X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=4577c5a0511f70bfa7302d01e6f2eee52a1ce8f8;hb=add6c88b334e9cf4ddb0ae1849f1380f9844f99c;hp=1c50ab555b50df2015b30e3f8a369d96717e7408;hpb=87f5ff9abfff1e2cb824083b999638ee2d9f415d;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 1c50ab55..4577c5a0 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2007/04/12 13:22:49 $ - Version: $Revision: 1.357 $ + Date: $Date: 2007/10/08 15:20:17 $ + Version: $Revision: 1.373 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -37,7 +37,7 @@ #include // for memset #endif -namespace gdcm +namespace GDCM_NAME_SPACE { //----------------------------------------------------------------------------- @@ -50,7 +50,7 @@ const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 /** * \brief This default constructor neither loads nor parses the file. - * You should then invoke \ref Document::Load. + * You should then invoke Document::Load. * */ Document::Document() @@ -70,6 +70,8 @@ Document::Document() LoadMode = LD_ALL; // default : load everything, later SetFileName(""); + changeFromUN=false; + UnexpectedEOF=false; } /** @@ -244,7 +246,7 @@ bool Document::DoTheLoadingDocumentJob( ) // Force Loading some more elements if user asked to. - gdcm::DocEntry *d; + GDCM_NAME_SPACE::DocEntry *d; for (ListElements::iterator it = UserForceLoadList.begin(); it != UserForceLoadList.end(); ++it) @@ -580,7 +582,7 @@ double Document::SwapDouble(double a) // // -----------------File I/O --------------- /** - * \brief Tries to open the file \ref Document::Filename and + * \brief Tries to open the file Document::Filename and * checks the preamble when existing, * or if the file starts with an ACR-NEMA look-like element. * @return The FILE pointer on success, 0 on failure. @@ -691,7 +693,7 @@ bool Document::CloseFile() * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) */ -void Document::WriteContent(std::ofstream *fp, FileType filetype) +void Document::WriteContent(std::ofstream *fp, FileType filetype, bool, bool) { // Skip if user wants to write an ACR-NEMA file @@ -719,8 +721,10 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) * --> was too much tricky / we were [in a hurry / too lazy] * --> We don't write the element 0x0000 (group length) */ - - ElementSet::WriteContent(fp, filetype); // This one is recursive + // This one is recursive + // false : outside MetaElements + // false : outside Sequence + ElementSet::WriteContent(fp, filetype, false, false); } // ----------------------------------------- @@ -849,7 +853,7 @@ void Document::LoadEntryBinArea(DataEntry *entry) //} /** - * \brief Compares two documents, according to \ref DicomDir rules + * \brief Compares two documents, according to DicomDir rules * \warning Does NOT work with ACR-NEMA files * \todo Find a trick to solve the pb (use RET fields ?) * @param document to compare with current one @@ -918,7 +922,7 @@ bool Document::operator<(Document &document) /** * \brief Reads a given length of bytes - * (in order to avoid to many CPU time consuming fread-s) + * (in order to avoid to many CPU time-consuming fread-s) * @param l length to read */ void Document::ReadBegBuffer(size_t l) @@ -1031,10 +1035,10 @@ int Document::ComputeGroup0002Length( ) vr = entry->GetVR(); //if ( (vr == "OB")||(vr == "OW")||(vr == "UT")||(vr == "SQ")) - // (no SQ, OW, UT in group 0x0002;) + // (no SQ, OW, OL, UT in group 0x0002;) if ( vr == "OB" ) { - // explicit VR AND (OB, OW, SQ, UT) : 4 more bytes + // explicit VR AND (OB, OW, OL, SQ, UT) : 4 more bytes groupLength += 4; } groupLength += 2 + 2 + 4 + entry->GetLength(); @@ -1282,11 +1286,11 @@ void Document::ParseDES(DocEntrySet *set, long offset, << " at offset 0x(" << std::hex << newDocEntry->GetOffset() << ")"); - ParseSQ( newSeqEntry, - newDocEntry->GetOffset(), - l, delim_mode_intern); + bool res = ParseSQ( newSeqEntry, + newDocEntry->GetOffset(), + l, delim_mode_intern); - gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern); + gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern << " -->return : " << res); } if ( !set->AddEntry( newSeqEntry ) ) { @@ -1318,15 +1322,18 @@ void Document::ParseDES(DocEntrySet *set, long offset, newDocEntry->Delete(); } first = false; + + if (UnexpectedEOF) // some terminator was missing + break; } // end While gdcmDebugMacro( "Exit from ParseDES, delim-mode " << delim_mode ); } /** * \brief Parses a Sequence ( SeqEntry after SeqEntry) - * @return parsed length for this level + * @return false if expected fff0,e000 not found */ -void Document::ParseSQ( SeqEntry *seqEntry, +bool Document::ParseSQ( SeqEntry *seqEntry, long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; @@ -1339,9 +1346,11 @@ void Document::ParseSQ( SeqEntry *seqEntry, DocEntry *newDocEntry = ReadNextDocEntry(); if ( !newDocEntry ) - { + { + // The most frequent is when a SQ terminator is missing (?!?) gdcmWarningMacro("in ParseSQ : should never get here!"); - break; + UnexpectedEOF = true; + return false; } if ( delim_mode ) { @@ -1389,6 +1398,7 @@ void Document::ParseSQ( SeqEntry *seqEntry, break; } } + return true; } /** @@ -1502,20 +1512,30 @@ void Document::FindDocEntryLength( DocEntry *entry ) { const VRKey &vr = entry->GetVR(); uint16_t length16; - if ( Filetype == ExplicitVR && !entry->IsImplicitVR() ) { - if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT" - || vr == "UN" ) + + // WARNING : + // + // For some images, length of UN elements is coded on 2 bytes (instead of 4) + // There are *not* readable ! + // You can make a quick and dirty patch, commenting out + //| vr == "UN" + // in the following line. + // (the 'straight' images will no longer be readable ...) + + if ( vr == "OB" || vr == "OW" || vr == "OL" || vr == "SQ" || vr == "UT" + || vr == "UN" || changeFromUN == true) { + changeFromUN = false; // 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::cur); // Once per OW,OB,SQ DocEntry - uint32_t length32 = ReadInt32(); // Once per OW,OB,SQ DocEntry + //Fp->seekg( 2L, std::ios::cur); // Once per OB,OW,OL,SQ DocEntry + uint32_t length32 = ReadInt32(); // Once per Ob,OW,OL,SQ DocEntry CurrentOffsetPosition+=4; - if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff ) + if ( (vr == "OB" || vr == "OW" || vr == "OL") && length32 == 0xffffffff ) { uint32_t lengthOB; try @@ -1549,11 +1569,9 @@ void Document::FindDocEntryLength( DocEntry *entry ) FixDocEntryFoundLength(entry, length32); return; } - // Length is encoded on 2 bytes. //length16 = ReadInt16(); length16 = GetInt16(); - // 0xffff means that we deal with 'No Length' Sequence // or 'No Length' SQItem if ( length16 == 0xffff) @@ -1603,7 +1621,8 @@ uint32_t Document::FindDocEntryLengthOBOrOW() uint16_t elem; try - { + { ///\todo make sure there is never OL encoded pixel data! + //group = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements //elem = ReadInt16(); // Once per fragment (if any) of OB,OW DataElements ReadBegBuffer(4); // Once per fragment (if any) of OB,OW DataElements @@ -2062,8 +2081,7 @@ bool Document::CheckSwap() s16 = *((uint16_t *)(deb)); gdcmDebugMacro("not a DicomV3 nor a 'clean' ACR/NEMA;" - << " (->despaired wild guesses !)"); - + << " (->despaired wild guesses !)"); switch ( s16 ) { case 0x0001 : @@ -2091,9 +2109,48 @@ bool Document::CheckSwap() Filetype = ACR; return true; default : - gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)"); - Filetype = Unknown; - return false; + + s16 = *((uint16_t *)(deb)); + if (s16 != 0x0000) + return false; + s16 = *((uint16_t *)(deb+2)); + + Fp->seekg ( 0L, std::ios::beg); // Once per Document + CurrentOffsetPosition = 0; + switch(s16) // try an other trick! + // -> to be able to decode 0029|1010 DataElement + // -> and be not less cleaver than dcmdump ;-) + { + case 0x0004 : + SwapCode = 1234; + break; + case 0x0400 : + SwapCode = 3412; + break; + default: + gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)"); + Filetype = Unknown; + return false; + } + // Check if next 2 bytes are a VR + // Probabely something more time-consuming exists with std::string + const char VRvalues[] = "AEASATCSDADTFLFDISLOLTPNSHSLSSSTTMUIULUSUTOBOWOLOFATUNSQRT"; + int nbVal = 29; + const char *pt = VRvalues; + for (int i=0;i= 0x0010 && CurrentElem <=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"; + // -> Better we fix the problem at Write time + + else if (CurrentGroup%2 == 1 ) + { + if (CurrentElem >= 0x0010 && CurrentElem <=0x00ff ) + // DICOM PS 3-5 7.8.1 a) states that : + // Private Creator Data Elements numbered (gggg,0010-00FF) (gggg is odd) + // attributes have to be LO (Long String) and the VM shall be equal to 1 + realVR = "LO"; + + // Seems not to be true + // Still in gdcmtk, David Clunnie disagrees, Marco Eichelberg says it's OK ... + // We let it for a while? + //(We should check length==4, for more security, but we don't have it yet !) + else if ( CurrentElem == 0x0001) + realVR = "UL"; // Private Group Length To End } - */ + else { DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);//only when ImplicitVR @@ -2214,6 +2280,26 @@ DocEntry *Document::ReadNextDocEntry() } } + // if UN found, let's check the dictionary, and trust it! + // (maybe a private dictionary exists?) + else if (vr == "UN") + { + DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem); + if ( dictEntry ) + { + realVR = dictEntry->GetVR(); + dictEntry->Unregister(); // GetDictEntry registered it + + // for VR = "UN", length is always stored on 4 bytes. + changeFromUN=true; + /// \todo : fixme If inside a supposed to be UN DataElement (but SQ according to a private dictionnary) + /// there is some more supposed to be UN DataElements, it will probabely fail. + /// --> find a -non time consuming- trick to store changeFromUN info at DataElement level, + /// not at the Document level. + } + } + + DocEntry *newEntry; //if ( Global::GetVR()->IsVROfSequence(realVR) ) if (realVR == "SQ")