X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=c9e7bddc598844cb4249e082b8e982e7d28352af;hb=f07febbce9f70fd0faee0f3ce3df674c1e7f8a13;hp=a92cf3db4aaae239b1044cd3246e9a84ecbd1cdc;hpb=3e7acd356052aa0836ba8ac2e71d955c8739eeda;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index a92cf3db..c9e7bddc 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2006/02/08 17:34:47 $ - Version: $Revision: 1.340 $ + Date: $Date: 2006/07/10 09:41:46 $ + Version: $Revision: 1.353 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -62,11 +62,13 @@ Document::Document() Initialize(); SwapCode = 1234; Filetype = ExplicitVR; + CurrentOffsetPosition = 0; // Load will set it to true if sucessfull Group0002Parsed = false; IsDocumentAlreadyLoaded = false; IsDocumentModified = true; LoadMode = LD_ALL; // default : load everything, later + SetFileName(""); } @@ -95,6 +97,23 @@ bool Document::Load( ) return DoTheLoadingDocumentJob( ); } + +//#ifndef GDCM_LEGACY_REMOVE +/** + * \brief Loader. (DEPRECATED : not to break the API) + * @param fileName 'Document' (File or DicomDir) to be open for parsing + * @return false if file cannot be open or no swap info was found, + * or no tag was found. + */ + /* +bool Document::Load( std::string const &fileName ) +{ + Filename = fileName; + return DoTheLoadingDocumentJob( ); +} +*/ +//#endif + /** * \brief Performs the Loading Job (internal use only) * @return false if file cannot be open or no swap info was found, @@ -118,7 +137,7 @@ bool Document::DoTheLoadingDocumentJob( ) Group0002Parsed = false; gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str()); - + // Computes the total length of the file Fp->seekg(0, std::ios::end); // Once per Document ! long lgt = Fp->tellg(); // Once per Document ! @@ -151,7 +170,7 @@ bool Document::DoTheLoadingDocumentJob( ) } IsDocumentAlreadyLoaded = true; - Fp->seekg( 0, std::ios::beg); // Once per Document + //Fp->seekg(0, std::ios::beg); // Once per Document! // Load 'non string' values @@ -204,13 +223,13 @@ bool Document::DoTheLoadingDocumentJob( ) } //FIXME later : how to use it? - SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000); + SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000); // Modality LUT Sequence if ( modLutSeq !=0 ) { SQItem *sqi= modLutSeq->GetFirstSQItem(); if ( sqi != 0 ) { - DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006); + DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006); // LUT Data if ( dataEntry != 0 ) { if ( dataEntry->GetLength() != 0 ) @@ -237,7 +256,7 @@ bool Document::DoTheLoadingDocumentJob( ) if ( d == NULL) { - gdcmWarningMacro( "You asked toForce Load " << std::hex + gdcmWarningMacro( "You asked to ForceLoad " << std::hex << (*it).Group <<"|"<< (*it).Elem << " that doesn't exist" ); continue; @@ -246,7 +265,7 @@ bool Document::DoTheLoadingDocumentJob( ) LoadDocEntry(d, true); } - CloseFile(); + CloseFile(); // ---------------------------- // Specific code to allow gdcm to read ACR-LibIDO formated images @@ -607,7 +626,6 @@ std::ifstream *Document::OpenFile() } //-- Broken ACR or DICOM with no Preamble; may start with a Shadow Group -- - // FIXME : We cannot be sure the preable is only zeroes.. // (see ACUSON-24-YBR_FULL-RLE.dcm ) if ( @@ -640,7 +658,7 @@ std::ifstream *Document::OpenFile() // -- Neither ACR/No Preamble Dicom nor DICOMV3 file CloseFile(); - // Don't user Warning nor Error, not to polute the output + // Don't user Warning nor Error, not to pollute the output // while directory recursive parsing ... gdcmDebugMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: " << Filename.c_str()); @@ -673,7 +691,7 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) // Skip if user wants to write an ACR-NEMA file if ( filetype == ImplicitVR || filetype == ExplicitVR || - filetype == JPEG ) + filetype == JPEG || filetype == JPEG2000 ) { // writing Dicom File Preamble char filePreamble[128]; @@ -681,7 +699,6 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) fp->write(filePreamble, 128); fp->write("DICM", 4); } - /* * \todo rewrite later, if really usefull * - 'Group Length' element is optional in DICOM @@ -735,20 +752,16 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) * @param entry Entry whose binArea is going to be loaded */ void Document::LoadEntryBinArea(DataEntry *entry) -{ +{ if( entry->GetBinArea() ) return; -// to be coherent with LoadEntryBinArea(uint16_t group, uint16_t elem) -// (and save time !) -// :-( -// TestAllReadCompareDicom hangs on rle16sti.dcm bool openFile = !Fp; if ( openFile ) OpenFile(); -// ------- - size_t o =(size_t)entry->GetOffset(); - Fp->seekg(o, std::ios::beg); // FIXME : for each BinEntry LoadEntryBinArea + + //size_t o =(size_t)entry->GetOffset(); + Fp->seekg((size_t)entry->GetOffset(), std::ios::beg); // FIXME : for each DataEntry ! size_t l = entry->GetLength(); uint8_t *data = new uint8_t[l]; @@ -808,13 +821,9 @@ void Document::LoadEntryBinArea(DataEntry *entry) } entry->SetBinArea(data); - -// to be coherent with LoadEntryBinArea(uint16_t group, uint16_t elem) -// (and save time !) - if ( openFile ) + if ( openFile ) // The file is left in the state (open/close) it was at entrance CloseFile(); -// --------------- } /** @@ -824,15 +833,15 @@ void Document::LoadEntryBinArea(DataEntry *entry) * \note seems to be unused!. * @param entry DocEntry whose value will be loaded. */ -void Document::LoadDocEntrySafe(DocEntry *entry) -{ - if ( Fp ) - { - long PositionOnEntry = Fp->tellg(); // LoadDocEntrySafe is not used - LoadDocEntry(entry); - Fp->seekg(PositionOnEntry, std::ios::beg); // LoadDocEntrySafe is not used - } -} +//void Document::LoadDocEntrySafe(DocEntry *entry) +//{ +// if ( Fp ) +// { +// long PositionOnEntry = Fp->tellg(); // LoadDocEntrySafe is not used +// LoadDocEntry(entry); +// Fp->seekg(PositionOnEntry, std::ios::beg); // LoadDocEntrySafe is not used +// } +//} /** * \brief Compares two documents, according to \ref DicomDir rules @@ -901,6 +910,27 @@ bool Document::operator<(Document &document) //----------------------------------------------------------------------------- // Protected + +/** + * \brief Reads a given length of bytes + * (in order to avoid to many CPU time consuming fread-s) + * @param l length to read + */ +void Document::ReadBegBuffer(size_t l) + throw( FormatError ) +{ + Fp->read (BegBuffer, (size_t)l); + if ( Fp->fail() ) + { + throw FormatError( "Document::ReadBegBuffer()", " file error." ); + } + if ( Fp->eof() ) + { + throw FormatError( "Document::ReadBegBuffer()", "EOF." ); + } + PtrBegBuffer = BegBuffer; + CurrentOffsetPosition+=l; +} /** * \brief Reads a supposed to be 16 Bits integer * (swaps it depending on processor endianness) @@ -923,6 +953,18 @@ uint16_t Document::ReadInt16() return g; } +/** + * \brief Gets from BegBuffer a supposed to be 16 Bits integer + * (swaps it depending on processor endianness) + * @return read value + */ +uint16_t Document::GetInt16() +{ + uint16_t g = *((uint16_t*)PtrBegBuffer); + g = SwapShort(g); + PtrBegBuffer+=2; + return g; +} /** * \brief Reads a supposed to be 32 Bits integer * (swaps it depending on processor endianness) @@ -945,6 +987,19 @@ uint32_t Document::ReadInt32() return g; } +/** + * \brief Gets from BegBuffer a supposed to be 32 Bits integer + * (swaps it depending on processor endianness) + * @return read value + */ +uint32_t Document::GetInt32() +{ + uint32_t g = *((uint32_t*)PtrBegBuffer); + g = SwapLong(g); + PtrBegBuffer+=4; + return g; +} + /** * \brief Re-computes the length of the Dicom group 0002. */ @@ -977,7 +1032,6 @@ int Document::ComputeGroup0002Length( ) // explicit VR AND (OB, OW, SQ, UT) : 4 more bytes groupLength += 4; } - groupLength += 2 + 2 + 4 + entry->GetLength(); } } @@ -1020,6 +1074,7 @@ void Document::CallEndMethod() // Private /** * \brief Loads all the needed Dictionaries + * \warning NOT end user intended method ! */ void Document::Initialize() { @@ -1041,42 +1096,53 @@ void Document::ParseDES(DocEntrySet *set, long offset, DocEntry *newDocEntry; DataEntry *newDataEntry; SeqEntry *newSeqEntry; - VRKey vr; + //VRKey vr; bool used; // will be set to false when something wrong happens to an Entry. // (Entry will then be deleted) bool delim_mode_intern = delim_mode; bool first = true; gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode - << " at offset " << std::hex << "0x(" << offset << ")" ); + << " at offset " << std::hex << "0x(" << offset << ")" ); while (true) { - // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry + ///\todo FIXME : On 64 bits processors, tellg gives unexpected results after a while ? + /// Probabely a bug in gdcm code somwhere (some memory erased ?) + +// Uncomment to track the bug +/* + if( Debug::GetDebugFlag() ) + std::cout << std::dec <<"(long)(Fp->tellg()) " << (long)(Fp->tellg()) // in Debug mode + << std::hex << " 0x(" <<(long)(Fp->tellg()) << ")" << std::endl; + */ + + // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry if ( !delim_mode ) // 'and then' doesn't exist in C++ :-( if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry, when no delim mode { break; } - newDocEntry = ReadNextDocEntry( ); - // Uncoment this cerr line to be able to 'follow' the DocEntries - // when something *very* strange happens - if( Debug::GetDebugFlag() ) - std::cerr<GetKey()<<" "<GetVR()<GetKey()<<" "<GetVR()<IsItemStarter() ) - { - // Debug message within the method ! - newDocEntry = Backtrack(newDocEntry); + { + // Debug message within the method ! + newDocEntry = Backtrack(newDocEntry); } else { @@ -1090,7 +1156,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, { //////////////////////////// DataEntry - vr = newDocEntry->GetVR(); + //vr = newDocEntry->GetVR(); // useless ? if ( !set->AddEntry( newDataEntry ) ) { @@ -1118,7 +1184,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, //if ( newDataEntry->IsUnfound() ) /?!? JPR { lgrGroup = atoi(strLgrGroup.c_str()); - Fp->seekg(lgrGroup, std::ios::cur); // Only when NOSHADOW + Fp->seekg(lgrGroup, std::ios::cur); // Once per Shadow group, when NOSHADOW RemoveEntry( newDocEntry ); // Remove and delete continue; } @@ -1216,7 +1282,6 @@ void Document::ParseDES(DocEntrySet *set, long offset, l, delim_mode_intern); gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern); - } if ( !set->AddEntry( newSeqEntry ) ) { @@ -1233,7 +1298,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry - if ( !delim_mode ) // andthen doesn't exist in C++ :-( + if ( !delim_mode ) // 'and then' doesn't exist in C++ :-( if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry when no delim mode { @@ -1282,12 +1347,14 @@ void Document::ParseSQ( SeqEntry *seqEntry, break; } } - if ( !delim_mode ) // andthen doesn't exist in C++ :-( + else // ! delim_mode + { if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SQItem when no delim mode { newDocEntry->Delete(); break; } + } // create the current SQItem SQItem *itemSQ = SQItem::New( seqEntry->GetDepthLevel() ); unsigned int l = newDocEntry->GetReadLength(); @@ -1300,16 +1367,12 @@ void Document::ParseSQ( SeqEntry *seqEntry, { dlm_mod = false; } - - // remove fff0,e000, created out of the SQItem - - //Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); //JPRx - + // fill up the current SQItem, starting at the beginning of fff0,e000 - + + Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); // Once per SQItem ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod); - - offsetStartCurrentSQItem = Fp->tellg(); // Once per SQItem + offsetStartCurrentSQItem = Fp->tellg(); // Once per SQItem seqEntry->AddSQItem( itemSQ, SQItemNumber ); itemSQ->Delete(); @@ -1352,8 +1415,7 @@ DocEntry *Document::Backtrack(DocEntry *docEntry) newEntry->SetOffset(offset); // Move back to the beginning of the Sequence - // Fp->seekg( 0, std::ios::beg); // JPRx - // Fp->seekg(offset, std::ios::cur); // JPRx + Fp->seekg(offset, std::ios::beg); // Only for Shadow Implicit VR SQ return newEntry; } @@ -1366,10 +1428,10 @@ DocEntry *Document::Backtrack(DocEntry *docEntry) */ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) { - uint16_t group = entry->GetGroup(); - uint16_t elem = entry->GetElement(); + uint16_t group = entry->GetGroup(); + uint16_t elem = entry->GetElement(); const VRKey &vr = entry->GetVR(); - uint32_t length = entry->GetLength(); + uint32_t length = entry->GetLength(); // Fp->seekg((long)entry->GetOffset(), std::ios::beg); // JPRx @@ -1377,7 +1439,6 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) // (fffe e000) tells us an Element is beginning // (fffe e00d) tells us an Element just ended // (fffe e0dd) tells us the current SeQuence just ended - // // (fffe 0000) is an 'impossible' tag value, // found in MR-PHILIPS-16-Multi-Seq.dcm @@ -1403,8 +1464,6 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) // The elements whose length is bigger than the specified upper bound // are not loaded. - std::ostringstream s; - if (!forceLoad) { if (length > MaxSizeLoadEntry) @@ -1412,13 +1471,20 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) dataEntryPtr->SetBinArea(NULL,true); dataEntryPtr->SetState(DataEntry::STATE_NOTLOADED); - // to be sure we are at the end of the value ... + // to be sure we are at the end of the value ... // Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), // std::ios::beg); //JPRx return; } } - + + /// \todo: a method that *doesn't* load anything (maybe with MaxSizeLoadEntry=0 ?) + /// + a ForceLoad call on the +/- 20 'usefull' fields + /// Allow user to tell the fields he wants to ForceLoad + /// during initial stage. + /// Later, a GetString or GetBinArea will load the value from disk, if not loaded + /// + a method that load *everything* that's not yet loaded + LoadEntryBinArea(dataEntryPtr); // last one, not to erase length ! } @@ -1440,10 +1506,10 @@ void Document::FindDocEntryLength( DocEntry *entry ) // The following reserved two bytes (see PS 3.5-2003, section // "7.1.2 Data element structure with explicit vr", p 27) must be // skipped before proceeding on reading the length on 4 bytes. - - Fp->seekg( 2L, std::ios::cur); // Once per OW,OB,SQ DocEntry - uint32_t length32 = ReadInt32(); + //Fp->seekg( 2L, std::ios::cur); // Once per OW,OB,SQ DocEntry + uint32_t length32 = ReadInt32(); // Once per OW,OB,SQ DocEntry + CurrentOffsetPosition+=4; if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) { uint32_t lengthOB; @@ -1480,8 +1546,9 @@ void Document::FindDocEntryLength( DocEntry *entry ) } // Length is encoded on 2 bytes. - length16 = ReadInt16(); - + //length16 = ReadInt16(); + length16 = GetInt16(); + // 0xffff means that we deal with 'No Length' Sequence // or 'No Length' SQItem if ( length16 == 0xffff) @@ -1503,22 +1570,25 @@ void Document::FindDocEntryLength( DocEntry *entry ) // Well ... group 0002 is always coded in 'Explicit VR Litle Endian' // even if Transfer Syntax is 'Implicit VR ...' // --> Except for 'Implicit VR Big Endian Transfer Syntax GE Private' - - FixDocEntryFoundLength( entry, ReadInt32() ); + // where Group 0x0002 is *also* encoded in Implicit VR ! + + FixDocEntryFoundLength( entry, GetInt32() /*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(); // Only for OB,OW DataElements + long positionOnEntry = Fp->tellg(); // Only for OB,OW DataElements + bool foundSequenceDelimiter = false; uint32_t totalLength = 0; @@ -1526,25 +1596,28 @@ uint32_t Document::FindDocEntryLengthOBOrOW() { uint16_t group; uint16_t elem; + try { - group = ReadInt16(); - elem = ReadInt16(); + //group = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements + //elem = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements + ReadBegBuffer(4); // Once per fragment (if any) of OB,OW DataElements } catch ( FormatError ) { throw FormatError("Unexpected end of file encountered during ", "Document::FindDocEntryLengthOBOrOW()"); } + group = GetInt16(); + elem = GetInt16(); + // We have to decount the group and element we just read totalLength += 4; if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { - // long filePosition = Fp->tellg(); JPRx gdcmWarningMacro( "Neither an Item tag nor a Sequence delimiter tag on :" << std::hex << group << " , " << elem - //<< ") -before- position x(" << filePosition // JPRx << ")" ); Fp->seekg(positionOnEntry, std::ios::beg); // Once per fragment (if any) of OB,OW DataElements @@ -1555,7 +1628,7 @@ uint32_t Document::FindDocEntryLengthOBOrOW() { foundSequenceDelimiter = true; } - uint32_t itemLength = ReadInt32(); + uint32_t itemLength = ReadInt32(); // Once per fragment (if any) of OB,OW DataElements // We add 4 bytes since we just read the ItemLength with ReadInt32 totalLength += itemLength + 4; SkipBytes(itemLength); @@ -1565,7 +1638,7 @@ uint32_t Document::FindDocEntryLengthOBOrOW() break; } } - Fp->seekg( positionOnEntry, std::ios::beg); // Only for OB,OW DataElements + Fp->seekg( positionOnEntry, std::ios::beg); // Only once for OB,OW DataElements return totalLength; } @@ -1576,15 +1649,17 @@ uint32_t Document::FindDocEntryLengthOBOrOW() VRKey Document::FindDocEntryVR() { if ( Filetype != ExplicitVR ) + { return GDCM_VRUNKNOWN; + } // Delimiters (0xfffe), are not explicit VR ... if ( CurrentGroup == 0xfffe ) return GDCM_VRUNKNOWN; - long positionOnEntry; - if( Debug::GetWarningFlag() ) - positionOnEntry = Fp->tellg(); // Only in Warning Mode + //long positionOnEntry; + //if( Debug::GetWarningFlag() ) + // positionOnEntry = Fp->tellg(); // Only in Warning Mode // Warning: we believe this is explicit VR (Value Representation) because // we used a heuristic that found "UL" in the first tag and/or @@ -1598,12 +1673,15 @@ VRKey Document::FindDocEntryVR() // if it happens not to be the case. VRKey vr; - Fp->read(&(vr[0]),(size_t)2); - - if ( !CheckDocEntryVR(vr) ) + //Fp->read(&(vr[0]),(size_t)2); + vr[0] = *PtrBegBuffer++; + vr[1] = *PtrBegBuffer++; + + //if ( !CheckDocEntryVR(vr) ) // avoid useless function call + if ( !Global::GetVR()->IsValidVR(vr) ) { /* - std::cout << "================================================================Unknown VR" +// std::cout << "================================================================Unknown VR" << std::hex << "0x(" << (unsigned int)vr[0] << "|" << (unsigned int)vr[1] << ")" << "for : " << CurrentGroup @@ -1613,12 +1691,13 @@ VRKey Document::FindDocEntryVR() gdcmWarningMacro( "Unknown VR " << std::hex << "0x(" << (unsigned int)vr[0] << "|" << (unsigned int)vr[1] << ")" - << " at offset : 0x(" << positionOnEntry<< ") for group " << CurrentGroup + << " at offset : 0x(" << CurrentOffsetPosition-4<< ") for group " << CurrentGroup ); //Fp->seekg(positionOnEntry, std::ios::beg); //JPRx - Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?) + //Fp->seekg((long)-2, std::ios::cur);// only for unrecognized VR (?!?) //see :MR_Philips_Intera_PrivateSequenceExplicitVR.dcm + PtrBegBuffer-=2; return GDCM_VRUNKNOWN; } return vr; @@ -1656,7 +1735,7 @@ void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) if ( l == -1 ) // length = 0xffff shouldn't appear here ... // ... but PMS imagers happen ! return; - Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg); //FIXME :each DocEntry + Fp->seekg((size_t)(currentDocEntry->GetOffset()), std::ios::beg); //FIXME :each DocEntry if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb { Fp->seekg( l,std::ios::cur); //FIXME :each DocEntry @@ -1668,17 +1747,21 @@ void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) * the parser went Jabberwocky) one can hope improving things by * applying some heuristics. * @param entry entry to check - * @param foundLength first assumption about length + * @param foundLength first assumption about length (before bug fix, or set to zero if =0xffffffff) */ void Document::FixDocEntryFoundLength(DocEntry *entry, uint32_t foundLength) { entry->SetReadLength( foundLength );// will be updated only if a bug is found + if ( foundLength == 0xffffffff) { - foundLength = 0; + //foundLength = 0; + //entry->SetLength(foundLength); + entry->SetLength(0); + return; // return ASAP; don't waist time on useless tests } - + uint16_t gr = entry->GetGroup(); uint16_t elem = entry->GetElement(); @@ -1708,26 +1791,37 @@ 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 ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) ) - { - foundLength = 4; - entry->SetReadLength(4); // a bug is to be fixed ! - } - + else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) ) + { + // Ideally we should check we are in Explicit and double check + // that VR=UL... this is done properly in gdcm2 + if( foundLength == 6 ) + { + gdcmWarningMacro( "Replacing Length from 6 into 4" ); + foundLength = 4; + entry->SetReadLength(4); // a bug is to be fixed ! + } + else if ( foundLength%4 ) + { + gdcmErrorMacro( "This looks like to a buggy Siemens DICOM file." + "The length of this tag seems to be wrong" ); + } + } + else if ( entry->GetVR() == "SQ" ) { - foundLength = 0; // ReadLength is unchanged - } - - //////// We encountered a 'delimiter' element i.e. a tag of the form + foundLength = 0; // ReadLength is unchanged + } + + //////// 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 ( 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 // causes extra troubles... - if ( entry->GetElement() != 0x0000 ) + if ( elem != 0x0000 ) { foundLength = 0; } @@ -1735,7 +1829,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, { foundLength=12; // to skip the mess that follows this bugged Tag ! } - } + } entry->SetLength(foundLength); } @@ -1771,6 +1865,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) // encounter such an ill-formed image, we simply display a warning // message and proceed on parsing (while crossing fingers). long filePosition = Fp->tellg(); // Only when elem 0x0000 length is not 4 (?!?) + (void)filePosition; gdcmWarningMacro( "Erroneous Group Length element length on : (" << std::hex << group << " , " << elem << ") -before- position x(" << filePosition << ")" @@ -1866,9 +1961,8 @@ bool Document::CheckSwap() // Position the file position indicator at first tag // (i.e. after the file preamble and the "DICM" string). - //Fp->seekg(0, std::ios::beg); // JPRx - Fp->seekg ( 132L, std::ios::beg); // Once per Document + CurrentOffsetPosition = 132; return true; } // ------------------------------- End of DicomV3 ---------------- @@ -1879,7 +1973,7 @@ bool Document::CheckSwap() gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)"); Fp->seekg(0, std::ios::beg); // Once per ACR-NEMA Document - + CurrentOffsetPosition = 0; // Let's check 'No Preamble Dicom File' : // Should start with group 0x0002 // and be Explicit Value Representation @@ -1959,6 +2053,9 @@ bool Document::CheckSwap() // Find a trick to tell it the caller... s16 = *((uint16_t *)(deb)); + + gdcmDebugMacro("not a DicomV3 nor a 'clean' ACR/NEMA;" + << " (->despaired wild guesses !)"); switch ( s16 ) { @@ -2022,7 +2119,7 @@ void Document::SwitchByteSwapCode() * \brief during parsing, Header Elements too long are not loaded in memory * @param newSize new size */ -void Document::SetMaxSizeLoadEntry(long newSize) +void Document::SetMaxSizeLoadEntry(long newSize) { if ( newSize < 0 ) { @@ -2041,34 +2138,37 @@ void Document::SetMaxSizeLoadEntry(long newSize) * (read the 'Group Number', the 'Element Number', * gets the Dict Entry * gets the VR, gets the length, gets the offset value) - * @return On succes : the newly created DocEntry, NULL on failure. + * @return On succes : the newly created DocEntry, NULL on failure. */ DocEntry *Document::ReadNextDocEntry() { try { - CurrentGroup = ReadInt16(); - CurrentElem = ReadInt16(); + ReadBegBuffer(8); // Avoid to many time consuming freads + //CurrentGroup = ReadInt16(); + //CurrentElem = ReadInt16(); } catch ( FormatError ) { - // We reached the EOF (or an error occured) therefore + // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. return 0; } - + + CurrentGroup = GetInt16(); + CurrentElem = GetInt16(); + // In 'true DICOM' files Group 0002 is always little endian - if ( HasDCMPreamble ) + if ( HasDCMPreamble ) { if ( !Group0002Parsed && CurrentGroup != 0x0002) // avoid calling a function when useless HandleOutOfGroup0002(CurrentGroup, CurrentElem); else // Sometimes file contains groups of tags with reversed endianess. - HandleBrokenEndian(CurrentGroup, CurrentElem); + HandleBrokenEndian(CurrentGroup, CurrentElem); } - + VRKey vr = FindDocEntryVR(); - VRKey realVR = vr; if ( vr == GDCM_VRUNKNOWN ) @@ -2077,9 +2177,14 @@ DocEntry *Document::ReadNextDocEntry() { realVR = "UL"; // must be UL } + else if (CurrentGroup == 0xfffe) // Don't get DictEntry for Delimitors + { + realVR = "UL"; + } + // Commented out in order not to generate 'Shadow Groups' where some // Data Elements are Explicit VR and some other ones Implicit VR - // (Stupid MatLab DICOM Reader couln't read gdcm-written images) + // (Stupid MatLab DICOM Reader couldn't read gdcm-written images) /* else if (CurrentGroup%2 == 1 && (CurrentElem >= 0x0010 && CurrentElem <=0x00ff )) @@ -2091,20 +2196,22 @@ DocEntry *Document::ReadNextDocEntry() */ else { - DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem); + DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);//only when ImplicitVR if ( dictEntry ) { realVR = dictEntry->GetVR(); - dictEntry->Unregister(); + dictEntry->Unregister(); // GetDictEntry registered it } } } - + DocEntry *newEntry; //if ( Global::GetVR()->IsVROfSequence(realVR) ) if (realVR == "SQ") + { newEntry = NewSeqEntry(CurrentGroup, CurrentElem); - else + } + else { newEntry = NewDataEntry(CurrentGroup, CurrentElem, realVR); static_cast(newEntry)->SetState(DataEntry::STATE_NOTLOADED); @@ -2116,14 +2223,14 @@ DocEntry *Document::ReadNextDocEntry() { // We thought this was explicit VR, but we end up with an // implicit VR tag. Let's backtrack. - if ( newEntry->GetGroup() != 0xfffe ) + + //if ( newEntry->GetGroup() != 0xfffe ) + if (CurrentGroup != 0xfffe) { - std::string msg; int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong - msg = Util::Format( - "Entry (%04x,%04x) at x(%x) should be Explicit VR\n", - newEntry->GetGroup(), newEntry->GetElement(), offset ); - gdcmWarningMacro( msg.c_str() ); + + gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x(" + << offset << ") should be Explicit VR"); } } newEntry->SetImplicitVR(); @@ -2141,7 +2248,6 @@ DocEntry *Document::ReadNextDocEntry() } newEntry->SetOffset(Fp->tellg()); // for each DocEntry - return newEntry; } @@ -2153,6 +2259,23 @@ DocEntry *Document::ReadNextDocEntry() */ void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) { + // for strange PMS Gyroscan Intera images + // Item 'starter' has a tag : 0x3f3f,0x3f00, for no apparent reason + + // --- Feel free to remove this test *on your own coy of gdcm* + // if you are sure you'll never face this problem. + + if ((group == 0x3f3f) && (elem == 0x3f00)) + { + // start endian swap mark for group found + gdcmDebugMacro( " delimiter 0x3f3f found." ); + // fix the tag + group = 0xfffe; + elem = 0xe000; + return; + } + // --- End of removable code + // Endian reversion. // Some files contain groups of tags with reversed endianess. static int reversedEndian = 0; @@ -2236,7 +2359,7 @@ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) group = SwapShort(group); elem = SwapShort(elem); } - + /// \todo find a trick to warn user and stop processing if ( s == TS::DeflatedExplicitVRLittleEndian)