X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.h;h=31d98776b929abe4033de7fd48f3c91a99a602f5;hb=aba8714645174c0c7d3c7aadf6af1832743e2971;hp=3e675c47310430c39e65fb7a8684f67a6407c4bf;hpb=1f5594f4e2bc55ccc70ff04cd66acc7cd8da74c8;p=gdcm.git diff --git a/src/gdcmHeader.h b/src/gdcmHeader.h index 3e675c47..31d98776 100644 --- a/src/gdcmHeader.h +++ b/src/gdcmHeader.h @@ -1,171 +1,245 @@ // gdcmHeader.h - +//----------------------------------------------------------------------------- #ifndef GDCMHEADER_H #define GDCMHEADER_H -#include #include "gdcmCommon.h" +#include "gdcmVR.h" +#include "gdcmTS.h" #include "gdcmException.h" #include "gdcmDictSet.h" #include "gdcmElValue.h" #include "gdcmElValSet.h" +#include -typedef string VRKey; -typedef string VRAtr; -typedef map VRHT; // Value Representation Hash Table - -/// The purpose of an instance of gdcmHeader is to act as a container of -/// all the DICOM 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 belongs to gdmcFile. -/// \note The various entries of the explicit value representation (VR) shall -/// be managed within a dictionary which is shared by all gdcmHeader -/// instances. -/// \note The gdcmHeader::Set*Tag* family members cannot be defined as -/// protected due to Swig limitations for as Has_a dependency between -/// gdcmFile and gdcmHeader. - +//----------------------------------------------------------------------------- +typedef std::string VRKey; +typedef std::string VRAtr; +typedef std::map VRHT; // Value Representation Hash Table + +//----------------------------------------------------------------------------- +/* + * The purpose of an instance of gdcmHeader is to act as a container of + * all the DICOM 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 belongs to gdmcFile. + * \note The various entries of the explicit value representation (VR) shall + * be managed within a dictionary which is shared by all gdcmHeader + * instances. + * \note The gdcmHeader::Set*Tag* family members cannot be defined as + * protected due to Swig limitations for as Has_a dependency between + * gdcmFile and gdcmHeader. + */ class GDCM_EXPORT gdcmHeader { - void SkipBytes(guint32); -private: - /// Pointer to the Value Representation Hash Table which contains all - /// the VR of the DICOM version3 public dictionary. - static VRHT *dicom_vr; - - /// Global dictionary container - gdcmDictSet* Dicts; - /// Public dictionary used to parse this header - gdcmDict* RefPubDict; - /// Optional "shadow dictionary" (private elements) used to parse this - /// header - gdcmDict* RefShaDict; +public: + gdcmHeader(bool exception_on_error = false); + gdcmHeader(const char *filename, + bool exception_on_error = false, + bool enable_sequences = false); + + virtual ~gdcmHeader(); - /// ELement VALueS parsed with the PUBlic dictionary. - gdcmElValSet PubElVals; - /// ELement VALueS parsed with the SHAdow dictionary. - gdcmElValSet ShaElVals; - /// Refering underlying filename. - string filename; +// Standard values and informations contained in the header + inline std::string GetFileName(void) {return filename;} + + bool IsReadable(void); + 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); + bool IsRLELossLessTransferSyntax(void); + bool IsJPEGLossless(void); + bool IsJPEG2000(void); + bool IsDicomV3(void); + FileType GetFileType(void); + + // Some heuristic based accessors, end user intended + // (to be move to gdcmHeaderHelper?) + int GetXSize(void); + int GetYSize(void); + int GetZSize(void); + int GetBitsStored(void); + int GetBitsAllocated(void); + int GetSamplesPerPixel(void); + int GetPlanarConfiguration(void); + + int GetPixelSize(void); + std::string GetPixelType(void); + size_t GetPixelOffset(void); + size_t GetPixelAreaLength(void); + + bool HasLUT(void); + int GetLUTNbits(void); + unsigned char * GetLUTRGBA(void); + + std::string GetTransfertSyntaxName(void); + + // When some proprietary shadow groups are disclosed, we can set up + // an additional specific dictionary to access extra information. + + // OK : we still have *ONE* ElValSet, + // with both Public and Shadow Elements + // parsed against THE Public Dictionary and A (single) Shadow Dictionary + + // TODO Swig int SetShaDict(std::string filename); + // TODO Swig int SetPubDict(std::string filename); + +// Public element value + std::string GetPubElValByName (std::string tagName); + std::string GetPubElValRepByName (std::string tagName); + std::string GetPubElValByNumber (guint16 group, guint16 element); + std::string GetPubElValRepByNumber(guint16 group, guint16 element); + + bool SetPubElValByName (std::string content, std::string tagName); + bool SetPubElValByNumber(std::string content, guint16 group, guint16 element); + bool SetPubElValLengthByNumber(guint32 lgr, guint16 group, guint16 element); + + inline ListTag & GetPubListElem(void) { return PubElValSet.GetListElem();}; + inline TagElValueHT & GetPubElVal(void) { return PubElValSet.GetTagHt(); }; + + void PrintPubElVal(std::ostream & os = std::cout); + void PrintPubDict (std::ostream & os = std::cout); + +// Element value + std::string GetElValByName (std::string tagName); + std::string GetElValRepByName (std::string tagName); + std::string GetElValByNumber (guint16 group, guint16 element); + std::string GetElValRepByNumber(guint16 group, guint16 element); + + bool SetElValueByName(std::string content,std::string tagName); +// bool SetElValueByNumber(std::string content,guint16 group, guint16 element); + +// inline ListTag & GetListElem(void) { return PubElValSet.GetListElem();}; +// inline TagElValueHT & GetElVal(void) { return PubElValSet.GetTagHt(); }; + +// Read (used in gdcmFile) + FILE *OpenFile(bool exception_on_error = false) throw(gdcmFileError); + bool CloseFile(void); + virtual void ParseHeader(bool exception_on_error = false) throw(gdcmFormatError); + +// Write (used in gdcmFile) + bool Write(FILE *, FileType); + void SetImageDataSize(size_t ExpectedSize); + +// System access + inline int GetSwapCode(void) { return sw; } + guint16 SwapShort(guint16); // needed by gdcmFile + guint32 SwapLong(guint32); // for JPEG Files + + // was protected + bool ReplaceOrCreateByNumber(std::string Value, guint16 Group, guint16 Elem); + bool ReplaceOrCreateByNumber( char * Value, guint16 Group, guint16 Elem); + bool ReplaceIfExistByNumber ( char * Value, guint16 Group, guint16 Elem); + +protected: + bool CheckIfExistByNumber(guint16 Group, guint16 Elem ); + gdcmElValue * GetElValueByNumber(guint16 group, guint16 element); + + int write(std::ostream&); + int anonymize(std::ostream&); // FIXME : anonymize should be a friend ? + + size_t GetPubElValOffsetByNumber (guint16 Group, guint16 Elem); + void * GetPubElValVoidAreaByNumber(guint16 Group, guint16 Elem); + void * LoadElementVoidArea (guint16 Group, guint16 Element); + + +// Variables FILE * fp; + FileType filetype; // ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown - // FIXME sw should be an enum e.g. - //enum EndianType { - //LittleEndian, - //BadLittleEndian, - //BigEndian, - //BadBigEndian}; - /// Swap code e.g. little, big, bad-big, bad-little endian). Warning: - /// this code is not fixed during header parsing. - int sw; +private: + // Read + void LoadElements (void); + void LoadElementValue (gdcmElValue *); + void LoadElementValueSafe(gdcmElValue *); + void FindLength (gdcmElValue *); + void FindVR (gdcmElValue *); - /// Size treshold above which an element value will NOT be loaded in - /// memory (to avoid loading the image/volume itself). By default, - /// this upper bound is fixed to 1024 bytes (which might look reasonable - /// when one considers the definition of the various VR contents). - guint32 MaxSizeLoadElementValue; + guint32 FindLengthOB(void); + + void SkipElementValue (gdcmElValue *); + void FixFoundLength (gdcmElValue *, guint32); + bool IsAnInteger (gdcmElValue *); guint16 ReadInt16(void); guint32 ReadInt32(void); - guint16 SwapShort(guint16); - guint32 SwapLong(guint32); - guint32 FindLengthOB(void); + void SkipBytes(guint32); + 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); + // Dict + gdcmDictEntry *GetDictEntryByName (std::string Name); + gdcmDictEntry *GetDictEntryByNumber(guint16, guint16); // ElValue related utilities - gdcmElValue * ReadNextElement(void); - gdcmElValue * NewElValueByKey(guint16 group, guint16 element); - gdcmElValue * NewElValueByName(string name); - void FindLength(gdcmElValue *); - void FindVR(gdcmElValue *); - void LoadElementValue(gdcmElValue *); - void LoadElementValueSafe(gdcmElValue *); - void SkipElementValue(gdcmElValue *); - void FixFoundLength(gdcmElValue*, guint32); - bool IsAnInteger(gdcmElValue *); + gdcmElValue *ReadNextElement (void); + gdcmElValue *NewElValueByNumber(guint16 group, guint16 element); + gdcmElValue *NewElValueByName (std::string Name); + gdcmElValue* GetElementByName (std::string Name); + + // Deprecated + gdcmElValue *NewManualElValToPubDict(std::string NewTagName, + std::string VR); + +// Variables + // Pointer to the Value Representation Hash Table which contains all + // the VR of the DICOM version3 public dictionary. + gdcmVR *dicom_vr; // Not a class member for thread-safety reasons - 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); + // Pointer to the Transfert Syntax Hash Table which contains all + // the TS of the DICOM version3 public dictionary. + gdcmTS *dicom_ts; // Not a class member for thread-safety reasons + + // Pointer to global dictionary container + gdcmDictSet *Dicts; // Not a class member for thread-safety reasons - bool IsJPEGLossless(void); - -protected: - // FIXME: is this enum still necessary ?? - 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(); + // Public dictionary used to parse this header + gdcmDict *RefPubDict; - size_t GetPixelOffset(void); - void GetPixels(size_t, void *); - int GetSwapCode(void) { return sw; } + // Optional "shadow dictionary" (private elements) used to parse this + // header + gdcmDict *RefShaDict; - // 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); + /// ELement VALueS parsed with the PUBlic dictionary. + gdcmElValSet PubElValSet; + + // Refering underlying filename. + std::string filename; + + int enableSequences; - string GetPubElValByName(string TagName); - string GetPubElValByNumber(guint16 group, guint16 element); - string GetPubElValRepByName(string TagName); - string GetPubElValRepByNumber(guint16 group, guint16 element); + // FIXME sw should be an enum e.g. + //enum EndianType { + //LittleEndian, + //BadLittleEndian, + //BigEndian, + //BadBigEndian}; + // Swap code e.g. little, big, bad-big, bad-little endian). Warning: + // this code is not fixed during header parsing. + int sw; - TagElValueHT & GetPubElVal(void) { return PubElVals.GetTagHt(); }; - void PrintPubElVal(ostream & os = cout); - void PrintPubDict(ostream & os = cout); - - // TODO Swig string* GetShaTagNames(); - string GetShaElValByName(string TagName); - string GetShaElValByNumber(guint16 group, guint16 element); - string GetShaElValRepByName(string TagName); - string GetShaElValRepByNumber(guint16 group, guint16 element); - - 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); - - int gdcmHeader::SetPubElValLengthByNumber(guint32 lgr, guint16 group, - guint16 element); + // Size treshold above which an element value will NOT be loaded in + // memory (to avoid loading the image/volume itself). By default, + // this upper bound is fixed to 1024 bytes (which might look reasonable + // when one considers the definition of the various VR contents). + guint32 MaxSizeLoadElementValue; - gdcmElValSet GetPubElVals() { return(PubElVals); } + static const unsigned int HEADER_LENGTH_TO_READ; + static const unsigned int MAX_SIZE_LOAD_ELEMENT_VALUE; }; +//----------------------------------------------------------------------------- #endif