X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=e561603b8384e10910d82ac1dbbc06568944339c;hb=edfc14dd195f9759cf02da0959d96d1499d572be;hp=854e6db28d1193494b02061ea6219ec690e3aed7;hpb=b8ca604b2c1c17790f19ac61b63dfb5b550ac6c0;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 854e6db2..e561603b 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/11/17 10:20:07 $ - Version: $Revision: 1.133 $ + Date: $Date: 2004/11/30 16:59:32 $ + Version: $Revision: 1.144 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -36,9 +36,12 @@ namespace gdcm { +//----------------------------------------------------------------------------- static const char *TransferSyntaxStrings[] = { // Implicit VR Little Endian "1.2.840.10008.1.2", + // Implicit VR Little Endian DLX G.E? + "1.2.840.113619.5.2", // Explicit VR Little Endian "1.2.840.10008.1.2.1", // Deflated Explicit VR Little Endian @@ -68,10 +71,10 @@ static const char *TransferSyntaxStrings[] = { // Unknown "Unknown Transfer Syntax" }; - + //----------------------------------------------------------------------------- // Refer to Document::CheckSwap() -const unsigned int Document::HEADER_LENGTH_TO_READ = 256; +//const unsigned int Document::HEADER_LENGTH_TO_READ = 256; // Refer to Document::SetMaxSizeLoadEntry() const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 @@ -98,19 +101,19 @@ 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 @@ -440,7 +443,7 @@ 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( memcmp(dicm, "DICM", 4) == 0 ) @@ -479,41 +482,22 @@ bool Document::CloseFile() * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -void Document::Write(std::ofstream* fp, FileType filetype) +void Document::WriteContent(std::ofstream* fp, FileType filetype) { /// \todo move the following lines (and a lot of others, to be written) /// to a future function CheckAndCorrectHeader /// (necessary if user wants to write a DICOM V3 file /// starting from an ACR-NEMA (V2) Header - if (filetype == ImplicitVR) - { - std::string ts = - Util::DicomString( TransferSyntaxStrings[ImplicitVRLittleEndian] ); - ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); - - /// \todo Refer to standards on page 21, chapter 6.2 - /// "Value representation": values with a VR of UI shall be - /// padded with a single trailing null - /// in the following case we have to padd manually with a 0 - - SetEntryLengthByNumber(18, 0x0002, 0x0010); - } - - if (filetype == ExplicitVR) + if ( filetype == ImplicitVR || filetype == ExplicitVR ) { - std::string ts = - Util::DicomString( TransferSyntaxStrings[ExplicitVRLittleEndian] ); - ReplaceOrCreateByNumber(ts, 0x0002, 0x0010); //LEAK - - /// \todo Refer to standards on page 21, chapter 6.2 - /// "Value representation": values with a VR of UI shall be - /// padded with a single trailing null - /// Dans le cas suivant on doit pader manuellement avec un 0 - - SetEntryLengthByNumber(20, 0x0002, 0x0010); + // writing Dicom File Preamble + char filePreamble[128]; + memset(filePreamble, 0, 128); + fp->write(filePreamble, 128); + fp->write("DICM", 4); } - + /** * \todo rewrite later, if really usefull * - 'Group Length' element is optional in DICOM @@ -526,8 +510,7 @@ void Document::Write(std::ofstream* fp, FileType filetype) * UpdateGroupLength(true,ACR); */ - ElementSet::Write(fp, filetype); // This one is recursive - + ElementSet::WriteContent(fp, filetype); // This one is recursive } /** @@ -755,6 +738,11 @@ bool Document::ReplaceIfExistByNumber(std::string const & value, return true; } +std::string Document::GetTransferSyntaxValue(TransferSyntaxType type) +{ + return TransferSyntaxStrings[type]; +} + //----------------------------------------------------------------------------- // Protected @@ -991,7 +979,7 @@ bool Document::SetEntryByNumber(uint8_t*content, int lgth, * @param element element number of the Entry to modify * @return true on success, false otherwise. */ -bool Document::SetEntryLengthByNumber(uint32_t l, +/*bool Document::SetEntryLengthByNumber(uint32_t l, uint16_t group, uint16_t element) { /// \todo use map methods, instead of multimap JPR @@ -1007,7 +995,7 @@ bool Document::SetEntryLengthByNumber(uint32_t l, ( ((TagHT.equal_range(key)).first)->second )->SetLength(l); return true ; -} +}*/ /** * \brief Gets (from Header) the offset of a 'non string' element value @@ -1016,7 +1004,7 @@ bool Document::SetEntryLengthByNumber(uint32_t l, * @param elem element number of the Entry * @return File Offset of the Element Value */ -size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) +/*size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) { DocEntry* entry = GetDocEntryByNumber(group, elem); if (!entry) @@ -1025,7 +1013,7 @@ size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) return 0; } return entry->GetOffset(); -} +}*/ /** * \brief Gets (from Header) a 'non string' element value @@ -1063,31 +1051,13 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) if ( !docElement ) return; - size_t o =(size_t)docElement->GetOffset(); - Fp->seekg( o, std::ios_base::beg); - size_t l = docElement->GetLength(); - uint8_t* a = new uint8_t[l]; - if(!a) - { - dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a"); - return; - } - - // Read the value - Fp->read((char*)a, l); - if( Fp->fail() || Fp->eof() )//Fp->gcount() == 1 - { - delete[] a; + BinEntry *binElement = dynamic_cast(docElement); + if( !binElement ) return; - } - // Set the value to the DocEntry - if( !SetEntryBinAreaByNumber( a, group, elem ) ) - { - delete[] a; - dbg.Verbose(0, "Document::LoadEntryBinArea setting failed."); - } + LoadEntryBinArea(binElement); } + /** * \brief Loads (from disk) the element content * when a string is not suitable @@ -1095,8 +1065,16 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) */ void Document::LoadEntryBinArea(BinEntry* element) { + if(element->GetBinArea()) + return; + + bool openFile = !Fp; + if(openFile) + 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]; if( !a ) @@ -1114,6 +1092,9 @@ void Document::LoadEntryBinArea(BinEntry* element) } element->SetBinArea(a); + + if(openFile) + CloseFile(); } /** @@ -1123,7 +1104,7 @@ void Document::LoadEntryBinArea(BinEntry* element) * @param element Element number of the searched Dicom Element * @return */ -bool Document::SetEntryBinAreaByNumber(uint8_t* area, +/*bool Document::SetEntryBinAreaByNumber(uint8_t* area, uint16_t group, uint16_t element) { DocEntry* currentEntry = GetDocEntryByNumber(group, element); @@ -1139,7 +1120,7 @@ bool Document::SetEntryBinAreaByNumber(uint8_t* area, } return false; -} +}*/ /** * \brief Update the entries with the shadow dictionary. @@ -1258,9 +1239,12 @@ ValEntry* Document::GetValEntryByNumber(uint16_t group, uint16_t element) */ void Document::LoadDocEntrySafe(DocEntry * entry) { - long PositionOnEntry = Fp->tellg(); - LoadDocEntry(entry); - Fp->seekg(PositionOnEntry, std::ios_base::beg); + if(Fp) + { + long PositionOnEntry = Fp->tellg(); + LoadDocEntry(entry); + Fp->seekg(PositionOnEntry, std::ios::beg); + } } /** @@ -1387,10 +1371,12 @@ void Document::ParseDES(DocEntrySet *set, long offset, if (delimitor) { + delete newDocEntry; break; } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + delete newDocEntry; break; } } @@ -1404,9 +1390,6 @@ void Document::ParseDES(DocEntrySet *set, long offset, } //////////////////// BinEntry or UNKOWN VR: -/* BinEntry* newBinEntry = - new BinEntry( newDocEntry->GetDictEntry() ); //LEAK - newBinEntry->Copy( newDocEntry );*/ BinEntry* newBinEntry = new BinEntry( newDocEntry ); //LEAK // When "this" is a Document the Key is simply of the @@ -1440,21 +1423,22 @@ 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 ); } } // Just to make sure we are at the beginning of next entry. SkipToNextDocEntry(newDocEntry); + //delete newDocEntry; } else { @@ -1506,6 +1490,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, set->AddEntry( newSeqEntry ); if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { + delete newDocEntry; break; } } @@ -1535,13 +1520,14 @@ void Document::ParseSQ( SeqEntry* seqEntry, { if ( newDocEntry->IsSequenceDelimitor() ) { - seqEntry->SetSequenceDelimitationItem( newDocEntry ); + seqEntry->SetSequenceDelimitationItem( newDocEntry ); break; } } if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { - break; + delete newDocEntry; + break; } SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); @@ -1563,6 +1549,7 @@ void Document::ParseSQ( SeqEntry* seqEntry, } ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod); + delete newDocEntry; seqEntry->AddEntry( itemSQ, SQItemNumber ); SQItemNumber++; @@ -1584,7 +1571,7 @@ 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 @@ -1638,7 +1625,7 @@ 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; } @@ -1766,7 +1753,7 @@ 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 ) @@ -1786,9 +1773,9 @@ 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; } @@ -1906,7 +1893,7 @@ void Document::FindDocEntryVR( DocEntry *entry ) if( !CheckDocEntryVR(entry, vr) ) { - Fp->seekg(positionOnEntry, std::ios_base::beg); + 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 @@ -2151,8 +2138,8 @@ 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); } /** @@ -2320,7 +2307,7 @@ 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."); @@ -2341,7 +2328,7 @@ uint32_t Document::FindDocEntryLengthOB() break; } } - Fp->seekg( positionOnEntry, std::ios_base::beg); + Fp->seekg( positionOnEntry, std::ios::beg); return totalLength; } @@ -2397,7 +2384,7 @@ 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); } /** @@ -2432,7 +2419,7 @@ bool Document::CheckSwap() uint32_t s32; uint16_t s16; - char deb[256]; //HEADER_LENGTH_TO_READ]; + char deb[256]; // First, compare HostByteOrder and NetworkByteOrder in order to // determine if we shall need to swap bytes (i.e. the Endian type). @@ -2447,7 +2434,7 @@ bool Document::CheckSwap() // The easiest case is the one of a DICOM header, since it possesses a // file preamble where it suffice to look for the string "DICM". - Fp->read(deb, HEADER_LENGTH_TO_READ); + Fp->read(deb, 256); char *entCur = deb + 128; if( memcmp(entCur, "DICM", (size_t)4) == 0 ) @@ -2511,8 +2498,8 @@ 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 @@ -2520,7 +2507,7 @@ 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. @@ -2532,7 +2519,7 @@ bool Document::CheckSwap() // representation of a 32 bits integer. Hence the following dirty // trick : s32 = *((uint32_t *)(entCur)); - + switch( s32 ) { case 0x00040000 : @@ -2609,6 +2596,7 @@ bool Document::CheckSwap() } + /** * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. @@ -2814,7 +2802,7 @@ 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; } @@ -3100,7 +3088,7 @@ void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, * Document. * * The structure used by a Document (through \ref ElementSet), - * in order to old the parsed entries of a Dicom header, is a recursive + * in order to hold 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 SQItem) add an extra complexity to the data