X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.h;h=ab2782a532b178ec3a3bdb4354b352fed0ecccb8;hb=56ad78cdf3b5de32f0a94a38cd32ddc9f403ffc3;hp=fdbe8ba89c79901e8639e2856fe95beaaaf81821;hpb=3c51b39e18ba55faf14c5bbac129662e824d3adb;p=gdcm.git diff --git a/src/gdcmDocument.h b/src/gdcmDocument.h index fdbe8ba8..ab2782a5 100644 --- a/src/gdcmDocument.h +++ b/src/gdcmDocument.h @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmDocument.h,v $ Language: C++ - Date: $Date: 2004/09/03 04:16:29 $ - Version: $Revision: 1.33 $ + Date: $Date: 2008/09/15 15:49:22 $ + Version: $Revision: 1.154 $ 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 @@ -16,246 +16,260 @@ =========================================================================*/ -#ifndef GDCMDOCUMENT_H -#define GDCMDOCUMENT_H +#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 "gdcmDebug.h" // for LEGACY +#include "gdcmCommandManager.h" #include #include +#include + +namespace GDCM_NAME_SPACE +{ +class SeqEntry; +class Dict; //----------------------------------------------------------------------------- /** - * \brief Derived by both gdcmHeader and gdcmDicomDir + * \brief Derived by both GDCM_NAME_SPACE::File and GDCM_NAME_SPACE::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; + gdcmTypeMacro(Document); - /// \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; +public: + typedef std::list ListElements; + +// Loading + //Deprecated : use SetFileName() + Load() +//#ifndef GDCM_LEGACY_REMOVE +// virtual bool Load( std::string const &filename ); +//#endif + virtual bool Load( ); + +// Dictionaries + Dict *GetPubDict(); + Dict *GetShaDict(); + bool SetShaDict(Dict *dict); + bool SetShaDict(DictKey const &dictName); + +// Informations contained in the GDCM_NAME_SPACE::Document + bool IsParsable(); + virtual bool IsReadable(); + bool IsDicomV3(); + bool IsPapyrus(); + FileType GetFileType(); + std::string GetTransferSyntax(); + /// Return the Transfer Syntax as a string + std::string GetTransferSyntaxName(); + +// Swap code + /// 'Swap code' accessor (see SwapCode ) + int GetSwapCode() { return SwapCode; } - /// \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; +// File I/O + /// Accessor to Filename + const std::string &GetFileName() const { return Filename; } + /// Accessor to Filename + virtual void SetFileName(std::string const &fileName) + { if (Filename != fileName) + Filename = fileName, IsDocumentModified = true; } + + std::ifstream *OpenFile(); + bool CloseFile(); + void WriteContent( std::ofstream *fp, FileType type, bool insideMetaElements, bool insideSequence ); + +// Data entries + virtual void LoadEntryBinArea(uint16_t group, uint16_t elem); + virtual void LoadEntryBinArea(DataEntry *entry); + + void SetMaxSizeLoadEntry(long); + void AddForceLoadElement(uint16_t group, uint16_t elem); + +// Ordering of Documents + bool operator<(Document &document); + +/** + * \brief Sets the LoadMode as a boolean string. + * LD_NOSEQ, LD_NOSHADOW, LD_NOSHADOWSEQ + ... (nothing more, right now) + * WARNING : before using NO_SHADOW, be sure *all* your files + * contain accurate values in the 0x0000 element (if any) + * of *each* Shadow Group. The parser will fail if the size is wrong ! + * @param mode Load mode to be used + */ + void SetLoadMode (int mode) { if (LoadMode != mode) + LoadMode=mode, IsDocumentModified = true; } protected: +// Methods + // Constructor and destructor are protected to forbid end user + // to instanciate from this class Document (only GDCM_NAME_SPACE::File and + // GDCM_NAME_SPACE::DicomDir are meaningfull). + Document(); + virtual ~Document(); + + virtual void CallStartMethod(); + virtual void CallProgressMethod(); + virtual void CallEndMethod(); + + uint16_t ReadInt16() throw ( FormatError ); + uint32_t ReadInt32() throw ( FormatError ); + + /// \brief skips bytes inside the source file + void SkipBytes(uint32_t nBytes) { Fp->seekg((long)nBytes, std::ios::cur);} + int ComputeGroup0002Length( ); + +// Variables /// 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. + /// \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; - /// File Pointer, opened during Header parsing. - FILE *Fp; + ///\brief whether we already parsed group 0002 (Meta Elements) + bool Group0002Parsed; + + ///\brief whether file has a DCM Preamble + bool HasDCMPreamble; + + /// File Pointer, opened during Document parsing. + std::ifstream *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; - /// \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; - - /// Will be set 1 if user asks to 'go inside' the 'sequences' (VR = "SQ") - int EnableSequences; + /// User supplied list of elements to Anonymize + ListElements UserAnonymizeList; - /// \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); - -// Dictionnaries - gdcmDict *GetPubDict(); - gdcmDict *GetShaDict(); - bool SetShaDict(gdcmDict *dict); - bool SetShaDict(DictKey const & dictName); - -// Informations contained in the parser - 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(); - - FileType GetFileType(); - - FILE* OpenFile(); - bool CloseFile(); + /// User supplied list of elements to force Load + ListElements UserForceLoadList; - void Write(FILE* fp, FileType type); - - gdcmValEntry* ReplaceOrCreateByNumber(std::string const & value, - uint16_t group, uint16_t elem); - - gdcmBinEntry* ReplaceOrCreateByNumber(void *voidArea, int lgth, - uint16_t group, uint16_t elem); - gdcmSeqEntry* ReplaceOrCreateByNumber(uint16_t group, uint16_t elem); - bool ReplaceIfExistByNumber ( std::string const & value, - uint16_t group, - uint16_t elem ); + /// \brief Bit string integer (each one considered as a boolean) + /// Bit 0 : Skip Sequences, if possible + /// Bit 1 : Skip Shadow Groups if possible + /// Probabely, some more to add + int LoadMode; - virtual void* LoadEntryVoidArea(uint16_t group, uint16_t elem); - virtual void* LoadEntryVoidArea(gdcmBinEntry* entry); - - // System access (meaning endian related !?) - 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 Whether the GDCM_NAME_SPACE::Document is already parsed/loaded : + /// False from the creation of the GDCM_NAME_SPACE::Document untill + /// GDCM_NAME_SPACE::Document:Load() + bool IsDocumentAlreadyLoaded; // FIXME : probabely useless now -protected: - // Constructor and destructor are protected to forbid end user - // to instanciate from this class gdcmDocument (only gdcmHeader and - // gdcmDicomDir are meaningfull). - gdcmDocument(); - gdcmDocument( std::string const & filename ); - virtual ~gdcmDocument(); - - void Parse7FE0 (); - // Entry - int CheckIfEntryExistByNumber(uint16_t group, uint16_t elem ); // int ! -public: - virtual std::string GetEntryByName (TagName const & tagName); - virtual std::string GetEntryVRByName (TagName const & 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 const & content, - std::string const & tagName); - virtual bool SetEntryByNumber(std::string const & 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); - - 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); - - virtual void UpdateShaEntries(); - - // Header entry - gdcmDocEntry* GetDocEntryByNumber(uint16_t group, uint16_t element); - gdcmDocEntry* GetDocEntryByName (std::string const & tagName); - - gdcmValEntry* GetValEntryByNumber(uint16_t group, uint16_t element); - gdcmBinEntry* GetBinEntryByNumber(uint16_t group, uint16_t element); - - void LoadDocEntrySafe(gdcmDocEntry* entry); + /// Whether the GDCM_NAME_SPACE::Document was modified since the last Load() + bool IsDocumentModified; 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); +// Methods + void Initialize(); + bool DoTheLoadingDocumentJob(); + + // System access (meaning endian related !?) + void ReadBegBuffer(size_t l) throw ( FormatError ); + uint16_t SwapShort(uint16_t); + uint32_t SwapLong(uint32_t); + double SwapDouble(double); + /// \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);} - void LoadDocEntry (gdcmDocEntry *); - void FindDocEntryLength(gdcmDocEntry *) throw ( gdcmFormatError ); - void FindDocEntryVR (gdcmDocEntry *); - bool CheckDocEntryVR (gdcmDocEntry *, gdcmVRKey); - - std::string GetDocEntryValue (gdcmDocEntry *); - std::string GetDocEntryUnvalue(gdcmDocEntry *); - - void SkipDocEntry (gdcmDocEntry *); - void SkipToNextDocEntry (gdcmDocEntry *); + // Read + void ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode); + bool ParseSQ (SeqEntry *seq, long offset, long l_max, bool delim_mode); - void FixDocEntryFoundLength(gdcmDocEntry *, uint32_t); - bool IsDocEntryAnInteger (gdcmDocEntry *); + void LoadDocEntry (DocEntry *e, bool forceLoad = false); + void FindDocEntryLength (DocEntry *e) throw ( FormatError ); + uint32_t FindDocEntryLengthOBOrOW() throw( FormatUnexpected ); + VRKey FindDocEntryVR(); + bool CheckDocEntryVR (const VRKey &k); - uint32_t FindDocEntryLengthOB() throw( gdcmFormatUnexpected ); + void SkipDocEntry (DocEntry *entry); + void SkipToNextDocEntry (DocEntry *entry); - uint16_t ReadInt16() throw ( gdcmFormatError ); - uint32_t ReadInt32() throw ( gdcmFormatError ); - 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 SetMaxSizeLoadEntry(long); - void SetMaxSizePrintEntry(long); + void SwitchByteSwapCode(); // DocEntry related utilities - gdcmDocEntry* ReadNextDocEntry(); - - uint32_t GenerateFreeTagKeyInGroup(uint16_t group); - -public: -// Accessors: - /// Accessor to \ref PrintLevel - void SetPrintLevel(int level) { PrintLevel = level; } + DocEntry *ReadNextDocEntry(); + uint16_t GetInt16(); + uint32_t GetInt32(); - /// Accessor to \ref Filename - const std::string &GetFileName() { return Filename; } + void HandleBrokenEndian (uint16_t &group, uint16_t &elem); + void HandleOutOfGroup0002(uint16_t &group, uint16_t &elem); + DocEntry *Backtrack(DocEntry *docEntry, DocEntrySet *set); - /// Accessor to \ref Filename - void SetFileName(std::string const & fileName) { Filename = fileName; } - - /// 'Swap code' accessor (see \ref SwapCode ) - int GetSwapCode() { return SwapCode; } +// Variables +protected: + /// value of the ??? for any progress bar + float Progress; + mutable bool Abort; - /// File pointer - FILE * GetFP() { return Fp; } + /// Public dictionary used to parse this header + Dict *RefPubDict; + /// \brief Optional "shadow dictionary" (private elements) used to parse + /// this header + Dict *RefShaDict; - bool operator<(gdcmDocument &document); + /// \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 to allow any inner method to know current tag Group number + uint16_t CurrentGroup; + /// \brief to allow any inner method to know current tag Element number + uint16_t CurrentElem; + +// uint32_t GenerateFreeTagKeyInGroup(uint16_t group); +// void BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, +// DocEntrySet *set ); +private: + /// \brief buffer to avoid some freads + char BegBuffer[8]; + char *PtrBegBuffer; + /// \brief to avoid time consuming ftellg + size_t CurrentOffsetPosition; + /// \brief to indicate if last supposed to be UN DataElement is not + /// (according to a private Dicom dictionary) + bool changeFromUN; + /// \brief whether an unexpected EOF was encountered + bool UnexpectedEOF; + /// \brief to avoid infinite loop when illegal UN stands for OB + size_t OffsetOfPreviousParseDES; }; +} // end namespace gdcm + //----------------------------------------------------------------------------- #endif