9 #include <netinet/in.h>
11 #include <cctype> // for isalpha
16 #define HEADER_LENGTH_TO_READ 256 // on ne lit plus que le debut
21 struct FileReadError {
22 FileReadError(FILE* fp, const char* Mesg) {
24 dbg.Verbose(1, "EOF encountered :", Mesg);
26 dbg.Verbose(1, "Error on reading :", Mesg);
31 //FIXME: this looks dirty to me...
32 #define str2num(str, typeNum) *((typeNum *)(str))
33 // str est un pointeur dans un tableau de caractères, qui doit contenir,
34 // à cet endroit la, la représentation binaire d'un entier (16 ou 32 bits)
35 // je veux récupérer ça ... dans un entier.
36 // s'il y a une autre solution, évitant des cast et les indirections,
39 VRHT * gdcmHeader::dicom_vr = (VRHT*)0;
40 gdcmDictSet* gdcmHeader::Dicts = new gdcmDictSet();
42 void gdcmHeader::Initialise(void) {
43 if (!gdcmHeader::dicom_vr)
45 RefPubDict = gdcmHeader::Dicts->GetDefaultPublicDict();
46 RefShaDict = (gdcmDict*)0;
49 gdcmHeader::gdcmHeader (const char* InFilename) {
50 SetMaxSizeLoadElementValue(1024);
51 filename = InFilename;
53 fp=fopen(InFilename,"rw");
54 dbg.Error(!fp, "gdcmHeader::gdcmHeader cannot open file", InFilename);
58 gdcmHeader::~gdcmHeader (void) {
63 void gdcmHeader::InitVRDict (void) {
65 dbg.Verbose(0, "gdcmHeader::InitVRDict:", "VR dictionary allready set");
69 (*vr)["AE"] = "Application Entity"; // At most 16 bytes
70 (*vr)["AS"] = "Age String"; // Exactly 4 bytes
71 (*vr)["AT"] = "Attribute Tag"; // 2 16-bit unsigned short integers
72 (*vr)["CS"] = "Code String"; // At most 16 bytes
73 (*vr)["DA"] = "Date"; // Exactly 8 bytes
74 (*vr)["DS"] = "Decimal String"; // At most 16 bytes
75 (*vr)["DT"] = "Date Time"; // At most 26 bytes
76 (*vr)["FL"] = "Floating Point Single"; // 32-bit IEEE 754:1985 float
77 (*vr)["FD"] = "Floating Point Double"; // 64-bit IEEE 754:1985 double
78 (*vr)["IS"] = "Integer String"; // At most 12 bytes
79 (*vr)["LO"] = "Long String"; // At most 64 chars
80 (*vr)["LT"] = "Long Text"; // At most 10240 chars
81 (*vr)["OB"] = "Other Byte String"; // String of bytes (vr independant)
82 (*vr)["OW"] = "Other Word String"; // String of 16-bit words (vr dep)
83 (*vr)["PN"] = "Person Name"; // At most 64 chars
84 (*vr)["SH"] = "Short String"; // At most 16 chars
85 (*vr)["SL"] = "Signed Long"; // Exactly 4 bytes
86 (*vr)["SQ"] = "Sequence of Items"; // Not Applicable
87 (*vr)["SS"] = "Signed Short"; // Exactly 2 bytes
88 (*vr)["ST"] = "Short Text"; // At most 1024 chars
89 (*vr)["TM"] = "Time"; // At most 16 bytes
90 (*vr)["UI"] = "Unique Identifier"; // At most 64 bytes
91 (*vr)["UL"] = "Unsigned Long "; // Exactly 4 bytes
92 (*vr)["UN"] = "Unknown"; // Any length of bytes
93 (*vr)["US"] = "Unsigned Short "; // Exactly 2 bytes
94 (*vr)["UT"] = "Unlimited Text"; // At most 2^32 -1 chars
100 * \brief Discover what the swap code is (among little endian, big endian,
101 * bad little endian, bad big endian).
104 void gdcmHeader::CheckSwap()
106 // The only guaranted way of finding the swap code is to find a
107 // group tag since we know it's length has to be of four bytes i.e.
108 // 0x00000004. Finding the swap code in then straigthforward. Trouble
109 // occurs when we can't find such group...
111 guint32 x=4; // x : pour ntohs
112 bool net2host; // true when HostByteOrder is the same as NetworkByteOrder
116 char deb[HEADER_LENGTH_TO_READ];
118 // First, compare HostByteOrder and NetworkByteOrder in order to
119 // determine if we shall need to swap bytes (i.e. the Endian type).
125 // The easiest case is the one of a DICOM header, since it possesses a
126 // file preamble where it suffice to look for the sting "DICM".
127 lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp);
130 if(memcmp(entCur, "DICM", (size_t)4) == 0) {
131 filetype = TrueDicom;
132 dbg.Verbose(1, "gdcmHeader::CheckSwap:", "looks like DICOM Version3");
135 dbg.Verbose(1, "gdcmHeader::CheckSwap:", "not a DICOM Version3 file");
138 if(filetype == TrueDicom) {
139 // Next, determine the value representation (VR). Let's skip to the
140 // first element (0002, 0000) and check there if we find "UL", in
141 // which case we (almost) know it is explicit VR.
142 // WARNING: if it happens to be implicit VR then what we will read
143 // is the length of the group. If this ascii representation of this
144 // length happens to be "UL" then we shall believe it is explicit VR.
145 // FIXME: in order to fix the above warning, we could read the next
146 // element value (or a couple of elements values) in order to make
147 // sure we are not commiting a big mistake.
149 // * the 128 bytes of File Preamble (often padded with zeroes),
150 // * the 4 bytes of "DICM" string,
151 // * the 4 bytes of the first tag (0002, 0000),
152 // i.e. a total of 136 bytes.
154 if(memcmp(entCur, "UL", (size_t)2) == 0) {
155 filetype = ExplicitVR;
156 dbg.Verbose(1, "gdcmHeader::CheckSwap:",
157 "explicit Value Representation");
159 filetype = ImplicitVR;
160 dbg.Verbose(1, "gdcmHeader::CheckSwap:",
161 "not an explicit Value Representation");
166 dbg.Verbose(1, "gdcmHeader::CheckSwap:",
167 "HostByteOrder != NetworkByteOrder");
170 dbg.Verbose(1, "gdcmHeader::CheckSwap:",
171 "HostByteOrder = NetworkByteOrder");
174 // Position the file position indicator at first tag (i.e.
175 // after the file preamble and the "DICM" string).
177 fseek (fp, 132L, SEEK_SET);
179 } // End of TrueDicom
181 // Alas, this is not a DicomV3 file and whatever happens there is no file
182 // preamble. We can reset the file position indicator to where the data
183 // is (i.e. the beginning of the file).
186 // Our next best chance would be to be considering a 'clean' ACR/NEMA file.
187 // By clean we mean that the length of the first tag is written down.
188 // If this is the case and since the length of the first group HAS to be
189 // four (bytes), then determining the proper swap code is straightforward.
192 s = str2num(entCur, guint32);
212 dbg.Verbose(0, "gdcmHeader::CheckSwap:",
213 "ACR/NEMA unfound swap info (time to raise bets)");
216 // We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
217 // It is time for despaired wild guesses. So, let's assume this file
218 // happens to be 'dirty' ACR/NEMA, i.e. the length of the group is
219 // not present. Then the only info we have is the net2host one.
227 void gdcmHeader::SwitchSwapToBigEndian(void) {
228 dbg.Verbose(1, "gdcmHeader::SwitchSwapToBigEndian",
229 "Switching to BigEndian mode.");
246 void gdcmHeader::GetPixels(size_t lgrTotale, void* _Pixels) {
248 pixelsOffset = GetPixelOffset();
249 printf("pixelsOffset %d\n",pixelsOffset);
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 ...
503 void gdcmHeader::FixFoundLength(ElValue * ElVal, guint32 FoundLength) {
504 // Heuristic: a final fix.
505 if ( FoundLength == 0xffffffff)
507 ElVal->SetLength(FoundLength);
510 guint32 gdcmHeader::FindLengthOB(void) {
511 // See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
514 long PositionOnEntry = ftell(fp);
515 bool FoundSequenceDelimiter = false;
516 guint32 TotalLength = 0;
519 while ( ! FoundSequenceDelimiter) {
522 TotalLength += 4; // We even have to decount the group and element
524 dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
525 "wrong group for an item sequence.");
526 throw Error::FileReadError(fp, "gdcmHeader::FindLengthOB");
529 FoundSequenceDelimiter = true;
530 else if ( n != 0xe000) {
531 dbg.Verbose(1, "gdcmHeader::FindLengthOB: ",
532 "wrong element for an item sequence.");
533 throw Error::FileReadError(fp, "gdcmHeader::FindLengthOB");
535 ItemLength = ReadInt32();
536 TotalLength += ItemLength + 4; // We add 4 bytes since we just read
537 // the ItemLength with ReadInt32
538 SkipBytes(ItemLength);
540 fseek(fp, PositionOnEntry, SEEK_SET);
544 void gdcmHeader::FindLength(ElValue * ElVal) {
545 guint16 element = ElVal->GetElement();
546 string vr = ElVal->GetVR();
549 if ( (filetype == ExplicitVR) && ! ElVal->IsImplicitVr() ) {
551 if ( (vr=="OB") || (vr=="OW") || (vr=="SQ") || (vr=="UN") ) {
552 // The following reserved two bytes (see PS 3.5-2001, section
553 // 7.1.2 Data element structure with explicit vr p27) must be
554 // skipped before proceeding on reading the length on 4 bytes.
555 fseek(fp, 2L, SEEK_CUR);
556 guint32 length32 = ReadInt32();
557 if ( (vr == "OB") && (length32 == 0xffffffff) ) {
558 ElVal->SetLength(FindLengthOB());
561 FixFoundLength(ElVal, length32);
565 // Length is encoded on 2 bytes.
566 length16 = ReadInt16();
568 // We can tell the current file is encoded in big endian (like
569 // Data/US-RGB-8-epicard) when we find the "Transfer Syntax" tag
570 // and it's value is the one of the encoding of a big endian file.
571 // In order to deal with such big endian encoded files, we have
572 // (at least) two strategies:
573 // * when we load the "Transfer Syntax" tag with value of big endian
574 // encoding, we raise the proper flags. Then we wait for the end
575 // of the META group (0x0002) among which is "Transfer Syntax",
576 // before switching the swap code to big endian. We have to postpone
577 // the switching of the swap code since the META group is fully encoded
578 // in little endian, and big endian coding only starts at the next
579 // group. The corresponding code can be hard to analyse and adds
580 // many additional unnecessary tests for regular tags.
581 // * the second strategy consist in waiting for trouble, that shall appear
582 // when we find the first group with big endian encoding. This is
583 // easy to detect since the length of a "Group Length" tag (the
584 // ones with zero as element number) has to be of 4 (0x0004). When we
585 // encouter 1024 (0x0400) chances are the encoding changed and we
586 // found a group with big endian encoding.
587 // We shall use this second strategy. In order make sure that we
588 // can interpret the presence of an apparently big endian encoded
589 // length of a "Group Length" without committing a big mistake, we
590 // add an additional check: we look in the allready parsed elements
591 // for the presence of a "Transfer Syntax" whose value has to be "big
592 // endian encoding". When this is the case, chances are we got our
593 // hands on a big endian encoded file: we switch the swap code to
594 // big endian and proceed...
595 if ( (element == 0x000) && (length16 == 0x0400) ) {
596 if ( ! IsExplicitVRBigEndianTransferSyntax() )
597 throw Error::FileReadError(fp, "gdcmHeader::FindLength");
599 SwitchSwapToBigEndian();
600 // Restore the unproperly loaded values i.e. the group, the element
601 // and the dictionary entry depending on them.
602 guint16 CorrectGroup = SwapShort(ElVal->GetGroup());
603 guint16 CorrectElem = SwapShort(ElVal->GetElement());
604 gdcmDictEntry * NewTag = IsInDicts(CorrectGroup, CorrectElem);
606 // This correct tag is not in the dictionary. Create a new one.
607 NewTag = new gdcmDictEntry(CorrectGroup, CorrectElem);
609 // FIXME this can create a memory leaks on the old entry that be
610 // left unreferenced.
611 ElVal->SetDictEntry(NewTag);
614 // Heuristic: well some files are really ill-formed.
615 if ( length16 == 0xffff) {
617 dbg.Verbose(0, "gdcmHeader::FindLength",
618 "Erroneous element length fixed.");
620 FixFoundLength(ElVal, (guint32)length16);
624 // Either implicit VR or a non DICOM conformal (see not below) explicit
625 // VR that ommited the VR of (at least) this element. Farts happen.
626 // [Note: according to the part 5, PS 3.5-2001, section 7.1 p25
627 // on Data elements "Implicit and Explicit VR Data Elements shall
628 // not coexist in a Data Set and Data Sets nested within it".]
629 // Length is on 4 bytes.
630 FixFoundLength(ElVal, ReadInt32());
634 * \ingroup gdcmHeader
635 * \brief Swaps back the bytes of 4-byte long integer accordingly to
638 * @return The suggested integer.
640 guint32 gdcmHeader::SwapLong(guint32 a) {
641 // FIXME: il pourrait y avoir un pb pour les entiers negatifs ...
646 a=( ((a<<24) & 0xff000000) | ((a<<8) & 0x00ff0000) |
647 ((a>>8) & 0x0000ff00) | ((a>>24) & 0x000000ff) );
651 a=( ((a<<16) & 0xffff0000) | ((a>>16) & 0x0000ffff) );
655 a=( ((a<<8) & 0xff00ff00) | ((a>>8) & 0x00ff00ff) );
658 dbg.Error(" gdcmHeader::SwapLong : unset swap code");
665 * \ingroup gdcmHeader
666 * \brief Swaps the bytes so they agree with the processor order
667 * @return The properly swaped 16 bits integer.
669 guint16 gdcmHeader::SwapShort(guint16 a) {
670 if ( (sw==4321) || (sw==2143) )
671 a =(((a<<8) & 0x0ff00) | ((a>>8)&0x00ff));
675 void gdcmHeader::SkipBytes(guint32 NBytes) {
676 //FIXME don't dump the returned value
677 (void)fseek(fp, (long)NBytes, SEEK_CUR);
680 void gdcmHeader::SkipElementValue(ElValue * ElVal) {
681 SkipBytes(ElVal->GetLength());
684 void gdcmHeader::SetMaxSizeLoadElementValue(long NewSize) {
687 if ((guint32)NewSize >= (guint32)0xffffffff) {
688 MaxSizeLoadElementValue = 0xffffffff;
691 MaxSizeLoadElementValue = NewSize;
695 * \ingroup gdcmHeader
696 * \brief Loads the element if it's size is not to big.
697 * @param ElVal Element whose value shall be loaded.
698 * @param MaxSize Size treshold above which the element value is not
699 * loaded in memory. The element value is allways loaded
700 * when MaxSize is equal to UINT32_MAX.
703 void gdcmHeader::LoadElementValue(ElValue * ElVal) {
705 guint16 group = ElVal->GetGroup();
706 guint16 elem = ElVal->GetElement();
707 string vr = ElVal->GetVR();
708 guint32 length = ElVal->GetLength();
709 bool SkipLoad = false;
711 fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
713 // Sequences not treated yet !
715 // Ne faudrait-il pas au contraire trouver immediatement
716 // une maniere 'propre' de traiter les sequences (vr = SQ)
717 // car commencer par les ignorer risque de conduire a qq chose
718 // qui pourrait ne pas etre generalisable
723 // Heuristic : a sequence "contains" a set of tags (called items). It looks
724 // like the last tag of a sequence (the one that terminates the sequence)
725 // has a group of 0xfffe (with a dummy length).
726 if( group == 0xfffe )
729 // The group length doesn't represent data to be loaded in memory, since
730 // each element of the group shall be loaded individualy.
735 // FIXME the following skip is not necessary
736 SkipElementValue(ElVal);
738 ElVal->SetValue("gdcm::Skipped");
742 // When the length is zero things are easy:
748 // Values bigger than specified are not loaded.
750 // En fait, c'est les elements dont la longueur est superieure
751 // a celle fixee qui ne sont pas charges
753 if (length > MaxSizeLoadElementValue) {
755 s << "gdcm::NotLoaded.";
756 s << " Address:" << (long)ElVal->GetOffset();
757 s << " Length:" << ElVal->GetLength();
758 //mesg += " Length:" + ElVal->GetLength();
759 ElVal->SetValue(s.str());
763 // When an integer is expected, read and convert the following two or
764 // four bytes properly i.e. as an integer as opposed to a string.
765 if ( IsAnInteger(ElVal) ) {
768 NewInt = ReadInt16();
769 } else if( length == 4 ) {
770 NewInt = ReadInt32();
772 dbg.Error(true, "LoadElementValue: Inconsistency when reading Int.");
774 //FIXME: make the following an util fonction
777 ElVal->SetValue(s.str());
781 // FIXME The exact size should be length if we move to strings or whatever
784 // QUESTION : y a-t-il une raison pour ne pas utiliser g_malloc ici ?
787 char* NewValue = (char*)malloc(length+1);
789 dbg.Verbose(1, "LoadElementValue: Failed to allocate NewValue");
794 item_read = fread(NewValue, (size_t)length, (size_t)1, fp);
795 if ( item_read != 1 ) {
797 Error::FileReadError(fp, "gdcmHeader::LoadElementValue");
798 ElVal->SetValue("gdcm::UnRead");
801 ElVal->SetValue(NewValue);
805 * \ingroup gdcmHeader
806 * \brief Loads the element while preserving the current
807 * underlying file position indicator as opposed to
808 * to LoadElementValue that modifies it.
809 * @param ElVal Element whose value shall be loaded.
812 void gdcmHeader::LoadElementValueSafe(ElValue * ElVal) {
813 long PositionOnEntry = ftell(fp);
814 LoadElementValue(ElVal);
815 fseek(fp, PositionOnEntry, SEEK_SET);
819 guint16 gdcmHeader::ReadInt16(void) {
822 item_read = fread (&g, (size_t)2,(size_t)1, fp);
823 if ( item_read != 1 )
824 throw Error::FileReadError(fp, "gdcmHeader::ReadInt16");
829 guint32 gdcmHeader::ReadInt32(void) {
832 item_read = fread (&g, (size_t)4,(size_t)1, fp);
833 if ( item_read != 1 )
834 throw Error::FileReadError(fp, "gdcmHeader::ReadInt32");
840 * \ingroup gdcmHeader
841 * \brief Read the next tag without loading it's value
842 * @return On succes the newly created ElValue, NULL on failure.
845 ElValue * gdcmHeader::ReadNextElement(void) {
854 catch ( Error::FileReadError ) {
855 // We reached the EOF (or an error occured) and header parsing
856 // has to be considered as finished.
860 // Find out if the tag we encountered is in the dictionaries:
861 gdcmDictEntry * NewTag = IsInDicts(g, n);
863 NewTag = new gdcmDictEntry(g, n);
865 NewElVal = new ElValue(NewTag);
867 dbg.Verbose(1, "ReadNextElement: failed to allocate ElValue");
872 try { FindLength(NewElVal); }
873 catch ( Error::FileReadError ) { // Call it quits
876 NewElVal->SetOffset(ftell(fp));
880 bool gdcmHeader::IsAnInteger(ElValue * ElVal) {
881 guint16 group = ElVal->GetGroup();
882 guint16 element = ElVal->GetElement();
883 string vr = ElVal->GetVR();
884 guint32 length = ElVal->GetLength();
886 // When we have some semantics on the element we just read, and if we
887 // a priori know we are dealing with an integer, then we shall be
888 // able to swap it's element value properly.
889 if ( element == 0 ) { // This is the group length of the group
893 dbg.Error("gdcmHeader::IsAnInteger",
894 "Erroneous Group Length element length.");
897 if ( group % 2 != 0 )
898 // We only have some semantics on documented elements, which are
902 if ( (length != 4) && ( length != 2) )
903 // Swapping only make sense on integers which are 2 or 4 bytes long.
906 if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
909 if ( (group == 0x0028) && (element == 0x0005) )
910 // This tag is retained from ACR/NEMA
911 // CHECKME Why should "Image Dimensions" be a single integer ?
913 // "Image Dimensions", c'est en fait le 'nombre de dimensions'
914 // de l'objet ACR-NEMA stocké
920 // DICOM V3 ne retient pas cette information
921 // Par defaut, tout est 'Image',
922 // C'est a l'utilisateur d'explorer l'ensemble des entetes
923 // pour savoir à quoi il a a faire
925 // Le Dicom Multiframe peut etre utilise pour stocker,
926 // dans un seul fichier, une serie temporelle (cardio vasculaire GE, p.ex)
927 // ou un volume (medecine Nucleaire, p.ex)
931 if ( (group == 0x0028) && (element == 0x0200) )
932 // This tag is retained from ACR/NEMA
939 * \ingroup gdcmHeader
940 * \brief Recover the offset (from the beginning of the file) of the pixels.
942 size_t gdcmHeader::GetPixelOffset(void) {
943 // If this file complies with the norm we should encounter the
944 // "Image Location" tag (0x0028, 0x0200). This tag contains the
945 // the group that contains the pixel data (hence the "Pixel Data"
946 // is found by indirection through the "Image Location").
947 // Inside the group pointed by "Image Location" the searched element
948 // is conventionally the element 0x0010 (when the norm is respected).
949 // When the "Image Location" is absent we default to group 0x7fe0.
952 string ImageLocation = GetPubElValByName("Image Location");
953 if ( ImageLocation == "gdcm::Unfound" ) {
956 grPixel = (guint16) atoi( ImageLocation.c_str() );
958 if (grPixel != 0x7fe0)
959 // FIXME is this still necessary ?
960 // Now, this looks like an old dirty fix for Philips imager
964 ElValue* PixelElement = PubElVals.GetElementByNumber(grPixel, numPixel);
966 return PixelElement->GetOffset();
971 gdcmDictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) {
973 // Y a-t-il une raison de lui passer des guint32
974 // alors que group et element sont des guint16?
976 gdcmDictEntry * found = (gdcmDictEntry*)0;
977 if (!RefPubDict && !RefShaDict) {
978 //FIXME build a default dictionary !
979 printf("FIXME in gdcmHeader::IsInDicts\n");
982 found = RefPubDict->GetTag(group, element);
987 found = RefShaDict->GetTag(group, element);
994 list<string> * gdcmHeader::GetPubTagNames(void) {
995 list<string> * Result = new list<string>;
996 TagHT entries = RefPubDict->GetEntries();
998 for (TagHT::iterator tag = entries.begin(); tag != entries.end(); ++tag){
999 Result->push_back( tag->second->GetName() );
1004 map<string, list<string> > * gdcmHeader::GetPubTagNamesByCategory(void) {
1005 map<string, list<string> > * Result = new map<string, list<string> >;
1006 TagHT entries = RefPubDict->GetEntries();
1008 for (TagHT::iterator tag = entries.begin(); tag != entries.end(); ++tag){
1009 (*Result)[tag->second->GetFourth()].push_back(tag->second->GetName());
1014 string gdcmHeader::GetPubElValByNumber(guint16 group, guint16 element) {
1015 return PubElVals.GetElValueByNumber(group, element);
1018 string gdcmHeader::GetPubElValRepByNumber(guint16 group, guint16 element) {
1019 ElValue* elem = PubElVals.GetElementByNumber(group, element);
1021 return "gdcm::Unfound";
1022 return elem->GetVR();
1025 string gdcmHeader::GetPubElValByName(string TagName) {
1026 return PubElVals.GetElValueByName(TagName);
1029 string gdcmHeader::GetPubElValRepByName(string TagName) {
1030 ElValue* elem = PubElVals.GetElementByName(TagName);
1032 return "gdcm::Unfound";
1033 return elem->GetVR();
1036 string gdcmHeader::GetShaElValByNumber(guint16 group, guint16 element) {
1037 return ShaElVals.GetElValueByNumber(group, element);
1040 string gdcmHeader::GetShaElValRepByNumber(guint16 group, guint16 element) {
1041 ElValue* elem = ShaElVals.GetElementByNumber(group, element);
1043 return "gdcm::Unfound";
1044 return elem->GetVR();
1047 string gdcmHeader::GetShaElValByName(string TagName) {
1048 return ShaElVals.GetElValueByName(TagName);
1051 string gdcmHeader::GetShaElValRepByName(string TagName) {
1052 ElValue* elem = ShaElVals.GetElementByName(TagName);
1054 return "gdcm::Unfound";
1055 return elem->GetVR();
1059 string gdcmHeader::GetElValByNumber(guint16 group, guint16 element) {
1060 string pub = GetPubElValByNumber(group, element);
1063 return GetShaElValByNumber(group, element);
1066 string gdcmHeader::GetElValRepByNumber(guint16 group, guint16 element) {
1067 string pub = GetPubElValRepByNumber(group, element);
1070 return GetShaElValRepByNumber(group, element);
1073 string gdcmHeader::GetElValByName(string TagName) {
1074 string pub = GetPubElValByName(TagName);
1077 return GetShaElValByName(TagName);
1080 string gdcmHeader::GetElValRepByName(string TagName) {
1081 string pub = GetPubElValRepByName(TagName);
1084 return GetShaElValRepByName(TagName);
1088 * \ingroup gdcmHeader
1089 * \brief Parses the header of the file but does NOT load element values.
1091 void gdcmHeader::ParseHeader(void) {
1092 ElValue * newElValue = (ElValue *)0;
1096 while ( (newElValue = ReadNextElement()) ) {
1097 SkipElementValue(newElValue);
1098 PubElVals.Add(newElValue);
1103 * \ingroup gdcmHeader
1104 * \brief Loads the element values of all the elements present in the
1105 * public tag based hash table.
1107 void gdcmHeader::LoadElements(void) {
1109 if (DEBUG) printf("LoadElements : Entree\n");
1112 if (DEBUG) printf("LoadElements : rewind\n");
1114 TagElValueHT ht = PubElVals.GetTagHt();
1116 if (DEBUG) printf("LoadElements : GetTagHt\n");
1118 for (TagElValueHT::iterator tag = ht.begin(); tag != ht.end(); ++tag) {
1119 LoadElementValue(tag->second);
1123 void gdcmHeader::PrintPubElVal(ostream & os) {
1124 PubElVals.Print(os);
1127 void gdcmHeader::PrintPubDict(ostream & os) {
1128 RefPubDict->Print(os);