icosio.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 <cstring>
#include "icosio.h"
#include "portable_fileio.h"
#include "geometry.h"
 
using namespace EMAN;
 
 
IcosIO::IcosIO(const string & fname, IOMode rw)
:       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        is_new_file = false;
        memset(&icosh, 0, sizeof(IcosHeader));
}
 
IcosIO::~IcosIO()
{
        if (file) {
                fclose(file);
                file = 0;
        }
}
 
void IcosIO::init()
{
        ENTERFUNC;
        if (initialized) {
                return ;
        }
 
        initialized = true;
        file = sfopen(filename, rw_mode, &is_new_file);
 
        if (!is_new_file) {
                if (fread(&icosh, sizeof(IcosHeader), 1, file) != 1) {
                        throw ImageReadException(filename, "ICOS header");
                }
 
                if (!is_valid(&icosh)) {
                        throw ImageReadException(filename, "invalid ICOS file");
                }
                is_big_endian = ByteOrder::is_data_big_endian(&icosh.stamp);
                become_host_endian((int *) &icosh, sizeof(IcosHeader) / sizeof(int));
        }
        EXITFUNC;
}
 
bool IcosIO::is_valid(const void *first_block)
{
        ENTERFUNC;
        bool result = false;
        if (!first_block) {
                result = false;
        }
        else {
                const int *data = static_cast < const int *>(first_block);
                int stamp = data[0];
                int stamp1 = data[19];
                int stamp2 = data[20];
                int stamp3 = data[26];
 
                bool data_big_endian = ByteOrder::is_data_big_endian(&stamp);
 
                if (data_big_endian != ByteOrder::is_host_big_endian()) {
                        ByteOrder::swap_bytes(&stamp);
                        ByteOrder::swap_bytes(&stamp1);
                        ByteOrder::swap_bytes(&stamp2);
                        ByteOrder::swap_bytes(&stamp3);
                }
 
                if (stamp == STAMP && stamp1 == STAMP1 && stamp2 == STAMP2 && stamp3 == STAMP3) {
                        result = true;
                }
        }
        EXITFUNC;
        return result;
}
 
int IcosIO::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();
 
        check_region(area, IntSize(icosh.nx, icosh.ny, icosh.nz),false,false);
 
        int xlen = 0, ylen = 0, zlen = 0;
        EMUtil::get_region_dims(area, icosh.nx, &xlen, icosh.ny, &ylen, icosh.nz, &zlen);
 
        dict["nx"] = xlen;
        dict["ny"] = ylen;
        dict["nz"] = zlen;
        dict["datatype"] = EMUtil::EM_FLOAT;
        dict["minimum"] = icosh.min;
        dict["maximum"] = icosh.max;
 
        EXITFUNC;
        return 0;
}
 
int IcosIO::write_header(const Dict & dict, int image_index, const Region* ,
                                                 EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        int err = 0;
        //single image format, index can only be zero
        if(image_index == -1) {
                image_index = 0;
        }
        if(image_index != 0) {
                throw ImageWriteException(filename, "ICOS file does not support stack.");
        }
        check_write_access(rw_mode, image_index, 1);
 
        icosh.stamp = STAMP;
        icosh.stamp1 = STAMP1;
        icosh.stamp2 = STAMP2;
        icosh.stamp3 = STAMP3;
 
        icosh.nx = dict["nx"];
        icosh.ny = dict["ny"];
        icosh.nz = dict["nz"];
 
        icosh.min = dict["minimum"];
        icosh.max = dict["maximum"];
 
        rewind(file);
 
        if (fwrite(&icosh, sizeof(IcosHeader), 1, file) != 1) {
                throw ImageWriteException(filename, "ICOS header write");
        }
 
        EXITFUNC;
        return err;
}
 
int IcosIO::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);
        check_region(area, IntSize(icosh.nx, icosh.ny, icosh.nz),false,false);
 
        portable_fseek(file, sizeof(IcosHeader), SEEK_SET);
 
        EMUtil::process_region_io((unsigned char *) data, file,
                                                          READ_ONLY, image_index,
                                                          sizeof(float), icosh.nx, icosh.ny, icosh.nz,
                                                          area, false, EMUtil::IMAGE_ICOS, sizeof(int), sizeof(int));
 
        int xlen = 0, ylen = 0, zlen = 0;
        EMUtil::get_region_dims(area, icosh.nx, &xlen, icosh.ny, &ylen, icosh.nz, &zlen);
        become_host_endian(data, xlen * ylen * zlen);
 
 
        EXITFUNC;
        return 0;
}
 
int IcosIO::write_data(float *data, int image_index, const Region* area,
                                           EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        //single image format, index can only be zero
        image_index = 0;
        check_write_access(rw_mode, image_index, 1, data);
        portable_fseek(file, sizeof(IcosHeader), SEEK_SET);
 
        EMUtil::process_region_io(data, file, rw_mode, image_index,
                                                          sizeof(float), icosh.nx, icosh.ny, icosh.nz, area,
                                                          false, EMUtil::IMAGE_ICOS, sizeof(int), sizeof(int));
 
#if 0
        size_t float_size = sizeof(float);
        int nx = icosh.nx;
        float *buf = new float[nx + 2];
        buf[0] = (float)float_size * nx;
        buf[nx + 1] = buf[0];
        int nrows = icosh.ny * icosh.nz;
 
        int row_size = (nx + 2) * float_size;
 
 
        for (int j = 0; j < nrows; j++) {
                memcpy(&buf[1], &data[nx * j], nx * float_size);
                if (fwrite(buf, row_size, 1, file) != 1) {
                        throw ImageWriteException(filename, "ICOS data");
                }
        }
 
        if( buf )
        {
                delete[]buf;
                buf = 0;
        }
#endif
        EXITFUNC;
        return 0;
}
 
void IcosIO::flush()
{
        fflush(file);
}
 
bool IcosIO::is_complex_mode()
{
        return false;
}
 
bool IcosIO::is_image_big_endian()
{
        init();
        return is_big_endian;
}