+// 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
#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 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:
+
+ // 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 GetElement(void){return element;};
string GetVR(void) {return vr; };
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) --> ligne du Dictionnaire Dicom
+
typedef map<TagKey, gdcmDictEntry*> TagHT;
class GDCM_EXPORT gdcmDict {
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,
// * 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?
+ //
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;
void SetDictEntry(gdcmDictEntry *NewEntry) { entry = NewEntry; };
bool IsVrUnknown(void) { return entry->IsVrUnknown(); };
- void SetLength(guint32 l){LgrElem = l; };
+ void SetLength(guint32 l){ LgrElem = l; };
void SetValue(string val){ value = val; };
void SetOffset(size_t of){ Offset = of; };
void SetImplicitVr(void) { ImplicitVr = true; };
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;
TagElValueHT & GetTagHt(void);
};
+
+//
+// ---------------------------------------------------- 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
+ // 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);
// 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 {
//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).
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
+ // 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);
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 &);
// 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
////// 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:
// 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;
+
+//
+// ---------------------------------------------------- gdcmMultiFrame
+//
+// un fichierMultiFrame EST_UN fichier
+//
+//
+
//class gdcmMultiFrame : gdcmFile;
+
+
+// gdcmHeader.cxx
+
#include "gdcm.h"
#include <stdio.h>
// For nthos:
#include <sstream>
#include "gdcmUtil.h"
-#define HEADER_LENGHT_TO_READ 256 // on ne lit plus que le debut
+#define HEADER_LENGTH_TO_READ 256 // on ne lit plus que le debut
namespace Error {
struct FileReadError {
/**
* \ingroup gdcmHeader
- * \brief Discover what the swap code is (among little endian, big endian,
+ * \brief Discover what the swap code is (among little endian, big endian,
* bad little endian, bad big endian).
+ *
*/
void gdcmHeader::CheckSwap()
{
int lgrLue;
char * entCur;
- char deb[HEADER_LENGHT_TO_READ];
+ char deb[HEADER_LENGTH_TO_READ];
// First, compare HostByteOrder and NetworkByteOrder in order to
// determine if we shall need to swap bytes (i.e. the Endian type).
// The easiest case is the one of a DICOM header, since it possesses a
// file preamble where it suffice to look for the sting "DICM".
- lgrLue = fread(deb, 1, HEADER_LENGHT_TO_READ, fp);
+ lgrLue = fread(deb, 1, HEADER_LENGTH_TO_READ, fp);
entCur = deb + 128;
if(memcmp(entCur, "DICM", (size_t)4) == 0) {
return;
default :
dbg.Verbose(0, "gdcmHeader::CheckSwap:",
- "ACE/NEMA unfound swap info (time to raise bets)");
+ "ACR/NEMA unfound swap info (time to raise bets)");
}
// We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
sw = 3412;
}
+void gdcmHeader::GetPixels(size_t lgrTotale, void* Pixels) {
+ size_t pixelsOffset;
+ pixelsOffset = GetPixelOffset();
+ fseek(fp, pixelsOffset, SEEK_SET);
+ fread(Pixels, 1, lgrTotale, fp);
+}
+
/**
* \ingroup gdcmHeader
* \brief Find the value representation of the current tag.
// a tag where we expect reading a VR but are in fact we read the
// first to bytes of the length. Then we will interogate (through find)
// the dicom_vr dictionary with oddities like "\004\0" which crashes
- // both GCC and VC++ implentations of the STL map. Hence when the
+ // both GCC and VC++ implementations of the STL map. Hence when the
// expected VR read happens to be non-ascii characters we consider
// we hit falsely explicit VR tag.
// endian encoding". When this is the case, chances are we got our
// hands on a big endian encoded file: we switch the swap code to
// big endian and proceed...
- if ( (element == 0) && (length16 == 1024) ) {
+ if ( (element == 0x000) && (length16 == 0x0400) ) {
if ( ! IsBigEndianTransferSyntax() )
throw Error::FileReadError(fp, "gdcmHeader::FindLength");
length16 = 4;
fseek(fp, (long)ElVal->GetOffset(), SEEK_SET);
// Sequences not treated yet !
+ //
+ // Ne faudrait-il pas au contraire trouver immediatement
+ // une maniere 'propre' de traiter les sequences (vr = SQ)
+ // car commencer par les ignorer risque de conduire a qq chose
+ // qui pourrait ne pas etre generalisable
+ //
if( vr == "SQ" )
SkipLoad = true;
}
// Values bigger than specified are not loaded.
+ //
+ // En fait, c'est les elements dont la longueur est superieure
+ // a celle fixee qui ne sont pas charges
+ //
if (length > MaxSizeLoadElementValue) {
ostringstream s;
s << "gdcm::NotLoaded.";
if ( (group == 0x0028) && (element == 0x0005) )
// This tag is retained from ACR/NEMA
// CHECKME Why should "Image Dimensions" be a single integer ?
+ //
+ // "Image Dimensions", c'est en fait le 'nombre de dimensions'
+ // de l'objet ACR-NEMA stocké
+ // 1 : Signal
+ // 2 : Image
+ // 3 : Volume
+ // 4 : Sequence
+ //
+ // DICOM V3 ne retient pas cette information
+ // Par defaut, tout est 'Image',
+ // C'est a l'utilisateur d'explorer l'ensemble des entetes
+ // pour savoir à quoi il a a faire
+ //
+ // Le Dicom Multiframe peut etre utilise pour stocker,
+ // dans un seul fichier, une serie temporelle (cardio vasculaire GE, p.ex)
+ // ou un volume (medecine Nucleaire, p.ex)
+ //
return true;
if ( (group == 0x0028) && (element == 0x0200) )
}
gdcmDictEntry * gdcmHeader::IsInDicts(guint32 group, guint32 element) {
+ //
+ // Y a-t-il une raison de lui passer des guint32
+ // alors que group et element sont des guint16?
+ //
gdcmDictEntry * found = (gdcmDictEntry*)0;
if (!RefPubDict && !RefShaDict) {
//FIXME build a default dictionary !
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff