X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmDocument.h;h=a1c445f729b2b9181e24eeffe3747cd556b13b2e;hb=d00078b5e19310b379c8339fa8fe38362e8ca392;hp=a8f7cb19a285287824828d26fd290580cbd6bac1;hpb=0d33ba5ffb1c6beac21f33bd3e3aad67b7608c9d;p=gdcm.git diff --git a/src/gdcmDocument.h b/src/gdcmDocument.h index a8f7cb19..a1c445f7 100644 --- a/src/gdcmDocument.h +++ b/src/gdcmDocument.h @@ -1,82 +1,177 @@ -// gdcmDocument.h -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmDocument.h,v $ + Language: C++ + Date: $Date: 2005/01/20 16:17:00 $ + Version: $Revision: 1.95 $ + + 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.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + #ifndef GDCMDOCUMENT_H #define GDCMDOCUMENT_H -#include "gdcmCommon.h" - #include "gdcmVR.h" -#include "gdcmTS.h" -#include "gdcmException.h" -#include "gdcmDictSet.h" -#include "gdcmDocEntry.h" -#include "gdcmDocEntrySet.h" +#include "gdcmDict.h" #include "gdcmElementSet.h" #include #include +#include - - -//----------------------------------------------------------------------------- -typedef std::string VRKey; -typedef std::string VRAtr; -typedef std::map VRHT; // Value Representation Hash Table - -typedef std::map TagDocEntryHT; -typedef std::pair PairHT; -typedef std::pair IterHT; -/// for linking together the Elements -typedef std::list ListTag; - -typedef std::string GroupKey; -typedef std::map GroupHT; +namespace gdcm +{ +class ValEntry; +class BinEntry; +class SeqEntry; +class Dict; +class RLEFramesInfo; +class JPEGFragmentsInfo; //----------------------------------------------------------------------------- /** - * \brief used by both gdcmHeader and gdcmDicomDir + * \brief Derived by both Header and DicomDir */ -class GDCM_EXPORT gdcmDocument : public gdcmElementSet +class GDCM_EXPORT Document : public ElementSet { -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; +public: +// Informations contained in the parser + virtual bool IsReadable(); + FileType GetFileType(); - /// \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). - guint32 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. - guint32 MaxSizePrintEntry; + std::string GetTransferSyntax(); + + RLEFramesInfo *GetRLEInfo() { return RLEInfo; } + JPEGFragmentsInfo *GetJPEGInfo() { return JPEGInfo; } + +// Dictionaries + virtual void PrintPubDict (std::ostream &os = std::cout); + virtual void PrintShaDict (std::ostream &os = std::cout); + + Dict* GetPubDict(); + Dict* GetShaDict(); + bool SetShaDict(Dict* dict); + bool SetShaDict(DictKey const &dictName); + +// Swap code + /// 'Swap code' accessor (see \ref SwapCode ) + int GetSwapCode() { return SwapCode; } + // System access (meaning endian related !?) + uint16_t SwapShort(uint16_t); // needed by Document + uint32_t SwapLong(uint32_t); // needed by Document + uint16_t UnswapShort(uint16_t); // needed by Document + uint32_t UnswapLong(uint32_t); // needed by Document +// Ordering of Documents + bool operator<(Document &document); + +public: +// 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 ); + +// Content entries + +// Oops ! Python is gonna cry : +// 4 methods with same name and different parameters ... +// Only C++ is aware! + + virtual bool SetEntry(std::string const &content, + uint16_t group, uint16_t elem); + virtual bool SetEntry(uint8_t *content, int lgth, + uint16_t group, uint16_t elem); + virtual bool SetEntry(std::string const &content, ValEntry *entry); + virtual bool SetEntry(uint8_t *content, int lgth, BinEntry *entry); + + virtual void *GetEntryBinArea(uint16_t group, uint16_t elem); + + virtual std::string GetEntry (uint16_t group, uint16_t elem); + virtual std::string GetEntryVR(uint16_t group, uint16_t elem); + virtual int GetEntryLength(uint16_t group, uint16_t elem); + + ValEntry *ReplaceOrCreate(std::string const &value, + uint16_t group, uint16_t elem, + TagName const &vr = GDCM_UNKNOWN); + BinEntry *ReplaceOrCreate(uint8_t* binArea, int lgth, + uint16_t group, uint16_t elem, + TagName const &vr = GDCM_UNKNOWN); + SeqEntry *ReplaceOrCreate(uint16_t group, uint16_t elem); + + bool ReplaceIfExist(std::string const &value, + uint16_t group, uint16_t elem ); + + bool CheckIfEntryExist(uint16_t group, uint16_t elem ); + virtual void LoadEntryBinArea(uint16_t group, uint16_t elem); + virtual void LoadEntryBinArea(BinEntry *entry); + + void LoadDocEntrySafe(DocEntry *entry); + /*TagDocEntryHT *BuildFlatHashTable();*/ + + /// Return the Transfer Syntax as a string + std::string GetTransferSyntaxName(); + + bool IsDicomV3(); protected: - /// Refering underlying filename. - std::string filename; +// Methods + // 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 - /// \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 sw; + int ComputeGroup0002Length( FileType filetype ); + +// Variables + /// Refering underlying filename. + std::string Filename; + + /// \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; + + ///\brief whether we already parsed group 0002 + bool Group0002Parsed; + + ///\brief whether file has a DCM Preamble + bool HasDCMPreamble; /// File Pointer, opened during Header parsing. - FILE *fp; + std::ifstream *Fp; /// ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown - FileType filetype; + FileType Filetype; /// After opening the file, we read HEADER_LENGTH_TO_READ bytes. static const unsigned int HEADER_LENGTH_TO_READ; @@ -87,209 +182,81 @@ protected: /// \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; - /// Hash Table (multimap), to provide fast access - TagDocEntryHT tagHT; - - /// Chained list, to keep the 'spacial' ordering - ListTag listEntries; - - /// Will be set 1 if user asks to 'go inside' the 'sequences' (VR = "SQ") - int enableSequences; + /// Store the RLE frames info obtained during parsing of pixels. + RLEFramesInfo *RLEInfo; - /// \brief Amount of printed details for each Header Entry (Dicom Element): - /// 0 : stands for the least detail level. - int printLevel; - -public: - - -// Print - // Canonical Printing method (see also gdcmDocument::SetPrintLevel) - // virtual void Print (std::ostream &os = std::cout); - // {PrintEntry(os);}; - - // no more Print method for gdcmDocument (inherits from gdcmElementSet - // virtual void PrintEntry (std::ostream &os = std::cout) - // { return Print(os);}; - - // the 2 following will be merged - virtual void PrintPubDict (std::ostream &os = std::cout); - virtual void PrintShaDict (std::ostream &os = std::cout); + /// Store the JPEG fragments info obtained during parsing of pixels. + JPEGFragmentsInfo *JPEGInfo; -// Dictionnaries - gdcmDict *GetPubDict(void); - gdcmDict *GetShaDict(void); - bool SetShaDict(gdcmDict *dict); - bool SetShaDict(DictKey dictName); - -// Informations contained in the parser - virtual bool IsReadable(void); - bool IsImplicitVRLittleEndianTransferSyntax(void); - bool IsExplicitVRLittleEndianTransferSyntax(void); - bool IsDeflatedExplicitVRLittleEndianTransferSyntax(void); - bool IsExplicitVRBigEndianTransferSyntax(void); - FileType GetFileType(void); - -// Read (used in gdcmFile, gdcmDicomDir) - FILE *OpenFile(bool exception_on_error = false) throw(gdcmFileError); - bool CloseFile(void); - -// Write (used in gdcmFile, gdcmDicomDir) - virtual bool Write(FILE *, FileType); - virtual void WriteEntryTagVRLength(gdcmDocEntry *tag, - FILE *_fp, FileType type); - virtual void WriteEntryValue(gdcmDocEntry *tag,FILE *_fp,FileType type); - virtual bool WriteEntry(gdcmDocEntry *tag,FILE *_fp,FileType type); - virtual bool WriteEntries(FILE *_fp,FileType type); - void WriteEntriesDeprecated(FILE *_fp,FileType type); // JPR - - gdcmDocEntry * ReplaceOrCreateByNumber(std::string Value, - guint16 Group, guint16 Elem); - bool ReplaceIfExistByNumber (char *Value, guint16 Group, guint16 Elem); - - virtual void *LoadEntryVoidArea (guint16 Group, guint16 Element); - void LoadVLEntry (gdcmDocEntry *entry); - -// System access - guint16 SwapShort(guint16); // needed by gdcmFile - guint32 SwapLong(guint32); // needed by gdcmFile - guint16 UnswapShort(guint16); // needed by gdcmFile - guint32 UnswapLong(guint32); // needed by gdcmFile - -protected: - // 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(const char *inFilename, - bool exception_on_error = false, - bool enable_sequences = false, - bool ignore_shadow = false); - virtual ~gdcmDocument(void); -// Entry - int CheckIfEntryExistByNumber(guint16 Group, guint16 Elem ); // int ! - virtual std::string GetEntryByName (std::string tagName); - virtual std::string GetEntryVRByName (std::string tagName); - virtual std::string GetEntryByNumber (guint16 group, guint16 element); - virtual std::string GetEntryVRByNumber(guint16 group, guint16 element); - virtual int GetEntryLengthByNumber(guint16 group, guint16 element); - - virtual bool SetEntryByName (std::string content, std::string tagName); - virtual bool SetEntryByNumber(std::string content, - guint16 group, guint16 element); - virtual bool SetEntryLengthByNumber(guint32 length, - guint16 group, guint16 element); - - virtual size_t GetEntryOffsetByNumber (guint16 Group, guint16 Elem); - virtual void *GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem); - virtual bool SetEntryVoidAreaByNumber(void *a, guint16 Group, guint16 Elem); - - virtual void UpdateShaEntries(void); - -// Header entry - gdcmDocEntry *GetDocEntryByNumber (guint16 group, guint16 element); - gdcmDocEntry *GetDocEntryByName (std::string Name); - IterHT GetDocEntrySameNumber(guint16 group, guint16 element); -// IterHT GetDocEntrySameName (std::string Name); - - void LoadDocEntrySafe(gdcmDocEntry *); - - // Probabely useless - //void UpdateGroupLength(bool SkipSequence = false, - // FileType type = ImplicitVR); - - //void AddDocEntry (gdcmDocEntry *); - - private: +// Methods // Read - //bool LoadHeaderEntries(bool exception_on_error = false) throw(gdcmFormatError); - // remplacé par ParseDES. - // What about exception_on_error ? - - long ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode); - long ParseSQ(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode); - - - void LoadDocEntry (gdcmDocEntry *); - void FindDocEntryLength(gdcmDocEntry *); - void FindDocEntryVR (gdcmDocEntry *); - bool CheckDocEntryVR (gdcmDocEntry *, VRKey); + void ParseDES(DocEntrySet *set,long offset, long l_max, bool delim_mode); + void ParseSQ (SeqEntry *seq, long offset, long l_max, bool delim_mode); - std::string GetDocEntryValue (gdcmDocEntry *); - std::string GetDocEntryUnvalue(gdcmDocEntry *); + void LoadDocEntry (DocEntry *e); + void FindDocEntryLength (DocEntry *e) throw ( FormatError ); + uint32_t FindDocEntryLengthOBOrOW() throw( FormatUnexpected ); + std::string FindDocEntryVR(); + bool CheckDocEntryVR (VRKey k); - void SkipDocEntry (gdcmDocEntry *); - void SkipToNextDocEntry (gdcmDocEntry *); + std::string GetDocEntryValue (DocEntry *entry); + std::string GetDocEntryUnvalue(DocEntry *entry); - void FixDocEntryFoundLength(gdcmDocEntry *, guint32); - bool IsDocEntryAnInteger (gdcmDocEntry *); - guint32 FindDocEntryLengthOB(void); + void SkipDocEntry (DocEntry *entry); + void SkipToNextDocEntry (DocEntry *entry); - guint16 ReadInt16(void); - guint32 ReadInt32(void); - void SkipBytes(guint32); + void FixDocEntryFoundLength(DocEntry *entry,uint32_t l); + bool IsDocEntryAnInteger (DocEntry *entry); - void Initialise(void); - bool CheckSwap(void); - void SwitchSwapToBigEndian(void); + 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 Initialize(); + bool CheckSwap(); + void SwitchByteSwapCode(); void SetMaxSizeLoadEntry(long); void SetMaxSizePrintEntry(long); - // DictEntry related utilities - - gdcmDictEntry *GetDictEntryByName (std::string Name); - gdcmDictEntry *GetDictEntryByNumber(guint16, guint16); - gdcmDictEntry *NewVirtualDictEntry(guint16 group, - guint16 element, - std::string vr = "unkn", - std::string fourth = "unkn", - std::string name = "unkn"); - //gdcmDictEntry *NewVirtualDictEntry(gdcmDocEntry *); // never defined - // DocEntry related utilities - - gdcmDocEntry *ReadNextDocEntry (void); - gdcmDocEntry *NewDocEntryByNumber(guint16 group, - guint16 element); - gdcmDocEntry *NewDocEntryByName (std::string Name); - - // Deprecated (Not used) --> commented out - //gdcmDocEntry *NewManualDocEntryToPubDict(std::string NewTagName, - // std::string VR); - - guint32 GenerateFreeTagKeyInGroup(guint16 group); + DocEntry *ReadNextDocEntry(); -public: -// Accessors: - /// Accessor to \ref printLevel - void SetPrintLevel(int level) { printLevel = level; }; - - /// Accessor to \ref filename - inline std::string GetFileName(void) {return filename;} - - /// Accessor to \ref filename - inline void SetFileName(char* fileName) {filename = fileName;} + uint32_t GenerateFreeTagKeyInGroup(uint16_t group); +/* void BuildFlatHashTableRecurse( TagDocEntryHT &builtHT, + DocEntrySet* set );*/ - /// Accessor to \ref gdcmDocument::tagHT - inline TagDocEntryHT &GetEntry(void) { return tagHT; }; + void HandleBrokenEndian(uint16_t &group, uint16_t &elem); + void HandleOutOfGroup0002(uint16_t &group, uint16_t &elem); - /// Accessor to \ref gdcmDocument::listEntries - inline ListTag &GetListEntry(void) { return listEntries; }; +// 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 ) - inline int GetSwapCode(void) { return sw; } + /// \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 - inline FILE * GetFP(void) { return fp; } + /// \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; +private: + friend class FileHelper; }; +} // end namespace gdcm //----------------------------------------------------------------------------- #endif