X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.h;h=273305c11160e301a8a4606606a4c462d4ff9e41;hb=e037a39af09b4df452992e1129fa2a370171c44e;hp=9f3603e966570ed0e5353566764a4944929a170d;hpb=54ce6e928bccc91bb12601c782b92c833678de40;p=gdcm.git diff --git a/src/gdcmHeader.h b/src/gdcmHeader.h index 9f3603e9..273305c1 100644 --- a/src/gdcmHeader.h +++ b/src/gdcmHeader.h @@ -4,21 +4,11 @@ #define GDCMHEADER_H #include "gdcmCommon.h" -#include "gdcmVR.h" -#include "gdcmTS.h" -#include "gdcmException.h" -#include "gdcmDictSet.h" -#include "gdcmHeaderEntry.h" -#include "gdcmHeaderEntrySet.h" -#include +#include "gdcmParser.h" //----------------------------------------------------------------------------- -typedef std::string VRKey; -typedef std::string VRAtr; -typedef std::map VRHT; // Value Representation Hash Table - -//----------------------------------------------------------------------------- -/* +/** + * \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 @@ -27,7 +17,7 @@ typedef std::map VRHT; // Value Representation Hash Table * 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 + * 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 @@ -36,23 +26,38 @@ typedef std::map VRHT; // Value Representation Hash Table * protected due to Swig limitations for as Has_a dependency between * gdcmFile and gdcmHeader. */ -class GDCM_EXPORT 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 enable_sequences = false, + bool skip_shadow = false); + virtual ~gdcmHeader(); -// 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); + // Standard values and informations contained in the header + virtual bool IsReadable(void); bool IsJPEGBaseLineProcess1TransferSyntax(void); bool IsJPEGExtendedProcess2_4TransferSyntax(void); bool IsJPEGExtendedProcess3_5TransferSyntax(void); @@ -61,11 +66,10 @@ public: 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); + // (to be moved to gdcmHeaderHelper?) + int GetXSize(void); int GetYSize(void); int GetZSize(void); int GetBitsStored(void); @@ -93,152 +97,61 @@ public: // TODO Swig int SetShaDict(std::string filename); // TODO Swig int SetPubDict(std::string filename); - -// Public element value - std::string GetPubEntryByName (std::string tagName); - std::string GetPubEntryVRByName (std::string tagName); - std::string GetPubEntryByNumber (guint16 group, guint16 element); - std::string GetPubEntryVRByNumber(guint16 group, guint16 element); - bool SetPubEntryByName (std::string content, std::string tagName); - bool SetPubEntryByNumber(std::string content, guint16 group, guint16 element); - bool SetPubEntryLengthByNumber(guint32 lgr, guint16 group, guint16 element); - - inline ListTag & GetPubListEntry(void) { return PubEntrySet.GetListEntry();}; - inline TagHeaderEntryHT & GetPubEntry(void) { return PubEntrySet.GetTagHT(); }; - - void PrintPubEntry(std::ostream & os = std::cout); - void PrintPubDict (std::ostream & os = std::cout); - -// Element value - std::string GetEntryByName (std::string tagName); - std::string GetEntryVRByName (std::string tagName); - std::string GetEntryByNumber (guint16 group, guint16 element); - std::string GetEntryVRByNumber(guint16 group, guint16 element); - - bool SetEntryByName(std::string content,std::string tagName); -// bool SetEntryByNumber(std::string content,guint16 group, guint16 element); - -// inline ListTag & GetListElem(void) { return PubHeaderEntrySet.GetListElem();}; -// inline TagHeaderEntryHT & GetElVal(void) { return PubHeaderEntrySet.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); - - 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); - -// System access - inline int GetSwapCode(void) { return sw; } - guint16 SwapShort(guint16); // needed by gdcmFile - guint32 SwapLong(guint32); // for JPEG Files + /// Accessor to \ref gdcmHeader::GrPixel + guint16 GetGrPixel(void) {return GrPixel;} -protected: - bool CheckIfExistByNumber(guint16 Group, guint16 Elem ); - - gdcmHeaderEntry *GetHeaderEntryByName (std::string Name); - gdcmHeaderEntry *GetHeaderEntryByNumber(guint16 group, guint16 element); - - int write(std::ostream&); - int anonymize(std::ostream&); // FIXME : anonymize should be a friend ? - - size_t GetPubEntryOffsetByNumber (guint16 Group, guint16 Elem); - void * GetPubEntryVoidAreaByNumber(guint16 Group, guint16 Elem); - void * LoadEntryVoidArea (guint16 Group, guint16 Element); + /// Accessor to \ref gdcmHeader::NumPixel + guint16 GetNumPixel(void) {return NumPixel;} + +// Entry + + 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); -// Variables - FILE * fp; - FileType filetype; // ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown - -private: - // Read - void LoadHeaderEntries (void); - void LoadHeaderEntry (gdcmHeaderEntry *); - void LoadHeaderEntrySafe (gdcmHeaderEntry *); - void FindHeaderEntryLength(gdcmHeaderEntry *); - void FindHeaderEntryVR (gdcmHeaderEntry *); - - void SkipHeaderEntry (gdcmHeaderEntry *); - void FixHeaderEntryFoundLength(gdcmHeaderEntry *, guint32); - bool IsHeaderEntryAnInteger (gdcmHeaderEntry *); - - guint32 FindHeaderEntryLengthOB(void); - - guint16 ReadInt16(void); - guint32 ReadInt32(void); - void SkipBytes(guint32); - - void Initialise(void); - void CheckSwap(void); - void SwitchSwapToBigEndian(void); - void SetMaxSizeLoadElementValue(long); - - // Dict - gdcmDictEntry *GetDictEntryByName (std::string Name); - gdcmDictEntry *GetDictEntryByNumber(guint16, guint16); - - // HeaderEntry related utilities - gdcmHeaderEntry *ReadNextHeaderEntry (void); - gdcmHeaderEntry *NewHeaderEntryByNumber(guint16 group, guint16 element); - gdcmHeaderEntry *NewHeaderEntryByName (std::string Name); - - // Deprecated (Not used) - gdcmHeaderEntry *NewManualHeaderEntryToPubDict(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 WriteEntry(gdcmHeaderEntry *tag,FILE *_fp,FileType type); - // 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 - // Public dictionary used to parse this header - gdcmDict *RefPubDict; + virtual void PrintEntryNoSQ (std::ostream &os = std::cout); + virtual void PrintEntryNiceSQ(std::ostream &os = std::cout); - // Optional "shadow dictionary" (private elements) used to parse this - // header - gdcmDict *RefShaDict; +protected: + //CLEANME int write(std::ostream&); + //CLEANME int anonymize(std::ostream&);//FIXME: anonymize should be a friend + bool anonymizeHeader(void); +private: - /// ELement VALueS parsed with the PUBlic dictionary. - gdcmHeaderEntrySet PubEntrySet; - - // Refering underlying filename. - std::string filename; - - int enableSequences; - - // 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; - - static const unsigned int HEADER_LENGTH_TO_READ; - static const unsigned int MAX_SIZE_LOAD_ELEMENT_VALUE; }; //-----------------------------------------------------------------------------