+// 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
#include <list>
#include <map>
+ // 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 <stdint.h>
#define guint16 uint16_t
#ifdef _MSC_VER
typedef unsigned short guint16;
-typedef unsigned int guint32;
+typedef unsigned int guint32;
#endif
#ifdef _MSC_VER
#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
// 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"
// 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<TagKey, gdcmDictEntry*> 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<DictKey, gdcmDict*> DictSetHT;
// 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;
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<TagKey, ElValue*> TagElValueHT;
typedef map<string, ElValue*> 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).
// * 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<TagKey, VRAtr> VRHT; // Value Representation Hash Table
+typedef map<VRKey, VRAtr> 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)
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,
//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;
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,
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<string> * GetPubTagNames(void);
map<string, list<string> > * 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 &);
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();
// 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;
+
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff