serio.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__serio_h__
#define eman__serio_h__ 1
 
#include "imageio.h"
 
#ifdef _WIN32
typedef unsigned long long uint64_t;
#else
#include "stdint.h"
#endif
 
namespace EMAN
{
        class SerIO : public ImageIO
        {
        public:
                explicit SerIO(const string & fname, IOMode rw_mode = READ_ONLY);
                ~SerIO();
 
                DEFINE_IMAGEIO_FUNC;
                static bool is_valid(const void *first_block);
                int get_nimg();
 
        private:
                enum SerImgMode {
                        oneD = 0x4120,
                        twoD = 0x4122
                };
 
                enum SerTagType {
                        timeOnly = 0x4152,
                        posTime  = 0x4122
                };
 
                enum SerDataMode {
                        SER_UCHAR = 1,
                        SER_USHORT,
                        SER_UINT,
                        SER_CHAR,
                        SER_SHORT,
                        SER_INT,
                        SER_FLOAT,
                        SER_DOUBLE,
                        SER_COMPLEX8,
                        SER_COMPLEX16,
                        UNKNOWN
                };
 
                //This header struct has an alignment issue. It's size is 32 instead of 30.
                //So we need read the item one by one.
                struct SerHeader {
                        short   ByteOrder;
                        short   SeriesID;
                        short   SeriesVersion;
                        int             DataTypeID;
                        int             TagTypeID;
                        int     TotalNumberElements;
                        int             ValidNumberElements;
                        int             OffsetArrayOffset;              // could also be 64 bits in new version, we don't actually use this header
                        int             NumberDimensions;
                };
 
                bool    is_new_file;
 
                SerHeader serh;
 
                uint64_t *  data_offset_array;
                uint64_t *  tag_offset_array;
 
                int nimg;       //total image number in this file
                int nx;
                int ny;
                int nz;
                int datatypeid; //1D or 2D image
                int datamode;   //data value mode (int, float, etc.)
 
                void read_dim_arr(Dict & dict, int idx);
 
                void read_data_element(Dict & dict);
 
                void read_data_tag(Dict & dict);
        };
 
}
 
#endif  //eman__serio_h__