X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=284fe5e6fee561ab73a129a052ac542318acbb84;hb=fd5c14391627c6e42283ced90561271af2a161a2;hp=993d55beda1daf0e1423f764918f3876e15c8e92;hpb=286692fea55fd500cd8cd01c0c985694ed3ead7c;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 993d55be..284fe5e6 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2008/01/04 13:32:01 $ - Version: $Revision: 1.378 $ + Date: $Date: 2011/03/29 07:36:00 $ + Version: $Revision: 1.386 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -284,10 +284,12 @@ bool Document::DoTheLoadingDocumentJob( ) std::string RecCode; RecCode = GetEntryString(0x0008, 0x0010); // recognition code (RET) + if(RecCode.find("ACRNEMA_LIBIDO") == 0 || // any version RecCode.find("CANRME_AILIBOD") == 0) // for brain-damaged softwares // with "little-endian strings" { + Filetype = ACR_LIBIDO; std::string rows = GetEntryString(0x0028, 0x0010); std::string columns = GetEntryString(0x0028, 0x0011); @@ -441,7 +443,7 @@ std::string Document::GetTransferSyntax() // happen at different stages): try loading and proceed with check... // Well ... - // (parsing and loading happen at the very same stage!) + // (parsing and loading happen at the very same stage!) //LoadDocEntrySafe(entry); //JPRx if (DataEntry *dataEntry = dynamic_cast(entry) ) { @@ -531,11 +533,11 @@ uint32_t Document::SwapLong(uint32_t a) // save CPU time a=( ( a<<24) | ((a<<8) & 0x00ff0000) | ((a>>8) & 0x0000ff00) | (a>>24) ); - break; + break; case 3412 : // a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) ); a=( (a<<16) | (a>>16) ); - break; + break; case 2143 : a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); break; @@ -544,7 +546,7 @@ uint32_t Document::SwapLong(uint32_t a) a = 0; } return a; -} +} /** * \brief Swaps back the bytes of 8-byte long 'double' accordingly to @@ -588,12 +590,12 @@ double Document::SwapDouble(double a) * \brief Tries to open the file Document::Filename and * checks the preamble when existing, * or if the file starts with an ACR-NEMA look-like element. - * @return The FILE pointer on success, 0 on failure. + * @return The FILE pointer on success, 0 on failure. */ std::ifstream *Document::OpenFile() { HasDCMPreamble = false; - if (Filename.length() == 0) + if (Filename.length() == 0) { return 0; } @@ -608,13 +610,13 @@ std::ifstream *Document::OpenFile() if ( ! *Fp ) { // Don't user gdcmErrorMacro : - // a spurious message will appear when you use, for instance + // a spurious message will appear when you use, for instance // gdcm::FileHelper *fh = new gdcm::FileHelper( outputFileName ); // to create outputFileName. - - // FIXME : if the upper comment is still usefull + + // FIXME : if the upper comment is still usefull // --> the constructor is not so good ... - + gdcmWarningMacro( "Cannot open file: " << Filename.c_str()); delete Fp; Fp = 0; @@ -622,7 +624,7 @@ std::ifstream *Document::OpenFile() //exit(1); // No function is allowed to leave the application instead // of warning the caller } - + uint16_t zero = 0; Fp->read((char*)&zero, (size_t)2); if ( Fp->eof() ) @@ -630,7 +632,7 @@ std::ifstream *Document::OpenFile() CloseFile(); return 0; } - + //-- DICOM -- Fp->seekg(126L, std::ios::cur); // Once per Document char dicm[4]; // = {' ',' ',' ',' '}; @@ -640,7 +642,7 @@ std::ifstream *Document::OpenFile() CloseFile(); return 0; } - + if ( memcmp(dicm, "DICM", 4) == 0 ) { HasDCMPreamble = true; @@ -650,13 +652,13 @@ 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 ( + 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 || zero == 0x0028 || 0x2800 // worse : some ACR-NEMA like files - // start 00028 group ?!? + // start 00028 group ?!? ) { std::string msg = Util::Format( @@ -665,19 +667,19 @@ std::ifstream *Document::OpenFile() gdcmWarningMacro( msg.c_str() ); return Fp; } - + // -- Neither ACR/No Preamble Dicom nor DICOMV3 file CloseFile(); // 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()); + << Filename.c_str()); return 0; } /** - * \brief closes the file - * @return TRUE if the close was successfull + * \brief closes the file + * @return TRUE if the close was successfull */ bool Document::CloseFile() { @@ -691,9 +693,9 @@ bool Document::CloseFile() } /** - * \brief Writes in a file all the Entries (Dicom Elements) + * \brief Writes in a file all the Entries (Dicom Elements) * @param fp file pointer on an already open file (actually: Output File Stream) - * @param filetype Type of the File to be written + * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) */ void Document::WriteContent(std::ofstream *fp, FileType filetype, bool, bool) @@ -1007,7 +1009,7 @@ uint32_t Document::ReadInt32() uint32_t Document::GetInt32() { uint32_t g = *((uint32_t*)PtrBegBuffer); - g = SwapLong(g); + g = SwapLong(g); PtrBegBuffer+=4; return g; } @@ -1015,7 +1017,7 @@ uint32_t Document::GetInt32() /** * \brief Re-computes the length of the Dicom group 0002. */ -int Document::ComputeGroup0002Length( ) +int Document::ComputeGroup0002Length( ) { uint16_t gr; VRKey vr; @@ -1102,7 +1104,7 @@ void Document::Initialize() * @param l_max length to parse (meaningless when we are in 'delimitor mode') * @param delim_mode : whether we are in 'delimitor mode' (l=0xffffff) or not */ -bool Document::ParseDES(DocEntrySet *set, long offset, +void Document::ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode) { DocEntry *newDocEntry; @@ -1113,9 +1115,8 @@ bool Document::ParseDES(DocEntrySet *set, long offset, // (Entry will then be deleted) bool delim_mode_intern = delim_mode; bool first = true; - bool successParseDES = true; gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode - << " at offset " << std::hex << "0x(" << offset << ")" ); + << " at offset " << std::hex << "0x(" << offset << ")" ); while (true) { @@ -1123,12 +1124,11 @@ bool Document::ParseDES(DocEntrySet *set, long offset, /// Probabely a bug in gdcm code somewhere (some memory erased ?) // Uncomment to track the bug - - if( Debug::GetDebugFlag() ) + + 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 @@ -1145,7 +1145,7 @@ bool Document::ParseDES(DocEntrySet *set, long offset, // Uncoment this cerr line to be able to 'follow' the DocEntries // when something *very* strange happens - if( Debug::GetDebugFlag() ) + if( Debug::GetDebugFlag() ) std::cerr<GetKey()<<" "<GetVR()<(newDocEntry); - if ( newDataEntry ) + if ( newDataEntry ) { //////////////////////////// DataEntry - + //vr = newDocEntry->GetVR(); // useless ? if ( !set->AddEntry( newDataEntry ) ) @@ -1205,7 +1205,7 @@ bool Document::ParseDES(DocEntrySet *set, long offset, } } - bool delimitor = newDataEntry->IsItemDelimitor(); + bool delimitor = newDataEntry->IsItemDelimitor(); bool outOfBounds = false; if (!delim_mode ) if ( ((long)(Fp->tellg())-offset) >= l_max ) //Once per DataEntry when no delim mode @@ -1282,8 +1282,7 @@ bool Document::ParseDES(DocEntrySet *set, long offset, { newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); } - - bool res = true; + if ( l != 0 ) { // Don't try to parse zero-length sequences @@ -1291,32 +1290,12 @@ bool Document::ParseDES(DocEntrySet *set, long offset, << " at offset 0x(" << std::hex << newDocEntry->GetOffset() << ")"); - res = ParseSQ( newSeqEntry, + bool res = ParseSQ( newSeqEntry, newDocEntry->GetOffset(), l, delim_mode_intern); gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern << " -->return : " << res); - } - - if ( !res ) - { - gdcmDebugMacro( "in ParseDES : ParseSQ failed " << newSeqEntry->GetKey() - << " (at offset : 0x(" << std::hex - << newSeqEntry->GetOffset() << ") )" ); - - successParseDES = false; - newDocEntry = BacktrackSQtoOB(newSeqEntry, set); - set->AddEntry( newDocEntry); /// \todo fixme : the whole process is not done - /// (check SQItem length, when the DataElement is inside a Sequence) - - // - // - // - - continue; - } - if ( !set->AddEntry( newSeqEntry ) ) { gdcmWarningMacro( "in ParseDES : cannot add a SeqEntry " @@ -1334,7 +1313,7 @@ bool Document::ParseDES(DocEntrySet *set, long offset, if ( !delim_mode ) // 'and then' doesn't exist in C++ :-( if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per SeqEntry when no delim mode - + { if ( !used ) newDocEntry->Delete(); @@ -1353,10 +1332,7 @@ bool Document::ParseDES(DocEntrySet *set, long offset, break; } } // end While - gdcmDebugMacro( "Exit from ParseDES, delim-mode " << delim_mode ); - - return successParseDES; } /** @@ -1376,7 +1352,7 @@ bool Document::ParseSQ( SeqEntry *seqEntry, DocEntry *newDocEntry = ReadNextDocEntry(); if ( !newDocEntry ) - { + { // The most frequent is when a SQ terminator is missing (?!?) gdcmWarningMacro("in ParseSQ : should never get here!"); UnexpectedEOF = true; @@ -1411,7 +1387,7 @@ bool Document::ParseSQ( SeqEntry *seqEntry, { dlm_mod = false; } - + // avoid infinite loop when Bad assumption was made on illegal 'unknown length' UN //JPRx if (offsetStartCurrentSQItem <= OffsetOfPreviousParseDES) @@ -1426,22 +1402,16 @@ bool Document::ParseSQ( SeqEntry *seqEntry, { OffsetOfPreviousParseDES = offsetStartCurrentSQItem; } - + // fill up the current SQItem, starting at the beginning of fff0,e000 - Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); // Once per SQItem - bool res = ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod); + ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod); offsetStartCurrentSQItem = Fp->tellg(); // Once per SQItem seqEntry->AddSQItem( itemSQ, SQItemNumber ); itemSQ->Delete(); newDocEntry->Delete(); SQItemNumber++; - if (!res) // to avoid extra -useless- work when illegal UN stands for OB ... - { - gdcmDebugMacro("in ParseSQ : ParseDES failed"); - return false; - } //if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) //JPRx if ( !delim_mode && (offsetStartCurrentSQItem-offset ) >= l_max ) { @@ -1452,8 +1422,7 @@ bool Document::ParseSQ( SeqEntry *seqEntry, } /** - * \brief When a private Sequence + Implicit VR - * (or UN + undefined length element) is encountered + * \brief When a private Sequence + Implicit VR is encountered * we cannot guess it's a Sequence till we find the first * Item Starter. We then backtrack to do the job. * @param docEntry Item Starter that warned us @@ -1485,56 +1454,7 @@ DocEntry *Document::Backtrack(DocEntry *docEntry, DocEntrySet *set) // Move back to the beginning of the Sequence Fp->seekg(offset, std::ios::beg); // Only for Shadow Implicit VR SQ - return newEntry; // It will be added where it has to be! -} - - -/** - * \brief When a private OB + Implicit VR - * (or UN + undefined length element) is encountered - * we made first a bad assumption -it should be a Sequence- - * When we realize we were wrong, we backtrack. - * WARNING : it will probabely fail if the element - * is embedded within a sequence - * @param docEntry Item Starter that warned us - * @param set DocEntrySet (ElementSet/SQItem) the DocEntry will belong - */ - -DataEntry *Document::BacktrackSQtoOB(SeqEntry *docEntry, DocEntrySet *set) -{ - // Get all info we can from SeqEntry - - uint16_t group = docEntry->GetGroup(); - uint16_t elem = docEntry->GetElement(); - uint32_t lgt = docEntry->GetLength(); - long offset = docEntry->GetOffset(); - - gdcmDebugMacro( "BacktrackSQtoOB(" << std::hex << group - << "|" << elem - << " at offset 0x(" <RemoveEntry( docEntry ); - docEntry->Delete(); // not yet included into a DocEntrySet ! - - // forge the OB Entry - DataEntry *newEntry = NewDataEntry(group, elem, "OB"); - newEntry->SetOffset(offset); - - // Move back to the beginning of the Element - Fp->seekg(offset, std::ios::beg); - - uint32_t lengthOB = FindDocEntryLengthOBOrOW();// for encapsulation of encoded pixel - - newEntry->SetReadLength(lengthOB); - newEntry->SetLength(lengthOB); - - Fp->seekg(offset, std::ios::beg); - LoadDocEntry(newEntry, true); // true : forceload - - /// \todo fixme : it will fail if the element - /// is embedded within a sequence (sequence length checking is not done) - - return newEntry; // It will be added (ElementSet/SQItem) where it has to be! + return newEntry; // It will added where it has to be! } /** @@ -1594,7 +1514,7 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) 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 @@ -1616,7 +1536,7 @@ void Document::FindDocEntryLength( DocEntry *entry ) uint16_t length16; if ( Filetype == ExplicitVR && !entry->IsImplicitVR() ) { - + // WARNING : // // For some images, length of UN elements is coded on 2 bytes (instead of 4) @@ -1625,9 +1545,9 @@ void Document::FindDocEntryLength( DocEntry *entry ) //| vr == "UN" // in the following line. // (the 'straight' images will no longer be readable ...) - + if ( vr == "OB" || vr == "OW" || vr == "OL" || vr == "SQ" || vr == "UT" - || vr == "UN" || changeFromUN == true) + || vr == "UN" || changeFromUN == true) { changeFromUN = false; // The following reserved two bytes (see PS 3.5-2003, section @@ -1782,11 +1702,11 @@ VRKey Document::FindDocEntryVR() // Delimiters (0xfffe), are not explicit VR ... if ( CurrentGroup == 0xfffe ) return GDCM_VRUNKNOWN; - - //long positionOnEntry; - //if( Debug::GetWarningFlag() ) + + //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 // 'Transfer Syntax' told us it is. @@ -1802,17 +1722,17 @@ VRKey Document::FindDocEntryVR() //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) ) - { + { gdcmWarningMacro( "Unknown VR " << vr.GetHexaRepresentation() << std::hex << " at offset : 0x(" << CurrentOffsetPosition-4 << ") for group " << std::hex << 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; @@ -1878,7 +1798,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, entry->SetLength(0); return; // return ASAP; don't waist time on useless tests } - + uint16_t gr = entry->GetGroup(); uint16_t elem = entry->GetElement(); @@ -1911,7 +1831,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, // 'Leonardo' source. Hence, one might consider commenting out the // following fix on efficiency reasons. 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 ) @@ -1919,7 +1839,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, 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." @@ -1985,7 +1905,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) // 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 : (" + gdcmWarningMacro( "Erroneous Group Length element length on : (" << std::hex << group << " , " << elem << ") -before- position x(" << filePosition << ")" << "lgt : " << length ); @@ -2174,9 +2094,9 @@ 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 !)"); + << " (->despaired wild guesses !)"); switch ( s16 ) { case 0x0001 : @@ -2189,7 +2109,9 @@ bool Document::CheckSwap() case 0x0008 : case 0x0028 : SwapCode = 1234; - Filetype = ACR; + // Brute hack to allow reading DICOM RT files + //Filetype = ACR; // DICOM RT are *not* ACR-Nema files! + Filetype = ExplicitVR; return true; case 0x0100 : case 0x0200 : @@ -2204,7 +2126,7 @@ bool Document::CheckSwap() Filetype = ACR; return true; default : - + s16 = *((uint16_t *)(deb)); if (s16 != 0x0000) return false; @@ -2221,7 +2143,7 @@ bool Document::CheckSwap() break; case 0x0400 : SwapCode = 3412; - break; + break; default: gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)"); Filetype = Unknown; @@ -2245,7 +2167,7 @@ bool Document::CheckSwap() } } Filetype = ImplicitVR; - return true; + return true; } } } @@ -2315,11 +2237,11 @@ DocEntry *Document::ReadNextDocEntry() // header parsing has to be considered as finished. return 0; } - + changeFromUN = false; CurrentGroup = GetInt16(); CurrentElem = GetInt16(); - + // In 'true DICOM' files Group 0002 is always little endian if ( HasDCMPreamble ) { @@ -2349,7 +2271,7 @@ DocEntry *Document::ReadNextDocEntry() // -> Better we fix the problem at Write time else if (CurrentGroup%2 == 1 ) - { + { if (CurrentElem >= 0x0010 && CurrentElem <=0x00ff ) { // DICOM PS 3-5 7.8.1 a) states that : @@ -2389,13 +2311,13 @@ DocEntry *Document::ReadNextDocEntry() } // if UN found, let's check the dictionary, and trust it! - // (maybe a private dictionary exists?) + // (maybe a private dictionary exists?) else if (vr == "UN") { DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem); if ( dictEntry ) { - realVR = dictEntry->GetVR(); + realVR = dictEntry->GetVR(); dictEntry->Unregister(); // GetDictEntry registered it // for VR = "UN", length is always stored on 4 bytes. @@ -2428,10 +2350,10 @@ 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) - { + { int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x(" @@ -2542,7 +2464,7 @@ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) if ( s == TS::ImplicitVRLittleEndian || - s == TS::ImplicitVRBigEndianPrivateGE + s == TS::ImplicitVRBigEndianPrivateGE ) { Filetype = ImplicitVR; @@ -2555,10 +2477,10 @@ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) // to trust manufacturers. // (we often find 'Implicit VR' tag, // even when Transfer Syntax tells us it's Explicit ... - + // NEVER trust the meta elements! // (see what ezDICOM does ...) - + /* if ( s == TS::ExplicitVRBigEndian ) { @@ -2579,34 +2501,34 @@ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) elem = SwapShort(elem); // not what we where told (by meta elements) ! gdcmDebugMacro("Transfer Syntax Name = [" - << GetTransferSyntaxName() << "]" ); + << GetTransferSyntaxName() << "]" ); } - + /// \todo find a trick to warn user and stop processing - + if ( s == TS::DeflatedExplicitVRLittleEndian) { gdcmWarningMacro("Transfer Syntax [" << GetTransferSyntaxName() << "] :" << " not yet dealt with "); - return; + return; } - + // The following shouldn't occur very often // Let's check at the very end. if ( ts == GDCM_UNKNOWN ) { gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " ); - return; + return; } - + if ( !Global::GetTS()->IsTransferSyntax(ts) ) { gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: [" << ts << "]"); return; - } + } } //-----------------------------------------------------------------------------