X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=e5e627e436fe4b9390379491fc5f5c4a84e05339;hb=99ac30f10909a566e9506776d33dfacc300d4502;hp=c5d391396cc11c60b7b040b24e07c9d19869ce90;hpb=0b01703cc07d46a6ae718e01c6beee14599a9da1;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index c5d39139..e5e627e4 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/11/24 11:17:47 $ - Version: $Revision: 1.136 $ + Date: $Date: 2004/12/10 13:49:07 $ + Version: $Revision: 1.150 $ 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 @@ -36,6 +43,7 @@ namespace gdcm { +//----------------------------------------------------------------------------- static const char *TransferSyntaxStrings[] = { // Implicit VR Little Endian "1.2.840.10008.1.2", @@ -70,10 +78,10 @@ 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 @@ -100,19 +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 @@ -410,7 +418,11 @@ FileType Document::GetFileType() */ std::ifstream* Document::OpenFile() { - if (Filename.length() == 0) return 0; + if (Filename.length() == 0) + { + return 0; + } + if(Fp) { dbg.Verbose( 0, @@ -419,17 +431,23 @@ 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( @@ -442,9 +460,14 @@ 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; @@ -481,41 +504,22 @@ 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 @@ -528,8 +532,7 @@ 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 } /** @@ -668,6 +671,7 @@ BinEntry* Document::ReplaceOrCreateByNumber( dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); } + delete currentEntry; } else { @@ -757,6 +761,11 @@ bool Document::ReplaceIfExistByNumber(std::string const & value, return true; } +std::string Document::GetTransferSyntaxValue(TransferSyntaxType type) +{ + return TransferSyntaxStrings[type]; +} + //----------------------------------------------------------------------------- // Protected @@ -830,7 +839,6 @@ 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; @@ -910,9 +918,6 @@ 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 ) { @@ -921,30 +926,7 @@ bool Document::SetEntryByNumber(std::string const& content, 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); + valEntry->SetValue(content); return true; } @@ -982,53 +964,6 @@ bool Document::SetEntryByNumber(uint8_t*content, int lgth, return true; } -/** - * \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. - */ -bool Document::SetEntryLengthByNumber(uint32_t l, - uint16_t group, uint16_t element) -{ - /// \todo use map methods, instead of multimap JPR - TagKey key = DictEntry::TranslateToKey(group, element); - if ( !TagHT.count(key) ) - { - return false; - } - if ( l % 2 ) - { - l++; // length must be even - } - ( ((TagHT.equal_range(key)).first)->second )->SetLength(l); - - return true ; -} - -/** - * \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 - */ -size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem) -{ - DocEntry* entry = GetDocEntryByNumber(group, elem); - if (!entry) - { - dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present."); - return 0; - } - return entry->GetOffset(); -} - /** * \brief Gets (from Header) a 'non string' element value * (LoadElementValues has already be executed) @@ -1070,30 +1005,6 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) return; LoadEntryBinArea(binElement); -/* 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; - return; - } - - // Set the value to the DocEntry - if( !SetEntryBinAreaByNumber( a, group, elem ) ) - { - delete[] a; - dbg.Verbose(0, "Document::LoadEntryBinArea setting failed."); - }*/ } /** @@ -1103,12 +1014,15 @@ 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]; @@ -1139,7 +1053,7 @@ 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); @@ -1155,7 +1069,7 @@ bool Document::SetEntryBinAreaByNumber(uint8_t* area, } return false; -} +}*/ /** * \brief Update the entries with the shadow dictionary. @@ -1274,9 +1188,12 @@ 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); + } } /** @@ -1422,9 +1339,6 @@ 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 @@ -1458,16 +1372,16 @@ 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 ); } } @@ -1606,7 +1520,7 @@ 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 @@ -1660,7 +1574,7 @@ 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; } @@ -1788,7 +1702,7 @@ 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 ) @@ -1808,9 +1722,9 @@ 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; } @@ -1922,13 +1836,12 @@ 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. - Fp->read (vr, (size_t)2); vr[2] = 0; 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 @@ -2173,8 +2086,8 @@ 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); } /** @@ -2342,7 +2255,7 @@ 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."); @@ -2363,7 +2276,7 @@ uint32_t Document::FindDocEntryLengthOB() break; } } - Fp->seekg( positionOnEntry, std::ios_base::beg); + Fp->seekg( positionOnEntry, std::ios::beg); return totalLength; } @@ -2419,7 +2332,7 @@ 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); } /** @@ -2432,6 +2345,7 @@ void Document::Initialise() RefShaDict = NULL; RLEInfo = new RLEFramesInfo; JPEGInfo = new JPEGFragmentsInfo; + Filetype = Unknown; } /** @@ -2454,7 +2368,7 @@ 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). @@ -2469,7 +2383,7 @@ 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 ) @@ -2533,8 +2447,8 @@ 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 @@ -2542,7 +2456,7 @@ 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. @@ -2554,7 +2468,7 @@ bool Document::CheckSwap() // representation of a 32 bits integer. Hence the following dirty // trick : s32 = *((uint32_t *)(entCur)); - + switch( s32 ) { case 0x00040000 : @@ -2725,7 +2639,6 @@ void Document::HandleBrokenEndian(uint16_t group, uint16_t elem) reversedEndian--; SwitchSwapToBigEndian(); } - } /** @@ -2837,7 +2750,7 @@ 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; }