#define GDCMHEADER_H
#include "gdcmCommon.h"
-#include "gdcmVR.h"
-#include "gdcmTS.h"
-#include "gdcmException.h"
-#include "gdcmDictSet.h"
-#include "gdcmHeaderEntry.h"
-#include "gdcmHeaderEntrySet.h"
-#include <map>
+#include "gdcmParser.h"
//-----------------------------------------------------------------------------
-typedef std::string VRKey;
-typedef std::string VRAtr;
-typedef std::map<VRKey, VRAtr> VRHT; // Value Representation Hash Table
-
-//-----------------------------------------------------------------------------
-/*
- * \defgroup gdcmHedaer
+/**
* \brief
* The purpose of an instance of gdcmHeader is to act as a container of
* all the DICOM elements and their corresponding values (and
* The typical usage of instances of class gdcmHeader is to classify a set of
* dicom files according to header information e.g. to create a file hierarchy
* reflecting the Patient/Study/Serie informations, or extracting a given
- * SerieId. Accesing the content (image[s] or volume[s]) is beyond the
+ * SerieId. Accessing the content (image[s] or volume[s]) is beyond the
* functionality of this class and belongs to gdmcFile.
* \note The various entries of the explicit value representation (VR) shall
* be managed within a dictionary which is shared by all gdcmHeader
* protected due to Swig limitations for as Has_a dependency between
* gdcmFile and gdcmHeader.
*/
-class GDCM_EXPORT gdcmHeader {
+class GDCM_EXPORT gdcmHeader : public gdcmParser
+{
+protected:
+ /// In some cases (e.g. for some ACR-NEMA images) the Header Entry Element
+ /// Number of the 'Pixel Element' is *not* found at 0x0010. In order to
+ /// make things easier the parser shall store the proper value in
+ /// NumPixel to provide a unique access facility. See also the constructor
+ /// \ref gdcmHeader::gdcmHeader
+ guint16 NumPixel;
+ /// In some cases (e.g. for some ACR-NEMA images) the header entry for
+ /// the group of pixels is *not* found at 0x7fe0. In order to
+ /// make things easier the parser shall store the proper value in
+ /// GrPixel to provide a unique access facility. See also the constructor
+ /// \ref gdcmHeader::gdcmHeader
+ guint16 GrPixel;
+ /// Some DICOM files may contain several images (e.g. a icon, followd by
+ /// the image itself. Hence the tag (GrPixel,NumPixel) might appear
+ /// several times. countGrPixel is the number of occurences of the
+ /// tag of pixels (i.e. (GrPixel,NumPixel)) contained in the header.
+ /// TODO : will be dealt with SQ tree-like stucture
+ int countGrPixel;
public:
gdcmHeader(bool exception_on_error = false);
gdcmHeader(const char *filename,
bool exception_on_error = false,
- bool enable_sequences = false);
-
+ bool enable_sequences = false,
+ bool skip_shadow = false);
+
virtual ~gdcmHeader();
-// Standard values and informations contained in the header
- inline std::string GetFileName(void) {return filename;}
-
- bool IsReadable(void);
- bool IsImplicitVRLittleEndianTransferSyntax(void);
- bool IsExplicitVRLittleEndianTransferSyntax(void);
- bool IsDeflatedExplicitVRLittleEndianTransferSyntax(void);
- bool IsExplicitVRBigEndianTransferSyntax(void);
+ // Standard values and informations contained in the header
+ virtual bool IsReadable(void);
bool IsJPEGBaseLineProcess1TransferSyntax(void);
bool IsJPEGExtendedProcess2_4TransferSyntax(void);
bool IsJPEGExtendedProcess3_5TransferSyntax(void);
bool IsJPEGLossless(void);
bool IsJPEG2000(void);
bool IsDicomV3(void);
- FileType GetFileType(void);
// Some heuristic based accessors, end user intended
- // (to be move to gdcmHeaderHelper?)
- int GetXSize(void);
+ // (to be moved to gdcmHeaderHelper?)
+ int GetXSize(void);
int GetYSize(void);
int GetZSize(void);
int GetBitsStored(void);
// TODO Swig int SetShaDict(std::string filename);
// TODO Swig int SetPubDict(std::string filename);
-
-// Public element value
- std::string GetPubEntryByName (std::string tagName);
- std::string GetPubEntryVRByName (std::string tagName);
- std::string GetPubEntryByNumber (guint16 group, guint16 element);
- std::string GetPubEntryVRByNumber(guint16 group, guint16 element);
- bool SetPubEntryByName (std::string content, std::string tagName);
- bool SetPubEntryByNumber(std::string content, guint16 group, guint16 element);
- bool SetPubEntryLengthByNumber(guint32 lgr, guint16 group, guint16 element);
-
- inline ListTag & GetPubListEntry(void) { return PubEntrySet.GetListEntry();};
- inline TagHeaderEntryHT & GetPubEntry(void) { return PubEntrySet.GetTagHT(); };
-
- void PrintPubEntry(std::ostream & os = std::cout);
- void PrintPubDict (std::ostream & os = std::cout);
-
-// Element value
- std::string GetEntryByName (std::string tagName);
- std::string GetEntryVRByName (std::string tagName);
- std::string GetEntryByNumber (guint16 group, guint16 element);
- std::string GetEntryVRByNumber(guint16 group, guint16 element);
-
- bool SetEntryByName(std::string content,std::string tagName);
-// bool SetEntryByNumber(std::string content,guint16 group, guint16 element);
-
-// inline ListTag & GetListEntry(void) { return PubHeaderEntrySet.GetListElem();};
-// inline TagHeaderEntryHT & GetListEntry(void) { return PubHeaderEntrySet.GetTagHt(); };
-
-// Read (used in gdcmFile)
- FILE *OpenFile(bool exception_on_error = false) throw(gdcmFileError);
- bool CloseFile(void);
- virtual void ParseHeader(bool exception_on_error = false) throw(gdcmFormatError);
-
-// Write (used in gdcmFile)
- bool Write(FILE *, FileType);
- void SetImageDataSize(size_t ExpectedSize);
-
- bool ReplaceOrCreateByNumber(std::string Value, guint16 Group, guint16 Elem);
- bool ReplaceOrCreateByNumber( char * Value, guint16 Group, guint16 Elem);
- bool ReplaceIfExistByNumber ( char * Value, guint16 Group, guint16 Elem);
-
-// System access
- inline int GetSwapCode(void) { return sw; }
- guint16 SwapShort(guint16); // needed by gdcmFile
- guint32 SwapLong(guint32); // for JPEG Files
+ /// Accessor to \ref gdcmHeader::GrPixel
+ guint16 GetGrPixel(void) {return GrPixel;}
-protected:
- bool CheckIfExistByNumber(guint16 Group, guint16 Elem );
-
- gdcmHeaderEntry *GetHeaderEntryByName (std::string Name);
- gdcmHeaderEntry *GetHeaderEntryByNumber(guint16 group, guint16 element);
-
- int write(std::ostream&);
- int anonymize(std::ostream&); // FIXME : anonymize should be a friend ?
-
- size_t GetPubEntryOffsetByNumber (guint16 Group, guint16 Elem);
- void * GetPubEntryVoidAreaByNumber(guint16 Group, guint16 Elem);
- void * LoadEntryVoidArea (guint16 Group, guint16 Element);
+ /// Accessor to \ref gdcmHeader::NumPixel
+ guint16 GetNumPixel(void) {return NumPixel;}
+
+// Entry
+
+// These functions are necessary for Python because
+// there are protected in the parent class
+
+ inline virtual std::string GetEntryByNumber (guint16 group, guint16 element)
+ { return(gdcmParser::GetEntryByNumber(group,element)); }
+
+ inline virtual std::string GetEntryVRByNumber(guint16 group, guint16 element)
+ { return(gdcmParser::GetEntryVRByNumber(group,element)); }
+
+ inline virtual int GetEntryLengthByNumber(guint16 group, guint16 element)
+ { return(gdcmParser::GetEntryLengthByNumber(group,element)); }
+
+ inline virtual std::string GetEntryByName (std::string tagName)
+ { return(gdcmParser::GetEntryByName(tagName)); }
+
+ inline virtual std::string GetEntryVRByName (std::string tagName)
+ { return(gdcmParser::GetEntryVRByName(tagName)); }
+
+ inline virtual bool SetEntryByNumber(std::string content,
+ guint16 group, guint16 element)
+ { return(gdcmParser::SetEntryByNumber(content,group,element)); }
+
+ inline virtual bool SetEntryByName(std::string content,std::string tagName)
+ { return(gdcmParser::SetEntryByName(content,tagName)); }
+
+ inline virtual bool SetEntryLengthByNumber(guint32 l,
+ guint16 group, guint16 element)
+ { return(gdcmParser::SetEntryLengthByNumber(l,group,element)); }
+
+ inline virtual void UpdateShaEntries(void)
+ { gdcmParser::UpdateShaEntries(); }
+
+ /// Read (used in gdcmFile)
+ void SetImageDataSize(size_t ExpectedSize);
+ bool operator<(gdcmHeader &header);
-// Variables
- FILE * fp;
- FileType filetype; // ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown
-
-private:
- // Read
- void LoadHeaderEntries (void);
- void LoadHeaderEntry (gdcmHeaderEntry *);
- void LoadHeaderEntrySafe (gdcmHeaderEntry *);
- void FindHeaderEntryLength(gdcmHeaderEntry *);
- void FindHeaderEntryVR (gdcmHeaderEntry *);
-
- void SkipHeaderEntry (gdcmHeaderEntry *);
- void FixHeaderEntryFoundLength(gdcmHeaderEntry *, guint32);
- bool IsHeaderEntryAnInteger (gdcmHeaderEntry *);
-
- guint32 FindHeaderEntryLengthOB(void);
-
- guint16 ReadInt16(void);
- guint32 ReadInt32(void);
- void SkipBytes(guint32);
-
- void Initialise(void);
- void CheckSwap(void);
- void SwitchSwapToBigEndian(void);
- void SetMaxSizeLoadElementValue(long);
-
- // Dict
- gdcmDictEntry *GetDictEntryByName (std::string Name);
- gdcmDictEntry *GetDictEntryByNumber(guint16, guint16);
-
- // HeaderEntry related utilities
- gdcmHeaderEntry *ReadNextHeaderEntry (void);
- gdcmHeaderEntry *NewHeaderEntryByNumber(guint16 group, guint16 element);
- gdcmHeaderEntry *NewHeaderEntryByName (std::string Name);
-
- // Deprecated (Not used)
- gdcmHeaderEntry *NewManualHeaderEntryToPubDict(std::string NewTagName,
- std::string VR);
-
-// Variables
- // Pointer to the Value Representation Hash Table which contains all
- // the VR of the DICOM version3 public dictionary.
- gdcmVR *dicom_vr; // Not a class member for thread-safety reasons
+ bool WriteEntry(gdcmHeaderEntry *tag,FILE *_fp,FileType type);
- // Pointer to the Transfert Syntax Hash Table which contains all
- // the TS of the DICOM version3 public dictionary.
- gdcmTS *dicom_ts; // Not a class member for thread-safety reasons
-
- // Pointer to global dictionary container
- gdcmDictSet *Dicts; // Not a class member for thread-safety reasons
- // Public dictionary used to parse this header
- gdcmDict *RefPubDict;
+ virtual void PrintEntryNoSQ (std::ostream &os = std::cout);
+ virtual void PrintEntryNiceSQ(std::ostream &os = std::cout);
- // Optional "shadow dictionary" (private elements) used to parse this
- // header
- gdcmDict *RefShaDict;
+protected:
+ //CLEANME int write(std::ostream&);
+ //CLEANME int anonymize(std::ostream&);//FIXME: anonymize should be a friend
+ bool anonymizeHeader(void);
+private:
- /// ELement VALueS parsed with the PUBlic dictionary.
- gdcmHeaderEntrySet PubEntrySet;
-
- // Refering underlying filename.
- std::string filename;
-
- int enableSequences;
- int wasUpdated; // true if a gdcmHeaderEntry was added post parsing
-
- // FIXME sw should be an enum e.g.
- //enum EndianType {
- //LittleEndian,
- //BadLittleEndian,
- //BigEndian,
- //BadBigEndian};
- // Swap code e.g. little, big, bad-big, bad-little endian). Warning:
- // this code is not fixed during header parsing.
- int sw;
-
- // Size treshold 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 MaxSizeLoadElementValue;
-
- static const unsigned int HEADER_LENGTH_TO_READ;
- static const unsigned int MAX_SIZE_LOAD_ELEMENT_VALUE;
};
//-----------------------------------------------------------------------------