X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2Fgdcm.h;h=1b387098e06b74288cbe19773152e69dc3643c06;hb=81ed6935092ed908ca5c1af450f04c84baacf568;hp=0c370c6603805560215bdffac716a8491519e851;hpb=25ae0e96617ff16547270adacb5fa4fd3d9ddc0a;p=gdcm.git diff --git a/src/gdcm.h b/src/gdcm.h index 0c370c66..1b387098 100644 --- a/src/gdcm.h +++ b/src/gdcm.h @@ -1,9 +1,11 @@ +// gdcm.h + // gdcmlib Intro: // * gdcmlib is a library dedicated to reading and writing dicom files. // * LGPL for the license -// * lightweigth as opposed to CTN or DCMTK wich come bundled which try +// * lightweigth as opposed to CTN or DCMTK which come bundled which try // to implement the full DICOM standard (networking...). gdcmlib concentrates -// on reading and +// on reading and writing // * Formats: this lib should be able to read ACR-NEMA v1 and v2, Dicom v3 (as // stated in part10). [cf dcmtk/dcmdata/docs/datadict.txt] // * Targeted plateforms: Un*xes and Win32/VC++6.0 @@ -26,6 +28,30 @@ using namespace std; // string type lives in the std namespace on VC++ #include #include + // The requirement for the hash table (or map) that + // we shall use: + // 1/ First, next, last (iterators) + // 2/ should be sortable (i.e. sorted by TagKey). This + // condition shall be droped since the Win32/VC++ + // implementation doesn't look a sorted one. Pffff.... + // 3/ Make sure we can setup some default size value, + // which should be around 4500 entries which is the + // average dictionary size (said JPR) + // + // En fait, je disais que dans LE Directory Dicom (dans son etat 2002) + // il y a 1600 entrees. + // Une valeur raisonable pour un majorant du nombre d'entrees + // dans une entete DICOM d'une image semble semble etre 300 + // Si on 'decortique' les elements SQ (ce qui ne semble pas etre fait pour le moment) + // on risque en fait de depasser ... un nombre non previsible dans le cas d'une entree SQ + // contenant lui même un tres grand nombre d'entrees ?!?) + // Quant au nombre d'entrees dans un DICOMDIR, c'est encore pire : il n'est limité + // que par la taille d'un CD-ROM (les DVD-ROM ne sont pas encore pris en compte) + // On peut s'attendre a 30 entrees par fichier dicom présent sur le CD-ROM + // REMARQUE : il faudra se pencher sur le pb de la creation du DICOMDIR lorsqu'on voudra + // exporter des images lisibles par les consoles cliniques + // et pas seulement importables dans e-film. + #ifdef __GNUC__ #include #define guint16 uint16_t @@ -34,7 +60,7 @@ using namespace std; // string type lives in the std namespace on VC++ #ifdef _MSC_VER typedef unsigned short guint16; -typedef unsigned int guint32; +typedef unsigned int guint32; #endif #ifdef _MSC_VER @@ -43,6 +69,13 @@ typedef unsigned int guint32; #define GDCM_EXPORT #endif +// +// ---------------------------------------------------- gdcmDictEntry +// +// c'est une ligne du Dictionnaire Dicom +// + + //////////////////////////////////////////////////////////////////////////// // Tag based hash tables. // We shall use as keys the strings (as the C++ type) obtained by @@ -52,12 +85,13 @@ typedef unsigned int guint32; // Then the corresponding TagKey shall be the string 0010|0010 (where // the | (pipe symbol) acts as a separator). Refer to // gdcmDictEntry::TranslateToKey for this conversion function. + typedef string TagKey; class GDCM_EXPORT gdcmDictEntry { private: guint16 group; // e.g. 0x0010 - guint16 element; // e.g. 0x0010 + guint16 element; // e.g. 0x0103 string vr; // Value Representation i.e. some clue about the nature // of the data represented e.g. "FD" short for // "Floating Point Double" @@ -80,45 +114,81 @@ private: // DcmDictRangeRestriction elementRestriction; // }; public: - gdcmDictEntry(guint16 group, guint16 element, + + // fabrique une ligne de Dictionnaire Dicom à partir des parametres en entrée + + gdcmDictEntry(guint16 group, + guint16 element, string vr = "Unknown", string fourth = "Unknown", string name = "Unknown"); + + // fabrique une 'clé' par concaténation du numGroupe et du numElement + static TagKey TranslateToKey(guint16 group, guint16 element); - guint16 GetGroup(void) { return group;}; + + guint16 GetGroup(void) { return group; }; guint16 GetElement(void){return element;}; - string GetVR(void) {return vr; }; + string GetVR(void) {return vr; }; void SetVR(string); + void SetKey(string k){ key = k; } bool IsVrUnknown(void); string GetFourth(void) {return fourth;}; - string GetName(void) {return name;}; - string GetKey(void) {return key;}; + string GetName(void) {return name; }; + string GetKey(void) {return key; }; }; +// +// ---------------------------------------------------- gdcmDict +// +// c'est le Dictionnaire Dicom +// + //////////////////////////////////////////////////////////////////////////// // A single DICOM dictionary i.e. a container for a collection of dictionary // entries. There should be a single public dictionary (THE dictionary of // the actual DICOM v3) but as many shadow dictionaries as imagers // combined with all software versions... + typedef map TagHT; + // Table de Hachage : (group,Elem) --> pointeur vers une ligne du Dictionnaire Dicom class GDCM_EXPORT gdcmDict { string name; string filename; TagHT entries; public: + // rempli le Dictionnaire Dicom à partir d'un fichier texte gdcmDict(const char* FileName); // Read Dict from disk - // TODO Swig int AppendEntry(gdcmDictEntry* NewEntry); + + int AddNewEntry (gdcmDictEntry* NewEntry); + int ReplaceEntry(gdcmDictEntry* NewEntry); + int RemoveEntry (TagKey k); + int RemoveEntry (guint16 group, guint16 element); + + // renvoie une ligne de Dictionnaire Dicom à partir de (numGroup, numElement) gdcmDictEntry * GetTag(guint32 group, guint32 element); + void Print(ostream&); TagHT & GetEntries(void) { return entries; } }; + +// +// ---------------------------------------------------- gdcmDictSet +// +// Ensemble de Dictionnaires Dicom (le public + 'des' privés) +// Au cas ou l'on traiterait un jour les 'dictionnaires privés' +// - pratiquement un par constructeur, par machine, et par version du logiciel - +// +// + //////////////////////////////////////////////////////////////////////////// // Container for managing a set of loaded dictionaries. Sharing dictionaries // should avoid : // * reloading an allready loaded dictionary, // * having many in memory representations of the same dictionary. + typedef string DictKey; typedef map DictSetHT; @@ -138,15 +208,36 @@ public: // TODO Swig int LoadDictFromName(string filename); // TODO Swig int LoadAllDictFromDirectory(string DirectoryName); // TODO Swig string* GetAllDictNames(); + // + // Question : ne faudra-t-il pas mettre LE dictionnaire DICOM dans un Directory + // et les eventuels 'dictionnaires prives' dans un autre? + // (pour eviter a un utilisateur mal dégourdi de tout saccager ?) + // int LoadDicomV3Dict(void); void Print(ostream&); gdcmDict* GetDict(DictKey DictName); gdcmDict* GetDefaultPublicDict(void); }; -//////////////////////////////////////////////////////////////////////////// + +// +// ---------------------------------------------------- ElValue +// +// C'est un Element Dicom +// (ce qu'on a trouve dans l'entete de l'image +// + ce qu'on est allé chercher dans le Dictionnaire Dicom) +// + +// QUESTION: +// +// Ne faudrait-il pas trouver un autre nom, qui preterait moins à confusion? +// ElValue n'EST PAS la 'valeur d'un Element', mais la reunion d'infos +// trouvees dans l'Entete du fichier ET dans le Dictionnaire DICOM +// + // The dicom header of a Dicom file contains a set of such ELement VALUES // (when successfuly parsed against a given Dicom dictionary) + class GDCM_EXPORT ElValue { private: gdcmDictEntry *entry; @@ -160,49 +251,82 @@ private: public: string value; // used to be char * valeurElem size_t Offset; // Offset from the begining of file for direct user access + ElValue(gdcmDictEntry*); void SetDictEntry(gdcmDictEntry *NewEntry) { entry = NewEntry; }; - bool IsVrUnknown(void) { return entry->IsVrUnknown(); }; - void SetLength(guint32 l){LgrElem = l; }; - void SetValue(string val){ value = val; }; - void SetOffset(size_t of){ Offset = of; }; void SetImplicitVr(void) { ImplicitVr = true; }; bool IsImplicitVr(void) { return ImplicitVr; }; - void SetVR(string); - string GetVR(void); - string GetValue(void) { return value; }; - guint32 GetLength(void) { return LgrElem; }; - size_t GetOffset(void) { return Offset; }; - guint16 GetGroup(void) { return entry->GetGroup(); }; + + guint16 GetGroup(void) { return entry->GetGroup(); }; guint16 GetElement(void) { return entry->GetElement(); }; - string GetKey(void) { return entry->GetKey(); }; - string GetName(void) { return entry->GetName();}; + string GetKey(void) { return entry->GetKey(); }; + string GetName(void) { return entry->GetName(); }; + + string GetVR(void) { return entry->GetVR(); }; + void SetVR(string v) { entry->SetVR(v); }; + + // Question : + // Un champ privé, accessible en consultation et en modif (sans restriction) + // interet par rapport à un champ public ? + // --> pouvoir en changer la définition sans toucher à l'API + + void SetLength(guint32 l){ LgrElem = l; }; + guint32 GetLength(void) { return LgrElem; }; + + void SetValue(string val){ value = val; }; + string GetValue(void) { return value; }; + + void SetOffset(size_t of){ Offset = of; }; + size_t GetOffset(void) { return Offset; }; + }; + +// +// ---------------------------------------------------- ElValSet +// +// ... un ensemble d'Elements Dicom +// ... le résultat de l'analyse d'une entete d'image, par exemple + //////////////////////////////////////////////////////////////////////////// -// Container for a set of succefully parsed ElValues. +// Container for a set of successfully parsed ElValues. typedef map TagElValueHT; typedef map TagElValueNameHT; class GDCM_EXPORT ElValSet { // We need both accesses with a TagKey and the Dictentry.Name + TagElValueHT tagHt; TagElValueNameHT NameHt; -public: - void Add(ElValue*); +public: + void Add(ElValue*); void Print(ostream &); void PrintByName(ostream &); + int Write(FILE *fp); ElValue* GetElementByNumber(guint32 group, guint32 element); - ElValue* GetElementByName(string); - string GetElValueByNumber(guint32 group, guint32 element); - string GetElValueByName(string); - TagElValueHT & GetTagHt(void); + ElValue* GetElementByName (string); + string GetElValueByNumber(guint32 group, guint32 element); + string GetElValueByName (string); + + TagElValueHT & GetTagHt(void); + + int SetElValueByNumber(string content, guint32 group, guint32 element); + int SetElValueByName(string content, string TagName); }; + +// +// ---------------------------------------------------- gdcmHeader +// +// C'est le Dicom Header d'une image donnée +// (tous les elements Dicom qui la composent +// + des info 'de service') +// + //////////////////////////////////////////////////////////////////////////// // The typical usage of instances of class gdcmHeader is to classify a set of -// dicom files according to header information e.g. to create a file hierachy +// dicom files according to header information e.g. to create a file hierarchy // reflecting the Patient/Study/Serie informations, or extracting a given // SerieId. Accesing the content (image[s] or volume[s]) is beyond the // functionality of this class and belong to gdmcFile (see below). @@ -212,15 +336,18 @@ public: // * the gdcmHeader::Set*Tag* family members cannot be defined as protected // (Swig limitations for as Has_a dependency between gdcmFile and gdcmHeader) + typedef string VRKey; typedef string VRAtr; -typedef map VRHT; // Value Representation Hash Table +typedef map VRHT; // Value Representation Hash Table + class GDCM_EXPORT gdcmHeader { void SkipBytes(guint32); private: static VRHT *dicom_vr; // Dictionaries of data elements: + static gdcmDictSet* Dicts; // global dictionary container gdcmDict* RefPubDict; // public dictionary gdcmDict* RefShaDict; // shadow dictionary (optional) @@ -229,13 +356,23 @@ private: ElValSet ShaElVals; // parsed with Shadow Dictionary string filename; // refering underlying file FILE * fp; - // The tag Image Location ((0028,0200) containing the address of - // the pixels) is not allways present. When we store this information + // The tag Image Location (0028,0200) - containing the address of + // the pixels - is not allways present. Then we store this information + // il etait facultatif en ACR-NEMA, il n'existe plus en DICOM 3 // FIXME + + // Question : + // Qu'y a-t-il a corriger ? + // // outside of the elements: + guint16 grPixel; guint16 numPixel; - // Swap code (little, big, big-bad endian): this code is not fixed + // Ne faudrait-il pas une indication sur la presence ou non + // du 'groupe des pixels' dans l'entete? + // (voir pb du DICOMDIR) + + // Swap code (little, big, bad-big, bad-little endian): this code is not fixed // during parsing.FIXME sw should be an enum e.g. //enum EndianType { //LittleEndian, @@ -243,7 +380,8 @@ private: //BigEndian, //BadBigEndian}; int sw; - // Only the elements whose size are below this bound shall be loaded. + + // Only the elements whose size is below this bound will be loaded. // By default, this upper bound is limited to 1024 (which looks reasonable // when one considers the definition of the various VR contents). guint32 MaxSizeLoadElementValue; @@ -264,11 +402,24 @@ private: void SwitchSwapToBigEndian(void); void FixFoundLength(ElValue*, guint32); bool IsAnInteger(ElValue *); - bool IsBigEndianTransferSyntax(void); + + bool IsImplicitVRLittleEndianTransferSyntax(void); + bool IsExplicitVRLittleEndianTransferSyntax(void); + bool IsDeflatedExplicitVRLittleEndianTransferSyntax(void); + bool IsExplicitVRBigEndianTransferSyntax(void); + bool IsJPEGBaseLineProcess1TransferSyntax(void); + bool IsJPEGExtendedProcess2_4TransferSyntax(void); + bool IsJPEGExtendedProcess3_5TransferSyntax(void); + bool IsJPEGSpectralSelectionProcess6_8TransferSyntax(void); +// +// Euhhhhhhh +// Il y en a encore DIX-SEPT, comme ça. +// Il faudrait trouver qq chose + rusé ... +// + void SetMaxSizeLoadElementValue(long); ElValue * ReadNextElement(void); gdcmDictEntry * IsInDicts(guint32, guint32); - size_t GetPixelOffset(void); protected: enum FileType { Unknown = 0, @@ -285,26 +436,34 @@ public: virtual void ParseHeader(void); gdcmHeader(const char* filename); virtual ~gdcmHeader(); + + size_t GetPixelOffset(void); + void GetPixels(size_t, void *); + int GetSwapCode(void) { return sw; } // TODO Swig int SetPubDict(string filename); - // When some proprietary shadow groups are disclosed, whe can set - // up an additional specific dictionary to access extra information. + // When some proprietary shadow groups are disclosed, we can set up + // an additional specific dictionary to access extra information. // TODO Swig int SetShaDict(string filename); // Retrieve all potentially available tag [tag = (group, element)] names - // from the standard (or public) dictionary. Typical usage: enable the + // from the standard (or public) dictionary. Typical usage : enable the // user of a GUI based interface to select his favorite fields for sorting - // or selection. + // or selecting. list * GetPubTagNames(void); map > * GetPubTagNamesByCategory(void); // Get the element values themselves: + string GetPubElValByName(string TagName); string GetPubElValByNumber(guint16 group, guint16 element); + // Getting the element value representation (VR) might be needed by caller - // to convert the string typed content to caller's native type (think - // of C/C++ vs Python). + // to convert the string typed content to caller's native type + // (think of C/C++ vs Python). + string GetPubElValRepByName(string TagName); string GetPubElValRepByNumber(guint16 group, guint16 element); + TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); }; void PrintPubElVal(ostream & os = cout); void PrintPubDict(ostream &); @@ -324,28 +483,48 @@ public: string GetElValRepByName(string TagName); string GetElValRepByNumber(guint16 group, guint16 element); - // TODO Swig int SetPubElValByName(string content, string TagName); - // TODO Swig int SetPubElValByNumber(string content, guint16 group, guint16 element); - // TODO Swig int SetShaElValByName(string content, string ShadowTagName); - // TODO Swig int SetShaElValByNumber(string content, guint16 group, guint16 element); + int SetPubElValByName(string content, string TagName); + int SetPubElValByNumber(string content, guint16 group, guint16 element); + int SetShaElValByName(string content, string ShadowTagName); + int SetShaElValByNumber(string content, guint16 group, guint16 element); - // TODO Swig int GetSwapCode(); + ElValSet GetPubElVals() { return(PubElVals); } }; +// +// ---------------------------------------------------- gdcmFile +// +// un fichier EST_UNE entete, ou A_UNE entete ? +// +// On dit 'EST_UNE' ... + + //////////////////////////////////////////////////////////////////////////// // In addition to Dicom header exploration, this class is designed // for accessing the image/volume content. One can also use it to // write Dicom files. -////// QUESTION: this looks still like an open question wether the +////// QUESTION: this looks still like an open question whether the ////// relationship between a gdcmFile and gdcmHeader is of ////// type IS_A or HAS_A ! -class GDCM_EXPORT gdcmFile: gdcmHeader + +class GDCM_EXPORT gdcmFile: public gdcmHeader { private: + // QUESTION : + // Data pointe sur quoi? + // sur les Pixels lus? + // --> j'ajoute un champ public : Pixels + // (il faudra que l'utilisateur puisse modifier les pixels ?) + void* Data; int Parsed; // weather allready parsed string OrigFileName; // To avoid file overwrite public: + // je ne suis pas sur d'avoir compris *où* il serait légitime de ranger ca. + // on pourra tjs le deplacer, et mettre des accesseurs + void * Pixels; + size_t lgrTotale; + // Constructor dedicated to writing a new DICOMV3 part10 compliant // file (see SetFileName, SetDcmTag and Write) // TODO Swig gdcmFile(); @@ -355,32 +534,78 @@ public: // the DICOM header is post-poned to first header information access. // This avoid a double parsing of public part of the header when // one sets an a posteriori shadow dictionary (efficiency can be - // seen a a side effect). + // seen as a side effect). + gdcmFile(string & filename); + // For promotion (performs a deepcopy of pointed header object) // TODO Swig gdcmFile(gdcmHeader* header); // TODO Swig ~gdcmFile(); // On writing purposes. When instance was created through // gdcmFile(string filename) then the filename argument MUST be different - // from the constructor's one (no overwriting aloud). + // from the constructor's one (no overwriting allowed). // TODO Swig int SetFileName(string filename); // Allocates necessary memory, copies the data (image[s]/volume[s]) to // newly allocated zone and return a pointer to it: - // TODO Swig void * GetImageData(); + + void * GetImageData(); + // Returns size (in bytes) of required memory to contain data // represented in this file. - // TODO Swig size_t GetImageDataSize(); + + size_t GetImageDataSize(); + // Copies (at most MaxSize bytes) of data to caller's memory space. // Returns an error code on failure (if MaxSize is not big enough) - // TODO Swig int PutImageDataHere(void* destination, size_t MaxSize ); + + int PutImageDataHere(void* destination, size_t MaxSize ); + + // Question : + // + // GetImageData et PutImageDataHere + // Get et Put pour 2 fonctions qui font presque la meme chose :-( + // + // Allocates ExpectedSize bytes of memory at this->Data and copies the // pointed data to it. + + // Question : + // Pourquoi dupliquer les pixels, alors qu'on les a deja en mémoire, + // et que Data (dans le gdcmHeader) est un pointeur ? + // TODO Swig int SetImageData(void * Data, size_t ExpectedSize); + // Push to disk. + // A NE PAS OUBLIER : que fait-on en cas de Transfert Syntax (dans l'entete) + // incohérente avec l'ordre des octets en mémoire // TODO Swig int Write(); + + // Ecrit sur disque les pixels d'UNE image + // Aucun test n'est fait sur l'"Endiannerie" du processeur. + // Ca sera à l'utilisateur d'appeler son Reader correctement + + int WriteRawData (string nomFichier); + int WriteDcm (string nomFichier); }; +// +// ---------------------------------------------------- gdcmSerie +// +// une serie EST_UN fichier ???? +// +// + //class gdcmSerie : gdcmFile; + +// +// ---------------------------------------------------- gdcmMultiFrame +// +// un fichierMultiFrame EST_UN fichier +// +// + //class gdcmMultiFrame : gdcmFile; + +