false; + + gdcmVerboseMacro( "Starting parsing of file: " << Filename.c_str()); + // Fp->seekg( 0, std::ios::beg); Fp->seekg(0, std::ios::end); long lgt = Fp->tellg(); Fp->seekg( 0, std::ios::beg); + CheckSwap(); long beg = Fp->tellg(); lgt -= beg; - 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 = GetEntry(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ) { LoadEntryBinArea(0x0028,0x1200); // gray LUT /// FIXME FIXME FIXME /// The tags refered by the three following lines used to be CORRECTLY /// defined as having an US Value Representation in the public - /// dictionnary. BUT the semantics implied by the three following + /// dictionary. BUT the semantics implied by the three following /// lines state that the corresponding tag contents are in fact /// the ones of a BinEntry. - /// In order to fix things "Quick and Dirty" the dictionnary was - /// altered on PURPOUS but now contains a WRONG value. + /// In order to fix things "Quick and Dirty" the dictionary was + /// altered on PURPOSE but now contains a WRONG value. /// In order to fix things and restore the dictionary to its /// correct value, one needs to decided of the semantics by deciding - /// wether the following tags are either: + /// whether the following tags are either: /// - multivaluated US, and hence loaded as ValEntry, but afterwards /// also used as BinEntry, which requires the proper conversion, /// - OW, and hence loaded as BinEntry, but afterwards also used @@ -170,16 +142,16 @@ Document::Document( std::string const &filename ) : ElementSet(-1) // we switch lineNumber and columnNumber // std::string RecCode; - RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code + RecCode = GetEntry(0x0008, 0x0010); // recognition code (RET) if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { Filetype = ACR_LIBIDO; - std::string rows = GetEntryByNumber(0x0028, 0x0010); - std::string columns = GetEntryByNumber(0x0028, 0x0011); - SetEntryByNumber(columns, 0x0028, 0x0010); - SetEntryByNumber(rows , 0x0028, 0x0011); + std::string rows = GetEntry(0x0028, 0x0010); + std::string columns = GetEntry(0x0028, 0x0011); + SetEntry(columns, 0x0028, 0x0010); + SetEntry(rows , 0x0028, 0x0011); } // ----------------- End of ACR-LibIDO kludge ------------------ } @@ -190,12 +162,16 @@ Document::Document( std::string const &filename ) : ElementSet(-1) */ Document::Document() : ElementSet(-1) { + RLEInfo = NULL; + JPEGInfo = NULL; + Fp = 0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - Initialise(); - SwapCode = 0; + Initialize(); + SwapCode = 1234; Filetype = ExplicitVR; + Group0002Parsed = false; } /** @@ -206,8 +182,10 @@ Document::~Document () RefPubDict = NULL; RefShaDict = NULL; - delete RLEInfo; - delete JPEGInfo; + if( RLEInfo ) + delete RLEInfo; + if( JPEGInfo ) + delete JPEGInfo; } //----------------------------------------------------------------------------- @@ -283,14 +261,14 @@ bool Document::IsReadable() { if( Filetype == Unknown) { - Debug::Verbose(0, "Document::IsReadable: wrong filetype"); + gdcmVerboseMacro( "Wrong filetype"); return false; } - if( TagHT.empty() ) - { - Debug::Verbose(0, "Document::IsReadable: no tags in internal" - " hash table."); + //if( TagHT.empty() ) + if ( IsEmpty() ) + { + gdcmVerboseMacro( "No tag in internal hash table."); return false; } @@ -303,12 +281,12 @@ bool Document::IsReadable() * value from disk when only parsing occured). * @return The encountered Transfer Syntax of the current document. */ -TransferSyntaxType Document::GetTransferSyntax() +std::string Document::GetTransferSyntax() { - DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); + DocEntry *entry = GetDocEntry(0x0002, 0x0010); if ( !entry ) { - return UnknownTS; + return GDCM_UNKNOWN; } // The entry might be present but not loaded (parsing and loading @@ -323,68 +301,15 @@ TransferSyntaxType Document::GetTransferSyntax() if ( transfer.length() == 0 ) { // for brain damaged headers - return UnknownTS; + return GDCM_UNKNOWN; } while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { transfer.erase(transfer.length()-1, 1); } - for (int i = 0; TransferSyntaxStrings[i] != NULL; i++) - { - if ( TransferSyntaxStrings[i] == transfer ) - { - return TransferSyntaxType(i); - } - } + return transfer; } - return UnknownTS; -} - -bool Document::IsJPEGLossless() -{ - TransferSyntaxType r = GetTransferSyntax(); - return r == JPEGFullProgressionProcess10_12 - || r == JPEGLosslessProcess14 - || r == JPEGLosslessProcess14_1; -} - -/** - * \brief Determines if the Transfer Syntax was already encountered - * and if it corresponds to a JPEG2000 one - * @return True when JPEG2000 (Lossly or LossLess) found. False in all - * other cases. - */ -bool Document::IsJPEG2000() -{ - TransferSyntaxType r = GetTransferSyntax(); - return r == JPEG2000Lossless || r == JPEG2000; -} - -/** - * \brief Determines if the Transfer Syntax corresponds to any form - * of Jpeg encoded Pixel data. - * @return True when any form of JPEG found. False otherwise. - */ -bool Document::IsJPEG() -{ - TransferSyntaxType r = GetTransferSyntax(); - return r == JPEGBaselineProcess1 - || r == JPEGExtendedProcess2_4 - || r == JPEGExtendedProcess3_5 - || r == JPEGSpectralSelectionProcess6_8 - || IsJPEGLossless() - || IsJPEG2000(); -} - -/** - * \brief Determines if the Transfer Syntax corresponds to encapsulated - * of encoded Pixel Data (as opposed to native). - * @return True when encapsulated. False when native. - */ -bool Document::IsEncapsulate() -{ - TransferSyntaxType r = GetTransferSyntax(); - return IsJPEG() || r == RLELossless; + return GDCM_UNKNOWN; } /** @@ -393,11 +318,28 @@ bool Document::IsEncapsulate() */ bool Document::IsDicomV3() { - // Checking if Transfert Syntax exists is enough + // Checking if Transfer Syntax exists is enough // Anyway, it's to late check if the 'Preamble' was found ... // And ... would it be a rich idea to check ? // (some 'no Preamble' DICOM images exist !) - return GetDocEntryByNumber(0x0002, 0x0010) != NULL; + return GetDocEntry(0x0002, 0x0010) != NULL; +} + +/** + * \brief Predicate for Papyrus file + * Dedicated to whomsoever it may concern + * @return True when the file is a Papyrus file. + */ +bool Document::IsPapyrus() +{ + // check for Papyrus private Sequence + DocEntry *e = GetDocEntry(0x0041, 0x1050); + if ( !e ) + return false; + // check if it's actually a Sequence + if ( !dynamic_cast(e) ) + return false; + return true; } /** @@ -417,6 +359,8 @@ FileType Document::GetFileType() */ std::ifstream *Document::OpenFile() { + + HasDCMPreamble = false; if (Filename.length() == 0) { return 0; @@ -424,17 +368,13 @@ std::ifstream *Document::OpenFile() if(Fp) { - Debug::Verbose( 0, - "Document::OpenFile is already opened when opening: ", - Filename.c_str()); + gdcmVerboseMacro( "File already open: " << Filename.c_str()); } Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); if( ! *Fp ) { - Debug::Verbose( 0, - "Document::OpenFile cannot open file: ", - Filename.c_str()); + gdcmDebugMacro( "Cannot open file: " << Filename.c_str()); delete Fp; Fp = 0; return 0; @@ -455,6 +395,9 @@ std::ifstream *Document::OpenFile() zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 || zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ) { + std::string msg + = Util::Format("ACR/DICOM with no preamble: (%04x)\n", zero); + gdcmVerboseMacro( msg.c_str() ); return Fp; } @@ -469,13 +412,12 @@ std::ifstream *Document::OpenFile() } if( memcmp(dicm, "DICM", 4) == 0 ) { + HasDCMPreamble = true; return Fp; } CloseFile(); - Debug::Verbose( 0, - "Document::OpenFile not DICOM/ACR (missing preamble)", - Filename.c_str()); + gdcmVerboseMacro( "Not DICOM/ACR (missing preamble)" << Filename.c_str()); return 0; } @@ -493,12 +435,12 @@ bool Document::CloseFile() 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. @@ -544,13 +486,13 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ -ValEntry *Document::ReplaceOrCreateByNumber(std::string const &value, - uint16_t group, - uint16_t elem, - TagName const &vr ) +ValEntry *Document::ReplaceOrCreate(std::string const &value, + uint16_t group, + uint16_t elem, + TagName const &vr ) { ValEntry *valEntry = 0; - DocEntry *currentEntry = GetDocEntryByNumber( group, elem); + DocEntry *currentEntry = GetDocEntry( group, elem); if (currentEntry) { @@ -566,8 +508,7 @@ ValEntry *Document::ReplaceOrCreateByNumber(std::string const &value, { if (!RemoveEntry(currentEntry)) { - Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); + gdcmVerboseMacro( "Removal of previous DocEntry failed."); return NULL; } @@ -577,12 +518,11 @@ ValEntry *Document::ReplaceOrCreateByNumber(std::string const &value, // Create a new valEntry if necessary if (!valEntry) { - valEntry = NewValEntryByNumber(group, elem, vr); + valEntry = NewValEntry(group, elem, vr); if ( !AddEntry(valEntry)) { - Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); + gdcmVerboseMacro("AddEntry failed although this is a creation."); delete valEntry; return NULL; @@ -599,20 +539,20 @@ ValEntry *Document::ReplaceOrCreateByNumber(std::string const &value, * when it exists. Create it with the given value when unexistant. * A copy of the binArea is made to be kept in the Document. * @param binArea (binary) value to be set - * @param Group Group number of the Entry - * @param Elem Element number of the Entry + * @param group Group number of the Entry + * @param elem Element number of the Entry * @param vr V(alue) R(epresentation) of the Entry -if private Entry- * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ -BinEntry *Document::ReplaceOrCreateByNumber(uint8_t *binArea, - int lgth, - uint16_t group, - uint16_t elem, - TagName const &vr ) +BinEntry *Document::ReplaceOrCreate(uint8_t *binArea, + int lgth, + uint16_t group, + uint16_t elem, + TagName const &vr ) { BinEntry *binEntry = 0; - DocEntry *currentEntry = GetDocEntryByNumber( group, elem); + DocEntry *currentEntry = GetDocEntry( group, elem); // Verify the currentEntry if (currentEntry) @@ -629,8 +569,7 @@ BinEntry *Document::ReplaceOrCreateByNumber(uint8_t *binArea, { if (!RemoveEntry(currentEntry)) { - Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); + gdcmVerboseMacro( "Removal of previous DocEntry failed."); return NULL; } @@ -640,12 +579,11 @@ BinEntry *Document::ReplaceOrCreateByNumber(uint8_t *binArea, // Create a new binEntry if necessary if (!binEntry) { - binEntry = NewBinEntryByNumber(group, elem, vr); + binEntry = NewBinEntry(group, elem, vr); if ( !AddEntry(binEntry)) { - Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); delete binEntry; return NULL; @@ -677,15 +615,15 @@ BinEntry *Document::ReplaceOrCreateByNumber(uint8_t *binArea, /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it when unexistant. - * @param Group Group number of the Entry - * @param Elem Element number of the Entry + * @param group Group number of the Entry + * @param elem Element number of the Entry * \return pointer to the modified/created SeqEntry (NULL when creation * failed). */ -SeqEntry *Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) +SeqEntry *Document::ReplaceOrCreate( uint16_t group, uint16_t elem) { SeqEntry *seqEntry = 0; - DocEntry *currentEntry = GetDocEntryByNumber( group, elem); + DocEntry *currentEntry = GetDocEntry( group, elem); // Verify the currentEntry if (currentEntry) @@ -702,29 +640,25 @@ SeqEntry *Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) { if (!RemoveEntry(currentEntry)) { - Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); + gdcmVerboseMacro( "Removal of previous DocEntry failed."); return NULL; } } } - // Create a new seqEntry if necessary if (!seqEntry) { - seqEntry = NewSeqEntryByNumber(group, elem); + seqEntry = NewSeqEntry(group, elem); if ( !AddEntry(seqEntry)) { - Debug::Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); + gdcmVerboseMacro( "AddEntry failed allthough this is a creation."); delete seqEntry; return NULL; } } - return seqEntry; } @@ -736,95 +670,56 @@ SeqEntry *Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) * @param elem element number of the Entry * \return boolean */ -bool Document::ReplaceIfExistByNumber(std::string const &value, - uint16_t group, uint16_t elem ) +bool Document::ReplaceIfExist(std::string const &value, + uint16_t group, uint16_t elem ) { - SetEntryByNumber(value, group, elem); + SetEntry(value, group, elem); return true; } -std::string Document::GetTransferSyntaxValue(TransferSyntaxType type) -{ - return TransferSyntaxStrings[type]; -} - //----------------------------------------------------------------------------- // Protected -/** - * \brief Checks if a given Dicom Element exists within the H table - * @param group Group number of the searched Dicom Element - * @param element Element number of the searched Dicom Element - * @return true is found - */ -bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) -{ - const std::string &key = DictEntry::TranslateToKey(group, element ); - return TagHT.count(key) != 0; -} - - -/** - * \brief Searches within Header Entries (Dicom Elements) parsed with - * the public and private dictionaries - * for the element value 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)) - { - return GDCM_UNFOUND; - } - - return ((ValEntry *)TagHT.find(key)->second)->GetValue(); -} - /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag.. - * * Obtaining the VR (Value Representation) might be needed by caller * to convert the string typed content to caller's native type * (think of C++ vs Python). The VR is actually of a higher level * of semantics than just the native C++ type. - * @param group Group number of the searched tag. - * @param element Element number of the searched tag. + * @param group Group number of the searched tag. + * @param elem Element number of the searched tag. * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element) +std::string Document::GetEntryVR(uint16_t group, uint16_t elem) { - DocEntry *elem = GetDocEntryByNumber(group, element); - if ( !elem ) + DocEntry *element = GetDocEntry(group, elem); + if ( !element ) { return GDCM_UNFOUND; } - return elem->GetVR(); + return element->GetVR(); } /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the value length of a given tag.. - * @param group Group number of the searched tag. - * @param element Element number of the searched tag. + * @param group Group number of the searched tag. + * @param elem Element number of the searched tag. * @return Corresponding element length; -2 if not found */ -int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element) +int Document::GetEntryLength(uint16_t group, uint16_t elem) { - DocEntry *elem = GetDocEntryByNumber(group, element); - if ( !elem ) + DocEntry *element = GetDocEntry(group, elem); + if ( !element ) { return -2; //magic number } - return elem->GetLength(); + return element->GetLength(); } /** @@ -832,17 +727,16 @@ int Document::GetEntryLengthByNumber(uint16_t group, uint16_t 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 + * @param group group number of the Dicom Element to modify + * @param elem element number of the Dicom Element to modify */ -bool Document::SetEntryByNumber(std::string const& content, - uint16_t group, uint16_t element) +bool Document::SetEntry(std::string const& content, + uint16_t group, uint16_t elem) { - ValEntry *entry = GetValEntryByNumber(group, element); + ValEntry *entry = GetValEntry(group, elem); if (!entry ) { - Debug::Verbose(0, "Document::SetEntryByNumber: no corresponding", - " ValEntry (try promotion first)."); + gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); return false; } return SetEntry(content,entry); @@ -854,17 +748,16 @@ bool Document::SetEntryByNumber(std::string const& content, * the given value. * @param content new value (void* -> uint8_t*) to substitute with * @param lgth new value length - * @param group group number of the Dicom Element to modify - * @param element element number of the Dicom Element to modify + * @param group group number of the Dicom Element to modify + * @param elem element number of the Dicom Element to modify */ -bool Document::SetEntryByNumber(uint8_t*content, int lgth, - uint16_t group, uint16_t element) +bool Document::SetEntry(uint8_t*content, int lgth, + uint16_t group, uint16_t elem) { - BinEntry *entry = GetBinEntryByNumber(group, element); + BinEntry *entry = GetBinEntry(group, elem); if (!entry ) { - Debug::Verbose(0, "Document::SetEntryByNumber: no corresponding", - " ValEntry (try promotion first)."); + gdcmVerboseMacro( "No corresponding ValEntry (try promotion first)."); return false; } @@ -877,7 +770,7 @@ bool Document::SetEntryByNumber(uint8_t*content, int lgth, * @param content new value (string) to substitute with * @param entry Entry to be modified */ -bool Document::SetEntry(std::string const &content,ValEntry *entry) +bool Document::SetEntry(std::string const &content, ValEntry *entry) { if(entry) { @@ -892,7 +785,7 @@ bool Document::SetEntry(std::string const &content,ValEntry *entry) * and modifies it's content with the given value. * @param content new value (void* -> uint8_t*) to substitute with * @param entry Entry to be modified - * @param lgth new value length + * @param lgth new value length */ bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry) { @@ -920,12 +813,12 @@ bool Document::SetEntry(uint8_t *content, int lgth, BinEntry *entry) * @param elem element number of the Entry * @return Pointer to the 'non string' area */ -void *Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) +void *Document::GetEntryBinArea(uint16_t group, uint16_t elem) { - DocEntry *entry = GetDocEntryByNumber(group, elem); + DocEntry *entry = GetDocEntry(group, elem); if (!entry) { - Debug::Verbose(1, "Document::GetDocEntryByNumber: no entry"); + gdcmVerboseMacro( "No entry"); return 0; } if ( BinEntry *binEntry = dynamic_cast(entry) ) @@ -937,15 +830,15 @@ void *Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) } /** - * \brief Loads (from disk) the element content - * when a string is not suitable + * \brief Loads (from disk) the element content + * when a string is not suitable * @param group group number of the Entry * @param elem element number of the Entry */ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { // Search the corresponding DocEntry - DocEntry *docElement = GetDocEntryByNumber(group, elem); + DocEntry *docElement = GetDocEntry(group, elem); if ( !docElement ) return; @@ -957,39 +850,39 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) } /** - * \brief Loads (from disk) the element content - * when a string is not suitable - * @param element Entry whose binArea is going to be loaded + * \brief Loads (from disk) the element content + * when a string is not suitable + * @param elem Entry whose binArea is going to be loaded */ -void Document::LoadEntryBinArea(BinEntry *element) +void Document::LoadEntryBinArea(BinEntry *elem) { - if(element->GetBinArea()) + if(elem->GetBinArea()) return; bool openFile = !Fp; if(openFile) OpenFile(); - size_t o =(size_t)element->GetOffset(); + size_t o =(size_t)elem->GetOffset(); Fp->seekg(o, std::ios::beg); - size_t l = element->GetLength(); + size_t l = elem->GetLength(); uint8_t *a = new uint8_t[l]; if( !a ) { - Debug::Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); + gdcmVerboseMacro( "Cannot allocate BinEntry content"); return; } /// \todo check the result Fp->read((char*)a, l); - if( Fp->fail() || Fp->eof()) //Fp->gcount() == 1 + if( Fp->fail() || Fp->eof()) { delete[] a; return; } - element->SetBinArea(a); + elem->SetBinArea(a); if(openFile) CloseFile(); @@ -998,14 +891,14 @@ void Document::LoadEntryBinArea(BinEntry *element) /** * \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 + * @param group Group number of the searched Dicom Element + * @param elem Element number of the searched Dicom Element * @return */ -/*bool Document::SetEntryBinAreaByNumber(uint8_t *area, - uint16_t group, uint16_t element) +/*bool Document::SetEntryBinArea(uint8_t *area, + uint16_t group, uint16_t elem) { - DocEntry *currentEntry = GetDocEntryByNumber(group, element); + DocEntry *currentEntry = GetDocEntry(group, elem); if ( !currentEntry ) { return false; @@ -1020,75 +913,12 @@ void Document::LoadEntryBinArea(BinEntry *element) return false; }*/ -/** - * \brief retrieves a Dicom Element (the first one) using (group, element) - * \warning (group, element) IS NOT an identifier inside the Dicom Header - * if you think it's NOT UNIQUE, check the count number - * and use iterators to retrieve ALL the Dicoms Elements within - * a given couple (group, element) - * @param group Group number of the searched Dicom Element - * @param element Element number of the searched Dicom Element - * @return - */ -DocEntry *Document::GetDocEntryByNumber(uint16_t group, uint16_t element) -{ - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key)) - { - return NULL; - } - return TagHT.find(key)->second; -} - -/** - * \brief Same as \ref Document::GetDocEntryByNumber except it only - * returns a result when the corresponding entry is of type - * ValEntry. - * @return When present, the corresponding ValEntry. - */ -ValEntry *Document::GetValEntryByNumber(uint16_t group, uint16_t element) -{ - DocEntry *currentEntry = GetDocEntryByNumber(group, element); - if ( !currentEntry ) - { - return 0; - } - if ( ValEntry *entry = dynamic_cast(currentEntry) ) - { - return entry; - } - Debug::Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry."); - - return 0; -} - -/** - * \brief Same as \ref Document::GetDocEntryByNumber except it only - * returns a result when the corresponding entry is of type - * BinEntry. - * @return When present, the corresponding BinEntry. - */ -BinEntry *Document::GetBinEntryByNumber(uint16_t group, uint16_t element) -{ - DocEntry *currentEntry = GetDocEntryByNumber(group, element); - if ( !currentEntry ) - { - return 0; - } - if ( BinEntry *entry = dynamic_cast(currentEntry) ) - { - return entry; - } - Debug::Verbose(0, "Document::GetBinEntryByNumber: unfound BinEntry."); - - return 0; -} /** - * \brief Loads the element while preserving the current - * underlying file position indicator as opposed to - * to LoadDocEntry that modifies it. - * @param entry Header Entry whose value shall be loaded. + * \brief Loads the element while preserving the current + * underlying file position indicator as opposed to + * LoadDocEntry that modifies it. + * @param entry Header Entry whose value will be loaded. * @return */ void Document::LoadDocEntrySafe(DocEntry *entry) @@ -1110,23 +940,20 @@ uint32_t Document::SwapLong(uint32_t a) { switch (SwapCode) { - case 0 : + case 1234 : break; case 4321 : a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) | ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) ); - break; - + break; case 3412 : a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) ); - break; - + break; case 2143 : a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); - break; + break; default : - //std::cout << "swapCode= " << SwapCode << std::endl; - Debug::Error(" Document::SwapLong : unset swap code"); + gdcmErrorMacro( "Unset swap code:" << SwapCode ); a = 0; } return a; @@ -1179,7 +1006,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, BinEntry *newBinEntry; SeqEntry *newSeqEntry; VRKey vr; - bool used=false; + bool used = false; while (true) { @@ -1188,8 +1015,9 @@ void Document::ParseDES(DocEntrySet *set, long offset, break; } - used=true; + used = true; newDocEntry = ReadNextDocEntry( ); + if ( !newDocEntry ) { break; @@ -1204,23 +1032,24 @@ void Document::ParseDES(DocEntrySet *set, long offset, { if ( newBinEntry ) { - if ( ! Global::GetVR()->IsVROfBinaryRepresentable(vr) ) + if ( Filetype == ExplicitVR && ! Global::GetVR()->IsVROfBinaryRepresentable(vr) ) { ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR - Debug::Verbose(0, "Document::ParseDES: neither Valentry, " - "nor BinEntry. Probably unknown VR."); + gdcmVerboseMacro( std::hex << newDocEntry->GetGroup() + << "|" << newDocEntry->GetElement() + << " : Neither Valentry, nor BinEntry." + "Probably unknown VR."); } //////////////////// BinEntry or UNKOWN VR: // When "this" is a Document the Key is simply of the // form ( group, elem )... - if (Document *dummy = dynamic_cast< Document* > ( set ) ) + if ( 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 + // valEntry in a sequence item, and the key has the // generalized form (refer to \ref BaseTagKey): if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { @@ -1241,9 +1070,8 @@ void Document::ParseDES(DocEntrySet *set, long offset, /////////////////////// ValEntry // 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 @@ -1281,15 +1109,15 @@ void Document::ParseDES(DocEntrySet *set, long offset, if ( ( newDocEntry->GetGroup() == 0x7fe0 ) && ( newDocEntry->GetElement() == 0x0010 ) ) { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts == RLELossless ) + std::string ts = GetTransferSyntax(); + if ( Global::GetTS()->IsRLELossless(ts) ) { long positionOnEntry = Fp->tellg(); Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeRLEInfo(); Fp->seekg( positionOnEntry, std::ios::beg ); } - else if ( IsJPEG() ) + else if ( Global::GetTS()->IsJPEG(ts) ) { long positionOnEntry = Fp->tellg(); Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); @@ -1323,13 +1151,13 @@ void Document::ParseDES(DocEntrySet *set, long offset, // 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 ) ) @@ -1366,10 +1194,13 @@ void Document::ParseSQ( SeqEntry *seqEntry, { 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 @@ -1379,7 +1210,7 @@ void Document::ParseSQ( SeqEntry *seqEntry, { if ( newDocEntry->IsSequenceDelimitor() ) { - seqEntry->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetDelimitationItem( newDocEntry ); break; } } @@ -1388,7 +1219,7 @@ void Document::ParseSQ( SeqEntry *seqEntry, delete newDocEntry; break; } - + // create the current SQItem SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); std::ostringstream newBase; newBase << seqEntry->GetKey() @@ -1406,11 +1237,23 @@ 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 ) { @@ -1478,8 +1321,8 @@ 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 ... @@ -1555,8 +1398,8 @@ void Document::LoadDocEntry(DocEntry *entry) if( length % 2 ) { newValue = Util::DicomString(str, length+1); - //Debug::Verbose(0, "Warning: bad length: ", length ); - Debug::Verbose(0, "For string :", newValue.c_str()); + gdcmVerboseMacro("Warning: bad length: " << length << + ",For string :" << newValue.c_str()); // Since we change the length of string update it length //entry->SetReadLength(length+1); } @@ -1568,10 +1411,9 @@ void Document::LoadDocEntry(DocEntry *entry) if ( ValEntry *valEntry = dynamic_cast(entry) ) { - if ( Fp->fail() || Fp->eof())//Fp->gcount() == 1 + if ( Fp->fail() || Fp->eof()) { - Debug::Verbose(1, "Document::LoadDocEntry", - "unread element value"); + gdcmVerboseMacro("Unread element value"); valEntry->SetValue(GDCM_UNREAD); return; } @@ -1588,8 +1430,7 @@ void Document::LoadDocEntry(DocEntry *entry) } else { - Debug::Error(true, "Document::LoadDocEntry" - "Should have a ValEntry, here !"); + gdcmErrorMacro( "Should have a ValEntry, here !"); } } @@ -1601,7 +1442,6 @@ void Document::LoadDocEntry(DocEntry *entry) void Document::FindDocEntryLength( DocEntry *entry ) throw ( FormatError ) { - uint16_t element = entry->GetElement(); std::string vr = entry->GetVR(); uint16_t length16; @@ -1649,6 +1489,14 @@ void Document::FindDocEntryLength( DocEntry *entry ) // Length is encoded on 2 bytes. length16 = ReadInt16(); + + // FIXME : This heuristic supposes that the first group following + // group 0002 *has* and element 0000. + // BUT ... Element 0000 is optionnal :-( + + + // Fixed using : HandleOutOfGroup0002() + // (first hereafter strategy ...) // We can tell the current file is encoded in big endian (like // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag @@ -1669,6 +1517,8 @@ void Document::FindDocEntryLength( DocEntry *entry ) // ones with zero as element number) has to be of 4 (0x0004). When we // encounter 1024 (0x0400) chances are the encoding changed and we // found a group with big endian encoding. + //---> Unfortunately, element 0000 is optional. + //---> This will not work when missing! // We shall use this second strategy. In order to make sure that we // can interpret the presence of an apparently big endian encoded // length of a "Group Length" without committing a big mistake, we @@ -1677,38 +1527,39 @@ void Document::FindDocEntryLength( DocEntry *entry ) // endian encoding". When this is the case, chances are we have got our // hands on a big endian encoded file: we switch the swap code to // big endian and proceed... - if ( element == 0x0000 && length16 == 0x0400 ) - { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts != ExplicitVRBigEndian ) - { - throw FormatError( "Document::FindDocEntryLength()", - " not explicit VR." ); - return; - } - length16 = 4; - SwitchSwapToBigEndian(); - - // Restore the unproperly loaded values i.e. the group, the element - // and the dictionary entry depending on them. - uint16_t correctGroup = SwapShort( entry->GetGroup() ); - uint16_t correctElem = SwapShort( entry->GetElement() ); - DictEntry *newTag = GetDictEntryByNumber( correctGroup, - correctElem ); - if ( !newTag ) - { - // This correct tag is not in the dictionary. Create a new one. - newTag = NewVirtualDictEntry(correctGroup, correctElem); - } - // FIXME this can create a memory leaks on the old entry that be - // left unreferenced. - entry->SetDictEntry( newTag ); - } - - // Heuristic: well, some files are really ill-formed. + +// if ( element == 0x0000 && length16 == 0x0400 ) +// { +// std::string ts = GetTransferSyntax(); +// if ( Global::GetTS()->GetSpecialTransferSyntax(ts) +// != TS::ExplicitVRBigEndian ) +// { +// throw FormatError( "Document::FindDocEntryLength()", +// " not explicit VR." ); +// return; +// } +// length16 = 4; +// SwitchByteSwapCode(); +// +// // Restore the unproperly loaded values i.e. the group, the element +// // and the dictionary entry depending on them. +// uint16_t correctGroup = SwapShort( entry->GetGroup() ); +// uint16_t correctElem = SwapShort( entry->GetElement() ); +// DictEntry *newTag = GetDictEntry( correctGroup, correctElem ); +// if ( !newTag ) +// { +// // This correct tag is not in the dictionary. Create a new one. +// newTag = NewVirtualDictEntry(correctGroup, correctElem); +// } +// // FIXME this can create a memory leaks on the old entry that be +// // left unreferenced. +// entry->SetDictEntry( newTag ); +// } + + // 0xffff means that we deal with 'No Length' Sequence + // or 'No Length' SQItem if ( length16 == 0xffff) - { - // 0xffff means that we deal with 'Unknown Length' Sequence + { length16 = 0; } FixDocEntryFoundLength( entry, (uint32_t)length16 ); @@ -1722,6 +1573,9 @@ void Document::FindDocEntryLength( DocEntry *entry ) // on Data elements "Implicit and Explicit VR Data Elements shall // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. + + // Well ... group 0002 is always coded in 'Explicit VR Litle Endian' + // even if Transfer Syntax is 'Implicit VR ...' FixDocEntryFoundLength( entry, ReadInt32() ); return; @@ -1735,7 +1589,7 @@ void Document::FindDocEntryLength( DocEntry *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 @@ -1753,9 +1607,9 @@ std::string Document::FindDocEntryVR() if( !CheckDocEntryVR(vr) ) { Fp->seekg(positionOnEntry, std::ios::beg); - return(GDCM_UNKNOWN); + return GDCM_UNKNOWN; } - return(vr); + return vr; } /** @@ -1921,14 +1775,13 @@ void Document::SkipDocEntry(DocEntry *entry) /** * \brief Skips to the begining of the next Header Entry * \warning NOT end user intended method ! - * @param offset start of skipping - * @param readLgth length to skip - + * @param currentDocEntry entry to skip */ -void Document::SkipToNextDocEntry(DocEntry *newDocEntry) +void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) { - Fp->seekg((long)(newDocEntry->GetOffset()), std::ios::beg); - Fp->seekg( (long)(newDocEntry->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); } /** @@ -1936,7 +1789,7 @@ void Document::SkipToNextDocEntry(DocEntry *newDocEntry) * 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) @@ -1952,17 +1805,14 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, if ( foundLength % 2) { - std::ostringstream s; - s << "Warning : Tag with uneven length " - << foundLength - << " in x(" << std::hex << gr << "," << elem <<")" << std::dec; - Debug::Verbose(0, s.str().c_str()); + gdcmVerboseMacro( "Warning : Tag with uneven length " << foundLength + << " in x(" << std::hex << gr << "," << elem <<")"); } //////// Fix for some naughty General Electric images. // Allthough not recent many such GE corrupted images are still present // on Creatis hard disks. Hence this fix shall remain when such images - // are no longer in user (we are talking a few years, here)... + // are no longer in use (we are talking a few years, here)... // Note: XMedCom probably uses such a trick since it is able to read // those pesky GE images ... if ( foundLength == 13) @@ -2015,7 +1865,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, */ bool Document::IsDocEntryAnInteger(DocEntry *entry) { - uint16_t element = entry->GetElement(); + uint16_t elem = entry->GetElement(); uint16_t group = entry->GetGroup(); const std::string &vr = entry->GetVR(); uint32_t length = entry->GetLength(); @@ -2023,7 +1873,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) // 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 ) { @@ -2038,13 +1888,11 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) // test is useless (and might even look a bit paranoid), when we // encounter such an ill-formed image, we simply display a warning // message and proceed on parsing (while crossing fingers). - std::ostringstream s; long filePosition = Fp->tellg(); - s << "Erroneous Group Length element length on : (" \ - << std::hex << group << " , " << element + gdcmVerboseMacro( "Erroneous Group Length element length on : (" + << std::hex << group << " , " << elem << ") -before- position x(" << filePosition << ")" - << "lgt : " << length; - Debug::Verbose(0, "Document::IsDocEntryAnInteger", s.str().c_str() ); + << "lgt : " << length ); } } @@ -2080,8 +1928,8 @@ uint32_t Document::FindDocEntryLengthOBOrOW() } catch ( FormatError ) { - throw FormatError("Document::FindDocEntryLengthOBOrOW()", - " group or element not present."); + throw FormatError("Unexpected end of file encountered during ", + "Document::FindDocEntryLengthOBOrOW()"); } // We have to decount the group and element we just read @@ -2089,12 +1937,13 @@ uint32_t Document::FindDocEntryLengthOBOrOW() if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { - Debug::Verbose(1, "Document::FindDocEntryLengthOBOrOW: neither an Item " - "tag nor a Sequence delimiter tag."); + long filePosition = Fp->tellg(); + gdcmVerboseMacro( "Neither an Item tag nor a Sequence delimiter tag on :" + << std::hex << group << " , " << elem + << ") -before- position x(" << filePosition << ")" ); + Fp->seekg(positionOnEntry, std::ios::beg); - throw FormatUnexpected("Document::FindDocEntryLengthOBOrOW()", - "Neither an Item tag nor a Sequence " - "delimiter tag."); + throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag."); } if ( elem == 0xe0dd ) @@ -2175,7 +2024,7 @@ void Document::SkipBytes(uint32_t nBytes) * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ -void Document::Initialise() +void Document::Initialize() { RefPubDict = Global::GetDicts()->GetDefaultPubDict(); RefShaDict = NULL; @@ -2217,25 +2066,24 @@ bool Document::CheckSwap() net2host = false; } - // The easiest case is the one of a DICOM header, since it possesses a - // file preamble where it suffice to look for the string "DICM". + // 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 ) { - Debug::Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3"); + gdcmVerboseMacro( "Looks like DICOM Version3 (preamble + DCM)" ); - // Next, determine the value representation (VR). Let's skip to the - // first element (0002, 0000) and check there if we find "UL" - // - or "OB" if the 1st one is (0002,0001) -, + // Group 0002 should always be VR, and the first element 0000 + // Let's be carefull (so many wrong headers ...) + // and determine the value representation (VR) : + // Let's skip to the first element (0002,0000) and check there if we find + // "UL" - or "OB" if the 1st one is (0002,0001) -, // in which case we (almost) know it is explicit VR. // WARNING: if it happens to be implicit VR then what we will read // is the length of the group. If this ascii representation of this // length happens to be "UL" then we shall believe it is explicit VR. - // FIXME: in order to fix the above warning, we could read the next - // element value (or a couple of elements values) in order to make - // sure we are not commiting a big mistake. // We need to skip : // * the 128 bytes of File Preamble (often padded with zeroes), // * the 4 bytes of "DICM" string, @@ -2243,46 +2091,42 @@ 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; - Debug::Verbose(1, "Document::CheckSwap:", - "explicit Value Representation"); + gdcmVerboseMacro( "Group 0002 : Explicit Value Representation"); } else { Filetype = ImplicitVR; - Debug::Verbose(1, "Document::CheckSwap:", - "not an explicit Value Representation"); + gdcmVerboseMacro( "Group 0002 :Not an explicit Value Representation;" + << "Looks like a bugged Header!"); } if ( net2host ) { SwapCode = 4321; - Debug::Verbose(1, "Document::CheckSwap:", - "HostByteOrder != NetworkByteOrder"); + gdcmVerboseMacro( "HostByteOrder != NetworkByteOrder"); } else { - SwapCode = 0; - Debug::Verbose(1, "Document::CheckSwap:", - "HostByteOrder = NetworkByteOrder"); + SwapCode = 1234; + gdcmVerboseMacro( "HostByteOrder = NetworkByteOrder"); } - // Position the file position indicator at first tag (i.e. - // after the file preamble and the "DICM" string). + // Position the file position indicator at first tag + // (i.e. after the file preamble and the "DICM" string). Fp->seekg(0, std::ios::beg); Fp->seekg ( 132L, std::ios::beg); return true; @@ -2291,7 +2135,7 @@ 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). - Debug::Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file"); + gdcmVerboseMacro( "Not a DICOM Version3 file"); Fp->seekg(0, std::ios::beg); // Our next best chance would be to be considering a 'clean' ACR/NEMA file. @@ -2320,7 +2164,7 @@ bool Document::CheckSwap() Filetype = ACR; return true; case 0x00000004 : - SwapCode = 0; + SwapCode = 1234; Filetype = ACR; return true; default : @@ -2351,7 +2195,7 @@ bool Document::CheckSwap() case 0x0006 : case 0x0007 : case 0x0008 : - SwapCode = 0; + SwapCode = 1234; Filetype = ACR; return true; case 0x0100 : @@ -2366,37 +2210,26 @@ bool Document::CheckSwap() Filetype = ACR; return true; default : - Debug::Verbose(0, "Document::CheckSwap:", - "ACR/NEMA unfound swap info (Really hopeless !)"); + gdcmVerboseMacro( "ACR/NEMA unfound swap info (Really hopeless !)"); Filetype = Unknown; return false; } - // Then the only info we have is the net2host one. - //if (! net2host ) - // SwapCode = 0; - //else - // SwapCode = 4321; - //return; } } - - /** - * \brief Restore the unproperly loaded values i.e. the group, the element - * and the dictionary entry depending on them. + * \brief Change the Byte Swap code. */ -void Document::SwitchSwapToBigEndian() +void Document::SwitchByteSwapCode() { - Debug::Verbose(1, "Document::SwitchSwapToBigEndian", - "Switching to BigEndian mode."); - if ( SwapCode == 0 ) + gdcmVerboseMacro( "Switching Byte Swap code from "<< SwapCode); + if ( SwapCode == 1234 ) { SwapCode = 4321; } else if ( SwapCode == 4321 ) { - SwapCode = 0; + SwapCode = 1234; } else if ( SwapCode == 3412 ) { @@ -2434,7 +2267,6 @@ void Document::SetMaxSizeLoadEntry(long newSize) */ void Document::SetMaxSizePrintEntry(long newSize) { - //DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME if ( newSize < 0 ) { return; @@ -2455,7 +2287,7 @@ void Document::SetMaxSizePrintEntry(long newSize) * apparent reason * @return no return */ -void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) +void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) { // Endian reversion. Some files contain groups of tags with reversed endianess. static int reversedEndian = 0; @@ -2464,23 +2296,92 @@ void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) { // start endian swap mark for group found reversedEndian++; - SwitchSwapToBigEndian(); + SwitchByteSwapCode(); // fix the tag group = 0xfffe; elem = 0xe000; } - else if ((group == 0xfffe) && (elem == 0xe00d) && reversedEndian) + else if (group == 0xfffe && elem == 0xe00d && reversedEndian) { // end of reversed endian group reversedEndian--; - SwitchSwapToBigEndian(); + SwitchByteSwapCode(); + } +} + +/** + * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS + * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID) + */ +std::string Document::GetTransferSyntaxName() +{ + // use the TS (TS : Transfer Syntax) + std::string transferSyntax = GetEntry(0x0002,0x0010); + + if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) ) + { + gdcmErrorMacro( "Transfer Syntax not loaded. " << std::endl + << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" ); + return "Uncompressed ACR-NEMA"; + } + if ( transferSyntax == GDCM_UNFOUND ) + { + gdcmVerboseMacro( "Unfound Transfer Syntax (0002,0010)"); + return "Uncompressed ACR-NEMA"; + } + + // we do it only when we need it + const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax ); + + // Global::GetTS() is a global static you shall never try to delete it! + return tsName; +} + +/** + * \brief Group 0002 is always coded Little Endian + * whatever Transfer Syntax is + * @return no return + */ +void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) +{ + // Endian reversion. Some files contain groups of tags with reversed endianess. + if ( !Group0002Parsed && group != 0x0002) + { + Group0002Parsed = true; + // we just came out of group 0002 + // if Transfer syntax is Big Endian we have to change CheckSwap + + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsTransferSyntax(ts) ) + { + gdcmVerboseMacro("True DICOM File, with NO Tansfer Syntax: " << ts ); + return; + } + + // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..." + + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian ) + { + Filetype = ImplicitVR; + } + + // FIXME Strangely, this works with + //'Implicit VR Transfer Syntax (GE Private) + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian ) + { + gdcmVerboseMacro("Transfer Syntax Name = [" + << GetTransferSyntaxName() << "]" ); + SwitchByteSwapCode(); + group = SwapShort(group); + elem = SwapShort(elem); + } } } /** * \brief Read the next tag but WITHOUT loading it's value * (read the 'Group Number', the 'Element Number', - * gets the Dict Entry + * gets the Dict Entry * gets the VR, gets the length, gets the offset value) * @return On succes the newly created DocEntry, NULL on failure. */ @@ -2502,35 +2403,44 @@ DocEntry *Document::ReadNextDocEntry() return 0; } + // Sometimes file contains groups of tags with reversed endianess. HandleBrokenEndian(group, elem); + +// In 'true DICOM' files Group 0002 is always little endian + if ( HasDCMPreamble ) + HandleOutOfGroup0002(group, elem); + std::string vr = FindDocEntryVR(); std::string realVR = vr; if( vr == GDCM_UNKNOWN) { - DictEntry *dictEntry = GetDictEntryByNumber(group,elem); + DictEntry *dictEntry = GetDictEntry(group,elem); if( dictEntry ) realVR = dictEntry->GetVR(); } DocEntry *newEntry; if( Global::GetVR()->IsVROfSequence(realVR) ) - newEntry = NewSeqEntryByNumber(group, elem); + newEntry = NewSeqEntry(group, elem); else if( Global::GetVR()->IsVROfStringRepresentable(realVR) ) - newEntry = NewValEntryByNumber(group, elem,vr); + newEntry = NewValEntry(group, elem,vr); else - newEntry = NewBinEntryByNumber(group, elem,vr); + 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()); - Debug::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()); + gdcmVerboseMacro( msg.c_str() ); + } } newEntry->SetImplicitVR(); } @@ -2552,25 +2462,25 @@ DocEntry *Document::ReadNextDocEntry() return newEntry; } - +//GenerateFreeTagKeyInGroup? What was it designed for ?!? /** * \brief Generate a free TagKey i.e. a TagKey that is not present * in the TagHt dictionary. * @param group The generated tag must belong to this group. * @return The element of tag with given group which is fee. */ -uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group) -{ - for (uint32_t elem = 0; elem < UINT32_MAX; elem++) - { - TagKey key = DictEntry::TranslateToKey(group, elem); - if (TagHT.count(key) == 0) - { - return elem; - } - } - return UINT32_MAX; -} +//uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group) +//{ +// for (uint32_t elem = 0; elem < UINT32_MAX; elem++) +// { +// TagKey key = DictEntry::TranslateToKey(group, elem); +// if (TagHT.count(key) == 0) +// { +// return elem; +// } +// } +// return UINT32_MAX; +//} /** * \brief Assuming the internal file pointer \ref Document::Fp @@ -2606,15 +2516,13 @@ bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) } if ( itemTagGroup != testGroup || itemTagElement != testElement ) { - std::ostringstream s; - s << " We should have found tag ("; - s << std::hex << testGroup << "," << testElement << ")" << std::endl; - s << " but instead we encountered tag ("; - s << std::hex << itemTagGroup << "," << itemTagElement << ")" - << std::endl; - s << " at address: " << (unsigned)currentPosition << std::endl; - Debug::Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:"); - Debug::Verbose(0, s.str().c_str()); + gdcmVerboseMacro( "Wrong Item Tag found:" + << " We should have found tag (" + << std::hex << testGroup << "," << testElement << ")" << std::endl + << " but instead we encountered tag (" + << std::hex << itemTagGroup << "," << itemTagElement << ")" + << " at address: " << " 0x(" << (unsigned int)currentPosition << ")" + ) ; Fp->seekg(positionOnEntry, std::ios::beg); return false; @@ -2638,8 +2546,6 @@ bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) */ uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement) { - long positionOnEntry = Fp->tellg(); - (void)positionOnEntry; if ( !ReadTag(testGroup, testElement) ) { @@ -2650,11 +2556,9 @@ uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement) long currentPosition = Fp->tellg(); uint32_t itemLength = ReadInt32(); { - std::ostringstream s; - s << "Basic Item Length is: " - << itemLength << std::endl; - s << " at address: " << (unsigned)currentPosition << std::endl; - Debug::Verbose(0, "Document::ReadItemTagLength: ", s.str().c_str()); + gdcmVerboseMacro( "Basic Item Length is: " + << itemLength << std::endl + << " at address: " << std::hex << (unsigned int)currentPosition); } return itemLength; } @@ -2684,12 +2588,8 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() { uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], uint32_t); - std::ostringstream s; - s << " Read one length: "; - s << std::hex << individualLength << std::endl; - Debug::Verbose(0, - "Document::ReadAndSkipEncapsulatedBasicOffsetTable: ", - s.str().c_str()); + gdcmVerboseMacro( "Read one length: " << + std::hex << individualLength ); } #endif //GDCM_DEBUG @@ -2704,8 +2604,8 @@ void Document::ReadAndSkipEncapsulatedBasicOffsetTable() */ void Document::ComputeRLEInfo() { - TransferSyntaxType ts = GetTransferSyntax(); - if ( ts != RLELossless ) + std::string ts = GetTransferSyntax(); + if ( !Global::GetTS()->IsRLELossless(ts) ) { return; } @@ -2746,7 +2646,7 @@ void Document::ComputeRLEInfo() if ( nbRleSegments > 16 ) { // There should be at most 15 segments (refer to RLEFrame class) - Debug::Verbose(0, "Document::ComputeRLEInfo: too many segments."); + gdcmVerboseMacro( "Too many segments."); } uint32_t rleSegmentOffsetTable[16]; @@ -2789,8 +2689,7 @@ void Document::ComputeRLEInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - Debug::Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); - Debug::Verbose(0, " item at end of RLE item sequence"); + gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence"); } } @@ -2803,7 +2702,8 @@ void Document::ComputeRLEInfo() void Document::ComputeJPEGFragmentInfo() { // If you need to, look for comments of ComputeRLEInfo(). - if ( ! IsJPEG() ) + std::string ts = GetTransferSyntax(); + if ( ! Global::GetTS()->IsJPEG(ts) ) { return; } @@ -2830,12 +2730,11 @@ void Document::ComputeJPEGFragmentInfo() // Delimiter Item': if ( !ReadTag(0xfffe, 0xe0dd) ) { - Debug::Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter "); - Debug::Verbose(0, " item at end of JPEG item sequence"); + gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence"); } } -/** +/* * \brief Walk recursively the given \ref DocEntrySet, and feed * the given hash table (\ref TagDocEntryHT) with all the * \ref DocEntry (Dicom entries) encountered. @@ -2844,7 +2743,7 @@ void Document::ComputeJPEGFragmentInfo() * when recursively walking the given set. * @param set The structure to be traversed (recursively). */ -void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, +/*void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, DocEntrySet *set ) { if (ElementSet *elementSet = dynamic_cast< ElementSet* > ( set ) ) @@ -2894,9 +2793,9 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, } } -} +}*/ -/** +/* * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current * Document. * @@ -2919,12 +2818,12 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, * \ref BuildFlatHashTable again... * @return The flat std::map<> we juste build. */ -TagDocEntryHT *Document::BuildFlatHashTable() +/*TagDocEntryHT *Document::BuildFlatHashTable() { TagDocEntryHT *FlatHT = new TagDocEntryHT; BuildFlatHashTableRecurse( *FlatHT, this ); return FlatHT; -} +}*/ @@ -2938,8 +2837,8 @@ TagDocEntryHT *Document::BuildFlatHashTable() bool Document::operator<(Document &document) { // Patient Name - std::string s1 = GetEntryByNumber(0x0010,0x0010); - std::string s2 = document.GetEntryByNumber(0x0010,0x0010); + std::string s1 = GetEntry(0x0010,0x0010); + std::string s2 = document.GetEntry(0x0010,0x0010); if(s1 < s2) { return true; @@ -2951,8 +2850,8 @@ bool Document::operator<(Document &document) else { // Patient ID - s1 = GetEntryByNumber(0x0010,0x0020); - s2 = document.GetEntryByNumber(0x0010,0x0020); + s1 = GetEntry(0x0010,0x0020); + s2 = document.GetEntry(0x0010,0x0020); if ( s1 < s2 ) { return true; @@ -2964,8 +2863,8 @@ bool Document::operator<(Document &document) else { // Study Instance UID - s1 = GetEntryByNumber(0x0020,0x000d); - s2 = document.GetEntryByNumber(0x0020,0x000d); + s1 = GetEntry(0x0020,0x000d); + s2 = document.GetEntry(0x0020,0x000d); if ( s1 < s2 ) { return true; @@ -2977,8 +2876,8 @@ bool Document::operator<(Document &document) else { // Serie Instance UID - s1 = GetEntryByNumber(0x0020,0x000e); - s2 = document.GetEntryByNumber(0x0020,0x000e); + s1 = GetEntry(0x0020,0x000e); + s2 = document.GetEntry(0x0020,0x000e); if ( s1 < s2 ) { return true; @@ -3007,10 +2906,7 @@ int Document::ComputeGroup0002Length( FileType filetype ) bool found0002 = false; // for each zero-level Tag in the DCM Header - DocEntry *entry; - - Initialize(); - entry = GetNextEntry(); + DocEntry *entry = GetFirstEntry(); while(entry) { gr = entry->GetGroup();