X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=c5d391396cc11c60b7b040b24e07c9d19869ce90;hb=0b01703cc07d46a6ae718e01c6beee14599a9da1;hp=2f0f843a333b40a1007b8c9fc55a6e2184d2a187;hpb=a9009b11831b3d20710bcc68a988b14724459afa;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 2f0f843a..c5d39139 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/10/22 04:13:25 $ - Version: $Revision: 1.109 $ + Date: $Date: 2004/11/24 11:17:47 $ + Version: $Revision: 1.136 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -28,7 +28,7 @@ #include // For nthos: -#ifdef _MSC_VER +#if defined(_MSC_VER) || defined(__BORLANDC__) #include #else #include @@ -39,6 +39,8 @@ 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 @@ -84,13 +86,13 @@ const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; * \brief constructor * @param filename file to be opened for parsing */ -Document::Document( std::string const & filename ) - : ElementSet(-1) +Document::Document( std::string const & filename ) : ElementSet(-1) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; Initialise(); + Fp = 0; if ( !OpenFile() ) { return; @@ -180,11 +182,14 @@ Document::Document( std::string const & filename ) * \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; + Filetype = ExplicitVR; PrintLevel = 1; // 'Medium' print level by default } @@ -196,13 +201,8 @@ Document::~Document () RefPubDict = NULL; RefShaDict = NULL; - // Recursive clean up of sequences - for (TagDocEntryHT::const_iterator it = TagHT.begin(); - it != TagHT.end(); ++it ) - { - //delete it->second; //temp remove - } - TagHT.clear(); + delete RLEInfo; + delete JPEGInfo; } //----------------------------------------------------------------------------- @@ -290,14 +290,11 @@ bool Document::IsReadable() return true; } - /** - * \brief Internal function that checks whether the Transfer Syntax given - * as argument is the one present in the current document. - * @param syntaxToCheck The transfert syntax we need to check against. - * @return True when SyntaxToCheck corresponds to the Transfer Syntax of - * the current document. False either when the document contains - * no Transfer Syntax, or when the Tranfer Syntaxes doesn't match. + * \brief Accessor to the Transfer Syntax (when present) of the + * current document (it internally handles reading the + * value from disk when only parsing occured). + * @return The encountered Transfer Syntax of the current document. */ TransferSyntaxType Document::GetTransferSyntax() { @@ -321,7 +318,7 @@ TransferSyntaxType Document::GetTransferSyntax() // for brain damaged headers return UnknownTS; } - while ( !isdigit(transfer[transfer.length()-1]) ) + while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { transfer.erase(transfer.length()-1, 1); } @@ -413,6 +410,14 @@ FileType Document::GetFileType() */ std::ifstream* Document::OpenFile() { + if (Filename.length() == 0) return 0; + if(Fp) + { + dbg.Verbose( 0, + "Document::OpenFile is already opened when opening: ", + Filename.c_str()); + } + Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); if(!Fp) @@ -426,8 +431,12 @@ std::ifstream* Document::OpenFile() uint16_t zero; Fp->read((char*)&zero, (size_t)2 ); - //ACR -- or DICOM with no Preamble -- - if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 ) + //ACR -- or DICOM with no Preamble; may start with a Shadow Group -- + if( + zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 || + zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 || + zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 || + zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ) { return Fp; } @@ -441,7 +450,7 @@ std::ifstream* Document::OpenFile() return Fp; } - Fp->close(); + CloseFile(); dbg.Verbose( 0, "Document::OpenFile not DICOM/ACR (missing preamble)", Filename.c_str()); @@ -455,11 +464,14 @@ std::ifstream* Document::OpenFile() */ bool Document::CloseFile() { - Fp->close(); - delete Fp; - Fp = 0; + if( Fp ) + { + Fp->close(); + delete Fp; + Fp = 0; + } - return true; //FIXME how do we detect a non-close ifstream ? + return true; //FIXME how do we detect a non-close ifstream ? } /** @@ -478,7 +490,8 @@ void Document::Write(std::ofstream* fp, FileType filetype) if (filetype == ImplicitVR) { - std::string ts = TransferSyntaxStrings[ImplicitVRLittleEndian]; + std::string ts = + Util::DicomString( TransferSyntaxStrings[ImplicitVRLittleEndian] ); ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); /// \todo Refer to standards on page 21, chapter 6.2 @@ -491,8 +504,9 @@ void Document::Write(std::ofstream* fp, FileType filetype) if (filetype == ExplicitVR) { - std::string ts = TransferSyntaxStrings[ExplicitVRLittleEndian]; - ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); + std::string ts = + Util::DicomString( TransferSyntaxStrings[ExplicitVRLittleEndian] ); + ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); //LEAK /// \todo Refer to standards on page 21, chapter 6.2 /// "Value representation": values with a VR of UI shall be @@ -524,7 +538,7 @@ void Document::Write(std::ofstream* fp, FileType filetype) * @param value (string) Value to be set * @param group Group number of the Entry * @param elem Element number of the Entry - * @param VR V(alue) R(epresentation) of the Entry -if private Entry- + * @param vr V(alue) R(epresentation) of the Entry -if private Entry- * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ @@ -532,7 +546,7 @@ ValEntry* Document::ReplaceOrCreateByNumber( std::string const & value, uint16_t group, uint16_t elem, - std::string const & VR ) + TagName const & vr ) { ValEntry* valEntry = 0; DocEntry* currentEntry = GetDocEntryByNumber( group, elem); @@ -548,7 +562,7 @@ ValEntry* Document::ReplaceOrCreateByNumber( DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); if (!dictEntry) { - currentEntry = NewDocEntryByNumber(group, elem,VR); + currentEntry = NewDocEntryByNumber(group, elem, vr); } else { @@ -561,11 +575,16 @@ ValEntry* Document::ReplaceOrCreateByNumber( " 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 @@ -579,12 +598,14 @@ ValEntry* Document::ReplaceOrCreateByNumber( 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; @@ -600,6 +621,7 @@ ValEntry* Document::ReplaceOrCreateByNumber( /* * \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 @@ -611,7 +633,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( int lgth, uint16_t group, uint16_t elem, - std::string const& VR ) + TagName const & vr ) { BinEntry* binEntry = 0; DocEntry* currentEntry = GetDocEntryByNumber( group, elem); @@ -628,7 +650,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( if (!dictEntry) { - currentEntry = NewDocEntryByNumber(group, elem, VR); + currentEntry = NewDocEntryByNumber(group, elem, vr); } else { @@ -671,7 +693,23 @@ BinEntry* Document::ReplaceOrCreateByNumber( } } - SetEntryByNumber(binArea, lgth, group, elem); + uint8_t *tmpArea; + if (lgth>0 && binArea) + { + tmpArea = new uint8_t[lgth]; + memcpy(tmpArea,binArea,lgth); + } + else + { + tmpArea = 0; + } + if (!SetEntryByNumber(tmpArea, lgth, group, elem)) + { + if (tmpArea) + { + delete[] tmpArea; + } + } return binEntry; } @@ -685,9 +723,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( * \return pointer to the modified/created SeqEntry (NULL when creation * failed). */ -SeqEntry* Document::ReplaceOrCreateByNumber( - uint16_t group, - uint16_t elem) +SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) { SeqEntry* b = 0; DocEntry* a = GetDocEntryByNumber( group, elem); @@ -714,7 +750,7 @@ SeqEntry* Document::ReplaceOrCreateByNumber( * \return boolean */ bool Document::ReplaceIfExistByNumber(std::string const & value, - uint16_t group, uint16_t elem ) + uint16_t group, uint16_t elem ) { SetEntryByNumber(value, group, elem); @@ -733,7 +769,7 @@ bool Document::ReplaceIfExistByNumber(std::string const & value, bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) { const std::string &key = DictEntry::TranslateToKey(group, element ); - return TagHT.count(key); + return TagHT.count(key) != 0; } /** @@ -745,7 +781,7 @@ bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string Document::GetEntryByName(TagName const& tagName) +std::string Document::GetEntryByName(TagName const & tagName) { DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) @@ -778,7 +814,7 @@ std::string Document::GetEntryVRByName(TagName const& tagName) } DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); + dictEntry->GetElement()); return elem->GetVR(); } @@ -850,7 +886,8 @@ int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element) * @param tagName name of the searched Dicom Element. * @return true when found */ -bool Document::SetEntryByName(std::string const & content,std::string const & tagName) +bool Document::SetEntryByName( std::string const & content, + TagName const & tagName) { DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) @@ -871,8 +908,7 @@ bool Document::SetEntryByName(std::string const & content,std::string const & ta * @param element element number of the Dicom Element to modify */ bool Document::SetEntryByNumber(std::string const& content, - uint16_t group, - uint16_t element) + uint16_t group, uint16_t element) { int c; int l; @@ -885,13 +921,10 @@ bool Document::SetEntryByNumber(std::string const& content, return false; } // Non even content must be padded with a space (020H)... - std::string finalContent = content; - if( finalContent.length() % 2 ) - { - finalContent += '\0'; // ... therefore we padd with (000H) .!?! - } + std::string finalContent = Util::DicomString( content.c_str() ); + assert( !(finalContent.size() % 2) ); valEntry->SetValue(finalContent); - + // Integers have a special treatement for their length: l = finalContent.length(); @@ -924,10 +957,8 @@ bool Document::SetEntryByNumber(std::string const& content, * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool Document::SetEntryByNumber(uint8_t*content, - int lgth, - uint16_t group, - uint16_t element) +bool Document::SetEntryByNumber(uint8_t*content, int lgth, + uint16_t group, uint16_t element) { (void)lgth; //not used TagKey key = DictEntry::TranslateToKey(group, element); @@ -943,10 +974,10 @@ bool Document::SetEntryByNumber(uint8_t*content, //content = content + '\0'; // fing a trick to enlarge a binary field? } */ - BinEntry* a = (BinEntry *)TagHT[key]; - a->SetBinArea(content); - a->SetLength(lgth); - a->SetValue(GDCM_BINLOADED); + BinEntry* entry = (BinEntry *)TagHT[key]; + entry->SetBinArea(content); + entry->SetLength(lgth); + entry->SetValue(GDCM_BINLOADED); return true; } @@ -963,8 +994,7 @@ bool Document::SetEntryByNumber(uint8_t*content, * @return true on success, false otherwise. */ bool Document::SetEntryLengthByNumber(uint32_t l, - uint16_t group, - uint16_t element) + uint16_t group, uint16_t element) { /// \todo use map methods, instead of multimap JPR TagKey key = DictEntry::TranslateToKey(group, element); @@ -1028,61 +1058,78 @@ void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) * @param group group number of the Entry * @param elem element number of the Entry */ -void* Document::LoadEntryBinArea(uint16_t group, uint16_t elem) +void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { + // Search the corresponding DocEntry DocEntry *docElement = GetDocEntryByNumber(group, elem); if ( !docElement ) - { - return NULL; - } - size_t o =(size_t)docElement->GetOffset(); + return; + + BinEntry *binElement = dynamic_cast(docElement); + if( !binElement ) + return; + + LoadEntryBinArea(binElement); +/* size_t o =(size_t)docElement->GetOffset(); Fp->seekg( o, std::ios_base::beg); size_t l = docElement->GetLength(); uint8_t* a = new uint8_t[l]; if(!a) { dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); - return NULL; + return; } + + // Read the value Fp->read((char*)a, l); if( Fp->fail() || Fp->eof() )//Fp->gcount() == 1 { delete[] a; - return NULL; + return; } - /// \todo Drop any already existing void area! JPR + + // Set the value to the DocEntry if( !SetEntryBinAreaByNumber( a, group, elem ) ) { + delete[] a; dbg.Verbose(0, "Document::LoadEntryBinArea setting failed."); - } - return a; + }*/ } + /** * \brief Loads (from disk) the element content * when a string is not suitable * @param element Entry whose binArea is going to be loaded */ -void* Document::LoadEntryBinArea(BinEntry* element) +void Document::LoadEntryBinArea(BinEntry* element) { + bool openFile = !Fp; + if(openFile) + OpenFile(); + size_t o =(size_t)element->GetOffset(); Fp->seekg(o, std::ios_base::beg); + size_t l = element->GetLength(); uint8_t* a = new uint8_t[l]; if( !a ) { dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); - return NULL; + return; } - element->SetBinArea((uint8_t*)a); + /// \todo check the result Fp->read((char*)a, l); if( Fp->fail() || Fp->eof()) //Fp->gcount() == 1 { delete[] a; - return NULL; + return; } - return a; + element->SetBinArea(a); + + if(openFile) + CloseFile(); } /** @@ -1093,20 +1140,21 @@ void* Document::LoadEntryBinArea(BinEntry* element) * @return */ bool Document::SetEntryBinAreaByNumber(uint8_t* area, - uint16_t group, - uint16_t element) + uint16_t group, uint16_t element) { DocEntry* currentEntry = GetDocEntryByNumber(group, element); if ( !currentEntry ) { return false; } + if ( BinEntry* binEntry = dynamic_cast(currentEntry) ) { binEntry->SetBinArea( area ); return true; } - return true; + + return false; } /** @@ -1164,7 +1212,7 @@ void Document::UpdateShaEntries() * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ -DocEntry* Document::GetDocEntryByName(std::string const & tagName) +DocEntry* Document::GetDocEntryByName(TagName const & tagName) { DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) @@ -1185,8 +1233,7 @@ DocEntry* Document::GetDocEntryByName(std::string const & tagName) * @param element Element number of the searched Dicom Element * @return */ -DocEntry* Document::GetDocEntryByNumber(uint16_t group, - uint16_t element) +DocEntry* Document::GetDocEntryByNumber(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); if ( !TagHT.count(key)) @@ -1202,8 +1249,7 @@ DocEntry* Document::GetDocEntryByNumber(uint16_t group, * ValEntry. * @return When present, the corresponding ValEntry. */ -ValEntry* Document::GetValEntryByNumber(uint16_t group, - uint16_t element) +ValEntry* Document::GetValEntryByNumber(uint16_t group, uint16_t element) { DocEntry* currentEntry = GetDocEntryByNumber(group, element); if ( !currentEntry ) @@ -1303,16 +1349,14 @@ uint16_t Document::UnswapShort(uint16_t a) * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) * @return length of the parsed set. */ -void Document::ParseDES(DocEntrySet *set, - long offset, - long l_max, - bool delim_mode) +void Document::ParseDES(DocEntrySet *set, long offset, + long l_max, bool delim_mode) { DocEntry *newDocEntry = 0; - + while (true) - { - if ( !delim_mode && (Fp->tellg()-offset) >= l_max) + { + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { break; } @@ -1330,7 +1374,7 @@ void Document::ParseDES(DocEntrySet *set, { /////////////////////// ValEntry ValEntry* newValEntry = - new ValEntry( newDocEntry->GetDictEntry() ); + new ValEntry( newDocEntry->GetDictEntry() ); //LEAK newValEntry->Copy( newDocEntry ); // When "set" is a Document, then we are at the top of the @@ -1349,14 +1393,22 @@ void Document::ParseDES(DocEntrySet *set, + newValEntry->GetKey() ); } - set->AddEntry( newValEntry ); LoadDocEntry( newValEntry ); - if (newValEntry->IsItemDelimitor()) + bool delimitor=newValEntry->IsItemDelimitor(); + if( !set->AddEntry( newValEntry ) ) { + // If here expect big troubles + delete newValEntry; //otherwise mem leak + } + + if (delimitor) + { + delete newDocEntry; break; } - if ( !delim_mode && (Fp->tellg()-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + delete newDocEntry; break; } } @@ -1370,9 +1422,10 @@ void Document::ParseDES(DocEntrySet *set, } //////////////////// BinEntry or UNKOWN VR: - BinEntry* newBinEntry = - new BinEntry( newDocEntry->GetDictEntry() ); - newBinEntry->Copy( newDocEntry ); +/* BinEntry* newBinEntry = + new BinEntry( newDocEntry->GetDictEntry() ); //LEAK + newBinEntry->Copy( newDocEntry );*/ + BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK // When "this" is a Document the Key is simply of the // form ( group, elem )... @@ -1390,8 +1443,12 @@ void Document::ParseDES(DocEntrySet *set, + newBinEntry->GetKey() ); } - set->AddEntry( newBinEntry ); LoadDocEntry( newBinEntry ); + if( !set->AddEntry( newBinEntry ) ) + { + //Expect big troubles if here + delete newBinEntry; + } } if ( ( newDocEntry->GetGroup() == 0x7fe0 ) @@ -1416,6 +1473,7 @@ void Document::ParseDES(DocEntrySet *set, // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); + //delete newDocEntry; } else { @@ -1465,8 +1523,9 @@ void Document::ParseDES(DocEntrySet *set, l, delim_mode); } set->AddEntry( newSeqEntry ); - if ( !delim_mode && (Fp->tellg()-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + delete newDocEntry; break; } } @@ -1479,7 +1538,7 @@ void Document::ParseDES(DocEntrySet *set, * @return parsed length for this level */ void Document::ParseSQ( SeqEntry* seqEntry, - long offset, long l_max, bool delim_mode) + long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; bool dlm_mod; @@ -1496,13 +1555,14 @@ void Document::ParseSQ( SeqEntry* seqEntry, { if ( newDocEntry->IsSequenceDelimitor() ) { - seqEntry->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetSequenceDelimitationItem( newDocEntry ); break; } } - if ( !delim_mode && (Fp->tellg()-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - break; + delete newDocEntry; + break; } SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); @@ -1524,10 +1584,11 @@ void Document::ParseSQ( SeqEntry* seqEntry, } ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); + delete newDocEntry; seqEntry->AddEntry( itemSQ, SQItemNumber ); SQItemNumber++; - if ( !delim_mode && ( Fp->tellg() - offset ) >= l_max ) + if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) { break; } @@ -1580,7 +1641,7 @@ void Document::LoadDocEntry(DocEntry* entry) s << " x(" << std::hex << entry->GetLength() << ")"; binEntryPtr->SetValue(s.str()); } - // Be carefull : a BinEntry IS_A ValEntry ... + // Be carefull : a BinEntry IS_A ValEntry ... else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { // s << "gdcm::NotLoaded. (ValEntry)"; @@ -1598,7 +1659,8 @@ void Document::LoadDocEntry(DocEntry* entry) } // to be sure we are at the end of the value ... - Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),std::ios_base::beg); + Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), + std::ios_base::beg); return; } @@ -1660,15 +1722,28 @@ void Document::LoadDocEntry(DocEntry* entry) return; } - // We need an additional byte for storing \0 that is not on disk + // FIXME: We need an additional byte for storing \0 that is not on disk char *str = new char[length+1]; Fp->read(str, (size_t)length); - str[length] = '\0'; - std::string newValue = str; + str[length] = '\0'; //this is only useful when length is odd + // Special DicomString call to properly handle \0 and even length + std::string newValue; + if( length % 2 ) + { + newValue = Util::DicomString(str, length+1); + //dbg.Verbose(0, "Warning: bad length: ", length ); + dbg.Verbose(0, "For string :", newValue.c_str()); + // Since we change the length of string update it length + entry->SetReadLength(length+1); + } + else + { + newValue = Util::DicomString(str, length); + } delete[] str; if ( ValEntry* valEntry = dynamic_cast(entry) ) - { + { if ( Fp->fail() || Fp->eof())//Fp->gcount() == 1 { dbg.Verbose(1, "Document::LoadDocEntry", @@ -1734,7 +1809,7 @@ void Document::FindDocEntryLength( DocEntry *entry ) // the length and proceed. long currentPosition = Fp->tellg(); Fp->seekg(0L,std::ios_base::end); - long lengthUntilEOF = Fp->tellg() - currentPosition; + long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; Fp->seekg(currentPosition, std::ios_base::beg); entry->SetLength(lengthUntilEOF); return; @@ -1889,7 +1964,7 @@ bool Document::CheckDocEntryVR(DocEntry *entry, VRKey vr) // expected VR read happens to be non-ascii characters we consider // we hit falsely explicit VR tag. - if ( !isalpha(vr[0]) && !isalpha(vr[1]) ) + if ( !isalpha((unsigned char)vr[0]) && !isalpha((unsigned char)vr[1]) ) { realExplicit = false; } @@ -2110,7 +2185,7 @@ void Document::SkipToNextDocEntry(DocEntry *entry) * @param foundLength fist assumption about length */ void Document::FixDocEntryFoundLength(DocEntry *entry, - uint32_t foundLength) + uint32_t foundLength) { entry->SetReadLength( foundLength ); // will be updated only if a bug is found if ( foundLength == 0xffffffff) @@ -2192,7 +2267,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) { uint16_t element = entry->GetElement(); uint16_t group = entry->GetGroup(); - std::string vr = entry->GetVR(); + const std::string & vr = entry->GetVR(); uint32_t length = entry->GetLength(); // When we have some semantics on the element we just read, and if we @@ -2304,7 +2379,7 @@ uint16_t Document::ReadInt16() Fp->read ((char*)&g, (size_t)2); if ( Fp->fail() ) { - throw FormatError( "Document::ReadInt16()", " file error." ); + throw FormatError( "Document::ReadInt16()", " file error." ); } if( Fp->eof() ) { @@ -2379,7 +2454,7 @@ bool Document::CheckSwap() uint32_t s32; uint16_t s16; - char deb[HEADER_LENGTH_TO_READ]; + char deb[256]; //HEADER_LENGTH_TO_READ]; // First, compare HostByteOrder and NetworkByteOrder in order to // determine if we shall need to swap bytes (i.e. the Endian type). @@ -2504,13 +2579,13 @@ bool Document::CheckSwap() // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA, // i.e. the 'group length' element is not present : - // check the supposed to be 'group number' - // 0x0002 or 0x0004 or 0x0008 + // check the supposed-to-be 'group number' + // in ( 0x0001 .. 0x0008 ) // to determine ' SwapCode' value . // Only 0 or 4321 will be possible // (no oportunity to check for the formerly well known // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian' - // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -4, 8-) + // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -3, 4, ..., 8-) // the file IS NOT ACR-NEMA nor DICOM V3 // Find a trick to tell it the caller... @@ -2518,22 +2593,32 @@ bool Document::CheckSwap() switch ( s16 ) { + case 0x0001 : case 0x0002 : + case 0x0003 : case 0x0004 : - case 0x0008 : + case 0x0005 : + case 0x0006 : + case 0x0007 : + case 0x0008 : SwapCode = 0; Filetype = ACR; return true; + case 0x0100 : case 0x0200 : + case 0x0300 : case 0x0400 : - case 0x0800 : + case 0x0500 : + case 0x0600 : + case 0x0700 : + case 0x0800 : SwapCode = 4321; Filetype = ACR; return true; default : dbg.Verbose(0, "Document::CheckSwap:", - "ACR/NEMA unfound swap info (Really hopeless !)"); - Filetype = Unknown; + "ACR/NEMA unfound swap info (Really hopeless !)"); + Filetype = Unknown; return false; } // Then the only info we have is the net2host one. @@ -2545,6 +2630,8 @@ bool Document::CheckSwap() } } + + /** * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. @@ -2612,6 +2699,35 @@ 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', @@ -2637,6 +2753,7 @@ DocEntry* Document::ReadNextDocEntry() return 0; } + HandleBrokenEndian(group, elem); DocEntry *newEntry = NewDocEntryByNumber(group, elem); FindDocEntryVR(newEntry); @@ -2697,8 +2814,18 @@ bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) //// Read the Item Tag group and element, and make // sure they are what we expected: - uint16_t itemTagGroup = ReadInt16(); - uint16_t itemTagElement = ReadInt16(); + 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; @@ -2838,8 +2965,13 @@ void Document::ComputeRLEInfo() 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[15]; + uint32_t rleSegmentOffsetTable[16]; for( int k = 1; k <= 15; k++ ) { rleSegmentOffsetTable[k] = ReadInt32(); @@ -2935,19 +3067,19 @@ void Document::ComputeJPEGFragmentInfo() * @param set The structure to be traversed (recursively). */ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, - DocEntrySet* set ) + DocEntrySet* set ) { if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) ) { - TagDocEntryHT* currentHT = elementSet->GetTagHT(); - for( TagDocEntryHT::const_iterator i = currentHT->begin(); - i != currentHT->end(); + 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) ) { - ListSQItem& items = seqEntry->GetSQItems(); + const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); item != items.end(); ++item) @@ -2963,15 +3095,15 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, if (SQItem* SQItemSet = dynamic_cast< SQItem* > ( set ) ) { - ListDocEntry& currentList = SQItemSet->GetDocEntries(); - for (ListDocEntry::iterator i = currentList.begin(); - i != currentList.end(); - ++i) + const ListDocEntry& currentList = SQItemSet->GetDocEntries(); + for (ListDocEntry::const_iterator i = currentList.begin(); + i != currentList.end(); + ++i) { DocEntry* entry = *i; if ( SeqEntry* seqEntry = dynamic_cast(entry) ) { - ListSQItem& items = seqEntry->GetSQItems(); + const ListSQItem& items = seqEntry->GetSQItems(); for( ListSQItem::const_iterator item = items.begin(); item != items.end(); ++item) @@ -2991,7 +3123,7 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, * Document. * * The structure used by a Document (through \ref ElementSet), - * in order to old the parsed entries of a Dicom header, is a recursive + * in order to hold the parsed entries of a Dicom header, is a recursive * one. This is due to the fact that the sequences (when present) * can be nested. Additionaly, the sequence items (represented in * gdcm as \ref SQItem) add an extra complexity to the data