X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=10fd52f39b03b6b8e7301947ab205a10aa755220;hb=ab62b1a706df8e2ab1fbf26fa5037d6c22293655;hp=ccd0b644be13c468d5c272c8c0223d3eff4a0451;hpb=220ad8c527f2b2edf1ba19af8897aca8f4a49cf7;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index ccd0b644..10fd52f3 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2004/07/30 16:09:27 $ - Version: $Revision: 1.60 $ + Date: $Date: 2004/08/02 16:42:14 $ + Version: $Revision: 1.65 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -25,7 +25,6 @@ #include "gdcmUtil.h" #include "gdcmDebug.h" -#include #include // For nthos: @@ -83,17 +82,15 @@ const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff; /** * \brief constructor * @param inFilename file to be opened for parsing - * @param exception_on_error whether we throw an exception or not */ -gdcmDocument::gdcmDocument( std::string const & filename, - bool exception_on_error) +gdcmDocument::gdcmDocument( std::string const & filename ) : gdcmElementSet(-1) { SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Filename = filename; Initialise(); - if ( !OpenFile(exception_on_error)) + if ( !OpenFile() ) { return; } @@ -110,7 +107,7 @@ gdcmDocument::gdcmDocument( std::string const & filename, long beg = ftell(Fp); lgt -= beg; - SQDepthLevel=0; + SQDepthLevel = 0; long l = ParseDES( this, beg, lgt, false); // le Load sera fait a la volee (void)l; //is l used anywhere ? @@ -137,7 +134,11 @@ gdcmDocument::gdcmDocument( std::string const & filename, CloseFile(); // -------------------------------------------------------------- - // Special Patch to allow gdcm to read ACR-LibIDO formated images + // Specific code to allow gdcm to read ACR-LibIDO formated images + // Note: ACR-LibIDO is an extension of the ACR standard that was + // used at CREATIS. For the time being (say a couple years) + // we keep this kludge to allow a smooth move to gdcm for + // CREATIS developpers (sorry folks). // // if recognition code tells us we deal with a LibIDO image // we switch lineNumber and columnNumber @@ -154,23 +155,20 @@ gdcmDocument::gdcmDocument( std::string const & filename, SetEntryByNumber(columns, 0x0028, 0x0010); SetEntryByNumber(rows , 0x0028, 0x0011); } - // ----------------- End of Special Patch ---------------- + // ----------------- End of ACR-LibIDO kludge ------------------ PrintLevel = 1; // 'Medium' print level by default } /** - * \brief constructor - * @param exception_on_error + * \brief This default constructor doesn't parse the file. You should + * then invoke \ref gdcmDocument::SetFileName and then the parsing. */ -gdcmDocument::gdcmDocument(bool exception_on_error) +gdcmDocument::gdcmDocument() :gdcmElementSet(-1) { - (void)exception_on_error; - SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE); Initialise(); - PrintLevel = 1; // 'Medium' print level by default } @@ -244,7 +242,7 @@ bool gdcmDocument::SetShaDict(gdcmDict *dict) * \brief Set the shadow dictionary used * \param dictName name of the dictionary to use in shadow */ -bool gdcmDocument::SetShaDict(DictKey dictName) +bool gdcmDocument::SetShaDict(DictKey const & dictName) { RefShaDict = gdcmGlobal::GetDicts()->GetDict(dictName); return !RefShaDict; @@ -463,58 +461,46 @@ FileType gdcmDocument::GetFileType() } /** - * \brief opens the file - * @param exception_on_error - * @return + * \brief Tries to open the file \ref gdcmDocument::Filename and + * checks the preamble when existing. + * @return The FILE pointer on success. */ -FILE *gdcmDocument::OpenFile(bool exception_on_error) - throw(gdcmFileError) +FILE* gdcmDocument::OpenFile() { - Fp = fopen(Filename.c_str(),"rb"); - - if(!Fp) - { - if(exception_on_error) - { - throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)"); - } - else - { - dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ", - Filename.c_str()); - return NULL; - } - } - - if ( Fp ) - { - uint16_t zero; - fread(&zero, (size_t)2, (size_t)1, Fp); - - //ACR -- or DICOM with no Preamble -- - if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 ) - { - return Fp; - } - - //DICOM - fseek(Fp, 126L, SEEK_CUR); - char dicm[4]; - fread(dicm, (size_t)4, (size_t)1, Fp); - if( memcmp(dicm, "DICM", 4) == 0 ) - { - return Fp; - } - - fclose(Fp); - dbg.Verbose(0, "gdcmDocument::OpenFile not DICOM/ACR", Filename.c_str()); - } - else - { - dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file", Filename.c_str()); - } + Fp = fopen(Filename.c_str(),"rb"); - return 0; + if(!Fp) + { + dbg.Verbose( 0, + "gdcmDocument::OpenFile cannot open file: ", + Filename.c_str()); + return 0; + } + + uint16_t zero; + fread(&zero, (size_t)2, (size_t)1, Fp); + + //ACR -- or DICOM with no Preamble -- + if( zero == 0x0008 || zero == 0x0800 || zero == 0x0002 || zero == 0x0200 ) + { + return Fp; + } + + //DICOM + fseek(Fp, 126L, SEEK_CUR); + char dicm[4]; + fread(dicm, (size_t)4, (size_t)1, Fp); + if( memcmp(dicm, "DICM", 4) == 0 ) + { + return Fp; + } + + fclose(Fp); + dbg.Verbose( 0, + "gdcmDocument::OpenFile not DICOM/ACR (missing preamble)", + Filename.c_str()); + + return 0; } /** @@ -524,7 +510,7 @@ FILE *gdcmDocument::OpenFile(bool exception_on_error) bool gdcmDocument::CloseFile() { int closed = fclose(Fp); - Fp = (FILE *)0; + Fp = 0; return closed; } @@ -599,7 +585,7 @@ void gdcmDocument::Write(FILE* fp,FileType filetype) */ gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber( - std::string value, + std::string const & value, uint16_t group, uint16_t elem ) { @@ -693,11 +679,10 @@ gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber( * @param Elem element number of the Entry * \return boolean */ -bool gdcmDocument::ReplaceIfExistByNumber(const char* value, uint16_t group, - uint16_t elem ) +bool gdcmDocument::ReplaceIfExistByNumber(std::string const & value, + uint16_t group, uint16_t elem ) { - const std::string v = value; - SetEntryByNumber(v, group, elem); + SetEntryByNumber(value, group, elem); return true; } @@ -713,7 +698,7 @@ bool gdcmDocument::ReplaceIfExistByNumber(const char* value, uint16_t group, */ int gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) { - std::string key = gdcmDictEntry::TranslateToKey(group, element ); + const std::string &key = gdcmDictEntry::TranslateToKey(group, element ); return TagHT.count(key); } @@ -726,7 +711,7 @@ int gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element ) * @return Corresponding element value when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryByName(TagName tagName) +std::string gdcmDocument::GetEntryByName(TagName const & tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) @@ -750,7 +735,7 @@ std::string gdcmDocument::GetEntryByName(TagName tagName) * @return Corresponding element value representation when it exists, * and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise. */ -std::string gdcmDocument::GetEntryVRByName(TagName tagName) +std::string gdcmDocument::GetEntryVRByName(TagName const & tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( dictEntry == NULL) @@ -758,8 +743,8 @@ std::string gdcmDocument::GetEntryVRByName(TagName tagName) return GDCM_UNFOUND; } - gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), - dictEntry->GetElement()); + gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(), + dictEntry->GetElement()); return elem->GetVR(); } @@ -832,7 +817,7 @@ int gdcmDocument::GetEntryLengthByNumber(uint16_t group, uint16_t element) * @param tagName name of the searched Dicom Element. * @return true when found */ -bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) +bool gdcmDocument::SetEntryByName(std::string const & content,std::string const & tagName) { gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName); if( !dictEntry ) @@ -852,7 +837,7 @@ bool gdcmDocument::SetEntryByName(std::string content,std::string tagName) * @param group group number of the Dicom Element to modify * @param element element number of the Dicom Element to modify */ -bool gdcmDocument::SetEntryByNumber(std::string content, +bool gdcmDocument::SetEntryByNumber(std::string const & content, uint16_t group, uint16_t element) { @@ -864,11 +849,12 @@ bool gdcmDocument::SetEntryByNumber(std::string content, return false; } // Non even content must be padded with a space (020H)... - if( content.length() % 2 ) + std::string evenContent = content; + if( evenContent.length() % 2 ) { - content += '\0'; // ... therefore we padd with (000H) .!?! + evenContent += '\0'; // ... therefore we padd with (000H) .!?! } - valEntry->SetValue(content); + valEntry->SetValue(evenContent); // Integers have a special treatement for their length: gdcmVRKey vr = valEntry->GetVR(); @@ -882,7 +868,7 @@ bool gdcmDocument::SetEntryByNumber(std::string content, } else { - valEntry->SetLength(content.length()); + valEntry->SetLength(evenContent.length()); } return true; @@ -916,10 +902,10 @@ bool gdcmDocument::SetEntryByNumber(void *content, //content = content + '\0'; // fing a trick to enlarge a binary field? } */ - gdcmBinEntry * a; - a = (gdcmBinEntry *)TagHT[key]; + gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key]; a->SetVoidArea(content); //a->SetLength(lgth); // ??? + return true; } @@ -1066,8 +1052,9 @@ bool gdcmDocument::SetEntryVoidAreaByNumber(void * area, { return false; } - // This was for multimap ? - (( gdcmBinEntry *)( ((TagHT.equal_range(key)).first)->second ))->SetVoidArea(area); + + // This was for multimap ? + (( gdcmBinEntry *)( ((TagHT.equal_range(key)).first)->second ))->SetVoidArea(area); return true; } @@ -1222,7 +1209,7 @@ uint32_t gdcmDocument::SwapLong(uint32_t a) default : std::cout << "swapCode= " << SwapCode << std::endl; dbg.Error(" gdcmDocument::SwapLong : unset swap code"); - a=0; + a = 0; } return a; } @@ -1245,7 +1232,7 @@ uint16_t gdcmDocument::SwapShort(uint16_t a) { if ( SwapCode == 4321 || SwapCode == 2143 ) { - a =((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) ); + a = ((( a << 8 ) & 0x0ff00 ) | (( a >> 8 ) & 0x00ff ) ); } return a; } @@ -1301,7 +1288,7 @@ long gdcmDocument::ParseDES(gdcmDocEntrySet *set, newValEntry->SetDepthLevel(depth); set->AddEntry(newValEntry); LoadDocEntry(newValEntry); - if (newValEntry->isItemDelimitor()) + if (newValEntry->IsItemDelimitor()) { break; } @@ -1411,7 +1398,7 @@ long gdcmDocument::ParseSQ(gdcmSeqEntry *set, } if( delim_mode ) { - if ( newDocEntry->isSequenceDelimitor() ) + if ( newDocEntry->IsSequenceDelimitor() ) { set->SetSequenceDelimitationItem( newDocEntry ); break; @@ -1498,8 +1485,12 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) } // to be sure we are at the end of the value ... fseek(Fp, (long)entry->GetOffset()+(long)entry->GetLength(), SEEK_SET); - - return; //FIXME FIXME FIXME FIXME ???? + // Following return introduced by JPR on version 1.25. Since the + // treatement of a ValEntry is never executed (doh!) this means + // we were lucky up to now because we NEVER encountered a ValEntry + // whose length was bigger thant MaxSizeLoadEntry !? I can't believe + // this could ever work... + return; //FIXME FIXME FIXME FIXME JPR ???? // Be carefull : a BinEntry IS_A ValEntry ... if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) ) @@ -1617,7 +1608,8 @@ void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry) * \brief Find the value Length of the passed Header Entry * @param Entry Header Entry whose length of the value shall be loaded. */ -void gdcmDocument::FindDocEntryLength (gdcmDocEntry *entry) +void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry ) + throw ( gdcmFormatError ) { uint16_t element = entry->GetElement(); std::string vr = entry->GetVR(); @@ -1636,8 +1628,12 @@ void gdcmDocument::FindDocEntryLength (gdcmDocEntry *entry) if ( vr == "OB" && length32 == 0xffffffff ) { - uint32_t lengthOB = FindDocEntryLengthOB(); - if ( errno == 1 ) + uint32_t lengthOB; + try + { + lengthOB = FindDocEntryLengthOB(); + } + catch ( gdcmFormatUnexpected ) { // Computing the length failed (this happens with broken // files like gdcm-JPEG-LossLess3a.dcm). We still have a @@ -1649,7 +1645,6 @@ void gdcmDocument::FindDocEntryLength (gdcmDocEntry *entry) long lengthUntilEOF = ftell(Fp) - currentPosition; fseek(Fp, currentPosition, SEEK_SET); entry->SetLength(lengthUntilEOF); - errno = 0; return; } entry->SetLength(lengthOB); @@ -1689,12 +1684,12 @@ void gdcmDocument::FindDocEntryLength (gdcmDocEntry *entry) // endian encoding". When this is the case, chances are we have got our // hands on a big endian encoded file: we switch the swap code to // big endian and proceed... - if ( (element == 0x0000) && (length16 == 0x0400) ) + if ( element == 0x0000 && length16 == 0x0400 ) { - if ( ! IsExplicitVRBigEndianTransferSyntax() ) + if ( !IsExplicitVRBigEndianTransferSyntax() ) { - dbg.Verbose(0, "gdcmDocument::FindLength", "not explicit VR"); - errno = 1; + throw gdcmFormatError( "gdcmDocument::FindDocEntryLength()", + " not explicit VR." ); return; } length16 = 4; @@ -1718,11 +1713,10 @@ void gdcmDocument::FindDocEntryLength (gdcmDocEntry *entry) // Heuristic: well, some files are really ill-formed. if ( length16 == 0xffff) { + // 0xffff means that we deal with 'Unknown Length' Sequence length16 = 0; - // Length16= 0xffff means that we deal with - // 'Unknown Length' Sequence } - FixDocEntryFoundLength(entry, (uint32_t)length16); + FixDocEntryFoundLength( entry, (uint32_t)length16 ); return; } else @@ -1734,7 +1728,7 @@ void gdcmDocument::FindDocEntryLength (gdcmDocEntry *entry) // not coexist in a Data Set and Data Sets nested within it".] // Length is on 4 bytes. - FixDocEntryFoundLength(entry, ReadInt32()); + FixDocEntryFoundLength( entry, ReadInt32() ); return; } } @@ -1802,7 +1796,7 @@ bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr) // expected VR read happens to be non-ascii characters we consider // we hit falsely explicit VR tag. - if ( (!isalpha(vr[0])) && (!isalpha(vr[1])) ) + if ( !isalpha(vr[0]) && !isalpha(vr[1]) ) { realExplicit = false; } @@ -2149,6 +2143,7 @@ bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *entry) */ uint32_t gdcmDocument::FindDocEntryLengthOB() + throw( gdcmFormatUnexpected ) { // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data. long positionOnEntry = ftell(Fp); @@ -2157,26 +2152,33 @@ uint32_t gdcmDocument::FindDocEntryLengthOB() while ( !foundSequenceDelimiter ) { - uint16_t g = ReadInt16(); - uint16_t n = ReadInt16(); - if ( errno == 1 ) + uint16_t group; + uint16_t elem; + try { - return 0; + group = ReadInt16(); + elem = ReadInt16(); + } + catch ( gdcmFormatError ) + { + throw gdcmFormatError("gdcmDocument::FindDocEntryLengthOB()", + " group or element not present."); } // We have to decount the group and element we just read totalLength += 4; - if ( g != 0xfffe || ( n != 0xe0dd && n != 0xe000 ) ) + if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) ) { - dbg.Verbose(1, "gdcmDocument::FindLengthOB: neither an Item tag " - "nor a Sequence delimiter tag."); + dbg.Verbose(1, "gdcmDocument::FindDocEntryLengthOB: neither an Item " + "tag nor a Sequence delimiter tag."); fseek(Fp, positionOnEntry, SEEK_SET); - errno = 1; - return 0; + throw gdcmFormatUnexpected("gdcmDocument::FindDocEntryLengthOB()", + "Neither an Item tag nor a Sequence " + "delimiter tag."); } - if ( n == 0xe0dd ) + if ( elem == 0xe0dd ) { foundSequenceDelimiter = true; } @@ -2201,6 +2203,7 @@ uint32_t gdcmDocument::FindDocEntryLengthOB() * @return read value */ uint16_t gdcmDocument::ReadInt16() + throw( gdcmFormatError ) { uint16_t g; size_t item_read = fread (&g, (size_t)2,(size_t)1, Fp); @@ -2208,12 +2211,10 @@ uint16_t gdcmDocument::ReadInt16() { if( ferror(Fp) ) { - dbg.Verbose(0, "gdcmDocument::ReadInt16", " File Error"); + throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." ); } - errno = 1; - return 0; + throw gdcmFormatError( "gdcmDocument::ReadInt16()", "EOF." ); } - errno = 0; g = SwapShort(g); return g; } @@ -2224,6 +2225,7 @@ uint16_t gdcmDocument::ReadInt16() * @return read value */ uint32_t gdcmDocument::ReadInt32() + throw( gdcmFormatError ) { uint32_t g; size_t item_read = fread (&g, (size_t)4,(size_t)1, Fp); @@ -2231,12 +2233,10 @@ uint32_t gdcmDocument::ReadInt32() { if( ferror(Fp) ) { - dbg.Verbose(0, "gdcmDocument::ReadInt32", " File Error"); + throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." ); } - errno = 1; - return 0; + throw gdcmFormatError( "gdcmDocument::ReadInt32()", "EOF." ); } - errno = 0; g = SwapLong(g); return g; } @@ -2523,28 +2523,39 @@ void gdcmDocument::SetMaxSizePrintEntry(long newSize) * gets the VR, gets the length, gets the offset value) * @return On succes the newly created DocEntry, NULL on failure. */ -gdcmDocEntry *gdcmDocument::ReadNextDocEntry() +gdcmDocEntry* gdcmDocument::ReadNextDocEntry() { - uint16_t g = ReadInt16(); - uint16_t n = ReadInt16(); + uint16_t group; + uint16_t elem; - if (errno == 1) + try + { + group = ReadInt16(); + elem = ReadInt16(); + } + catch ( gdcmFormatError e ) { // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. + std::cout << e; return 0; } - gdcmDocEntry *newEntry = NewDocEntryByNumber(g, n); + gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem); FindDocEntryVR(newEntry); - FindDocEntryLength(newEntry); - if (errno == 1) + try + { + FindDocEntryLength(newEntry); + } + catch ( gdcmFormatError e ) { // Call it quits + std::cout << e; delete newEntry; - return NULL; + return 0; } + newEntry->SetOffset(ftell(Fp)); return newEntry; @@ -2626,8 +2637,8 @@ bool gdcmDocument::ReadTag(uint16_t testGroup, uint16_t testElement) */ uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement) { - long PositionOnEntry = ftell(Fp); - (void)PositionOnEntry; + long positionOnEntry = ftell(Fp); + (void)positionOnEntry; if ( !ReadTag(testGroup, testElement) ) { @@ -2744,7 +2755,7 @@ void gdcmDocument::Parse7FE0 () // Make sure that at the end of the item we encounter a 'Sequence // Delimiter Item': - if ( ! ReadTag(0xfffe, 0xe0dd) ) + if ( !ReadTag(0xfffe, 0xe0dd) ) { dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item"); dbg.Verbose(0, " at end of RLE item sequence"); @@ -2764,7 +2775,7 @@ void gdcmDocument::Parse7FE0 () bool gdcmDocument::operator<(gdcmDocument &document) { // Patient Name - std::string s1 = this->GetEntryByNumber(0x0010,0x0010); + std::string s1 = GetEntryByNumber(0x0010,0x0010); std::string s2 = document.GetEntryByNumber(0x0010,0x0010); if(s1 < s2) { @@ -2777,7 +2788,7 @@ bool gdcmDocument::operator<(gdcmDocument &document) else { // Patient ID - s1 = this->GetEntryByNumber(0x0010,0x0020); + s1 = GetEntryByNumber(0x0010,0x0020); s2 = document.GetEntryByNumber(0x0010,0x0020); if ( s1 < s2 ) { @@ -2790,7 +2801,7 @@ bool gdcmDocument::operator<(gdcmDocument &document) else { // Study Instance UID - s1 = this->GetEntryByNumber(0x0020,0x000d); + s1 = GetEntryByNumber(0x0020,0x000d); s2 = document.GetEntryByNumber(0x0020,0x000d); if ( s1 < s2 ) { @@ -2803,7 +2814,7 @@ bool gdcmDocument::operator<(gdcmDocument &document) else { // Serie Instance UID - s1 = this->GetEntryByNumber(0x0020,0x000e); + s1 = GetEntryByNumber(0x0020,0x000e); s2 = document.GetEntryByNumber(0x0020,0x000e); if ( s1 < s2 ) {