X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=8ac4b2296ae0d43209ef487b7bfed0319bf1e90c;hb=880f6dfe2e061712fafbf75ab9547aadf170fc40;hp=3803b0a705673a36a062262c0c5d2c00e6fdabbb;hpb=79d1ce76dfcb136e8b77aaeac859ba59973e7ae4;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 3803b0a7..8ac4b229 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2006/02/09 10:48:04 $ - Version: $Revision: 1.341 $ + Date: $Date: 2006/05/05 22:13:55 $ + Version: $Revision: 1.347 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -95,6 +95,20 @@ 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 +132,7 @@ 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 ! @@ -640,7 +654,7 @@ 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()); @@ -681,7 +695,6 @@ 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 @@ -969,7 +982,6 @@ int Document::ComputeGroup0002Length( ) // explicit VR AND (OB, OW, SQ, UT) : 4 more bytes groupLength += 4; } - groupLength += 2 + 2 + 4 + entry->GetLength(); } } @@ -1012,6 +1024,7 @@ void Document::CallEndMethod() // Private /** * \brief Loads all the needed Dictionaries + * \warning NOT end user intended method ! */ void Document::Initialize() { @@ -1039,11 +1052,21 @@ void Document::ParseDES(DocEntrySet *set, long offset, 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 { @@ -1066,9 +1089,9 @@ void Document::ParseDES(DocEntrySet *set, long offset, // but we didn't get it (private Sequence + Implicit VR) // we have to backtrack. if ( !first && newDocEntry->IsItemStarter() ) - { - // Debug message within the method ! - newDocEntry = Backtrack(newDocEntry); + { + // Debug message within the method ! + newDocEntry = Backtrack(newDocEntry); } else { @@ -1208,7 +1231,6 @@ void Document::ParseDES(DocEntrySet *set, long offset, l, delim_mode_intern); gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern); - } if ( !set->AddEntry( newSeqEntry ) ) { @@ -1274,12 +1296,14 @@ 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(); @@ -1292,16 +1316,12 @@ 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(); @@ -1344,8 +1364,7 @@ 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; } @@ -1369,7 +1388,6 @@ 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 @@ -1437,7 +1455,7 @@ 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(); @@ -1500,6 +1518,7 @@ 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' + // where Group 0x0002 is *also* encoded in Implicit VR ! FixDocEntryFoundLength( entry, ReadInt32() ); return; @@ -1508,6 +1527,7 @@ void Document::FindDocEntryLength( DocEntry *entry ) /** * \brief Find the Length till the next sequence delimiter + * \warning NOT end user intended method ! * @return */ uint32_t Document::FindDocEntryLengthOBOrOW() @@ -1515,7 +1535,7 @@ uint32_t Document::FindDocEntryLengthOBOrOW() { // 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 - + bool foundSequenceDelimiter = false; uint32_t totalLength = 0; @@ -1537,11 +1557,9 @@ uint32_t Document::FindDocEntryLengthOBOrOW() 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 @@ -1573,7 +1591,9 @@ uint32_t Document::FindDocEntryLengthOBOrOW() VRKey Document::FindDocEntryVR() { if ( Filetype != ExplicitVR ) + { return GDCM_VRUNKNOWN; + } // Delimiters (0xfffe), are not explicit VR ... if ( CurrentGroup == 0xfffe ) @@ -1600,7 +1620,7 @@ VRKey Document::FindDocEntryVR() if ( !CheckDocEntryVR(vr) ) { /* - std::cout << "================================================================Unknown VR" +// std::cout << "================================================================Unknown VR" << std::hex << "0x(" << (unsigned int)vr[0] << "|" << (unsigned int)vr[1] << ")" << "for : " << CurrentGroup @@ -1665,17 +1685,21 @@ 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(); @@ -1705,26 +1729,37 @@ 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; } @@ -1732,7 +1767,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, { foundLength=12; // to skip the mess that follows this bugged Tag ! } - } + } entry->SetLength(foundLength); } @@ -1863,8 +1898,6 @@ 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 return true; } // ------------------------------- End of DicomV3 ---------------- @@ -2019,7 +2052,7 @@ 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 ) { @@ -2038,7 +2071,7 @@ 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() { @@ -2049,23 +2082,22 @@ DocEntry *Document::ReadNextDocEntry() } 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; } // 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 ) @@ -2074,9 +2106,14 @@ 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 )) @@ -2088,20 +2125,22 @@ 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); @@ -2113,14 +2152,14 @@ 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(); @@ -2233,7 +2272,7 @@ 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)