X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.h;h=3d8564140d646e4667f2b6484dabee3427d903b1;hb=279aed8cb3483318205a8b652e05457a7fc94dec;hp=5e43f564460f3fec9966d1ef1766e0a9ccad7f7a;hpb=595f90023c498f01bba240043841088ba5d45872;p=gdcm.git diff --git a/src/gdcmHeader.h b/src/gdcmHeader.h index 5e43f564..3d856414 100644 --- a/src/gdcmHeader.h +++ b/src/gdcmHeader.h @@ -1,170 +1,161 @@ // gdcmHeader.h - +//----------------------------------------------------------------------------- #ifndef GDCMHEADER_H #define GDCMHEADER_H -#include #include "gdcmCommon.h" -#include "gdcmException.h" -#include "gdcmDictSet.h" -#include "gdcmElValue.h" -#include "gdcmElValSet.h" - -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. - -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; +#include "gdcmParser.h" + +//----------------------------------------------------------------------------- +/** + * \brief + * 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. Accessing 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 : public gdcmParser +{ +protected: + /// In some cases (e.g. for some ACR-NEMA images) the Header Entry Element + /// Number of the 'Pixel Element' is *not* found at 0x0010. In order to + /// make things easier the parser shall store the proper value in + /// NumPixel to provide a unique access facility. See also the constructor + /// \ref gdcmHeader::gdcmHeader + guint16 NumPixel; + /// In some cases (e.g. for some ACR-NEMA images) the header entry for + /// the group of pixels is *not* found at 0x7fe0. In order to + /// make things easier the parser shall store the proper value in + /// GrPixel to provide a unique access facility. See also the constructor + /// \ref gdcmHeader::gdcmHeader + guint16 GrPixel; + /// Some DICOM files may contain several images (e.g. a icon, followd by + /// the image itself. Hence the tag (GrPixel,NumPixel) might appear + /// several times. countGrPixel is the number of occurences of the + /// tag of pixels (i.e. (GrPixel,NumPixel)) contained in the header. + /// TODO : will be dealt with SQ tree-like stucture + int countGrPixel; +public: + gdcmHeader(bool exception_on_error = false); + gdcmHeader(const char *filename, + bool exception_on_error = false, + bool enable_sequences = false, + bool skip_shadow = false); - /// 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; - - /// ELement VALueS parsed with the PUBlic dictionary. - gdcmElValSet PubElValSet; - /// ELement VALueS parsed with the SHAdow dictionary. - gdcmElValSet ShaElValSet; - /// Refering underlying filename. - string filename; - FILE * fp; - - // 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; - - /// 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; - - 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); - // CLEAN ME: NewManualElValToPubDict is NOT called any more. - gdcmElValue* NewManualElValToPubDict(string NewTagName, string VR); - void SetMaxSizeLoadElementValue(long); - - gdcmDictEntry * GetDictEntryByKey(guint16, guint16); - gdcmDictEntry * GetDictEntryByName(string name); - - // 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 *); - void LoadElements(void); - - bool IsImplicitVRLittleEndianTransferSyntax(void); - bool IsExplicitVRLittleEndianTransferSyntax(void); - bool IsDeflatedExplicitVRLittleEndianTransferSyntax(void); - bool IsExplicitVRBigEndianTransferSyntax(void); + virtual ~gdcmHeader(); + + // Standard values and informations contained in the header + virtual bool IsReadable(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); - -protected: - FileType filetype; - int write(ostream&); - int anonymize(ostream&); // FIXME : anonymize should be a friend ? -public: - bool IsReadable(void); - virtual void ParseHeader(bool exception_on_error = false) - throw(gdcmFormatError); - gdcmHeader(const char *filename, bool exception_on_error = false) - throw(gdcmFileError); - virtual ~gdcmHeader(); - + + // Some heuristic based accessors, end user intended + // (to be moved 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); - void GetPixels(size_t, void *); - int GetSwapCode(void) { return sw; } + size_t GetPixelAreaLength(void); + + bool HasLUT(void); + int GetLUTNbits(void); + unsigned char * GetLUTRGBA(void); + + std::string GetTransfertSyntaxName(void); - // 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); - - string GetPubElValByName(string TagName); - string GetPubElValByNumber(guint16 group, guint16 element); - string GetPubElValRepByName(string TagName); - string GetPubElValRepByNumber(guint16 group, guint16 element); - - TagElValueHT & GetPubElVal(void) { return PubElValSet.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 SetPubElValLengthByNumber(guint32 lgr, guint16 group, guint16 element); - int ReplaceOrCreateByNumber(string Value, guint16 Group, guint16 Elem); - int GetXSize(void); - int GetYSize(void); - int GetZSize(void); - string GetPixelType(void); - int Write(FILE *, FileType); + // OK : we still have *ONE* HeaderEntrySet, + // 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); + + /// Accessor to \ref gdcmHeader::GrPixel + guint16 GetGrPixel(void) {return GrPixel;} + /// Accessor to \ref gdcmHeader::NumPixel + guint16 GetNumPixel(void) {return NumPixel;} + +// Entry + +// These functions are necessary for Python because +// there are protected in the parent class + + inline virtual std::string GetEntryByNumber (guint16 group, guint16 element) + { return(gdcmParser::GetEntryByNumber(group,element)); } + + inline virtual std::string GetEntryVRByNumber(guint16 group, guint16 element) + { return(gdcmParser::GetEntryVRByNumber(group,element)); } + + inline virtual int GetEntryLengthByNumber(guint16 group, guint16 element) + { return(gdcmParser::GetEntryLengthByNumber(group,element)); } + + inline virtual std::string GetEntryByName (std::string tagName) + { return(gdcmParser::GetEntryByName(tagName)); } + + inline virtual std::string GetEntryVRByName (std::string tagName) + { return(gdcmParser::GetEntryVRByName(tagName)); } + + inline virtual bool SetEntryByNumber(std::string content, + guint16 group, guint16 element) + { return(gdcmParser::SetEntryByNumber(content,group,element)); } + + inline virtual bool SetEntryByName(std::string content,std::string tagName) + { return(gdcmParser::SetEntryByName(content,tagName)); } + + inline virtual bool SetEntryLengthByNumber(guint32 l, + guint16 group, guint16 element) + { return(gdcmParser::SetEntryLengthByNumber(l,group,element)); } + + inline virtual void UpdateShaEntries(void) + { gdcmParser::UpdateShaEntries(); } + + /// Read (used in gdcmFile) + void SetImageDataSize(size_t ExpectedSize); + + bool operator<(gdcmHeader &header); + + bool WriteEntry(gdcmHeaderEntry *tag,FILE *_fp,FileType type); + + + virtual void PrintEntryNoSQ (std::ostream &os = std::cout); + virtual void PrintEntryNiceSQ(std::ostream &os = std::cout); + +protected: + //CLEANME int write(std::ostream&); + //CLEANME int anonymize(std::ostream&);//FIXME: anonymize should be a friend + bool anonymizeHeader(void); +private: + }; +//----------------------------------------------------------------------------- #endif