salio.cpp

Go to the documentation of this file.

/*
 * 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 "salio.h"
#include "util.h"
#include "geometry.h"
 
#ifndef WIN32
#include <sys/param.h>
#else
#define  MAXPATHLEN (MAX_PATH * 4)
#endif
 
#include <cstdio>
#include <climits>
#include <cstring>
 
using namespace EMAN;
 
const char *SalIO::HDR_EXT = "hdr";
const char *SalIO::IMG_EXT = "img";
const char *SalIO::MAGIC = " IDENTIFICATION";
 
 
SalIO::SalIO(const string & fname, IOMode rw)
:       ImageIO(fname, rw)
{
        nx = 0;
        ny = 0;
        record_length = 512;
        scan_mode = NON_RASTER_SCAN;
        pixel = 4.6667f;
}
 
SalIO::~SalIO()
{
        if (file) {
                fclose(file);
                file = 0;
        }
}
 
void SalIO::init()
{
        ENTERFUNC;
 
        if (initialized) {
                return;
        }
 
        initialized = true;
 
        string hdr_filename = Util::change_filename_ext(filename, HDR_EXT);
        string img_filename = Util::change_filename_ext(filename, IMG_EXT);
 
        bool is_new_file = false;
        file = sfopen(hdr_filename, rw_mode, &is_new_file);
 
        char scan_type[MAXPATHLEN];
        ScanAxis axis = X_SCAN_AXIS;
 
        if (!is_new_file) {
                char buf[MAXPATHLEN];
                if (fgets(buf, MAXPATHLEN, file)) {
                        if (!is_valid(buf)) {
                                throw ImageReadException(filename, "ivalid SAL");
                        }
                }
 
                while (fgets(buf, MAXPATHLEN, file)) {
                        const char *buf1 = buf + 1;
 
                        if (Util::sstrncmp(buf1, "NXP")) {
                                sscanf(strchr(buf, '=') + 1, " %d", &nx);
                        }
                        else if (Util::sstrncmp(buf1, "NYP")) {
                                sscanf(strchr(buf, '=') + 1, " %d", &ny);
                        }
                        else if (Util::sstrncmp(buf1, "AXSCAN")) {
                                char *t = strrchr(buf, '\'');
                                if (t && t[-1] == 'Y') {
                                        axis = Y_SCAN_AXIS;
                                }
                        }
                        else if (Util::sstrncmp(buf1, "FILE REC LEN")) {
                                sscanf(strchr(buf, '=') + 1, " %d", &record_length);
                        }
                        else if (Util::sstrncmp(buf1, "SCAN TYPE")) {
                                sscanf(strchr(buf, '\'') + 1, " %s", scan_type);
                                if (scan_type[0] == 'R') {
                                        scan_mode = RASTER_SCAN;
                                }
                        }
                        else if (Util::sstrncmp(buf1, "DELTAX")) {
                                sscanf(strchr(buf, '=') + 1, " %f", &pixel);
                                pixel /= 3.0;
                        }
                }
 
 
                if (axis == Y_SCAN_AXIS) {
                        int t = nx;
                        nx = ny;
                        ny = t;
                }
        }
        fclose(file);
        file = sfopen(img_filename, rw_mode);
 
        EXITFUNC;
}
 
bool SalIO::is_valid(const void *first_block)
{
        ENTERFUNC;
        bool result = false;
 
        if (!first_block) {
                result = false;
        }
        result = Util::check_file_by_magic(first_block, MAGIC);
        EXITFUNC;
        return result;
}
 
int SalIO::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(nx, ny));
 
        int xlen = 0, ylen = 0;
        EMUtil::get_region_dims(area, nx, &xlen, ny, &ylen);
 
        dict["nx"] = xlen;
        dict["ny"] = ylen;
        dict["nz"] = 1;
        dict["datatype"] = EMUtil::EM_SHORT;
        dict["SAL.pixel"] = pixel;
 
        EXITFUNC;
        return 0;
}
 
int SalIO::write_header(const Dict &, int, const Region* , EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        LOGWARN("SAL write is not supported.");
        EXITFUNC;
        return 1;
}
 
int SalIO::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(nx, ny));
 
        if (scan_mode != NON_RASTER_SCAN) {
                LOGERR("only NON_RASTER_SCAN scan mode is supported in a SAL image");
                return 1;
        }
 
        rewind(file);
 
        int mode_size = (int)sizeof(short);
        unsigned char *cdata = (unsigned char *) data;
        short *sdata = (short *) data;
        size_t row_size = nx * mode_size;
        size_t block_size = (((row_size - 1) / record_length) + 1) * record_length;
        size_t post_row = block_size - row_size;
 
        EMUtil::process_region_io(cdata, file, READ_ONLY, image_index,
                                                          mode_size, nx, ny, 1, area, false,
                                                          EMUtil::IMAGE_SAL, 0, post_row);
 
#if 0
        int row_size = nx * mode_size;
        int block_size = (((row_size - 1) / record_length) + 1) * record_length;
 
        for (int j = 0; j < ny; j++) {
                if (fread(&cdata[j * row_size], block_size, 1, file) != 1) {
                        LOGERR("Incomplete SAL data read %d/%d blocks", j, ny);
                        return 1;
                }
        }
#endif
 
        int xlen = 0, ylen = 0;
        EMUtil::get_region_dims(area, nx, &xlen, ny, &ylen);
 
        if (scan_mode == NON_RASTER_SCAN) {
                become_host_endian(sdata, xlen * ylen);
 
                for (int i = 0; i < ylen; i += 2) {
                        for (int j = 0; j < xlen / 2; j++) {
                                short sw = sdata[i * xlen + j];
                                sdata[i * xlen + j] = sdata[i * xlen + xlen - j - 1];
                                sdata[i * xlen + xlen - j - 1] = sw;
                        }
                }
        }
 
        for (int i = xlen * ylen - 1; i >= 0; i--) {
                data[i] = static_cast < float >((cdata[i * 2 + 1] * UCHAR_MAX) + cdata[i * 2]);
        }
        EXITFUNC;
        return 0;
}
 
int SalIO::write_data(float *, int, const Region* , EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        LOGWARN("SAL write is not supported.");
        EXITFUNC;
        return 1;
}
 
void SalIO::flush()
{
}
 
 
bool SalIO::is_complex_mode()
{
        return false;
}
 
bool SalIO::is_image_big_endian()
{
        return false;
}