+// 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
// 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
// the declaration once you provided the definition of the method...
#include <string>
+#ifdef _MSC_VER
+using namespace std; // string type lives in the std namespace on VC++
+#endif
+
#include <iostream>
#include <stddef.h> // For size_t
-#include <glib.h>
-#include <stdio.h> // CLEANME
-#include <map> // The requirement for the hash table (or map) that
+#include <stdio.h> // FIXME For FILE on GCC only
+#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
// 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 _MSC_VER
- using namespace std; // string type lives in the std namespace on VC++
+
+#ifdef __GNUC__
+#include <stdint.h>
+#define guint16 uint16_t
+#define guint32 uint32_t
#endif
+
+#ifdef _MSC_VER
+typedef unsigned short guint16;
+typedef unsigned int guint32;
+#endif
+
#ifdef _MSC_VER
#define GDCM_EXPORT __declspec( dllexport )
#else
#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
// concatenating the group value and the element value (both of type
// 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"
- // CLEAN ME: find the official dicom name for this field !
+ // CLEANME: find the official dicom name for this field !
string fourth; // Fourth field containing some semantics.
string name; // e.g. "Patient_Name"
- TagKey key; // This is redundant zith (group, element) but we add
+ TagKey key; // Redundant with (group, element) but we add it
// on efficiency purposes.
// DCMTK has many fields for handling a DictEntry (see below). What are the
// relevant ones for gdcmlib ?
// struct DBI_SimpleEntry {
- // Uint16 group;
- // Uint16 element;
// Uint16 upperGroup;
// Uint16 upperElement;
// DcmEVR evr;
// DcmDictRangeRestriction elementRestriction;
// };
public:
- //CLEANME gdcmDictEntry();
+
+ // fabrique une ligne de Dictionnaire Dicom à partir des parametres en entrée
+
+
gdcmDictEntry(guint16 group, guint16 element,
- string vr, string fourth, string name);
+ 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 GetElement(void){return element;};
string GetVR(void) {return vr; };
- void SetVR(string in){vr = in; };
+ void SetVR(string);
+ bool IsVrUnknown(void);
string GetFourth(void) {return fourth;};
string GetName(void) {return name;};
string GetKey(void) {return key;};
};
-typedef map<TagKey, gdcmDictEntry*> TagHT;
+//
+// ---------------------------------------------------- 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) --> ligne du Dictionnaire Dicom
+
+typedef map<TagKey, gdcmDictEntry*> TagHT;
+
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);
+
+ // 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.
+// * reloading an allready loaded dictionary,
// * having many in memory representations of the same dictionary.
+
typedef string DictKey;
typedef map<DictKey, gdcmDict*> DictSetHT;
+
class GDCM_EXPORT gdcmDictSet {
private:
string DictPath; // Directory path to dictionaries
public:
gdcmDictSet(void); // loads THE DICOM v3 dictionary
// TODO Swig int LoadDictFromFile(string filename);
-///// QUESTION: the following function might not be thread safe !? Maybe
-///// we need some mutex here, to avoid concurent creation of
-///// the same dictionary !?!?!
+ // QUESTION: the following function might not be thread safe !? Maybe
+ // we need some mutex here, to avoid concurent creation of
+ // the same dictionary !?!?!
// 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?
+ //
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)
+//
+
+
// 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;
guint32 LgrElem;
+ bool ImplicitVr; // Even when reading explicit vr files, some
+ // elements happen to be implicit. Flag them here
+ // since we can't use the entry->vr without breaking
+ // the underlying dictionary.
// Might prove of some interest (see _ID_DCM_ELEM)
// int Swap;
public:
string value; // used to be char * valeurElem
size_t Offset; // Offset from the begining of file for direct user access
ElValue(gdcmDictEntry*);
- void SetVR(string);
- string GetVR(void);
- void SetLength(guint32 l){LgrElem = l; };
+ 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; };
+ guint32 GetLength(void) { return LgrElem; };
size_t GetOffset(void) { return Offset; };
guint16 GetGroup(void) { return entry->GetGroup(); };
guint16 GetElement(void) { return entry->GetElement(); };
string GetName(void) { return entry->GetName();};
};
+
+//
+// ---------------------------------------------------- ElValSet
+//
+// ... un ensemble d'Elements Dicom
+//
+
+////////////////////////////////////////////////////////////////////////////
+// Container for a set of succefully parsed ElValues.
typedef map<TagKey, ElValue*> TagElValueHT;
typedef map<string, ElValue*> TagElValueNameHT;
-// Container for a set of succefully parsed ElValues.
+
class GDCM_EXPORT ElValSet {
- // We need both accesses with a TagKey and the Dicentry.Name
+ // We need both accesses with a TagKey and the Dictentry.Name
TagElValueHT tagHt;
TagElValueNameHT NameHt;
public:
void Add(ElValue*);
void Print(ostream &);
void PrintByName(ostream &);
- ElValue* GetElement(guint32 group, guint32 element);
- string GetElValue(guint32 group, guint32 element);
- string GetElValue(string);
+ ElValue* GetElementByNumber(guint32 group, guint32 element);
+ ElValue* GetElementByName(string);
+ string GetElValueByNumber(guint32 group, guint32 element);
+ string GetElValueByName(string);
TagElValueHT & GetTagHt(void);
};
-// The various entries of the explicit value representation (VR) shall
-// be managed within a dictionary.
-typedef string VRKey;
-typedef string VRAtr;
-typedef map<TagKey, VRAtr> VRHT; // Value Representation Hash Table
-// The typical usage of objects of this class is to classify a set of
-// dicom files according to header information e.g. to create a file hierachy
+//
+// ---------------------------------------------------- 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 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 (see dmcFile below).
+// functionality of this class and belong to gdmcFile (see below).
// Notes:
+// * the various entries of the explicit value representation (VR) shall
+// be managed within a dictionary which is shared by all gdcmHeader instances
// * the gdcmHeader::Set*Tag* family members cannot be defined as protected
// (Swig limitations for as Has_a dependency between gdcmFile and gdcmHeader)
-class GDCM_EXPORT gdcmHeader {
-//FIXME sw should be qn EndianType !!!
- //enum EndianType {
- //LittleEndian,
- //BadLittleEndian,
- //BigEndian,
- //BadBigEndian};
+
+
+typedef string VRKey;
+typedef string VRAtr;
+typedef map<TagKey, VRAtr> VRHT; // Value Representation Hash Table
+ // Cette Table de Hachage ne devrait servir qu'a determiner
+ // si deux caractères correspondent à une VR existante ?
+
+class GDCM_EXPORT gdcmHeader {
+ void SkipBytes(guint32);
private:
- // All instances share the same value representation dictionary
static VRHT *dicom_vr;
- static gdcmDictSet* Dicts; // Global dictionary container
- gdcmDict* RefPubDict; // Public Dictionary
- gdcmDict* RefShaDict; // Shadow Dictionary (optional)
- ElValSet PubElVals; // Element Values parsed with Public Dictionary
- ElValSet ShaElVals; // Element Values parsed with Shadow Dictionary
- // In order to inspect/navigate through the file
- string filename;
+ // Dictionaries of data elements:
+ static gdcmDictSet* Dicts; // global dictionary container
+ gdcmDict* RefPubDict; // public dictionary
+ gdcmDict* RefShaDict; // shadow dictionary (optional)
+ // Parsed element values:
+ ElValSet PubElVals; // parsed with Public Dictionary
+ ElValSet ShaElVals; // parsed with Shadow Dictionary
+ string filename; // refering underlying file
FILE * fp;
- // The tag Image Location ((0028,0200) containing the adress of
+ // The tag Image Location ((0028,0200) containing the address of
// the pixels) is not allways present. When we store this information
// FIXME
// outside of the elements:
guint16 grPixel;
guint16 numPixel;
+
+ // Swap code (little, big, big-bad endian): this code is not fixed
+ // during parsing.FIXME sw should be an enum e.g.
+ //enum EndianType {
+ //LittleEndian,
+ //BadLittleEndian,
+ //BigEndian,
+ //BadBigEndian};
int sw;
+ // Only the elements whose size are below this bound shall 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;
+
guint16 ReadInt16(void);
guint32 ReadInt32(void);
guint16 SwapShort(guint16);
void Initialise(void);
void CheckSwap(void);
void FindLength(ElValue *);
+ guint32 FindLengthOB(void);
void FindVR(ElValue *);
void LoadElementValue(ElValue *);
+ void LoadElementValueSafe(ElValue *);
void SkipElementValue(ElValue *);
void InitVRDict(void);
- bool IsAnInteger(guint16, guint16, string, guint32);
- ElValue * ReadNextElement(void);
+ void SwitchSwapToBigEndian(void);
+ void FixFoundLength(ElValue*, guint32);
+ bool IsAnInteger(ElValue *);
+ bool IsBigEndianTransferSyntax(void);
+ void SetMaxSizeLoadElementValue(long);
+ ElValue * ReadNextElement(void);
gdcmDictEntry * IsInDicts(guint32, guint32);
- size_t GetPixelOffset(void);
protected:
enum FileType {
Unknown = 0,
ExplicitVR,
ImplicitVR,
ACR,
- ACR_LIBIDO};
+ ACR_LIBIDO}; // CLEANME
FileType filetype;
-///// QUESTION: Maybe Print is a better name than write !?
int write(ostream&);
-///// QUESTION: Maybe anonymize should be a friend function !?!?
-///// See below for an example of how anonymize might be implemented.
- int anonymize(ostream&);
+ int anonymize(ostream&); // FIXME : anonymize should be a friend ?
public:
void LoadElements(void);
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
+ // 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 (hence static). Typical usage:
- // enable the user of a GUI based interface to select his favorite fields
- // for sorting or selection.
- // TODO Swig string* GetPubTagNames();
+ // 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.
+ 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);
- // Get the element value representation: (VR) might be needed by caller
+
+ // 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).
- // TODO Swig string GetPubElValRepByName(string TagName);
- // TODO Swig string GetPubElValRepByNumber(guint16 group, guint16 element);
+
+ string GetPubElValRepByName(string TagName);
+ string GetPubElValRepByNumber(guint16 group, guint16 element);
+
TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); };
void PrintPubElVal(ostream & os = cout);
void PrintPubDict(ostream &);
// Same thing with the shadow :
// TODO Swig string* GetShaTagNames();
- // TODO Swig string GetShaElValByName(string TagName);
- // TODO Swig string GetShaElValByNumber(guint16 group, guint16 element);
- // TODO Swig string GetShaElValRepByName(string TagName);
- // TODO Swig string GetShaElValRepByNumber(guint16 group, guint16 element);
-
- // Wrappers of the above (both public and shadow) to avoid bugging the
- // caller with knowing if ElVal is from the public or shadow dictionary.
- // TODO Swig string GetElValByName(string TagName);
- // TODO Swig string GetElValByNumber(guint16 group, guint16 element);
- // TODO Swig string GetElValRepByName(string TagName);
- // TODO Swig string GetElValRepByNumber(guint16 group, guint16 element);
+ string GetShaElValByName(string TagName);
+ string GetShaElValByNumber(guint16 group, guint16 element);
+ string GetShaElValRepByName(string TagName);
+ string GetShaElValRepByNumber(guint16 group, guint16 element);
+
+ // Wrappers of the above (public is privileged over shadow) to avoid
+ // bugging the caller with knowing if ElVal is from the public or shadow
+ // dictionary.
+ string GetElValByName(string TagName);
+ string GetElValByNumber(guint16 group, guint16 element);
+ 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 GetSwapCode();
};
+//
+// ---------------------------------------------------- gdcmFile
+//
+// un fichier EST_UNE entete, ou A_UNE entete ?
+//
+//
+
+
+////////////////////////////////////////////////////////////////////////////
// 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
////// relationship between a gdcmFile and gdcmHeader is of
////// type IS_A or HAS_A !
+
class GDCM_EXPORT gdcmFile: gdcmHeader
{
private:
void* Data;
- int Parsed; // weather allready parsed
- string OrigFileName; // To avoid file overwrite
+ int Parsed; // weather allready parsed
+ string OrigFileName; // To avoid file overwrite
public:
// Constructor dedicated to writing a new DICOMV3 part10 compliant
// file (see SetFileName, SetDcmTag and Write)
// 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();
// Allocates necessary memory, copies the data (image[s]/volume[s]) to
// newly allocated zone and return a pointer to it:
// TODO Swig void * GetImageData();
+
// Returns size (in bytes) of required memory to contain data
// represented in this file.
// TODO Swig 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 );
+
// Allocates ExpectedSize bytes of memory at this->Data and copies the
// pointed data to it.
// TODO Swig int SetImageData(void * Data, size_t ExpectedSize);
// TODO Swig int Write();
};
+//
+// ---------------------------------------------------- gdcmSerie
+//
+// une serie EST_UN fichier ????
+//
+//
+
//class gdcmSerie : gdcmFile;
-//class gdcmMultiFrame : gdcmFile;
//
-//Examples:
-// * gdcmFile WriteDicom;
-// WriteDicom.SetFileName("MyDicomFile.dcm");
-// string * AllTags = gdcmHeader.GetDcmTagNames();
-// WriteDicom.SetDcmTag(AllTags[5], "253");
-// WriteDicom.SetDcmTag("Patient Name", "bozo");
-// WriteDicom.SetDcmTag("Patient Name", "bozo");
-// WriteDicom.SetImageData(Image);
-// WriteDicom.Write();
-//
-//
-// Anonymize(ostream& output) {
-// a = gdcmFile("toto1");
-// a.SetPubValueByName("Patient Name", "");
-// a.SetPubValueByName("Date", "");
-// a.SetPubValueByName("Study Date", "");
-// a.write(output);
-// }
+// ---------------------------------------------------- gdcmMultiFrame
+//
+// un fichierMultiFrame EST_UN fichier
+//
+//
+
+//class gdcmMultiFrame : gdcmFile;
+
+
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff