9 #include <netinet/in.h>
11 #include <cctype> // for isalpha
16 #define HEADER_LENGTH_TO_READ 256 // on ne lit plus que le debut
17 #define _MaxSizeLoadElementValue_ 1024 // longueur au dela de laquelle on ne charge plus les valeurs
20 struct FileReadError {
21 FileReadError(FILE* fp, const char* Mesg) {
23 dbg.Verbose(1, "EOF encountered :", Mesg);
25 dbg.Verbose(1, "Error on reading :", Mesg);
30 //FIXME: this looks dirty to me...
32 #define str2num(str, typeNum) *((typeNum *)(str))
34 // str est un pointeur dans un tableau de caractères, qui doit contenir,
35 // à cet endroit la, la représentation binaire d'un entier (16 ou 32 bits)
36 // je veux récupérer ça ... dans un entier.
37 // s'il y a une autre solution, évitant des cast et les indirections,
40 VRHT * gdcmHeader::dicom_vr = (VRHT*)0;
41 gdcmDictSet* gdcmHeader::Dicts = new gdcmDictSet();
43 void gdcmHeader::Initialise(void) {
44 if (!gdcmHeader::dicom_vr)
46 RefPubDict = gdcmHeader::Dicts->GetDefaultPublicDict();
47 RefShaDict = (gdcmDict*)0;
50 gdcmHeader::gdcmHeader (const char* InFilename) {
51 SetMaxSizeLoadElementValue(_MaxSizeLoadElementValue_);
52 filename = InFilename;
54 fp=fopen(InFilename,"rw");
55 dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename);
59 gdcmHeader::~gdcmHeader (void) {
64 void gdcmHeader::InitVRDict (void) {
66 dbg.Verbose(0, "gdcmHeader::InitVRDict:", "VR dictionary allready set");
70 (*vr)["AE"] = "Application Entity"; // At most 16 bytes
71 (*vr)["AS"] = "Age String"; // Exactly 4 bytes
72 (*vr)["AT"] = "Attribute Tag"; // 2 16-bit unsigned short integers
73 (*vr)["CS"] = "Code String"; // At most 16 bytes
74 (*vr)["DA"] = "Date"; // Exactly 8 bytes
75 (*vr)["DS"] = "Decimal String"; // At most 16 bytes
76 (*vr)["DT"] = "Date Time"; // At most 26 bytes
77 (*vr)["FL"] = "Floating Point Single"; // 32-bit IEEE 754:1985 float
78 (*vr)["FD"] = "Floating Point Double"; // 64-bit IEEE 754:1985 double
79 (*vr)["IS"] = "Integer String"; // At most 12 bytes
80 (*vr)["LO"] = "Long String"; // At most 64 chars
81 (*vr)["LT"] = "Long Text"; // At most 10240 chars
82 (*vr)["OB"] = "Other Byte String"; // String of bytes (vr independant)
83 (*vr)["OW"] = "Other Word String"; // String of 16-bit words (vr dep)
84 (*vr)["PN"] = "Person Name"; // At most 64 chars
85 (*vr)["SH"] = "Short String"; // At most 16 chars
86 (*vr)["SL"] = "Signed Long"; // Exactly 4 bytes
87 (*vr)["SQ"] = "Sequence of Items"; // Not Applicable
88 (*vr)["SS"] = "Signed Short"; // Exactly 2 bytes
89 (*vr)["ST"] = "Short Text"; // At most 1024 chars
90 (*vr)["TM"] = "Time"; // At most 16 bytes
91 (*vr)["UI"] = "Unique Identifier"; // At most 64 bytes
92 (*vr)["UL"] = "Unsigned Long "; // Exactly 4 bytes
93 (*vr)["UN"] = "Unknown"; // Any length of bytes
94 (*vr)["US"] = "Unsigned Short "; // Exactly 2 bytes
95 (*vr)["UT"] = "Unlimited Text"; // At most 2^32 -1 chars
100 * \ingroup gdcmHeader
101 * \brief Discover what the swap code is (among little endian, big endian,
102 * bad little endian, bad big endian).
105 void gdcmHeader::CheckSwap()
107 // The only guaranted way of finding the swap code is to find a
108 // group tag since we know it's length has to be of four bytes i.e.
109 // 0x00000004. Finding the swap code in then straigthforward. Trouble
110 // occurs when we can't find such group...
112 guint32 x=4; // x : pour ntohs
113 bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
117 char deb[HEADER_LENGTH_TO_READ];
119 // First, compare HostByteOrder and NetworkByteOrder in order to
120 // determine if we shall need to swap bytes (i.e. the Endian type).
126 // The easiest case is the one of a DICOM header, since it possesses a
127 // file preamble where it suffice to look for the string "DICM".
128 lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp);
131 if(memcmp(entCur, "DICM", (size_t)4) == 0) {
132 filetype = TrueDicom;
133 dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
136 dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
139 if(filetype == TrueDicom) {
140 // Next, determine the value representation (VR). Let's skip to the
141 // first element (0002, 0000) and check there if we find "UL", in
142 // which case we (almost) know it is explicit VR.
143 // WARNING: if it happens to be implicit VR then what we will read
144 // is the length of the group. If this ascii representation of this
145 // length happens to be "UL" then we shall believe it is explicit VR.
146 // FIXME: in order to fix the above warning, we could read the next
147 // element value (or a couple of elements values) in order to make
148 // sure we are not commiting a big mistake.
150 // * the 128 bytes of File Preamble (often padded with zeroes),
151 // * the 4 bytes of "DICM" string,
152 // * the 4 bytes of the first tag (0002, 0000),
153 // i.e. a total of 136 bytes.
155 if(memcmp(entCur, "UL", (size_t)2) == 0) {
156 filetype = ExplicitVR;
157 dbg.Verbose(1, "gdcmHeader::CheckSwap:",
158 "explicit Value Representation");
160 filetype = ImplicitVR;
161 dbg.Verbose(1, "gdcmHeader::CheckSwap:",
162 "not an explicit Value Representation");
167 dbg.Verbose(1, "gdcmHeader::CheckSwap:",
168 "HostByteOrder != NetworkByteOrder");
171 dbg.Verbose(1, "gdcmHeader::CheckSwap:",
172 "HostByteOrder = NetworkByteOrder");
175 // Position the file position indicator at first tag (i.e.
176 // after the file preamble and the "DICM" string).
178 fseek (fp, 132L, SEEK_SET);
180 } // End of TrueDicom
182 // Alas, this is not a DicomV3 file and whatever happens there is no file
183 // preamble. We can reset the file position indicator to where the data
184 // is (i.e. the beginning of the file).
187 // Our next best chance would be to be considering a 'clean' ACR/NEMA file.
188 // By clean we mean that the length of the first tag is written down.
189 // If this is the case and since the length of the first group HAS to be
190 // four (bytes), then determining the proper swap code is straightforward.
193 s = str2num(entCur, guint32);
213 dbg.Verbose(0, "gdcmHeader::CheckSwap:",
214 "ACR/NEMA unfound swap info (time to raise bets)");
217 // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
218 // It is time for despaired wild guesses. So, let's assume this file
219 // happens to be 'dirty' ACR/NEMA, i.e. the length of the group is
220 // not present. Then the only info we have is the net2host one.
228 void gdcmHeader::SwitchSwapToBigEndian(void) {
229 dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian",
230 "Switching to BigEndian mode.");
247 void gdcmHeader::GetPixels(size_t lgrTotale, void* _Pixels) {
249 pixelsOffset = GetPixelOffset();
250 fseek(fp, pixelsOffset, SEEK_SET);
251 fread(_Pixels, 1, lgrTotale, fp);
257 * \ingroup gdcmHeader
258 * \brief Find the value representation of the current tag.
260 * @param sw code swap
261 * @param skippedLength pointeur sur nombre d'octets que l'on a saute qd
262 * la lecture est finie
263 * @param longueurLue pointeur sur longueur (en nombre d'octets)
265 * @return longueur retenue pour le champ
270 // --> C'etait la description de quoi, ca?
273 void gdcmHeader::FindVR( ElValue *ElVal) {
274 if (filetype != ExplicitVR)
280 long PositionOnEntry = ftell(fp);
281 // Warning: we believe this is explicit VR (Value Representation) because
282 // we used a heuristic that found "UL" in the first tag. Alas this
283 // doesn't guarantee that all the tags will be in explicit VR. In some
284 // cases (see e-film filtered files) one finds implicit VR tags mixed
285 // within an explicit VR file. Hence we make sure the present tag
286 // is in explicit VR and try to fix things if it happens not to be
288 bool RealExplicit = true;
290 lgrLue=fread (&VR, (size_t)2,(size_t)1, fp);
294 // Assume we are reading a falsely explicit VR file i.e. we reached
295 // a tag where we expect reading a VR but are in fact we read the
296 // first to bytes of the length. Then we will interogate (through find)
297 // the dicom_vr dictionary with oddities like "\004\0" which crashes
298 // both GCC and VC++ implementations of the STL map. Hence when the
299 // expected VR read happens to be non-ascii characters we consider
300 // we hit falsely explicit VR tag.
302 if ( (!isalpha(VR[0])) && (!isalpha(VR[1])) )
303 RealExplicit = false;
305 // CLEANME searching the dicom_vr at each occurence is expensive.
306 // PostPone this test in an optional integrity check at the end
307 // of parsing or only in debug mode.
308 if ( RealExplicit && !dicom_vr->count(vr) )
309 RealExplicit = false;
311 if ( RealExplicit ) {
312 if ( ElVal->IsVrUnknown() ) {
313 // When not a dictionary entry, we can safely overwrite the vr.
317 if ( ElVal->GetVR() == vr ) {
318 // The vr we just read and the dictionary agree. Nothing to do.
321 // The vr present in the file and the dictionary disagree. We assume
322 // the file writer knew best and use the vr of the file. Since it would
323 // be unwise to overwrite the vr of a dictionary (since it would
324 // compromise it's next user), we need to clone the actual DictEntry
325 // and change the vr for the read one.
326 gdcmDictEntry* NewTag = new gdcmDictEntry(ElVal->GetGroup(),
331 ElVal->SetDictEntry(NewTag);
335 // We thought this was explicit VR, but we end up with an
336 // implicit VR tag. Let's backtrack.
337 dbg.Verbose(1, "gdcmHeader::FindVR:", "Falsely explicit vr file");
338 fseek(fp, PositionOnEntry, SEEK_SET);
339 // When this element is known in the dictionary we shall use, e.g. for
340 // the semantics (see the usage of IsAnInteger), the vr proposed by the
341 // dictionary entry. Still we have to flag the element as implicit since
342 // we know now our assumption on expliciteness is not furfilled.
344 if ( ElVal->IsVrUnknown() )
345 ElVal->SetVR("Implicit");
346 ElVal->SetImplicitVr();
350 * \ingroup gdcmHeader
351 * \brief Determines if the Transfer Syntax was allready encountered
352 * and if it corresponds to a ImplicitVRLittleEndian one.
354 * @return True when ImplicitVRLittleEndian found. False in all other cases.
356 bool gdcmHeader::IsImplicitVRLittleEndianTransferSyntax(void) {
357 ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010);
360 LoadElementValueSafe(Element);
361 string Transfer = Element->GetValue();
362 if ( Transfer == "1.2.840.10008.1.2" )
368 * \ingroup gdcmHeader
369 * \brief Determines if the Transfer Syntax was allready encountered
370 * and if it corresponds to a ExplicitVRLittleEndian one.
372 * @return True when ExplicitVRLittleEndian found. False in all other cases.
374 bool gdcmHeader::IsExplicitVRLittleEndianTransferSyntax(void) {
375 ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010);
378 LoadElementValueSafe(Element);
379 string Transfer = Element->GetValue();
380 if ( Transfer == "1.2.840.10008.1.2.1" )
386 * \ingroup gdcmHeader
387 * \brief Determines if the Transfer Syntax was allready encountered
388 * and if it corresponds to a DeflatedExplicitVRLittleEndian one.
390 * @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
392 bool gdcmHeader::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) {
393 ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010);
396 LoadElementValueSafe(Element);
397 string Transfer = Element->GetValue();
398 if ( Transfer == "1.2.840.10008.1.2.1.99" )
405 * \ingroup gdcmHeader
406 * \brief Determines if the Transfer Syntax was allready encountered
407 * and if it corresponds to a Explicit VR Big Endian one.
409 * @return True when big endian found. False in all other cases.
411 bool gdcmHeader::IsExplicitVRBigEndianTransferSyntax(void) {
412 ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010);
415 LoadElementValueSafe(Element);
416 string Transfer = Element->GetValue();
417 if ( Transfer == "1.2.840.10008.1.2.2" )
424 * \ingroup gdcmHeader
425 * \brief Determines if the Transfer Syntax was allready encountered
426 * and if it corresponds to a JPEGBaseLineProcess1 one.
428 * @return True when JPEGBaseLineProcess1found. False in all other cases.
430 bool gdcmHeader::IsJPEGBaseLineProcess1TransferSyntax(void) {
431 ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010);
434 LoadElementValueSafe(Element);
435 string Transfer = Element->GetValue();
436 if ( Transfer == "1.2.840.10008.1.2.4.50" )
442 * \ingroup gdcmHeader
443 * \brief Determines if the Transfer Syntax was allready encountered
444 * and if it corresponds to a JPEGExtendedProcess2-4 one.
446 * @return True when JPEGExtendedProcess2-4 found. False in all other cases.
448 bool gdcmHeader::IsJPEGExtendedProcess2_4TransferSyntax(void) {
449 ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010);
452 LoadElementValueSafe(Element);
453 string Transfer = Element->GetValue();
454 if ( Transfer == "1.2.840.10008.1.2.4.51" )
461 * \ingroup gdcmHeader
462 * \brief Determines if the Transfer Syntax was allready encountered
463 * and if it corresponds to a JPEGExtendeProcess3-5 one.
465 * @return True when JPEGExtendedProcess3-5 found. False in all other cases.
467 bool gdcmHeader::IsJPEGExtendedProcess3_5TransferSyntax(void) {
468 ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010);
471 LoadElementValueSafe(Element);
472 string Transfer = Element->GetValue();
473 if ( Transfer == "1.2.840.10008.1.2.4.52" )
479 * \ingroup gdcmHeader
480 * \brief Determines if the Transfer Syntax was allready encountered
481 * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one.
483 * @return True when JPEGSpectralSelectionProcess6-8 found. False in all other cases.
485 bool gdcmHeader::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void) {
486 ElValue* Element = PubElVals.GetElementByNumber(0x0002, 0x0010);
489 LoadElementValueSafe(Element);
490 string Transfer = Element->GetValue();
491 if ( Transfer == "1.2.840.10008.1.2.4.53" )
498 // Il y en a encore DIX-SEPT, comme ça.
499 // Il faudrait trouver qq chose + rusé ...
501 // --> probablement TOUS les supprimer (Eric dixit)
505 void gdcmHeader::FixFoundLength(ElValue * ElVal, guint32 FoundLength) {
506 // Heuristic: a final fix.
507 if ( FoundLength == 0xffffffff)
509 ElVal->SetLength(FoundLength);
512 guint32 gdcmHeader::FindLengthOB(void) {
513 // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
516 long PositionOnEntry = ftell(fp);
517 bool FoundSequenceDelimiter = false;
518 guint32 TotalLength = 0;
521 while ( ! FoundSequenceDelimiter) {
524 TotalLength += 4; // We even have to decount the group and element
526 dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
527 "wrong group for an item sequence.");
528 throw Error::FileReadError(fp, "gdcmHeader::FindLengthOB");
531 FoundSequenceDelimiter = true;
532 else if ( n != 0xe000) {
533 dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
534 "wrong element for an item sequence.");
535 throw Error::FileReadError(fp, "gdcmHeader::FindLengthOB");
537 ItemLength = ReadInt32();
538 TotalLength += ItemLength + 4; // We add 4 bytes since we just read
539 // the ItemLength with ReadInt32
540 SkipBytes(ItemLength);
542 fseek(fp, PositionOnEntry, SEEK_SET);
546 void gdcmHeader::FindLength(ElValue * ElVal) {
547 guint16 element = ElVal->GetElement();
548 string vr = ElVal->GetVR();
551 if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) {
553 if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) {
554 // The following reserved two bytes (see PS 3.5-2001, section
555 // 7.1.2 Data element structure with explicit vr p27) must be
556 // skipped before proceeding on reading the length on 4 bytes.
557 fseek(fp, 2L, SEEK_CUR);
558 guint32 length32 = ReadInt32();
559 if ( (vr == "OB") && (length32 == 0xffffffff) ) {
560 ElVal->SetLength(FindLengthOB());
563 FixFoundLength(ElVal, length32);
567 // Length is encoded on 2 bytes.
568 length16 = ReadInt16();
570 // We can tell the current file is encoded in big endian (like
571 // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag
572 // and it's value is the one of the encoding of a big endian file.
573 // In order to deal with such big endian encoded files, we have
574 // (at least) two strategies:
575 // * when we load the "Transfer Syntax" tag with value of big endian
576 // encoding, we raise the proper flags. Then we wait for the end
577 // of the META group (0x0002) among which is "Transfer Syntax",
578 // before switching the swap code to big endian. We have to postpone
579 // the switching of the swap code since the META group is fully encoded
580 // in little endian, and big endian coding only starts at the next
581 // group. The corresponding code can be hard to analyse and adds
582 // many additional unnecessary tests for regular tags.
583 // * the second strategy consists in waiting for trouble, that shall appear
584 // when we find the first group with big endian encoding. This is
585 // easy to detect since the length of a "Group Length" tag (the
586 // ones with zero as element number) has to be of 4 (0x0004). When we
587 // encouter 1024 (0x0400) chances are the encoding changed and we
588 // found a group with big endian encoding.
589 // We shall use this second strategy. In order make sure that we
590 // can interpret the presence of an apparently big endian encoded
591 // length of a "Group Length" without committing a big mistake, we
592 // add an additional check: we look in the allready parsed elements
593 // for the presence of a "Transfer Syntax" whose value has to be "big
594 // endian encoding". When this is the case, chances are we got our
595 // hands on a big endian encoded file: we switch the swap code to
596 // big endian and proceed...
597 if ( (element == 0x000) && (length16 == 0x0400) ) {
598 if ( ! IsExplicitVRBigEndianTransferSyntax() )
599 throw Error::FileReadError(fp, "gdcmHeader::FindLength");
601 SwitchSwapToBigEndian();
602 // Restore the unproperly loaded values i.e. the group, the element
603 // and the dictionary entry depending on them.
604 guint16 CorrectGroup = SwapShort(ElVal->GetGroup());
605 guint16 CorrectElem = SwapShort(ElVal->GetElement());
606 gdcmDictEntry * NewTag = IsInDicts(CorrectGroup, CorrectElem);
608 // This correct tag is not in the dictionary. Create a new one.
609 NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem);
611 // FIXME this can create a memory leaks on the old entry that be
612 // left unreferenced.
613 ElVal->SetDictEntry(NewTag);
616 // Heuristic: well some files are really ill-formed.
617 if ( length16 == 0xffff) {
619 dbg.Verbose(0, "gdcmHeader::FindLength",
620 "Erroneous element length fixed.");
622 FixFoundLength(ElVal, (guint32)length16);
626 // Either implicit VR or a non DICOM conformal (see not below) explicit
627 // VR that ommited the VR of (at least) this element. Farts happen.
628 // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25
629 // on Data elements "Implicit and Explicit VR Data Elements shall
630 // not coexist in a Data Set and Data Sets nested within it".]
631 // Length is on 4 bytes.
632 FixFoundLength(ElVal, ReadInt32());
636 * \ingroup gdcmHeader
637 * \brief Swaps back the bytes of 4-byte long integer accordingly to
640 * @return The suggested integer.
642 guint32 gdcmHeader::SwapLong(guint32 a) {
643 // FIXME: il pourrait y avoir un pb pour les entiers negatifs ...
648 a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
649 ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
653 a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
657 a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
660 dbg.Error(" gdcmHeader::SwapLong : unset swap code");
667 * \ingroup gdcmHeader
668 * \brief Swaps the bytes so they agree with the processor order
669 * @return The properly swaped 16 bits integer.
671 guint16 gdcmHeader::SwapShort(guint16 a) {
672 if ( (sw==4321) || (sw==2143) )
673 a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
677 void gdcmHeader::SkipBytes(guint32 NBytes) {
678 //FIXME don't dump the returned value
679 (void)fseek(fp, (long)NBytes, SEEK_CUR);
682 void gdcmHeader::SkipElementValue(ElValue * ElVal) {
683 SkipBytes(ElVal->GetLength());
686 void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
689 if ((guint32)NewSize >= (guint32)0xffffffff) {
690 MaxSizeLoadElementValue = 0xffffffff;
693 MaxSizeLoadElementValue = NewSize;
697 * \ingroup gdcmHeader
698 * \brief Loads the element if it's size is not to big.
699 * @param ElVal Element whose value shall be loaded.
700 * @param MaxSize Size treshold above which the element value is not
701 * loaded in memory. The element value is allways loaded
702 * when MaxSize is equal to UINT32_MAX.
705 void gdcmHeader::LoadElementValue(ElValue * ElVal) {
707 guint16 group = ElVal->GetGroup();
708 guint16 elem = ElVal->GetElement();
709 string vr = ElVal->GetVR();
710 guint32 length = ElVal->GetLength();
711 bool SkipLoad = false;
713 fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
715 // Sequences not treated yet !
717 // Ne faudrait-il pas au contraire trouver immediatement
718 // une maniere 'propre' de traiter les sequences (vr = SQ)
719 // car commencer par les ignorer risque de conduire a qq chose
720 // qui pourrait ne pas etre generalisable
725 // Heuristic : a sequence "contains" a set of tags (called items). It looks
726 // like the last tag of a sequence (the one that terminates the sequence)
727 // has a group of 0xfffe (with a dummy length).
728 if( group == 0xfffe )
731 // The group length doesn't represent data to be loaded in memory, since
732 // each element of the group shall be loaded individualy.
734 //SkipLoad = true; // modif sauvage JPR
735 // On charge la longueur du groupe
736 // quand l'element 0x0000 est présent !
739 // FIXME the following skip is not necessary
740 SkipElementValue(ElVal);
742 ElVal->SetValue("gdcm::Skipped");
746 // When the length is zero things are easy:
752 // Values bigger than specified are not loaded.
754 // En fait, c'est les elements dont la longueur est superieure
755 // a celle fixee qui ne sont pas charges
757 if (length > MaxSizeLoadElementValue) {
759 s << "gdcm::NotLoaded.";
760 s << " Address:" << (long)ElVal->GetOffset();
761 s << " Length:" << ElVal->GetLength();
762 //mesg += " Length:" + ElVal->GetLength();
763 ElVal->SetValue(s.str());
767 // When an integer is expected, read and convert the following two or
768 // four bytes properly i.e. as an integer as opposed to a string.
769 if ( IsAnInteger(ElVal) ) {
772 NewInt = ReadInt16();
773 } else if( length == 4 ) {
774 NewInt = ReadInt32();
776 dbg.Error(true, "LoadElementValue: Inconsistency when reading Int.");
778 //FIXME: make the following an util fonction
781 ElVal->SetValue(s.str());
785 // FIXME The exact size should be length if we move to strings or whatever
788 // QUESTION : y a-t-il une raison pour ne pas utiliser g_malloc ici ?
791 char* NewValue = (char*)malloc(length+1);
793 dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue");
798 item_read = fread(NewValue, (size_t)length, (size_t)1, fp);
799 if ( item_read != 1 ) {
801 Error::FileReadError(fp, "gdcmHeader::LoadElementValue");
802 ElVal->SetValue("gdcm::UnRead");
805 ElVal->SetValue(NewValue);
809 * \ingroup gdcmHeader
810 * \brief Loads the element while preserving the current
811 * underlying file position indicator as opposed to
812 * to LoadElementValue that modifies it.
813 * @param ElVal Element whose value shall be loaded.
816 void gdcmHeader::LoadElementValueSafe(ElValue * ElVal) {
817 long PositionOnEntry = ftell(fp);
818 LoadElementValue(ElVal);
819 fseek(fp, PositionOnEntry, SEEK_SET);
823 guint16 gdcmHeader::ReadInt16(void) {
826 item_read = fread (&g, (size_t)2,(size_t)1, fp);
827 if ( item_read != 1 )
828 throw Error::FileReadError(fp, "gdcmHeader::ReadInt16");
833 guint32 gdcmHeader::ReadInt32(void) {
836 item_read = fread (&g, (size_t)4,(size_t)1, fp);
837 if ( item_read != 1 )
838 throw Error::FileReadError(fp, "gdcmHeader::ReadInt32");
844 * \ingroup gdcmHeader
845 * \brief Read the next tag without loading it's value
846 * @return On succes the newly created ElValue, NULL on failure.
849 ElValue * gdcmHeader::ReadNextElement(void) {
858 catch ( Error::FileReadError ) {
859 // We reached the EOF (or an error occured) and header parsing
860 // has to be considered as finished.
864 // Find out if the tag we encountered is in the dictionaries:
865 gdcmDictEntry * NewTag = IsInDicts(g, n);
867 NewTag = new gdcmDictEntry(g, n);
869 NewElVal = new ElValue(NewTag);
871 dbg.Verbose(1, "ReadNextElement: failed to allocate ElValue");
876 try { FindLength(NewElVal); }
877 catch ( Error::FileReadError ) { // Call it quits
880 NewElVal->SetOffset(ftell(fp));
884 bool gdcmHeader::IsAnInteger(ElValue * ElVal) {
885 guint16 group = ElVal->GetGroup();
886 guint16 element = ElVal->GetElement();
887 string vr = ElVal->GetVR();
888 guint32 length = ElVal->GetLength();
890 // When we have some semantics on the element we just read, and if we
891 // a priori know we are dealing with an integer, then we shall be
892 // able to swap it's element value properly.
893 if ( element == 0 ) { // This is the group length of the group
897 dbg.Error("gdcmHeader::IsAnInteger",
898 "Erroneous Group Length element length.");
901 if ( group % 2 != 0 )
902 // We only have some semantics on documented elements, which are
906 if ( (length != 4) && ( length != 2) )
907 // Swapping only make sense on integers which are 2 or 4 bytes long.
910 if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
913 if ( (group == 0x0028) && (element == 0x0005) )
914 // This tag is retained from ACR/NEMA
915 // CHECKME Why should "Image Dimensions" be a single integer ?
917 // "Image Dimensions", c'est en fait le 'nombre de dimensions'
918 // de l'objet ACR-NEMA stocké
924 // DICOM V3 ne retient pas cette information
925 // Par defaut, tout est 'Image',
926 // C'est a l'utilisateur d'explorer l'ensemble des entetes
927 // pour savoir à quoi il a a faire
929 // Le Dicom Multiframe peut etre utilise pour stocker,
930 // dans un seul fichier, une serie temporelle (cardio vasculaire GE, p.ex)
931 // ou un volume (medecine Nucleaire, p.ex)
935 if ( (group == 0x0028) && (element == 0x0200) )
936 // This tag is retained from ACR/NEMA
943 * \ingroup gdcmHeader
944 * \brief Recover the offset (from the beginning of the file) of the pixels.
946 size_t gdcmHeader::GetPixelOffset(void) {
947 // If this file complies with the norm we should encounter the
948 // "Image Location" tag (0x0028, 0x0200). This tag contains the
949 // the group that contains the pixel data (hence the "Pixel Data"
950 // is found by indirection through the "Image Location").
951 // Inside the group pointed by "Image Location" the searched element
952 // is conventionally the element 0x0010 (when the norm is respected).
953 // When the "Image Location" is absent we default to group 0x7fe0.
956 string ImageLocation = GetPubElValByName("Image Location");
957 if ( ImageLocation == "gdcm::Unfound" ) {
960 grPixel = (guint16) atoi( ImageLocation.c_str() );
962 if (grPixel != 0x7fe0)
963 // FIXME is this still necessary ?
964 // Now, this looks like an old dirty fix for Philips imager
968 ElValue* PixelElement = PubElVals.GetElementByNumber(grPixel, numPixel);
970 return PixelElement->GetOffset();
975 gdcmDictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) {
977 // Y a-t-il une raison de lui passer des guint32
978 // alors que group et element sont des guint16?
980 gdcmDictEntry * found = (gdcmDictEntry*)0;
981 if (!RefPubDict && !RefShaDict) {
982 //FIXME build a default dictionary !
983 printf("FIXME in gdcmHeader::IsInDicts\n");
986 found = RefPubDict->GetTag(group, element);
991 found = RefShaDict->GetTag(group, element);
998 list<string> * gdcmHeader::GetPubTagNames(void) {
999 list<string> * Result = new list<string>;
1000 TagHT entries = RefPubDict->GetEntries();
1002 for (TagHT::iterator tag = entries.begin(); tag != entries.end(); ++tag){
1003 Result->push_back( tag->second->GetName() );
1008 map<string, list<string> > * gdcmHeader::GetPubTagNamesByCategory(void) {
1009 map<string, list<string> > * Result = new map<string, list<string> >;
1010 TagHT entries = RefPubDict->GetEntries();
1012 for (TagHT::iterator tag = entries.begin(); tag != entries.end(); ++tag){
1013 (*Result)[tag->second->GetFourth()].push_back(tag->second->GetName());
1018 string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
1019 return PubElVals.GetElValueByNumber(group, element);
1022 string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) {
1023 ElValue* elem = PubElVals.GetElementByNumber(group, element);
1025 return "gdcm::Unfound";
1026 return elem->GetVR();
1029 string gdcmHeader::GetPubElValByName(string TagName) {
1030 return PubElVals.GetElValueByName(TagName);
1033 string gdcmHeader::GetPubElValRepByName(string TagName) {
1034 ElValue* elem = PubElVals.GetElementByName(TagName);
1036 return "gdcm::Unfound";
1037 return elem->GetVR();
1040 string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) {
1041 return ShaElVals.GetElValueByNumber(group, element);
1044 string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) {
1045 ElValue* elem = ShaElVals.GetElementByNumber(group, element);
1047 return "gdcm::Unfound";
1048 return elem->GetVR();
1051 string gdcmHeader::GetShaElValByName(string TagName) {
1052 return ShaElVals.GetElValueByName(TagName);
1055 string gdcmHeader::GetShaElValRepByName(string TagName) {
1056 ElValue* elem = ShaElVals.GetElementByName(TagName);
1058 return "gdcm::Unfound";
1059 return elem->GetVR();
1063 string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) {
1064 string pub = GetPubElValByNumber(group, element);
1067 return GetShaElValByNumber(group, element);
1070 string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) {
1071 string pub = GetPubElValRepByNumber(group, element);
1074 return GetShaElValRepByNumber(group, element);
1077 string gdcmHeader::GetElValByName(string TagName) {
1078 string pub = GetPubElValByName(TagName);
1081 return GetShaElValByName(TagName);
1084 string gdcmHeader::GetElValRepByName(string TagName) {
1085 string pub = GetPubElValRepByName(TagName);
1088 return GetShaElValRepByName(TagName);
1092 * \ingroup gdcmHeader
1093 * \brief Modifie la valeur d'un ElValue déja existant
1094 * \ dans le PubElVals du gdcmHeader,
1095 * \ accédé par ses numero de groupe et d'element.
1097 int gdcmHeader::SetPubElValByNumber(string content, guint16 group, guint16 element) {
1098 //TagKey key = gdcmDictEntry::TranslateToKey(group, element);
1099 //PubElVals.tagHt[key]->SetValue(content);
1101 return ( PubElVals.SetElValueByNumber (content, group, element) );
1106 * \ingroup gdcmHeader
1107 * \brief Modifie la valeur d'un ElValue déja existant
1108 * \ dans le PubElVals du gdcmHeader,
1109 * \ accédé par son nom
1111 int gdcmHeader::SetPubElValByName(string content, string TagName) {
1112 //TagKey key = gdcmDictEntry::TranslateToKey(group, element);
1113 //PubElVals.tagHt[key]->SetValue(content);
1115 return ( PubElVals.SetElValueByName (content, TagName) );
1120 * \ingroup gdcmHeader
1121 * \brief Modifie la valeur d'un ElValue déja existant
1122 * \ dans le ShaElVals du gdcmHeader,
1123 * \ accédé par ses numero de groupe et d'element.
1125 int gdcmHeader::SetShaElValByNumber(string content, guint16 group, guint16 element) {
1127 return ( ShaElVals.SetElValueByNumber (content, group, element) );
1132 * \ingroup gdcmHeader
1133 * \brief Modifie la valeur d'un ElValue déja existant
1134 * \ dans le ShaElVals du gdcmHeader,
1135 * \ accédé par son nom
1137 int gdcmHeader::SetShaElValByName(string content, string TagName) {
1139 return ( ShaElVals.SetElValueByName (content, TagName) );
1142 * \ingroup gdcmHeader
1143 * \brief Parses the header of the file but does NOT load element values.
1145 void gdcmHeader::ParseHeader(void) {
1146 ElValue * newElValue = (ElValue *)0;
1150 while ( (newElValue = ReadNextElement()) ) {
1151 SkipElementValue(newElValue);
1152 PubElVals.Add(newElValue);
1157 * \ingroup gdcmHeader
1158 * \brief Loads the element values of all the elements present in the
1159 * public tag based hash table.
1161 void gdcmHeader::LoadElements(void) {
1165 TagElValueHT ht = PubElVals.GetTagHt();
1167 for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
1168 LoadElementValue(tag->second);
1172 void gdcmHeader::PrintPubElVal(ostream & os) {
1173 PubElVals.Print(os);
1176 void gdcmHeader::PrintPubDict(ostream & os) {
1177 RefPubDict->Print(os);