X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=fd3758e0eaa6d336679e9d959083c6392e9c6f60;hb=9599017adda887d012139a8a452e5a18242dec3b;hp=95b8efec2fc3470081a5bc4c0df1da349f969901;hpb=75a7803826f63fcbcbe3b1b8ce198e96c38b9920;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 95b8efec..fd3758e0 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2005/05/25 12:54:17 $ - Version: $Revision: 1.241 $ + Date: $Date: 2005/06/24 10:53:46 $ + Version: $Revision: 1.251 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -35,8 +35,6 @@ namespace gdcm { //----------------------------------------------------------------------------- -// Refer to Document::CheckSwap() -//const unsigned int Document::HEADER_LENGTH_TO_READ = 256; // Refer to Document::SetMaxSizeLoadEntry() const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 @@ -67,7 +65,7 @@ Document::Document() /** * \brief Constructor (not to break the API) - * @param filename 'Document' (File or DicomDir) to be opened for parsing + * @param fileName 'Document' (File or DicomDir) to be open for parsing */ Document::Document( std::string const &fileName ) :ElementSet(-1) @@ -85,11 +83,6 @@ Document::Document( std::string const &fileName ) IsDocumentAlreadyLoaded = false; Load(fileName); - - // Normaly (?) Fp should be already deleted by CloseFile() - if ( Fp != 0 ) - delete Fp; - Fp = 0; } /** * \brief Canonical destructor. @@ -105,7 +98,7 @@ Document::~Document () /** * \brief Loader - * @param filename 'Document' (File or DicomDir) to be opened for parsing + * @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. */ @@ -113,14 +106,14 @@ bool Document::Load( std::string const &fileName ) { // We should clean out anything that already exists. // Check IsDocumentAlreadyLoaded to be sure. - if( IsDocumentAlreadyLoaded ) + if ( IsDocumentAlreadyLoaded ) { gdcmWarningMacro( "A file was already parsed inside this " - << "gdcm::Document (previous name was: " - << Filename.c_str() << ". New name is :" - << fileName ); + << "gdcm::Document (previous name was: " + << Filename.c_str() << ". New name is :" + << fileName ); // todo : clean out the 'Document' - // We should call ClearEntry() on the parent object ?!? + // Should we call ClearEntry() on the parent object ?!? } Filename = fileName; @@ -174,10 +167,14 @@ bool Document::Load( std::string const &fileName ) // Load 'non string' values std::string PhotometricInterpretation = GetEntryValue(0x0028,0x0004); - if( PhotometricInterpretation == "PALETTE COLOR " ) + if ( PhotometricInterpretation == "PALETTE COLOR " ) { - LoadEntryBinArea(0x0028,0x1200); // gray LUT - /// FIXME FIXME FIXME + // FIXME + // Probabely this line should be outside the 'if' + // Try to find an image sample holding a 'gray LUT' + LoadEntryBinArea(0x0028,0x1200); // gray LUT + + /// FIXME /// 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 @@ -202,9 +199,25 @@ bool Document::Load( std::string const &fileName ) LoadEntryBinArea(0x0028,0x1222); // Segmented Blue Palette Color LUT Data LoadEntryBinArea(0x0028,0x1223); - } + } + //FIXME later : how to use it? - LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent) + SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000); + if ( modLutSeq !=0 ) + { + SQItem *sqi= modLutSeq->GetFirstSQItem(); + if ( sqi != 0 ) + { + BinEntry *b = sqi->GetBinEntry(0x0028,0x3006); + if ( b != 0 ) + { + if ( b->GetLength() != 0 ) + { + LoadEntryBinArea(b); //LUT Data (CTX dependent) + } + } + } + } CloseFile(); @@ -280,7 +293,7 @@ bool Document::SetShaDict(DictKey const &dictName) */ bool Document::IsReadable() { - if( Filetype == Unknown) + if ( Filetype == Unknown ) { gdcmWarningMacro( "Wrong filetype"); return false; @@ -463,14 +476,14 @@ std::ifstream *Document::OpenFile() return 0; } - if(Fp) + if ( Fp ) { gdcmWarningMacro( "File already open: " << Filename.c_str()); CloseFile(); } Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); - if( ! *Fp ) + if ( ! *Fp ) { // Don't user gdcmErrorMacro : // a spurious message will appear when you use, for instance @@ -486,14 +499,14 @@ std::ifstream *Document::OpenFile() uint16_t zero = 0; Fp->read((char*)&zero, (size_t)2); - if( Fp->eof() ) + if ( Fp->eof() ) { CloseFile(); return 0; } //-- ACR or DICOM with no Preamble; may start with a Shadow Group -- - 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 || @@ -509,12 +522,12 @@ std::ifstream *Document::OpenFile() Fp->seekg(126L, std::ios::cur); char dicm[4] = {' ',' ',' ',' '}; Fp->read(dicm, (size_t)4); - if( Fp->eof() ) + if ( Fp->eof() ) { CloseFile(); return 0; } - if( memcmp(dicm, "DICM", 4) == 0 ) + if ( memcmp(dicm, "DICM", 4) == 0 ) { HasDCMPreamble = true; return Fp; @@ -533,7 +546,7 @@ std::ifstream *Document::OpenFile() */ bool Document::CloseFile() { - if( Fp ) + if ( Fp ) { Fp->close(); delete Fp; @@ -597,7 +610,7 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) return; BinEntry *binElement = dynamic_cast(docElement); - if( !binElement ) + if ( !binElement ) return; LoadEntryBinArea(binElement); @@ -610,11 +623,11 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) */ void Document::LoadEntryBinArea(BinEntry *elem) { - if(elem->GetBinArea()) + if (elem->GetBinArea() ) return; bool openFile = !Fp; - if(openFile) + if ( openFile ) OpenFile(); size_t o =(size_t)elem->GetOffset(); @@ -622,14 +635,14 @@ void Document::LoadEntryBinArea(BinEntry *elem) size_t l = elem->GetLength(); uint8_t *a = new uint8_t[l]; - if( !a ) + if ( !a ) { gdcmWarningMacro( "Cannot allocate BinEntry content"); return; } Fp->read((char*)a, l); - if( Fp->fail() || Fp->eof()) + if ( Fp->fail() || Fp->eof() ) { delete[] a; return; @@ -637,7 +650,7 @@ void Document::LoadEntryBinArea(BinEntry *elem) elem->SetBinArea(a); - if(openFile) + if ( openFile ) CloseFile(); } @@ -649,7 +662,7 @@ void Document::LoadEntryBinArea(BinEntry *elem) */ void Document::LoadDocEntrySafe(DocEntry *entry) { - if(Fp) + if ( Fp ) { long PositionOnEntry = Fp->tellg(); LoadDocEntry(entry); @@ -669,11 +682,11 @@ bool Document::operator<(Document &document) // Patient Name std::string s1 = GetEntryValue(0x0010,0x0010); std::string s2 = document.GetEntryValue(0x0010,0x0010); - if(s1 < s2) + if (s1 < s2) { return true; } - else if( s1 > s2 ) + else if ( s1 > s2 ) { return false; } @@ -699,7 +712,7 @@ bool Document::operator<(Document &document) { return true; } - else if( s1 > s2 ) + else if ( s1 > s2 ) { return false; } @@ -712,7 +725,7 @@ bool Document::operator<(Document &document) { return true; } - else if( s1 > s2 ) + else if ( s1 > s2 ) { return false; } @@ -738,7 +751,7 @@ uint16_t Document::ReadInt16() { throw FormatError( "Document::ReadInt16()", " file error." ); } - if( Fp->eof() ) + if ( Fp->eof() ) { throw FormatError( "Document::ReadInt16()", "EOF." ); } @@ -760,7 +773,7 @@ uint32_t Document::ReadInt32() { throw FormatError( "Document::ReadInt32()", " file error." ); } - if( Fp->eof() ) + if ( Fp->eof() ) { throw FormatError( "Document::ReadInt32()", "EOF." ); } @@ -797,19 +810,19 @@ int Document::ComputeGroup0002Length( FileType filetype ) { gr = entry->GetGroup(); - if( gr == 0x0002 ) + if ( gr == 0x0002 ) { found0002 = true; - if( entry->GetElement() != 0x0000 ) + if ( entry->GetElement() != 0x0000 ) { vr = entry->GetVR(); - if( filetype == ExplicitVR ) + if ( filetype == ExplicitVR ) { - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || (vr == "UT") ) { - // explicit VR AND OB, OW, SQ : 4 more bytes + // explicit VR AND OB, OW, SQ, UT : 4 more bytes groupLength += 4; } } @@ -905,7 +918,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, } LoadDocEntry( newBinEntry ); - if( !set->AddEntry( newBinEntry ) ) + if ( !set->AddEntry( newBinEntry ) ) { //Expect big troubles if here //delete newBinEntry; @@ -947,7 +960,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, if ( strLgrGroup != GDCM_UNFOUND) { lgrGroup = atoi(strLgrGroup.c_str()); - Fp->seekg(lgrGroup , std::ios::cur); + Fp->seekg(lgrGroup, std::ios::cur); used = false; continue; } @@ -955,7 +968,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, } } - if( !set->AddEntry( newValEntry ) ) + if ( !set->AddEntry( newValEntry ) ) { // If here expect big troubles // delete newValEntry; //otherwise mem leak @@ -964,13 +977,13 @@ void Document::ParseDES(DocEntrySet *set, long offset, if (delimitor) { - if(!used) + if ( !used ) delete newDocEntry; break; } - if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max ) { - if(!used) + if ( !used ) delete newDocEntry; break; } @@ -1030,20 +1043,20 @@ void Document::ParseDES(DocEntrySet *set, long offset, newDocEntry->GetOffset(), l, delim_mode); } - if( !set->AddEntry( newSeqEntry ) ) + if ( !set->AddEntry( newSeqEntry ) ) { used = false; } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - if( !used ) + if ( !used ) delete newDocEntry; break; } } - if( !used ) + if ( !used ) delete newDocEntry; } } @@ -1069,7 +1082,7 @@ void Document::ParseSQ( SeqEntry *seqEntry, // FIXME Should warn user break; } - if( delim_mode ) + if ( delim_mode ) { if ( newDocEntry->IsSequenceDelimitor() ) { @@ -1136,7 +1149,7 @@ void Document::LoadDocEntry(DocEntry *entry) // (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 - if( group == 0xfffe ) + if ( group == 0xfffe ) { // NO more value field for SQ ! return; @@ -1158,7 +1171,6 @@ void Document::LoadDocEntry(DocEntry *entry) { if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) ) { - //s << "gdcm::NotLoaded (BinEntry)"; s << GDCM_NOTLOADED; s << " Ad.:" << (long)entry->GetOffset(); s << " x(" << std::hex << entry->GetOffset() << ")"; @@ -1167,10 +1179,8 @@ void Document::LoadDocEntry(DocEntry *entry) s << " x(" << std::hex << entry->GetLength() << ")"; binEntryPtr->SetValue(s.str()); } - // Be carefull : a BinEntry IS_A ValEntry ... else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) ) { - // s << "gdcm::NotLoaded. (ValEntry)"; s << GDCM_NOTLOADED; s << " Address:" << (long)entry->GetOffset(); s << " Length:" << entry->GetLength(); @@ -1204,7 +1214,7 @@ void Document::LoadDocEntry(DocEntry *entry) uint32_t NewInt; int nbInt; // When short integer(s) are expected, read and convert the following - // n *two characters properly i.e. consider them as short integers as + // (n * 2) characters properly i.e. consider them as short integers as // opposed to strings. // Elements with Value Multiplicity > 1 // contain a set of integers (not a single one) @@ -1253,11 +1263,11 @@ void Document::LoadDocEntry(DocEntry *entry) str[length] = '\0'; //this is only useful when length is odd // Special DicomString call to properly handle \0 and even length std::string newValue; - if( length % 2 ) + if ( length % 2 ) { newValue = Util::DicomString(str, length+1); gdcmWarningMacro("Warning: bad length: " << length << - ",For string :" << newValue.c_str()); + " For string :" << newValue.c_str()); // Since we change the length of string update it length //entry->SetReadLength(length+1); } @@ -1271,12 +1281,17 @@ void Document::LoadDocEntry(DocEntry *entry) { if ( Fp->fail() || Fp->eof()) { - gdcmWarningMacro("Unread element value"); + if ( Fp->fail() ) + gdcmWarningMacro("--> fail"); + + gdcmWarningMacro("Unread element value " << valEntry->GetKey() + << " lgt : " << valEntry->GetReadLength() + << " at " << std::hex << valEntry->GetOffset()); valEntry->SetValue(GDCM_UNREAD); return; } - if( vr == "UI" ) + if ( vr == "UI" ) { // Because of correspondance with the VR dic valEntry->SetValue(newValue); @@ -1288,7 +1303,9 @@ void Document::LoadDocEntry(DocEntry *entry) } else { - gdcmErrorMacro( "Should have a ValEntry, here !"); + gdcmWarningMacro("Should have a ValEntry, here ! " << valEntry->GetKey() + << " lgt : " << valEntry->GetReadLength() + << " at " << std::hex << valEntry->GetOffset()); } } @@ -1304,7 +1321,7 @@ void Document::FindDocEntryLength( DocEntry *entry ) if ( Filetype == ExplicitVR && !entry->IsImplicitVR() ) { - if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" ) + if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT" || vr == "UN" ) { // The following reserved two bytes (see PS 3.5-2003, section // "7.1.2 Data element structure with explicit vr", p 27) must be @@ -1454,7 +1471,7 @@ std::string Document::FindDocEntryVR() Fp->read (vr, (size_t)2); vr[2] = 0; - if( !CheckDocEntryVR(vr) ) + if ( !CheckDocEntryVR(vr) ) { Fp->seekg(positionOnEntry, std::ios::beg); return GDCM_UNKNOWN; @@ -1502,14 +1519,14 @@ std::string Document::GetDocEntryValue(DocEntry *entry) // Elements with Value Multiplicity > 1 // contain a set of short integers (not a single one) - if( vr == "US" || vr == "SS" ) + if ( vr == "US" || vr == "SS" ) { uint16_t newInt16; nbInt = length / 2; for (int i=0; i < nbInt; i++) { - if( i != 0 ) + if ( i != 0 ) { s << '\\'; } @@ -1525,14 +1542,14 @@ std::string Document::GetDocEntryValue(DocEntry *entry) // as usual for standard multivaluated filels // Elements with Value Multiplicity > 1 // contain a set of integers (not a single one) - else if( vr == "UL" || vr == "SL" ) + else if ( vr == "UL" || vr == "SL" ) { uint32_t newInt32; nbInt = length / 4; for (int i=0; i < nbInt; i++) { - if( i != 0) + if ( i != 0) { s << '\\'; } @@ -1659,7 +1676,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, // Allthough not recent many such GE corrupted images are still present // on Creatis hard disks. Hence this fix shall remain when such images // are no longer in use (we are talking a few years, here)... - // Note: XMedCom probably uses such a trick since it is able to read + // Note: XMedCon probably uses such a trick since it is able to read // those pesky GE images ... if ( foundLength == 13) { @@ -1689,12 +1706,12 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, //////// 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 ) + 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 ( entry->GetElement() != 0x0000 ) { foundLength = 0; } @@ -1757,12 +1774,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) * true when we hope ours assuptions are OK */ bool Document::CheckSwap() -{ - // The only guaranted way of finding the swap code is to find a - // group tag since we know it's length has to be of four bytes i.e. - // 0x00000004. Finding the swap code in then straigthforward. Trouble - // occurs when we can't find such group... - +{ uint32_t s32; uint16_t s16; @@ -1777,7 +1789,7 @@ bool Document::CheckSwap() Fp->read(deb, 256); char *entCur = deb + 128; - if( memcmp(entCur, "DICM", (size_t)4) == 0 ) + if ( memcmp(entCur, "DICM", (size_t)4) == 0 ) { gdcmWarningMacro( "Looks like DICOM Version3 (preamble + DCM)" ); @@ -1801,11 +1813,11 @@ bool Document::CheckSwap() // even if elem 0002,0010 (Transfer Syntax) tells us the file is // *Implicit* VR (see former 'gdcmData/icone.dcm') - if( memcmp(entCur, "UL", (size_t)2) == 0 || - memcmp(entCur, "OB", (size_t)2) == 0 || - memcmp(entCur, "UI", (size_t)2) == 0 || - memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later - // when Write DCM *adds* + if ( memcmp(entCur, "UL", (size_t)2) == 0 || + memcmp(entCur, "OB", (size_t)2) == 0 || + memcmp(entCur, "UI", (size_t)2) == 0 || + memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later + // when Write DCM *adds* // FIXME // Use Document::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? group 0000 @@ -1867,12 +1879,12 @@ bool Document::CheckSwap() if ( SwapCode != 0 ) { - if( memcmp(entCur, "UL", (size_t)2) == 0 || - memcmp(entCur, "OB", (size_t)2) == 0 || - memcmp(entCur, "UI", (size_t)2) == 0 || - memcmp(entCur, "SH", (size_t)2) == 0 || - memcmp(entCur, "AE", (size_t)2) == 0 || - memcmp(entCur, "OB", (size_t)2) == 0 ) + if ( memcmp(entCur, "UL", (size_t)2) == 0 || + memcmp(entCur, "OB", (size_t)2) == 0 || + memcmp(entCur, "UI", (size_t)2) == 0 || + memcmp(entCur, "SH", (size_t)2) == 0 || + memcmp(entCur, "AE", (size_t)2) == 0 || + memcmp(entCur, "OB", (size_t)2) == 0 ) { Filetype = ExplicitVR; gdcmWarningMacro( "Group 0002 : Explicit Value Representation"); @@ -1964,7 +1976,8 @@ bool Document::CheckSwap() */ void Document::SwitchByteSwapCode() { - gdcmWarningMacro( "Switching Byte Swap code from "<< SwapCode); + gdcmWarningMacro( "Switching Byte Swap code from "<< SwapCode + << " at :" <tellg() ); if ( SwapCode == 1234 ) { SwapCode = 4321; @@ -2035,37 +2048,38 @@ DocEntry *Document::ReadNextDocEntry() std::string vr = FindDocEntryVR(); std::string realVR = vr; - if( vr == GDCM_UNKNOWN) + if ( vr == GDCM_UNKNOWN ) { if ( elem == 0x0000 ) // Group Length realVR = "UL"; // must be UL else { DictEntry *dictEntry = GetDictEntry(group,elem); - if( dictEntry ) + if ( dictEntry ) realVR = dictEntry->GetVR(); } } DocEntry *newEntry; - if( Global::GetVR()->IsVROfSequence(realVR) ) + if ( Global::GetVR()->IsVROfSequence(realVR) ) newEntry = NewSeqEntry(group, elem); - else if( Global::GetVR()->IsVROfStringRepresentable(realVR) ) + else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) ) newEntry = NewValEntry(group, elem,vr); else newEntry = NewBinEntry(group, elem,vr); - if( vr == GDCM_UNKNOWN ) + if ( vr == GDCM_UNKNOWN ) { - if( Filetype == ExplicitVR ) + if ( Filetype == ExplicitVR ) { // We thought this was explicit VR, but we end up with an // implicit VR tag. Let's backtrack. if ( newEntry->GetGroup() != 0xfffe ) { std::string msg; - msg = Util::Format("Entry (%04x,%04x) should be Explicit VR\n", - newEntry->GetGroup(), newEntry->GetElement()); + int offset = Fp->tellg(); + msg = Util::Format("Entry (%04x,%04x) at %x should be Explicit VR\n", + newEntry->GetGroup(), newEntry->GetElement(), offset ); gdcmWarningMacro( msg.c_str() ); } }