X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmParser.cxx;h=9a1c07cea4a1934d63cfb10120e64333ab917198;hb=5154dc89c0a2a565e9e79024ba8910f405279dd2;hp=d75aae58f79d7a057f6c70dfcc3803658b036ea1;hpb=4f48626ba6d2dc26d40f07b780b0fdb5fcc04911;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index d75aae58..9a1c07ce 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; //----------------------------------------------------------------------------- @@ -44,11 +44,12 @@ const unsigned int gdcmParser::MAX_SIZE_PRINT_ELEMENT_VALUE = 64; /** * \brief constructor - * @param inFilename + * @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 + * \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 @@ -68,9 +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 @@ -78,11 +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); @@ -93,7 +93,6 @@ gdcmParser::gdcmParser(bool exception_on_error) { } /** - * \ingroup gdcmParser * \brief Canonical destructor. */ gdcmParser::~gdcmParser (void) { @@ -104,13 +103,11 @@ 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(); @@ -119,11 +116,11 @@ void gdcmParser::PrintEntry(std::ostream & 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); @@ -401,7 +406,7 @@ gdcmHeaderEntry * gdcmParser::ReplaceOrCreateByNumber( gdcmHeaderEntry* a; a = GetHeaderEntryByNumber( Group, Elem); if (a == NULL) { - gdcmHeaderEntry *a = NewHeaderEntryByNumber(Group, Elem); + a =NewHeaderEntryByNumber(Group, Elem); if (a == NULL) return NULL; AddHeaderEntry(a); @@ -442,7 +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. @@ -460,7 +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. @@ -485,7 +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. @@ -502,7 +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.. @@ -524,7 +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.. @@ -539,7 +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. @@ -555,7 +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. @@ -606,7 +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 @@ -631,7 +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 @@ -651,7 +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 @@ -683,17 +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; } @@ -701,7 +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 @@ -720,7 +714,6 @@ bool gdcmParser::SetEntryVoidAreaByNumber(void * area, } /** - * \ingroup gdcmParser * \brief Update the entries with the shadow dictionary. * Only non even entries are analyzed */ @@ -764,7 +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. @@ -780,7 +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 @@ -799,7 +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. @@ -812,7 +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. @@ -874,7 +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... @@ -911,7 +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 @@ -948,8 +937,14 @@ void gdcmParser::WriteEntryTagVRLength(gdcmHeaderEntry *tag, 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 + fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp); //element if ( type == ExplicitVR ) { @@ -959,12 +954,6 @@ void gdcmParser::WriteEntryTagVRLength(gdcmHeaderEntry *tag, // Hence we skip writing the VR and length and we pad by writing // 0xffffffff - if (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 ignore spurious fffe|0000 tag ! - return; - int ff=0xffffffff; fwrite (&ff,(size_t)4 ,(size_t)1 ,_fp); return; @@ -1002,6 +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(); @@ -1012,7 +1002,6 @@ void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) if (group == 0xfffe) // Delimiters have no associated value: return; - void *voidArea; voidArea = tag->GetVoidArea(); @@ -1024,6 +1013,9 @@ 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 '\' + // 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, "\\"); @@ -1036,7 +1028,9 @@ void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) tokens.clear(); return; } - + // some 'Integer' fields may be mulivaluated + // 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") { std::vector tokens; @@ -1050,8 +1044,7 @@ void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) } tokens.clear(); return; - } - + } fwrite (tag->GetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value } @@ -1098,8 +1091,8 @@ 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) @@ -1111,13 +1104,10 @@ bool gdcmParser::WriteEntries(FILE *_fp,FileType type) 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; @@ -1126,7 +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. @@ -1150,13 +1139,10 @@ void gdcmParser::WriteEntriesDeprecated(FILE *_fp,FileType type) { 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 ((*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; @@ -1164,7 +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. @@ -1193,7 +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. @@ -1203,7 +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. */ @@ -1214,7 +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. */ @@ -1225,12 +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; @@ -1241,27 +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 @@ -1273,7 +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) // -------------------------------------------------------------- @@ -1285,7 +1258,8 @@ 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; std::string rows = GetEntryByNumber(0x0028, 0x0010); @@ -1293,11 +1267,11 @@ void gdcmParser::LoadHeaderEntries(void) { 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 @@ -1307,25 +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; } @@ -1348,18 +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(); @@ -1372,6 +1333,10 @@ void gdcmParser::LoadHeaderEntry(gdcmHeaderEntry *Entry) { } } } + // 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(); @@ -1408,7 +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 @@ -1424,15 +1388,15 @@ 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()) ) { @@ -1536,7 +1500,6 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { } /** - * \ingroup gdcmParser * \brief Find the Value Representation of the current Dicom Element. * @param Entry */ @@ -1573,7 +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. @@ -1645,7 +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 ! @@ -1662,6 +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; @@ -1677,6 +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; @@ -1702,7 +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 @@ -1756,7 +1729,6 @@ std::string gdcmParser::GetHeaderEntryUnvalue(gdcmHeaderEntry *Entry) } /** - * \ingroup gdcmParser * \brief Skip a given Header Entry * \warning NOT end user intended method ! * @param entry @@ -1767,15 +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; } @@ -1791,7 +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... @@ -1819,20 +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. @@ -1876,7 +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 @@ -1928,7 +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 @@ -1949,7 +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 @@ -1970,7 +1937,6 @@ guint32 gdcmParser::ReadInt32(void) { } /** - * \ingroup gdcmParser * \brief skips bytes inside the source file * \warning NOT end user intended method ! * @return @@ -1981,7 +1947,6 @@ void gdcmParser::SkipBytes(guint32 NBytes) { } /** - * \ingroup gdcmParser * \brief Loads all the needed Dictionaries * \warning NOT end user intended method ! */ @@ -1992,7 +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 @@ -2176,7 +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. */ @@ -2204,7 +2167,6 @@ void gdcmParser::SwitchSwapToBigEndian(void) } /** - * \ingroup gdcmParser * \brief during parsing, Header Elements too long are not loaded in memory * @param NewSize */ @@ -2222,13 +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) @@ -2244,7 +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. @@ -2275,7 +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 @@ -2308,7 +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. */ @@ -2345,7 +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. @@ -2368,7 +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 @@ -2385,7 +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. @@ -2409,9 +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. @@ -2444,7 +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.