Program: gdcm
Module: $RCSfile: gdcmDocument.h,v $
Language: C++
- Date: $Date: 2004/11/25 13:12:02 $
- Version: $Revision: 1.63 $
+ 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
=========================================================================*/
-#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"
-#include "gdcmRLEFramesInfo.h"
-#include "gdcmJPEGFragmentsInfo.h"
-#include "gdcmDocEntrySet.h"
+#include "gdcmDict.h"
#include "gdcmElementSet.h"
-
-class ValEntry;
-class BinEntry;
-class SeqEntry;
+#include "gdcmException.h"
+#include "gdcmDebug.h" // for LEGACY
+#include "gdcmCommandManager.h"
#include <map>
#include <list>
#include <fstream>
-namespace gdcm
+namespace GDCM_NAME_SPACE
{
-
-enum TransferSyntaxType {
- ImplicitVRLittleEndian = 0,
- ImplicitVRLittleEndianDLXGE,
- ExplicitVRLittleEndian,
- DeflatedExplicitVRLittleEndian,
- ExplicitVRBigEndian,
- JPEGBaselineProcess1,
- JPEGExtendedProcess2_4,
- JPEGExtendedProcess3_5,
- JPEGSpectralSelectionProcess6_8,
- JPEGFullProgressionProcess10_12,
- JPEGLosslessProcess14,
- JPEGLosslessProcess14_1,
- JPEG2000Lossless,
- JPEG2000,
- RLELossless,
- UnknownTS
-};
-
-static const char *TransferSyntaxStrings[] = {
- // Implicit VR Little Endian
- "1.2.840.10008.1.2",
- // Implicit VR Little Endian DLX G.E?
- "1.2.840.113619.5.2",
- // Explicit VR Little Endian
- "1.2.840.10008.1.2.1",
- // Deflated Explicit VR Little Endian
- "1.2.840.10008.1.2.1.99",
- // Explicit VR Big Endian
- "1.2.840.10008.1.2.2",
- // JPEG Baseline (Process 1)
- "1.2.840.10008.1.2.4.50",
- // JPEG Extended (Process 2 & 4)
- "1.2.840.10008.1.2.4.51",
- // JPEG Extended (Process 3 & 5)
- "1.2.840.10008.1.2.4.52",
- // JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8)
- "1.2.840.10008.1.2.4.53",
- // JPEG Full Progression, Non-Hierarchical (Process 10 & 12)
- "1.2.840.10008.1.2.4.55",
- // JPEG Lossless, Non-Hierarchical (Process 14)
- "1.2.840.10008.1.2.4.57",
- // JPEG Lossless, Hierarchical, First-Order Prediction (Process 14, [Selection Value 1])
- "1.2.840.10008.1.2.4.70",
- // JPEG 2000 Lossless
- "1.2.840.10008.1.2.4.90",
- // JPEG 2000
- "1.2.840.10008.1.2.4.91",
- // RLE Lossless
- "1.2.840.10008.1.2.5",
- // Unknown
- "Unknown Transfer Syntax"
-};
+class SeqEntry;
+class Dict;
//-----------------------------------------------------------------------------
/**
- * \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<DicomElement> 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;
+ /// User supplied list of elements to Anonymize
+ ListElements UserAnonymizeList;
- /// Store the RLE frames info obtained during parsing of pixels.
- RLEFramesInfo* RLEInfo;
+ /// User supplied list of elements to force Load
+ ListElements UserForceLoadList;
- /// Store the JPEG fragments info obtained during parsing of pixels.
- JPEGFragmentsInfo* JPEGInfo;
-
- /// \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
- 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 Write( std::ofstream* fp, FileType type );
-
- ValEntry* ReplaceOrCreateByNumber(std::string const & value,
- uint16_t group, uint16_t elem,
- TagName const & vr = "unkn");
-
- BinEntry* ReplaceOrCreateByNumber(uint8_t* binArea, int lgth,
- uint16_t group, uint16_t elem,
- TagName const & vr = "unkn");
-
- SeqEntry* 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 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
-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 bool SetEntryLengthByNumber(uint32_t length,
- uint16_t group, uint16_t element);
-
- virtual size_t GetEntryOffsetByNumber(uint16_t group, uint16_t elem);
- virtual void* GetEntryBinAreaByNumber(uint16_t group, uint16_t elem);
- 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 ParseDES(DocEntrySet *set, long offset, long l_max, bool delim_mode);
+ bool 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);
+ 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);
- std::string GetDocEntryValue (DocEntry *);
- std::string GetDocEntryUnvalue(DocEntry *);
+ void SkipDocEntry (DocEntry *entry);
+ void SkipToNextDocEntry (DocEntry *entry);
- void SkipDocEntry (DocEntry *);
- void SkipToNextDocEntry (DocEntry *);
+ void FixDocEntryFoundLength(DocEntry *entry, uint32_t l);
+ bool IsDocEntryAnInteger (DocEntry *entry);
- void FixDocEntryFoundLength(DocEntry *, uint32_t);
- bool IsDocEntryAnInteger (DocEntry *);
-
- uint32_t FindDocEntryLengthOB() throw( FormatUnexpected );
-
- 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 PrintLevel
- void SetPrintLevel(int level) { PrintLevel = level; }
-
- /// 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
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff