gatan2io.cpp

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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
 * 
 * */
 
#include "gatan2io.h"
#include "geometry.h"
#include "portable_fileio.h"
#include <cstring>
 
using namespace EMAN;
 
Gatan2IO::Gatan2IO(const string & fname, IOMode rw)
:       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        memset(&gatanh, 0, sizeof(Gatan2Header));
}
 
Gatan2IO::~Gatan2IO()
{
        if (file) {
                fclose(file);
                file = 0;
        }
}
 
void Gatan2IO::init()
{
        ENTERFUNC;
        
        if (initialized) {
                return;
        }
        
        initialized = true;
 
        bool is_new_file = false;
        file = sfopen(filename, rw_mode, &is_new_file);
 
        if (!is_new_file) {
                if (fread(&gatanh, sizeof(Gatan2Header), 1, file) != 1) {
                        throw ImageReadException(filename, "Gatan2 Header");
                }
 
                if (!is_valid(&gatanh)) {
                        throw ImageReadException(filename, "invalid Gatan2 file");
                }
 
                is_big_endian = ByteOrder::is_data_big_endian(&gatanh.len);
                become_host_endian((short *) &gatanh, sizeof(Gatan2Header) / sizeof(short));
        }
        EXITFUNC;
}
 
bool Gatan2IO::is_valid(const void *first_block)
{
        ENTERFUNC;
        bool result = false;
        
        if (!first_block) {
                result = false;
        }
        else {
                const short *data = static_cast < const short *>(first_block);
                short len = data[5];
                short type = data[6];
 
                bool data_big_endian = ByteOrder::is_data_big_endian(&len);
 
                if (data_big_endian != ByteOrder::is_host_big_endian()) {
                        ByteOrder::swap_bytes(&len);
                        ByteOrder::swap_bytes(&type);
                }
 
                int double_size = sizeof(double);
                if (len > 0 && len <= double_size && type > 0 && type <= GATAN2_INVALID) {
                        result = true;
                }
        }
        EXITFUNC;
        return result;
}
 
int Gatan2IO::read_header(Dict & dict, int image_index, const Region * area, bool)
{
        ENTERFUNC;
        //single image format, index can only be zero
        if(image_index == -1) {
                image_index = 0;
        }
 
        if(image_index != 0) {
                throw ImageReadException(filename, "no stack allowed for MRC image. For take 2D slice out of 3D image, read the 3D image first, then use get_clip().");
        }
 
        init();
        
        if (is_complex_mode()) {
                throw ImageReadException(filename, "Cannot read complex Gatan2 files");
        }
        else {
                check_region(area, IntSize(gatanh.nx, gatanh.ny));
 
                int xlen = 0, ylen = 0;
                EMUtil::get_region_dims(area, gatanh.nx, &xlen, gatanh.ny, &ylen);
                                
                dict["nx"] = xlen;
                dict["ny"] = ylen;
                dict["nz"] = 1;
                dict["datatype"] = to_em_datatype(gatanh.type); 
        }
        
        EXITFUNC;
        return 0;
}
 
int Gatan2IO::write_header(const Dict &, int, const Region* , EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        LOGWARN("Gatan2 write is not supported.");
        EXITFUNC;
        return 1;
}
 
int Gatan2IO::read_data(float *data, int image_index, const Region * area, bool )
{
        ENTERFUNC;
        //single image format, index can only be zero
        image_index = 0;
        check_read_access(image_index, data);
 
        if (is_complex_mode()) {
                throw ImageReadException(filename, "Cannot read complex Gatan2 files");
        }
        
        check_region(area, IntSize(gatanh.nx, gatanh.ny));
        
        portable_fseek(file, sizeof(Gatan2Header), SEEK_SET);
 
#if 0
        if (fread(data, gatanh.nx * gatanh.len, gatanh.ny, file) != (unsigned int) gatanh.ny) {
                LOGDEBUG("Data read incomplete in Gatan file '%s'", filename.c_str());
                return 1;
        }
#endif
 
        int size = gatanh.nx * gatanh.ny;
        short *sdata = (short *) data;
        unsigned char *cdata = (unsigned char *) data;
        int *ldata = (int *) data;
 
        EMUtil::process_region_io(cdata, file, READ_ONLY, image_index, gatanh.len,
                                                          gatanh.nx, gatanh.ny, 1, area);
 
        switch (gatanh.type) {
        case GATAN2_SHORT:
                become_host_endian((short *) data, size);
                for (int i = size - 1; i >= 0; i--) {
                        data[i] = static_cast < float >(sdata[i]);
                }
                break;
        case GATAN2_FLOAT:
                become_host_endian(data, size);
                break;
        case GATAN2_CHAR:
                for (int i = size - 1; i >= 0; i--) {
                        data[i] = static_cast < float >(cdata[i]);
                }
                break;
        case GATAN2_INT:
                become_host_endian((int *) data, size);
                for (int i = size - 1; i >= 0; i--) {
                        data[i] = static_cast < float >(ldata[i]);
                }
                break;
        default:
                throw ImageReadException(filename, "unsupported Gatan2 data type");
        }
        EXITFUNC;
        return 0;
}
 
int Gatan2IO::write_data(float *, int, const Region*, EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        LOGWARN("Gatan2 write is not supported.");
        EXITFUNC;
        return 1;
}
 
void Gatan2IO::flush()
{
}
 
bool Gatan2IO::is_complex_mode()
{
        init();
        if (gatanh.type == GATAN2_COMPLEX || gatanh.type == GATAN2_PACKED_COMPLEX) {
                return true;
        }
        return false;
}
 
bool Gatan2IO::is_image_big_endian()
{
        init();
        return is_big_endian;
}
 
 
 
int Gatan2IO::to_em_datatype(int gatan_type)
{
        switch (gatan_type) {
        case GATAN2_SHORT:
                return EMUtil::EM_SHORT;
 
        case GATAN2_FLOAT:
                return EMUtil::EM_FLOAT;
 
        case GATAN2_CHAR:
                return EMUtil::EM_CHAR;
 
        case GATAN2_INT:
                return EMUtil::EM_INT;
        }
 
        return EMUtil::EM_UNKNOWN;
}