X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.h;h=00a74ffc4bc499b58a17520f9ee8c563d3010f49;hb=75a92c136f26236dda738889f9d7144e31705b87;hp=c999b59134f928d3fa671124660cfd6631987f18;hpb=4c8c80589b3770976ea27fc03b290b97db5da3e6;p=gdcm.git diff --git a/src/gdcmDocument.h b/src/gdcmDocument.h index c999b591..00a74ffc 100644 --- a/src/gdcmDocument.h +++ b/src/gdcmDocument.h @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmDocument.h,v $ Language: C++ - Date: $Date: 2004/07/30 11:40:13 $ - Version: $Revision: 1.24 $ + Date: $Date: 2005/06/02 13:42:18 $ + Version: $Revision: 1.111 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR @@ -19,241 +19,212 @@ #ifndef GDCMDOCUMENT_H #define GDCMDOCUMENT_H -#include "gdcmCommon.h" #include "gdcmVR.h" -#include "gdcmTS.h" -#include "gdcmException.h" -#include "gdcmDictSet.h" -#include "gdcmDocEntry.h" - -class gdcmValEntry; -class gdcmBinEntry; -class gdcmSeqEntry; - -#include "gdcmDocEntrySet.h" +#include "gdcmDict.h" #include "gdcmElementSet.h" +#include "gdcmException.h" #include #include +#include + +#define NO_SEQ 0x0000001 +#define NO_SHADOW 0x00000002 + +namespace gdcm +{ +class ValEntry; +class BinEntry; +class SeqEntry; +class Dict; //----------------------------------------------------------------------------- /** - * \brief Derived by both gdcmHeader and gdcmDicomDir + * \brief Derived by both gdcm::File and gdcm::DicomDir */ -class GDCM_EXPORT gdcmDocument : public gdcmElementSet +class GDCM_EXPORT Document : public ElementSet { -friend class gdcmFile; -private: - /// Public dictionary used to parse this header - gdcmDict *RefPubDict; - - /// \brief Optional "shadow dictionary" (private elements) used to parse - /// this header - gdcmDict *RefShaDict; - - /// \brief Equals =1 if user wants to skip shadow groups while parsing - /// (to save space) - int IgnoreShadow; - - /// \brief Size threshold 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). - uint32_t MaxSizeLoadEntry; - - /// \brief Size threshold above which an element value will NOT be *printed* - /// in order no to polute the screen output. By default, this upper bound - /// is fixed to 64 bytes. - uint32_t MaxSizePrintEntry; - -protected: - /// Refering underlying filename. - std::string Filename; - - /// \brief SWap code (e.g. Big Endian, Little Endian, Bad Big Endian, - /// Bad Little Endian) according to the processor Endianity and - /// what is written on disc. - int SwapCode; - - /// File Pointer, opened during Header parsing. - FILE *Fp; - - /// ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown - FileType Filetype; - - /// After opening the file, we read HEADER_LENGTH_TO_READ bytes. - static const unsigned int HEADER_LENGTH_TO_READ; - - /// \brief Elements whose value is longer than MAX_SIZE_LOAD_ELEMENT_VALUE - /// are NOT loaded. - static const unsigned int MAX_SIZE_LOAD_ELEMENT_VALUE; +public: - /// \brief Elements whose value is longer than MAX_SIZE_PRINT_ELEMENT_VALUE - /// are NOT printed. - /// \todo Currently not used since collides with #define in - /// \ref gdcmDocEntry.cxx. See also - /// \ref gdcmDocument::SetMaxSizePrintEntry() - static const unsigned int MAX_SIZE_PRINT_ELEMENT_VALUE; +typedef std::list ListElements; - /// Will be set 1 if user asks to 'go inside' the 'sequences' (VR = "SQ") - int EnableSequences; +// Loading + virtual bool Load( std::string const &filename ); - /// \brief Amount of printed details for each Header Entry (Dicom Element): - /// 0 : stands for the least detail level. - int PrintLevel; - -public: -// the 2 following will be merged - virtual void PrintPubDict (std::ostream &os = std::cout); - virtual void PrintShaDict (std::ostream &os = std::cout); +// Dictionaries + Dict *GetPubDict(); + Dict *GetShaDict(); + bool SetShaDict(Dict *dict); + bool SetShaDict(DictKey const &dictName); -// Dictionnaries - gdcmDict *GetPubDict(); - gdcmDict *GetShaDict(); - bool SetShaDict(gdcmDict *dict); - bool SetShaDict(DictKey dictName); - -// Informations contained in the parser +// Informations contained in the gdcm::Document virtual bool IsReadable(); - bool IsGivenTransferSyntax(std::string const & SyntaxToCheck); - bool IsImplicitVRLittleEndianTransferSyntax(); - bool IsExplicitVRLittleEndianTransferSyntax(); - bool IsDeflatedExplicitVRLittleEndianTransferSyntax(); - bool IsExplicitVRBigEndianTransferSyntax(); - bool IsJPEGBaseLineProcess1TransferSyntax(); - bool IsJPEGExtendedProcess2_4TransferSyntax(); - bool IsJPEGExtendedProcess3_5TransferSyntax(); - bool IsJPEGSpectralSelectionProcess6_8TransferSyntax(); - bool IsRLELossLessTransferSyntax(); - bool IsJPEGLossless(); - bool IsJPEG2000(); bool IsDicomV3(); - + bool IsPapyrus(); FileType GetFileType(); + std::string GetTransferSyntax(); + /// Return the Transfer Syntax as a string + std::string GetTransferSyntaxName(); - FILE* OpenFile(bool exception_on_error = false) throw(gdcmFileError); +// Swap code + /// 'Swap code' accessor (see \ref SwapCode ) + int GetSwapCode() { return SwapCode; } + // System access (meaning endian related !?) + uint16_t SwapShort(uint16_t); + uint32_t SwapLong(uint32_t); + /// \brief Unswaps back the bytes of 2-bytes long integer + /// so they agree with the processor order. + uint16_t UnswapShort(uint16_t a) { return SwapShort(a);} + /// \brief Unswaps back the bytes of 4-byte long integer + /// so they agree with the processor order. + uint32_t UnswapLong(uint32_t a) { return SwapLong(a);} + +// File I/O + /// Accessor to \ref Filename + const std::string &GetFileName() const { return Filename; } + /// Accessor to \ref Filename + void SetFileName(std::string const &fileName) { Filename = fileName; } + + std::ifstream *OpenFile(); bool CloseFile(); + void WriteContent( std::ofstream *fp, FileType type ); - void Write(FILE* fp, FileType type); +// Content entries + virtual void LoadEntryBinArea(uint16_t group, uint16_t elem); + virtual void LoadEntryBinArea(BinEntry *entry); - gdcmValEntry* ReplaceOrCreateByNumber(std::string value, - uint16_t group, uint16_t elem); + void LoadDocEntrySafe(DocEntry *entry); + +// Ordering of Documents + bool operator<(Document &document); - gdcmBinEntry* ReplaceOrCreateByNumber(void *voidArea, int lgth, - uint16_t group, uint16_t elem); - bool ReplaceIfExistByNumber (const char* value, uint16_t group, uint16_t elem); - - virtual void* LoadEntryVoidArea(uint16_t group, uint16_t elem); - virtual void* LoadEntryVoidArea(gdcmBinEntry* entry); - - // System access - uint16_t SwapShort(uint16_t); // needed by gdcmFile - uint32_t SwapLong(uint32_t); // needed by gdcmFile - uint16_t UnswapShort(uint16_t); // needed by gdcmFile - uint32_t UnswapLong(uint32_t); // needed by gdcmFile +/** + * \brief \brief Sets the LoadMode as a boolean string. + * NO_SEQ, NO_SHADOW, ... (nothing more, right now) + * WARNING : before using NO_SHADOW, be sure *all* your files + * contain accurate values in the 0x0000 element + * of each Shadow Group. The paser will fail if the size is wrong ! + * @param mode Load mode to be used + */ + void SetLoadMode (int mode) { LoadMode = mode; } protected: +// Methods // Constructor and destructor are protected to forbid end user - // to instanciate from this class gdcmDocument (only gdcmHeader and - // gdcmDicomDir are meaningfull). - gdcmDocument(bool exception_on_error = false); - gdcmDocument(std::string const & filename, - bool exception_on_error = false, - bool ignore_shadow = false); - virtual ~gdcmDocument(); + // to instanciate from this class Document (only gdcm::File and + // gdcm::DicomDir are meaningfull). + Document(); + Document( std::string const &filename ); + virtual ~Document(); - void gdcmDocument::Parse7FE0 (); - // Entry - int CheckIfEntryExistByNumber(uint16_t group, uint16_t elem ); // int ! -public: - virtual std::string GetEntryByName (TagName tagName); - virtual std::string GetEntryVRByName (TagName tagName); - virtual std::string GetEntryByNumber (uint16_t group, uint16_t elem); - virtual std::string GetEntryVRByNumber(uint16_t group, uint16_t elem); - virtual int GetEntryLengthByNumber(uint16_t group, uint16_t elem); -protected: - virtual bool SetEntryByName (std::string content, std::string tagName); - virtual bool SetEntryByNumber(std::string content, - uint16_t group, uint16_t element); - virtual bool SetEntryByNumber(void *content, int lgth, - uint16_t group, uint16_t element); - virtual bool SetEntryLengthByNumber(uint32_t length, - uint16_t group, uint16_t element); + uint16_t ReadInt16() throw ( FormatError ); + uint32_t ReadInt32() throw ( FormatError ); + void SkipBytes(uint32_t); + int ComputeGroup0002Length( FileType filetype ); + +// Variables + /// Refering underlying filename. + std::string Filename; - virtual size_t GetEntryOffsetByNumber(uint16_t group, uint16_t elem); - virtual void* GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem); - virtual bool SetEntryVoidAreaByNumber(void* a, uint16_t group, - uint16_t elem); + /// \brief Swap code gives an information on the byte order of a + /// supposed to be an int32, as it's read on disc + /// (depending on the image Transfer Syntax *and* on the processor endianess) + /// as opposed as it should in memory to be dealt as an int32. + /// For instance : + /// - a 'Little Endian' image, read with a little endian processor + /// will have a SwapCode= 1234 (the order is OK; nothing to do) + /// - a 'Little Endian' image, read with a big endian procesor + /// will have a SwapCode= 4321 (the order is wrong; int32 an int16 must be + /// swapped) + /// note : values 2143, 4321, 3412 remain for the ACR-NEMA time, and + /// the well known 'Bad Big Endian' and 'Bad Little Endian' codes + int SwapCode; - virtual void UpdateShaEntries(); + ///\brief whether we already parsed group 0002 (Meta Elements) + bool Group0002Parsed; - // Header entry - gdcmDocEntry* GetDocEntryByNumber(uint16_t group, uint16_t element); - gdcmDocEntry* GetDocEntryByName (std::string const & tagName); + ///\brief whether file has a DCM Preamble + bool HasDCMPreamble; - gdcmValEntry* GetValEntryByNumber(uint16_t group, uint16_t element); - gdcmBinEntry* GetBinEntryByNumber(uint16_t group, uint16_t element); + /// File Pointer, opened during Document parsing. + std::ifstream *Fp; - void LoadDocEntrySafe(gdcmDocEntry* entry); + /// ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown + FileType Filetype; -private: - // Read - long ParseDES(gdcmDocEntrySet *set, long offset, long l_max,bool delim_mode); - long ParseSQ(gdcmSeqEntry *seq, long offset, long l_max, bool delim_mode); + /// After opening the file, we read HEADER_LENGTH_TO_READ bytes. + static const unsigned int HEADER_LENGTH_TO_READ; + /// \brief Elements whose value is longer than MAX_SIZE_LOAD_ELEMENT_VALUE + /// are NOT loaded. + static const unsigned int MAX_SIZE_LOAD_ELEMENT_VALUE; + + /// List of elements to Anonymize + ListElements AnonymizeList; + + /// \brief Bit string integer (each one considered as a boolean) + /// Bit 0 : Skip Sequences, if possible + /// Bit 1 : Skip Shadow Groups if possible + /// Some more to add + int LoadMode; - void LoadDocEntry (gdcmDocEntry *); - void FindDocEntryLength(gdcmDocEntry *); - void FindDocEntryVR (gdcmDocEntry *); - bool CheckDocEntryVR (gdcmDocEntry *, gdcmVRKey); + /// Whether the gdcm::Document is already parsed/loaded + /// - False from the creation of the gdcm::Document untill + /// gdcm::Document:Load() + bool IsDocumentAlreadyLoaded; + +private: +// Methods + void Initialize(); - std::string GetDocEntryValue (gdcmDocEntry *); - std::string GetDocEntryUnvalue(gdcmDocEntry *); + // Read + void ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode); + void ParseSQ (SeqEntry *seq, long offset, long l_max, bool delim_mode); - void SkipDocEntry (gdcmDocEntry *); - void SkipToNextDocEntry (gdcmDocEntry *); + void LoadDocEntry (DocEntry *e); + void FindDocEntryLength (DocEntry *e) throw ( FormatError ); + uint32_t FindDocEntryLengthOBOrOW() throw( FormatUnexpected ); + std::string FindDocEntryVR(); + bool CheckDocEntryVR (VRKey k); - void FixDocEntryFoundLength(gdcmDocEntry *, uint32_t); - bool IsDocEntryAnInteger (gdcmDocEntry *); + std::string GetDocEntryValue (DocEntry *entry); + std::string GetDocEntryUnvalue(DocEntry *entry); - uint32_t FindDocEntryLengthOB(); + void SkipDocEntry (DocEntry *entry); + void SkipToNextDocEntry (DocEntry *entry); - uint16_t ReadInt16(); - uint32_t ReadInt32(); - void SkipBytes(uint32_t); - bool ReadTag(uint16_t, uint16_t); - uint32_t ReadTagLength(uint16_t, uint16_t); + void FixDocEntryFoundLength(DocEntry *entry, uint32_t l); + bool IsDocEntryAnInteger (DocEntry *entry); - void Initialise(); bool CheckSwap(); - void SwitchSwapToBigEndian(); + void SwitchByteSwapCode(); void SetMaxSizeLoadEntry(long); - void SetMaxSizePrintEntry(long); // DocEntry related utilities - gdcmDocEntry* ReadNextDocEntry(); + DocEntry *ReadNextDocEntry(); - uint32_t GenerateFreeTagKeyInGroup(uint16_t group); + void HandleBrokenEndian (uint16_t &group, uint16_t &elem); + void HandleOutOfGroup0002(uint16_t &group, uint16_t &elem); -public: -// Accessors: - /// Accessor to \ref printLevel - void SetPrintLevel(int level) { PrintLevel = level; } - - /// Accessor to \ref Filename - const std::string &GetFileName() { return Filename; } - - /// Accessor to \ref Filename - void SetFileName(std::string const & fileName) { Filename = fileName; } +// Variables + /// Public dictionary used to parse this header + Dict *RefPubDict; + /// \brief Optional "shadow dictionary" (private elements) used to parse + /// this header + Dict *RefShaDict; - /// 'Swap code' accessor (see \ref sw ) - int GetSwapCode() { return SwapCode; } + /// \brief Size threshold 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). + uint32_t MaxSizeLoadEntry; - /// File pointer - FILE * GetFP() { return Fp; } - - bool operator<(gdcmDocument &document); +// uint32_t GenerateFreeTagKeyInGroup(uint16_t group); +// void BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, +// DocEntrySet *set ); }; +} // end namespace gdcm + //----------------------------------------------------------------------------- #endif