X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmDocument.cxx;h=e29c08bfc24dd287b2ecbacc27528ac6955d67ea;hb=65f457a97152fce4878d7aa20ec02f4ccda20705;hp=9dd23bbcd964189f379acf978a324b37bf020e95;hpb=8e1fe98f7659cec85bcbce8551e28f8e45971370;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 9dd23bbc..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" @@ -51,7 +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)) //----------------------------------------------------------------------------- @@ -80,23 +95,23 @@ 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()); + Filename.c_str()); rewind(fp); fseek(fp,0L,SEEK_END); @@ -110,6 +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(); // -------------------------------------------------------------- @@ -124,7 +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); @@ -159,17 +194,8 @@ gdcmDocument::~gdcmDocument (void) { // Recursive clean up of sequences for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it ) - { - gdcmDocEntry * entry = it->second; - if ( gdcmSeqEntry* SeqEntry = dynamic_cast(entry) ) - { - delete SeqEntry; - RemoveEntry(SeqEntry); - } - else - { - RemoveEntry(entry); - } + { + delete it->second; } tagHT.clear(); } @@ -236,7 +262,7 @@ bool gdcmDocument::SetShaDict(DictKey dictName){ * false otherwise. */ bool gdcmDocument::IsReadable(void) { - if(filetype==gdcmUnknown) { + if(Filetype==gdcmUnknown) { dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype"); return(false); } @@ -249,6 +275,7 @@ bool gdcmDocument::IsReadable(void) { return(true); } + /** * \brief Internal function that checks whether the Transfer Syntax given * as argument is the one present in the current document. @@ -382,11 +409,12 @@ bool gdcmDocument::IsRLELossLessTransferSyntax(void) * @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_90) ); + || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_70) ); // was 90 } /** @@ -419,7 +447,7 @@ bool gdcmDocument::IsDicomV3(void) { * @return the FileType code */ FileType gdcmDocument::GetFileType(void) { - return(filetype); + return Filetype; } /** @@ -430,7 +458,7 @@ 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) { @@ -438,11 +466,9 @@ FILE *gdcmDocument::OpenFile(bool 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; } } @@ -453,22 +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; } /** @@ -485,34 +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); @@ -525,7 +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); @@ -540,19 +560,22 @@ 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; } /** @@ -568,7 +591,8 @@ bool gdcmDocument::Write(FILE *fp, FileType type) { gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( std::string Value, guint16 Group, - guint16 Elem ){ + guint16 Elem ) +{ gdcmDocEntry* CurrentEntry; gdcmValEntry* ValEntry; @@ -581,7 +605,7 @@ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to" " NewDocEntryByNumber failed."); - return (gdcmValEntry *)0; + return NULL; } ValEntry = new gdcmValEntry(CurrentEntry); if ( !AddEntry(ValEntry)) @@ -601,13 +625,13 @@ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal" " of previous DocEntry failed."); - return (gdcmValEntry *)0; + return NULL; } if ( !AddEntry(ValEntry)) { dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding" " promoted ValEntry failed."); - return (gdcmValEntry *)0; + return NULL; } } } @@ -626,26 +650,27 @@ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( * \return pointer to the modified/created Header Entry (NULL when creation * failed). */ - - gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( void *voidArea, int lgth, guint16 Group, - guint16 Elem ){ + guint16 Elem) +{ gdcmDocEntry* a; - gdcmBinEntry* b; + gdcmBinEntry* b; a = GetDocEntryByNumber( Group, Elem); if (a == NULL) { a =NewBinEntryByNumber(Group, Elem); if (a == NULL) return NULL; - b = new gdcmBinEntry(a); + + b = new gdcmBinEntry(a); AddEntry(b); } SetEntryByNumber(voidArea, lgth, Group, Elem); b->SetVoidArea(voidArea); - return (gdcmBinEntry*)b; + + return b; } @@ -676,7 +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); } /** @@ -693,7 +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()); } /** @@ -709,7 +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; @@ -782,8 +807,8 @@ 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()); } /** @@ -837,10 +862,11 @@ bool gdcmDocument::SetEntryByNumber(void *content, 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). { @@ -891,8 +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(); @@ -910,8 +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(); @@ -930,11 +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); @@ -949,7 +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 @@ -972,7 +997,7 @@ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, * Only non even entries are analyzed */ void gdcmDocument::UpdateShaEntries(void) { - gdcmDictEntry *entry; + //gdcmDictEntry *entry; std::string vr; /// \todo TODO : still any use to explore recursively the whole structure? @@ -1079,236 +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(); - 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. @@ -1336,7 +1131,7 @@ guint32 gdcmDocument::SwapLong(guint32 a) { a=0; } return(a); -} +} /** * \brief Unswaps back the bytes of 4-byte long integer accordingly to @@ -1370,17 +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(); @@ -1394,17 +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) { @@ -1431,9 +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 { @@ -1441,7 +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 @@ -1461,6 +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); @@ -1469,8 +1275,8 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool break; } } + delete NewDocEntry; } - delete NewDocEntry; return l; // ?? } @@ -1482,19 +1288,21 @@ 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; } @@ -1505,7 +1313,6 @@ 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) @@ -1515,7 +1322,7 @@ 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; @@ -1530,7 +1337,8 @@ 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(); @@ -1544,9 +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; } @@ -1559,21 +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) ) { @@ -1647,7 +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") ) { @@ -1754,7 +1579,7 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) { */ void gdcmDocument::FindDocEntryVR( gdcmDocEntry *Entry) { - if (filetype != gdcmExplicitVR) + if (Filetype != gdcmExplicitVR) return; char VR[3]; @@ -1998,16 +1823,6 @@ 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 @@ -2186,7 +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); @@ -2206,7 +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); @@ -2238,7 +2053,7 @@ void gdcmDocument::SkipBytes(guint32 NBytes) { void gdcmDocument::Initialise(void) { RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict(); - RefShaDict = (gdcmDict*)0; + RefShaDict = NULL; } /** @@ -2311,13 +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"); } @@ -2362,19 +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 : @@ -2400,18 +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; } @@ -2505,15 +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); @@ -2527,117 +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; -} - - -/** - * \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 @@ -2657,68 +2352,6 @@ 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. - */ -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), @@ -2786,7 +2419,7 @@ guint32 gdcmDocument::ReadItemTagLength(void) } /** - * \brief Read the length of an exptected Sequence Delimiter tag i.e. + * \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 @@ -2804,6 +2437,7 @@ guint32 gdcmDocument::ReadSequenceDelimiterTagLength(void) * No other way so 'skip' the Data * */ + void gdcmDocument::Parse7FE0 (void) { gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010); @@ -2827,7 +2461,7 @@ 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){ + for (unsigned int i=0; i < ItemLength; i += 4){ guint32 IndividualLength; IndividualLength = str2num(&BasicOffsetTableItemValue[i],guint32); std::ostringstream s; @@ -2842,7 +2476,7 @@ void gdcmDocument::Parse7FE0 (void) // JPEG Image //// We then skip (not reading them) all the fragments of images: - while ( ItemLength = ReadItemTagLength() ) + while ( (ItemLength = ReadItemTagLength()) ) { SkipBytes(ItemLength); } @@ -2855,7 +2489,7 @@ void gdcmDocument::Parse7FE0 (void) long RleSegmentLength[15], fragmentLength; // while 'Sequence Delimiter Item' (fffe,e0dd) not found - while ( fragmentLength = ReadSequenceDelimiterTagLength() ) + while ( (fragmentLength = ReadSequenceDelimiterTagLength()) ) { // Parse fragments of the current Fragment (Frame) //------------------ scanning (not reading) fragment pixels @@ -2894,9 +2528,10 @@ void gdcmDocument::Parse7FE0 (void) SkipBytes(RleSegmentLength[nbRleSegments]); } } - return; } + + /** * \brief Compares two documents, according to \ref gdcmDicomDir rules * \warning Does NOT work with ACR-NEMA files @@ -2904,47 +2539,48 @@ 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; }