X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmDocument.cxx;h=5b79c5f8dca126fa23f51cc451fbce1e1e995ff3;hb=14900333988858a95935ec735224433cf308c21c;hp=834a3d1ee13b168e63cf21c765698512da512624;hpb=2012716d624d631dcdb825fdd4470908e115a717;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 834a3d1e..5b79c5f8 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/06/20 18:08:47 $ - Version: $Revision: 1.19 $ + Date: $Date: 2004/07/16 15:18:05 $ + Version: $Revision: 1.49 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -66,7 +66,7 @@ #define UI1_2_840_10008_1_2_4_91 "1.2.840.10008.1.2.4.91" // RLE Lossless #define UI1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5" - +// UI1_1_2_840_10008_1_2_5 #define str2num(str, typeNum) *((typeNum *)(str)) //----------------------------------------------------------------------------- @@ -74,9 +74,8 @@ const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256; // Refer to gdcmDocument::SetMaxSizeLoadEntry() -const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096; - -const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; +const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096 +const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; //----------------------------------------------------------------------------- // Constructor / Destructor @@ -95,23 +94,25 @@ const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; * with a FALSE value for the 'enable_sequence' param. * ('public elements' may be embedded in 'shadow Sequences') */ -gdcmDocument::gdcmDocument(const char *inFilename, - bool exception_on_error, - bool enable_sequences, - bool ignore_shadow) - : gdcmElementSet(-1) { - enableSequences=enable_sequences; - ignoreShadow =ignore_shadow; - +gdcmDocument::gdcmDocument(std::string const & inFilename, + bool exception_on_error, + bool enable_sequences, + bool ignore_shadow) + : gdcmElementSet(-1) +{ + IgnoreShadow = ignore_shadow; + //enableSequences=enable_sequences; + (void)enable_sequences; + enableSequences = true; // JPR // TODO : remove params out of the constructor SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); - filename = inFilename; + Filename = inFilename; Initialise(); if ( !OpenFile(exception_on_error)) return; dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ", - filename.c_str()); + Filename.c_str()); rewind(fp); fseek(fp,0L,SEEK_END); @@ -125,6 +126,27 @@ gdcmDocument::gdcmDocument(const char *inFilename, SQDepthLevel=0; long l=ParseDES( this, beg, lgt, false); // le Load sera fait a la volee + (void)l; //is l used anywhere ? + + rewind(fp); + + // Load 'non string' values + + std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); + if( PhotometricInterpretation == "PALETTE COLOR " ) + { + LoadEntryVoidArea(0x0028,0x1200); // gray LUT + LoadEntryVoidArea(0x0028,0x1201); // R LUT + LoadEntryVoidArea(0x0028,0x1202); // G LUT + LoadEntryVoidArea(0x0028,0x1203); // B LUT + + LoadEntryVoidArea(0x0028,0x1221); // Segmented Red Palette Color LUT Data + LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data + LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data + } + //FIXME later : how to use it? + LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent) + CloseFile(); // -------------------------------------------------------------- @@ -139,7 +161,7 @@ gdcmDocument::gdcmDocument(const char *inFilename, RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares // with "little-endian strings" { - filetype = gdcmACR_LIBIDO; + Filetype = gdcmACR_LIBIDO; std::string rows = GetEntryByNumber(0x0028, 0x0010); std::string columns = GetEntryByNumber(0x0028, 0x0011); SetEntryByNumber(columns, 0x0028, 0x0010); @@ -155,9 +177,10 @@ gdcmDocument::gdcmDocument(const char *inFilename, * @param exception_on_error */ gdcmDocument::gdcmDocument(bool exception_on_error) - :gdcmElementSet(-1) { + :gdcmElementSet(-1) +{ (void)exception_on_error; - enableSequences=0; + //enableSequences=0; // ?!? JPR SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); @@ -168,14 +191,16 @@ gdcmDocument::gdcmDocument(bool exception_on_error) /** * \brief Canonical destructor. */ -gdcmDocument::~gdcmDocument (void) { +gdcmDocument::~gdcmDocument () +{ RefPubDict = NULL; RefShaDict = NULL; // Recursive clean up of sequences - for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it ) - { - delete (it->second); + for (TagDocEntryHT::const_iterator it = tagHT.begin(); + it != tagHT.end(); ++it ) + { + delete it->second; } tagHT.clear(); } @@ -187,7 +212,8 @@ gdcmDocument::~gdcmDocument (void) { * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return */ -void gdcmDocument::PrintPubDict(std::ostream & os) { +void gdcmDocument::PrintPubDict(std::ostream & os) +{ RefPubDict->Print(os); } @@ -195,7 +221,8 @@ void gdcmDocument::PrintPubDict(std::ostream & os) { * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ -void gdcmDocument::PrintShaDict(std::ostream & os) { +void gdcmDocument::PrintShaDict(std::ostream & os) +{ RefShaDict->Print(os); } @@ -204,33 +231,37 @@ void gdcmDocument::PrintShaDict(std::ostream & os) { /** * \brief Get the public dictionary used */ -gdcmDict *gdcmDocument::GetPubDict(void) { - return(RefPubDict); +gdcmDict *gdcmDocument::GetPubDict() +{ + return RefPubDict; } /** * \brief Get the shadow dictionary used */ -gdcmDict *gdcmDocument::GetShaDict(void) { - return(RefShaDict); +gdcmDict *gdcmDocument::GetShaDict() +{ + return RefShaDict; } /** * \brief Set the shadow dictionary used * \param dict dictionary to use in shadow */ -bool gdcmDocument::SetShaDict(gdcmDict *dict){ - RefShaDict=dict; - return(!RefShaDict); +bool gdcmDocument::SetShaDict(gdcmDict *dict) +{ + RefShaDict = dict; + return !RefShaDict; } /** * \brief Set the shadow dictionary used * \param dictName name of the dictionary to use in shadow */ -bool gdcmDocument::SetShaDict(DictKey dictName){ - RefShaDict=gdcmGlobal::GetDicts()->GetDict(dictName); - return(!RefShaDict); +bool gdcmDocument::SetShaDict(DictKey dictName) +{ + RefShaDict = gdcmGlobal::GetDicts()->GetDict(dictName); + return !RefShaDict; } /** @@ -241,20 +272,27 @@ bool gdcmDocument::SetShaDict(DictKey dictName){ * @return true when gdcmDocument is the one of a reasonable Dicom/Acr file, * false otherwise. */ -bool gdcmDocument::IsReadable(void) { - if(filetype==gdcmUnknown) { +bool gdcmDocument::IsReadable() +{ + if( Filetype == gdcmUnknown) + { + std::cout << " gdcmDocument::IsReadable: Filetype " << Filetype + << " " << "gdcmUnknown " << gdcmUnknown << std::endl; //JPR dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype"); - return(false); + return false; } - if(!tagHT.empty()<=0) { + + if(tagHT.empty()) + { dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal" " hash table."); - return(false); + return false; } - return(true); + return true; } + /** * \brief Internal function that checks whether the Transfer Syntax given * as argument is the one present in the current document. @@ -263,27 +301,32 @@ bool gdcmDocument::IsReadable(void) { * the current document. False either when the document contains * no Transfer Syntax, or when the Tranfer Syntaxes don't match. */ -bool gdcmDocument::IsGivenTransferSyntax(const std::string & SyntaxToCheck) +bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck) { - gdcmDocEntry *Entry = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Entry ) + gdcmDocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010); + if ( !entry ) + { return false; + } // The entry might be present but not loaded (parsing and loading // happen at differente stages): try loading and proceed with check... - LoadDocEntrySafe(Entry); - if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(Entry) ) + LoadDocEntrySafe(entry); + if (gdcmValEntry* valEntry = dynamic_cast< gdcmValEntry* >(entry) ) { - std::string Transfer = ValEntry->GetValue(); + std::string transfer = valEntry->GetValue(); + // 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... - while ( ! isdigit(Transfer[Transfer.length()-1]) ) + while ( ! isdigit(transfer[transfer.length()-1]) ) { - Transfer.erase(Transfer.length()-1, 1); + transfer.erase(transfer.length()-1, 1); } - if ( Transfer == SyntaxToCheck ) + if ( transfer == syntaxToCheck ) + { return true; + } } return false; } @@ -295,7 +338,7 @@ bool gdcmDocument::IsGivenTransferSyntax(const std::string & SyntaxToCheck) * \sa \ref gdcmDocument::IsGivenTransferSyntax. * @return True when ImplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) +bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2); } @@ -305,7 +348,7 @@ bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) * and if it corresponds to a ExplicitVRLittleEndian one. * @return True when ExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) +bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1); } @@ -315,7 +358,7 @@ bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) * and if it corresponds to a DeflatedExplicitVRLittleEndian one. * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) +bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99); } @@ -325,7 +368,7 @@ bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) * and if it corresponds to a Explicit VR Big Endian one. * @return True when big endian found. False in all other cases. */ -bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) +bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2); } @@ -335,7 +378,7 @@ bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) * and if it corresponds to a JPEGBaseLineProcess1 one. * @return True when JPEGBaseLineProcess1found. False in all other cases. */ -bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax(void) +bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50); } @@ -345,7 +388,7 @@ bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax(void) * and if it corresponds to a JPEGExtendedProcess2-4 one. * @return True when JPEGExtendedProcess2-4 found. False in all other cases. */ -bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax(void) +bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51); } @@ -355,7 +398,7 @@ bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax(void) * and if it corresponds to a JPEGExtendeProcess3-5 one. * @return True when JPEGExtendedProcess3-5 found. False in all other cases. */ -bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax(void) +bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52); } @@ -366,7 +409,7 @@ bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax(void) * @return True when JPEGSpectralSelectionProcess6-8 found. False in all * other cases. */ -bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) +bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53); } @@ -377,7 +420,7 @@ bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) * @return True when RLE Lossless found. False in all * other cases. */ -bool gdcmDocument::IsRLELossLessTransferSyntax(void) +bool gdcmDocument::IsRLELossLessTransferSyntax() { return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); } @@ -388,11 +431,12 @@ bool gdcmDocument::IsRLELossLessTransferSyntax(void) * @return True when RLE Lossless found. False in all * other cases. */ -bool gdcmDocument::IsJPEGLossless(void) + +bool gdcmDocument::IsJPEGLossless() { return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55) || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57) - || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) ); + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70) ); } /** @@ -401,7 +445,7 @@ bool gdcmDocument::IsJPEGLossless(void) * @return True when JPEG2000 (Lossly or LossLess) found. False in all * other cases. */ -bool gdcmDocument::IsJPEG2000(void) +bool gdcmDocument::IsJPEG2000() { return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); @@ -411,12 +455,13 @@ bool gdcmDocument::IsJPEG2000(void) * \brief Predicate for dicom version 3 file. * @return True when the file is a dicom version 3. */ -bool gdcmDocument::IsDicomV3(void) { +bool gdcmDocument::IsDicomV3() +{ // Checking if Transfert Syntax exists is enough // Anyway, it's to late check if the 'Preamble' was found ... // And ... would it be a rich idea to check ? // (some 'no Preamble' DICOM images exist !) - return (GetDocEntryByNumber(0x0002, 0x0010) != NULL); + return GetDocEntryByNumber(0x0002, 0x0010) != NULL; } /** @@ -424,8 +469,9 @@ bool gdcmDocument::IsDicomV3(void) { * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) * @return the FileType code */ -FileType gdcmDocument::GetFileType(void) { - return(filetype); +FileType gdcmDocument::GetFileType() +{ + return Filetype; } /** @@ -436,89 +482,83 @@ FileType gdcmDocument::GetFileType(void) { FILE *gdcmDocument::OpenFile(bool exception_on_error) throw(gdcmFileError) { - fp=fopen(filename.c_str(),"rb"); + fp = fopen(Filename.c_str(),"rb"); if(!fp) { - if(exception_on_error) + if(exception_on_error) + { throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)"); + } else { - std::cout <<"gdcmDocument::OpenFile cannot open file: " - << filename.c_str() << std::endl; dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ", - filename.c_str()); - return (NULL); + Filename.c_str()); + return NULL; } } if ( fp ) { - guint16 zero; + uint16_t zero; fread(&zero, (size_t)2, (size_t)1, fp); //ACR -- or DICOM with no Preamble -- if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200) - return(fp); + { + return fp; + } //DICOM fseek(fp, 126L, SEEK_CUR); char dicm[4]; fread(dicm, (size_t)4, (size_t)1, fp); if( memcmp(dicm, "DICM", 4) == 0 ) - return(fp); + { + return fp; + } fclose(fp); - dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", filename.c_str()); + dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", Filename.c_str()); } - else { - dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", filename.c_str()); + else + { + dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", Filename.c_str()); } - return(NULL); + + return 0; } /** * \brief closes the file * @return TRUE if the close was successfull */ -bool gdcmDocument::CloseFile(void) { +bool gdcmDocument::CloseFile() +{ int closed = fclose(fp); fp = (FILE *)0; - if (! closed) - return false; - return true; + + return closed; } /** * \brief Writes in a file all the Header Entries (Dicom Elements) - * of the Chained List * @param fp file pointer on an already open file - * @param type Type of the File to be written + * @param filetype Type of the File to be written * (ACR-NEMA, ExplicitVR, ImplicitVR) * \return Always true. */ -bool gdcmDocument::Write(FILE *fp, FileType type) { -/// \todo -/// ============== -/// The stuff will have to be rewritten using the SeQuence based -/// tree-like stucture instead of the chained list . -/// (so we shall remove the Group*HT from the gdcmDocument) -/// To be checked -/// ============= - +void gdcmDocument::Write(FILE* fp,FileType filetype) +{ /// \todo move the following lines (and a lot of others, to be written) /// to a future function CheckAndCorrectHeader - /// \todo - /// Question : - /// Comment pourrait-on savoir si le DcmHeader vient d'un fichier - /// DicomV3 ou non (FileType est un champ de gdcmDocument ...) /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA - /// no way + /// no way (check : FileType est un champ de gdcmDocument ...) /// a moins de se livrer a un tres complique ajout des champs manquants. - /// faire un CheckAndCorrectHeader (?) - - if (type == gdcmImplicitVR) + /// faire un CheckAndCorrectHeader (?) + + if (filetype == gdcmImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); @@ -526,12 +566,12 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { /// \todo Refer to standards on page 21, chapter 6.2 /// "Value representation": values with a VR of UI shall be /// padded with a single trailing null - /// Dans le cas suivant on doit pader manuellement avec un 0 + /// in the following case we have to padd manually with a 0 SetEntryLengthByNumber(18, 0x0002, 0x0010); } - if (type == gdcmExplicitVR) + if (filetype == gdcmExplicitVR) { std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); @@ -543,22 +583,21 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { SetEntryLengthByNumber(20, 0x0002, 0x0010); } - + /** * \todo rewrite later, if really usefull + * - 'Group Length' element is optional in DICOM + * - but un-updated odd groups lengthes can causes pb + * (xmedcon breaker) * - * --> Warning : un-updated odd groups lengths can causes pb - * --> (xmedcon breaks) - * --> to be re- written with future org. - * - * if ( (type == ImplicitVR) || (type == ExplicitVR) ) - * UpdateGroupLength(false,type); - * if ( type == ACR) + * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) ) + * UpdateGroupLength(false,filetype); + * if ( filetype == ACR) * UpdateGroupLength(true,ACR); */ + + gdcmElementSet::Write(fp,filetype); // This one is recursive - WriteEntries(fp,type); - return(true); } /** @@ -572,25 +611,25 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { */ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( - std::string Value, - guint16 Group, - guint16 Elem ){ - gdcmDocEntry* CurrentEntry; - gdcmValEntry* ValEntry; - - CurrentEntry = GetDocEntryByNumber( Group, Elem); - if (!CurrentEntry) + std::string value, + uint16_t group, + uint16_t elem ) +{ + gdcmValEntry* valEntry; + + gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem); + if (!currentEntry) { // The entry wasn't present and we simply create the required ValEntry: - CurrentEntry = NewDocEntryByNumber(Group, Elem); - if (!CurrentEntry) + currentEntry = NewDocEntryByNumber(group, elem); + if (!currentEntry) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" " NewDocEntryByNumber failed."); - return (gdcmValEntry *)0; + return NULL; } - ValEntry = new gdcmValEntry(CurrentEntry); - if ( !AddEntry(ValEntry)) + valEntry = new gdcmValEntry(currentEntry); + if ( !AddEntry(valEntry)) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" " failed allthough this is a creation."); @@ -598,29 +637,29 @@ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( } else { - ValEntry = dynamic_cast< gdcmValEntry* >(CurrentEntry); - if ( !ValEntry ) + valEntry = dynamic_cast< gdcmValEntry* >(currentEntry); + if ( !valEntry ) { // We need to promote the gdcmDocEntry to a gdcmValEntry: - ValEntry = new gdcmValEntry(CurrentEntry); - if (!RemoveEntry(CurrentEntry)) + valEntry = new gdcmValEntry(currentEntry); + if (!RemoveEntry(currentEntry)) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" " of previous DocEntry failed."); - return (gdcmValEntry *)0; + return NULL; } - if ( !AddEntry(ValEntry)) + if ( !AddEntry(valEntry)) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" " promoted ValEntry failed."); - return (gdcmValEntry *)0; + return NULL; } } } - SetEntryByNumber(Value, Group, Elem); + SetEntryByNumber(value, group, elem); - return ValEntry; + return valEntry; } /* @@ -635,25 +674,28 @@ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( void *voidArea, int lgth, - guint16 Group, - guint16 Elem) -{ - gdcmDocEntry* a; - gdcmBinEntry* b; - a = GetDocEntryByNumber( Group, Elem); - if (a == NULL) { - a =NewBinEntryByNumber(Group, Elem); - if (a == NULL) - return NULL; - b = new gdcmBinEntry(a); + uint16_t group, + uint16_t elem) +{ + gdcmBinEntry* b = 0; + gdcmDocEntry* a = GetDocEntryByNumber( group, elem); + if (!a) + { + a = NewBinEntryByNumber(group, elem); + if (!a) + { + return 0; + } + + b = new gdcmBinEntry(a); AddEntry(b); + b->SetVoidArea(voidArea); } - SetEntryByNumber(voidArea, lgth, Group, Elem); - b->SetVoidArea(voidArea); - return (gdcmBinEntry*)b; -} - + SetEntryByNumber(voidArea, lgth, group, elem); + //b->SetVoidArea(voidArea); //what if b == 0 !! + return b; +} /** * \brief Set a new value if the invoked element exists @@ -663,10 +705,11 @@ gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( * @param Elem element number of the Entry * \return boolean */ -bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) +bool gdcmDocument::ReplaceIfExistByNumber(const char* value, uint16_t group, + uint16_t elem ) { - std::string v = Value; - SetEntryByNumber(v, Group, Elem); + std::string v = value; + SetEntryByNumber(v, group, elem); return true; } @@ -679,9 +722,10 @@ bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 El * @param element Element number of the searched Dicom Element * @return number of occurences */ -int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { +int gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) +{ std::string key = gdcmDictEntry::TranslateToKey(group, element ); - return (tagHT.count(key)); + return tagHT.count(key); } /** @@ -693,12 +737,15 @@ int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryByName(std::string tagName) { +std::string gdcmDocument::GetEntryByName(TagName tagName) +{ gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); - if( dictEntry == NULL) + if( !dictEntry ) + { return GDCM_UNFOUND; + } - return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); + return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); } /** @@ -714,7 +761,8 @@ std::string gdcmDocument::GetEntryByName(std::string tagName) { * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByName(std::string tagName) { +std::string gdcmDocument::GetEntryVRByName(TagName tagName) +{ gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return GDCM_UNFOUND; @@ -734,8 +782,10 @@ std::string gdcmDocument::GetEntryVRByName(std::string tagName) { * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){ - TagKey key = gdcmDictEntry::TranslateToKey(group, element); +std::string gdcmDocument::GetEntryByNumber(uint16_t group, uint16_t element) +{ + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); + /// \todo use map methods, instead of multimap JPR if ( ! tagHT.count(key)) return GDCM_UNFOUND; return ((gdcmValEntry *)tagHT.find(key)->second)->GetValue(); @@ -755,7 +805,8 @@ std::string gdcmDocument::GetEntryByNumber(guint16 group, guint16 element){ * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) { +std::string gdcmDocument::GetEntryVRByNumber(uint16_t group, uint16_t element) +{ gdcmDocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) return GDCM_UNFOUND; @@ -770,7 +821,8 @@ std::string gdcmDocument::GetEntryVRByNumber(guint16 group, guint16 element) { * @param element Element number of the searched tag. * @return Corresponding element length; -2 if not found */ -int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) { +int gdcmDocument::GetEntryLengthByNumber(uint16_t group, uint16_t element) +{ gdcmDocEntry* elem = GetDocEntryByNumber(group, element); if ( !elem ) return -2; @@ -782,13 +834,14 @@ int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) { * @param tagName name of the searched Dicom Element. * @return true when found */ -bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) { +bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) +{ gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return false; - return(SetEntryByNumber(content,dictEntry->GetGroup(), - dictEntry->GetElement())); + return SetEntryByNumber(content,dictEntry->GetGroup(), + dictEntry->GetElement()); } /** @@ -800,8 +853,8 @@ bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) { * @param element element number of the Dicom Element to modify */ bool gdcmDocument::SetEntryByNumber(std::string content, - guint16 group, - guint16 element) + uint16_t group, + uint16_t element) { gdcmValEntry* ValEntry = GetValEntryByNumber(group, element); if (!ValEntry) @@ -810,15 +863,14 @@ bool gdcmDocument::SetEntryByNumber(std::string content, " ValEntry (try promotion first)."); return false; } - // Non even content must be padded with a space (020H). - if((content.length())%2) + if((content.length())%2) { content = content + '\0'; - + } ValEntry->SetValue(content); // Integers have a special treatement for their length: - VRKey vr = ValEntry->GetVR(); + gdcmVRKey vr = ValEntry->GetVR(); if( (vr == "US") || (vr == "SS") ) ValEntry->SetLength(2); else if( (vr == "UL") || (vr == "SL") ) @@ -834,19 +886,21 @@ bool gdcmDocument::SetEntryByNumber(std::string content, * through it's (group, element) and modifies it's content with * the given value. * @param content new value (void *) to substitute with + * @param lgth new value length * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ bool gdcmDocument::SetEntryByNumber(void *content, - int lgth, - guint16 group, - guint16 element) + int lgth, + uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); + (void)lgth; //not used + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; - -/* Hope Binray field length is never wrong + +/* Hope Binaray field length is *never* wrong if(lgth%2) // Non even length are padded with a space (020H). { lgth++; @@ -871,11 +925,12 @@ bool gdcmDocument::SetEntryByNumber(void *content, * @param element element number of the Entry to modify * @return true on success, false otherwise. */ -bool gdcmDocument::SetEntryLengthByNumber(guint32 l, - guint16 group, - guint16 element) +bool gdcmDocument::SetEntryLengthByNumber(uint32_t l, + uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); + /// \todo use map methods, instead of multimap JPR + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; if (l%2) l++; // length must be even @@ -891,13 +946,12 @@ bool gdcmDocument::SetEntryLengthByNumber(guint32 l, * @param Elem element number of the Entry * @return File Offset of the Element Value */ -size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) +size_t gdcmDocument::GetEntryOffsetByNumber(uint16_t Group, uint16_t Elem) { gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem); if (!Entry) { - dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber", - "failed to Locate gdcmDocEntry"); + dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry present."); return (size_t)0; } return Entry->GetOffset(); @@ -910,13 +964,12 @@ size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) * @param Elem element number of the Entry * @return Pointer to the 'non string' area */ -void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) +void * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t Group, uint16_t Elem) { gdcmDocEntry* Entry = GetDocEntryByNumber(Group, Elem); if (!Entry) { - dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber", - "failed to Locate gdcmDocEntry"); + dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry"); return (NULL); } return ((gdcmBinEntry *)Entry)->GetVoidArea(); @@ -928,19 +981,45 @@ void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) * @param Group group number of the Entry * @param Elem element number of the Entry */ -void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem) +void *gdcmDocument::LoadEntryVoidArea(uint16_t Group, uint16_t Elem) { gdcmDocEntry * Element= GetDocEntryByNumber(Group, Elem); if ( !Element ) return NULL; size_t o =(size_t)Element->GetOffset(); fseek(fp, o, SEEK_SET); - size_t l=Element->GetLength(); + size_t l = Element->GetLength(); char* a = new char[l]; - if(!a) + if(!a) { + dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); return NULL; - + } + size_t l2 = fread(a, 1, l ,fp); + if(l != l2) + { + delete[] a; + return NULL; + } + /// \todo Drop any allready existing void area! JPR SetEntryVoidAreaByNumber(a, Group, Elem); + return a; +} +/** + * \brief Loads (from disk) the element content + * when a string is not suitable + * @param Element Entry whose voidArea is going to be loaded + */ +void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *Element) +{ + size_t o =(size_t)Element->GetOffset(); + fseek(fp, o, SEEK_SET); + size_t l = Element->GetLength(); + char* a = new char[l]; + if(!a) { + dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a"); + return NULL; + } + Element->SetVoidArea((void *)a); /// \todo check the result size_t l2 = fread(a, 1, l ,fp); if(l != l2) @@ -948,22 +1027,21 @@ void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem) delete[] a; return NULL; } - return a; } /** * \brief Sets a 'non string' value to a given Dicom Element - * @param area + * @param area area containing the 'non string' value * @param group Group number of the searched Dicom Element * @param element Element number of the searched Dicom Element * @return */ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, - guint16 group, - guint16 element) + uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; // This was for multimap ? @@ -976,8 +1054,8 @@ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, * \brief Update the entries with the shadow dictionary. * Only non even entries are analyzed */ -void gdcmDocument::UpdateShaEntries(void) { - gdcmDictEntry *entry; +void gdcmDocument::UpdateShaEntries() { + //gdcmDictEntry *entry; std::string vr; /// \todo TODO : still any use to explore recursively the whole structure? @@ -1026,7 +1104,8 @@ void gdcmDocument::UpdateShaEntries(void) { * @return Corresponding Dicom Element when it exists, and NULL * otherwise. */ - gdcmDocEntry *gdcmDocument::GetDocEntryByName(std::string tagName) { +gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string tagName) +{ gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) return NULL; @@ -1044,9 +1123,10 @@ void gdcmDocument::UpdateShaEntries(void) { * @param element Element number of the searched Dicom Element * @return */ -gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element) +gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(uint16_t group, + uint16_t element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return NULL; return tagHT.find(key)->second; @@ -1058,7 +1138,8 @@ gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element) * ValEntry. * @return When present, the corresponding ValEntry. */ -gdcmValEntry* gdcmDocument::GetValEntryByNumber(guint16 group, guint16 element) +gdcmValEntry* gdcmDocument::GetValEntryByNumber(uint16_t group, + uint16_t element) { gdcmDocEntry* CurrentEntry = GetDocEntryByNumber(group, element); if (! CurrentEntry) @@ -1078,248 +1159,20 @@ gdcmValEntry* gdcmDocument::GetValEntryByNumber(guint16 group, guint16 element) * @param entry Header Entry whose value shall be loaded. * @return */ -void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) { +void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry) +{ long PositionOnEntry = ftell(fp); LoadDocEntry(entry); fseek(fp, PositionOnEntry, SEEK_SET); } - -/** - * \brief Writes in a file (according to the requested format) - * the group, the element, the value representation and the length - * of a single gdcmDocEntry passed as argument. - * @param tag pointer on the gdcmDocEntry to be written - * @param _fp already open file pointer - * @param type type of the File to be written - */ -void gdcmDocument::WriteEntryTagVRLength(gdcmDocEntry *tag, - FILE *_fp, - FileType type) -{ - guint16 group = tag->GetGroup(); - VRKey vr = tag->GetVR(); - guint16 el = tag->GetElement(); - guint32 lgr = tag->GetReadLength(); - - if ( (group == 0xfffe) && (el == 0x0000) ) - // Fix in order to make some MR PHILIPS images e-film readable - // see gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm: - // we just *always* ignore spurious fffe|0000 tag ! - return; - - fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group - fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element - - if ( type == gdcmExplicitVR ) { - - // Special case of delimiters: - if (group == 0xfffe) { - // Delimiters have NO Value Representation and have NO length. - // Hence we skip writing the VR and length and we pad by writing - // 0xffffffff - - int ff=0xffffffff; - fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp); - return; - } - - guint16 z=0; - guint16 shortLgr = lgr; - if (vr == "unkn") { // Unknown was 'written' - // deal with Little Endian - fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); - fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); - } else { - fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp); - if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) - { - fwrite ( &z, (size_t)2 ,(size_t)1 ,_fp); - fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); - } else { - fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); - } - } - } - else // IMPLICIT VR - { - fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); - } -} - -/** - * \brief Writes in a file (according to the requested format) - * the value of a single gdcmDocEntry passed as argument. - * @param tag Pointer on the gdcmDocEntry to be written - * @param _fp Already open file pointer - * @param type type of the File to be written - */ - -// \todo TODO : to be re -written recursively ! -void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type) -{ - (void)type; - guint16 group = tag->GetGroup(); - VRKey vr = tag->GetVR(); - guint32 lgr = tag->GetReadLength(); - - if (vr == "SQ") - // SeQuences have no value: - return; - if (group == 0xfffe) - // Delimiters have no associated value: - return; - - //-------------------------------- - // - // FIXME :right now, both value and voidArea belong to gdcmValue - // - // ------------------------------- - -// if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) ) { - void *voidArea; - gdcmBinEntry *BinEntry= (gdcmBinEntry *)tag;; - voidArea = BinEntry->GetVoidArea(); - if (voidArea != NULL) - { // there is a 'non string' LUT, overlay, etc - fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value - return; - } -// } - - if (vr == "US" || vr == "SS") - { - // some 'Short integer' fields may be mulivaluated - // each single value is separated from the next one by '\' - // we split the string and write each value as a short int - std::vector tokens; - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\"); - for (unsigned int i=0; i tokens; - tokens.erase(tokens.begin(),tokens.end()); // clean any previous value - Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\"); - for (unsigned int i=0; iGetValue().c_str(), - (size_t)lgr ,(size_t)1, _fp); // Elem value -} - -/** - * \brief Writes in a file (according to the requested format) - * a single gdcmDocEntry passed as argument. - * \sa WriteEntryValue, WriteEntryTagVRLength. - * @param tag Pointer on the gdcmDocEntry to be written - * @param _fp Already open file pointer - * @param type type of the File to be written - */ - -bool gdcmDocument::WriteEntry(gdcmDocEntry *tag, FILE *_fp,FileType type) -{ - guint32 length = tag->GetLength(); - - if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(tag) ) - { - // The value of a tag MUST (see the DICOM norm) be an odd number of - // bytes. When this is not the case, pad with an additional byte: - if(length%2==1) { - ValEntry->SetValue(ValEntry->GetValue()+"\0"); - ValEntry->SetLength(ValEntry->GetReadLength()+1); - } - WriteEntryTagVRLength(ValEntry, _fp, type); - WriteEntryValue(ValEntry, _fp, type); - return true; - } - - if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) ) - { - /// \todo FIXME : when voidArea belong to gdcmBinEntry only, fix - /// voidArea length - // - // The value of a tag MUST (see the DICOM norm) be an odd number of - // bytes. When this is not the case, pad with an additional byte: -/* - if(length%2==1) { - tag->SetValue(tag->GetValue()+"\0"); - tag->SetLength(tag->GetReadLength()+1); - } -*/ - WriteEntryTagVRLength(tag, _fp, type); - WriteEntryValue(tag, _fp, type); - return true; - } -} - -/** - * \brief writes on disc according to the requested format - * (ACR-NEMA, ExplicitVR, ImplicitVR) the image - * using the Chained List - * \warning does NOT add the missing elements in the header : - * it's up to the user doing it ! - * (function CheckHeaderCoherence to be written) - * \warning DON'T try, right now, to write a DICOM image - * from an ACR Header (meta elements will be missing!) - * @param type type of the File to be written - * (ACR-NEMA, ExplicitVR, ImplicitVR) - * @param _fp already open file pointer - */ - -bool gdcmDocument::WriteEntries(FILE *_fp,FileType type) -{ - /// \todo FIXME : explore recursively the whole structure... - /// \todo (?) check write failures (after *each* fwrite) - - dbg.Verbose(0, "gdcmDocument::WriteEntries: entering."); - for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it ) - { - gdcmDocEntry * entry = it->second; - - if ( type == gdcmACR ){ - if (entry->GetGroup() < 0x0008) - // Ignore pure DICOM V3 groups - continue; - if (entry->GetGroup() %2) - // Ignore the "shadow" groups - continue; - if (entry->GetVR() == "SQ" ) // ignore Sequences - continue; - } - if (! WriteEntry(entry, _fp, type) ) { - dbg.Verbose(0, "gdcmDocument::WriteEntries: write failure."); - return false; - } - } - return true; -} - - /** * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly swaped 32 bits integer. */ -guint32 gdcmDocument::SwapLong(guint32 a) { +uint32_t gdcmDocument::SwapLong(uint32_t a) +{ switch (sw) { case 0 : break; @@ -1340,34 +1193,37 @@ guint32 gdcmDocument::SwapLong(guint32 a) { dbg.Error(" gdcmDocument::SwapLong : unset swap code"); a=0; } - return(a); -} + return a; +} /** * \brief Unswaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly unswaped 32 bits integer. */ -guint32 gdcmDocument::UnswapLong(guint32 a) { - return (SwapLong(a)); +uint32_t gdcmDocument::UnswapLong(uint32_t a) +{ + return SwapLong(a); } /** * \brief Swaps the bytes so they agree with the processor order * @return The properly swaped 16 bits integer. */ -guint16 gdcmDocument::SwapShort(guint16 a) { +uint16_t gdcmDocument::SwapShort(uint16_t a) +{ if ( (sw==4321) || (sw==2143) ) a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff)); - return (a); + return a; } /** * \brief Unswaps the bytes so they agree with the processor order * @return The properly unswaped 16 bits integer. */ -guint16 gdcmDocument::UnswapShort(guint16 a) { - return (SwapShort(a)); +uint16_t gdcmDocument::UnswapShort(uint16_t a) +{ + return SwapShort(a); } //----------------------------------------------------------------------------- @@ -1375,17 +1231,20 @@ guint16 gdcmDocument::UnswapShort(guint16 a) { /** * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries) - * @return false if file is not ACR-NEMA / PAPYRUS / DICOM + * @return length of the parsed set. */ -long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) { - +long gdcmDocument::ParseDES(gdcmDocEntrySet *set, + long offset, + long l_max, + bool delim_mode) +{ gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; gdcmValEntry *NewValEntry = (gdcmValEntry *)0; gdcmBinEntry *bn; gdcmSeqEntry *sq; - VRKey vr; - long l; + gdcmVRKey vr; + unsigned long l = 0; int depth; depth = set->GetDepthLevel(); @@ -1410,7 +1269,7 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool NewValEntry->SetDepthLevel(depth); set->AddEntry(NewValEntry); LoadDocEntry(NewValEntry); - if (/*!delim_mode && */NewValEntry->isItemDelimitor()) + if (NewValEntry->isItemDelimitor()) break; if ( !delim_mode && ftell(fp)-offset >= l_max) { @@ -1436,10 +1295,17 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool if (NewDocEntry->GetGroup() == 0x7fe0 && NewDocEntry->GetElement() == 0x0010 ) { - if (NewDocEntry->GetLength()==0xffffffff) + if (NewDocEntry->GetReadLength()==0xffffffff) + { // Broken US.3405.1.dcm Parse7FE0(); // to skip the pixels // (multipart JPEG/RLE are trouble makers) + } + else + { + SkipToNextDocEntry(NewDocEntry); + l = NewDocEntry->GetFullLength(); + } } else { @@ -1469,8 +1335,8 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool long lgt = ParseSQ( sq, NewDocEntry->GetOffset(), l, delim_mode); + (void)lgt; //not used... } - // FIXME : on en fait quoi, de lgt ? set->AddEntry(sq); if ( !delim_mode && ftell(fp)-offset >= l_max) { @@ -1479,7 +1345,7 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool } delete NewDocEntry; } - return l; // ?? + return l; // Probably useless } /** @@ -1490,19 +1356,22 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, long offset, long l_max, bool delim_mode) { int SQItemNumber = 0; - + gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; gdcmSQItem *itemSQ; bool dlm_mod; - int lgr, l, lgth; + int lgr, lgth; + unsigned int l; int depth = set->GetDepthLevel(); + (void)depth; //not used while (true) { + NewDocEntry = ReadNextDocEntry(); + if (!NewDocEntry) + break; if(delim_mode) { if (NewDocEntry->isSequenceDelimitor()) { - /// \todo add the Sequence Delimitor - /// \todo find the trick to put it properly ! set->SetSequenceDelimitationItem(NewDocEntry); break; } @@ -1513,7 +1382,6 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, itemSQ = new gdcmSQItem(set->GetDepthLevel()); itemSQ->AddEntry(NewDocEntry); - /// \todo no value, no voidArea. Think of it while printing ! l= NewDocEntry->GetReadLength(); if (l == 0xffffffff) @@ -1523,14 +1391,14 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod); - set->AddEntry(itemSQ,SQItemNumber); + set->AddEntry(itemSQ,SQItemNumber); SQItemNumber ++; if (!delim_mode && (ftell(fp)-offset) >= l_max) { break; } } lgth = ftell(fp) - offset; - return(lgth); + return lgth; } /** @@ -1538,12 +1406,12 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, * the value specified with gdcmDocument::SetMaxSizeLoadEntry() * @param Entry Header Entry (Dicom Element) to be dealt with */ -void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) +void gdcmDocument::LoadDocEntry(gdcmDocEntry* Entry) { size_t item_read; - guint16 group = Entry->GetGroup(); - std::string vr= Entry->GetVR(); - guint32 length = Entry->GetLength(); + uint16_t group = Entry->GetGroup(); + std::string vr = Entry->GetVR(); + uint32_t length = Entry->GetLength(); fseek(fp, (long)Entry->GetOffset(), SEEK_SET); @@ -1551,16 +1419,15 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) // (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 ) + { // NO more value field for SQ ! - //Entry->SetValue("gdcm::Skipped"); - // appel recursif de Load Value - // (meme pb que pour le parsing) return; } // When the length is zero things are easy: - if ( length == 0 ) { + if ( length == 0 ) + { ((gdcmValEntry *)Entry)->SetValue(""); return; } @@ -1568,53 +1435,81 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) // The elements whose length is bigger than the specified upper bound // are not loaded. Instead we leave a short notice of the offset of // the element content and it's length. - if (length > MaxSizeLoadEntry) { + + std::ostringstream s; + if (length > MaxSizeLoadEntry) + { + if (gdcmBinEntry* BinEntryPtr = dynamic_cast< gdcmBinEntry* >(Entry) ) + { + s << "gdcm::NotLoaded (BinEntry)"; + s << " Address:" << (long)Entry->GetOffset(); + s << " Length:" << Entry->GetLength(); + s << " x(" << std::hex << Entry->GetLength() << ")"; + BinEntryPtr->SetValue(s.str()); + } + // to be sure we are at the end of the value ... + fseek(fp, (long)Entry->GetOffset()+(long)Entry->GetLength(), SEEK_SET); + return; + // Be carefull : a BinEntry IS_A ValEntry ... if (gdcmValEntry* ValEntryPtr = dynamic_cast< gdcmValEntry* >(Entry) ) { - std::ostringstream s; - s << "gdcm::NotLoaded."; + s << "gdcm::NotLoaded. (ValEntry)"; s << " Address:" << (long)Entry->GetOffset(); s << " Length:" << Entry->GetLength(); s << " x(" << std::hex << Entry->GetLength() << ")"; ValEntryPtr->SetValue(s.str()); } // to be sure we are at the end of the value ... - fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET); - + fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET); + return; + } + + // When we find a BinEntry not very much can be done : + if (gdcmBinEntry* BinEntryPtr = dynamic_cast< gdcmBinEntry* >(Entry) ) + { + + LoadEntryVoidArea(BinEntryPtr); + s << "gdcm::Loaded (BinEntry)"; + BinEntryPtr->SetValue(s.str()); return; } - // Any compacter code suggested (?) - if ( IsDocEntryAnInteger(Entry) ) { - guint32 NewInt; + /// \todo Any compacter code suggested (?) + if ( IsDocEntryAnInteger(Entry) ) + { + uint32_t NewInt; std::ostringstream s; int nbInt; - // When short integer(s) are expected, read and convert the following - // n *two characters properly i.e. 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") { + // When short integer(s) are expected, read and convert the following + // n *two 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++) { + if (nbInt > 1) + { + for (int i=1; i < nbInt; i++) + { s << '\\'; NewInt = ReadInt16(); s << NewInt; } } } - // When integer(s) are expected, read and convert the following - // n * four characters properly i.e. as integers as opposed to strings. - // Elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - else if (vr == "UL" || vr == "SL") { + // 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++) { + if (nbInt > 1) + { + for (int i=1; i < nbInt; i++) + { s << '\\'; NewInt = ReadInt32(); s << NewInt; @@ -1632,16 +1527,26 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) // We need an additional byte for storing \0 that is not on disk std::string NewValue(length,0); item_read = fread(&(NewValue[0]), (size_t)length, (size_t)1, fp); - if ( item_read != 1 ) { - dbg.Verbose(1, "gdcmDocument::LoadElementValue","unread element value"); - ((gdcmValEntry *)Entry)->SetValue("gdcm::UnRead"); - return; - } + if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(Entry) ) + { + if ( item_read != 1 ) + { + dbg.Verbose(1, "gdcmDocument::LoadDocEntry", + "unread element value"); + ValEntry->SetValue("gdcm::UnRead"); + return; + } - if( (vr == "UI") ) // Because of correspondance with the VR dic - ((gdcmValEntry *)Entry)->SetValue(NewValue.c_str()); + if( (vr == "UI") ) // Because of correspondance with the VR dic + ValEntry->SetValue(NewValue.c_str()); + else + ValEntry->SetValue(NewValue); + } else - ((gdcmValEntry *)Entry)->SetValue(NewValue); + { + dbg.Error(true, "gdcmDocument::LoadDocEntry" + "Should have a ValEntry, here !"); + } } @@ -1649,14 +1554,14 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) * \brief Find the value Length of the passed Header Entry * @param Entry Header Entry whose length of the value shall be loaded. */ - void gdcmDocument::FindDocEntryLength (gdcmDocEntry *Entry) { - guint16 element = Entry->GetElement(); - //guint16 group = Entry->GetGroup(); //FIXME +void gdcmDocument::FindDocEntryLength (gdcmDocEntry *Entry) +{ + uint16_t element = Entry->GetElement(); std::string vr = Entry->GetVR(); - guint16 length16; + uint16_t length16; - if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) ) + if ( (Filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) ) { if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { @@ -1664,11 +1569,27 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) // 7.1.2 Data element structure with explicit vr p27) must be // skipped before proceeding on reading the length on 4 bytes. fseek(fp, 2L, SEEK_CUR); - guint32 length32 = ReadInt32(); + uint32_t length32 = ReadInt32(); if ( (vr == "OB") && (length32 == 0xffffffff) ) { - Entry->SetLength(FindDocEntryLengthOB()); + uint32_t LengthOB = FindDocEntryLengthOB(); + if ( errno == 1 ) + { + // Computing the length failed (this happens with broken + // files like gdcm-JPEG-LossLess3a.dcm). We still have a + // 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. + long CurrentPosition = ftell(fp); + fseek(fp,0L,SEEK_END); + long LengthUntilEOF = ftell(fp) - CurrentPosition; + fseek(fp, CurrentPosition, SEEK_SET); + Entry->SetLength(LengthUntilEOF); + errno = 0; + return; + } + Entry->SetLength(LengthOB); return; } FixDocEntryFoundLength(Entry, length32); @@ -1717,8 +1638,8 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) SwitchSwapToBigEndian(); // Restore the unproperly loaded values i.e. the group, the element // and the dictionary entry depending on them. - guint16 CorrectGroup = SwapShort(Entry->GetGroup()); - guint16 CorrectElem = SwapShort(Entry->GetElement()); + uint16_t CorrectGroup = SwapShort(Entry->GetGroup()); + uint16_t CorrectElem = SwapShort(Entry->GetElement()); gdcmDictEntry * NewTag = GetDictEntryByNumber(CorrectGroup, CorrectElem); if (!NewTag) @@ -1731,16 +1652,14 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) Entry->SetDictEntry(NewTag); } - // Heuristic: well some files are really ill-formed. + // Heuristic: well, some files are really ill-formed. if ( length16 == 0xffff) { length16 = 0; - //dbg.Verbose(0, "gdcmDocument::FindLength", - // "Erroneous element length fixed."); - // Actually, length= 0xffff means that we deal with - // Unknown Sequence Length + // Length16= 0xffff means that we deal with + // 'Unknown Length' Sequence } - FixDocEntryFoundLength(Entry, (guint32)length16); + FixDocEntryFoundLength(Entry, (uint32_t)length16); return; } else @@ -1763,7 +1682,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) */ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry) { - if (filetype != gdcmExplicitVR) + if (Filetype != gdcmExplicitVR) return; char VR[3]; @@ -1802,7 +1721,7 @@ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry) * @return false if the VR is incorrect of if the VR isn't referenced * otherwise, it returns true */ -bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, VRKey vr) +bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, gdcmVRKey vr) { char msg[100]; // for sprintf bool RealExplicit = true; @@ -1837,7 +1756,7 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, VRKey vr) "UL","FIXME","Group Length"); Entry->SetDictEntry(NewEntry); } - return(false); + return false; } if ( Entry->IsVRUnknown() ) @@ -1861,7 +1780,7 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *Entry, VRKey vr) vr,"FIXME",Entry->GetName()); Entry->SetDictEntry(NewEntry); } - return(true); + return true; } /** @@ -1877,7 +1796,7 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry) { std::string val=((gdcmValEntry *)Entry)->GetValue(); std::string vr=Entry->GetVR(); - guint32 length = Entry->GetLength(); + uint32_t length = Entry->GetLength(); std::ostringstream s; int nbInt; @@ -1890,7 +1809,7 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry) if (vr == "US" || vr == "SS") { - guint16 NewInt16; + uint16_t NewInt16; nbInt = length / 2; for (int i=0; i < nbInt; i++) @@ -1911,7 +1830,7 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry) // contain a set of integers (not a single one) else if (vr == "UL" || vr == "SL") { - guint32 NewInt32; + uint32_t NewInt32; nbInt = length / 4; for (int i=0; i < nbInt; i++) @@ -1927,10 +1846,10 @@ std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *Entry) #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM - return(s.str()); + return s.str(); } - return(((gdcmValEntry *)Entry)->GetValue()); + return ((gdcmValEntry *)Entry)->GetValue(); } /** @@ -1951,7 +1870,7 @@ std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry) if (vr == "US" || vr == "SS") { - guint16 NewInt16; + uint16_t NewInt16; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\"); @@ -1964,7 +1883,7 @@ std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry) } if (vr == "UL" || vr == "SL") { - guint32 NewInt32; + uint32_t NewInt32; tokens.erase(tokens.begin(),tokens.end()); // clean any previous value Tokenize (((gdcmValEntry *)Entry)->GetValue(), tokens, "\\"); @@ -1980,10 +1899,10 @@ std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry *Entry) #ifdef GDCM_NO_ANSI_STRING_STREAM s << std::ends; // to avoid oddities on Solaris #endif //GDCM_NO_ANSI_STRING_STREAM - return(s.str()); + return s.str(); } - return(((gdcmValEntry *)Entry)->GetValue()); + return ((gdcmValEntry *)Entry)->GetValue(); } /** @@ -2007,31 +1926,21 @@ void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry) (void)fseek(fp, (long)(entry->GetReadLength()), SEEK_CUR); } -/** - * \brief Loads the value for a a given VLEntry - * \warning NOT end user intended method ! - * @param entry - */ -void gdcmDocument::LoadVLEntry(gdcmDocEntry *entry) -{ - //SkipBytes(entry->GetLength()); - LoadDocEntry(entry); -} /** * \brief When the length of an element value is obviously wrong (because * the parser went Jabberwocky) one can hope improving things by * applying some heuristics. */ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, - guint32 FoundLength) + uint32_t FoundLength) { Entry->SetReadLength(FoundLength); // will be updated only if a bug is found if ( FoundLength == 0xffffffff) { FoundLength = 0; } - guint16 gr =Entry->GetGroup(); - guint16 el =Entry->GetElement(); + uint16_t gr =Entry->GetGroup(); + uint16_t el =Entry->GetElement(); if (FoundLength%2) { std::ostringstream s; @@ -2102,10 +2011,10 @@ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, * @return The result of the heuristical predicate. */ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { - guint16 element = Entry->GetElement(); - guint16 group = Entry->GetGroup(); - std::string vr = Entry->GetVR(); - guint32 length = Entry->GetLength(); + uint16_t element = Entry->GetElement(); + uint16_t group = Entry->GetGroup(); + 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 @@ -2145,14 +2054,14 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { * @return */ - guint32 gdcmDocument::FindDocEntryLengthOB(void) { +uint32_t gdcmDocument::FindDocEntryLengthOB() { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. - guint16 g; - guint16 n; + uint16_t g; + uint16_t n; long PositionOnEntry = ftell(fp); bool FoundSequenceDelimiter = false; - guint32 TotalLength = 0; - guint32 ItemLength; + uint32_t TotalLength = 0; + uint32_t ItemLength; while ( ! FoundSequenceDelimiter) { @@ -2160,31 +2069,30 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { n = ReadInt16(); if (errno == 1) return 0; - TotalLength += 4; // We even have to decount the group and element + + // We have to decount the group and element we just read + TotalLength += 4; - if ( g != 0xfffe && g!=0xb00c ) //for bogus header + if ( ( g != 0xfffe ) + || ( ( n != 0xe0dd ) && ( n != 0xe000 ) ) ) { - char msg[100]; // for sprintf. Sorry - sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n); - dbg.Verbose(1, "gdcmDocument::FindLengthOB: ",msg); + dbg.Verbose(1, "gdcmDocument::FindLengthOB: neither an Item tag " + "nor a Sequence delimiter tag."); + fseek(fp, PositionOnEntry, SEEK_SET); errno = 1; return 0; } - if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) // for bogus header + + if ( n == 0xe0dd ) FoundSequenceDelimiter = true; - else if ( n != 0xe000 ) - { - char msg[100]; // for sprintf. Sorry - sprintf(msg,"wrong element (%04x) for an item sequence (%04x,%04x)\n", - n, g,n); - dbg.Verbose(1, "gdcmDocument::FindLengthOB: ",msg); - errno = 1; - return 0; - } + ItemLength = ReadInt32(); - TotalLength += ItemLength + 4; // We add 4 bytes since we just read - // the ItemLength with ReadInt32 + // We add 4 bytes since we just read the ItemLength with ReadInt32 + TotalLength += ItemLength + 4; SkipBytes(ItemLength); + + if ( FoundSequenceDelimiter ) + break; } fseek(fp, PositionOnEntry, SEEK_SET); return TotalLength; @@ -2195,8 +2103,8 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { * (swaps it depending on processor endianity) * @return read value */ -guint16 gdcmDocument::ReadInt16(void) { - guint16 g; +uint16_t gdcmDocument::ReadInt16() { + uint16_t g; size_t item_read; item_read = fread (&g, (size_t)2,(size_t)1, fp); if ( item_read != 1 ) { @@ -2215,8 +2123,8 @@ guint16 gdcmDocument::ReadInt16(void) { * (swaps it depending on processor endianity) * @return read value */ -guint32 gdcmDocument::ReadInt32(void) { - guint32 g; +uint32_t gdcmDocument::ReadInt32() { + uint32_t g; size_t item_read; item_read = fread (&g, (size_t)4,(size_t)1, fp); if ( item_read != 1 ) { @@ -2235,7 +2143,7 @@ guint32 gdcmDocument::ReadInt32(void) { * \warning NOT end user intended method ! * @return */ -void gdcmDocument::SkipBytes(guint32 NBytes) { +void gdcmDocument::SkipBytes(uint32_t NBytes) { //FIXME don't dump the returned value (void)fseek(fp, (long)NBytes, SEEK_CUR); } @@ -2244,10 +2152,10 @@ void gdcmDocument::SkipBytes(guint32 NBytes) { * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ -void gdcmDocument::Initialise(void) +void gdcmDocument::Initialise() { RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); - RefShaDict = (gdcmDict*)0; + RefShaDict = NULL; } /** @@ -2265,10 +2173,10 @@ bool gdcmDocument::CheckSwap() { // 0x00000004. Finding the swap code in then straigthforward. Trouble // occurs when we can't find such group... - guint32 x=4; // x : for ntohs + uint32_t x=4; // x : for ntohs bool net2host; // true when HostByteOrder is the same as NetworkByteOrder - guint32 s32; - guint16 s16; + uint32_t s32; + uint16_t s16; int lgrLue; char *entCur; @@ -2320,13 +2228,13 @@ bool gdcmDocument::CheckSwap() { // Use gdcmDocument::dicom_vr to test all the possibilities // instead of just checking for UL, OB and UI !? group 0000 { - filetype = gdcmExplicitVR; + Filetype = gdcmExplicitVR; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "explicit Value Representation"); } else { - filetype = gdcmImplicitVR; + Filetype = gdcmImplicitVR; dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not an explicit Value Representation"); } @@ -2366,24 +2274,24 @@ bool gdcmDocument::CheckSwap() { // We assume the array of char we are considering contains the binary // representation of a 32 bits integer. Hence the following dirty // trick : - s32 = *((guint32 *)(entCur)); + s32 = *((uint32_t *)(entCur)); switch (s32) { case 0x00040000 : sw = 3412; - filetype = gdcmACR; + Filetype = gdcmACR; return true; case 0x04000000 : sw = 4321; - filetype = gdcmACR; + Filetype = gdcmACR; return true; case 0x00000400 : sw = 2143; - filetype = gdcmACR; + Filetype = gdcmACR; return true; case 0x00000004 : sw = 0; - filetype = gdcmACR; + Filetype = gdcmACR; return true; default : @@ -2402,25 +2310,25 @@ bool gdcmDocument::CheckSwap() { // the file IS NOT ACR-NEMA nor DICOM V3 // Find a trick to tell it the caller... - s16 = *((guint16 *)(deb)); + s16 = *((uint16_t *)(deb)); switch (s16) { case 0x0002 : case 0x0004 : case 0x0008 : sw = 0; - filetype = gdcmACR; + Filetype = gdcmACR; return true; case 0x0200 : case 0x0400 : case 0x0800 : sw = 4321; - filetype = gdcmACR; + Filetype = gdcmACR; return true; default : dbg.Verbose(0, "gdcmDocument::CheckSwap:", "ACR/NEMA unfound swap info (Really hopeless !)"); - filetype = gdcmUnknown; + Filetype = gdcmUnknown; return false; } @@ -2437,7 +2345,7 @@ bool gdcmDocument::CheckSwap() { * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. */ -void gdcmDocument::SwitchSwapToBigEndian(void) +void gdcmDocument::SwitchSwapToBigEndian() { dbg.Verbose(1, "gdcmDocument::SwitchSwapToBigEndian", "Switching to BigEndian mode."); @@ -2468,7 +2376,7 @@ void gdcmDocument::SetMaxSizeLoadEntry(long NewSize) { if (NewSize < 0) return; - if ((guint32)NewSize >= (guint32)0xffffffff) + if ((uint32_t)NewSize >= (uint32_t)0xffffffff) { MaxSizeLoadEntry = 0xffffffff; return; @@ -2486,7 +2394,7 @@ void gdcmDocument::SetMaxSizePrintEntry(long NewSize) { if (NewSize < 0) return; - if ((guint32)NewSize >= (guint32)0xffffffff) + if ((uint32_t)NewSize >= (uint32_t)0xffffffff) { MaxSizePrintEntry = 0xffffffff; return; @@ -2503,11 +2411,10 @@ void gdcmDocument::SetMaxSizePrintEntry(long NewSize) * gets the VR, gets the length, gets the offset value) * @return On succes the newly created DocEntry, NULL on failure. */ -gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) { - guint16 g,n; +gdcmDocEntry *gdcmDocument::ReadNextDocEntry() { + uint16_t g = ReadInt16(); + uint16_t n = ReadInt16(); gdcmDocEntry *NewEntry; - g = ReadInt16(); - n = ReadInt16(); if (errno == 1) // We reached the EOF (or an error occured) therefore @@ -2518,7 +2425,8 @@ gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) { FindDocEntryVR(NewEntry); FindDocEntryLength(NewEntry); - if (errno == 1) { + if (errno == 1) + { // Call it quits delete NewEntry; return NULL; @@ -2527,221 +2435,46 @@ gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) { return NewEntry; } -/** - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Name Name of the underlying DictEntry - */ -gdcmDocEntry *gdcmDocument::NewDocEntryByName(std::string Name) -{ - gdcmDictEntry *NewTag = GetDictEntryByName(Name); - if (!NewTag) - NewTag = NewVirtualDictEntry(0xffff, 0xffff, "LO", "unkn", Name); - - gdcmDocEntry* NewEntry = new gdcmDocEntry(NewTag); - if (!NewEntry) - { - dbg.Verbose(1, "gdcmDocument::ObtainDocEntryByName", - "failed to allocate gdcmDocEntry"); - return (gdcmDocEntry *)0; - } - return NewEntry; -} - -/** - * \brief Request a new virtual dict entry to the dict set - * @param group group number of the underlying DictEntry - * @param element element number of the underlying DictEntry - * @param vr VR of the underlying DictEntry - * @param fourth owner group - * @param name english name - */ -gdcmDictEntry *gdcmDocument::NewVirtualDictEntry(guint16 group, guint16 element, - std::string vr, - std::string fourth, - std::string name) -{ - return gdcmGlobal::GetDicts()->NewVirtualDictEntry(group,element,vr,fourth,name); -} - -/** - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Group group number of the underlying DictEntry - * @param Elem element number of the underlying DictEntry - */ -gdcmDocEntry* gdcmDocument::NewDocEntryByNumber(guint16 Group, guint16 Elem) -{ - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); - if (!DictEntry) - DictEntry = NewVirtualDictEntry(Group, Elem); - - gdcmDocEntry *NewEntry = new gdcmDocEntry(DictEntry); - if (!NewEntry) - { - dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber", - "failed to allocate gdcmDocEntry"); - return (gdcmDocEntry*)0; - } - return NewEntry; -} - - -/** - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Group group number of the underlying DictEntry - * @param Elem element number of the underlying DictEntry - */ -gdcmValEntry *gdcmDocument::NewValEntryByNumber(guint16 Group, guint16 Elem) -{ - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); - if (!DictEntry) - DictEntry = NewVirtualDictEntry(Group, Elem); - - gdcmValEntry *NewEntry = new gdcmValEntry(DictEntry); - if (!NewEntry) - { - dbg.Verbose(1, "gdcmDocument::NewValEntryByNumber", - "failed to allocate gdcmValEntry"); - return NULL; - } - return NewEntry; -} - - -/** - * \brief Build a new Element Value from all the low level arguments. - * Check for existence of dictionary entry, and build - * a default one when absent. - * @param Group group number of the underlying DictEntry - * @param Elem element number of the underlying DictEntry - */ -gdcmBinEntry *gdcmDocument::NewBinEntryByNumber(guint16 Group, guint16 Elem) -{ - // Find out if the tag we encountered is in the dictionaries: - gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem); - if (!DictEntry) - DictEntry = NewVirtualDictEntry(Group, Elem); - - gdcmBinEntry *NewEntry = new gdcmBinEntry(DictEntry); - if (!NewEntry) - { - dbg.Verbose(1, "gdcmDocument::NewBinEntryByNumber", - "failed to allocate gdcmBinEntry"); - return NULL; - } - return NewEntry; -} /** - * \brief Generate a free TagKey i.e. a TagKey that is not present + * \brief Generate a free gdcmTagKey i.e. a gdcmTagKey that is not present * in the TagHt dictionary. * @param group The generated tag must belong to this group. * @return The element of tag with given group which is fee. */ -guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group) +uint32_t gdcmDocument::GenerateFreeTagKeyInGroup(uint16_t group) { - for (guint32 elem = 0; elem < UINT32_MAX; elem++) + for (uint32_t elem = 0; elem < UINT32_MAX; elem++) { - TagKey key = gdcmDictEntry::TranslateToKey(group, elem); + gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, elem); if (tagHT.count(key) == 0) return elem; } return UINT32_MAX; } - -/** - * \brief Searches both the public and the shadow dictionary (when they - * exist) for the presence of the DictEntry with given name. - * The public dictionary has precedence on the shadow one. - * @param Name name of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. - */ -gdcmDictEntry *gdcmDocument::GetDictEntryByName(std::string Name) -{ - gdcmDictEntry *found = (gdcmDictEntry *)0; - if (!RefPubDict && !RefShaDict) - { - dbg.Verbose(0, "gdcmDocument::GetDictEntry", - "we SHOULD have a default dictionary"); - } - if (RefPubDict) - { - found = RefPubDict->GetDictEntryByName(Name); - if (found) - return found; - } - if (RefShaDict) - { - found = RefShaDict->GetDictEntryByName(Name); - if (found) - return found; - } - return found; -} - -/** - * \brief Searches both the public and the shadow dictionary (when they - * exist) for the presence of the DictEntry with given - * group and element. The public dictionary has precedence on the - * shadow one. - * @param group group number of the searched DictEntry - * @param element element number of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. - */ -gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element) -{ - gdcmDictEntry *found = (gdcmDictEntry *)0; - if (!RefPubDict && !RefShaDict) - { - dbg.Verbose(0, "gdcmDocument::GetDictEntry", - "we SHOULD have a default dictionary"); - } - if (RefPubDict) - { - found = RefPubDict->GetDictEntryByNumber(group, element); - if (found) - return found; - } - if (RefShaDict) - { - found = RefShaDict->GetDictEntryByNumber(group, element); - if (found) - return found; - } - return found; -} - /** * \brief Assuming the internal file pointer \ref gdcmDocument::fp - * is placed at the beginning of a tag (TestGroup, TestElement), - * read the length associated to the Tag. + * is placed at the beginning of a tag check whether this + * tag is (TestGroup, TestElement). * \warning On success the internal file pointer \ref gdcmDocument::fp - * is modified to point after the tag and it's length. + * is modified to point after the tag. * On failure (i.e. when the tag wasn't the expected tag * (TestGroup, TestElement) the internal file pointer * \ref gdcmDocument::fp is restored to it's original position. * @param TestGroup The expected group of the tag. * @param TestElement The expected Element of the tag. - * @return On success returns the length associated to the tag. On failure - * returns 0. + * @return True on success, false otherwise. */ -guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement) +bool gdcmDocument::ReadTag(uint16_t TestGroup, uint16_t TestElement) { - guint16 ItemTagGroup; - guint16 ItemTagElement; + uint16_t ItemTagGroup; + uint16_t ItemTagElement; long PositionOnEntry = ftell(fp); long CurrentPosition = ftell(fp); // On debugging purposes //// Read the Item Tag group and element, and make - // sure they are respectively 0xfffe and 0xe000: + // sure they are what we expected: ItemTagGroup = ReadInt16(); ItemTagElement = ReadInt16(); if ( (ItemTagGroup != TestGroup) || (ItemTagElement != TestElement ) ) @@ -2756,12 +2489,38 @@ guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement) dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:"); dbg.Verbose(0, s.str().c_str()); fseek(fp, PositionOnEntry, SEEK_SET); + return false; + } + return true; +} + +/** + * \brief Assuming the internal file pointer \ref gdcmDocument::fp + * is placed at the beginning of a tag (TestGroup, TestElement), + * read the length associated to the Tag. + * \warning On success the internal file pointer \ref gdcmDocument::fp + * is modified to point after the tag and it's length. + * On failure (i.e. when the tag wasn't the expected tag + * (TestGroup, TestElement) the internal file pointer + * \ref gdcmDocument::fp is restored to it's original position. + * @param TestGroup The expected group of the tag. + * @param TestElement The expected Element of the tag. + * @return On success returns the length associated to the tag. On failure + * returns 0. + */ +uint32_t gdcmDocument::ReadTagLength(uint16_t TestGroup, uint16_t TestElement) +{ + long PositionOnEntry = ftell(fp); + (void)PositionOnEntry; + + if ( !ReadTag(TestGroup, TestElement) ) + { return 0; } //// Then read the associated Item Length - CurrentPosition=ftell(fp); - guint32 ItemLength; + long CurrentPosition = ftell(fp); + uint32_t ItemLength; ItemLength = ReadInt32(); { std::ostringstream s; @@ -2773,38 +2532,12 @@ guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement) return ItemLength; } -/** - * \brief Read the length of an exptected Item tag i.e. (0xfffe, 0xe000). - * \sa \ref gdcmDocument::ReadTagLength - * \warning See warning of \ref gdcmDocument::ReadTagLength - * @return On success returns the length associated to the item tag. - * On failure returns 0. - */ -guint32 gdcmDocument::ReadItemTagLength(void) -{ - return ReadTagLength(0xfffe, 0xe000); -} - -/** - * \brief Read the length of an exptected Sequence Delimiter tag i.e. - * (0xfffe, 0xe0dd). - * \sa \ref gdcmDocument::ReadTagLength - * \warning See warning of \ref gdcmDocument::ReadTagLength - * @return On success returns the length associated to the Sequence - * Delimiter tag. On failure returns 0. - */ -guint32 gdcmDocument::ReadSequenceDelimiterTagLength(void) -{ - return ReadTagLength(0xfffe, 0xe0dd); -} - - /** * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files * No other way so 'skip' the Data * */ -void gdcmDocument::Parse7FE0 (void) +void gdcmDocument::Parse7FE0 () { gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) @@ -2815,11 +2548,11 @@ void gdcmDocument::Parse7FE0 (void) || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier ! || IsDeflatedExplicitVRLittleEndianTransferSyntax() ) return; - + // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels //// Read the Basic Offset Table Item Tag length... - guint32 ItemLength = ReadItemTagLength(); + uint32_t ItemLength = ReadTagLength(0xfffe, 0xe000); //// ... and then read length[s] itself[themselves]. We don't use // the values read (BTW what is the purpous of those lengths ?) @@ -2827,9 +2560,9 @@ void gdcmDocument::Parse7FE0 (void) // BTW, what is the purpous of those length anyhow !? char * BasicOffsetTableItemValue = new char[ItemLength + 1]; fread(BasicOffsetTableItemValue, ItemLength, 1, fp); - for (int i=0; i < ItemLength; i += 4){ - guint32 IndividualLength; - IndividualLength = str2num(&BasicOffsetTableItemValue[i],guint32); + for (unsigned int i=0; i < ItemLength; i += 4){ + uint32_t IndividualLength; + IndividualLength = str2num(&BasicOffsetTableItemValue[i],uint32_t); std::ostringstream s; s << " Read one length: "; s << std::hex << IndividualLength << std::endl; @@ -2842,11 +2575,10 @@ void gdcmDocument::Parse7FE0 (void) // JPEG Image //// We then skip (not reading them) all the fragments of images: - while ( ItemLength = ReadItemTagLength() ) + while ( (ItemLength = ReadTagLength(0xfffe, 0xe000)) ) { SkipBytes(ItemLength); } - } else { @@ -2854,22 +2586,18 @@ void gdcmDocument::Parse7FE0 (void) long ftellRes; long RleSegmentLength[15], fragmentLength; - // while 'Sequence Delimiter Item' (fffe,e0dd) not found - while ( fragmentLength = ReadSequenceDelimiterTagLength() ) + // While we find some items: + while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) ) { // Parse fragments of the current Fragment (Frame) //------------------ scanning (not reading) fragment pixels - guint32 nbRleSegments = ReadInt32(); - printf(" Nb of RLE Segments : %d\n",nbRleSegments); + uint32_t nbRleSegments = ReadInt32(); //// Reading RLE Segments Offset Table - guint32 RleSegmentOffsetTable[15]; + uint32_t RleSegmentOffsetTable[15]; for(int k=1; k<=15; k++) { ftellRes=ftell(fp); RleSegmentOffsetTable[k] = ReadInt32(); - printf(" at : %x Offset Segment %d : %d (%x)\n", - (unsigned)ftellRes,k,RleSegmentOffsetTable[k], - RleSegmentOffsetTable[k]); } // skipping (not reading) RLE Segments @@ -2878,9 +2606,6 @@ void gdcmDocument::Parse7FE0 (void) RleSegmentLength[k]= RleSegmentOffsetTable[k+1] - RleSegmentOffsetTable[k]; ftellRes=ftell(fp); - printf (" Segment %d : Length = %d x(%x) Start at %x\n", - k,(unsigned)RleSegmentLength[k], - (unsigned)RleSegmentLength[k], (unsigned)ftellRes); SkipBytes(RleSegmentLength[k]); } } @@ -2888,15 +2613,21 @@ void gdcmDocument::Parse7FE0 (void) RleSegmentLength[nbRleSegments]= fragmentLength - RleSegmentOffsetTable[nbRleSegments]; ftellRes=ftell(fp); - printf (" Segment %d : Length = %d x(%x) Start at %x\n", - nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments], - (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes); SkipBytes(RleSegmentLength[nbRleSegments]); } + + // Make sure that at the end of the item we encounter a 'Sequence + // Delimiter Item': + if ( ! ReadTag(0xfffe, 0xe0dd) ) + { + dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item"); + dbg.Verbose(0, " at end of RLE item sequence"); + } } - return; } + + /** * \brief Compares two documents, according to \ref gdcmDicomDir rules * \warning Does NOT work with ACR-NEMA files @@ -2904,47 +2635,48 @@ void gdcmDocument::Parse7FE0 (void) * @param document * @return true if 'smaller' */ - bool gdcmDocument::operator<(gdcmDocument &document){ +bool gdcmDocument::operator<(gdcmDocument &document) +{ std::string s1,s2; // Patient Name s1=this->GetEntryByNumber(0x0010,0x0010); s2=document.GetEntryByNumber(0x0010,0x0010); if(s1 < s2) - return(true); + return true; else if(s1 > s2) - return(false); + return false; else { // Patient ID s1=this->GetEntryByNumber(0x0010,0x0020); s2=document.GetEntryByNumber(0x0010,0x0020); if (s1 < s2) - return(true); + return true; else if (s1 > s2) - return(1); + return true; else { // Study Instance UID s1=this->GetEntryByNumber(0x0020,0x000d); s2=document.GetEntryByNumber(0x0020,0x000d); if (s1 < s2) - return(true); + return true; else if(s1 > s2) - return(false); + return false; else { // Serie Instance UID s1=this->GetEntryByNumber(0x0020,0x000e); s2=document.GetEntryByNumber(0x0020,0x000e); if (s1 < s2) - return(true); + return true; else if(s1 > s2) - return(false); + return false; } } } - return(false); + return false; }