X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmParser.cxx;h=332b415adc257c92d47d68a429b73744bb9bf236;hb=801fe2221ca70b34c5c644b6f522aa1b7233945b;hp=3fa3cc97621bca32a74bda46cb621f3b772b966d;hpb=491d5e5c2e844e42a028babd349d91cccb9663dd;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index 3fa3cc97..332b415a 100644 --- a/src/gdcmParser.cxx +++ b/src/gdcmParser.cxx @@ -1,8 +1,15 @@ // gdcmParser.cxx //----------------------------------------------------------------------------- +//#define UINT32_MAX (4294967295U) + + #include "gdcmParser.h" +#include "gdcmGlobal.h" #include "gdcmUtil.h" +#include "gdcmDebug.h" + #include +#include // For nthos: #ifdef _MSC_VER @@ -11,12 +18,6 @@ #include #endif -#ifdef GDCM_NO_ANSI_STRING_STREAM -# include -# define ostringstream ostrstream -# else -# include -#endif # include #define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" @@ -24,58 +25,10 @@ #define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2" #define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" - // Fourth semantics: - // - // ---> Warning : This fourth field is NOT part - // of the 'official' Dicom Dictionnary - // and should NOT be used. - // (Not defined for all the groups - // may be removed in a future release) - // - // CMD Command - // META Meta Information - // DIR Directory - // ID - // PAT Patient - // ACQ Acquisition - // REL Related - // IMG Image - // SDY Study - // VIS Visit - // WAV Waveform - // PRC - // DEV Device - // NMI Nuclear Medicine - // MED - // BFS Basic Film Session - // BFB Basic Film Box - // BIB Basic Image Box - // BAB - // IOB - // PJ - // PRINTER - // RT Radio Therapy - // DVH - // SSET - // RES Results - // CRV Curve - // OLY Overlays - // PXL Pixels - // DL Delimiters - // - - // Other usefull abreviations : - // Radiographic view associated with Patient Position (0018,5100). - // Defined Terms: - // - // AP = Anterior/Posterior - // PA = Posterior/Anterior - // LL = Left Lateral - // RL = Right Lateral - // RLD = Right Lateral Decubitus - // LLD = Left Lateral Decubitus - // RLO = Right Lateral Oblique - // LLO = Left Lateral Oblique +typedef struct { + guint32 totalSQlength; + guint32 alreadyParsedlength; +} pileElem; //----------------------------------------------------------------------------- // Refer to gdcmParser::CheckSwap() @@ -84,43 +37,40 @@ const unsigned int gdcmParser::HEADER_LENGTH_TO_READ = 256; // Refer to gdcmParser::SetMaxSizeLoadEntry() const unsigned int gdcmParser::MAX_SIZE_LOAD_ELEMENT_VALUE = 4096; -// Refer to gdcmParser::SetMaxSizePrintEntry() -// TODO : Right now, better see "define, in gdcmHederEntry.cxx const unsigned int gdcmParser::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; //----------------------------------------------------------------------------- // Constructor / Destructor /** - * \ingroup gdcmParser - * \brief constructor - * @param inFilename + * \brief constructor + * @param inFilename file to be opened for parsing * @param exception_on_error whether we throw an exception or not * @param enable_sequences = true to allow the header - * to be parsed *inside* the SeQuences, + * to be parsed *inside* the SeQuences, * when they have an actual length - * @param ignore_shadow to allow skipping the shadow elements, - * to save memory space. - * \warning The TRUE value for this param has to be used - * with a FALSE value for the 'enable_sequence' param. - * ('public elements' may be embedded in 'shadow Sequences') + * \warning enable_sequences *has to be* true for reading PAPYRUS 3.0 files + * @param ignore_shadow to allow skipping the shadow elements, + * to save memory space. + * \warning The TRUE value for this param has to be used + * with a FALSE value for the 'enable_sequence' param. + * ('public elements' may be embedded in 'shadow Sequences') */ gdcmParser::gdcmParser(const char *inFilename, bool exception_on_error, bool enable_sequences, - bool ignore_shadow) { + bool ignore_shadow) { enableSequences=enable_sequences; ignoreShadow =ignore_shadow; - SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); + SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); filename = inFilename; Initialise(); if ( !OpenFile(exception_on_error)) return; - if (ParseHeader()) { - LoadHeaderEntries(); - } + + LoadHeaderEntries(); CloseFile(); wasUpdated = 0; // will be set to 1 if user adds an entry @@ -128,11 +78,11 @@ gdcmParser::gdcmParser(const char *inFilename, } /** - * \ingroup gdcmParser * \brief constructor * @param exception_on_error */ gdcmParser::gdcmParser(bool exception_on_error) { + (void)exception_on_error; enableSequences=0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); @@ -143,7 +93,6 @@ gdcmParser::gdcmParser(bool exception_on_error) { } /** - * \ingroup gdcmParser * \brief Canonical destructor. */ gdcmParser::~gdcmParser (void) { @@ -154,27 +103,24 @@ gdcmParser::~gdcmParser (void) { //----------------------------------------------------------------------------- // Print /** - * \ingroup gdcmParser * \brief Prints the Header Entries (Dicom Elements) - * both from the H Table and the chained list + * from the chained list * @return */ void gdcmParser::PrintEntry(std::ostream & os) { - std::ostringstream s; - + for (ListTag::iterator i = listEntries.begin(); - i != listEntries.end(); - ++i) + i != listEntries.end(); + ++i) { - (*i)->SetPrintLevel(printLevel); - (*i)->Print(os); + (*i)->SetPrintLevel(printLevel); + (*i)->Print(os); } - os< Warning : un-updated odd groups lengths can causes pb + * --> (xmedcon breaks) + * --> to be re- written with future org. + * + * if ( (type == ImplicitVR) || (type == ExplicitVR) ) + * UpdateGroupLength(false,type); + * if ( type == ACR) + * UpdateGroupLength(true,ACR); + */ WriteEntries(fp,type); return(true); - } +} /** - * \ingroup gdcmParser * \brief Modifies the value of a given Header Entry (Dicom Element) - * if it exists; Creates it with the given value if it doesn't - * \warning : adds the Header Entry to the HTable, NOT to the chained List - * @param Value passed as a std::string - * @param Group group of the Entry - * @param Elem element of the Entry - * \return pointer to the created Header Entry - * NULL if creation failed + * when it exists. Create it with the given value when unexistant. + * \warning Adds the Header Entry to the HTable, NOT to the chained List + * @param Value Value to be set + * @param Group Group of the Entry + * @param Elem Element of the Entry + * \return pointer to the modified/created Header Entry (NULL when creation + * failed). */ gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber( std::string Value, guint16 Group, - guint16 Elem ){ + guint16 Elem ){ gdcmHeaderEntry* a; - a = GetHeaderEntryByNumber( Group, Elem); + a = GetHeaderEntryByNumber( Group, Elem); if (a == NULL) { - gdcmHeaderEntry *a =NewHeaderEntryByNumber(Group, Elem); + a =NewHeaderEntryByNumber(Group, Elem); if (a == NULL) return NULL; AddHeaderEntry(a); } - //SetEntryByNumber(Value, Group, Elem); + //CLEANME SetEntryByNumber(Value, Group, Elem); a->SetValue(Value); return(a); } /** - * \ingroup gdcmParser - * \brief Modifies the value of a given Header Entry (Dicom Element) - * if it exists; Creates it with the given value if it doesn't - * @param Value passed as a char* - * @param Group group of the Entry - * @param Elem element of the Entry - * \return pointer to the created Header Entry - * NULL if creation failed - * - */ -gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber( - char* Value, - guint16 Group, - guint16 Elem ) { - gdcmHeaderEntry* nvHeaderEntry=NewHeaderEntryByNumber(Group, Elem); - - if(!nvHeaderEntry) - return(NULL); - - AddHeaderEntry(nvHeaderEntry); - - std::string v = Value; - SetEntryByNumber(v, Group, Elem); - return(nvHeaderEntry); -} - -/** - * \ingroup gdcmParser - * \brief Set a new value if the invoked element exists - * Seems to be useless !!! + * \brief Set a new value if the invoked element exists + * Seems to be useless !!! * @param Value new element value * @param Group group of the Entry * @param Elem element of the Entry @@ -515,7 +426,7 @@ gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber( */ bool gdcmParser::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem ) { - std::string v = Value; + std::string v = Value; SetEntryByNumber(v, Group, Elem); return true; } @@ -524,7 +435,6 @@ bool gdcmParser::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem // Protected /** - * \ingroup gdcmParser * \brief Checks if a given Dicom Element exists * within the H table * @param group Group number of the searched Dicom Element @@ -532,12 +442,11 @@ bool gdcmParser::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem * @return number of occurences */ int gdcmParser::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { - std::string key = gdcmDictEntry::TranslateToKey(group, element ); - return (tagHT.count(key)); + std::string key = gdcmDictEntry::TranslateToKey(group, element ); + return (tagHT.count(key)); } /** - * \ingroup gdcmParser * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value of a given tag. @@ -555,7 +464,6 @@ std::string gdcmParser::GetEntryByName(std::string tagName) { } /** - * \ingroup gdcmParser * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag. @@ -574,13 +482,12 @@ std::string gdcmParser::GetEntryVRByName(std::string tagName) { return GDCM_UNFOUND; gdcmHeaderEntry* elem = GetHeaderEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); + dictEntry->GetElement()); return elem->GetVR(); } /** - * \ingroup gdcmParser * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag. @@ -597,7 +504,6 @@ std::string gdcmParser::GetEntryByNumber(guint16 group, guint16 element){ } /** - * \ingroup gdcmParser * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value representation of a given tag.. @@ -619,7 +525,6 @@ std::string gdcmParser::GetEntryVRByNumber(guint16 group, guint16 element) { } /** - * \ingroup gdcmParser * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the value length of a given tag.. @@ -634,7 +539,6 @@ int gdcmParser::GetEntryLengthByNumber(guint16 group, guint16 element) { return elem->GetLength(); } /** - * \ingroup gdcmParser * \brief Sets the value (string) of the Header Entry (Dicom Element) * @param content string value of the Dicom Element * @param tagName name of the searched Dicom Element. @@ -643,14 +547,13 @@ int gdcmParser::GetEntryLengthByNumber(guint16 group, guint16 element) { bool gdcmParser::SetEntryByName(std::string content,std::string tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) - return false; + return false; return(SetEntryByNumber(content,dictEntry->GetGroup(), dictEntry->GetElement())); } /** - * \ingroup gdcmParser * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element) * through it's (group, element) and modifies it's content with * the given value. @@ -694,14 +597,13 @@ bool gdcmParser::SetEntryByNumber(std::string content, else if( (vr == "UL") || (vr == "SL") ) lgr = 4; else - lgr = l; + lgr = l; a->SetLength(lgr); return true; -} +} /** - * \ingroup gdcmParser * \brief Accesses an existing gdcmHeaderEntry (i.e. a Dicom Element) * in the PubHeaderEntrySet of this instance * through it's (group, element) and modifies it's length with @@ -714,19 +616,18 @@ bool gdcmParser::SetEntryByNumber(std::string content, */ bool gdcmParser::SetEntryLengthByNumber(guint32 l, guint16 group, - guint16 element) + guint16 element) { TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; if (l%2) l++; // length must be even - ( ((tagHT.equal_range(key)).first)->second )->SetLength(l); - - return true ; + ( ((tagHT.equal_range(key)).first)->second )->SetLength(l); + + return true ; } /** - * \ingroup gdcmParser * \brief Gets (from Header) the offset of a 'non string' element value * (LoadElementValues has already be executed) * @param Group group of the Entry @@ -735,7 +636,7 @@ bool gdcmParser::SetEntryLengthByNumber(guint32 l, */ size_t gdcmParser::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) { - gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); + gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); if (!Entry) { dbg.Verbose(1, "gdcmParser::GetHeaderEntryByNumber", @@ -746,7 +647,6 @@ size_t gdcmParser::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) } /** - * \ingroup gdcmParser * \brief Gets (from Header) a 'non string' element value * (LoadElementValues has already be executed) * @param Group group of the Entry @@ -755,7 +655,7 @@ size_t gdcmParser::GetEntryOffsetByNumber(guint16 Group, guint16 Elem) */ void * gdcmParser::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) { - gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); + gdcmHeaderEntry* Entry = GetHeaderEntryByNumber(Group, Elem); if (!Entry) { dbg.Verbose(1, "gdcmParser::GetHeaderEntryByNumber", @@ -766,7 +666,6 @@ void * gdcmParser::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem) } /** - * \ingroup gdcmParser * \brief Loads (from disk) the element content * when a string is not suitable * @param Group group of the Entry @@ -779,25 +678,24 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) return NULL; size_t o =(size_t)Element->GetOffset(); fseek(fp, o, SEEK_SET); - int l=Element->GetLength(); - void * a = malloc(l); + size_t l=Element->GetLength(); + char* a = new char[l]; if(!a) - return NULL; + return NULL; SetEntryVoidAreaByNumber(a, Group, Elem); - // TODO check the result + /// \todo check the result size_t l2 = fread(a, 1, l ,fp); if(l != l2) { - free(a); - return NULL; + delete[] a; + return NULL; } return a; } /** - * \ingroup gdcmParser * \brief Sets a 'non string' value to a given Dicom Element * @param area * @param group Group number of the searched Dicom Element @@ -806,17 +704,16 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) */ bool gdcmParser::SetEntryVoidAreaByNumber(void * area, guint16 group, - guint16 element) + guint16 element) { TagKey key = gdcmDictEntry::TranslateToKey(group, element); if ( ! tagHT.count(key)) return false; - ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area); + ( ((tagHT.equal_range(key)).first)->second )->SetVoidArea(area); return true; } /** - * \ingroup gdcmParser * \brief Update the entries with the shadow dictionary. * Only non even entries are analyzed */ @@ -860,7 +757,6 @@ void gdcmParser::UpdateShaEntries(void) { } /** - * \ingroup gdcmParser * \brief Searches within the Header Entries for a Dicom Element of * a given tag. * @param tagName name of the searched Dicom Element. @@ -876,7 +772,6 @@ void gdcmParser::UpdateShaEntries(void) { } /** - * \ingroup gdcmParser * \brief retrieves a Dicom Element (the first one) using (group, element) * \warning (group, element) IS NOT an identifier inside the Dicom Header * if you think it's NOT UNIQUE, check the count number @@ -895,7 +790,6 @@ gdcmHeaderEntry* gdcmParser::GetHeaderEntryByNumber(guint16 group, guint16 eleme } /** - * \ingroup gdcmParser * \brief retrieves the Dicom Elements (all of them) using (group, element) * @param group Group number of the searched Dicom Element. * @param element Element number of the searched Dicom Element. @@ -908,7 +802,6 @@ IterHT gdcmParser::GetHeaderEntrySameNumber(guint16 group, guint16 element){ } /** - * \ingroup gdcmParser * \brief Loads the element while preserving the current * underlying file position indicator as opposed to * to LoadHeaderEntry that modifies it. @@ -922,7 +815,6 @@ void gdcmParser::LoadHeaderEntrySafe(gdcmHeaderEntry * entry) { } /** - * \ingroup gdcmParser * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader * \warning : to be re-written using the chained list instead of the H table. * \warning : DO NOT use (doesn't work any longer because of the multimap) @@ -958,7 +850,7 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) { vr = elem->GetVR(); sprintf(trash, "%04x", gr); - key = trash; // generate 'group tag' + key = trash; // generate 'group tag' // if the caller decided not to take SEQUENCEs into account // e.g : he wants to write an ACR-NEMA File @@ -971,7 +863,7 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) { // since it's at the end of the Hash Table // (fffe,e0dd) - // pas SEQUENCE en ACR-NEMA + // there is SEQUENCE in ACR-NEMA // WARNING : // --> la descente a l'interieur' des SQ // devrait etre faite avec une liste chainee, pas avec une HTable... @@ -979,8 +871,8 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) { if ( groupHt.count(key) == 0) // we just read the first elem of a given group { if (el == 0x0000) // the first elem is 0x0000 - { - groupHt[key] = 0; // initialize group length + { + groupHt[key] = 0; // initialize group length } else { @@ -989,7 +881,7 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) { } else // any elem but the first { - if (type == ExplicitVR) + if (type == gdcmExplicitVR) { if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) { @@ -1008,15 +900,15 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) { { // FIXME: g++ -Wall -Wstrict-prototypes reports on following line: // warning: unsigned int format, different type arg - sscanf(g->first.c_str(),"%x",&gr_bid); - tk = g->first + "|0000"; // generate the element full tag + sscanf(g->first.c_str(),"%x",&gr_bid); //FIXME + tk = g->first + "|0000"; // generate the element full tag if ( tagHT.count(tk) == 0) // if element 0x0000 not found - { + { gdcmDictEntry * tagZ = new gdcmDictEntry(gr_bid, 0x0000, "UL"); elemZ = new gdcmHeaderEntry(tagZ); elemZ->SetLength(4); - AddHeaderEntry(elemZ); // create it + AddHeaderEntry(elemZ); // create it } else { @@ -1029,146 +921,160 @@ void gdcmParser::UpdateGroupLength(bool SkipSequence, FileType type) { } /** - * \ingroup gdcmParser - * \brief writes on disc according to the requested format - * (ACR-NEMA, ExplicitVR, ImplicitVR) ONE - * gdcmHeaderEntry - * @param tag pointer on the gdcmHeaderEntry to be written - * @param type type of the File to be written - * (ACR-NEMA, ExplicitVR, ImplicitVR) - * @param _fp already open file pointer + * \brief Writes in a file (according to the requested format) + * the group, the element, the value representation and the length + * of a single gdcmHeaderEntry passed as argument. + * @param tag pointer on the gdcmHeaderEntry to be written + * @param _fp already open file pointer + * @param type type of the File to be written */ -void gdcmParser::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type) +void gdcmParser::WriteEntryTagVRLength(gdcmHeaderEntry *tag, + FILE *_fp, + FileType type) { - guint16 gr, el; - guint32 lgr; - std::string value; - const char * val; - std::string vr; - guint32 val_uint32; - guint16 val_uint16; - guint16 valZero =0; - void *voidArea; - std::vector tokens; + 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 ) { - void *ptr; - int ff=0xffffffff; - // TODO (?) tester les echecs en ecriture (apres chaque fwrite) - int compte =0; - itsTimeToWritePixels = false; - - // === Deal with the length - // -------------------- - if((tag->GetLength())%2==1) - { - tag->SetValue(tag->GetValue()+"\0"); - tag->SetLength(tag->GetReadLength()+1); - } + // 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 - gr = tag->GetGroup(); - el = tag->GetElement(); - lgr = tag->GetReadLength(); - val = tag->GetValue().c_str(); - vr = tag->GetVR(); - voidArea = tag->GetVoidArea(); - - if ( type == ACR ) - { - if (gr < 0x0008) return; // ignore pure DICOM V3 groups - if (gr %2) return; // ignore shadow groups - if (vr == "SQ" ) return; // ignore Sequences - // TODO : find a trick to *skip* the SeQuences ! - // Not only ignore the SQ element - if (gr == 0xfffe ) return; // ignore delimiters - } + int ff=0xffffffff; + fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp); + return; + } - fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp); //group - fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element - - if ( (type == ExplicitVR) || (type == DICOMDIR) ) { - // EXPLICIT VR - guint16 z=0, shortLgr; - - if (gr == 0xfffe) { // NO Value Representation for 'delimiters' - // no length : write ffffffff - fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp); - return; // NO value for 'delimiters' - } - - shortLgr=lgr; - if (vr == "unkn") { // Unknown was 'written' - // deal with Little Endian - fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); + guint16 z=0; + guint16 shortLgr = lgr; + if (vr == "unkn") { // Unfound 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 (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); - } + fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp); } - } - else // IMPLICIT VR - { - fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); } + } + else // IMPLICIT VR + { + fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp); + } +} - // === Deal with the value - // ------------------- - if (vr == "SQ") return; // no "value" to write for the SEQuences - if (gr == 0xfffe)return; // no "value" to write for the delimiters +/** + * \brief Writes in a file (according to the requested format) + * the value of a single gdcmHeaderEntry passed as argument. + * @param tag Pointer on the gdcmHeaderEntry to be written + * @param _fp Already open file pointer + * @param type type of the File to be written + */ +void gdcmParser::WriteEntryValue(gdcmHeaderEntry *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; - if (voidArea != NULL) - { // there is a 'non string' LUT, overlay, etc - fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value - return; - } + void *voidArea; + voidArea = tag->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") + 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 (tag->GetValue(), tokens, "\\"); + for (unsigned int i=0; iGetValue(), tokens, "\\"); - for (unsigned int i=0; i tokens; + tokens.erase(tokens.begin(),tokens.end()); // clean any previous value + Tokenize (tag->GetValue(), tokens, "\\"); + for (unsigned int i=0; iGetValue(), 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 gdcmHeaderEntry passed as argument. + * \sa WriteEntryValue, WriteEntryTagVRLength. + * @param tag Pointer on the gdcmHeaderEntry to be written + * @param _fp Already open file pointer + * @param type type of the File to be written + */ + +bool gdcmParser::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type) +{ + guint32 length = tag->GetLength(); + + // 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; } /** - * \ingroup gdcmParser * \brief writes on disc according to the requested format * (ACR-NEMA, ExplicitVR, ImplicitVR) the image * using the Chained List @@ -1183,22 +1089,33 @@ void gdcmParser::WriteEntry(gdcmHeaderEntry *tag, FILE *_fp,FileType type) * @param _fp already open file pointer */ -void gdcmParser::WriteEntries(FILE *_fp,FileType type) +bool gdcmParser::WriteEntries(FILE *_fp,FileType type) { - // TODO (?) tester les echecs en ecriture (apres chaque fwrite) - + /// \todo (?) check write failures (after *each* fwrite) + for (ListTag::iterator tag2=listEntries.begin(); tag2 != listEntries.end(); ++tag2) { - WriteEntry(*tag2,_fp,type); - if (itsTimeToWritePixels) - break; + if ( type == gdcmACR ){ + if ((*tag2)->GetGroup() < 0x0008) + // Ignore pure DICOM V3 groups + continue; + if ((*tag2)->GetElement() %2) + // Ignore the "shadow" groups + continue; + if ((*tag2)->GetVR() == "SQ" ) // ignore Sequences + continue; + if ((*tag2)->GetSQDepthLevel() != 0) // Not only ignore the SQ element + continue; + } + if (! WriteEntry(*tag2,_fp,type) ) + return false; } + return true; } /** - * \ingroup gdcmParser * \brief writes on disc according to the requested format * (ACR-NEMA, ExplicitVR, ImplicitVR) the image, * using only the last synonym of each mutimap H Table post. @@ -1221,14 +1138,18 @@ void gdcmParser::WriteEntriesDeprecated(FILE *_fp,FileType type) { for (TagHeaderEntryHT::iterator tag2=tagHT.begin(); tag2 != tagHT.end(); ++tag2){ - WriteEntry(tag2->second,_fp,type); - if (itsTimeToWritePixels) + if ( type == gdcmACR ){ + if ((*tag2->second).GetGroup() < 0x0008) continue; // ignore pure DICOM V3 groups + if ((*tag2->second).GetElement() %2) continue; // ignore shadow groups + if ((*tag2->second).GetVR() == "SQ" ) continue; // ignore Sequences + if ((*tag2->second).GetSQDepthLevel() != 0) continue; // Not only ignore the SQ element + } + if ( ! WriteEntry(tag2->second,_fp,type)) break; } } /** - * \ingroup gdcmParser * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly swaped 32 bits integer. @@ -1257,7 +1178,6 @@ guint32 gdcmParser::SwapLong(guint32 a) { } /** - * \ingroup gdcmParser * \brief Unswaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly unswaped 32 bits integer. @@ -1267,7 +1187,6 @@ guint32 gdcmParser::UnswapLong(guint32 a) { } /** - * \ingroup gdcmParser * \brief Swaps the bytes so they agree with the processor order * @return The properly swaped 16 bits integer. */ @@ -1278,7 +1197,6 @@ guint16 gdcmParser::SwapShort(guint16 a) { } /** - * \ingroup gdcmParser * \brief Unswaps the bytes so they agree with the processor order * @return The properly unswaped 16 bits integer. */ @@ -1289,12 +1207,11 @@ guint16 gdcmParser::UnswapShort(guint16 a) { //----------------------------------------------------------------------------- // Private /** - * \ingroup gdcmParser - * \brief Parses the header of the file but WITHOUT loading element values. - * @return false if file is not ACR-NEMA / DICOM + * \brief Parses the header of the file and load element values. + * @return false if file is not ACR-NEMA / PAPYRUS / DICOM */ -bool gdcmParser::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { - +bool gdcmParser::LoadHeaderEntries(bool exception_on_error) throw(gdcmFormatError) { + (void)exception_on_error; rewind(fp); if (!CheckSwap()) return false; @@ -1304,28 +1221,20 @@ bool gdcmParser::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { SkipHeaderEntry(newHeaderEntry); if ( (ignoreShadow==0) || (newHeaderEntry->GetGroup()%2) == 0) { AddHeaderEntry(newHeaderEntry); - } - } - return true; -} - -/** - * \ingroup gdcmParser - * \brief Loads the element values of all the Header Entries pointed in the - * public Chained List. - */ -void gdcmParser::LoadHeaderEntries(void) { - rewind(fp); - for (ListTag::iterator i = GetListEntry().begin(); - i != GetListEntry().end(); - ++i) - { - LoadHeaderEntry(*i); - } - + } + } rewind(fp); - - // Load 'non string' values + // Be carefull : merging this two loops may cause troubles ... + for (ListTag::iterator i = GetListEntry().begin(); + i != GetListEntry().end(); + ++i) + { + LoadHeaderEntry(*i); + } + rewind(fp); + + // Load 'non string' values + std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004); if( PhotometricInterpretation == "PALETTE COLOR " ) { LoadEntryVoidArea(0x0028,0x1200); // gray LUT @@ -1337,7 +1246,7 @@ void gdcmParser::LoadHeaderEntries(void) { LoadEntryVoidArea(0x0028,0x1222); // Segmented Green Palette Color LUT Data LoadEntryVoidArea(0x0028,0x1223); // Segmented Blue Palette Color LUT Data } - //FIXME : how to use it? + //FIXME later : how to use it? LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent) // -------------------------------------------------------------- @@ -1346,22 +1255,23 @@ void gdcmParser::LoadHeaderEntries(void) { // if recognition code tells us we deal with a LibIDO image // we switch lineNumber and columnNumber // - std::string RecCode; + std::string RecCode; RecCode = GetEntryByNumber(0x0008, 0x0010); // recognition code if (RecCode == "ACRNEMA_LIBIDO_1.1" || - RecCode == "CANRME_AILIBOD1_1." ) + RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares + // with "little-endian strings" { - filetype = ACR_LIBIDO; + filetype = gdcmACR_LIBIDO; std::string rows = GetEntryByNumber(0x0028, 0x0010); std::string columns = GetEntryByNumber(0x0028, 0x0011); SetEntryByNumber(columns, 0x0028, 0x0010); SetEntryByNumber(rows , 0x0028, 0x0011); } - // ----------------- End of Special Patch ---------------- + // ----------------- End of Special Patch ---------------- + return true; } /** - * \ingroup gdcmParser * \brief Loads the element content if its length doesn't exceed * the value specified with gdcmParser::SetMaxSizeLoadEntry() * @param Entry Header Entry (Dicom Element) to be dealt with @@ -1371,25 +1281,14 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { guint16 group = Entry->GetGroup(); std::string vr= Entry->GetVR(); guint32 length = Entry->GetLength(); - bool SkipLoad = false; fseek(fp, (long)Entry->GetOffset(), SEEK_SET); - - // the test was commented out to 'go inside' the SeQuences - // we don't any longer skip them ! - - // if( vr == "SQ" ) // (DO NOT remove this comment) - // SkipLoad = true; // A SeQuence "contains" a set of Elements. // (fffe e000) tells us an Element is beginning // (fffe e00d) tells us an Element just ended // (fffe e0dd) tells us the current SeQuence just ended - if( group == 0xfffe ) - SkipLoad = true; - - if ( SkipLoad ) { - Entry->SetLength(0); + if( group == 0xfffe ) { Entry->SetValue("gdcm::Skipped"); return; } @@ -1412,18 +1311,16 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { Entry->SetValue(s.str()); return; } - - // When integer(s) are expected, read and convert the following - // n *(two or four bytes) - // properly i.e. as integers as opposed to strings. - // Elements with Value Multiplicity > 1 - // contain a set of integers (not a single one) - + // Any compacter code suggested (?) if ( IsHeaderEntryAnInteger(Entry) ) { guint32 NewInt; std::ostringstream s; int nbInt; + // When short integer(s) are expected, read and convert the following + // n *two characters properly i.e. as short integers as opposed to strings. + // Elements with Value Multiplicity > 1 + // contain a set of integers (not a single one) if (vr == "US" || vr == "SS") { nbInt = length / 2; NewInt = ReadInt16(); @@ -1434,8 +1331,12 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { NewInt = ReadInt16(); s << NewInt; } - } + } } + // When integer(s) are expected, read and convert the following + // n * four characters properly i.e. as integers as opposed to strings. + // Elements with Value Multiplicity > 1 + // contain a set of integers (not a single one) else if (vr == "UL" || vr == "SL") { nbInt = length / 4; NewInt = ReadInt32(); @@ -1453,7 +1354,7 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { #endif //GDCM_NO_ANSI_STRING_STREAM Entry->SetValue(s.str()); - return; + return; } // We need an additional byte for storing \0 that is not on disk @@ -1466,13 +1367,12 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { } if( (vr == "UI") ) // Because of correspondance with the VR dic - Entry->SetValue(NewValue.c_str()); // ??? JPR ??? + Entry->SetValue(NewValue.c_str()); else Entry->SetValue(NewValue); } /** - * \ingroup gdcmParser * \brief add a new Dicom Element pointer to * the H Table and at the end of the chained List * \warning push_bash in listEntries ONLY during ParseHeader @@ -1488,24 +1388,17 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { } /** - * \ingroup gdcmParser * \brief Find the value Length of the passed Header Entry * @param Entry Header Entry whose length of the value shall be loaded. */ void gdcmParser::FindHeaderEntryLength (gdcmHeaderEntry *Entry) { guint16 element = Entry->GetElement(); - guint16 group = Entry->GetGroup(); + //guint16 group = Entry->GetGroup(); //FIXME std::string vr = Entry->GetVR(); guint16 length16; + - if( (element == NumPixel) && (group == GrPixel) ) - { - dbg.SetDebug(GDCM_DEBUG); - dbg.Verbose(2, "gdcmParser::FindLength: ", - "we reached (GrPixel,NumPixel)"); - } - - if ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) ) + if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) ) { if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { @@ -1587,7 +1480,7 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { //dbg.Verbose(0, "gdcmParser::FindLength", // "Erroneous element length fixed."); // Actually, length= 0xffff means that we deal with - // Unknown Sequence Length + // Unfound Sequence Length } FixHeaderEntryFoundLength(Entry, (guint32)length16); return; @@ -1607,13 +1500,12 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { } /** - * \ingroup gdcmParser * \brief Find the Value Representation of the current Dicom Element. * @param Entry */ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) { - if (filetype != ExplicitVR) + if (filetype != gdcmExplicitVR) return; char VR[3]; @@ -1627,7 +1519,7 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) // is in explicit VR and try to fix things if it happens not to be // the case. - int lgrLue=fread (&VR, (size_t)2,(size_t)1, fp); // lgrLue not used + (void)fread (&VR, (size_t)2,(size_t)1, fp); VR[2]=0; if(!CheckHeaderEntryVR(Entry,VR)) { @@ -1644,7 +1536,6 @@ void gdcmParser::FindHeaderEntryVR( gdcmHeaderEntry *Entry) } /** - * \ingroup gdcmParser * \brief Check the correspondance between the VR of the header entry * and the taken VR. If they are different, the header entry is * updated with the new VR. @@ -1686,7 +1577,7 @@ bool gdcmParser::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr) gdcmDictEntry* NewEntry = NewVirtualDictEntry( Entry->GetGroup(),Entry->GetElement(), "UL","FIXME","Group Length"); - Entry->SetDictEntry(NewEntry); + Entry->SetDictEntry(NewEntry); } return(false); } @@ -1716,7 +1607,6 @@ bool gdcmParser::CheckHeaderEntryVR(gdcmHeaderEntry *Entry, VRKey vr) } /** - * \ingroup gdcmParser * \brief Get the transformed value of the header entry. The VR value * is used to define the transformation to operate on the value * \warning NOT end user intended method ! @@ -1733,6 +1623,13 @@ std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry) std::ostringstream s; int nbInt; + // When short integer(s) are expected, read and convert the following + // n * 2 bytes properly i.e. as a multivaluated strings + // (each single value is separated fromthe next one by '\' + // as usual for standard multivaluated filels + // Elements with Value Multiplicity > 1 + // contain a set of short integers (not a single one) + if (vr == "US" || vr == "SS") { guint16 NewInt16; @@ -1748,6 +1645,12 @@ std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry) } } + // When integer(s) are expected, read and convert the following + // n * 4 bytes properly i.e. as a multivaluated strings + // (each single value is separated fromthe next one by '\' + // as usual for standard multivaluated filels + // Elements with Value Multiplicity > 1 + // contain a set of integers (not a single one) else if (vr == "UL" || vr == "SL") { guint32 NewInt32; @@ -1773,7 +1676,6 @@ std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry) } /** - * \ingroup gdcmParser * \brief Get the reverse transformed value of the header entry. The VR * value is used to define the reverse transformation to operate on * the value @@ -1827,7 +1729,6 @@ std::string gdcmParser::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry) } /** - * \ingroup gdcmParser * \brief Skip a given Header Entry * \warning NOT end user intended method ! * @param entry @@ -1838,15 +1739,13 @@ void gdcmParser::SkipHeaderEntry(gdcmHeaderEntry *entry) } /** - * \ingroup gdcmParser * \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. */ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 FoundLength) { - Entry->SetReadLength(FoundLength); // will be updated only if a bug is found - + Entry->SetReadLength(FoundLength); // will be updated only if a bug is found if ( FoundLength == 0xffffffff) { FoundLength = 0; } @@ -1862,7 +1761,7 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Found } // Sorry for the patch! - // XMedCom did the trick to read some nasty GE images ... + // 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... @@ -1882,28 +1781,28 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Found Entry->SetReadLength(4); // 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 + FoundLength =0; // ReadLength is unchanged } - // a SeQuence Element is beginning - // fffe|e000 is just a marker, its length *should be* zero + // we found a 'delimiter' element + // fffe|xxxx is just a marker, we don't take its length 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; - } + // causes extra troubles :-( + FoundLength =0; + } + Entry->SetUsableLength(FoundLength); } /** - * \ingroup gdcmParser * \brief Apply some heuristics to predict whether the considered * element value contains/represents an integer or not. * @param Entry The element value on which to apply the predicate. @@ -1924,22 +1823,21 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { else { std::ostringstream s; - int filePosition = ftell(fp); + 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("gdcmParser::IsHeaderEntryAnInteger", - // s.str().c_str()); + << ") -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("gdcmParser::IsHeaderEntryAnInteger", + // s.str().c_str()); } } if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") ) @@ -1948,7 +1846,6 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { return false; } /** - * \ingroup gdcmParser * \brief Find the Length till the next sequence delimiter * \warning NOT end user intended method ! * @return @@ -1971,7 +1868,7 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { return 0; TotalLength += 4; // We even have to decount the group and element - if ( g != 0xfffe && g!=0xb00c ) /*for bogus header */ + if ( g != 0xfffe && g!=0xb00c ) //for bogus header { char msg[100]; // for sprintf. Sorry sprintf(msg,"wrong group (%04x) for an item sequence (%04x,%04x)\n",g, g,n); @@ -1979,7 +1876,7 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { errno = 1; return 0; } - if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) /* for bogus header */ + if ( n == 0xe0dd || ( g==0xb00c && n==0x0eb6 ) ) // for bogus header FoundSequenceDelimiter = true; else if ( n != 0xe000 ) { @@ -2000,7 +1897,6 @@ bool gdcmParser::IsHeaderEntryAnInteger(gdcmHeaderEntry *Entry) { } /** - * \ingroup gdcmParser * \brief Reads a supposed to be 16 Bits integer * (swaps it depending on processor endianity) * @return read value @@ -2021,7 +1917,6 @@ guint16 gdcmParser::ReadInt16(void) { } /** - * \ingroup gdcmParser * \brief Reads a supposed to be 32 Bits integer * (swaps it depending on processor endianity) * @return read value @@ -2042,7 +1937,6 @@ guint32 gdcmParser::ReadInt32(void) { } /** - * \ingroup gdcmParser * \brief skips bytes inside the source file * \warning NOT end user intended method ! * @return @@ -2053,7 +1947,6 @@ void gdcmParser::SkipBytes(guint32 NBytes) { } /** - * \ingroup gdcmParser * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ @@ -2064,7 +1957,6 @@ void gdcmParser::Initialise(void) } /** - * \ingroup gdcmParser * \brief Discover what the swap code is (among little endian, big endian, * bad little endian, bad big endian). * sw is set @@ -2122,26 +2014,25 @@ bool gdcmParser::CheckSwap() { // FIXME : FIXME: // Sometimes (see : gdcmData/icone.dcm) group 0x0002 *is* Explicit VR, - // but elem 0002,0010 (Transfert Syntax) tells us the file is *Implicit* VR. - // -and it is !- + // but elem 0002,0010 (Transfert Syntax) tells us the file is + // *Implicit* VR. -and it is !- if( (memcmp(entCur, "UL", (size_t)2) == 0) || - (memcmp(entCur, "OB", (size_t)2) == 0) || - (memcmp(entCur, "UI", (size_t)2) == 0) || - (memcmp(entCur, "CS", (size_t)2) == 0) ) // CS, to remove later - // when Write DCM *adds* + (memcmp(entCur, "OB", (size_t)2) == 0) || + (memcmp(entCur, "UI", (size_t)2) == 0) || + (memcmp(entCur, "CS", (size_t)2) == 0) ) // CS, to remove later + // when Write DCM *adds* // FIXME // Use gdcmParser::dicom_vr to test all the possibilities - // instead of just checking for UL, OB and UI !? // group 0000 - + // instead of just checking for UL, OB and UI !? group 0000 { - filetype = ExplicitVR; + filetype = gdcmExplicitVR; dbg.Verbose(1, "gdcmParser::CheckSwap:", "explicit Value Representation"); } else { - filetype = ImplicitVR; + filetype = gdcmImplicitVR; dbg.Verbose(1, "gdcmParser::CheckSwap:", "not an explicit Value Representation"); } @@ -2186,22 +2077,22 @@ bool gdcmParser::CheckSwap() { switch (s32) { case 0x00040000 : sw = 3412; - filetype = ACR; + filetype = gdcmACR; return true; case 0x04000000 : sw = 4321; - filetype = ACR; + filetype = gdcmACR; return true; case 0x00000400 : sw = 2143; - filetype = ACR; + filetype = gdcmACR; return true; case 0x00000004 : sw = 0; - filetype = ACR; + filetype = gdcmACR; return true; default : - + // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file. // It is time for despaired wild guesses. // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA, @@ -2217,39 +2108,38 @@ bool gdcmParser::CheckSwap() { // the file IS NOT ACR-NEMA nor DICOM V3 // Find a trick to tell it the caller... - s16 = *((guint16 *)(deb)); + s16 = *((guint16 *)(deb)); + + switch (s16) { + case 0x0002 : + case 0x0004 : + case 0x0008 : + sw = 0; + filetype = gdcmACR; + return true; + case 0x0200 : + case 0x0400 : + case 0x0800 : + sw = 4321; + filetype = gdcmACR; + return true; + default : + dbg.Verbose(0, "gdcmParser::CheckSwap:", + "ACR/NEMA unfound swap info (Really hopeless !)"); + filetype = gdcmUnknown; + return false; + } - switch (s16) { - case 0x0002 : - case 0x0004 : - case 0x0008 : - sw = 0; - filetype = ACR; - return true; - case 0x0200 : - case 0x0400 : - case 0x0800 : - sw = 4321; - filetype = ACR; - return true; - default : - dbg.Verbose(0, "gdcmParser::CheckSwap:", - "ACR/NEMA unfound swap info (Really hopeless !)"); - filetype = Unknown; - return false; - } - - // Then the only info we have is the net2host one. - //if (! net2host ) + // Then the only info we have is the net2host one. + //if (! net2host ) // sw = 0; //else // sw = 4321; - //return; + //return; } } /** - * \ingroup gdcmParser * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. */ @@ -2277,7 +2167,6 @@ void gdcmParser::SwitchSwapToBigEndian(void) } /** - * \ingroup gdcmParser * \brief during parsing, Header Elements too long are not loaded in memory * @param NewSize */ @@ -2295,13 +2184,8 @@ void gdcmParser::SetMaxSizeLoadEntry(long NewSize) /** - * \ingroup gdcmParser * \brief Header Elements too long will not be printed - * \warning - * \todo : not yet usable - * (see MAX_SIZE_PRINT_ELEMENT_VALUE - * in gdcmHeaderEntry gdcmLoadEntry) - * + * \todo See comments of \ref gdcmParser::MAX_SIZE_PRINT_ELEMENT_VALUE * @param NewSize */ void gdcmParser::SetMaxSizePrintEntry(long NewSize) @@ -2317,7 +2201,6 @@ void gdcmParser::SetMaxSizePrintEntry(long NewSize) } /** - * \ingroup gdcmParser * \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. @@ -2348,7 +2231,6 @@ gdcmDictEntry *gdcmParser::GetDictEntryByName(std::string Name) } /** - * \ingroup gdcmParser * \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 @@ -2381,7 +2263,6 @@ gdcmDictEntry *gdcmParser::GetDictEntryByNumber(guint16 group,guint16 element) } /** - * \ingroup gdcmParser * \brief Read the next tag but WITHOUT loading it's value * @return On succes the newly created HeaderEntry, NULL on failure. */ @@ -2396,19 +2277,19 @@ gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) { // header parsing has to be considered as finished. return (gdcmHeaderEntry *)0; -/* Pb : how to propagate the element length (used in SkipHeaderEntry) +// Pb : how to propagate the element length (used in SkipHeaderEntry) // direct call to SkipBytes ? - if (ignoreShadow == 1 && g%2 ==1) //JPR +// 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 (gdcmHeaderEntry *)1; // to tell caller it's NOT finished -*/ +// return (gdcmHeaderEntry *)1; // to tell caller it's NOT finished + NewEntry = NewHeaderEntryByNumber(g, n); FindHeaderEntryVR(NewEntry); FindHeaderEntryLength(NewEntry); - + if (errno == 1) { // Call it quits return NULL; @@ -2418,7 +2299,6 @@ gdcmHeaderEntry *gdcmParser::ReadNextHeaderEntry(void) { } /** - * \ingroup gdcmParser * \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. @@ -2441,7 +2321,6 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByName(std::string Name) } /** - * \ingroup gdcmParser * \brief Request a new virtual dict entry to the dict set * @param group group of the underlying DictEntry * @param element element of the underlying DictEntry @@ -2458,7 +2337,6 @@ gdcmDictEntry *gdcmParser::NewVirtualDictEntry(guint16 group, guint16 element, } /** - * \ingroup gdcmParser * \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. @@ -2482,9 +2360,8 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) return NewEntry; } -// Never used; commented out, waiting for removal. +/// \todo Never used; commented out, waiting for removal. /** - * \ingroup gdcmParser * \brief Small utility function that creates a new manually crafted * (as opposed as read from the file) gdcmHeaderEntry with user * specified name and adds it to the public tag hash table. @@ -2517,7 +2394,6 @@ gdcmHeaderEntry *gdcmParser::NewHeaderEntryByNumber(guint16 Group, guint16 Elem) //} /** - * \ingroup gdcmParser * \brief Generate a free TagKey i.e. a TagKey that is not present * in the TagHt dictionary. * @param group The generated tag must belong to this group.