X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=693d425e6ecf27530982d04c4e9ef331138f98fa;hb=a61fbd6eb8daabbe9a6df9ebc91300875dc1c560;hp=5f40b723e6d3ed4d141162ca360b947af9b3d0b0;hpb=f3cc252fad08c3e8dbc395f2ca7cabf47bf95302;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 5f40b723..693d425e 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 15:13:09 $ - Version: $Revision: 1.273 $ + Date: $Date: 2005/10/18 10:43:31 $ + Version: $Revision: 1.291 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -17,8 +17,6 @@ =========================================================================*/ #include "gdcmDocument.h" -#include "gdcmValEntry.h" -#include "gdcmBinEntry.h" #include "gdcmSeqEntry.h" #include "gdcmGlobal.h" #include "gdcmUtil.h" @@ -27,6 +25,7 @@ #include "gdcmDictSet.h" #include "gdcmDocEntrySet.h" #include "gdcmSQItem.h" +#include "gdcmDataEntry.h" #include #include @@ -51,7 +50,7 @@ const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 * */ Document::Document() - :ElementSet(-1) + :ElementSet() { Fp = 0; @@ -67,36 +66,12 @@ Document::Document() SetFileName(""); } -/** - * \brief Constructor (DEPRECATED : not to break the API) - * @param fileName 'Document' (File or DicomDir) to be open 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 = LD_ALL; // Load everything, later - - // Load will set it to true if sucessfull - IsDocumentAlreadyLoaded = false; - IsDocumentModified = true; - - SetFileName(fileName); - Load( ); -} /** * \brief Canonical destructor. */ Document::~Document () { - RefPubDict = NULL; - RefShaDict = NULL; + CloseFile(); } //----------------------------------------------------------------------------- @@ -138,21 +113,6 @@ bool Document::DoTheLoadingDocumentJob( ) if ( ! IsDocumentModified ) // Nothing to do ! return true; - // if ( Filename == fileName ) - // { - // gdcmWarningMacro( "The file was already parsed inside this " - // << "gdcm::Document (its name is: " - // << Filename.c_str() ); - // return true; - // } - - //gdcmWarningMacro( "A file was already parsed inside this " - // << "gdcm::Document (previous name was: " - // << Filename.c_str() << ". New name is :" - // << fileName ); - // clean out the Entries, if already parsed - // (probabely a mistake from the user) - ClearEntry(); Fp = 0; @@ -205,7 +165,7 @@ bool Document::DoTheLoadingDocumentJob( ) // Load 'non string' values - std::string PhotometricInterpretation = GetEntryValue(0x0028,0x0004); + std::string PhotometricInterpretation = GetEntryString(0x0028,0x0004); if ( PhotometricInterpretation == "PALETTE COLOR " ) { // FIXME @@ -218,16 +178,16 @@ bool Document::DoTheLoadingDocumentJob( ) /// defined as having an US Value Representation in the public /// dictionary. BUT the semantics implied by the three following /// lines state that the corresponding tag contents are in fact - /// the ones of a BinEntry. + /// the ones of a DataEntry. /// In order to fix things "Quick and Dirty" the dictionary was /// altered on PURPOSE but now contains a WRONG value. /// In order to fix things and restore the dictionary to its /// correct value, one needs to decided of the semantics by deciding /// whether the following tags are either : - /// - multivaluated US, and hence loaded as ValEntry, but afterwards - /// also used as BinEntry, which requires the proper conversion, - /// - OW, and hence loaded as BinEntry, but afterwards also used - /// as ValEntry, which requires the proper conversion. + /// - multivaluated US, and hence loaded as DataEntry, but afterwards + /// also used as DataEntry, which requires the proper conversion, + /// - OW, and hence loaded as DataEntry, but afterwards also used + /// as DataEntry, which requires the proper conversion. LoadEntryBinArea(0x0028,0x1201); // R LUT LoadEntryBinArea(0x0028,0x1202); // G LUT LoadEntryBinArea(0x0028,0x1203); // B LUT @@ -247,12 +207,12 @@ bool Document::DoTheLoadingDocumentJob( ) SQItem *sqi= modLutSeq->GetFirstSQItem(); if ( sqi != 0 ) { - BinEntry *b = sqi->GetBinEntry(0x0028,0x3006); - if ( b != 0 ) + DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006); + if ( dataEntry != 0 ) { - if ( b->GetLength() != 0 ) + if ( dataEntry->GetLength() != 0 ) { - LoadEntryBinArea(b); //LUT Data (CTX dependent) + LoadEntryBinArea(dataEntry); //LUT Data (CTX dependent) } } } @@ -265,28 +225,20 @@ 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) - continue; - - if ( dynamic_cast(d) ) { - LoadDocEntry(d, true); + gdcmWarningMacro( "You asked toForce Load " << std::hex + << (*it).Group <<"|"<< (*it).Elem + << " that doesn't exist" ); continue; } - if ( dynamic_cast(d) ) - { - LoadEntryBinArea((*it).Group, (*it).Elem); - continue; - } - - if ( dynamic_cast(d) ) - { - gdcmWarningMacro( "You cannot 'ForceLoad' a SeqEntry "); - continue; - } + LoadDocEntry(d, true); } CloseFile(); @@ -302,16 +254,16 @@ bool Document::DoTheLoadingDocumentJob( ) // we switch lineNumber and columnNumber // std::string RecCode; - RecCode = GetEntryValue(0x0008, 0x0010); // recognition code (RET) + RecCode = GetEntryString(0x0008, 0x0010); // recognition code (RET) if (RecCode == "ACRNEMA_LIBIDO_1.1" || RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { Filetype = ACR_LIBIDO; - std::string rows = GetEntryValue(0x0028, 0x0010); - std::string columns = GetEntryValue(0x0028, 0x0011); - SetValEntry(columns, 0x0028, 0x0010); - SetValEntry(rows , 0x0028, 0x0011); + std::string rows = GetEntryString(0x0028, 0x0010); + std::string columns = GetEntryString(0x0028, 0x0011); + SetEntryString(columns, 0x0028, 0x0010); + SetEntryString(rows , 0x0028, 0x0011); } // --- End of ACR-LibIDO kludge --- return true; @@ -447,9 +399,9 @@ std::string Document::GetTransferSyntax() // The entry might be present but not loaded (parsing and loading // happen at different stages): try loading and proceed with check... LoadDocEntrySafe(entry); - if (ValEntry *valEntry = dynamic_cast< ValEntry* >(entry) ) + if (DataEntry *dataEntry = dynamic_cast(entry) ) { - std::string transfer = valEntry->GetValue(); + std::string transfer = dataEntry->GetString(); // The actual transfer (as read from disk) might be padded. We // first need to remove the potential padding. We can make the // weak assumption that padding was not executed with digits... @@ -461,6 +413,11 @@ std::string Document::GetTransferSyntax() while ( !isdigit((unsigned char)transfer[transfer.length()-1]) ) { transfer.erase(transfer.length()-1, 1); + if ( transfer.length() == 0 ) + { + // for brain damaged headers + return GDCM_UNKNOWN; + } } return transfer; } @@ -474,7 +431,7 @@ std::string Document::GetTransferSyntax() std::string Document::GetTransferSyntaxName() { // use the TS (TS : Transfer Syntax) - std::string transferSyntax = GetEntryValue(0x0002,0x0010); + std::string transferSyntax = GetEntryString(0x0002,0x0010); if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) ) { @@ -595,14 +552,14 @@ 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 +595,14 @@ 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 ) { @@ -687,15 +639,21 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) { // Search the corresponding DocEntry - DocEntry *docElement = GetDocEntry(group, elem); - if ( !docElement ) + DocEntry *docEntry = GetDocEntry(group, elem); + if ( !docEntry ) + { + gdcmWarningMacro(std::hex << group << "|" << elem + << "doesn't exist" ); return; - - BinEntry *binElement = dynamic_cast(docElement); - if ( !binElement ) + } + DataEntry *dataEntry = dynamic_cast(docEntry); + if ( !dataEntry ) + { + gdcmWarningMacro(std::hex << group << "|" << elem + << "is NOT a DataEntry"); return; - - LoadEntryBinArea(binElement); + } + LoadEntryBinArea(dataEntry); } /** @@ -703,36 +661,70 @@ void Document::LoadEntryBinArea(uint16_t group, uint16_t elem) * when a string is not suitable * @param elem Entry whose binArea is going to be loaded */ -void Document::LoadEntryBinArea(BinEntry *elem) +void Document::LoadEntryBinArea(DataEntry *entry) { - if (elem->GetBinArea() ) + if( entry->GetBinArea() ) return; bool openFile = !Fp; if ( openFile ) OpenFile(); - size_t o =(size_t)elem->GetOffset(); + size_t o =(size_t)entry->GetOffset(); Fp->seekg(o, std::ios::beg); - size_t l = elem->GetLength(); - uint8_t *a = new uint8_t[l]; - if ( !a ) + size_t l = entry->GetLength(); + uint8_t *data = new uint8_t[l]; + if ( !data ) { - gdcmWarningMacro( "Cannot allocate BinEntry content for : " - << std::hex << elem->GetGroup() - << "|" << elem->GetElement() ); + gdcmWarningMacro( "Cannot allocate DataEntry content for : " + << std::hex << entry->GetGroup() + << "|" << entry->GetElement() ); return; } - Fp->read((char*)a, l); + // Read the datas + Fp->read((char*)data, l); if ( Fp->fail() || Fp->eof() ) { - delete[] a; + delete[] data; + entry->SetState(DataEntry::STATE_UNREAD); return; } - elem->SetBinArea(a); + // Swap the data content if necessary + uint32_t i; + unsigned short vrLgth = Global::GetVR()->GetAtomicElementLength(entry->GetVR()); + if( entry->GetVR() == "OW" ) + vrLgth = 1; + + switch(vrLgth) + { + case 2: + { + uint16_t *data16 = (uint16_t *)data; + for(i=0;iSetBinArea(data); if ( openFile ) CloseFile(); @@ -764,8 +756,8 @@ void Document::LoadDocEntrySafe(DocEntry *entry) bool Document::operator<(Document &document) { // Patient Name - std::string s1 = GetEntryValue(0x0010,0x0010); - std::string s2 = document.GetEntryValue(0x0010,0x0010); + std::string s1 = GetEntryString(0x0010,0x0010); + std::string s2 = document.GetEntryString(0x0010,0x0010); if (s1 < s2) { return true; @@ -777,8 +769,8 @@ bool Document::operator<(Document &document) else { // Patient ID - s1 = GetEntryValue(0x0010,0x0020); - s2 = document.GetEntryValue(0x0010,0x0020); + s1 = GetEntryString(0x0010,0x0020); + s2 = document.GetEntryString(0x0010,0x0020); if ( s1 < s2 ) { return true; @@ -790,8 +782,8 @@ bool Document::operator<(Document &document) else { // Study Instance UID - s1 = GetEntryValue(0x0020,0x000d); - s2 = document.GetEntryValue(0x0020,0x000d); + s1 = GetEntryString(0x0020,0x000d); + s2 = document.GetEntryString(0x0020,0x000d); if ( s1 < s2 ) { return true; @@ -803,8 +795,8 @@ bool Document::operator<(Document &document) else { // Serie Instance UID - s1 = GetEntryValue(0x0020,0x000e); - s2 = document.GetEntryValue(0x0020,0x000e); + s1 = GetEntryString(0x0020,0x000e); + s2 = document.GetEntryString(0x0020,0x000e); if ( s1 < s2 ) { return true; @@ -878,9 +870,8 @@ 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 +892,19 @@ 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(); } } @@ -945,13 +940,15 @@ void Document::ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode) { DocEntry *newDocEntry; - ValEntry *newValEntry; - BinEntry *newBinEntry; + DataEntry *newDataEntry; 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 +958,13 @@ void Document::ParseDES(DocEntrySet *set, long offset, newDocEntry = ReadNextDocEntry( ); + // FIXME : + // Private tag, in IMplicit VR are defaulted as a DataEntry, + // Very often they are only composed of Printable characters, + // and could be defaulted as a DataEntry. + // It's too late to do the Job + // (we should check the value, but we know it after LoadDocEntry ...) + // Uncoment this printf line to be able to 'follow' the DocEntries // when something *very* strange happens @@ -973,7 +977,7 @@ 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. @@ -987,123 +991,66 @@ void Document::ParseDES(DocEntrySet *set, long offset, } used = true; - newValEntry = dynamic_cast(newDocEntry); - newBinEntry = dynamic_cast(newDocEntry); + newDataEntry = dynamic_cast(newDocEntry); - if ( newValEntry || newBinEntry ) + if ( newDataEntry ) { - //////////////////////////// ContentEntry - if ( newBinEntry ) - { - vr = newDocEntry->GetVR(); - if ( Filetype == ExplicitVR && - !Global::GetVR()->IsVROfBinaryRepresentable(vr) ) - { - ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR - gdcmWarningMacro( std::hex << newDocEntry->GetGroup() - << "|" << newDocEntry->GetElement() - << " : Neither Valentry, nor BinEntry." - "Probably unknown VR."); - } - - //////////////////// BinEntry or UNKOWN VR: - - // When "this" is a Document the Key is simply of the - // form ( group, elem )... - //if ( set == this ) // ( dynamic_cast< Document* > ( set ) ) - //{ - // newBinEntry->SetKey( newBinEntry->GetKey() ); - //} - // but when "this" is a SQItem, we are inserting this new - // valEntry in a sequence item, and the key has the - // generalized form (refer to \ref BaseTagKey): + //////////////////////////// DataEntry + vr = newDocEntry->GetVR(); + if ( Filetype == ExplicitVR && + !Global::GetVR()->IsVROfBinaryRepresentable(vr) ) + { + ////// No DataEntry: should mean UNKOWN VR + gdcmWarningMacro( std::hex << newDocEntry->GetGroup() + << "|" << newDocEntry->GetElement() + << " : No DataEntry." + "Probably unknown VR."); + } - // time waste hunting - //if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) - //{ - // newBinEntry->SetKey( parentSQItem->GetBaseTagKey() - // + newBinEntry->GetKey() ); - //} - - if ( !set->AddEntry( newBinEntry ) ) - { - gdcmWarningMacro( "in ParseDES : cannot add a BinEntry " - << newBinEntry->GetKey() - << " (at offset : " - << newBinEntry->GetOffset() << " )" ); - used=false; - } - else - { - // Load only if we can add (not a duplicate key) - LoadDocEntry( newBinEntry ); - } - } // end BinEntry + if ( !set->AddEntry( newDataEntry ) ) + { + gdcmWarningMacro( "in ParseDES : cannot add a DataEntry " + << newDataEntry->GetKey() + << " (at offset : " + << newDataEntry->GetOffset() << " )" ); + used=false; + } 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 ( set == this ) // ( dynamic_cast< Document* > ( set ) ) - //{ - // newValEntry->SetKey( newValEntry->GetKey() ); - //} - // ...but when "set" is a SQItem, we are inserting this new - // valEntry in a sequence item. Hence the key has the - // generalized form (refer to \ref BaseTagKey): - - // time waste hunting - //if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) ) - //{ - // newValEntry->SetKey( parentSQItem->GetBaseTagKey() - // + newValEntry->GetKey() ); - //} - - if ( !set->AddEntry( newValEntry ) ) - { - gdcmWarningMacro( "in ParseDES : cannot add a ValEntry " - << newValEntry->GetKey() - << " (at offset : " - << newValEntry->GetOffset() << " )" ); - used=false; - } - else - { - // Load only if we can add (not a duplicate key) - LoadDocEntry( newValEntry ); - } + // Load only if we can add (not a duplicate key) + LoadDocEntry( newDataEntry ); + } - if ( newValEntry->GetElement() == 0x0000 ) // if on group length + if ( newDataEntry->GetElement() == 0x0000 ) // if on group length + { + if ( newDataEntry->GetGroup()%2 != 0 ) // if Shadow Group { - if ( newValEntry->GetGroup()%2 != 0 ) // if Shadow Group + if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr { - if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr + std::string strLgrGroup = newDataEntry->GetString(); + int lgrGroup; + if ( newDataEntry->IsUnfound() ) { - std::string strLgrGroup = newValEntry->GetValue(); - int lgrGroup; - if ( strLgrGroup != GDCM_UNFOUND) - { - lgrGroup = atoi(strLgrGroup.c_str()); - Fp->seekg(lgrGroup, std::ios::cur); - used = false; - RemoveEntry( newDocEntry ); - newDocEntry = 0; - continue; - } + lgrGroup = atoi(strLgrGroup.c_str()); + Fp->seekg(lgrGroup, std::ios::cur); + //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 = newDataEntry->IsItemDelimitor(); - if ( (delimitor) || - (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) - { - if ( !used ) - delete newDocEntry; - break; - } + if ( (delimitor) || + (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) ) + { + if ( !used ) + delete newDocEntry; + break; } // Just to make sure we are at the beginning of next entry. @@ -1132,7 +1079,8 @@ 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 +1088,8 @@ 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 +1123,17 @@ 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 +1144,7 @@ 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 +1158,7 @@ void Document::ParseDES(DocEntrySet *set, long offset, } first = false; } // end While + gdcmWarningMacro( "Exit from ParseDES, delim-mode " << delim_mode ); } /** @@ -1240,14 +1198,6 @@ void Document::ParseSQ( SeqEntry *seqEntry, } // create the current SQItem SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() ); -/* - std::ostringstream newBase; - newBase << seqEntry->GetKey() - << "/" - << SQItemNumber - << "#"; - itemSQ->SetBaseTagKey( newBase.str() ); -*/ unsigned int l = newDocEntry->GetReadLength(); if ( l == 0xffffffff ) @@ -1311,15 +1261,14 @@ DocEntry *Document::Backtrack(DocEntry *docEntry) Fp->seekg( 0, std::ios::beg); Fp->seekg(offset, std::ios::cur); -return newEntry; + 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) { @@ -1333,16 +1282,22 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) // (fffe e000) tells us an Element is beginning // (fffe e00d) tells us an Element just ended // (fffe e0dd) tells us the current SeQuence just ended - if ( group == 0xfffe ) + if ( group == 0xfffe || vr == "SQ" ) { // NO more value field for SQ ! return; } + DataEntry *dataEntryPtr = dynamic_cast< DataEntry* >(entry); + if( !dataEntryPtr ) + { + return; + } + // When the length is zero things are easy: if ( length == 0 ) { - ((ValEntry *)entry)->SetValue(""); + dataEntryPtr->SetBinArea(NULL,true); return; } @@ -1356,30 +1311,8 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) { if (length > MaxSizeLoadEntry) { - if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) ) - { - s << GDCM_NOTLOADED; - s << " Ad.:" << (long)entry->GetOffset(); - s << " x(" << std::hex << entry->GetOffset() << ")"; - s << std::dec; - s << " Lgt:" << entry->GetLength(); - s << " x(" << std::hex << entry->GetLength() << ")"; - binEntryPtr->SetValue(s.str()); - } - else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) ) - { - s << GDCM_NOTLOADED; - s << " Address:" << (long)entry->GetOffset(); - s << " Length:" << entry->GetLength(); - s << " x(" << std::hex << entry->GetLength() << ")"; - valEntryPtr->SetValue(s.str()); - } - else - { - // fusible - gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry " - << "nor a ValEntry ?! Should never print that !" ); - } + dataEntryPtr->SetBinArea(NULL,true); + dataEntryPtr->SetState(DataEntry::STATE_NOTLOADED); // to be sure we are at the end of the value ... Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(), @@ -1388,117 +1321,11 @@ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) } } - // When we find a BinEntry not very much can be done : - if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) ) - { - s << GDCM_BINLOADED; - binEntryPtr->SetValue(s.str()); - LoadEntryBinArea(binEntryPtr); // last one, not to erase length ! - return; - } - - if ( IsDocEntryAnInteger(entry) ) - { - uint32_t NewInt; - int nbInt; - // When short integer(s) are expected, read and convert the following - // (n * 2) characters properly i.e. consider them as short integers as - // opposed to strings. - // Elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - if (vr == "US" || vr == "SS") - { - nbInt = length / 2; - NewInt = ReadInt16(); - s << NewInt; - if (nbInt > 1) - { - for (int i=1; i < nbInt; i++) - { - s << '\\'; - NewInt = ReadInt16(); - s << NewInt; - } - } - } - // See above comment on multiple integers (mutatis mutandis). - else if (vr == "UL" || vr == "SL") - { - nbInt = length / 4; - NewInt = ReadInt32(); - s << NewInt; - if (nbInt > 1) - { - for (int i=1; i < nbInt; i++) - { - s << '\\'; - NewInt = ReadInt32(); - s << NewInt; - } - } - } -#ifdef GDCM_NO_ANSI_STRING_STREAM - s << std::ends; // to avoid oddities on Solaris -#endif //GDCM_NO_ANSI_STRING_STREAM - - ((ValEntry *)entry)->SetValue(s.str()); - return; - } - - // FIXME: We need an additional byte for storing \0 that is not on disk - char *str = new char[length+1]; - Fp->read(str, (size_t)length); - str[length] = '\0'; //this is only useful when length is odd - // Special DicomString call to properly handle \0 and even length - std::string newValue; - if ( length % 2 ) - { - newValue = Util::DicomString(str, length+1); - gdcmWarningMacro("Warning: bad length: " << length << - " For string :" << newValue.c_str()); - // Since we change the length of string update it length - //entry->SetReadLength(length+1); - } - else - { - newValue = Util::DicomString(str, length); - } - delete[] str; - - if ( ValEntry *valEntry = dynamic_cast(entry) ) - { - if ( Fp->fail() || Fp->eof()) - { - if ( Fp->fail() ) - gdcmWarningMacro("--> fail"); - - gdcmWarningMacro("Unread element value " << valEntry->GetKey() - << " lgt : " << valEntry->GetReadLength() - << " at " << std::hex << valEntry->GetOffset()); - valEntry->SetValue(GDCM_UNREAD); - return; - } - - if ( vr == "UI" ) - { - // Because of correspondance with the VR dic - valEntry->SetValue(newValue); - } - else - { - valEntry->SetValue(newValue); - } - } - else - { - gdcmWarningMacro("Should have a ValEntry, here ! " << valEntry->GetKey() - << " lgt : " << valEntry->GetReadLength() - << " at " << std::hex << valEntry->GetOffset()); - } + LoadEntryBinArea(dataEntryPtr); // last one, not to erase length ! } /** - * \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 +1336,8 @@ 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 +1359,9 @@ 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 +1503,7 @@ 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) @@ -1683,136 +1514,6 @@ bool Document::CheckDocEntryVR(VRKey vr) return true; } -/** - * \brief Get the transformed value of the header entry. The VR value - * is used to define the transformation to operate on the value - * \warning NOT end user intended method ! - * @param entry entry to tranform - * @return Transformed entry value - */ -std::string Document::GetDocEntryValue(DocEntry *entry) -{ - if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) - { - std::string val = ((ValEntry *)entry)->GetValue(); - std::string vr = entry->GetVR(); - uint32_t length = entry->GetLength(); - std::ostringstream s; - int nbInt; - - // When short integer(s) are expected, read and convert the following - // n * 2 bytes properly i.e. as a multivaluated strings - // (each single value is separated fromthe next one by '\' - // as usual for standard multivaluated filels - // Elements with Value Multiplicity > 1 - // contain a set of short integers (not a single one) - - if ( vr == "US" || vr == "SS" ) - { - uint16_t newInt16; - - nbInt = length / 2; - for (int i=0; i < nbInt; i++) - { - if ( i != 0 ) - { - s << '\\'; - } - newInt16 = ( val[2*i+0] & 0xFF ) + ( ( val[2*i+1] & 0xFF ) << 8); - newInt16 = SwapShort( newInt16 ); - s << newInt16; - } - } - - // When integer(s) are expected, read and convert the following - // n * 4 bytes properly i.e. as a multivaluated strings - // (each single value is separated fromthe next one by '\' - // as usual for standard multivaluated filels - // Elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - else if ( vr == "UL" || vr == "SL" ) - { - uint32_t newInt32; - - nbInt = length / 4; - for (int i=0; i < nbInt; i++) - { - if ( i != 0) - { - s << '\\'; - } - newInt32 = ( val[4*i+0] & 0xFF ) - + (( val[4*i+1] & 0xFF ) << 8 ) - + (( val[4*i+2] & 0xFF ) << 16 ) - + (( val[4*i+3] & 0xFF ) << 24 ); - newInt32 = SwapLong( newInt32 ); - s << newInt32; - } - } -#ifdef GDCM_NO_ANSI_STRING_STREAM - s << std::ends; // to avoid oddities on Solaris -#endif //GDCM_NO_ANSI_STRING_STREAM - return s.str(); - } - return ((ValEntry *)entry)->GetValue(); -} - -/** - * \brief Get the reverse transformed value of the header entry. The VR - * value is used to define the reverse transformation to operate on - * the value - * \warning NOT end user intended method ! - * @param entry Entry to reverse transform - * @return Reverse transformed entry value - */ -std::string Document::GetDocEntryUnvalue(DocEntry *entry) -{ - if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() ) - { - std::string vr = entry->GetVR(); - std::vector tokens; - std::ostringstream s; - - if ( vr == "US" || vr == "SS" ) - { - uint16_t newInt16; - - tokens.erase( tokens.begin(), tokens.end()); // clean any previous value - Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\"); - for (unsigned int i=0; i> 8 ) & 0xFF ); - } - tokens.clear(); - } - if ( vr == "UL" || vr == "SL") - { - uint32_t newInt32; - - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\"); - for (unsigned int i=0; i> 8 ) & 0xFF ) - << (char)(( newInt32 >> 16 ) & 0xFF ) - << (char)(( newInt32 >> 24 ) & 0xFF ); - } - tokens.clear(); - } - -#ifdef GDCM_NO_ANSI_STRING_STREAM - s << std::ends; // to avoid oddities on Solaris -#endif //GDCM_NO_ANSI_STRING_STREAM - return s.str(); - } - - return ((ValEntry *)entry)->GetValue(); -} - /** * \brief Skip a given Header Entry * \warning NOT end user intended method ! @@ -2158,7 +1859,7 @@ 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 +1892,7 @@ 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 +1926,7 @@ 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 +1946,15 @@ 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); @@ -2259,10 +1968,11 @@ DocEntry *Document::ReadNextDocEntry() DocEntry *newEntry; if ( Global::GetVR()->IsVROfSequence(realVR) ) newEntry = NewSeqEntry(group, elem); - else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) ) - newEntry = NewValEntry(group, elem,vr); - else - newEntry = NewBinEntry(group, elem,vr); + else + { + newEntry = NewDataEntry(group, elem, realVR); + static_cast(newEntry)->SetState(DataEntry::STATE_NOTLOADED); + } if ( vr == GDCM_UNKNOWN ) { @@ -2286,7 +1996,7 @@ DocEntry *Document::ReadNextDocEntry() { FindDocEntryLength(newEntry); } - catch ( FormatError e ) + catch ( FormatError ) { // Call it quits delete newEntry; @@ -2324,6 +2034,22 @@ 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." ); + } } /** @@ -2347,7 +2073,7 @@ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) return; } - // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..." + // Group 0002 is always 'Explicit ...' even when Transfer Syntax says 'Implicit ..." if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian ) { @@ -2355,7 +2081,10 @@ void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem) } // FIXME Strangely, this works with - //'Implicit VR Transfer Syntax (GE Private) + //'Implicit VR BigEndian Transfer Syntax (GE Private) + // + // --> Probabely normal, since we considered we never have to trust manufacturers. + // (we find very often 'Implicit VR' tag, even when Transfer Syntax tells us it's Explicit ... if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian ) { gdcmWarningMacro("Transfer Syntax Name = ["