X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=8896d14d0fe73c9b7cb730984dfedc78f6b85c85;hb=21d241b3fdcf675d8d91a6daf6dfd6f448b68195;hp=51c8cbf86bd95d9e9d025bd3edda0e4eb365be79;hpb=c4fa2e74a4ce56a0a8db54e4a70d404bec9fc8dd;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 51c8cbf8..8896d14d 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2005/08/30 14:40:33 $ - Version: $Revision: 1.272 $ + Date: $Date: 2005/10/10 10:49:24 $ + Version: $Revision: 1.286 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -63,7 +63,7 @@ Document::Document() Group0002Parsed = false; IsDocumentAlreadyLoaded = false; IsDocumentModified = true; - LoadMode = GDCM_LD_ALL; // default : load everything, later + LoadMode = LD_ALL; // default : load everything, later SetFileName(""); } @@ -81,7 +81,7 @@ Document::Document( std::string const &fileName ) SwapCode = 1234; Filetype = ExplicitVR; Group0002Parsed = false; - LoadMode = GDCM_LD_ALL; // Load everything, later + LoadMode = LD_ALL; // Load everything, later // Load will set it to true if sucessfull IsDocumentAlreadyLoaded = false; @@ -95,8 +95,7 @@ Document::Document( std::string const &fileName ) */ Document::~Document () { - RefPubDict = NULL; - RefShaDict = NULL; + CloseFile(); } //----------------------------------------------------------------------------- @@ -265,26 +264,37 @@ bool Document::DoTheLoadingDocumentJob( ) it != UserForceLoadList.end(); ++it) { + gdcmWarningMacro( "Force Load " << std::hex + << (*it).Group << "|" <<(*it).Elem ); + d = GetDocEntry( (*it).Group, (*it).Elem); - + if ( d == NULL) + { + gdcmWarningMacro( "You asked toForce Load " << std::hex + << (*it).Group <<"|"<< (*it).Elem + << " that doesn't exist" ); continue; + } - if ( dynamic_cast(d) ) + if ( dynamic_cast(d) ) { LoadDocEntry(d, true); continue; } - if ( dynamic_cast(d) ) + BinEntry *b = dynamic_cast(d); + if ( b ) { - LoadEntryBinArea((*it).Group, (*it).Elem); + LoadEntryBinArea(b); + b->SetValue(GDCM_BINLOADED); continue; } if ( dynamic_cast(d) ) { - gdcmWarningMacro( "You cannot 'ForceLoad' a SeqEntry "); + gdcmWarningMacro( "You cannot 'ForceLoad' a SeqEntry :" << std::hex + << (*it).Group <<"|"<< (*it).Elem ); continue; } } @@ -595,14 +605,14 @@ std::ifstream *Document::OpenFile() zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 ) { std::string msg = Util::Format( - "ACR/DICOM starting at the begining of the file:(%04x)\n", zero); + "ACR/DICOM starting at the beginning of the file:(%04x)\n", zero); gdcmWarningMacro( msg.c_str() ); return Fp; } //-- DICOM -- Fp->seekg(126L, std::ios::cur); - char dicm[4] = {' ',' ',' ',' '}; + char dicm[4]; // = {' ',' ',' ',' '}; Fp->read(dicm, (size_t)4); if ( Fp->eof() ) { @@ -638,19 +648,14 @@ bool Document::CloseFile() } /** - * \brief Writes in a file all the Header Entries (Dicom Elements) + * \brief Writes in a file all the Entries (Dicom Elements) * @param fp file pointer on an already open file (actually: Output File Stream) * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) - * @return Always true. */ 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 + // Skip if user wants to write an ACR-NEMA file if ( filetype == ImplicitVR || filetype == ExplicitVR ) { @@ -689,12 +694,18 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) // Search the corresponding DocEntry DocEntry *docElement = GetDocEntry(group, elem); if ( !docElement ) + { + gdcmWarningMacro(std::hex << group << "|" << elem + << "doesn't exist" ); return; - + } BinEntry *binElement = dynamic_cast(docElement); if ( !binElement ) + { + gdcmWarningMacro(std::hex << group << "|" << elem + << "is NOT a BinEntry"); return; - + } LoadEntryBinArea(binElement); } @@ -878,9 +889,8 @@ void Document::SkipBytes(uint32_t nBytes) /** * \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 ) +int Document::ComputeGroup0002Length( /*FileType filetype*/ ) { uint16_t gr; std::string vr; @@ -901,15 +911,19 @@ int Document::ComputeGroup0002Length( FileType filetype ) if ( entry->GetElement() != 0x0000 ) { vr = entry->GetVR(); + + // FIXME : group 0x0002 is *always* Explicit VR! - if ( filetype == ExplicitVR ) - { - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || (vr == "UT") ) + //if ( filetype == ExplicitVR ) + //{ + // if ( (vr == "OB") || (vr == "OW") || (vr == "UT") || (vr == "SQ") ) + // (no SQ, OW, UT in group 0x0002;) + if ( vr == "OB" ) { // explicit VR AND OB, OW, SQ, UT : 4 more bytes groupLength += 4; } - } + //} groupLength += 2 + 2 + 4 + entry->GetLength(); } } @@ -949,9 +963,12 @@ void Document::ParseDES(DocEntrySet *set, long offset, BinEntry *newBinEntry; SeqEntry *newSeqEntry; VRKey vr; - bool used; + bool used; // will be set to false when something wrong happens to an Entry. + // (Entry will then be deleted) bool delim_mode_intern = delim_mode; bool first = true; + gdcmWarningMacro( "Enter in ParseDES, delim-mode " << delim_mode + << " at offset " << std::hex << offset ); while (true) { if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) @@ -961,6 +978,14 @@ void Document::ParseDES(DocEntrySet *set, long offset, newDocEntry = ReadNextDocEntry( ); + // FIXME : + // Private tag, in IMplicit VR are defaulted as a BinEntry, + // Very often they are only composed of Printable characters, + // and could be defaulted as a ValEntry. + // It's too late to do the Job + // (we should check the value, but we know it after LoadDocEntry ...) + // --> in next gdcm major release let's unify ValEntry and BinEntry ! + // Uncoment this printf line to be able to 'follow' the DocEntries // when something *very* strange happens @@ -973,7 +998,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, break; } - // an Item Starter found elsewhere but the first postition + // an Item Starter found elsewhere but the first position // of a SeqEntry means previous entry was a Sequence // but we didn't get it (private Sequence + Implicit VR) // we have to backtrack. @@ -1086,16 +1111,17 @@ void Document::ParseDES(DocEntrySet *set, long offset, { lgrGroup = atoi(strLgrGroup.c_str()); Fp->seekg(lgrGroup, std::ios::cur); - used = false; - RemoveEntry( newDocEntry ); - newDocEntry = 0; + //used = false; // never used + RemoveEntry( newDocEntry ); // Remove and delete + // bcc 5.5 is right "assigned a value that's never used" + // newDocEntry = 0; continue; } } } } - bool delimitor=newValEntry->IsItemDelimitor(); + bool delimitor = newValEntry->IsItemDelimitor(); if ( (delimitor) || (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) @@ -1132,7 +1158,8 @@ void Document::ParseDES(DocEntrySet *set, long offset, if ( newDocEntry->GetGroup()%2 != 0 ) { Fp->seekg( l, std::ios::cur); - used = false; + RemoveEntry( newDocEntry ); // Remove and delete + //used = false; // never used continue; } } @@ -1140,7 +1167,8 @@ void Document::ParseDES(DocEntrySet *set, long offset, { // User asked to skip *any* SeQuence Fp->seekg( l, std::ios::cur); - used = false; + //used = false; // never used + RemoveEntry( newDocEntry ); // Remove and delete continue; } // delay the dynamic cast as late as possible @@ -1174,9 +1202,17 @@ void Document::ParseDES(DocEntrySet *set, long offset, if ( l != 0 ) { // Don't try to parse zero-length sequences + + gdcmWarningMacro( "Entry in ParseSQ, delim " << delim_mode_intern + << " at offset " << std::hex + << newDocEntry->GetOffset() ); + ParseSQ( newSeqEntry, newDocEntry->GetOffset(), l, delim_mode_intern); + + gdcmWarningMacro( "Exit from ParseSQ, delim " << delim_mode_intern); + } if ( !set->AddEntry( newSeqEntry ) ) { @@ -1187,7 +1223,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, used = false; } - if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { if ( !used ) delete newDocEntry; @@ -1201,6 +1237,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, } first = false; } // end While + gdcmWarningMacro( "Exit from ParseDES, delim-mode " << delim_mode ); } /** @@ -1318,8 +1355,7 @@ return newEntry; * \brief Loads (or not) the element content depending if its length exceeds * or not the value specified with Document::SetMaxSizeLoadEntry() * @param entry Header Entry (Dicom Element) to be dealt with - * @param forceLoad wheter we want to load its content even if its length - * exceeds the value specified with Document::SetMaxSizeLoadEntry() + * @param forceLoad whether you want to force loading of 'long' elements */ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) { @@ -1498,7 +1534,7 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) } /** - * \brief Find the value Length of the passed Header Entry + * \brief Find the value Length of the passed Doc Entry * @param entry Header Entry whose length of the value shall be loaded. */ void Document::FindDocEntryLength( DocEntry *entry ) @@ -1509,7 +1545,8 @@ void Document::FindDocEntryLength( DocEntry *entry ) if ( Filetype == ExplicitVR && !entry->IsImplicitVR() ) { - if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT" || vr == "UN" ) + if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT" + /*|| vr == "UN"*/ ) { // The following reserved two bytes (see PS 3.5-2003, section // "7.1.2 Data element structure with explicit vr", p 27) must be @@ -1531,6 +1568,9 @@ void Document::FindDocEntryLength( DocEntry *entry ) // chance to get the pixels by deciding the element goes // until the end of the file. Hence we artificially fix the // the length and proceed. + gdcmWarningMacro( " Computing the length failed for " << + entry->GetKey() <<" in " <tellg(); Fp->seekg(0L,std::ios::end); @@ -1672,7 +1712,7 @@ std::string Document::FindDocEntryVR() * and the taken VR. If they are different, the header entry is * updated with the new VR. * @param vr Dicom Value Representation - * @return false if the VR is incorrect of if the VR isn't referenced + * @return false if the VR is incorrect or if the VR isn't referenced * otherwise, it returns true */ bool Document::CheckDocEntryVR(VRKey vr) @@ -2158,7 +2198,7 @@ bool Document::CheckSwap() Filetype = ACR; return true; default : - gdcmWarningMacro( "ACR/NEMA unfound swap info (Really hopeless !)"); + gdcmWarningMacro("ACR/NEMA unfound swap info (Really hopeless !)"); Filetype = Unknown; return false; } @@ -2191,7 +2231,7 @@ void Document::SwitchByteSwapCode() } /** - * \brief during parsing, Header Elements too long are not loaded in memory + * \brief during parsing, Header Elements too long are not loaded in memory * @param newSize new size */ void Document::SetMaxSizeLoadEntry(long newSize) @@ -2225,7 +2265,7 @@ DocEntry *Document::ReadNextDocEntry() group = ReadInt16(); elem = ReadInt16(); } - catch ( FormatError e ) + catch ( FormatError ) { // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. @@ -2245,7 +2285,15 @@ DocEntry *Document::ReadNextDocEntry() if ( vr == GDCM_UNKNOWN ) { if ( elem == 0x0000 ) // Group Length + { realVR = "UL"; // must be UL + } + else if (group%2 == 1 && (elem >= 0x0010 && elem <=0x00ff )) + { + // DICOM PS 3-5 7.8.1 a) states that those + // (gggg-0010->00FF where gggg is odd) attributes have to be LO + realVR = "LO"; + } else { DictEntry *dictEntry = GetDictEntry(group,elem); @@ -2260,9 +2308,9 @@ DocEntry *Document::ReadNextDocEntry() if ( Global::GetVR()->IsVROfSequence(realVR) ) newEntry = NewSeqEntry(group, elem); else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) ) - newEntry = NewValEntry(group, elem,vr); + newEntry = NewValEntry(group, elem, realVR); else - newEntry = NewBinEntry(group, elem,vr); + newEntry = NewBinEntry(group, elem, realVR); if ( vr == GDCM_UNKNOWN ) { @@ -2286,7 +2334,7 @@ DocEntry *Document::ReadNextDocEntry() { FindDocEntryLength(newEntry); } - catch ( FormatError e ) + catch ( FormatError ) { // Call it quits delete newEntry; @@ -2324,6 +2372,22 @@ void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) reversedEndian--; SwitchByteSwapCode(); } + else if (group == 0xfeff && elem == 0xdde0) + { + // reversed Sequence Terminator found + // probabely a bug in the header ! + // Do what you want, it breaks ! + //reversedEndian--; + //SwitchByteSwapCode(); + gdcmWarningMacro( "Should never get here! reversed Sequence Terminator!" ); + // fix the tag + group = 0xfffe; + elem = 0xe0dd; + } + else if (group == 0xfffe && elem == 0xe0dd) + { + gdcmWarningMacro( "Straight Sequence Terminator." ); + } } /**