Program: gdcm
Module: $RCSfile: gdcmFile.h,v $
Language: C++
- Date: $Date: 2004/10/22 13:56:46 $
- Version: $Revision: 1.66 $
+ 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
=========================================================================*/
-#ifndef GDCMFILE_H
-#define GDCMFILE_H
+#ifndef _GDCMFILE_H_
+#define _GDCMFILE_H_
-#include "gdcmCommon.h"
-#include "gdcmHeader.h"
-#include "gdcmPixelConvert.h"
+#include "gdcmDebug.h"
+#include "gdcmDocument.h"
+#include "gdcmTagKey.h"
-namespace gdcm
-{
-//-----------------------------------------------------------------------------
-/*
- * 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.
- */
-class GDCM_EXPORT File
+namespace GDCM_NAME_SPACE
{
-public:
- File( Header* header );
- File( std::string const& filename );
-
- virtual ~File();
-
- /// Accessor to \ref Header
- Header* GetHeader() { return HeaderInternal; }
-
- /// Accessor to \ref ImageDataSize
- size_t GetImageDataSize(){ return ImageDataSize; };
-
- /// Accessor to \ref ImageDataSizeRaw
- size_t GetImageDataSizeRaw(){ return ImageDataSizeRaw; };
- /// Accessor to \ref PixelConverter
- PixelConvert* GetPixelConverter(){ return PixelConverter; };
+class RLEFramesInfo;
+class JPEGFragmentsInfo;
- uint8_t* GetImageData();
- size_t GetImageDataIntoVector(void* destination, size_t maxSize);
- uint8_t* GetImageDataRaw();
+//-----------------------------------------------------------------------------
+// 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
+};
- // see also Header::SetImageDataSize ?!?
- bool SetImageData (uint8_t* 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);
+/**
+ * \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 File : public Document
+{
+ gdcmTypeMacro(File);
- virtual bool SetEntryByNumber(std::string const& content,
- uint16_t group, uint16_t element)
- {
- HeaderInternal->SetEntryByNumber(content,group,element);
- return true;
- }
- uint8_t* GetLutRGBA();
+public:
+ 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 SaveInitialValues(); // will belong to the future PixelData class
- void RestoreInitialValues(); // will belong to the future PixelData class
- void DeleteInitialValues(); // will belong to the future PixelData class
- uint8_t* GetDecompressed();
- int ComputeDecompressedPixelDataSizeFromHeader();
-
-private:
-// members variables:
-
- /// Header to use to load the file
- Header *HeaderInternal;
-
- /// \brief Whether the underlying \ref Header was loaded by
- /// the constructor or passed to the constructor. When false
- /// the destructor is in charge of deletion.
- bool SelfHeader;
+ bool GetImageOrientationPatient( float iop[6] );
+ bool GetImagePositionPatient( float ipp[3] );
- /// Wether already parsed or not
- bool Parsed;
-
- /// Utility pixel converter
- PixelConvert* PixelConverter;
+ 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);
-/// FIXME
-// --------------- Will be moved to a PixelData class
-//
+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; }
+
+ /// 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
- DocEntry* InitialRedLUTDescr;
- /// \brief Green Palette Color Lookup Table Descriptor 0028 1102 as read
- DocEntry* InitialGreenLUTDescr;
- /// \brief Blue Palette Color Lookup Table Descriptor 0028 1103 as read
- DocEntry* InitialBlueLUTDescr;
-
- /// \brief Red Palette Color Lookup Table Data 0028 1201 as read
- DocEntry* InitialRedLUTData;
- /// \brief Green Palette Color Lookup Table Data 0028 1202 as read
- DocEntry* InitialGreenLUTData;
- /// \brief Blue Palette Color Lookup Table Data 0028 1203 as read
- DocEntry* InitialBlueLUTData;
-
-//
-// --------------- end of future PixelData 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
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff