X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=e29c08bfc24dd287b2ecbacc27528ac6955d67ea;hb=65f457a97152fce4878d7aa20ec02f4ccda20705;hp=3b4c2d4a7c9ccef460ac9a6274d43ec550fd797e;hpb=9f596ccd6001b165eca959c6a7b104eb10ff9911;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 3b4c2d4a..e29c08bf 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -1,5 +1,20 @@ -// gdcmDocument.cxx -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDocument.cxx,v $ + Language: C++ + Date: $Date: 2004/06/23 15:01:57 $ + Version: $Revision: 1.29 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ #include "gdcmDocument.h" #include "gdcmValEntry.h" @@ -22,12 +37,36 @@ # include +// Implicit VR Little Endian #define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" +// Explicit VR Little Endian #define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1" -#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2" +// Deflated Explicit VR Little Endian #define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" -#define UI1_1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5" - +// Explicit VR Big Endian +#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2" +// JPEG Baseline (Process 1) +#define UI1_2_840_10008_1_2_4_50 "1.2.840.10008.1.2.4.50" +// JPEG Extended (Process 2 & 4) +#define UI1_2_840_10008_1_2_4_51 "1.2.840.10008.1.2.4.51" +// JPEG Extended (Process 3 & 5) +#define UI1_2_840_10008_1_2_4_52 "1.2.840.10008.1.2.4.52" +// JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8) +#define UI1_2_840_10008_1_2_4_53 "1.2.840.10008.1.2.4.53" +// JPEG Full Progression, Non-Hierarchical (Process 10 & 12) +#define UI1_2_840_10008_1_2_4_55 "1.2.840.10008.1.2.4.55" +// JPEG Lossless, Non-Hierarchical (Process 14) +#define UI1_2_840_10008_1_2_4_57 "1.2.840.10008.1.2.4.57" +// JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, +// [Selection Value 1]) +#define UI1_2_840_10008_1_2_4_70 "1.2.840.10008.1.2.4.70" +// JPEG 2000 Lossless +#define UI1_2_840_10008_1_2_4_90 "1.2.840.10008.1.2.4.90" +// JPEG 2000 +#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)) //----------------------------------------------------------------------------- @@ -56,24 +95,24 @@ 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) +gdcmDocument::gdcmDocument(std::string const & inFilename, + bool exception_on_error, + bool enable_sequences, + bool ignore_shadow) : gdcmElementSet(-1) { enableSequences=enable_sequences; - ignoreShadow =ignore_shadow; + IgnoreShadow =ignore_shadow; 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()); rewind(fp); - //if (!CheckSwap()) - // return false; // to go on compiling fseek(fp,0L,SEEK_END); long lgt = ftell(fp); @@ -86,6 +125,26 @@ 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(); // -------------------------------------------------------------- @@ -100,7 +159,7 @@ 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); @@ -132,12 +191,17 @@ gdcmDocument::gdcmDocument(bool exception_on_error) gdcmDocument::~gdcmDocument (void) { RefPubDict = NULL; RefShaDict = NULL; + + // Recursive clean up of sequences + for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it ) + { + delete it->second; + } + tagHT.clear(); } //----------------------------------------------------------------------------- // Print -/** - /** * \brief Prints The Dict Entries of THE public Dicom Dictionary @@ -198,50 +262,73 @@ bool gdcmDocument::SetShaDict(DictKey dictName){ * false otherwise. */ bool gdcmDocument::IsReadable(void) { - if(filetype==gdcmUnknown) { - std::cout << "wrong filetype" <GetValue(); - if ( Transfer == UI1_2_840_10008_1_2 ) - return true; + // 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) ) + { + 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]) ) + { + Transfer.erase(Transfer.length()-1, 1); + } + if ( Transfer == SyntaxToCheck ) + return true; + } return false; } +/** + * \brief Determines if the Transfer Syntax of the present document + * corresponds to a Implicit Value Representation of + * Little Endian. + * \sa \ref gdcmDocument::IsGivenTransferSyntax. + * @return True when ImplicitVRLittleEndian found. False in all other cases. + */ +bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2); +} + /** * \brief Determines if the Transfer Syntax was already encountered * and if it corresponds to a ExplicitVRLittleEndian one. * @return True when ExplicitVRLittleEndian found. False in all other cases. */ -bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_1 ) - return true; - return false; +bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1); } /** @@ -249,16 +336,9 @@ 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) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); - - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_1_99 ) - return true; - return false; +bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99); } /** @@ -266,16 +346,99 @@ 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) { - gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); - if ( !Element ) - return false; - LoadDocEntrySafe(Element); +bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2); +} - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier ! - return true; - return false; +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGBaseLineProcess1 one. + * @return True when JPEGBaseLineProcess1found. False in all other cases. + */ +bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * 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) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * 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) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one. + * @return True when JPEGSpectralSelectionProcess6-8 found. False in all + * other cases. + */ +bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53); +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a RLE Lossless one. + * @return True when RLE Lossless found. False in all + * other cases. + */ +bool gdcmDocument::IsRLELossLessTransferSyntax(void) +{ + return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5); +} + +/** + * \brief Determines if Transfer Syntax was already encountered + * and if it corresponds to a JPEG Lossless one. + * @return True when RLE Lossless found. False in all + * other cases. + */ + +bool gdcmDocument::IsJPEGLossless(void) +{ + 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_70) ); // was 90 +} + +/** + * \brief Determines if the Transfer Syntax was already encountered + * and if it corresponds to a JPEG2000 one + * @return True when JPEG2000 (Lossly or LossLess) found. False in all + * other cases. + */ +bool gdcmDocument::IsJPEG2000(void) +{ + return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) ); +} + +/** + * \brief Predicate for dicom version 3 file. + * @return True when the file is a dicom version 3. + */ +bool gdcmDocument::IsDicomV3(void) { + // 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); } /** @@ -284,7 +447,7 @@ bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) { * @return the FileType code */ FileType gdcmDocument::GetFileType(void) { - return(filetype); + return Filetype; } /** @@ -295,11 +458,18 @@ FileType gdcmDocument::GetFileType(void) { FILE *gdcmDocument::OpenFile(bool exception_on_error) throw(gdcmFileError) { - fp=fopen(filename.c_str(),"rb"); - if(exception_on_error) + fp=fopen(Filename.c_str(),"rb"); + + if(!fp) { - if(!fp) - throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)"); + if(exception_on_error) + throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)"); + else + { + dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ", + Filename.c_str()); + return NULL; + } } if ( fp ) @@ -309,22 +479,22 @@ FILE *gdcmDocument::OpenFile(bool exception_on_error) //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()); + dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", Filename.c_str()); } - return(NULL); + return NULL; } /** @@ -341,34 +511,28 @@ bool gdcmDocument::CloseFile(void) { /** * \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) { +bool gdcmDocument::WriteF(FileType filetype) { /// \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) +/// ============== +/// The stuff is rewritten using the SeQuence based +/// tree-like stucture (cf : Print ) /// To be checked /// ============= /// \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) + if (filetype == gdcmImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); @@ -381,7 +545,7 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { SetEntryLengthByNumber(18, 0x0002, 0x0010); } - if (type == gdcmExplicitVR) + if (filetype == gdcmExplicitVR) { std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); @@ -396,48 +560,120 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { /** * \todo rewrite later, if really usefull + * ('Group Length' element is optional in DICOM) * - * --> Warning : un-updated odd groups lengths can causes pb + * --> Warning : un-updated odd groups lengthes 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); - WriteEntries(fp,type); - return(true); + /// WriteEntries(fp,type); // old stuff + return true; } /** * \brief Modifies the value of a given Header Entry (Dicom Element) * when it exists. Create it with the given value when unexistant. - * @param Value Value to be set + * @param Value (string) Value to be set * @param Group Group number of the Entry * @param Elem Element number of the Entry * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ - - -gdcmDocEntry * gdcmDocument::ReplaceOrCreateByNumber( + +gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( std::string Value, guint16 Group, - guint16 Elem ){ + guint16 Elem ) +{ + gdcmDocEntry* CurrentEntry; + gdcmValEntry* ValEntry; + + CurrentEntry = GetDocEntryByNumber( Group, Elem); + if (!CurrentEntry) + { + // The entry wasn't present and we simply create the required ValEntry: + CurrentEntry = NewDocEntryByNumber(Group, Elem); + if (!CurrentEntry) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" + " NewDocEntryByNumber failed."); + return NULL; + } + ValEntry = new gdcmValEntry(CurrentEntry); + if ( !AddEntry(ValEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry" + " failed allthough this is a creation."); + } + } + else + { + ValEntry = dynamic_cast< gdcmValEntry* >(CurrentEntry); + if ( !ValEntry ) + { + // We need to promote the gdcmDocEntry to a gdcmValEntry: + ValEntry = new gdcmValEntry(CurrentEntry); + if (!RemoveEntry(CurrentEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" + " of previous DocEntry failed."); + return NULL; + } + if ( !AddEntry(ValEntry)) + { + dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" + " promoted ValEntry failed."); + return NULL; + } + } + } + + SetEntryByNumber(Value, Group, Elem); + + return ValEntry; +} + +/* + * \brief Modifies the value of a given Header Entry (Dicom Element) + * when it exists. Create it with the given value when unexistant. + * @param voidArea (binary) value to be set + * @param Group Group number of the Entry + * @param Elem Element number of the Entry + * \return pointer to the modified/created Header Entry (NULL when creation + * failed). + */ +gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( + void *voidArea, + int lgth, + guint16 Group, + guint16 Elem) +{ gdcmDocEntry* a; + gdcmBinEntry* b; a = GetDocEntryByNumber( Group, Elem); if (a == NULL) { - a =NewDocEntryByNumber(Group, Elem); + a =NewBinEntryByNumber(Group, Elem); if (a == NULL) return NULL; - AddEntry(a); + + b = new gdcmBinEntry(a); + AddEntry(b); } - SetEntryByNumber(Value, Group, Elem); - //a->SetValue(Value); - return(a); -} + SetEntryByNumber(voidArea, lgth, Group, Elem); + b->SetVoidArea(voidArea); + + return b; +} + + /** * \brief Set a new value if the invoked element exists @@ -465,7 +701,7 @@ bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 El */ int gdcmDocument::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { std::string key = gdcmDictEntry::TranslateToKey(group, element ); - return (tagHT.count(key)); + return tagHT.count(key); } /** @@ -482,7 +718,7 @@ std::string gdcmDocument::GetEntryByName(std::string tagName) { if( dictEntry == NULL) return GDCM_UNFOUND; - return(GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement())); + return GetEntryByNumber(dictEntry->GetGroup(),dictEntry->GetElement()); } /** @@ -498,7 +734,7 @@ 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; @@ -571,15 +807,15 @@ bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) { if( dictEntry == NULL) return false; - return(SetEntryByNumber(content,dictEntry->GetGroup(), - dictEntry->GetElement())); + return SetEntryByNumber(content,dictEntry->GetGroup(), + dictEntry->GetElement()); } /** * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. - * @param content new value to substitute with + * @param content new value (string) to substitute with * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ @@ -587,34 +823,63 @@ bool gdcmDocument::SetEntryByNumber(std::string content, guint16 group, guint16 element) { - TagKey key = gdcmDictEntry::TranslateToKey(group, element); - if ( ! tagHT.count(key)) + gdcmValEntry* ValEntry = GetValEntryByNumber(group, element); + if (!ValEntry) + { + dbg.Verbose(0, "gdcmDocument::SetEntryByNumber: no corresponding", + " ValEntry (try promotion first)."); return false; - int l = content.length(); - if(l%2) // Non even length are padded with a space (020H). - { - l++; - content = content + '\0'; } + + // Non even content must be padded with a space (020H). + if((content.length())%2) + content = content + '\0'; - gdcmDocEntry * a; - a = tagHT[key]; - - ((gdcmValEntry*)a)->SetValue(content); - - std::string vr = a->GetVR(); + ValEntry->SetValue(content); - guint32 lgr; + // Integers have a special treatement for their length: + VRKey vr = ValEntry->GetVR(); if( (vr == "US") || (vr == "SS") ) - lgr = 2; + ValEntry->SetLength(2); else if( (vr == "UL") || (vr == "SL") ) - lgr = 4; + ValEntry->SetLength(4); else - lgr = l; + ValEntry->SetLength(content.length()); - a->SetLength(lgr); return true; -} +} + +/** + * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) + * through it's (group, element) and modifies it's content with + * the given value. + * @param content new value (void *) to substitute with + * @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) +{ + (void)lgth; //not used + TagKey key = gdcmDictEntry::TranslateToKey(group, element); + if ( ! tagHT.count(key)) + return false; + +/* Hope Binray field length is never wrong + if(lgth%2) // Non even length are padded with a space (020H). + { + lgth++; + //content = content + '\0'; // fing a trick to enlarge a binary field? + } +*/ + gdcmBinEntry * a; + a = (gdcmBinEntry *)tagHT[key]; + a->SetVoidArea(content); + //a->SetLength(lgth); // ??? + return true; +} /** * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element) @@ -652,8 +917,7 @@ size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 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(); @@ -671,8 +935,7 @@ void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 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(); @@ -691,11 +954,12 @@ void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem) 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; - + } SetEntryVoidAreaByNumber(a, Group, Elem); /// \todo check the result size_t l2 = fread(a, 1, l ,fp); @@ -710,7 +974,7 @@ void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem) /** * \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 @@ -733,10 +997,10 @@ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, * Only non even entries are analyzed */ void gdcmDocument::UpdateShaEntries(void) { - gdcmDictEntry *entry; + //gdcmDictEntry *entry; std::string vr; - // TODO : if still any use (?) explore recursively the whole structure + /// \todo TODO : still any use to explore recursively the whole structure? /* for(ListTag::iterator it=listEntries.begin(); it!=listEntries.end(); @@ -764,7 +1028,7 @@ void gdcmDocument::UpdateShaEntries(void) { CheckDocEntryVR(*it,vr); (*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling - + } else { @@ -808,6 +1072,25 @@ gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(guint16 group, guint16 element) return tagHT.find(key)->second; } +/** + * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only + * returns a result when the corresponding entry is of type + * ValEntry. + * @return When present, the corresponding ValEntry. + */ +gdcmValEntry* gdcmDocument::GetValEntryByNumber(guint16 group, guint16 element) +{ + gdcmDocEntry* CurrentEntry = GetDocEntryByNumber(group, element); + if (! CurrentEntry) + return (gdcmValEntry*)0; + if ( gdcmValEntry* ValEntry = dynamic_cast(CurrentEntry) ) + { + return ValEntry; + } + dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry."); + return (gdcmValEntry*)0; +} + /** * \brief Loads the element while preserving the current * underlying file position indicator as opposed to @@ -821,227 +1104,6 @@ void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * 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(); - std::string 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 : to be re -written recursively ! - -void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type) -{ - (void)type; - guint16 group = tag->GetGroup(); - std::string 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 - // - // ------------------------------- - - -/* // to go on compiling - void *voidArea; - voidArea = tag->GetVoidArea(); // to go on compiling - 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(); - gdcmValEntry * Vtag = (gdcmValEntry *) tag; -std::cout << "gdcmDocument::WriteEntry Vtag->GetValue() " << Vtag->GetValue() << std::endl; - // 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) - { - Vtag->SetValue(Vtag->GetValue()+"\0"); - Vtag->SetLength(Vtag->GetReadLength()+1); - } - - WriteEntryTagVRLength(Vtag, _fp, type); - std::cout << "after WriteEntryTagVRLength " << std::endl; - WriteEntryValue(Vtag, _fp, type); - std::cout << "after WriteEntryValue " << std::endl; - 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) -{ - -// FIXME : explore recursively the whole structure... - - /// \todo (?) check write failures (after *each* fwrite) - - std::cout << "--------------------- gdcmDocument::WriteEntries " << std::endl; - for (TagDocEntryHT::iterator tag2=tagHT.begin(); - tag2 != tagHT.end(); - ++tag2) - { - - (*tag2).second->Print(); - - if ( type == gdcmACR ){ - if ((*tag2).second->GetGroup() < 0x0008) - // Ignore pure DICOM V3 groups - continue; - if ((*tag2).second->GetGroup() %2) - // Ignore the "shadow" groups - continue; - if ((*tag2).second->GetVR() == "SQ" ) // ignore Sequences - continue; - //if ((*tag2).second->GetDepthLevel() != 0) // Not only ignore the SQ element - // continue; - } - if (! WriteEntry((*tag2).second,_fp,type) ) { - std::cout << "Write Failure " << std::endl; - return false; - } else { - - } - } - return true; -} - - /** * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. @@ -1069,7 +1131,7 @@ guint32 gdcmDocument::SwapLong(guint32 a) { a=0; } return(a); -} +} /** * \brief Unswaps back the bytes of 4-byte long integer accordingly to @@ -1103,17 +1165,17 @@ 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) { gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0; - gdcmValEntry *vl; + gdcmValEntry *NewValEntry = (gdcmValEntry *)0; gdcmBinEntry *bn; gdcmSeqEntry *sq; VRKey vr; - long l; + unsigned long l; int depth; depth = set->GetDepthLevel(); @@ -1127,17 +1189,18 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool break; vr = NewDocEntry->GetVR(); - if (vr!="SQ") { + if (vr!="SQ") + { if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) ) { /////// ValEntry - vl= new gdcmValEntry(NewDocEntry->GetDictEntry()); - vl->Copy(NewDocEntry); - vl->SetDepthLevel(depth); - set->AddEntry(vl); - LoadDocEntry(vl); - if (/*!delim_mode && */vl->isItemDelimitor()) + NewValEntry = new gdcmValEntry(NewDocEntry->GetDictEntry()); + NewValEntry->Copy(NewDocEntry); + NewValEntry->SetDepthLevel(depth); + set->AddEntry(NewValEntry); + LoadDocEntry(NewValEntry); + if (NewValEntry->isItemDelimitor()) break; if ( !delim_mode && ftell(fp)-offset >= l_max) { @@ -1164,9 +1227,16 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool NewDocEntry->GetElement() == 0x0010 ) { if (NewDocEntry->GetLength()==0xffffffff) + { // Broken US.3405.1.dcm Parse7FE0(); // to skip the pixels // (multipart JPEG/RLE are trouble makers) + } + else + { + SkipToNextDocEntry(NewDocEntry); + l = NewDocEntry->GetFullLength(); + } } else { @@ -1174,7 +1244,9 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool SkipToNextDocEntry(NewDocEntry); l = NewDocEntry->GetFullLength(); } - } else { // VR = "SQ" + } + else + { // VR = "SQ" l=NewDocEntry->GetReadLength(); if (l != 0) // don't mess the delim_mode for zero-length sequence @@ -1194,6 +1266,7 @@ 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); @@ -1202,8 +1275,8 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool break; } } + delete NewDocEntry; } - delete NewDocEntry; return l; // ?? } @@ -1211,42 +1284,49 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool * \brief Parses a Sequence ( SeqEntry after SeqEntry) * @return parsed length for this level */ -long gdcmDocument::ParseSQ(gdcmSeqEntry *set, long offset, long l_max, bool delim_mode) { +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()) { - //add the Sequence Delimitor // TODO : find the trick to put it properly ! - set->SetSequenceDelimitationItem(NewDocEntry); - break; - } - } + if (NewDocEntry->isSequenceDelimitor()) { + set->SetSequenceDelimitationItem(NewDocEntry); + break; + } + } if (!delim_mode && (ftell(fp)-offset) >= l_max) { - break; + break; } + itemSQ = new gdcmSQItem(set->GetDepthLevel()); - itemSQ->AddEntry(NewDocEntry); // no value, no voidArea. Think of it while printing ! + itemSQ->AddEntry(NewDocEntry); l= NewDocEntry->GetReadLength(); - if (l ==0xffffffff) + if (l == 0xffffffff) dlm_mod = true; else dlm_mod=false; - + lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod); - set->AddEntry(itemSQ); - SQItemNumber ++; // a voir + set->AddEntry(itemSQ,SQItemNumber); + SQItemNumber ++; if (!delim_mode && (ftell(fp)-offset) >= l_max) { break; - } + } } lgth = ftell(fp) - offset; return(lgth); @@ -1257,7 +1337,8 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, long offset, long l_max, bool deli * 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(); @@ -1271,9 +1352,6 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) { // (fffe e0dd) tells us the current SeQuence just ended 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; } @@ -1286,21 +1364,41 @@ 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) { + if (gdcmBinEntry* BinEntryPtr = dynamic_cast< gdcmBinEntry* >(Entry) ) + { + std::ostringstream s; + 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->GetGroup(),BinEntryPtr->GetElement()); + return; + } + // Any compacter code suggested (?) if ( IsDocEntryAnInteger(Entry) ) { @@ -1374,7 +1472,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) { guint16 length16; - if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) ) + if ( (Filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) ) { if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { @@ -1481,7 +1579,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) { */ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry) { - if (filetype != gdcmExplicitVR) + if (Filetype != gdcmExplicitVR) return; char VR[3]; @@ -1725,22 +1823,13 @@ 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 this heuristic. + * applying some heuristics. */ -void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, guint32 FoundLength) +void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, + guint32 FoundLength) { Entry->SetReadLength(FoundLength); // will be updated only if a bug is found if ( FoundLength == 0xffffffff) { @@ -1752,48 +1841,61 @@ void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, guint32 FoundLeng if (FoundLength%2) { std::ostringstream s; - s << "Warning : Tag with uneven length " << FoundLength - << " in x(" << std::hex << gr << "," << el <<")" << std::dec; - dbg.Verbose(0,s.str().c_str()); + s << "Warning : Tag with uneven length " + << FoundLength + << " in x(" << std::hex << gr << "," << el <<")" << std::dec; + dbg.Verbose(0, s.str().c_str()); } - // Sorry for the patch! - // XMedCom did the trick to read some naughty GE images ... - if (FoundLength == 13) { - // The following 'if' will be removed when there is no more - // images on Creatis HDs with a 13 length for Manufacturer... - if ( (Entry->GetGroup() != 0x0008) || - ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){ - // end of remove area - FoundLength =10; - Entry->SetReadLength(10); // a bug is to be fixed + //////// Fix for some naughty General Electric images. + // Allthough not recent many such GE corrupted images are still present + // on Creatis hard disks. Hence this fix shall remain when such images + // are no longer in user (we are talking a few years, here)... + // Note: XMedCom probably uses such a trick since it is able to read + // those pesky GE images ... + if (FoundLength == 13) { // Only happens for this length ! + if ( (Entry->GetGroup() != 0x0008) + || ( (Entry->GetElement() != 0x0070) + && (Entry->GetElement() != 0x0080) ) ) + { + FoundLength = 10; + Entry->SetReadLength(10); /// \todo a bug is to be fixed !? } } - // to fix some garbage 'Leonardo' Siemens images - // May be commented out to avoid overhead - else if ( (Entry->GetGroup() == 0x0009) && - ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){ - FoundLength =4; - Entry->SetReadLength(4); // a bug is to be fixed + //////// Fix for some brain-dead 'Leonardo' Siemens images. + // Occurence of such images is quite low (unless one leaves close to a + // 'Leonardo' source. Hence, one might consider commenting out the + // following fix on efficiency reasons. + else + if ( (Entry->GetGroup() == 0x0009) + && ( (Entry->GetElement() == 0x1113) + || (Entry->GetElement() == 0x1114) ) ) + { + FoundLength = 4; + Entry->SetReadLength(4); /// \todo a bug is to be fixed !? } - // end of fix - // to try to 'go inside' SeQuences (with length), and not to skip them - else if ( Entry->GetVR() == "SQ") - { - if (enableSequences) // only if the user does want to ! - FoundLength =0; // ReadLength is unchanged + //////// Deal with sequences, but only on users request: + else + if ( ( Entry->GetVR() == "SQ") && enableSequences) + { + FoundLength = 0; // ReadLength is unchanged } - // we found a 'delimiter' element - // fffe|xxxx is just a marker, we don't take its length into account - else if(Entry->GetGroup() == 0xfffe) + //////// We encountered a 'delimiter' element i.e. a tag of the form + // "fffe|xxxx" which is just a marker. Delimiters length should not be + // taken into account. + else + if(Entry->GetGroup() == 0xfffe) { - // *normally, fffe|0000 doesn't exist ! - if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm - // causes extra troubles :-( - FoundLength =0; + // According to the norm, fffe|0000 shouldn't exist. BUT the Philips + // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to + // causes extra troubles... + if( Entry->GetElement() != 0x0000 ) + { + FoundLength = 0; + } } Entry->SetUsableLength(FoundLength); @@ -1810,6 +1912,7 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { guint16 group = Entry->GetGroup(); std::string vr = Entry->GetVR(); guint32 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 // able to swap it's element value properly. @@ -1819,29 +1922,29 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { return true; else { + // Allthough this should never happen, still some images have a + // corrupted group length [e.g. have a glance at offset x(8336) of + // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm]. + // Since for dicom compliant and well behaved headers, the present + // test is useless (and might even look a bit paranoid), when we + // encounter such an ill-formed image, we simply display a warning + // message and proceed on parsing (while crossing fingers). std::ostringstream s; int filePosition = ftell(fp); s << "Erroneous Group Length element length on : (" \ << std::hex << group << " , " << element << ") -before- position x(" << filePosition << ")" << "lgt : " << length; - // These 2 lines commented out : a *very dirty* patch - // to go on PrintHeader'ing gdcm-MR-PHILIPS-16-Multi-Seq.dcm. - // have a glance at offset x(8336) ... - // For *regular* headers, the test is useless.. - // lets's print a warning message and go on, - // instead of giving up with an error message - - //std::cout << s.str().c_str() << std::endl; - // dbg.Error("gdcmDocument::IsDocEntryAnInteger", - // s.str().c_str()); + dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() ); } } + if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) return true; return false; } + /** * \brief Find the Length till the next sequence delimiter * \warning NOT end user intended method ! @@ -1898,7 +2001,7 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *Entry) { * (swaps it depending on processor endianity) * @return read value */ -guint16 gdcmDocument::ReadInt16(void) { +guint16 gdcmDocument::ReadInt16() { guint16 g; size_t item_read; item_read = fread (&g, (size_t)2,(size_t)1, fp); @@ -1918,7 +2021,7 @@ guint16 gdcmDocument::ReadInt16(void) { * (swaps it depending on processor endianity) * @return read value */ -guint32 gdcmDocument::ReadInt32(void) { +guint32 gdcmDocument::ReadInt32() { guint32 g; size_t item_read; item_read = fread (&g, (size_t)4,(size_t)1, fp); @@ -1950,7 +2053,7 @@ void gdcmDocument::SkipBytes(guint32 NBytes) { void gdcmDocument::Initialise(void) { RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); - RefShaDict = (gdcmDict*)0; + RefShaDict = NULL; } /** @@ -2023,13 +2126,13 @@ 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"); } @@ -2074,19 +2177,19 @@ bool gdcmDocument::CheckSwap() { 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 : @@ -2112,18 +2215,18 @@ bool gdcmDocument::CheckSwap() { 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; } @@ -2217,15 +2320,6 @@ gdcmDocEntry *gdcmDocument::ReadNextDocEntry(void) { // header parsing has to be considered as finished. return (gdcmDocEntry *)0; -// Pb : how to propagate the element length (used in SkipDocEntry) -// direct call to SkipBytes ? - -// if (ignoreShadow == 1 && g%2 ==1) - // if user wants to skip shadow groups - // and current element *is* a shadow element - // we don't create anything -// return (gdcmDocEntry *)1; // to tell caller it's NOT finished - NewEntry = NewDocEntryByNumber(g, n); FindDocEntryVR(NewEntry); FindDocEntryLength(NewEntry); @@ -2239,100 +2333,6 @@ 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 NULL; - } - return NewEntry; -} - -/// \todo Never used; commented out, waiting for removal. -/** - * \brief Small utility function that creates a new manually crafted - * (as opposed as read from the file) gdcmDocEntry with user - * specified name and adds it to the public tag hash table. - * \note A fake TagKey is generated so the PubDict can keep it's coherence. - * @param NewTagName The name to be given to this new tag. - * @param VR The Value Representation to be given to this new tag. - * @return The newly hand crafted Element Value. - */ -//gdcmDocEntry *gdcmDocument::NewManualDocEntryToPubDict(std::string NewTagName, -// std::string VR) -//{ -// gdcmDocEntry *NewEntry = NULL; -// guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info -// guint32 FreeElem = 0; -// gdcmDictEntry *DictEntry = NULL; -// -// FreeElem = GenerateFreeTagKeyInGroup(StuffGroup); -// if (FreeElem == UINT32_MAX) -// { -// dbg.Verbose(1, "gdcmHeader::NewManualDocEntryToPubDict", -// "Group 0xffff in Public Dict is full"); -// return NULL; -// } -// -// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem, -// VR, "GDCM", NewTagName); -// NewEntry = new gdcmDocEntry(DictEntry); -// AddEntry(NewEntry); -// return NewEntry; -//} /** * \brief Generate a free TagKey i.e. a TagKey that is not present @@ -2353,274 +2353,235 @@ guint32 gdcmDocument::GenerateFreeTagKeyInGroup(guint16 group) /** - * \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. + * \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. */ -gdcmDictEntry *gdcmDocument::GetDictEntryByName(std::string Name) +guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement) { - gdcmDictEntry *found = (gdcmDictEntry *)0; - if (!RefPubDict && !RefShaDict) - { - dbg.Verbose(0, "gdcmDocument::GetDictEntry", - "we SHOULD have a default dictionary"); - } - if (RefPubDict) + guint16 ItemTagGroup; + guint16 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: + ItemTagGroup = ReadInt16(); + ItemTagElement = ReadInt16(); + if ( (ItemTagGroup != TestGroup) || (ItemTagElement != TestElement ) ) { - found = RefPubDict->GetDictEntryByName(Name); - if (found) - return found; + std::ostringstream s; + s << " We should have found tag ("; + s << std::hex << TestGroup << "," << TestElement << ")" << std::endl; + s << " but instead we encountered tag ("; + s << std::hex << ItemTagGroup << "," << ItemTagElement << ")" + << std::endl; + s << " at address: " << (unsigned)CurrentPosition << std::endl; + dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:"); + dbg.Verbose(0, s.str().c_str()); + fseek(fp, PositionOnEntry, SEEK_SET); + return 0; } - if (RefShaDict) + + //// Then read the associated Item Length + CurrentPosition=ftell(fp); + guint32 ItemLength; + ItemLength = ReadInt32(); { - found = RefShaDict->GetDictEntryByName(Name); - if (found) - return found; + std::ostringstream s; + s << "Basic Item Length is: " + << ItemLength << std::endl; + s << " at address: " << (unsigned)CurrentPosition << std::endl; + dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: ", s.str().c_str()); } - return found; + 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 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 of the searched DictEntry - * @param element element of the searched DictEntry - * @return Corresponding DictEntry when it exists, NULL otherwise. + * \brief Read the length of an expected 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. */ -gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element) +guint32 gdcmDocument::ReadSequenceDelimiterTagLength(void) { - 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; + return ReadTagLength(0xfffe, 0xe0dd); } /** - * \ingroup gdcmDocument * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files - * \ No other way so 'skip' the Data + * No other way so 'skip' the Data * */ -void gdcmDocument::Parse7FE0 (void) { +void gdcmDocument::Parse7FE0 (void) +{ gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); if ( !Element ) return; - std::string Transfer = ((gdcmValEntry *)Element)->GetValue(); - if (Transfer == UI1_2_840_10008_1_2 ) - return; - if ( Transfer == UI1_2_840_10008_1_2_1 ) - return; - if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier ! - return; - if ( Transfer == UI1_2_840_10008_1_2_1_99 ) + if ( IsImplicitVRLittleEndianTransferSyntax() + || IsExplicitVRLittleEndianTransferSyntax() + || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier ! + || IsDeflatedExplicitVRLittleEndianTransferSyntax() ) return; - int nb; - std::string str_nb=GetEntryByNumber(0x0028,0x0100); - if (str_nb == GDCM_UNFOUND ) { - nb = 16; - } else { - nb = atoi(str_nb.c_str() ); - if (nb == 12) nb =16; + // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels + + //// Read the Basic Offset Table Item Tag length... + guint32 ItemLength = ReadItemTagLength(); + + //// ... and then read length[s] itself[themselves]. We don't use + // the values read (BTW what is the purpous of those lengths ?) + if (ItemLength != 0) { + // BTW, what is the purpous of those length anyhow !? + char * BasicOffsetTableItemValue = new char[ItemLength + 1]; + fread(BasicOffsetTableItemValue, ItemLength, 1, fp); + for (unsigned int i=0; i < ItemLength; i += 4){ + guint32 IndividualLength; + IndividualLength = str2num(&BasicOffsetTableItemValue[i],guint32); + std::ostringstream s; + s << " Read one length: "; + s << std::hex << IndividualLength << std::endl; + dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str()); + } } - - guint16 ItemTagGr,ItemTagEl; - int ln; - long ftellRes; - - // -------------------- for Parsing : Position on begining of Jpeg/RLE Pixels - if ( Transfer != UI1_1_2_840_10008_1_2_5 ) { // !RLELossLessTransferSyntax + if ( ! IsRLELossLessTransferSyntax() ) + { // JPEG Image - ftellRes=ftell(fp); - fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr - fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El - if(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n", - (unsigned)ftellRes,ItemTagGr,ItemTagEl ); - ftellRes=ftell(fp); - fread(&ln,4,1,fp); - if(GetSwapCode()) - ln=SwapLong(ln); // Basic Offset Table Item Length - printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n", - (unsigned)ftellRes,ln,ln); - if (ln != 0) { - // What is it used for ?? - char * BasicOffsetTableItemValue= new char[ln+1]; - fread(BasicOffsetTableItemValue,ln,1,fp); - guint32 a; - for (int i=0;i1) { // skipping (not reading) RLE Segments - for(unsigned int k=1; k<=nbRleSegments-1; k++) { + // skipping (not reading) RLE Segments + if (nbRleSegments>1) { + for(unsigned int k=1; k<=nbRleSegments-1; k++) { 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); - fseek(fp,RleSegmentLength[k],SEEK_CUR); + k,(unsigned)RleSegmentLength[k], + (unsigned)RleSegmentLength[k], (unsigned)ftellRes); + SkipBytes(RleSegmentLength[k]); } } + 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); - - fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR); - - // ------------------ end of scanning fragment pixels - - ftellRes=ftell(fp); - fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr - fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El - if(GetSwapCode()) { - ItemTagGr=SwapShort(ItemTagGr); - ItemTagEl=SwapShort(ItemTagEl); - } - printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n", - (unsigned)ftellRes,ItemTagGr,ItemTagEl ); + nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments], + (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes); + SkipBytes(RleSegmentLength[nbRleSegments]); } } - return; } +/** + * \brief Compares two documents, according to \ref gdcmDicomDir rules + * \warning Does NOT work with ACR-NEMA files + * \todo Find a trick to solve the pb (use RET fields ?) + * @param document + * @return true if 'smaller' + */ +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; + else if(s1 > s2) + return false; + else + { + // Patient ID + s1=this->GetEntryByNumber(0x0010,0x0020); + s2=document.GetEntryByNumber(0x0010,0x0020); + if (s1 < s2) + return true; + else if (s1 > s2) + return true; + else + { + // Study Instance UID + s1=this->GetEntryByNumber(0x0020,0x000d); + s2=document.GetEntryByNumber(0x0020,0x000d); + if (s1 < s2) + return true; + else if(s1 > s2) + return false; + else + { + // Serie Instance UID + s1=this->GetEntryByNumber(0x0020,0x000e); + s2=document.GetEntryByNumber(0x0020,0x000e); + if (s1 < s2) + return true; + else if(s1 > s2) + return false; + } + } + } + return false; +} + + //-----------------------------------------------------------------------------