matrix.h

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/* @(#)matrix.h 1.5 2/8/93 */
 
/* prevent recursive definition */
#ifndef         matrix_ecat7_h
#define         matrix_ecat7_h
/*  19-sep-2002: 
 * Merge with bug fixes and support for CYGWIN provided by Kris Thielemans@csc.mrc.ac.uk
 * 09-jan-2003:
 * in #define W_MODE, replace "wb" and "w" by "wb+" and "w+" respectively  for windows and unix
 * 12-sep-2003:
 * Remove ntohs and ntohl declarations for Windows
 */
 
#include <stdio.h>
#include <sys/types.h>
#include <ecat/kernel/machine_indep.h>
 
/*
#define R_MODE "rb"
#define RW_MODE "rb+"
#define W_MODE "wb+"
*/
#ifdef _WIN32
#define swab _swab
#define strdup _strdup
#ifndef __CYGWIN__
typedef char *caddr_t;
// typedef unsigned char u_char;
// typedef unsigned short u_short;
#endif /* __CYGWIN__ */
// extern unsigned short ntohs(unsigned short);
// extern unsigned long ntohl(unsigned long);
#else /* _WIN32 */
#include <netinet/in.h>
#endif
 
#define         MatBLKSIZE 512
#define         MatFirstDirBlk 2
#define         MatMagic 0x67452301
#define V7 70
#define MagicNumLen 14
#define NameLen 32
#define IDLen 16
#define NumDataMasks 12
 
#define MAX_FRAMES  512
#define MAX_SLICES  1024
#define MAX_GATES   32
#define MAX_BED_POS 32
 
 
typedef enum {
        NoData, Sinogram, PetImage, AttenCor, Normalization,
        PolarMap, ByteVolume, PetVolume, ByteProjection,
        PetProjection, ByteImage, Short3dSinogram, Byte3dSinogram, Norm3d,
        Float3dSinogram,InterfileImage, NumDataSetTypes
} DataSetType;
 
/*
typedef enum {
        UnknownMatDataType, ByteData, VAX_Ix2, VAX_Ix4,
        VAX_Rx4, IeeeFloat, SunShort, SunLong, NumMatrixDataTypes, ColorData,
        BitData
} MatrixDataType;
*/
typedef enum {
        UnknownMatDataType, ByteData, VAX_Ix2, VAX_Ix4,
        VAX_Rx4, IeeeFloat, SunShort, SunLong,  NumMatrixDataTypes,
/*      Unsigned Short Big and Little Endian, PseudoColor, TrueColor,   BitData*/
        UShort_BE, UShort_LE, Color_24, Color_8, BitData
} MatrixDataType;
 
enum CalibrationStatus {Uncalibrated, Calibrated, Processed,
            NumCalibrationStatus};
 
 
enum ScanType {UndefScan, BlankScan,
        TransmissionScan, StaticEmission,
        DynamicEmission, GatedEmission,
        TransRectilinear, EmissionRectilinear,
        NumScanTypes};
 
enum CurrentModels {E921, E961, E953, E953B, E951, E951R,
                    E962, E925, NumEcatModels};
 
 
enum OldDisplayUnits {TotalCounts, UnknownEcfUnits, EcatCountsPerSec,
        UCiPerCC, LMRGlu, LMRGluUmol, LMRGluMg, NCiPerCC, WellCounts,
        BecquerelsPerCC, MlPerMinPer100g, MlPerMinPer1g, NumOldUnits};
 
enum PatientOrientation {FeetFirstProne, HeadFirstProne,
            FeetFirstSupine, HeadFirstSupine,
            FeetFirstRight, HeadFirstRight,
            FeetFirstLeft, HeadFirstLeft, UnknownOrientation, NumOrientations};
 
enum SeptaPos {SeptaExtended, SeptaRetracted, NoSeptaInstalled};
 
enum Sino3dOrder {ElAxVwRd, ElVwAxRd, NumSino3dOrders};
 
typedef enum {
                MAT_OK,
                MAT_READ_ERROR,
                MAT_WRITE_ERROR,
                MAT_INVALID_DIRBLK,
                MAT_ACS_FILE_NOT_FOUND,
                MAT_INTERFILE_OPEN_ERR,
                MAT_FILE_TYPE_NOT_MATCH,
                MAT_READ_FROM_NILFPTR,
                MAT_NOMHD_FILE_OBJECT,
                MAT_NIL_SHPTR,
                MAT_NIL_DATA_PTR,
                MAT_MATRIX_NOT_FOUND,
                MAT_UNKNOWN_FILE_TYPE,
                MAT_ACS_CREATE_ERR,
                MAT_BAD_ATTRIBUTE,
                MAT_BAD_FILE_ACCESS_MODE,
                MAT_INVALID_DIMENSION,
                MAT_NO_SLICES_FOUND,
                MAT_INVALID_DATA_TYPE,
                MAT_INVALID_MBED_POSITION
    }
MatrixErrorCode;
 
enum ProcessingCode { NotProc=0, Norm=1, Atten_Meas=2, Atten_Calc=4,
        Smooth_X=8, Smooth_Y=16, Smooth_Z=32, Scat2d=64, Scat3d=128,
        ArcPrc=256, DecayPrc=512, OnComPrc=1024,  RandomSub=2048 };
 
 
extern int numDisplayUnits;
extern char* datasettype[NumDataSetTypes];
extern char* dstypecode[NumDataSetTypes];
extern char* scantype[NumScanTypes];
extern char* scantypecode[NumScanTypes];
extern char* customDisplayUnits[];
extern float ecfconverter[NumOldUnits];
extern char* calstatus[NumCalibrationStatus];
extern char* sexcode;
extern char* dexteritycode;
extern char* typeFilterLabel[NumDataMasks];
 
extern MatrixErrorCode matrix_errno;
extern char matrix_errtxt[];
 
 
/*
 ecat 6.4 compatibility definitions
*/
typedef enum {        /* matrix data types */
            GENERIC,
            BYTE_TYPE,
            VAX_I2,
            VAX_I4,
            VAX_R4,
            SUN_R4,
            SUN_I2,
            SUN_I4
              }
MatrixDataType_64;
 
#define MAT_SUB_HEADER 255  /* operation to sub-header only */
 
typedef enum {        /* matrix file types */
            MAT_UNKNOWN_FTYPE,
            MAT_SCAN_DATA,
            MAT_IMAGE_DATA,
            MAT_ATTN_DATA,
            MAT_NORM_DATA
              }
MatrixFileType_64;
 
/*
        end of ecat 6.4 definitions
*/
 
struct  MatDir {
        int matnum;
        int strtblk;
        int endblk;
        int matstat; };
 
 
struct matdir
        { int   nmats,
                nmax;
          struct MatDir *entry;
        };
 
 
struct Matval {
        int frame, plane, gate, data, bed;
        };
 
struct Matlimits {
                int     framestart, frameend;
                int     planestart, planeend;
                int     gatestart , gateend;
                int     datastart , dataend;
                int     bedstart  , bedend;
        };
 
 
typedef
        struct matdirnode
        {
                int             matnum ;
                int             strtblk ;
                int             endblk ;
                int             matstat ;
                struct matdirnode *next ;
        }
MatDirNode ;
 
typedef
        struct matdirlist
        {
                int     nmats ;
                MatDirNode *first ;
                MatDirNode *last ;
        }
MatDirList ;
 
typedef
        struct matdirblk
        {
                int     nfree, nextblk, prvblk, nused ;
                struct  MatDir matdir[31] ;
        }
MatDirBlk ;
 
typedef enum {          /* matrix file access modes */
                MAT_READ_WRITE,         /* allow read and/or write */
                MAT_READ_ONLY,          /* only allow read */
                MAT_CREATE,             /* create if non-existant */
                MAT_OPEN_EXISTING,      /* open existing file read/write */
                MAT_CREATE_NEW_FILE     /* force new file creation */
                  }
MatrixFileAccessMode;
 
/* object creation attributes */
 
typedef enum
        {
                MAT_NULL,
                MAT_XDIM,
                MAT_YDIM,
                MAT_ZDIM,
                MAT_DATA_TYPE,
                MAT_SCALE_FACTOR,
                MAT_PIXEL_SIZE,
                MAT_Y_SIZE,
                MAT_Z_SIZE,
                MAT_DATA_MAX,
                MAT_DATA_MIN,
                MAT_PROTO
        }
MatrixObjectAttribute;
 
typedef struct XMAIN_HEAD {
        char magic_number[14];
        char original_file_name[32];
        short sw_version;
        short system_type;
        short file_type;
        char serial_number[10];
        short align_0;                                          /* 4 byte alignment purpose */
        unsigned int scan_start_time;
        char isotope_code[8];
        float isotope_halflife;
        char radiopharmaceutical[32];
        float gantry_tilt;
        float gantry_rotation;
        float bed_elevation;
        float intrinsic_tilt;
        short wobble_speed;
        short transm_source_type;
        float distance_scanned;
        float transaxial_fov;
        short angular_compression;
        short coin_samp_mode;
        short axial_samp_mode;
        short align_1;
        float calibration_factor;
        short calibration_units;
        short calibration_units_label;
        short compression_code;
        char study_name[12];
        char patient_id[16];
        char patient_name[32];
        char patient_sex[1];
        char patient_dexterity[1];
        float patient_age;
        float patient_height;
        float patient_weight;
        int patient_birth_date;
        char physician_name[32];
        char operator_name[32];
        char study_description[32];
        short acquisition_type;
        short patient_orientation;
        char facility_name[20];
        short num_planes;
        short num_frames;
        short num_gates;
        short num_bed_pos;
        float init_bed_position;
        float bed_offset[15];
        float plane_separation;
        short lwr_sctr_thres;
        short lwr_true_thres;
        short upr_true_thres;
        char user_process_code[10];
        short acquisition_mode;
        short align_2;
        float bin_size;
        float branching_fraction;
        unsigned int dose_start_time;
        float dosage;
        float well_counter_factor;
        char data_units[32];
        short septa_state;
        short align_3;
} Main_header;
 
typedef struct XSCAN_SUB {
        short data_type;
        short num_dimensions;
        short num_r_elements;
        short num_angles;
        short corrections_applied;
        short num_z_elements;
        short ring_difference;
        short align_0;
        float x_resolution;
        float y_resolution;
        float z_resolution;
        float w_resolution;
        unsigned int gate_duration;
        int r_wave_offset;
        int num_accepted_beats;
        float scale_factor;
        short scan_min;
        short scan_max;
        int prompts;
        int delayed;
        int multiples;
        int net_trues;
        float cor_singles[16];
        float uncor_singles[16];
        float tot_avg_cor;
        float tot_avg_uncor;
        int total_coin_rate;
        unsigned int frame_start_time;
        unsigned int frame_duration;
        float loss_correction_fctr;
        short phy_planes[8];
} Scan_subheader;
 
typedef struct X3DSCAN_SUB {
        short data_type;
        short num_dimensions;
        short num_r_elements;
        short num_angles;
        short corrections_applied;
        short num_z_elements[64];
        short ring_difference;
        short storage_order;
        short axial_compression;
        float x_resolution;
        float v_resolution;
        float z_resolution;
        float w_resolution;
        unsigned int gate_duration;
        int r_wave_offset;
        int num_accepted_beats;
        float scale_factor;
        short scan_min;
        short scan_max;
        int prompts;
        int delayed;
        int multiples;
        int net_trues;
        float tot_avg_cor;
        float tot_avg_uncor;
        int total_coin_rate;
        unsigned int frame_start_time;
        unsigned int frame_duration;
        float loss_correction_fctr;
        float uncor_singles[128];
} Scan3D_subheader;
 
typedef struct XIMAGE_SUB {
        short data_type;
        short num_dimensions;
        short x_dimension;
        short y_dimension;
        short z_dimension;
        short align_0;
        float z_offset;
        float x_offset;
        float y_offset;
        float recon_zoom;
        float scale_factor;
        short image_min;
        short image_max;
        float x_pixel_size;
        float y_pixel_size;
        float z_pixel_size;
        unsigned int frame_duration;
        unsigned int frame_start_time;
        short filter_code;
        short align_1;
        float x_resolution;
        float y_resolution;
        float z_resolution;
        float num_r_elements;
        float num_angles;
        float z_rotation_angle;
        float decay_corr_fctr;
        int processing_code;
        unsigned int gate_duration;
        int r_wave_offset;
        int num_accepted_beats;
        float filter_cutoff_frequency;
        float filter_resolution;
        float filter_ramp_slope;
        short filter_order;
        short align_2;
        float filter_scatter_fraction;
        float filter_scatter_slope;
        char annotation[40];
        float mt_1_1;
        float mt_1_2;
        float mt_1_3;
        float mt_2_1;
        float mt_2_2;
        float mt_2_3;
        float mt_3_1;
        float mt_3_2;
        float mt_3_3;
        float rfilter_cutoff;
        float rfilter_resolution;
        short rfilter_code;
        short rfilter_order;
        float zfilter_cutoff;
        float zfilter_resolution;
        short zfilter_code;
        short zfilter_order;
        float mt_1_4;
        float mt_2_4;
        float mt_3_4;
        short scatter_type;
        short recon_type;
        short recon_views;
        short align_3;
} Image_subheader;
 
typedef struct XNORM_SUB {
        short data_type;
        short num_dimensions;
        short num_r_elements;
        short num_angles;
        short num_z_elements;
        short ring_difference;
        float scale_factor;
        float norm_min;
        float norm_max;
        float fov_source_width;
        float norm_quality_factor;
        short norm_quality_factor_code;
        short storage_order;
        short span;
        short z_elements[64];
        short align_0;
} Norm_subheader;
 
typedef struct X3DNORM_SUB {
        short data_type;
        short num_r_elements;
        short num_transaxial_crystals;
        short num_crystal_rings;
        short crystals_per_ring;
        short num_geo_corr_planes;
        short uld;
        short lld;
        short scatter_energy;
        short norm_quality_factor_code;
        float norm_quality_factor;
        float ring_dtcor1[32];
        float ring_dtcor2[32];
        float crystal_dtcor[8];
        short span;
        short max_ring_diff;
} Norm3D_subheader;
 
typedef struct XATTEN_SUB {
        short data_type;
        short num_dimensions;
        short attenuation_type;
        short num_r_elements;
        short num_angles;
        short num_z_elements;
        short ring_difference;
        short align_0;
        float x_resolution;
        float y_resolution;
        float z_resolution;
        float w_resolution;
        float scale_factor;
        float x_offset;
        float y_offset;
        float x_radius;
        float y_radius;
        float tilt_angle;
        float attenuation_coeff;
        float attenuation_min;
        float attenuation_max;
        float skull_thickness;
        short num_additional_atten_coeff;
        short align_1;
        float additional_atten_coeff[8];
        float edge_finding_threshold;
        short storage_order;
        short span;
        short z_elements[64];
} Attn_subheader;
 
typedef enum { ECAT6, ECAT7, Interfile } FileFormat;
typedef
        struct matrix_file
        {
                char            *fname ;        /* file path */
                Main_header     *mhptr ;        /* pointer to main header */
                MatDirList      *dirlist ;      /* directory */
                FILE            *fptr ;         /* file ptr for I/O calls */
                int             acs ;           /* ACS flag for ACS files */
                FileFormat file_format;
                char **interfile_header;
        }
MatrixFile ;
 
typedef
        struct matrixdata
        {
                int             matnum ;        /* matrix number */
                MatrixFile      *matfile ;      /* pointer to parent */
                DataSetType     mat_type ;      /* type of matrix? */
                MatrixDataType  data_type ;     /* type of data */
                caddr_t         shptr ;         /* pointer to sub-header */
                caddr_t         data_ptr ;      /* pointer to data */
                int             data_size ;     /* size of data in bytes */
                int             xdim;           /* dimensions of data */
                int             ydim;           /* y dimension */
                int             zdim;           /* for volumes */
                float           scale_factor ;  /* valid if data is int? */
                float           pixel_size;     /* xdim data spacing (cm) */
                float           y_size;         /* ydim data spacing (cm) */
                float           z_size;         /* zdim data spacing (cm) */
                float           data_min;       /* min value of data */
                float           data_max;       /* max value of data */
                float       x_origin;       /* x origin of data */
                float       y_origin;       /* y origin of data */
                float       z_origin;       /* z origin of data */
        }
MatrixData ;
 
#if defined(sun) && !defined(__SVR4)       /* sunos 4.1 */
#define OLD_C 1
#endif
 
#if !defined(OLD_C) || defined(__cplusplus)
#if defined(__cplusplus)
extern "C" {
/*
 * high level user functions
 */
#endif
void SWAB(const void *from, void *to, int len);
void SWAW(const short *from, short *to, int len);
int find_bmin(const u_char*, int size);
int find_bmax(const u_char*, int size);
int find_smin(const short*, int size);
int find_smax(const short*, int size);
int find_imin(const int*, int size);
int find_imax(const int*, int size);
float find_fmin(const float*, int size);
float find_fmax(const float*, int size);
int matspec(const char* specs, char* fname ,int* matnum);
char* is_analyze(const char* );
MatrixFile* matrix_create(const char*,int,Main_header*);
MatrixFile* matrix_open(const char*,int,int);
MatrixData* matrix_read(MatrixFile*, int matnum, int type);
MatrixData* matrix_read_slice(MatrixFile*, MatrixData* volume, int slice_num,
        int segment);
MatrixData* matrix_read_view(MatrixFile*, MatrixData* volume, int view,
        int segment);
int matrix_write(MatrixFile*, int matnum, MatrixData*);
int mat_numcod(int frame, int plane, int gate, int data, int bed);
int mat_numdoc(int, struct Matval*);
void free_matrix_data(MatrixData*);
void matrix_perror(const char*);
int matrix_close(MatrixFile*);
int matrix_find(MatrixFile*, int matnum, struct MatDir*);
int crash(char *fmt, ...);
MatrixData *load_volume7(MatrixFile *matrix_file, int frame, int gate, int data, int bedstart, int bedend);
int save_volume7( MatrixFile *mfile, Image_subheader *shptr, float *data_ptr, int frame, int gate, int data, int bed );
 
 
/*
 * low level functions prototypes, don't use
 */
int unmap64_main_header(char *buf, Main_header *h);
int unmap64_scan_header(char *buf, Scan_subheader*, Main_header*);
int unmap64_attn_header(char *buf, Attn_subheader*, Main_header*);
int unmap64_image_header(char *buf, Image_subheader*, Main_header*);
int unmap64_norm_header(char *buf, Norm_subheader*, Main_header*);
int map64_main_header(char *buf, Main_header *h);
int map64_scan_header(char *buf, Scan_subheader*, Main_header*);
int map64_attn_header(char *buf, Attn_subheader*, Main_header*);
int map64_image_header(char *buf, Image_subheader*, Main_header*);
int map64_norm_header(char *buf, Norm_subheader*, Main_header*);
int unmap_main_header(char *buf, Main_header *h);
int unmap_Scan3D_header(char *buf, Scan3D_subheader*);
int unmap_scan_header(char *buf, Scan_subheader*);
int unmap_image_header(char *buf, Image_subheader*);
int unmap_attn_header(char *buf, Attn_subheader*);
int unmap_norm3d_header(char *buf, Norm3D_subheader*);
int unmap_norm_header(char *buf, Norm_subheader*);
int mat_read_main_header(FILE *fptr, Main_header *h);
int mat_read_scan_subheader( FILE *, Main_header*, int blknum, Scan_subheader*);
int mat_read_Scan3D_subheader( FILE *, Main_header*, int blknum, Scan3D_subheader*);
int mat_read_image_subheader(FILE *, Main_header*, int blknum, Image_subheader*);
int mat_read_attn_subheader(FILE *, Main_header*, int blknum, Attn_subheader*);
int mat_read_norm_subheader(FILE *, Main_header*, int blknum, Norm_subheader*);
int mat_read_norm3d_subheader(FILE *, Main_header*, int blknum, Norm3D_subheader*);
int mat_write_main_header(FILE *fptr, Main_header *h);
int mat_write_scan_subheader( FILE *, Main_header*, int blknum, Scan_subheader*);
int mat_write_Scan3D_subheader( FILE *, Main_header*, int blknum, Scan3D_subheader*);
int mat_write_image_subheader(FILE *, Main_header*, int blknum, Image_subheader*);
int mat_write_attn_subheader(FILE *, Main_header*, int blknum, Attn_subheader*);
int mat_write_norm_subheader(FILE *, Main_header*, int blknum, Norm_subheader*);
struct matdir *mat_read_dir(FILE *, Main_header*, char *selector);
int mat_read_matrix_data(FILE *, Main_header*, int blk, int nblks, short* bufr);
int mat_enter(FILE *, Main_header *mhptr, int matnum, int nblks);
int mat_lookup(FILE *fptr, Main_header *mhptr, int matnum,  struct MatDir *entry);
int mat_rblk(FILE *fptr, int blkno, char *bufr,  int nblks);
int mat_wblk(FILE *fptr, int blkno, char *bufr,  int nblks);
void swaw(short *from, short *to, int length);
int insert_mdir(struct MatDir   matdir,MatDirList       *dirlist);
 
#if defined(__cplusplus)
}
#endif
#else /* __cplusplus */
extern float find_fmin(), find_fmax();
extern MatrixFile *matrix_open(), *matrix_create();
extern MatrixData *matrix_read(), *matrix_object_create();
extern MatrixData *matrix_read_slice(), *matrix_read_view();
extern Main_header *matrix_init_main_header();
extern FILE* mat_open();
extern MatDirList *mat_read_directory();
extern char* is_analyze();
extern void free_matrix_data();
#endif  /* __cplusplus */
extern int ecat_default_version;
#endif  /*      matrix_ecat7_h */