rwSPIDER.h

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/*
 Based on rwSPIDER.h
 Header file for reading and writing SPIDER files
 Format: 3D image file format for the SPIDER package
 Author: Bernard Heymann
 Created: 19990410  Modified: 20010928
*/

#ifndef CORE_RWSPIDER_H
#define CORE_RWSPIDER_H

#define SPIDERSIZE 1024 // Minimum size of the SPIDER header (variable)

struct SPIDERhead
{                    // file header for SPIDER data
    float nslice;    //  0      slices in volume (image = 1)
    float nrow;      //  1      rows per slice
    float irec;      //  2      # records in file (unused)
    float nhistrec;  //  3      (obsolete)
    float iform;     //  4      file type specifier
    float imami;     //  5      max/min flag (=1 if calculated)
    float fmax;      //  6      maximum
    float fmin;      //  7      minimum
    float av;        //  8      average
    float sig;       //  9      standard deviation (=-1 if not calculated)
    float ihist;     // 10      (obsolete)
    float nsam;      // 11      pixels per row
    float labrec;    // 12      # records in header
    float iangle;    // 13      flag: tilt angles filled
    float phi;       // 14      tilt angles
    float theta;     // 15
    float gamma;     // 16      (=psi)
    float xoff;      // 17      translation
    float yoff;      // 18
    float zoff;      // 19
    float scale;     // 20      scaling
    float labbyt;    // 21      # bytes in header
    float lenbyt;    // 22      record length in bytes (row length)
    float istack;    // 23      indicates stack of images
    float inuse;     // 24      indicates this image in stack is used (not used)
    float maxim;     // 25      max image in stack used
    float imgnum;    // 26      number of current image
    float unused[2]; // 27-28     (unused)
    float kangle;    // 29      flag: additional angles set
    float phi1;      // 30      additional angles
    float theta1;    // 31
    float psi1;      // 32
    float phi2;      // 33
    float theta2;    // 34
    float psi2;      // 35

    double fGeo_matrix[3][3]; // x9 = 72 bytes: Geometric info
    float fAngle1; // angle info

    float fr1;
    float fr2; // lift up cosine mask parameters

    float RTflag; // 1=RT, 2=FFT(RT)
    float Astart;
    float Aend;
    float Ainc;
    float Rsigma; // 4*7 = 28 bytes
    float Tstart;
    float Tend;
    float Tinc; // 4*3 = 12, 12+28 = 40B

    float weight; // For Maximum-Likelihood refinement
    float flip;   // 0=no flipping operation (false), 1=flipping (true)

    char fNada2[576]; // empty 700-76-40=624-40-8= 576 bytes

    char cdat[12];   // 211-213   creation date
    char ctim[8];  // 214-215   creation time
    char ctit[160];  // 216-255   title
} ;

/************************************************************************
@Function: readSPIDER
@Description:
 Reading a SPIDER image file format.
@Algorithm:
 A 3D multi-image format used in electron microscopy.
 Header size:    1024 bytes (not same as data offset!).
 Data offset:    sizeof(float)*x_size*ceil(1024/x_size)
 File format extensions:   .spi
 Byte order determination: File type and third dimension values
        must be less than 256*256.
 Data type:      only float.
 Transform type:    Hermitian
        The x-dimension contains the x-size
        of the full transform
 A multi-image file has a global header followed by a header and data
 for each sub-image.
@Arguments:
 Bimage* p   the image structure.
 size_t select_img  image selection in multi-image file (-1 = all images).
@Returns:
 int     error code (<0 means failure).
**************************************************************************/
int  readSPIDER(size_t select_img);

/************************************************************************
@Function: readSPIDER
@Description:
 Reading a SPIDER image file format in batches.
@Arguments:
 size_t start_img  Number of first image in the batch.
 size_t batch_size Specifies how many sub-images will be read.
    If batch_size = ALL_IMAGES, then images from `start_img` to the last one will be read.
@Returns:
 int     error code (<0 means failure).
**************************************************************************/
int  readSPIDER(size_t start_img, size_t batch_size);

/************************************************************************
@Function: writeSPIDER
@Description:
 Writing a SPIDER image file format.
@Algorithm:
 A 3D image format used in electron microscopy.
@Arguments:
@Returns:
 int     error code (<0 means failure).
**************************************************************************/
int  writeSPIDER(size_t select_img = ALL_IMAGES, bool isStack=false, int mode=WRITE_OVERWRITE);
#endif