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 wich 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.
58 #define guint16 uint16_t
59 #define guint32 uint32_t
63 typedef unsigned short guint16;
64 typedef unsigned int guint32;
68 #define GDCM_EXPORT __declspec( dllexport )
75 // ---------------------------------------------------- gdcmDictEntry
77 // c'est une ligne du Dictionnaire Dicom
81 ////////////////////////////////////////////////////////////////////////////
82 // Tag based hash tables.
83 // We shall use as keys the strings (as the C++ type) obtained by
84 // concatenating the group value and the element value (both of type
85 // unsigned 16 bit integers in Dicom) expressed in hexadecimal.
86 // Example: consider the tag given as (group, element) = (0x0010, 0x0010).
87 // Then the corresponding TagKey shall be the string 0010|0010 (where
88 // the | (pipe symbol) acts as a separator). Refer to
89 // gdcmDictEntry::TranslateToKey for this conversion function.
91 typedef string TagKey;
93 class GDCM_EXPORT gdcmDictEntry {
95 guint16 group; // e.g. 0x0010
96 guint16 element; // e.g. 0x0103
97 string vr; // Value Representation i.e. some clue about the nature
98 // of the data represented e.g. "FD" short for
99 // "Floating Point Double"
100 // CLEANME: find the official dicom name for this field !
101 string fourth; // Fourth field containing some semantics.
102 string name; // e.g. "Patient_Name"
103 TagKey key; // Redundant with (group, element) but we add it
104 // on efficiency purposes.
105 // DCMTK has many fields for handling a DictEntry (see below). What are the
106 // relevant ones for gdcmlib ?
107 // struct DBI_SimpleEntry {
108 // Uint16 upperGroup;
109 // Uint16 upperElement;
111 // const char* tagName;
114 // const char* standardVersion;
115 // DcmDictRangeRestriction groupRestriction;
116 // DcmDictRangeRestriction elementRestriction;
120 // fabrique une ligne de Dictionnaire Dicom à partir des parametres en entrée
123 gdcmDictEntry(guint16 group, guint16 element,
124 string vr = "Unknown",
125 string fourth = "Unknown",
126 string name = "Unknown");
128 // fabrique une 'clé' par concaténation du numGroupe et du numElement
130 static TagKey TranslateToKey(guint16 group, guint16 element);
132 guint16 GetGroup(void) { return group;};
133 guint16 GetElement(void){return element;};
134 string GetVR(void) {return vr; };
136 bool IsVrUnknown(void);
137 string GetFourth(void) {return fourth;};
138 string GetName(void) {return name;};
139 string GetKey(void) {return key;};
143 // ---------------------------------------------------- gdcmDict
145 // c'est le Dictionnaire Dicom
149 ////////////////////////////////////////////////////////////////////////////
150 // A single DICOM dictionary i.e. a container for a collection of dictionary
151 // entries. There should be a single public dictionary (THE dictionary of
152 // the actual DICOM v3) but as many shadow dictionaries as imagers
153 // combined with all software versions...
155 typedef map<TagKey, gdcmDictEntry*> TagHT;
156 // Table de Hachage (group,Elem) --> ligne du Dictionnaire Dicom
158 typedef map<TagKey, gdcmDictEntry*> TagHT;
160 class GDCM_EXPORT gdcmDict {
165 // rempli le Dictionnaire Dicom à partir d'un fichier texte
166 gdcmDict(const char* FileName); // Read Dict from disk
168 // TODO Swig int AppendEntry(gdcmDictEntry* NewEntry);
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?
215 int LoadDicomV3Dict(void);
216 void Print(ostream&);
217 gdcmDict* GetDict(DictKey DictName);
218 gdcmDict* GetDefaultPublicDict(void);
223 // ---------------------------------------------------- ElValue
225 // C'est un Element Dicom
226 // (ce qu'on a trouve dans l'entete de l'image
227 // + ce qu'on est allé chercher dans le Dictionnaire Dicom)
232 // Ne faudrait-il pas trouver un autre nom, qui preterait moins à confusion?
233 // ElValue n'EST PAS la 'valeur d'un Element', mais la reunion d'infos
234 // trouvees dans l'Entete" du fichier ET dans le Dictionnaire
237 // The dicom header of a Dicom file contains a set of such ELement VALUES
238 // (when successfuly parsed against a given Dicom dictionary)
240 class GDCM_EXPORT ElValue {
242 gdcmDictEntry *entry;
244 bool ImplicitVr; // Even when reading explicit vr files, some
245 // elements happen to be implicit. Flag them here
246 // since we can't use the entry->vr without breaking
247 // the underlying dictionary.
248 // Might prove of some interest (see _ID_DCM_ELEM)
251 string value; // used to be char * valeurElem
252 size_t Offset; // Offset from the begining of file for direct user access
253 ElValue(gdcmDictEntry*);
254 void SetDictEntry(gdcmDictEntry *NewEntry) { entry = NewEntry; };
256 bool IsVrUnknown(void) { return entry->IsVrUnknown(); };
257 void SetLength(guint32 l){ LgrElem = l; };
258 void SetValue(string val){ value = val; };
259 void SetOffset(size_t of){ Offset = of; };
260 void SetImplicitVr(void) { ImplicitVr = true; };
261 bool IsImplicitVr(void) { return ImplicitVr; };
264 string GetValue(void) { return value; };
265 guint32 GetLength(void) { return LgrElem; };
266 size_t GetOffset(void) { return Offset; };
267 guint16 GetGroup(void) { return entry->GetGroup(); };
268 guint16 GetElement(void) { return entry->GetElement(); };
269 string GetKey(void) { return entry->GetKey(); };
270 string GetName(void) { return entry->GetName();};
275 // ---------------------------------------------------- ElValSet
277 // ... un ensemble d'Elements Dicom
280 ////////////////////////////////////////////////////////////////////////////
281 // Container for a set of successfully parsed ElValues.
282 typedef map<TagKey, ElValue*> TagElValueHT;
283 typedef map<string, ElValue*> TagElValueNameHT;
285 class GDCM_EXPORT ElValSet {
286 // We need both accesses with a TagKey and the Dictentry.Name
288 TagElValueNameHT NameHt;
291 void Print(ostream &);
292 void PrintByName(ostream &);
293 ElValue* GetElementByNumber(guint32 group, guint32 element);
294 ElValue* GetElementByName (string);
295 string GetElValueByNumber(guint32 group, guint32 element);
296 string GetElValueByName (string);
297 TagElValueHT & GetTagHt(void);
302 // ---------------------------------------------------- gdcmHeader
304 // C'est le Dicom Header d'une image donnée
305 // (tous les elements Dicom qui la composent
306 // + des info 'de service')
309 ////////////////////////////////////////////////////////////////////////////
310 // The typical usage of instances of class gdcmHeader is to classify a set of
311 // dicom files according to header information e.g. to create a file hierarchy
312 // reflecting the Patient/Study/Serie informations, or extracting a given
313 // SerieId. Accesing the content (image[s] or volume[s]) is beyond the
314 // functionality of this class and belong to gdmcFile (see below).
316 // * the various entries of the explicit value representation (VR) shall
317 // be managed within a dictionary which is shared by all gdcmHeader instances
318 // * the gdcmHeader::Set*Tag* family members cannot be defined as protected
319 // (Swig limitations for as Has_a dependency between gdcmFile and gdcmHeader)
322 typedef string VRKey;
323 typedef string VRAtr;
324 typedef map<TagKey, VRAtr> VRHT; // Value Representation Hash Table
325 // Cette Table de Hachage ne devrait servir qu'a determiner
326 // si deux caractères correspondent à une VR existante ?
328 class GDCM_EXPORT gdcmHeader {
329 void SkipBytes(guint32);
331 static VRHT *dicom_vr;
332 // Dictionaries of data elements:
333 static gdcmDictSet* Dicts; // global dictionary container
334 gdcmDict* RefPubDict; // public dictionary
335 gdcmDict* RefShaDict; // shadow dictionary (optional)
336 // Parsed element values:
337 ElValSet PubElVals; // parsed with Public Dictionary
338 ElValSet ShaElVals; // parsed with Shadow Dictionary
339 string filename; // refering underlying file
341 // The tag Image Location ((0028,0200) containing the address of
342 // the pixels) is not allways present. When we store this information
344 // outside of the elements:
347 // Ne faudrait-il pas une indication sur la presence ou non
348 // du 'groupe des pixels' dans l'entete?
349 // (voir pb du DICOMDIR)
351 // Swap code (little, big, big-bad endian): this code is not fixed
352 // during parsing.FIXME sw should be an enum e.g.
360 // Only the elements whose size are below this bound shall be loaded.
361 // By default, this upper bound is limited to 1024 (which looks reasonable
362 // when one considers the definition of the various VR contents).
363 guint32 MaxSizeLoadElementValue;
365 guint16 ReadInt16(void);
366 guint32 ReadInt32(void);
367 guint16 SwapShort(guint16);
368 guint32 SwapLong(guint32);
369 void Initialise(void);
370 void CheckSwap(void);
371 void FindLength(ElValue *);
372 guint32 FindLengthOB(void);
373 void FindVR(ElValue *);
374 void LoadElementValue(ElValue *);
375 void LoadElementValueSafe(ElValue *);
376 void SkipElementValue(ElValue *);
377 void InitVRDict(void);
378 void SwitchSwapToBigEndian(void);
379 void FixFoundLength(ElValue*, guint32);
380 bool IsAnInteger(ElValue *);
382 bool IsImplicitVRLittleEndianTransferSyntax(void);
383 bool IsExplicitVRLittleEndianTransferSyntax(void);
384 bool IsDeflatedExplicitVRLittleEndianTransferSyntax(void);
385 bool IsExplicitVRBigEndianTransferSyntax(void);
386 bool IsJPEGBaseLineProcess1TransferSyntax(void);
387 bool IsJPEGExtendedProcess2_4TransferSyntax(void);
388 bool IsJPEGExtendedProcess3_5TransferSyntax(void);
389 bool IsJPEGSpectralSelectionProcess6_8TransferSyntax(void);
392 // Il y en a encore DIX-SEPT, comme ça.
393 // Il faudrait trouver qq chose + rusé ...
398 void SetMaxSizeLoadElementValue(long);
399 ElValue * ReadNextElement(void);
400 gdcmDictEntry * IsInDicts(guint32, guint32);
408 ACR_LIBIDO}; // CLEANME
411 int anonymize(ostream&); // FIXME : anonymize should be a friend ?
413 void LoadElements(void);
414 virtual void ParseHeader(void);
415 gdcmHeader(const char* filename);
416 virtual ~gdcmHeader();
418 size_t GetPixelOffset(void);
419 void GetPixels(size_t, void *);
420 int GetSwapCode(void) { return sw; }
422 // TODO Swig int SetPubDict(string filename);
423 // When some proprietary shadow groups are disclosed, we can set
424 // up an additional specific dictionary to access extra information.
425 // TODO Swig int SetShaDict(string filename);
427 // Retrieve all potentially available tag [tag = (group, element)] names
428 // from the standard (or public) dictionary. Typical usage: enable the
429 // user of a GUI based interface to select his favorite fields for sorting
431 list<string> * GetPubTagNames(void);
432 map<string, list<string> > * GetPubTagNamesByCategory(void);
433 // Get the element values themselves:
435 string GetPubElValByName(string TagName);
436 string GetPubElValByNumber(guint16 group, guint16 element);
438 // Getting the element value representation (VR) might be needed by caller
439 // to convert the string typed content to caller's native type (think
440 // of C/C++ vs Python).
442 string GetPubElValRepByName(string TagName);
443 string GetPubElValRepByNumber(guint16 group, guint16 element);
445 TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); };
446 void PrintPubElVal(ostream & os = cout);
447 void PrintPubDict(ostream &);
449 // Same thing with the shadow :
450 // TODO Swig string* GetShaTagNames();
451 string GetShaElValByName(string TagName);
452 string GetShaElValByNumber(guint16 group, guint16 element);
453 string GetShaElValRepByName(string TagName);
454 string GetShaElValRepByNumber(guint16 group, guint16 element);
456 // Wrappers of the above (public is privileged over shadow) to avoid
457 // bugging the caller with knowing if ElVal is from the public or shadow
459 string GetElValByName(string TagName);
460 string GetElValByNumber(guint16 group, guint16 element);
461 string GetElValRepByName(string TagName);
462 string GetElValRepByNumber(guint16 group, guint16 element);
464 // TODO Swig int SetPubElValByName(string content, string TagName);
465 // TODO Swig int SetPubElValByNumber(string content, guint16 group, guint16 element);
466 // TODO Swig int SetShaElValByName(string content, string ShadowTagName);
467 // TODO Swig int SetShaElValByNumber(string content, guint16 group, guint16 element);
469 // TODO Swig int GetSwapCode();
473 // ---------------------------------------------------- gdcmFile
475 // un fichier EST_UNE entete, ou A_UNE entete ?
480 ////////////////////////////////////////////////////////////////////////////
481 // In addition to Dicom header exploration, this class is designed
482 // for accessing the image/volume content. One can also use it to
483 // write Dicom files.
484 ////// QUESTION: this looks still like an open question wether the
485 ////// relationship between a gdcmFile and gdcmHeader is of
486 ////// type IS_A or HAS_A !
488 class GDCM_EXPORT gdcmFile: public gdcmHeader
492 int Parsed; // weather allready parsed
493 string OrigFileName; // To avoid file overwrite
495 // Constructor dedicated to writing a new DICOMV3 part10 compliant
496 // file (see SetFileName, SetDcmTag and Write)
497 // TODO Swig gdcmFile();
498 // Opens (in read only and when possible) an existing file and checks
499 // for DICOM compliance. Returns NULL on failure.
500 // Note: the in-memory representation of all available tags found in
501 // the DICOM header is post-poned to first header information access.
502 // This avoid a double parsing of public part of the header when
503 // one sets an a posteriori shadow dictionary (efficiency can be
504 // seen as a side effect).
506 gdcmFile(string & filename);
508 // For promotion (performs a deepcopy of pointed header object)
509 // TODO Swig gdcmFile(gdcmHeader* header);
510 // TODO Swig ~gdcmFile();
512 // On writing purposes. When instance was created through
513 // gdcmFile(string filename) then the filename argument MUST be different
514 // from the constructor's one (no overwriting aloud).
515 // TODO Swig int SetFileName(string filename);
517 // Allocates necessary memory, copies the data (image[s]/volume[s]) to
518 // newly allocated zone and return a pointer to it:
520 void * GetImageData();
522 // Returns size (in bytes) of required memory to contain data
523 // represented in this file.
525 size_t GetImageDataSize();
527 // Copies (at most MaxSize bytes) of data to caller's memory space.
528 // Returns an error code on failure (if MaxSize is not big enough)
529 // TODO Swig int PutImageDataHere(void* destination, size_t MaxSize );
531 // Allocates ExpectedSize bytes of memory at this->Data and copies the
532 // pointed data to it.
533 // TODO Swig int SetImageData(void * Data, size_t ExpectedSize);
535 // TODO Swig int Write();
539 // ---------------------------------------------------- gdcmSerie
541 // une serie EST_UN fichier ????
545 //class gdcmSerie : gdcmFile;
548 // ---------------------------------------------------- gdcmMultiFrame
550 // un fichierMultiFrame EST_UN fichier
554 //class gdcmMultiFrame : gdcmFile;