2 // * gdcmlib is a library dedicated to reading and writing dicom files.
3 // * LGPL for the license
4 // * lightweigth as opposed to CTN or DCMTK wich come bundled which try
5 // to implement the full DICOM standard (networking...). gdcmlib concentrates
7 // * Formats: this lib should be able to read ACR-NEMA v1 and v2, Dicom v3 (as
8 // stated in part10). [cf dcmtk/dcmdata/docs/datadict.txt]
9 // * Targeted plateforms: Un*xes and Win32/VC++6.0
13 // The declarations commented out and starting with "TODO Swig" needed
14 // to be temporarily removed for swig to proceed correctly (in fact
15 // problems appears at loading of _gdcm.[so/dll]). So, simply uncomment
16 // the declaration once you provided the definition of the method...
20 #include <stddef.h> // For size_t
22 #include <stdio.h> // CLEANME
23 #include <map> // The requirement for the hash table (or map) that
25 // 1/ First, next, last (iterators)
26 // 2/ should be sortable (i.e. sorted by TagKey). This
27 // condition shall be droped since the Win32/VC++
28 // implementation doesn't look a sorted one. Pffff....
29 // 3/ Make sure we can setup some default size value,
30 // which should be around 4500 entries which is the
31 // average dictionary size (said JPR)
34 using namespace std; // string type lives in the std namespace on VC++
37 #define GDCM_EXPORT __declspec( dllexport )
42 // Tag based hash tables.
43 // We shall use as keys the strings (as the C++ type) obtained by
44 // concatenating the group value and the element value (both of type
45 // unsigned 16 bit integers in Dicom) expressed in hexadecimal.
46 // Example: consider the tag given as (group, element) = (0x0010, 0x0010).
47 // Then the corresponding TagKey shall be the string 0010|0010 (where
48 // the | (pipe symbol) acts as a separator). Refer to
49 // gdcmDictEntry::TranslateToKey for this conversion function.
50 typedef string TagKey;
52 class GDCM_EXPORT gdcmDictEntry {
54 guint16 group; // e.g. 0x0010
55 guint16 element; // e.g. 0x0010
56 string vr; // Value Representation i.e. some clue about the nature
57 // of the data represented e.g. "FD" short for
58 // "Floating Point Double"
59 // CLEAN ME: find the official dicom name for this field !
60 string fourth; // Fourth field containing some semantics.
61 string name; // e.g. "Patient_Name"
62 TagKey key; // This is redundant zith (group, element) but we add
63 // on efficiency purposes.
64 // DCMTK has many fields for handling a DictEntry (see below). What are the
65 // relevant ones for gdcmlib ?
66 // struct DBI_SimpleEntry {
70 // Uint16 upperElement;
72 // const char* tagName;
75 // const char* standardVersion;
76 // DcmDictRangeRestriction groupRestriction;
77 // DcmDictRangeRestriction elementRestriction;
80 //CLEANME gdcmDictEntry();
81 gdcmDictEntry(guint16 group, guint16 element,
82 string vr, string fourth, string name);
83 static TagKey TranslateToKey(guint16 group, guint16 element);
84 guint16 GetGroup(void) { return group;};
85 guint16 GetElement(void){return element;};
86 string GetVR(void) {return vr; };
87 void SetVR(string in){vr = in; };
88 string GetFourth(void) {return fourth;};
89 string GetName(void) {return name;};
90 string GetKey(void) {return key;};
93 typedef map<TagKey, gdcmDictEntry*> TagHT;
95 // A single DICOM dictionary i.e. a container for a collection of dictionary
96 // entries. There should be a single public dictionary (THE dictionary of
97 // the actual DICOM v3) but as many shadow dictionaries as imagers
98 // combined with all software versions...
99 class GDCM_EXPORT gdcmDict {
104 gdcmDict(const char* FileName); // Read Dict from disk
105 // TODO Swig int AppendEntry(gdcmDictEntry* NewEntry);
106 gdcmDictEntry * GetTag(guint32 group, guint32 element);
107 void Print(ostream&);
110 // Container for managing a set of loaded dictionaries. Sharing dictionaries
112 // * reloading an allready loaded dictionary.
113 // * having many in memory representations of the same dictionary.
114 typedef string DictKey;
115 typedef map<DictKey, gdcmDict*> DictSetHT;
116 class GDCM_EXPORT gdcmDictSet {
118 string DictPath; // Directory path to dictionaries
120 int AppendDict(gdcmDict* NewDict);
121 int LoadDictFromFile(string filename, DictKey);
122 void SetDictPath(void);
124 gdcmDictSet(void); // loads THE DICOM v3 dictionary
125 // TODO Swig int LoadDictFromFile(string filename);
126 ///// QUESTION: the following function might not be thread safe !? Maybe
127 ///// we need some mutex here, to avoid concurent creation of
128 ///// the same dictionary !?!?!
129 // TODO Swig int LoadDictFromName(string filename);
130 // TODO Swig int LoadAllDictFromDirectory(string DirectoryName);
131 // TODO Swig string* GetAllDictNames();
132 int LoadDicomV3Dict(void);
133 void Print(ostream&);
134 gdcmDict* GetDict(DictKey DictName);
135 gdcmDict* GetDefaultPublicDict(void);
138 // The dicom header of a Dicom file contains a set of such ELement VALUES
139 // (when successfuly parsed against a given Dicom dictionary)
140 class GDCM_EXPORT ElValue {
142 gdcmDictEntry *entry;
144 // Might prove of some interest (see _ID_DCM_ELEM)
147 string value; // used to be char * valeurElem
148 size_t Offset; // Offset from the begining of file for direct user access
149 ElValue(gdcmDictEntry*);
152 void SetLength(guint32 l){LgrElem = l; };
153 void SetValue(string val){ value = val; };
154 void SetOffset(size_t of){ Offset = of; };
155 string GetValue(void) { return value; };
156 guint32 GetLength(void) { return LgrElem; };
157 size_t GetOffset(void) { return Offset; };
158 guint16 GetGroup(void) { return entry->GetGroup(); };
159 guint16 GetElement(void) { return entry->GetElement(); };
160 string GetKey(void) { return entry->GetKey(); };
161 string GetName(void) { return entry->GetName();};
164 typedef map<TagKey, ElValue*> TagElValueHT;
165 typedef map<string, ElValue*> TagElValueNameHT;
166 // Container for a set of succefully parsed ElValues.
167 class GDCM_EXPORT ElValSet {
168 // We need both accesses with a TagKey and the Dicentry.Name
170 TagElValueNameHT NameHt;
173 void Print(ostream &);
174 void PrintByName(ostream &);
175 ElValue* GetElement(guint32 group, guint32 element);
176 string GetElValue(guint32 group, guint32 element);
177 string GetElValue(string);
178 TagElValueHT & GetTagHt(void);
181 // The various entries of the explicit value representation (VR) shall
182 // be managed within a dictionary.
183 typedef string VRKey;
184 typedef string VRAtr;
185 typedef map<TagKey, VRAtr> VRHT; // Value Representation Hash Table
187 // The typical usage of objects of this class is to classify a set of
188 // dicom files according to header information e.g. to create a file hierachy
189 // reflecting the Patient/Study/Serie informations, or extracting a given
190 // SerieId. Accesing the content (image[s] or volume[s]) is beyond the
191 // functionality of this class (see dmcFile below).
193 // * the gdcmHeader::Set*Tag* family members cannot be defined as protected
194 // (Swig limitations for as Has_a dependency between gdcmFile and gdcmHeader)
195 class GDCM_EXPORT gdcmHeader {
196 //FIXME sw should be qn EndianType !!!
203 // All instances share the same value representation dictionary
204 static VRHT *dicom_vr;
205 static gdcmDictSet* Dicts; // Global dictionary container
206 gdcmDict* RefPubDict; // Public Dictionary
207 gdcmDict* RefShaDict; // Shadow Dictionary (optional)
208 ElValSet PubElVals; // Element Values parsed with Public Dictionary
209 ElValSet ShaElVals; // Element Values parsed with Shadow Dictionary
210 // In order to inspect/navigate through the file
213 // The tag Image Location ((0028,0200) containing the adress of
214 // the pixels) is not allways present. When we store this information
216 // outside of the elements:
221 guint16 ReadInt16(void);
222 guint32 ReadInt32(void);
223 guint16 SwapShort(guint16);
224 guint32 SwapLong(guint32);
225 void Initialise(void);
226 void CheckSwap(void);
227 void FindLength(ElValue *);
228 void FindVR(ElValue *);
229 void LoadElementValue(ElValue *);
230 void SkipElementValue(ElValue *);
231 void InitVRDict(void);
232 bool IsAnInteger(guint16, guint16, string, guint32);
233 ElValue * ReadNextElement(void);
234 gdcmDictEntry * IsInDicts(guint32, guint32);
235 size_t GetPixelOffset(void);
245 ///// QUESTION: Maybe Print is a better name than write !?
247 ///// QUESTION: Maybe anonymize should be a friend function !?!?
248 ///// See below for an example of how anonymize might be implemented.
249 int anonymize(ostream&);
251 void LoadElements(void);
252 virtual void ParseHeader(void);
253 gdcmHeader(const char* filename);
254 virtual ~gdcmHeader();
256 // TODO Swig int SetPubDict(string filename);
257 // When some proprietary shadow groups are disclosed, whe can set
258 // up an additional specific dictionary to access extra information.
259 // TODO Swig int SetShaDict(string filename);
261 // Retrieve all potentially available tag [tag = (group, element)] names
262 // from the standard (or public) dictionary (hence static). Typical usage:
263 // enable the user of a GUI based interface to select his favorite fields
264 // for sorting or selection.
265 // TODO Swig string* GetPubTagNames();
266 // Get the element values themselves:
267 string GetPubElValByName(string TagName);
268 string GetPubElValByNumber(guint16 group, guint16 element);
269 // Get the element value representation: (VR) might be needed by caller
270 // to convert the string typed content to caller's native type (think
271 // of C/C++ vs Python).
272 // TODO Swig string GetPubElValRepByName(string TagName);
273 // TODO Swig string GetPubElValRepByNumber(guint16 group, guint16 element);
274 TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); };
275 void PrintPubElVal(ostream & os = cout);
276 void PrintPubDict(ostream &);
278 // Same thing with the shadow :
279 // TODO Swig string* GetShaTagNames();
280 // TODO Swig string GetShaElValByName(string TagName);
281 // TODO Swig string GetShaElValByNumber(guint16 group, guint16 element);
282 // TODO Swig string GetShaElValRepByName(string TagName);
283 // TODO Swig string GetShaElValRepByNumber(guint16 group, guint16 element);
285 // Wrappers of the above (both public and shadow) to avoid bugging the
286 // caller with knowing if ElVal is from the public or shadow dictionary.
287 // TODO Swig string GetElValByName(string TagName);
288 // TODO Swig string GetElValByNumber(guint16 group, guint16 element);
289 // TODO Swig string GetElValRepByName(string TagName);
290 // TODO Swig string GetElValRepByNumber(guint16 group, guint16 element);
292 // TODO Swig int SetPubElValByName(string content, string TagName);
293 // TODO Swig int SetPubElValByNumber(string content, guint16 group, guint16 element);
294 // TODO Swig int SetShaElValByName(string content, string ShadowTagName);
295 // TODO Swig int SetShaElValByNumber(string content, guint16 group, guint16 element);
297 // TODO Swig int GetSwapCode();
300 // In addition to Dicom header exploration, this class is designed
301 // for accessing the image/volume content. One can also use it to
302 // write Dicom files.
303 ////// QUESTION: this looks still like an open question wether the
304 ////// relationship between a gdcmFile and gdcmHeader is of
305 ////// type IS_A or HAS_A !
306 class GDCM_EXPORT gdcmFile: gdcmHeader
310 int Parsed; // weather allready parsed
311 string OrigFileName; // To avoid file overwrite
313 // Constructor dedicated to writing a new DICOMV3 part10 compliant
314 // file (see SetFileName, SetDcmTag and Write)
315 // TODO Swig gdcmFile();
316 // Opens (in read only and when possible) an existing file and checks
317 // for DICOM compliance. Returns NULL on failure.
318 // Note: the in-memory representation of all available tags found in
319 // the DICOM header is post-poned to first header information access.
320 // This avoid a double parsing of public part of the header when
321 // one sets an a posteriori shadow dictionary (efficiency can be
322 // seen a a side effect).
323 gdcmFile(string & filename);
324 // For promotion (performs a deepcopy of pointed header object)
325 // TODO Swig gdcmFile(gdcmHeader* header);
326 // TODO Swig ~gdcmFile();
328 // On writing purposes. When instance was created through
329 // gdcmFile(string filename) then the filename argument MUST be different
330 // from the constructor's one (no overwriting aloud).
331 // TODO Swig int SetFileName(string filename);
333 // Allocates necessary memory, copies the data (image[s]/volume[s]) to
334 // newly allocated zone and return a pointer to it:
335 // TODO Swig void * GetImageData();
336 // Returns size (in bytes) of required memory to contain data
337 // represented in this file.
338 // TODO Swig size_t GetImageDataSize();
339 // Copies (at most MaxSize bytes) of data to caller's memory space.
340 // Returns an error code on failure (if MaxSize is not big enough)
341 // TODO Swig int PutImageDataHere(void* destination, size_t MaxSize );
342 // Allocates ExpectedSize bytes of memory at this->Data and copies the
343 // pointed data to it.
344 // TODO Swig int SetImageData(void * Data, size_t ExpectedSize);
346 // TODO Swig int Write();
349 //class gdcmSerie : gdcmFile;
350 //class gdcmMultiFrame : gdcmFile;
354 // * gdcmFile WriteDicom;
355 // WriteDicom.SetFileName("MyDicomFile.dcm");
356 // string * AllTags = gdcmHeader.GetDcmTagNames();
357 // WriteDicom.SetDcmTag(AllTags[5], "253");
358 // WriteDicom.SetDcmTag("Patient Name", "bozo");
359 // WriteDicom.SetDcmTag("Patient Name", "bozo");
360 // WriteDicom.SetImageData(Image);
361 // WriteDicom.Write();
364 // Anonymize(ostream& output) {
365 // a = gdcmFile("toto1");
366 // a.SetPubValueByName("Patient Name", "");
367 // a.SetPubValueByName("Date", "");
368 // a.SetPubValueByName("Study Date", "");