X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.h;h=ab2782a532b178ec3a3bdb4354b352fed0ecccb8;hb=6278320cc85da00d2d56ffbf07806e84966892c3;hp=490fbc74c867d851c11e82847660bcfa08a709e6;hpb=a2040ffd26fc9a3c835b6c45b92a808f1d001b36;p=gdcm.git diff --git a/src/gdcmDocument.h b/src/gdcmDocument.h index 490fbc74..ab2782a5 100644 --- a/src/gdcmDocument.h +++ b/src/gdcmDocument.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmDocument.h,v $ Language: C++ - Date: $Date: 2005/01/05 15:38:28 $ - Version: $Revision: 1.70 $ + 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 @@ -16,258 +16,259 @@ =========================================================================*/ -#ifndef GDCMDOCUMENT_H -#define GDCMDOCUMENT_H +#ifndef _GDCMDOCUMENT_H_ +#define _GDCMDOCUMENT_H_ #include "gdcmVR.h" #include "gdcmDict.h" #include "gdcmElementSet.h" +#include "gdcmException.h" +#include "gdcmDebug.h" // for LEGACY +#include "gdcmCommandManager.h" #include #include #include -namespace gdcm +namespace GDCM_NAME_SPACE { -class ValEntry; -class BinEntry; class SeqEntry; class Dict; -class RLEFramesInfo; -class JPEGFragmentsInfo; - -enum TransferSyntaxType { - ImplicitVRLittleEndian = 0, - ImplicitVRLittleEndianDLXGE, - ExplicitVRLittleEndian, - DeflatedExplicitVRLittleEndian, - ExplicitVRBigEndian, - JPEGBaselineProcess1, - JPEGExtendedProcess2_4, - JPEGExtendedProcess3_5, - JPEGSpectralSelectionProcess6_8, - JPEGFullProgressionProcess10_12, - JPEGLosslessProcess14, - JPEGLosslessProcess14_1, - JPEG2000Lossless, - JPEG2000, - RLELossless, - UnknownTS -}; //----------------------------------------------------------------------------- /** - * \brief Derived by both Header and DicomDir + * \brief Derived by both GDCM_NAME_SPACE::File and GDCM_NAME_SPACE::DicomDir */ class GDCM_EXPORT Document : public ElementSet { -friend class File; -private: - /// Public dictionary used to parse this header - Dict* RefPubDict; - - /// \brief Optional "shadow dictionary" (private elements) used to parse - /// this header - Dict* RefShaDict; + 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. - std::ifstream* 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 - /// class DocEntry . See also - /// method ref Document::SetMaxSizePrintEntry() - static const unsigned int MAX_SIZE_PRINT_ELEMENT_VALUE; - - /// Store the RLE frames info obtained during parsing of pixels. - RLEFramesInfo* RLEInfo; - - /// Store the JPEG fragments info obtained during parsing of pixels. - JPEGFragmentsInfo* JPEGInfo; - -public: -// the 2 following will be merged - virtual void PrintPubDict (std::ostream &os = std::cout); - virtual void PrintShaDict (std::ostream &os = std::cout); - -// Dictionnaries - Dict* GetPubDict(); - Dict* GetShaDict(); - bool SetShaDict(Dict* dict); - bool SetShaDict(DictKey const & dictName); - -// Informations contained in the parser - virtual bool IsReadable(); - TransferSyntaxType GetTransferSyntax(); - bool IsJPEGLossless(); - bool IsJPEG2000(); - bool IsJPEG(); - bool IsEncapsulate(); - bool IsDicomV3(); - - FileType GetFileType(); - - std::ifstream * OpenFile(); - bool CloseFile(); - - void WriteContent( std::ofstream* fp, FileType type ); - - ValEntry* ReplaceOrCreateByNumber(std::string const & value, - uint16_t group, uint16_t elem, - TagName const & vr = GDCM_UNKNOWN); - - BinEntry* ReplaceOrCreateByNumber(uint8_t* binArea, int lgth, - uint16_t group, uint16_t elem, - TagName const & vr = GDCM_UNKNOWN); + /// User supplied list of elements to Anonymize + ListElements UserAnonymizeList; - SeqEntry* ReplaceOrCreateByNumber(uint16_t group, uint16_t elem); + /// User supplied list of elements to force Load + ListElements UserForceLoadList; - 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 LoadEntryBinArea(uint16_t group, uint16_t elem); - virtual void LoadEntryBinArea(BinEntry* entry); - - // System access (meaning endian related !?) - uint16_t SwapShort(uint16_t); // needed by File - uint32_t SwapLong(uint32_t); // needed by File - uint16_t UnswapShort(uint16_t); // needed by File - uint32_t UnswapLong(uint32_t); // needed by File + /// \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 - static std::string GetTransferSyntaxValue(TransferSyntaxType type); - -protected: - // Constructor and destructor are protected to forbid end user - // to instanciate from this class Document (only Header and - // DicomDir are meaningfull). - Document(); - Document( std::string const & filename ); - virtual ~Document(); - - void ReadAndSkipEncapsulatedBasicOffsetTable(); - void ComputeRLEInfo(); - void ComputeJPEGFragmentInfo(); - // Entry - bool CheckIfEntryExistByNumber(uint16_t group, uint16_t elem ); -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, - TagName const & tagName ); - virtual bool SetEntryByNumber(std::string const & content, - uint16_t group, uint16_t element); - virtual bool SetEntryByNumber(uint8_t* content, int lgth, - uint16_t group, uint16_t element); - virtual void* GetEntryBinAreaByNumber(uint16_t group, uint16_t elem); - // FIXME - // Verify the usefull of this method... otherwise remove it - // It's body is commented in the .xx - //virtual bool SetEntryBinAreaByNumber(uint8_t* a, uint16_t group, - // uint16_t elem); - - virtual void UpdateShaEntries(); - - // Header entry - DocEntry* GetDocEntryByNumber(uint16_t group, uint16_t element); - DocEntry* GetDocEntryByName (TagName const & tagName); - - ValEntry* GetValEntryByNumber(uint16_t group, uint16_t element); - //BinEntry* GetBinEntryByNumber(uint16_t group, uint16_t element); - RLEFramesInfo* GetRLEInfo() { return RLEInfo; } - JPEGFragmentsInfo* GetJPEGInfo() { return JPEGInfo; } - - void LoadDocEntrySafe(DocEntry* entry); - TagDocEntryHT* BuildFlatHashTable(); + /// Whether the GDCM_NAME_SPACE::Document was modified since the last Load() + bool IsDocumentModified; private: +// 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);} + // 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 LoadDocEntry (DocEntry *); - void FindDocEntryLength(DocEntry *) throw ( FormatError ); - void FindDocEntryVR (DocEntry *); - bool CheckDocEntryVR (DocEntry *, VRKey); - - std::string GetDocEntryValue (DocEntry *); - std::string GetDocEntryUnvalue(DocEntry *); + 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 SkipDocEntry (DocEntry *); - void SkipToNextDocEntry (DocEntry *); + 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); - void FixDocEntryFoundLength(DocEntry *, uint32_t); - bool IsDocEntryAnInteger (DocEntry *); + void SkipDocEntry (DocEntry *entry); + void SkipToNextDocEntry (DocEntry *entry); - uint32_t FindDocEntryLengthOB() throw( FormatUnexpected ); + void FixDocEntryFoundLength(DocEntry *entry, uint32_t l); + bool IsDocEntryAnInteger (DocEntry *entry); - uint16_t ReadInt16() throw ( FormatError ); - uint32_t ReadInt32() throw ( FormatError ); - void SkipBytes(uint32_t); - bool ReadTag(uint16_t, uint16_t); - uint32_t ReadTagLength(uint16_t, uint16_t); - - void Initialise(); bool CheckSwap(); - void SwitchSwapToBigEndian(); - void SetMaxSizeLoadEntry(long); - void SetMaxSizePrintEntry(long); + void SwitchByteSwapCode(); // DocEntry related utilities - DocEntry* ReadNextDocEntry(); + DocEntry *ReadNextDocEntry(); + uint16_t GetInt16(); + uint32_t GetInt32(); - uint32_t GenerateFreeTagKeyInGroup(uint16_t group); - void BuildFlatHashTableRecurse( TagDocEntryHT& builtHT, - DocEntrySet* set ); + void HandleBrokenEndian (uint16_t &group, uint16_t &elem); + void HandleOutOfGroup0002(uint16_t &group, uint16_t &elem); + DocEntry *Backtrack(DocEntry *docEntry, DocEntrySet *set); - void HandleBrokenEndian(uint16_t group, uint16_t elem); -public: -// Accessors: - /// Accessor to \ref Filename - const std::string &GetFileName() const { return Filename; } +// Variables +protected: + /// value of the ??? for any progress bar + float Progress; + mutable bool Abort; + + /// Public dictionary used to parse this header + Dict *RefPubDict; + /// \brief Optional "shadow dictionary" (private elements) used to parse + /// this header + Dict *RefShaDict; - /// Accessor to \ref Filename - void SetFileName(std::string const & fileName) { Filename = fileName; } + /// \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; - /// 'Swap code' accessor (see \ref SwapCode ) - int GetSwapCode() { return SwapCode; } - - bool operator<(Document &document); + /// \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 //-----------------------------------------------------------------------------