mitkAnalyzeImageReader.h

/*=========================================================================

  Program:   3DMed
  Date:      $Date: 2014-02-25 18:30:00 +0800 $
  Version:   $Version: 4.6.0 $
  Copyright: MIPG, Institute of Automation, Chinese Academy of Sciences

=========================================================================*/


#ifndef __mitkAnalyzeImageReader_h
#define __mitkAnalyzeImageReader_h

#include "mitkVolumeReader.h"



// ******************************** Definition of Analyze Header File ***************************************

namespace AnalyzeImageIO
{
enum DataTypeKeyValues  {
    ANALYZE_DT_UNKNOWN      =0,  
    ANALYZE_DT_BINARY       =1,  
    ANALYZE_DT_UNSIGNED_CHAR=2,  
    ANALYZE_DT_SIGNED_SHORT =4,  
    ANALYZE_DT_SIGNED_INT   =8,  
    ANALYZE_DT_FLOAT        =16, 
    ANALYZE_DT_COMPLEX      =32, 
    ANALYZE_DT_DOUBLE       =64, 
    ANALYZE_DT_RGB          =128,
    ANALYZE_DT_ALL          =255,
    //Obsolete, using SPM, B2ANALYZE_DT_UNSIGNED_SHORT =6,  /**< Deontes that the data type is unsigned short in brains2 analyze extensions*/
    //Obsolete, using SPM, B2ANALYZE_DT_UNSIGNED_INT   =12, /**< Deontes that the data type is unsigned int in brains2 analyze extensions*/
    SPMANALYZE_DT_UNSIGNED_SHORT=132,
    SPMANALYZE_DT_UNSIGNED_INT  =136 
};

enum DataTypeIndex  {
    ANALYZE_DT_INDEX_UNKNOWN       =0,
    ANALYZE_DT_INDEX_BINARY        =1,
    ANALYZE_DT_INDEX_UNSIGNED_CHAR =2,
    ANALYZE_DT_INDEX_SIGNED_SHORT  =3,
    ANALYZE_DT_INDEX_SIGNED_INT    =4,
    ANALYZE_DT_INDEX_FLOAT         =5,
    ANALYZE_DT_INDEX_COMPLEX       =6,
    ANALYZE_DT_INDEX_DOUBLE        =7,
    ANALYZE_DT_INDEX_RGB           =8,
    ANALYZE_DT_INDEX_ALL           =9,
    //Obsolete, using SPM, B2ANALYZE_DT_INDEX_UNSIGNED_SHORT=10,
    //Obsolete, using SPM, B2ANALYZE_DT_INDEX_UNSIGNED_INT  =11,
    SPMANALYZE_DT_INDEX_UNSIGNED_SHORT   =10,
    SPMANALYZE_DT_INDEX_UNSIGNED_INT     =11
};

typedef enum 
{
    ANALYZE_ORIENTATION_RPI_TRANSVERSE=0,        
    ANALYZE_ORIENTATION_RIP_CORONAL   =1,        
    ANALYZE_ORIENTATION_PIR_SAGITTAL  =2,        
    ANALYZE_ORIENTATION_RAI_TRANSVERSE_FLIPPED=3,
    ANALYZE_ORIENTATION_RSP_CORONAL_FLIPPED=4,   
    ANALYZE_ORIENTATION_PIL_SAGITTAL_FLIPPED=5   
} /*ValidAnalyzeOrientationFlags*/;

struct header_key              /*      header_key       */
{/*off + size*/
    /*0 + 4  */int sizeof_hdr;         
    /*4 + 10 */char data_type[10];     
    /*14 + 18*/char db_name[18];       
    /*32 + 4 */int extents;            
    /*36 + 2 */short int session_error;
    /*38 + 1 */char regular;           
    /*39 + 1 */char hkey_un0;          
};/* total=40  */

struct image_dimension         /*      image_dimension  */
{                              /* off + size*/
    /*0 + 16 */ short int dim[8];  
    /*16 + 4 */ char vox_units[4]; 
    /*20 + 4 */ char cal_units[8]; 
    /*24 + 2 */ short int unused1; 
    /*30 + 2 */ short int datatype;
    /*32 + 2 */ short int bitpix;  
    /*34 + 2 */ short int dim_un0; 
    /*36 + 32*/ float pixdim[8];   
    /*68 + 4 */ float vox_offset;  
    /*72 + 4 */ float roi_scale;   
    /*76 + 4 */ float funused1;    
    /*80 + 4 */ float funused2;    
    /*84 + 4 */ float cal_max;     
    /*88 + 4 */ float cal_min;     
    /*92 + 4 */ int compressed;    
    /*96 + 4 */ int verified;      
    /*100 + 4*/ int glmax;         
    /*104 + 4*/ int glmin;         
}/*total=108 */;

struct data_history   /* data_history     */
{/*off + size*/
    /*0 + 80  */char descrip[80];   
    /*80 + 24 */char aux_file[24];  
    /*104 + 1 */char orient;        
    /*105 + 10*/char originator[10];
    /*115 + 10*/char generated[10]; 
    /*125 + 10*/char scannum[10];   
    /*135 + 10*/char patient_id[10];
    /*145 + 10*/char exp_date[10];  
    /*155 + 10*/char exp_time[10];  
    /*165 + 3 */char hist_un0[3];   
    /*168 + 4 */int views;          
    /*172 + 4 */int vols_added;     
    /*176 + 4 */int start_field;    
    /*180 + 4 */int field_skip;     
    /*184 + 4 */int omax;           
    /*188 + 4 */int omin;           
    /*192 + 4 */int smax;           
    /*196 + 4 */int smin;           
};/* total=200 */

struct dsr/*      dsr              */
{/* off + size*/
    /*0 + 40   */ struct header_key hk;        
    /*40 + 108 */ struct image_dimension dime; 
    /*148 + 200*/ struct data_history hist;    
}/*total=348*/;

}
// ******************************** Definition of Analyze Header File ***************************************

using namespace AnalyzeImageIO;


class MITK_COMMON_API mitkAnalyzeImageReader : public mitkVolumeReader
{
public:
    MITK_TYPE(mitkAnalyzeImageReader, mitkVolumeReader)

    virtual void PrintSelf(ostream &os);

    mitkAnalyzeImageReader();

    typedef std::streamoff SizeType;

    typedef enum { BigEndian, LittleEndian, OrderNotApplicable } ByteOrder;

    typedef enum { ASCII, Binary, TypeNotApplicable } FileType;

    const char * GetFileExtensions() { return ".hdr .img .img.gz"; }

    unsigned long long GetDataBytes();

protected:
    virtual ~mitkAnalyzeImageReader();

    virtual bool Execute();
    bool ReadInfo();
    bool ReadData();

    bool ReadBufferAsBinary(std::istream& os, void *buffer, SizeType numberOfBytesToBeRead);
    ByteOrder CheckAnalyzeEndian(const struct dsr &temphdr);
    void SwapHeaderBytesIfNecessary( struct dsr * const imageheader );
    void SwapBytesIfNecessary( void* buffer, unsigned long numberOfPixels );

    int             m_ComponentType;
    unsigned int    m_NumberOfComponents;
    unsigned int    m_NumberOfDimensions;
    int             m_Dimensions[3];
    float           m_Spacing[3];

private:
    mitkAnalyzeImageReader(const mitkAnalyzeImageReader&);
    void operator = (const mitkAnalyzeImageReader&);

    ByteOrder       m_ByteOrder;
    FileType        m_FileType;

    struct dsr      m_Hdr;
    ByteOrder       m_MachineByteOrder;
};


#endif

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