1 /*=========================================================================
4 Module: $RCSfile: gdcmDocument.cxx,v $
6 Date: $Date: 2005/11/05 13:23:30 $
7 Version: $Revision: 1.325 $
9 Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
10 l'Image). All rights reserved. See Doc/License.txt or
11 http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
13 This software is distributed WITHOUT ANY WARRANTY; without even
14 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 PURPOSE. See the above copyright notices for more information.
17 =========================================================================*/
19 #include "gdcmDocument.h"
20 #include "gdcmSeqEntry.h"
21 #include "gdcmGlobal.h"
23 #include "gdcmDebug.h"
25 #include "gdcmDictSet.h"
26 #include "gdcmDocEntrySet.h"
27 #include "gdcmSQItem.h"
28 #include "gdcmDataEntry.h"
33 #include <ctype.h> // for isdigit
34 #include <stdlib.h> // for atoi
38 //-----------------------------------------------------------------------------
40 // Refer to Document::SetMaxSizeLoadEntry()
41 const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
43 //-----------------------------------------------------------------------------
44 // Constructor / Destructor
45 // Constructors and destructors are protected to avoid user to invoke directly
48 * \brief This default constructor neither loads nor parses the file.
49 * You should then invoke \ref Document::Load.
57 SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
60 Filetype = ExplicitVR;
61 // Load will set it to true if sucessfull
62 Group0002Parsed = false;
63 IsDocumentAlreadyLoaded = false;
64 IsDocumentModified = true;
65 LoadMode = LD_ALL; // default : load everything, later
70 * \brief Canonical destructor.
72 Document::~Document ()
77 //-----------------------------------------------------------------------------
80 * \brief Loader. use SetLoadMode(), SetFileName() before !
81 * @return false if file cannot be open or no swap info was found,
82 * or no tag was found.
84 bool Document::Load( )
86 if ( GetFileName() == "" )
88 gdcmWarningMacro( "Use SetFileName, before !" );
91 return DoTheLoadingDocumentJob( );
94 * \brief Loader. (DEPRECATED : not to break the API)
95 * @param fileName 'Document' (File or DicomDir) to be open for parsing
96 * @return false if file cannot be open or no swap info was found,
97 * or no tag was found.
99 bool Document::Load( std::string const &fileName )
102 return DoTheLoadingDocumentJob( );
106 * \brief Performs the Loading Job (internal use only)
107 * @return false if file cannot be open or no swap info was found,
108 * or no tag was found.
110 bool Document::DoTheLoadingDocumentJob( )
112 if ( ! IsDocumentModified ) // Nothing to do !
120 // warning already performed in OpenFile()
125 Group0002Parsed = false;
127 gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str());
129 Fp->seekg(0, std::ios::end);
130 long lgt = Fp->tellg(); // total length of the file
132 Fp->seekg(0, std::ios::beg);
134 // CheckSwap returns a boolean
135 // (false if no swap info of any kind was found)
138 gdcmWarningMacro( "Neither a DICOM V3 nor an ACR-NEMA file: "
139 << Filename.c_str());
144 long beg = Fp->tellg(); // just after DICOM preamble (if any)
146 lgt -= beg; // remaining length to parse
149 // Loading is done during parsing
150 ParseDES( this, beg, lgt, false); // delim_mode is first defaulted to false
154 gdcmErrorMacro( "No tag in internal hash table for: "
155 << Filename.c_str());
159 IsDocumentAlreadyLoaded = true;
161 Fp->seekg( 0, std::ios::beg);
163 // Load 'non string' values
165 std::string PhotometricInterpretation = GetEntryString(0x0028,0x0004);
166 if ( PhotometricInterpretation == "PALETTE COLOR " )
169 // Probabely this line should be outside the 'if'
170 // Try to find an image sample holding a 'gray LUT'
171 LoadEntryBinArea(0x0028,0x1200); // gray LUT
174 /// --> FIXME : The difference between BinEntry and DataEntry
175 /// --> no longer exists, but the alteration of Dicom Dictionary remains.
176 /// --> Old comment restored on purpose.
177 /// --> New one (replacing both BinEntry and ValEntry by DataEntry)
178 /// --> had absolutely no meaning.
179 /// --> The whole comment will be removed when the stuff is cleaned !
181 /// The tags refered by the three following lines used to be CORRECTLY
182 /// defined as having an US Value Representation in the public
183 /// dictionary. BUT the semantics implied by the three following
184 /// lines state that the corresponding tag contents are in fact
185 /// the ones of a BinEntry.
186 /// In order to fix things "Quick and Dirty" the dictionary was
187 /// altered on PURPOSE but now contains a WRONG value.
188 /// In order to fix things and restore the dictionary to its
189 /// correct value, one needs to decide of the semantics by deciding
190 /// whether the following tags are either :
191 /// - multivaluated US, and hence loaded as ValEntry, but afterwards
192 /// also used as BinEntry, which requires the proper conversion,
193 /// - OW, and hence loaded as BinEntry, but afterwards also used
194 /// as ValEntry, which requires the proper conversion.
196 // --> OB (byte aray) or OW (short int aray)
197 // The actual VR has to be deduced from other entries.
198 // Our way of loading them may fail in some cases :
199 // We must or not SwapByte depending on other field values.
201 LoadEntryBinArea(0x0028,0x1201); // R LUT
202 LoadEntryBinArea(0x0028,0x1202); // G LUT
203 LoadEntryBinArea(0x0028,0x1203); // B LUT
205 // Segmented Red Palette Color LUT Data
206 LoadEntryBinArea(0x0028,0x1221);
207 // Segmented Green Palette Color LUT Data
208 LoadEntryBinArea(0x0028,0x1222);
209 // Segmented Blue Palette Color LUT Data
210 LoadEntryBinArea(0x0028,0x1223);
213 //FIXME later : how to use it?
214 SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000);
217 SQItem *sqi= modLutSeq->GetFirstSQItem();
220 DataEntry *dataEntry = sqi->GetDataEntry(0x0028,0x3006);
221 if ( dataEntry != 0 )
223 if ( dataEntry->GetLength() != 0 )
225 // FIXME : CTX dependent means : contexted dependant.
226 // see upper comment.
227 LoadEntryBinArea(dataEntry); //LUT Data (CTX dependent)
233 // Force Loading some more elements if user asked to.
236 for (ListElements::iterator it = UserForceLoadList.begin();
237 it != UserForceLoadList.end();
240 gdcmDebugMacro( "Force Load " << std::hex
241 << (*it).Group << "|" <<(*it).Elem );
243 d = GetDocEntry( (*it).Group, (*it).Elem);
247 gdcmWarningMacro( "You asked toForce Load " << std::hex
248 << (*it).Group <<"|"<< (*it).Elem
249 << " that doesn't exist" );
253 LoadDocEntry(d, true);
258 // ----------------------------
259 // Specific code to allow gdcm to read ACR-LibIDO formated images
260 // Note: ACR-LibIDO is an extension of the ACR standard that was
261 // used at CREATIS. For the time being (say a couple of years)
262 // we keep this kludge to allow CREATIS users
263 // reading their old images.
265 // if recognition code tells us we deal with a LibIDO image
266 // we switch lineNumber and columnNumber
269 RecCode = GetEntryString(0x0008, 0x0010); // recognition code (RET)
270 if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
271 RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
272 // with "little-endian strings"
274 Filetype = ACR_LIBIDO;
275 std::string rows = GetEntryString(0x0028, 0x0010);
276 std::string columns = GetEntryString(0x0028, 0x0011);
277 SetEntryString(columns, 0x0028, 0x0010);
278 SetEntryString(rows , 0x0028, 0x0011);
280 // --- End of ACR-LibIDO kludge ---
286 * \brief Adds a new element we want to load anyway
287 * @param group Group number of the target tag.
288 * @param elem Element number of the target tag.
290 void Document::AddForceLoadElement (uint16_t group, uint16_t elem)
295 UserForceLoadList.push_back(el);
298 * \brief Get the public dictionary used
300 Dict *Document::GetPubDict()
306 * \brief Get the shadow dictionary used
308 Dict *Document::GetShaDict()
314 * \brief Set the shadow dictionary used
315 * @param dict dictionary to use in shadow
317 bool Document::SetShaDict(Dict *dict)
324 * \brief Set the shadow dictionary used
325 * @param dictName name of the dictionary to use in shadow
327 bool Document::SetShaDict(DictKey const &dictName)
329 RefShaDict = Global::GetDicts()->GetDict(dictName);
334 * \brief This predicate tells us whether or not the current Document
335 * was properly parsed and contains at least *one* Dicom Element
336 * (and nothing more, sorry).
337 * @return false when we're 150 % sure it's NOT a Dicom/Acr file,
340 bool Document::IsReadable()
342 if ( Filetype == Unknown )
344 gdcmErrorMacro( "Wrong filetype for " << GetFileName());
350 gdcmErrorMacro( "No tag in internal hash table.");
358 * \brief Predicate for dicom version 3 file.
359 * @return True when the file is a dicom version 3.
361 bool Document::IsDicomV3()
363 // Checking if Transfer Syntax exists is enough
364 // Anyway, it's too late check if the 'Preamble' was found ...
365 // And ... would it be a rich idea to check ?
366 // (some 'no Preamble' DICOM images exist !)
367 return GetDocEntry(0x0002, 0x0010) != NULL;
371 * \brief Predicate for Papyrus file
372 * Dedicated to whomsoever it may concern
373 * @return True when the file is a Papyrus file.
375 bool Document::IsPapyrus()
377 // check for Papyrus private Sequence
378 DocEntry *e = GetDocEntry(0x0041, 0x1050);
381 // check if it's actually a Sequence
382 if ( !dynamic_cast<SeqEntry*>(e) )
388 * \brief returns the File Type
389 * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
390 * @return the FileType code
392 FileType Document::GetFileType()
398 * \brief Accessor to the Transfer Syntax (when present) of the
399 * current document (it internally handles reading the
400 * value from disk when only parsing occured).
401 * @return The encountered Transfer Syntax of the current document, if DICOM.
402 * GDCM_UNKNOWN for ACR-NEMA files (or broken headers ...)
404 std::string Document::GetTransferSyntax()
406 DocEntry *entry = GetDocEntry(0x0002, 0x0010);
412 // The entry might be present but not loaded (parsing and loading
413 // happen at different stages): try loading and proceed with check...
414 LoadDocEntrySafe(entry);
415 if (DataEntry *dataEntry = dynamic_cast<DataEntry *>(entry) )
417 std::string transfer = dataEntry->GetString();
418 // The actual transfer (as read from disk) might be padded. We
419 // first need to remove the potential padding. We can make the
420 // weak assumption that padding was not executed with digits...
421 if ( transfer.length() == 0 )
423 // for brain damaged headers
424 gdcmWarningMacro( "Transfer Syntax has length = 0.");
427 while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
429 transfer.erase(transfer.length()-1, 1);
430 if ( transfer.length() == 0 )
432 // for brain damaged headers
433 gdcmWarningMacro( "Transfer Syntax contains no valid character.");
443 * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS
444 * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
446 std::string Document::GetTransferSyntaxName()
448 // use the TS (TS : Transfer Syntax)
449 std::string transferSyntax = GetEntryString(0x0002,0x0010);
451 if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) )
453 gdcmErrorMacro( "Transfer Syntax not loaded. " << std::endl
454 << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" );
455 return "Uncompressed ACR-NEMA";
457 if ( transferSyntax == GDCM_UNFOUND )
459 gdcmDebugMacro( "Unfound Transfer Syntax (0002,0010)");
460 return "Uncompressed ACR-NEMA";
463 // we do it only when we need it
464 const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax );
466 // Global::GetTS() is a global static you shall never try to delete it!
470 // --------------- Swap Code ------------------
472 * \brief Swaps the bytes so they agree with the processor order
473 * @return The properly swaped 16 bits integer.
475 uint16_t Document::SwapShort(uint16_t a)
477 if ( SwapCode == 4321 || SwapCode == 2143 )
479 //a = ((( a << 8 ) & 0xff00 ) | (( a >> 8 ) & 0x00ff ) );
481 a = ( a << 8 ) | ( a >> 8 );
487 * \brief Swaps back the bytes of 4-byte long integer accordingly to
489 * @return The properly swaped 32 bits integer.
491 uint32_t Document::SwapLong(uint32_t a)
498 // a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
499 // ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
501 a=( ( a<<24) | ((a<<8) & 0x00ff0000) |
502 ((a>>8) & 0x0000ff00) | (a>>24) );
505 // a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
506 a=( (a<<16) | (a>>16) );
509 a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
512 gdcmErrorMacro( "Unexpected swap code:" << SwapCode );
519 * \brief Swaps back the bytes of 8-byte long 'double' accordingly to
521 * @return The properly swaped 64 bits double.
523 double Document::SwapDouble(double a)
527 // There were no 'double' at ACR-NEMA time.
528 // We just have to deal with 'straight Little Endian' and
529 // 'straight Big Endian'
534 char *beg = (char *)&a;
537 for (unsigned int i = 0; i<7; i++)
548 gdcmErrorMacro( "Unexpected swap code:" << SwapCode );
555 // -----------------File I/O ---------------
557 * \brief Tries to open the file \ref Document::Filename and
558 * checks the preamble when existing.
559 * @return The FILE pointer on success.
561 std::ifstream *Document::OpenFile()
563 HasDCMPreamble = false;
564 if (Filename.length() == 0)
571 gdcmDebugMacro( "File already open: " << Filename.c_str());
575 Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
578 // Don't user gdcmErrorMacro :
579 // a spurious message will appear when you use, for instance
580 // gdcm::FileHelper *fh = new gdcm::FileHelper( outputFileName );
581 // to create outputFileName.
583 // FIXME : if the upper comment is still usefull
584 // --> the constructor is not so good ...
586 gdcmWarningMacro( "Cannot open file: " << Filename.c_str());
590 //exit(1); // No function is allowed to leave the application instead
591 // of warning the caller
595 Fp->read((char*)&zero, (size_t)2);
602 //-- Broken ACR or DICOM with no Preamble; may start with a Shadow Group --
604 // FIXME : We cannot be sure the preable is only zeroes..
605 // (see ACUSON-24-YBR_FULL-RLE.dcm )
607 zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 ||
608 zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 ||
609 zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 ||
610 zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 )
612 std::string msg = Util::Format(
613 "ACR/DICOM starting by 0x(%04x) at the beginning of the file\n", zero);
614 // FIXME : is it a Warning message, or a Debug message?
615 gdcmWarningMacro( msg.c_str() );
620 Fp->seekg(126L, std::ios::cur);
621 char dicm[4]; // = {' ',' ',' ',' '};
622 Fp->read(dicm, (size_t)4);
628 if ( memcmp(dicm, "DICM", 4) == 0 )
630 HasDCMPreamble = true;
634 // -- Neither ACR/No Preamble Dicom nor DICOMV3 file
636 // Don't user Warning nor Error, not to polute the output
637 // while directory recursive parsing ...
638 gdcmDebugMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
639 << Filename.c_str());
644 * \brief closes the file
645 * @return TRUE if the close was successfull
647 bool Document::CloseFile()
659 * \brief Writes in a file all the Entries (Dicom Elements)
660 * @param fp file pointer on an already open file (actually: Output File Stream)
661 * @param filetype Type of the File to be written
662 * (ACR-NEMA, ExplicitVR, ImplicitVR)
664 void Document::WriteContent(std::ofstream *fp, FileType filetype)
666 // Skip if user wants to write an ACR-NEMA file
668 if ( filetype == ImplicitVR || filetype == ExplicitVR ||
671 // writing Dicom File Preamble
672 char filePreamble[128];
673 memset(filePreamble, 0, 128);
674 fp->write(filePreamble, 128);
675 fp->write("DICM", 4);
679 * \todo rewrite later, if really usefull
680 * - 'Group Length' element is optional in DICOM
681 * - but un-updated odd groups lengthes can causes pb
684 * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) )
685 * UpdateGroupLength(false,filetype);
686 * if ( filetype == ACR)
687 * UpdateGroupLength(true,ACR);
689 * --> Computing group length for groups with embeded Sequences
690 * --> was too much tricky / we were [in a hurry / too lazy]
691 * --> We don't write the element 0x0000 (group length)
694 ElementSet::WriteContent(fp, filetype); // This one is recursive
697 // -----------------------------------------
700 * \brief Loads (from disk) the element content
701 * when a string is not suitable
702 * @param group group number of the Entry
703 * @param elem element number of the Entry
705 void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
707 // Search the corresponding DocEntry
708 DocEntry *docEntry = GetDocEntry(group, elem);
711 gdcmWarningMacro(std::hex << group << "|" << elem
712 << "doesn't exist" );
715 DataEntry *dataEntry = dynamic_cast<DataEntry *>(docEntry);
718 gdcmWarningMacro(std::hex << group << "|" << elem
719 << "is NOT a DataEntry");
722 LoadEntryBinArea(dataEntry);
726 * \brief Loads (from disk) the element content
727 * when a string is not suitable
728 * @param entry Entry whose binArea is going to be loaded
730 void Document::LoadEntryBinArea(DataEntry *entry)
732 if( entry->GetBinArea() )
739 size_t o =(size_t)entry->GetOffset();
740 Fp->seekg(o, std::ios::beg);
742 size_t l = entry->GetLength();
743 uint8_t *data = new uint8_t[l];
746 gdcmWarningMacro( "Cannot allocate DataEntry content for : "
747 << std::hex << entry->GetGroup()
748 << "|" << entry->GetElement() );
753 Fp->read((char*)data, l);
754 if ( Fp->fail() || Fp->eof() )
757 entry->SetState(DataEntry::STATE_UNREAD);
761 // Swap the data content if necessary
763 unsigned short vrLgth =
764 Global::GetVR()->GetAtomicElementLength(entry->GetVR());
766 // FIXME : trouble expected if we read an ... OW Entry (LUT, etc ..)
767 // if( entry->GetVR() == "OW" )
778 uint16_t *data16 = (uint16_t *)data;
779 for(i=0;i<l/vrLgth;i++)
780 data16[i] = SwapShort(data16[i]);
785 uint32_t *data32 = (uint32_t *)data;
786 for(i=0;i<l/vrLgth;i++)
787 data32[i] = SwapLong(data32[i]);
792 double *data64 = (double *)data;
793 for(i=0;i<l/vrLgth;i++)
794 data64[i] = SwapDouble(data64[i]);
799 entry->SetBinArea(data);
806 * \brief Loads the element while preserving the current
807 * underlying file position indicator as opposed to
808 * LoadDocEntry that modifies it.
809 * @param entry DocEntry whose value will be loaded.
811 void Document::LoadDocEntrySafe(DocEntry *entry)
815 long PositionOnEntry = Fp->tellg();
817 Fp->seekg(PositionOnEntry, std::ios::beg);
822 * \brief Compares two documents, according to \ref DicomDir rules
823 * \warning Does NOT work with ACR-NEMA files
824 * \todo Find a trick to solve the pb (use RET fields ?)
825 * @param document to compare with current one
826 * @return true if 'smaller'
828 bool Document::operator<(Document &document)
831 std::string s1 = GetEntryString(0x0010,0x0010);
832 std::string s2 = document.GetEntryString(0x0010,0x0010);
844 s1 = GetEntryString(0x0010,0x0020);
845 s2 = document.GetEntryString(0x0010,0x0020);
856 // Study Instance UID
857 s1 = GetEntryString(0x0020,0x000d);
858 s2 = document.GetEntryString(0x0020,0x000d);
869 // Serie Instance UID
870 s1 = GetEntryString(0x0020,0x000e);
871 s2 = document.GetEntryString(0x0020,0x000e);
886 //-----------------------------------------------------------------------------
889 * \brief Reads a supposed to be 16 Bits integer
890 * (swaps it depending on processor endianness)
893 uint16_t Document::ReadInt16()
897 Fp->read ((char*)&g, (size_t)2);
900 throw FormatError( "Document::ReadInt16()", " file error." );
904 throw FormatError( "Document::ReadInt16()", "EOF." );
911 * \brief Reads a supposed to be 32 Bits integer
912 * (swaps it depending on processor endianness)
915 uint32_t Document::ReadInt32()
919 Fp->read ((char*)&g, (size_t)4);
922 throw FormatError( "Document::ReadInt32()", " file error." );
926 throw FormatError( "Document::ReadInt32()", "EOF." );
933 * \brief skips bytes inside the source file
934 * \warning NOT end user intended method !
937 void Document::SkipBytes(uint32_t nBytes)
939 //FIXME don't dump the returned value
940 Fp->seekg((long)nBytes, std::ios::cur);
944 * \brief Re-computes the length of the Dicom group 0002.
946 int Document::ComputeGroup0002Length( )
952 bool found0002 = false;
954 // for each zero-level Tag in the DCM Header
955 DocEntry *entry = GetFirstEntry();
958 gr = entry->GetGroup();
964 if ( entry->GetElement() != 0x0000 )
968 //if ( (vr == "OB")||(vr == "OW")||(vr == "UT")||(vr == "SQ"))
969 // (no SQ, OW, UT in group 0x0002;)
972 // explicit VR AND (OB, OW, SQ, UT) : 4 more bytes
976 groupLength += 2 + 2 + 4 + entry->GetLength();
982 entry = GetNextEntry();
987 //-----------------------------------------------------------------------------
990 * \brief Loads all the needed Dictionaries
991 * \warning NOT end user intended method !
993 void Document::Initialize()
995 RefPubDict = Global::GetDicts()->GetDefaultPubDict();
1001 * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
1002 * @param set DocEntrySet we are going to parse ('zero level' or a SQItem)
1003 * @param offset start of parsing
1004 * @param l_max length to parse (meaningless when we are in 'delimitor mode')
1005 * @param delim_mode : whether we are in 'delimitor mode' (l=0xffffff) or not
1007 void Document::ParseDES(DocEntrySet *set, long offset,
1008 long l_max, bool delim_mode)
1010 DocEntry *newDocEntry;
1011 DataEntry *newDataEntry;
1012 SeqEntry *newSeqEntry;
1014 bool used; // will be set to false when something wrong happens to an Entry.
1015 // (Entry will then be deleted)
1016 bool delim_mode_intern = delim_mode;
1018 gdcmDebugMacro( "Enter in ParseDES, delim-mode " << delim_mode
1019 << " at offset " << std::hex << offset );
1022 if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
1027 newDocEntry = ReadNextDocEntry( );
1029 // Uncoment this cerr line to be able to 'follow' the DocEntries
1030 // when something *very* strange happens
1031 if( Debug::GetDebugFlag() )
1032 std::cerr<<newDocEntry->GetKey()<<" "<<newDocEntry->GetVR()<<std::endl;
1039 // an Item Starter found elsewhere but the first position
1040 // of a SeqEntry means previous entry was a Sequence
1041 // but we didn't get it (private Sequence + Implicit VR)
1042 // we have to backtrack.
1043 if ( !first && newDocEntry->IsItemStarter() )
1045 // Debug message within the method !
1046 newDocEntry = Backtrack(newDocEntry);
1050 PreviousDocEntry = newDocEntry;
1054 newDataEntry = dynamic_cast<DataEntry*>(newDocEntry);
1058 //////////////////////////// DataEntry
1060 vr = newDocEntry->GetVR();
1062 if ( !set->AddEntry( newDataEntry ) )
1064 gdcmDebugMacro( "in ParseDES : cannot add a DataEntry "
1065 << newDataEntry->GetKey()
1067 << newDataEntry->GetOffset() << " )" );
1072 newDataEntry->Delete();
1073 // Load only if we can add (not a duplicate key)
1074 LoadDocEntry( newDataEntry );
1077 if ( newDataEntry->GetElement() == 0x0000 ) // if on group length
1079 if ( newDataEntry->GetGroup()%2 != 0 ) // if Shadow Group
1081 if ( LoadMode & LD_NOSHADOW ) // if user asked to skip shad.gr
1083 std::string strLgrGroup = newDataEntry->GetString();
1085 if ( newDataEntry->IsUnfound() )
1087 lgrGroup = atoi(strLgrGroup.c_str());
1088 Fp->seekg(lgrGroup, std::ios::cur);
1089 //used = false; // never used
1090 RemoveEntry( newDocEntry ); // Remove and delete
1091 // bcc 5.5 is right "assigned a value that's never used"
1099 bool delimitor = newDataEntry->IsItemDelimitor();
1102 (!delim_mode && ((long)(Fp->tellg())-offset) >= l_max) )
1105 newDocEntry->Delete();
1109 // Just to make sure we are at the beginning of next entry.
1110 SkipToNextDocEntry(newDocEntry);
1114 /////////////////////// SeqEntry : VR = "SQ"
1116 unsigned long l = newDocEntry->GetReadLength();
1117 if ( l != 0 ) // don't mess the delim_mode for 'zero-length sequence'
1119 if ( l == 0xffffffff )
1121 delim_mode_intern = true;
1125 delim_mode_intern = false;
1129 if ( (LoadMode & LD_NOSHADOWSEQ) && ! delim_mode_intern )
1131 // User asked to skip SeQuences *only* if they belong to Shadow Group
1132 if ( newDocEntry->GetGroup()%2 != 0 )
1134 Fp->seekg( l, std::ios::cur);
1135 newDocEntry->Delete(); // Delete, not in the set
1139 if ( (LoadMode & LD_NOSEQ) && ! delim_mode_intern )
1141 // User asked to skip *any* SeQuence
1142 Fp->seekg( l, std::ios::cur);
1143 newDocEntry->Delete(); // Delete, not in the set
1146 // delay the dynamic cast as late as possible
1147 newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
1149 // no other way to create the Delimitor ...
1150 newSeqEntry->SetDelimitorMode( delim_mode_intern );
1152 // At the top of the hierarchy, stands a Document. When "set"
1153 // is a Document, then we are building the first depth level.
1154 // Hence the SeqEntry we are building simply has a depth
1156 if ( set == this ) // ( dynamic_cast< Document* > ( set ) )
1158 newSeqEntry->SetDepthLevel( 1 );
1160 // But when "set" is already a SQItem, we are building a nested
1161 // sequence, and hence the depth level of the new SeqEntry
1162 // we are building, is one level deeper:
1164 // time waste hunting
1165 else if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
1167 newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
1171 { // Don't try to parse zero-length sequences
1173 gdcmDebugMacro( "Entry in ParseSQ, delim " << delim_mode_intern
1174 << " at offset " << std::hex
1175 << newDocEntry->GetOffset() );
1177 ParseSQ( newSeqEntry,
1178 newDocEntry->GetOffset(),
1179 l, delim_mode_intern);
1181 gdcmDebugMacro( "Exit from ParseSQ, delim " << delim_mode_intern);
1184 if ( !set->AddEntry( newSeqEntry ) )
1186 gdcmWarningMacro( "in ParseDES : cannot add a SeqEntry "
1187 << newSeqEntry->GetKey()
1189 << newSeqEntry->GetOffset() << " )" );
1194 newDocEntry->Delete();
1197 if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
1200 newDocEntry->Delete();
1203 } // end SeqEntry : VR = "SQ"
1207 newDocEntry->Delete();
1211 gdcmDebugMacro( "Exit from ParseDES, delim-mode " << delim_mode );
1215 * \brief Parses a Sequence ( SeqEntry after SeqEntry)
1216 * @return parsed length for this level
1218 void Document::ParseSQ( SeqEntry *seqEntry,
1219 long offset, long l_max, bool delim_mode)
1221 int SQItemNumber = 0;
1223 long offsetStartCurrentSQItem = offset;
1227 // the first time, we read the fff0,e000 of the first SQItem
1228 DocEntry *newDocEntry = ReadNextDocEntry();
1232 gdcmWarningMacro("in ParseSQ : should never get here!");
1237 if ( newDocEntry->IsSequenceDelimitor() )
1239 seqEntry->SetDelimitationItem( newDocEntry );
1240 newDocEntry->Delete();
1244 if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
1246 newDocEntry->Delete();
1249 // create the current SQItem
1250 SQItem *itemSQ = SQItem::New( seqEntry->GetDepthLevel() );
1251 unsigned int l = newDocEntry->GetReadLength();
1253 if ( l == 0xffffffff )
1262 // remove fff0,e000, created out of the SQItem
1263 Fp->seekg(offsetStartCurrentSQItem, std::ios::beg);
1264 // fill up the current SQItem, starting at the beginning of fff0,e000
1266 ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod);
1268 offsetStartCurrentSQItem = Fp->tellg();
1270 seqEntry->AddSQItem( itemSQ, SQItemNumber );
1272 newDocEntry->Delete();
1274 if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
1282 * \brief When a private Sequence + Implicit VR is encountered
1283 * we cannot guess it's a Sequence till we find the first
1284 * Item Starter. We then backtrack to do the job.
1285 * @param docEntry Item Starter that warned us
1287 DocEntry *Document::Backtrack(DocEntry *docEntry)
1289 // delete the Item Starter, built erroneously out of any Sequence
1290 // it's not yet in the HTable/chained list
1293 // Get all info we can from PreviousDocEntry
1294 uint16_t group = PreviousDocEntry->GetGroup();
1295 uint16_t elem = PreviousDocEntry->GetElement();
1296 uint32_t lgt = PreviousDocEntry->GetLength();
1297 long offset = PreviousDocEntry->GetOffset();
1299 gdcmDebugMacro( "Backtrack :" << std::hex << group
1301 << " at offset " << offset );
1302 RemoveEntry( PreviousDocEntry );
1304 // forge the Seq Entry
1305 DocEntry *newEntry = NewSeqEntry(group, elem);
1306 newEntry->SetLength(lgt);
1307 newEntry->SetOffset(offset);
1309 // Move back to the beginning of the Sequence
1310 Fp->seekg( 0, std::ios::beg);
1311 Fp->seekg(offset, std::ios::cur);
1317 * \brief Loads (or not) the element content depending if its length exceeds
1318 * or not the value specified with Document::SetMaxSizeLoadEntry()
1319 * @param entry Header Entry (Dicom Element) to be dealt with
1320 * @param forceLoad whether you want to force loading of 'long' elements
1322 void Document::LoadDocEntry(DocEntry *entry, bool forceLoad)
1324 uint16_t group = entry->GetGroup();
1325 uint16_t elem = entry->GetElement();
1326 const VRKey &vr = entry->GetVR();
1327 uint32_t length = entry->GetLength();
1329 Fp->seekg((long)entry->GetOffset(), std::ios::beg);
1331 // A SeQuence "contains" a set of Elements.
1332 // (fffe e000) tells us an Element is beginning
1333 // (fffe e00d) tells us an Element just ended
1334 // (fffe e0dd) tells us the current SeQuence just ended
1336 // (fffe 0000) is an 'impossible' tag value,
1337 // found in MR-PHILIPS-16-Multi-Seq.dcm
1339 if ( (group == 0xfffe && elem != 0x0000 ) || vr == "SQ" )
1341 // NO more value field for SQ !
1345 DataEntry *dataEntryPtr = dynamic_cast< DataEntry* >(entry);
1351 // When the length is zero things are easy:
1354 dataEntryPtr->SetBinArea(NULL,true);
1358 // The elements whose length is bigger than the specified upper bound
1361 std::ostringstream s;
1365 if (length > MaxSizeLoadEntry)
1367 dataEntryPtr->SetBinArea(NULL,true);
1368 dataEntryPtr->SetState(DataEntry::STATE_NOTLOADED);
1370 // to be sure we are at the end of the value ...
1371 Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
1377 LoadEntryBinArea(dataEntryPtr); // last one, not to erase length !
1381 * \brief Find the value Length of the passed Doc Entry
1382 * @param entry Header Entry whose length of the value shall be loaded.
1384 void Document::FindDocEntryLength( DocEntry *entry )
1385 throw ( FormatError )
1387 const VRKey &vr = entry->GetVR();
1390 if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
1392 if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT"
1395 // The following reserved two bytes (see PS 3.5-2003, section
1396 // "7.1.2 Data element structure with explicit vr", p 27) must be
1397 // skipped before proceeding on reading the length on 4 bytes.
1398 Fp->seekg( 2L, std::ios::cur);
1399 uint32_t length32 = ReadInt32();
1401 if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
1406 lengthOB = FindDocEntryLengthOBOrOW();
1408 catch ( FormatUnexpected )
1410 // Computing the length failed (this happens with broken
1411 // files like gdcm-JPEG-LossLess3a.dcm). We still have a
1412 // chance to get the pixels by deciding the element goes
1413 // until the end of the file. Hence we artificially fix the
1414 // the length and proceed.
1415 gdcmWarningMacro( " Computing the length failed for " <<
1416 entry->GetKey() <<" in " <<GetFileName());
1418 long currentPosition = Fp->tellg();
1419 Fp->seekg(0L,std::ios::end);
1421 long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
1422 Fp->seekg(currentPosition, std::ios::beg);
1424 entry->SetReadLength(lengthUntilEOF);
1425 entry->SetLength(lengthUntilEOF);
1428 entry->SetReadLength(lengthOB);
1429 entry->SetLength(lengthOB);
1432 FixDocEntryFoundLength(entry, length32);
1436 // Length is encoded on 2 bytes.
1437 length16 = ReadInt16();
1439 // 0xffff means that we deal with 'No Length' Sequence
1440 // or 'No Length' SQItem
1441 if ( length16 == 0xffff)
1445 FixDocEntryFoundLength( entry, (uint32_t)length16 );
1450 // Either implicit VR or a non DICOM conformal (see note below) explicit
1451 // VR that ommited the VR of (at least) this element. Farts happen.
1452 // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25
1453 // on Data elements "Implicit and Explicit VR Data Elements shall
1454 // not coexist in a Data Set and Data Sets nested within it".]
1455 // Length is on 4 bytes.
1457 // Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
1458 // even if Transfer Syntax is 'Implicit VR ...'
1459 // --> Except for 'Implicit VR Big Endian Transfer Syntax GE Private'
1461 FixDocEntryFoundLength( entry, ReadInt32() );
1467 * \brief Find the Length till the next sequence delimiter
1468 * \warning NOT end user intended method !
1471 uint32_t Document::FindDocEntryLengthOBOrOW()
1472 throw( FormatUnexpected )
1474 // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
1475 long positionOnEntry = Fp->tellg();
1476 bool foundSequenceDelimiter = false;
1477 uint32_t totalLength = 0;
1479 while ( !foundSequenceDelimiter )
1485 group = ReadInt16();
1488 catch ( FormatError )
1490 throw FormatError("Unexpected end of file encountered during ",
1491 "Document::FindDocEntryLengthOBOrOW()");
1493 // We have to decount the group and element we just read
1495 if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
1497 long filePosition = Fp->tellg();
1499 "Neither an Item tag nor a Sequence delimiter tag on :"
1500 << std::hex << group << " , " << elem
1501 << ") -before- position x(" << filePosition << ")" );
1503 Fp->seekg(positionOnEntry, std::ios::beg);
1504 throw FormatUnexpected(
1505 "Neither an Item tag nor a Sequence delimiter tag.");
1507 if ( elem == 0xe0dd )
1509 foundSequenceDelimiter = true;
1511 uint32_t itemLength = ReadInt32();
1512 // We add 4 bytes since we just read the ItemLength with ReadInt32
1513 totalLength += itemLength + 4;
1514 SkipBytes(itemLength);
1516 if ( foundSequenceDelimiter )
1521 Fp->seekg( positionOnEntry, std::ios::beg);
1526 * \brief Find the Value Representation of the current Dicom Element.
1527 * @return Value Representation of the current Entry
1529 VRKey Document::FindDocEntryVR()
1531 if ( Filetype != ExplicitVR )
1532 return GDCM_VRUNKNOWN;
1534 long positionOnEntry = Fp->tellg();
1535 // Warning: we believe this is explicit VR (Value Representation) because
1536 // we used a heuristic that found "UL" in the first tag and/or
1537 // 'Transfer Syntax' told us it is.
1538 // Alas this doesn't guarantee that all the tags will be in explicit VR.
1539 // In some cases one finds implicit VR tags mixed within an explicit VR file.
1540 // Hence we make sure the present tag is in explicit VR and try to fix things
1541 // if it happens not to be the case.
1544 Fp->read(&(vr[0]),(size_t)2);
1546 if ( !CheckDocEntryVR(vr) )
1548 // Don't warn user with useless messages
1549 // Often, delimiters (0xfffe), are not explicit VR ...
1550 if ( CurrentGroup != 0xfffe )
1551 gdcmWarningMacro( "Unknown VR " << std::hex << "0x("
1552 << (unsigned int)vr[0] << "|" << (unsigned int)vr[1]
1553 << ") at offset :" << positionOnEntry );
1554 Fp->seekg(positionOnEntry, std::ios::beg);
1555 return GDCM_VRUNKNOWN;
1561 * \brief Check the correspondance between the VR of the header entry
1562 * and the taken VR. If they are different, the header entry is
1563 * updated with the new VR.
1564 * @param vr Dicom Value Representation
1565 * @return false if the VR is incorrect or if the VR isn't referenced
1566 * otherwise, it returns true
1568 bool Document::CheckDocEntryVR(const VRKey &vr)
1570 return Global::GetVR()->IsValidVR(vr);
1574 * \brief Skip a given Header Entry
1575 * \warning NOT end user intended method !
1576 * @param entry entry to skip
1578 void Document::SkipDocEntry(DocEntry *entry)
1580 SkipBytes(entry->GetLength());
1584 * \brief Skips to the beginning of the next Header Entry
1585 * \warning NOT end user intended method !
1586 * @param currentDocEntry entry to skip
1588 void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
1590 int l = currentDocEntry->GetReadLength();
1591 if ( l == -1 ) // length = 0xffff shouldn't appear here ...
1592 // ... but PMS imagers happen !
1594 Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
1595 if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb
1597 Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur);
1602 * \brief When the length of an element value is obviously wrong (because
1603 * the parser went Jabberwocky) one can hope improving things by
1604 * applying some heuristics.
1605 * @param entry entry to check
1606 * @param foundLength first assumption about length
1608 void Document::FixDocEntryFoundLength(DocEntry *entry,
1609 uint32_t foundLength)
1611 entry->SetReadLength( foundLength );// will be updated only if a bug is found
1612 if ( foundLength == 0xffffffff)
1617 uint16_t gr = entry->GetGroup();
1618 uint16_t elem = entry->GetElement();
1620 if ( foundLength % 2)
1622 gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength
1623 << " in x(" << std::hex << gr << "," << elem <<")");
1626 //////// Fix for some naughty General Electric images.
1627 // Allthough not recent many such GE corrupted images are still present
1628 // on Creatis hard disks. Hence this fix shall remain when such images
1629 // are no longer in use (we are talking a few years, here)...
1630 // Note: XMedCon probably uses such a trick since it is able to read
1631 // those pesky GE images ...
1632 if ( foundLength == 13)
1634 // Only happens for this length !
1635 if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) )
1638 entry->SetReadLength(10); // a bug is to be fixed !?
1642 //////// Fix for some brain-dead 'Leonardo' Siemens images.
1643 // Occurence of such images is quite low (unless one leaves close to a
1644 // 'Leonardo' source. Hence, one might consider commenting out the
1645 // following fix on efficiency reasons.
1646 else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
1649 entry->SetReadLength(4); // a bug is to be fixed !
1652 else if ( entry->GetVR() == "SQ" )
1654 foundLength = 0; // ReadLength is unchanged
1657 //////// We encountered a 'delimiter' element i.e. a tag of the form
1658 // "fffe|xxxx" which is just a marker. Delimiters length should not be
1659 // taken into account.
1660 else if ( gr == 0xfffe )
1662 // According to the norm, fffe|0000 shouldn't exist. BUT the Philips
1663 // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to
1664 // causes extra troubles...
1665 if ( entry->GetElement() != 0x0000 )
1671 foundLength=12; // to skip the mess that follows this bugged Tag !
1674 entry->SetLength(foundLength);
1678 * \brief Apply some heuristics to predict whether the considered
1679 * element value contains/represents an integer or not.
1680 * @param entry The element value on which to apply the predicate.
1681 * @return The result of the heuristical predicate.
1683 bool Document::IsDocEntryAnInteger(DocEntry *entry)
1685 uint16_t elem = entry->GetElement();
1686 uint16_t group = entry->GetGroup();
1687 const VRKey &vr = entry->GetVR();
1688 uint32_t length = entry->GetLength();
1690 // When we have some semantics on the element we just read, and if we
1691 // a priori know we are dealing with an integer, then we shall be
1692 // able to swap it's element value properly.
1693 if ( elem == 0 ) // This is the group length of the group
1701 // Although this should never happen, still some images have a
1702 // corrupted group length [e.g. have a glance at offset x(8336) of
1703 // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
1704 // Since for dicom compliant and well behaved headers, the present
1705 // test is useless (and might even look a bit paranoid), when we
1706 // encounter such an ill-formed image, we simply display a warning
1707 // message and proceed on parsing (while crossing fingers).
1708 long filePosition = Fp->tellg();
1709 gdcmWarningMacro( "Erroneous Group Length element length on : ("
1710 << std::hex << group << " , " << elem
1711 << ") -before- position x(" << filePosition << ")"
1712 << "lgt : " << length );
1716 if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" )
1724 * \brief Discover what the swap code is (among little endian, big endian,
1725 * bad little endian, bad big endian).
1727 * @return false when we are absolutely sure
1728 * it's neither ACR-NEMA nor DICOM
1729 * true when we hope ours assuptions are OK
1731 bool Document::CheckSwap()
1738 // First, compare HostByteOrder and NetworkByteOrder in order to
1739 // determine if we shall need to swap bytes (i.e. the Endian type).
1740 bool net2host = Util::IsCurrentProcessorBigEndian();
1742 // The easiest case is the one of a 'true' DICOM header, we just have
1743 // to look for the string "DICM" inside the file preamble.
1746 char *entCur = deb + 128;
1747 if ( memcmp(entCur, "DICM", (size_t)4) == 0 )
1749 gdcmDebugMacro( "Looks like DICOM Version3 (preamble + DCM)" );
1751 // Group 0002 should always be VR, and the first element 0000
1752 // Let's be carefull (so many wrong headers ...)
1753 // and determine the value representation (VR) :
1754 // Let's skip to the first element (0002,0000) and check there if we find
1755 // "UL" - or "OB" if the 1st one is (0002,0001) -,
1756 // in which case we (almost) know it is explicit VR.
1757 // WARNING: if it happens to be implicit VR then what we will read
1758 // is the length of the group. If this ascii representation of this
1759 // length happens to be "UL" then we shall believe it is explicit VR.
1760 // We need to skip :
1761 // * the 128 bytes of File Preamble (often padded with zeroes),
1762 // * the 4 bytes of "DICM" string,
1763 // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001)
1764 // i.e. a total of 136 bytes.
1767 // group 0x0002 *is always* Explicit VR Sometimes ,
1768 // even if elem 0002,0010 (Transfer Syntax) tells us the file is
1769 // *Implicit* VR (see former 'gdcmData/icone.dcm')
1771 if ( memcmp(entCur, "UL", (size_t)2) == 0 ||
1772 memcmp(entCur, "OB", (size_t)2) == 0 ||
1773 memcmp(entCur, "UI", (size_t)2) == 0 ||
1774 memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later
1775 // when Write DCM *adds*
1777 // Use Document::dicom_vr to test all the possibilities
1778 // instead of just checking for UL, OB and UI !? group 0000
1780 Filetype = ExplicitVR;
1781 gdcmDebugMacro( "Group 0002 : Explicit Value Representation");
1785 Filetype = ImplicitVR;
1786 gdcmWarningMacro( "Group 0002 :Not an explicit Value Representation;"
1787 << "Looks like a bugged Header!");
1793 gdcmDebugMacro( "HostByteOrder != NetworkByteOrder, SwapCode = 4321");
1798 gdcmDebugMacro( "HostByteOrder = NetworkByteOrder, SwapCode = 1234");
1801 // Position the file position indicator at first tag
1802 // (i.e. after the file preamble and the "DICM" string).
1804 Fp->seekg(0, std::ios::beg); // FIXME : Is it usefull?
1806 Fp->seekg ( 132L, std::ios::beg);
1808 } // ------------------------------- End of DicomV3 ----------------
1810 // Alas, this is not a DicomV3 file and whatever happens there is no file
1811 // preamble. We can reset the file position indicator to where the data
1812 // is (i.e. the beginning of the file).
1814 gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)");
1816 Fp->seekg(0, std::ios::beg);
1818 // Let's check 'No Preamble Dicom File' :
1819 // Should start with group 0x0002
1820 // and be Explicit Value Representation
1822 s16 = *((uint16_t *)(deb));
1835 if ( SwapCode != 0 )
1837 if ( memcmp(entCur, "UL", (size_t)2) == 0 ||
1838 memcmp(entCur, "OB", (size_t)2) == 0 ||
1839 memcmp(entCur, "UI", (size_t)2) == 0 ||
1840 memcmp(entCur, "SH", (size_t)2) == 0 ||
1841 memcmp(entCur, "AE", (size_t)2) == 0 ||
1842 memcmp(entCur, "OB", (size_t)2) == 0 )
1844 Filetype = ExplicitVR;
1845 gdcmDebugMacro( "Group 0002 : Explicit Value Representation");
1849 // ------------------------------- End of 'No Preamble' DicomV3 -------------
1851 // Our next best chance would be to be considering a 'clean' ACR/NEMA file.
1852 // By clean we mean that the length of the first group is written down.
1853 // If this is the case and since the length of the first group HAS to be
1854 // four (bytes), then determining the proper swap code is straightforward.
1857 // We assume the array of char we are considering contains the binary
1858 // representation of a 32 bits integer. Hence the following dirty
1860 s32 = *((uint32_t *)(entCur));
1880 // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
1881 // It is time for despaired wild guesses.
1882 // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA,
1883 // i.e. the 'group length' element is not present :
1885 // check the supposed-to-be 'group number'
1886 // in ( 0x0001 .. 0x0008 )
1887 // to determine ' SwapCode' value .
1888 // Only 0 or 4321 will be possible
1889 // (no oportunity to check for the formerly well known
1890 // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
1891 // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc-3, 4, ..., 8-)
1892 // the file IS NOT ACR-NEMA nor DICOM V3
1893 // Find a trick to tell it the caller...
1895 s16 = *((uint16_t *)(deb));
1922 gdcmWarningMacro("ACR/NEMA unfound swap info (Hopeless !)");
1930 * \brief Change the Byte Swap code.
1932 void Document::SwitchByteSwapCode()
1934 gdcmDebugMacro( "Switching Byte Swap code from "<< SwapCode
1935 << " at: 0x" << std::hex << Fp->tellg() );
1936 if ( SwapCode == 1234 )
1940 else if ( SwapCode == 4321 )
1944 else if ( SwapCode == 3412 )
1948 else if ( SwapCode == 2143 )
1952 gdcmDebugMacro( " Into: "<< SwapCode );
1956 * \brief during parsing, Header Elements too long are not loaded in memory
1957 * @param newSize new size
1959 void Document::SetMaxSizeLoadEntry(long newSize)
1965 if ((uint32_t)newSize >= (uint32_t)0xffffffff )
1967 MaxSizeLoadEntry = 0xffffffff;
1970 MaxSizeLoadEntry = newSize;
1974 * \brief Read the next tag WITHOUT loading it's value
1975 * (read the 'Group Number', the 'Element Number',
1976 * gets the Dict Entry
1977 * gets the VR, gets the length, gets the offset value)
1978 * @return On succes : the newly created DocEntry, NULL on failure.
1980 DocEntry *Document::ReadNextDocEntry()
1984 CurrentGroup = ReadInt16();
1985 CurrentElem = ReadInt16();
1987 catch ( FormatError )
1989 // We reached the EOF (or an error occured) therefore
1990 // header parsing has to be considered as finished.
1994 // Sometimes file contains groups of tags with reversed endianess.
1995 HandleBrokenEndian(CurrentGroup, CurrentElem);
1997 // In 'true DICOM' files Group 0002 is always little endian
1998 if ( HasDCMPreamble )
1999 HandleOutOfGroup0002(CurrentGroup, CurrentElem);
2001 VRKey vr = FindDocEntryVR();
2005 if ( vr == GDCM_VRUNKNOWN )
2007 if ( CurrentElem == 0x0000 ) // Group Length
2009 realVR = "UL"; // must be UL
2011 else if (CurrentGroup%2 == 1 &&
2012 (CurrentElem >= 0x0010 && CurrentElem <=0x00ff ))
2014 // DICOM PS 3-5 7.8.1 a) states that those
2015 // (gggg-0010->00FF where gggg is odd) attributes have to be LO
2020 DictEntry *dictEntry = GetDictEntry(CurrentGroup,CurrentElem);
2023 realVR = dictEntry->GetVR();
2024 dictEntry->Unregister();
2028 // gdcmDebugMacro( "Found VR: " << vr << " / Real VR: " << realVR );
2031 if ( Global::GetVR()->IsVROfSequence(realVR) )
2032 newEntry = NewSeqEntry(CurrentGroup, CurrentElem);
2035 newEntry = NewDataEntry(CurrentGroup, CurrentElem, realVR);
2036 static_cast<DataEntry *>(newEntry)->SetState(DataEntry::STATE_NOTLOADED);
2039 if ( vr == GDCM_VRUNKNOWN )
2041 if ( Filetype == ExplicitVR )
2043 // We thought this was explicit VR, but we end up with an
2044 // implicit VR tag. Let's backtrack.
2045 if ( newEntry->GetGroup() != 0xfffe )
2048 int offset = Fp->tellg();
2050 "Entry (%04x,%04x) at x(%x) should be Explicit VR\n",
2051 newEntry->GetGroup(), newEntry->GetElement(), offset );
2052 gdcmWarningMacro( msg.c_str() );
2055 newEntry->SetImplicitVR();
2060 FindDocEntryLength(newEntry);
2062 catch ( FormatError )
2069 newEntry->SetOffset(Fp->tellg());
2075 * \brief Handle broken private tag from Philips NTSCAN
2076 * where the endianess is being switched to BigEndian
2077 * for no apparent reason
2080 void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
2082 // Endian reversion.
2083 // Some files contain groups of tags with reversed endianess.
2084 static int reversedEndian = 0;
2085 // try to fix endian switching in the middle of headers
2086 if ((group == 0xfeff) && (elem == 0x00e0))
2088 // start endian swap mark for group found
2089 gdcmDebugMacro( "Start endian swap mark found." );
2091 SwitchByteSwapCode();
2096 else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
2098 // end of reversed endian group
2099 gdcmDebugMacro( "End of reversed endian." );
2101 SwitchByteSwapCode();
2103 else if (group == 0xfeff && elem == 0xdde0)
2105 // reversed Sequence Terminator found
2106 // probabely a bug in the header !
2107 // Do what you want, it breaks !
2109 //SwitchByteSwapCode();
2110 gdcmWarningMacro( "Should never get here! reversed Sequence Terminator!" );
2115 else if (group == 0xfffe && elem == 0xe0dd)
2117 gdcmDebugMacro( "Straight Sequence Terminator." );
2122 * \brief Group 0002 is always coded Little Endian
2123 * whatever Transfer Syntax is
2126 void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem)
2128 // Endian reversion.
2129 // Some files contain groups of tags with reversed endianess.
2130 if ( !Group0002Parsed && group != 0x0002)
2132 Group0002Parsed = true;
2133 // we just came out of group 0002
2134 // if Transfer Syntax is Big Endian we have to change CheckSwap
2136 std::string ts = GetTransferSyntax();
2137 if ( ts == GDCM_UNKNOWN )
2139 gdcmDebugMacro("True DICOM File, with NO Transfer Syntax (?!) " );
2142 if ( !Global::GetTS()->IsTransferSyntax(ts) )
2144 gdcmWarningMacro("True DICOM File, with illegal Transfer Syntax: ["
2149 // Group 0002 is always 'Explicit ...'
2150 // even when Transfer Syntax says 'Implicit ..."
2152 if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
2153 TS::ImplicitVRLittleEndian )
2155 Filetype = ImplicitVR;
2158 // FIXME Strangely, this works with
2159 //'Implicit VR BigEndian Transfer Syntax (GE Private)
2161 // --> Probabely normal, since we considered we never have
2162 // to trust manufacturers.
2163 // (we find very often 'Implicit VR' tag,
2164 // even when Transfer Syntax tells us it's Explicit ...
2165 if ( Global::GetTS()->GetSpecialTransferSyntax(ts) ==
2166 TS::ExplicitVRBigEndian )
2168 gdcmDebugMacro("Transfer Syntax Name = ["
2169 << GetTransferSyntaxName() << "]" );
2170 SwitchByteSwapCode();
2171 group = SwapShort(group);
2172 elem = SwapShort(elem);
2177 //-----------------------------------------------------------------------------
2180 //-----------------------------------------------------------------------------
2181 } // end namespace gdcm