spiderio.h

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/*
 * Author: Steven Ludtke, 04/10/2003 (sludtke@bcm.edu)
 * Copyright (c) 2000-2006 Baylor College of Medicine
 * 
 * This software is issued under a joint BSD/GNU license. You may use the
 * source code in this file under either license. However, note that the
 * complete EMAN2 and SPARX software packages have some GPL dependencies,
 * so you are responsible for compliance with the licenses of these packages
 * if you opt to use BSD licensing. The warranty disclaimer below holds
 * in either instance.
 * 
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 * 
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 * 
 * */
 
#ifndef eman__spiderio_h__
#define eman__spiderio_h__ 1
 
#include "imageio.h"
 
namespace EMAN
{
        class SpiderIO : public ImageIO
        {
          public:
                explicit SpiderIO(const string & fname, IOMode rw_mode = READ_ONLY);
                ~SpiderIO();
 
                DEFINE_IMAGEIO_FUNC;
                static bool is_valid(const void *first_block);
                
                bool is_single_image_format() const { return false;     }
                
                int get_nimg();
 
        protected:
                struct SpiderHeader
                {
                        float nslice;           // number of slices in volume; 1 for a 2D image.
                        float nrow;         // nrow, number of rows per slice 
                        float irec;                     // total number of records in the file (unused)
                        float nhistrec;     // obsolete, unused
                        
                        float type;             //iform, file type
                        
                        float mmvalid;          // imami, max/min flag.
                        float max;          // fmax, max value
                        float min;          // fmin, min value
                        float mean;         // av, average value
                        float sigma;            // sig, std dev, -1=unknown
                        float ihist;        // obsolete, no longer used
                        float nsam;         // nsam, number of pixels per row
                        float headrec;          // labrec, number of records in header
                        float angvalid;         // iangle, flag, 1 if tilt angles have been computed
                        float phi;          // tilt angle
                        float theta;        // tilt angle
                        float gamma;        // tilt angle  (also called psi).
                        float dx;           // xoff, x translation
                        float dy;           // yoff, y translation
                        float dz;                       // zoff, z translation
                        float scale;        // scale factor
                        float headlen;          // labbyt, header length in bytes
                        float reclen;       // lenbyt, record length in bytes
 
                        float istack;
                        float inuse;        // not used
                        float maxim;
                        float imgnum;
                        
                        float lastindx;    
                        
                        float u6;                  // unused
                        float u7;          // unused
                        
                        float Kangle;   
                        float phi1;
                        float theta1;
                        float psi1;
                        float phi2;
                        float theta2;
                        float psi2;
                        char  u8[48];           //unused
                        float xf[27];           // reserved for Jose Maria's transforms
                        float u9[135];      // unused
                        char date[11];      // creation date e.g. 27-MAY-1999 
                        char time[8];       // creation time e.g. 09:43:19 
                        char title[160];    
                };
 
                enum SpiderType
                {
                        IMAGE_2D                        =   1,
                        IMAGE_3D                        =   3,
                        IMAGE_2D_FFT_ODD        = -11,
                        IMAGE_2D_FFT_EVEN       = -12,
                        IMAGE_3D_FFT_ODD        = -21,
                        IMAGE_3D_FFT_EVEN       = -22
                };
 
                enum
                {
                        SINGLE_IMAGE_HEADER             =   0,
                        OVERALL_STACK_HEADER    =       2,
                        NUM_FLOATS_IN_HEADER    = 211
                };
                
                //ISTACK, MAXIM, IMGNUM only useful for overall stack header
                int write_single_header(const Dict & dict, const Region* area, int image_index, size_t offset,
                                                                SpiderHeader *& hp,     int ISTACK, int MAXIM=1, int IMGNUM=1, bool use_host_endian=true);      
                
                int write_single_data(float *data, const Region * area, SpiderHeader *& hp,
                                                                size_t offset, int img_index, int max_nimg, bool use_host_endian=true);
                
                virtual bool is_valid_spider(const void *first_block);
 
          protected:
                bool need_swap() const;
                void swap_data(float *data, size_t nitems);
                void swap_header(SpiderHeader * header);
 
          protected:
 
                SpiderHeader *first_h; // overall image header
                SpiderHeader *cur_h;   // the current reading/writing image header
                
                bool is_big_endian;
                bool is_new_file;
        };
}
 
#endif  //eman__spiderio_h__