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)
231 // The dicom header of a Dicom file contains a set of such ELement VALUES
232 // (when successfuly parsed against a given Dicom dictionary)
234 class GDCM_EXPORT ElValue {
236 gdcmDictEntry *entry;
238 bool ImplicitVr; // Even when reading explicit vr files, some
239 // elements happen to be implicit. Flag them here
240 // since we can't use the entry->vr without breaking
241 // the underlying dictionary.
242 // Might prove of some interest (see _ID_DCM_ELEM)
245 string value; // used to be char * valeurElem
246 size_t Offset; // Offset from the begining of file for direct user access
247 ElValue(gdcmDictEntry*);
248 void SetDictEntry(gdcmDictEntry *NewEntry) { entry = NewEntry; };
250 bool IsVrUnknown(void) { return entry->IsVrUnknown(); };
251 void SetLength(guint32 l){ LgrElem = l; };
252 void SetValue(string val){ value = val; };
253 void SetOffset(size_t of){ Offset = of; };
254 void SetImplicitVr(void) { ImplicitVr = true; };
255 bool IsImplicitVr(void) { return ImplicitVr; };
258 string GetValue(void) { return value; };
259 guint32 GetLength(void) { return LgrElem; };
260 size_t GetOffset(void) { return Offset; };
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();};
269 // ---------------------------------------------------- ElValSet
271 // ... un ensemble d'Elements Dicom
274 ////////////////////////////////////////////////////////////////////////////
275 // Container for a set of succefully parsed ElValues.
276 typedef map<TagKey, ElValue*> TagElValueHT;
277 typedef map<string, ElValue*> TagElValueNameHT;
279 class GDCM_EXPORT ElValSet {
280 // We need both accesses with a TagKey and the Dictentry.Name
282 TagElValueNameHT NameHt;
285 void Print(ostream &);
286 void PrintByName(ostream &);
287 ElValue* GetElementByNumber(guint32 group, guint32 element);
288 ElValue* GetElementByName(string);
289 string GetElValueByNumber(guint32 group, guint32 element);
290 string GetElValueByName(string);
291 TagElValueHT & GetTagHt(void);
296 // ---------------------------------------------------- gdcmHeader
298 // C'est le Dicom Header d'une image donnée
299 // (tous les elements Dicom qui la composent
300 // + des info 'de service')
303 ////////////////////////////////////////////////////////////////////////////
304 // The typical usage of instances of class gdcmHeader is to classify a set of
305 // dicom files according to header information e.g. to create a file hierarchy
306 // reflecting the Patient/Study/Serie informations, or extracting a given
307 // SerieId. Accesing the content (image[s] or volume[s]) is beyond the
308 // functionality of this class and belong to gdmcFile (see below).
310 // * the various entries of the explicit value representation (VR) shall
311 // be managed within a dictionary which is shared by all gdcmHeader instances
312 // * the gdcmHeader::Set*Tag* family members cannot be defined as protected
313 // (Swig limitations for as Has_a dependency between gdcmFile and gdcmHeader)
316 typedef string VRKey;
317 typedef string VRAtr;
318 typedef map<TagKey, VRAtr> VRHT; // Value Representation Hash Table
319 // Cette Table de Hachage ne devrait servir qu'a determiner
320 // si deux caractères correspondent à une VR existante ?
322 class GDCM_EXPORT gdcmHeader {
323 void SkipBytes(guint32);
325 static VRHT *dicom_vr;
326 // Dictionaries of data elements:
327 static gdcmDictSet* Dicts; // global dictionary container
328 gdcmDict* RefPubDict; // public dictionary
329 gdcmDict* RefShaDict; // shadow dictionary (optional)
330 // Parsed element values:
331 ElValSet PubElVals; // parsed with Public Dictionary
332 ElValSet ShaElVals; // parsed with Shadow Dictionary
333 string filename; // refering underlying file
335 // The tag Image Location ((0028,0200) containing the address of
336 // the pixels) is not allways present. When we store this information
338 // outside of the elements:
342 // Swap code (little, big, big-bad endian): this code is not fixed
343 // during parsing.FIXME sw should be an enum e.g.
351 // Only the elements whose size are below this bound shall be loaded.
352 // By default, this upper bound is limited to 1024 (which looks reasonable
353 // when one considers the definition of the various VR contents).
354 guint32 MaxSizeLoadElementValue;
356 guint16 ReadInt16(void);
357 guint32 ReadInt32(void);
358 guint16 SwapShort(guint16);
359 guint32 SwapLong(guint32);
360 void Initialise(void);
361 void CheckSwap(void);
362 void FindLength(ElValue *);
363 guint32 FindLengthOB(void);
364 void FindVR(ElValue *);
365 void LoadElementValue(ElValue *);
366 void LoadElementValueSafe(ElValue *);
367 void SkipElementValue(ElValue *);
368 void InitVRDict(void);
369 void SwitchSwapToBigEndian(void);
370 void FixFoundLength(ElValue*, guint32);
371 bool IsAnInteger(ElValue *);
372 bool IsBigEndianTransferSyntax(void);
373 void SetMaxSizeLoadElementValue(long);
374 ElValue * ReadNextElement(void);
375 gdcmDictEntry * IsInDicts(guint32, guint32);
383 ACR_LIBIDO}; // CLEANME
386 int anonymize(ostream&); // FIXME : anonymize should be a friend ?
388 void LoadElements(void);
389 virtual void ParseHeader(void);
390 gdcmHeader(const char* filename);
391 virtual ~gdcmHeader();
393 size_t GetPixelOffset(void);
394 void GetPixels(size_t, void *);
395 int GetSwapCode(void) { return sw; }
397 // TODO Swig int SetPubDict(string filename);
398 // When some proprietary shadow groups are disclosed, we can set
399 // up an additional specific dictionary to access extra information.
400 // TODO Swig int SetShaDict(string filename);
402 // Retrieve all potentially available tag [tag = (group, element)] names
403 // from the standard (or public) dictionary. Typical usage: enable the
404 // user of a GUI based interface to select his favorite fields for sorting
406 list<string> * GetPubTagNames(void);
407 map<string, list<string> > * GetPubTagNamesByCategory(void);
408 // Get the element values themselves:
410 string GetPubElValByName(string TagName);
411 string GetPubElValByNumber(guint16 group, guint16 element);
413 // Getting the element value representation (VR) might be needed by caller
414 // to convert the string typed content to caller's native type (think
415 // of C/C++ vs Python).
417 string GetPubElValRepByName(string TagName);
418 string GetPubElValRepByNumber(guint16 group, guint16 element);
420 TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); };
421 void PrintPubElVal(ostream & os = cout);
422 void PrintPubDict(ostream &);
424 // Same thing with the shadow :
425 // TODO Swig string* GetShaTagNames();
426 string GetShaElValByName(string TagName);
427 string GetShaElValByNumber(guint16 group, guint16 element);
428 string GetShaElValRepByName(string TagName);
429 string GetShaElValRepByNumber(guint16 group, guint16 element);
431 // Wrappers of the above (public is privileged over shadow) to avoid
432 // bugging the caller with knowing if ElVal is from the public or shadow
434 string GetElValByName(string TagName);
435 string GetElValByNumber(guint16 group, guint16 element);
436 string GetElValRepByName(string TagName);
437 string GetElValRepByNumber(guint16 group, guint16 element);
439 // TODO Swig int SetPubElValByName(string content, string TagName);
440 // TODO Swig int SetPubElValByNumber(string content, guint16 group, guint16 element);
441 // TODO Swig int SetShaElValByName(string content, string ShadowTagName);
442 // TODO Swig int SetShaElValByNumber(string content, guint16 group, guint16 element);
444 // TODO Swig int GetSwapCode();
448 // ---------------------------------------------------- gdcmFile
450 // un fichier EST_UNE entete, ou A_UNE entete ?
455 ////////////////////////////////////////////////////////////////////////////
456 // In addition to Dicom header exploration, this class is designed
457 // for accessing the image/volume content. One can also use it to
458 // write Dicom files.
459 ////// QUESTION: this looks still like an open question wether the
460 ////// relationship between a gdcmFile and gdcmHeader is of
461 ////// type IS_A or HAS_A !
463 class GDCM_EXPORT gdcmFile: gdcmHeader
467 int Parsed; // weather allready parsed
468 string OrigFileName; // To avoid file overwrite
470 // Constructor dedicated to writing a new DICOMV3 part10 compliant
471 // file (see SetFileName, SetDcmTag and Write)
472 // TODO Swig gdcmFile();
473 // Opens (in read only and when possible) an existing file and checks
474 // for DICOM compliance. Returns NULL on failure.
475 // Note: the in-memory representation of all available tags found in
476 // the DICOM header is post-poned to first header information access.
477 // This avoid a double parsing of public part of the header when
478 // one sets an a posteriori shadow dictionary (efficiency can be
479 // seen as a side effect).
481 gdcmFile(string & filename);
483 // For promotion (performs a deepcopy of pointed header object)
484 // TODO Swig gdcmFile(gdcmHeader* header);
485 // TODO Swig ~gdcmFile();
487 // On writing purposes. When instance was created through
488 // gdcmFile(string filename) then the filename argument MUST be different
489 // from the constructor's one (no overwriting aloud).
490 // TODO Swig int SetFileName(string filename);
492 // Allocates necessary memory, copies the data (image[s]/volume[s]) to
493 // newly allocated zone and return a pointer to it:
494 // TODO Swig void * GetImageData();
496 // Returns size (in bytes) of required memory to contain data
497 // represented in this file.
498 // TODO Swig size_t GetImageDataSize();
500 // Copies (at most MaxSize bytes) of data to caller's memory space.
501 // Returns an error code on failure (if MaxSize is not big enough)
502 // TODO Swig int PutImageDataHere(void* destination, size_t MaxSize );
504 // Allocates ExpectedSize bytes of memory at this->Data and copies the
505 // pointed data to it.
506 // TODO Swig int SetImageData(void * Data, size_t ExpectedSize);
508 // TODO Swig int Write();
512 // ---------------------------------------------------- gdcmSerie
514 // une serie EST_UN fichier ????
518 //class gdcmSerie : gdcmFile;
521 // ---------------------------------------------------- gdcmMultiFrame
523 // un fichierMultiFrame EST_UN fichier
527 //class gdcmMultiFrame : gdcmFile;