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);
170 // renvoie une ligne de Dictionnaire Dicom à partir de (numGroup, numElement)
171 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(); };
268 void SetVR(string v) { entry->SetVR(v); };
271 // Un champ privé, accessible en consultation et en modif (sans restriction)
272 // interet par rapport à un champ public ?
273 // --> pouvoir en changer la définition sans toucher à l'API
275 void SetLength(guint32 l){ LgrElem = l; };
276 guint32 GetLength(void) { return LgrElem; };
278 void SetValue(string val){ value = val; };
279 string GetValue(void) { return value; };
281 void SetOffset(size_t of){ Offset = of; };
282 size_t GetOffset(void) { return Offset; };
288 // ---------------------------------------------------- ElValSet
290 // ... un ensemble d'Elements Dicom
291 // ... le résultat de l'analyse d'une entete d'image, par exemple
293 ////////////////////////////////////////////////////////////////////////////
294 // Container for a set of successfully parsed ElValues.
295 typedef map<TagKey, ElValue*> TagElValueHT;
296 typedef map<string, ElValue*> TagElValueNameHT;
298 class GDCM_EXPORT ElValSet {
299 // We need both accesses with a TagKey and the Dictentry.Name
302 TagElValueNameHT NameHt;
305 void Print(ostream &);
306 void PrintByName(ostream &);
308 ElValue* GetElementByNumber(guint32 group, guint32 element);
309 ElValue* GetElementByName (string);
310 string GetElValueByNumber(guint32 group, guint32 element);
311 string GetElValueByName (string);
313 TagElValueHT & GetTagHt(void);
315 int SetElValueByNumber(string content, guint32 group, guint32 element);
316 int SetElValueByName(string content, string TagName);
321 // ---------------------------------------------------- gdcmHeader
323 // C'est le Dicom Header d'une image donnée
324 // (tous les elements Dicom qui la composent
325 // + des info 'de service')
328 ////////////////////////////////////////////////////////////////////////////
329 // The typical usage of instances of class gdcmHeader is to classify a set of
330 // dicom files according to header information e.g. to create a file hierarchy
331 // reflecting the Patient/Study/Serie informations, or extracting a given
332 // SerieId. Accesing the content (image[s] or volume[s]) is beyond the
333 // functionality of this class and belong to gdmcFile (see below).
335 // * the various entries of the explicit value representation (VR) shall
336 // be managed within a dictionary which is shared by all gdcmHeader instances
337 // * the gdcmHeader::Set*Tag* family members cannot be defined as protected
338 // (Swig limitations for as Has_a dependency between gdcmFile and gdcmHeader)
341 typedef string VRKey;
342 typedef string VRAtr;
343 typedef map<VRKey, VRAtr> VRHT; // Value Representation Hash Table
346 class GDCM_EXPORT gdcmHeader {
347 void SkipBytes(guint32);
349 static VRHT *dicom_vr;
350 // Dictionaries of data elements:
352 static gdcmDictSet* Dicts; // global dictionary container
353 gdcmDict* RefPubDict; // public dictionary
354 gdcmDict* RefShaDict; // shadow dictionary (optional)
355 // Parsed element values:
356 ElValSet PubElVals; // parsed with Public Dictionary
357 ElValSet ShaElVals; // parsed with Shadow Dictionary
358 string filename; // refering underlying file
360 // The tag Image Location (0028,0200) - containing the address of
361 // the pixels - is not allways present. Then we store this information
366 // Qu'y a-t-il a corriger ?
368 // outside of the elements:
372 // Ne faudrait-il pas une indication sur la presence ou non
373 // du 'groupe des pixels' dans l'entete?
374 // (voir pb du DICOMDIR)
376 // Swap code (little, big, bad-big, bad-little endian): this code is not fixed
377 // during parsing.FIXME sw should be an enum e.g.
385 // Only the elements whose size is below this bound will be loaded.
386 // By default, this upper bound is limited to 1024 (which looks reasonable
387 // when one considers the definition of the various VR contents).
388 guint32 MaxSizeLoadElementValue;
390 guint16 ReadInt16(void);
391 guint32 ReadInt32(void);
392 guint16 SwapShort(guint16);
393 guint32 SwapLong(guint32);
394 void Initialise(void);
395 void CheckSwap(void);
396 void FindLength(ElValue *);
397 guint32 FindLengthOB(void);
398 void FindVR(ElValue *);
399 void LoadElementValue(ElValue *);
400 void LoadElementValueSafe(ElValue *);
401 void SkipElementValue(ElValue *);
402 void InitVRDict(void);
403 void SwitchSwapToBigEndian(void);
404 void FixFoundLength(ElValue*, guint32);
405 bool IsAnInteger(ElValue *);
407 bool IsImplicitVRLittleEndianTransferSyntax(void);
408 bool IsExplicitVRLittleEndianTransferSyntax(void);
409 bool IsDeflatedExplicitVRLittleEndianTransferSyntax(void);
410 bool IsExplicitVRBigEndianTransferSyntax(void);
411 bool IsJPEGBaseLineProcess1TransferSyntax(void);
412 bool IsJPEGExtendedProcess2_4TransferSyntax(void);
413 bool IsJPEGExtendedProcess3_5TransferSyntax(void);
414 bool IsJPEGSpectralSelectionProcess6_8TransferSyntax(void);
417 // Il y en a encore DIX-SEPT, comme ça.
418 // Il faudrait trouver qq chose + rusé ...
421 void SetMaxSizeLoadElementValue(long);
422 ElValue * ReadNextElement(void);
423 gdcmDictEntry * IsInDicts(guint32, guint32);
431 ACR_LIBIDO}; // CLEANME
434 int anonymize(ostream&); // FIXME : anonymize should be a friend ?
436 void LoadElements(void);
437 virtual void ParseHeader(void);
438 gdcmHeader(const char* filename);
439 virtual ~gdcmHeader();
441 size_t GetPixelOffset(void);
442 void GetPixels(size_t, void *);
443 int GetSwapCode(void) { return sw; }
445 // TODO Swig int SetPubDict(string filename);
446 // When some proprietary shadow groups are disclosed, we can set up
447 // an additional specific dictionary to access extra information.
448 // TODO Swig int SetShaDict(string filename);
450 // Retrieve all potentially available tag [tag = (group, element)] names
451 // from the standard (or public) dictionary. Typical usage : enable the
452 // user of a GUI based interface to select his favorite fields for sorting
454 list<string> * GetPubTagNames(void);
455 map<string, list<string> > * GetPubTagNamesByCategory(void);
456 // Get the element values themselves:
458 string GetPubElValByName(string TagName);
459 string GetPubElValByNumber(guint16 group, guint16 element);
461 // Getting the element value representation (VR) might be needed by caller
462 // to convert the string typed content to caller's native type
463 // (think of C/C++ vs Python).
465 string GetPubElValRepByName(string TagName);
466 string GetPubElValRepByNumber(guint16 group, guint16 element);
468 TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); };
469 void PrintPubElVal(ostream & os = cout);
470 void PrintPubDict(ostream &);
472 // Same thing with the shadow :
473 // TODO Swig string* GetShaTagNames();
474 string GetShaElValByName(string TagName);
475 string GetShaElValByNumber(guint16 group, guint16 element);
476 string GetShaElValRepByName(string TagName);
477 string GetShaElValRepByNumber(guint16 group, guint16 element);
479 // Wrappers of the above (public is privileged over shadow) to avoid
480 // bugging the caller with knowing if ElVal is from the public or shadow
482 string GetElValByName(string TagName);
483 string GetElValByNumber(guint16 group, guint16 element);
484 string GetElValRepByName(string TagName);
485 string GetElValRepByNumber(guint16 group, guint16 element);
487 int SetPubElValByName(string content, string TagName);
488 int SetPubElValByNumber(string content, guint16 group, guint16 element);
489 int SetShaElValByName(string content, string ShadowTagName);
490 int SetShaElValByNumber(string content, guint16 group, guint16 element);
492 ElValSet GetPubElVals() { return(PubElVals); }
496 // ---------------------------------------------------- gdcmFile
498 // un fichier EST_UNE entete, ou A_UNE entete ?
500 // On dit 'EST_UNE' ...
503 ////////////////////////////////////////////////////////////////////////////
504 // In addition to Dicom header exploration, this class is designed
505 // for accessing the image/volume content. One can also use it to
506 // write Dicom files.
507 ////// QUESTION: this looks still like an open question whether the
508 ////// relationship between a gdcmFile and gdcmHeader is of
509 ////// type IS_A or HAS_A !
511 class GDCM_EXPORT gdcmFile: public gdcmHeader
515 // Data pointe sur quoi?
516 // sur les Pixels lus?
517 // --> j'ajoute un champ public : Pixels
518 // (il faudra que l'utilisateur puisse modifier les pixels ?)
521 int Parsed; // weather allready parsed
522 string OrigFileName; // To avoid file overwrite
524 // je ne suis pas sur d'avoir compris *où* il serait légitime de ranger ca.
525 // on pourra tjs le deplacer, et mettre des accesseurs
529 // Constructor dedicated to writing a new DICOMV3 part10 compliant
530 // file (see SetFileName, SetDcmTag and Write)
531 // TODO Swig gdcmFile();
532 // Opens (in read only and when possible) an existing file and checks
533 // for DICOM compliance. Returns NULL on failure.
534 // Note: the in-memory representation of all available tags found in
535 // the DICOM header is post-poned to first header information access.
536 // This avoid a double parsing of public part of the header when
537 // one sets an a posteriori shadow dictionary (efficiency can be
538 // seen as a side effect).
540 gdcmFile(string & filename);
542 // For promotion (performs a deepcopy of pointed header object)
543 // TODO Swig gdcmFile(gdcmHeader* header);
544 // TODO Swig ~gdcmFile();
546 // On writing purposes. When instance was created through
547 // gdcmFile(string filename) then the filename argument MUST be different
548 // from the constructor's one (no overwriting allowed).
549 // TODO Swig int SetFileName(string filename);
551 // Allocates necessary memory, copies the data (image[s]/volume[s]) to
552 // newly allocated zone and return a pointer to it:
554 void * GetImageData();
556 // Returns size (in bytes) of required memory to contain data
557 // represented in this file.
559 size_t GetImageDataSize();
561 // Copies (at most MaxSize bytes) of data to caller's memory space.
562 // Returns an error code on failure (if MaxSize is not big enough)
564 int PutImageDataHere(void* destination, size_t MaxSize );
568 // GetImageData et PutImageDataHere
569 // Get et Put pour 2 fonctions qui font presque la meme chose :-(
572 // Allocates ExpectedSize bytes of memory at this->Data and copies the
573 // pointed data to it.
576 // Pourquoi dupliquer les pixels, alors qu'on les a deja en mémoire,
577 // et que Data (dans le gdcmHeader) est un pointeur ?
579 // TODO Swig int SetImageData(void * Data, size_t ExpectedSize);
582 // A NE PAS OUBLIER : que fait-on en cas de Transfert Syntax (dans l'entete)
583 // incohérente avec l'ordre des octets en mémoire
584 // TODO Swig int Write();
586 // Ecrit sur disque les pixels d'UNE image
587 // Aucun test n'est fait sur l'"Endiannerie" du processeur.
588 // Ca sera à l'utilisateur d'appeler son Reader correctement
590 int WriteRawData (string nomFichier);
591 int WriteDcm (string nomFichier);
595 // ---------------------------------------------------- gdcmSerie
597 // une serie EST_UN fichier ????
601 //class gdcmSerie : gdcmFile;
604 // ---------------------------------------------------- gdcmMultiFrame
606 // un fichierMultiFrame EST_UN fichier
610 //class gdcmMultiFrame : gdcmFile;