From 7ad80376db5efb1b6f98e910a82886bf3cc68a26 Mon Sep 17 00:00:00 2001 From: jpr Date: Tue, 22 Mar 2005 11:29:37 +0000 Subject: [PATCH] * FIX : element 0x0000 of shadow groups is now force to a ValEntry, and it's VR is forced to UL * ENH : user id now allowed to tell he doesn't want to deal with Sequences and/or with Shadow groups use SetLoadMode (NO_SEQ | NO-SHADOW); --- src/gdcmDocument.cxx | 260 ++++++++++++++++++++----------------------- 1 file changed, 118 insertions(+), 142 deletions(-) diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 588e92ed..0147abbe 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2005/03/09 19:31:54 $ - Version: $Revision: 1.232 $ + Date: $Date: 2005/03/22 11:29:37 $ + Version: $Revision: 1.233 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -40,21 +40,69 @@ namespace gdcm // Refer to Document::SetMaxSizeLoadEntry() const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 -const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; //----------------------------------------------------------------------------- // Constructor / Destructor // Constructors and destructors are protected to avoid user to invoke directly + /** - * \brief constructor - * @param filename 'Document' (File or DicomDir) to be opened for parsing + * \brief This default constructor neither loads nor parses the file. + * You should then invoke \ref Document::SetFileName + * and \ref Document::Load. + * */ -Document::Document( std::string const &filename ) +Document::Document() :ElementSet(-1) { - SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - Filename = filename; + Fp = 0; + + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialize(); + SwapCode = 1234; + Filetype = ExplicitVR; + Group0002Parsed = false; + LoadMode = 0x00000000; // Load everything +} + +/** + * \brief Constructor (not to break the API) + * @param filename 'Document' (File or DicomDir) to be opened for parsing + */ +Document::Document( std::string const &filename ) + :ElementSet(-1) +{ + Fp = 0; + + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); + Initialize(); + SwapCode = 1234; + Filetype = ExplicitVR; + Group0002Parsed = false; + LoadMode = 0x00000000; // Load everything + + Load(filename); +} +/** + * \brief Canonical destructor. + */ +Document::~Document () +{ + RefPubDict = NULL; + RefShaDict = NULL; +} + +//----------------------------------------------------------------------------- +// Public + +/** + * \brief Loader + * @param filename 'Document' (File or DicomDir) to be opened for parsing + */ +void Document::Load( std::string const &filename ) +{ + Filename = filename; + + // We should clean out anything that already exists. Fp = 0; if ( !OpenFile() ) @@ -67,17 +115,18 @@ Document::Document( std::string const &filename ) gdcmWarningMacro( "Starting parsing of file: " << Filename.c_str()); Fp->seekg(0, std::ios::end); - long lgt = Fp->tellg(); - + long lgt = Fp->tellg(); // total length of the file + Fp->seekg(0, std::ios::beg); CheckSwap(); - long beg = Fp->tellg(); - lgt -= beg; - + long beg = Fp->tellg(); // just after DICOM preamble (if any) + + lgt -= beg; // remaining length to parse + ParseDES( this, beg, lgt, false); // Loading is done during parsing - Fp->seekg( 0, std::ios::beg); + Fp->seekg( 0, std::ios::beg); // Load 'non string' values @@ -141,33 +190,6 @@ Document::Document( std::string const &filename ) // --- End of ACR-LibIDO kludge --- } -/** - * \brief This default constructor doesn't parse the file. You should - * then invoke \ref Document::SetFileName and then the parsing. - */ -Document::Document() - :ElementSet(-1) -{ - Fp = 0; - - SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - Initialize(); - SwapCode = 1234; - Filetype = ExplicitVR; - Group0002Parsed = false; -} - -/** - * \brief Canonical destructor. - */ -Document::~Document () -{ - RefPubDict = NULL; - RefShaDict = NULL; -} - -//----------------------------------------------------------------------------- -// Public /** * \brief Get the public dictionary used */ @@ -766,7 +788,10 @@ void Document::Initialize() /** * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) - * @return length of the parsed set. + * @param set DocEntrySet we are going to parse ('zero level' or a SQItem) + * @param offset start of parsing + * @param l_max length to parse + * @param delim_mode : whether we are in 'delimitor mode' (l=0xffffff) or not */ void Document::ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode) @@ -839,6 +864,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, else { /////////////////////// ValEntry + // When "set" is a Document, then we are at the top of the // hierarchy and the Key is simply of the form ( group, elem )... if ( dynamic_cast< Document* > ( set ) ) @@ -856,10 +882,32 @@ void Document::ParseDES(DocEntrySet *set, long offset, LoadDocEntry( newValEntry ); bool delimitor=newValEntry->IsItemDelimitor(); + + if ( LoadMode & NO_SHADOW ) // User asked to skip, if possible, + // shadow groups ( if possible : + // whether element 0x0000 exits) + { + if ( newValEntry->GetGroup()%2 != 0 ) + { + if ( newValEntry->GetElement() == 0x0000 ) + { + std::string strLgrGroup = newValEntry->GetValue(); + int lgrGroup; + if ( strLgrGroup != GDCM_UNFOUND) + { + lgrGroup = atoi(strLgrGroup.c_str()); + Fp->seekg(lgrGroup , std::ios::cur); + used = false; + continue; + } + } + } + } + if( !set->AddEntry( newValEntry ) ) { // If here expect big troubles - //delete newValEntry; //otherwise mem leak + // delete newValEntry; //otherwise mem leak used=false; } @@ -883,7 +931,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, else { // VR = "SQ" - unsigned long l = newDocEntry->GetReadLength(); + unsigned long l = newDocEntry->GetReadLength(); if ( l != 0 ) // don't mess the delim_mode for zero-length sequence { if ( l == 0xffffffff ) @@ -895,6 +943,14 @@ void Document::ParseDES(DocEntrySet *set, long offset, delim_mode = false; } } + + if ( (LoadMode & NO_SEQ) && ! delim_mode ) // User asked to skip SQ + { + Fp->seekg( l, std::ios::cur); + used = false; + continue; + } + // no other way to create it ... newSeqEntry->SetDelimitorMode( delim_mode ); @@ -902,9 +958,8 @@ void Document::ParseDES(DocEntrySet *set, long offset, // is a Document, then we are building the first depth level. // Hence the SeqEntry we are building simply has a depth // level of one: - if (/*Document *dummy =*/ dynamic_cast< Document* > ( set ) ) + if ( dynamic_cast< Document* > ( set ) ) { - //(void)dummy; newSeqEntry->SetDepthLevel( 1 ); newSeqEntry->SetKey( newSeqEntry->GetKey() ); } @@ -928,6 +983,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, { used = false; } + if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) { if( !used ) @@ -1237,72 +1293,6 @@ void Document::FindDocEntryLength( DocEntry *entry ) // Length is encoded on 2 bytes. length16 = ReadInt16(); - - // FIXME : This heuristic supposes that the first group following - // group 0002 *has* and element 0000. - // BUT ... Element 0000 is optionnal :-( - - - // Fixed using : HandleOutOfGroup0002() - // (first hereafter strategy ...) - - // We can tell the current file is encoded in big endian (like - // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag - // and it's value is the one of the encoding of a big endian file. - // In order to deal with such big endian encoded files, we have - // (at least) two strategies: - // * when we load the "Transfer Syntax" tag with value of big endian - // encoding, we raise the proper flags. Then we wait for the end - // of the META group (0x0002) among which is "Transfer Syntax", - // before switching the swap code to big endian. We have to postpone - // the switching of the swap code since the META group is fully encoded - // in little endian, and big endian coding only starts at the next - // group. The corresponding code can be hard to analyse and adds - // many additional unnecessary tests for regular tags. - // * the second strategy consists in waiting for trouble, that shall - // appear when we find the first group with big endian encoding. This - // is easy to detect since the length of a "Group Length" tag (the - // ones with zero as element number) has to be of 4 (0x0004). When we - // encounter 1024 (0x0400) chances are the encoding changed and we - // found a group with big endian encoding. - //---> Unfortunately, element 0000 is optional. - //---> This will not work when missing! - // We shall use this second strategy. In order to make sure that we - // can interpret the presence of an apparently big endian encoded - // length of a "Group Length" without committing a big mistake, we - // add an additional check: we look in the already parsed elements - // for the presence of a "Transfer Syntax" whose value has to be "big - // endian encoding". When this is the case, chances are we have got our - // hands on a big endian encoded file: we switch the swap code to - // big endian and proceed... - -// if ( element == 0x0000 && length16 == 0x0400 ) -// { -// std::string ts = GetTransferSyntax(); -// if ( Global::GetTS()->GetSpecialTransferSyntax(ts) -// != TS::ExplicitVRBigEndian ) -// { -// throw FormatError( "Document::FindDocEntryLength()", -// " not explicit VR." ); -// return; -// } -// length16 = 4; -// SwitchByteSwapCode(); -// -// // Restore the unproperly loaded values i.e. the group, the element -// // and the dictionary entry depending on them. -// uint16_t correctGroup = SwapShort( entry->GetGroup() ); -// uint16_t correctElem = SwapShort( entry->GetElement() ); -// DictEntry *newTag = GetDictEntry( correctGroup, correctElem ); -// if ( !newTag ) -// { -// // This correct tag is not in the dictionary. Create a new one. -// newTag = NewVirtualDictEntry(correctGroup, correctElem); -// } -// // FIXME this can create a memory leaks on the old entry that be -// // left unreferenced. -// entry->SetDictEntry( newTag ); -// } // 0xffff means that we deal with 'No Length' Sequence // or 'No Length' SQItem @@ -1362,12 +1352,14 @@ uint32_t Document::FindDocEntryLengthOBOrOW() if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { long filePosition = Fp->tellg(); - gdcmWarningMacro( "Neither an Item tag nor a Sequence delimiter tag on :" + gdcmWarningMacro( + "Neither an Item tag nor a Sequence delimiter tag on :" << std::hex << group << " , " << elem << ") -before- position x(" << filePosition << ")" ); Fp->seekg(positionOnEntry, std::ios::beg); - throw FormatUnexpected( "Neither an Item tag nor a Sequence delimiter tag."); + throw FormatUnexpected( + "Neither an Item tag nor a Sequence delimiter tag."); } if ( elem == 0xe0dd ) { @@ -1665,10 +1657,10 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, */ bool Document::IsDocEntryAnInteger(DocEntry *entry) { - uint16_t elem = entry->GetElement(); - uint16_t group = entry->GetGroup(); - const std::string &vr = entry->GetVR(); - uint32_t length = entry->GetLength(); + uint16_t elem = entry->GetElement(); + uint16_t group = entry->GetGroup(); + const std::string &vr = entry->GetVR(); + uint32_t length = entry->GetLength(); // When we have some semantics on the element we just read, and if we // a priori know we are dealing with an integer, then we shall be @@ -1920,26 +1912,6 @@ void Document::SetMaxSizeLoadEntry(long newSize) MaxSizeLoadEntry = newSize; } -/** - * \brief Header Elements too long will not be printed - * See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE - * @param newSize new size - */ -void Document::SetMaxSizePrintEntry(long newSize) -{ - if ( newSize < 0 ) - { - return; - } - if ((uint32_t)newSize >= (uint32_t)0xffffffff ) - { - MaxSizePrintEntry = 0xffffffff; - return; - } - MaxSizePrintEntry = newSize; -} - - /** * \brief Read the next tag but WITHOUT loading it's value * (read the 'Group Number', the 'Element Number', @@ -1976,9 +1948,14 @@ DocEntry *Document::ReadNextDocEntry() if( vr == GDCM_UNKNOWN) { - DictEntry *dictEntry = GetDictEntry(group,elem); - if( dictEntry ) - realVR = dictEntry->GetVR(); + if ( elem == 0x0000 ) // Group Length + realVR = "UL"; // must be UL + else + { + DictEntry *dictEntry = GetDictEntry(group,elem); + if( dictEntry ) + realVR = dictEntry->GetVR(); + } } DocEntry *newEntry; @@ -2013,7 +1990,6 @@ DocEntry *Document::ReadNextDocEntry() catch ( FormatError e ) { // Call it quits - //std::cout << e; delete newEntry; return 0; } -- 2.45.1