X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmParser.cxx;h=327a37534531f3e366e43edf50576f340a8bfcd8;hb=8b0d3c6c373474dc31af9eb56cf949298a723a76;hp=e413ee1edd704ea5cd92a3067000686f2c036351;hpb=73d23d0da1d6ff657c01d1fb78f6ec876736afb3;p=gdcm.git diff --git a/src/gdcmParser.cxx b/src/gdcmParser.cxx index e413ee1e..327a3753 100644 --- a/src/gdcmParser.cxx +++ b/src/gdcmParser.cxx @@ -1,5 +1,10 @@ // gdcmParser.cxx //----------------------------------------------------------------------------- +#include "gdcmParser.h" +#include "gdcmGlobal.h" +#include "gdcmUtil.h" +#include "gdcmDebug.h" + #include #include @@ -10,24 +15,18 @@ #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; @@ -44,11 +43,12 @@ 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 @@ -70,7 +70,7 @@ gdcmParser::gdcmParser(const char *inFilename, return; if (ParseHeader()) { LoadHeaderEntries(); - } + } CloseFile(); wasUpdated = 0; // will be set to 1 if user adds an entry @@ -83,6 +83,7 @@ gdcmParser::gdcmParser(const char *inFilename, * @param exception_on_error */ gdcmParser::gdcmParser(bool exception_on_error) { + (void)exception_on_error; enableSequences=0; SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); @@ -106,11 +107,10 @@ gdcmParser::~gdcmParser (void) { /** * \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 +119,152 @@ void gdcmParser::PrintEntry(std::ostream & os) { (*i)->SetPrintLevel(printLevel); (*i)->Print(os); } - os<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 any SeQuence + * \warning : will be removed + * @return + */ +void gdcmParser::PrintEntryNiceSQ(std::ostream & os) { + pileElem pile[50]; // Hope embedded sequence depth is no more than 50 + int top =-1; + int countSQ = 0; + int currentParsedlength = 0; + int totalElementlength; + std::ostringstream tab; + tab << " "; + + int DEBUG = 0; // Sorry; Dealing with e-film breaker images + // will (certainly) cause a lot of troubles ... + // I prefer keeping my 'trace' on . + + for (ListTag::iterator i = listEntries.begin(); + i != listEntries.end(); + ++i) { + if ( (*i)->GetVR() == "SQ" && (*i)->GetReadLength() != 0) { // SQ found + countSQ++; + top ++; + if ( top >= 50) { + std::cout << "Kaie ! Kaie! SQ stack overflow" << std::endl; + return; + } + if (DEBUG) std::cout << "\n >>>>> empile niveau " << top + << "; Lgr SeQ: " << (*i)->GetReadLength() + << "\n" <GetReadLength(); + pile[top].alreadyParsedlength = 0; + currentParsedlength = 0; + + } else { // non SQ found + + if (countSQ != 0) { // we are 'inside a SeQuence' + if ( (*i)->GetGroup()==0xfffe && (*i)->GetElement()==0xe0dd){ + // we just found 'end of SeQuence' + + if (DEBUG) + std::cout << "fffe,e0dd : depile" << std::endl; + currentParsedlength += 8; // gr:2 elem:2 vr:2 lgt:2 + countSQ --; + top --; + pile[top].alreadyParsedlength += currentParsedlength; + } else { + // we are on a 'standard' elem + // or a Zero-length SeQuence + + totalElementlength = (*i)->GetFullLength(); + currentParsedlength += totalElementlength; + pile[top].alreadyParsedlength += totalElementlength; + + if (pile[top].totalSQlength == 0xffffffff) { + if (DEBUG) + std::cout << "totalSeQlength == 0xffffffff" + << std::endl; + } else { + if (DEBUG) + std::cout << "alrdyPseLgt:" + << pile[top].alreadyParsedlength << " totSeQlgt: " + << pile[top].totalSQlength << " curPseLgt: " + << currentParsedlength + << std::endl; + while (pile[top].alreadyParsedlength==pile[top].totalSQlength) { + + if (DEBUG) + std::cout << " \n<<<<<< On depile niveau " << top + << "\n" << std::endl; + + currentParsedlength = pile[top].alreadyParsedlength; + countSQ --; + top --; + if (top >=0) { + + pile[top].alreadyParsedlength += currentParsedlength +12; + // 12 : length of 'SQ embedded' SQ element + currentParsedlength += 8; // gr:2 elem:2 vr:2 lgt:2 + + if (DEBUG) + std::cout << pile[top].alreadyParsedlength << " " + << pile[top].totalSQlength << " " + << currentParsedlength + << std::endl; + } + if (top == -1) { + currentParsedlength = 0; + break; + } + } + } + } + } // end : 'inside a SeQuence' + } + + if (countSQ != 0) { + for (int i=0;iSetPrintLevel(printLevel); + (*i)->Print(os); + + } // end for +} + + + +/** + * \brief Prints The Dict Entries of THE public Dicom Dictionary * @return */ void gdcmParser::PrintPubDict(std::ostream & os) { @@ -131,7 +272,7 @@ void gdcmParser::PrintPubDict(std::ostream & os) { } /** - * \brief Prints The Dict Entries of THE shadow Dicom Dictionnary + * \brief Prints The Dict Entries of THE shadow Dicom Dictionary * @return */ void gdcmParser::PrintShaDict(std::ostream & os) { @@ -687,8 +828,8 @@ 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; @@ -697,7 +838,7 @@ void *gdcmParser::LoadEntryVoidArea(guint16 Group, guint16 Elem) size_t l2 = fread(a, 1, l ,fp); if(l != l2) { - free(a); + delete[] a; return NULL; } @@ -878,7 +1019,7 @@ 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... @@ -915,7 +1056,7 @@ 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 @@ -1006,6 +1147,7 @@ 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(); @@ -1016,7 +1158,6 @@ void gdcmParser::WriteEntryValue(gdcmHeaderEntry *tag, FILE *_fp,FileType type) if (group == 0xfffe) // Delimiters have no associated value: return; - void *voidArea; voidArea = tag->GetVoidArea(); @@ -1028,6 +1169,9 @@ 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, "\\"); @@ -1040,7 +1184,9 @@ 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; @@ -1054,8 +1200,7 @@ 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 } @@ -1234,7 +1379,7 @@ guint16 gdcmParser::UnswapShort(guint16 a) { * @return false if file is not ACR-NEMA / DICOM */ bool gdcmParser::ParseHeader(bool exception_on_error) throw(gdcmFormatError) { - + (void)exception_on_error; rewind(fp); if (!CheckSwap()) return false; @@ -1311,25 +1456,14 @@ 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; } @@ -1352,18 +1486,16 @@ 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(); @@ -1376,6 +1508,10 @@ 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(); @@ -1434,9 +1570,10 @@ void gdcmParser::AddHeaderEntry(gdcmHeaderEntry *newHeaderEntry) { */ 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()) ) { @@ -1666,6 +1803,13 @@ 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; @@ -1681,6 +1825,12 @@ 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; @@ -1778,8 +1928,7 @@ void gdcmParser::SkipHeaderEntry(gdcmHeaderEntry *entry) */ 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; } @@ -1795,7 +1944,7 @@ 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... @@ -1823,15 +1972,16 @@ 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); }