imagicio.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__imagicio_h__
#define eman__imagicio_h__ 1
 
#include "imageio.h"
 
namespace EMAN
{
        class ImagicIO : public ImageIO
        {
          public:
                static const char *HED_EXT;
                static const char *IMG_EXT;
                
                explicit ImagicIO(const string & fname, IOMode rw_mode = READ_ONLY);
                ~ImagicIO();
 
                DEFINE_IMAGEIO_FUNC;
                static bool is_valid(const void *first_block);
                
                bool is_single_image_format() const
                {
                        return false;
                }
                
                int get_nimg();
                
          private:
                static const char *REAL_TYPE_MAGIC;
                static const char *CTF_MAGIC;
 
 
                enum DataType
                {
                        IMAGIC_UCHAR,
                        IMAGIC_USHORT,
                        IMAGIC_FLOAT,
                        IMAGIC_FLOAT_COMPLEX,
                        IMAGIC_FFT_FLOAT_COMPLEX,
                        IMAGIC_UNKNOWN_TYPE
                };
 
                enum
                {
                        NUM_4BYTES_PRE_IXOLD = 14,
                        NUM_4BYTES_AFTER_IXOLD = 14,
                        NUM_4BYTES_AFTER_SPACE = 207
                };
 
                struct ImagicHeader
                {
                        int imgnum;                     // image number, [1,n]
                        int count;                      // total number of images - 1 (only first image), [0,n-1]
                        int error;                      // Error code for this image
                        int headrec;            // # of header records/image (always 1)
                        int mday;                       // image creation time
                        int month;
                        int year;
                        int hour;
                        int minute;
                        int sec;
                        int reals;                      // image size in reals
                        int pixels;                     // image size in pixels
                        int ny;                         // # of lines / image
                        int nx;                         // # of pixels / line
                        char type[4];           // PACK, INTG, REAL, COMP, RECO
                        int ixold;                      // Top left X-coord. in image before windowing 
                        int iyold;                      // Top left Y-coord. in image before windowing 
                        float avdens;           // average density
                        float sigma;            // deviation of density
                        float varia;            // variance of density
                        float oldav;            // old average density
                        float max;                      // max density
                        float min;                      // min density
                        int complex;            // not used
                        float cellx;            // not used
                        float celly;            // not used
                        float cellz;            // not used
                        float cella1;           // not used
                        float cella2;           // not used
                        char label[80];         // image id string
                        int space[8];
                        float mrc1[4];
                        int mrc2;
                        int space2[7];
                        int lbuf;                       // effective buffer len = nx
                        int inn;                        // lines in buffer = 1
                        int iblp;                       // buffer lines/image = ny
                        int ifb;                        // 1st line in buf = 0
                        int lbr;                        // last buf line read = -1
                        int lbw;                        // last buf line written = 0
                        int lastlr;                     // last line called for read = -1
                        int lastlw;                     // last line called for write = 1
                        int ncflag;                     // decode to complex = 0
                        int num;                        // file number = 40 (?)
                        int nhalf;                      // leff/2
                        int ibsd;                       // record size for r/w (words) = nx*2
                        int ihfl;                       // file # = 8
                        int lcbr;                       // lin count read buf = -1
                        int lcbw;                       // lin count wr buf = 1
                        int imstr;                      // calc stat on rd = -1
                        int imstw;                      // calc stat on wr = -1
                        int istart;                     // begin line in buf = 1
                        int iend;                       // end line in buf = nx
                        int leff;                       // eff line len = nx
                        int linbuf;                     // line len (16 bit) nx *2
                        int ntotbuf;            // total buf in pgm = -1
                        int space3[5];
                        int icstart;            // complex line start = 1
                        int icend;                      // complex line end = nx/2
                        int rdonly;                     // read only = 0
                        int misc[157];          // Remainder of header (EMAN1 specific settings not supported)
                };
 
                size_t get_datatype_size(DataType t);
                int to_em_datatype(DataType t);
                void make_header_host_endian(ImagicHeader & hed);
                void swap_header(ImagicHeader & hed);
                DataType get_datatype_from_name(const char *name);
 
                Ctf * read_ctf(const ImagicHeader& hed) const;
                void write_ctf(const Ctf * const ctf, int image_index = 0);
                
          private:
                string hed_filename;
                string img_filename;
 
                FILE *hed_file;
                FILE *img_file;
 
                ImagicHeader imagich;
                bool is_big_endian;
                bool is_new_hed;
                bool is_new_img;
 
                DataType datatype;
                int nz;
        };
 
}
 
 
#endif  //eman__imagicio_h__