X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.h;h=86866908f34f68c5ded235aab4d5862a13ba5657;hb=df832cf7f90b4ca5aca2f628c1756fb276779fac;hp=c814acbb6d4aa8b17600b80350b3dfc7660c16bf;hpb=6bbf9cb61993d024630bf9b05b82e4346559c5b2;p=gdcm.git diff --git a/src/gdcmFile.h b/src/gdcmFile.h index c814acbb..86866908 100644 --- a/src/gdcmFile.h +++ b/src/gdcmFile.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: gdcmFile.h,v $ Language: C++ - Date: $Date: 2004/10/08 08:56:48 $ - Version: $Revision: 1.56 $ + Date: $Date: 2007/09/17 12:16:02 $ + Version: $Revision: 1.134 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -16,207 +16,215 @@ =========================================================================*/ -#ifndef GDCMFILE_H -#define GDCMFILE_H +#ifndef _GDCMFILE_H_ +#define _GDCMFILE_H_ -#include "gdcmCommon.h" -#include "gdcmHeader.h" +#include "gdcmDebug.h" +#include "gdcmDocument.h" +#include "gdcmTagKey.h" + + +namespace GDCM_NAME_SPACE +{ + +class RLEFramesInfo; +class JPEGFragmentsInfo; //----------------------------------------------------------------------------- -/* - * In addition to Dicom header exploration, this class is designed - * for accessing the image/volume content. One can also use it to - * write Dicom/ACR-NEMA/RAW files. +// 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 +}; + +//----------------------------------------------------------------------------- + +/** + * \brief 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 File 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. Accessing the content (image[s] or volume[s]) is beyond the + * functionality of this class and belongs to gdcm::FileHelper. + * \note The various entries of the explicit value representation (VR) shall + * be managed within a dictionary which is shared by all File + * instances. + * \note The File::Set*Tag* family members cannot be defined as + * protected due to Swig limitations for as Has_a dependency between + * File and FileHelper. */ -class GDCM_EXPORT gdcmFile +class GDCM_EXPORT File : public Document { + gdcmTypeMacro(File); + public: - gdcmFile( gdcmHeader *header ); - gdcmFile( std::string const& filename ); - - virtual ~gdcmFile(); - - /// Accessor to \ref Header - gdcmHeader* GetHeader() { return Header; } - - int ComputeDecompressedPixelDataSizeFromHeader(); - - void ConvertRGBPlanesToRGBPixels( uint8_t* source, uint8_t* destination ); - void ConvertYcBcRPlanesToRGBPixels( uint8_t* source, uint8_t* destination ); - void ConvertReArrangeBits( - uint8_t* pixelZone, - size_t imageDataSize, - int numberBitsStored, - int numberBitsAllocated, - int highBitPosition ) throw ( gdcmFormatError ); - void ConvertReorderEndianity( - uint8_t* pixelZone, - size_t imageDataSize, - int numberBitsStored, - int numberBitsAllocated, - bool signedPixel ); - void ConvertDecompress12BitsTo16Bits( - uint8_t* pixelZone, - int sizeX, - int sizeY, - FILE* filePtr) throw ( gdcmFormatError); - - /// Accessor to \ref ImageDataSize - size_t GetImageDataSize(){ return ImageDataSize; }; - - /// Accessor to \ref ImageDataSizeRaw - size_t GetImageDataSizeRaw(){ return ImageDataSizeRaw; }; - - uint8_t* GetImageData(); - size_t GetImageDataIntoVector(void* destination, size_t maxSize); - uint8_t* GetImageDataRaw(); - size_t GetImageDataIntoVectorRaw(void* destination, size_t maxSize); - - // see also gdcmHeader::SetImageDataSize ?!? - bool SetImageData (uint8_t* data, size_t expectedSize); - - /// \todo When the caller is aware we simply point to the data: - /// int SetImageDataNoCopy (void* Data, size_t ExpectedSize); - - // Write pixels of ONE image on hard drive - // No test is made on processor "endianity" - // The user must call his reader correctly - bool WriteRawData (std::string const& fileName); - bool WriteDcmImplVR(std::string const& fileName); - bool WriteDcmExplVR(std::string const& fileName); - bool WriteAcr (std::string const& fileName); - - // Don't look any longer for the code : - // It's in file gdcmParsePixels.cxx - bool ParsePixelData(); - - virtual bool SetEntryByNumber(std::string const& content, - uint16_t group, uint16_t element) - { - Header->SetEntryByNumber(content,group,element); - return true; - } + static File *New() {return new File();} + + // Loading + // GDCM_LEGACY(bool Load( std::string const &filename )) + bool Load(); + // Standard values and informations contained in the header + bool IsReadable(); + + void SetFourthDimensionLocation(uint16_t group, uint16_t elem) { + FourthDimensionLocation = TagKey(group, elem); } + + // Some heuristic based accessors, end user intended + int GetImageNumber(); + ModalityType GetModality(); + + int GetXSize(); + int GetYSize(); + int GetZSize(); + int GetTSize(); // unnormalized in DICOM V3 + + bool GetSpacing(float &xspacing, float &yspacing, float &zspacing); + float GetXSpacing(); + float GetYSpacing(); + float GetZSpacing(); + + float GetXOrigin(); + float GetYOrigin(); + float GetZOrigin(); + + float GetXCosineOnX(); + float GetXCosineOnY(); + float GetXCosineOnZ(); + float GetYCosineOnX(); + float GetYCosineOnY(); + float GetYCosineOnZ(); -protected: - bool WriteBase(std::string const& fileName, FileType type); - -private: - void Initialise(); - void SwapZone(void* im, int swap, int lgr, int nb); - - bool ReadPixelData(void* destination); + bool GetImageOrientationPatient( float iop[6] ); + bool GetImagePositionPatient( float ipp[3] ); - // For JPEG 8 Bits, body in file gdcmJpeg.cxx - bool gdcm_read_JPEG_file (FILE* fp, void* image_buffer); - bool gdcm_write_JPEG_file (FILE* fp, void* image_buffer, - int image_width, int image_heigh, - int quality); - - // For JPEG 12 Bits, body in file gdcmJpeg12.cxx - bool gdcm_read_JPEG_file12 (FILE* fp, void* image_buffer); - bool gdcm_write_JPEG_file12 (FILE* fp, void* image_buffer, - int image_width, int image_height, - int quality); - - // For JPEG 2000, body in file gdcmJpeg2000.cxx - bool gdcm_read_JPEG2000_file (FILE* fp, void* image_buffer); - - // For Run Length Encoding - bool gdcm_read_RLE_file (FILE* fp, void* image_buffer); -// FIXME : *sure* it's NOT static (C++) -// (would be static in C, or embedded in ADA) -// It's NOT a method, but a not user intended fonction. -// How do we write that in C++ ?) - static bool gdcm_read_RLE_fragment( uint8_t** decodedZone, - long fragmentSize, - long uncompressedSegmentSize, FILE* fp); - - void SaveInitialValues(); // will belong to the future gdcmPixelData class - void RestoreInitialValues(); // will belong to the future gdcmPixelData class - void DeleteInitialValues(); // will belong to the future gdcmPixelData class - -// members variables: - - /// \brief Header to use to load the file - gdcmHeader *Header; - - /// \brief Whether the underlying \ref gdcmHeader was loaded by - /// the constructor or passed to the constructor. When false - /// the destructor is in charge of deletion. - bool SelfHeader; - - /// wether already parsed - bool Parsed; + int GetBitsStored(); + int GetBitsAllocated(); + int GetHighBitPosition(); + int GetSamplesPerPixel(); + int GetPlanarConfiguration(); + int GetPixelSize(); + std::string GetPixelType(); + bool IsSignedPixelData(); + bool IsMonochrome(); + bool IsMonochrome1(); + bool IsPaletteColor(); + bool IsYBRFull(); + + bool HasLUT(); + int GetLUTNbits(); + + // For rescaling graylevel: + bool GetRescaleSlopeIntercept(double &slope, double &intercept); + double GetRescaleIntercept(); + double GetRescaleSlope(); + + int GetNumberOfScalarComponents(); + int GetNumberOfScalarComponentsRaw(); + + /// Accessor to File::GrPixel + uint16_t GetGrPixel() { return GrPixel; } + /// Accessor to File::NumPixel + uint16_t GetNumPixel() { return NumPixel; } + + size_t GetPixelOffset(); + size_t GetPixelAreaLength(); + + /// returns the RLE info + RLEFramesInfo *GetRLEInfo() { return RLEInfo; } + /// Returns the JPEG Fragments info + JPEGFragmentsInfo *GetJPEGInfo() { return JPEGInfo; } + +// Anonymization process + void AddAnonymizeElement (uint16_t group, uint16_t elem, + std::string const &value); + /// Clears the list of elements to be anonymized + void ClearAnonymizeList() { UserAnonymizeList.clear(); } + void AnonymizeNoLoad(); + /// Replace patient's own information by info from the Anonymization list + bool AnonymizeFile(); + + bool Write(std::string fileName, FileType filetype); + +protected: + File(); + virtual ~File(); + /// \brief Protect the Writer from writing illegal groups + bool MayIWrite(uint16_t group) + { if (group < 8 && group !=2 ) return false; else return true; } -// -// --------------- Will be moved to a gdcmPixelData class -// + /// Store the RLE frames info obtained during parsing of pixels. + RLEFramesInfo *RLEInfo; + /// Store the JPEG fragments info obtained during parsing of pixels. + JPEGFragmentsInfo *JPEGInfo; + + /// \brief In some cases (e.g. for some ACR-NEMA images) the 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. + 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. + uint16_t GrPixel; + /// \brief allows user to tell gdcm in which DataElement is stored + ///the -unnormalized- 4th Dimension + TagKey FourthDimensionLocation; - /// \brief to hold the Pixels (when read) - uint8_t* Pixel_Data; // (was PixelData) - - /// \brief Size (in bytes) of required memory to hold the Gray Level pixels - /// represented in this file. This is used when the user DOESN'T want - /// the RGB pixels image when it's stored as a PALETTE COLOR image - size_t ImageDataSizeRaw; - - /// \brief Size (in bytes) of requited memory to hold the the pixels - /// of this image in it's RGB convertion either from: - /// - Plane R, Plane G, Plane B - /// - Grey Plane + Palette Color - /// - YBR Pixels (or from RGB Pixels, as well) - size_t ImageDataSize; - - /// \brief ==1 if GetImageDataRaw was used - /// ==0 if GetImageData was used - /// ==-1 if ImageData never read - int PixelRead; - - /// \brief length of the last allocated area devoided to receive Pixels - /// ( to allow us not to (free + new) if un necessary ) - size_t LastAllocatedPixelDataLength; - - // Initial values of some fields that can be modified during reading process - // if user asked to transform gray level + LUT image into RGB image - - /// \brief Samples Per Pixel (0x0028,0x0002), as found on disk - std::string InitialSpp; - /// \brief Photometric Interpretation (0x0028,0x0004), as found on disk - std::string InitialPhotInt; - /// \brief Planar Configuration (0x0028,0x0006), as found on disk - std::string InitialPlanConfig; - - // Initial values of some fields that can be modified during reading process - // if the image was a 'strange' ACR-NEMA - // (Bits Allocated=12, High Bit not equal to Bits stored +1) - /// \brief Bits Allocated (0x0028,0x0100), as found on disk - std::string InitialBitsAllocated; - /// \brief High Bit (0x0028,0x0102), as found on disk - std::string InitialHighBit; - - // some DocEntry that can be moved out of the H table during reading process - // if user asked to transform gray level + LUT image into RGB image - // We keep a pointer on them for a future use. - - /// \brief Red Palette Color Lookup Table Descriptor 0028 1101 as read - gdcmDocEntry* InitialRedLUTDescr; - /// \brief Green Palette Color Lookup Table Descriptor 0028 1102 as read - gdcmDocEntry* InitialGreenLUTDescr; - /// \brief Blue Palette Color Lookup Table Descriptor 0028 1103 as read - gdcmDocEntry* InitialBlueLUTDescr; - - /// \brief Red Palette Color Lookup Table Data 0028 1201 as read - gdcmDocEntry* InitialRedLUTData; - /// \brief Green Palette Color Lookup Table Data 0028 1202 as read - gdcmDocEntry* InitialGreenLUTData; - /// \brief Blue Palette Color Lookup Table Data 0028 1203 as read - gdcmDocEntry* InitialBlueLUTData; - -// -// --------------- end of future gdcmPixelData class -// +private: + bool DoTheLoadingJob(); + void ComputeRLEInfo(); + void ComputeJPEGFragmentInfo(); + bool ReadTag(uint16_t, uint16_t); + uint32_t ReadTagLength(uint16_t, uint16_t); + void ReadEncapsulatedBasicOffsetTable(); + uint32_t *BasicOffsetTableItemValue; }; +} // end namespace gdcm //----------------------------------------------------------------------------- #endif