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...
27 #include <stddef.h> // For size_t
28 #include <stdio.h> // FIXME For FILE on GCC only
31 #include "gdcmException.h"
34 // The requirement for the hash table (or map) that
36 // 1/ First, next, last (iterators)
37 // 2/ should be sortable (i.e. sorted by TagKey). This
38 // condition shall be droped since the Win32/VC++
39 // implementation doesn't look a sorted one. Pffff....
40 // 3/ Make sure we can setup some default size value,
41 // which should be around 4500 entries which is the
42 // average dictionary size (said JPR)
44 // En fait, je disais que dans LE Directory Dicom (dans son etat 2001)
45 // il y a +/- 1600 entrees.
46 // Une valeur raisonable pour un majorant du nombre d'entrees
47 // dans une entete DICOM d'une image semble semble etre 300
48 // Si on 'decortique' les elements SQ (ce qui ne semble pas etre fait pour le moment)
49 // on risque en fait de depasser ... un nombre non previsible dans le cas d'une entree SQ
50 // contenant lui même un tres grand nombre d'entrees ?!?)
51 // Quant au nombre d'entrees dans un DICOMDIR, c'est encore pire : il n'est limité
52 // que par la taille d'un CD-ROM (les DVD-ROM ne sont pas encore pris en compte)
53 // On peut s'attendre a 30 entrees par fichier dicom présent sur le CD-ROM
54 // REMARQUE : il faudra se pencher sur le pb de la creation du DICOMDIR lorsqu'on voudra
55 // exporter des images lisibles par les consoles cliniques
56 // et pas seulement importables dans e-film.
60 #define guint16 uint16_t
61 #define guint32 uint32_t
65 typedef unsigned short guint16;
66 typedef unsigned int guint32;
70 #define GDCM_EXPORT __declspec( dllexport )
75 ////////////////////////////////////////////////////////////////////////////
76 // Tag based hash tables.
77 // We shall use as keys the strings (as the C++ type) obtained by
78 // concatenating the group value and the element value (both of type
79 // unsigned 16 bit integers in Dicom) expressed in hexadecimal.
80 // Example: consider the tag given as (group, element) = (0x0010, 0x0010).
81 // Then the corresponding TagKey shall be the string 0010|0010 (where
82 // the | (pipe symbol) acts as a separator). Refer to
83 // gdcmDictEntry::TranslateToKey for this conversion function.
85 typedef string TagKey;
86 typedef string TagName;
88 class GDCM_EXPORT gdcmDictEntry {
90 guint16 group; // e.g. 0x0010
91 guint16 element; // e.g. 0x0103
92 string vr; // Value Representation i.e. some clue about the nature
93 // of the data represented e.g. "FD" short for
94 // "Floating Point Double"
95 // CLEANME: find the official dicom name for this field !
96 string fourth; // Fourth field containing some semantics.
97 string name; // e.g. "Patient_Name"
98 TagKey key; // Redundant with (group, element) but we add it
99 // on efficiency purposes.
100 // DCMTK has many fields for handling a DictEntry (see below). What are the
101 // relevant ones for gdcmlib ?
102 // struct DBI_SimpleEntry {
103 // Uint16 upperGroup;
104 // Uint16 upperElement;
106 // const char* tagName;
109 // const char* standardVersion;
110 // DcmDictRangeRestriction groupRestriction;
111 // DcmDictRangeRestriction elementRestriction;
114 gdcmDictEntry(guint16 group,
116 string vr = "Unknown",
117 string fourth = "Unknown",
118 string name = "Unknown");
119 // fabrique une 'clé' par concaténation du numGroupe et du numElement
120 static TagKey TranslateToKey(guint16 group, guint16 element);
122 guint16 GetGroup(void) { return group; };
123 guint16 GetElement(void){return element;};
124 string GetVR(void) {return vr; };
126 void SetKey(string k){ key = k; }
127 bool IsVrUnknown(void);
128 string GetFourth(void) {return fourth;};
129 string GetName(void) {return name; };
130 string GetKey(void) {return key; };
133 ////////////////////////////////////////////////////////////////////////////
134 // A single DICOM dictionary i.e. a container for a collection of dictionary
135 // entries. There should be a single public dictionary (THE dictionary of
136 // the actual DICOM v3) but as many shadow dictionaries as imagers
137 // combined with all software versions...
139 typedef map<TagKey, gdcmDictEntry*> TagKeyHT;
140 typedef map<TagName, gdcmDictEntry*> TagNameHT;
142 class GDCM_EXPORT gdcmDict {
145 TagKeyHT KeyHt; // Both accesses with a TagKey or with a
146 TagNameHT NameHt; // TagName are required.
148 gdcmDict(const char* FileName); // Reads Dict from ascii file
149 int AddNewEntry (gdcmDictEntry* NewEntry);
150 int ReplaceEntry(gdcmDictEntry* NewEntry);
151 int RemoveEntry (TagKey key);
152 int RemoveEntry (guint16 group, guint16 element);
153 gdcmDictEntry * GetTagByKey(guint16 group, guint16 element);
154 gdcmDictEntry * GetTagByName(TagName name);
155 void Print(ostream&);
156 void PrintByKey(ostream&);
157 void PrintByName(ostream&);
158 TagKeyHT & GetEntries(void) { return KeyHt; }
162 ////////////////////////////////////////////////////////////////////////////
163 // Container for managing a set of loaded dictionaries. Sharing dictionaries
165 // * reloading an allready loaded dictionary,
166 // * having many in memory representations of the same dictionary.
168 typedef string DictKey;
169 typedef map<DictKey, gdcmDict*> DictSetHT;
171 class GDCM_EXPORT gdcmDictSet {
174 int AppendDict(gdcmDict* NewDict);
175 void LoadDictFromFile(string filename, DictKey);
177 static string DictPath; // Directory path to dictionaries
178 static string BuildDictPath(void);
179 static gdcmDict* DefaultPubDict;
181 static list<string> * GetPubDictTagNames(void);
182 static map<string, list<string> >* GetPubDictTagNamesByCategory(void);
183 static gdcmDict* LoadDefaultPubDict(void);
186 // TODO Swig int LoadDictFromFile(string filename);
187 // QUESTION: the following function might not be thread safe !? Maybe
188 // we need some mutex here, to avoid concurent creation of
189 // the same dictionary !?!?!
190 // TODO Swig int LoadDictFromName(string filename);
191 // TODO Swig int LoadAllDictFromDirectory(string DirectoryName);
192 // TODO Swig string* GetAllDictNames();
194 void Print(ostream&);
195 gdcmDict* GetDict(DictKey DictName);
196 gdcmDict* GetDefaultPubDict(void);
199 ///////////////////////////////////////////////////////////////////////////
200 // The dicom header of a Dicom file contains a set of such ELement VALUES
201 // (when successfuly parsed against a given Dicom dictionary)
202 class GDCM_EXPORT ElValue {
204 gdcmDictEntry *entry;
206 bool ImplicitVr; // Even when reading explicit vr files, some
207 // elements happen to be implicit. Flag them here
208 // since we can't use the entry->vr without breaking
209 // the underlying dictionary.
212 size_t Offset; // Offset from the begining of file for direct user access
214 ElValue(gdcmDictEntry*);
215 void SetDictEntry(gdcmDictEntry *NewEntry) { entry = NewEntry; };
216 bool IsVrUnknown(void) { return entry->IsVrUnknown(); };
217 void SetImplicitVr(void) { ImplicitVr = true; };
218 bool IsImplicitVr(void) { return ImplicitVr; };
220 guint16 GetGroup(void) { return entry->GetGroup(); };
221 guint16 GetElement(void) { return entry->GetElement();};
222 string GetKey(void) { return entry->GetKey(); };
223 string GetName(void) { return entry->GetName(); };
224 string GetVR(void) { return entry->GetVR(); };
225 void SetVR(string v) { entry->SetVR(v); };
226 void SetLength(guint32 l){ LgrElem = l; };
227 guint32 GetLength(void) { return LgrElem; };
229 // Question : SetLength est public
230 // (sinon, on ne pourrait pas l'appeler dans ElValSet)
231 // alors que *personne* ne devrait s'en servir !
232 // c'est *forcément* la lgr de la string 'value', non?
234 void SetValue(string val){ value = val; };
235 string GetValue(void) { return value;};
237 void SetOffset(size_t of){ Offset = of; };
238 size_t GetOffset(void) { return Offset;};
239 // Question : SetOffset est public ...
240 // Quel utilisateur serait ammené à modifier l'Offset ?
244 ////////////////////////////////////////////////////////////////////////////
245 // Container for a set of successfully parsed ElValues.
246 typedef map<TagKey, ElValue*> TagElValueHT;
247 typedef map<string, ElValue*> TagElValueNameHT;
249 class GDCM_EXPORT ElValSet {
250 TagElValueHT tagHt; // Both accesses with a TagKey or with a
251 TagElValueNameHT NameHt; // the DictEntry.Name are required.
254 void Print(ostream &);
255 void PrintByName(ostream &);
257 ElValue* GetElementByNumber(guint32 group, guint32 element);
258 ElValue* GetElementByName (string);
259 string GetElValueByNumber(guint32 group, guint32 element);
260 string GetElValueByName (string);
262 TagElValueHT & GetTagHt(void);
264 int SetElValueByNumber(string content, guint32 group, guint32 element);
265 int SetElValueByName (string content, string TagName);
267 int SetElValueLengthByNumber(guint32 l, guint32 group, guint32 element);
268 int SetElValueLengthByName (guint32 l, string TagName);
272 ////////////////////////////////////////////////////////////////////////////
273 // The purpous of an instance of gdcmHeader is to act as a container of
274 // all the elements and their corresponding values (and additionaly the
275 // corresponding DICOM dictionary entry) of the header of a DICOM file.
277 // The typical usage of instances of class gdcmHeader is to classify a set of
278 // dicom files according to header information e.g. to create a file hierarchy
279 // reflecting the Patient/Study/Serie informations, or extracting a given
280 // SerieId. Accesing the content (image[s] or volume[s]) is beyond the
281 // functionality of this class and belong to gdmcFile (see below).
283 // * the various entries of the explicit value representation (VR) shall
284 // be managed within a dictionary which is shared by all gdcmHeader instances
285 // * the gdcmHeader::Set*Tag* family members cannot be defined as protected
286 // (Swig limitations for as Has_a dependency between gdcmFile and gdcmHeader)
288 typedef string VRKey;
289 typedef string VRAtr;
290 typedef map<VRKey, VRAtr> VRHT; // Value Representation Hash Table
292 class GDCM_EXPORT gdcmHeader {
293 void SkipBytes(guint32);
295 static VRHT *dicom_vr;
296 // Dictionaries of data elements:
298 gdcmDictSet* Dicts; // global dictionary container
299 gdcmDict* RefPubDict; // public dictionary
300 gdcmDict* RefShaDict; // shadow dictionary (optional)
301 // Parsed element values:
302 ElValSet PubElVals; // parsed with Public Dictionary
303 ElValSet ShaElVals; // parsed with Shadow Dictionary
304 string filename; // refering underlying file
308 // Ne faudrait-il pas une indication sur la presence ou non
309 // du 'groupe des pixels' dans l'entete?
310 // (voir pb du DICOMDIR)
312 // Swap code (little, big, bad-big, bad-little endian): this code is not fixed
313 // during parsing.FIXME sw should be an enum e.g.
321 // Only the elements whose size is below this bound will be loaded.
322 // By default, this upper bound is limited to 1024 (which looks reasonable
323 // when one considers the definition of the various VR contents).
324 guint32 MaxSizeLoadElementValue;
326 guint16 ReadInt16(void);
327 guint32 ReadInt32(void);
328 guint16 SwapShort(guint16);
329 guint32 SwapLong(guint32);
330 guint32 FindLengthOB(void);
331 void Initialise(void);
332 void CheckSwap(void);
333 void InitVRDict(void);
334 void SwitchSwapToBigEndian(void);
335 void AddAndDefaultElements(void);
336 void SetMaxSizeLoadElementValue(long);
338 gdcmDictEntry * GetDictEntryByKey(guint16, guint16);
339 gdcmDictEntry * GetDictEntryByName(string name);
341 // ElValue related utilities
342 ElValue * ReadNextElement(void);
343 ElValue * NewElValueByKey(guint16 group, guint16 element);
344 ElValue * NewElValueByName(string name);
345 void FindLength(ElValue *);
346 void FindVR(ElValue *);
347 void LoadElementValue(ElValue *);
348 void LoadElementValueSafe(ElValue *);
349 void SkipElementValue(ElValue *);
350 void FixFoundLength(ElValue*, guint32);
351 bool IsAnInteger(ElValue *);
353 bool IsImplicitVRLittleEndianTransferSyntax(void);
354 bool IsExplicitVRLittleEndianTransferSyntax(void);
355 bool IsDeflatedExplicitVRLittleEndianTransferSyntax(void);
356 bool IsExplicitVRBigEndianTransferSyntax(void);
357 bool IsJPEGBaseLineProcess1TransferSyntax(void);
358 bool IsJPEGExtendedProcess2_4TransferSyntax(void);
359 bool IsJPEGExtendedProcess3_5TransferSyntax(void);
360 bool IsJPEGSpectralSelectionProcess6_8TransferSyntax(void);
369 ACR_LIBIDO}; // CLEANME
372 int anonymize(ostream&); // FIXME : anonymize should be a friend ?
374 void LoadElements(void);
375 virtual void ParseHeader(bool exception_on_error = false)
376 throw(gdcmFormatError);
377 gdcmHeader(const char *filename, bool exception_on_error = false)
378 throw(gdcmFileError);
379 virtual ~gdcmHeader();
381 size_t GetPixelOffset(void);
382 void GetPixels(size_t, void *);
383 int GetSwapCode(void) { return sw; }
385 // TODO Swig int SetPubDict(string filename);
386 // When some proprietary shadow groups are disclosed, we can set up
387 // an additional specific dictionary to access extra information.
388 // TODO Swig int SetShaDict(string filename);
390 // Get the element values themselves:
391 string GetPubElValByName(string TagName);
392 string GetPubElValByNumber(guint16 group, guint16 element);
394 // Getting the element value representation (VR) might be needed by caller
395 // to convert the string typed content to caller's native type
396 // (think of C/C++ vs Python).
398 string GetPubElValRepByName(string TagName);
399 string GetPubElValRepByNumber(guint16 group, guint16 element);
401 TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); };
402 void PrintPubElVal(ostream & os = cout);
403 void PrintPubDict(ostream & os = cout);
405 // Same thing with the shadow :
406 // TODO Swig string* GetShaTagNames();
407 string GetShaElValByName(string TagName);
408 string GetShaElValByNumber(guint16 group, guint16 element);
409 string GetShaElValRepByName(string TagName);
410 string GetShaElValRepByNumber(guint16 group, guint16 element);
412 // Wrappers of the above (public is privileged over shadow) to avoid
413 // bugging the caller with knowing if ElVal is from the public or shadow
415 string GetElValByName(string TagName);
416 string GetElValByNumber(guint16 group, guint16 element);
417 string GetElValRepByName(string TagName);
418 string GetElValRepByNumber(guint16 group, guint16 element);
420 int SetPubElValByName(string content, string TagName);
421 int SetPubElValByNumber(string content, guint16 group, guint16 element);
422 int SetShaElValByName(string content, string ShadowTagName);
423 int SetShaElValByNumber(string content, guint16 group, guint16 element);
425 ElValSet GetPubElVals() { return(PubElVals); }
429 // ---------------------------------------------------- gdcmFile
431 // un fichier EST_UNE entete, ou A_UNE entete ?
433 // On dit 'EST_UNE' ...
436 ////////////////////////////////////////////////////////////////////////////
437 // In addition to Dicom header exploration, this class is designed
438 // for accessing the image/volume content. One can also use it to
439 // write Dicom files.
440 ////// QUESTION: this looks still like an open question whether the
441 ////// relationship between a gdcmFile and gdcmHeader is of
442 ////// type IS_A or HAS_A !
444 class GDCM_EXPORT gdcmFile: public gdcmHeader
448 // Data pointe sur quoi?
449 // sur les Pixels lus?
450 // --> j'ajoute un champ public : Pixels
451 // (il faudra que l'utilisateur puisse modifier les pixels ?)
454 int Parsed; // weather allready parsed
455 string OrigFileName; // To avoid file overwrite
457 // je ne suis pas sur d'avoir compris *où* il serait légitime de ranger ca.
458 // on pourra tjs le deplacer, et mettre des accesseurs
462 // Constructor dedicated to writing a new DICOMV3 part10 compliant
463 // file (see SetFileName, SetDcmTag and Write)
464 // TODO Swig gdcmFile();
465 // Opens (in read only and when possible) an existing file and checks
466 // for DICOM compliance. Returns NULL on failure.
467 // Note: the in-memory representation of all available tags found in
468 // the DICOM header is post-poned to first header information access.
469 // This avoid a double parsing of public part of the header when
470 // one sets an a posteriori shadow dictionary (efficiency can be
471 // seen as a side effect).
473 gdcmFile(string & filename);
475 // For promotion (performs a deepcopy of pointed header object)
476 // TODO Swig gdcmFile(gdcmHeader* header);
477 // TODO Swig ~gdcmFile();
479 // On writing purposes. When instance was created through
480 // gdcmFile(string filename) then the filename argument MUST be different
481 // from the constructor's one (no overwriting allowed).
482 // TODO Swig int SetFileName(string filename);
484 // Allocates necessary memory, copies the data (image[s]/volume[s]) to
485 // newly allocated zone and return a pointer to it:
487 void * GetImageData();
489 // Returns size (in bytes) of required memory to contain data
490 // represented in this file.
492 size_t GetImageDataSize();
494 // Copies (at most MaxSize bytes) of data to caller's memory space.
495 // Returns an error code on failure (if MaxSize is not big enough)
497 int GetImageDataIntoVector(void* destination, size_t MaxSize );
501 // GetImageData et GetImageDataIntoVector
502 // Get et Put pour 2 fonctions qui font presque la meme chose :-(
505 // Allocates ExpectedSize bytes of memory at this->Data and copies the
506 // pointed data to it.
509 // Pourquoi dupliquer les pixels, alors qu'on les a deja en mémoire,
510 // et que Data (dans le gdcmHeader) est un pointeur ?
512 // TODO Swig int SetImageData(void * Data, size_t ExpectedSize);
515 // A NE PAS OUBLIER : que fait-on en cas de Transfert Syntax (dans l'entete)
516 // incohérente avec l'ordre des octets en mémoire
517 // TODO Swig int Write();
519 // Ecrit sur disque les pixels d'UNE image
520 // Aucun test n'est fait sur l'"Endiannerie" du processeur.
521 // Ca sera à l'utilisateur d'appeler son Reader correctement
523 int WriteRawData (string nomFichier);
524 int WriteDcm (string nomFichier);
528 // ---------------------------------------------------- gdcmSerie
530 // une serie EST_UN fichier ????
534 //class gdcmSerie : gdcmFile;
537 // ---------------------------------------------------- gdcmMultiFrame
539 // un fichierMultiFrame EST_UN fichier
543 //class gdcmMultiFrame : gdcmFile;
546 #endif // #ifndef GDCM_H