X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=11b88a2e6fefc1d8b1aebba0dd568c1c0cdeda05;hb=6278320cc85da00d2d56ffbf07806e84966892c3;hp=4d88d9c8d623b85b76f12f8117f19fbefb591302;hpb=a4cc79200b40be00c490fa4a9116dca626e1c5cf;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 4d88d9c8..11b88a2e 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2007/09/17 12:16:02 $ - Version: $Revision: 1.369 $ + Date: $Date: 2008/09/15 15:49:22 $ + Version: $Revision: 1.381 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -63,6 +63,7 @@ Document::Document() SwapCode = 1234; Filetype = ExplicitVR; CurrentOffsetPosition = 0; + OffsetOfPreviousParseDES =0; // Load will set it to true if sucessfull Group0002Parsed = false; IsDocumentAlreadyLoaded = false; @@ -161,6 +162,7 @@ bool Document::DoTheLoadingDocumentJob( ) // Recursive call. // Loading is done during parsing + OffsetOfPreviousParseDES = beg; ParseDES( this, beg, lgt, false); // delim_mode is first defaulted to false if ( IsEmpty() ) @@ -281,10 +283,13 @@ bool Document::DoTheLoadingDocumentJob( ) // std::string RecCode; RecCode = GetEntryString(0x0008, 0x0010); // recognition code (RET) - if (RecCode == "ACRNEMA_LIBIDO_1.1" || - RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares - // with "little-endian strings" + + + 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); @@ -693,7 +698,7 @@ bool Document::CloseFile() * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) */ -void Document::WriteContent(std::ofstream *fp, FileType filetype) +void Document::WriteContent(std::ofstream *fp, FileType filetype, bool, bool) { // Skip if user wants to write an ACR-NEMA file @@ -1035,10 +1040,10 @@ int Document::ComputeGroup0002Length( ) vr = entry->GetVR(); //if ( (vr == "OB")||(vr == "OW")||(vr == "UT")||(vr == "SQ")) - // (no SQ, OW, UT in group 0x0002;) + // (no SQ, OW, OL, UT in group 0x0002;) if ( vr == "OB" ) { - // explicit VR AND (OB, OW, SQ, UT) : 4 more bytes + // explicit VR AND (OB, OW, OL, SQ, UT, UN) : 4 more bytes groupLength += 4; } groupLength += 2 + 2 + 4 + entry->GetLength(); @@ -1116,14 +1121,14 @@ void Document::ParseDES(DocEntrySet *set, long offset, { ///\todo FIXME : On 64 bits processors, tellg gives unexpected results after a while ? - /// Probabely a bug in gdcm code somwhere (some memory erased ?) + /// Probabely a bug in gdcm code somewhere (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++ :-( @@ -1151,7 +1156,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, if ( !first && newDocEntry->IsItemStarter() ) { // Debug message within the method ! - newDocEntry = Backtrack(newDocEntry); + newDocEntry = Backtrack(newDocEntry, set); } else { @@ -1225,7 +1230,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, { /////////////////////// SeqEntry : VR = "SQ" - unsigned long l = newDocEntry->GetReadLength(); + unsigned long l = newDocEntry->GetReadLength(); if ( l != 0 ) // don't mess the delim_mode for 'zero-length sequence' { if ( l == 0xffffffff ) @@ -1324,7 +1329,9 @@ void Document::ParseDES(DocEntrySet *set, long offset, first = false; if (UnexpectedEOF) // some terminator was missing + { break; + } } // end While gdcmDebugMacro( "Exit from ParseDES, delim-mode " << delim_mode ); } @@ -1382,8 +1389,22 @@ 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) + { + gdcmWarningMacro("Bad assumption was made on illegal 'unknown length' UN!" << std::endl << + "OffsetOfPreviousParseDES " << std::hex << OffsetOfPreviousParseDES + << " offsetStartCurrentSQItem " << offsetStartCurrentSQItem); + /// \todo when "Bad assumption (SQ) on illegal 'unknown length' UN", Backtrack again + try OB + return false; + } + else + { + OffsetOfPreviousParseDES = offsetStartCurrentSQItem; + } + // 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 @@ -1405,9 +1426,10 @@ bool Document::ParseSQ( SeqEntry *seqEntry, * \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 + * @param docEntry Item Starter that warned us + * @param set DocEntrySet (ElementSet/SQItem) the DocEntry will belong */ -DocEntry *Document::Backtrack(DocEntry *docEntry) +DocEntry *Document::Backtrack(DocEntry *docEntry, DocEntrySet *set) { // delete the Item Starter, built erroneously out of any Sequence // it's not yet in the HTable/chained list @@ -1422,7 +1444,8 @@ DocEntry *Document::Backtrack(DocEntry *docEntry) gdcmDebugMacro( "Backtrack :" << std::hex << group << "|" << elem << " at offset 0x(" <RemoveEntry( PreviousDocEntry ); // forge the Seq Entry DocEntry *newEntry = NewSeqEntry(group, elem); @@ -1432,7 +1455,7 @@ DocEntry *Document::Backtrack(DocEntry *docEntry) // Move back to the beginning of the Sequence Fp->seekg(offset, std::ios::beg); // Only for Shadow Implicit VR SQ - return newEntry; + return newEntry; // It will added where it has to be! } /** @@ -1524,18 +1547,18 @@ void Document::FindDocEntryLength( DocEntry *entry ) // in the following line. // (the 'straight' images will no longer be readable ...) - if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT" - || vr == "UN" || changeFromUN == true) + if ( vr == "OB" || vr == "OW" || vr == "OL" || vr == "SQ" || vr == "UT" + || vr == "UN" || changeFromUN == true) { changeFromUN = false; // 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(); // Once per OW,OB,SQ DocEntry + //Fp->seekg( 2L, std::ios::cur); // Once per OB,OW,OL,UT,UN,SQ DocEntry + uint32_t length32 = ReadInt32(); // Once per OB,OW,OL,UT,UN,SQ DocEntry CurrentOffsetPosition+=4; - if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) + if ( (vr == "OB" || vr == "OW" || vr == "OL") && length32 == 0xffffffff ) { uint32_t lengthOB; try @@ -1621,7 +1644,8 @@ uint32_t Document::FindDocEntryLengthOBOrOW() uint16_t elem; try - { + { ///\todo make sure there is never OL encoded pixel data! + //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 @@ -1640,8 +1664,8 @@ uint32_t Document::FindDocEntryLengthOBOrOW() { gdcmWarningMacro( "Neither an Item tag nor a Sequence delimiter tag on :" - << std::hex << group << " , " << elem - << ")" ); + << std::hex << group << "|" << elem << ") Pos. on entry was 0x(" <seekg(positionOnEntry, std::ios::beg); // Once per fragment (if any) of OB,OW DataElements throw FormatUnexpected( @@ -1702,21 +1726,12 @@ VRKey Document::FindDocEntryVR() //if ( !CheckDocEntryVR(vr) ) // avoid useless function call if ( !Global::GetVR()->IsValidVR(vr) ) - { -/* -// std::cout << "================================================================Unknown VR" - << std::hex << "0x(" - << (unsigned int)vr[0] << "|" << (unsigned int)vr[1] - << ")" << "for : " << CurrentGroup - << " at offset : 0x(" << positionOnEntry << ")" - << std::endl; -*/ - gdcmWarningMacro( "Unknown VR " << std::hex << "0x(" - << (unsigned int)vr[0] << "|" << (unsigned int)vr[1] - << ")" - << " at offset : 0x(" << CurrentOffsetPosition-4<< ") for group " << CurrentGroup - ); + { + 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 (?!?) //see :MR_Philips_Intera_PrivateSequenceExplicitVR.dcm @@ -1755,7 +1770,7 @@ void Document::SkipDocEntry(DocEntry *entry) void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) { long l = currentDocEntry->GetReadLength(); - if ( l == -1 ) // length = 0xffff shouldn't appear here ... + if ( (uint32_t) l == (uint32_t)-1 ) // length = 0xffff shouldn't appear here ... // ... but PMS imagers happen ! return; Fp->seekg((size_t)(currentDocEntry->GetOffset()), std::ios::beg); //FIXME :each DocEntry @@ -1790,10 +1805,12 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, if ( foundLength % 2) { - gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength - << " in x(" << std::hex << gr << "," << elem <<")"); + gdcmWarningMacro( "Warning : Tag (" << std::hex << gr << "|" << elem << ") with uneven length " + << std::dec << foundLength << " 0x(" << std::hex << foundLength << ") " + //<< " at offset x(" << offset << ")" + ); } - + //////// 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 @@ -2133,17 +2150,20 @@ bool Document::CheckSwap() } // Check if next 2 bytes are a VR // Probabely something more time-consuming exists with std::string - const char VRvalues[] = "AEASCSDADSFLFDISLOLTPNSHSLSSSTTMUIULUSUTOBOWOFATUNSQ"; - int nbVal = 26; + const char VRvalues[] = "AEASATCSDADTFLFDISLOLTPNSHSLSSSTTMUIULUSUTOBOWOLOFATUNSQRT"; + int nbVal = 29; const char *pt = VRvalues; for (int i=0;i= 0x0010 && CurrentElem <=0x00ff ) + { // DICOM PS 3-5 7.8.1 a) states that : // Private Creator Data Elements numbered (gggg,0010-00FF) (gggg is odd) // attributes have to be LO (Long String) and the VM shall be equal to 1 @@ -2261,8 +2282,20 @@ DocEntry *Document::ReadNextDocEntry() // Still in gdcmtk, David Clunnie disagrees, Marco Eichelberg says it's OK ... // We let it for a while? //(We should check length==4, for more security, but we don't have it yet !) + } else if ( CurrentElem == 0x0001) - realVR = "UL"; // Private Group Length To End + { + realVR = "UL"; // Private Group Length To End + } + else // check the private dictionary for shadow elements when Implicit VR! + { + DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem); + if ( dictEntry ) + { + realVR = dictEntry->GetVR(); + dictEntry->Unregister(); // GetDictEntry registered it + } + } } else @@ -2283,19 +2316,21 @@ DocEntry *Document::ReadNextDocEntry() 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. + // remember this info, in order not to crash later changeFromUN=true; - /// \todo : fixme If inside a supposed to be UN DataElement (but SQ according to a private dictionnary) - /// there is some more supposed to be UN DataElements, it will probabely fail. + /// \todo : fixme If inside a vr = "UN" DataElement (but SQ according to a private dictionnary) + /// there is some more vr = "UN" DataElements, it will probabely fail. /// --> find a -non time consuming- trick to store changeFromUN info at DataElement level, /// not at the Document level. + /// --> ?!? JPR + } } - DocEntry *newEntry; //if ( Global::GetVR()->IsVROfSequence(realVR) ) if (realVR == "SQ") @@ -2321,7 +2356,7 @@ DocEntry *Document::ReadNextDocEntry() int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x(" - << offset << ") should be Explicit VR"); + << std::hex << offset << ") should be Explicit VR"); } } newEntry->SetImplicitVR();