X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmParser.cxx;h=332b415adc257c92d47d68a429b73744bb9bf236;hb=801fe2221ca70b34c5c644b6f522aa1b7233945b;hp=c84cbb287b40f26811d7ad25bcb48dc39a5edef0;hpb=5ac719be199bf3cd4f9c9c68c88eff4dc7227531;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index c84cbb28..332b415a 100644 --- a/src/gdcmParser.cxx +++ b/src/gdcmParser.cxx @@ -1,5 +1,13 @@ // gdcmParser.cxx //----------------------------------------------------------------------------- +//#define UINT32_MAX (4294967295U) + + +#include "gdcmParser.h" +#include "gdcmGlobal.h" +#include "gdcmUtil.h" +#include "gdcmDebug.h" + #include #include @@ -10,24 +18,18 @@ #include #endif -#ifdef GDCM_NO_ANSI_STRING_STREAM -# include -# define ostringstream ostrstream -# else -# include -#endif # include -#include "gdcmParser.h" -#include "gdcmGlobal.h" -#include "gdcmUtil.h" -#include "gdcmDebug.h" - #define UI1_2_840_10008_1_2 "1.2.840.10008.1.2" #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" #define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99" +typedef struct { + guint32 totalSQlength; + guint32 alreadyParsedlength; +} pileElem; + //----------------------------------------------------------------------------- // Refer to gdcmParser::CheckSwap() const unsigned int gdcmParser::HEADER_LENGTH_TO_READ = 256; @@ -35,8 +37,6 @@ 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; //----------------------------------------------------------------------------- @@ -69,9 +69,8 @@ gdcmParser::gdcmParser(const char *inFilename, if ( !OpenFile(exception_on_error)) return; - if (ParseHeader()) { - LoadHeaderEntries(); - } + + LoadHeaderEntries(); CloseFile(); wasUpdated = 0; // will be set to 1 if user adds an entry @@ -79,11 +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); @@ -94,7 +93,6 @@ gdcmParser::gdcmParser(bool exception_on_error) { } /** - * \ingroup gdcmParser * \brief Canonical destructor. */ gdcmParser::~gdcmParser (void) { @@ -105,7 +103,6 @@ gdcmParser::~gdcmParser (void) { //----------------------------------------------------------------------------- // Print /** - * \ingroup gdcmParser * \brief Prints the Header Entries (Dicom Elements) * from the chained list * @return @@ -121,71 +118,7 @@ void gdcmParser::PrintEntry(std::ostream & os) { } } -/** - * \ingroup gdcmParser - * \brief Prints the Header Entries (Dicom Elements) - * from the chained list - * and skips the elements belonging to a SeQuence - * @return - */ -void gdcmParser::PrintEntryNoSQ(std::ostream & os) { - int countSQ = 0; - for (ListTag::iterator i = listEntries.begin(); - i != listEntries.end(); - ++i) - { - if ( (*i)->GetVR() == "SQ"){ - countSQ ++; - } - - if ( (*i)->GetGroup() == 0xfffe && (*i)->GetElement() == 0xe0dd){ - countSQ --; - continue; - } - - if (countSQ == 0) { - (*i)->SetPrintLevel(printLevel); - (*i)->Print(os); - } - } -} -/** - * \ingroup gdcmParser - * \brief Prints the Header Entries (Dicom Elements) - * from the chained list - * and indents the elements belonging to a SeQuence - * @return - */ -void gdcmParser::PrintEntryNiceSQ(std::ostream & os) { - int countSQ = 0; - std::ostringstream tab; - tab << " "; - for (ListTag::iterator i = listEntries.begin(); - i != listEntries.end(); - ++i) - { - // we ignore '0 length' SeQuences - if ( (*i)->GetVR() == "SQ" && (*i)->GetReadLength()!=0){ - countSQ ++; - } - // a SeQuence is over when a Sequence Delimiter Item is found - // pb : 'actual length' Sequence have NO Sequence Delimiter - // --> They 'never' finish : check the global length ! - if ( (*i)->GetGroup() == 0xfffe && (*i)->GetElement() == 0xe0dd){ - countSQ --; - continue; - } - - - if (countSQ != 0) { - for (int i=0;iSetPrintLevel(printLevel); - (*i)->Print(os); - } -} /** * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return @@ -245,7 +178,7 @@ bool gdcmParser::SetShaDict(DictKey dictName){ * false otherwise. */ bool gdcmParser::IsReadable(void) { - if(filetype==Unknown) { + if(filetype==gdcmUnknown) { return(false); } if(listEntries.size()<=0) { @@ -273,7 +206,6 @@ bool gdcmParser::IsImplicitVRLittleEndianTransferSyntax(void) { } /** - * \ingroup gdcmParser * \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. @@ -326,7 +258,7 @@ bool gdcmParser::IsExplicitVRBigEndianTransferSyntax(void) { /** * \brief returns the File Type - * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown) + * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unfound) * @return the FileType code */ FileType gdcmParser::GetFileType(void) { @@ -394,59 +326,64 @@ bool gdcmParser::CloseFile(void) { * \return Always true. */ bool gdcmParser::Write(FILE *fp, FileType type) { -// ============== -// TODO The stuff was rewritten using the chained list instead -// of the H table -// so we could remove the GroupHT from the gdcmParser -// To be checked -// ============= - - // TODO : move the following lines (and a lot of others, to be written) - // to a future function CheckAndCorrectHeader +/// \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 GroupHT from the gdcmParser) +/// To be checked +/// ============= + + /// \todo move the following lines (and a lot of others, to be written) + /// to a future function CheckAndCorrectHeader - // Question : - // Comment pourrait-on savoir si le DcmHeader vient d'un fichier - // DicomV3 ou non (FileType est un champ de gdcmParser ...) - // WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA - // no way - // a moins de se livrer a un tres complique ajout des champs manquants. - // faire un CheckAndCorrectHeader (?) - - if (type == ImplicitVR) + /// \todo + /// Question : + /// Comment pourrait-on savoir si le DcmHeader vient d'un fichier + /// DicomV3 ou non (FileType est un champ de gdcmParser ...) + /// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA + /// no way + /// a moins de se livrer a un tres complique ajout des champs manquants. + /// faire un CheckAndCorrectHeader (?) + + if (type == gdcmImplicitVR) { std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2; ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010); - //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": - // values with a VR of UI shall be padded with a single trailing null - // Dans le cas suivant on doit pader manuellement avec un 0 + /// \todo Refer to standards on page 21, chapter 6.2 + /// "Value representation": values with a VR of UI shall be + /// padded with a single trailing null + /// Dans le cas suivant on doit pader manuellement avec un 0 SetEntryLengthByNumber(18, 0x0002, 0x0010); } - if (type == ExplicitVR) + if (type == gdcmExplicitVR) { std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1; ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010); - //FIXME Refer to standards on page 21, chapter 6.2 "Value representation": - // values with a VR of UI shall be padded with a single trailing null - // Dans le cas suivant on doit pader manuellement avec un 0 + /// \todo Refer to standards on page 21, chapter 6.2 + /// "Value representation": values with a VR of UI shall be + /// padded with a single trailing null + /// Dans le cas suivant on doit pader manuellement avec un 0 SetEntryLengthByNumber(20, 0x0002, 0x0010); } -/* TODO : rewrite later, if really usefull - ---> 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); -*/ +/** + * \todo rewrite later, if really usefull + * + * --> 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); @@ -510,7 +447,6 @@ int gdcmParser::CheckIfEntryExistByNumber(guint16 group, guint16 element ) { } /** - * \ingroup gdcmParser * \brief Searches within Header Entries (Dicom Elements) parsed with * the public and private dictionaries * for the element value of a given tag. @@ -528,7 +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. @@ -553,7 +488,6 @@ std::string gdcmParser::GetEntryVRByName(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. @@ -570,7 +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.. @@ -592,7 +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.. @@ -607,7 +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. @@ -623,7 +554,6 @@ bool gdcmParser::SetEntryByName(std::string content,std::string tagName) { } /** - * \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. @@ -674,7 +604,6 @@ bool gdcmParser::SetEntryByNumber(std::string content, } /** - * \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 @@ -699,7 +628,6 @@ bool gdcmParser::SetEntryLengthByNumber(guint32 l, } /** - * \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 @@ -719,7 +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 @@ -751,17 +678,17 @@ 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; 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); + delete[] a; return NULL; } @@ -769,7 +696,6 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) } /** - * \ingroup gdcmParser * \brief Sets a 'non string' value to a given Dicom Element * @param area * @param group Group number of the searched Dicom Element @@ -788,7 +714,6 @@ bool gdcmParser::SetEntryVoidAreaByNumber(void * area, } /** - * \ingroup gdcmParser * \brief Update the entries with the shadow dictionary. * Only non even entries are analyzed */ @@ -832,7 +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. @@ -848,7 +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 @@ -867,7 +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. @@ -880,7 +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. @@ -960,7 +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") ) { @@ -979,7 +900,7 @@ 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); + 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 @@ -1025,7 +946,7 @@ void gdcmParser::WriteEntryTagVRLength(gdcmHeaderEntry *tag, fwrite ( &group,(size_t)2 ,(size_t)1 ,_fp); //group fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element - if ( type == ExplicitVR ) { + if ( type == gdcmExplicitVR ) { // Special case of delimiters: if (group == 0xfffe) { @@ -1040,7 +961,7 @@ void gdcmParser::WriteEntryTagVRLength(gdcmHeaderEntry *tag, guint16 z=0; guint16 shortLgr = lgr; - if (vr == "unkn") { // Unknown was 'written' + 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); @@ -1070,6 +991,7 @@ void gdcmParser::WriteEntryTagVRLength(gdcmHeaderEntry *tag, */ void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) { + (void)type; guint16 group = tag->GetGroup(); std::string vr = tag->GetVR(); guint32 lgr = tag->GetReadLength(); @@ -1092,7 +1014,7 @@ void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) if (vr == "US" || vr == "SS") { // some 'Short integer' fields may be mulivaluated - // each single value is separated from the next one by \ + // 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 @@ -1107,7 +1029,7 @@ void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) return; } // some 'Integer' fields may be mulivaluated - // each single value is separated from the next one by \ + // each single value is separated from the next one by '\' // we split the string and write each value as an int if (vr == "UL" || vr == "SL") { @@ -1169,26 +1091,23 @@ bool gdcmParser::WriteEntry(gdcmHeaderEntry *tag, 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) { - if ( type == ACR ){ + 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" ) - // For the time being sequences are simply ignored - // TODO : find a trick not to *skip* the SeQuences ! - continue; - if ((*tag2)->GetGroup() == 0xfffe ) - // Ignore the documented delimiter + 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; @@ -1197,7 +1116,6 @@ bool gdcmParser::WriteEntries(FILE *_fp,FileType type) } /** - * \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. @@ -1220,14 +1138,11 @@ void gdcmParser::WriteEntriesDeprecated(FILE *_fp,FileType type) { for (TagHeaderEntryHT::iterator tag2=tagHT.begin(); tag2 != tagHT.end(); ++tag2){ - if ( type == ACR ){ - 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 - // TODO : find a trick to *skip* the SeQuences ! - // Not only ignore the SQ element - // --> will be done with the next organization - if ((*tag2->second).GetGroup() == 0xfffe ) continue; // ignore delimiters + 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; @@ -1235,7 +1150,6 @@ void gdcmParser::WriteEntriesDeprecated(FILE *_fp,FileType type) { } /** - * \ingroup gdcmParser * \brief Swaps back the bytes of 4-byte long integer accordingly to * processor order. * @return The properly swaped 32 bits integer. @@ -1264,7 +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. @@ -1274,7 +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. */ @@ -1285,7 +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. */ @@ -1296,12 +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; @@ -1312,27 +1222,19 @@ bool gdcmParser::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { 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 @@ -1344,7 +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) // -------------------------------------------------------------- @@ -1356,19 +1258,20 @@ void gdcmParser::LoadHeaderEntries(void) { 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 @@ -1378,25 +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; } @@ -1481,7 +1373,6 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { } /** - * \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 @@ -1497,17 +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 ( (filetype == ExplicitVR) && (! Entry->IsImplicitVR()) ) + if ( (filetype == gdcmExplicitVR) && (! Entry->IsImplicitVR()) ) { if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) { @@ -1589,7 +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; @@ -1609,13 +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]; @@ -1646,7 +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. @@ -1718,7 +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 ! @@ -1737,7 +1625,7 @@ std::string gdcmParser::GetHeaderEntryValue(gdcmHeaderEntry *Entry) // 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 \ + // (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) @@ -1759,7 +1647,7 @@ 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 \ + // (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) @@ -1788,7 +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 @@ -1842,7 +1729,6 @@ std::string gdcmParser::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry) } /** - * \ingroup gdcmParser * \brief Skip a given Header Entry * \warning NOT end user intended method ! * @param entry @@ -1853,15 +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; } @@ -1877,7 +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... @@ -1905,20 +1789,20 @@ void gdcmParser::FixHeaderEntryFoundLength(gdcmHeaderEntry *Entry, guint32 Found 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. @@ -1962,7 +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 @@ -2014,7 +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 @@ -2035,7 +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 @@ -2056,7 +1937,6 @@ guint32 gdcmParser::ReadInt32(void) { } /** - * \ingroup gdcmParser * \brief skips bytes inside the source file * \warning NOT end user intended method ! * @return @@ -2067,7 +1947,6 @@ void gdcmParser::SkipBytes(guint32 NBytes) { } /** - * \ingroup gdcmParser * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ @@ -2078,7 +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 @@ -2148,13 +2026,13 @@ bool gdcmParser::CheckSwap() { // Use gdcmParser::dicom_vr to test all the possibilities // 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"); } @@ -2199,19 +2077,19 @@ 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 : @@ -2230,27 +2108,27 @@ bool gdcmParser::CheckSwap() { // the file IS NOT ACR-NEMA nor DICOM V3 // Find a trick to tell it the caller... - s16 = *((guint16 *)(deb)); - - 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; - } + 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; + } // Then the only info we have is the net2host one. //if (! net2host ) @@ -2262,7 +2140,6 @@ bool gdcmParser::CheckSwap() { } /** - * \ingroup gdcmParser * \brief Restore the unproperly loaded values i.e. the group, the element * and the dictionary entry depending on them. */ @@ -2290,7 +2167,6 @@ void gdcmParser::SwitchSwapToBigEndian(void) } /** - * \ingroup gdcmParser * \brief during parsing, Header Elements too long are not loaded in memory * @param NewSize */ @@ -2308,13 +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) @@ -2330,7 +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. @@ -2361,7 +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 @@ -2394,7 +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. */ @@ -2431,7 +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. @@ -2454,7 +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 @@ -2471,7 +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. @@ -2495,9 +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. @@ -2530,7 +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.