* src/gdcmHeader.cxx added a post header parsing AddAndDefaultElements

[gdcm.git] / src / gdcm.h

// 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 which come bundled which try
//   to implement the full DICOM standard (networking...). gdcmlib concentrates
//   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
//
//
// TODO
// The declarations commented out and starting with "TODO Swig" needed
// to be temporarily removed for swig to proceed correctly (in fact
// problems appears at loading of _gdcm.[so/dll]). So, simply uncomment
// 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 <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
                      //    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
#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

////////////////////////////////////////////////////////////////////////////
// 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
// unsigned 16 bit integers in Dicom) expressed in hexadecimal.
// Example: consider the tag given as (group, element) = (0x0010, 0x0010).
// 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;
typedef string TagName;

class GDCM_EXPORT gdcmDictEntry {
private:
        guint16 group;    // 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"
        // CLEANME: find the official dicom name for this field !
        string  fourth;   // Fourth field containing some semantics.
        string  name;     // e.g. "Patient_Name"
        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 upperGroup;
        //         Uint16 upperElement;
        //         DcmEVR evr;
        //         const char* tagName;
        //         int vmMin;
        //         int vmMax;
        //         const char* standardVersion;
        //         DcmDictRangeRestriction groupRestriction;
        //         DcmDictRangeRestriction elementRestriction;
        //       };
public:
        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 GetElement(void){return element;};
        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;   };
};
  
////////////////////////////////////////////////////////////////////////////
// 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*> TagKeyHT;
typedef map<TagName, gdcmDictEntry*> TagNameHT;

class GDCM_EXPORT gdcmDict {
        string name;
        string filename;
        TagKeyHT  KeyHt;                // Both accesses with a TagKey or with a
        TagNameHT NameHt;               // TagName are required.
public:
        gdcmDict(const char* FileName);   // Reads Dict from ascii file
        int AddNewEntry (gdcmDictEntry* NewEntry);
        int ReplaceEntry(gdcmDictEntry* NewEntry);
        int RemoveEntry (TagKey key);
        int RemoveEntry (guint16 group, guint16 element);
        gdcmDictEntry * GetTagByKey(guint16 group, guint16 element);
        gdcmDictEntry * GetTagByName(TagName name);
        void Print(ostream&);
        void PrintByKey(ostream&);
        void PrintByName(ostream&);
        TagKeyHT & GetEntries(void) { return KeyHt; }
};


////////////////////////////////////////////////////////////////////////////
// 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;

class GDCM_EXPORT gdcmDictSet {
private:
        string DictPath;      // Directory path to dictionaries
        DictSetHT dicts;
        int AppendDict(gdcmDict* NewDict);
        int LoadDictFromFile(string filename, DictKey);
        void SetDictPath(void);
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 !?!?!
        // 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);
};

///////////////////////////////////////////////////////////////////////////
// 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.
public:
        string  value;
        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 SetImplicitVr(void) { ImplicitVr = true; };
        bool  IsImplicitVr(void) { return ImplicitVr; };
        
        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  GetVR(void)      { return entry->GetVR();     };
        void    SetVR(string v)  { entry->SetVR(v);           }; 
        void SetLength(guint32 l){ LgrElem = l;               };
        guint32 GetLength(void)  { return LgrElem;            };
        
        // Question : SetLength est public 
        // (sinon, on ne pourrait pas l'appeler dans ElValSet)
        // alors que *personne* ne devrait s'en servir !
        // c'est *forcément* la lgr de la string 'value', non?

        void SetValue(string val){ value = val; };
        string  GetValue(void)   { return value;};

        void SetOffset(size_t of){ Offset = of; };
        size_t  GetOffset(void)  { return Offset;};
        // Question : SetOffset est public ...
        // Quel utilisateur serait ammené à modifier l'Offset ?
};


////////////////////////////////////////////////////////////////////////////
// Container for a set of successfully parsed ElValues.
typedef map<TagKey, ElValue*> TagElValueHT;
typedef map<string, ElValue*> TagElValueNameHT;

class GDCM_EXPORT ElValSet {
        TagElValueHT tagHt;             // Both accesses with a TagKey or with a
        TagElValueNameHT NameHt;        // the DictEntry.Name are required.
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);  
        
        int SetElValueByNumber(string content, guint32 group, guint32 element);
        int SetElValueByName(string content, string TagName);
};

////////////////////////////////////////////////////////////////////////////
// The purpous of an instance of gdcmHeader is to act as a container of
// all the elements and their corresponding values (and additionaly the
// corresponding DICOM dictionary entry) of the header of a DICOM file.
//
// 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 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)

typedef string VRKey;
typedef string VRAtr;
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)
        // Parsed element values:
        ElValSet PubElVals;         // parsed with Public Dictionary
        ElValSet ShaElVals;         // parsed with Shadow Dictionary
        string filename;            // refering underlying file
        FILE * fp;
        guint16 grPixel;
        guint16 numPixel;
        // 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, 
                //BadLittleEndian,
                //BigEndian, 
                //BadBigEndian};
        int sw;

        // 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;

        guint16 ReadInt16(void);
        guint32 ReadInt32(void);
        guint16 SwapShort(guint16);
        guint32 SwapLong(guint32);
        guint32 FindLengthOB(void);
        void Initialise(void);
        void CheckSwap(void);
        void InitVRDict(void);
        void SwitchSwapToBigEndian(void);
        void AddAndDefaultElements(void);
        void SetMaxSizeLoadElementValue(long);

        gdcmDictEntry * GetDictEntryByKey(guint16, guint16);
        gdcmDictEntry * GetDictEntryByName(string name);

        // ElValue related utilities
        ElValue * ReadNextElement(void);
        ElValue * NewElValueByKey(guint16 group, guint16 element);
        ElValue * NewElValueByName(string name);
        void FindLength(ElValue *);
        void FindVR(ElValue *);
        void LoadElementValue(ElValue *);
        void LoadElementValueSafe(ElValue *);
        void SkipElementValue(ElValue *);
        void FixFoundLength(ElValue*, guint32);
        bool IsAnInteger(ElValue *);
        
        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);     
                
protected:
        enum FileType {
                Unknown = 0,
                TrueDicom,
                ExplicitVR,
                ImplicitVR,
                ACR,
                ACR_LIBIDO};  // CLEANME
        FileType filetype;
        int write(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, 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
        // user of a GUI based interface to select his favorite fields for sorting
        // 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).

        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(); 
        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);

        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);

        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 whether the
//////           relationship between a gdcmFile and gdcmHeader is of
//////           type IS_A or HAS_A !

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();
        // Opens (in read only and when possible) an existing file and checks
        // for DICOM compliance. Returns NULL on failure.
        // Note: the in-memory representation of all available tags found in
        //    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 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 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:
        
         void * GetImageData();
        
        // Returns size (in bytes) of required memory to contain data
        // represented in this file.
        
        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)
        
        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;