X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=34b18e5f2d2dd451484efdeb672e8b431275d18e;hb=507c357466602345e4bd9de6c475e0887cf2ba36;hp=3f49d22649bfa5808acf1204d7d15b16d7cc7be6;hpb=1b14200990537794a9f66d43c89b030459237edc;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 3f49d226..34b18e5f 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2005/10/18 11:10:45 $ - Version: $Revision: 1.292 $ + Date: $Date: 2005/12/14 10:00:28 $ + Version: $Revision: 1.334 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -76,7 +76,6 @@ Document::~Document () //----------------------------------------------------------------------------- // Public - /** * \brief Loader. use SetLoadMode(), SetFileName() before ! * @return false if file cannot be open or no swap info was found, @@ -90,17 +89,6 @@ bool Document::Load( ) return false; } return DoTheLoadingDocumentJob( ); -} -/** - * \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( ); } /** @@ -119,15 +107,13 @@ bool Document::DoTheLoadingDocumentJob( ) if ( !OpenFile() ) { // warning already performed in OpenFile() - //gdcmWarningMacro( "Unable to open as an ACR/DICOM file: " - // << Filename.c_str() ); Filetype = Unknown; return false; } Group0002Parsed = false; - gdcmWarningMacro( "Starting parsing of file: " << Filename.c_str()); + gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str()); Fp->seekg(0, std::ios::end); long lgt = Fp->tellg(); // total length of the file @@ -154,7 +140,7 @@ bool Document::DoTheLoadingDocumentJob( ) if ( IsEmpty() ) { - gdcmWarningMacro( "No tag in internal hash table for: " + gdcmErrorMacro( "No tag in internal hash table for: " << Filename.c_str()); CloseFile(); return false; @@ -174,20 +160,33 @@ bool Document::DoTheLoadingDocumentJob( ) LoadEntryBinArea(0x0028,0x1200); // gray LUT /// FIXME + /// --> FIXME : The difference between BinEntry and DataEntry + /// --> no longer exists, but the alteration of Dicom Dictionary remains. + /// --> Old comment restored on purpose. + /// --> New one (replacing both BinEntry and ValEntry by DataEntry) + /// --> had absolutely no meaning. + /// --> The whole comment will be removed when the stuff is cleaned ! + /// --> /// The tags refered by the three following lines used to be CORRECTLY /// defined as having an US Value Representation in the public /// dictionary. BUT the semantics implied by the three following /// lines state that the corresponding tag contents are in fact - /// the ones of a DataEntry. + /// the ones of a BinEntry. /// In order to fix things "Quick and Dirty" the dictionary was /// altered on PURPOSE but now contains a WRONG value. /// In order to fix things and restore the dictionary to its - /// correct value, one needs to decided of the semantics by deciding + /// correct value, one needs to decide of the semantics by deciding /// whether the following tags are either : - /// - multivaluated US, and hence loaded as DataEntry, but afterwards - /// also used as DataEntry, which requires the proper conversion, - /// - OW, and hence loaded as DataEntry, but afterwards also used - /// as DataEntry, which requires the proper conversion. + /// - multivaluated US, and hence loaded as ValEntry, but afterwards + /// also used as BinEntry, which requires the proper conversion, + /// - OW, and hence loaded as BinEntry, but afterwards also used + /// as ValEntry, which requires the proper conversion. + + // --> OB (byte aray) or OW (short int aray) + // The actual VR has to be deduced from other entries. + // Our way of loading them may fail in some cases : + // We must or not SwapByte depending on other field values. + LoadEntryBinArea(0x0028,0x1201); // R LUT LoadEntryBinArea(0x0028,0x1202); // G LUT LoadEntryBinArea(0x0028,0x1203); // B LUT @@ -212,6 +211,8 @@ bool Document::DoTheLoadingDocumentJob( ) { if ( dataEntry->GetLength() != 0 ) { + // FIXME : CTX dependent means : contexted dependant. + // see upper comment. LoadEntryBinArea(dataEntry); //LUT Data (CTX dependent) } } @@ -225,7 +226,7 @@ bool Document::DoTheLoadingDocumentJob( ) it != UserForceLoadList.end(); ++it) { - gdcmWarningMacro( "Force Load " << std::hex + gdcmDebugMacro( "Force Load " << std::hex << (*it).Group << "|" <<(*it).Elem ); d = GetDocEntry( (*it).Group, (*it).Elem); @@ -277,7 +278,7 @@ bool Document::DoTheLoadingDocumentJob( ) */ void Document::AddForceLoadElement (uint16_t group, uint16_t elem) { - Element el; + DicomElement el; el.Group = group; el.Elem = elem; UserForceLoadList.push_back(el); @@ -325,11 +326,11 @@ bool Document::SetShaDict(DictKey const &dictName) * @return false when we're 150 % sure it's NOT a Dicom/Acr file, * true otherwise. */ -bool Document::IsReadable() +bool Document::IsParsable() { if ( Filetype == Unknown ) { - gdcmWarningMacro( "Wrong filetype"); + gdcmWarningMacro( "Wrong filetype for " << GetFileName()); return false; } @@ -341,6 +342,17 @@ bool Document::IsReadable() return true; } +/** + * \brief This predicate tells us whether or not the current Document + * was properly parsed and contains at least *one* Dicom Element + * (and nothing more, sorry). + * @return false when we're 150 % sure it's NOT a Dicom/Acr file, + * true otherwise. + */ +bool Document::IsReadable() +{ + return IsParsable(); +} /** * \brief Predicate for dicom version 3 file. @@ -386,7 +398,8 @@ FileType Document::GetFileType() * \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. + * @return The encountered Transfer Syntax of the current document, if DICOM. + * GDCM_UNKNOWN for ACR-NEMA files (or broken headers ...) */ std::string Document::GetTransferSyntax() { @@ -408,6 +421,7 @@ std::string Document::GetTransferSyntax() if ( transfer.length() == 0 ) { // for brain damaged headers + gdcmWarningMacro( "Transfer Syntax has length = 0."); return GDCM_UNKNOWN; } while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) @@ -416,6 +430,7 @@ std::string Document::GetTransferSyntax() if ( transfer.length() == 0 ) { // for brain damaged headers + gdcmWarningMacro( "Transfer Syntax contains no valid character."); return GDCM_UNKNOWN; } } @@ -441,7 +456,7 @@ std::string Document::GetTransferSyntaxName() } if ( transferSyntax == GDCM_UNFOUND ) { - gdcmWarningMacro( "Unfound Transfer Syntax (0002,0010)"); + gdcmDebugMacro( "Unfound Transfer Syntax (0002,0010)"); return "Uncompressed ACR-NEMA"; } @@ -494,12 +509,48 @@ uint32_t Document::SwapLong(uint32_t a) a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) ); break; default : - gdcmErrorMacro( "Unset swap code:" << SwapCode ); + gdcmErrorMacro( "Unexpected swap code:" << SwapCode ); a = 0; } return a; } +/** + * \brief Swaps back the bytes of 8-byte long 'double' accordingly to + * processor order. + * @return The properly swaped 64 bits double. + */ +double Document::SwapDouble(double a) +{ + switch (SwapCode) + { + // There were no 'double' at ACR-NEMA time. + // We just have to deal with 'straight Little Endian' and + // 'straight Big Endian' + case 1234 : + break; + case 4321 : + { + char *beg = (char *)&a; + char *end = beg + 7; + char t; + for (unsigned int i = 0; i<7; i++) + { + t = *beg; + *beg = *end; + *end = t; + beg++, + end--; + } + } + break; + default : + gdcmErrorMacro( "Unexpected swap code:" << SwapCode ); + a = 0.; + } + return a; +} + // // -----------------File I/O --------------- /** @@ -517,7 +568,7 @@ std::ifstream *Document::OpenFile() if ( Fp ) { - gdcmWarningMacro( "File already open: " << Filename.c_str()); + gdcmDebugMacro( "File already open: " << Filename.c_str()); CloseFile(); } @@ -528,6 +579,10 @@ std::ifstream *Document::OpenFile() // 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 + // --> the constructor is not so good ... + gdcmWarningMacro( "Cannot open file: " << Filename.c_str()); delete Fp; Fp = 0; @@ -544,7 +599,10 @@ std::ifstream *Document::OpenFile() return 0; } - //-- ACR or DICOM with no Preamble; may start with a Shadow Group -- + //-- 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 ( zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 || zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 || @@ -552,7 +610,8 @@ std::ifstream *Document::OpenFile() zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ) { std::string msg = Util::Format( - "ACR/DICOM starting at the beginning of the file:(%04x)\n", zero); + "ACR/DICOM starting by 0x(%04x) at the beginning of the file\n", zero); + // FIXME : is it a Warning message, or a Debug message? gdcmWarningMacro( msg.c_str() ); return Fp; } @@ -574,7 +633,9 @@ std::ifstream *Document::OpenFile() // -- Neither ACR/No Preamble Dicom nor DICOMV3 file CloseFile(); - gdcmWarningMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: " + // Don't user Warning nor Error, not to polute the output + // while directory recursive parsing ... + gdcmDebugMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: " << Filename.c_str()); return 0; } @@ -604,7 +665,8 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) { // Skip if user wants to write an ACR-NEMA file - if ( filetype == ImplicitVR || filetype == ExplicitVR ) + if ( filetype == ImplicitVR || filetype == ExplicitVR || + filetype == JPEG ) { // writing Dicom File Preamble char filePreamble[128]; @@ -623,6 +685,10 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) * UpdateGroupLength(false,filetype); * if ( filetype == ACR) * UpdateGroupLength(true,ACR); + * + * --> Computing group length for groups with embeded Sequences + * --> was too much tricky / we were [in a hurry / too lazy] + * --> We don't write the element 0x0000 (group length) */ ElementSet::WriteContent(fp, filetype); // This one is recursive @@ -642,15 +708,15 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) DocEntry *docEntry = GetDocEntry(group, elem); if ( !docEntry ) { - gdcmWarningMacro(std::hex << group << "|" << elem - << "doesn't exist" ); + gdcmDebugMacro(std::hex << group << "|" << elem + << " doesn't exist" ); return; } DataEntry *dataEntry = dynamic_cast(docEntry); if ( !dataEntry ) { gdcmWarningMacro(std::hex << group << "|" << elem - << "is NOT a DataEntry"); + << " is NOT a DataEntry"); return; } LoadEntryBinArea(dataEntry); @@ -659,7 +725,7 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) /** * \brief Loads (from disk) the element content * when a string is not suitable - * @param elem Entry whose binArea is going to be loaded + * @param entry Entry whose binArea is going to be loaded */ void Document::LoadEntryBinArea(DataEntry *entry) { @@ -683,7 +749,7 @@ void Document::LoadEntryBinArea(DataEntry *entry) return; } - // Read the datas + // Read the data Fp->read((char*)data, l); if ( Fp->fail() || Fp->eof() ) { @@ -694,12 +760,19 @@ void Document::LoadEntryBinArea(DataEntry *entry) // Swap the data content if necessary uint32_t i; - unsigned short vrLgth = Global::GetVR()->GetAtomicElementLength(entry->GetVR()); - if( entry->GetVR() == "OW" ) - vrLgth = 1; + unsigned short vrLgth = + Global::GetVR()->GetAtomicElementLength(entry->GetVR()); + +// FIXME : trouble expected if we read an ... OW Entry (LUT, etc ..) +// if( entry->GetVR() == "OW" ) +// vrLgth = 1; switch(vrLgth) { + case 1: + { + break; + } case 2: { uint16_t *data16 = (uint16_t *)data; @@ -716,10 +789,9 @@ void Document::LoadEntryBinArea(DataEntry *entry) } case 8: { - gdcmWarningMacro("Can't swap 64 bits datas"); -/* uint64_t *data64 = (uint64_t *)data; + double *data64 = (double *)data; for(i=0;iGetVR(); - // FIXME : group 0x0002 is *always* Explicit VR! - - //if ( filetype == ExplicitVR ) - //{ - // if ( (vr == "OB") || (vr == "OW") || (vr == "UT") || (vr == "SQ") ) + //if ( (vr == "OB")||(vr == "OW")||(vr == "UT")||(vr == "SQ")) // (no SQ, OW, UT in group 0x0002;) if ( vr == "OB" ) { - // explicit VR AND OB, OW, SQ, UT : 4 more bytes + // explicit VR AND (OB, OW, SQ, UT) : 4 more bytes groupLength += 4; } - //} + groupLength += 2 + 2 + 4 + entry->GetLength(); } } @@ -916,11 +983,37 @@ int Document::ComputeGroup0002Length( /*FileType filetype*/ ) return groupLength; } +/** + * \brief CallStartMethod + */ +void Document::CallStartMethod() +{ + Progress = 0.0f; + Abort = false; + CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS); +} + +/** + * \brief CallProgressMethod + */ +void Document::CallProgressMethod() +{ + CommandManager::ExecuteCommand(this,CMD_PROGRESS); +} + +/** + * \brief CallEndMethod + */ +void Document::CallEndMethod() +{ + Progress = 1.0f; + CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS); +} + //----------------------------------------------------------------------------- // Private /** * \brief Loads all the needed Dictionaries - * \warning NOT end user intended method ! */ void Document::Initialize() { @@ -947,8 +1040,8 @@ void Document::ParseDES(DocEntrySet *set, long offset, // (Entry will then be deleted) bool delim_mode_intern = delim_mode; bool first = true; - gdcmWarningMacro( "Enter in ParseDES, delim-mode " << delim_mode - << " at offset " << std::hex << offset ); + gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode + << " at offset " << std::hex << "0x(" << offset << ")" ); while (true) { if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) @@ -958,19 +1051,10 @@ void Document::ParseDES(DocEntrySet *set, long offset, newDocEntry = ReadNextDocEntry( ); - // FIXME : - // Private tag, in IMplicit VR are defaulted as a DataEntry, - // Very often they are only composed of Printable characters, - // and could be defaulted as a DataEntry. - // It's too late to do the Job - // (we should check the value, but we know it after LoadDocEntry ...) - - // Uncoment this printf line to be able to 'follow' the DocEntries + // Uncoment this cerr line to be able to 'follow' the DocEntries // when something *very* strange happens - - //printf( "%04x|%04x %s\n",newDocEntry->GetGroup(), - // newDocEntry->GetElement(), - // newDocEntry->GetVR().c_str() ); + if( Debug::GetDebugFlag() ) + std::cerr<GetKey()<<" "<GetVR()<IsItemStarter() ) - { - newDocEntry = Backtrack(newDocEntry); + { + // Debug message within the method ! + newDocEntry = Backtrack(newDocEntry); } else { @@ -996,31 +1081,23 @@ void Document::ParseDES(DocEntrySet *set, long offset, if ( newDataEntry ) { //////////////////////////// DataEntry + vr = newDocEntry->GetVR(); - if ( Filetype == ExplicitVR && - !Global::GetVR()->IsVROfBinaryRepresentable(vr) ) - { - ////// No DataEntry: should mean UNKOWN VR - gdcmWarningMacro( std::hex << newDocEntry->GetGroup() - << "|" << newDocEntry->GetElement() - << " : No DataEntry." - "Probably unknown VR."); - } if ( !set->AddEntry( newDataEntry ) ) { - gdcmWarningMacro( "in ParseDES : cannot add a DataEntry " + gdcmDebugMacro( "in ParseDES : cannot add a DataEntry " << newDataEntry->GetKey() - << " (at offset : " - << newDataEntry->GetOffset() << " )" ); + << " (at offset : 0x(" + << newDataEntry->GetOffset() << ") )" ); used=false; } else { + newDataEntry->Delete(); // Load only if we can add (not a duplicate key) LoadDocEntry( newDataEntry ); } - if ( newDataEntry->GetElement() == 0x0000 ) // if on group length { if ( newDataEntry->GetGroup()%2 != 0 ) // if Shadow Group @@ -1028,8 +1105,9 @@ void Document::ParseDES(DocEntrySet *set, long offset, if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr { std::string strLgrGroup = newDataEntry->GetString(); + int lgrGroup; - if ( newDataEntry->IsUnfound() ) + //if ( newDataEntry->IsUnfound() ) /?!? JPR { lgrGroup = atoi(strLgrGroup.c_str()); Fp->seekg(lgrGroup, std::ios::cur); @@ -1049,7 +1127,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) { if ( !used ) - delete newDocEntry; + newDocEntry->Delete(); break; } @@ -1079,8 +1157,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, if ( newDocEntry->GetGroup()%2 != 0 ) { Fp->seekg( l, std::ios::cur); - RemoveEntry( newDocEntry ); // Remove and delete - //used = false; // never used + newDocEntry->Delete(); // Delete, not in the set continue; } } @@ -1088,8 +1165,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, { // User asked to skip *any* SeQuence Fp->seekg( l, std::ios::cur); - //used = false; // never used - RemoveEntry( newDocEntry ); // Remove and delete + newDocEntry->Delete(); // Delete, not in the set continue; } // delay the dynamic cast as late as possible @@ -1102,11 +1178,9 @@ void Document::ParseDES(DocEntrySet *set, long offset, // is a Document, then we are building the first depth level. // Hence the SeqEntry we are building simply has a depth // level of one: -// SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ); if ( set == this ) // ( dynamic_cast< Document* > ( set ) ) { newSeqEntry->SetDepthLevel( 1 ); - // newSeqEntry->SetKey( newSeqEntry->GetKey() ); } // But when "set" is already a SQItem, we are building a nested // sequence, and hence the depth level of the new SeqEntry @@ -1116,49 +1190,50 @@ void Document::ParseDES(DocEntrySet *set, long offset, else if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) { newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); - - // newSeqEntry->SetKey( parentSQItem->GetBaseTagKey() - // + newSeqEntry->GetKey() ); } if ( l != 0 ) { // Don't try to parse zero-length sequences - gdcmWarningMacro( "Entry in ParseSQ, delim " << delim_mode_intern - << " at offset " << std::hex - << newDocEntry->GetOffset() ); + gdcmDebugMacro( "Entry in ParseSQ, delim " << delim_mode_intern + << " at offset 0x(" << std::hex + << newDocEntry->GetOffset() << ")"); ParseSQ( newSeqEntry, newDocEntry->GetOffset(), l, delim_mode_intern); - gdcmWarningMacro( "Exit from ParseSQ, delim " << delim_mode_intern); + gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern); } if ( !set->AddEntry( newSeqEntry ) ) { gdcmWarningMacro( "in ParseDES : cannot add a SeqEntry " << newSeqEntry->GetKey() - << " (at offset : " - << newSeqEntry->GetOffset() << " )" ); + << " (at offset : 0x(" + << newSeqEntry->GetOffset() << ") )" ); used = false; } + else + { + newDocEntry->Delete(); + } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { if ( !used ) - delete newDocEntry; - break; + newDocEntry->Delete(); + break; } } // end SeqEntry : VR = "SQ" if ( !used ) { - delete newDocEntry; + newDocEntry->Delete(); } first = false; } // end While - gdcmWarningMacro( "Exit from ParseDES, delim-mode " << delim_mode ); + gdcmDebugMacro( "Exit from ParseDES, delim-mode " << delim_mode ); } /** @@ -1179,7 +1254,6 @@ void Document::ParseSQ( SeqEntry *seqEntry, if ( !newDocEntry ) { - // FIXME Should warn user gdcmWarningMacro("in ParseSQ : should never get here!"); break; } @@ -1188,16 +1262,17 @@ void Document::ParseSQ( SeqEntry *seqEntry, if ( newDocEntry->IsSequenceDelimitor() ) { seqEntry->SetDelimitationItem( newDocEntry ); + newDocEntry->Delete(); break; } } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - delete newDocEntry; + newDocEntry->Delete(); break; } // create the current SQItem - SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); + SQItem *itemSQ = SQItem::New( seqEntry->GetDepthLevel() ); unsigned int l = newDocEntry->GetReadLength(); if ( l == 0xffffffff ) @@ -1209,18 +1284,17 @@ void Document::ParseSQ( SeqEntry *seqEntry, dlm_mod = false; } - // Let's try :------------ // remove fff0,e000, created out of the SQItem - delete newDocEntry; Fp->seekg(offsetStartCurrentSQItem, std::ios::beg); // fill up the current SQItem, starting at the beginning of fff0,e000 ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod); offsetStartCurrentSQItem = Fp->tellg(); - // end try ----------------- seqEntry->AddSQItem( itemSQ, SQItemNumber ); + itemSQ->Delete(); + newDocEntry->Delete(); SQItemNumber++; if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max ) { @@ -1239,7 +1313,7 @@ DocEntry *Document::Backtrack(DocEntry *docEntry) { // delete the Item Starter, built erroneously out of any Sequence // it's not yet in the HTable/chained list - delete docEntry; + docEntry->Delete(); // Get all info we can from PreviousDocEntry uint16_t group = PreviousDocEntry->GetGroup(); @@ -1247,9 +1321,9 @@ DocEntry *Document::Backtrack(DocEntry *docEntry) uint32_t lgt = PreviousDocEntry->GetLength(); long offset = PreviousDocEntry->GetOffset(); - gdcmWarningMacro( "Backtrack :" << std::hex << group - << "|" << elem - << " at offset " << offset ); + gdcmDebugMacro( "Backtrack :" << std::hex << group + << "|" << elem + << " at offset 0x(" <GetGroup(); uint16_t elem = entry->GetElement(); - std::string vr = entry->GetVR(); + const VRKey &vr = entry->GetVR(); uint32_t length = entry->GetLength(); Fp->seekg((long)entry->GetOffset(), std::ios::beg); @@ -1285,7 +1359,7 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) // (fffe e0dd) tells us the current SeQuence just ended // // (fffe 0000) is an 'impossible' tag value, - // found in MR-PHILIPS-16-Multi-Seq.dcm + // found in MR-PHILIPS-16-Multi-Seq.dcm if ( (group == 0xfffe && elem != 0x0000 ) || vr == "SQ" ) { @@ -1307,8 +1381,7 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) } // The elements whose length is bigger than the specified upper bound - // are not loaded. Instead we leave a short notice on the offset of - // the element content and it's length. + // are not loaded. std::ostringstream s; @@ -1336,7 +1409,7 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) void Document::FindDocEntryLength( DocEntry *entry ) throw ( FormatError ) { - std::string vr = entry->GetVR(); + const VRKey &vr = entry->GetVR(); uint16_t length16; if ( Filetype == ExplicitVR && !entry->IsImplicitVR() ) @@ -1407,7 +1480,8 @@ void Document::FindDocEntryLength( DocEntry *entry ) // Length is on 4 bytes. // Well ... group 0002 is always coded in 'Explicit VR Litle Endian' - // even if Transfer Syntax is 'Implicit VR ...' + // even if Transfer Syntax is 'Implicit VR ...' + // --> Except for 'Implicit VR Big Endian Transfer Syntax GE Private' FixDocEntryFoundLength( entry, ReadInt32() ); return; @@ -1416,7 +1490,6 @@ 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() @@ -1477,28 +1550,33 @@ uint32_t Document::FindDocEntryLengthOBOrOW() * \brief Find the Value Representation of the current Dicom Element. * @return Value Representation of the current Entry */ -std::string Document::FindDocEntryVR() +VRKey Document::FindDocEntryVR() { if ( Filetype != ExplicitVR ) - return GDCM_UNKNOWN; + return GDCM_VRUNKNOWN; long positionOnEntry = Fp->tellg(); // Warning: we believe this is explicit VR (Value Representation) because - // we used a heuristic that found "UL" in the first tag. Alas this - // doesn't guarantee that all the tags will be in explicit VR. In some - // cases (see e-film filtered files) one finds implicit VR tags mixed - // within an explicit VR file. Hence we make sure the present tag - // is in explicit VR and try to fix things if it happens not to be - // the case. + // we used a heuristic that found "UL" in the first tag and/or + // 'Transfer Syntax' told us it is. + // Alas this doesn't guarantee that all the tags will be in explicit VR. + // In some cases one finds implicit VR tags mixed within an explicit VR file. + // Hence we make sure the present tag is in explicit VR and try to fix things + // if it happens not to be the case. - char vr[3]; - Fp->read (vr, (size_t)2); - vr[2] = 0; + VRKey vr; + Fp->read(&(vr[0]),(size_t)2); if ( !CheckDocEntryVR(vr) ) { + // Don't warn user with useless messages + // Often, delimiters (0xfffe), are not explicit VR ... + if ( CurrentGroup != 0xfffe ) + gdcmWarningMacro( "Unknown VR " << std::hex << "0x(" + << (unsigned int)vr[0] << "|" << (unsigned int)vr[1] + << ") at offset : 0x(" << positionOnEntry<< ")" ); Fp->seekg(positionOnEntry, std::ios::beg); - return GDCM_UNKNOWN; + return GDCM_VRUNKNOWN; } return vr; } @@ -1511,17 +1589,13 @@ std::string Document::FindDocEntryVR() * @return false if the VR is incorrect or if the VR isn't referenced * otherwise, it returns true */ -bool Document::CheckDocEntryVR(VRKey vr) +bool Document::CheckDocEntryVR(const VRKey &vr) { - if ( !Global::GetVR()->IsValidVR(vr) ) - return false; - - return true; + return Global::GetVR()->IsValidVR(vr); } /** * \brief Skip a given Header Entry - * \warning NOT end user intended method ! * @param entry entry to skip */ void Document::SkipDocEntry(DocEntry *entry) @@ -1531,7 +1605,6 @@ void Document::SkipDocEntry(DocEntry *entry) /** * \brief Skips to the beginning of the next Header Entry - * \warning NOT end user intended method ! * @param currentDocEntry entry to skip */ void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) @@ -1557,7 +1630,7 @@ void Document::SkipToNextDocEntry(DocEntry *currentDocEntry) void Document::FixDocEntryFoundLength(DocEntry *entry, uint32_t foundLength) { - entry->SetReadLength( foundLength ); // will be updated only if a bug is found + entry->SetReadLength( foundLength );// will be updated only if a bug is found if ( foundLength == 0xffffffff) { foundLength = 0; @@ -1568,7 +1641,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, if ( foundLength % 2) { - gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength + gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength << " in x(" << std::hex << gr << "," << elem <<")"); } @@ -1633,7 +1706,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) { uint16_t elem = entry->GetElement(); uint16_t group = entry->GetGroup(); - const std::string &vr = entry->GetVR(); + const VRKey &vr = entry->GetVR(); uint32_t length = entry->GetLength(); // When we have some semantics on the element we just read, and if we @@ -1647,9 +1720,9 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) } else { - // Allthough this should never happen, still some images have a + // Although this should never happen, still some images have a // corrupted group length [e.g. have a glance at offset x(8336) of - // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm]. + // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm. // Since for dicom compliant and well behaved headers, the present // test is useless (and might even look a bit paranoid), when we // encounter such an ill-formed image, we simply display a warning @@ -1695,7 +1768,7 @@ bool Document::CheckSwap() char *entCur = deb + 128; if ( memcmp(entCur, "DICM", (size_t)4) == 0 ) { - gdcmWarningMacro( "Looks like DICOM Version3 (preamble + DCM)" ); + gdcmDebugMacro( "Looks like DICOM Version3 (preamble + DCM)" ); // Group 0002 should always be VR, and the first element 0000 // Let's be carefull (so many wrong headers ...) @@ -1727,7 +1800,7 @@ bool Document::CheckSwap() // instead of just checking for UL, OB and UI !? group 0000 { Filetype = ExplicitVR; - gdcmWarningMacro( "Group 0002 : Explicit Value Representation"); + gdcmDebugMacro( "Group 0002 : Explicit Value Representation"); } else { @@ -1739,12 +1812,12 @@ bool Document::CheckSwap() if ( net2host ) { SwapCode = 4321; - gdcmWarningMacro( "HostByteOrder != NetworkByteOrder"); + gdcmDebugMacro( "HostByteOrder != NetworkByteOrder, SwapCode = 4321"); } else { SwapCode = 1234; - gdcmWarningMacro( "HostByteOrder = NetworkByteOrder"); + gdcmDebugMacro( "HostByteOrder = NetworkByteOrder, SwapCode = 1234"); } // Position the file position indicator at first tag @@ -1791,7 +1864,7 @@ bool Document::CheckSwap() memcmp(entCur, "OB", (size_t)2) == 0 ) { Filetype = ExplicitVR; - gdcmWarningMacro( "Group 0002 : Explicit Value Representation"); + gdcmDebugMacro( "Group 0002 : Explicit Value Representation"); return true; } } @@ -1837,7 +1910,7 @@ bool Document::CheckSwap() // 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 -3, 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... @@ -1868,7 +1941,7 @@ bool Document::CheckSwap() Filetype = ACR; return true; default : - gdcmWarningMacro("ACR/NEMA unfound swap info (Really hopeless !)"); + gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)"); Filetype = Unknown; return false; } @@ -1880,8 +1953,8 @@ bool Document::CheckSwap() */ void Document::SwitchByteSwapCode() { - gdcmWarningMacro( "Switching Byte Swap code from "<< SwapCode - << " at :" <tellg() ); + gdcmDebugMacro( "Switching Byte Swap code from "<< SwapCode + << " at: 0x" << std::hex << Fp->tellg() ); if ( SwapCode == 1234 ) { SwapCode = 4321; @@ -1898,6 +1971,7 @@ void Document::SwitchByteSwapCode() { SwapCode = 3412; } + gdcmDebugMacro( " Into: "<< SwapCode ); } /** @@ -1927,13 +2001,10 @@ void Document::SetMaxSizeLoadEntry(long newSize) */ DocEntry *Document::ReadNextDocEntry() { - uint16_t group; - uint16_t elem; - try { - group = ReadInt16(); - elem = ReadInt16(); + CurrentGroup = ReadInt16(); + CurrentElem = ReadInt16(); } catch ( FormatError ) { @@ -1943,22 +2014,24 @@ DocEntry *Document::ReadNextDocEntry() } // Sometimes file contains groups of tags with reversed endianess. - HandleBrokenEndian(group, elem); + HandleBrokenEndian(CurrentGroup, CurrentElem); // In 'true DICOM' files Group 0002 is always little endian if ( HasDCMPreamble ) - HandleOutOfGroup0002(group, elem); + HandleOutOfGroup0002(CurrentGroup, CurrentElem); - std::string vr = FindDocEntryVR(); - std::string realVR = vr; + VRKey vr = FindDocEntryVR(); + + VRKey realVR = vr; - if ( vr == GDCM_UNKNOWN ) + if ( vr == GDCM_VRUNKNOWN ) { - if ( elem == 0x0000 ) // Group Length + if ( CurrentElem == 0x0000 ) // Group Length { realVR = "UL"; // must be UL } - else if (group%2 == 1 && (elem >= 0x0010 && elem <=0x00ff )) + else if (CurrentGroup%2 == 1 && + (CurrentElem >= 0x0010 && CurrentElem <=0x00ff )) { // DICOM PS 3-5 7.8.1 a) states that those // (gggg-0010->00FF where gggg is odd) attributes have to be LO @@ -1966,24 +2039,26 @@ DocEntry *Document::ReadNextDocEntry() } else { - DictEntry *dictEntry = GetDictEntry(group,elem); + DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem); if ( dictEntry ) { realVR = dictEntry->GetVR(); + dictEntry->Unregister(); } } } + // gdcmDebugMacro( "Found VR: " << vr << " / Real VR: " << realVR ); DocEntry *newEntry; if ( Global::GetVR()->IsVROfSequence(realVR) ) - newEntry = NewSeqEntry(group, elem); + newEntry = NewSeqEntry(CurrentGroup, CurrentElem); else { - newEntry = NewDataEntry(group, elem, realVR); + newEntry = NewDataEntry(CurrentGroup, CurrentElem, realVR); static_cast(newEntry)->SetState(DataEntry::STATE_NOTLOADED); } - if ( vr == GDCM_UNKNOWN ) + if ( vr == GDCM_VRUNKNOWN ) { if ( Filetype == ExplicitVR ) { @@ -1993,8 +2068,9 @@ DocEntry *Document::ReadNextDocEntry() { std::string msg; int offset = Fp->tellg(); - msg = Util::Format("Entry (%04x,%04x) at 0x(%x) should be Explicit VR\n", - newEntry->GetGroup(), newEntry->GetElement(), offset ); + msg = Util::Format( + "Entry (%04x,%04x) at x(%x) should be Explicit VR\n", + newEntry->GetGroup(), newEntry->GetElement(), offset ); gdcmWarningMacro( msg.c_str() ); } } @@ -2008,7 +2084,7 @@ DocEntry *Document::ReadNextDocEntry() catch ( FormatError ) { // Call it quits - delete newEntry; + newEntry->Delete(); return 0; } @@ -2025,12 +2101,14 @@ DocEntry *Document::ReadNextDocEntry() */ void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) { - // Endian reversion. Some files contain groups of tags with reversed endianess. + // 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 + gdcmDebugMacro( "Start endian swap mark found." ); reversedEndian++; SwitchByteSwapCode(); // fix the tag @@ -2040,6 +2118,7 @@ void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) else if (group == 0xfffe && elem == 0xe00d && reversedEndian) { // end of reversed endian group + gdcmDebugMacro( "End of reversed endian." ); reversedEndian--; SwitchByteSwapCode(); } @@ -2050,14 +2129,14 @@ void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) // Do what you want, it breaks ! //reversedEndian--; //SwitchByteSwapCode(); - gdcmWarningMacro( "Should never get here! reversed Sequence Terminator!" ); + gdcmWarningMacro( "Should never get here! reversed Sequence Terminator!" ); // fix the tag group = 0xfffe; elem = 0xe0dd; } else if (group == 0xfffe && elem == 0xe0dd) { - gdcmWarningMacro( "Straight Sequence Terminator." ); + gdcmDebugMacro( "Straight Sequence Terminator." ); } } @@ -2068,35 +2147,47 @@ void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) */ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) { - // Endian reversion. Some files contain groups of tags with reversed endianess. + // Endian reversion. + // Some files contain groups of tags with reversed endianess. if ( !Group0002Parsed && group != 0x0002) { Group0002Parsed = true; // we just came out of group 0002 - // if Transfer syntax is Big Endian we have to change CheckSwap + // if Transfer Syntax is Big Endian we have to change CheckSwap std::string ts = GetTransferSyntax(); + if ( ts == GDCM_UNKNOWN ) + { + gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " ); + return; + } if ( !Global::GetTS()->IsTransferSyntax(ts) ) { - gdcmWarningMacro("True DICOM File, with NO Tansfer Syntax: " << ts ); + gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: [" + << ts << "]"); return; } - // Group 0002 is always 'Explicit ...' even when Transfer Syntax says 'Implicit ..." + // Group 0002 is always 'Explicit ...' + // even when Transfer Syntax says 'Implicit ..." - if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian ) - { - Filetype = ImplicitVR; - } + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == + TS::ImplicitVRLittleEndian ) + { + Filetype = ImplicitVR; + } // FIXME Strangely, this works with //'Implicit VR BigEndian Transfer Syntax (GE Private) // - // --> Probabely normal, since we considered we never have to trust manufacturers. - // (we find very often 'Implicit VR' tag, even when Transfer Syntax tells us it's Explicit ... - if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian ) + // --> Probabely normal, since we considered we never have + // to trust manufacturers. + // (we find very often 'Implicit VR' tag, + // even when Transfer Syntax tells us it's Explicit ... + if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == + TS::ExplicitVRBigEndian ) { - gdcmWarningMacro("Transfer Syntax Name = [" + gdcmDebugMacro("Transfer Syntax Name = [" << GetTransferSyntaxName() << "]" ); SwitchByteSwapCode(); group = SwapShort(group);