X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmHeader.h;h=cbd36527205e66477f2cdeb1823967515084d3f8;hb=8da9df62c47908e7b9a67238a6c12b92ba6cae7a;hp=9f3603e966570ed0e5353566764a4944929a170d;hpb=54ce6e928bccc91bb12601c782b92c833678de40;p=gdcm.git diff --git a/src/gdcmHeader.h b/src/gdcmHeader.h index 9f3603e9..cbd36527 100644 --- a/src/gdcmHeader.h +++ b/src/gdcmHeader.h @@ -1,245 +1,194 @@ -// gdcmHeader.h -//----------------------------------------------------------------------------- +/*========================================================================= + + Program: gdcm + Module: $RCSfile: gdcmHeader.h,v $ + Language: C++ + Date: $Date: 2004/11/25 13:12:02 $ + Version: $Revision: 1.94 $ + + 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 GDCMHEADER_H #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 - -//----------------------------------------------------------------------------- -typedef std::string VRKey; -typedef std::string VRAtr; -typedef std::map VRHT; // Value Representation Hash Table +#include "gdcmDocument.h" +namespace gdcm +{ //----------------------------------------------------------------------------- -/* - * The purpose of an instance of gdcmHeader is to act as a container of +/** + * \brief + * The purpose of an instance of Header is to act as a container of * all the DICOM elements and their corresponding values (and * additionaly the corresponding DICOM dictionary entry) of the header * of a DICOM file. * - * The typical usage of instances of class gdcmHeader is to classify a set of + * The typical usage of instances of class Header 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 + * be managed within a dictionary which is shared by all Header * instances. - * \note The gdcmHeader::Set*Tag* family members cannot be defined as + * \note The Header::Set*Tag* family members cannot be defined as * protected due to Swig limitations for as Has_a dependency between - * gdcmFile and gdcmHeader. + * File and Header. */ -class GDCM_EXPORT gdcmHeader { -public: - gdcmHeader(bool exception_on_error = false); - gdcmHeader(const char *filename, - bool exception_on_error = false, - bool enable_sequences = 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); - bool IsJPEGBaseLineProcess1TransferSyntax(void); - bool IsJPEGExtendedProcess2_4TransferSyntax(void); - bool IsJPEGExtendedProcess3_5TransferSyntax(void); - bool IsJPEGSpectralSelectionProcess6_8TransferSyntax(void); - bool IsRLELossLessTransferSyntax(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); - int GetYSize(void); - int GetZSize(void); - int GetBitsStored(void); - int GetBitsAllocated(void); - int GetSamplesPerPixel(void); - int GetPlanarConfiguration(void); - - int GetPixelSize(void); - std::string GetPixelType(void); - size_t GetPixelOffset(void); - size_t GetPixelAreaLength(void); - - bool HasLUT(void); - int GetLUTNbits(void); - unsigned char * GetLUTRGBA(void); - - std::string GetTransfertSyntaxName(void); - - // When some proprietary shadow groups are disclosed, we can set up - // an additional specific dictionary to access extra information. - - // OK : we still have *ONE* HeaderEntrySet, - // with both Public and Shadow Elements - // parsed against THE Public Dictionary and A (single) Shadow Dictionary - - // 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 & GetListElem(void) { return PubHeaderEntrySet.GetListElem();}; -// inline TagHeaderEntryHT & GetElVal(void) { return PubHeaderEntrySet.GetTagHt(); }; +//----------------------------------------------------------------------------- +// Dicom Part 3.3 Compliant +enum ModalityType { + Unknow, + AU, // Voice Audio + AS, // Angioscopy + BI, // Biomagnetic Imaging + CF, // Cinefluorography + CP, // Culposcopy + CR, // Computed Radiography + CS, // Cystoscopy + CT, // Computed Tomography + DD, // Duplex Dopler + DF, // Digital Fluoroscopy + DG, // Diaphanography + DM, // Digital Microscopy + DS, // Digital Substraction Angiography + DX, // Digital Radiography + ECG, // Echocardiography + EPS, // Basic Cardiac EP + ES, // Endoscopy + FA, // Fluorescein Angiography + FS, // Fundoscopy + HC, // Hard Copy + HD, // Hemodynamic + LP, // Laparoscopy + LS, // Laser Surface Scan + MA, // Magnetic Resonance Angiography + MR, // Magnetic Resonance + NM, // Nuclear Medicine + OT, // Other + PT, // Positron Emission Tomography + RF, // Radio Fluoroscopy + RG, // Radiographic Imaging + RTDOSE, // Radiotherapy Dose + RTIMAGE, // Radiotherapy Image + RTPLAN, // Radiotherapy Plan + RTSTRUCT, // Radiotherapy Structure Set + SM, // Microscopic Imaging + ST, // Single-photon Emission Computed Tomography + TG, // Thermography + US, // Ultrasound + VF, // Videofluorography + XA, // X-Ray Angiography + XC // Photographic Imaging +}; +//----------------------------------------------------------------------------- -// 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); +class GDCM_EXPORT Header : public Document +{ +protected: + /// \brief 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 Header::Header + uint16_t NumPixel; + /// \brief 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 Header::Header + uint16_t GrPixel; -// Write (used in gdcmFile) - bool Write(FILE *, FileType); - void SetImageDataSize(size_t ExpectedSize); +public: + Header(); + Header( std::string const & filename ); + + ~Header(); - 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); + // Standard values and informations contained in the header + bool IsReadable(); -// System access - inline int GetSwapCode(void) { return sw; } - guint16 SwapShort(guint16); // needed by gdcmFile - guint32 SwapLong(guint32); // for JPEG Files + // Some heuristic based accessors, end user intended + int GetBitsStored(); + int GetBitsAllocated(); + int GetSamplesPerPixel(); + int GetPlanarConfiguration(); + int GetPixelSize(); + int GetHighBitPosition(); + bool IsSignedPixelData(); + bool IsMonochrome(); + bool IsPaletteColor(); + bool IsYBRFull(); + + std::string GetPixelType(); + size_t GetPixelOffset(); + size_t GetPixelAreaLength(); + + //Some image informations needed for third package imaging library + int GetXSize(); + int GetYSize(); + int GetZSize(); + + float GetXSpacing(); + float GetYSpacing(); + float GetZSpacing(); + + // Useful for rescaling graylevel: + float GetRescaleIntercept(); + float GetRescaleSlope(); + + int GetNumberOfScalarComponents(); + int GetNumberOfScalarComponentsRaw(); + + int GetImageNumber(); + ModalityType GetModality(); + + float GetXOrigin(); + float GetYOrigin(); + float GetZOrigin(); + + bool HasLUT(); + int GetLUTNbits(); + + /// Return the Transfer Syntax as a string + std::string GetTransfertSyntaxName(); + + /// Accessor to \ref Header::GrPixel + uint16_t GetGrPixel() { return GrPixel; } -protected: - bool CheckIfExistByNumber(guint16 Group, guint16 Elem ); + /// Accessor to \ref Header::NumPixel + uint16_t GetNumPixel() { return NumPixel; } - gdcmHeaderEntry *GetHeaderEntryByName (std::string Name); - gdcmHeaderEntry *GetHeaderEntryByNumber(guint16 group, guint16 element); + /// Read (used in File) + void SetImageDataSize(size_t expectedSize); - int write(std::ostream&); - int anonymize(std::ostream&); // FIXME : anonymize should be a friend ? + bool Write(std::string fileName, FileType filetype); - size_t GetPubEntryOffsetByNumber (guint16 Group, guint16 Elem); - void * GetPubEntryVoidAreaByNumber(guint16 Group, guint16 Elem); - void * LoadEntryVoidArea (guint16 Group, guint16 Element); + /// Initialize DICOM header when none + void InitializeDefaultHeader(); + +protected: + /// Replace patient's specific information by 'anonymous' + bool AnonymizeHeader(); + /// Helper function needed to organize DICOM files based on + /// their x,y,z position + void GetImageOrientationPatient( float iop[6] ); -// 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 - - // 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; - - // Optional "shadow dictionary" (private elements) used to parse this - // header - gdcmDict *RefShaDict; - - /// ELement VALueS parsed with the PUBlic dictionary. - gdcmHeaderEntrySet PubEntrySet; - - // Refering underlying filename. - std::string filename; - - int enableSequences; - - // 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; + friend class SerieHeader; }; +} // end namespace gdcm //----------------------------------------------------------------------------- #endif