* python/demo/*.py load.py extracted from test.py. Added explore.py

[gdcm.git] / src / 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 
// * 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>
#include <iostream>
#include <stddef.h>   // For size_t
#include <stdio.h>    // FIXME For FILE on GCC only
#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)
#ifdef __GNUC__
#include <stdint.h>
#define guint16 uint16_t
#define guint32 uint32_t
#define g_malloc malloc
#define g_free   free
#endif
#ifdef _MSC_VER
#include <glib.h>
#endif

#ifdef _MSC_VER
        using namespace std;  // string type lives in the std namespace on VC++
#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;

class GDCM_EXPORT gdcmDictEntry {
private:
        guint16 group;    // e.g. 0x0010
        guint16 element;  // e.g. 0x0010
        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 !
        string  fourth;   // Fourth field containing some semantics.
        string  name;     // e.g. "Patient_Name"
        TagKey  key;      // This is redundant zith (group, element) but we add
                          // 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;
        //         const char* tagName;
        //         int vmMin;
        //         int vmMax;
        //         const char* standardVersion;
        //         DcmDictRangeRestriction groupRestriction;
        //         DcmDictRangeRestriction elementRestriction;
        //       };
public:
        //CLEANME gdcmDictEntry();
        gdcmDictEntry(guint16 group, guint16 element,
                      string vr     = "Unknown",
                                          string fourth = "Unknown",
                                          string name   = "Unknown");
        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);
        bool    IsVrUnknown(void);
        string  GetFourth(void) {return fourth;};
        string  GetName(void)   {return name;};
        string  GetKey(void)    {return key;};
};
  
typedef map<TagKey, gdcmDictEntry*> TagHT;

// 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...
class GDCM_EXPORT gdcmDict {
        string name;
        string filename;
        TagHT entries;
public:
        gdcmDict(const char* FileName);   // Read Dict from disk
        // TODO Swig int AppendEntry(gdcmDictEntry* NewEntry);
        gdcmDictEntry * GetTag(guint32 group, guint32 element);
        void Print(ostream&);
};

// 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();
        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.
        // 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 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 GetElement(void) { return entry->GetElement(); };
        string  GetKey(void)     { return entry->GetKey(); };
        string  GetName(void)    { return entry->GetName();};
};

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 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);
        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
// 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).
// Notes:
// * 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};
private:
        // All instances share the same Value Representation dictionary
        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
        // In order to inspect/navigate through the file
        string filename;
        FILE * fp;
        // The tag Image Location ((0028,0200) containing the adress 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.
        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);
        guint32 SwapLong(guint32);
        void Initialise(void);
        void CheckSwap(void);
        void FindLength(ElValue *);
        void FindVR(ElValue *);
        void LoadElementValue(ElValue *);
        void LoadElementValueSafe(ElValue *);
        void SkipElementValue(ElValue *);
        void InitVRDict(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,
                TrueDicom,
                ExplicitVR,
                ImplicitVR,
                ACR,
                ACR_LIBIDO};
        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&);
public:
        void LoadElements(void);
        virtual void ParseHeader(void);
        gdcmHeader(const char* filename);
        virtual ~gdcmHeader();

        // 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.
        // 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();
        // 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
        // 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);
        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);

        // 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);

        // TODO Swig int GetSwapCode();
};

// 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
public:
        // 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 a 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).
        // 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();
        // 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);
        // Push to disk.
        // TODO Swig int Write();
};

//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);
//   }