X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFile.h;h=86866908f34f68c5ded235aab4d5862a13ba5657;hb=df832cf7f90b4ca5aca2f628c1756fb276779fac;hp=b7a395827c8a4488c26e522afad87fc4de0f6118;hpb=220ad8c527f2b2edf1ba19af8897aca8f4a49cf7;p=gdcm.git diff --git a/src/gdcmFile.h b/src/gdcmFile.h index b7a39582..86866908 100644 --- a/src/gdcmFile.h +++ b/src/gdcmFile.h @@ -3,12 +3,12 @@ Program: gdcm Module: $RCSfile: gdcmFile.h,v $ Language: C++ - Date: $Date: 2004/07/30 16:09:27 $ - Version: $Revision: 1.40 $ + 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 - http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details. + 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 @@ -16,118 +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, - bool exception_on_error = false); - - virtual ~gdcmFile(); - - /// Accessor to \ref Header - gdcmHeader* GetHeader() { return Header; } - - void SetPixelDataSizeFromHeader(); - size_t GetImageDataSize(); - size_t GetImageDataSizeRaw(); - - void * GetImageData(); - size_t GetImageDataIntoVector(void* destination, size_t maxSize); - void * GetImageDataRaw(); - size_t GetImageDataIntoVectorRaw(void* destination, size_t maxSize); - - // Allocates ExpectedSize bytes of memory at this->Data and copies the - // pointed data to it. Copying the image might look useless but - // the caller might destroy it's image (without knowing it: think - // of a complicated interface where display is done with a library - // e.g. VTK) before calling the Write - - // voir gdcmHeader::SetImageDataSize ?!? - bool SetImageData (void * 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(); + bool GetImageOrientationPatient( float iop[6] ); + bool GetImagePositionPatient( float ipp[3] ); + + 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: - bool WriteBase(std::string const & fileName, FileType type); + 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; } + + /// 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; private: - void SwapZone(void* im, int swap, int lgr, int nb); - - bool ReadPixelData(void * destination); - - // For JPEG 8 Bits, body in file gdcmJpeg.cxx - bool gdcm_read_JPEG_file (FILE *fp, void * image_buffer); - static int gdcm_read_RLE_fragment(char **areaToRead, long lengthToDecode, - long uncompressedSegmentSize, FILE *fp); - // For JPEG 12 Bits, body in file gdcmJpeg12.cxx - bool gdcm_read_JPEG_file12 (FILE *fp, void* image_buffer); - // For JPEG 2000, body in file gdcmJpeg2000.cxx - bool gdcm_read_JPEG2000_file (FILE *fp, void* image_buffer); - - // For Run Length Encoding (TOCHECK) - bool gdcm_read_RLE_file (FILE *fp, void* image_buffer); - -// 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; - - /// \brief to hold the Pixels (when read) - void* PixelData; - - /// \brief Area length to receive the pixels - size_t ImageDataSizeRaw; - - /// \brief Area length to receive the RGB pixels - /// from Grey Plane + Palette Color - size_t ImageDataSize; - - /// \brief ==1 if GetImageDataRaw was used - /// ==0 if GetImageData was used - /// ==-1 if ImageData never read - int PixelRead; - - /// wether already parsed - int Parsed; + 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