X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=857f12de05ca1a44e4acbc750d1599e2752f1c29;hb=d65508e83c169bde30eecaed0ca1c5ce6d0eebcb;hp=9b5b2ac4e7f03d731f94e20a56c93b2a3b378f87;hpb=f4618aed21f60eeca799cf5807b3dca987831591;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 9b5b2ac4..857f12de 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/09/10 18:54:38 $ - Version: $Revision: 1.74 $ + Date: $Date: 2004/10/06 22:31:31 $ + Version: $Revision: 1.96 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -20,7 +20,6 @@ #include "gdcmValEntry.h" #include "gdcmBinEntry.h" #include "gdcmSeqEntry.h" - #include "gdcmGlobal.h" #include "gdcmUtil.h" #include "gdcmDebug.h" @@ -107,10 +106,7 @@ gdcmDocument::gdcmDocument( std::string const & filename ) long beg = ftell(Fp); lgt -= beg; - SQDepthLevel = 0; - - long l = ParseDES( this, beg, lgt, false); // le Load sera fait a la volee - (void)l; //is l used anywhere ? + ParseDES( this, beg, lgt, false); // le Load sera fait a la volee rewind(Fp); @@ -119,17 +115,35 @@ gdcmDocument::gdcmDocument( std::string const & filename ) std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ) { - LoadEntryVoidArea(0x0028,0x1200); // gray LUT - LoadEntryVoidArea(0x0028,0x1201); // R LUT - LoadEntryVoidArea(0x0028,0x1202); // G LUT - LoadEntryVoidArea(0x0028,0x1203); // B LUT + LoadEntryBinArea(0x0028,0x1200); // gray LUT + /// FIXME FIXME FIXME + /// The tags refered by the three following lines used to be CORRECTLY + /// defined as having an US Value Representation in the public + /// dictionnary. BUT the semantics implied by the three following + /// lines state that the corresponding tag contents are in fact + /// the ones of a gdcmBinEntry. + /// In order to fix things "Quick and Dirty" the dictionnary was + /// altered on PURPOUS 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 + /// wether the following tags are either: + /// - multivaluated US, and hence loaded as gdcmValEntry, but afterwards + /// also used as gdcmBinEntry, which requires the proper conversion, + /// - OW, and hence loaded as gdcmBinEntry, but afterwards also used + /// as gdcmValEntry, which requires the proper conversion. + LoadEntryBinArea(0x0028,0x1201); // R LUT + LoadEntryBinArea(0x0028,0x1202); // G LUT + LoadEntryBinArea(0x0028,0x1203); // B LUT - LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data - LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data - LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data + // Segmented Red Palette Color LUT Data + LoadEntryBinArea(0x0028,0x1221); + // Segmented Green Palette Color LUT Data + LoadEntryBinArea(0x0028,0x1222); + // Segmented Blue Palette Color LUT Data + LoadEntryBinArea(0x0028,0x1223); } //FIXME later : how to use it? - LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent) + LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent) CloseFile(); @@ -184,7 +198,7 @@ gdcmDocument::~gdcmDocument () for (TagDocEntryHT::const_iterator it = TagHT.begin(); it != TagHT.end(); ++it ) { - delete it->second; + //delete it->second; //temp remove } TagHT.clear(); } @@ -215,7 +229,7 @@ void gdcmDocument::PrintShaDict(std::ostream & os) /** * \brief Get the public dictionary used */ -gdcmDict *gdcmDocument::GetPubDict() +gdcmDict* gdcmDocument::GetPubDict() { return RefPubDict; } @@ -223,7 +237,7 @@ gdcmDict *gdcmDocument::GetPubDict() /** * \brief Get the shadow dictionary used */ -gdcmDict *gdcmDocument::GetShaDict() +gdcmDict* gdcmDocument::GetShaDict() { return RefShaDict; } @@ -435,6 +449,22 @@ bool gdcmDocument::IsJPEG2000() || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); } +/** + * \brief Determines if the Transfer Syntax corresponds to encapsulated + * of encoded Pixel Data (as opposed to native). + * @return True when encapsulated. False when native. + */ +bool gdcmDocument::IsEncapsulateTransferSyntax() +{ + return ( IsJPEGBaseLineProcess1TransferSyntax() + || IsJPEGExtendedProcess2_4TransferSyntax() + || IsJPEGExtendedProcess3_5TransferSyntax() + || IsJPEGSpectralSelectionProcess6_8TransferSyntax() + || IsRLELossLessTransferSyntax() + || IsJPEGLossless() + || IsJPEG2000() ); +} + /** * \brief Predicate for dicom version 3 file. * @return True when the file is a dicom version 3. @@ -523,13 +553,10 @@ bool gdcmDocument::CloseFile() void gdcmDocument::Write(FILE* fp,FileType filetype) { /// \todo move the following lines (and a lot of others, to be written) - /// to a future function CheckAndCorrectHeader - - /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA - /// no way (check : FileType est un champ de gdcmDocument ...) - /// a moins de se livrer a un tres complique ajout des champs manquants. - /// faire un CheckAndCorrectHeader (?) - + /// to a future function CheckAndCorrectHeader + /// (necessary if user wants to write a DICOM V3 file + /// starting from an ACR-NEMA (V2) gdcmHeader + if (filetype == gdcmImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; @@ -578,22 +605,37 @@ void gdcmDocument::Write(FILE* fp,FileType filetype) * @param value (string) 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). - */ - -gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( + */ +gdcmValEntry* gdcmDocument::ReplaceOrCreateByNumber( std::string const & value, uint16_t group, - uint16_t elem ) + uint16_t elem, + std::string const & VR ) { gdcmValEntry* valEntry = 0; gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem); if (!currentEntry) { - // The entry wasn't present and we simply create the required ValEntry: - currentEntry = NewDocEntryByNumber(group, elem); + // check if (group,element) DictEntry exists + // if it doesn't, create an entry in gdcmDictSet::VirtualEntry + // and use it + + // Find out if the tag we received is in the dictionaries: + gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); + gdcmDictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem); + if (!dictEntry) + { + currentEntry = NewDocEntryByNumber(group, elem,VR); + } + else + { + currentEntry = NewDocEntryByNumber(group, elem); + } + if (!currentEntry) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" @@ -639,36 +681,80 @@ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( /* * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. - * @param voidArea (binary) value to be set + * @param binArea (binary) value to be set * @param Group Group number of the Entry * @param Elem Element number of the Entry * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ -gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( - void *voidArea, +gdcmBinEntry* gdcmDocument::ReplaceOrCreateByNumber( + uint8_t* binArea, int lgth, uint16_t group, - uint16_t elem) + uint16_t elem, + std::string const& VR ) { - gdcmBinEntry* b = 0; - gdcmDocEntry* a = GetDocEntryByNumber( group, elem); - if (!a) + gdcmBinEntry* binEntry = 0; + gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem); + if (!currentEntry) { - a = NewBinEntryByNumber(group, elem); - if (!a) + + // check if (group,element) DictEntry exists + // if it doesn't, create an entry in gdcmDictSet::VirtualEntry + // and use it + + // Find out if the tag we received is in the dictionaries: + gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); + gdcmDictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem); + + if (!dictEntry) { - return 0; + currentEntry = NewDocEntryByNumber(group, elem, VR); + } + else + { + currentEntry = NewDocEntryByNumber(group, elem); + } + if (!currentEntry) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" + " NewDocEntryByNumber failed."); + return NULL; } + binEntry = new gdcmBinEntry(currentEntry); + if ( !AddEntry(binEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" + " failed allthough this is a creation."); + } + } + else + { + binEntry = dynamic_cast< gdcmBinEntry* >(currentEntry); + if ( !binEntry ) // Euuuuh? It wasn't a BinEntry + // then we change it to a BinEntry ? + // Shouldn't it be considered as an error ? + { + // We need to promote the gdcmDocEntry to a gdcmBinEntry: + binEntry = new gdcmBinEntry(currentEntry); + if (!RemoveEntry(currentEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" + " of previous DocEntry failed."); + return NULL; + } + if ( !AddEntry(binEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" + " promoted BinEntry failed."); + return NULL; + } + } + } - b = new gdcmBinEntry(a); - AddEntry(b); - b->SetVoidArea(voidArea); - } - SetEntryByNumber(voidArea, lgth, group, elem); - //b->SetVoidArea(voidArea); //what if b == 0 !! + SetEntryByNumber(binArea, lgth, group, elem); - return b; + return binEntry; } @@ -680,7 +766,7 @@ gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( * \return pointer to the modified/created SeqEntry (NULL when creation * failed). */ -gdcmSeqEntry * gdcmDocument::ReplaceOrCreateByNumber( +gdcmSeqEntry* gdcmDocument::ReplaceOrCreateByNumber( uint16_t group, uint16_t elem) { @@ -740,9 +826,9 @@ bool gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryByName(TagName const & tagName) +std::string gdcmDocument::GetEntryByName(TagName const& tagName) { - gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); + gdcmDictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) { return GDCM_UNFOUND; @@ -764,7 +850,7 @@ std::string gdcmDocument::GetEntryByName(TagName const & tagName) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByName(TagName const & tagName) +std::string gdcmDocument::GetEntryVRByName(TagName const& tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) @@ -777,7 +863,6 @@ std::string gdcmDocument::GetEntryVRByName(TagName const & tagName) return elem->GetVR(); } - /** * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries @@ -866,10 +951,13 @@ bool gdcmDocument::SetEntryByName(std::string const & content,std::string const * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool gdcmDocument::SetEntryByNumber(std::string const & content, +bool gdcmDocument::SetEntryByNumber(std::string const& content, uint16_t group, uint16_t element) { + int c; + int l; + gdcmValEntry* valEntry = GetValEntryByNumber(group, element); if (!valEntry ) { @@ -878,30 +966,31 @@ bool gdcmDocument::SetEntryByNumber(std::string const & content, return false; } // Non even content must be padded with a space (020H)... - std::string evenContent = content; - if( evenContent.length() % 2 ) + std::string finalContent = content; + if( finalContent.length() % 2 ) { - evenContent += '\0'; // ... therefore we padd with (000H) .!?! + finalContent += '\0'; // ... therefore we padd with (000H) .!?! } - valEntry->SetValue(evenContent); + valEntry->SetValue(finalContent); // Integers have a special treatement for their length: - gdcmVRKey vr = valEntry->GetVR(); - if( vr == "US" || vr == "SS" ) - { - int c = CountSubstring(content, "\\"); // for multivaluated items - valEntry->SetLength((c+1)*2); - } - else if( vr == "UL" || vr == "SL" ) - { - int c = CountSubstring(content, "\\"); // for multivaluated items - valEntry->SetLength((c+1)*4); - } - else - { - valEntry->SetLength(evenContent.length()); - } + l = finalContent.length(); + if ( l != 0) // To avoid to be cheated by 'zero length' integers + { + gdcmVRKey vr = valEntry->GetVR(); + if( vr == "US" || vr == "SS" ) + { + c = CountSubstring(content, "\\") + 1; // for multivaluated items + l = c*2; + } + else if( vr == "UL" || vr == "SL" ) + { + c = CountSubstring(content, "\\") + 1; // for multivaluated items + l = c*4;; + } + } + valEntry->SetLength(l); return true; } @@ -909,12 +998,12 @@ bool gdcmDocument::SetEntryByNumber(std::string const & content, * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. - * @param content new value (void *) to substitute with + * @param content new value (void* -> uint8_t*) to substitute with * @param lgth new value length * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool gdcmDocument::SetEntryByNumber(void *content, +bool gdcmDocument::SetEntryByNumber(uint8_t*content, int lgth, uint16_t group, uint16_t element) @@ -934,8 +1023,9 @@ bool gdcmDocument::SetEntryByNumber(void *content, } */ gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key]; - a->SetVoidArea(content); - //a->SetLength(lgth); // ??? + a->SetBinArea(content); + a->SetLength(lgth); + a->SetValue(GDCM_BINLOADED); return true; } @@ -995,7 +1085,7 @@ size_t gdcmDocument::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) * @param elem element number of the Entry * @return Pointer to the 'non string' area */ -void * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem) +void* gdcmDocument::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem) { gdcmDocEntry* entry = GetDocEntryByNumber(group, elem); if (!entry) @@ -1003,7 +1093,7 @@ void * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem) dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry"); return 0; } - return ((gdcmBinEntry *)entry)->GetVoidArea(); + return ((gdcmBinEntry *)entry)->GetBinArea(); } /** @@ -1012,7 +1102,7 @@ void * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem) * @param group group number of the Entry * @param elem element number of the Entry */ -void *gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem) +void* gdcmDocument::LoadEntryBinArea(uint16_t group, uint16_t elem) { gdcmDocEntry *docElement = GetDocEntryByNumber(group, elem); if ( !docElement ) @@ -1022,10 +1112,10 @@ void *gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem) size_t o =(size_t)docElement->GetOffset(); fseek(Fp, o, SEEK_SET); size_t l = docElement->GetLength(); - char* a = new char[l]; + uint8_t* a = new uint8_t[l]; if(!a) { - dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); + dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea cannot allocate a"); return NULL; } size_t l2 = fread(a, 1, l , Fp); @@ -1034,28 +1124,30 @@ void *gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem) delete[] a; return NULL; } - /// \TODO Drop any already existing void area! JPR - SetEntryVoidAreaByNumber(a, group, elem); - + /// \todo Drop any already existing void area! JPR + if( !SetEntryBinAreaByNumber( a, group, elem ) ); + { + dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea setting failed."); + } return a; } /** * \brief Loads (from disk) the element content * when a string is not suitable - * @param element Entry whose voidArea is going to be loaded + * @param element Entry whose binArea is going to be loaded */ -void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element) +void* gdcmDocument::LoadEntryBinArea(gdcmBinEntry* element) { size_t o =(size_t)element->GetOffset(); fseek(Fp, o, SEEK_SET); size_t l = element->GetLength(); - char* a = new char[l]; + uint8_t* a = new uint8_t[l]; if( !a ) { - dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); + dbg.Verbose(0, "gdcmDocument::LoadEntryBinArea cannot allocate a"); return NULL; } - element->SetVoidArea((void *)a); + element->SetBinArea((uint8_t*)a); /// \todo check the result size_t l2 = fread(a, 1, l , Fp); if( l != l2 ) @@ -1074,19 +1166,20 @@ void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element) * @param element Element number of the searched Dicom Element * @return */ -bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, +bool gdcmDocument::SetEntryBinAreaByNumber(uint8_t* area, uint16_t group, uint16_t element) { - gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key)) + gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element); + if ( !currentEntry ) { return false; } - - // This was for multimap ? - (( gdcmBinEntry *)( ((TagHT.equal_range(key)).first)->second ))->SetVoidArea(area); - + if ( gdcmBinEntry* binEntry = dynamic_cast(currentEntry) ) + { + binEntry->SetBinArea( area ); + return true; + } return true; } @@ -1284,17 +1377,13 @@ uint16_t gdcmDocument::UnswapShort(uint16_t a) * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) * @return length of the parsed set. */ - -long gdcmDocument::ParseDES(gdcmDocEntrySet *set, +void gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) { gdcmDocEntry *newDocEntry = 0; - gdcmValEntry *newValEntry = 0; - unsigned long l = 0; - int depth = set->GetDepthLevel(); while (true) { if ( !delim_mode && (ftell(Fp)-offset) >= l_max) @@ -1313,12 +1402,29 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) ) { - /////// ValEntry - newValEntry = new gdcmValEntry(newDocEntry->GetDictEntry()); - newValEntry->Copy(newDocEntry); - newValEntry->SetDepthLevel(depth); - set->AddEntry(newValEntry); - LoadDocEntry(newValEntry); + /////////////////////// ValEntry + gdcmValEntry* newValEntry = + new gdcmValEntry( newDocEntry->GetDictEntry() ); + newValEntry->Copy( newDocEntry ); + + // When "set" is a gdcmDocument, then we are at the top of the + // hierarchy and the Key is simply of the form ( group, elem )... + if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) ) + { + (void)dummy; + newValEntry->SetKey( newValEntry->GetKey() ); + } + // ...but when "set" is a gdcmSQItem, we are inserting this new + // valEntry in a sequence item. Hence the key has the + // generalized form (refer to \ref gdcmBaseTagKey): + if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) ) + { + newValEntry->SetKey( parentSQItem->GetBaseTagKey() + + newValEntry->GetKey() ); + } + + set->AddEntry( newValEntry ); + LoadDocEntry( newValEntry ); if (newValEntry->IsItemDelimitor()) { break; @@ -1337,39 +1443,55 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, "nor BinEntry. Probably unknown VR."); } - ////// BinEntry or UNKOWN VR: - gdcmBinEntry *bn = new gdcmBinEntry(newDocEntry->GetDictEntry()); - bn->Copy(newDocEntry); - set->AddEntry(bn); - LoadDocEntry(bn); + //////////////////// BinEntry or UNKOWN VR: + gdcmBinEntry* newBinEntry = + new gdcmBinEntry( newDocEntry->GetDictEntry() ); + newBinEntry->Copy( newDocEntry ); + + // When "this" is a gdcmDocument the Key is simply of the + // form ( group, elem )... + if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) ) + { + newBinEntry->SetKey( newBinEntry->GetKey() ); + } + // but when "this" is a SQItem, we are inserting this new + // valEntry in a sequence item, and the kay has the + // generalized form (refer to \ref gdcmBaseTagKey): + if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) ) + { + newBinEntry->SetKey( parentSQItem->GetBaseTagKey() + + newBinEntry->GetKey() ); + } + + set->AddEntry( newBinEntry ); + LoadDocEntry( newBinEntry ); } if (newDocEntry->GetGroup() == 0x7fe0 && newDocEntry->GetElement() == 0x0010 ) { - if (newDocEntry->GetReadLength()==0xffffffff) + if ( IsRLELossLessTransferSyntax() ) { - // Broken US.3405.1.dcm - Parse7FE0(); // to skip the pixels - // (multipart JPEG/RLE are trouble makers) + long PositionOnEntry = ftell(Fp); + fseek(Fp, newDocEntry->GetOffset(), SEEK_SET); + ComputeRLEInfo(); + fseek(Fp, PositionOnEntry, SEEK_SET); } else { SkipToNextDocEntry(newDocEntry); - l = newDocEntry->GetFullLength(); } } else { // to be sure we are at the beginning SkipToNextDocEntry(newDocEntry); - l = newDocEntry->GetFullLength(); } } else { // VR = "SQ" - l = newDocEntry->GetReadLength(); + unsigned long l = newDocEntry->GetReadLength(); if ( l != 0 ) // don't mess the delim_mode for zero-length sequence { if ( l == 0xffffffff ) @@ -1382,20 +1504,38 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, } } // no other way to create it ... - gdcmSeqEntry *sq = new gdcmSeqEntry(newDocEntry->GetDictEntry(), - set->GetDepthLevel()); - sq->Copy(newDocEntry); - sq->SetDelimitorMode(delim_mode); - sq->SetDepthLevel(depth); + gdcmSeqEntry* newSeqEntry = + new gdcmSeqEntry( newDocEntry->GetDictEntry() ); + newSeqEntry->Copy( newDocEntry ); + newSeqEntry->SetDelimitorMode( delim_mode ); + + // At the top of the hierarchy, stands a gdcmDocument. When "set" + // is a gdcmDocument, then we are building the first depth level. + // Hence the gdcmSeqEntry we are building simply has a depth + // level of one: + if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) ) + { + (void)dummy; + newSeqEntry->SetDepthLevel( 1 ); + newSeqEntry->SetKey( newSeqEntry->GetKey() ); + } + // But when "set" is allready a SQItem, we are building a nested + // sequence, and hence the depth level of the new gdcmSeqEntry + // we are building, is one level deeper: + if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) ) + { + newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 ); + newSeqEntry->SetKey( parentSQItem->GetBaseTagKey() + + newSeqEntry->GetKey() ); + } if ( l != 0 ) { // Don't try to parse zero-length sequences - long lgt = ParseSQ( sq, - newDocEntry->GetOffset(), - l, delim_mode); - (void)lgt; //not used... + ParseSQ( newSeqEntry, + newDocEntry->GetOffset(), + l, delim_mode); } - set->AddEntry(sq); + set->AddEntry( newSeqEntry ); if ( !delim_mode && (ftell(Fp)-offset) >= l_max) { break; @@ -1403,24 +1543,21 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, } delete newDocEntry; } - return l; // Probably useless } /** * \brief Parses a Sequence ( SeqEntry after SeqEntry) * @return parsed length for this level */ -long gdcmDocument::ParseSQ(gdcmSeqEntry *set, - long offset, long l_max, bool delim_mode) +void gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry, + long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; bool dlm_mod; - //int depth = set->GetDepthLevel(); - //(void)depth; //not used while (true) { - gdcmDocEntry *newDocEntry = ReadNextDocEntry(); + gdcmDocEntry* newDocEntry = ReadNextDocEntry(); if ( !newDocEntry ) { // FIXME Should warn user @@ -1430,7 +1567,7 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, { if ( newDocEntry->IsSequenceDelimitor() ) { - set->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetSequenceDelimitationItem( newDocEntry ); break; } } @@ -1439,8 +1576,13 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, break; } - gdcmSQItem *itemSQ = new gdcmSQItem(set->GetDepthLevel()); - itemSQ->AddEntry(newDocEntry); + gdcmSQItem *itemSQ = new gdcmSQItem( seqEntry->GetDepthLevel() ); + std::ostringstream newBase; + newBase << seqEntry->GetKey() + << "/" + << SQItemNumber + << "#"; + itemSQ->SetBaseTagKey( newBase.str() ); unsigned int l = newDocEntry->GetReadLength(); if ( l == 0xffffffff ) @@ -1452,19 +1594,15 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, dlm_mod = false; } - int lgr = ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); - (void)lgr; //FIXME not used + ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); - set->AddEntry(itemSQ, SQItemNumber); + seqEntry->AddEntry( itemSQ, SQItemNumber ); SQItemNumber++; - if ( !delim_mode && (ftell(Fp)-offset) >= l_max) + if ( !delim_mode && ( ftell(Fp) - offset ) >= l_max ) { break; } } - - int lgth = ftell(Fp) - offset; - return lgth; } /** @@ -1539,9 +1677,9 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) // When we find a BinEntry not very much can be done : if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) ) { - s << "gdcm::Loaded (BinEntry)"; + s << GDCM_BINLOADED; binEntryPtr->SetValue(s.str()); - LoadEntryVoidArea(binEntryPtr); // last one, not to erase length ! + LoadEntryBinArea(binEntryPtr); // last one, not to erase length ! return; } @@ -1549,7 +1687,6 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) if ( IsDocEntryAnInteger(entry) ) { uint32_t NewInt; - //std::ostringstream s; //shadow previous declaration 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 @@ -1653,11 +1790,13 @@ void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) fseek(Fp, 2L, SEEK_CUR); uint32_t length32 = ReadInt32(); - if ( vr == "OB" && length32 == 0xffffffff ) + if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) { uint32_t lengthOB; try { + /// \todo rename that to FindDocEntryLengthOBOrOW since + /// the above test is on both OB and OW... lengthOB = FindDocEntryLengthOB(); } catch ( gdcmFormatUnexpected ) @@ -2688,110 +2827,213 @@ uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement) } /** - * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files - * No other way so 'skip' the Data - * + * \brief Parse pixel data from disk of [multi-]fragment RLE encoding. + * Compute the RLE extra information and store it in \ref RLEInfo + * for later pixel retrieval usage. */ -void gdcmDocument::Parse7FE0 () +void gdcmDocument::ComputeRLEInfo() { - gdcmDocEntry* element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !element ) - { - // Should warn user FIXME - return; - } - - if ( IsImplicitVRLittleEndianTransferSyntax() - || IsExplicitVRLittleEndianTransferSyntax() - || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier ! - || IsDeflatedExplicitVRLittleEndianTransferSyntax() ) + if ( ! IsRLELossLessTransferSyntax() ) { return; } - - // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels + // Encoded pixel data: for the time being we are only concerned with + // Jpeg or RLE Pixel data encodings. + // As stated in ps-3.3, 8.2: + // "If sent in Encapsulated Format (i.e. other than the Native Format) the + // value representation OB is used". + // Hence we expect an OB value representation. Concerning OB VR, + // the section PS3.3, A.4.c (p58 and p59), states: + // "For the Value Representations OB and OW, the encoding shall meet the + // following specifications depending on the Data element tag:" + // [...snip...] + // - the first item in the sequence of items before the encoded pixel + // data stream shall be basic offset table item. The basic offset table + // item value, however, is not required to be present" //// Read the Basic Offset Table Item Tag length... uint32_t itemLength = ReadTagLength(0xfffe, 0xe000); - //// ... and then read length[s] itself[themselves]. We don't use - // the values read (BTW what is the purpous of those lengths ?) + // When present, read the basic offset table itself. + // Notes: - since the presence of this basic offset table is optional + // we can't rely on it for the implementation, and we will simply + // trash it's content (when present). + // - still, when present, we could add some further checks on the + // lengths, but we won't bother with such fuses for the time being. if ( itemLength != 0 ) { - // BTW, what is the purpous of those length anyhow !? char* basicOffsetTableItemValue = new char[itemLength + 1]; fread(basicOffsetTableItemValue, itemLength, 1, Fp); for (unsigned int i=0; i < itemLength; i += 4 ) { - uint32_t individualLength = str2num(&basicOffsetTableItemValue[i],uint32_t); + uint32_t individualLength = str2num( &basicOffsetTableItemValue[i], + uint32_t); std::ostringstream s; s << " Read one length: "; s << std::hex << individualLength << std::endl; - dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str()); + dbg.Verbose(0, "gdcmDocument::ComputeRLEInfo: ", s.str().c_str()); } delete[] basicOffsetTableItemValue; } - if ( ! IsRLELossLessTransferSyntax() ) - { - // JPEG Image - - //// We then skip (not reading them) all the fragments of images: - while ( (itemLength = ReadTagLength(0xfffe, 0xe000)) ) + // Encapsulated RLE Compressed Images (see PS-3.3, Annex G). + // Loop on the frame[s] and store the parsed information in a + // gdcmRLEFramesInfo. + long frameLength; + + // Loop on the individual frame[s] and store the information + // on the RLE fragments in a gdcmRLEFramesInfo. + // Note: - when only a single frame is present, this is a + // classical image. + // - when more than one frame are present, then we are in + // the case of a multi-frame image. + while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) ) + { + // Parse the RLE Header and store the corresponding RLE Segment + // Offset Table information on fragments of this current Frame. + // Note that the fragment pixels themselves are not loaded + // (but just skipped). + long frameOffset = ftell(Fp); + + uint32_t nbRleSegments = ReadInt32(); + + uint32_t rleSegmentOffsetTable[15]; + for( int k = 1; k <= 15; k++ ) { - SkipBytes(itemLength); + rleSegmentOffsetTable[k] = ReadInt32(); } + + // Deduce from both the RLE Header and the frameLength the + // fragment length, and again store this info in a + // gdcmRLEFramesInfo. + long rleSegmentLength[15]; + // skipping (not reading) RLE Segments + if ( nbRleSegments > 1) + { + for(unsigned int k = 1; k <= nbRleSegments-1; k++) + { + rleSegmentLength[k] = rleSegmentOffsetTable[k+1] + - rleSegmentOffsetTable[k]; + SkipBytes(rleSegmentLength[k]); + } + } + + rleSegmentLength[nbRleSegments] = frameLength + - rleSegmentOffsetTable[nbRleSegments]; + SkipBytes(rleSegmentLength[nbRleSegments]); + + // Store the collected info + gdcmRLEFrame* newFrameInfo = new gdcmRLEFrame; + newFrameInfo->NumberFragments = nbRleSegments; + for( unsigned int k = 1; k <= nbRleSegments; k++ ) + { + newFrameInfo->Offset[k] = frameOffset + rleSegmentOffsetTable[k]; + newFrameInfo->Length[k] = rleSegmentLength[k]; + } + RLEInfo.Frames.push_back( newFrameInfo ); } - else + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( !ReadTag(0xfffe, 0xe0dd) ) { - // RLE Image - long ftellRes; - long rleSegmentLength[15], fragmentLength; + dbg.Verbose(0, "gdcmDocument::ComputeRLEInfo: no sequence delimiter "); + dbg.Verbose(0, " item at end of RLE item sequence"); + } +} - // While we find some items: - while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) - { - // Parse fragments of the current Fragment (Frame) - //------------------ scanning (not reading) fragment pixels - uint32_t nbRleSegments = ReadInt32(); - - //// Reading RLE Segments Offset Table - uint32_t rleSegmentOffsetTable[15]; - for(int k=1; k<=15; k++) +/** + * \brief Walk recursively the given \ref gdcmDocEntrySet, and feed + * the given hash table (\ref TagDocEntryHT) with all the + * \ref gdcmDocEntry (Dicom entries) encountered. + * This method does the job for \ref BuildFlatHashTable. + * @param builtHT Where to collect all the \ref gdcmDocEntry encountered + * when recursively walking the given set. + * @param set The structure to be traversed (recursively). + */ +void gdcmDocument::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, + gdcmDocEntrySet* set ) +{ + if (gdcmElementSet* elementSet = dynamic_cast< gdcmElementSet* > ( set ) ) + { + TagDocEntryHT* currentHT = elementSet->GetTagHT(); + for( TagDocEntryHT::const_iterator i = currentHT->begin(); + i != currentHT->end(); + ++i) + { + gdcmDocEntry* entry = i->second; + if ( gdcmSeqEntry* seqEntry = dynamic_cast(entry) ) { - ftellRes = ftell(Fp); - rleSegmentOffsetTable[k] = ReadInt32(); + ListSQItem& items = seqEntry->GetSQItems(); + for( ListSQItem::const_iterator item = items.begin(); + item != items.end(); + ++item) + { + BuildFlatHashTableRecurse( builtHT, *item ); + } + continue; } + builtHT[entry->GetKey()] = entry; + } + return; + } - // skipping (not reading) RLE Segments - if ( nbRleSegments > 1) + if (gdcmSQItem* SQItemSet = dynamic_cast< gdcmSQItem* > ( set ) ) + { + ListDocEntry& currentList = SQItemSet->GetDocEntries(); + for (ListDocEntry::iterator i = currentList.begin(); + i != currentList.end(); + ++i) + { + gdcmDocEntry* entry = *i; + if ( gdcmSeqEntry* seqEntry = dynamic_cast(entry) ) { - for(unsigned int k = 1; k <= nbRleSegments-1; k++) + ListSQItem& items = seqEntry->GetSQItems(); + for( ListSQItem::const_iterator item = items.begin(); + item != items.end(); + ++item) { - rleSegmentLength[k] = rleSegmentOffsetTable[k+1] - - rleSegmentOffsetTable[k]; - ftellRes = ftell(Fp); - SkipBytes(rleSegmentLength[k]); - } - } - - rleSegmentLength[nbRleSegments] = fragmentLength - - rleSegmentOffsetTable[nbRleSegments]; - ftellRes = ftell(Fp); - SkipBytes(rleSegmentLength[nbRleSegments]); + BuildFlatHashTableRecurse( builtHT, *item ); + } + continue; + } + builtHT[entry->GetKey()] = entry; } - // Make sure that at the end of the item we encounter a 'Sequence - // Delimiter Item': - if ( !ReadTag(0xfffe, 0xe0dd) ) - { - dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item"); - dbg.Verbose(0, " at end of RLE item sequence"); - } } } +/** + * \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current + * gdcmDocument. + * + * The structure used by a gdcmDocument (through \ref gdcmElementSet), + * in order to old the parsed entries of a Dicom header, is a recursive + * one. This is due to the fact that the sequences (when present) + * can be nested. Additionaly, the sequence items (represented in + * gdcm as \ref gdcmSQItem) add an extra complexity to the data + * structure. Hence, a gdcm user whishing to visit all the entries of + * a Dicom header will need to dig in the gdcm internals (which + * implies exposing all the internal data structures to the API). + * In order to avoid this burden to the user, \ref BuildFlatHashTable + * recursively builds a temporary hash table, which holds all the + * Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a + * std::map<>). + * \warning Of course there is NO integrity constrain between the + * returned \ref TagDocEntryHT and the \ref gdcmElementSet used + * to build it. Hence if the underlying \ref gdcmElementSet is + * altered, then it is the caller responsability to invoke + * \ref BuildFlatHashTable again... + * @return The flat std::map<> we juste build. + */ +TagDocEntryHT* gdcmDocument::BuildFlatHashTable() +{ + TagDocEntryHT* FlatHT = new TagDocEntryHT; + BuildFlatHashTableRecurse( *FlatHT, this ); + return FlatHT; +} + /**