X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.cxx;h=57193f206eb4a86fa4e1eb873c334147eb6f108e;hb=81b83abc1f19db44870ea35907c5f6a102ba5c64;hp=06a91f83695301b25ba07cf7a7f7a1301888b2f7;hpb=725267b12a1928251820ad7a3fc363de5fcdf8dc;p=gdcm.git diff --git a/src/gdcmDocument.cxx b/src/gdcmDocument.cxx index 06a91f83..57193f20 100644 --- a/src/gdcmDocument.cxx +++ b/src/gdcmDocument.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.cxx,v $ Language: C++ - Date: $Date: 2006/03/14 12:09:18 $ - Version: $Revision: 1.345 $ + Date: $Date: 2006/06/15 14:22:33 $ + Version: $Revision: 1.350 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -95,19 +95,22 @@ bool Document::Load( ) return DoTheLoadingDocumentJob( ); } -#ifndef GDCM_LEGACY_REMOVE + +//#ifndef GDCM_LEGACY_REMOVE /** * \brief Loader. (DEPRECATED : not to break the API) * @param fileName 'Document' (File or DicomDir) to be open for parsing * @return false if file cannot be open or no swap info was found, * or no tag was found. */ + /* bool Document::Load( std::string const &fileName ) { Filename = fileName; return DoTheLoadingDocumentJob( ); } -#endif +*/ +//#endif /** * \brief Performs the Loading Job (internal use only) @@ -260,7 +263,7 @@ bool Document::DoTheLoadingDocumentJob( ) LoadDocEntry(d, true); } - CloseFile(); + CloseFile(); // ---------------------------- // Specific code to allow gdcm to read ACR-LibIDO formated images @@ -621,7 +624,6 @@ std::ifstream *Document::OpenFile() } //-- Broken ACR or DICOM with no Preamble; may start with a Shadow Group -- - // FIXME : We cannot be sure the preable is only zeroes.. // (see ACUSON-24-YBR_FULL-RLE.dcm ) if ( @@ -695,7 +697,6 @@ void Document::WriteContent(std::ofstream *fp, FileType filetype) fp->write(filePreamble, 128); fp->write("DICM", 4); } - /* * \todo rewrite later, if really usefull * - 'Group Length' element is optional in DICOM @@ -1047,13 +1048,13 @@ void Document::ParseDES(DocEntrySet *set, long offset, DocEntry *newDocEntry; DataEntry *newDataEntry; SeqEntry *newSeqEntry; - VRKey vr; + //VRKey vr; bool used; // will be set to false when something wrong happens to an Entry. // (Entry will then be deleted) bool delim_mode_intern = delim_mode; bool first = true; gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode - << " at offset " << std::hex << "0x(" << offset << ")" ); + << " at offset " << std::hex << "0x(" << offset << ")" ); while (true) { @@ -1063,29 +1064,30 @@ void Document::ParseDES(DocEntrySet *set, long offset, // Uncomment to track the bug /* if( Debug::GetDebugFlag() ) - std::cout << std::dec <<"(long)(Fp->tellg()) " << (long)(Fp->tellg()) + std::cout << std::dec <<"(long)(Fp->tellg()) " << (long)(Fp->tellg()) // in Debug mode << std::hex << " 0x(" <<(long)(Fp->tellg()) << ")" << std::endl; -*/ - + */ + // if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry if ( !delim_mode ) // 'and then' doesn't exist in C++ :-( if ( ((long)(Fp->tellg())-offset) >= l_max) // Once per DocEntry, when no delim mode { break; } - newDocEntry = ReadNextDocEntry( ); - // Uncoment this cerr line to be able to 'follow' the DocEntries - // when something *very* strange happens - if( Debug::GetDebugFlag() ) - std::cerr<GetKey()<<" "<GetVR()<GetKey()<<" "<GetVR()<GetVR(); + //vr = newDocEntry->GetVR(); // useless ? if ( !set->AddEntry( newDataEntry ) ) { @@ -1232,7 +1234,6 @@ void Document::ParseDES(DocEntrySet *set, long offset, l, delim_mode_intern); gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern); - } if ( !set->AddEntry( newSeqEntry ) ) { @@ -1379,10 +1380,10 @@ DocEntry *Document::Backtrack(DocEntry *docEntry) */ void Document::LoadDocEntry(DocEntry *entry, bool forceLoad) { - uint16_t group = entry->GetGroup(); - uint16_t elem = entry->GetElement(); + uint16_t group = entry->GetGroup(); + uint16_t elem = entry->GetElement(); const VRKey &vr = entry->GetVR(); - uint32_t length = entry->GetLength(); + uint32_t length = entry->GetLength(); // Fp->seekg((long)entry->GetOffset(), std::ios::beg); // JPRx @@ -1593,7 +1594,9 @@ uint32_t Document::FindDocEntryLengthOBOrOW() VRKey Document::FindDocEntryVR() { if ( Filetype != ExplicitVR ) + { return GDCM_VRUNKNOWN; + } // Delimiters (0xfffe), are not explicit VR ... if ( CurrentGroup == 0xfffe ) @@ -1620,7 +1623,7 @@ VRKey Document::FindDocEntryVR() if ( !CheckDocEntryVR(vr) ) { /* - std::cout << "================================================================Unknown VR" +// std::cout << "================================================================Unknown VR" << std::hex << "0x(" << (unsigned int)vr[0] << "|" << (unsigned int)vr[1] << ")" << "for : " << CurrentGroup @@ -1744,18 +1747,18 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, gdcmErrorMacro( "This looks like to a buggy Siemens DICOM file." "The length of this tag seems to be wrong" ); } - } - + } + else if ( entry->GetVR() == "SQ" ) { - foundLength = 0; // ReadLength is unchanged - } - - //////// We encountered a 'delimiter' element i.e. a tag of the form + foundLength = 0; // ReadLength is unchanged + } + + //////// We encountered a 'delimiter' element i.e. a tag of the form // "fffe|xxxx" which is just a marker. Delimiters length should not be // taken into account. else if ( gr == 0xfffe ) - { + { // According to the norm, fffe|0000 shouldn't exist. BUT the Philips // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to // causes extra troubles... @@ -1767,7 +1770,7 @@ void Document::FixDocEntryFoundLength(DocEntry *entry, { foundLength=12; // to skip the mess that follows this bugged Tag ! } - } + } entry->SetLength(foundLength); } @@ -1803,6 +1806,7 @@ bool Document::IsDocEntryAnInteger(DocEntry *entry) // encounter such an ill-formed image, we simply display a warning // message and proceed on parsing (while crossing fingers). long filePosition = Fp->tellg(); // Only when elem 0x0000 length is not 4 (?!?) + (void)filePosition; gdcmWarningMacro( "Erroneous Group Length element length on : (" << std::hex << group << " , " << elem << ") -before- position x(" << filePosition << ")" @@ -2052,7 +2056,7 @@ void Document::SwitchByteSwapCode() * \brief during parsing, Header Elements too long are not loaded in memory * @param newSize new size */ -void Document::SetMaxSizeLoadEntry(long newSize) +void Document::SetMaxSizeLoadEntry(long newSize) { if ( newSize < 0 ) { @@ -2071,7 +2075,7 @@ void Document::SetMaxSizeLoadEntry(long newSize) * (read the 'Group Number', the 'Element Number', * gets the Dict Entry * gets the VR, gets the length, gets the offset value) - * @return On succes : the newly created DocEntry, NULL on failure. + * @return On succes : the newly created DocEntry, NULL on failure. */ DocEntry *Document::ReadNextDocEntry() { @@ -2082,11 +2086,11 @@ DocEntry *Document::ReadNextDocEntry() } catch ( FormatError ) { - // We reached the EOF (or an error occured) therefore + // We reached the EOF (or an error occured) therefore // header parsing has to be considered as finished. return 0; } - + // In 'true DICOM' files Group 0002 is always little endian if ( HasDCMPreamble ) { @@ -2094,11 +2098,10 @@ DocEntry *Document::ReadNextDocEntry() HandleOutOfGroup0002(CurrentGroup, CurrentElem); else // Sometimes file contains groups of tags with reversed endianess. - HandleBrokenEndian(CurrentGroup, CurrentElem); + HandleBrokenEndian(CurrentGroup, CurrentElem); } - + VRKey vr = FindDocEntryVR(); - VRKey realVR = vr; if ( vr == GDCM_VRUNKNOWN ) @@ -2107,6 +2110,11 @@ DocEntry *Document::ReadNextDocEntry() { realVR = "UL"; // must be UL } + else if (CurrentGroup == 0xfffe) // Don't get DictEntry for Delimitors + { + realVR = "UL"; + } + // Commented out in order not to generate 'Shadow Groups' where some // Data Elements are Explicit VR and some other ones Implicit VR // (Stupid MatLab DICOM Reader couldn't read gdcm-written images) @@ -2121,11 +2129,11 @@ DocEntry *Document::ReadNextDocEntry() */ else { - DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem); + DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);//only when ImplicitVR if ( dictEntry ) { realVR = dictEntry->GetVR(); - dictEntry->Unregister(); + dictEntry->Unregister(); // GetDictEntry registered it } } } @@ -2133,8 +2141,10 @@ DocEntry *Document::ReadNextDocEntry() DocEntry *newEntry; //if ( Global::GetVR()->IsVROfSequence(realVR) ) if (realVR == "SQ") + { newEntry = NewSeqEntry(CurrentGroup, CurrentElem); - else + } + else { newEntry = NewDataEntry(CurrentGroup, CurrentElem, realVR); static_cast(newEntry)->SetState(DataEntry::STATE_NOTLOADED); @@ -2146,14 +2156,14 @@ DocEntry *Document::ReadNextDocEntry() { // We thought this was explicit VR, but we end up with an // implicit VR tag. Let's backtrack. - if ( newEntry->GetGroup() != 0xfffe ) + + //if ( newEntry->GetGroup() != 0xfffe ) + if (CurrentGroup != 0xfffe) { - std::string msg; int offset = Fp->tellg();//Only when heuristic for Explicit/Implicit was wrong - msg = Util::Format( - "Entry (%04x,%04x) at x(%x) should be Explicit VR\n", - newEntry->GetGroup(), newEntry->GetElement(), offset ); - gdcmWarningMacro( msg.c_str() ); + + gdcmWarningMacro("Entry (" << newEntry->GetKey() << ") at x(" + << offset << ") should be Explicit VR"); } } newEntry->SetImplicitVR(); @@ -2171,7 +2181,6 @@ DocEntry *Document::ReadNextDocEntry() } newEntry->SetOffset(Fp->tellg()); // for each DocEntry - return newEntry; } @@ -2183,6 +2192,23 @@ DocEntry *Document::ReadNextDocEntry() */ void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem) { + // for strange PMS Gyroscan Intera images + // Item 'starter' has a tag : 0x3f3f,0x3f00, for no apparent reason + + // --- Feel free to remove this test *on your own coy of gdcm* + // if you are sure you'll never face this problem. + + if ((group == 0x3f3f) && (elem == 0x3f00)) + { + // start endian swap mark for group found + gdcmDebugMacro( " delimiter 0x3f3f found." ); + // fix the tag + group = 0xfffe; + elem = 0xe000; + return; + } + // --- End of removable code + // Endian reversion. // Some files contain groups of tags with reversed endianess. static int reversedEndian = 0;