pifio.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__pifio_h__
#define eman__pifio_h__ 1
 
#include "imageio.h"
 
namespace EMAN
{
        class PifIO : public ImageIO
        {
          public:
                explicit PifIO(const string & fname, IOMode rw_mode = READ_ONLY);
                ~PifIO();
 
                DEFINE_IMAGEIO_FUNC;
                static bool is_valid(const void *first_block);
 
                bool is_single_image_format() const
                {
                        return false;
                }
                int get_nimg();
                
          private:
                enum
                {
                        PIF_MAGIC_NUM = 8
                };
 
                enum PifDataMode
                {
                        PIF_CHAR = 0,
                        PIF_SHORT = 1,
                        PIF_FLOAT_INT = 2,
                        PIF_SHORT_COMPLEX = 3,
                        PIF_FLOAT_INT_COMPLEX = 4,
                        PIF_BOXED_DATA = 6,                     // byte, read as 0
                        PIF_SHORT_FLOAT = 7,
                        PIF_SHORT_FLOAT_COMPLEX = 8,
                        PIF_FLOAT = 9,
                        PIF_FLOAT_COMPLEX = 10,
                        PIF_MAP_FLOAT_SHORT = 20,
                        PIF_MAP_FLOAT_INT = 21,
                        PIF_MAP_FLOAT_INT_2 = 40,                       // 4 byte floatint, read as 2
                        PIF_BOXED_FLOAT_INT = 46,               // 4 byte floatint, read as 2
                        PIF_INVALID
                };
 
                // note there are no floats in these files. Floats are stored as ints with
                // a scaling factor.
                struct PifFileHeader
                {
                        int magic[2];           // magic number; identify PIF file
                        char scalefactor[16];   // to convert float ints -> floats
                        int nimg;                       // number of images in file
                        int endian;                     // endianness, 0 -> vax,intel (little), 1 -> SGI, PowerPC (big)
                        char program[32];       // program which generated image
                        int htype;                      // 1 - all images same number of pixels and depth, 0 - otherwise
                        int nx;                         // number of columns
                        int ny;                         // number of rows
                        int nz;                         // number of sections
                        int mode;                       // image data type
 
                        int even;
                        int mrcX;                       // MRC X dim
                        int mrcY;                       // MRC Y dim
                        int mrcZ;                       // MRC Z dim
                        char scale_fac[16];
                        char ctf_a0[13];
                        char ctf_a1[13];
                        char ctf_a2[13];
                        char ctf_a3[13];
                        char ctf_a4[13];
                        char ctf_a5[13];
                        char pad[318];
                };
 
                struct PifColorMap
                {                                               // color map for depthcued images
                        short r[256];
                        short g[256];
                        short b[256];
                };
 
                struct PifImageHeader
                {
                        int nx;
                        int ny;
                        int nz;                         // size of this image
                        int mode;                       // image data type
                        int bkg;                        // background value
                        int radius;                     // boxed image radius
                        int xstart;
                        int ystart;
                        int zstart;                     // starting number of each axis
                        int mx;
                        int my;
                        int mz;                         // intervals along x,y,z
                        int xlen;
                        int ylen;
                        int zlen;                       // cell dimensions (floatints)
                        int alpha;
                        int beta;
                        int gamma;                      // angles (floatints)
                        int mapc;
                        int mapr;
                        int maps;                       // axes->sections (1,2,3=x,y,z)
                        int min;
                        int max;
                        int mean;
                        int sigma;                      // statistics (floatints)
                        int ispg;                       // spacegroup
                        int nsymbt;                     // bytes for symmetry ops
                        int xorigin;
                        int yorigin;            // origin (floatint)
                        char title[80];
                        char time[32];
                        char imagenum[16];      // unique micrograph number
                        char scannum[8];        // scan number of micrograph
                        int aoverb;
                        int mapabang;
                        int pad[63];            // later use
                };
          
                int get_mode_size(PifDataMode mode);
                bool is_float_int(int mode);
                void fseek_to(int image_index);
                int to_em_datatype(int pif_datatype);
                int to_pif_datatype(int em_datatype);
 
            string filename;
                PifFileHeader pfh;
                int mode_size;
                bool is_big_endian;
                bool is_new_file;
                float real_scale_factor;
        };
 
}
 
 
#endif  //eman__pifio_h__