1 /*=========================================================================
4 Module: $RCSfile: gdcmDocument.cxx,v $
6 Date: $Date: 2005/07/02 16:51:16 $
7 Version: $Revision: 1.253 $
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 "gdcmValEntry.h"
21 #include "gdcmBinEntry.h"
22 #include "gdcmSeqEntry.h"
23 #include "gdcmGlobal.h"
25 #include "gdcmDebug.h"
27 #include "gdcmDictSet.h"
28 #include "gdcmDocEntrySet.h"
29 #include "gdcmSQItem.h"
34 #include <ctype.h> // for isdigit
35 #include <stdlib.h> // for atoi
39 //-----------------------------------------------------------------------------
41 // Refer to Document::SetMaxSizeLoadEntry()
42 const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
44 //-----------------------------------------------------------------------------
45 // Constructor / Destructor
46 // Constructors and destructors are protected to avoid user to invoke directly
49 * \brief This default constructor neither loads nor parses the file.
50 * You should then invoke \ref Document::Load.
58 SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
61 Filetype = ExplicitVR;
62 // Load will set it to true if sucessfull
63 Group0002Parsed = false;
64 IsDocumentAlreadyLoaded = false;
65 LoadMode = 0x00000000; // default : load everything, later
69 * \brief Constructor (not to break the API)
70 * @param fileName 'Document' (File or DicomDir) to be open for parsing
72 Document::Document( std::string const &fileName )
77 SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
80 Filetype = ExplicitVR;
81 Group0002Parsed = false;
82 LoadMode = 0x00000000; // Load everything
84 // Load will set it to true if sucessfull
85 IsDocumentAlreadyLoaded = false;
90 * \brief Canonical destructor.
92 Document::~Document ()
98 //-----------------------------------------------------------------------------
103 * @param fileName 'Document' (File or DicomDir) to be open for parsing
104 * @return false if file cannot be open or no swap info was found,
105 * or no tag was found.
107 bool Document::Load( std::string const &fileName )
109 // We should clean out anything that already exists.
110 // Check IsDocumentAlreadyLoaded to be sure.
111 if ( IsDocumentAlreadyLoaded )
113 gdcmWarningMacro( "A file was already parsed inside this "
114 << "gdcm::Document (previous name was: "
115 << Filename.c_str() << ". New name is :"
117 // todo : clean out the 'Document'
118 // Should we call ClearEntry() on the parent object ?!?
126 // warning already performed in OpenFile()
127 //gdcmWarningMacro( "Unable to open as an ACR/DICOM file: "
128 // << Filename.c_str() );
133 Group0002Parsed = false;
135 gdcmWarningMacro( "Starting parsing of file: " << Filename.c_str());
137 Fp->seekg(0, std::ios::end);
138 long lgt = Fp->tellg(); // total length of the file
140 Fp->seekg(0, std::ios::beg);
142 // CheckSwap returns a boolean
143 // (false if no swap info of any kind was found)
146 gdcmWarningMacro( "Neither a DICOM V3 nor an ACR-NEMA file: "
147 << Filename.c_str());
152 long beg = Fp->tellg(); // just after DICOM preamble (if any)
154 lgt -= beg; // remaining length to parse
156 ParseDES( this, beg, lgt, false); // Loading is done during parsing
160 gdcmWarningMacro( "No tag in internal hash table for: "
161 << Filename.c_str());
165 IsDocumentAlreadyLoaded = true;
167 Fp->seekg( 0, std::ios::beg);
169 // Load 'non string' values
171 std::string PhotometricInterpretation = GetEntryValue(0x0028,0x0004);
172 if ( PhotometricInterpretation == "PALETTE COLOR " )
175 // Probabely this line should be outside the 'if'
176 // Try to find an image sample holding a 'gray LUT'
177 LoadEntryBinArea(0x0028,0x1200); // gray LUT
180 /// The tags refered by the three following lines used to be CORRECTLY
181 /// defined as having an US Value Representation in the public
182 /// dictionary. BUT the semantics implied by the three following
183 /// lines state that the corresponding tag contents are in fact
184 /// the ones of a BinEntry.
185 /// In order to fix things "Quick and Dirty" the dictionary was
186 /// altered on PURPOSE but now contains a WRONG value.
187 /// In order to fix things and restore the dictionary to its
188 /// correct value, one needs to decided of the semantics by deciding
189 /// whether the following tags are either:
190 /// - multivaluated US, and hence loaded as ValEntry, but afterwards
191 /// also used as BinEntry, which requires the proper conversion,
192 /// - OW, and hence loaded as BinEntry, but afterwards also used
193 /// as ValEntry, which requires the proper conversion.
194 LoadEntryBinArea(0x0028,0x1201); // R LUT
195 LoadEntryBinArea(0x0028,0x1202); // G LUT
196 LoadEntryBinArea(0x0028,0x1203); // B LUT
198 // Segmented Red Palette Color LUT Data
199 LoadEntryBinArea(0x0028,0x1221);
200 // Segmented Green Palette Color LUT Data
201 LoadEntryBinArea(0x0028,0x1222);
202 // Segmented Blue Palette Color LUT Data
203 LoadEntryBinArea(0x0028,0x1223);
206 //FIXME later : how to use it?
207 SeqEntry *modLutSeq = GetSeqEntry(0x0028,0x3000);
210 SQItem *sqi= modLutSeq->GetFirstSQItem();
213 BinEntry *b = sqi->GetBinEntry(0x0028,0x3006);
216 if ( b->GetLength() != 0 )
218 LoadEntryBinArea(b); //LUT Data (CTX dependent)
226 // ----------------------------
227 // Specific code to allow gdcm to read ACR-LibIDO formated images
228 // Note: ACR-LibIDO is an extension of the ACR standard that was
229 // used at CREATIS. For the time being (say a couple years)
230 // we keep this kludge to allow CREATIS users
231 // reading their old images.
233 // if recognition code tells us we deal with a LibIDO image
234 // we switch lineNumber and columnNumber
237 RecCode = GetEntryValue(0x0008, 0x0010); // recognition code (RET)
238 if (RecCode == "ACRNEMA_LIBIDO_1.1" ||
239 RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
240 // with "little-endian strings"
242 Filetype = ACR_LIBIDO;
243 std::string rows = GetEntryValue(0x0028, 0x0010);
244 std::string columns = GetEntryValue(0x0028, 0x0011);
245 SetValEntry(columns, 0x0028, 0x0010);
246 SetValEntry(rows , 0x0028, 0x0011);
248 // --- End of ACR-LibIDO kludge ---
254 * \brief Get the public dictionary used
256 Dict *Document::GetPubDict()
262 * \brief Get the shadow dictionary used
264 Dict *Document::GetShaDict()
270 * \brief Set the shadow dictionary used
271 * @param dict dictionary to use in shadow
273 bool Document::SetShaDict(Dict *dict)
280 * \brief Set the shadow dictionary used
281 * @param dictName name of the dictionary to use in shadow
283 bool Document::SetShaDict(DictKey const &dictName)
285 RefShaDict = Global::GetDicts()->GetDict(dictName);
290 * \brief This predicate tells us whether or not the current Document
291 * was properly parsed and contains at least *one* Dicom Element
292 * (and nothing more, sorry).
293 * @return false when we're 150 % sure it's NOT a Dicom/Acr file,
296 bool Document::IsReadable()
298 if ( Filetype == Unknown )
300 gdcmWarningMacro( "Wrong filetype");
306 gdcmWarningMacro( "No tag in internal hash table.");
314 * \brief Predicate for dicom version 3 file.
315 * @return True when the file is a dicom version 3.
317 bool Document::IsDicomV3()
319 // Checking if Transfer Syntax exists is enough
320 // Anyway, it's too late check if the 'Preamble' was found ...
321 // And ... would it be a rich idea to check ?
322 // (some 'no Preamble' DICOM images exist !)
323 return GetDocEntry(0x0002, 0x0010) != NULL;
327 * \brief Predicate for Papyrus file
328 * Dedicated to whomsoever it may concern
329 * @return True when the file is a Papyrus file.
331 bool Document::IsPapyrus()
333 // check for Papyrus private Sequence
334 DocEntry *e = GetDocEntry(0x0041, 0x1050);
337 // check if it's actually a Sequence
338 if ( !dynamic_cast<SeqEntry*>(e) )
344 * \brief returns the File Type
345 * (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
346 * @return the FileType code
348 FileType Document::GetFileType()
354 * \brief Accessor to the Transfer Syntax (when present) of the
355 * current document (it internally handles reading the
356 * value from disk when only parsing occured).
357 * @return The encountered Transfer Syntax of the current document.
359 std::string Document::GetTransferSyntax()
361 DocEntry *entry = GetDocEntry(0x0002, 0x0010);
367 // The entry might be present but not loaded (parsing and loading
368 // happen at different stages): try loading and proceed with check...
369 LoadDocEntrySafe(entry);
370 if (ValEntry *valEntry = dynamic_cast< ValEntry* >(entry) )
372 std::string transfer = valEntry->GetValue();
373 // The actual transfer (as read from disk) might be padded. We
374 // first need to remove the potential padding. We can make the
375 // weak assumption that padding was not executed with digits...
376 if ( transfer.length() == 0 )
378 // for brain damaged headers
381 while ( !isdigit((unsigned char)transfer[transfer.length()-1]) )
383 transfer.erase(transfer.length()-1, 1);
391 * \brief Accesses the info from 0002,0010 : Transfer Syntax and TS
392 * @return The full Transfer Syntax Name (as opposed to Transfer Syntax UID)
394 std::string Document::GetTransferSyntaxName()
396 // use the TS (TS : Transfer Syntax)
397 std::string transferSyntax = GetEntryValue(0x0002,0x0010);
399 if ( (transferSyntax.find(GDCM_NOTLOADED) < transferSyntax.length()) )
401 gdcmErrorMacro( "Transfer Syntax not loaded. " << std::endl
402 << "Better you increase MAX_SIZE_LOAD_ELEMENT_VALUE" );
403 return "Uncompressed ACR-NEMA";
405 if ( transferSyntax == GDCM_UNFOUND )
407 gdcmWarningMacro( "Unfound Transfer Syntax (0002,0010)");
408 return "Uncompressed ACR-NEMA";
411 // we do it only when we need it
412 const TSKey &tsName = Global::GetTS()->GetValue( transferSyntax );
414 // Global::GetTS() is a global static you shall never try to delete it!
418 // --------------- Swap Code ------------------
420 * \brief Swaps the bytes so they agree with the processor order
421 * @return The properly swaped 16 bits integer.
423 uint16_t Document::SwapShort(uint16_t a)
425 if ( SwapCode == 4321 || SwapCode == 2143 )
427 //a = ((( a << 8 ) & 0xff00 ) | (( a >> 8 ) & 0x00ff ) );
429 a = ( a << 8 ) | ( a >> 8 );
435 * \brief Swaps back the bytes of 4-byte long integer accordingly to
437 * @return The properly swaped 32 bits integer.
439 uint32_t Document::SwapLong(uint32_t a)
446 // a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
447 // ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
449 a=( ( a<<24) | ((a<<8) & 0x00ff0000) |
450 ((a>>8) & 0x0000ff00) | (a>>24) );
453 // a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
454 a=( (a<<16) | (a>>16) );
457 a=( ((a<< 8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
460 gdcmErrorMacro( "Unset swap code:" << SwapCode );
467 // -----------------File I/O ---------------
469 * \brief Tries to open the file \ref Document::Filename and
470 * checks the preamble when existing.
471 * @return The FILE pointer on success.
473 std::ifstream *Document::OpenFile()
475 HasDCMPreamble = false;
476 if (Filename.length() == 0)
483 gdcmWarningMacro( "File already open: " << Filename.c_str());
487 Fp = new std::ifstream(Filename.c_str(), std::ios::in | std::ios::binary);
490 // Don't user gdcmErrorMacro :
491 // a spurious message will appear when you use, for instance
492 // gdcm::FileHelper *fh = new gdcm::FileHelper( outputFileName );
493 // to create outputFileName.
494 gdcmWarningMacro( "Cannot open file: " << Filename.c_str());
498 //exit(1); // No function is allowed to leave the application instead
499 // of warning the caller
503 Fp->read((char*)&zero, (size_t)2);
510 //-- ACR or DICOM with no Preamble; may start with a Shadow Group --
512 zero == 0x0001 || zero == 0x0100 || zero == 0x0002 || zero == 0x0200 ||
513 zero == 0x0003 || zero == 0x0300 || zero == 0x0004 || zero == 0x0400 ||
514 zero == 0x0005 || zero == 0x0500 || zero == 0x0006 || zero == 0x0600 ||
515 zero == 0x0007 || zero == 0x0700 || zero == 0x0008 || zero == 0x0800 )
517 std::string msg = Util::Format(
518 "ACR/DICOM starting at the begining of the file:(%04x)\n", zero);
519 gdcmWarningMacro( msg.c_str() );
524 Fp->seekg(126L, std::ios::cur);
525 char dicm[4] = {' ',' ',' ',' '};
526 Fp->read(dicm, (size_t)4);
532 if ( memcmp(dicm, "DICM", 4) == 0 )
534 HasDCMPreamble = true;
538 // -- Neither ACR/No Preamble Dicom nor DICOMV3 file
540 gdcmWarningMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
541 << Filename.c_str());
546 * \brief closes the file
547 * @return TRUE if the close was successfull
549 bool Document::CloseFile()
561 * \brief Writes in a file all the Header Entries (Dicom Elements)
562 * @param fp file pointer on an already open file (actually: Output File Stream)
563 * @param filetype Type of the File to be written
564 * (ACR-NEMA, ExplicitVR, ImplicitVR)
565 * @return Always true.
567 void Document::WriteContent(std::ofstream *fp, FileType filetype)
569 // \TODO move the following lines (and a lot of others, to be written)
570 // to a future function CheckAndCorrectHeader
572 // (necessary if user wants to write a DICOM V3 file
573 // starting from an ACR-NEMA (V2) Header
575 if ( filetype == ImplicitVR || filetype == ExplicitVR )
577 // writing Dicom File Preamble
578 char filePreamble[128];
579 memset(filePreamble, 0, 128);
580 fp->write(filePreamble, 128);
581 fp->write("DICM", 4);
585 * \todo rewrite later, if really usefull
586 * - 'Group Length' element is optional in DICOM
587 * - but un-updated odd groups lengthes can causes pb
590 * if ( (filetype == ImplicitVR) || (filetype == ExplicitVR) )
591 * UpdateGroupLength(false,filetype);
592 * if ( filetype == ACR)
593 * UpdateGroupLength(true,ACR);
596 ElementSet::WriteContent(fp, filetype); // This one is recursive
599 // -----------------------------------------
602 * \brief Loads (from disk) the element content
603 * when a string is not suitable
604 * @param group group number of the Entry
605 * @param elem element number of the Entry
607 void Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
609 // Search the corresponding DocEntry
610 DocEntry *docElement = GetDocEntry(group, elem);
614 BinEntry *binElement = dynamic_cast<BinEntry *>(docElement);
618 LoadEntryBinArea(binElement);
622 * \brief Loads (from disk) the element content
623 * when a string is not suitable
624 * @param elem Entry whose binArea is going to be loaded
626 void Document::LoadEntryBinArea(BinEntry *elem)
628 if (elem->GetBinArea() )
635 size_t o =(size_t)elem->GetOffset();
636 Fp->seekg(o, std::ios::beg);
638 size_t l = elem->GetLength();
639 uint8_t *a = new uint8_t[l];
642 gdcmWarningMacro( "Cannot allocate BinEntry content");
646 Fp->read((char*)a, l);
647 if ( Fp->fail() || Fp->eof() )
660 * \brief Loads the element while preserving the current
661 * underlying file position indicator as opposed to
662 * LoadDocEntry that modifies it.
663 * @param entry DocEntry whose value will be loaded.
665 void Document::LoadDocEntrySafe(DocEntry *entry)
669 long PositionOnEntry = Fp->tellg();
671 Fp->seekg(PositionOnEntry, std::ios::beg);
676 * \brief Compares two documents, according to \ref DicomDir rules
677 * \warning Does NOT work with ACR-NEMA files
678 * \todo Find a trick to solve the pb (use RET fields ?)
679 * @param document to compare with current one
680 * @return true if 'smaller'
682 bool Document::operator<(Document &document)
685 std::string s1 = GetEntryValue(0x0010,0x0010);
686 std::string s2 = document.GetEntryValue(0x0010,0x0010);
698 s1 = GetEntryValue(0x0010,0x0020);
699 s2 = document.GetEntryValue(0x0010,0x0020);
710 // Study Instance UID
711 s1 = GetEntryValue(0x0020,0x000d);
712 s2 = document.GetEntryValue(0x0020,0x000d);
723 // Serie Instance UID
724 s1 = GetEntryValue(0x0020,0x000e);
725 s2 = document.GetEntryValue(0x0020,0x000e);
740 //-----------------------------------------------------------------------------
743 * \brief Reads a supposed to be 16 Bits integer
744 * (swaps it depending on processor endianness)
747 uint16_t Document::ReadInt16()
751 Fp->read ((char*)&g, (size_t)2);
754 throw FormatError( "Document::ReadInt16()", " file error." );
758 throw FormatError( "Document::ReadInt16()", "EOF." );
765 * \brief Reads a supposed to be 32 Bits integer
766 * (swaps it depending on processor endianness)
769 uint32_t Document::ReadInt32()
773 Fp->read ((char*)&g, (size_t)4);
776 throw FormatError( "Document::ReadInt32()", " file error." );
780 throw FormatError( "Document::ReadInt32()", "EOF." );
787 * \brief skips bytes inside the source file
788 * \warning NOT end user intended method !
791 void Document::SkipBytes(uint32_t nBytes)
793 //FIXME don't dump the returned value
794 Fp->seekg((long)nBytes, std::ios::cur);
798 * \brief Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
799 * @param filetype Type of the File to be written
801 int Document::ComputeGroup0002Length( FileType filetype )
807 bool found0002 = false;
809 // for each zero-level Tag in the DCM Header
810 DocEntry *entry = GetFirstEntry();
813 gr = entry->GetGroup();
819 if ( entry->GetElement() != 0x0000 )
823 if ( filetype == ExplicitVR )
825 if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") || (vr == "UT") )
827 // explicit VR AND OB, OW, SQ, UT : 4 more bytes
831 groupLength += 2 + 2 + 4 + entry->GetLength();
837 entry = GetNextEntry();
842 //-----------------------------------------------------------------------------
845 * \brief Loads all the needed Dictionaries
846 * \warning NOT end user intended method !
848 void Document::Initialize()
850 RefPubDict = Global::GetDicts()->GetDefaultPubDict();
856 * \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
857 * @param set DocEntrySet we are going to parse ('zero level' or a SQItem)
858 * @param offset start of parsing
859 * @param l_max length to parse
860 * @param delim_mode : whether we are in 'delimitor mode' (l=0xffffff) or not
862 void Document::ParseDES(DocEntrySet *set, long offset,
863 long l_max, bool delim_mode)
865 DocEntry *newDocEntry;
866 ValEntry *newValEntry;
867 BinEntry *newBinEntry;
868 SeqEntry *newSeqEntry;
874 if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
880 newDocEntry = ReadNextDocEntry( );
887 vr = newDocEntry->GetVR();
888 newValEntry = dynamic_cast<ValEntry*>(newDocEntry);
889 newBinEntry = dynamic_cast<BinEntry*>(newDocEntry);
890 newSeqEntry = dynamic_cast<SeqEntry*>(newDocEntry);
892 if ( newValEntry || newBinEntry )
896 if ( Filetype == ExplicitVR &&
897 !Global::GetVR()->IsVROfBinaryRepresentable(vr) )
899 ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
900 gdcmWarningMacro( std::hex << newDocEntry->GetGroup()
901 << "|" << newDocEntry->GetElement()
902 << " : Neither Valentry, nor BinEntry."
903 "Probably unknown VR.");
906 //////////////////// BinEntry or UNKOWN VR:
907 // When "this" is a Document the Key is simply of the
908 // form ( group, elem )...
909 if ( dynamic_cast< Document* > ( set ) )
911 newBinEntry->SetKey( newBinEntry->GetKey() );
913 // but when "this" is a SQItem, we are inserting this new
914 // valEntry in a sequence item, and the key has the
915 // generalized form (refer to \ref BaseTagKey):
916 if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
918 newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
919 + newBinEntry->GetKey() );
922 LoadDocEntry( newBinEntry );
923 if ( !set->AddEntry( newBinEntry ) )
925 //Expect big troubles if here
926 //delete newBinEntry;
932 /////////////////////// ValEntry
934 // When "set" is a Document, then we are at the top of the
935 // hierarchy and the Key is simply of the form ( group, elem )...
936 if ( dynamic_cast< Document* > ( set ) )
938 newValEntry->SetKey( newValEntry->GetKey() );
940 // ...but when "set" is a SQItem, we are inserting this new
941 // valEntry in a sequence item. Hence the key has the
942 // generalized form (refer to \ref BaseTagKey):
943 if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
945 newValEntry->SetKey( parentSQItem->GetBaseTagKey()
946 + newValEntry->GetKey() );
949 LoadDocEntry( newValEntry );
950 bool delimitor=newValEntry->IsItemDelimitor();
952 if ( LoadMode & NO_SHADOW ) // User asked to skip, if possible,
953 // shadow groups ( if possible :
954 // whether element 0x0000 exits)
956 if ( newValEntry->GetGroup()%2 != 0 )
958 if ( newValEntry->GetElement() == 0x0000 )
960 std::string strLgrGroup = newValEntry->GetValue();
962 if ( strLgrGroup != GDCM_UNFOUND)
964 lgrGroup = atoi(strLgrGroup.c_str());
965 Fp->seekg(lgrGroup, std::ios::cur);
973 if ( !set->AddEntry( newValEntry ) )
975 // If here expect big troubles
976 // delete newValEntry; //otherwise mem leak
986 if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max )
994 // Just to make sure we are at the beginning of next entry.
995 SkipToNextDocEntry(newDocEntry);
999 /////////////////////// SeqEntry : VR = "SQ"
1001 unsigned long l = newDocEntry->GetReadLength();
1002 if ( l != 0 ) // don't mess the delim_mode for zero-length sequence
1004 if ( l == 0xffffffff )
1014 if ( (LoadMode & NO_SHADOWSEQ) && ! delim_mode )
1016 // User asked to skip SQ only if they belong to Shadow group
1017 if ( newDocEntry->GetGroup()%2 != 0 )
1019 Fp->seekg( l, std::ios::cur);
1025 if ( (LoadMode & NO_SEQ) && ! delim_mode )
1027 // User asked to skip *any* SeQuence
1028 Fp->seekg( l, std::ios::cur);
1033 // no other way to create it ...
1034 newSeqEntry->SetDelimitorMode( delim_mode );
1036 // At the top of the hierarchy, stands a Document. When "set"
1037 // is a Document, then we are building the first depth level.
1038 // Hence the SeqEntry we are building simply has a depth
1040 if ( dynamic_cast< Document* > ( set ) )
1042 newSeqEntry->SetDepthLevel( 1 );
1043 newSeqEntry->SetKey( newSeqEntry->GetKey() );
1045 // But when "set" is already a SQItem, we are building a nested
1046 // sequence, and hence the depth level of the new SeqEntry
1047 // we are building, is one level deeper:
1048 if (SQItem *parentSQItem = dynamic_cast< SQItem* > ( set ) )
1050 newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
1051 newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
1052 + newSeqEntry->GetKey() );
1056 { // Don't try to parse zero-length sequences
1057 ParseSQ( newSeqEntry,
1058 newDocEntry->GetOffset(),
1061 if ( !set->AddEntry( newSeqEntry ) )
1066 if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
1080 * \brief Parses a Sequence ( SeqEntry after SeqEntry)
1081 * @return parsed length for this level
1083 void Document::ParseSQ( SeqEntry *seqEntry,
1084 long offset, long l_max, bool delim_mode)
1086 int SQItemNumber = 0;
1088 long offsetStartCurrentSQItem = offset;
1092 // the first time, we read the fff0,e000 of the first SQItem
1093 DocEntry *newDocEntry = ReadNextDocEntry();
1097 // FIXME Should warn user
1102 if ( newDocEntry->IsSequenceDelimitor() )
1104 seqEntry->SetDelimitationItem( newDocEntry );
1108 if ( !delim_mode && ((long)(Fp->tellg())-offset) >= l_max)
1113 // create the current SQItem
1114 SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
1115 std::ostringstream newBase;
1116 newBase << seqEntry->GetKey()
1120 itemSQ->SetBaseTagKey( newBase.str() );
1121 unsigned int l = newDocEntry->GetReadLength();
1123 if ( l == 0xffffffff )
1132 // Let's try :------------
1133 // remove fff0,e000, created out of the SQItem
1135 Fp->seekg(offsetStartCurrentSQItem, std::ios::beg);
1136 // fill up the current SQItem, starting at the beginning of fff0,e000
1137 ParseDES(itemSQ, offsetStartCurrentSQItem, l+8, dlm_mod);
1138 offsetStartCurrentSQItem = Fp->tellg();
1139 // end try -----------------
1141 seqEntry->AddSQItem( itemSQ, SQItemNumber );
1143 if ( !delim_mode && ((long)(Fp->tellg())-offset ) >= l_max )
1151 * \brief Loads the element content if its length doesn't exceed
1152 * the value specified with Document::SetMaxSizeLoadEntry()
1153 * @param entry Header Entry (Dicom Element) to be dealt with
1155 void Document::LoadDocEntry(DocEntry *entry)
1157 uint16_t group = entry->GetGroup();
1158 std::string vr = entry->GetVR();
1159 uint32_t length = entry->GetLength();
1161 Fp->seekg((long)entry->GetOffset(), std::ios::beg);
1163 // A SeQuence "contains" a set of Elements.
1164 // (fffe e000) tells us an Element is beginning
1165 // (fffe e00d) tells us an Element just ended
1166 // (fffe e0dd) tells us the current SeQuence just ended
1167 if ( group == 0xfffe )
1169 // NO more value field for SQ !
1173 // When the length is zero things are easy:
1176 ((ValEntry *)entry)->SetValue("");
1180 // The elements whose length is bigger than the specified upper bound
1181 // are not loaded. Instead we leave a short notice of the offset of
1182 // the element content and it's length.
1184 std::ostringstream s;
1185 if (length > MaxSizeLoadEntry)
1187 if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
1189 s << GDCM_NOTLOADED;
1190 s << " Ad.:" << (long)entry->GetOffset();
1191 s << " x(" << std::hex << entry->GetOffset() << ")";
1193 s << " Lgt:" << entry->GetLength();
1194 s << " x(" << std::hex << entry->GetLength() << ")";
1195 binEntryPtr->SetValue(s.str());
1197 else if (ValEntry *valEntryPtr = dynamic_cast< ValEntry* >(entry) )
1199 s << GDCM_NOTLOADED;
1200 s << " Address:" << (long)entry->GetOffset();
1201 s << " Length:" << entry->GetLength();
1202 s << " x(" << std::hex << entry->GetLength() << ")";
1203 valEntryPtr->SetValue(s.str());
1208 gdcmErrorMacro( "MaxSizeLoadEntry exceeded, neither a BinEntry "
1209 << "nor a ValEntry ?! Should never print that !" );
1212 // to be sure we are at the end of the value ...
1213 Fp->seekg((long)entry->GetOffset()+(long)entry->GetLength(),
1218 // When we find a BinEntry not very much can be done :
1219 if (BinEntry *binEntryPtr = dynamic_cast< BinEntry* >(entry) )
1221 s << GDCM_BINLOADED;
1222 binEntryPtr->SetValue(s.str());
1223 LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
1227 if ( IsDocEntryAnInteger(entry) )
1231 // When short integer(s) are expected, read and convert the following
1232 // (n * 2) characters properly i.e. consider them as short integers as
1233 // opposed to strings.
1234 // Elements with Value Multiplicity > 1
1235 // contain a set of integers (not a single one)
1236 if (vr == "US" || vr == "SS")
1239 NewInt = ReadInt16();
1243 for (int i=1; i < nbInt; i++)
1246 NewInt = ReadInt16();
1251 // See above comment on multiple integers (mutatis mutandis).
1252 else if (vr == "UL" || vr == "SL")
1255 NewInt = ReadInt32();
1259 for (int i=1; i < nbInt; i++)
1262 NewInt = ReadInt32();
1267 #ifdef GDCM_NO_ANSI_STRING_STREAM
1268 s << std::ends; // to avoid oddities on Solaris
1269 #endif //GDCM_NO_ANSI_STRING_STREAM
1271 ((ValEntry *)entry)->SetValue(s.str());
1275 // FIXME: We need an additional byte for storing \0 that is not on disk
1276 char *str = new char[length+1];
1277 Fp->read(str, (size_t)length);
1278 str[length] = '\0'; //this is only useful when length is odd
1279 // Special DicomString call to properly handle \0 and even length
1280 std::string newValue;
1283 newValue = Util::DicomString(str, length+1);
1284 gdcmWarningMacro("Warning: bad length: " << length <<
1285 " For string :" << newValue.c_str());
1286 // Since we change the length of string update it length
1287 //entry->SetReadLength(length+1);
1291 newValue = Util::DicomString(str, length);
1295 if ( ValEntry *valEntry = dynamic_cast<ValEntry* >(entry) )
1297 if ( Fp->fail() || Fp->eof())
1300 gdcmWarningMacro("--> fail");
1302 gdcmWarningMacro("Unread element value " << valEntry->GetKey()
1303 << " lgt : " << valEntry->GetReadLength()
1304 << " at " << std::hex << valEntry->GetOffset());
1305 valEntry->SetValue(GDCM_UNREAD);
1311 // Because of correspondance with the VR dic
1312 valEntry->SetValue(newValue);
1316 valEntry->SetValue(newValue);
1321 gdcmWarningMacro("Should have a ValEntry, here ! " << valEntry->GetKey()
1322 << " lgt : " << valEntry->GetReadLength()
1323 << " at " << std::hex << valEntry->GetOffset());
1328 * \brief Find the value Length of the passed Header Entry
1329 * @param entry Header Entry whose length of the value shall be loaded.
1331 void Document::FindDocEntryLength( DocEntry *entry )
1332 throw ( FormatError )
1334 std::string vr = entry->GetVR();
1337 if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
1339 if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UT" || vr == "UN" )
1341 // The following reserved two bytes (see PS 3.5-2003, section
1342 // "7.1.2 Data element structure with explicit vr", p 27) must be
1343 // skipped before proceeding on reading the length on 4 bytes.
1344 Fp->seekg( 2L, std::ios::cur);
1345 uint32_t length32 = ReadInt32();
1347 if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
1352 lengthOB = FindDocEntryLengthOBOrOW();
1354 catch ( FormatUnexpected )
1356 // Computing the length failed (this happens with broken
1357 // files like gdcm-JPEG-LossLess3a.dcm). We still have a
1358 // chance to get the pixels by deciding the element goes
1359 // until the end of the file. Hence we artificially fix the
1360 // the length and proceed.
1361 long currentPosition = Fp->tellg();
1362 Fp->seekg(0L,std::ios::end);
1364 long lengthUntilEOF = (long)(Fp->tellg())-currentPosition;
1365 Fp->seekg(currentPosition, std::ios::beg);
1367 entry->SetReadLength(lengthUntilEOF);
1368 entry->SetLength(lengthUntilEOF);
1371 entry->SetReadLength(lengthOB);
1372 entry->SetLength(lengthOB);
1375 FixDocEntryFoundLength(entry, length32);
1379 // Length is encoded on 2 bytes.
1380 length16 = ReadInt16();
1382 // 0xffff means that we deal with 'No Length' Sequence
1383 // or 'No Length' SQItem
1384 if ( length16 == 0xffff)
1388 FixDocEntryFoundLength( entry, (uint32_t)length16 );
1393 // Either implicit VR or a non DICOM conformal (see note below) explicit
1394 // VR that ommited the VR of (at least) this element. Farts happen.
1395 // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25
1396 // on Data elements "Implicit and Explicit VR Data Elements shall
1397 // not coexist in a Data Set and Data Sets nested within it".]
1398 // Length is on 4 bytes.
1400 // Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
1401 // even if Transfer Syntax is 'Implicit VR ...'
1403 FixDocEntryFoundLength( entry, ReadInt32() );
1409 * \brief Find the Length till the next sequence delimiter
1410 * \warning NOT end user intended method !
1413 uint32_t Document::FindDocEntryLengthOBOrOW()
1414 throw( FormatUnexpected )
1416 // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
1417 long positionOnEntry = Fp->tellg();
1418 bool foundSequenceDelimiter = false;
1419 uint32_t totalLength = 0;
1421 while ( !foundSequenceDelimiter )
1427 group = ReadInt16();
1430 catch ( FormatError )
1432 throw FormatError("Unexpected end of file encountered during ",
1433 "Document::FindDocEntryLengthOBOrOW()");
1435 // We have to decount the group and element we just read
1437 if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
1439 long filePosition = Fp->tellg();
1441 "Neither an Item tag nor a Sequence delimiter tag on :"
1442 << std::hex << group << " , " << elem
1443 << ") -before- position x(" << filePosition << ")" );
1445 Fp->seekg(positionOnEntry, std::ios::beg);
1446 throw FormatUnexpected(
1447 "Neither an Item tag nor a Sequence delimiter tag.");
1449 if ( elem == 0xe0dd )
1451 foundSequenceDelimiter = true;
1453 uint32_t itemLength = ReadInt32();
1454 // We add 4 bytes since we just read the ItemLength with ReadInt32
1455 totalLength += itemLength + 4;
1456 SkipBytes(itemLength);
1458 if ( foundSequenceDelimiter )
1463 Fp->seekg( positionOnEntry, std::ios::beg);
1468 * \brief Find the Value Representation of the current Dicom Element.
1469 * @return Value Representation of the current Entry
1471 std::string Document::FindDocEntryVR()
1473 if ( Filetype != ExplicitVR )
1474 return GDCM_UNKNOWN;
1476 long positionOnEntry = Fp->tellg();
1477 // Warning: we believe this is explicit VR (Value Representation) because
1478 // we used a heuristic that found "UL" in the first tag. Alas this
1479 // doesn't guarantee that all the tags will be in explicit VR. In some
1480 // cases (see e-film filtered files) one finds implicit VR tags mixed
1481 // within an explicit VR file. Hence we make sure the present tag
1482 // is in explicit VR and try to fix things if it happens not to be
1486 Fp->read (vr, (size_t)2);
1489 if ( !CheckDocEntryVR(vr) )
1491 Fp->seekg(positionOnEntry, std::ios::beg);
1492 return GDCM_UNKNOWN;
1498 * \brief Check the correspondance between the VR of the header entry
1499 * and the taken VR. If they are different, the header entry is
1500 * updated with the new VR.
1501 * @param vr Dicom Value Representation
1502 * @return false if the VR is incorrect of if the VR isn't referenced
1503 * otherwise, it returns true
1505 bool Document::CheckDocEntryVR(VRKey vr)
1507 if ( !Global::GetVR()->IsValidVR(vr) )
1514 * \brief Get the transformed value of the header entry. The VR value
1515 * is used to define the transformation to operate on the value
1516 * \warning NOT end user intended method !
1517 * @param entry entry to tranform
1518 * @return Transformed entry value
1520 std::string Document::GetDocEntryValue(DocEntry *entry)
1522 if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
1524 std::string val = ((ValEntry *)entry)->GetValue();
1525 std::string vr = entry->GetVR();
1526 uint32_t length = entry->GetLength();
1527 std::ostringstream s;
1530 // When short integer(s) are expected, read and convert the following
1531 // n * 2 bytes properly i.e. as a multivaluated strings
1532 // (each single value is separated fromthe next one by '\'
1533 // as usual for standard multivaluated filels
1534 // Elements with Value Multiplicity > 1
1535 // contain a set of short integers (not a single one)
1537 if ( vr == "US" || vr == "SS" )
1542 for (int i=0; i < nbInt; i++)
1548 newInt16 = ( val[2*i+0] & 0xFF ) + ( ( val[2*i+1] & 0xFF ) << 8);
1549 newInt16 = SwapShort( newInt16 );
1554 // When integer(s) are expected, read and convert the following
1555 // n * 4 bytes properly i.e. as a multivaluated strings
1556 // (each single value is separated fromthe next one by '\'
1557 // as usual for standard multivaluated filels
1558 // Elements with Value Multiplicity > 1
1559 // contain a set of integers (not a single one)
1560 else if ( vr == "UL" || vr == "SL" )
1565 for (int i=0; i < nbInt; i++)
1571 newInt32 = ( val[4*i+0] & 0xFF )
1572 + (( val[4*i+1] & 0xFF ) << 8 )
1573 + (( val[4*i+2] & 0xFF ) << 16 )
1574 + (( val[4*i+3] & 0xFF ) << 24 );
1575 newInt32 = SwapLong( newInt32 );
1579 #ifdef GDCM_NO_ANSI_STRING_STREAM
1580 s << std::ends; // to avoid oddities on Solaris
1581 #endif //GDCM_NO_ANSI_STRING_STREAM
1584 return ((ValEntry *)entry)->GetValue();
1588 * \brief Get the reverse transformed value of the header entry. The VR
1589 * value is used to define the reverse transformation to operate on
1591 * \warning NOT end user intended method !
1592 * @param entry Entry to reverse transform
1593 * @return Reverse transformed entry value
1595 std::string Document::GetDocEntryUnvalue(DocEntry *entry)
1597 if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
1599 std::string vr = entry->GetVR();
1600 std::vector<std::string> tokens;
1601 std::ostringstream s;
1603 if ( vr == "US" || vr == "SS" )
1607 tokens.erase( tokens.begin(), tokens.end()); // clean any previous value
1608 Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
1609 for (unsigned int i=0; i<tokens.size(); i++)
1611 newInt16 = atoi(tokens[i].c_str());
1612 s << ( newInt16 & 0xFF )
1613 << (( newInt16 >> 8 ) & 0xFF );
1617 if ( vr == "UL" || vr == "SL")
1621 tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
1622 Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
1623 for (unsigned int i=0; i<tokens.size();i++)
1625 newInt32 = atoi(tokens[i].c_str());
1626 s << (char)( newInt32 & 0xFF )
1627 << (char)(( newInt32 >> 8 ) & 0xFF )
1628 << (char)(( newInt32 >> 16 ) & 0xFF )
1629 << (char)(( newInt32 >> 24 ) & 0xFF );
1634 #ifdef GDCM_NO_ANSI_STRING_STREAM
1635 s << std::ends; // to avoid oddities on Solaris
1636 #endif //GDCM_NO_ANSI_STRING_STREAM
1640 return ((ValEntry *)entry)->GetValue();
1644 * \brief Skip a given Header Entry
1645 * \warning NOT end user intended method !
1646 * @param entry entry to skip
1648 void Document::SkipDocEntry(DocEntry *entry)
1650 SkipBytes(entry->GetLength());
1654 * \brief Skips to the beginning of the next Header Entry
1655 * \warning NOT end user intended method !
1656 * @param currentDocEntry entry to skip
1658 void Document::SkipToNextDocEntry(DocEntry *currentDocEntry)
1660 Fp->seekg((long)(currentDocEntry->GetOffset()), std::ios::beg);
1661 if (currentDocEntry->GetGroup() != 0xfffe) // for fffe pb
1662 Fp->seekg( (long)(currentDocEntry->GetReadLength()),std::ios::cur);
1666 * \brief When the length of an element value is obviously wrong (because
1667 * the parser went Jabberwocky) one can hope improving things by
1668 * applying some heuristics.
1669 * @param entry entry to check
1670 * @param foundLength first assumption about length
1672 void Document::FixDocEntryFoundLength(DocEntry *entry,
1673 uint32_t foundLength)
1675 entry->SetReadLength( foundLength ); // will be updated only if a bug is found
1676 if ( foundLength == 0xffffffff)
1681 uint16_t gr = entry->GetGroup();
1682 uint16_t elem = entry->GetElement();
1684 if ( foundLength % 2)
1686 gdcmWarningMacro( "Warning : Tag with uneven length " << foundLength
1687 << " in x(" << std::hex << gr << "," << elem <<")");
1690 //////// Fix for some naughty General Electric images.
1691 // Allthough not recent many such GE corrupted images are still present
1692 // on Creatis hard disks. Hence this fix shall remain when such images
1693 // are no longer in use (we are talking a few years, here)...
1694 // Note: XMedCon probably uses such a trick since it is able to read
1695 // those pesky GE images ...
1696 if ( foundLength == 13)
1698 // Only happens for this length !
1699 if ( gr != 0x0008 || ( elem != 0x0070 && elem != 0x0080 ) )
1702 entry->SetReadLength(10); // a bug is to be fixed !?
1706 //////// Fix for some brain-dead 'Leonardo' Siemens images.
1707 // Occurence of such images is quite low (unless one leaves close to a
1708 // 'Leonardo' source. Hence, one might consider commenting out the
1709 // following fix on efficiency reasons.
1710 else if ( gr == 0x0009 && ( elem == 0x1113 || elem == 0x1114 ) )
1713 entry->SetReadLength(4); // a bug is to be fixed !?
1716 else if ( entry->GetVR() == "SQ" )
1718 foundLength = 0; // ReadLength is unchanged
1721 //////// We encountered a 'delimiter' element i.e. a tag of the form
1722 // "fffe|xxxx" which is just a marker. Delimiters length should not be
1723 // taken into account.
1724 else if ( gr == 0xfffe )
1726 // According to the norm, fffe|0000 shouldn't exist. BUT the Philips
1727 // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to
1728 // causes extra troubles...
1729 if ( entry->GetElement() != 0x0000 )
1734 entry->SetLength(foundLength);
1738 * \brief Apply some heuristics to predict whether the considered
1739 * element value contains/represents an integer or not.
1740 * @param entry The element value on which to apply the predicate.
1741 * @return The result of the heuristical predicate.
1743 bool Document::IsDocEntryAnInteger(DocEntry *entry)
1745 uint16_t elem = entry->GetElement();
1746 uint16_t group = entry->GetGroup();
1747 const std::string &vr = entry->GetVR();
1748 uint32_t length = entry->GetLength();
1750 // When we have some semantics on the element we just read, and if we
1751 // a priori know we are dealing with an integer, then we shall be
1752 // able to swap it's element value properly.
1753 if ( elem == 0 ) // This is the group length of the group
1761 // Allthough this should never happen, still some images have a
1762 // corrupted group length [e.g. have a glance at offset x(8336) of
1763 // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm].
1764 // Since for dicom compliant and well behaved headers, the present
1765 // test is useless (and might even look a bit paranoid), when we
1766 // encounter such an ill-formed image, we simply display a warning
1767 // message and proceed on parsing (while crossing fingers).
1768 long filePosition = Fp->tellg();
1769 gdcmWarningMacro( "Erroneous Group Length element length on : ("
1770 << std::hex << group << " , " << elem
1771 << ") -before- position x(" << filePosition << ")"
1772 << "lgt : " << length );
1776 if ( vr == "UL" || vr == "US" || vr == "SL" || vr == "SS" )
1784 * \brief Discover what the swap code is (among little endian, big endian,
1785 * bad little endian, bad big endian).
1787 * @return false when we are absolutely sure
1788 * it's neither ACR-NEMA nor DICOM
1789 * true when we hope ours assuptions are OK
1791 bool Document::CheckSwap()
1798 // First, compare HostByteOrder and NetworkByteOrder in order to
1799 // determine if we shall need to swap bytes (i.e. the Endian type).
1800 bool net2host = Util::IsCurrentProcessorBigEndian();
1802 // The easiest case is the one of a 'true' DICOM header, we just have
1803 // to look for the string "DICM" inside the file preamble.
1806 char *entCur = deb + 128;
1807 if ( memcmp(entCur, "DICM", (size_t)4) == 0 )
1809 gdcmWarningMacro( "Looks like DICOM Version3 (preamble + DCM)" );
1811 // Group 0002 should always be VR, and the first element 0000
1812 // Let's be carefull (so many wrong headers ...)
1813 // and determine the value representation (VR) :
1814 // Let's skip to the first element (0002,0000) and check there if we find
1815 // "UL" - or "OB" if the 1st one is (0002,0001) -,
1816 // in which case we (almost) know it is explicit VR.
1817 // WARNING: if it happens to be implicit VR then what we will read
1818 // is the length of the group. If this ascii representation of this
1819 // length happens to be "UL" then we shall believe it is explicit VR.
1820 // We need to skip :
1821 // * the 128 bytes of File Preamble (often padded with zeroes),
1822 // * the 4 bytes of "DICM" string,
1823 // * the 4 bytes of the first tag (0002, 0000),or (0002, 0001)
1824 // i.e. a total of 136 bytes.
1827 // group 0x0002 *is always* Explicit VR Sometimes ,
1828 // even if elem 0002,0010 (Transfer Syntax) tells us the file is
1829 // *Implicit* VR (see former 'gdcmData/icone.dcm')
1831 if ( memcmp(entCur, "UL", (size_t)2) == 0 ||
1832 memcmp(entCur, "OB", (size_t)2) == 0 ||
1833 memcmp(entCur, "UI", (size_t)2) == 0 ||
1834 memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later
1835 // when Write DCM *adds*
1837 // Use Document::dicom_vr to test all the possibilities
1838 // instead of just checking for UL, OB and UI !? group 0000
1840 Filetype = ExplicitVR;
1841 gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
1845 Filetype = ImplicitVR;
1846 gdcmWarningMacro( "Group 0002 :Not an explicit Value Representation;"
1847 << "Looks like a bugged Header!");
1853 gdcmWarningMacro( "HostByteOrder != NetworkByteOrder");
1858 gdcmWarningMacro( "HostByteOrder = NetworkByteOrder");
1861 // Position the file position indicator at first tag
1862 // (i.e. after the file preamble and the "DICM" string).
1864 Fp->seekg(0, std::ios::beg); // FIXME : Is it usefull?
1866 Fp->seekg ( 132L, std::ios::beg);
1868 } // ------------------------------- End of DicomV3 ----------------
1870 // Alas, this is not a DicomV3 file and whatever happens there is no file
1871 // preamble. We can reset the file position indicator to where the data
1872 // is (i.e. the beginning of the file).
1874 gdcmWarningMacro( "Not a Kosher DICOM Version3 file (no preamble)");
1876 Fp->seekg(0, std::ios::beg);
1878 // Let's check 'No Preamble Dicom File' :
1879 // Should start with group 0x0002
1880 // and be Explicit Value Representation
1882 s16 = *((uint16_t *)(deb));
1895 if ( SwapCode != 0 )
1897 if ( memcmp(entCur, "UL", (size_t)2) == 0 ||
1898 memcmp(entCur, "OB", (size_t)2) == 0 ||
1899 memcmp(entCur, "UI", (size_t)2) == 0 ||
1900 memcmp(entCur, "SH", (size_t)2) == 0 ||
1901 memcmp(entCur, "AE", (size_t)2) == 0 ||
1902 memcmp(entCur, "OB", (size_t)2) == 0 )
1904 Filetype = ExplicitVR;
1905 gdcmWarningMacro( "Group 0002 : Explicit Value Representation");
1909 // ------------------------------- End of 'No Preamble' DicomV3 -------------
1911 // Our next best chance would be to be considering a 'clean' ACR/NEMA file.
1912 // By clean we mean that the length of the first group is written down.
1913 // If this is the case and since the length of the first group HAS to be
1914 // four (bytes), then determining the proper swap code is straightforward.
1917 // We assume the array of char we are considering contains the binary
1918 // representation of a 32 bits integer. Hence the following dirty
1920 s32 = *((uint32_t *)(entCur));
1940 // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
1941 // It is time for despaired wild guesses.
1942 // So, let's check if this file wouldn't happen to be 'dirty' ACR/NEMA,
1943 // i.e. the 'group length' element is not present :
1945 // check the supposed-to-be 'group number'
1946 // in ( 0x0001 .. 0x0008 )
1947 // to determine ' SwapCode' value .
1948 // Only 0 or 4321 will be possible
1949 // (no oportunity to check for the formerly well known
1950 // ACR-NEMA 'Bad Big Endian' or 'Bad Little Endian'
1951 // if unsuccessfull (i.e. neither 0x0002 nor 0x0200 etc -3, 4, ..., 8-)
1952 // the file IS NOT ACR-NEMA nor DICOM V3
1953 // Find a trick to tell it the caller...
1955 s16 = *((uint16_t *)(deb));
1982 gdcmWarningMacro( "ACR/NEMA unfound swap info (Really hopeless !)");
1990 * \brief Change the Byte Swap code.
1992 void Document::SwitchByteSwapCode()
1994 gdcmWarningMacro( "Switching Byte Swap code from "<< SwapCode
1995 << " at :" <<std::hex << Fp->tellg() );
1996 if ( SwapCode == 1234 )
2000 else if ( SwapCode == 4321 )
2004 else if ( SwapCode == 3412 )
2008 else if ( SwapCode == 2143 )
2015 * \brief during parsing, Header Elements too long are not loaded in memory
2016 * @param newSize new size
2018 void Document::SetMaxSizeLoadEntry(long newSize)
2024 if ((uint32_t)newSize >= (uint32_t)0xffffffff )
2026 MaxSizeLoadEntry = 0xffffffff;
2029 MaxSizeLoadEntry = newSize;
2033 * \brief Read the next tag but WITHOUT loading it's value
2034 * (read the 'Group Number', the 'Element Number',
2035 * gets the Dict Entry
2036 * gets the VR, gets the length, gets the offset value)
2037 * @return On succes the newly created DocEntry, NULL on failure.
2039 DocEntry *Document::ReadNextDocEntry()
2046 group = ReadInt16();
2049 catch ( FormatError e )
2051 // We reached the EOF (or an error occured) therefore
2052 // header parsing has to be considered as finished.
2056 // Sometimes file contains groups of tags with reversed endianess.
2057 HandleBrokenEndian(group, elem);
2059 // In 'true DICOM' files Group 0002 is always little endian
2060 if ( HasDCMPreamble )
2061 HandleOutOfGroup0002(group, elem);
2063 std::string vr = FindDocEntryVR();
2064 std::string realVR = vr;
2066 if ( vr == GDCM_UNKNOWN )
2068 if ( elem == 0x0000 ) // Group Length
2069 realVR = "UL"; // must be UL
2072 DictEntry *dictEntry = GetDictEntry(group,elem);
2074 realVR = dictEntry->GetVR();
2079 if ( Global::GetVR()->IsVROfSequence(realVR) )
2080 newEntry = NewSeqEntry(group, elem);
2081 else if ( Global::GetVR()->IsVROfStringRepresentable(realVR) )
2082 newEntry = NewValEntry(group, elem,vr);
2084 newEntry = NewBinEntry(group, elem,vr);
2086 if ( vr == GDCM_UNKNOWN )
2088 if ( Filetype == ExplicitVR )
2090 // We thought this was explicit VR, but we end up with an
2091 // implicit VR tag. Let's backtrack.
2092 if ( newEntry->GetGroup() != 0xfffe )
2095 int offset = Fp->tellg();
2096 msg = Util::Format("Entry (%04x,%04x) at %x should be Explicit VR\n",
2097 newEntry->GetGroup(), newEntry->GetElement(), offset );
2098 gdcmWarningMacro( msg.c_str() );
2101 newEntry->SetImplicitVR();
2106 FindDocEntryLength(newEntry);
2108 catch ( FormatError e )
2115 newEntry->SetOffset(Fp->tellg());
2121 * \brief Handle broken private tag from Philips NTSCAN
2122 * where the endianess is being switched to BigEndian for no
2126 void Document::HandleBrokenEndian(uint16_t &group, uint16_t &elem)
2128 // Endian reversion. Some files contain groups of tags with reversed endianess.
2129 static int reversedEndian = 0;
2130 // try to fix endian switching in the middle of headers
2131 if ((group == 0xfeff) && (elem == 0x00e0))
2133 // start endian swap mark for group found
2135 SwitchByteSwapCode();
2140 else if (group == 0xfffe && elem == 0xe00d && reversedEndian)
2142 // end of reversed endian group
2144 SwitchByteSwapCode();
2149 * \brief Group 0002 is always coded Little Endian
2150 * whatever Transfer Syntax is
2153 void Document::HandleOutOfGroup0002(uint16_t &group, uint16_t &elem)
2155 // Endian reversion. Some files contain groups of tags with reversed endianess.
2156 if ( !Group0002Parsed && group != 0x0002)
2158 Group0002Parsed = true;
2159 // we just came out of group 0002
2160 // if Transfer syntax is Big Endian we have to change CheckSwap
2162 std::string ts = GetTransferSyntax();
2163 if ( !Global::GetTS()->IsTransferSyntax(ts) )
2165 gdcmWarningMacro("True DICOM File, with NO Tansfer Syntax: " << ts );
2169 // Group 0002 is always 'Explicit ...' enven when Transfer Syntax says 'Implicit ..."
2171 if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ImplicitVRLittleEndian )
2173 Filetype = ImplicitVR;
2176 // FIXME Strangely, this works with
2177 //'Implicit VR Transfer Syntax (GE Private)
2178 if ( Global::GetTS()->GetSpecialTransferSyntax(ts) == TS::ExplicitVRBigEndian )
2180 gdcmWarningMacro("Transfer Syntax Name = ["
2181 << GetTransferSyntaxName() << "]" );
2182 SwitchByteSwapCode();
2183 group = SwapShort(group);
2184 elem = SwapShort(elem);
2189 //-----------------------------------------------------------------------------
2192 //-----------------------------------------------------------------------------
2193 } // end namespace gdcm