X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDataEntry.cxx;h=106310443eca7167723e73e1f45ff1da4ff8cdc3;hb=b06cbd9177331d793223eac6bf8b2bccf874e7e3;hp=cf6a3689d36bf28cdaa8aaf350a2a0d22b2fb0a5;hpb=42741e5f9bddec6ff604bffe74977848db3edf0a;p=gdcm.git diff --git a/src/gdcmDataEntry.cxx b/src/gdcmDataEntry.cxx index cf6a3689..10631044 100644 --- a/src/gdcmDataEntry.cxx +++ b/src/gdcmDataEntry.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDataEntry.cxx,v $ Language: C++ - Date: $Date: 2005/10/21 14:15:41 $ - Version: $Revision: 1.6 $ + Date: $Date: 2007/09/14 08:22:19 $ + Version: $Revision: 1.48 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -25,7 +25,13 @@ #include -namespace gdcm +#if defined(__BORLANDC__) + #include // for memcpy + #include // for atof + #include // for isdigit +#endif + +namespace GDCM_NAME_SPACE { //----------------------------------------------------------------------------- #define MAX_SIZE_PRINT_ELEMENT_VALUE 0x7fffffff @@ -34,15 +40,19 @@ uint32_t DataEntry::MaxSizePrintEntry = MAX_SIZE_PRINT_ELEMENT_VALUE; //----------------------------------------------------------------------------- // Constructor / Destructor /** - * \brief Constructor for a given DictEntry - * @param e Pointer to existing dictionary entry + * \brief Constructor for a given DataEntry + * @param group group number of the Data Entry to be created + * @param elem element number of the Data Entry to be created + * @param vr Value Representation of the Data Entry to be created */ -DataEntry::DataEntry(DictEntry *e) - : DocEntry(e) +DataEntry::DataEntry(uint16_t group,uint16_t elem, + VRKey const &vr) + : DocEntry(group,elem,vr) { State = STATE_LOADED; Flag = FLAG_NONE; + StrArea = 0; BinArea = 0; SelfArea = true; } @@ -52,10 +62,12 @@ DataEntry::DataEntry(DictEntry *e) * @param e Pointer to existing Doc entry */ DataEntry::DataEntry(DocEntry *e) - : DocEntry(e->GetDictEntry()) + //: DocEntry(e->GetDictEntry()) + : DocEntry(e->GetGroup(),e->GetElement(), e->GetVR() ) { - Flag = 0; + Flag = FLAG_NONE; BinArea = 0; + SelfArea = true; Copy(e); @@ -67,15 +79,18 @@ DataEntry::DataEntry(DocEntry *e) DataEntry::~DataEntry () { DeleteBinArea(); + } -//----------------------------------------------------------------------------- -// Print - //----------------------------------------------------------------------------- // Public /** - * \brief Sets the value (non string) of the current Dicom Header Entry + * \brief Sets the value (non string) of the current DataEntry + * @param area area + * @param self self=true : The area : *belongs" to the DataEntry + * : will be delete with the DataEntry + * self=false The area *is not* deleted with the DataEntry + * */ void DataEntry::SetBinArea( uint8_t *area, bool self ) { @@ -86,7 +101,11 @@ void DataEntry::SetBinArea( uint8_t *area, bool self ) State = STATE_LOADED; } - +/** + * \brief Inserts the value (non string) into the current DataEntry + * @param area area + * @param length length + */ void DataEntry::CopyBinArea( uint8_t *area, uint32_t length ) { DeleteBinArea(); @@ -99,13 +118,18 @@ void DataEntry::CopyBinArea( uint8_t *area, uint32_t length ) NewBinArea(); memcpy(BinArea,area,length); if( length!=lgh ) - BinArea[length]=0; + BinArea[length]=0; // padd with zero State = STATE_LOADED; } } -void DataEntry::SetValue(const uint32_t &id,const double &val) +/** + * \brief Inserts the elementary (non string) value into the current DataEntry + * @param id index of the elementary value to be set + * @param val value, passed as a double + */ +void DataEntry::SetValue(const uint32_t &id, const double &val) { if( !BinArea ) NewBinArea(); @@ -113,7 +137,7 @@ void DataEntry::SetValue(const uint32_t &id,const double &val) if( id > GetValueCount() ) { - gdcmErrorMacro("Index (" << id << ")is greater than the data size"); + gdcmErrorMacro("Index (" << id << ") is greater than the data size"); return; } @@ -147,23 +171,36 @@ void DataEntry::SetValue(const uint32_t &id,const double &val) BinArea[id] = (uint8_t)val; } } - +/** + * \brief returns, as a double one of the values + * (when entry is multivaluated), identified by its index. + * Returns 0.0 if index is wrong + * @param id id + */ double DataEntry::GetValue(const uint32_t &id) const { if( !BinArea ) { - gdcmErrorMacro("BinArea not set. Can't get the value"); - return 0; + if (GetLength() != 0) // avoid stupid messages + /// \todo warn the user there was a problem ! + gdcmErrorMacro("BinArea not set " << std::hex + << GetGroup() << " " << GetElement() + << " Can't get the value"); + return 0.0; } uint32_t count = GetValueCount(); if( id > count ) { - gdcmErrorMacro("Index (" << id << ")is greater than the data size"); - return 0; + gdcmErrorMacro("Index (" << id << ") is greater than the data size"); + return 0.0; } + // if user *knows* that entry contains a US, + // he just has to cast the double he receives + const VRKey &vr = GetVR(); + if( vr == "US" || vr == "SS" ) return ((uint16_t *)BinArea)[id]; else if( vr == "UL" || vr == "SL" ) @@ -174,10 +211,11 @@ double DataEntry::GetValue(const uint32_t &id) const return ((double *)BinArea)[id]; else if( Global::GetVR()->IsVROfStringRepresentable(vr) ) { + // this is for VR = "DS", ... if( GetLength() ) { // Don't use std::string to accelerate processing - double val = 0.0; + double val; char *tmp = new char[GetLength()+1]; memcpy(tmp,BinArea,GetLength()); tmp[GetLength()]=0; @@ -219,28 +257,72 @@ double DataEntry::GetValue(const uint32_t &id) const return BinArea[id]; } -bool DataEntry::IsValueCountValid() const +/** + * \brief Checks if the multiplicity of the value follows Dictionary VM + */ +bool DataEntry::IsValueCountValid() /*const*/ { uint32_t vm; - std::istringstream os; - os.str( GetVM() ); - os >> vm; - return vm == GetValueCount(); + const std::string &strVM = GetVM(); + uint32_t vc = GetValueCount(); + bool valid = vc == 0; + if( valid ) + return true; + + // FIXME : what shall we do with VM = "2-n", "3-n", etc + + if( strVM == "1-n" ) + { + // make sure there is at least one ??? FIXME + valid = vc >= 1; + } + else + { + std::istringstream os; + os.str( strVM ); + os >> vm; + // Two cases: + // vm respects the one from the dict + // vm is 0 (we need to check if this element is allowed to be empty) FIXME + + // note (JPR) + // ---- + // Entries whose type is 1 are mandatory, with a mandatory value. + // Entries whose type is 1c are mandatory-inside-a-Sequence, + // with a mandatory value. + // Entries whose type is 2 are mandatory, with an optional value. + // Entries whose type is 2c are mandatory-inside-a-Sequence, + // with an optional value. + // Entries whose type is 3 are optional. + + // case vc == 0 is only applicable for 'type 2' entries. + // Problem : entry type may depend on the modality and/or the Sequence + // it's embedded in ! + // (Get the information in the 'Conformance Statements' ...) + valid = vc == vm; + } + return valid; } -uint32_t DataEntry::GetValueCount(void) const +/** + * \brief returns the number of elementary values + */ +uint32_t DataEntry::GetValueCount( ) const { const VRKey &vr = GetVR(); if( vr == "US" || vr == "SS" ) return GetLength()/sizeof(uint16_t); else if( vr == "UL" || vr == "SL" ) return GetLength()/sizeof(uint32_t); - else if( vr == "FL" ) - return GetLength()/sizeof(float); + else if( vr == "FL" || vr == "OF" ) + return GetLength()/4 ; // FL has a *4* length! sizeof(float); else if( vr == "FD" ) - return GetLength()/sizeof(double); + return GetLength()/8; // FD has a *8* length! sizeof(double); else if( Global::GetVR()->IsVROfStringRepresentable(vr) ) { + // Some element in DICOM are allowed to be empty + if( !GetLength() ) + return 0; // Don't use std::string to accelerate processing uint32_t count = 1; for(uint32_t i=0;i &valueVector) + { + /// \todo rewrite the whole method, in order *not to use* std::string ! + std::vector tokens; + + if (GetVR() != "DS") // never trust a user ! + return false; + + Util::Tokenize ( GetString().c_str(), tokens, "\\" ); + + int nbValues= tokens.size(); + if (nbValues == 0) + return false; + + for (int loop=0; loop 0 ) - { - std::string finalVal = Util::DicomString( value.c_str() ); - SetLength(finalVal.size()); - NewBinArea(); - - memcpy(BinArea, &(finalVal[0]), finalVal.size()); - } + { + size_t l = value.size(); + SetLength(l + l%2); + NewBinArea(); + memcpy(BinArea, value.c_str(), l); + if (l%2) // padded with blank except for UI + if ( vr == "UI" ) + BinArea[l] = '\0'; + else + BinArea[l] = ' '; } State = STATE_LOADED; } - +/** + * \brief returns as a string (when possible) the value of the DataEntry + */ std::string const &DataEntry::GetString() const { - static std::ostringstream s; - const VRKey &vr = GetVR(); - - s.str(""); - StrArea=""; - - if( !BinArea ) - return StrArea; - - if( vr == "US" || vr == "SS" ) - { - uint16_t *data=(uint16_t *)BinArea; - - for (unsigned int i=0; i < GetValueCount(); i++) - { - if( i!=0 ) - s << '\\'; - s << data[i]; - } - StrArea=s.str(); - } - // See above comment on multiple integers (mutatis mutandis). - else if( vr == "UL" || vr == "SL" ) - { - uint32_t *data=(uint32_t *)BinArea; - - for (unsigned int i=0; i < GetValueCount(); i++) - { - if( i!=0 ) - s << '\\'; - s << data[i]; - } - StrArea=s.str(); - } - else if( vr == "FL" ) - { - float *data=(float *)BinArea; - - for (unsigned int i=0; i < GetValueCount(); i++) - { - if( i!=0 ) - s << '\\'; - s << data[i]; - } - StrArea=s.str(); - } - else if( vr == "FD" ) - { - double *data=(double *)BinArea; - - for (unsigned int i=0; i < GetValueCount(); i++) - { - if( i!=0 ) - s << '\\'; - s << data[i]; - } - StrArea=s.str(); - } - else - StrArea.append((const char *)BinArea,GetLength()); - - return StrArea; + static std::ostringstream s; + const VRKey &vr = GetVR(); + s.str(""); + + if (!StrArea) + StrArea = new std::string(); + else + *StrArea=""; + + if( !BinArea ) + return *StrArea; + // When short integer(s) are stored, convert the following (n * 2) characters + // as a displayable string, the values being separated by a back-slash + if( vr == "US" ) + { + uint16_t *data=(uint16_t *)BinArea; + for (unsigned int i=0; i < GetValueCount(); i++) + { + if( i!=0 ) + s << '\\'; + s << data[i]; + } + *StrArea=s.str(); + } + else if (vr == "SS" ) + { + int16_t *data=(int16_t *)BinArea; + for (unsigned int i=0; i < GetValueCount(); i++) + { + if( i!=0 ) + s << '\\'; + s << data[i]; + } + *StrArea=s.str(); + } // See above comment on multiple short integers (mutatis mutandis). + else if( vr == "UL" ) + { + uint32_t *data=(uint32_t *)BinArea; + for (unsigned int i=0; i < GetValueCount(); i++) + { + if( i!=0 ) + s << '\\'; + s << data[i]; + } + *StrArea=s.str(); + } + else if( vr == "SL" ) + { + int32_t *data=(int32_t *)BinArea; + for (unsigned int i=0; i < GetValueCount(); i++) + { + if( i!=0 ) + s << '\\'; + s << data[i]; + } + *StrArea=s.str(); + } else if( vr == "FL" ) + { + float *data=(float *)BinArea; + for (unsigned int i=0; i < GetValueCount(); i++) + { + if( i!=0 ) + s << '\\'; + s << data[i]; + } + *StrArea=s.str(); + } + else if( vr == "FD" ) + { + double *data=(double *)BinArea; + for (unsigned int i=0; i < GetValueCount(); i++) + { + if( i!=0 ) + s << '\\'; + s << data[i]; + } + *StrArea=s.str(); + } + else + { + StrArea->append((const char *)BinArea,GetLength()); + // to avoid gdcm to propagate oddities in lengthes + if ( GetLength()%2) + StrArea->append(" ",1); } + return *StrArea; } + +/** + * \brief Copies all the attributes from an other DocEntry + * @param doc entry to copy from + * @remarks The content BinArea is copied too (StrArea is not) + */ void DataEntry::Copy(DocEntry *doc) { DocEntry::Copy(doc); @@ -396,96 +537,132 @@ void DataEntry::Copy(DocEntry *doc) { State = entry->State; Flag = entry->Flag; - CopyBinArea(entry->BinArea,entry->GetLength()); + CopyBinArea(entry->BinArea,entry->GetLength()); } } -void DataEntry::WriteContent(std::ofstream *fp, FileType filetype) +/** + * \brief Writes the 'common part' + the 'value' area of a DataEntry + * @param fp already open ofstream pointer + * @param filetype type of the file (ACR, ImplicitVR, ExplicitVR, ...) + */ +void DataEntry::WriteContent(std::ofstream *fp, FileType filetype, + bool insideMetaElements, bool insideSequence) { - DocEntry::WriteContent(fp, filetype); + // writes the 'common part' + DocEntry::WriteContent(fp, filetype, insideMetaElements, insideSequence); if ( GetGroup() == 0xfffe ) { return; //delimitors have NO value } - - uint8_t *binArea8 = BinArea; //safe notation - size_t lgr = GetLength(); - if (BinArea) // the binArea was *actually* loaded - { - - // The same operation should be done if we wanted - // to write image with Big Endian Transfer Syntax, - // while working on Little Endian Processor + + // --> We only deal with Little Endian writting. // --> forget Big Endian Transfer Syntax writting! // Next DICOM version will give it up ... - - // --> FIXME - // The stuff looks nice, but it's probably bugged, - // since troubles occur on big endian processors (SunSparc, Motorola) - // while reading the pixels of a - // gdcm-written Little-Endian 16 bits per pixel image - + + // WARNING - For Implicit VR private element, + // we have *no choice* but considering them as + // something like 'OB' values. + // we rewrite them as we found them on disc. + // Some trouble will occur if element was + // *actually* OW, if image was produced + // on Big endian based processor, read and writen + // on Little endian based processor + // and, later on, somebody needs + // this 'OW' Implicit VR private element (?!?) + // (Same stuff, mutatis mutandis, for Little/Big) + + // 8/16 bits Pixels problem should be solved automatiquely, + // since we ensure the VR (OB vs OW) is conform to Pixel size. + + uint8_t *data = BinArea; //safe notation + size_t l = GetLength(); +// gdcmDebugMacro("in DataEntry::WriteContent " << GetKey() << " AtomicLength: " +// << Global::GetVR()->GetAtomicElementLength(this->GetVR() ) // << " BinArea in :" << &BinArea +// ); + if (BinArea) // the binArea was *actually* loaded + { #if defined(GDCM_WORDS_BIGENDIAN) || defined(GDCM_FORCE_BIGENDIAN_EMULATION) - - /// \todo FIXME : Right now, we only care of Pixels element - /// we should deal with *all* the BinEntries - /// Well, not really since we are not interpreting values read... - - // 8 Bits Pixels *are* OB, 16 Bits Pixels *are* OW - // -value forced while Reading process- - - // --> WARNING - // --> the following lines *looked* very clever, - // --> but they don't work on big endian processors. - // --> since I've no access for the moment to a big endian proc :-( - // --> I comment them out, to see the result on the dash board - // --> - - // --> Revert to initial code : TestWriteSimple hangs on Darwin :-( - if (GetGroup() == 0x7fe0 && GetVR() == "OW") - { - uint16_t *binArea16 = (uint16_t*)binArea8; - binary_write (*fp, binArea16, lgr ); - } - else - { - // For any other VR, DataEntry is re-written as-is - binary_write (*fp, binArea8, lgr ); + unsigned short vrLgth = + Global::GetVR()->GetAtomicElementLength(this->GetVR()); + unsigned int i; + switch(vrLgth) + { + case 1: + { + binary_write (*fp, data, l ); + break; + } + case 2: + { + uint16_t *data16 = (uint16_t *)data; + for(i=0;i WARNING - // --> remove the following line, an uncomment the previous ones, - // --> if it doesn't work better - // --> - /*binary_write ( *fp, binArea8, lgr ); // Elem value*/ - #else - binary_write ( *fp, binArea8, lgr ); // Elem value + binary_write (*fp, data, l ); #endif //GDCM_WORDS_BIGENDIAN + } else { - // nothing was loaded, but we need to skip space on disc - + // nothing was loaded, but we need to skip space on disc + if (l != 0) + { // --> WARNING : nothing is written; // --> the initial data (on the the source image) is lost - // --> user is *not* informed ! - - fp->seekp(lgr, std::ios::cur); + // --> user is *not* informed ! + gdcmDebugMacro ("Nothing was loaded, but we need to skip space on disc. " + << "Length =" << l << " for " << GetKey() ); + fp->seekp(l, std::ios::cur); // At Write time, for unloaded elems + } } + // to avoid gdcm to propagate oddities + // (length was already modified) + if (l%2) + fp->seekp(1, std::ios::cur); // At Write time, for non even length elems +} + +/** + * \brief Compute the full length of the elementary DataEntry (not only value + * length) depending on the VR. + */ +uint32_t DataEntry::ComputeFullLength() +{ + return GetFullLength(); } //----------------------------------------------------------------------------- // Protected -void DataEntry::NewBinArea(void) + +/// \brief Creates a DataEntry owned BinArea +/// (remove previous one if any and relevant StrArea if any) +void DataEntry::NewBinArea( ) { DeleteBinArea(); if( GetLength() > 0 ) BinArea = new uint8_t[GetLength()]; SelfArea = true; } - +/// \brief Removes the BinArea, if owned by the DataEntry, +/// and the relevant StrArea if any void DataEntry::DeleteBinArea(void) { if (BinArea && SelfArea) @@ -493,6 +670,11 @@ void DataEntry::DeleteBinArea(void) delete[] BinArea; BinArea = NULL; } + if (StrArea) + { + delete StrArea; + StrArea = 0; + } } //----------------------------------------------------------------------------- @@ -507,7 +689,9 @@ void DataEntry::DeleteBinArea(void) */ void DataEntry::Print(std::ostream &os, std::string const & ) { - os << "D "; + //os << "D "; + + // First, Print the common part (vr [length offset] name). DocEntry::Print(os); uint16_t g = GetGroup(); @@ -524,34 +708,40 @@ void DataEntry::Print(std::ostream &os, std::string const & ) v = GetString(); const VRKey &vr = GetVR(); - if( vr == "US" || vr == "SS" ) - s << " [" << GetString() << "]"; - else if( vr == "UL" || vr == "SL" ) - s << " [" << GetString() << "]"; - else if ( vr == "FL" ) - s << " [" << GetString() << "]"; - else if ( vr == "FD" ) + if( vr == "US" || vr == "SS" || vr == "UL" || vr == "SL" + || vr == "FL" || vr == "FD") s << " [" << GetString() << "]"; else { if(Global::GetVR()->IsVROfStringRepresentable(vr)) { - std::string cleanString = Util::CreateCleanString(v); // replace non printable characters by '.' + // replace non printable characters by '.' + std::string cleanString = Util::CreateCleanString(v); if ( cleanString.length() <= GetMaxSizePrintEntry() - || PrintLevel >= 3 - || IsNotLoaded() ) + || PrintLevel >= 3 + || IsNotLoaded() ) + // FIXME : when IsNotLoaded(), you create a Clean String ?!? + // FIXME : PrintLevel<2 *does* print the values + // (3 is only for extra offsets printing) + // What do you wanted to do ? JPR { s << " [" << cleanString << "]"; } else { - s << " [gdcm::too long for print (" << cleanString.length() << ") ]"; + s << " [GDCM_NAME_SPACE::too long for print (" << cleanString.length() << ") ]"; } } else { - if ( Util::IsCleanArea( GetBinArea(),GetLength() ) ) + // A lot of Private elements (with no VR) contain actually + // only printable characters; + // Let's deal with them as is they were VR std::string representable + + if ( Util::IsCleanArea( GetBinArea(), GetLength() ) ) { + // FIXME : since the 'Area' *is* clean, just use + // a 'CreateString' method, to save CPU time. std::string cleanString = Util::CreateCleanString( BinArea,GetLength() ); s << " [" << cleanString << "]";