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...
19 #include <stddef.h> // For size_t
23 // The requirement for the hash table (or map) that we shall use:
24 // 1/ First, next, last (iterators)
25 // 2/ should be sortable (i.e. sorted by TagKey). This condition
26 // shall be droped since the Win32/VC++ implementation doesn't look
27 // a sorted one. Pffff....
28 // 3/ Make sure we can setup some default size value, which should be
29 // around 4500 entries which is the average dictionary size (said JPR)
33 // Tag based hash tables.
34 // We shall use as keys the strings (as the C++ type) obtained by
35 // concatenating the group value and the element value (both of type
36 // unsigned 16 bit integers in Dicom) expressed in hexadecimal.
37 // Example: consider the tag given as (group, element) = (0x0010, 0x0010).
38 // Then the corresponding TagKey shall be the string 0010|0010 (where
39 // the | (pipe symbol) acts as a separator). Refer to
40 // gdcmDictEntry::TranslateToKey for this conversion function.
41 typedef string TagKey;
45 guint16 group; // e.g. 0x0010
46 guint16 element; // e.g. 0x0010
47 string vr; // Value Representation i.e. some clue about the nature
48 // of the data represented e.g. "FD" short for
49 // "Floating Point Double"
50 // CLEAN ME: find the official dicom name for this field !
51 string fourth; // Fourth field containing some semantics.
52 string name; // e.g. "Patient_Name"
53 TagKey key; // This is redundant zith (group, element) but we add
54 // on efficiency purposes.
55 // DCMTK has many fields for handling a DictEntry (see below). What are the
56 // relevant ones for gdcmlib ?
57 // struct DBI_SimpleEntry {
61 // Uint16 upperElement;
63 // const char* tagName;
66 // const char* standardVersion;
67 // DcmDictRangeRestriction groupRestriction;
68 // DcmDictRangeRestriction elementRestriction;
71 //CLEANME gdcmDictEntry();
72 gdcmDictEntry(guint16 group, guint16 element,
73 string vr, string fourth, string vr);
74 static TagKey TranslateToKey(guint16 group, guint16 element);
75 guint16 GetGroup(void) { return group;};
76 guint16 GetElement(void){return element;};
77 string GetVR(void) {return vr; };
78 void SetVR(string in){vr = in; };
79 string GetFourth(void) {return fourth;};
80 string GetName(void) {return name;};
81 string GetKey(void) {return key;};
84 typedef map<TagKey, gdcmDictEntry*> TagHT;
86 // A single DICOM dictionary i.e. a container for a collection of dictionary
87 // entries. There should be a single public dictionary (THE dictionary of
88 // the actual DICOM v3) but as many shadow dictionaries as imagers
89 // combined with all software versions...
95 gdcmDict(const char* FileName); // Read Dict from disk
96 // TODO Swig int AppendEntry(gdcmDictEntry* NewEntry);
97 gdcmDictEntry * GetTag(guint32 group, guint32 element);
101 // Container for managing a set of loaded dictionaries. Sharing dictionaries
103 // * reloading an allready loaded dictionary.
104 // * having many in memory representations of the same dictionary.
105 typedef string DictKey;
106 typedef map<DictKey, gdcmDict*> DictSetHT;
109 string DictPath; // Directory path to dictionaries
111 int AppendDict(gdcmDict* NewDict);
112 int LoadDictFromFile(string filename, DictKey);
113 void SetDictPath(void);
115 gdcmDictSet(void); // loads THE DICOM v3 dictionary
116 // TODO Swig int LoadDictFromFile(string filename);
117 ///// QUESTION: the following function might not be thread safe !? Maybe
118 ///// we need some mutex here, to avoid concurent creation of
119 ///// the same dictionary !?!?!
120 // TODO Swig int LoadDictFromName(string filename);
121 // TODO Swig int LoadAllDictFromDirectory(string DirectoryName);
122 // TODO Swig string* GetAllDictNames();
123 int LoadDicomV3Dict(void);
124 void Print(ostream&);
125 gdcmDict* GetDict(DictKey DictName);
126 gdcmDict* GetDefaultPublicDict(void);
129 // The dicom header of a Dicom file contains a set of such ELement VALUES
130 // (when successfuly parsed against a given Dicom dictionary)
133 gdcmDictEntry *entry;
135 // Might prove of some interest (see _ID_DCM_ELEM)
138 string value; // used to be char * valeurElem
139 size_t Offset; // Offset from the begining of file for direct user access
140 ElValue(gdcmDictEntry*);
143 void SetLength(guint32 l){LgrElem = l; };
144 void SetValue(string val){ value = val; };
145 void SetOffset(size_t of){ Offset = of; };
146 string GetValue(void) { return value; };
147 guint32 GetLength(void) { return LgrElem; };
148 size_t GetOffset(void) { return Offset; };
149 guint16 GetGroup(void) { return entry->GetGroup(); };
150 guint16 GetElement(void) { return entry->GetElement(); };
151 string GetKey(void) { return entry->GetKey(); };
152 string GetName(void) { return entry->GetName();};
155 typedef map<TagKey, ElValue*> TagElValueHT;
156 typedef map<string, ElValue*> TagElValueNameHT;
157 // Container for a set of succefully parsed ElValues.
159 // We need both accesses with a TagKey and the Dicentry.Name
161 TagElValueNameHT NameHt;
164 void Print(ostream &);
165 void PrintByName(ostream &);
166 ElValue* GetElement(guint32 group, guint32 element);
167 string GetElValue(guint32 group, guint32 element);
168 string GetElValue(string);
169 TagElValueHT & GetTagHt(void);
172 // The various entries of the explicit value representation (VR) shall
173 // be managed within a dictionary.
174 typedef string VRKey;
175 typedef string VRAtr;
176 typedef map<TagKey, VRAtr> VRHT; // Value Representation Hash Table
178 // The typical usage of objects of this class is to classify a set of
179 // dicom files according to header information e.g. to create a file hierachy
180 // reflecting the Patient/Study/Serie informations, or extracting a given
181 // SerieId. Accesing the content (image[s] or volume[s]) is beyond the
182 // functionality of this class (see dmcFile below).
184 // * the gdcmHeader::Set*Tag* family members cannot be defined as protected
185 // (Swig limitations for as Has_a dependency between gdcmFile and gdcmHeader)
187 //FIXME sw should be qn EndianType !!!
194 // All instances share the same value representation dictionary
195 static VRHT *dicom_vr;
196 static gdcmDictSet* Dicts; // Global dictionary container
197 gdcmDict* RefPubDict; // Public Dictionary
198 gdcmDict* RefShaDict; // Shadow Dictionary (optional)
199 ElValSet PubElVals; // Element Values parsed with Public Dictionary
200 ElValSet ShaElVals; // Element Values parsed with Shadow Dictionary
201 // In order to inspect/navigate through the file
204 // The tag Image Location ((0028,0200) containing the adress of
205 // the pixels) is not allways present. When we store this information
207 // outside of the elements:
212 guint16 ReadInt16(void);
213 guint32 ReadInt32(void);
214 guint16 SwapShort(guint16);
215 guint32 SwapLong(guint32);
216 void Initialise(void);
217 void CheckSwap(void);
218 void FindLength(ElValue *);
219 void FindVR(ElValue *);
220 void LoadElementValue(ElValue *);
221 void SkipElementValue(ElValue *);
222 void InitVRDict(void);
223 bool IsAnInteger(guint16, guint16, string, guint32);
224 ElValue * ReadNextElement(void);
225 gdcmDictEntry * IsInDicts(guint32, guint32);
226 size_t GetPixelOffset(void);
236 ///// QUESTION: Maybe Print is a better name than write !?
238 ///// QUESTION: Maybe anonymize should be a friend function !?!?
239 ///// See below for an example of how anonymize might be implemented.
240 int anonymize(ostream&);
242 void LoadElements(void);
243 virtual void ParseHeader(void);
244 gdcmHeader(const char* filename);
245 virtual ~gdcmHeader();
247 // TODO Swig int SetPubDict(string filename);
248 // When some proprietary shadow groups are disclosed, whe can set
249 // up an additional specific dictionary to access extra information.
250 // TODO Swig int SetShaDict(string filename);
252 // Retrieve all potentially available tag [tag = (group, element)] names
253 // from the standard (or public) dictionary (hence static). Typical usage:
254 // enable the user of a GUI based interface to select his favorite fields
255 // for sorting or selection.
256 // TODO Swig string* GetPubTagNames();
257 // Get the element values themselves:
258 string GetPubElValByName(string TagName);
259 string GetPubElValByNumber(guint16 group, guint16 element);
260 // Get the element value representation: (VR) might be needed by caller
261 // to convert the string typed content to caller's native type (think
262 // of C/C++ vs Python).
263 // TODO Swig string GetPubElValRepByName(string TagName);
264 // TODO Swig string GetPubElValRepByNumber(guint16 group, guint16 element);
265 TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); };
266 void PrintPubElVal(ostream & os = std::cout);
267 void PrintPubDict(ostream &);
269 // Same thing with the shadow :
270 // TODO Swig string* GetShaTagNames();
271 // TODO Swig string GetShaElValByName(string TagName);
272 // TODO Swig string GetShaElValByNumber(guint16 group, guint16 element);
273 // TODO Swig string GetShaElValRepByName(string TagName);
274 // TODO Swig string GetShaElValRepByNumber(guint16 group, guint16 element);
276 // Wrappers of the above (both public and shadow) to avoid bugging the
277 // caller with knowing if ElVal is from the public or shadow dictionary.
278 // TODO Swig string GetElValByName(string TagName);
279 // TODO Swig string GetElValByNumber(guint16 group, guint16 element);
280 // TODO Swig string GetElValRepByName(string TagName);
281 // TODO Swig string GetElValRepByNumber(guint16 group, guint16 element);
283 // TODO Swig int SetPubElValByName(string content, string TagName);
284 // TODO Swig int SetPubElValByNumber(string content, guint16 group, guint16 element);
285 // TODO Swig int SetShaElValByName(string content, string ShadowTagName);
286 // TODO Swig int SetShaElValByNumber(string content, guint16 group, guint16 element);
288 // TODO Swig int GetSwapCode();
291 // In addition to Dicom header exploration, this class is designed
292 // for accessing the image/volume content. One can also use it to
293 // write Dicom files.
294 ////// QUESTION: this looks still like an open question wether the
295 ////// relationship between a gdcmFile and gdcmHeader is of
296 ////// type IS_A or HAS_A !
297 class gdcmFile: gdcmHeader
301 int Parsed; // weather allready parsed
302 string OrigFileName; // To avoid file overwrite
304 // Constructor dedicated to writing a new DICOMV3 part10 compliant
305 // file (see SetFileName, SetDcmTag and Write)
306 // TODO Swig gdcmFile();
307 // Opens (in read only and when possible) an existing file and checks
308 // for DICOM compliance. Returns NULL on failure.
309 // Note: the in-memory representation of all available tags found in
310 // the DICOM header is post-poned to first header information access.
311 // This avoid a double parsing of public part of the header when
312 // one sets an a posteriori shadow dictionary (efficiency can be
313 // seen a a side effect).
314 gdcmFile(string & filename);
315 // For promotion (performs a deepcopy of pointed header object)
316 // TODO Swig gdcmFile(gdcmHeader* header);
317 // TODO Swig ~gdcmFile();
319 // On writing purposes. When instance was created through
320 // gdcmFile(string filename) then the filename argument MUST be different
321 // from the constructor's one (no overwriting aloud).
322 // TODO Swig int SetFileName(string filename);
324 // Allocates necessary memory, copies the data (image[s]/volume[s]) to
325 // newly allocated zone and return a pointer to it:
326 // TODO Swig void * GetImageData();
327 // Returns size (in bytes) of required memory to contain data
328 // represented in this file.
329 // TODO Swig size_t GetImageDataSize();
330 // Copies (at most MaxSize bytes) of data to caller's memory space.
331 // Returns an error code on failure (if MaxSize is not big enough)
332 // TODO Swig int PutImageDataHere(void* destination, size_t MaxSize );
333 // Allocates ExpectedSize bytes of memory at this->Data and copies the
334 // pointed data to it.
335 // TODO Swig int SetImageData(void * Data, size_t ExpectedSize);
337 // TODO Swig int Write();
340 //class gdcmSerie : gdcmFile;
341 //class gdcmMultiFrame : gdcmFile;
345 // * gdcmFile WriteDicom;
346 // WriteDicom.SetFileName("MyDicomFile.dcm");
347 // string * AllTags = gdcmHeader.GetDcmTagNames();
348 // WriteDicom.SetDcmTag(AllTags[5], "253");
349 // WriteDicom.SetDcmTag("Patient Name", "bozo");
350 // WriteDicom.SetDcmTag("Patient Name", "bozo");
351 // WriteDicom.SetImageData(Image);
352 // WriteDicom.Write();
355 // Anonymize(ostream& output) {
356 // a = gdcmFile("toto1");
357 // a.SetPubValueByName("Patient Name", "");
358 // a.SetPubValueByName("Date", "");
359 // a.SetPubValueByName("Study Date", "");