4 // * gdcmlib is a library dedicated to reading and writing dicom files.
5 // * LGPL for the license
6 // * lightweigth as opposed to CTN or DCMTK which come bundled which try
7 // to implement the full DICOM standard (networking...). gdcmlib concentrates
8 // on reading and writing
9 // * Formats: this lib should be able to read ACR-NEMA v1 and v2, Dicom v3 (as
10 // stated in part10). [cf dcmtk/dcmdata/docs/datadict.txt]
11 // * Targeted plateforms: Un*xes and Win32/VC++6.0
15 // The declarations commented out and starting with "TODO Swig" needed
16 // to be temporarily removed for swig to proceed correctly (in fact
17 // problems appears at loading of _gdcm.[so/dll]). So, simply uncomment
18 // the declaration once you provided the definition of the method...
22 using namespace std; // string type lives in the std namespace on VC++
26 #include <stddef.h> // For size_t
27 #include <stdio.h> // FIXME For FILE on GCC only
31 // The requirement for the hash table (or map) that
33 // 1/ First, next, last (iterators)
34 // 2/ should be sortable (i.e. sorted by TagKey). This
35 // condition shall be droped since the Win32/VC++
36 // implementation doesn't look a sorted one. Pffff....
37 // 3/ Make sure we can setup some default size value,
38 // which should be around 4500 entries which is the
39 // average dictionary size (said JPR)
41 // En fait, je disais que dans LE Directory Dicom (dans son etat 2002)
42 // il y a 1600 entrees.
43 // Une valeur raisonable pour un majorant du nombre d'entrees
44 // dans une entete DICOM d'une image semble semble etre 300
45 // Si on 'decortique' les elements SQ (ce qui ne semble pas etre fait pour le moment)
46 // on risque en fait de depasser ... un nombre non previsible dans le cas d'une entree SQ
47 // contenant lui même un tres grand nombre d'entrees ?!?)
48 // Quant au nombre d'entrees dans un DICOMDIR, c'est encore pire : il n'est limité
49 // que par la taille d'un CD-ROM (les DVD-ROM ne sont pas encore pris en compte)
50 // On peut s'attendre a 30 entrees par fichier dicom présent sur le CD-ROM
51 // REMARQUE : il faudra se pencher sur le pb de la creation du DICOMDIR lorsqu'on voudra
52 // exporter des images lisibles par les consoles cliniques
53 // et pas seulement importables dans e-film.
57 #define guint16 uint16_t
58 #define guint32 uint32_t
62 typedef unsigned short guint16;
63 typedef unsigned int guint32;
67 #define GDCM_EXPORT __declspec( dllexport )
73 // ---------------------------------------------------- gdcmDictEntry
75 // c'est une ligne du Dictionnaire Dicom
79 ////////////////////////////////////////////////////////////////////////////
80 // Tag based hash tables.
81 // We shall use as keys the strings (as the C++ type) obtained by
82 // concatenating the group value and the element value (both of type
83 // unsigned 16 bit integers in Dicom) expressed in hexadecimal.
84 // Example: consider the tag given as (group, element) = (0x0010, 0x0010).
85 // Then the corresponding TagKey shall be the string 0010|0010 (where
86 // the | (pipe symbol) acts as a separator). Refer to
87 // gdcmDictEntry::TranslateToKey for this conversion function.
89 typedef string TagKey;
91 class GDCM_EXPORT gdcmDictEntry {
93 guint16 group; // e.g. 0x0010
94 guint16 element; // e.g. 0x0103
95 string vr; // Value Representation i.e. some clue about the nature
96 // of the data represented e.g. "FD" short for
97 // "Floating Point Double"
98 // CLEANME: find the official dicom name for this field !
99 string fourth; // Fourth field containing some semantics.
100 string name; // e.g. "Patient_Name"
101 TagKey key; // Redundant with (group, element) but we add it
102 // on efficiency purposes.
103 // DCMTK has many fields for handling a DictEntry (see below). What are the
104 // relevant ones for gdcmlib ?
105 // struct DBI_SimpleEntry {
106 // Uint16 upperGroup;
107 // Uint16 upperElement;
109 // const char* tagName;
112 // const char* standardVersion;
113 // DcmDictRangeRestriction groupRestriction;
114 // DcmDictRangeRestriction elementRestriction;
118 // fabrique une ligne de Dictionnaire Dicom à partir des parametres en entrée
120 gdcmDictEntry(guint16 group,
122 string vr = "Unknown",
123 string fourth = "Unknown",
124 string name = "Unknown");
126 // fabrique une 'clé' par concaténation du numGroupe et du numElement
128 static TagKey TranslateToKey(guint16 group, guint16 element);
130 guint16 GetGroup(void) { return group; };
131 guint16 GetElement(void){return element;};
132 string GetVR(void) {return vr; };
134 void SetKey(string k){ key = k; }
135 bool IsVrUnknown(void);
136 string GetFourth(void) {return fourth;};
137 string GetName(void) {return name; };
138 string GetKey(void) {return key; };
142 // ---------------------------------------------------- gdcmDict
144 // c'est le Dictionnaire Dicom
147 ////////////////////////////////////////////////////////////////////////////
148 // A single DICOM dictionary i.e. a container for a collection of dictionary
149 // entries. There should be a single public dictionary (THE dictionary of
150 // the actual DICOM v3) but as many shadow dictionaries as imagers
151 // combined with all software versions...
153 typedef map<TagKey, gdcmDictEntry*> TagHT;
154 // Table de Hachage : (group,Elem) --> pointeur vers une ligne du Dictionnaire Dicom
156 class GDCM_EXPORT gdcmDict {
161 // rempli le Dictionnaire Dicom à partir d'un fichier texte
162 gdcmDict(const char* FileName); // Read Dict from disk
164 int AddNewEntry (gdcmDictEntry* NewEntry);
165 int ReplaceEntry(gdcmDictEntry* NewEntry);
166 int RemoveEntry (TagKey k);
167 int RemoveEntry (guint16 group, guint16 element);
169 // renvoie une ligne de Dictionnaire Dicom à partir de (numGroup, numElement)
170 gdcmDictEntry * GetTag(guint32 group, guint32 element);
172 void Print(ostream&);
173 TagHT & GetEntries(void) { return entries; }
178 // ---------------------------------------------------- gdcmDictSet
180 // Ensemble de Dictionnaires Dicom (le public + 'des' privés)
181 // Au cas ou l'on traiterait un jour les 'dictionnaires privés'
182 // - pratiquement un par constructeur, par machine, et par version du logiciel -
186 ////////////////////////////////////////////////////////////////////////////
187 // Container for managing a set of loaded dictionaries. Sharing dictionaries
189 // * reloading an allready loaded dictionary,
190 // * having many in memory representations of the same dictionary.
192 typedef string DictKey;
193 typedef map<DictKey, gdcmDict*> DictSetHT;
195 class GDCM_EXPORT gdcmDictSet {
197 string DictPath; // Directory path to dictionaries
199 int AppendDict(gdcmDict* NewDict);
200 int LoadDictFromFile(string filename, DictKey);
201 void SetDictPath(void);
203 gdcmDictSet(void); // loads THE DICOM v3 dictionary
204 // TODO Swig int LoadDictFromFile(string filename);
205 // QUESTION: the following function might not be thread safe !? Maybe
206 // we need some mutex here, to avoid concurent creation of
207 // the same dictionary !?!?!
208 // TODO Swig int LoadDictFromName(string filename);
209 // TODO Swig int LoadAllDictFromDirectory(string DirectoryName);
210 // TODO Swig string* GetAllDictNames();
212 // Question : ne faudra-t-il pas mettre LE dictionnaire DICOM dans un Directory
213 // et les eventuels 'dictionnaires prives' dans un autre?
214 // (pour eviter a un utilisateur mal dégourdi de tout saccager ?)
216 int LoadDicomV3Dict(void);
217 void Print(ostream&);
218 gdcmDict* GetDict(DictKey DictName);
219 gdcmDict* GetDefaultPublicDict(void);
224 // ---------------------------------------------------- ElValue
226 // C'est un Element Dicom
227 // (ce qu'on a trouve dans l'entete de l'image
228 // + ce qu'on est allé chercher dans le Dictionnaire Dicom)
233 // Ne faudrait-il pas trouver un autre nom, qui preterait moins à confusion?
234 // ElValue n'EST PAS la 'valeur d'un Element', mais la reunion d'infos
235 // trouvees dans l'Entete du fichier ET dans le Dictionnaire DICOM
238 // The dicom header of a Dicom file contains a set of such ELement VALUES
239 // (when successfuly parsed against a given Dicom dictionary)
241 class GDCM_EXPORT ElValue {
243 gdcmDictEntry *entry;
245 bool ImplicitVr; // Even when reading explicit vr files, some
246 // elements happen to be implicit. Flag them here
247 // since we can't use the entry->vr without breaking
248 // the underlying dictionary.
249 // Might prove of some interest (see _ID_DCM_ELEM)
252 string value; // used to be char * valeurElem
253 size_t Offset; // Offset from the begining of file for direct user access
255 ElValue(gdcmDictEntry*);
256 void SetDictEntry(gdcmDictEntry *NewEntry) { entry = NewEntry; };
257 bool IsVrUnknown(void) { return entry->IsVrUnknown(); };
258 void SetImplicitVr(void) { ImplicitVr = true; };
259 bool IsImplicitVr(void) { return ImplicitVr; };
261 guint16 GetGroup(void) { return entry->GetGroup(); };
262 guint16 GetElement(void) { return entry->GetElement(); };
263 string GetKey(void) { return entry->GetKey(); };
264 string GetName(void) { return entry->GetName(); };
266 string GetVR(void) { return entry->GetVR(); };
267 void SetVR(string v) { entry->SetVR(v); };
270 // Un champ privé, accessible en consultation et en modif (sans restriction)
271 // interet par rapport à un champ public ?
272 // --> pouvoir en changer la définition sans toucher à l'API
274 void SetLength(guint32 l){ LgrElem = l; };
275 guint32 GetLength(void) { return LgrElem; };
277 // Question : SetLength est public
278 // (sinon, on ne pourrait pas l'appeler dans ElValSet)
279 // alors que *personne* ne devrait s'en servir !
280 // c'est *forcément* la lgr de la string 'value', non?
282 void SetValue(string val){ value = val; };
283 string GetValue(void) { return value; };
285 void SetOffset(size_t of){ Offset = of; };
286 size_t GetOffset(void) { return Offset; };
287 // Question : SetOffset est public ...
288 // Quel utilisateur serait ammené à modifier l'Offset ?
293 // ---------------------------------------------------- ElValSet
295 // ... un ensemble d'Elements Dicom
296 // ... le résultat de l'analyse d'une entete d'image, par exemple
298 ////////////////////////////////////////////////////////////////////////////
299 // Container for a set of successfully parsed ElValues.
300 typedef map<TagKey, ElValue*> TagElValueHT;
301 typedef map<string, ElValue*> TagElValueNameHT;
303 class GDCM_EXPORT ElValSet {
304 // We need both accesses with a TagKey and the Dictentry.Name
307 TagElValueNameHT NameHt;
310 void Print(ostream &);
311 void PrintByName(ostream &);
313 ElValue* GetElementByNumber(guint32 group, guint32 element);
314 ElValue* GetElementByName (string);
315 string GetElValueByNumber(guint32 group, guint32 element);
316 string GetElValueByName (string);
318 TagElValueHT & GetTagHt(void);
320 int SetElValueByNumber(string content, guint32 group, guint32 element);
321 int SetElValueByName(string content, string TagName);
326 // ---------------------------------------------------- gdcmHeader
328 // C'est le Dicom Header d'une image donnée
329 // (tous les elements Dicom qui la composent
330 // + des info 'de service')
333 ////////////////////////////////////////////////////////////////////////////
334 // The typical usage of instances of class gdcmHeader is to classify a set of
335 // dicom files according to header information e.g. to create a file hierarchy
336 // reflecting the Patient/Study/Serie informations, or extracting a given
337 // SerieId. Accesing the content (image[s] or volume[s]) is beyond the
338 // functionality of this class and belong to gdmcFile (see below).
340 // * the various entries of the explicit value representation (VR) shall
341 // be managed within a dictionary which is shared by all gdcmHeader instances
342 // * the gdcmHeader::Set*Tag* family members cannot be defined as protected
343 // (Swig limitations for as Has_a dependency between gdcmFile and gdcmHeader)
346 typedef string VRKey;
347 typedef string VRAtr;
348 typedef map<VRKey, VRAtr> VRHT; // Value Representation Hash Table
351 class GDCM_EXPORT gdcmHeader {
352 void SkipBytes(guint32);
354 static VRHT *dicom_vr;
355 // Dictionaries of data elements:
357 static gdcmDictSet* Dicts; // global dictionary container
358 gdcmDict* RefPubDict; // public dictionary
359 gdcmDict* RefShaDict; // shadow dictionary (optional)
360 // Parsed element values:
361 ElValSet PubElVals; // parsed with Public Dictionary
362 ElValSet ShaElVals; // parsed with Shadow Dictionary
363 string filename; // refering underlying file
365 // The tag Image Location (0028,0200) - containing the address of
366 // the pixels - is not allways present. Then we store this information
367 // il etait facultatif en ACR-NEMA, il n'existe plus en DICOM 3
371 // Qu'y a-t-il a corriger ?
373 // outside of the elements:
377 // Ne faudrait-il pas une indication sur la presence ou non
378 // du 'groupe des pixels' dans l'entete?
379 // (voir pb du DICOMDIR)
381 // Swap code (little, big, bad-big, bad-little endian): this code is not fixed
382 // during parsing.FIXME sw should be an enum e.g.
390 // Only the elements whose size is below this bound will be loaded.
391 // By default, this upper bound is limited to 1024 (which looks reasonable
392 // when one considers the definition of the various VR contents).
393 guint32 MaxSizeLoadElementValue;
395 guint16 ReadInt16(void);
396 guint32 ReadInt32(void);
397 guint16 SwapShort(guint16);
398 guint32 SwapLong(guint32);
399 void Initialise(void);
400 void CheckSwap(void);
401 void FindLength(ElValue *);
402 guint32 FindLengthOB(void);
403 void FindVR(ElValue *);
404 void LoadElementValue(ElValue *);
405 void LoadElementValueSafe(ElValue *);
406 void SkipElementValue(ElValue *);
407 void InitVRDict(void);
408 void SwitchSwapToBigEndian(void);
409 void FixFoundLength(ElValue*, guint32);
410 bool IsAnInteger(ElValue *);
412 bool IsImplicitVRLittleEndianTransferSyntax(void);
413 bool IsExplicitVRLittleEndianTransferSyntax(void);
414 bool IsDeflatedExplicitVRLittleEndianTransferSyntax(void);
415 bool IsExplicitVRBigEndianTransferSyntax(void);
416 bool IsJPEGBaseLineProcess1TransferSyntax(void);
417 bool IsJPEGExtendedProcess2_4TransferSyntax(void);
418 bool IsJPEGExtendedProcess3_5TransferSyntax(void);
419 bool IsJPEGSpectralSelectionProcess6_8TransferSyntax(void);
422 // Il y en a encore DIX-SEPT, comme ça.
423 // Il faudrait trouver qq chose + rusé ...
426 void SetMaxSizeLoadElementValue(long);
427 ElValue * ReadNextElement(void);
428 gdcmDictEntry * IsInDicts(guint32, guint32);
436 ACR_LIBIDO}; // CLEANME
439 int anonymize(ostream&); // FIXME : anonymize should be a friend ?
441 void LoadElements(void);
442 virtual void ParseHeader(void);
443 gdcmHeader(const char* filename);
444 virtual ~gdcmHeader();
446 size_t GetPixelOffset(void);
447 void GetPixels(size_t, void *);
448 int GetSwapCode(void) { return sw; }
450 // TODO Swig int SetPubDict(string filename);
451 // When some proprietary shadow groups are disclosed, we can set up
452 // an additional specific dictionary to access extra information.
453 // TODO Swig int SetShaDict(string filename);
455 // Retrieve all potentially available tag [tag = (group, element)] names
456 // from the standard (or public) dictionary. Typical usage : enable the
457 // user of a GUI based interface to select his favorite fields for sorting
459 list<string> * GetPubTagNames(void);
460 map<string, list<string> > * GetPubTagNamesByCategory(void);
461 // Get the element values themselves:
463 string GetPubElValByName(string TagName);
464 string GetPubElValByNumber(guint16 group, guint16 element);
466 // Getting the element value representation (VR) might be needed by caller
467 // to convert the string typed content to caller's native type
468 // (think of C/C++ vs Python).
470 string GetPubElValRepByName(string TagName);
471 string GetPubElValRepByNumber(guint16 group, guint16 element);
473 TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); };
474 void PrintPubElVal(ostream & os = cout);
475 void PrintPubDict(ostream &);
477 // Same thing with the shadow :
478 // TODO Swig string* GetShaTagNames();
479 string GetShaElValByName(string TagName);
480 string GetShaElValByNumber(guint16 group, guint16 element);
481 string GetShaElValRepByName(string TagName);
482 string GetShaElValRepByNumber(guint16 group, guint16 element);
484 // Wrappers of the above (public is privileged over shadow) to avoid
485 // bugging the caller with knowing if ElVal is from the public or shadow
487 string GetElValByName(string TagName);
488 string GetElValByNumber(guint16 group, guint16 element);
489 string GetElValRepByName(string TagName);
490 string GetElValRepByNumber(guint16 group, guint16 element);
492 int SetPubElValByName(string content, string TagName);
493 int SetPubElValByNumber(string content, guint16 group, guint16 element);
494 int SetShaElValByName(string content, string ShadowTagName);
495 int SetShaElValByNumber(string content, guint16 group, guint16 element);
497 ElValSet GetPubElVals() { return(PubElVals); }
501 // ---------------------------------------------------- gdcmFile
503 // un fichier EST_UNE entete, ou A_UNE entete ?
505 // On dit 'EST_UNE' ...
508 ////////////////////////////////////////////////////////////////////////////
509 // In addition to Dicom header exploration, this class is designed
510 // for accessing the image/volume content. One can also use it to
511 // write Dicom files.
512 ////// QUESTION: this looks still like an open question whether the
513 ////// relationship between a gdcmFile and gdcmHeader is of
514 ////// type IS_A or HAS_A !
516 class GDCM_EXPORT gdcmFile: public gdcmHeader
520 // Data pointe sur quoi?
521 // sur les Pixels lus?
522 // --> j'ajoute un champ public : Pixels
523 // (il faudra que l'utilisateur puisse modifier les pixels ?)
526 int Parsed; // weather allready parsed
527 string OrigFileName; // To avoid file overwrite
529 // je ne suis pas sur d'avoir compris *où* il serait légitime de ranger ca.
530 // on pourra tjs le deplacer, et mettre des accesseurs
534 // Constructor dedicated to writing a new DICOMV3 part10 compliant
535 // file (see SetFileName, SetDcmTag and Write)
536 // TODO Swig gdcmFile();
537 // Opens (in read only and when possible) an existing file and checks
538 // for DICOM compliance. Returns NULL on failure.
539 // Note: the in-memory representation of all available tags found in
540 // the DICOM header is post-poned to first header information access.
541 // This avoid a double parsing of public part of the header when
542 // one sets an a posteriori shadow dictionary (efficiency can be
543 // seen as a side effect).
545 gdcmFile(string & filename);
547 // For promotion (performs a deepcopy of pointed header object)
548 // TODO Swig gdcmFile(gdcmHeader* header);
549 // TODO Swig ~gdcmFile();
551 // On writing purposes. When instance was created through
552 // gdcmFile(string filename) then the filename argument MUST be different
553 // from the constructor's one (no overwriting allowed).
554 // TODO Swig int SetFileName(string filename);
556 // Allocates necessary memory, copies the data (image[s]/volume[s]) to
557 // newly allocated zone and return a pointer to it:
559 void * GetImageData();
561 // Returns size (in bytes) of required memory to contain data
562 // represented in this file.
564 size_t GetImageDataSize();
566 // Copies (at most MaxSize bytes) of data to caller's memory space.
567 // Returns an error code on failure (if MaxSize is not big enough)
569 int PutImageDataHere(void* destination, size_t MaxSize );
573 // GetImageData et PutImageDataHere
574 // Get et Put pour 2 fonctions qui font presque la meme chose :-(
577 // Allocates ExpectedSize bytes of memory at this->Data and copies the
578 // pointed data to it.
581 // Pourquoi dupliquer les pixels, alors qu'on les a deja en mémoire,
582 // et que Data (dans le gdcmHeader) est un pointeur ?
584 // TODO Swig int SetImageData(void * Data, size_t ExpectedSize);
587 // A NE PAS OUBLIER : que fait-on en cas de Transfert Syntax (dans l'entete)
588 // incohérente avec l'ordre des octets en mémoire
589 // TODO Swig int Write();
591 // Ecrit sur disque les pixels d'UNE image
592 // Aucun test n'est fait sur l'"Endiannerie" du processeur.
593 // Ca sera à l'utilisateur d'appeler son Reader correctement
595 int WriteRawData (string nomFichier);
596 int WriteDcm (string nomFichier);
600 // ---------------------------------------------------- gdcmSerie
602 // une serie EST_UN fichier ????
606 //class gdcmSerie : gdcmFile;
609 // ---------------------------------------------------- gdcmMultiFrame
611 // un fichierMultiFrame EST_UN fichier
615 //class gdcmMultiFrame : gdcmFile;