X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=2a2c88e1be9607f3d61d47d79ca7d94c705abb58;hb=74e3bc05fade5a18f193e7d1122c74756c0e689e;hp=6d5841a82f76ac4fbafeece947c4b0ac0ec2595e;hpb=f5c7e83afd484a025285c64a09a89bd227087245;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 6d5841a8..2a2c88e1 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/12/16 13:46:37 $ - Version: $Revision: 1.151 $ + Date: $Date: 2005/01/06 16:05:06 $ + Version: $Revision: 1.158 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -47,7 +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", @@ -535,7 +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 @@ -544,79 +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; } @@ -627,75 +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."); - } - delete currentEntry; - } - 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) { @@ -706,7 +663,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( { tmpArea = 0; } - if (!SetEntryByNumber(tmpArea, lgth, group, elem)) + if (!SetEntry(tmpArea,lgth,binEntry)) { if (tmpArea) { @@ -717,7 +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. @@ -728,20 +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; } /** @@ -917,16 +901,14 @@ bool Document::SetEntryByName( std::string const & content, bool Document::SetEntryByNumber(std::string const& content, uint16_t group, uint16_t element) { - 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)... - valEntry->SetValue(content); - return true; + return SetEntry(content,entry); } /** @@ -941,27 +923,56 @@ 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? + return SetEntry(content,lgth,entry); +} + +/** + * \brief Accesses an existing DocEntry (i.e. a Dicom Element) + * and modifies it's content with the given value. + * @param content new value (string) to substitute with + */ +bool Document::SetEntry(std::string const & content,ValEntry* entry) +{ + if(entry) + { + entry->SetValue(content); + return true; } -*/ - BinEntry* entry = (BinEntry *)TagHT[key]; - entry->SetBinArea(content); - entry->SetLength(lgth); - entry->SetValue(GDCM_BINLOADED); + return false; +} - return true; -} +/** + * \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 lgth new value length + */ +bool Document::SetEntry(uint8_t* content, int lgth,BinEntry* entry) +{ + if(entry) + { + // 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 false; +} /** * \brief Gets (from Header) a 'non string' element value @@ -1070,54 +1081,6 @@ 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. @@ -1169,15 +1132,37 @@ 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 @@ -1816,16 +1801,12 @@ 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 @@ -1835,104 +1816,34 @@ 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::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(); + 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; } @@ -2213,8 +2124,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" ) { return true; - } - + } return false; } @@ -2666,8 +2576,22 @@ 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 { @@ -3127,6 +3051,52 @@ 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 //-----------------------------------------------------------------------------