-// 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...
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcm.h,v $
+ Language: C++
+ Date: $Date: 2005/11/18 14:40:36 $
+ Version: $Revision: 1.56 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
#ifndef GDCM_H
#define GDCM_H
-#include <string>
-using namespace std;
-
-#include <iostream>
-#include <stddef.h> // For size_t
-#include <stdio.h> // FIXME For FILE on GCC only
-#include <list>
-#include <map>
-#include "gdcmException.h"
-
-
- // 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 2001)
- // 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 ?
-};
-
+// General purpose include file. This file should be included by
+// external users of gdcm. It exposes the necessary API.
-////////////////////////////////////////////////////////////////////////////
-// Container for a set of successfully parsed ElValues.
-typedef map<TagKey, ElValue*> TagElValueHT;
-typedef map<string, ElValue*> TagElValueNameHT;
+// No user should use any ".h" file that doesn't appear here!
-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);
-
- int SetElValueLengthByNumber(guint32 l, guint32 group, guint32 element);
- int SetElValueLengthByName (guint32 l, string TagName);
+#include "gdcmCommon.h"
+#include "gdcmUtil.h"
+#include "gdcmDebug.h"
-};
+#include "gdcmDictEntry.h"
+#include "gdcmDict.h"
+#include "gdcmDictSet.h"
-////////////////////////////////////////////////////////////////////////////
-// 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)
+#include "gdcmDataEntry.h"
+#include "gdcmSeqEntry.h"
+#include "gdcmSQItem.h"
-typedef string VRKey;
-typedef string VRAtr;
-typedef map<VRKey, VRAtr> VRHT; // Value Representation Hash Table
+#include "gdcmDocument.h"
+#include "gdcmFile.h"
-class GDCM_EXPORT gdcmHeader {
- void SkipBytes(guint32);
-private:
- static VRHT *dicom_vr;
- // Dictionaries of data elements:
+#include "gdcmFileHelper.h"
+#include "gdcmSerieHelper.h"
+#include "gdcmOrientation.h"
- 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;
+#include "gdcmDicomDir.h"
+#include "gdcmDicomDirPatient.h"
+#include "gdcmDicomDirStudy.h"
+#include "gdcmDicomDirSerie.h"
+#include "gdcmDicomDirImage.h"
+#include "gdcmDicomDirVisit.h"
- // 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;
+#include "gdcmValidator.h"
- 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(bool exception_on_error = false)
- throw(gdcmFormatError);
- gdcmHeader(const char *filename, bool exception_on_error = false)
- throw(gdcmFileError);
- 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 GetImageDataIntoVector(void* destination, size_t MaxSize );
-
- // Question :
- //
- // GetImageData et GetImageDataIntoVector
- // 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;
-
-
-#endif // #ifndef GDCM_H
+#endif
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff