X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=0098a5720af7654286537d6192db3731e2ffe43a;hb=0bbf3772212391cff69ed451c0a089279ee0c27c;hp=92ee5d3c76bc438716d4692399421c788b36380f;hpb=bba6b52311989034cfaca84d1ab1e492d94c1873;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 92ee5d3c..0098a572 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/11/30 16:24:31 $ - Version: $Revision: 1.143 $ + Date: $Date: 2005/01/06 16:33:54 $ + Version: $Revision: 1.159 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -23,6 +23,13 @@ #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" +#include "gdcmTS.h" +#include "gdcmException.h" +#include "gdcmDictSet.h" +#include "gdcmRLEFramesInfo.h" +#include "gdcmJPEGFragmentsInfo.h" +#include "gdcmDocEntrySet.h" +#include "gdcmSQItem.h" #include #include @@ -40,7 +47,7 @@ namespace gdcm static const char *TransferSyntaxStrings[] = { // Implicit VR Little Endian "1.2.840.10008.1.2", - // Implicit VR Little Endian DLX G.E? + // Implicit VR Big Endian DLX G.E? "1.2.840.113619.5.2", // Explicit VR Little Endian "1.2.840.10008.1.2.1", @@ -101,19 +108,19 @@ Document::Document( std::string const & filename ) : ElementSet(-1) dbg.Verbose(0, "Document::Document: starting parsing of file: ", Filename.c_str()); - Fp->seekg( 0, std::ios_base::beg); + Fp->seekg( 0, std::ios::beg); - Fp->seekg(0, std::ios_base::end); + Fp->seekg(0, std::ios::end); long lgt = Fp->tellg(); - Fp->seekg( 0, std::ios_base::beg); + Fp->seekg( 0, std::ios::beg); CheckSwap(); long beg = Fp->tellg(); lgt -= beg; ParseDES( this, beg, lgt, false); // le Load sera fait a la volee - Fp->seekg( 0, std::ios_base::beg); + Fp->seekg( 0, std::ios::beg); // Load 'non string' values @@ -175,8 +182,6 @@ Document::Document( std::string const & filename ) : ElementSet(-1) SetEntryByNumber(rows , 0x0028, 0x0011); } // ----------------- End of ACR-LibIDO kludge ------------------ - - PrintLevel = 1; // 'Medium' print level by default } /** @@ -191,7 +196,6 @@ Document::Document() : ElementSet(-1) Initialise(); SwapCode = 0; Filetype = ExplicitVR; - PrintLevel = 1; // 'Medium' print level by default } /** @@ -215,6 +219,7 @@ Document::~Document () */ void Document::PrintPubDict(std::ostream & os) { + RefPubDict->SetPrintLevel(PrintLevel); RefPubDict->Print(os); } @@ -224,6 +229,7 @@ void Document::PrintPubDict(std::ostream & os) */ void Document::PrintShaDict(std::ostream & os) { + RefShaDict->SetPrintLevel(PrintLevel); RefShaDict->Print(os); } @@ -411,7 +417,11 @@ FileType Document::GetFileType() */ std::ifstream* Document::OpenFile() { - if (Filename.length() == 0) return 0; + if (Filename.length() == 0) + { + return 0; + } + if(Fp) { dbg.Verbose( 0, @@ -420,17 +430,23 @@ std::ifstream* Document::OpenFile() } Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary); - - if(!Fp) + if( ! *Fp ) { dbg.Verbose( 0, "Document::OpenFile cannot open file: ", Filename.c_str()); + delete Fp; + Fp = 0; return 0; } uint16_t zero; - Fp->read((char*)&zero, (size_t)2 ); + Fp->read((char*)&zero, (size_t)2); + if( Fp->eof() ) + { + CloseFile(); + return 0; + } //ACR -- or DICOM with no Preamble; may start with a Shadow Group -- if( @@ -443,9 +459,14 @@ std::ifstream* Document::OpenFile() } //DICOM - Fp->seekg(126L, std::ios_base::cur); + Fp->seekg(126L, std::ios::cur); char dicm[4]; Fp->read(dicm, (size_t)4); + if( Fp->eof() ) + { + CloseFile(); + return 0; + } if( memcmp(dicm, "DICM", 4) == 0 ) { return Fp; @@ -514,7 +535,7 @@ void Document::WriteContent(std::ofstream* fp, FileType filetype) } /** - * \brief Modifies the value of a given Header Entry (Dicom Element) + * \brief Modifies the value of a given Doc Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. * @param value (string) Value to be set * @param group Group number of the Entry @@ -523,79 +544,53 @@ void Document::WriteContent(std::ofstream* fp, FileType filetype) * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ -ValEntry* Document::ReplaceOrCreateByNumber( - std::string const & value, - uint16_t group, - uint16_t elem, - TagName const & vr ) +ValEntry* Document::ReplaceOrCreateByNumber(std::string const & value, + uint16_t group, + uint16_t elem, + TagName const & vr ) { ValEntry* valEntry = 0; DocEntry* currentEntry = GetDocEntryByNumber( group, elem); - if (!currentEntry) + if (currentEntry) { - // check if (group,element) DictEntry exists - // if it doesn't, create an entry in DictSet::VirtualEntry - // and use it + valEntry = dynamic_cast< ValEntry* >(currentEntry); - // Find out if the tag we received is in the dictionaries: - Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); - DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); - if (!dictEntry) - { - currentEntry = NewDocEntryByNumber(group, elem, vr); - } - else - { - currentEntry = NewDocEntryByNumber(group, elem); - } + // Verify the VR + if( valEntry ) + if( valEntry->GetVR()!=vr ) + valEntry=NULL; - if (!currentEntry) + // if currentEntry doesn't correspond to the requested valEntry + if( !valEntry) { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; + if (!RemoveEntry(currentEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" + " of previous DocEntry failed."); + + return NULL; + } } + } - valEntry = new ValEntry(currentEntry); - delete currentEntry; + // Create a new valEntry if necessary + if (!valEntry) + { + valEntry = NewValEntryByNumber(group, elem, vr); if ( !AddEntry(valEntry)) { - delete valEntry; dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); + + delete valEntry; return NULL; } } - else - { - valEntry = dynamic_cast< ValEntry* >(currentEntry); - if ( !valEntry ) // Euuuuh? It wasn't a ValEntry - // then we change it to a ValEntry ? - // Shouldn't it be considered as an error ? - { - // We need to promote the DocEntry to a ValEntry: - valEntry = new ValEntry(currentEntry); - if (!RemoveEntry(currentEntry)) - { - delete valEntry; - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" - " of previous DocEntry failed."); - return NULL; - } - if ( !AddEntry(valEntry)) - { - delete valEntry; - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" - " promoted ValEntry failed."); - return NULL; - } - } - } - - SetEntryByNumber(value, group, elem); + // Set the binEntry value + SetEntry(value, valEntry); return valEntry; } @@ -606,74 +601,58 @@ ValEntry* Document::ReplaceOrCreateByNumber( * @param binArea (binary) value to be set * @param Group Group number of the Entry * @param Elem Element number of the Entry + * @param vr V(alue) R(epresentation) of the Entry -if private Entry- * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ -BinEntry* Document::ReplaceOrCreateByNumber( - uint8_t* binArea, - int lgth, - uint16_t group, - uint16_t elem, - TagName const & vr ) +BinEntry* Document::ReplaceOrCreateByNumber(uint8_t* binArea, + int lgth, + uint16_t group, + uint16_t elem, + TagName const & vr ) { BinEntry* binEntry = 0; DocEntry* currentEntry = GetDocEntryByNumber( group, elem); - if (!currentEntry) - { - - // check if (group,element) DictEntry exists - // if it doesn't, create an entry in DictSet::VirtualEntry - // and use it - // Find out if the tag we received is in the dictionaries: - Dict *pubDict = Global::GetDicts()->GetDefaultPubDict(); - DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem); - - if (!dictEntry) - { - currentEntry = NewDocEntryByNumber(group, elem, vr); - } - else - { - currentEntry = NewDocEntryByNumber(group, elem); - } - if (!currentEntry) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to" - " NewDocEntryByNumber failed."); - return NULL; - } - binEntry = new BinEntry(currentEntry); - if ( !AddEntry(binEntry)) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" - " failed allthough this is a creation."); - } - } - else + // Verify the currentEntry + if (currentEntry) { binEntry = dynamic_cast< BinEntry* >(currentEntry); - if ( !binEntry ) // Euuuuh? It wasn't a BinEntry - // then we change it to a BinEntry ? - // Shouldn't it be considered as an error ? + + // Verify the VR + if( binEntry ) + if( binEntry->GetVR()!=vr ) + binEntry=NULL; + + // if currentEntry doesn't correspond to the requested valEntry + if( !binEntry) { - // We need to promote the DocEntry to a BinEntry: - binEntry = new BinEntry(currentEntry); if (!RemoveEntry(currentEntry)) { dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" " of previous DocEntry failed."); - return NULL; - } - if ( !AddEntry(binEntry)) - { - dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding" - " promoted BinEntry failed."); + return NULL; } } } + // Create a new binEntry if necessary + if (!binEntry) + { + binEntry = NewBinEntryByNumber(group, elem, vr); + + if ( !AddEntry(binEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" + " failed allthough this is a creation."); + + delete binEntry; + return NULL; + } + } + + // Set the binEntry value uint8_t *tmpArea; if (lgth>0 && binArea) { @@ -684,7 +663,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( { tmpArea = 0; } - if (!SetEntryByNumber(tmpArea, lgth, group, elem)) + if (!SetEntry(tmpArea,lgth,binEntry)) { if (tmpArea) { @@ -695,7 +674,6 @@ BinEntry* Document::ReplaceOrCreateByNumber( return binEntry; } - /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it when unexistant. @@ -706,20 +684,48 @@ BinEntry* Document::ReplaceOrCreateByNumber( */ SeqEntry* Document::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) { - SeqEntry* b = 0; - DocEntry* a = GetDocEntryByNumber( group, elem); - if (!a) + SeqEntry* seqEntry = 0; + DocEntry* currentEntry = GetDocEntryByNumber( group, elem); + + // Verify the currentEntry + if (currentEntry) { - a = NewSeqEntryByNumber(group, elem); - if (!a) + seqEntry = dynamic_cast< SeqEntry* >(currentEntry); + + // Verify the VR + if( seqEntry ) + if( seqEntry->GetVR()!="SQ" ) + seqEntry=NULL; + + // if currentEntry doesn't correspond to the requested valEntry + if( !seqEntry) { - return 0; + if (!RemoveEntry(currentEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal" + " of previous DocEntry failed."); + + return NULL; + } } + } - b = new SeqEntry(a, 1); // FIXME : 1 (Depth) - AddEntry(b); - } - return b; + // Create a new seqEntry if necessary + if (!seqEntry) + { + seqEntry = NewSeqEntryByNumber(group, elem); + + if ( !AddEntry(seqEntry)) + { + dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" + " failed allthough this is a creation."); + + delete seqEntry; + return NULL; + } + } + + return seqEntry; } /** @@ -816,7 +822,6 @@ std::string Document::GetEntryVRByName(TagName const& tagName) std::string Document::GetEntryByNumber(uint16_t group, uint16_t element) { TagKey key = DictEntry::TranslateToKey(group, element); - /// \todo use map methods, instead of multimap JPR if ( !TagHT.count(key)) { return GDCM_UNFOUND; @@ -896,42 +901,14 @@ bool Document::SetEntryByName( std::string const & content, bool Document::SetEntryByNumber(std::string const& content, uint16_t group, uint16_t element) { - int c; - int l; - - ValEntry* valEntry = GetValEntryByNumber(group, element); - if (!valEntry ) + ValEntry* entry = GetValEntryByNumber(group, element); + if (!entry ) { dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding", " ValEntry (try promotion first)."); return false; } - // Non even content must be padded with a space (020H)... - std::string finalContent = Util::DicomString( content.c_str() ); - assert( !(finalContent.size() % 2) ); - valEntry->SetValue(finalContent); - - // Integers have a special treatement for their length: - - l = finalContent.length(); - if ( l != 0) // To avoid to be cheated by 'zero length' integers - { - VRKey vr = valEntry->GetVR(); - if( vr == "US" || vr == "SS" ) - { - // for multivaluated items - c = Util::CountSubstring(content, "\\") + 1; - l = c*2; - } - else if( vr == "UL" || vr == "SL" ) - { - // for multivaluated items - c = Util::CountSubstring(content, "\\") + 1; - l = c*4;; - } - } - valEntry->SetLength(l); - return true; + return SetEntry(content,entry); } /** @@ -946,74 +923,58 @@ bool Document::SetEntryByNumber(std::string const& content, bool Document::SetEntryByNumber(uint8_t*content, int lgth, uint16_t group, uint16_t element) { - (void)lgth; //not used - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key)) + BinEntry* entry = GetBinEntryByNumber(group, element); + if (!entry ) { + dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding", + " ValEntry (try promotion first)."); return false; } -/* Hope Binary field length is *never* wrong - if(lgth%2) // Non even length are padded with a space (020H). - { - lgth++; - //content = content + '\0'; // fing a trick to enlarge a binary field? - } -*/ - BinEntry* entry = (BinEntry *)TagHT[key]; - entry->SetBinArea(content); - entry->SetLength(lgth); - entry->SetValue(GDCM_BINLOADED); - - return true; + return SetEntry(content,lgth,entry); } /** * \brief Accesses an existing DocEntry (i.e. a Dicom Element) - * in the PubDocEntrySet of this instance - * through it's (group, element) and modifies it's length with - * the given value. - * \warning Use with extreme caution. - * @param l new length to substitute with - * @param group group number of the Entry to modify - * @param element element number of the Entry to modify - * @return true on success, false otherwise. + * and modifies it's content with the given value. + * @param content new value (string) to substitute with + * @param entry Entry to be modified */ -/*bool Document::SetEntryLengthByNumber(uint32_t l, - uint16_t group, uint16_t element) +bool Document::SetEntry(std::string const & content,ValEntry* entry) { - /// \todo use map methods, instead of multimap JPR - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key) ) - { - return false; - } - if ( l % 2 ) + if(entry) { - l++; // length must be even + entry->SetValue(content); + return true; } - ( ((TagHT.equal_range(key)).first)->second )->SetLength(l); - - return true ; -}*/ + return false; +} /** - * \brief Gets (from Header) the offset of a 'non string' element value - * (LoadElementValues has already be executed) - * @param group group number of the Entry - * @param elem element number of the Entry - * @return File Offset of the Element Value + * \brief Accesses an existing BinEntry (i.e. a Dicom Element) + * and modifies it's content with the given value. + * @param content new value (void* -> uint8_t*) to substitute with + * @param entry Entry to be modified + * @param lgth new value length */ -/*size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) +bool Document::SetEntry(uint8_t* content, int lgth, BinEntry* entry) { - DocEntry* entry = GetDocEntryByNumber(group, elem); - if (!entry) + if(entry) { - dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present."); - return 0; + // Hope Binary field length is *never* wrong + /*if(lgth%2) // Non even length are padded with a space (020H). + { + lgth++; + //content = content + '\0'; // fing a trick to enlarge a binary field? + }*/ + + entry->SetBinArea(content); + entry->SetLength(lgth); + entry->SetValue(GDCM_BINLOADED); + return true; } - return entry->GetOffset(); -}*/ + return false; +} /** * \brief Gets (from Header) a 'non string' element value @@ -1073,7 +1034,7 @@ void Document::LoadEntryBinArea(BinEntry* element) OpenFile(); size_t o =(size_t)element->GetOffset(); - Fp->seekg(o, std::ios_base::beg); + Fp->seekg(o, std::ios::beg); size_t l = element->GetLength(); uint8_t* a = new uint8_t[l]; @@ -1122,54 +1083,6 @@ void Document::LoadEntryBinArea(BinEntry* element) return false; }*/ -/** - * \brief Update the entries with the shadow dictionary. - * Only non even entries are analyzed - */ -void Document::UpdateShaEntries() -{ - //DictEntry *entry; - std::string vr; - - /// \todo TODO : still any use to explore recursively the whole structure? -/* - for(ListTag::iterator it=listEntries.begin(); - it!=listEntries.end(); - ++it) - { - // Odd group => from public dictionary - if((*it)->GetGroup()%2==0) - continue; - - // Peer group => search the corresponding dict entry - if(RefShaDict) - entry=RefShaDict->GetDictEntryByNumber((*it)->GetGroup(),(*it)->GetElement()); - else - entry=NULL; - - if((*it)->IsImplicitVR()) - vr="Implicit"; - else - vr=(*it)->GetVR(); - - (*it)->SetValue(GetDocEntryUnvalue(*it)); // to go on compiling - if(entry){ - // Set the new entry and the new value - (*it)->SetDictEntry(entry); - CheckDocEntryVR(*it,vr); - - (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling - - } - else - { - // Remove precedent value transformation - (*it)->SetDictEntry(NewVirtualDictEntry((*it)->GetGroup(),(*it)->GetElement(),vr)); - } - } -*/ -} - /** * \brief Searches within the Header Entries for a Dicom Element of * a given tag. @@ -1221,15 +1134,37 @@ ValEntry* Document::GetValEntryByNumber(uint16_t group, uint16_t element) { return 0; } - if ( ValEntry* valEntry = dynamic_cast(currentEntry) ) + if ( ValEntry* entry = dynamic_cast(currentEntry) ) { - return valEntry; + return entry; } dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry."); return 0; } +/** + * \brief Same as \ref Document::GetDocEntryByNumber except it only + * returns a result when the corresponding entry is of type + * BinEntry. + * @return When present, the corresponding BinEntry. + */ +BinEntry* Document::GetBinEntryByNumber(uint16_t group, uint16_t element) +{ + DocEntry* currentEntry = GetDocEntryByNumber(group, element); + if ( !currentEntry ) + { + return 0; + } + if ( BinEntry* entry = dynamic_cast(currentEntry) ) + { + return entry; + } + dbg.Verbose(0, "Document::GetBinEntryByNumber: unfound BinEntry."); + + return 0; +} + /** * \brief Loads the element while preserving the current * underlying file position indicator as opposed to @@ -1243,7 +1178,7 @@ void Document::LoadDocEntrySafe(DocEntry * entry) { long PositionOnEntry = Fp->tellg(); LoadDocEntry(entry); - Fp->seekg(PositionOnEntry, std::ios_base::beg); + Fp->seekg(PositionOnEntry, std::ios::beg); } } @@ -1423,16 +1358,16 @@ void Document::ParseDES(DocEntrySet *set, long offset, if ( ts == RLELossless ) { long PositionOnEntry = Fp->tellg(); - Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); + Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeRLEInfo(); - Fp->seekg( PositionOnEntry, std::ios_base::beg ); + Fp->seekg( PositionOnEntry, std::ios::beg ); } else if ( IsJPEG() ) { long PositionOnEntry = Fp->tellg(); - Fp->seekg( newDocEntry->GetOffset(), std::ios_base::beg ); + Fp->seekg( newDocEntry->GetOffset(), std::ios::beg ); ComputeJPEGFragmentInfo(); - Fp->seekg( PositionOnEntry, std::ios_base::beg ); + Fp->seekg( PositionOnEntry, std::ios::beg ); } } @@ -1571,7 +1506,7 @@ void Document::LoadDocEntry(DocEntry* entry) std::string vr = entry->GetVR(); uint32_t length = entry->GetLength(); - Fp->seekg((long)entry->GetOffset(), std::ios_base::beg); + Fp->seekg((long)entry->GetOffset(), std::ios::beg); // A SeQuence "contains" a set of Elements. // (fffe e000) tells us an Element is beginning @@ -1625,7 +1560,7 @@ void Document::LoadDocEntry(DocEntry* entry) // to be sure we are at the end of the value ... Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), - std::ios_base::beg); + std::ios::beg); return; } @@ -1753,7 +1688,7 @@ 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_base::cur); + Fp->seekg( 2L, std::ios::cur); uint32_t length32 = ReadInt32(); if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) @@ -1773,9 +1708,9 @@ void Document::FindDocEntryLength( DocEntry *entry ) // until the end of the file. Hence we artificially fix the // the length and proceed. long currentPosition = Fp->tellg(); - Fp->seekg(0L,std::ios_base::end); + Fp->seekg(0L,std::ios::end); long lengthUntilEOF = (long)(Fp->tellg())-currentPosition; - Fp->seekg(currentPosition, std::ios_base::beg); + Fp->seekg(currentPosition, std::ios::beg); entry->SetLength(lengthUntilEOF); return; } @@ -1868,16 +1803,12 @@ void Document::FindDocEntryLength( DocEntry *entry ) /** * \brief Find the Value Representation of the current Dicom Element. - * @param entry + * @return Value Representation of the current Entry */ -void Document::FindDocEntryVR( DocEntry *entry ) +std::string Document::FindDocEntryVR() { if ( Filetype != ExplicitVR ) - { - return; - } - - char vr[3]; + return(GDCM_UNKNOWN); long positionOnEntry = Fp->tellg(); // Warning: we believe this is explicit VR (Value Representation) because @@ -1887,105 +1818,34 @@ void Document::FindDocEntryVR( DocEntry *entry ) // 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; - if( !CheckDocEntryVR(entry, vr) ) + if( !CheckDocEntryVR(vr) ) { - Fp->seekg(positionOnEntry, std::ios_base::beg); - // When this element is known in the dictionary we shall use, e.g. for - // the semantics (see the usage of IsAnInteger), the VR proposed by the - // dictionary entry. Still we have to flag the element as implicit since - // we know now our assumption on expliciteness is not furfilled. - // avoid . - if ( entry->IsVRUnknown() ) - { - entry->SetVR("Implicit"); - } - entry->SetImplicitVR(); + Fp->seekg(positionOnEntry, std::ios::beg); + return(GDCM_UNKNOWN); } + return(vr); } /** * \brief Check the correspondance between the VR of the header entry * and the taken VR. If they are different, the header entry is * updated with the new VR. - * @param entry Header Entry to check * @param vr Dicom Value Representation * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ -bool Document::CheckDocEntryVR(DocEntry *entry, VRKey vr) +bool Document::CheckDocEntryVR(VRKey vr) { - std::string msg; - bool realExplicit = true; - - // Assume we are reading a falsely explicit VR file i.e. we reached - // a tag where we expect reading a VR but are in fact we read the - // first to bytes of the length. Then we will interogate (through find) - // the dicom_vr dictionary with oddities like "\004\0" which crashes - // both GCC and VC++ implementations of the STL map. Hence when the - // expected VR read happens to be non-ascii characters we consider - // we hit falsely explicit VR tag. - - if ( !isalpha((unsigned char)vr[0]) && !isalpha((unsigned char)vr[1]) ) - { - realExplicit = false; - } - // CLEANME searching the dicom_vr at each occurence is expensive. // PostPone this test in an optional integrity check at the end // of parsing or only in debug mode. - if ( realExplicit && !Global::GetVR()->Count(vr) ) - { - realExplicit = false; - } - - if ( !realExplicit ) - { - // We thought this was explicit VR, but we end up with an - // implicit VR tag. Let's backtrack. - msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", - entry->GetGroup(), entry->GetElement()); - dbg.Verbose(1, "Document::FindVR: ", msg.c_str()); - - if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000) - { - // Group length is UL ! - DictEntry* newEntry = NewVirtualDictEntry( - entry->GetGroup(), entry->GetElement(), - "UL", "FIXME", "Group Length"); - entry->SetDictEntry( newEntry ); - } + if ( !Global::GetVR()->IsValidVR(vr) ) return false; - } - - if ( entry->IsVRUnknown() ) - { - // When not a dictionary entry, we can safely overwrite the VR. - if( entry->GetElement() == 0x0000 ) - { - // Group length is UL ! - entry->SetVR("UL"); - } - else - { - entry->SetVR(vr); - } - } - else if ( entry->GetVR() != vr ) - { - // The VR present in the file and the dictionary disagree. We assume - // the file writer knew best and use the VR of the file. Since it would - // be unwise to overwrite the VR of a dictionary (since it would - // compromise it's next user), we need to clone the actual DictEntry - // and change the VR for the read one. - DictEntry* newEntry = NewVirtualDictEntry( - entry->GetGroup(), entry->GetElement(), - vr, "FIXME", entry->GetName()); - entry->SetDictEntry(newEntry); - } return true; } @@ -2138,8 +1998,8 @@ void Document::SkipDocEntry(DocEntry *entry) */ void Document::SkipToNextDocEntry(DocEntry *entry) { - Fp->seekg((long)(entry->GetOffset()), std::ios_base::beg); - Fp->seekg( (long)(entry->GetReadLength()), std::ios_base::cur); + Fp->seekg((long)(entry->GetOffset()), std::ios::beg); + Fp->seekg( (long)(entry->GetReadLength()), std::ios::cur); } /** @@ -2266,8 +2126,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" ) { return true; - } - + } return false; } @@ -2307,7 +2166,7 @@ uint32_t Document::FindDocEntryLengthOB() { dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item " "tag nor a Sequence delimiter tag."); - Fp->seekg(positionOnEntry, std::ios_base::beg); + Fp->seekg(positionOnEntry, std::ios::beg); throw FormatUnexpected("Document::FindDocEntryLengthOB()", "Neither an Item tag nor a Sequence " "delimiter tag."); @@ -2328,7 +2187,7 @@ uint32_t Document::FindDocEntryLengthOB() break; } } - Fp->seekg( positionOnEntry, std::ios_base::beg); + Fp->seekg( positionOnEntry, std::ios::beg); return totalLength; } @@ -2384,7 +2243,7 @@ uint32_t Document::ReadInt32() void Document::SkipBytes(uint32_t nBytes) { //FIXME don't dump the returned value - Fp->seekg((long)nBytes, std::ios_base::cur); + Fp->seekg((long)nBytes, std::ios::cur); } /** @@ -2397,6 +2256,7 @@ void Document::Initialise() RefShaDict = NULL; RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; + Filetype = Unknown; } /** @@ -2498,8 +2358,8 @@ 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_base::beg); - Fp->seekg ( 132L, std::ios_base::beg); + Fp->seekg(0, std::ios::beg); + Fp->seekg ( 132L, std::ios::beg); return true; } // End of DicomV3 @@ -2507,7 +2367,7 @@ bool Document::CheckSwap() // preamble. We can reset the file position indicator to where the data // is (i.e. the beginning of the file). dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file"); - Fp->seekg(0, std::ios_base::beg); + Fp->seekg(0, std::ios::beg); // Our next best chance would be to be considering a 'clean' ACR/NEMA file. // By clean we mean that the length of the first tag is written down. @@ -2690,7 +2550,6 @@ void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) reversedEndian--; SwitchSwapToBigEndian(); } - } /** @@ -2719,8 +2578,22 @@ DocEntry* Document::ReadNextDocEntry() } HandleBrokenEndian(group, elem); - DocEntry *newEntry = NewDocEntryByNumber(group, elem); - FindDocEntryVR(newEntry); + std::string vr=FindDocEntryVR(); + + DocEntry *newEntry = NewDocEntryByNumber(group, elem, vr); + if( vr == GDCM_UNKNOWN ) + { + if( Filetype == ExplicitVR ) + { + // We thought this was explicit VR, but we end up with an + // implicit VR tag. Let's backtrack. + std::string msg; + msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n", + newEntry->GetGroup(), newEntry->GetElement()); + dbg.Verbose(1, "Document::FindVR: ", msg.c_str()); + } + newEntry->SetImplicitVR(); + } try { @@ -2802,7 +2675,7 @@ bool Document::ReadTag(uint16_t testGroup, uint16_t testElement) s << " at address: " << (unsigned)currentPosition << std::endl; dbg.Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:"); dbg.Verbose(0, s.str().c_str()); - Fp->seekg(positionOnEntry, std::ios_base::beg); + Fp->seekg(positionOnEntry, std::ios::beg); return false; } @@ -3180,6 +3053,52 @@ bool Document::operator<(Document &document) return false; } + +/** + * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader + * @param filetype Type of the File to be written + */ +int Document::ComputeGroup0002Length( FileType filetype ) +{ + uint16_t gr, el; + std::string vr; + + int groupLength = 0; + bool found0002 = false; + + // for each zero-level Tag in the DCM Header + DocEntry *entry; + + Initialize(); + entry = GetNextEntry(); + while(entry) + { + gr = entry->GetGroup(); + + if (gr == 0x0002) + { + found0002 = true; + + el = entry->GetElement(); + vr = entry->GetVR(); + + if (filetype == ExplicitVR) + { + if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) + { + groupLength += 4; // explicit VR AND OB, OW, SQ : 4 more bytes + } + } + groupLength += 2 + 2 + 4 + entry->GetLength(); + } + else if (found0002 ) + break; + + entry = GetNextEntry(); + } + return groupLength; +} + } // end namespace gdcm //-----------------------------------------------------------------------------