-// gdcmFile.h
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmFile.h,v $
+ Language: C++
+ 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.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 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"
-////////////////////////////////////////////////////////////////////////////
-// In addition to Dicom header exploration, this class is designed
-// for accessing the image/volume content. One can also use it to
-// write Dicom files.
-////// QUESTION: this looks still like an open question whether the
-////// relationship between a gdcmFile and gdcmHeader is of
-////// type IS_A or HAS_A !
-class GDCM_EXPORT gdcmFile: public gdcmHeader
+namespace GDCM_NAME_SPACE
{
-private:
- // QUESTION :
- // Data pointe sur quoi?
- // sur les Pixels lus?
- // --> j'ajoute un champ public : Pixels
- // (il faudra que l'utilisateur puisse modifier les pixels ?)
-
- void* Data;
- int Parsed; // weather allready parsed
- string OrigFileName; // To avoid file overwrite
-protected:
- int WriteBase(string FileName, FileType type);
+
+class RLEFramesInfo;
+class JPEGFragmentsInfo;
+
+//-----------------------------------------------------------------------------
+// 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 File : public Document
+{
+ gdcmTypeMacro(File);
+
public:
- // je ne suis pas sur d'avoir compris *où* il serait légitime de ranger ca.
- // on pourra tjs le deplacer, et mettre des accesseurs
- void * Pixels;
- size_t lgrTotale;
-
- // Constructor dedicated to writing a new DICOMV3 part10 compliant
- // file (see SetFileName, SetDcmTag and Write)
- // TODO Swig gdcmFile();
- // Opens (in read only and when possible) an existing file and checks
- // for DICOM compliance. Returns NULL on failure.
- // Note: the in-memory representation of all available tags found in
- // the DICOM header is post-poned to first header information access.
- // This avoid a double parsing of public part of the header when
- // one sets an a posteriori shadow dictionary (efficiency can be
- // seen as a side effect).
-
- gdcmFile(string & filename);
- gdcmFile(const char * filename);
-
- // For promotion (performs a deepcopy of pointed header object)
- // TODO Swig gdcmFile(gdcmHeader* header);
- // TODO Swig ~gdcmFile();
-
- // On writing purposes. When instance was created through
- // gdcmFile(string filename) then the filename argument MUST be different
- // from the constructor's one (no overwriting allowed).
- // TODO Swig int SetFileName(string filename);
-
- // Allocates necessary memory, copies the data (image[s]/volume[s]) to
- // newly allocated zone and return a pointer to it:
-
- void * GetImageData();
-
- // Returns size (in bytes) of required memory to contain data
- // represented in this file.
-
- size_t GetImageDataSize();
-
- // Copies (at most MaxSize bytes) of data to caller's memory space.
- // Returns an error code on failure (if MaxSize is not big enough)
-
- int GetImageDataIntoVector(void* destination, size_t MaxSize );
-
- // Allocates ExpectedSize bytes of memory at this->Data and copies the
- // pointed data to it.
-
- // Question :
- // Pourquoi dupliquer les pixels, alors qu'on les a deja en mémoire,
- // et que Data (dans le gdcmHeader) est un pointeur ?
-
- int SetImageData (void * Data, size_t ExpectedSize);
- void SetImageDataSize (size_t ExpectedSize);
-
- // Push to disk.
- // A NE PAS OUBLIER : que fait-on en cas de Transfert Syntax (dans l'entete)
- // incohérente avec l'ordre des octets en mémoire
- // TODO Swig int Write();
-
- // Ecrit sur disque les pixels d'UNE image
- // Aucun test n'est fait sur l'"Endiannerie" du processeur.
- // Ca sera à l'utilisateur d'appeler son Reader correctement
-
- int WriteRawData (string nomFichier);
- int WriteDcmImplVR(string nomFichier);
- int WriteDcmImplVR(const char * nomFichier);
- int WriteDcmExplVR(string nomFichier);
- int WriteAcr (string nomFichier);
+ 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:
+ 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:
+ 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